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Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Abdominal microbial communities in ants depend on colony membership rather than caste and are linked to colony productivity

inferredcites →https://doi.org/10.1002/ece3.6305openalex-snapshot

Effects of diet, habitat, and phylogeny on the fecal microbiome of wild African savanna (Loxodonta africana) and forest elephants (L. cyclotis)

inferredcites →https://doi.org/10.1002/ece3.6413openalex-snapshot

Gut microbiomes of sympatric Amazonian wood‐eating catfishes (Loricariidae) reflect host identity and little role in wood digestion

inferredcites →https://doi.org/10.1002/ece3.7373openalex-snapshot

Gut microbial ecology of the Critically Endangered Fijian crested iguana (Brachylophus vitiensis): Effects of captivity status and host reintroduction on endogenous microbiomes

inferredcites →https://doi.org/10.1002/evl3.127openalex-snapshot

Evolution of diet across the animal tree of life

inferredcites →https://doi.org/10.1002/mbo3.994openalex-snapshot

Cabbage looper (Trichoplusia ni Hübner) labial glands contain unique bacterial flora in contrast with their alimentary canal, mandibular glands, and Malpighian tubules

inferredcites →https://doi.org/10.1002/mnfr.201700184openalex-snapshot

Microbiota, metabolome, and immune alterations in obese mice fed a high‐fat diet containing type 2 resistant starch

inferredcites →https://doi.org/10.1007/s00114-020-01714-wopenalex-snapshot

No impact of a short-term climatic “El Niño” fluctuation on gut microbial diversity in populations of the Galápagos marine iguana (Amblyrhynchus cristatus)

inferredcites →https://doi.org/10.1007/s00203-020-01931-xopenalex-snapshot

Human microbiome: an academic update on human body site specific surveillance and its possible role

inferredcites →https://doi.org/10.1007/s00203-021-02526-wopenalex-snapshot

Contrasting gut microbiota in captive Eurasian otters (Lutra lutra) by age

inferredcites →https://doi.org/10.1007/s00248-017-1041-8openalex-snapshot

Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species

inferredcites →https://doi.org/10.1007/s00248-019-01436-1openalex-snapshot

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

inferredcites →https://doi.org/10.1007/s00248-019-01456-xopenalex-snapshot

Variation in the Slimy Salamander (Plethodon spp.) Skin and Gut-Microbial Assemblages Is Explained by Geographic Distance and Host Affinity

inferredcites →https://doi.org/10.1007/s00248-019-01460-1openalex-snapshot

The Gut Microbiota Composition of the Moth Brithys crini Reflects Insect Metamorphosis

inferredcites →https://doi.org/10.1007/s00248-020-01553-2openalex-snapshot

Direct Comparison of Fecal and Gut Microbiota in the Blue Mussel (Mytilus edulis) Discourages Fecal Sampling as a Proxy for Resident Gut Community

inferredcites →https://doi.org/10.1007/s00248-020-01569-8openalex-snapshot

Effects of Urbanization and Landscape on Gut Microbiomes in White-Crowned Sparrows

inferredcites →https://doi.org/10.1007/s00248-021-01896-4openalex-snapshot

Invasive Amphibian Gut Microbiota and Functions Shift Differentially in an Expanding Population but Remain Conserved Across Established Populations

inferredcites →https://doi.org/10.1007/s00248-021-01910-9openalex-snapshot

Gut Microbiome of Wild Baltic Salmon (Salmo salar L.) Parr

inferredcites →https://doi.org/10.1007/s00284-021-02531-8openalex-snapshot

Tapirus bairdii-Associated Fecal Microbiome from a Critical Conservation Area: Calakmul, México

inferredcites →https://doi.org/10.1007/s00338-021-02200-zopenalex-snapshot

Comparative analysis of the gut microbiota composition between two sea snakes, Hydrophis curtus, and Hydrophis cyanocinctus

inferredcites →https://doi.org/10.1007/s11160-019-09558-yopenalex-snapshot

Rainbow trout (Oncorhynchus mykiss) gut microbiota is modulated by insect meal from Hermetia illucens prepupae in the diet

inferredcites →https://doi.org/10.1007/s11274-016-2054-zopenalex-snapshot

Spatial dynamics of the bacterial community structure in the gastrointestinal tract of red kangaroo (Macropus rufus)

inferredcites →https://doi.org/10.1007/s12275-020-0524-3openalex-snapshot

Distinct gut microbiotas between southern elephant seals and Weddell seals of Antarctica

inferredcites →https://doi.org/10.1016/j.aqrep.2016.12.003openalex-snapshot

Effects of microbe- and mussel-based diets on the gut microbiota in Arctic charr ( Salvelinus alpinus )

inferredcites →https://doi.org/10.1016/j.aquaculture.2016.07.017openalex-snapshot

Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr (Salmo salar L.)

inferredcites →https://doi.org/10.1016/j.aquaculture.2020.736245openalex-snapshot

The intestinal microbiome of Australian abalone, Haliotis laevigata and Haliotis laevigata × Haliotis rubra, over a 1-year period in aquaculture.

inferredcites →https://doi.org/10.1016/j.aspen.2021.101863openalex-snapshot

Characterization of the gut microbiome in the beet armyworm Spodoptera exigua in response to the short-term thermal stress

inferredcites →https://doi.org/10.1016/j.cbd.2021.100789openalex-snapshot

Characterization of the intestinal digesta and mucosal microbiome of the grass carp (Ctenopharyngodon idella)

inferredcites →https://doi.org/10.1016/j.chemosphere.2020.126891openalex-snapshot

16S rRNA gene sequencing reveals the relationship between gut microbiota and ovarian development in the swimming crab Portunus trituberculatus

inferredcites →https://doi.org/10.1016/j.chom.2020.06.013openalex-snapshot

Co-evolution and Co-speciation of Host-Gut Bacteria Systems

inferredcites →https://doi.org/10.1016/j.chom.2023.03.016openalex-snapshot

Cross-feeding in the gut microbiome: Ecology and mechanisms

inferredcites →https://doi.org/10.1016/j.cub.2019.04.017openalex-snapshot

Understanding Competition and Cooperation within the Mammalian Gut Microbiome

inferredcites →https://doi.org/10.1016/j.dib.2020.106690openalex-snapshot

Metagenomic 16S rDNA amplicon data of microbial diversity of guts in Vietnamese humans with type 2 diabetes and nondiabetic adults

inferredcites →https://doi.org/10.1016/j.dsr.2019.103081openalex-snapshot

Comparative analysis of the gut microbial communities between two dominant amphipods from the Challenger Deep, Mariana Trench

inferredcites →https://doi.org/10.1016/j.gecco.2022.e02125openalex-snapshot

Insights into the composition of gut microbiota in response to environmental temperature: The case of the Mongolia racerunner (Eremias argus)

inferredcites →https://doi.org/10.1016/j.jclepro.2023.136104openalex-snapshot

Yellow mealworms (Tenebrio molitor) as an alternative animal feed source: A comprehensive characterization of nutritional values and the larval gut microbiome

inferredcites →https://doi.org/10.1016/j.marenvres.2023.106128openalex-snapshot

Response of moulting genes and gut microbiome to nano-plastics and copper in juvenile horseshoe crab Tachypleus tridentatus

inferredcites →https://doi.org/10.1016/j.marpolbul.2021.112522openalex-snapshot

Nutrient pollution alters the gut microbiome of a territorial reef fish

inferredcites →https://doi.org/10.1016/j.marpolbul.2022.114022openalex-snapshot

Gut microbiome and metabolome of sea cucumber (Stichopus ocellatus) as putative markers for monitoring the marine sediment pollution in Pahang, Malaysia

inferredcites →https://doi.org/10.1016/j.nmni.2021.100928openalex-snapshot

The importance of Faecalibacterium prausnitzii in human health and diseases

inferredcites →https://doi.org/10.1016/j.scitotenv.2020.138301openalex-snapshot

Insights into the earthworm gut multi-kingdom microbial communities

inferredcites →https://doi.org/10.1016/j.scitotenv.2020.140142openalex-snapshot

Environmental and host factors shaping the gut microbiota diversity of brown frog Rana dybowskii

inferredcites →https://doi.org/10.1016/j.scitotenv.2020.140873openalex-snapshot

Gut microbial composition in different castes and developmental stages of the invasive hornet Vespa velutina nigrithorax

inferredcites →https://doi.org/10.1016/j.scitotenv.2020.143250openalex-snapshot

Bioaccumulation of trace elements affects chick body condition and gut microbiome in greater flamingos

inferredcites →https://doi.org/10.1016/j.scitotenv.2021.149471openalex-snapshot

Impacts of benzo(a)pyrene exposure on scallop (Chlamys farreri) gut health and gut microbiota composition

inferredcites →https://doi.org/10.1016/j.tim.2015.06.004openalex-snapshot

The giant panda gut microbiome

inferredcites →https://doi.org/10.1021/acs.est.8b06695openalex-snapshot

Effects of Arsenic on Gut Microbiota and Its Biotransformation Genes in EarthwormMetaphire sieboldi

inferredcites →https://doi.org/10.1038/ismej.2011.33openalex-snapshot

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

inferredcites →https://doi.org/10.1038/ismej.2016.176openalex-snapshot

Faecalibacterium prausnitzii : from microbiology to diagnostics and prognostics

inferredcites →https://doi.org/10.1038/nature24621openalex-snapshot

A communal catalogue reveals Earth’s multiscale microbial diversity

inferredcites →https://doi.org/10.1038/ncomms13699openalex-snapshot

Amphibian gut microbiota shifts differentially in community structure but converges on habitat-specific predicted functions

