Animal Microbiome

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

The sustainability of Atlantic salmon (Salmo salar) farming is threatened by infectious diseases, environmental stressors, feed limitations, and regulatory or economic constraints. Although current health monitoring is improving with AI-powered camera systems that analyze behavior and nutrition, these tools typically identify stress responses rather than early signs of disease states. Because the microbial community undergoes successional reassembly in response to physiological disruptions before host barriers are breached, the microbiome offers a proactive early warning approach. In this study, a comparative cohort design was employed using a total of 171 individuals (n= 85 "healthy"; n=86 "lesioned") collected from a commercial marine facility and classified based on external clinical signs. The microbiome of multiple body sites (gills, skin, urogenital pore, and mucosa) from healthy and lesioned salmon were profiled using 16S rRNA amplicon sequencing. No differences in alpha diversity were observed between tissues and conditions. However, beta diversity was significantly different in clinical status, and the interaction of tissue with the status. Conversely, the mucosa and urogenital microbiomes were compositionally similar to each other, as were the gill and skin microbiomes, suggesting that urogenital swabs could serve as a non-invasive proxy for gut microbiome profiling, and skin for gill microbiomes. Several supervised models were trained on these profiles and used to classify salmon status with high accuracy. Based on these data, two Salmon Microbiome Health Score were developed that accurately differentiated the two cohorts. These scores are proposed as a novel biomarker, enabling proactive health management in aquaculture and complementing emerging technological monitoring systems.

The cattle gastrointestinal tract harbors a diverse community of microorganisms, including pathogenic and commensal strains of Escherichia coli. Antimicrobial use in cattle can disrupt the gut microbiome leading to shifts in bacterial diversity and abundance. Here, we combined shotgun metagenomics and single-cell sequencing to assess how ceftiofur antibiotic treatment impacted microbial diversity and structure. At the start of the experiment, ceftiofur was administered intramuscularly in parallel with the inoculation of a cocktail of extended-beta-lactamase-producing E. coli strains, to simulate environmental exposure and acquisition of resistant strains while animals are under antibiotic treatment. Fecal samples were collected from both the antibiotic-treated (ceftiofur and inoculation) and control (inoculation only) calves over the course of 35 days. Read mapping to genome and gene databases showed substantial differences in microbial richness and beta diversity between treatment groups. Treatment group-enriched taxa included Bacteroidaceae and Fibrobacter, which were more abundant in samples that did not receive ceftiofur, and Akkermansia in ceftiofur-treated calves. In ceftiofur-exposed animals, we observed a gradual loss of virulence factors alongside increased abundances of beta-lactam resistance genes, including cfxA5 and cfxA6 likely encoded by CAG-485 (Muribaculaceae). We further profiled individual cells using single-cell sequencing, which revealed a high number of Clostridium carrying macrolide resistance genes lnu(P) and mph(N) in both ceftiofur-treated and control samples. Overall, our complementary approaches reveal distinct remodeling of the calf microbiome following antibiotic and E. coli administration, tied to key functional genes that can be assigned to specific genera or recurrently detected across diverse taxa. IMPORTANCECattle serve as natural reservoirs of zoonotic strains of E. coli, which can cause severe gastrointestinal infections in humans. Antibiotic usage on cattle farms can drive the emergence of antimicrobial resistant bacterial strains and alter the underlying cattle gastrointestinal microbiome. Consequently, there is a need to understand how antibiotic administration impacts population dynamics of cattle rumen and intestinal microbes. In this study, we combined both shotgun metagenomics and single-cell genomics on feces from ruminating calves to determine microbiome changes following administration of both ceftiofur and E. coli cocktails. We observed considerable variation in prevalence and abundance of virulence factors, antimicrobial resistance-related genes, and taxa with key roles in animal nutrition and health between the microbiomes of antibiotic-treated and antibiotic-free calves, with potential implications for their subsequent development and overall well-being.

