Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters

Using patterns of shared taxa to infer bacterial dispersal in human living environment in urban and rural areas

Contact with environmental microbial communities primes the human immune system. Factors determining the distribution of microorganisms, such as dispersal, are thus important for human health. Here, we used the relative number of bacteria shared between environmental and human samples as a measure of bacterial dispersal and studied these associations with living environment and lifestyles. We analyzed amplicon sequence variants (ASVs) of the V4 region of 16S rDNA gene from 347 samples of doormat dust as well as samples of saliva, skin swabs, and feces from 53 elderly people in urban and rural areas in Finland at three timepoints. We first enumerated the ASVs shared between doormat and one of the human sample types (i.e., saliva, skin swab, or feces) of each individual subject and calculated the shared ASVs as a proportion of all ASVs in the given sample type of that individual. We observed that the patterns for the proportions of shared ASVs differed among seasons and human sample type. In skin samples, there was a negative association between the proportion of shared ASVs and the coverage of built environment (a proxy for degree of urbanization), whereas in saliva data, this association was positive. We discuss these findings in the context of differing species pools in urban and rural environments.

IMPORTANCE

Understanding how environmental microorganisms reach and interact with humans is a key question when aiming to increase human contacts with natural microbiota. Few methods are suitable for studying microbial dispersal at relatively large spatial scales. Thus, we tested an indirect method and studied patterns of bacterial taxa that are shared between humans and their living environment.

Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses

Gut microbiomes are widely hypothesised to influence host fitness and have been experimentally shown to affect host health and phenotypes under laboratory conditions. However, the extent to which they do so in free-living animal populations and the proximate mechanisms involved remain open questions. In this study, using long-term, individual-based life history and shallow shotgun metagenomic sequencing data (2394 fecal samples from 794 individuals collected between 2013-2019), we quantify relationships between gut microbiome variation and survival in a feral population of horses under natural food limitation (Sable Island, Canada), and test metagenome-derived predictions using short-chain fatty acid data. We report detailed evidence that variation in the gut microbiome is associated with a host fitness proxy in nature and outline hypotheses of pathogenesis and methanogenesis as key causal mechanisms which may underlie such patterns in feral horses, and perhaps, wild herbivores more generally.

Long-distance movement dynamics shape host microbiome richness and turnover

Host-associated microbial communities are shaped by host migratory movements. These movements can have contrasting impacts on microbiota, and understanding such patterns can provide insight into the ecological processes that contribute to community diversity. Furthermore, long-distance movements to new environments are anticipated to occur with increasing frequency due to host distribution shifts resulting from climate change. Understanding how hosts transport their microbiota with them could be of importance when examining biological invasions. Although microbial community shifts are well-documented, the underlying mechanisms that lead to the restructuring of these communities remain relatively unexplored. Using literature and ecological simulations, we develop a framework to elucidate the major factors that lead to community change. We group host movements into two types-regular (repeated/cyclical migratory movements, as found in many birds and mammals) and irregular (stochastic/infrequent movements that do not occur on a cyclical basis, as found in many insects and plants). Ecological simulations and prior research suggest that movement type and frequency, alongside environmental exposure (e.g. internal/external microbiota) are key considerations for understanding movement-associated community changes. From our framework, we derive a series of testable hypotheses, and suggest means to test them, to facilitate future research into host movement and microbial community dynamics.

Linking microbiome temporal dynamics to host ecology in the wild

Ignoring the dynamic nature of microbial communities risks underestimating the power of microbes to impact the health of their hosts. Microbiomes are thought to be important for host fitness, yet the coarse temporal scale and population-level focus of many studies precludes the ability to investigate the importance of among-individual variation in stability and identify the ecological contexts in which this variation matters. Here we briefly summarise current knowledge of temporal dynamics in wild host-associated microbial communities. We then discuss the implications of among-individual variation in microbiota stability and suggest analytical approaches for understanding these patterns. One major requirement is for future studies to conduct individual-level longitudinal analyses, with some systems already well set up for answering these questions.