inferredcites →https://doi.org/10.1038/ncomms14319openalex-snapshot

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

inferredcites →https://doi.org/10.1038/nrmicro2537openalex-snapshot

The skin microbiome

inferredcites →https://doi.org/10.1038/s41396-018-0175-0openalex-snapshot

Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes

inferredcites →https://doi.org/10.1038/s41396-018-0239-1openalex-snapshot

Astrovirus infections induce age-dependent dysbiosis in gut microbiomes of bats

inferredcites →https://doi.org/10.1038/s41396-019-0345-8openalex-snapshot

Effects of the captive and wild environment on diversity of the gut microbiome of deer mice (Peromyscus maniculatus)

inferredcites →https://doi.org/10.1038/s41396-019-0546-1openalex-snapshot

Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster ( Homarus gammarus )

inferredcites →https://doi.org/10.1038/s41396-019-0568-8openalex-snapshot

Gut microbiota structure differs between honeybees in winter and summer

inferredcites →https://doi.org/10.1038/s41396-020-0634-2openalex-snapshot

The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography

inferredcites →https://doi.org/10.1038/s41396-022-01208-9openalex-snapshot

Experimental evaluation of ecological principles to understand and modulate the outcome of bacterial strain competition in gut microbiomes

inferredcites →https://doi.org/10.1038/s41467-019-10191-3openalex-snapshot

Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades

inferredcites →https://doi.org/10.1038/s41467-020-18871-1openalex-snapshot

Health and disease markers correlate with gut microbiome composition across thousands of people

inferredcites →https://doi.org/10.1038/s41467-021-22510-8openalex-snapshot

Diet and gut microbiome enterotype are associated at the population level in African buffalo

inferredcites →https://doi.org/10.1038/s41467-022-34557-2openalex-snapshot

Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species

inferredcites →https://doi.org/10.1038/s41522-021-00237-0openalex-snapshot

The structure of Brazilian Amazonian gut microbiomes in the process of urbanisation

inferredcites →https://doi.org/10.1038/s41559-017-0340-2openalex-snapshot

The microbiome beyond the horizon of ecological and evolutionary theory

inferredcites →https://doi.org/10.1038/s41564-023-01388-wopenalex-snapshot

Widespread extinctions of co-diversified primate gut bacterial symbionts from humans

inferredcites →https://doi.org/10.1038/s41579-018-0029-9openalex-snapshot

Best practices for analysing microbiomes

inferredcites →https://doi.org/10.1038/s41579-021-00562-3openalex-snapshot

Host specificity of the gut microbiome

inferredcites →https://doi.org/10.1038/s41587-019-0209-9openalex-snapshot

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

inferredcites →https://doi.org/10.1038/s41587-023-01845-1openalex-snapshot

Greengenes2 unifies microbial data in a single reference tree

inferredcites →https://doi.org/10.1038/s41598-017-09355-2openalex-snapshot

Microbiota in the coelomic fluid of two common coastal starfish species and characterization of an abundant Helicobacter-related taxon

inferredcites →https://doi.org/10.1038/s41598-017-09791-0openalex-snapshot

Bacterial Community Structure in the Asian Rice Gall Midge Reveals a Varied Microbiome Rich in Proteobacteria

inferredcites →https://doi.org/10.1038/s41598-017-11805-wopenalex-snapshot

Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions

inferredcites →https://doi.org/10.1038/s41598-018-28720-3openalex-snapshot

16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus

inferredcites →https://doi.org/10.1038/s41598-018-32747-xopenalex-snapshot

First insight into microbiome profile of fungivorous thrips Hoplothrips carpathicus (Insecta: Thysanoptera) at different developmental stages: molecular evidence of Wolbachia endosymbiosis

inferredcites →https://doi.org/10.1038/s41598-019-40347-6openalex-snapshot

Intensity of Nosema ceranae infection is associated with specific honey bee gut bacteria and weakly associated with gut microbiome structure

inferredcites →https://doi.org/10.1038/s41598-019-43875-3openalex-snapshot

Gut microbiome differences between wild and captive black rhinoceros – implications for rhino health

inferredcites →https://doi.org/10.1038/s41598-019-46388-1openalex-snapshot

Community analysis of gut microbiota in hornets, the largest eusocial wasps, Vespa mandarinia and V. simillima

inferredcites →https://doi.org/10.1038/s41598-019-55940-yopenalex-snapshot

Habitat filtering shapes the differential structure of microbial communities in the Xilingol grassland

