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.

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.

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 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

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.

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.

The gut microbiota is crucial for immune development and overall health in chickens. In commercial production, birds routinely receive multiple vaccines during early life. While individual vaccines are known to affect microbial composition, the impact of complex, multi-vaccine programs, as used in the poultry industry, is not well understood. This longitudinal study examined the impact of multiple live and inactivated vaccines, given at commercially relevant times from an early age, on gut microbial diversity and composition in layer chickens. We characterised microbiota profiles using 16S rRNA gene sequencing at pre- and post-vaccination timepoints across different vaccine groups. Overall, microbial diversity remained stable across most vaccines, indicating strong resilience of the gut microbiota to repeated immunological interventions. Differential abundance analyses identified changes in selected bacterial taxa following vaccination, with responses varying among vaccine groups. Notably, these changes were not sustained, as the gut microbial community returned to a stable state after the vaccination schedule. These findings underscore the robustness of the chicken gut ecosystem and lay a foundation for future research into microbiome-vaccine interactions and their implications for poultry health, immunity, and production efficiency.

Environmental change exposes ecosystems, including host-associated microbiomes, to stressors that occur repeatedly and in sequence, yet it remains unclear whether prior stressor history conditions host-microbiome responses to later perturbation. We used adult zebrafish (Danio rerio) to test whether sequential exposure to antibiotics, heat stress, the intestinal nematode Pseudocapillaria tomentosa, or pairwise stressor combinations altered gut microbiome structure, intestinal host gene expression, and host health outcomes. Across eight exposure regimes, prior stressor history and parasite exposure were associated with gut microbiome composition, while increasing prior stressor history was associated with reduced gut microbial diversity and convergence in community composition. Host intestinal transcriptional responses to parasite exposure were historically contingent, with parasite-associated differential gene expression varying non-linearly across prior stressor histories. Cumulative mortality increased with prior stressor history, whereas infection prevalence among surviving hosts decreased. Integrating microbial abundance, host gene expression, mortality, and neutral-community modeling identified Cetobacterium, Culicoidibacter, Flavobacterium, and Shewanella as candidate host-linked taxa associated with host response and survival. Collectively, these findings indicate that prior environmental stressor history shapes vertebrate host-microbiome responses to future perturbation and highlight specific gut microbial members as potential biomarkers or functional targets for follow-up studies.

Chlamydiota are obligate intracellular bacteria detected in snake cloacal microbiota, yet their biological significance remains poorly understood. Members range from recognised pathogens, such as Chlamydia serpentis, to potential environmental symbionts, raising questions about whether they represent transient contaminants, persistent colonisers, or subclinical infectious agents. Despite the cloaca serving as a primary site of chlamydial shedding in snakes, its interaction with the broader cloacal microbiota remains unexplored. Following pan-Chlamydiota PCR screening of 137 captive snakes across five collections, 52 samples (caenophidian snakes) (27 Chlamydiota-positive, 25 Chlamydiota-negative) were retained after V3-V4 16S rRNA sequencing and quality filtering. Presence of Chlamydiota was not associated with significant differences in alpha diversity or overall community composition, though it was related to greater within-community compositional heterogeneity. Differential abundance and multivariate analyses identified several enriched and depleted genera, with Lachnospiraceae and Copromonas consistently negatively associated with Chlamydiota across all three methods. Co-occurrence network analysis recovered more associations and a higher proportion of positive edges in the presence of Chlamydiota, with an expansion of anaerobic taxa. Inferred functional composition did not differ globally between groups; however, elastic net stability selection identified subtle pathway-specific differences, including enrichment of proteolytic and mycobacterial pathways in infected snakes. Our findings suggest subtle infection-associated community shifts that do not fully conform to established mammalian paradigms in which Chlamydia species behave either as gastrointestinal commensals or as cervicovaginal pathogens, highlighting the need for multi-omics approaches in larger cohorts of caenophidian and henophidian wild and captive snakes to better characterise the mechanistic basis and generalisability of these associations.