Distinct Gut Microbial Enterotypes and Functional Dynamics in Wild Striped Field Mice (Apodemus agrarius) across Diverse Populations

Rodents, including the striped field mouse (Apodemus agrarius), play vital roles in ecosystem functioning, with their gut microbiota contributing significantly to various ecological processes. Here, we investigated the structure and function of 94 wild A. agrarius individuals from 7 geographic populations (45°57' N, 126°48' E; 45°87' N, 126°37' E; 45°50' N, 125°31' E; 45°59' N, 124°37' E; 46°01' N, 124°88' E; 46°01' N, 124°88' E; 46°01' N, 124°88' E), revealing two distinct enterotypes (Type1 and Type2) for the first time. Each enterotype showed unique microbial diversity, functions, and assembly processes. Firmicutes and Bacteroidetes dominated, with a significant presence of Lactobacillus and Muribaculaceae. Functional analysis highlighted metabolic differences, with Type1 emphasizing nutrient processing and Type2 showing higher energy production capacity. The analysis of the neutral model and the null model revealed a mix of stochastic (drift and homogenizing dispersal) and deterministic processes (homogenous selection) that shape the assembly of the microbiota, with subtle differences in the assembly processes between the two enterotypes. Correlation analysis showed that elevation and BMI were associated with the phylogenetic turnover of microbial communities, suggesting that variations in these factors may influence the composition and diversity of the gut microbiota in A. agrarius. Our study sheds light on gut microbial dynamics in wild A. agrarius populations, highlighting the importance of considering ecological and physiological factors in understanding host-microbiota interactions.

Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions

The study of microbiomes across organisms and environments has become a prominent focus in molecular ecology. This perspective article explores common challenges, methodological advancements, and future directions in the field. Key research areas include understanding the drivers of microbiome community assembly, linking microbiome composition to host genetics, exploring microbial functions, transience and spatial partitioning, and disentangling non-bacterial components of the microbiome. Methodological advancements, such as quantifying absolute abundances, sequencing complete genomes, and utilizing novel statistical approaches, are also useful tools for understanding complex microbial diversity patterns. Our aims are to encourage robust practices in microbiome studies and inspire researchers to explore the next frontier of this rapidly changing field.

The influence of diet on gut microbiome and body mass dynamics in a capital-breeding migratory bird

Gut-associated microbial communities are known to play a vital role in the health and fitness of their hosts. Though studies investigating the factors associated with among-individual variation in microbiome structure in wild animal species are increasing, knowledge of this variation at the individual level is scarce, despite the clear link between microbiome and nutritional status uncovered in humans and model organisms. Here, we combine detailed observational data on life history and foraging preference with 16S rRNA profiling of the faecal microbiome to investigate the relationship between diet, microbiome stability and rates of body mass gain in a migratory capital-breeding bird, the light-bellied Brent goose (Branta bernicla hrota). Our findings suggest that generalist feeders have microbiomes that are intermediate in diversity and composition between two foraging specialisms, and also show higher within-individual plasticity. We also suggest a link between foraging phenotype and the rates of mass gain during the spring staging of a capital breeder. This study offers rare insight into individual-level temporal dynamics of the gut microbiome of a wild host. Further work is needed to uncover the functional link between individual dietary choices, gut microbiome structure and stability, and the implications this has for the reproductive success of this capital breeder.

Does ecological drift explain variation in microbiome composition among groups in a social host species?

Within a given species, considerable inter-individual, spatial, and temporal variation in the composition of the host microbiome exists. In group-living animals, social interactions homogenize microbiome composition among group members, nevertheless divergence in microbiome composition among related groups arise. Such variation can result from deterministic and stochastic processes. Stochastic changes, or ecological drift, can occur among symbionts with potential for colonizing a host and within individual hosts, and drive divergence in microbiome composition among hosts or host groups. We tested whether ecological drift associated with dispersal and foundation of new groups cause divergence in microbiome composition between natal and newly formed groups in the social spider Stegodyphus dumicola. We simulated the initiation of new groups by splitting field-collected nests into groups of 1, 3, and 10 individuals respectively, and compared variation in microbiome composition among and within groups after 6 weeks using 16S rRNA gene sequencing. Theory predicts that ecological drift increases with decreasing group size. We found that microbiome composition among single founders was more dissimilar than among individuals kept in groups, supporting this prediction. Divergence in microbiome composition from the natal nest was mainly driven by a higher number of non-core symbionts. This suggests that stochastic divergence in host microbiomes can arise during the process of group formation by individual founders, which could explain the existence of among-group variation in microbiome composition in the wild. Individual founders appear to harbour higher relative abundances of non-core symbionts compared with founders in small groups, some of which are possible pathogens. These symbionts vary in occurrence with group size, indicating that group dynamics influence various core and non-core symbionts differently.

Gut microbial community structure and function of Przewalski's horses varied across reintroduced sites in China

Host-associated microbiota can significantly impact host fitness. Therefore, naturally occurring variations in microbiota may influence the health and persistence of their hosts. This finding is particularly important in reintroduced animals, as they typically experience habitat changes during translocations. However, little is known about how microbiomes are altered in response to conservation translocation. Here, we accessed the gut microbiome of Przewalski's horse (Equus przewalskii) populations in China from three nature reserves (i.e. Xinjiang Kalamaili Nature Reserve, KNR; Dunhuang Xihu National Nature Reserve, DXNNR; and Anxi Extreme-arid Desert Nature Reserve, AENR) using 16s rRNA gene and metagenome sequencing. The results showed that the microbial composition and function differed significantly across locations, while a subset of core taxa was consistently present in most of the samples. The abundance of genes encoding microbe-produced enzymes involved in the metabolism of carbohydrates, especially for glycoside hydrolases, was significantly higher in open-spaced KNR populations than in more confined AENR individuals. This study offers detailed and significant differential characters related to the microbial community and metabolic pathways in various reintroduced sites of Przewalski's horse, which might provide a basis for future microecological and conservation research on endangered reintroduced animals.

Seasonal assembly of skin microbiota driven by neutral and selective processes in the greater horseshoe bat

Skin microbiota play an important role in protecting bat hosts from the fungal pathogen Pseudogymnoascus destructans, which has caused dramatic bat population declines and extinctions. Recent studies have provided insights into the bacterial communities of bat skin, but variation in skin bacterial community structure in the context of the seasonal dynamics of fungal invasion, as well as the processes that drive such variation, remain largely unexplored. In this study, we characterized bat skin microbiota over the course of the bat hibernation and active season stages and used a neutral model of community ecology to determine the relative roles of neutral and selective processes in driving microbial community variation. Our results showed significant seasonal shifts in skin community structure, as well as less diverse microbiota in hibernation than in the active season. Skin microbiota were influenced by the environmental bacterial reservoir. During both the hibernation and active season stages, more than 78% of ASVs in bat skin microbiota were consistent with neutral distribution, implying that neutral processes, that is, dispersal or ecological drift contributing the most to shifts in skin microbiota. In addition, the neutral model showed that some ASVs were actively selected by the bats from the environmental bacterial reservoir, accounting for approximately 20% and 31% of the total community during hibernation and active season stages, respectively. Overall, this research provides insights into the assemblage of bat-associated bacterial communities and will aid in the development of conservation strategies against fungal disease.

Maternal transmission gives way to social transmission during gut microbiota assembly in wild mice

BACKGROUND

The mammalian gut microbiota influences a wide array of phenotypes which are relevant to fitness, yet knowledge about the transmission routes by which gut microbes colonise hosts in natural populations remains limited. Here, we use an intensively studied wild population of wood mice (Apodemus sylvaticus) to examine how vertical (maternal) and horizontal (social) transmission routes influence gut microbiota composition throughout life.

RESULTS

We identify independent signals of maternal transmission (sharing of taxa between a mother and her offspring) and social transmission (sharing of taxa predicted by the social network), whose relative magnitudes shift as hosts age. In early life, gut microbiota composition is predicted by both maternal and social relationships, but by adulthood the impact of maternal transmission becomes undetectable, leaving only a signal of social transmission. By exploring which taxa drive the maternal transmission signal, we identify a candidate maternally-transmitted bacterial family in wood mice, the Muribaculaceae.

CONCLUSION

Overall, our findings point to an ontogenetically shifting transmission landscape in wild mice, with a mother's influence on microbiota composition waning as offspring age, while the relative impact of social contacts grows.

Positive associations matter: Microbial relationships drive tick microbiome composition

Untangling how factors such as environment, host, associations among bacterial species and dispersal predict microbial composition is a fundamental challenge. In this study, we use complementary machine-learning approaches to quantify the relative role of these factors in shaping microbiome variation of the blacklegged tick Ixodes scapularis. I. scapularis is the most important vector for Borrelia burgdorferi (the causative agent for Lyme disease) in the U.S. as well as a range of other important zoonotic pathogens. Yet the relative role of the interactions between pathogens and symbionts compared to other ecological forces is unknown. We found that positive associations between microbes where the occurrence of one microbe increases the probability of observing another, including between both pathogens and symbionts, was by far the most important factor shaping the tick microbiome. Microclimate and host factors played an important role for a subset of the tick microbiome including Borrelia (Borreliella) and Ralstonia, but for the majority of microbes, environmental and host variables were poor predictors at a regional scale. This study provides new hypotheses on how pathogens and symbionts might interact within tick species, as well as valuable predictions for how some taxa may respond to changing climate.

Out of the stable: Social disruption and concurrent shifts in the feral mare (Equus caballus) fecal microbiota

The disruption of animals' symbiotic bacterial communities (their microbiota) has been associated with myriad factors including changes to the diet, hormone levels, and various stressors. The maintenance of healthy bacterial communities may be especially challenging for social species as their microbiotas are also affected by group membership, social relationships, microbial transfer between individuals, and social stressors such as increased competition and rank maintenance. We investigated the effects of increased social instability, as determined by the number of group changes made by females, on the microbiota in free-living, feral horses (Equus caballus) on Shackleford Banks, a barrier island off the North Carolina coast. Females leaving their groups to join new ones had fecal microbial communities that were similarly diverse but compositionally different than those of females that did not change groups. Changing groups was also associated with the increased abundance of a several bacterial genera and families. These changes may be significant as horses are heavily dependent upon their microbial communities for nutrient absorption. Though we cannot identify the particular mechanism(s) driving these changes, to the best of our knowledge, ours is the first study to demonstrate an association between acute social perturbations and the microbiota in a free-ranging mammal.

Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights

Prevailing 16S rRNA gene-amplicon methods for characterizing the bacterial microbiome of wildlife are economical, but result in coarse taxonomic classifications, are subject to primer and 16S copy number biases, and do not allow for direct estimation of microbiome functional potential. While deep shotgun metagenomic sequencing can overcome many of these limitations, it is prohibitively expensive for large sample sets. Here we evaluated the ability of shallow shotgun metagenomic sequencing to characterize taxonomic and functional patterns in the faecal microbiome of a model population of feral horses (Sable Island, Canada). Since 2007, this unmanaged population has been the subject of an individual-based, long-term ecological study. Using deep shotgun metagenomic sequencing, we determined the sequencing depth required to accurately characterize the horse microbiome. In comparing conventional vs. high-throughput shotgun metagenomic library preparation techniques, we validate the use of more cost-effective laboratory methods. Finally, we characterize similarities between 16S amplicon and shallow shotgun characterization of the microbiome, and demonstrate that the latter recapitulates biological patterns first described in a published amplicon data set. Unlike for amplicon data, we further demonstrate how shallow shotgun metagenomic data provide useful insights regarding microbiome functional potential which support previously hypothesized diet effects in this study system.

Phylogenetically under-dispersed gut microbiomes are not correlated with host genomic heterozygosity in a genetically diverse reptile community

While key elements of fitness in vertebrate animals are impacted by their microbiomes, the host genetic characteristics that factor into microbiome composition are not fully understood. Here, we correlate host genomic heterozygosity and gut microbiome phylogenetic diversity across a community of reptiles in southwestern New Mexico to test hypotheses about the behaviour of host genes that drive microbiome assembly. We find that microbiome communities are phylogenetically under-dispersed relative to random expectations, and that host heterozygosity is not correlated with microbiome diversity. Our analyses reinforce results from functional genomic work that identify conserved host immune and nonimmune genes as key players in microbiome assembly, rather than gene families that rely on heterozygosity for their function.

Synchronous Seasonality in the Gut Microbiota of Wild Mouse Populations

The gut microbiome performs many important functions in mammalian hosts, with community composition shaping its functional role. However, the factors that drive individual microbiota variation in wild animals and to what extent these are predictable or idiosyncratic across populations remains poorly understood. Here, we use a multi-population dataset from a common rodent species (the wood mouse, Apodemus sylvaticus), to test whether a consistent “core” gut microbiota is identifiable in this species, and to what extent the predictors of microbiota variation are consistent across populations. Between 2014 and 2018 we used capture-mark-recapture and 16S rRNA profiling to intensively monitor two wild wood mouse populations and their gut microbiota, as well as characterising the microbiota from a laboratory-housed colony of the same species. Although the microbiota was broadly similar at high taxonomic levels, the two wild populations did not share a single bacterial amplicon sequence variant (ASV), despite being only 50km apart. Meanwhile, the laboratory-housed colony shared many ASVs with one of the wild populations from which it is thought to have been founded decades ago. Despite not sharing any ASVs, the two wild populations shared a phylogenetically more similar microbiota than either did with the colony, and the factors predicting compositional variation in each wild population were remarkably similar. We identified a strong and consistent pattern of seasonal microbiota restructuring that occurred at both sites, in all years, and within individual mice. While the microbiota was highly individualised, some seasonal convergence occurred in late winter/early spring. These findings reveal highly repeatable seasonal gut microbiota dynamics in multiple populations of this species, despite different taxa being involved. This provides a platform for future work to understand the drivers and functional implications of such predictable seasonal microbiome restructuring, including whether it might provide the host with adaptive seasonal phenotypic plasticity.

Microbiota composition and diversity of multiple body sites vary according to reproductive performance in a seabird

The microbiota is suggested to be a fundamental contributor to host reproduction and survival, but associations between microbiota and fitness are rare, especially for wild animals. Here, we tested the association between microbiota and two proxies of breeding performance in multiple body sites of the black-legged kittiwake, a seabird species. First we found that, in females, nonbreeders (i.e., birds that did not lay eggs) hosted different microbiota composition to that of breeders in neck and flank feathers, in the choanae, in the outer-bill and in the cloacae, but not in preen feathers and tracheae. These differences in microbiota might reflect variations in age or individual quality between breeders and nonbreeders. Second, we found that better female breeders (i.e., with higher body condition, earlier laying date, heavier eggs, larger clutch, and higher hatching success) had lower abundance of several Corynebacteriaceae in cloaca than poorer female breeders, suggesting that these bacteria might be pathogenic. Third, in females, better breeders had different microbiota composition and lower microbiota diversity in feathers, especially in preen feathers. They had also reduced dispersion in microbiota composition across body sites. These results might suggest that good breeding females are able to control their feather microbiota-potentially through preen secretions-more tightly than poor breeding females. We did not find strong evidence for an association between reproductive outcome and microbiota in males. Our results are consistent with the hypothesis that natural variation in the microbiota is associated with differences in host fitness in wild animals, but the causal relationships remain to be investigated.

