Animal microbiome

A draft collection of some remarkable animal microbiomes. Highly biased for cute or scary animals and recent papers or reviews. Please free to leave suggestions for others in the comments. Created December 2015, updated February 2018.

General mammalian gut microbiomes

Rates of gut microbiome divergence in mammals – Alex H. Nishida – Molecular Ecology – January 2018

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time – Mathieu Groussin – Nature Communications – February 2017

Review: The functionality of the gastrointestinal microbiome in non-human animals – Irene Hanning and Sandra Diaz-Sanchez – Microbiome – November 2015

33 mammalian species: Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans – Brian D. Muegge – Science – May 2011

60 mammalian species, clone libraries – Ruth E. Ley – Science – June 2008

Primate microbiome

LemursPatterns of Gut Bacterial Colonization in Three Primate Species – Erin A. McKenney – PLOS ONE – May 2015

Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology – Andres Gomez – Molecular Ecology – April 2015

Application of the Human Intestinal Tract Chip to the non-human primate gut microbiota – T.D.J. Bello González – Beneficial Microbes – December 2014

Gorilla gorilla gorilla gut: a potential reservoir of pathogenic bacteria as revealed using culturomics and molecular tools – Fadi Bittar – Scientific Reports – November 2014

Fecal microbial diversity and putative function in captive western lowland gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas) and binturongs (Arctictis binturong) – Erin A.McKenney – Integrative Zoology – November 2014

The saliva microbiome of Pan and Homo – Jing Li – BMC Microbiology – September 2013

Pet mammals (Cats, dogs, rabbits)

Review: Understanding the canine intestinal microbiota and its modification by pro-, pre- and synbiotics – what is the evidence? – Silke Schmitz – Veterinary Medicine and Science – January 2016

A Pyrosequencing Investigation of Differences in the Feline Subgingival Microbiota in Health, Gingivitis and Mild Periodontitis – Stephen Harris – PLOS ONE – November 2015

Overweight and the feline gut microbiome – a pilot study – I. N. Kieler – Journal of Animal Physiology and Animal Nutrition – October 2015

A longitudinal assessment of changes in bacterial community composition associated with the development of periodontal disease in dogs – Corrin Wallis – Veterinary Microbiology – September 2015

Impact of dietary fiber/starch ratio in shaping caecal microbiota in rabbits – Yanli Zhu – Canadian Journal of Microbiology – August 2015

Comparison of the Oral Microbiomes of Canines and Their Owners Using Next-Generation Sequencing – Changin Oh- PLOS ONE – July 2015

The bacterial communities associated with fecal types and body weight of rex rabbits – Bo Zen – Scientific Reports – March 2015

Review: Current state of knowledge: the canine gastrointestinal microbiome – Seema Hooda – Animal Health Research Reviews – June 2012

The Canine Oral Microbiome – Floyd E. Dewhirst – PLOS ONE – April 2012

Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats  – Stefanie Handl – FEMS Microbiology Ecology – May 2011

Agricultural mammals

A reference gene catalogue of the pig gut microbiome – Liang Xiao – Nature Microbiology – September 2016

Vaginal microbial communities from synchronized-heifers and cows with reproductive disorders – Candelaria Gonzalez Moreno – Journal of Applied Microbiology – September 2016

The pig gut microbial diversity: Understanding the pig gut microbial ecology through the next generation high throughput sequencing – Hyeun Bum Kim – Veterinary Microbiology – June 2015

Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function – Shengyong Mao- Scientific Reports – November 2015

Cute, scary, or other mammals

The Tasmanian devil microbiome—implications for conservation and management – Yuanyuan Cheng – Microbiome – December 2015

Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies – Mario Carrillo-Araujo – Frontiers in Microbiology – May 2015 (HT: François-J. Lapointe)

The Bamboo-Eating Giant Panda Harbors a Carnivore-Like Gut Microbiota, with Excessive Seasonal Variations – Zhengsheng Xue – mBio – May 2015

The evolution of the gut microbiota in the giant and the red pandas – Ying Li – Scientific Reports – May 2015

Variation in koala microbiomes within and between individuals: effect of body region and captivity status – Niccoló Alfano – Scientific Reports – May 2015

In-depth diversity analysis of the bacterial community resident in the camel rumen – Javad Gharechahi – Systematic and Applied Microbiology – February 2015

Armadillos/aardvarks/etc: Convergence of gut microbiomes in myrmecophagous mammals – Frédéric Delsuc – Molecular Ecology – October 2013 (HT: François-J. Lapointe)

The Microbial Community in the Feces of the White Rhinoceros (Ceratotherium simum) as Determined by Barcoded Pyrosequencing Analysis – Gaorui Bian – PLOS ONE – July 2013

Marine mammals

Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome – Natasha K.Dudek – Current Biology – December 2017

