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Joja M, Grant ET, Desai MS. Living on the edge: Mucus-associated microbes in the colon. Mucosal Immunol 2025:S1933-0219(25)00041-8. [PMID: 40233878 DOI: 10.1016/j.mucimm.2025.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Revised: 03/28/2025] [Accepted: 04/09/2025] [Indexed: 04/17/2025]
Abstract
The colonic mucus layer acts as a physicochemical barrier to pathogen invasion and as a habitat for mucus-associated microbes. This mucosal microbiome plays a crucial role in moderating mucus production, maintaining barrier integrity, and shaping the host immune response. However, unchecked mucin foraging may render the host vulnerable to disease. To better understand these dynamics in the mucus layer, it is essential to advance fundamental knowledge on how commensals bind to and utilize mucin as well as their interactions with both the host and their microbial neighbors. We present an overview of approaches for surveying mucus-associated bacteria and assessing their mucin-utilizing capacity, alongside a discussion of the limitations of existing methods. Additionally, we highlight how diet and host secretory immunoglobulin A interact with the mucosal bacterial community in the colon. Insights into this subset of the microbial community can guide therapeutic strategies to optimally support and modulate mucosal barrier integrity.
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Affiliation(s)
- Mihovil Joja
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - Erica T Grant
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Mahesh S Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
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2
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Kreimeyer H, Llorente C, Schnabl B. Influence of Alcohol on the Intestinal Immune System. Alcohol Res 2025; 45:03. [PMID: 40151622 PMCID: PMC11913448 DOI: 10.35946/arcr.v45.1.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2025] Open
Abstract
PURPOSE Alcohol misuse is associated with disruption of the microbial homeostasis (dysbiosis) and microbial overgrowth in the gut, gut barrier disruption, and translocation of microbes into the systemic circulation. It also induces changes in regulatory mechanisms of the gut, which is the largest peripheral immune organ. The gut-liver axis is important for health and disease, and alterations in the intestinal immune system contribute to alcohol-associated liver disease (ALD). Understanding these changes might help discover new targets for drugs and therapeutic approaches. SEARCH METHODS A systematic literature search was conducted in PubMed, Medline, and Embase of manuscripts published between January 2000 and November 2023 using the terms ("alcohol" or "ethanol") AND ("immune" or "immunol") AND ("intestine," "colon," or "gut"). Eligible manuscripts included studies and reviews that discussed the effects of ethanol on immune cells in the intestine. SEARCH RESULTS A total of 506 publications were found in the databases on November 20, 2023. After excluding duplicates and research not covering ALD (415 articles), 91 studies were reviewed. Also included were manuscripts covering specific immune cells in the context of ALD. DISCUSSION AND CONCLUSIONS Balancing immune tolerance vs. initiating an immune response challenges the intestinal immune system. Alcohol induces disruption of the intestinal barrier, which is accompanied by a thicker mucus layer and reduced anti-microbial peptides. This leads to longer attachment of bacteria to epithelial cells and consequently greater translocation into the circulation. Bacterial translocation activates the immune system, reducing the activity of regulatory T cells and inducing T helper 17 response via a variety of pathways. The role of innate immune cells, especially Type 3 innate lymphoid cells, and of specific B- and T-cell subsets in ALD remains elusive. Gut dysbiosis, translocation of viable bacteria and bacterial products into the circulation, and changes in the intestinal barrier have been linked to immune deficiency and infections in patients with cirrhosis. Modifying the intestinal immune system could reduce intestinal inflammation and alcohol-induced liver injury. Understanding the underlying pathophysiology can help to detect new targets for drugs and design therapeutic strategies.
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Affiliation(s)
- Henriette Kreimeyer
- Department of Medicine, University of California San Diego, La Jolla, California
| | - Cristina Llorente
- Department of Medicine, University of California San Diego, La Jolla, California
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, California
- Department of Medicine, U.S. Department of Veterans Affairs San Diego Healthcare System, San Diego, California
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3
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Wang Z, Xie N, Liang X, Shu Q, Hong Y, Shi H, Wang J, Fan D, Liu N, Xu F. Gut mechanoimmunology: Shaping immune response through physical cues. Phys Life Rev 2024; 50:13-26. [PMID: 38821019 DOI: 10.1016/j.plrev.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 06/02/2024]
Abstract
The gut immune system embodies a complex interplay between the gut mucosal barrier, the host's immune cells, and gut microbiota. These components exist within a dynamic environment characterized by a variety of physical cues, e.g., compression, tension, shear stress, stiffness, and viscoelasticity. The physical cues can be modified under specific pathological conditions. Given their dynamic nature, comprehending the specific effects of these physical cues on the gut immune system is critical for pathological and therapeutic studies of intestinal immune-related diseases. This review aims to discuss how physical cues influence gut immunology by affecting the gut mucosal barrier, host immune cells, and gut microbiota, defining this concept as gut mechanoimmunology. This review seeks to highlight that an enhanced understanding of gut mechanoimmunology carries therapeutic implications, not only for intestinal diseases but also for extraintestinal diseases.
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Affiliation(s)
- Ziwei Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an Jiaotong University, Xi'an, China; The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, China
| | - Ning Xie
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an Jiaotong University, Xi'an, China; The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, China
| | - Xiru Liang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an Jiaotong University, Xi'an, China
| | - Qiuai Shu
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an Jiaotong University, Xi'an, China
| | - Yijie Hong
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an Jiaotong University, Xi'an, China
| | - Haitao Shi
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an Jiaotong University, Xi'an, China
| | - Jinhai Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an Jiaotong University, Xi'an, China
| | - Daiming Fan
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China.
| | - Na Liu
- Department of Gastroenterology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, China.
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, China.
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Llorente C. The Imperative for Innovative Enteric Nervous System-Intestinal Organoid Co-Culture Models: Transforming GI Disease Modeling and Treatment. Cells 2024; 13:820. [PMID: 38786042 PMCID: PMC11119846 DOI: 10.3390/cells13100820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/29/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
This review addresses the need for innovative co-culture systems integrating the enteric nervous system (ENS) with intestinal organoids. The breakthroughs achieved through these techniques will pave the way for a transformative era in gastrointestinal (GI) disease modeling and treatment strategies. This review serves as an introduction to the companion protocol paper featured in this journal. The protocol outlines the isolation and co-culture of myenteric and submucosal neurons with small intestinal organoids. This review provides an overview of the intestinal organoid culture field to establish a solid foundation for effective protocol application. Remarkably, the ENS surpasses the number of neurons in the spinal cord. Referred to as the "second brain", the ENS orchestrates pivotal roles in GI functions, including motility, blood flow, and secretion. The ENS is organized into myenteric and submucosal plexuses. These plexuses house diverse subtypes of neurons. Due to its proximity to the gut musculature and its cell type complexity, there are methodological intricacies in studying the ENS. Diverse approaches such as primary cell cultures, three-dimensional (3D) neurospheres, and induced ENS cells offer diverse insights into the multifaceted functionality of the ENS. The ENS exhibits dynamic interactions with the intestinal epithelium, the muscle layer, and the immune system, influencing epithelial physiology, motility, immune responses, and the microbiome. Neurotransmitters, including acetylcholine (ACh), serotonin (5-HT), and vasoactive intestinal peptide (VIP), play pivotal roles in these intricate interactions. Understanding these dynamics is imperative, as the ENS is implicated in various diseases, ranging from neuropathies to GI disorders and neurodegenerative diseases. The emergence of organoid technology presents an unprecedented opportunity to study ENS interactions within the complex milieu of the small and large intestines. This manuscript underscores the urgent need for standardized protocols and advanced techniques to unravel the complexities of the ENS and its dynamic relationship with the gut ecosystem. The insights gleaned from such endeavors hold the potential to revolutionize GI disease modeling and treatment paradigms.
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Affiliation(s)
- Cristina Llorente
- Department of Medicine, University of California San Diego, MC0063, 9500 Gilman Drive, La Jolla, CA 92093, USA
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Abstract
Biogeography is the study of species distribution and diversity within an ecosystem and is at the core of how we understand ecosystem dynamics and interactions at the macroscale. In gut microbial communities, a historical reliance on bulk sequencing to probe community composition and dynamics has overlooked critical processes whereby microscale interactions affect systems-level microbiota function and the relationship with the host. In recent years, higher-resolution sequencing and novel single-cell level data have uncovered an incredible heterogeneity in microbial composition and have enabled a more nuanced spatial understanding of the gut microbiota. In an era when spatial transcriptomics and single-cell imaging and analysis have become key tools in mammalian cell and tissue biology, many of these techniques are now being applied to the microbiota. This fresh approach to intestinal biogeography has given important insights that span temporal and spatial scales, from the discovery of mucus encapsulation of the microbiota to the quantification of bacterial species throughout the gut. In this Review, we highlight emerging knowledge surrounding gut biogeography enabled by the observation and quantification of heterogeneity across multiple scales.
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Affiliation(s)
- Giselle McCallum
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carolina Tropini
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
- Humans and the Microbiome Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada.
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Ribardo DA, Johnson JJ, Hendrixson DR. Viscosity-dependent determinants of Campylobacter jejuni impacting the velocity of flagellar motility. mBio 2024; 15:e0254423. [PMID: 38085029 PMCID: PMC10790790 DOI: 10.1128/mbio.02544-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/06/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Bacteria can adapt flagellar motor output in response to the load that the extracellular milieu imparts on the flagellar filament to enable propulsion. Bacteria can adapt flagellar motor output in response to the load that the extracellular milieu imparts on the flagellar filament to enable propulsion through diverse environments. These changes may involve increasing power and torque in high-viscosity environments or reducing power and flagellar rotation upon contact with a surface. C. jejuni swimming velocity in low-viscosity environments is comparable to other bacterial flagellates and increases significantly as external viscosity increases. In this work, we provide evidence that the mechanics of the C. jejuni flagellar motor has evolved to naturally promote high swimming velocity in high-viscosity environments. We found that C. jejuni produces VidA and VidB as auxiliary proteins to specifically affect flagellar motor activity in low viscosity to reduce swimming velocity. Our findings provide some of the first insights into different mechanisms that exist in bacteria to alter the mechanics of a flagellar motor, depending on the viscosity of extracellular environments.
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Affiliation(s)
- Deborah A. Ribardo
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jeremiah J. Johnson
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - David R. Hendrixson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Barker T, Bulling M, Thomas V, Sweet M. The Effect of Pollen on Coral Health. BIOLOGY 2023; 12:1469. [PMID: 38132295 PMCID: PMC10740922 DOI: 10.3390/biology12121469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Corals are facing a range of threats, including rises in sea surface temperature and ocean acidification. Some now argue that keeping corals ex situ (in aquaria), may be not only important but necessary to prevent local extinction, for example in the Florida Reef Tract. Such collections or are already becoming common place, especially in the Caribbean, and may act as an ark, preserving and growing rare or endangered species in years to come. However, corals housed in aquaria face their own unique set of threats. For example, hobbyists (who have housed corals for decades) have noticed seasonal mortality is commonplace, incidentally following months of peak pollen production. So, could corals suffer from hay fever? If so, what does the future hold? In short, the answer to the first question is simple, and it is no, corals cannot suffer from hay fever, primarily because corals lack an adaptive immune system, which is necessary for the diagnosis of such an allergy. However, the threat from pollen could still be real. In this review, we explore how such seasonal mortality could play out. We explore increases in reactive oxygen species, the role of additional nutrients and how the microbiome of the pollen may introduce disease or cause dysbiosis in the holobiont.