The respiratory microbiome plays important roles in poultry health, immune regulation, and pathogen resistance, yet its development throughout the broiler production cycle remains poorly understood. This study investigated temporal changes in the tracheal microbiome of broiler chickens across production phases. Tracheal samples were collected during the starter (day 12), grower (day 21), early finisher (day 26), and late finisher (day 35) phases and analyzed using 16S ribosomal RNA gene sequencing. Tracheal microbial richness, diversity, community structure, and taxonomic composition changed significantly across broiler production stages, including starter, grower, early finisher, and late finisher feeding phases. Alpha diversity increased progressively throughout production, with significant increases in richness, diversity, and phylogenetic diversity during later stages. Beta diversity analysis revealed distinct microbial communities associated with each production phase, with starter-phase samples clearly separated from later phases. Taxonomic profiling showed dominance of Proteobacteria during the starter and grower phases, with enrichment of Methylobacterium-Methylorubrum and Pseudomonas during the starter phase and of Escherichia-Shigella during the grower phase. In contrast, the finisher phases exhibited reduced Proteobacteria abundance and increased Firmicutes and Actinobacteriota, including Lactobacillus, Ligilactobacillus, Faecalibacterium, Streptococcus, Staphylococcus, Romboutsia, and Corynebacterium. Overall, the tracheal microbiome underwent progressive maturation, shifting from a Proteobacteria-dominated community to a more diverse, complex, Firmicutes-rich ecosystem. These findings provide new insights into the development of the respiratory microbiome in broiler chickens and may support strategies to improve poultry respiratory health. Because dietary transitions occurred concurrently with age progression, the observed microbiome shifts should be interpreted as production-stage-associated changes rather than diet-specific effects.

Host-associated microbiomes play vital roles in organismal health, ecological interactions, and evolution, yet little is known about how microbial communities shift during the transition from aquatic to increasingly terrestrial habitats. Here, we characterize the skin microbiomes of three combtooth blenny species (Blenniella paula, Praealticus labrovittatus, and Alticus arnoldorum) that occupy distinct positions along the intertidal gradient in Guam--from fully subtidal (and exclusively aquatic) to intertidal (amphibious) and supratidal environments (exclusively terrestrial). Using 16S rRNA amplicon sequencing, we compared skin-associated bacterial communities with those in surrounding seawater and substrate biofilms to assess habitat influences on microbiome structure. Skin microbiomes were distinct from environmental microbial communities, indicating strong ecological filtering by the host. The divergence between skin and substrate microbiomes in the three species parallels their distribution along progressively higher zones of the intertidal gradient. The most divergent skin microbiome was that of the supratidal fish A. arnoldorum, characterized by higher Gammaproteobacteria abundance and enrichment of epiphytic and mucus-associated taxa. Across all species, we identified 32 microbial orders significantly enriched on the skin relative to environmental samples, including taxa commonly associated with fish mucosa (e.g., Vibrio, Alteromonas, Cetobacterium) and others rarely reported in aquatic marine fish (e.g., Rubritalea, Granulosicoccus). Several rare taxa with potential pathogenicity were also detected at low abundances. Together, these findings suggest that habitat-specific selective pressures strongly shape fish skin microbiomes along subtidal (aquatic) to supratidal (terrestrial) habitats and suggest that microbial symbionts may contribute to the ecological and physiological adaptations enabling amphibious lifestyles. This study provides the first comparative assessment of skin microbiome divergence across amphibious fish species along an intertidal gradient and offers a framework for predicting microbiome responses to environmental change.

The fish skin microbiome serves as a protective barrier, influencing host health and facilitating interactions between the host and its environment. While several studies have characterised the composition and roles of the fish skin microbiome, there remains a paucity of data on how environmental variation influences these microbes in natural populations. Here, we used 16S rRNA gene sequencing to characterise the skin microbiome of wild three-spined stickleback populations and examine how environmental factors influence microbial diversity and community composition across 17 freshwater lochs on the island of North Uist, Scotland. Analysis of 239 samples revealed a set of dominant bacterial genera commonly associated with other fish species, including Janthinobacterium, Pseudomonas, Acinetobacter, and Psychrobacter, that constituted a core skin microbiota across lochs. Microbiome composition was primarily shaped by environmental variables, particularly habitat, water pH, conductivity, and metal concentrations, with pH emerging as a key driver of community structure. Host sex also influenced microbiome variation, with several taxa differing in relative abundance between males and females. Alpha-diversity was higher among stickleback fish from lochs with a neutral pH compared with those from alkaline and acidic environments. Differential abundance analyses identified 27 and 24 amplicon sequence variants (ASVs), respectfully, associated with variations in pH and host sex, including members of Psychrobacter, Sphingobacterium, Carnobacterium, Chryseobacterium, and Arthrobacter, highlighting the combined influence of environmental and host factors on microbiome composition in wild fish populations in freshwater environments.