Temporal and regional variability in the skin microbiome of humpback whales along the Western Antarctic Peninsula – K. C. Bierlich – Applied and Environmental Microbiology – December 2017

Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring – Amy Apprill – mSystems – October 2017

The microbiome of a striped dolphin (Stenella coeruleoalba) stranded in Portugal –  Filipa Godoy-Vitorino – Research in Microbiology – January 2017

Analysis of the microbial diversity in faecal material of the endangered blue whale, Balaenoptera musculus – Olivia Guass – Antonie van Leeuwenhoek – June 2016

The bottlenose dolphin (Tursiops truncatus) faecal microbiota – Matteo Soverini – FEMS Microbiology Ecology – April 2016

Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea – Elisabeth M. Bik – Nature Communications – February 2016

Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores – Jon G Sanders – Nature Communications – September 2015

Review: The marine mammal microbiome: current knowledge and future directions – Tiffanie M. Nelson – Microbiology Australia – March 2015

Diet and phylogeny shape the gut microbiota of Antarctic seals: a comparison of wild and captive animals – Tiffanie M. Nelson – Environmental Microbiology – November 2012


Comparative Gut Microbiota of 59 Neotropical Bird Species – Sarah M. Hird – Frontiers in Microbiology – December 2015

Review: Exploring the avian gut microbiota: current trends and future directions – David W. Waite – Frontiers in Microbiology – July 2015

Review: The chicken gastrointestinal microbiome – Brian B. Oakley – FEMS Microbiology Letters – November 2014

Characterizing the avian gut microbiota: membership, driving influences, and potential function – David W. Waite – Frontiers in Microbiology – May 2014

Influence of Hand Rearing and Bird Age on the Fecal Microbiota of the Critically Endangered Kakapo – David W. Waite – Applied and Environmental Microbiology – May 2014

Sea gulls: Age-related differences in the cloacal microbiota of a wild bird species – Wouter FD van Dongen – BMC Ecology – March 2013

Review: Diversity and function of the avian gut microbiota – Kevin D. Kohl – Journal of Comparative Physiology B – July 2012


Metagenomic analysis of the gut microbiota of the Timber Rattlesnake, Crotalus horridus – Richard William McLaughlin – Molecular Biology Reports – July 2015

Kinship, inbreeding and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise – Michael L. Yuan – Molecular Ecology – April 2015

Aerobic Bacterial Microbiota Isolated from the Cloaca of the European Pond Turtle (Emys orbicularis) in Poland – Aneta Nowakiewicz – Journal of Wildlife Diseases – January 2015

Postprandial remodeling of the gut microbiota in Burmese pythons – Elizabeth K Costello – The ISME Journal – June 2010

The alligator gut microbiome and implications for archosaur symbioses – Sarah W. Keenan – Scientific Reports – October 2013


Panamanian frog species host unique skin bacterial communities – Lisa K. Belden – Frontiers in Microbiology


Exploring fish microbial communities to mitigate emerging diseases in aquaculture
Irene de Bruijn –  FEMS Microbial Ecology – November 2017

Fish intestinal microbiome: diversity and symbiosis unravelled by metagenomics
A.M. Tarnecki – Journal of Applied Microbiology – May 2017

The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels – Han Liu – Scientific Reports, April 2016

Transition from freshwater to seawater reshapes the skin-associated microbiota of Atlantic salmon – Jep Lokesh – Scientific Reports – January 2016

Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota – Chris CR Smith – ISME J – November 2015

A new view of the fish gut microbiome: Advances from next-generation sequencing – Mahdi Ghanbari – Aquaculture – November 2015

Book Chapter: The fish microbiome and its interactions with mucosal tissues – Daniel L. Merrifield – Mucosal Health in Aquaculture – 2015

Noninvasive analysis of metabolic changes following nutrient input into diverse fish species, as investigated by metabolic and microbial profiling approaches – Taiga Asakura – 2014 – PeerJ

Review: Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries – Martin S. Llewellyn – Frontiers in Microbiology – June 2014

The intestinal microbiome of fish under starvation – Jun Hong Xia – BMC Genomics – April 2014

Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis – Karen E Sullam – Molecular Ecology – April 2012


Review: Insect symbionts in food webs – Ailsa H. C. McLean – Philosophical Transactions of the Royal Society B – August 2016

Review: Lower Termite Associations with Microbes: Synergy, Protection, and Interplay – Brittany F. Peterson – Frontiers in Microbiology – April 2016

Gut bacteria mediate aggregation in the German cockroach – Ayako Wada-Katsumata – PNAS – December 2015

Evaluation of the bacterial microbiome of two flea species using different DNA-isolation techniques provides insights into flea host ecology – Andrea L. Lawrence – FEMS Microbiology Ecology – November 2015

Host genetic control of the microbiota mediates Drosophila nutritional phenotype – John M. Chaston – Applied and Environmental Microbiology – November 2015