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Affiliation(s)
- Triona Barker
- Aquatic Research Facility, Nature-Based Solutions Research Centre, University of Derby, Derby DE22 1GB, UK
| | - Mark Bulling
- Aquatic Research Facility, Nature-Based Solutions Research Centre, University of Derby, Derby DE22 1GB, UK
| | - Vincent Thomas
- Coral Spawning Lab, Unit 6 Midas Metro Centre, 193 Garth Road, Morden SM4 4NE, UK
| | - Michael Sweet
- Aquatic Research Facility, Nature-Based Solutions Research Centre, University of Derby, Derby DE22 1GB, UK
- Coral Spawning Lab, Unit 6 Midas Metro Centre, 193 Garth Road, Morden SM4 4NE, UK
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8
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Tao H, Wang J, Bao Z, Jin Y, Xiao Y. Acute chlorothalonil exposure had the potential to influence the intestinal barrier function and micro-environment in mice. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 894:165038. [PMID: 37355131 DOI: 10.1016/j.scitotenv.2023.165038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/02/2023] [Accepted: 06/18/2023] [Indexed: 06/26/2023]
Abstract
The intestinal barrier maintains intestinal homeostasis and metabolism and protects against harmful pollutants. Some environmental pollutants seriously affect intestinal barrier function. However, it remains unclear whether or how chlorothalonil (CTL) impacts the intestinal barrier function in animals. Herein, 6-week-old male mice were acutely exposed to different CTL concentrations (100 and 300 mg/kg BW) via intragastric administration once a day for 7 days. Histopathological examination revealed obvious inflammation in the mice' colon and ileum. Most notably, CTL exposure increased the intestinal permeability, particularly in the CTL-300 group. CTL exposure reduced the secretion of colonic epithelial mucus and changed the transcription levels of genes bound up with ion transport and ileal antimicrobial peptide (AMP) secretion, indicating intestinal chemical barrier damage. The results of terminal deoxynucleotidyl transferase dUTP nick end labelling (TUNEL) assay and Ki67 staining revealed abnormal apoptosis and increased intestinal epithelial cell proliferation, suggesting that CTL exposure led to cytotoxicity and inflammation. The results of 16S rRNA sequencing revealed that CTL exposure altered the intestinal microbiota composition and reduced its diversity and richness in the colon contents. Thus, acute CTL exposure affected the different intestinal barrier- and gut microenvironment-related endpoints in mice.
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Affiliation(s)
- Huaping Tao
- Key Laboratory of Organ Development and Regeneration of Zhejiang Province, College of Life and Environmental Sciences, Hangzhou Normal University, 311121 Hangzhou, China; College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Juntao Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhiwei Bao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yuanxiang Jin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China.
| | - Yingping Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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Inaba R, Vujakovic S, Bergstrom K. The gut mucus network: A dynamic liaison between microbes and the immune system. Semin Immunol 2023; 69:101807. [PMID: 37478802 DOI: 10.1016/j.smim.2023.101807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 06/24/2023] [Accepted: 07/08/2023] [Indexed: 07/23/2023]
Abstract
A complex mucus network made up of large polymers of the mucin-family glycoprotein MUC2 exists between the large intestinal microbial mass and epithelial and immune cells. This has long been understood as an innate immune defense barrier against the microbiota and other luminal threats that reinforces the barrier function of the epithelium and limits microbiota contact with the tissues. However, past and recent studies have provided new evidence of how critical the mucus network is to act as a 'liaison' between host and microbe to mediate anti-inflammatory, mutualistic interactions with the microbiota and protection from pathogens. This review summarizes historical and recent insights into the formation of the gut mucus network, how the microbes and immune system influence mucus, and in turn, how the mucus influences immune responses to the microbiota.
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Affiliation(s)
- Rain Inaba
- Department of Biology, University of British Columbia, Okanagan Campus, 3187 University Way, Kelowna V1V 1V7, British Columbia, Canada
| | - Sara Vujakovic
- Department of Biology, University of British Columbia, Okanagan Campus, 3187 University Way, Kelowna V1V 1V7, British Columbia, Canada
| | - Kirk Bergstrom
- Department of Biology, University of British Columbia, Okanagan Campus, 3187 University Way, Kelowna V1V 1V7, British Columbia, Canada.
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10
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Abo H, Muraki A, Harusato A, Imura T, Suzuki M, Takahashi K, Denning TL, Kawashima H. N-acetylglucosamine-6-O sulfation on intestinal mucins prevents obesity and intestinal inflammation by regulating gut microbiota. JCI Insight 2023; 8:e165944. [PMID: 37463055 PMCID: PMC10543739 DOI: 10.1172/jci.insight.165944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 07/11/2023] [Indexed: 08/23/2023] Open
Abstract
Intestinal mucins play an essential role in the defense against bacterial invasion and the maintenance of gut microbiota, which is instrumental in the regulation of host immune systems; hence, its dysregulation is a hallmark of metabolic disease and intestinal inflammation. However, the mechanism by which intestinal mucins control the gut microbiota as well as disease phenotypes remains nebulous. Herein, we report that N-acetylglucosamine (GlcNAc)-6-O sulfation of O-glycans on intestinal mucins performs a protective role against obesity and intestinal inflammation. Chst4-/- mice, lacking GlcNAc-6-O sulfation of the mucin O-glycans, showed significant weight gain and increased susceptibility to dextran sodium sulfate-induced colitis as well as colitis-associated cancer accompanied by significantly reduced immunoglobulin A (IgA) production caused by an impaired T follicular helper cell-mediated IgA response. Interestingly, the protective effects of GlcNAc-6-O sulfation against obesity and intestinal inflammation depend on the gut microbiota, evidenced by the modulation of the gut microbiota by cohousing or microbiota transplantation reversing disease phenotypes and IgA production. Collectively, our findings provide insight into the significance of host glycosylation, more specifically GlcNAc-6-O sulfation on intestinal mucins, in protecting against obesity and intestinal inflammation via regulation of the gut microbiota.
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Affiliation(s)
- Hirohito Abo
- Laboratory of Microbiology and Immunology, Graduate School of Pharmaceutical Science, Chiba University, Chiba, Japan
| | - Aoi Muraki
- Laboratory of Microbiology and Immunology, Graduate School of Pharmaceutical Science, Chiba University, Chiba, Japan
| | | | - Tetsuya Imura
- Department of Surgical Pathology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Maki Suzuki
- Laboratory of Microbiology and Immunology, Graduate School of Pharmaceutical Science, Chiba University, Chiba, Japan
| | - Kohta Takahashi
- Laboratory of Microbiology and Immunology, Graduate School of Pharmaceutical Science, Chiba University, Chiba, Japan
| | - Timothy L. Denning
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA
| | - Hiroto Kawashima
- Laboratory of Microbiology and Immunology, Graduate School of Pharmaceutical Science, Chiba University, Chiba, Japan
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Madzak C, Poiret S, Salomé Desnoulez S, Foligné B, Lafont F, Daniel C. Study of the persistence and dynamics of recombinant mCherry-producing Yarrowia lipolytica strains in the mouse intestine using fluorescence imaging. Microb Biotechnol 2023; 16:618-631. [PMID: 36541039 PMCID: PMC9948224 DOI: 10.1111/1751-7915.14178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022] Open
Abstract
Yarrowia lipolytica is a dimorphic oleaginous non-conventional yeast widely used as a powerful host for expressing heterologous proteins, as well as a promising source of engineered cell factories for various applications. This microorganism has a documented use in Feed and Food and a GRAS (generally recognized as safe) status. Moreover, in vivo studies demonstrated a beneficial effect of this yeast on animal health. However, despite the focus on Y. lipolytica for the industrial manufacturing of heterologous proteins and for probiotic effects, its potential for oral delivery of recombinant therapeutic proteins has seldom been evaluated in mammals. As the first steps towards this aim, we engineered two Y. lipolytica strains, a dairy strain and a laboratory strain, to produce the model fluorescent protein mCherry. We demonstrated that both Y. lipolytica strains transiently persisted for at least 1 week after four daily oral administrations and they maintained the active expression of mCherry in the mouse intestine. We used confocal microscopy to image individual Y. lipolytica cells of freshly collected intestinal tissues. They were found essentially in the lumen and they were rarely in contact with epithelial cells while transiting through the ileum, caecum and colon of mice. Taken as a whole, our results have shown that fluorescent Y. lipolytica strains constitute novel tools to study the persistence and dynamics of orally administered yeasts which could be used in the future as oral delivery vectors for the secretion of active therapeutic proteins in the gut.
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Affiliation(s)
- Catherine Madzak
- INRAE, AgroParisTech, Paris-Saclay University, UMR 782 SayFood, Thiverval-Grignon, France
| | - Sabine Poiret
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - Center for Infection and Immunity of Lille, Lille, France
| | - Sophie Salomé Desnoulez
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, Lille, France
| | - Benoit Foligné
- Univ. Lille, INSERM, CHU Lille, U1286 - Infinite - Institute for Translational Research in Inflammation, Lille, France
| | - Frank Lafont
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - Center for Infection and Immunity of Lille, Lille, France.,Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, Lille, France
| | - Catherine Daniel
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - Center for Infection and Immunity of Lille, Lille, France
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12
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Gong J, Shaik VA, Elfring GJ. Active particles crossing sharp viscosity gradients. Sci Rep 2023; 13:596. [PMID: 36631505 PMCID: PMC9834246 DOI: 10.1038/s41598-023-27423-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023] Open
Abstract
Active particles (living or synthetic) often move through inhomogeneous environments, such as gradients in light, heat or nutrient concentration, that can lead to directed motion (or taxis). Recent research has explored inhomogeneity in the rheological properties of a suspending fluid, in particular viscosity, as a mechanical (rather than biological) mechanism for taxis. Theoretical and experimental studies have shown that gradients in viscosity can lead to reorientation due to asymmetric viscous forces. In particular, recent experiments with Chlamydomonas Reinhardtii algae swimming across sharp viscosity gradients have observed that the microorganisms are redirected and scattered due to the viscosity change. Here we develop a simple theoretical model to explain these experiments. We model the swimmers as spherical squirmers and focus on small, but sharp, viscosity changes. We derive a law, analogous to Snell's law of refraction, that governs the orientation of active particles in the presence of a viscosity interface. Theoretical predictions show good agreement with experiments and provide a mechanistic understanding of the observed reorientation process.
