• blood-borne pathogens
• microarray
• multiplex detection
• resequencing microarray
• targeted sequencing

• Climate change
• Coral reef
• Microbiome
• Pathogens
• Remote sensing
• Reservoirs

• Bioremediation
• Fluxomics
• Marine bacteria
• Metabolomics
• Metagenomics
• Proteomics
• Transcriptomics

The current pandemic caused by the SARS CoV-2, tracing back its origin possibly to a coronavirus associated with bats, has ignited renewed interest in understanding zoonotic spillovers across the globe. While research is more directed towards solving the problem at hand by finding therapeutic strategies and novel vaccine techniques, it is important to address the environmental drivers of pathogen spillover and the complex biotic and abiotic drivers of zoonoses. The availability of cutting-edge genomic technologies has contributed enormously to preempt viral emergence from wildlife. However, there is still a dearth of studies from species-rich South Asian countries, especially from India. In this review, we outline the importance of studying disease dynamics through environmental sampling from wildlife in India and how ecological parameters of both the virus and the host community may play a role in mediating cross-species spillovers. Non-invasive sampling using feces, urine, shed hair, saliva, shed skin, and feathers has been instrumental in providing genetic information for both the host and their associated pathogens. Here, we discuss the advances made in environmental sampling protocols and strategies to generate genetic data from such samples towards the surveillance and characterization of potentially zoonotic pathogens. We primarily focus on bat-borne or small mammal-borne zoonoses and propose a conceptual framework for non-invasive strategies to tackle the threat of emerging zoonotic infections.

• Foods
• Gut bacteria
• Human studies
• Intestinal microbes
• Microbiome
• Microbiota
• Prebiotics
• Probiotics

• Food
• Gastrointestinal Microbiome
• Gastrointestinal Tract
• Humans
• Microbiota
• Prebiotics
• Probiotics

• Bioremediation
• Biotechnological application
• Environment
• Metagenome
• Xenobiotics

• Biodiversity
• Ecosystem
• Microarray
• Microorganisms
• Monitoring
• Sediment

• Biodiversity
• Ecosystem
• Environmental Monitoring
• Eukaryota
• Geologic Sediments
• Phylogeny

• Absolute quantification
• Competitive PCR
• Hybridization affinity ratio
• Microarray

• Bacteria/genetics
• Bacteria/isolation & purification
• DNA, Bacterial/analysis
• Genome, Bacterial
• Humans
• Microbiota/genetics
• Oligonucleotide Array Sequence Analysis
• Polymerase Chain Reaction/methods
• RNA, Ribosomal, 16S/analysis

• infectious diseases
• microbial genetics
• next-generation sequencing
• metagenomics

• Animals
• Anti-Bacterial Agents/therapeutic use
• Bacteria/genetics
• Bacteria/isolation & purification
• Communicable Diseases/diagnosis
• Communicable Diseases/genetics
• Communicable Diseases/microbiology
• Communicable Diseases/virology
• DNA/genetics
• DNA/isolation & purification
• Drug Resistance, Multiple, Bacterial/genetics
• Fungi/genetics
• Fungi/isolation & purification
• Helminths/genetics
• Helminths/isolation & purification
• High-Throughput Nucleotide Sequencing/methods
• Host-Pathogen Interactions
• Humans
• Medical Laboratory Science/instrumentation
• Medical Laboratory Science/methods
• Metagenome
• Metagenomics/instrumentation
• Metagenomics/methods
• Public Health/trends
• Viruses/genetics
• Viruses/isolation & purification

• R01 HL105704 NHLBI NIH HHS
• R33 AI120977 NIAID NIH HHS

• Canonical correlation analysis
• Crohn's disease
• Microbiome
• Volatile organic compounds