inferredcites →https://doi.org/10.1038/s41598-020-75203-5openalex-snapshot

Unravelling the gut bacteriome of Ips (Coleoptera: Curculionidae: Scolytinae): identifying core bacterial assemblage and their ecological relevance

inferredcites →https://doi.org/10.1038/s41598-021-02015-6openalex-snapshot

Diversity and compositional changes in the gut microbiota of wild and captive vertebrates: a meta-analysis

inferredcites →https://doi.org/10.1038/s41598-021-83497-2openalex-snapshot

Effects of maize (Zea mays) genotypes and microbial sources in shaping fall armyworm (Spodoptera frugiperda) gut bacterial communities

inferredcites →https://doi.org/10.1038/s41598-021-83675-2openalex-snapshot

Microbiome diversity of cotton aphids (Aphis gossypii) is associated with host alternation

inferredcites →https://doi.org/10.1038/s41598-021-91387-wopenalex-snapshot

Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca

inferredcites →https://doi.org/10.1038/s41598-021-94395-yopenalex-snapshot

Gut microbial communities associated with phenotypically divergent populations of the striped stem borer Chilo suppressalis (Walker, 1863)

inferredcites →https://doi.org/10.1038/s41598-021-98995-6openalex-snapshot

Diet diversity and environment determine the intestinal microbiome and bacterial pathogen load of fire salamanders

inferredcites →https://doi.org/10.1038/s41598-022-08761-5openalex-snapshot

Rumen and lower gut microbiomes relationship with feed efficiency and production traits throughout the lactation of Holstein dairy cows

inferredcites →https://doi.org/10.1038/s41598-022-24518-6openalex-snapshot

Wild microbiomes of striped plateau lizards vary with reproductive season, sex, and body size

inferredcites →https://doi.org/10.1038/s41598-022-24723-3openalex-snapshot

Lack of host phylogenetic structure in the gut bacterial communities of New Zealand cicadas and their interspecific hybrids

inferredcites →https://doi.org/10.1038/s41598-022-25408-7openalex-snapshot

The ground beetle Pseudoophonus rufipes gut microbiome is influenced by the farm management system

inferredcites →https://doi.org/10.1038/s41598-022-26861-0openalex-snapshot

Microbial rewilding in the gut microbiomes of captive ring-tailed lemurs (Lemur catta) in Madagascar

inferredcites →https://doi.org/10.1038/s41598-023-29663-0openalex-snapshot

Gut microbiome composition associates with corticosteroid treatment, morbidity, and senescence in Chinook salmon (Oncorhynchus tshawytscha)

inferredcites →https://doi.org/10.1038/s41598-023-31826-yopenalex-snapshot

Composition and function of the Galapagos penguin gut microbiome vary with age, location, and a putative bacterial pathogen

inferredcites →https://doi.org/10.1038/srep31448openalex-snapshot

Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets

inferredcites →https://doi.org/10.1038/srep32191openalex-snapshot

RETRACTED ARTICLE: Gut microbiome and dietary patterns in different Saudi populations and monkeys

inferredcites →https://doi.org/10.1073/pnas.1300926110openalex-snapshot

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

inferredcites →https://doi.org/10.1073/pnas.1419136111openalex-snapshot

Rapid changes in the gut microbiome during human evolution

inferredcites →https://doi.org/10.1073/pnas.1521835113openalex-snapshot

Captivity humanizes the primate microbiome

inferredcites →https://doi.org/10.1073/pnas.1905666116openalex-snapshot

Covariation of diet and gut microbiome in African megafauna

inferredcites →https://doi.org/10.1093/femsec/fiab021openalex-snapshot

Changes in the gut microbial community of the eastern newt (Notophthalmus viridescens) across its three distinct life stages

inferredcites →https://doi.org/10.1093/femsec/fix159openalex-snapshot

Developmental and gut-related changes to microbiomes of the cultured juvenile spiny lobster Panulirus ornatus

inferredcites →https://doi.org/10.1093/femsec/fiy213openalex-snapshot

Host blood meal source has a strong impact on gut microbiota of Aedes aegypti

inferredcites →https://doi.org/10.1093/femsec/fiz086openalex-snapshot

Gestation alters the gut microbiota of an oviparous lizard

inferredcites →https://doi.org/10.1093/femsec/fiz179openalex-snapshot

Age, gut location and diet impact the gut microbiome of a tropical herbivorous surgeonfish

inferredcites →https://doi.org/10.1093/femsle/fnab121openalex-snapshot

The effects of captivity on the microbiome of the endangered Comal Springs riffle beetle ( Heterelmis comalensis )

inferredcites →https://doi.org/10.1093/gerona/glaa319openalex-snapshot

Association Between Gut Microbiome and Frailty in the Older Adult Population in Korea