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Affiliation(s)
- Jiahao Gong
- Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, BC, V6T 1Z2, Canada
| | - Vaseem A Shaik
- Department of Mechanical Engineering, Institute of Applied Mathematics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Gwynn J Elfring
- Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, BC, V6T 1Z2, Canada. .,Department of Mechanical Engineering, Institute of Applied Mathematics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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13
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Gerner RR, Hossain S, Sargun A, Siada K, Norton GJ, Zheng T, Neumann W, Nuccio SP, Nolan EM, Raffatellu M. Siderophore Immunization Restricted Colonization of Adherent-Invasive Escherichia coli and Ameliorated Experimental Colitis. mBio 2022; 13:e0218422. [PMID: 36094114 PMCID: PMC9600343 DOI: 10.1128/mbio.02184-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 11/20/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are characterized by chronic inflammation of the gastrointestinal tract and profound alterations to the gut microbiome. Adherent-invasive Escherichia coli (AIEC) is a mucosa-associated pathobiont that colonizes the gut of patients with Crohn's disease, a form of IBD. Because AIEC exacerbates gut inflammation, strategies to reduce the AIEC bloom during colitis are highly desirable. To thrive in the inflamed gut, Enterobacteriaceae acquire the essential metal nutrient iron by producing and releasing siderophores. Here, we implemented an immunization-based strategy to target the siderophores enterobactin and its glucosylated derivative salmochelin to reduce the AIEC bloom in the inflamed gut. Using chemical (dextran sulfate sodium) and genetic (Il10-/- mice) IBD mouse models, we showed that immunization with enterobactin conjugated to the mucosal adjuvant cholera toxin subunit B potently elicited mucosal and serum antibodies against these siderophores. Siderophore-immunized mice exhibited lower AIEC gut colonization, diminished AIEC association with the gut mucosa, and reduced colitis severity. Moreover, Peyer's patches and the colonic lamina propria harbored enterobactin-specific B cells that could be identified by flow cytometry. The beneficial effect of siderophore immunization was primarily B cell-dependent because immunized muMT-/- mice, which lack mature B lymphocytes, were not protected during AIEC infection. Collectively, our study identified siderophores as a potential therapeutic target to reduce AIEC colonization and its association with the gut mucosa, which ultimately may reduce colitis exacerbation. Moreover, this work provides the foundation for developing monoclonal antibodies against siderophores, which could provide a narrow-spectrum strategy to target the AIEC bloom in Crohn's disease patients. IMPORTANCE Adherent-invasive Escherichia coli (AIEC) is abnormally prevalent in patients with ileal Crohn's disease and exacerbates intestinal inflammation, but treatment strategies that selectively target AIEC are unavailable. Iron is an essential micronutrient for most living organisms, and bacterial pathogens have evolved sophisticated strategies to capture iron from the host environment. AIEC produces siderophores, small, secreted molecules with a high affinity for iron. Here, we showed that immunization to elicit antibodies against siderophores promoted a reduction of the AIEC bloom, interfered with AIEC association with the mucosa, and mitigated colitis in experimental mouse models. We also established a flow cytometry-based approach to visualize and isolate siderophore-specific B cells, a prerequisite for engineering monoclonal antibodies against these molecules. Together, this work could lead to a more selective and antibiotic-sparing strategy to target AIEC in Crohn's disease patients.
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Affiliation(s)
- Romana R. Gerner
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, California, USA
| | - Suzana Hossain
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, California, USA
| | - Artur Sargun
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kareem Siada
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, California, USA
| | - Grant J. Norton
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, California, USA
| | - Tengfei Zheng
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Wilma Neumann
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sean-Paul Nuccio
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, California, USA
| | - Elizabeth M. Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Manuela Raffatellu
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Chiba University-University of California-San Diego Center for Mucosal Immunology, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, California, USA
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14
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Bucheli JEV, Todorov SD, Holzapfel WH. Role of gastrointestinal microbial populations, a terra incognita of the human body in the management of intestinal bowel disease and metabolic disorders. Benef Microbes 2022; 13:295-318. [PMID: 35866598 DOI: 10.3920/bm2022.0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Intestinal bowel disease (IBD) is a chronic immune-mediated clinical condition that affects the gastrointestinal tract and is mediated by an inflammatory response. Although it has been extensively studied, the multifactorial aetiology of this disorder makes it difficult to fully understand all the involved mechanisms in its development and therefore its treatment. In recent years, the fundamental role played by the human microbiota in the pathogenesis of IBD has been emphasised. Microbial imbalances in the gut bacterial communities and a lower species diversity in patients suffering from inflammatory gastrointestinal disorders compared to healthy individuals have been reported as principal factors in the development of IBD. These served to support scientific arguments for the use of probiotic microorganisms in alternative approaches for the prevention and treatment of IBD. In a homeostatic environment, the presence of bacteria (including probiotics) on the intestinal epithelial surface activates a cascade of processes by which immune responses inhibited and thereby commensal organisms maintained. At the same time these processes may support activities against specific pathogenic bacteria. In dysbiosis, these underlying mechanisms will serve to provoke a proinflammatory response, that, in combination with the use of antibiotics and the genetic predisposition of the host, will culminate in the development of IBD. In this review, we summarised the main causes of IBD, the physiological mechanisms involved and the related bacterial groups most frequently associated with these processes. The intention was to enable a better understanding of the interaction between the intestinal microbiota and the host, and to suggest possibilities by which this knowledge can be useful for the development of new therapeutic treatments.
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Affiliation(s)
- J E Vazquez Bucheli
- Human Effective Microbes, Department of Advanced Convergence, Handong Global University, Pohang, Gyeongbuk 37554, Republic of Korea
| | - S D Todorov
- ProBacLab, Department of Advanced Convergence, Handong Global University, Pohang, Gyeongbuk 37554, Republic of Korea
| | - W H Holzapfel
- Human Effective Microbes, Department of Advanced Convergence, Handong Global University, Pohang, Gyeongbuk 37554, Republic of Korea
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15
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Sardelli L, Vangosa FB, Merli M, Ziccarelli A, Visentin S, Visai L, Petrini P. Bioinspired in vitro intestinal mucus model for 3D-dynamic culture of bacteria. BIOMATERIALS ADVANCES 2022; 139:213022. [PMID: 35891596 DOI: 10.1016/j.bioadv.2022.213022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 05/27/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
The intestinal mucus is a biological barrier that supports the intestinal microbiota growth and filters molecules. To perform these functions, mucus possesses optimized microstructure and viscoelastic properties and it is steadily replenished thus flowing along the gut. The available in vitro intestinal mucus models are useful tools in investigating the microbiota-human cells interaction, and are used as matrices for bacterial culture or as static component of microfluidic devices like gut-on-chips. The aim of this work is to engineer an in vitro mucus models (I-Bac3Gel) addressing in a single system physiological viscoelastic properties (i.e., 2-200 Pa), 3D structure and suitability for dynamic bacterial culture. Homogeneously crosslinked alginate hydrogels are optimized in composition to obtain target viscoelastic and microstructural properties. Then, rheological tests are exploited to assess a priori the hydrogels capability to withstand the flow dynamic condition. We experimentally assess the suitability of I-Bac3Gels in the evolving field of microfluidics by applying a dynamic flow to a bacterial-loaded mucus model and by monitoring E. coli growth and survival. The engineered models represent a step forward in the modelling of the mucus, since they can answer to different urgent needs such as a 3D structure, bioinspired properties and compatibility with dynamic system.
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Affiliation(s)
- Lorenzo Sardelli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy.
| | - Francesco Briatico Vangosa
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
| | - Marta Merli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
| | - Anna Ziccarelli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
| | - Sonja Visentin
- Molecular Biotechnology and Health Sciences Department, University of Torino, Torino, Italy
| | - Livia Visai
- Molecular Medicine Department (DMM), Center for Health Technologies (CHT), UdR INSTM, University of Pavia, Pavia, Italy; Department of Occupational Medicine, Toxicology and Environmental Risks, Istituti Clinici Scientifici (ICS) Maugeri, IRCCS, Pavia, Italy
| | - Paola Petrini
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
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16
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Li J, Qu Z, Liu F, Jing H, Pan Y, Guo S, Ho CL. Diet‐Based Microbiome Modulation: You are What You Eat. PRINCIPLES IN MICROBIOME ENGINEERING 2022:1-46. [DOI: 10.1002/9783527825462.ch1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
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17
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Fox E, Lyte M. Variation in spatial organization of the gut microbiota along the longitudinal and transverse axes of the intestines. Arch Microbiol 2022; 204:424. [PMID: 35750957 DOI: 10.1007/s00203-022-02952-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 11/02/2022]
Abstract
Elucidation of the mechanisms by which the microbiota-gut-brain axis influences behavior requires understanding the anatomical relationship of bacteria with mucosal elements. We herein report that microbes were mainly associated with food or fecal matter in the intestinal lumen. In the small intestine, bacterial density increased from proximal-to-distal levels and was much higher in the large intestine. A mucus layer was present between the mucosal epithelium and fecal boluses in the large intestine, but not between food and the mucosal epithelium in the small intestine. In contrast, in all intestinal regions lacking food or fecal boluses, the lumen was small, or absent, and contained little or no bacteria or mucus. The association of bacteria with food was tested in the small intestine by examining the effect of fasting on it. Bacterial density was equivalent in the ileum of fasted and fed mice, but fasting greatly reduced the amount of food containing bacteria, suggesting the amount of bacteria was reduced. Critically, this study provides evidence that the vast majority of the microbiota in the intestines are associated with the food matrix thereby raising questions regarding how the gut microbiota can potentially signal the brain and influence behavior. Given their spatial location within the lumen, which keeps them at a great distance from neuronal elements in the mucosa, combined with immune and mucus barriers, microbiota more likely to influence behavior through secretion of bacterial products that can traverse the spatial difference to interact with gut neurons and not through direct physical association.
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Affiliation(s)
- Edward Fox
- Department of Psychological Sciences, Purdue University, 703 Third Street, West Lafayette, IN, 47907, USA.
| | - Mark Lyte
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, 50011, USA
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18
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Three-dimensional imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa. Proc Natl Acad Sci U S A 2022; 119:e2118483119. [PMID: 35476531 PMCID: PMC9171773 DOI: 10.1073/pnas.2118483119] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Many human diseases are causally linked to the gut microbiota, yet the field still lacks mechanistic understanding of the underlying complex interactions, because existing tools cannot simultaneously quantify microbial communities and their native context. In this work, we provide an approach to tissue clearing and preservation that enables 3D visualization of the biogeography of the host–microbiota interface. We combine this tool with sequencing and multiplexed microbial labeling to provide the field with a platform on which to discover patterns in the spatial distribution of microbes. We validated this platform by quantifying bacterial distribution in cecal mucosa at different stages of antibiotic exposure. This approach may enable researchers to formulate and test new hypotheses about host–microbe and microbe–microbe interactions. Improving our understanding of host–microbe relationships in the gut requires the ability to both visualize and quantify the spatial organization of microbial communities in their native orientation with the host tissue. We developed a systematic procedure to quantify the three-dimensional (3D) spatial structure of the native mucosal microbiota in any part of the intestines with taxonomic and high spatial resolution. We performed a 3D biogeographical analysis of the microbiota of mouse cecal crypts at different stages of antibiotic exposure. By tracking eubacteria and four dominant bacterial taxa, we found that the colonization of crypts by native bacteria is a dynamic and spatially organized process. Ciprofloxacin treatment drastically reduced bacterial loads and eliminated Muribaculaceae (or all Bacteroidetes entirely) even 10 d after recovery when overall bacterial loads returned to preantibiotic levels. Our 3D quantitative imaging approach revealed that the bacterial colonization of crypts is organized in a spatial pattern that consists of clusters of adjacent colonized crypts that are surrounded by unoccupied crypts, and that this spatial pattern is resistant to the elimination of Muribaculaceae or of all Bacteroidetes by ciprofloxacin. Our approach also revealed that the composition of cecal crypt communities is diverse and that Lactobacilli were found closer to the lumen than Bacteroidetes, Ruminococcaceae, and Lachnospiraceae, regardless of antibiotic exposure. Finally, we found that crypts communities with similar taxonomic composition were physically closer to each other than communities that were taxonomically different.
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19
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Profiling of the Bacterial Microbiota along the Murine Alimentary Tract. Int J Mol Sci 2022; 23:ijms23031783. [PMID: 35163705 PMCID: PMC8836272 DOI: 10.3390/ijms23031783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 12/13/2022] Open
Abstract
Here, the spatial distribution of the bacterial flora along the murine alimentary tract was evaluated using high throughput sequencing in wild-type and Tff3-deficient (Tff3KO) animals. Loss of Tff3 was linked to increased dextran sodium sulfate-induced colitis. This systematic study shows the results of 13 different regions from the esophagus to the rectum. The number of bacterial species (richness) increased from the esophagus to the rectum, from 50 to 200, respectively. Additionally, the bacterial community structure changed continuously; the highest changes were between the upper/middle and lower gastrointestinal compartments when comparing adjacent regions. Lactobacillus was the major colonizer in the upper/middle gastrointestinal tract, especially in the esophagus and stomach. From the caecum, a drastic diminution of Lactobacillus occurred, while members of Lachnospiraceae significantly increased. A significant change occurred in the bacterial community between the ascending and the transverse colon with Bacteroidetes being the major colonizers with relative constant abundance until the rectum. Interestingly, wild-type and Tff3KO animals did not show significant differences in their bacterial communities, suggesting that Tff3 is not involved in alterations of intraluminal or adhesive microbiota but is obviously important for mucosal protection, e.g., of the sensitive stem cells in the colonic crypts probably by a mucus plume.