The gastrointestinal (GI) tract, including the rumen and the other intestinal segments of cattle, harbors a diverse, complex, and dynamic microbiome that drives feed digestion and fermentation in cattle, determining feed efficiency and output of pollutants. This microbiome also plays an important role in affecting host health. Research has been conducted for more than a century to understand the microbiome and its relationship to feed efficiency and host health. The traditional cultivation-based research elucidated some of the major metabolism, but studies using molecular biology techniques conducted from late 1980’s to the late early 2000’s greatly expanded our view of the diversity of the rumen and intestinal microbiome of cattle. Recently, metagenomics has been the primary technology to characterize the GI microbiome and its relationship with host nutrition and health. This review addresses the main methods/techniques in current use, the knowledge gained, and some of the challenges that remain. Most of the primers used in quantitative real-time polymerase chain reaction quantification and diversity analysis using metagenomics of ruminal bacteria, archaea, fungi, and protozoa were also compiled.

• Cattle
• Gastrointestinal
• Metagenomics
• Microbiome
• Nutrition
• Rumen

• ArrayTube
• Ralstonia solanacearum
• diagnostic
• microarray
• multiplexing

Gut microbiota is the normal flora in the human body, has a great effect on gut digestion and metabolism, and plays an important role in human health and diseases. Advances in research of gut microbiota has led to a better understanding of the relationship between gut microbiota and host immunity and diseases. This article aims to review the association of gut microbiota with the host immunity and related diseases, emphasizing the importance of gut microbiota.

• Gut microbiota
• Toll-like receptor
• Type 1 diabetes

• DNA microarrays
• Explorative probe
• HiSpOD
• KASpOD
• Probe design

• Algorithms
• Oligonucleotide Array Sequence Analysis/methods
• Oligonucleotide Probes/genetics
• Proteins/genetics

• blood-borne
• multiplex diagnostics
• nucleic acid tests
• pathogen

In a previous study origanum oil (ORO), garlic oil (GAO), and peppermint oil (PEO) were shown to effectively lower methane production, decrease abundance of methanogens, and change abundances of several bacterial populations important to feed digestion in vitro. In this study, the impact of these essential oils (EOs, at 0.50 g/L) on the rumen bacterial community composition and population was further examined using the recently developed RumenBactArray. Species richness (expressed as number of operational taxonomic units, OTUs) in the phylum Firmicutes, especially those in the class Clostridia, was decreased by ORO and GAO, but increased by PEO, while that in the phylum Bacteroidetes was increased by ORO and PEO. Species richness in the genus Butyrivibrio was lowered by all the EOs. Increases of Bacteroidetes OTUs mainly resulted from increases of Prevotella OTUs. Overall, 67 individual OTUs showed significant differences (P ≤ 0.05) in relative abundance across the EO treatments. The predominant OTUs affected by EOs were diverse, including those related to Syntrophococcus sucromutans, Succiniclasticum ruminis, and Lachnobacterium bovis, and those classified to Prevotella, Clostridium, Roseburia, Pseudobutyrivibrio, Lachnospiraceae, Ruminococcaceae, Prevotellaceae, Bacteroidales, and Clostridiales. In total, 60 OTUs were found significantly (P ≤ 0.05) correlated with feed degradability, ammonia concentration, and molar percentage of volatile fatty acids. Taken together, this study demonstrated extensive impact of EOs on rumen bacterial communities in an EO type-dependent manner, especially those in the predominant families Prevotellaceae, Lachnospiraceae, and Ruminococcaceae. The information from this study may aid in understanding the effect of EOs on feed digestion and fermentation by rumen bacteria.

