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

Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans

(2016) Ron Sender et al.   CELL

Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea

(2016) Elisabeth M. Bik et al.   Nature Communications

Correlation between microbiota and growth in Mangrove Killifish (Kryptolebias marmoratus) and Atlantic cod (Gadus morhua)

(2016) Torunn Forberg et al.   Scientific Reports

Topographical Mapping of the Rainbow Trout (Oncorhynchus mykiss) Microbiome Reveals a Diverse Bacterial Community with Antifungal Properties in the Skin

(2015) Liam Lowrey et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2015) Mahdi Ghanbari et al.   AQUACULTURE

Using bacteria to study consistent variation in individual behavior

(2015) Gunnar De Winter et al.   BEHAVIORAL ECOLOGY

Daily rhythms of locomotor activity and the influence of a light and dark cycle on gut microbiota species in tambaqui (Colossoma macropomum)

(2015) R. Fortes-Silva et al.   BIOLOGICAL RHYTHM RESEARCH

Larval exposure to polychlorinated biphenyl 126 (PCB-126) causes persistent alteration of the amphibian gut microbiota

(2015) Kevin D. Kohl et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Disease alters macroecological patterns of North American bats

(2015) Winifred F. Frick et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

The Good, the Bad, and the Unknown: Microbial Symbioses of the American Alligator

(2015) S. W. Keenan et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies

(2015) Karen E Sullam et al.   ISME Journal

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

Community Structure of Skin Microbiome of Gulf Killifish, Fundulus grandis, Is Driven by Seasonality and Not Exposure to Oiled Sediments in a Louisiana Salt Marsh

(2015) Andrea M. Larsen et al.   MICROBIAL ECOLOGY

Diet is the primary determinant of bacterial community structure in the guts of higher termites

(2015) Aram Mikaelyan et al.   MOLECULAR ECOLOGY

Kinship, inbreeding and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise

(2015) Michael L. Yuan et al.   MOLECULAR ECOLOGY

Microbiology: Create a global microbiome effort

(2015) Nicole Dubilier et al.   NATURE

Cloacal Microbiome Structure in a Long-Distance Migratory Bird Assessed Using Deep 16sRNA Pyrosequencing

(2015) Jakub Kreisinger et al.   PLoS One

A unified initiative to harness Earth's microbiomes

(2015) A. P. Alivisatos et al.   SCIENCE

Identification of Population Bottlenecks and Colonization Factors during Assembly of Bacterial Communities within the Zebrafish Intestine

(2015) W. Zac Stephens et al.   mBio

Exploring the avian gut microbiota: current trends and future directions

(2015) David W. Waite et al.   Frontiers in Microbiology

Microbiota disbiosis is associated with colorectal cancer

(2015) Zhiguang Gao et al.   Frontiers in Microbiology

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

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

Microbiota and Mucosal Immunity in Amphibians

(2015) Bruno M. Colombo et al.   Frontiers in Immunology

The functionality of the gastrointestinal microbiome in non-human animals

(2015) Irene Hanning et al.   Microbiome

Bacteria Isolated from Bats Inhibit the Growth of Pseudogymnoascus destructans, the Causative Agent of White-Nose Syndrome

(2015) Joseph R. Hoyt et al.   PLoS One

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 development of the gut microbiota in rainbow trout (Oncorhynchus mykiss) is affected by first feeding and diet type

(2014) H.-C. Ingerslev et al.   AQUACULTURE

Daily torpor and hibernation in birds and mammals

(2014) Thomas Ruf et al.   BIOLOGICAL REVIEWS

The intestinal microbiome of fish under starvation

(2014) Jun Xia et al.   BMC GENOMICS

You Are What You Host: Microbiome Modulation of the Aging Process

(2014) Caroline Heintz et al.   CELL

Interspecific variations in the faecal microbiota ofProcellariiformseabirds

(2014) Meagan L. Dewar et al.   FEMS MICROBIOLOGY ECOLOGY

Unique and shared responses of the gut microbiota to prolonged fasting: a comparative study across five classes of vertebrate hosts

(2014) Kevin D. Kohl et al.   FEMS MICROBIOLOGY ECOLOGY

Amphibian skin may select for rare environmental microbes

(2014) Jenifer B Walke et al.   ISME Journal

Characterization of the gut microbiota of three commercially valuable warmwater fish species

(2014) A.M. Larsen et al.   JOURNAL OF APPLIED MICROBIOLOGY

Microbiome investigation in the ecological speciation context of lake whitefish (Coregonus clupeaformis) using next-generation sequencing

(2014) M. Sevellec et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Hibernation alters the diversity and composition of mucosa-associated bacteria while enhancing antimicrobial defence in the gut of 13-lined ground squirrels

(2014) Kimberly A. Dill-McFarland et al.   MOLECULAR ECOLOGY

Mosquitoes rely on their gut microbiota for development

(2014) Kerri L. Coon et al.   MOLECULAR ECOLOGY

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

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

Humpback Whale Populations Share a Core Skin Bacterial Community: Towards a Health Index for Marine Mammals?