inferredcites →https://doi.org/10.1093/icb/icx090openalex-snapshot

The Effects of Captivity on the Mammalian Gut Microbiome

inferredcites →https://doi.org/10.1093/ismejo/wrae042openalex-snapshot

Niche differentiation in microbial communities with stable genomic traits over time in engineered systems

inferredcites →https://doi.org/10.1093/jee/toac103openalex-snapshot

Gut Bacterial Diversity and Community Structure of Spodoptera exigua (Lepidoptera: Noctuidae) in the Welsh Onion-producing Areas of North China

inferredcites →https://doi.org/10.1093/jisesa/ieac015openalex-snapshot

Intercolony Comparisons of Gut Microbiome Composition From Lab Reared Eastern Subterranean Termites (Blattodea: Rhinotermitidae)

inferredcites →https://doi.org/10.1093/jmammal/gyad097openalex-snapshot

Firmicutes and Bacteroidetes contribute to mass gain variation in female obligate hibernators

inferredcites →https://doi.org/10.1093/nar/gkab1009openalex-snapshot

AMDB: a database of animal gut microbial communities with manually curated metadata

inferredcites →https://doi.org/10.1093/nar/gkf436openalex-snapshot

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

inferredcites →https://doi.org/10.1098/rspb.2018.0241openalex-snapshot

Urea hydrolysis by gut bacteria in a hibernating frog: evidence for urea-nitrogen recycling in Amphibia

inferredcites →https://doi.org/10.1098/rspb.2019.0431openalex-snapshot

Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species

inferredcites →https://doi.org/10.1098/rspb.2019.2438openalex-snapshot

Disrupting butterfly caterpillar microbiomes does not impact their survival and development

inferredcites →https://doi.org/10.1098/rspb.2020.2886openalex-snapshot

Application of ecological and evolutionary theory to microbiome community dynamics across systems

inferredcites →https://doi.org/10.1111/1462-2920.14797openalex-snapshot

Developmental stages and gut microenvironments influence gut microbiota dynamics in the invasive beetle Popillia japonica Newman (Coleoptera: Scarabaeidae)

inferredcites →https://doi.org/10.1111/1462-2920.15952openalex-snapshot

Temporal variations shape the gut microbiome ecology of the moth Brithys crini

inferredcites →https://doi.org/10.1111/1751-7915.13687openalex-snapshot

Environment and host species identity shape gut microbiota diversity in sympatric herbivorous mammals

inferredcites →https://doi.org/10.1111/1755-0998.12744openalex-snapshot

Measuring the gut microbiome in birds: Comparison of faecal and cloacal sampling

inferredcites →https://doi.org/10.1111/fwb.13905openalex-snapshot

The gut bacterial microbiome of the Threeridge mussel, Amblema plicata, varies between rivers but shows a consistent core community

inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05552.xopenalex-snapshot

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

inferredcites →https://doi.org/10.1111/jam.13738openalex-snapshot

Dietary live yeast and increased water temperature influence the gut microbiota of rainbow trout

inferredcites →https://doi.org/10.1111/jen.13057openalex-snapshot

Analysis of the gut microbiome of susceptible and resistant honeybees (Apis cerana) against sacbrood virus disease

inferredcites →https://doi.org/10.1111/mec.12501openalex-snapshot

Convergence of gut microbiomes in myrmecophagous mammals

inferredcites →https://doi.org/10.1111/mec.13050openalex-snapshot

Diet strongly influences the gut microbiota of surgeonfishes

inferredcites →https://doi.org/10.1111/mec.13181openalex-snapshot

Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology

inferredcites →https://doi.org/10.1111/mec.13730openalex-snapshot

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

inferredcites →https://doi.org/10.1111/mec.14278openalex-snapshot

Gut microbiomes of free‐ranging and captive Namibian cheetahs: Diversity, putative functions and occurrence of potential pathogens

inferredcites →https://doi.org/10.1111/mec.15240openalex-snapshot

City life alters the gut microbiome and stable isotope profiling of the eastern water dragon (Intellagama lesueurii)

inferredcites →https://doi.org/10.1111/mec.15385openalex-snapshot

Early sexual dimorphism in the developing gut microbiome of northern elephant seals

inferredcites →https://doi.org/10.1111/mec.15487openalex-snapshot

Gut microbiota of invasive bullfrog tadpoles responds more rapidly to temperature than a noninvasive congener

inferredcites →https://doi.org/10.1111/mec.16394openalex-snapshot

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

inferredcites →https://doi.org/10.1111/mec.17153openalex-snapshot

16S rRNA gene‐based meta‐analysis of the reptile gut microbiota reveals environmental effects, host influences and a limited core microbiota

inferredcites →https://doi.org/10.1111/mec.17520openalex-snapshot

Host diet drives gut microbiome convergence between coral reef fishes and mammals