• RumenBactArray
• bacterial composition
• essential oil
• microarray
• rumen

Although pelvic irradiation is effective for the treatment of various cancer types, many patients who receive radiotherapy experience serious complications. Gut microbial dysbiosis was hypothesized to be related to the occurrence of radiation-induced complications in cancer patients. Given the lack of clinical or experimental data on the impact of radiation on gut microbiota, a prospective observational study of gut microbiota was performed in gynecological cancer patients receiving pelvic radiotherapy. In the current study, the overall composition and alteration of gut microbiota in cancer patients receiving radiation were investigated by 454 pyrosequencing. Gut microbial composition showed significant differences (P < 0.001) between cancer patients and healthy individuals. The numbers of species-level taxa were severely reduced after radiotherapy (P < 0.045), and the abundance of each community largely changed. In particular, the phyla Firmicutes and Fusobacterium were significantly decreased by 10% and increased by 3% after radiation therapy, respectively. In addition, overall gut microbial composition was gradually remolded after the full treatment course of pelvic radiotherapy. In this set of cancer patients, dysbiosis of the gut microbiota was linked to health status, and the gut microbiota was influenced by pelvic radiotherapy. Although further studies are needed to elucidate the relationship between dysbiosis and complications induced by pelvic radiotherapy, the current study may offer insights into the treatment of cancer patients suffering from complications after radiation therapy.

• Adult
• Female
• Gastrointestinal Tract/microbiology
• Genital Neoplasms, Female/microbiology
• Genital Neoplasms, Female/radiotherapy
• Humans
• Microbiota/genetics
• Middle Aged
• RNA, Ribosomal, 16S/genetics

There has been a dramatic rise in the prevalence of IgE-mediated food allergy over recent decades, particularly among infants and young children. The cause of this increase is unknown but one putative factor is a change in the composition, richness and balance of the microbiota that colonize the human gut during early infancy. The coevolution of the human gastrointestinal tract and commensal microbiota has resulted in a symbiotic relationship in which gut microbiota play a vital role in early life immune development and function, as well as maintenance of gut wall epithelial integrity. Since IgE mediated food allergy is associated with immune dysregulation and impaired gut epithelial integrity there is substantial interest in the potential link between gut microbiota and food allergy. Although the exact link between gut microbiota and food allergy is yet to be established in humans, recent experimental evidence suggests that specific patterns of gut microbiota colonization may influence the risk and manifestations of food allergy. An understanding of the relationship between gut microbiota and food allergy has the potential to inform both the prevention and treatment of food allergy. In this paper we review the theory and evidence linking gut microbiota and IgE-mediated food allergy in early life. We then consider the implications and challenges for future research, including the techniques of measuring and analyzing gut microbiota, and the types of studies required to advance knowledge in the field.

The microflora in environmental water consists of a high density and diversity of bacterial species that form the foundation of the water ecosystem. Because the majority of these species cannot be cultured in vitro, a different approach is needed to identify prokaryotes in environmental water. A novel DNA microarray was developed as a simplified detection protocol. Multiple DNA probes were designed against each of the 97,927 sequences in the DNA Data Bank of Japan and mounted on a glass chip in duplicate. Evaluation of the microarray was performed using the DNA extracted from one liter of environmental water samples collected from seven sites in Japan. The extracted DNA was uniformly amplified using whole genome amplification (WGA), labeled with Cy3-conjugated 16S rRNA specific primers and hybridized to the microarray. The microarray successfully identified soil bacteria and environment-specific bacteria clusters. The DNA microarray described herein can be a useful tool in evaluating the diversity of prokaryotes and assessing environmental changes such as global warming.

• Environmental Monitoring/instrumentation
• Environmental Monitoring/methods
• Gene Expression Profiling/methods
• Harmful Algal Bloom
• Microalgae/classification
• Microalgae/genetics
• Microalgae/growth & development
• Nucleic Acid Hybridization
• Oligonucleotide Array Sequence Analysis
• Signal-To-Noise Ratio
• Water Pollution/analysis

