Animal Microbiome

Advances in metagenomic sequencing have transformed our understanding of host-associated microbiota, revealing critical roles in immune regulation, nutrient metabolism, and gastrointestinal (GI) homeostasis. However, the gut microbiome of large non-model species, particularly elephants, remains poorly characterized. Captivity introduces dietary, environmental, and management-related perturbations that may disrupt microbial balance and contribute to GI dysfunction. Here, we performed a longitudinal analysis of the fecal microbiome in five captive Asian elephants (Elephas maximus) at the Oregon Zoo exhibiting chronic fecal abnormalities, including mucus and inconsistent stool formation. Over 14 weeks, weekly fecal samples were collected and compared with samples from clinically normal elephants housed at three other zoological institutions. Using 16S rRNA gene sequencing, we identified marked differences in microbial community composition between affected and control elephants. Dysbiosis in Oregon Zoo elephants was characterized by enrichment of Akkermansia muciniphila and multiple members of the order Clostridiales, including taxa previously associated with gastrointestinal disorders. Administration of a commercially available probiotic formulation was associated with transient improvement in fecal characteristics and pronounced shifts in microbial composition, including a significant post-treatment reduction in overall microbial diversity and decreased abundance of several taxa linked to GI abnormalities. Notably, probiotic strains themselves were not detected, suggesting indirect or short-lived functional effects rather than durable colonization. Together, these findings provide one of the first longitudinal characterizations of gut microbiome dysbiosis in captive Asian elephants and identify candidate microbial contributors to chronic GI dysfunction in captivity, with implications for husbandry, dietary management, and microbiome-informed interventions in megafauna. Additionally, our study underscores the potential, although limited and likely indirect, benefit of probiotics when treating GI disorders in monograstric megavertebrates.

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.

Stress during the beef pre-harvest period can induce an inflammatory response and acidotic conditions in the gastrointestinal tract (GIT), which affects the gastrointestinal tract microbiome. The objective of this study was to characterize the status of the GIT microbiome at harvest in beef cattle entering a small USDA processing facility. Nine beef cattle were shipped from a producer in Columbia County, WI to the USDA processing facility at University of Wisconsin-Madison and were harvested across four dates. Digesta samples were collected from eight GIT locations: rumen solids, rumen liquids, abomasum, duodenum, jejunum, ileum, cecum, and large intestines. After DNA extraction with the DNeasy Blood & Tissue Kit, the V4 region of the 16S rRNA gene was amplified and sequenced on the Illumina MiSeq platform. Sequences were analyzed for alpha and beta diversity metrics (ANOVA and ADONOS), core microbiome, ANCOM, and co-occurrence network analyses. Harvest date and GIT location had a significant impact on microbial diversity and community composition (P<0.05), and there was an interaction between GIT location and harvest date (P<0.05). Taxonomic composition shifted throughout the GIT, though Prevotella and Treponema were core members in several different GIT locations. The co-occurrence analysis revealed microorganisms potentially associated with clinical infections, such as Moryella in the rumen and Acinetobacter in the hindgut, were considered keystone species. These results suggest that the pre-harvest period may negatively impact the beef cattle GIT microbiome. Modulating the GIT microbiome during the pre-harvest period may offer an opportunity to improve food safety.

Diet influences the composition, diversity, and functional capacity of the cattle gut microbiome. However, the extent to which feeding practices affect the microbial community and resistome under real-world conditions remains poorly understood, particularly in low- and middle-income settings. Here, we applied metagenomics to fecal samples from Bangladeshi cattle fed either a natural or a mixed diet to examine differences in microbial composition, functional potential, and resistome associated with feed type. Natural-fed cattle harbored higher microbial diversity and distinct bacterial phyla, including Bacteroidota, Campylobacteriota, and Mycoplasmatota. Acinetobacter, Aliarcobacter, Comamonas, Dysosmobacter, and Sharpea were enriched in natural-fed cattle, whereas Anaerotignum, Aristaeella, Oscillibacter, and Clostridium were more abundant in the mixed-fed group. Notably, the emerging zoonotic genus Aliarcobacter was detected in the natural-fed cohort. Alpha diversity analysis showed higher richness and evenness in natural-fed cattle, and a clear separation between dietary groups in beta diversity analysis (PERMANOVA, p = 0.01). Differential analysis identified Oscillibacter ruminantium as a biomarker of natural feeding, while Succinivibrio faecicola and Anaerovibrio slackiae for mixed feeding. Resistome profiles demonstrated clear differences. Mixed-fed cattle showed a consistent enrichment of tetracycline resistance genes, whereas the natural-fed group displayed a more variable resistome. Functional analysis suggested diet-associated differences in metabolic potential, with glutathione metabolism enriched in natural-fed cattle (p<0.05) and bile secretion and fatty acid metabolism moderately enriched in the mixed-fed group. These findings indicate that feeding practices are associated with differences in rumen microbial communities and resistome profiles in Bangladeshi cattle, providing baseline insights into microbiome-resistome relationships under field conditions.

Coccidiosis, caused by Eimeria parasites, poses significant economic and welfare challenges in poultry farming. Beyond its direct impact on health, Eimeria infection disrupts enteric microbial populations leading to dysbiosis and increases vulnerability to secondary diseases such as necrotic enteritis, caused by Clostridium perfringens. The impact of Eimeria infection or anticoccidial vaccination on host gastrointestinal phenotypes and enteric microbiota remains understudied. In this study, the metabolomic profiles and microbiota composition of chicken caecal tissue and contents were evaluated concurrently during a controlled experimental vaccination and challenge trial. Cobb500 broilers were vaccinated with a Saccharomyces cerevisiae-vectored anticoccidial vaccine and challenged with 15,000 Eimeria tenella oocysts. Assessment of caecal pathology and quantification of parasite load revealed correlations with alterations to caecal microbiota and host metabolome linked to infection and vaccination status. Infection heightened microbiota richness with increases in potentially pathogenic species, while vaccination elevated beneficial Bifidobacterium. Using a multi-omics factor analysis (MOFA) machine learning model, data on caecal microbiota and host metabolome were integrated and distinct profiles for healthy, infected, and recovering chickens were identified. Healthy and recovering chickens exhibited higher vitamin B metabolism linked to short-chain fatty acid-producing bacteria, whereas essential amino acid and cell membrane lipid metabolisms were prominent in infected and vaccinated chickens. Notably, vaccinated chickens showed distinct metabolites related to the enrichment of sphingolipids, important components of nerve cells and cell membranes. Our integrated multi-omics model revealed latent biomarkers indicative of vaccination and infection status, offering potential tools for diagnosing infection, monitoring vaccination efficacy, and guiding the development of novel treatments or controls.

BackgroundThe freshwater snail Biomphalaria glabrata is an important natural vector for the human parasitic trematode Schistosoma mansoni, which causes schistosomiasis. In the laboratory, B. glabrata are routinely maintained on simple lettuce diets. We aimed to explore and compare the impact of alternative diets on snail performance, global gene expression, and microbiome. MethodsSnails were raised in groups on fresh lettuce (FL), fish food (FF) and artificial snail gel (SG) diet for eight weeks, while measuring dietary impacts on growth, survival, and fecundity. RNA sequencing (RNA-Seq) was performed to correlate dietary phenotypes with changes in the snail transcriptome and associated microbial metatranscriptome. ResultsRelative to FL, FF and SG diets markedly enhanced growth, survival, and fecundity, with FF generating the highest fecundity rate. RNA-Seq identified 21,887 nutritionally modulated genes in the snail transcriptome. Fish food (FF) and SG diets drove upregulation of genes associated with antimicrobial immunity, growth, and reproduction, while elevated expression of genes linked to xenobiotic metabolism and oxidative stress was observed in FL-fed snails. Metatranscriptomic analysis identified 104 microbial classes, with a total of twenty-three classes significantly enriched in FF and SG snails, including short-chain fatty acid-producing and nutrient-cycling bacteria. Significant correlation (r = 0.63, p = 0.001) linked differentially expressed genes with enriched microbial taxa, highlighting the impact of diet on key snail health and performance metrics. ConclusionsThis work is the first nutritranscriptomic analysis of laboratory-bred B. glabrata. We describe key insights into the diet-phenotype-transcriptome-microbiome axis, which will inform dietary precision and optimisation for laboratory culture of B. glabrata. These data also highlight fundamental aspects of snail biology which could be exploited for molecular snail control approaches.