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20
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Dubbelboer IR, Barmpatsalou V, Rodler A, Karlsson E, Filipe Nunes S, Holmberg J, Häggström J, A. S. Bergström C. Gastrointestinal mucus in dog: physiological characteristics, composition, and structural properties. Eur J Pharm Biopharm 2022; 173:92-102. [DOI: 10.1016/j.ejpb.2022.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/17/2021] [Accepted: 02/23/2022] [Indexed: 11/27/2022]
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21
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Salomé-Desnoulez S, Poiret S, Foligné B, Muharram G, Peucelle V, Lafont F, Daniel C. Persistence and dynamics of fluorescent Lactobacillus plantarum in the healthy versus inflamed gut. Gut Microbes 2022; 13:1-16. [PMID: 33779491 PMCID: PMC8009120 DOI: 10.1080/19490976.2021.1897374] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The gastrointestinal tract is the main ecological niche in which Lactobacillus strains may provide health benefits in mammals. There is currently a need to characterize host-microbe interactions in space and time by tracking these bacteria in vivo. We combined noninvasive whole-body imaging with ex vivo fluorescence confocal microscopy imaging to monitor the impact of intestinal inflammation on the persistence of orally administered Lactobacillus plantarum NCIMB8826 in healthy and inflamed mouse colons. We developed fluorescent L. plantarum strains and demonstrated that mCherry is the best system for in vivo imaging and ex vivo fluorescence confocal microscopy of these bacteria. We also used whole-body imaging to show that this anti-inflammatory, orally administered strain persists for longer and at higher counts in the inflamed colon than in the healthy colon. We confirmed these results by the ex vivo confocal imaging of colons from mice with experimental colitis for 3 days after induction. Moreover, extended orthogonal view projections enabled us to localize individual L. plantarum in sites that differed for healthy versus inflamed guts. In healthy colons, orally administered bacteria were localized in the lumen (in close contact with commensal bacteria) and sometimes in the crypts (albeit very rarely in contact with intestinal cells). The bacteria were observed within and outside the mucus layer. In contrast, L. plantarum bacteria in the inflamed colon were mostly located in the lumen and (in less inflamed areas) within the mucus layer. In more intensely inflamed areas (i.e., where the colon had undergone structural damage), the L. plantarum were in direct contact with damaged epithelial cells. Taken as a whole, our results show that fluorescently labeled L. plantarum can be used to study the persistence of these bacteria in inflamed guts using both noninvasive whole-body imaging and ex vivo fluorescence confocal microscopy.
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Affiliation(s)
- Sophie Salomé-Desnoulez
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, F-59000 Lille, France
| | - Sabine Poiret
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Benoit Foligné
- Univ. Lille, INSERM, CHU Lille, U1286 - Infinite - Institute for Translational Research in Inflammation, F-59000 Lille, France
| | - Ghaffar Muharram
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Véronique Peucelle
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Frank Lafont
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, F-59000 Lille, France,Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Catherine Daniel
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – Center for Infection and Immunity of Lille, F-59000 Lille, France,CONTACT Daniel C Center for Infection and Immunity of Lille, Institut Pasteur de Lille, 1 rue du Professeur Calmette- CS50447, 59021 Lille cedex, France
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22
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Ni H, Chen Y, Xia W, Wang C, Hu C, Sun L, Tang W, Cui H, Shen T, Liu Y, Li J. SATB2 Defect Promotes Colitis and Colitis-associated Colorectal Cancer by Impairing Cl-/HCO3- Exchange and Homeostasis of Gut Microbiota. J Crohns Colitis 2021; 15:2088-2102. [PMID: 34019628 DOI: 10.1093/ecco-jcc/jjab094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND SATB2 is a diagnostic biomarker and a favourable prognostic marker for colorectal cancer [CRC], but its role in colitis and colitis-associated colorectal cancer [CAC] is unknown. METHODS Colitis was induced in intestinal epithelial-specific Satb2 knockout [Satb2 IEC-KO] and control mice using dextran sulphate sodium [DSS]. RNA-seq analysis was performed on colonic tissues, and 16S rDNA-Seq on faecal bacterial DNA from Satb2 IEC-KO and control mice. Immunohistochemistry and flow cytometry were performed to reveal the proportions of different immune cells. Chromatin immunoprecipitation [ChIP] and luciferase reporter were applied to show the regulatory role of SATB2 on SLC26A3, of which the Cl-/HCO3- exchange activity was measured fluorometrically by the pHi-sensitive dye. Bacteroides were detected by fluorescence in situ hybridisation [FISH] on colonic tissue. RESULTS Satb2 IEC-KO mice suffered from intestinal epithelial damage spontaneously, and developed more severe colitis and CAC. The expression of SLC26A3 correlated well with SATB2 revealed by RNA-seq and The Cancer Genome Atlas [TCGA] data, and was governed by SATB2 confirmed by ChIP and luciferase reporter experiments. Decreased intestinal flora diversity was seen in Satb2 IEC-KO mice. Bacteroides were more abundant and could colonise into the inner layer of colonic mucosa in Satb2 IEC-KO mice. Faecal microbiome transplantation from Satb2 IEC-KO mice aggravated colitis and M1 macrophages infiltration. CONCLUSIONS SATB2 plays a vital role in maintaining intestinal homeostasis, and its deficiency promotes the development of colitis and CAC by influencing the intestinal luminal environment and gut flora.
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Affiliation(s)
- Hengli Ni
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China.,Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yongyu Chen
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Wei Xia
- Department of Pathology, Second Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Chuyi Wang
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Caihong Hu
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Lina Sun
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Wen Tang
- Department of Gastroenterology, Second Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Hongxia Cui
- Department of Pathology, Second Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Tong Shen
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China
| | - Yao Liu
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China.,Department of Pathology, Second Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Jianming Li
- Department of Pathology and Pathophysiology, Medical College of Soochow University, Soochow University, Suzhou, People's Republic of China.,Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
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23
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Béchon N, Ghigo JM. Gut biofilms: Bacteroides as model symbionts to study biofilm formation by intestinal anaerobes. FEMS Microbiol Rev 2021; 46:6440158. [PMID: 34849798 DOI: 10.1093/femsre/fuab054] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/09/2021] [Indexed: 02/06/2023] Open
Abstract
Bacterial biofilms are communities of adhering bacteria that express distinct properties compared to their free-living counterparts, including increased antibiotic tolerance and original metabolic capabilities. Despite the potential impact of the biofilm lifestyle on the stability and function of the dense community of micro-organisms constituting the mammalian gut microbiota, the overwhelming majority of studies performed on biofilm formation by gut bacteria focused either on minor and often aerobic members of the community or on pathogenic bacteria. In this review, we discuss the reported evidence for biofilm-like structures formed by gut bacteria, the importance of considering the anaerobic nature of gut biofilms and we present the most recent advances on biofilm formation by Bacteroides, one of the most abundant genera of the human gut microbiota. Bacteroides species can be found attached to food particles and colonizing the mucus layer and we propose that Bacteroides symbionts are relevant models to probe the physiology of gut microbiota biofilms.
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Affiliation(s)
- Nathalie Béchon
- Institut Pasteur, Université de Paris, UMR CNRS2001, Genetics of Biofilms Laboratory 75015 Paris, France
| | - Jean-Marc Ghigo
- Institut Pasteur, Université de Paris, UMR CNRS2001, Genetics of Biofilms Laboratory 75015 Paris, France
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24
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Sibinelli-Sousa S, de Araújo-Silva AL, Hespanhol JT, Bayer-Santos E. Revisiting the steps of Salmonella gut infection with a focus on antagonistic interbacterial interactions. FEBS J 2021; 289:4192-4211. [PMID: 34546626 DOI: 10.1111/febs.16211] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/12/2021] [Accepted: 09/20/2021] [Indexed: 12/20/2022]
Abstract
A commensal microbial community is established in the mammalian gut during its development, and these organisms protect the host against pathogenic invaders. The hallmark of noninvasive Salmonella gut infection is the induction of inflammation via effector proteins secreted by the type III secretion system, which modulate host responses to create a new niche in which the pathogen can overcome the colonization resistance imposed by the microbiota. Several studies have shown that endogenous microbes are important to control Salmonella infection by competing for resources. However, there is limited information about antimicrobial mechanisms used by commensals and pathogens during these in vivo disputes for niche control. This review aims to revisit the steps that Salmonella needs to overcome during gut colonization-before and after the induction of inflammation-to achieve an effective infection. We focus on a series of reported and hypothetical antagonistic interbacterial interactions in which both contact-independent and contact-dependent mechanisms might define the outcome of the infection.
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Affiliation(s)
| | | | - Julia Takuno Hespanhol
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil
| | - Ethel Bayer-Santos
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil
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25
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Guimarães-Lopes VDP, Gomes MRVS, Kagueyama M, Faria RDCV, Ribeiro Filho OP, Melo FRD, Sartori SSR. Histometric parameters of the large intestine of hybrid marmosets Callithrix sp. under the influence of seasonality. Anat Histol Embryol 2021; 50:888-896. [PMID: 34462952 DOI: 10.1111/ahe.12732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/01/2022]
Abstract
Morphofunctional characteristics of the large intestine are rarely explored to understand the physiology, behavior and ecology of neotropical primates. In this study, we analyzed the histometric parameters of the large intestine of hybrid marmosets (Callithrix sp.) captured in forest fragments of Viçosa-Brazil, under seasonal interference. These animals were predominantly insectivorous in the rainy season and gummivores in the dry season. Large intestine fragments were collected and processed according to histological methods and stained with toluidine blue for general analysis, periodic acid of Schiff (PAS) and Alcian blue (AB) for goblet cells, Grimelius and Masson Fontana for argyrophil and argentaffin endocrine cells. Several histometric parameters were more expressive in the large intestine of the rainy season marmosets: greater thickness of the parietal layers, greater number of argyrophil and argentaffin endocrine cells, and AB-positive goblet cells, characteristics favor secretomotor functions and reduce the passage time of the fecal bolus, which is consistent with an insectivorous diet. In contrast, parameters such as crypt width, height of the absorptive cells and striated border, and the number of PAS-positive cells were more expressive in the dry season marmosets, reflecting the need for longer passage time for digestion and absorption of food items from tree gum, which are more complex and demand the action of microorganisms present in the large intestine, as well as greater protection against the abrasive action of dietary fibers and against microorganisms. Thus, it can be said that the marmoset's large intestine has morphological adaptations to maximize energy intake from the diet, which alternates under the influence of seasonality.
