Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution

Rates of gut microbiome divergence in mammals

(2018) Alex H. Nishida et al.   MOLECULAR ECOLOGY

Microbiome Structural and Functional Interactions across Host Dietary Niche Space

(2017) Caleb D. Phillips et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

Gut microbial communities of American pikas (Ochotona princeps ): Evidence for phylosymbiosis and adaptations to novel diets

(2017) Kevin D. Kohl et al.   JOURNAL OF ANIMAL ECOLOGY

Dispersal limitation promotes the diversification of the mammalian gut microbiota

(2017) Andrew H. Moeller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania

(2017) Samuel A. Smits et al.   SCIENCE

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

(2017) Mathieu Groussin et al.   Nature Communications

Evolutionary Biology Needs Wild Microbiomes

(2017) Sarah M. Hird   Frontiers in Microbiology

Host genetic variation in mucosal immunity pathways influences the upper airway microbiome

(2017) Catherine Igartua et al.   Microbiome

Optimizing methods and dodging pitfalls in microbiome research

(2017) Dorothy Kim et al.   Microbiome

16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform

(2016) Fiona Fouhy et al.   BMC MICROBIOLOGY

2016 Guidelines of the American Society of Mammalogists for the use of wild mammals in research and education:

(2016) Robert S. Sikes et al.   JOURNAL OF MAMMALOGY

Microbiome evolution along divergent branches of the vertebrate tree of life: what is known and unknown

(2016) Timothy J. Colston et al.   MOLECULAR ECOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Cospeciation of gut microbiota with hominids

(2016) A. H. Moeller et al.   SCIENCE

Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples

(2016) Angela Glassing et al.   Gut Pathogens

Gut Microbiota Diversity and Human Diseases: Should We Reintroduce Key Predators in Our Ecosystem?

(2016) Alexis Mosca et al.   Frontiers in Microbiology

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies

(2016) Se Jin Song et al.   mSystems

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

Biogeography of the Intestinal Mucosal and Lumenal Microbiome in the Rhesus Macaque

(2015) Koji Yasuda et al.   Cell Host & Microbe

Diet Dominates Host Genotype in Shaping the Murine Gut Microbiota

(2015) Rachel N. Carmody et al.   Cell Host & Microbe

Speciation dynamics during the global radiation of extant bats

(2015) Jeff J. Shi et al.   EVOLUTION

Validating the use of trap-collected feces for studying the gut microbiota of a small mammal (Neotoma lepida)

(2015) Kevin D. Kohl et al.   JOURNAL OF MAMMALOGY

Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores

(2015) Jon G. Sanders et al.   Nature Communications

Shifts in the gut microbiome observed in wildlife faecal samples exposed to natural weather conditions: lessons from time-series analyses using next-generation sequencing for application in field studies

(2015) Sebastian Menke et al.   Methods in Ecology and Evolution

Variation in koala microbiomes within and between individuals: effect of body region and captivity status

(2015) Niccoló Alfano et al.   Scientific Reports

Sample storage conditions significantly influence faecal microbiome profiles

(2015) Jocelyn M Choo et al.   Scientific Reports

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies

(2015) Mario Carrillo-Araujo et al.   Frontiers in Microbiology

Comparative Gut Microbiota of 59 Neotropical Bird Species

(2015) Sarah M. Hird et al.   Frontiers in Microbiology

Intra- and Interindividual Variations Mask Interspecies Variation in the Microbiota of Sympatric Peromyscus Populations

(2014) Nielson T. Baxter et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

Comparison of methods for fecal microbiome biospecimen collection

(2014) Christine Dominianni et al.   BMC MICROBIOLOGY

The Gut Microbiota Appears to Compensate for Seasonal Diet Variation in the Wild Black Howler Monkey (Alouatta pigra)

(2014) Katherine R. Amato et al.   MICROBIAL ECOLOGY

Trophic niche flexibility inGlossophaga soricina: how a nectar seeker sneaks an insect snack

(2013) Elizabeth L. Clare et al.   FUNCTIONAL ECOLOGY

Sympatric chimpanzees and gorillas harbor convergent gut microbial communities

(2013) A. H. Moeller et al.   GENOME RESEARCH

Convergence of gut microbiomes in myrmecophagous mammals

(2013) Frédéric Delsuc et al.   MOLECULAR ECOLOGY

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

The gut microbiota — masters of host development and physiology

(2013) Felix Sommer et al.   NATURE REVIEWS MICROBIOLOGY

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

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

Microbiome analysis among bats describes influences of host phylogeny, life history, physiology and geography

(2012) CALEB D. PHILLIPS et al.   MOLECULAR ECOLOGY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

A Core Human Microbiome as Viewed through 16S rRNA Sequence Clusters

(2012) Susan M. Huse et al.   PLoS One

Interactions Between the Microbiota and the Immune System

(2012) L. V. Hooper et al.   SCIENCE

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Assessing Gut Microbial Diversity from Feces and Rectal Mucosa

(2010) Ana Durbán et al.   MICROBIAL ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial populations and metabolites in the feces of free roaming and captive grizzly bears

(2009) Clarissa Schwab et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE