• B. flexus
• PGPR traits
• antioxidant
• metabolites
• salt stress

• 16S rRNA sequencing
• 16S-ITS-23S
• Oxford Nanopore Technology (ONT)
• PacBio
• RRN operon
• long-read sequencing

• RNA, Ribosomal, 16S/genetics
• Microbiota/genetics
• Operon
• High-Throughput Nucleotide Sequencing/methods
• Bacteria/genetics
• Bacteria/classification
• RNA, Ribosomal, 23S/genetics
• Sequence Analysis, DNA/methods
• rRNA Operon
• Phylogeny

• 2020018 Teagasc Walsh Scholar Scheme
• SFI/16/RC/3835 Science Foundation Ireland, VistaMilk
• SFI/12/RC/2273_P2 Science Foundation Ireland, APC Microbiome

• Abdominal infection
• Broad-spectrum bacterial nucleic acid detection
• Children
• Diagnosis and treatment
• Psychological stress

• bioinformatics analysis
• experimental procedures
• gut microecology
• technical specifications

• Bacterial antibiotic resistance
• Host immunity
• Host-phage interaction
• Microbial single-cell sequencing
• Microorganisms
• Single cell
• Single-cell sequencing technology

• Next Generation Sequencing
• celiac disease
• culture
• gastrointestinal microbiome
• polymerase chain reaction

• ICI immunotherapy
• biomarkers
• computational models
• prediction of treatment effectiveness
• tumor

• Humans
• B7-H1 Antigen/metabolism
• Neoplasms/drug therapy
• Neoplasms/genetics
• Biomarkers, Tumor/genetics
• Immunotherapy/methods
• Immune Checkpoint Inhibitors/pharmacology
• Immune Checkpoint Inhibitors/therapeutic use
• Tumor Microenvironment

• 16S rRNA gene
• Ancient DNA
• Bioinformatics
• Dental calculus
• Hybridization capture
• Oral microbiome
• Paleomicrobiology
• Shotgun metagenomics

• Humans
• RNA, Ribosomal, 16S/genetics
• Benchmarking
• Genes, rRNA
• Dental Calculus
• Microbiota
• DNA, Ancient

• 16S rRNA
• forensic microbiome
• individual identification
• machine learning
• review

• microbiome analysis
• network diagram
• parasitic tick
• questing tick
• symbiotic bacteria

• National Natural Science Foundation of China

• Gut-brain axis
• Liquid chromatography-mass spectrometry
• Metabolomics
• Microbiome
• Schizophrenia

• Humans
• Feces/microbiology
• RNA, Ribosomal, 16S/genetics
• RNA, Ribosomal, 16S/metabolism
• Schizophrenia
• Dysbiosis/complications
• Dysbiosis/microbiology
• Metabolomics

• Shanghai Key Laboratory of Psychotic Disorders Open Grant
• Natural Science Research Projects in Anhui Universities
• Applied Medicine Research Project of Hefei Health Committee
• Applied medicine research project of Anhui Health Committee
• Key Research and Development Plan of Anhui Provincial Department of Science and Technology
• Academy of Forensic Science

• Acinetobacter
• Bacillus
• Baijiu production
• Daqu
• high-throughput sequencing
• specific primer PCR

• Wastewater
• RNA, Ribosomal, 16S/genetics
• Phylogeny
• Permissiveness
• Plasmids/genetics
• Microbiota
• Gene Transfer, Horizontal

• MR/P028195/1 Medical Research Council
• Joint Programming Initiative on Antimicrobial Resistance
• Danish Innovation Foundation

• Climate change
• Metagenomics
• Microbial communities
• Rhizosphere
• Soil microbiome

• Ecosystem
• Climate Change
• Soil/chemistry
• Forests
• Microbiota
• Nitrogen/analysis
• Soil Microbiology
• Carbon

• Breg cells
• Bregs cytokines
• Bregs phonotypes
• cancers
• microbiota
• parasite diseases

• Immunotherapy

• bronchoalveolar lavage fluid
• children
• drug resistance
• hematological malignancies
• lower respiratory tract infection
• lung microbiome
• microbial tolerance
• unfavorable environment

• Natural Science Foundation of Shandong Province
• Qilu Hospital of Shandong University

• Community ecology
• Data curation
• Database management
• Ecosystem-specific database
• Meta-omics
• Microbiome
• Microbiota

• Joyce 2017-00242 Svenska Forskningsrådet Formas
• Joyce 2017-00242 Svenska Forskningsrådet Formas
• Joyce 2020-03175 European Union ERA-Net Cofund on Food Systems and Climate Project
• Joyce 2020-03175 European Union ERA-Net Cofund on Food Systems and Climate Project
• Institut Français de Recherche pour l'Exploitation de la Mer
• University of Gothenburg

• Aryl hydrocarbon receptor
• Bacterial function
• Gastrointestinal motility
• Gut microbiota
• Polychlorinated biphenyl 126

• Animals
• Dioxins
• Environmental Pollutants/toxicity
• Gastrointestinal Microbiome
• Male
• Mice
• Mice, Inbred C57BL
• Polychlorinated Biphenyls/toxicity
• Polychlorinated Dibenzodioxins/toxicity
• Receptors, Aryl Hydrocarbon/genetics
• Receptors, Aryl Hydrocarbon/metabolism

As screens are increasingly integrated into every facet of modern life, there is growing concern over the potential effects of high screen time. Previous studies have largely utilized self-report data on mood and behavioral aspects of screen time, and no molecular theory has yet been developed. In this study, we explored the fecal microbiome and metabolome of a diverse group of 60 college students, classified by high (≥ 75 min/day) or low (0–75 min/day) self-reported screen time using 16S rRNA amplicon sequencing, targeted liquid chromatography-tandem mass spectrometry, and targeted detection of short-chain fatty acids using gas chromatography-mass spectrometry. Several key taxa and metabolites were significantly altered between groups and found to be highly co-occurrent. Results of pathway and enzyme enrichment analyses were synthesized to articulate an integrated hypothesis indicating widespread mitochondrial dysfunction and aberrant amino acid metabolism. High screen time was also predicted to be significantly associated with type I diabetes, obesity, chronic fatigue syndrome, and various manifestations of inflammatory bowel. This is the first-ever study to report the effects of high screen time at the molecular level, and these results provide a data-driven hypothesis for future experimental research.

• metagenomics
• microbiome
• next generation sequencing
• prostate cancer

• Genitalia, Male/microbiology
• Humans
• Male
• Metagenomics/methods
• Microbiota/genetics
• Precision Medicine
• Prostatic Neoplasms/genetics
• Prostatic Neoplasms/metabolism
• Prostatic Neoplasms/therapy

In cancer patients, the clinical response to checkpoint-based immunotherapy is associated with the composition and functional quality of the host microbiome. While the relevance of the gut microbiome for checkpoint immunotherapy outcome has been addressed intensively, data on the role of the local tumor microbiome are missing. Here, we set out to molecularly characterize the local non-small cell lung cancer microbiome using 16S rRNA gene amplicon sequencing of bronchoscopic tumor biopsies from patients treated with PD-1/PD-L1-targeted checkpoint inhibitors. Our analyses showed significant diversity of the tumor microbiome with high proportions of Firmicutes, Bacteroidetes and Proteobacteria. Correlations with clinical data revealed that high microbial diversity was associated with improved patient survival irrespective of radiology-based treatment response. Moreover, we found that the presence of Gammaproteobacteria correlated with low PD-L1 expression and poor response to checkpoint-based immunotherapy, translating into poor survival. Our study suggests novel microbiome-specific/derived biomarkers for checkpoint immunotherapy response prediction and prognosis in lung cancer. In a broader sense, our data draw attention to the local tumor microbial habitat as an important addition to the spatially separated microbiome of the gut compartment.

Over the past decades, a large amount of data has been accumulated in various subfields of glycobiology. However, much clinically relevant data and many tools are still not widely used in medicine. Synthetic glycoconjugates with the known structure of glycans are an accurate tool for the study of glycan-binding proteins. We used polyacrylamide glycoconjugates (PGs) including PGs with tumour-associated glycans (TAGs) in immunoassays to assess the prognostic potential of the serum level of anti-glycan antibodies (AG Abs) in gastrointestinal cancer patients and found an association of AG Abs with survival. The specificity of affinity-isolated AG Abs was investigated using synthetic and natural glycoconjugates. AG Abs showed mainly a low specificity to tumour-associated and tumour-derived mucins; therefore, the protective role of the examined circulating AG Abs against cancer remains a challenge. In this review, our findings are analysed and discussed in the context of the contribution of bacteria to the AG Abs stimulus and cancer progression. Examples of the influence of pathogenic bacteria colonising tumours on cancer progression and patient survival through mechanisms of interaction with tumours and dysregulated immune response are considered. The possibilities and problems of the integrative study of AG Abs and the microbiome using high-performance technologies are discussed.