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Affiliation(s)
- Vanessa de Paula Guimarães-Lopes
- Departamento de Biologia Animal, Universidade Federal de Viçosa, Viçosa, Brazil.,Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Mislene Kagueyama
- Departamento de Biologia Animal, Universidade Federal de Viçosa, Viçosa, Brazil
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The Interplay between Nutrition, Innate Immunity, and the Commensal Microbiota in Adaptive Intestinal Morphogenesis. Nutrients 2021; 13:nu13072198. [PMID: 34206809 PMCID: PMC8308283 DOI: 10.3390/nu13072198] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 12/15/2022] Open
Abstract
The gastrointestinal tract is a functionally and anatomically segmented organ that is colonized by microbial communities from birth. While the genetics of mouse gut development is increasingly understood, how nutritional factors and the commensal gut microbiota act in concert to shape tissue organization and morphology of this rapidly renewing organ remains enigmatic. Here, we provide an overview of embryonic mouse gut development, with a focus on the intestinal vasculature and the enteric nervous system. We review how nutrition and the gut microbiota affect the adaptation of cellular and morphologic properties of the intestine, and how these processes are interconnected with innate immunity. Furthermore, we discuss how nutritional and microbial factors impact the renewal and differentiation of the epithelial lineage, influence the adaptation of capillary networks organized in villus structures, and shape the enteric nervous system and the intestinal smooth muscle layers. Intriguingly, the anatomy of the gut shows remarkable flexibility to nutritional and microbial challenges in the adult organism.
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27
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Bossink EGBM, Zakharova M, de Bruijn DS, Odijk M, Segerink LI. Measuring barrier function in organ-on-chips with cleanroom-free integration of multiplexable electrodes. LAB ON A CHIP 2021; 21:2040-2049. [PMID: 33861228 DOI: 10.1016/j.ooc.2021.100013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Transepithelial/transendothelial electrical resistance (TEER) measurements can be applied in organ-on-chips (OoCs) to estimate the barrier properties of a tissue or cell layer in a continuous, non-invasive, and label-free manner. Assessing the barrier integrity in in vitro models is valuable for studying and developing barrier targeting drugs. Several systems for measuring the TEER have been shown, but each of them having their own drawbacks. This article presents a cleanroom-free fabrication method for the integration of platinum electrodes in a polydimethylsiloxane OoC, allowing the real-time assessment of the barrier function by employing impedance spectroscopy. The proposed method and electrode arrangement allow visual inspection of the cells cultured in the device at the site of the electrodes, and multiplexing of both the electrodes in one OoC and the number of OoCs in one device. The effectiveness of our system is demonstrated by lining the OoC with intestinal epithelial cells, creating a gut-on-chip, where we monitored the formation, as well as the disruption and recovery of the cell barrier during a 21 day culture period. The application is further expanded by creating a blood-brain-barrier, to show that the proposed fabrication method can be applied to monitor the barrier formation in the OoC for different types of biological barriers.
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Affiliation(s)
- Elsbeth G B M Bossink
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, Technical Medical Center and Max Planck Institute for Complex Fluid Dynamics, University of Twente, The Netherlands.
| | - Mariia Zakharova
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, Technical Medical Center and Max Planck Institute for Complex Fluid Dynamics, University of Twente, The Netherlands.
| | - Douwe S de Bruijn
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, Technical Medical Center and Max Planck Institute for Complex Fluid Dynamics, University of Twente, The Netherlands.
| | - Mathieu Odijk
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, Technical Medical Center and Max Planck Institute for Complex Fluid Dynamics, University of Twente, The Netherlands.
| | - Loes I Segerink
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, Technical Medical Center and Max Planck Institute for Complex Fluid Dynamics, University of Twente, The Netherlands.
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28
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Fang J, Wang H, Zhou Y, Zhang H, Zhou H, Zhang X. Slimy partners: the mucus barrier and gut microbiome in ulcerative colitis. Exp Mol Med 2021; 53:772-787. [PMID: 34002011 PMCID: PMC8178360 DOI: 10.1038/s12276-021-00617-8] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/14/2021] [Accepted: 01/31/2021] [Indexed: 02/08/2023] Open
Abstract
Ulcerative colitis (UC) is a chronic recurrent intestinal inflammatory disease characterized by high incidence and young onset age. Recently, there have been some interesting findings in the pathogenesis of UC. The mucus barrier, which is composed of a mucin complex rich in O-glycosylation, not only provides nutrients and habitat for intestinal microbes but also orchestrates the taming of germs. In turn, the gut microbiota modulates the production and secretion of mucins and stratification of the mucus layers. Active bidirectional communication between the microbiota and its 'slimy' partner, the mucus barrier, seems to be a continually performed concerto, maintaining homeostasis of the gut ecological microenvironment. Any abnormalities may induce a disorder in the gut community, thereby causing inflammatory damage. Our review mainly focuses on the complicated communication between the mucus barrier and gut microbiome to explore a promising new avenue for UC therapy.
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Affiliation(s)
- Jian Fang
- grid.203507.30000 0000 8950 5267Department of Preventive Medicine, Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang People’s Republic of China ,grid.412551.60000 0000 9055 7865College of Medicine, Shaoxing University, 508 Huancheng Road, Shaoxing, Zhejiang Province People’s Republic of China
| | - Hui Wang
- grid.415644.60000 0004 1798 6662Department of Colorectal Surgery, Shaoxing people’s Hospital, 568 North Zhongxing Road, Shaoxing, Zhejiang Province People’s Republic of China
| | - Yuping Zhou
- grid.203507.30000 0000 8950 5267The Affiliated Hospital of Medical School, Ningbo University, 247 Renmin Road, Ningbo, Zhejiang People’s Republic of China
| | - Hui Zhang
- grid.203507.30000 0000 8950 5267Department of Preventive Medicine, Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang People’s Republic of China
| | - Huiting Zhou
- grid.203507.30000 0000 8950 5267Department of Preventive Medicine, Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang People’s Republic of China
| | - Xiaohong Zhang
- grid.203507.30000 0000 8950 5267Department of Preventive Medicine, Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang People’s Republic of China
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ICOS ligand and IL-10 synergize to promote host-microbiota mutualism. Proc Natl Acad Sci U S A 2021; 118:2018278118. [PMID: 33753483 DOI: 10.1073/pnas.2018278118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Genome-wide association studies have identified ICOSLG, which encodes the inducible costimulator ligand (ICOSLG or ICOSL) as a susceptibility locus for inflammatory bowel disease. ICOSL has been implicated in the enhancement of pattern recognition receptor signaling in dendritic cells, induction of IL-10 production by CD4 T cells, and the generation of high-affinity antibodies to specific antigens-all of which can potentially explain its involvement in gastrointestinal inflammation. Here, we show that murine ICOSL deficiency results in significant enrichment of IL-10-producing CD4 T cells particularly in the proximal large intestine. Transient depletion of IL-10-producing cells from adult ICOSL-deficient mice induced severe colonic inflammation that was prevented when mice were first treated with metronidazole. ICOSL-deficient mice displayed reduced IgA and IgG antibodies in the colon mucus and impaired serum antibody recognition of microbial antigens, including flagellins derived from mucus-associated bacteria of the Lachnospiraceae family. Confirming the synergy between ICOSL and IL-10, ICOSL deficiency coupled with CD4-specific deletion of the Il10 gene resulted in juvenile onset colitis that was impeded when pups were fostered by ICOSL-sufficient dams. In this setting, we found that both maternally acquired and host-derived antibodies contribute to the life anti-commensal antibody repertoire that mediates this protection in early life. Collectively, our findings reveal a partnership between ICOSL-dependent anti-commensal antibodies and IL-10 in adaptive immune regulation of the microbiota in the large intestine. Furthermore, we identify ICOSL deficiency as an effective platform for exploring the functions of anti-commensal antibodies in host-microbiota mutualism.
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30
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Nanoparticles in the Food Industry and Their Impact on Human Gut Microbiome and Diseases. Int J Mol Sci 2021; 22:ijms22041942. [PMID: 33669290 PMCID: PMC7920074 DOI: 10.3390/ijms22041942] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/02/2021] [Accepted: 02/10/2021] [Indexed: 12/11/2022] Open
Abstract
The use of inorganic nanoparticles (NPs) has expanded into various industries including food manufacturing, agriculture, cosmetics, and construction. This has allowed NPs access to the human gastrointestinal tract, yet little is known about how they may impact human health. As the gut microbiome continues to be increasingly implicated in various diseases of unknown etiology, researchers have begun studying the potentially toxic effects of these NPs on the gut microbiome. Unfortunately, conflicting results have limited researcher’s ability to evaluate the true impact of NPs on the gut microbiome in relation to health. This review focuses on the impact of five inorganic NPs (silver, iron oxide, zinc oxide, titanium dioxide, and silicon dioxide) on the gut microbiome and gastrointestinal tract with consideration for various methodological differences within the literature. This is important as NP-induced changes to the gut could lead to various gut-related diseases. These include irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), celiac disease, and colorectal cancer. Research in this area is necessary as the use of NPs in various industries continues to grow along with the number of people suffering from chronic gastrointestinal diseases.
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31
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Hero JS, Pisa JH, Raimondo EE, Martínez MA. Proteomic analysis of secretomes from Bacillus sp. AR03: characterization of enzymatic cocktails active on complex carbohydrates for xylooligosaccharides production. Prep Biochem Biotechnol 2021; 51:871-880. [PMID: 33439095 DOI: 10.1080/10826068.2020.1870136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Bacillus sp. AR03 have been described as an important producer of carbohydrate-active enzymes (CAZymes) when growing in a peptone-based medium supplemented with simple sugars and/or carboxymethyl cellulose (CMC) as carbon sources. This work aimed to identify the extracellular enzymatic cocktails through shotgun proteomics. The proteomic analysis showed that enzymes involved in cellulose and xylan degradation were among the most abundant proteins. These enzymes included an endo-glucanase GH5_2 and a glucuronoxylanase GH30_8, which were found in all conditions. In addition, several proteins were differentially expressed in the three evaluated culture media, indicating microbial metabolic changes due to the different supplied carbon sources, particularly, in the presence of CMC. Finally, the capability of the crude enzymatic cocktails from culture media to degrade birchwood xylan was assessed, which produced mostly xylooligosaccharides containing among 3-5 xylose units. Consequently, this work shows the potential of the extracellular enzymes from Bacillus sp. AR03 for producing emergent prebiotics.
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Affiliation(s)
- Johan S Hero
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Tucumán, Argentina
| | - José H Pisa
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Tucumán, Argentina
| | - Enzo E Raimondo
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Tucumán, Argentina.,Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - M Alejandra Martínez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Tucumán, Argentina.,Facultad de Ciencias Exactas y Tecnología, Universidad Nacional de Tucumán, Tucumán, Argentina
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32
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Gomez CL, Neufeld KL. Elevated adenomatous polyposis coli in goblet cells is associated with inflammation in mouse and human colon. Exp Physiol 2020; 105:2154-2167. [PMID: 33150708 DOI: 10.1113/ep088970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/21/2020] [Indexed: 11/08/2022]
Abstract
NEW FINDINGS What is the central question of this study? What is the localization and distribution pattern of adenomatous polyposis coli (APC) in intestinal epithelial cells? Does this distribution change in different regions of the colon or in the condition of inflammation? What is the main finding and its importance? Colonic epithelia from mice and humans contain a subset of goblet cells displaying high APC levels. The number of APChigh goblet cells increases in inflamed tissue, which also displays increased GRP78, indicating potential stress from mucin production. In cultured human colon cells, expression of interleukin 1 pathway components (inducers of MUC2 expression) is reduced upon APC depletion raising the potential for APC participation in an inflammatory response. ABSTRACT Adenomatous polyposis coli (APC) serves as a gatekeeper of intestinal homeostasis by promoting cellular differentiation and maintaining crypt architecture. Although appreciated as a critical colon tumour suppressor, roles for APC in disease states such as inflammation have yet to be fully delineated. This study aimed to characterize the localization of APC protein in gastrointestinal tissues from human patients with active inflammatory bowel disease and mice with dextran sodium sulfate (DSS)-induced colitis. Fluorescence immunohistochemistry revealed a subset of goblet cells with elevated Apc staining intensity in the small intestines and proximal/medial colons of mice. Upon induction of colitis with DSS, these 'APChigh ' goblet cells remained in the proximal and medial colon, but now were also observed in the distal colon. This phenotype was recapitulated in humans, with APChigh goblet cells observed only in the descending colons of patients with active ulcerative colitis. In cultured human colon cells derived from normal tissue, APC depletion reduced expression of mRNAs encoding the interleukin 1 (IL1) signalling pathway components IL1β and interleukin-1 receptor (IL1R), known regulators of Muc2 expression. Treating cancer cells lacking wild-type APC with IL1β, or induction of full-length APC in these cells led to increases in IL1R and MUC2 expression. Combining IL1β treatment with APC induction led to an increase of MUC2 expression greater than expected for additive affects, suggesting that APC sensitizes cells to IL1 signalling. These findings suggest that APC has novel roles in maintaining proper goblet cell function, thus providing further evidence for APC as an important factor in intestinal tissue homeostasis and disease.
