Animal Microbiome

Flying birds and bats have simplified gastrointestinal tracts (GITs) and low intestinal mass to support flight. While previous work showed reduced GIT passage times in birds relative to other vertebrates, GIT passage times have never been collectively quantified for bats. We conducted a meta-analysis of published digesta passage times across vertebrates, comparing volant and non-volant vertebrates, while considering the effects of body mass and diet. We hypothesized that, like flying birds, bats have significantly faster digesta passage times relative to nonvolant vertebrates, likely due to their adaptations for flight. Our study supports this, revealing significant differences in passage times among flying and non-flying groups, with bats exhibiting faster transit times compared to non-volant vertebrates. Using a phylogenetic comparative analysis, we show that flight and diet have a strong effect on GIT transit times across diverse taxa, while body mass plays a more limited role. Accelerated transit times in bats likely promote the rapid turnover of gut contents, which may contribute to their distinct GIT microbe compositions. Unique among mammals, bat GIT microbiomes are dominated by Pseudomonadota bacteria, a pattern also observed in flying birds. We hypothesize this convergence may result from rapid GIT transit times quantified here for volant taxa.

This review explores the profound effects of domestication and urbanization on the gut microbiota of animals. It delves into the complex interplay between these two processes and their transformative impact on the microorganisms residing in the gastrointestinal tracts of a wide range of species. Domestication, the centuries-old practice of taming and breeding animals for human use, has led to significant shifts in the gut microbiomes of domesticated animals. This shift is a result of altered diets, living conditions, and reduced exposure to natural environments. The paper examines the consequences of these changes on animal health, behavior, and their adaptation to domestic life. Conversely, urbanization, characterized by the rapid expansion of cities and human habitats, has driven wild animals to adapt to urban environments. This review investigates how the urban landscape, pollution, and dietary changes reshape the gut microbiomes of urban wildlife. It explores the potential implications of these alterations on the animals resilience to urban stressors and disease. Drawing parallels between domestication and urbanization, the paper reveals intriguing similarities and differences in gut microbiome transformations across various species. It also assesses the broader implications of these shifts on ecological dynamics, zoonotic disease transmission, and the potential for microbial interactions between domesticated animals, urban wildlife, and humans. Ultimately, this review consolidates current knowledge on the topic, shedding light on the shared mechanisms and unique adaptations that drive microbial changes in animals undergoing domestication and those adapting to urban environments. It concludes with a discussion of the implications for animal conservation, animal-human interactions, and the One Health perspective, emphasizing the importance of understanding these intricate icrobial relationships in our ever-changing world. By enhancing our comprehension of these complex dynamics, this paper contributes to the growing body of knowledge that informs our coexistence with the animals we share our lives and cities with, highlighting the critical role of gut microbiota in these processes.

Dysbiosis in the vertebrate gut microbiome has been associated with several diseases. However, it is unclear whether particular gut regions or specific time periods during ontogeny are responsible for the development of dysbiosis, especially in non-model organisms. Here we examine the microbiome associated with dysbiosis in different parts of the gastrointestinal tract (ileum, caecum, colon) in a long-lived bird with high juvenile mortality, the ostrich. Individuals that died of gut disease (n=68) had substantially different microbial composition from age-matched controls (n=50) throughout the gut. Several taxa were associated with mortality (Enterobacteriaceae, Peptostreptococcaceae, Porphyromonadaceae, Clostridium) and some with survival (Lachnospiraceae, Ruminococcaceae, Erysipelotrichaceae, Turicibacter). Repeated faecal sampling showed that pathobionts were already present shortly after hatching and proliferated in individuals with low diversity, resulting in mortality weeks later. The factors influencing seeding of the gut microbiota may therefore be key to understanding dysbiosis and host development.

The gut microbiota is vital to host health, yet the relative influence of host traits and environmental factors on fish gut microbiota dynamics remains underexplored. We investigated the ecological dynamics of Atlantic salmon (Salmo salar) gut microbiota, by analysing 847 samples from wild and farmed salmon across diverse geographic regions, developmental phases, and associated diet and environmental microbiota. Farmed salmon exhibits reduced microbial diversity and distinct community composition with increased Firmicutes and reduced Proteobacteria compared to wild salmon. Microbial diversity declined with advancing developmental phases notably due to reduced Proteobacteria and expanded Mycoplasma. Diet was the primary contributor ([~]23%) to farmed salmon microbiota, with environmental inputs varying by region and phase. These findings highlight the importance of aquaculture practices guided by microbiota insights, while emphasize the need to preserve microbial diversity in wild populations to enhance resilience against environmental pressures, contributing to both sustainable farming and conservation strategies.