• antibodies
• cancer
• glycoconjugates
• prognosis
• survival
• tumour microbiota

• Animals
• Antibodies/immunology
• Bacteria/immunology
• Gastrointestinal Neoplasms/immunology
• Gastrointestinal Neoplasms/microbiology
• Glycoconjugates/immunology
• Humans
• Microbiota/immunology
• Polysaccharides/immunology

Ankylosing spondylitis is a chronic, debilitating arthritis with a predilection for the axial skeleton. It has a strong genetic predisposition, but the precise pathogenetic mechanisms involved in its development have not yet been fully elucidated. This has implications both for early diagnosis and for effective management. Recently, alterations in the intestinal microbiome have been implicated in disease pathogenesis. In this review, we summarize studies assessing the intestinal microbiome in AS pathogenesis, in addition to synthesizing the literature exploring the postulated mechanisms by which it exerts it pathogenic potential. Finally, we review studies analysing manipulation of the microbiome as a potential therapeutic avenue in AS management.

• ankylosing spondylitis
• intestinal dysbiosis
• intestinal microbiome
• intestinal microbiota
• pathogenesis
• spondyloarthropathy

Although metagenomics and metatranscriptomics are commonly used to identify bacteria and viruses in human samples, few studies directly compare these strategies. We wished to compare DNA and RNA sequencing of bacterial and viral metagenomes and metatranscriptomes in the human cervix. Total nucleic acids from six human cervical samples were subjected to DNA and RNA sequencing. The effect of DNase-treatment before reverse transcription to cDNA were also analyzed. Similarities and differences in the metagenomic findings with the three different sequencing approaches were evaluated. A higher proportion of human sequences were detected by DNA sequencing (93%) compared to RNA sequencing without (76%) and with prior DNase-treatment (11%). On the contrary, bacterial sequences increased 17 and 91 times. However, the number of detected bacterial genera were less by RNA sequencing, suggesting that only a few contribute to most of the bacterial transcripts. The viral sequences were less by RNA sequencing, still twice as many virus genera were detected, including some RNA viruses that were missed by DNA sequencing. Metatranscriptomics of total cDNA provided improved detection of mainly transcribed bacteria and viruses in cervical swabs as well as detection of RNA viruses, compared to metagenomics.

• Adult
• Aged
• Arthroplasty, Replacement, Hip
• Arthroplasty, Replacement, Knee
• Artifacts
• Bacteria/genetics
• Bacteria/isolation & purification
• Female
• Hip Joint/microbiology
• Humans
• Knee Joint/microbiology
• Male
• Microbiota
• Middle Aged
• Polymerase Chain Reaction
• Prosthesis-Related Infections/microbiology
• Prosthesis-Related Infections/pathology
• RNA, Ribosomal, 16S/chemistry
• RNA, Ribosomal, 16S/genetics
• RNA, Ribosomal, 16S/metabolism
• Sequence Analysis, DNA

• Schulich School of Medicine and Dentistry

• butyrate
• functional capacity
• gut microbiota

• Adolescent
• Adult
• Butyrates/metabolism
• DNA, Bacterial/genetics
• Feces/microbiology
• Gastrointestinal Microbiome/genetics
• Gene Dosage
• Genes, Bacterial
• Humans
• Middle Aged
• Obesity/microbiology
• Phenotype
• Phylogeny
• Polymerase Chain Reaction
• Reproducibility of Results
• Statistics, Nonparametric
• Vegans
• Young Adult

• HLA
• autoimmune connective tissue diseases
• autoimmune diseases
• microRNA
• microbiome
• next-generation sequencing

• 16S
• Bowen
• Hunter
• Illumina
• PERMANOVA
• SILVA
• UniFrac
• deep lake
• stratification
• thermistor

• Hashimoto’s thyroiditis
• Th17 cells
• immune
• intestinal flora
• metformin

• Machine learning
• Metagenomics
• Phenotype prediction
• R-package
• Sample classification