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

Modern broiler breeds allow for high feed efficiency and rapid growth, but come at a cost of increased susceptibility to pathogens and disease. Broiler growth rate, feed efficiency, and health are furthermore affected by the composition of the gut microbiota, which in turn is influenced by diet composition. In this study we therefore assessed how diet composition alters the broiler jejunal gut microbiota. A total of 96 broiler chickens were divided into four diet groups: control, coated butyrate supplementation, medium chain fatty acid supplementation, or a high-fibre low-protein content. Diet groups were sub-divided into age groups (4, 12 and 33 days of age) resulting in groups of 8 broilers per diet per age. The jejunum content jejunum was used for metagenomic shotgun sequencing to determine the microbiota composition on species level. Among all diet groups, a total of 104 differential abundant bacterial species were detected. Most notably were the changes in the jejunal microbiota induced by butyrate supplementation when compared to the control diet, resulting in the reduced relative abundance of mainly Enterococcus faecium and the opportunistic pathogen Enterococcus hirae in broilers 4 days post-hatch. At this early stage of development, the immune system is still immature thereby highlighting the importance to study the relation of diet and the jejunal microbiota. Future studies should furthermore elucidate how diet can be used to promote a beneficial microbiota in the early stages of broiler development.

Anthropogenic pressures are increasingly reshaping wildlife habitats worldwide. These transformations reduce natural areas, but also create new ecological niches, food resources, and environmental stressors, with potential consequences for wildlife behavior, physiology, and morphology. These changes may affect the gut microbiome, a critical component of host health, yet such effects are often inconsistent across species, particularly in wild non-human primates, and remain poorly understood. Here, we investigated how the gut microbiome of chacma baboons (Papio ursinus ursinus), an ecologically flexible generalist, responds to an anthropization gradient. We analyzed 512 fecal samples collected from 33 wild troops across a broad range of anthropogenic environments in the Western Cape, South Africa. Using a multi-metric approach including the Human Footprint Index, land-use variables and dietary proxies derived from stable isotopes, we assessed gut microbial diversity and composition based on 16S rRNA gene (V4) sequencing. Human-altered environments characterized by high Human Footprint and built-up areas were associated with reduced microbial diversity, and compositional and functional shifts, including decline in fiber-degrading taxa and increase in bacteria associated with simple carbohydrate and dairy metabolism. In contrast, highly cultivated areas showed no diversity difference and distinct microbial assemblages, while dietary variation had weaker effects, primarily altering rare taxa. Our results demonstrate that different components of anthropogenic pressure exert contrasting effects on the baboon gut microbiome, reflecting multiple ecological pathways extending beyond diet alone. Microbiome shifts may have implications for host health, potentially increasing susceptibility to pathogens or inflammatory diseases, with consequences for wildlife populations.

The effective control of rodent populations on farms is a critical component of food- safety, as rodents are reservoirs and vectors for many foodborne pathogens in addition to several zoonotic pathogens. The functional role of rodents in the amplification and transmission of pathogens is likely underappreciated. Clear links have been identified between rodents and outbreaks of pathogens throughout Europe and Asia, however, comparatively little research has been devoted to studying this rodent-agricultural interface in the USA, particularly across the Midwest. Here, we address this existing knowledge gap by characterizing the metagenomic communities of rodent pests collected from Minnesota and Wisconsin food animal farms. We leveraged the Oxford Nanopore MinION sequencer to provide a rapid real-time survey of the putative zoonotic food- borne and other human pathogens. Rodents (mice and rats) were live trapped from three dairy and mixed animal farms. Tissues and fecal samples were collected from all rodents. DNA extraction was performed on 90 rodent colons along with 2 shrew colons included as outgroups in the study. Full-length 16S amplicon sequencing was performed with the MinION. Our data suggests the presence of putative foodborne pathogens including Salmonella spp., Campylobacter spp., Staphylococcus aureus, and Clostridium spp., along with many important mastitis pathogens. A critically important observation is that we discovered these pathogens within all five species of rodents (Microtus pennsylvanicus, Mus musculus, Peromyscus leucopus, Peromyscus maniculatus, and Rattus norvegicus) and shrew (Blarina brevicauda) in varying abundances. Interestingly, we observed a higher abundance of enteric pathogens (e.g. Salmonella) in shrew feces compared to the rodents analyzed in our study, however more data is required to establish that connection. Knowledge gained from our research efforts will directly inform and improve upon farm-level biosecurity efforts and public health interventions to reduce future outbreaks of foodborne and zoonotic disease.

The gut microbiome is increasingly recognized as a pivotal modulator of animal behaviour, yet its influence on wild fauna remains largely unexplored. We investigated the correlational relationship between gut microbiota, behavioural phenotypes, and management practices in 26 captive endangered Iberian lynxs (Lynx pardinus) maintained within the ex-situ Iberian breeding program facilities, in two geographically distant stations in SW Spain. Behavioural observations were intensively recorded over two years, and three personality profiles emerged, i.e., (i) anomalous (with the highest frequencies for stereotypies), and (ii) sedentary and (iii) active (with the highest frequencies for sedentarism and for locomotion and surveillance, respectively). Fecal samples were analyzed for biweekly periods by 16S rRNA gene amplicon sequencing to profile bacterial composition and predicted functional pathways, and significant associations were found for each of the behavioural phenotypes. Both breeding station and local environment influenced gut microbial communities and personality profiles, underscoring the influence of management practices and local habitat in shaping the microbiome-behaviour nexus. Specific bacterial taxa and metabolic pathways were consistently associated with each behavioural phenotype, suggesting that microbial fecal signatures could serve as non invasive biomarkers for individual personality monitoring. This work constitutes the first comprehensive, multi layered examination of the interplay among behaviour, gut microbiota, and environmental factors in a large, wild carnivore. This integrative approach may help conservation programmes to optimize management decisions and improve reintroduction success

Germ-free (GF) animal models are indispensable for dissecting host-microbiota interactions and their roles in health and disease. The small teleost fish medaka (Oryzias latipes) provides unique advantages for establishing GF models across developmental stages, yet the functions of its intestinal microbiota and metabolites remain poorly characterized. Here, we developed both early-life and chronic GF medaka models to systematically characterize host biology in the absence of microbiota and evaluate the contribution of gut-derived metabolites to growth and immune development. Using a refined sterile feeding and verification protocol, we successfully maintained GF medaka for up to 57 days post-fertilization (dpf). As anticipated, GF fish displayed developmental delays, impaired organogenesis, reduced immune competence, and metabolic dysregulation. Supplementation with sterile gut-derived metabolites partially alleviated these deficits, as evidenced by enhanced locomotor activity and immune responses. Mechanistically, recovery was associated with improved ribosome biogenesis, tricarboxylic acid cycle activity, and histidine and pyruvate metabolism, suggesting enhanced protein synthesis and immune maturation. However, metabolite supplementation also elevated oxidative stress and inflammatory responses and failed to fully restore long-term survival or organ development. Our findings support the use of GF medaka as a versatile platform for investigating microbiota-host interactions across life stages. By integrating metabolite interventions, this model provides critical insights into the functional roles of gut microbiota and offers a valuable tool for advancing microbiome research in health and disease.

Primates are central to both human evolutionary research and ecosystem functioning, serving as seed dispersers, predators, pollinators, and prey. Despite their value to human and ecosystem science, global primate populations continue to decline, with [~]65% of species currently threatened with extinction. Conservation biology increasingly recognises that survival depends not only on protecting habitats and populations, but also on safeguarding the microbial communities that underpin host health, nutrition, and resilience. The gut bacterial microbiome plays a critical role in digestion, immune function, and adaptation to environmental change, making it an important dimension of primate conservation. Here, we systematically and quantitatively assessed the taxonomic and geographic coverage of primate gut bacterial microbiome research to identify key knowledge gaps relevant to primate conservation. Between 2001 and 2025, 261 articles were published across 100 journals. While taxonomic coverage is high at the family level, it declines substantially at the finer taxonomic scales. Currently, [~]34.5% of species have been studied, leaving gut bacterial biodiversity undocumented for 344 species. Moreover, approximately one-third of studied species have exclusively been studied in captivity, limiting insights into natural microbiome variation and reducing the conservation relevance of these findings. Geographic biases further hinder conservation applications, with megadiverse countries such as Brazil, the Democratic Republic of Congo, and Indonesia underrepresented. In addition, study methodology and reporting standards remain inconsistent. To address these challenges, a framework for the standardised reporting of a minimum set of data for primate gut bacterial microbiome research is included in this review. Adoption of this framework will improve transparency, comparability, and data accessibility, thereby enhancing the utility of microbiome research for primate conservation. By integrating microbial ecology into conservation biology, we highlight the microbiome as a potential critical frontier for safeguarding primate health, evolutionary potential, and long-term survival.

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.

BackgroundAnthropogenic habitat modification and associated resources can exert selection pressures on wildlife and their microbiomes, altering their diversity, resulting in homogenization and making them resemble the human microbiome. Diet is an important predictor of the microbiomes of volant vertebrates, mainly for birds, but for bats, results remain inconclusive. In spite of Indias exceptional bat diversity, there is little understanding of how their microbiomes respond to anthropogenic habitats. Therefore, we investigated the trends of taxonomic and functional diversity and their relationships with host feeding-guild and phylogeny for six wide-ranging bat species across six anthropogenically modified sites in Southern India by generating 16S barcode sequences from their fecal samples. ResultsEubacteria dominated samples with diet-specific taxonomic composition. Frugivore microbiomes contained large proportions of Cyanobacteria, possibly sourced from consumed plant matter or polluted drinking-water sources, and Lactobacillales dominated insectivore microbiomes, while Gammaproteobacteria were abundant regardless of host feeding guild. We found human pathogens in our samples possibly transferred from polluted water to the guts of bats foraging in nearby areas. We observed diet-specific taxonomic, phylogenetic, and functional composition. However, functional composition incorporating abundances displayed a high degree of overlap across feeding-guilds, suggesting functional homogenisation of microbiomes across feeding guilds, possibly due to anthropogenicity. Sample-wise diversity indices were significantly different with respect to diet only when samples from the same roost were not pooled together. However, in all cases, microbiomes from the same diet types displayed significant taxonomic and phylogenetic similarity to each other. Lastly, we observed limited concordance of microbiome diversity with chiropteran phylogeny. ConclusionsBecause of these potential signatures of pollution on bat microbiomes such as pathogens, we recommend their monitoring, especially because Cyanobacteria play a known role in bat and human disease. Our study is one of the first to study microbiome composition and function from bat species common around human inhabitation in South India, and establishes baselines in this region.

Probiotics are widely used in food animal production to support gut health and immune function, but the indicators of probiotic efficacy and the conditions under which they translate to host benefit remain unclear. Microbiota composition is the most accessible data supporting probiotic effects, yet whether compositional change reliably predicts host outcomes is not well understood. We investigated this question in broiler chickens fed two nutritionally similar basal diets, with or without a commercial probiotic. Microbiota composition was profiled across 6 gastrointestinal regions using 16S rRNA sequencing. To assess systemic functional effects, an in vitro assay building on prior observations of elevated circulating immune cell ATP in probiotic-fed animals was developed. In this assay, serum from each treatment group was applied to a chicken T-lymphocyte cell line before ATP quantitation. Basal diet was the primary driver of microbial community structure, with probiotic-induced compositional shifts observed predominantly in one diet context but minimally in the other. Despite this difference, serum from probiotic-supplemented animals increased T-lymphocyte ATP production across both diets, supporting prior findings and revealing a systemic immunometabolic response independent of broad microbiota restructuring. Functional predictions revealed enrichment of pathways related to mevalonate and carbohydrate metabolism in probiotic-supplemented birds within the more responsive diet context, driven largely by Lactobacillaceae family taxa. These findings demonstrate that basal diet modulates the detectability and nature of probiotic effects on the microbiota, but not the physiological host response. This disconnect has implications for how probiotic efficacy is evaluated and for microbiome targeted interventions across species. ImportanceProbiotics are used widely in food animal production to support gut health and immune function, yet predicting which probiotic preparations will produce meaningful effects remains a challenge. Microbiota composition, profiled by 16S rRNA sequencing, is the most accessible measure of probiotic activity, but it captures only one aspect of the host-microbe dynamic. These data demonstrate that probiotic-induced compositional changes vary substantially between basal diets, while the host immunometabolic response is consistent across diets, demonstrating that compositional readouts alone cannot reliably predict host outcomes. The findings have practical implications for how probiotic efficacy is evaluated and inform the broader effort to design microbiome targeted interventions across both veterinary and human contexts.