inferredcites →https://doi.org/10.1126/sciadv.abd3431openalex-snapshot

The gut microbiome defines social group membership in honey bee colonies

inferredcites →https://doi.org/10.1126/science.1155725openalex-snapshot

Evolution of Mammals and Their Gut Microbes

inferredcites →https://doi.org/10.1126/science.1198719openalex-snapshot

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

inferredcites →https://doi.org/10.1126/science.1224203openalex-snapshot

The Application of Ecological Theory Toward an Understanding of the Human Microbiome

inferredcites →https://doi.org/10.1126/science.aaf3951openalex-snapshot

Cospeciation of gut microbiota with hominids

inferredcites →https://doi.org/10.1126/science.aan4834openalex-snapshot

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

inferredcites →https://doi.org/10.1126/science.abb5352openalex-snapshot

Diversity and functional landscapes in the microbiota of animals in the wild

inferredcites →https://doi.org/10.1128/aem.00101-15openalex-snapshot

Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico

inferredcites →https://doi.org/10.1128/aem.00530-22openalex-snapshot

Sustained Drought, but Not Short-Term Warming, Alters the Gut Microbiomes of Wild Anolis Lizards

inferredcites →https://doi.org/10.1128/aem.00789-20openalex-snapshot

Fish Skin and Gut Microbiomes Show Contrasting Signatures of Host Species and Habitat

inferredcites →https://doi.org/10.1128/aem.01037-18openalex-snapshot

Overlapping Community Compositions of Gut and Fecal Microbiomes in Lab-Reared and Field-Collected German Cockroaches

inferredcites →https://doi.org/10.1128/aem.01181-20openalex-snapshot

The Lizard Gut Microbiome Changes with Temperature and Is Associated with Heat Tolerance

inferredcites →https://doi.org/10.1128/aem.01837-16openalex-snapshot

The Core Gut Microbiome of the American Cockroach, Periplaneta americana, Is Stable and Resilient to Dietary Shifts

inferredcites →https://doi.org/10.1128/aem.01864-20openalex-snapshot

Multi-omics Approaches To Decipher the Impact of Diet and Host Physiology on the Mammalian Gut Microbiome

inferredcites →https://doi.org/10.1128/aem.02082-20openalex-snapshot

Macrobdella decora : Old World Leech Gut Microbial Community Structure Conserved in a New World Leech

inferredcites →https://doi.org/10.1128/aem.02479-18openalex-snapshot

Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut

inferredcites →https://doi.org/10.1128/jcm.01769-21openalex-snapshot

The Clinical Utility of Two High-Throughput 16S rRNA Gene Sequencing Workflows for Taxonomic Assignment of Unidentifiable Bacterial Pathogens in Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

inferredcites →https://doi.org/10.1128/mbio.01667-20openalex-snapshot

Higher-Order Interactions Dampen Pairwise Competition in the Zebrafish Gut Microbiome

inferredcites →https://doi.org/10.1128/mbio.02502-22openalex-snapshot

Ecological Stability Emerges at the Level of Strains in the Human Gut Microbiome

inferredcites →https://doi.org/10.1128/mbio.02901-19openalex-snapshot

Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats

inferredcites →https://doi.org/10.1128/mra.00256-22openalex-snapshot

Gut Microbiome 16S rRNA Gene Amplicon Taxonomic Profiling of Hospitalized Moroccan COVID-19 Patients

inferredcites →https://doi.org/10.1128/mra.00374-21openalex-snapshot

16S rRNA Gene Amplicon Sequencing of Gut Microbiota from Naked Carp (Gymnocypris przewalskii) in Qinghai Lake, China

inferredcites →https://doi.org/10.1128/mra.01260-20openalex-snapshot

16S rRNA Gene Amplicon Sequencing of Gut Microbiota in Three Species of Deep-Sea Fish in Suruga Bay, Japan

inferredcites →https://doi.org/10.1128/msphere.00418-17openalex-snapshot

Effect of Environmental Factors and an Emerging Parasitic Disease on Gut Microbiome of Wild Salmonid Fish

inferredcites →https://doi.org/10.1128/msphere.00730-19openalex-snapshot

Gut Microbiomes of the Eastern Oyster ( Crassostrea virginica ) and the Blue Mussel ( Mytilus edulis ): Temporal Variation and the Influence of Marine Aggregate-Associated Microbial Communities

inferredcites →https://doi.org/10.1128/msystems.00633-21openalex-snapshot

Cross-Scale Analyses of Animal and Human Gut Microbiome Assemblies from Metacommunity to Global Landscape

inferredcites →https://doi.org/10.1128/msystems.00917-21openalex-snapshot

Molting Alters the Microbiome, Immune Response, and Digestive Enzyme Activity in Mud Crab ( Scylla paramamosain )

inferredcites →https://doi.org/10.1128/spectrum.00266-22openalex-snapshot

Species Identity Dominates over Environment in Driving Bacterial Community Assembly in Wild Invasive Leaf Miners

inferredcites →https://doi.org/10.1128/spectrum.03585-22openalex-snapshot

Gut Microbiome Composition of the Fire Ant Solenopsis invicta: an Integrated Analysis of Host Genotype and Geographical Distribution

inferredcites →https://doi.org/10.1146/annurev-ecolsys-110411-160307openalex-snapshot