(2014) Amy Apprill et al.   PLoS One

Ex situ Diet Influences the Bacterial Community Associated with the Skin of Red-Eyed Tree Frogs (Agalychnis callidryas)

(2014) Rachael E. Antwis et al.   PLoS One

Inter Individual Variations of the Fish Skin Microbiota: Host Genetics Basis of Mutualism?

(2014) Sébastien Boutin et al.   PLoS One

Microbiomes are true to type

(2014) Andrew H. Moeller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The pathogenBatrachochytrium dendrobatidisdisturbs the frog skin microbiome during a natural epidemic and experimental infection

(2014) Andrea J. Jani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The microbiome of New World vultures

(2014) Michael Roggenbuck et al.   Nature Communications

Characterizing the avian gut microbiota: membership, driving influences, and potential function

(2014) David W. Waite et al.   Frontiers in Microbiology

Sampling locality is more detectable than taxonomy or ecology in the gut microbiota of the brood-parasitic Brown-headed Cowbird (Molothrus ater)

(2014) Sarah M. Hird et al.   PeerJ

Early origin of viviparity and multiple reversions to oviparity in squamate reptiles

(2013) R. Alexander Pyron et al.   ECOLOGY LETTERS

Determination of antimicrobial and heavy metal resistance profiles of some bacteria isolated from aquatic amphibian and reptile species

(2013) Nurcihan Hacioglu et al.   ENVIRONMENTAL MONITORING AND ASSESSMENT

Diversity of the skin microbiota of fishes: evidence for host species specificity

(2013) Andrea Larsen et al.   FEMS MICROBIOLOGY ECOLOGY

Factors influencing the grass carp gut microbiome and its effect on metabolism

(2013) Jiajia Ni et al.   FEMS MICROBIOLOGY ECOLOGY

Microbial genes, brain & behaviour - epigenetic regulation of the gut-brain axis

(2013) R. M. Stilling et al.   GENES BRAIN AND BEHAVIOR

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

Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes

(2013) Jon G. Sanders et al.   MOLECULAR ECOLOGY

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Global Taxonomic Diversity of Living Reptiles

(2013) Daniel Pincheira-Donoso et al.   PLoS One

Mapping the Global Emergence of Batrachochytrium dendrobatidis, the Amphibian Chytrid Fungus

(2013) Deanna H. Olson et al.   PLoS One

A horizon scan of global conservation issues for 2014

(2013) William J. Sutherland et al.   TRENDS IN ECOLOGY & EVOLUTION

Gut–brain axis: how the microbiome influences anxiety and depression

(2013) Jane A. Foster et al.   TRENDS IN NEUROSCIENCES

Microbiome diversity ofAphis glycineswith extensive superinfection in native and invasive populations

(2013) Raman Bansal et al.   Environmental Microbiology Reports

Restructuring of the amphibian gut microbiota through metamorphosis

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

Commensal Clostridia: leading players in the maintenance of gut homeostasis

(2013) Loris R Lopetuso et al.   Gut Pathogens

The alligator gut microbiome and implications for archosaur symbioses

(2013) Sarah W. Keenan et al.   Scientific Reports

Microbial Endocrinology in the Microbiome-Gut-Brain Axis: How Bacterial Production and Utilization of Neurochemicals Influence Behavior

(2013) Mark Lyte   PLoS Pathogens

Age-related differences in the cloacal microbiota of a wild bird species

(2013) Wouter FD van Dongen et al.   BMC ECOLOGY

Interspecific variations in the gastrointestinal microbiota in penguins

(2013) Meagan L. Dewar et al.   MicrobiologyOpen

The Impact of the Gut Microbiota on Human Health: An Integrative View

(2012) Jose C. Clemente et al.   CELL

Changes in cutaneous microbial abundance with sloughing: possible implications for infection and disease in amphibians

(2012) EA Meyer et al.   DISEASES OF AQUATIC ORGANISMS

Diversity and function of the avian gut microbiota

(2012) Kevin D. Kohl   JOURNAL OF COMPARATIVE PHYSIOLOGY B-BIOCHEMICAL SYSTEMIC AND ENVIRONMENTAL PHYSIOLOGY

Highly similar microbial communities are shared among related and trophically similar ant species

(2012) KIRK E. ANDERSON et al.   MOLECULAR ECOLOGY

Do diet and taxonomy influence insect gut bacterial communities?

(2012) D. R. Colman et al.   MOLECULAR ECOLOGY

Ecological drift and local exposures drive enteric bacterial community differences within species of Galápagos iguanas

(2012) EMILY W. LANKAU et al.   MOLECULAR ECOLOGY

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

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

Intestinal microbiota composition in fishes is influenced by host ecology and environment

(2012) SANDI WONG et al.   MOLECULAR ECOLOGY

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

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

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Gut Microbiome of the Critically Endangered New Zealand Parrot, the Kakapo (Strigops habroptilus)

(2012) David W. Waite et al.   PLoS One

Phylogenetic Analysis of Microbial Communities in Different Regions of the Gastrointestinal Tract in Panaque nigrolineatus, a Wood-Eating Fish