Seasonal variations in the composition and functional profiles of gut microbiota reflect dietary changes in plateau pikas

Seasonal variations in gut microbiota of small mammals and how it is influenced by environmental variables is relatively poorly understood. We sampled 162 wild plateau pikas (Ochotona curzoniae) in four seasons over two and a half years and recorded the air temperature, precipitation, and nutrient content in edible vegetation at the sampling site. After conducting 16S rRNA and shotgun metagenomic sequencing, we found that the highest alpha diversity, the relative abundance of Firmicutes, and the simplest co-occurrence network occurred in winter, whereas that the highest relative abundance of Proteobacteria and the most complex network structure was observed in spring. The highest relative abundance of Verrucomicrobiota and Spirochaetota were seen in summer and autumn, respectively. Air temperature, precipitation, and the contents of crude protein, crude fiber, and polysaccharide in vegetation had significant effects on the seasonal changes in gut microbiota. Diet contributed more to microbial variation than climatic factors. Metagenomic analysis revealed that the amino acid metabolism pathway and axillary activity enzymes were most abundant in summer, while abundance of carbohydrate-binding modules and carbohydrate esterases were highest in spring. These microbial variations were related to the changes in dietary nutrition, indicating that gut microbiota of plateau pika contribute to the efficient use of food resources. This study provides new evidence of how external environmental factors affect the intestinal environment of small mammals. This article is protected by copyright. All rights reserved.

Host, microbiome, and complex space: applying population and landscape genetic approaches to gut microbiome research in wild populations

In recent years, emerging sequencing technologies and computational tools have driven a tidal wave of research on host-associated microbiomes, particularly the gut microbiome. These studies demonstrate numerous connections between the gut microbiome and vital host functions, primarily in humans, model organisms, and domestic animals. As the adaptive importance of the gut microbiome becomes clearer, interest in studying the gut microbiomes of wild populations has increased, in part due to the potential for discovering conservation applications. The study of wildlife gut microbiomes holds many new challenges and opportunities due to the complex genetic, spatial, and environmental structure of wild host populations, and the potential for these factors to interact with the microbiome. The emerging picture of adaptive coevolution in host-microbiome relationships highlights the importance of understanding microbiome variation in the context of host population genetics and landscape heterogeneity across a wide range of host populations. We propose a conceptual framework for understanding wildlife gut microbiomes in relation to landscape variables and host population genetics, including the potential of approaches derived from landscape genetics. We use this framework to review current research, synthesize important trends, highlight implications for conservation, and recommend future directions for research. Specifically, we focus on how spatial structure and environmental variation interact with host population genetics and microbiome variation in natural populations, and what we can learn from how these patterns of covariation differ depending on host ecological and evolutionary traits.

Feed and Host Genetics Drive Microbiome Diversity with Resultant Consequences for Production Traits in Mass-Reared Black Soldier Fly (Hermetia illucens) Larvae

Mass rearing the black soldier fly, Hermetia illucens, for waste bioremediation and valorisation is gaining traction on a global scale. While the health and productivity of this species are underpinned by associations with microbial taxa, little is known about the factors that govern gut microbiome assembly, function, and contributions towards host phenotypic development in actively feeding larvae. In the present study, a 16S rDNA gene sequencing approach applied to a study system incorporating both feed substrate and genetic variation is used to address this knowledge gap. It is determined that the alpha diversity of larval gut bacterial communities is driven primarily by features of the larval feed substrate, including the diversity of exogenous bacterial populations. Microbiome beta diversity, however, demonstrated patterns of differentiation consistent with an influence of diet, larval genetic background, and a potential interaction between these factors. Moreover, evidence for an association between microbiome structure and the rate of larval fat accumulation was uncovered. Taxonomic enrichment analysis and clustering of putative functional gut profiles further suggested that feed-dependent turnover in microbiome communities is most likely to impact larval characteristics. Taken together, these findings indicate that host-microbiome interactions in this species are complex yet relevant to larval trait emergence.