The gut microbiome (hereafter, GM) varies across individuals of the same species and this pattern has been observed in multiple wild species. Evidence shows that the GM connects to individual health and survival especially in captive species, but more research is needed to understand how the GM connects to host fitness in wild species. We used long-term monitoring data to investigate whether the GM of collared flycatchers Ficedula albicollis associates with annual and lifetime reproductive success (LRS), and survival to the following breeding season. This is the first study that 1) characterized the collared flycatcher GM, and 2) investigated how variation in the GM related to LRS in wild birds. Our results showed that higher GM diversity was associated with a higher annual and lifetime reproductive success in especially male collared flycatchers. We also found that the compositional variation in collared flycatcher GMs was explained by sex, age, and breeding habitat, but not by annual or lifetime reproductive success. Individuals that died before the next breeding season had higher abundances of ASVs belonging to the pathogenic families Enterobacteriaceae and Parachlamydiaceae, and the genera Corynebacteria and Sphingomonas. Our results show that the GM associates with different aspects of host fitness in a wild bird population. More research is needed to evaluate if there is a causal relationship between the GM and individual fitness. These findings also contribute to our understanding of the GMs role in evolution by elucidating the connection between the GM (trait) and reproductive success.

The gut microbiome is increasingly being appreciated as a master regulator of animal health. However, most avian gut microbiome studies have focused on birds of economic importance while the gut microbiomes of raptors remain underexplored. Here we examine the gut microbiota of 29 samples from four Falco species including hybrid birds-- raptors of historic importance --in the context of avian evolution by sequencing the 16S rDNA V4 region. Our results reveal that evolutionary histories and diet are significantly associated with avian gut microbiota in general, whereas diet plays a major role in shaping the falcon gut microbiota. Multiple analyses revealed that gut microbial diversity, composition, and abundance of key diet-discriminating bacterial genera in the falcon gut closely resemble those of carnivorous raptors rather than those of their closest phylogenetic relatives. Furthermore, the falcon microbiota is dominated by Firmicutes and consists of Salmonella at appreciable levels. Salmonella presence may potentially alter the functional capacity of the falcon gut microbiota as its abundance is associated with depletion of multiple predicted metabolic pathways involved in protein mass buildup, muscle maintenance, and enrichment of antimicrobial compound degradation, thus increasing the pathogenic potential of the falcon gut and presents a potential risk to human health. Author Summary in Arabic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/517295v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1440126org.highwire.dtl.DTLVardef@1a76b91org.highwire.dtl.DTLVardef@870bccorg.highwire.dtl.DTLVardef@17ac82_HPS_FORMAT_FIGEXP M_FIG C_FIG

Characterization of the gut microbiome may aid understanding and management of natural and experimental disease states in research animals, thereby promoting reproducibility. In this study, the rectal bacterial communities of three separate common marmoset (Callithrix jacchus) breeding colonies were defined using 16S rRNA sequencing of rectal swab samples. Study animals originated from two German colonies and a United States colony (JHU). The two German cohorts, previously fed the same diet, were imported into the JHU facility; they were then isolated, transitioned onto JHU diet, and then moved into rooms housing JHU animals. To dissect the contributions of diet and integration in shaping the rectal bacterial community, samples were collected from German origin marmosets upon JHU arrival (baseline), following diet transition (100 d), and following cohousing (390 d). Baseline and 390 d samples were collected from stably maintained JHU marmosets. Bacterial community composition was distinct between all three cohorts at baseline, suggesting that factors other than primary diet confer significant differences between captive populations. Beta-diversity of the animals from the two German colonies converged by 100 d but remained distinct from JHU sample beta-diversity throughout the 390-d study, indicating that diet had greater influence on bacterial community composition than did housing animals within the same room. Our results demonstrate substantial differences in gut bacteria between different captive marmoset colonies, with persistence of these differences following husbandry standardization and housing integration. Goals of rigor and reproducibility in research underscore the need to consider microbial differences between marmosets of diverse origin. ImportanceCharacterizing gut microbial populations is expected to promote health and enhance research reproducibility in animal studies. As use of common marmosets as animal models of human diseases expands, evaluating the marmoset gut bacterial community will be critical for interpreting research findings, especially as marmosets are prone to gastrointestinal inflammation. In this study, using 16S rRNA sequencing of rectal swab samples, we compared bacterial community among three captive colonies of marmosets at baseline and following importation of cohorts from two of the colonies into the third colony. Diet history had sustained influence on bacterial community composition, while housing the animals within the same room over a period of eight months did not appear to be a major factor. These persistent differences in marmoset gut bacterial community highlight the need for careful consideration of animal origin as a variable in marmoset research studies.

Probiotic supplementation supports poultry gut health by modulating microbiome and promoting immune development, yet limited information is known about the effects of early, particularly embryonic, supplementation. In this study, we investigated the effects of administering a lactobacilli cocktail in ovo (embryonic day 18), post-hatch, or both on gut immunity and the succession of the cecal microbiota in broilers over five weeks. 16S rRNA gene-based sequencing of cecal contents revealed a steady increase in Shannon diversity during the first three weeks (PERMANOVA, p < 0.005), with community structure stabilizing by week 3 across all groups. In ovo lactobacilli administration improved early hatch rates and modulated microbial composition during early succession, including reductions in Klebsiella and Enterococcus, and enrichment of Lactobacillus, during the first two weeks (MaAsLin2, q < 0.25). These microbiome shifts were accompanied by a reduced expression of pro-inflammatory cytokines (IFN-{gamma}, IL-1{beta}, and IL-8) in cecal tonsils. These findings highlight the transient yet critical role of early-life probiotic interventions in shaping gut microbial colonization and immune response in broiler chickens. More importantly, a single in ovo lactobacilli dose yielded effects comparable to weekly oral or combined administration.

BackgroundThe gut microbiome forms at an early stage, yet data on the environmental factors influencing the development of wild avian microbiomes is limited. As the gut microbiome is a vital part of organismal health, it is important to understand how it may connect to host performance. The early studies with wild gut microbiome have shown that the rearing environment may be of importance in gut microbiome formation, yet the results vary across taxa, and the effects of specific environmental factors have not been characterized. Here, wild great tit (Parus major) broods were manipulated to either reduce or enlarge the original brood soon after hatching. We investigated if brood size was associated with nestling bacterial gut microbiome, and whether gut microbiome diversity predicted survival. Fecal samples were collected at mid-nestling stage and sequenced with the 16S rRNA gene amplicon sequencing, and nestling growth and survival were measured. ResultsGut microbiome diversity showed high variation between individuals, but this variation was not significantly explained by brood size or body mass. Additionally, we did not find a significant effect of brood size on body mass or gut microbiome composition. We also demonstrated that early handling had no impact on nestling performance or gut microbiome. Furthermore, we found no significant association between gut microbiome diversity and short-term (survival to fledging) or mid-term (apparent juvenile) survival. ConclusionsWe found no clear association between early-life environment, offspring condition and gut microbiome. This suggests that brood size is not a significantly contributing factor to great tit nestling condition, and that other environmental and genetic factors may be more strongly linked to offspring condition and gut microbiome. Future studies should expand into other early-life environmental factors e.g., diet composition and quality, and parental influences.

This study assessed the genetic relatedness, evolutionary dynamics, and virulence profile of Salmonella isolated from lymph nodes and ground beef from apparently healthy cattle over two years. For this purpose, we used a set of isolates of nine different serovars: Anatum (n=23), Reading (n=22), Typhimurium (n=10), London (n=9), Kentucky (n=6), Fresno (n=4), Give, Muenster, and monophasic 1,4,[5],12:i- (n=1 each). These isolates were subjected to whole genome sequencing, and assembled and annotated genomes were used for downstream bioinformatic analyses. Although lymph nodes and ground beef were collected and analyzed separately, we still observed clonality between isolates from both sources. This finding suggests that some Salmonella circulating in the gut may reach the lymphatic system, creating a dual reservoir for ground beef contamination. We also found evidence of Salmonella persistence across cattle cohorts, as we observed clonality between isolates collected in different years. Variation in the virulence and pathogenicity island profiles was limited, with minor differences that could not be associated with attenuated virulence in the bovine host. Conversely, isolates of all serovars, except Fresno, were genetically close to strains involved in human salmonellosis in different countries, highlighting the risk to public health posed by strains associated with the carrier state in cattle. Further research is needed to reveal the mechanisms by which Salmonella causes subclinical infections in cattle and persists for long periods within farm environments.