• Animals
• Animals, Newborn
• Colon/immunology
• Colon/metabolism
• Colon/microbiology
• Escherichia coli/growth & development
• Escherichia coli/immunology
• Gastrointestinal Tract/immunology
• Gastrointestinal Tract/metabolism
• Gastrointestinal Tract/microbiology
• Immunity, Innate/immunology
• Intestine, Small/immunology
• Intestine, Small/metabolism
• Intestine, Small/microbiology
• Microbiota/genetics
• Microbiota/immunology
• Mucins/genetics
• Mucins/immunology
• Mucins/metabolism
• Mucus/immunology
• Mucus/metabolism
• Mucus/microbiology
• Peptides/genetics
• Peptides/immunology
• Peptides/metabolism
• Rats
• Trefoil Factor-2
• Up-Regulation/genetics
• Up-Regulation/immunology
• alpha-Defensins/genetics
• alpha-Defensins/immunology
• alpha-Defensins/metabolism

• 100140 Wellcome Trust
• U01 AI095473 NIAID NIH HHS
• G0400268 Medical Research Council

Evaluating the composition of the human gut microbiota greatly facilitates studies on its role in human pathophysiology, and is heavily reliant on culture-independent molecular methods. A microarray designated the Human Gut Chip (HuGChip) was developed to analyze and compare human gut microbiota samples. The PhylArray software was used to design specific and sensitive probes. The DNA chip was composed of 4,441 probes (2,442 specific and 1,919 explorative probes) targeting 66 bacterial families. A mock community composed of 16S rRNA gene sequences from intestinal species was used to define the threshold criteria to be used to analyze complex samples. This was then experimentally verified with three human faecal samples and results were compared (i) with pyrosequencing of the V4 hypervariable region of the 16S rRNA gene, (ii) metagenomic data, and (iii) qPCR analysis of three phyla. When compared at both the phylum and the family level, high Pearson's correlation coefficients were obtained between data from all methods. The HuGChip development and validation showed that it is not only able to assess the known human gut microbiota but could also detect unknown species with the explorative probes to reveal the large number of bacterial sequences not yet described in the human gut microbiota, overcoming the main inconvenience encountered when developing microarrays.

• Analysis of Variance
• Bacteria/classification
• Bacteria/genetics
• Base Sequence
• Feces/microbiology
• Gastrointestinal Tract/microbiology
• Humans
• Microarray Analysis
• Microbiota/genetics
• Molecular Sequence Data
• Oligonucleotide Array Sequence Analysis/instrumentation
• Oligonucleotide Array Sequence Analysis/methods
• Phylogeny
• RNA, Ribosomal, 16S/genetics

Metagenomics which combines the power of genomics, bioinformatics, and systems biology, provide new access to the microbial world. Metagenomics permit the genetic analysis of complex microbial populations without requiring prior cultivation. Through the conceptual innovations in metagenomics and the improvements in DNA high-throughput sequencing and bioinformatics analysis technology, gastrointestinal microbiology has entered the metagenomics era and become a hot topic worldwide. Human microbiome research is underway, however, most studies in this area have focused on the composition and function of the intestinal microbiota and the relationship between intestinal microbiota and metabolic diseases (obesity, diabetes, metabolic syndrome, etc.) and intestinal disorders [inflammatory bowel disease, colorectal cancer, irritable bowel syndrome (IBS), etc.]. Few investigations on microbiota have been conducted within the upper gastrointestinal tract (esophagus, stomach and duodenum). The upper gastrointestinal microbiota is essential for several gastrointestinal illnesses, including esophagitis, Barrett’s esophagus, and esophageal carcinoma, gastritis and gastric cancer, small intestinal bacterial overgrowth, IBS and celiac disease. However, the constitution and diversity of the microbiota in different sections of the upper gastrointestinal tract under health and various disease states, as well as the function of microbiota in the pathogenesis of various digestive diseases are still undefined. The current article provides an overview of the recent findings regarding the relationship between upper gastrointestinal microbiota and gastrointestinal diseases; and discusses the study limitations and future directions of upper gastrointestinal microbiota research.