(2012) Ryan McDonald et al.   PLoS One

Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes

(2012) P. Jeraldo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cultivable microbiota of Lithobates catesbeianus and advances in the selection of lactic acid bacteria as biological control agents in raniculture

(2012) Gabriela Montel Mendoza et al.   RESEARCH IN VETERINARY SCIENCE

Speciation by symbiosis

(2012) Robert M. Brucker et al.   TRENDS IN ECOLOGY & EVOLUTION

Phylogenetic Insights on Evolutionary Novelties in Lizards and Snakes: Sex, Birth, Bodies, Niches, and Venom

(2011) Jack W. Sites et al.   Annual Review of Ecology Evolution and Systematics

Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

(2011) Andrea K. Bartram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative fecal metagenomics unveils unique functional capacity of the swine gut

(2011) Regina Lamendella et al.   BMC MICROBIOLOGY

Microbial consortia of gorgonian corals from the Aleutian islands

(2011) Michael A. Gray et al.   FEMS MICROBIOLOGY ECOLOGY

Oral tolerance

(2011) Howard L. Weiner et al.   IMMUNOLOGICAL REVIEWS

Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows

(2011) Filipa Godoy-Vitorino et al.   ISME Journal

Co-habiting amphibian species harbor unique skin bacterial communities in wild populations

(2011) Valerie J McKenzie et al.   ISME Journal

Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the Galápagos Islands using 16S rRNA-based pyrosequencing

(2011) Pei-Ying Hong et al.   ISME Journal

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

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

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

The Human Gut Microbiome: Ecology and Recent Evolutionary Changes

(2010) Jens Walter et al.   Annual Review of Microbiology

Why bacteria matter in animal development and evolution

(2010) Sebastian Fraune et al.   BIOESSAYS

Toxic hydrogen sulfide and dark caves: life-history adaptations in a livebearing fish (Poecilia mexicana, Poeciliidae)

(2010) Rüdiger Riesch et al.   ECOLOGY

Sexually transmitted bacteria affect female cloacal assemblages in a wild bird

(2010) Joël White et al.   ECOLOGY LETTERS

Accelerated rates of climatic-niche evolution underlie rapid species diversification

(2010) Kenneth H. Kozak et al.   ECOLOGY LETTERS

The presence of bifidobacteria in social insects, fish and reptiles

(2010) J. Kopečný et al.   FOLIA MICROBIOLOGICA

Postprandial remodeling of the gut microbiota in Burmese pythons

(2010) Elizabeth K Costello et al.   ISME Journal

Diversity and temporal stability of bacterial communities in a model passerine bird, the zebra finch

(2010) CLARE McW. H. BENSKIN et al.   MOLECULAR ECOLOGY

Microbiome Profiling by Illumina Sequencing of Combinatorial Sequence-Tagged PCR Products

(2010) Gregory B. Gloor et al.   PLoS One

Enzootic and epizootic dynamics of the chytrid fungal pathogen of amphibians

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

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

(2010) C. De Filippo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Succession of microbial consortia in the developing infant gut microbiome

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

Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities

(2010) Howard Ochman et al.   PLOS BIOLOGY

Response of Gut Microbiota to Fasting and Hibernation in Syrian Hamsters

(2009) K. Sonoyama et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Culture-Independent Characterization of Bacterial Communities Associated with the Cold-Water Coral Lophelia pertusa in the Northeastern Gulf of Mexico

(2009) C. A. Kellogg et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Skin microbes on frogs prevent morbidity and mortality caused by a lethal skin fungus

(2009) Reid N Harris et al.   ISME Journal

Evidence for Ecological Speciation and Its Alternative

(2009) D. Schluter   SCIENCE

TOXIC HYDROGEN SULFIDE AND DARK CAVES: PHENOTYPIC AND GENETIC DIVERGENCE ACROSS TWO ABIOTIC ENVIRONMENTAL GRADIENTS INPOECILIA MEXICANA

(2008) Michael Tobler et al.   EVOLUTION

Amphibian Chemical Defense: Antifungal Metabolites of the Microsymbiont Janthinobacterium lividum on the Salamander Plethodon cinereus

(2008) Robert M. Brucker et al.   JOURNAL OF CHEMICAL ECOLOGY

Isolation and Characterization of a New Fungal Species, Chrysosporium ophiodiicola, from a Mycotic Granuloma of a Black Rat Snake (Elaphe obsoleta obsoleta)

(2008) S. Rajeev et al.   JOURNAL OF CLINICAL MICROBIOLOGY

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Worlds within worlds: evolution of the vertebrate gut microbiota

(2008) Ruth E. Ley et al.   NATURE REVIEWS MICROBIOLOGY

Hibernation in an Antarctic Fish: On Ice for Winter

(2008) Hamish A. Campbell et al.   PLoS One

The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome

(2008) D. A. Sela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE

Interactions between commensal bacteria and the gut-associated immune system of the chicken

(2008) Jennifer T. Brisbin et al.   ANIMAL HEALTH RESEARCH REVIEWS

Determination of fish origin by using 16S rDNA fingerprinting of bacterial communities by PCR-DGGE: An application on Pangasius fish from Viet Nam

(2007) Doan Duy Le Nguyen et al.   FOOD CONTROL