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Affiliation(s)
- Christian L Gomez
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Kristi L Neufeld
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
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33
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Labarta-Bajo L, Gramalla-Schmitz A, Gerner RR, Kazane KR, Humphrey G, Schwartz T, Sanders K, Swafford A, Knight R, Raffatellu M, Zúñiga EI. CD8 T cells drive anorexia, dysbiosis, and blooms of a commensal with immunosuppressive potential after viral infection. Proc Natl Acad Sci U S A 2020; 117:24998-25007. [PMID: 32958643 PMCID: PMC7547153 DOI: 10.1073/pnas.2003656117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Infections elicit immune adaptations to enable pathogen resistance and/or tolerance and are associated with compositional shifts of the intestinal microbiome. However, a comprehensive understanding of how infections with pathogens that exhibit distinct capability to spread and/or persist differentially change the microbiome, the underlying mechanisms, and the relative contribution of individual commensal species to immune cell adaptations is still lacking. Here, we discovered that mouse infection with a fast-spreading and persistent (but not a slow-spreading acute) isolate of lymphocytic choriomeningitis virus induced large-scale microbiome shifts characterized by increased Verrucomicrobia and reduced Firmicute/Bacteroidetes ratio. Remarkably, the most profound microbiome changes occurred transiently after infection with the fast-spreading persistent isolate, were uncoupled from sustained viral loads, and were instead largely caused by CD8 T cell responses and/or CD8 T cell-induced anorexia. Among the taxa enriched by infection with the fast-spreading virus, Akkermansia muciniphila, broadly regarded as a beneficial commensal, bloomed upon starvation and in a CD8 T cell-dependent manner. Strikingly, oral administration of A. muciniphila suppressed selected effector features of CD8 T cells in the context of both infections. Our findings define unique microbiome differences after chronic versus acute viral infections and identify CD8 T cell responses and downstream anorexia as driver mechanisms of microbial dysbiosis after infection with a fast-spreading virus. Our data also highlight potential context-dependent effects of probiotics and suggest a model in which changes in host behavior and downstream microbiome dysbiosis may constitute a previously unrecognized negative feedback loop that contributes to CD8 T cell adaptations after infections with fast-spreading and/or persistent pathogens.
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Affiliation(s)
- Lara Labarta-Bajo
- Division of Biological Sciences, University of California San Diego, La Jolla, San Diego, CA 92093
| | - Anna Gramalla-Schmitz
- Division of Biological Sciences, University of California San Diego, La Jolla, San Diego, CA 92093
| | - Romana R Gerner
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093
- Division of Host-Microbe Systems & Therapeutics, University of California San Diego, La Jolla, CA 92093
| | - Katelynn R Kazane
- Division of Biological Sciences, University of California San Diego, La Jolla, San Diego, CA 92093
| | - Gregory Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093
| | - Tara Schwartz
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093
| | - Karenina Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093
| | - Austin Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA 92093
| | - Manuela Raffatellu
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093
- Division of Host-Microbe Systems & Therapeutics, University of California San Diego, La Jolla, CA 92093
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093
- Center for Mucosal Immunology, Allergy, and Vaccines, Chiba University-University of California San Diego, La Jolla, CA 92093
| | - Elina I Zúñiga
- Division of Biological Sciences, University of California San Diego, La Jolla, San Diego, CA 92093;
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34
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Kennedy MS, Chang EB. The microbiome: Composition and locations. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 176:1-42. [PMID: 33814111 DOI: 10.1016/bs.pmbts.2020.08.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The human body is home to a diverse and functionally important assemblage of symbiotic microbes that varies predictably over different spatial scales, both within and across body sites. The composition of these spatially distinct microbial consortia can be impacted by a variety of stochastic and deterministic forces, including dispersal from different source communities, and selection by regionally-specific host processes for the enrichment of physiologically significant taxa. In this chapter, we review the composition, function, and assembly of the healthy human gastrointestinal, skin, vaginal, and respiratory microbiomes, with special emphasis on the regional distribution of microbes throughout the gastrointestinal tract.
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Affiliation(s)
- Megan S Kennedy
- Medical Scientist Training Program, Pritzker School of Medicine, The University of Chicago, Chicago, IL, United States; Department of Ecology & Evolution, The University of Chicago, Chicago, IL, United States
| | - Eugene B Chang
- Department of Medicine, Knapp Center for Biomedical Discovery, The University of Chicago, Chicago, IL, United States.
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35
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Cambeiro-Pérez N, Hidalgo-Cantabrana C, Moro-García MA, Blanco-Míguez A, Fdez-Riverola F, Riestra S, Lourenço A, Alonso-Arias R, Margolles A, Martínez-Carballo E, Sánchez B. In silico and functional analyses of immunomodulatory peptides encrypted in the human gut metaproteome. J Funct Foods 2020. [DOI: 10.1016/j.jff.2020.103969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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36
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Spatial Compartmentalization of the Microbiome between the Lumen and Crypts Is Lost in the Murine Cecum following the Process of Surgery, Including Overnight Fasting and Exposure to Antibiotics. mSystems 2020; 5:5/3/e00377-20. [PMID: 32518197 PMCID: PMC7289591 DOI: 10.1128/msystems.00377-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The cecum is a unique region in the mammalian intestinal tract in which the microbiome is localized to two compartments, the lumen and the crypts. The microbiome within crypts is particularly important as it is in direct contact with lining epithelial cells including stem cells. Here, we analyzed the microbiome in cecum of mice using multiple techniques including metagenomics. The lumen microbiome comprised Firmicutes and Bacteroidetes whereas the crypts were dominated by Proteobacteria and Deferribacteres, and the mucus comprised a mixture of these 4 phyla. The lumen microbial functional potential comprised mainly carbon metabolism, while the crypt microbiome was enriched for genes encoding stress resistance. In order to determine how this structure, assembly, and function are altered under provocative conditions, we exposed mice to overnight starvation (S), antibiotics (A), and a major surgical injury (partial hepatectomy [H]), as occurs with major surgery in humans. We have previously demonstrated that the combined effect of this "SAH" treatment leads to a major disturbance of the cecal microbiota at the bottom of crypts in a manner that disrupts crypt cell homeostasis. Here, we applied the SAH conditions and observed a loss of compartmentalization in both composition and function of the cecal microbiome associated with major shifts in local physicochemical cues including decrease of hypoxia, increase of pH, and loss of butyrate production. Taken together, these studies demonstrated a defined order, structure, and function of the cecal microbiome that can be disrupted under provocative conditions such as major surgery and its attendant exposures.IMPORTANCE The proximal colon and cecum are two intestinal regions in which the microbiome localizes to two spatially distinct compartments, the lumen and crypts. The differences in composition and function of luminal and crypt microbiome in the cecum and the effect of physiological stress on their compartmentalization remain poorly characterized. Here, we characterized the composition and function of the lumen-, mucus-, and crypt-associated microbiome in the cecum of mice. We observed a highly ordered microbial architecture within the cecum whose assembly and function become markedly disrupted when provoked by physiological stress such as surgery and its attendant preoperative treatments (i.e., overnight fasting and antibiotics). Major shifts in local physicochemical cues including a decrease in hypoxia levels, an increase in pH, and a loss of butyrate production were associated with the loss of compositional and functional compartmentalization of the cecal microbiome.
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37
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Herath M, Hosie S, Bornstein JC, Franks AE, Hill-Yardin EL. The Role of the Gastrointestinal Mucus System in Intestinal Homeostasis: Implications for Neurological Disorders. Front Cell Infect Microbiol 2020; 10:248. [PMID: 32547962 PMCID: PMC7270209 DOI: 10.3389/fcimb.2020.00248] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/29/2020] [Indexed: 12/19/2022] Open
Abstract
Mucus is integral to gut health and its properties may be affected in neurological disease. Mucus comprises a hydrated network of polymers including glycosylated mucin proteins. We propose that factors that influence the nervous system may also affect the volume, viscosity, porosity of mucus composition and subsequently, gastrointestinal (GI) microbial populations. The gut has its own intrinsic neuronal network, the enteric nervous system, which extends the length of the GI tract and innervates the mucosal epithelium. The ENS regulates gut function including mucus secretion and renewal. Both dysbiosis and gut dysfunction are commonly reported in several neurological disorders such as Parkinson's and Alzheimer's disease as well in patients with neurodevelopmental disorders including autism. Since some microbes use mucus as a prominent energy source, changes in mucus properties could alter, and even exacerbate, dysbiosis-related gut symptoms in neurological disorders. This review summarizes existing knowledge of the structure and function of the mucus of the GI tract and highlights areas to be addressed in future research to better understand how intestinal homeostasis is impacted in neurological disorders.
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Affiliation(s)
- Madushani Herath
- Department of Physiology, University of Melbourne, Parkville, VIC, Australia
| | - Suzanne Hosie
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Joel C Bornstein
- Department of Physiology, University of Melbourne, Parkville, VIC, Australia
| | - Ashley E Franks
- School of Life Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Elisa L Hill-Yardin
- Department of Physiology, University of Melbourne, Parkville, VIC, Australia.,School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
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38
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Kämpfer AAM, Busch M, Schins RPF. Advanced In Vitro Testing Strategies and Models of the Intestine for Nanosafety Research. Chem Res Toxicol 2020; 33:1163-1178. [PMID: 32383381 DOI: 10.1021/acs.chemrestox.0c00079] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
There is growing concern about the potential adverse effects of oral exposure to engineered nanomaterials (ENM). Recent years have witnessed major developments in and advancement of intestinal in vitro models for nanosafety evaluation. The present paper reviews the key factors that should be considered for inclusion in nonanimal alternative testing approaches to reliably reflect the in vivo dynamics of the physicochemical properties of ENM as well the intestinal physiology and morphology. Currently available models range from simple cell line-based monocultures to advanced 3D systems and organoids. In addition, in vitro approaches exist to replicate the mucous barrier, digestive processes, luminal flow, peristalsis, and interactions of ENM with the intestinal microbiota. However, while the inclusion of a multitude of individual factors/components of particle (pre)treatment, exposure approach, and cell model approximates in vivo-like conditions, such increasing complexity inevitably affects the system's robustness and reproducibility. The selection of the individual modules to build the in vitro testing strategy should be driven and justified by the specific purpose of the study and, not least, the intended or actual application of the investigated ENM. Studies that address health hazards of ingested ENM likely require different approaches than research efforts to unravel the fundamental interactions or toxicity mechanisms of ENM in the intestine. Advanced reliable and robust in vitro models of the intestine, especially when combined in an integrated testing approach, offer great potential to further improve the field of nanosafety research.