• Humans
• Machine Learning
• Metagenome
• Metagenomics
• Phenotype
• RNA, Ribosomal, 16S/genetics

• 1564894 National Science Foundation

The nature of the relationship between the communities of microorganisms making up the microbiota in and on a host body has been increasingly explored in recent years. Microorganisms, including bacteria, archaea, viruses, parasites and fungi, have often long co-evolved with their hosts. In human, the structure and diversity of microbiota vary according to the host’s immunity, diet, environment, age, physiological and metabolic status, medical practices (e.g., antibiotic treatment), climate, season and host genetics. The recent advent of next generation sequencing (NGS) technologies enhanced observational capacities and allowed for a better understanding of the relationship between distinct microorganisms within microbiota. The interaction between the host and their microbiota has become a field of research into microorganisms with therapeutic and preventive interest for public health applications. This review aims at assessing the current knowledge on interactions between prokaryotic and eukaryotic communities. After a brief description of the metagenomic methods used in the studies were analysed, we summarise the findings of available publications describing the interaction between the bacterial communities and protozoa, helminths and fungi, either in vitro, in experimental models, or in humans. Overall, we observed the existence of a beneficial effect in situations where some microorganisms can improve the health status of the host, while the presence of other microorganisms has been associated with pathologies, resulting in an adverse effect on human health.

• NGS
• culturomics
• host
• interactions
• metabarcoding
• metagenomics
• microbiota
• mycobiota

• 16S rRNA gene
• Bacterial diversity
• Hypervariable regions
• Ion Torrent PGM
• Next-generation sequencing
• Vaginal microbiota

Emerging evidence supports that oral microbiota are associated with health and diseases of the esophagus. How oral microbiota change in Chinese patients with esophageal cancer (EC) is unknown, neither is their biomarker role. For an objective to understand alterations of oral microbiota in Chinese EC patients, we conducted a case-control study including saliva samples from 39 EC patients and 51 healthy volunteers. 16S rDNA genes of V3-V4 variable regions were sequenced to identify taxon. Relationship between oral flora and disease was analyzed according to alpha diversity and beta diversity. Resultantly, the Shannon index (p = 0.2) and the Simpson diversity index (p = 0.071) were not significant between the two groups. Yet we still found several species different in abundance between the two groups. For the EC group, the most significantly increased taxa were Firmicutes, Negativicutes, Selenomonadales, Prevotellaceae, Prevotella, and Veillonellaceae, while the most significantly decreased taxa were Proteobacteria, Betaproteobacteria, Neisseriales, Neisseriaceae, and Neisseria. In conclusion, there are significant alterations in abundance of some oral microbiomes between the EC patients and the healthy controls in the studied Chinese participants, which may be meaningful for predicting the development of EC, and the potential roles of these species in EC development deserve further studies.

• 16S rDNA gene
• alteration
• esophageal cancer
• indicator
• oral microbiota

• 16S rRNA sequencing
• fecal samples
• metagenomics
• microbiome
• transplantation

The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada is an appealing ecosystem for studying how microbial communities and metabolic processes are related to environmental change. Ocean and climate variability result in large spatiotemporal variations in environmental conditions and oceanographic processes. The EGSL is also exposed to a variety of additional human pressures that threaten its integrity and sustainable use, including shipping, aquiculture, coastal development, and oil exploration. To monitor and perhaps mitigate the impacts of these human activities on the EGSL, a comprehensive understanding of the biological communities is required. In this study, we provide the first comprehensive view of bacterial diversity in the EGSL and describe the distinct bacterial assemblages associated with different environmental habitats. This work therefore provides an important baseline ecological framework for bacterial communities in the EGSL useful for further studies on how these communities may respond to environmental change.