A tightly regulated inflammatory response occurs during and following parturition; however, excessive or prolonged inflammation negatively affects herd health and productivity. The gut microbiota plays an important role in host immunity and metabolism and undergoes substantial changes during the transition period. However, the relationship between systemic inflammation, measured by serum acute-phase proteins, and gut microbial dynamics during early lactation remains poorly understood. We investigated fecal microbiota dynamics in relation to systemic inflammation in early postpartum dairy cows. Fecal and blood samples were collected from 71 Holstein cows on days 1 and 3 in milk (DIM). The V3-V4 region of the 16S rRNA gene was sequenced and microbial diversity, differential abundance, and microbial interaction networks were evaluated. Inflammatory status, defined by fibrinogen, haptoglobin, and their combined classification, was associated with significant alterations in fecal microbial composition during the immediate postpartum period, independent of body condition score, parity, DIM, and DNA extraction parameters. Differential abundance analyses revealed extensive taxonomic restructuring, while network analyses identified increased modularity, altered keystone taxa distribution, and greater compartmentalization of microbial interactions in animals with elevated inflammatory markers. Several taxa were consistently associated with inflammatory status across analytical approaches. Notably, Ruminococcaceae UCG-002 and Dielma were associated with inflammatory states, whereas Xylanibacter, Marvinbryantia, Akkermansia, and Oscillibacter were associated with non-inflammatory status. This study identifies an association between systemic inflammation and fecal microbiota composition in early transition dairy cows, providing a foundation for future microbiome-based biomarkers of inflammatory status. IMPORTANCESubclinical systemic inflammation during early postpartum can negatively affect dairy cow health and productivity, yet current monitoring relies on repeated blood sampling and transient inflammatory biomarkers. For the first time association of systemic inflammation, assessed using fibrinogen, haptoglobin, and their combined classification, with alterations in fecal microbial composition, microbial interaction networks, and keystone taxa distribution during the early postpartum period was established. Several bacterial taxa were consistently associated with either elevated or normal inflammatory states across differential abundance, network, and odds ratio analyses. Many of these taxa remain poorly characterized in dairy cattle, highlighting the need for future mechanistic studies. This study demonstrates that systemic inflammation during early postpartum is associated with measurable alterations in the fecal microbiota. This work provides a foundation for developing microbiome-based biomarkers for detecting and monitoring subclinical systemic inflammation in dairy cattle.

The evolutionary divergence between Henophidia (non-venomous) and Caenophidia (venomous) snakes has produced distinct cranial morphologies, digestive strategies, and presence of specialised venom systems in Caenophidia, yet the extent to which these long-standing diverging trajectories have shaped cloacal microbiota assembly remains poorly understood. We characterised cloacal microbiota in 70 captive snakes (52 Caenophidia, 18 Henophidia) by 16S rRNA amplicon sequencing. Beta diversity was tested by PERMANOVA, differential abundance by ANCOM-BC2, community types by Dirichlet Multinomial Mixture modelling (DMM), and microbial interactions by SparCC co-occurrence networks. Predicted functional potential (PICRUSt2) was analysed by ALDEx2 differential abundance testing and elastic net feature selection. Henophidia exhibited significantly higher bacterial richness and greater compositional variability than Caenophidia. Community composition showed clade-associated differences (PERMANOVA) and partitioned into two distinct DMM community types. The Henophidia network was 11.9-fold denser and more modular, with Burkholderiaceae as a keystone hub, whereas the Caenophidia network was sparse. Henophidia showed predicted enrichment in C1 metabolic pathways (ethylmalonyl-CoA, formaldehyde assimilation I, glycine betaine degradation I, methylaspartate cycle), aromatic compound catabolism, and nitrogen recycling, whilst Caenophidia showed enrichment in allantoin and glucuronate degradation. This multi-method analysis suggests Burkholderiaceae as a candidate keystone taxon in Henophidia and indicates that phylogenetic clade is a major contributor to cloacal microbiota structure. The lower richness in Caenophidia raises a testable hypothesis that broad-spectrum antimicrobial activity of their venom components may selectively filter susceptible microbial lineages, motivating future shotgun metagenomic studies in wild populations of snakes.