Sloths, with their ruminant-like digestive systems, possess the slowest digestion among mammals due to their low metabolic rate, minimal food intake, and extremely low-energy diet. However, no comprehensive studies have characterized the sloths gut microbiota, including fungi, and their role in digestion. This study hypothesized that effective plant fiber-degrading fungi (e.g., Neocallimastigomycota) would be scarce in the sloths gut. The aim was to describe the gut microbiota of three-toed (Bradypus variegatus) and two-toed (Choloepus hoffmanni) sloths to understand their link to slow digestion. Microbial composition and functionality were analyzed using shotgun metagenomics, metatranscriptomics, fungal metabarcoding (ITS 1 and 2 nrDNA), and cellulose degradation analysis. Microbial communities were dominated by bacteria (92-97%), followed by viruses (1-7%). Fungi accounted for only 0.06-0.5% of metagenomic reads and 0.1% of transcripts. Functional analysis revealed minimal CAZy abundance (1.7-1.9% in metagenomes, 0.2% in metatranscriptomes), with no fungal CAZys or glycoside hydrolases detected. Neocallimastigomycota had negligible abundance in metagenomic data and was absent in metatranscriptomic or ITS metabarcoding data. Bradypus variegatus showed overall lower CAZy abundance and fungal presence compared to Choloepus hoffmanni. Lastly, cellulose degradation analyses revealed that only [~]5-35% of the intake was digested. This study highlights the unique microbial ecosystem in sloths guts, showing minimal presence of plant fiber-degrading anaerobic fungi and limited microbial CAZys, aligning with their slow digestion and low metabolic rate, thus enhancing our understanding of their digestive efficiency and metabolic adaptations.

Ulcerative conditions present a major challenge in Norwegian salmon farming. Probiotic Aliivibrio species have previously been demonstrated to provide health benefits in both Atlantic salmon and lumpfish, although the underlying mechanisms and the host-bacteria interactions remain unclear. This study aimed to investigate whether these bacteria could colonize Atlantic salmon following bath administration, determine the tissue tropism, and assess the duration of colonization. We examined the host microbiota using culture-based methods, qPCR and immunohistochemistry techniques specifically designed to target the applied Aliivibrio strains. Our findings reveal that the probiotic bacteria can successfully colonize Atlantic salmon and persist for at least nine months post-administration. We identified the administered strains in the skin and underlying tissue with all three methods. The probiotics were also identified in the distal intestine and the visceral organs. Additionally, we isolated the probiotic Aliivibrio species from mixed cultures in ulcerated areas. While viable bacteria were recoverable from recently euthanized fish, tissue decay promoted bacterial recovery of the administered species across all experiments. Given prior evidence on ulcer reduction associated with these probiotics, competitive exclusion appears to be a plausible mechanism of action, though further investigation is warranted.

Reintroducing captive-bred animals into the wild often faces limited success, with the underlying causes frequently unclear. One emerging hypothesis is that maladapted gut microbiota may play a significant role in these challenges. To investigate this possibility, we employed genome-resolved metagenomics to analyse the taxonomic and functional differences in the gut microbiota of wild and captive European hares (Lepus europaeus), as well as to assess the impact of a dietary switch to grass aimed at pre-adapting captive hares to wild conditions. Our analyses recovered 860 metagenome-assembled genomes, with 87% of them representing novel species. We found significant taxonomic and functional differences between the gut microbiota of wild and captive hares, notably the absence of Spirochaetota in captive animals and differences in amino acid and sugar degradation capacities. While the dietary switch to grass induced some minor changes in the gut microbiota, it did not result in a shift towards a more wild-like microbial community. The increased capacity for degrading amino acids and specific sugars observed in wild hares suggest that, instead of bulk grass, dietary interventions tailored to their specific dietary preferences might be necessary for pre-adapting hare gut microbiota to wild conditions. ImportanceThis study sheds light on the critical role of gut microbiota in the success of reintroducing captive-bred animals into the wild. By comparing the gut microbiota of wild and captive European hares, we identified significant taxonomic and functional differences, including the absence of key microbial groups in captive hares. Dietary interventions, such as switching to grass, showed limited success in restoring a wild-like microbiota, highlighting the need for tailored approaches to mimic natural diets. With 87% of recovered microbial genomes representing novel species, this research also enriches our understanding of microbial diversity in wildlife. These findings emphasise that maladapted gut microbiota may hinder the survival and adaptation of reintroduced animals, suggesting that microbiome-targeted strategies could improve conservation efforts and the success of animal rewilding programs.