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Affiliation(s)
- Angela A M Kämpfer
- Leibniz Research Institute for Environmental Medicine, IUF, 40225 Düsseldorf, Germany
| | - Mathias Busch
- Leibniz Research Institute for Environmental Medicine, IUF, 40225 Düsseldorf, Germany
| | - Roel P F Schins
- Leibniz Research Institute for Environmental Medicine, IUF, 40225 Düsseldorf, Germany
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Swimming motility of a gut bacterial symbiont promotes resistance to intestinal expulsion and enhances inflammation. PLoS Biol 2020; 18:e3000661. [PMID: 32196484 PMCID: PMC7112236 DOI: 10.1371/journal.pbio.3000661] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/01/2020] [Accepted: 02/24/2020] [Indexed: 01/07/2023] Open
Abstract
Some of the densest microbial ecosystems in nature thrive within the intestines of humans and other animals. To protect mucosal tissues and maintain immune tolerance, animal hosts actively sequester bacteria within the intestinal lumen. In response, numerous bacterial pathogens and pathobionts have evolved strategies to subvert spatial restrictions, thereby undermining immune homeostasis. However, in many cases, it is unclear how escaping host spatial control benefits gut bacteria and how changes in intestinal biogeography are connected to inflammation. A better understanding of these processes could uncover new targets for treating microbiome-mediated inflammatory diseases. To this end, we investigated the spatial organization and dynamics of bacterial populations within the intestine using larval zebrafish and live imaging. We discovered that a proinflammatory Vibrio symbiont native to zebrafish governs its own spatial organization using swimming motility and chemotaxis. Surprisingly, we found that Vibrio’s motile behavior does not enhance its growth rate but rather promotes its persistence by enabling it to counter intestinal flow. In contrast, Vibrio mutants lacking motility traits surrender to host spatial control, becoming aggregated and entrapped within the lumen. Consequently, nonmotile and nonchemotactic mutants are susceptible to intestinal expulsion and experience large fluctuations in absolute abundance. Further, we found that motile Vibrio cells induce expression of the proinflammatory cytokine tumor necrosis factor alpha (TNFα) in gut-associated macrophages and the liver. Using inducible genetic switches, we demonstrate that swimming motility can be manipulated in situ to modulate the spatial organization, persistence, and inflammatory activity of gut bacterial populations. Together, our findings suggest that host spatial control over resident microbiota plays a broader role in regulating the abundance and persistence of gut bacteria than simply protecting mucosal tissues. Moreover, we show that intestinal flow and bacterial motility are potential targets for therapeutically managing bacterial spatial organization and inflammatory activity within the gut. The use of live imaging and bacteria engineered to carry inducible genetic switches reveals how a gut symbiont uses swimming motility to escape the host's spatial control and persist within the physically dynamic confines of the intestine.
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Dai Z, Zhang J, Wu Q, Chen J, Liu J, Wang L, Chen C, Xu J, Zhang H, Shi C, Li Z, Fang H, Lin C, Tang D, Wang D. The role of microbiota in the development of colorectal cancer. Int J Cancer 2019; 145:2032-2041. [PMID: 30474116 PMCID: PMC6899977 DOI: 10.1002/ijc.32017] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 10/25/2018] [Accepted: 11/13/2018] [Indexed: 02/05/2023]
Abstract
Colorectal cancer is the third largest cancer in worldwide and has been proven to be closely related to the intestinal microbiota. Many reports and clinical studies have shown that intestinal microbial behavior may lead to pathological changes in the host intestines. The changes can be divided into epigenetic changes and carcinogenic changes at the gene level, which ultimately promote the production and development of colorectal cancer. This article reviews the pathways of microbial signaling in the intestinal epithelial barrier, the role of microbiota in inflammatory colorectal tumors, and typical microbial carcinogenesis. Finally, by gaining a deeper understanding of the intestinal microbiota, we hope to achieve the goal of treating colorectal cancer using current microbiota technologies, such as fecal microbiological transplantation.
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Affiliation(s)
- Zhujiang Dai
- Clinical Medical CollegeYangzhou UniversityYangzhouJiangsu ProvinceChina
| | - Jingqiu Zhang
- Department of General SurgeryInstitute of General Surgery, Clinical Medical College, Yangzhou University, Northern Jiangsu People's HospitalYangzhouChina
| | - Qi Wu
- Clinical Medical CollegeYangzhou UniversityYangzhouJiangsu ProvinceChina
| | - Juan Chen
- Department of GastroenterologyClinical Medical College, Yangzhou University, Northern Jiangsu People's HospitalYangzhouChina
| | - Jun Liu
- Department of GastroenterologyClinical Medical College, Yangzhou University, Northern Jiangsu People's HospitalYangzhouChina
| | - Lu Wang
- Department of GastroenterologyClinical Medical College, Yangzhou University, Northern Jiangsu People's HospitalYangzhouChina
| | - Chaowu Chen
- Department of GastroenterologyClinical Medical College, Yangzhou University, Northern Jiangsu People's HospitalYangzhouChina
| | - Jiaming Xu
- Department of General SurgeryInstitute of General Surgery, Clinical Medical College, Yangzhou University, Northern Jiangsu People's HospitalYangzhouChina
| | - Hongpeng Zhang
- Department of General SurgeryInstitute of General Surgery, Clinical Medical College, Yangzhou University, Northern Jiangsu People's HospitalYangzhouChina
| | - Chunfeng Shi
- Clinical Medical CollegeYangzhou UniversityYangzhouJiangsu ProvinceChina
| | - Zhen Li
- Clinical Medical CollegeYangzhou UniversityYangzhouJiangsu ProvinceChina
| | - Huiwen Fang
- Clinical Medical CollegeYangzhou UniversityYangzhouJiangsu ProvinceChina
| | - Chaobiao Lin
- Clinical Medical CollegeYangzhou UniversityYangzhouJiangsu ProvinceChina
| | - Dong Tang
- Department of General SurgeryInstitute of General Surgery, Clinical Medical College, Yangzhou University, Northern Jiangsu People's HospitalYangzhouChina
| | - Daorong Wang
- Department of General SurgeryInstitute of General Surgery, Clinical Medical College, Yangzhou University, Northern Jiangsu People's HospitalYangzhouChina
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Datt C, Elfring GJ. Active Particles in Viscosity Gradients. PHYSICAL REVIEW LETTERS 2019; 123:158006. [PMID: 31702312 DOI: 10.1103/physrevlett.123.158006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Indexed: 06/10/2023]
Abstract
Microswimmers in nature often experience spatial gradients of viscosity. In this Letter we develop theoretical results for the dynamics of active particles, biological or otherwise, swimming through viscosity gradients. We model the active particles using the squirmer model, and show how viscosity gradients lead to viscotaxis for squirmers, and how the effects of viscosity gradients depend on the swimming gait of the microswimmers. We also show how such gradients in viscosity can be used to control active particles and suggest a mechanism to sort them based on their swimming style.
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Affiliation(s)
- Charu Datt
- Department of Mechanical Engineering and Institute of Applied Mathematics, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Gwynn J Elfring
- Department of Mechanical Engineering and Institute of Applied Mathematics, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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Courson DS, Pokhrel A, Scott C, Madrill M, Rinehold AJ, Tamayo R, Cheney RE, Purcell EB. Single cell analysis of nutrient regulation of Clostridioides (Clostridium) difficile motility. Anaerobe 2019; 59:205-211. [PMID: 31386902 PMCID: PMC6785396 DOI: 10.1016/j.anaerobe.2019.102080] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/10/2019] [Accepted: 07/25/2019] [Indexed: 11/24/2022]
Abstract
Regulation of bacterial motility to maximize nutrient acquisition or minimize exposure to harmful substances plays an important role in microbial proliferation and host colonization. The technical difficulties of performing high-resolution live microscopy on anaerobes have hindered mechanistic studies of motility in Clostridioides (formerly Clostridium) difficile. Here, we present a widely applicable protocol for live cell imaging of anaerobic bacteria that has allowed us to characterize C. difficile swimming at the single-cell level. This accessible method for anaerobic live cell microscopy enables inquiry into previously inaccessible aspects of C. difficile physiology and behavior. We present the first report that vegetative C. difficile are capable of regulated motility in the presence of different nutrients. We demonstrate that the epidemic C. difficile strain R20291 exhibits regulated motility in the presence of multiple nutrient sources by modulating its swimming velocity. This is a powerful illustration of the ability of single-cell studies to explain population-wide phenomena such as dispersal through the environment.
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Affiliation(s)
- David S Courson
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Astha Pokhrel
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Cody Scott
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Melissa Madrill
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Alden J Rinehold
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Richard E Cheney
- Department of Cell Biology and Physiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Erin B Purcell
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA.
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Predicting the Longitudinally and Radially Varying Gut Microbiota Composition Using Multi-Scale Microbial Metabolic Modeling. Processes (Basel) 2019. [DOI: 10.3390/pr7070394] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background: The gut microbiota is a heterogeneous group of microbes that is spatially distributed along various sections of the intestines and across the mucosa and lumen in each section. Understanding the dynamics between the spatially differential microbial populations and the driving forces for the observed spatial organization will provide valuable insights into important questions such as the nature of colonization of the infant gut and different types of inflammatory bowel disease localized in different regions of the intestines. However, in most studies, the microbiota is sampled only at a single site (often feces) or from a particular anatomical site of the intestines. Differential oxygen availability is putatively a key factor shaping the spatial organization. Results: To test this hypothesis, we constructed a community genome-scale metabolic model consisting of representative organisms for the major phyla present in the human gut microbiome. By solving step-wise optimization problems embedded in a dynamic framework to predict community metabolism and integrate the mucosally-adherent with the luminal microbiome between consecutive sections along the intestines, we were able to capture (i) the essential features of the spatially differential composition of obligate anaerobes vs. facultative anaerobes and aerobes determined experimentally, and (ii) the accumulation of microbial biomass in the lumen. Sensitivity analysis suggests that the spatial organization depends primarily on the oxygen-per-microbe availability in each region. Oxygen availability is reduced relative to the ~100-fold increase in mucosal microbial density along the intestines, causing the switch between aerobes and anaerobes. Conclusion: The proposed integrated dynamic framework is able to predict spatially differential gut microbiota composition using microbial genome-scale metabolic models and test hypotheses regarding the dynamics of the gut microbiota. It can potentially become a valuable tool for exploring therapeutic strategies for site-specific perturbation of the gut microbiota and the associated metabolic activities.
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Microbiota: Overview and Implication in Immunotherapy-Based Cancer Treatments. Int J Mol Sci 2019; 20:ijms20112699. [PMID: 31159348 PMCID: PMC6600175 DOI: 10.3390/ijms20112699] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/17/2019] [Accepted: 05/26/2019] [Indexed: 12/12/2022] Open
Abstract
During the last few years, the gut microbiota has gained increasing attention as a consequence of its emerging role as a modulator of the immune system. With the advent of the era of checkpoint inhibitors immunotherapy and adoptive cell transfer (ACT) in oncology, these findings became of primary relevance in light of experimental data that suggested the microbiota involvement as a plausible predictor of a good or poor response. These remarks justify the efforts to pinpoint the specific actions of the microbiota and to identify new strategies to favorably edit its composition.
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Miller KA, Vicentini FA, Hirota SA, Sharkey KA, Wieser ME. Antibiotic treatment affects the expression levels of copper transporters and the isotopic composition of copper in the colon of mice. Proc Natl Acad Sci U S A 2019; 116:5955-5960. [PMID: 30850515 PMCID: PMC6442602 DOI: 10.1073/pnas.1814047116] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Copper is a critical enzyme cofactor in the body but also a potent cellular toxin when intracellularly unbound. Thus, there is a delicate balance of intracellular copper, maintained by a series of complex interactions between the metal and specific copper transport and binding proteins. The gastrointestinal (GI) tract is the primary site of copper entry into the body and there has been considerable progress in understanding the intricacies of copper metabolism in this region. The GI tract is also host to diverse bacterial populations, and their role in copper metabolism is not well understood. In this study, we compared the isotopic fractionation of copper in the GI tract of mice with intestinal microbiota significantly depleted by antibiotic treatment to that in mice not receiving such treatment. We demonstrated variability in copper isotopic composition along the length of the gut. A significant difference, ∼1.0‰, in copper isotope abundances was measured in the proximal colon of antibiotic-treated mice. The changes in copper isotopic composition in the colon are accompanied by changes in copper transporters. Both CTR1, a copper importer, and ATP7A, a copper transporter across membranes, were significantly down-regulated in the colon of antibiotic-treated mice. This study demonstrated that isotope abundance measurements of metals can be used as an indicator of changes in metabolic processes in vivo. These measurements revealed a host-microbial interaction in the GI tract involved in the regulation of copper transport.
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Affiliation(s)
- Kerri A Miller
- Department of Physics and Astronomy, University of Calgary, Calgary, AB, Canada T2N 1N4;
| | - Fernando A Vicentini
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada T2N 4N1
| | - Simon A Hirota
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada T2N 4N1
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada T2N 4N1
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada T2N 4N1
| | - Keith A Sharkey
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada T2N 4N1
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada T2N 4N1
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada T2N 4N1
| | - Michael E Wieser
- Department of Physics and Astronomy, University of Calgary, Calgary, AB, Canada T2N 1N4
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The interaction between smoking, alcohol and the gut microbiome. Best Pract Res Clin Gastroenterol 2017; 31:579-588. [PMID: 29195678 DOI: 10.1016/j.bpg.2017.10.006] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/17/2017] [Accepted: 10/20/2017] [Indexed: 02/08/2023]
Abstract
The gastrointestinal microbiome is a complex echosystem that establishes a symbiotic, mutually beneficial relation with the host, being rather stable in health, but affected by age, drugs, diet, alcohol, and smoking. Alcohol and smoking contribute to changes in the stomach and affect H pylori-related disorders including the risk of gastric cancer. In the small intestine and in the colon alcohol causes depletion of bacteria with anti-inflammatory activity, eventually resulting in intestinal damage with "leaky gut". These changes contribute to hepatic damage in both alcoholic and non-alcoholic liver disease and have been associated with other disorders. Lactobacillus GG and A. muciniphila exert a protective effect in this setting. Smoking leads to modifications of the gut microbiome linked with a protective effect toward ulcerative colitis and deleterious for Crohn's disease. The exact cause-effect relation between alcohol and smoking and changes of the gastrointestinal microbiome needs further exploration with high throughput methodologies, and controlled studies are necessary to define the role of microbiome modulation on the immune response and systemic activation of pro-inflammatory pathways.
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47
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Tropini C, Earle KA, Huang KC, Sonnenburg JL. The Gut Microbiome: Connecting Spatial Organization to Function. Cell Host Microbe 2017; 21:433-442. [PMID: 28407481 DOI: 10.1016/j.chom.2017.03.010] [Citation(s) in RCA: 408] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The first rudimentary evidence that the human body harbors a microbiota hinted at the complexity of host-associated microbial ecosystems. Now, almost 400 years later, a renaissance in the study of microbiota spatial organization, driven by coincident revolutions in imaging and sequencing technologies, is revealing functional relationships between biogeography and health, particularly in the vertebrate gut. In this Review, we present our current understanding of principles governing the localization of intestinal bacteria, and spatial relationships between bacteria and their hosts. We further discuss important emerging directions that will enable progressing from the inherently descriptive nature of localization and -omics technologies to provide functional, quantitative, and mechanistic insight into this complex ecosystem.
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Affiliation(s)
- Carolina Tropini
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kristen A Earle
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
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Interaction Between Familial Transmission and a Constitutively Active Immune System Shapes Gut Microbiota in Drosophila melanogaster. Genetics 2017; 206:889-904. [PMID: 28413160 PMCID: PMC5499193 DOI: 10.1534/genetics.116.190215] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 03/31/2017] [Indexed: 12/14/2022] Open
Abstract
Resident gut bacteria are constantly influencing the immune system, yet the role of the immune system in shaping microbiota composition during an organism’s life span has remained unclear. Experiments in mice have been inconclusive due to differences in husbandry schemes that led to conflicting results. We used Drosophila as a genetically tractable system with a simpler gut bacterial population structure streamlined genetic backgrounds and established cross schemes to address this issue. We found that, depending on their genetic background, young flies had microbiota of different diversities that converged with age to the same Acetobacteraceae-dominated pattern in healthy flies. This pattern was accelerated in immune-compromised flies with higher bacterial load and gut cell death. Nevertheless, immune-compromised flies resembled their genetic background, indicating that familial transmission was the main force regulating gut microbiota. In contrast, flies with a constitutively active immune system had microbiota readily distinguishable from their genetic background with the introduction and establishment of previously undetectable bacterial families. This indicated the influence of immunity over familial transmission. Moreover, hyperactive immunity and increased enterocyte death resulted in the highest bacterial load observed starting from early adulthood. Cohousing experiments showed that the microenvironment also played an important role in the structure of the microbiota where flies with constitutive immunity defined the gut microbiota of their cohabitants. Our data show that, in Drosophila, constitutively active immunity shapes the structure and density of gut microbiota.
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Moschen AR, Gerner RR, Wang J, Klepsch V, Adolph TE, Reider SJ, Hackl H, Pfister A, Schilling J, Moser PL, Kempster SL, Swidsinski A, Orth Höller D, Weiss G, Baines JF, Kaser A, Tilg H. Lipocalin 2 Protects from Inflammation and Tumorigenesis Associated with Gut Microbiota Alterations. Cell Host Microbe 2016; 19:455-69. [PMID: 27078067 DOI: 10.1016/j.chom.2016.03.007] [Citation(s) in RCA: 255] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/29/2016] [Accepted: 03/24/2016] [Indexed: 12/12/2022]
Abstract
High mucosal and fecal concentrations of the antimicrobial siderophore-binding peptide Lipocalin-2 (Lcn2) are observed in inflammatory bowel disease. However, Lcn2 function in chronic intestinal inflammation remains unclear. Here, we demonstrate that Lcn2 protects from early-onset colitis and spontaneous emergence of right-sided colonic tumors resulting from IL-10 deficiency. Exacerbated inflammation in Lcn2(-/-)/Il10(-/-) mice is driven by IL-6, which also controls tumorigenesis. Lcn2(-/-)/Il10(-/-) mice exhibit profound alterations in gut microbial composition, which contributes to inflammation and tumorigenesis, as demonstrated by the transmissibility of the phenotype and protection conferred by antibiotics. Specifically, facultative pathogenic Alistipes spp. utilize enterobactin as iron source, bloom in Lcn2(-/-)/Il10(-/-) mice, and are sufficient to induce colitis and right-sided tumors when transferred into Il10(-/-) mice. Our results demonstrate that Lcn2 protects against intestinal inflammation and tumorigenesis associated with alterations in the microbiota.
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Affiliation(s)
- Alexander R Moschen
- Division of Internal Medicine I (Gastroenterology, Endocrinology and Metabolism), Department of Medicine, Medical University Innsbruck, Innsbruck 6020, Austria.
| | - Romana R Gerner
- Division of Internal Medicine I (Gastroenterology, Endocrinology and Metabolism), Department of Medicine, Medical University Innsbruck, Innsbruck 6020, Austria
| | - Jun Wang
- Max Planck Institute for Evolutionary Biology, Plön 24308, Germany; Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel 24118, Germany
| | - Victoria Klepsch
- Department of Medical Genetics, Molecular and Clinical Pharmacology, Division of Translational Cell Genetics, Medical University Innsbruck, Innsbruck 6020, Austria
| | - Timon E Adolph
- Division of Internal Medicine I (Gastroenterology, Endocrinology and Metabolism), Department of Medicine, Medical University Innsbruck, Innsbruck 6020, Austria
| | - Simon J Reider
- Division of Internal Medicine I (Gastroenterology, Endocrinology and Metabolism), Department of Medicine, Medical University Innsbruck, Innsbruck 6020, Austria
| | - Hubert Hackl
- Division of Bioinformatics, Biocenter Innsbruck, Medical University Innsbruck, Innsbruck 6020, Austria
| | - Alexandra Pfister
- Division of Internal Medicine I (Gastroenterology, Endocrinology and Metabolism), Department of Medicine, Medical University Innsbruck, Innsbruck 6020, Austria
| | - Johannes Schilling
- Charité Hospital, CCM, Laboratory for Molecular Genetics, Polymicrobial Infections and Bacterial Biofilms and Department of Medicine, Gastroenterology, Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Patrizia L Moser
- Department of Pathology, Medical University Innsbruck, Innsbruck 6020, Austria
| | - Sarah L Kempster
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Alexander Swidsinski
- Charité Hospital, CCM, Laboratory for Molecular Genetics, Polymicrobial Infections and Bacterial Biofilms and Department of Medicine, Gastroenterology, Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Dorothea Orth Höller
- Division of Hygiene and Medical Microbiology, Department of Hygiene, Microbiology and Social Medicine, Medical University Innsbruck, Innsbruck 6020, Austria
| | - Günter Weiss
- Division of Internal Medicine VI (Infectious Diseases, Immunology, Rheumatology and Pneumology), Department of Medicine, Medical University Innsbruck, Innsbruck 6020, Austria
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, Plön 24308, Germany; Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel 24118, Germany
| | - Arthur Kaser
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Herbert Tilg
- Division of Internal Medicine I (Gastroenterology, Endocrinology and Metabolism), Department of Medicine, Medical University Innsbruck, Innsbruck 6020, Austria.
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Aguirre Valadez JM, Rivera-Espinosa L, Méndez-Guerrero O, Chávez-Pacheco JL, García Juárez I, Torre A. Intestinal permeability in a patient with liver cirrhosis. Ther Clin Risk Manag 2016; 12:1729-1748. [PMID: 27920543 PMCID: PMC5125722 DOI: 10.2147/tcrm.s115902] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Liver cirrhosis is a worldwide public health problem, and patients with this disease are at high risk of developing complications, bacterial translocation from the intestinal lumen to the mesenteric nodes, and systemic circulation, resulting in the development of severe complications related to high mortality rate. The intestinal barrier is a structure with a physical and biochemical activity to maintain balance between the external environment, including bacteria and their products, and the internal environment. Patients with liver cirrhosis develop a series of alterations in different components of the intestinal barrier directly associated with the severity of liver disease that finally increased intestinal permeability. A "leaky gut" is an effect produced by damaged intestinal barrier; alterations in the function of tight junction proteins are related to bacterial translocation and their products. Instead, increasing serum proinflammatory cytokines and hemodynamics modification, which results in the appearance of complications of liver cirrhosis such as hepatic encephalopathy, variceal hemorrhage, bacterial spontaneous peritonitis, and hepatorenal syndrome. The intestinal microbiota plays a fundamental role in maintaining the proper function of the intestinal barrier; bacterial overgrowth and dysbiosis are two phenomena often present in people with liver cirrhosis favoring bacterial translocation. Increased intestinal permeability has an important role in the genesis of these complications, and treating it could be the base for prevention and partial treatment of these complications.
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Affiliation(s)
| | | | - Osvely Méndez-Guerrero
- Department of Gastroenterology, Instituto Nacional de Ciencias Médicas y Nutrición”Salvador Zubirán
| | | | - Ignacio García Juárez
- Department of Gastroenterology, Instituto Nacional de Ciencias Médicas y Nutrición”Salvador Zubirán
| | - Aldo Torre
- Department of Gastroenterology, Instituto Nacional de Ciencias Médicas y Nutrición”Salvador Zubirán
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