An Introductory “How-to” Guide for Incorporating Microbiome Research into Integrative and Comparative Biology

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!

(2017) John Vollmers et al.   PLoS One

Stress and the microbiome: linking glucocorticoids to bacterial community dynamics in wild red squirrels

(2016) Mason R. Stothart et al.   Biology Letters

Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes

(2016) Chenhong Zhang et al.   ISME Journal

A place for host–microbe symbiosis in the comparative physiologist's toolbox

(2016) Kevin D. Kohl et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Effects of field conditions on fecal microbiota

(2016) Vanessa L. Hale et al.   JOURNAL OF MICROBIOLOGICAL METHODS

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

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

Captivity humanizes the primate microbiome

(2016) Jonathan B. Clayton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Do Vertebrate Gut Metagenomes Confer Rapid Ecological Adaptation?

(2016) Antton Alberdi et al.   TRENDS IN ECOLOGY & EVOLUTION

Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data

(2016) Ran Blekhman et al.   Scientific Reports

The Gut Microbiota Modulates Energy Metabolism in the Hibernating Brown Bear Ursus arctos

(2016) Felix Sommer et al.   Cell Reports

Metabarcoding of fungal communities associated with bark beetles

(2016) Kirsten E. Miller et al.   Ecology and Evolution

Fecal Transplants: What Is Being Transferred?

(2016) Diana P. Bojanova et al.   PLOS BIOLOGY

An optimized approach to germ-free rearing in the jewel waspNasonia

(2016) J. Dylan Shropshire et al.   PeerJ

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

(2016) Patrick D. Schloss et al.   PeerJ

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota

(2016) Abigail P. Lauder et al.   Microbiome

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

(2016) Se Jin Song et al.   mSystems

Bacterial and Archaeal Diversity in the Gastrointestinal Tract of the North American Beaver (Castor canadensis)

(2016) Robert J. Gruninger et al.   PLoS One

Spatial Heterogeneity of Gut Microbial Composition along the Gastrointestinal Tract in Natural Populations of House Mice

(2016) Taichi A. Suzuki et al.   PLoS One

An evaluation of the accuracy and speed of metagenome analysis tools

(2016) Stinus Lindgreen et al.   Scientific Reports

Innate immune responses to gut microbiota differ between oceanic and freshwater threespine stickleback populations

(2015) Kathryn Milligan-Myhre et al.   Disease Models & Mechanisms

Inoculation of tannin-degrading bacteria into novel hosts increases performance on tannin-rich diets

(2015) Kevin D. Kohl et al.   ENVIRONMENTAL MICROBIOLOGY

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

Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8weeks

(2015) Vanessa L. Hale et al.   JOURNAL OF MICROBIOLOGICAL METHODS

The microbiome of the urinary tract—a role beyond infection

(2015) Samantha A. Whiteside et al.   Nature Reviews Urology

Sample storage conditions significantly influence faecal microbiome profiles

(2015) Jocelyn M Choo et al.   Scientific Reports

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease

(2015) Xochitl C Morgan et al.   GENOME BIOLOGY

Phylogenetic Analysis of Bacterial Communities in Different Regions of the Gastrointestinal Tract of Agkistrodon piscivorus, the Cottonmouth Snake

(2015) Timothy J. Colston et al.   PLoS One

The effect of captivity on the cutaneous bacterial community of the critically endangered Panamanian golden frog (Atelopus zeteki)

(2014) Matthew H. Becker et al.   BIOLOGICAL CONSERVATION

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Gut microbes of mammalian herbivores facilitate intake of plant toxins

(2014) Kevin D. Kohl et al.   ECOLOGY LETTERS

A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses

(2014) Pier Luigi Buttigieg et al.   FEMS MICROBIOLOGY ECOLOGY

Variation in gut microbial communities and its association with pathogen infection in wild bumble bees (Bombus)

(2014) Daniel P Cariveau et al.   ISME Journal

Which is more important for classifying microbial communities: who’s there or what they can do?

(2014) Zhenjiang Xu et al.   ISME Journal

Metamorphosis of a Butterfly-Associated Bacterial Community

(2014) Tobin J. Hammer et al.   PLoS One

The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16S rRNA Gene Sequencing

(2014) Nicholas A. Kennedy et al.   PLoS One

The Placenta Harbors a Unique Microbiome

(2014) K. Aagaard et al.   Science Translational Medicine

Divining the Essence of Symbiosis: Insights from the Squid-Vibrio Model

(2014) Margaret McFall-Ngai   PLOS BIOLOGY

The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types

(2014) Jenna M. Lang et al.   PeerJ

Captivity results in disparate loss of gut microbial diversity in closely related hosts

(2014) K. D. Kohl et al.   Conservation Physiology

A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets

(2013) Milkha M Leimena et al.   BMC GENOMICS

Herbivorous rodents (Neotoma spp.) harbour abundant and active foregut microbiota

(2013) Kevin D. Kohl et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus)

(2013) Andrew H Loudon et al.   ISME Journal

Convergence of gut microbiomes in myrmecophagous mammals

(2013) Frédéric Delsuc et al.   MOLECULAR ECOLOGY

The amphibian skin-associated microbiome across species, space and life history stages

(2013) Jordan G. Kueneman et al.   MOLECULAR ECOLOGY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Symbiotic bacteria appear to mediate hyena social odors

(2013) K. R. Theis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Animals in a bacterial world, a new imperative for the life sciences

(2013) Margaret McFall-Ngai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Wild-caught rodents retain a majority of their natural gut microbiota upon entrance into captivity

(2013) Kevin D. Kohl et al.   Environmental Microbiology Reports

Diet and phylogeny shape the gut microbiota of Antarctic seals: a comparison of wild and captive animals

(2012) Tiffanie M. Nelson et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity of cloacal microbial community in migratory shorebirds that use the Tagus estuary as stopover habitat and their potential to harbor and disperse pathogenic microorganisms

(2012) Susana S. Santos et al.   FEMS MICROBIOLOGY ECOLOGY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Evaluation of different storage methods to characterize the fecal bacterial communities of captive western lowland gorillas (Gorilla gorilla gorilla)

(2012) Klára Vlčková et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Unlocking the potential of metagenomics through replicated experimental design

(2012) Rob Knight et al.   NATURE BIOTECHNOLOGY

Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome

(2012) Sanqing Yuan et al.   PLoS One

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

Human nutrition, the gut microbiome and the immune system

(2011) Andrew L. Kau et al.   NATURE

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

The bacterial microbiota in the ceca of Capercaillie (Tetrao urogallus) differs between wild and captive birds

(2011) Tobias Wienemann et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Reshaping the gut microbiome with bacterial transplantation and antibiotic intake

(2010) C. Manichanh et al.   GENOME RESEARCH

Changes in the Intestinal Microbiota of Wild Atlantic cod Gadus morhua L. Upon Captive Rearing

(2010) Anusha K. S. Dhanasiri et al.   MICROBIAL ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Molecular characterization of the cloacal microbiota of wild and captive parrots

(2010) Panagiotis G. Xenoulis et al.   VETERINARY MICROBIOLOGY

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

Wolbachia as a bacteriocyte-associated nutritional mutualist

(2009) T. Hosokawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diet-Induced Obesity Is Linked to Marked but Reversible Alterations in the Mouse Distal Gut Microbiome

(2008) Peter J. Turnbaugh et al.   Cell Host & Microbe

The minimum information about a genome sequence (MIGS) specification

(2008) Dawn Field et al.   NATURE BIOTECHNOLOGY

Methods for generating and colonizing gnotobiotic zebrafish

(2008) Linh N Pham et al.   Nature Protocols