Anaerobic gut fungi (AGF) are key members of the herbivorous gut microbiome. While AGF communities have been well-studied in foregut and hindgut fermenters, they remain poorly characterized in pseudoruminants such as camels. Here, we present a comprehensive culture-independent diversity survey of 142 fecal samples from all three extant camel species (Camelus dromedarius, Camelus bactrianus, and Camelus ferus). The AGF community in Camelus was highly diverse, with representatives of 42 AGF genera identified. However, this diversity was unevenly distributed, with three genera (Neocallimastix, Caecomyces, and Orpinomyces) accounting for 70.7% of sequences encountered, and only 12 genera exceeding 1% relative abundance in the entire dataset. While several of the genera identified as major components of the AGF community in camels are highly ubiquitous in all herbivores, others, such as Oontomyces, Aestipascuomyces, Liebetanzomyces, and the yet uncultured genera NY09, NY03, and JV-2025d are extremely rare in ruminants and hindgut fermenters, hinting at their preference and potential co-evolution with the Camelidae. Ordination approaches identified host species and biogeography as key determinants driving AGF community structure differences between various camel species. Comparative community structure analysis between AGF community in camels versus reference foregut and hindgut fermenters identified the relative enrichment of the genera Oontomyces and Aestipascuomyces in pseudoruminants datasets. Our results demonstrate a distinct AGF community composition in Camelidae, elucidate factors impacting AGF diversity and community structure variations in Camelus, and identify key distinct taxa differentially enriched in psuedoruminants compared to ruminants and hindgut fermenters. The ecological and evolutionary drivers of such patterns are discussed.

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.

Host-microbe interactions are shaped by both host and environmental factors. However, little is known about how host-microbe interactions vary across populations within a species. Here, we characterized the gut microbiota of 191 wild threespine stickleback fish (Gasterosteus aculeatus) from six populations from Alaskan lakes spanning a gradient of surface area. We tested how environmental context (lake size and ecotype) and host traits (sex, body mass, gravidity, Schistocephalus solidus (S. solidus) infection, and fibrosis) influence stickleback gut microbial composition using 16S rRNA gene sequencing. We found that the lake surface area strongly predicted fish gut microbial alpha diversity. Fish from intermediate-sized lakes harbored significantly more diverse microbiota than those from small and large lakes, independent of ecotype. Body mass was associated with gut microbial diversity. Model-predicted marginal effects from the mass and lake surface area interaction analysis showed that the association between fish mass and microbial alpha diversity was strongly negative in the smallest lakes, weakest in intermediate-sized lakes, and strongly positive in the largest lakes. In addition, sex and S. solidus infection were significantly associated with gut microbiota alpha and beta diversity, whereas fibrosis and gravidity showed minimal effects. Differential abundance analysis revealed lake size-dependent associations between body mass and individual taxa. Together, these results demonstrate that both habitat context and host variation interactively shape stickleback gut microbial communities in the wild. Integrating lake-level and individual-level analyses reveals how ecological setting modulates host-microbe associations, offering insights into the role of the gut microbiota in host adaptation and population divergence.

Snail-borne diseases affect more than a quarter of a billion people worldwide and pose a high burden in the livestock industry. A fundamental understanding of the drivers of the epidemiology of these diseases is crucial for the development of sustainable control measures. The microbiome is increasingly being recognized as an important player in the tripartite interaction between parasitic flatworms, snail intermediate hosts and the snail microbiome. In order to better understand these interactions, transplant experiments are needed, which rely on the development of a reliable and reproducible protocol to obtain microbiome-disturbed snails. Here we report on the first successful snail microbiome transplants, which indicate that Biomphalaria glabrata can accrue novel bacterial assemblies depending on the available environmental bacteria obtained from donor snails. Moreover, the phylogenetic relatedness to the donor significantly affected the survival probability of the recipients, corroborating the phylosymbiosis pattern in freshwater snails. The transplant technique described here, complemented by field-based studies, could facilitate future research endeavors to investigate the role of specific bacteria or bacterial communities in parasitic flatworm resistance of B. glabrata and might ultimately pave the way for microbiome-mediated control of snail-borne diseases.