Diet is the primary determinant of bacterial community structure in the guts of higher termites – Aram Mikaelyan – October 2015

Review: The Gut Microbiota of Termites: Digesting the Diversity in the Light of Ecology and Evolution – Andreas Brune – Annual Review of Microbiology – October 2015

Review: Functional symbiosis and communication in microbial ecosystems. The case of wood-eating termites and cockroaches – Mercedes Berlanga – International Microbiology – Fall 2015

French invasive Asian tiger mosquito populations harbor reduced bacterial microbiota and genetic diversity compared to Vietnamese autochthonous relatives – G. Minard – Frontiers in Microbiology – September 2015

Developmental succession of the microbiome of Culex mosquitoes – Dagne Duguma – BMC Microbiology – July 2015

Diet shapes the gut microbiota of the omnivorous cockroach Blattella germanica – Ana Elena Pérez-Cobas – FEMS Microbiology Ecology – February 2015

Bacterial Communities and Midgut Microbiota Associated with Mosquito Populations from Waste Tires in East-Central Illinois – Chang-Hyun Kim – January 2015

Convergent Bacterial Microbiotas in the Fungal Agricultural Systems of Insects – Frank O. Aylward – mBio – November 2014

Identifying the core microbial community in the gut of fungus-growing termites – Saria Otani – Molecular Ecology – August 2014

Review: The impact of microbial symbionts on host plant utilization by herbivorous insects – Allison K. Hansen – Molecular Ecology – March 2014

Do diet and taxonomy influence insect gut bacterial communities? – D. R. Colman – Molecular Ecology – September 2012

Highly similar microbial communities are shared among related and trophically similar ant species – Anderson KE –  Molecular Ecology – January 2012

Anthropogenic effects on interaction outcomes: examples from insect-microbial symbioses in forest and savanna ecosystems – Diana L. Six – Symbiosis – June 2011

Review: Toward the functional analysis of uncultivable, symbiotic microorganisms in the termite gut – Yuichi Hongoh – Cellular and Molecular Life Sciences – March 2011

Molluscs and Annelids

Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk – Roberta M. O’Connor – PNAS – November 2014

Analysis of Stomach and Gut Microbiomes of the Eastern Oyster (Crassostrea virginica) from Coastal Louisiana, USA – Gary M. King – PLOS ONE — December 2012


The Gut of Geographically Disparate Ciona intestinalis Harbors a Core Microbiota – Larry J. Dishaw – PLOS ONE – April 2014 (HT: Larry J. Dishaw)

Corals, sponges, jellyfish

CoralsBacterial community diversity of the deep-sea octocoral Paramuricea placomus – Christina A. Kellogg – PeerJ – September 2016

Review: The Sponge Hologenome – Nicole S. Webster – mBio – April 2016

Biogeographic variation in the microbiome of the ecologically important sponge, Carteriospongia foliascens – Heidi M. Luter – PeerJ – December 2015

Stable and sporadic symbiotic communities of coral and algal holobionts
Eric R Hester – the ISME Journal – November 2015

Review: Coral—the world’s most diverse symbiotic ecosystem –  Linda L. Blackall – Molecular Ecology – October 2015

Review: Nitrogen cycling in corals: the key to understanding holobiont functioning?
Nils Rädecker – Trends in Microbiology – August 2015

Pyrosequencing Characterization of the Microbiota from Atlantic Intertidal Marine Sponges Reveals High Microbial Diversity and the Lack of Co-Occurrence Patterns – Anoop Alex – PLOS ONE – May 2015

Review: Microbes in the coral holobiont: partners through evolution, development, and ecological interactions – Janelle R. Thompson – Frontiers in Cellular and Infection Microbiology – January 2015

Review: Coral-associated micro-organisms and their roles in promoting coral health and thwarting diseases – Cory J. Krediet – Proceedings of the Royal Society B – January 2013

Review: Genomic insights into the marine sponge microbiome – Ute Hentschel – Nature Reviews Microbiology – September 2012

Review: Multi-Partner Interactions in Corals in the Face of Climate Change – Koty H. Sharp – The Biological Bulletin – August 2012

Coral-Associated Bacterial Assemblages: Current Knowledge and the Potential for Climate-Driven Impacts – Morgan E. Mouchka – Integrative and Comparative Biology – June 2010

Review: An environmental genomics perspective on the diversity and function of marine sponge-associated microbiota – Lubomir Grozdanov – Current Opinion in Microbiology – June 2007

Review: Sponge-Associated Microorganisms: Evolution, Ecology, and Biotechnological Potential – Michael W. Taylor – Microbiology and Molecular Biology Reviews – June 2007


The Microbial Community of Tardigrades: Environmental Influence and Species Specificity of Microbiome Structure and Composition – Matteo Vecchi – Microbial Ecology – January 2018