Industrialization has reshaped human gut microbiomes, but its effects on other human-associated mammals remain poorly understood. Domestic dogs provide an informative comparative system because they have shared human environments and food systems for millennia yet retain distinct host biology. However, most canine microbiome studies have focused on industrialized companion animals, limiting our understanding of the ecological range of the domestic dog gut microbiome. We analyzed fecal 16S rRNA gene profiles from 261 dogs sampled across Nepal, Thailand, the United Arab Emirates, and the United States, spanning forager, agrarian, pastoralist, urban, and industrialized lifestyles; 257 dogs remained after excluding recent antibiotic exposure. Lifestyle was the strongest measured correlate of canine gut microbiome composition, and this structure persisted in restricted analyses of mature, non-shelter dogs sampled from temperate climate regions. Industrialized dogs differed from non-industrialized dogs through directional genus-level turnover, restructuring of VANISH- and BloSSUM-like microbial guilds, and shifts in predicted functional potential. Non-industrialized dogs were not microbiologically uniform: pastoralist dogs carried non-industrialized microbiome profiles but diverged from a simple forager-to-industrialized continuum. Cross-species comparisons with humans sampled across matched lifestyle categories showed parallel lifestyle-associated restructuring in both hosts, but host species remained the dominant axis of variation and the genera responding to industrialization were largely host-specific. These findings expand the ecological baseline for the domestic dog gut microbiome and identify industrialization as a major axis of microbiome restructuring in a long-term human-associated mammal. More broadly, they show that shared lifestyle transitions can impose parallel ecological pressures across host species without overriding host-specific community assembly.

Although the roles of host-associated microbiomes in animal health are increasingly recognised, the factors influencing their variation remain understudied. The relatively simple microbiome of honey bees is a relevant system to address this gap. In particular, the relationship between variations in microbiome composition and the ectoparasite Varroa destructor, the main threat to honey bee health worldwide, is poorly established. In this study, we used metagenomic and statistical analyses of 1442 European honey bee colonies to investigate the relationships between the honey bee microbiome, temporality, location, V. destructor load, and behavioural response to its infestation by the host. While season, year, and location were identified as the main drivers of microbiome variation, V. destructor load emerged as a significant factor associated with microbiome variation. Notably, we identify several pathogens and opportunists that correlated positively with V. destructor load, while the core symbiont Bombilactobacillus correlated negatively. This is compatible with a shift in the microbiome toward dysbiosis, which may be driven by or promote V. destructor parasitism. By contrast, we found only limited evidence of an association between the microbiome and resistance behaviours of the host against this parasite. While the study cannot establish causal relationships, we present the largest metagenomic analysis of honey bee microbiomes to date, providing robust, generalisable evidence about the factors driving variation in the microbiome composition of this ecologically and economically important pollinator. These findings may serve as additional markers in selective breeding programs targeting V. destructor resistance, which could ultimately improve honey bee health.

Illegal wildlife trade and habitat degradation displace thousands of animals annually in Southeast Asia, with many confiscated primates housed in rehabilitation centers that increasingly function as long-term holding environments. In slow lorises, dental clipping associated with the pet trade may generate persistent disruption along the oral-gut axis, potentially undermining physiological readiness for release in ways not captured by conventional screening. Here, we evaluated whether microbiome structure provides an integrative marker of release readiness in rehabilitating Javan slow lorises (Nycticebus javanicus). From June to October 2024, we collected fecal (n = 26) and saliva (n = 18) samples from 19 adults housed at YIARI, including 10 release candidates and 9 non-candidates classified primarily based on tooth loss, medical history, and possibility of release. Bacterial communities were characterized using 16S rRNA (V3-V4) amplicon sequencing, with alpha and beta diversity, taxonomic enrichment (LEfSe), and predicted functional profiles (PICRUSt2) assessed. Microbiome composition was strongly compartmentalized by body site, with higher alpha diversity in the gut. Release candidacy was associated with modest gut compositional differences, whereas oral microbiomes showed pronounced divergence between candidates and non-candidates. Non-candidates were enriched in dysbiosis-associated taxa and degradation-oriented functional pathways, while candidates showed enrichment of biosynthetic and central energy metabolism pathways. Gut microbiome structure was stable across pre-release and soft-release phases. These findings indicate that oral and gut microbiomes represent distinct physiological niches and that persistent oral microbiome alteration is a sensitive marker of long-term dental perturbation. Integrating microbiome-informed metrics may improve multidimensional assessment of release readiness.