The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada are among the largest and most productive coastal ecosystems in the world. Very little information on bacterial diversity exists, hampering our understanding of the relationships between bacterial community structure and biogeochemical function in the EGSL. During the productive spring period, we investigated free-living and particle-associated bacterial communities across the stratified waters of the Lower St. Lawrence Estuary, including the particle-rich surface and bottom boundary layers. Modelling of community structure based on 16S rRNA gene and transcript diversity identified bacterial assemblages specifically associated with four habitat types defined by water mass (upper water or lower water column) and size fraction (free living or particle associated). Assemblages from the upper waters represent sets of cooccurring bacterial populations that are widely distributed across Lower St. Lawrence Estuary surface waters and likely key contributors to organic matter degradation during the spring. In addition, we provide strong evidence that particles in deep hypoxic waters and the bottom boundary layer support a metabolically active bacterial community that is compositionally distinct from those of surface particles and the free-living communities. Among the distinctive features of the bacterial assemblage associated with lower-water particles was the presence of uncultivated lineages of Deltaproteobacteria, including marine myxobacteria. Overall, these results provide an important ecological framework for further investigations of the biogeochemical contributions of bacterial populations in this important coastal marine ecosystem.

IMPORTANCE The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada is an appealing ecosystem for studying how microbial communities and metabolic processes are related to environmental change. Ocean and climate variability result in large spatiotemporal variations in environmental conditions and oceanographic processes. The EGSL is also exposed to a variety of additional human pressures that threaten its integrity and sustainable use, including shipping, aquiculture, coastal development, and oil exploration. To monitor and perhaps mitigate the impacts of these human activities on the EGSL, a comprehensive understanding of the biological communities is required. In this study, we provide the first comprehensive view of bacterial diversity in the EGSL and describe the distinct bacterial assemblages associated with different environmental habitats. This work therefore provides an important baseline ecological framework for bacterial communities in the EGSL useful for further studies on how these communities may respond to environmental change.

• bacterial diversity
• estuary
• marine microbiology

We present TaxPhlAn, a new method and bioinformatics pipeline for design and analysis of single-locus sequence typing (SLST) markers to type and profile bacteria beyond the species-level in a complex microbial community background. TaxPhlAn can be applied to any group of phylogenetically-related bacteria, provided reference genomes are available. As TaxPhlAn requires the SLST targets identified to fit the phylogenetic pattern as determined through comprehensive evolutionary reconstruction of input genomes, TaxPhlAn allows for the identification and phylogenetic inference of new biodiversity. Here, we present a clinically relevant case study of high-resolution Staphylococcus profiling on skin of atopic dermatitis (AD) patients. We demonstrate that SLST enables profiling of cutaneous Staphylococcus members at (sub)species level and provides higher resolution than current 16S-based techniques. With the higher discriminative ability provided by our approach, we further show that the presence of Staphylococcus capitis on the skin together with Staphylococcus aureus associates with AD disease.

• Maternal immune response
• Microbiome
• Preterm births
• Preterm prelabour rupture of membranes
• Spontaneous preterm birth
• Vaginal microbiota

Leprosy is an infectious disease that has predilection in skin and peripheral nerves. Skin has its own microbiome, however it is not extensively studied in Indian leprosy patients. Here, by using next-generation 16S rDNA sequencing, we have attempted to assess the skin associated microbial diversity pertaining to affected and unaffected skin of Indian leprosy patients. A total of 90 skin swab samples were collected from 60 individuals (30 healthy controls, 30 patients) residing in Hyderabad and Miraj, two distinct geographical locations in India to assess the homo/heterogeneity of skin microbial signatures. While a large increase in genus Methylobacterium and Pseudomonas was seen in patients from Miraj and Hyderabad respectively, a considerable decrease in genus Staphylococcus in the leprosy patients (as compared to controls) from both geographical locations was also observed. We expect that, these datasets can not-only provide further interesting insights, but will also help to observe dynamics of microbiome in the diseased state and generate hypotheses to test for skin microbiome transplantation studies in leprosy.

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9897089

• Bayes Theorem
• DNA, Bacterial/genetics
• Databases, Factual
• Gastrointestinal Microbiome/genetics
• High-Throughput Nucleotide Sequencing
• Humans
• Internet
• Microbial Consortia/genetics
• Microbiota/genetics
• Multivariate Analysis
• Phylogeny
• RNA, Ribosomal, 16S/genetics
• Sequence Analysis, DNA

• fetal development
• healthy status
• metagenomics
• prenatal microbiome

• advantages
• analysis
• drawbacks
• gut microbiota
• methods

• Gastrointestinal Microbiome/genetics
• Gastrointestinal Microbiome/physiology
• Gastrointestinal Tract/microbiology
• High-Throughput Nucleotide Sequencing/methods
• Humans
• Microbiota/genetics
• Microbiota/physiology