From Animalcules to an Ecosystem: Application of Ecological Concepts to the Human Microbiome

inferredcites →https://doi.org/10.1155/2014/872725openalex-snapshot

Association between Faecalibacterium prausnitzii Reduction and Inflammatory Bowel Disease: A Meta-Analysis and Systematic Review of the Literature

inferredcites →https://doi.org/10.1186/gm228openalex-snapshot

Gut microbiome-host interactions in health and disease

inferredcites →https://doi.org/10.1186/s12864-016-3318-6openalex-snapshot

Functional analysis for gut microbes of the brown tree frog (Polypedates megacephalus) in artificial hibernation

inferredcites →https://doi.org/10.1186/s12864-019-6219-7openalex-snapshot

High-throughput sequencing reveals the core gut microbiota of the mud crab (Scylla paramamosain) in different coastal regions of southern China

inferredcites →https://doi.org/10.1186/s12866-021-02259-2openalex-snapshot

Composition and diversity of gut microbiota in Pomacea canaliculata in sexes and between developmental stages

inferredcites →https://doi.org/10.1186/s12866-022-02571-5openalex-snapshot

Bacterial diversity in Haemagogus leucocelaenus (Diptera: Culicidae) from Vale do Ribeira, São Paulo, Brazil

inferredcites →https://doi.org/10.1186/s13059-019-1908-8openalex-snapshot

Host-associated microbiomes are predicted by immune system complexity and climate

inferredcites →https://doi.org/10.1186/s13099-020-00351-yopenalex-snapshot

Gut microbiome of native Arab Kuwaitis

inferredcites →https://doi.org/10.1186/s40168-018-0427-2openalex-snapshot

Holobionts and ecological speciation: the intestinal microbiota of lake whitefish species pairs

inferredcites →https://doi.org/10.1186/s40168-018-0430-7openalex-snapshot

Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore

inferredcites →https://doi.org/10.1186/s40168-018-0454-zopenalex-snapshot

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

inferredcites →https://doi.org/10.1186/s40168-019-0622-9openalex-snapshot

A longitudinal assessment of host-microbe-parasite interactions resolves the zebrafish gut microbiome’s link to Pseudocapillaria tomentosa infection and pathology

inferredcites →https://doi.org/10.1186/s40168-020-00897-8openalex-snapshot

Parallel and non-parallel changes of the gut microbiota during trophic diversification in repeated young adaptive radiations of sympatric cichlid fish

inferredcites →https://doi.org/10.1186/s40168-020-0783-6openalex-snapshot

Dietary effects on gut microbiota of the mesquite lizard Sceloporus grammicus (Wiegmann, 1828) across different altitudes

inferredcites →https://doi.org/10.1186/s40168-021-01113-xopenalex-snapshot

Host habitat is the major determinant of the gut microbiome of fish

inferredcites →https://doi.org/10.1186/s40168-021-01214-7openalex-snapshot

Robust host source tracking building on the divergent and non-stochastic assembly of gut microbiomes in wild and farmed large yellow croaker

inferredcites →https://doi.org/10.1186/s40657-021-00287-0openalex-snapshot

The gut microbiome and metabolome of Himalayan Griffons (Gyps himalayensis): insights into the adaptation to carrion-feeding habits in avian scavengers

inferredcites →https://doi.org/10.1186/s40779-017-0122-9openalex-snapshot

Interaction between the gut microbiome and mucosal immune system

inferredcites →https://doi.org/10.1186/s42523-021-00094-4openalex-snapshot

Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales

inferredcites →https://doi.org/10.1186/s42523-021-00149-6openalex-snapshot

Gut microbiome composition, not alpha diversity, is associated with survival in a natural vertebrate population

inferredcites →https://doi.org/10.1186/s42523-021-00156-7openalex-snapshot

Interactions between reproductive biology and microbiomes in wild animal species

inferredcites →https://doi.org/10.1186/s42523-022-00168-xopenalex-snapshot

Microbiome structure in large pelagic sharks with distinct feeding ecologies

inferredcites →https://doi.org/10.1186/s42523-022-00184-xopenalex-snapshot

Host phylogeny, habitat, and diet are main drivers of the cephalopod and mollusk gut microbiome

inferredcites →https://doi.org/10.1186/s42523-022-00200-0openalex-snapshot

Gut microbiome reflect adaptation of earthworms to cave and surface environments

inferredcites →https://doi.org/10.1186/s42523-022-00218-4openalex-snapshot

Characterization of the gut microbiome and resistome of Galapagos marine iguanas (Amblyrhynchus cristatus) from uninhabited islands

inferredcites →https://doi.org/10.1194/jlr.r036012openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pcbi.1004365openalex-snapshot