Tick-borne pathogens can reshape vector microbiomes in ways that influence pathogen colonisation and transmission, yet the interplay between Ehrlichia ruminantium and the microbiota of its tick vectors remains uncharacterised. We profiled bacterial communities in haemolymph, midgut, and salivary glands of infected (n = 11) and uninfected (n = 12) Am. gemma ticks, a vector of E. ruminantium in East Africa, collected from cattle in Kajiado County, Kenya, using near-full-length 16S rRNA gene amplicon sequencing on the Oxford Nanopore platform. Community composition, alpha and beta diversity, co-occurrence networks, keystone taxa, and PICRUSt2-inferred functional profiles were compared across tissue-infection status groups. We identified 226 bacterial genera dominated by Coxiella, Pseudomonas, Acinetobacter, Proteus, and Rickettsia. Infection was associated with tissue-specific shifts in community composition (PERMANOVA R{superscript 2} = 0.14, p < 0.001) and co-occurrence network structure, with midgut networks showing complete hub taxon turnover (Jaccard = 0.000, p = 0.043). Haemolymph communities converged around Luteimonas as a keystone taxon, while opportunistic Proteobacteria, including Acinetobacter and Serratia, emerged as keystones in infected midgut. Endosymbiotic Rickettsia was near-absent in infected tissues (0.3% vs 9.3% mean relative abundance in midgut), consistent with competitive exclusion. Functional inference identified FDR-significant enrichment of predicted aerobactin siderophore biosynthesis, antimicrobial efflux, and oxidative stress response gene families in infected microbiota. These findings show tissue-specific restructuring of the Am. gemma microbiome associated with E. ruminantium infection and point to candidate targets for microbiome-based interventions against heartwater. ImportanceHeartwater, caused by the bacterium Ehrlichia ruminantium and transmitted by Amblyomma ticks, kills up to 90% of susceptible ruminants and is one of the most devastating tick-borne diseases in sub-Saharan Africa. Controlling heartwater requires understanding how the pathogen interacts with the microbial communities living inside its tick vector. In this exploratory study, we show that E. ruminantium infection is associated with tissue-specific shifts in the Amblyomma tick microbiome, including reduced abundance of beneficial symbionts, elevated representation of opportunistic bacteria among community hubs, and enrichment of iron acquisition and antimicrobial resistance functions. The midgut, the first tissue colonised during infection, showed the most marked structural reorganisation. These tissue-resolved microbiome signatures point to potential targets for novel control strategies, such as anti-microbiota vaccines or approaches that reinforce natural colonisation resistance, offering new strategies to reduce heartwater transmission and protect livestock livelihoods across Africa.

BackgroundRaw broiler meat products are highly perishable, and microbial activity is the main factor limiting their shelf lives. The spoilage microbiomes of broiler meat products have been studied mainly using traditional culturing methods and 16S rRNA gene amplicon sequencing, neither of which can show the activity of whole microbiome. Previous metatranscriptomic research of broiler spoilage has also remained limited to specific spoilage organisms rather than entire microbiomes. ResultsOur longitudinal study of broiler meat spoilage discovered the successions of active bacterial microbiomes and metabolic pathway activities of spoilers at 4{degrees}C and 6{degrees}C. Samples taken daily were subjected to metatranscriptomic analyses in combination with non-targeted metabolomic, traditional microbiology, and sensory analyses until advanced spoilage took place. Carnobacterium divergens, Carnobacterium maltaromaticum and Vagococcus proximus were the most active species at both temperatures. Carnobacteria are known poultry spoilers whereas Vagococcus proximus, a species recently described, played an unexpected active role in the microbiome. It became dominant in samples stored at 6{degrees}C and its activity increased also at 4{degrees}C after the use-by date. Central carbohydrate metabolism was the most common KEGG orthology pathway module of the microbiome at both temperatures. C. divergens and C. maltaromaticum showed stable metabolic profiles during the spoilage process, whereas V. proximus displayed a shift from high ATP synthesis activity to increased fatty acid and carbohydrate metabolism when spoilage advanced in samples stored at 4{degrees}C. Non-targeted metabolomics showed similar metabolomic trends across both temperatures. At 6{degrees}C, time-dependent changes were generally more pronounced, and the spoilage markers tyramine and spermidine showed greater accumulation. ConclusionsAs expected, the rate of spoilage is higher at 6 than 4{degrees}C, however we did not anticipate a similar overall trajectory of the spoilage processes. Our results link V. proximus as a key active spoiler in broiler meat and demonstrate the efficacy of using RNA-seq together with metabolomics to decode the function of a meat spoilage microbiome. This demonstrates that spoilage microbiomes consist of active species we have been neglecting due to the technological limitations of the standard methods. Future studies targeting to the metabolism and detecting of Vagococcus are warranted.