• Microbiota
• Upper gastrointestinal tract
• Digestive diseases
• 16S rDNA
• Metagenomics

• Animals
• Bacteria/classification
• Bacteria/genetics
• Bacteria/growth & development
• Gastrointestinal Diseases/microbiology
• Gastrointestinal Tract/microbiology
• Gene Expression Regulation, Bacterial
• Genome, Bacterial
• Host-Pathogen Interactions
• Humans
• Metagenomics/methods
• Risk Factors

Next-generation sequencing (NGS) allows faster acquisition of metagenomic data, but complete exploration of complex ecosystems is hindered by the extraordinary diversity of microorganisms. To reduce the environmental complexity, we created an innovative solution hybrid selection (SHS) method that is combined with NGS to characterize large DNA fragments harbouring biomarkers of interest. The quality of enrichment was evaluated after fragments containing the methyl coenzyme M reductase subunit A gene (mcrA), the biomarker of methanogenesis, were captured from a Methanosarcina strain and a metagenomic sample from a meromictic lake. The methanogen diversity was compared with direct metagenome and mcrA-based amplicon pyrosequencing strategies. The SHS approach resulted in the capture of DNA fragments up to 2.5 kb with an enrichment efficiency between 41 and 100%, depending on the sample complexity. Compared with direct metagenome and amplicons sequencing, SHS detected broader mcrA diversity, and it allowed efficient sampling of the rare biosphere and unknown sequences. In contrast to amplicon-based strategies, SHS is less biased and GC independent, and it recovered complete biomarker sequences in addition to conserved regions. Because this method can also isolate the regions flanking the target sequences, it could facilitate operon reconstructions.

Bacteria colonizing the human intestinal tract exhibit a high phylogenetic diversity that reflects their immense metabolic potentials. The catalytic activity of gut microbes has an important impact on gastrointestinal (GI) functions and host health. The microbial conversion of carbohydrates and other food components leads to the formation of a large number of compounds that affect the host metabolome and have beneficial or adverse effects on human health. Metabolomics is a metabolic-biology system approach focused on the metabolic responses understanding of living systems to physio-pathological stimuli by using multivariate statistical data on human body fluids obtained by different instrumental techniques. A metabolomic approach based on an analytical platform could be able to separate, detect, characterize and quantify a wide range of metabolites and its metabolic pathways. This approach has been recently applied to study the metabolic changes triggered in the gut microbiota by specific diet components and diet variations, specific diseases, probiotic and synbiotic food intake. This review describes the metabolomic data obtained by analyzing human fluids by using different techniques and particularly Gas Chromatography Mass Spectrometry Solid-phase Micro Extraction (GC-MS/SPME), Proton Nuclear Magnetic Resonance (¹H-NMR) Spectroscopy and Fourier Transform Infrared (FTIR) Spectroscopy. This instrumental approach has a good potential in the identification and detection of specific food intake and diseases biomarkers.

• biomarkers
• diet
• gut microbiota
• instrumental methods
• metabolites

Bacteria that utilize sunlight to supplement metabolic activity are now being described in a range of ecosystems. While it is likely that phototrophy provides an important competitive advantage, the contribution that these microorganisms make to the bioenergetics of polar marine ecosystems is unknown. In this minireview, we discuss recent advances in our understanding of phototrophic bacteria and highlight the need for future research.

• Base Sequence
• Escherichia coli K12/genetics
• Escherichia coli K12/isolation & purification
• Formamides/pharmacology
• Models, Statistical
• Nucleic Acid Denaturation/drug effects
• Nucleic Acid Hybridization/methods
• Oligonucleotide Array Sequence Analysis/methods
• Oligonucleotide Probes/chemistry
• Oligonucleotide Probes/genetics
• RNA, Bacterial/chemistry
• RNA, Bacterial/genetics
• RNA, Ribosomal, 16S/chemistry
• RNA, Ribosomal, 16S/genetics
• Rhodobacter sphaeroides/genetics
• Rhodobacter sphaeroides/isolation & purification
• Thermodynamics
• Transition Temperature

• P 20185 Austrian Science Fund FWF