Shades of grey: host phenotype dependent effect of urbanization on the bacterial microbiome of a wild mammal

BACKGROUND

Host-associated microbiota are integral to the ecology of their host and may help wildlife species cope with rapid environmental change. Urbanization is a globally replicated form of severe environmental change which we can leverage to better understand wildlife microbiomes. Does the colonization of separate cities result in parallel changes in the intestinal microbiome of wildlife, and if so, does within-city habitat heterogeneity matter? Using 16S rRNA gene amplicon sequencing, we quantified the effect of urbanization (across three cities) on the microbiome of eastern grey squirrels (Sciurus carolinensis). Grey squirrels are ubiquitous in rural and urban environments throughout their native range, across which they display an apparent coat colour polymorphism (agouti, black, intermediate).

RESULTS

Grey squirrel microbiomes differed between rural and city environments; however, comparable variation was explained by habitat heterogeneity within cities. Our analyses suggest that operational taxonomic unit (OTU) community structure was more strongly influenced by local environmental conditions (rural and city forests versus human built habitats) than urbanization of the broader landscape (city versus rural). The bacterial genera characterizing the microbiomes of built-environment squirrels are thought to specialize on host-derived products and have been linked in previous research to low fibre diets. However, despite an effect of urbanization at fine spatial scales, phylogenetic patterns in the microbiome were coat colour phenotype dependent. City and built-environment agouti squirrels displayed greater phylogenetic beta-dispersion than those in rural or forest environments, and null modelling results indicated that the phylogenetic structure of urban agouti squirrels did not differ greatly from stochastic expectations.

CONCLUSIONS

Squirrel microbiomes differed between city and rural environments, but differences of comparable magnitude were observed between land classes at a within-city scale. We did not observe strong evidence that inter-environmental differences were the result of disparate selective pressures. Rather, our results suggest that microbiota dispersal and ecological drift are integral to shaping the inter-environmental differences we observed. However, these processes were partly mediated by squirrel coat colour phenotype. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide a useful free-living system with which to study how host genetics mediate environment x microbiome interactions.

Effects of Pasture Grass, Silage, and Hay Diet on Equine Fecal Microbiota

Simple Summary

The intestinal microbial community in horses is very complex and interacts closely with diets. Apart from traditional forage diets, such as hay and pasture grass, silage is used to feed horses in China and other areas of the world for economic reasons or convenience of storage. Additionally, silage is also used for its convenience of harvesting and its nutrient components, including lactic acid and volatile fatty acids. In this study, we detected the characteristic composition of a fecal microbial community in horses that were fed silage with the use of a relatively new sequencing technique; we compared this result with that from horses that were fed hay and pasture grass. This study revealed some characteristic findings on the fecal microbial composition in horses that were given each of type of diet and showed significant differences between the groups. Our results provided novel data about the fecal microbial composition in horses on the silage diet. We hope that these could help balance the intestinal microbiota in horses that are mainly fed silage in combination with other types of forages in order to maintain intestinal health.

Abstract

Diet is an important factor affecting intestinal microbiota in horses. Fecal microbiota is commonly used as a substitute for studying hindgut microbiota when investigating the relationship between intestinal microbial changes and host health. So far, no study has compared the difference between the fecal microbiota found in horses that are fed pasture grass, silage, and hay. The present study aims to characterize the fecal microbiota in horses that were exclusively on one of the three forage diets, and to analyze the potential impact of these forages, especially silage, on horse intestinal health. There were 36 horses randomly assigned to each of the three groups; each group was fed only one type of forage for 8 weeks. High throughput sequencing was applied to analyze the bacterial taxa in fecal samples collected from the horses at the end of the feeding trial. The Lachnospiraceae family was statistically more abundant in horses fed with hay, while it was the least abundant in horses fed with silage. The Streptococcaceae spp., considered a core microbial component in equine intestinal microbiota, were present in significantly lower quantities in feces from horses that were fed pasture grass as compared to those from horses fed hay or silage. The novel data may help promote the balancing of horse intestinal microbiota and the maintenance of intestinal health in horses.