Amphibious animals, such as frogs, are found at the intersection of aquatic and terrestrial ecosystems. They often serve as keystone and sentinel species, essential in nutrient cycling and food webs. In recent decades, amphibians have experienced drastic population declines due to habitat loss, climate change, and disease. These declines have prompted investments in ex situ conservation and captive breeding programs, which aim to reduce extinction risk by creating assurance colonies and reintroducing individuals once threats are mitigated. A critical component of these programs is proper husbandry, which ensures the health and longevity of captive populations and their ability to produce offspring that can be reintroduced into the wild. The artificial environment in captivity can profoundly impact animal behavior and health, particularly in relation to diet and nutrition. Diet not only provides nutrients and energy but also shapes the hosts gut microbial community, which in turn impacts digestive health. Complex microbial communities, collectively known as the microbiome, are characterized by the high biodiversity of prokaryotes, microscopic fungi, and viruses. The diet-associated microbiome is increasingly studied for its role in captive animal health and behavior, although research has focused more on bacteria than fungal communities, or the "mycobiome". Here, we investigated the core mycobiome using metabarcoding of fungal communities in 15 wild-caught Anaxyrus fowleri (Fowlers Toad), documenting shifts as toads transitioned from wild to captive settings. We identified a core set of fungal taxa and observed distinct changes in non-core fungi associated with dietary differences. These findings highlight the dynamic nature of the amphibian mycobiome and the significant impact captivity can have on microbial composition, providing a framework for understanding the role of the amphibian mycobiome in future conservation efforts.

Gut microbial communities regulate host physiology and health of humans and laboratory animals. The functional significance of these collective bacterial genomes (i.e. the microbiome) to the adaptive potential of wildlife hosts is still unknown. Studies demonstrating convincing examples of microbial flexibility to environmental change so far lack the experimental approaches to demonstrate the effect on host physiology. Invasive species provide natural experiments to tease apart these host-microbe relationships. However, no studies have investigated how microbial symbionts might mediate responses of invasive hosts physiology to environmental change. In this study, we examine whether invasive gut microbiomes have significantly diverged in their ability to respond to novel environmental change (i.e. a dietary challenge) compared to native gut microbiomes by performing reciprocal faecal microbial transplant (FMT) experiments in native and invasive guttural toad (Sclerophrys gutturalis) populations. Subsequently, we determine how the microbiome regulates host physiological changes in response to a dietary challenge. We show that invasive gut microbiomes exhibit higher microbial compositional and predicted functional flexibility to novel dietary change, compared to native gut microbiomes. This increased microbial flexibility is coupled with significant flexibility in energy harvesting. Furthermore, our results indicate that overall invasive gut microbiomes significantly upregulate energy harvesting and physiological performance of hosts, compared to native microbiomes. Our study is the first identifying gut microbiota as the sole factor contributing to the adaptive physiology of a vertebrate using a unique study design. These findings provide novel insights into the key role of gut microbial symbionts in increasing the invasive potential of its vertebrate host.

Shorebirds migrate long distances twice annually, which requires intense physiological and morphological adaptations, including the ability to rapidly gain weight via fat deposition at stopover locations. The role of the microbiome in weight gain in avian hosts is unresolved, but there is substantial evidence to support the hypothesis that the microbiome is involved with host weight from mammalian microbiome literature. Here, we collected 100 fecal samples of Ruddy Turnstones to investigate microbiome composition and function during stopover weight gain in Delaware Bay, USA. Using 16S rRNA sequencing on 90 of these samples and metatranscriptomic sequencing on 22, we show that taxonomic composition of the microbiome shifts during weight gain, as do functional aspects of the metatranscriptome. We identified ten genes that are associated with weight class and polyunsaturated fatty acid biosynthesis in the microbiota is significantly increasing as birds gain weight. Our results support that the microbiome is a dynamic feature of host biology that interacts with both the host and the environment and may be involved in the rapid weight gain of shorebirds.

