Distinct microbiota composition and fermentation products indicate functional compartmentalization in the hindgut of a marine herbivorous fish

Red seaweed (Asparagopsis taxiformis) supplementation reduces enteric methane by over 80 percent in beef steers

(2021) Breanna M. Roque et al.   PLoS One

Histology and ultrastructure of the gastrointestinal tract in four temperate marine herbivorous fishes

(2021) Kate S. Johnson et al.   JOURNAL OF MORPHOLOGY

Effects of dietary sodium acetate on food intake, weight gain, intestinal digestive enzyme activities, energy metabolism and gut microbiota in cultured fish: Zebrafish as a model

(2020) Hongling Zhang et al.   AQUACULTURE

Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling

(2020) Ching Jian et al.   PLoS One

A role for gut microbiota in host niche differentiation

(2020) Lydia K. Greene et al.   ISME Journal

Intestinal microbes: an axis of functional diversity among large marine consumers

(2020) Jarrod J. Scott et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The role of the gut microbiome in sustainable teleost aquaculture

(2020) William Bernard Perry et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities

(2020) Jacob T. Barlow et al.   Nature Communications

Mitigating the carbon footprint and improving productivity of ruminant livestock agriculture using a red seaweed

(2020) Robert D. Kinley et al.   JOURNAL OF CLEANER PRODUCTION

Analysis of compositions of microbiomes with bias correction

(2020) Huang Lin et al.   Nature Communications

The Beta-Diversity of Siganus fuscescens-Associated Microbial Communities From Different Habitats Increases With Body Weight

(2020) Yongjie Wu et al.   Frontiers in Microbiology

The Genus Alistipes: Gut Bacteria With Emerging Implications to Inflammation, Cancer, and Mental Health

(2020) Bianca J. Parker et al.   Frontiers in Immunology

Few Herbivore Species Consume Dominant Macroalgae on a Caribbean Coral Reef

(2020) Claire L. A. Dell et al.   Frontiers in Marine Science

The herbivorous fish family Kyphosidae (Teleostei: Perciformes) represents a recent radiation from higher latitudes

(2019) Steen Wilhelm Knudsen et al.   JOURNAL OF BIOGEOGRAPHY

Gut Microbiota of Migrating Wild Rabbit Fish (Siganus guttatus) Larvae Have Low Spatial and Temporal Variability

(2019) Duy Le et al.   MICROBIAL ECOLOGY

Ancient acquisition of “alginate utilization loci” by human gut microbiota

(2018) Sophie Mathieu et al.   Scientific Reports

Comparative Analysis of the Microbiota Between Sheep Rumen and Rabbit Cecum Provides New Insight Into Their Differential Methane Production

(2018) Lan Mi et al.   Frontiers in Microbiology

Fast acquisition of a polysaccharide fermenting gut microbiome by juvenile green turtles Chelonia mydas after settlement in coastal habitats

(2018) Patricia Campos et al.   Microbiome

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Fecal microbiota transplantation confers beneficial metabolic effects of diet and exercise on diet-induced obese mice

(2018) Zi-Lun Lai et al.   Scientific Reports

The Microbiome of the Gastrointestinal Tract of a Range-Shifting Marine Herbivorous Fish

(2018) Jacquelyn Jones et al.   Frontiers in Microbiology

Changes in microbiota along the intestine of grass carp (Ctenopharyngodon idella): Community, interspecific interactions, and functions

(2018) Gang Yang et al.   AQUACULTURE

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

(2018) Rolf Henrik Nilsson et al.   NUCLEIC ACIDS RESEARCH

Genomic diversification of giant enteric symbionts reflects host dietary lifestyles

(2017) David Kamanda Ngugi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

mixOmics: An R package for ‘omics feature selection and multiple data integration

(2017) Florian Rohart et al.   PLoS Computational Biology

The Gut Microbiota of Healthy Chilean Subjects Reveals a High Abundance of the Phylum Verrucomicrobia

(2017) Sayaka Fujio-Vejar et al.   Frontiers in Microbiology

Microbiome patterns across the gastrointestinal tract of the rabbitfish Siganus fuscescens

(2017) Shaun Nielsen et al.   PeerJ

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Formation of propionate and butyrate by the human colonic microbiota

(2016) Petra Louis et al.   ENVIRONMENTAL MICROBIOLOGY

Absolute quantification of microbial taxon abundances

(2016) Ruben Props et al.   ISME Journal

Microbiome and metabolic disease: revisiting the bacterial phylum Bacteroidetes

(2016) Elizabeth L. Johnson et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Diet drives quick changes in the metabolic activity and composition of human gut microbiota in a validated in vitro gut model

(2016) Marisol Aguirre et al.   RESEARCH IN MICROBIOLOGY

The Potential Role of Seaweeds in the Natural Manipulation of Rumen Fermentation and Methane Production

(2016) Margarida R. G. Maia et al.   Scientific Reports

A new view of the fish gut microbiome: Advances from next-generation sequencing

(2015) Mahdi Ghanbari et al.   AQUACULTURE

The biogeography of the atlantic salmon (Salmo salar) gut microbiome

(2015) Martin S Llewellyn et al.   ISME Journal

Comparison of the gut microbiomes of 12 bony fish and 3 shark species

(2015) CE Givens et al.   MARINE ECOLOGY PROGRESS SERIES

Diet strongly influences the gut microbiota of surgeonfishes

(2015) Sou Miyake et al.   MOLECULAR ECOLOGY

Gut biogeography of the bacterial microbiota

(2015) Gregory P. Donaldson et al.   NATURE REVIEWS MICROBIOLOGY

Comparison of the gut microbiomes of 12 bony fish and 3 shark species

(2015) CE Givens et al.   MARINE ECOLOGY PROGRESS SERIES

Mucin glycan foraging in the human gut microbiome

(2015) Louise E. Tailford et al.   Frontiers in Genetics

An Expanded Genomic Representation of the Phylum Cyanobacteria

(2014) Rochelle M. Soo et al.   Genome Biology and Evolution

Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men

(2014) Anne Salonen et al.   ISME Journal

Intestinal microbiota in fishes: what's known and what's not

(2014) Kendall D. Clements et al.   MOLECULAR ECOLOGY

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

(2014) M. Vital et al.   mBio

Fish gut microbiota analysis differentiates physiology and behavior of invasive Asian carp and indigenous American fish

(2013) Lin Ye et al.   ISME Journal

The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism

(2013) Gijs den Besten et al.   JOURNAL OF LIPID RESEARCH

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

“Methanoplasmatales,” Thermoplasmatales-Related Archaea in Termite Guts and Other Environments, Are the Seventh Order of Methanogens

(2012) Kristina Paul et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis

(2012) KAREN E. SULLAM et al.   MOLECULAR ECOLOGY

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Visualising associations between paired ‘omics’ data sets

(2012) Ignacio González et al.   BioData Mining

Utilisation of mannitol by temperate marine herbivorous fishes

(2010) W.L. White et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

(2009) Jennifer M. Brulc et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular characterization of the autochthonous microbiota in the gastrointestinal tract of adult yellow grouper (Epinephelus awoara) cultured in cages

(2008) Zhigang Zhou et al.   AQUACULTURE