Neutral Models of Microbiome Evolution

inferredcites →https://doi.org/10.1371/journal.pone.0183117openalex-snapshot

Microbiota of little penguins and short-tailed shearwaters during development

inferredcites →https://doi.org/10.1371/journal.pone.0187842openalex-snapshot

Diversity and characterization of bacteria associated with the deep-sea hydrothermal vent crab Austinograea sp. comparing with those of two shallow-water crabs by 16S ribosomal DNA analysis

inferredcites →https://doi.org/10.1371/journal.pone.0188919openalex-snapshot

Bacterial community composition in the gut content of Lampetra japonica revealed by 16S rRNA gene pyrosequencing

inferredcites →https://doi.org/10.1371/journal.pone.0208011openalex-snapshot

Characterization of the intestinal microbiota of the sea cucumber Holothuria glaberrima

inferredcites →https://doi.org/10.1371/journal.pone.0208917openalex-snapshot

The hindgut microbiota of praying mantids is highly variable and includes both prey-associated and host-specific microbes

inferredcites →https://doi.org/10.1371/journal.pone.0260792openalex-snapshot

Divergence together with microbes: A comparative study of the associated microbiomes in the closely related Littorina species

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What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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The role of microbiomes in animal invasions: a scoping review

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Bridging the gap: improving methodologies for future avian microbiome research

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Decoding the Gut Microbiome and Its Interactions in Animals: Mechanisms of Action

inferred← citeshttps://doi.org/10.1007/s00253-026-13948-1openalex-snapshot

Metagenomics comparison identifies shared pathogenic microbiome in humans, pigs and chickens

inferred← citeshttps://doi.org/10.1016/b978-0-443-22376-1.00014-3openalex-snapshot

Metagenomics, microbiomes, and symbioses

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Hierarchical drivers of the Baltic blue mussel (Mytilus trossulus) microbiome: Host filtering, seasonal dynamics, and anthropogenic impact

inferred← citeshttps://doi.org/10.1038/s42003-025-08185-7openalex-snapshot

Gut microbiome and diet contribute to ecological niche differentiation between argali (Ovis ammon hodgsoni) and blue sheep (Pseudois nayaur) on the Qinghai-Tibet Plateau

inferred← citeshttps://doi.org/10.1093/femsle/fnag049openalex-snapshot

The lizard microbiome: patterns, drivers, and functional implications

inferred← citeshttps://doi.org/10.1093/ismejo/wraf247openalex-snapshot

Host-microbiota matching and epigenetic modulation drive Daphnia magna responses to cyanobacterial stress

inferred← citeshttps://doi.org/10.1099/ijsem.0.007260openalex-snapshot

Aleya cavernae gen. nov., sp. nov., and Lacrimispora cavernae sp. nov., novel taxa isolated from bat guano

inferred← citeshttps://doi.org/10.1111/mec.17741openalex-snapshot

Blurred Lines Between Determinism and Stochasticity in an Amphibian Phylosymbiosis Under Pathogen Infection

inferred← citeshttps://doi.org/10.3389/fmars.2026.1866986openalex-snapshot

Microbiome baseline for an Arctic sentinel: spatial patterning of nasal and anal microbiomes in ringed seals

inferred← citeshttps://doi.org/10.3389/fpubh.2026.1746385openalex-snapshot

The resistome bridge between livestock and workers: novel frameworks for early detection and monitoring of antimicrobial resistance

inferred← citeshttps://doi.org/10.3390/insects17080871openalex-snapshot

Effect of Protein Supplementation on the Gut Microbiome of Omnivorous and Herbivorous Goliath Beetles

inferred← citeshttps://doi.org/10.3390/v17111508openalex-snapshot

Viromic Insights into Gut RNA Virus Diversity Among Three Corvid Species

inferred← citeshttps://doi.org/10.64898/2026.04.29.721755openalex-snapshot

An expansive animal gut microbiome dataset elucidates major compositional shifts across bilaterian evolution

inferred← citeshttps://doi.org/10.64898/2026.06.18.733207openalex-snapshot

The primate gut bacterial microbiome: a systematic review of research methodologies, taxonomic coverage, and conservation implications

inferred← citeshttps://doi.org/10.64898/2026.08.24.746638openalex-snapshot

Host ecological context influences taxonomic diversity and functional conservation of gut microbiome across anthropogenic habitats in macaques

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