As the global population continues to grow exponentially, the competition for resources between livestock and humans has become increasingly intense. Breeding efficient animal breeds, fully utilizing feed resources, and reducing environmental damage are major challenges facing the livestock industry. To address these issues, enhancing the feed utilization efficiency in the poultry industry is crucial. Recent studies have elucidated the pivotal role of gut microbiota in modulating the feeding behavior of their host organisms. Thus, we used metagenomics, transcriptomics, and metabolomics to explore how the intestinal microbiome affects the feed utilization efficiency in ducks. Our metagenomic analysis revealed a significant up-regulation of Elusimicrobiota at the phylum level within the high residual feed intake (HRFI) group, in comparison to the low residual feed intake (LRFI) group. Additionally, functional analysis using Clusters of Orthologous Groups of proteins (COG) indicated prominent disparities in the category of secondary metabolites biosynthesis, transport, and catabolism between the HRFI and LRFI groups. Furthermore, our metabolomics investigation identified an upregulated expression of the secondary metabolite 15-deoxy-{Delta}12,14-prostaglandin J2 (15d-PGJ2) in the HRFI group compared to the LRFI group. Liver transcriptome analysis identified prostaglandin-endoperoxide synthase 2 (PTGS2) as a key hub gene, exerting significant regulatory influence within the arachidonic acid pathway. Notably, the metabolite 15d-PGJ2 is a terminal product in the metabolic pathway of arachidonic acid. The correlation analysis between the cecal microbiota and differential metabolites revealed a significant negative correlation between Elusimicrobiota and the metabolite 15d-PGJ2. In summary, we assumed that the intestinal microbiome Elusimicrobiota regulates the expression of the PTGS2 gene, consequently inducing variations in PTGS2 efficiency between the HRFI and LRFI groups, ultimately leading to diverse residual feed intake levels in ducks. IMPORTANCEThis investigation utilizes metabolomics to elucidate the interplay between genes and microbiome communities. We present evidence of disparities in the composition of microbial consortia among ducks RFI, alongside identification of pivotal genes within the liver that potentially modulate RFI. These results provide novel perspectives on the processes through which the cecum and liver influence RFI.

Mass mortality events in wildlife can be indications of an emerging infectious disease. During the spring and summer of 2021, hundreds of dead passerines were reported across the eastern US. Birds exhibited a range of clinical signs including swollen conjunctiva, ocular discharge, ataxia, and nystagmus. As part of the diagnostic investigation, high-throughput metagenomic next-generation sequencing was performed across three molecular laboratories on samples from affected birds. Many potentially pathogenic microbes were detected, with bacteria comprising the largest proportion; however, no singular agent was consistently identified, with many of the detected microbes also found in unaffected (control) birds, and thus considered to be subclinical infections. Congruent results across laboratories have helped drive further investigation into alternative causes including environmental contaminants and nutritional deficiencies. This work highlights the utility of metagenomic approaches in investigations of emerging diseases and provides a framework for future wildlife mortality events. Article Summary LineThe causative agent of a mass mortality event in passerines remains inconclusive after metagenomic high-throughput sequencing with results prompting further investigation into non-pathogenic causes.

Vertebrate gut microbiome has significant effects on host development, health, and fitness. Multiple external factors contribute to gut microbiome variation, and the role of ambient temperature has gained increasing attention. Yet, temperature effects are often tested in extremes and in captive systems. We experimentally studied the effect of subtle temperature decreases during post-natal development on gut microbiome diversity and composition in wild pied flycatchers (Ficedula hypoleuca). We also performed partial cross-fostering to study the relative contribution of genetic and rearing environment on microbiome. Nest-box cold treatment did not influence gut microbiome diversity or composition, which may be due to the small temperature change, ontogenetic stage, or other factors, such as diet, causing large variation in the data. Rearing environment explained more of the variation in gut microbiome than genetic background, but the variance explained was relatively small. Future studies need to further address the drivers of the large intraspecific variation in microbiome in natural populations.

Animals from a wide taxonomic range can sense earths magnetic field, however the underlying mechanism remains one of sensory-biology greatest mysteries. One hypothesis suggests that Magnetotactic bacteria (MTB) serve as the underlying mechanism. This hypothesis predicts that MTB will be detected in animal microbiomes and might show a phylogenetic relationship with their hosts. We examined the phylogenetic relationship between various MTB species across 4,048 avian species using databases of MTB genetic presence across the tree of life and an avian phylogenetic tree. We documented 12 genera of MTB in association with 185 avian species. Three genera, Magnetospirillum, Magnetovibrio and Solidesulfovibrio, were found at relative high prevalence of positive samples (84%, 33%, 12% respectively). Further, Magnetospirillum showed a significant phylogenetic relationship with avian species in general and specifically within Psittaciformes, and Passeriformes. Our results demonstrate the power of harnessing the newly published MTB-database, with specific host-related queries. This analysis, to the best of our knowledge has never been done, and could be replicated across the animal kingdom. The relationship detected suggests an evolutionary and ecological relationship between MTB and avian hosts. These results are consistent with the symbiotic magnetic sensing hypothesis and highlights the potential role of microbiome in sensory physiology.