BackgroundWildlife rehabilitation can influence host-associated microbiota, yet little is known about how the gut microbiome of insectivorous bats responds to rehabilitation during temporary managed care. This study applied shotgun metagenomics to evaluate the impact of temporary managed care on the gut microbiome of wild and rehabilitated bats in Yorkshire, UK. ResultsWe analysed 25 faecal metagenomes from Myotis daubentonii, Pipistrellus pipistrellus, Nyctalus noctula and N. leisleri, including wild baseline bats and bats sampled during temporary managed care (1-49 days in rehabilitation). Microbial communities clustered strongly by host species and roost location, but not by rehabilitation status. Bacterial alpha diversity did not differ between wild bats, and bats in care (H = 2.30, p = 0.32). Archaeal communities were highly uniform across samples, showing far lower interindividual variation than bacterial communities (12.2% vs. 41.8% coefficient of variation). Rehabilitated bats showed increased relative abundance of Yersiniaceae and Lactobacillaceae, while environmental families such as Pseudomonadaceae and Erwiniaceae decreased, indicating modest but non-disruptive changes consistent with a controlled diet and reduced environmental exposure. ConclusionsAcross temporary managed care, the core gut microbiome of insectivorous bats remained stable, demonstrating notable microbial resilience. These findings provide an important baseline for monitoring microbiome health in wildlife rehabilitation and supporting post-release conservation programmes in the UK and beyond.

Understanding the patterns and drivers of infectious disease dynamics at different levels of life organization is a fundamental disease ecology challenge. In this study, we performed a multi-infectious agents (IA) screening of 1,983 individuals belonging to 18 seabird species, sampled between 2017 and 2022 across five sub-Antarctic islands in the Southern Indian and Atlantic Oceans. Our aim was to identify the drivers of IA community in these seabirds by considering intrinsic and extrinsic factors on three dimensions: distance between seabird metapopulations and within-island sites, macro-community (host functional traits based on feeding and breeding features) and intra-host IA community composition. Samples were screened for 24 DNA-based IAs using a high-throughput real-time PCR method, followed by subsequent hierarchical modelling of species communities. Campylobacter lari, Escherichia coli, Pasteurella multocida, Chlamydiaceae and Mycobacterium spp. were found to be present on all islands in some, but not all, species. However, only E. coli was detected in all species. According to our modelling results, the influence of year and within-island site had limited influence on IA presence/absence, accounting respectively for an average of 1.0% and 1.8% of the variation in IA community. Including host species as a response variable produced a better model fit than including host species functional traits, highlighting the difficulty in simplifying systems by focusing on high-level functional categories. Model outputs show how each species influences IA distribution depending on IA traits, but no clear trend has emerged. Interestingly, burrowing species were less frequently infected with directly transmitted IAs, probably due to the low frequency of transmission events associated with their breeding features and limited social contacts. Our findings pave the way for further multi-dimension studies that would combine complementary approaches to disentangle the complex processes at play in the dynamics of hosts and IAs interactions.

1.Amplicon-based profiling of airway microbiota is increasingly used to assess respiratory health in mammals, yet baseline data for free-ranging baleen whales remain scarce. We characterised the exhaled-breath ("blow") microbiota of rorqual whales in the Gulf of St. Lawrence (Canada) and examined associations with individual health indicators. Blow samples were collected opportunistically from six whales (two blue, two fin and two humpback), with seawater and air controls. The V4 region of the 16S rRNA gene was sequenced on an Illumina MiSeq platform and processed in R (v4.5) using the DADA2 pipeline for quality filtering, denoising and amplicon sequence variant (ASV) inference. Alpha diversity varied among individuals (Shannon = 2.72 - 4.33) and beta-diversity analyses revealed a significant effect of environment (whale blow vs. seawater) on community composition (PERMANOVA: R2 = 0.140, F = 1.31, p = 0.030). The relative abundance of pathobionts (22.8-48.8%) was negatively correlated with alpha diversity (Spearman {rho} = -0.88 to -0.94, p < 0.05), while higher diversity correlated positively with good skin condition ({rho} = 0.84, p = 0.03). These findings provide the first baseline description of rorqual respiratory microbiota in the Gulf of St. Lawrence and support blow microbiome metrics as non-invasive health biomarkers.

Sarbecoviruses, a subgenus of Betacoronavirus, display both respiratory and gastrointestinal tropism, suggesting potential interactions with host gut microbial communities. However, ecological signatures of infection in wild bats remain poorly understood. We investigated associations between Sarbecovirus infection status, gut microbiome structure, and diet composition in Rhinolophus shameli roosting in northeastern Cambodia. Fecal samples collected across dry and wet seasons (2023-2024) were subject to full-length 16S rRNA gene sequencing and arthropod DNA metabarcoding. Sarbecovirus-positive bats exhibited stable alpha diversity but consistent shifts in gut community composition and increased interindividual variability consistent with the Anna Karenina Principle, suggesting infection-associated destabilization of community assembly rather than diversity erosion. Infection status was associated with enrichment of Shigella and Escherichia species, taxa linked to inflammatory or epithelial stress states in bats. In contrast, dietary composition showed no strong global structuring by infection status and weak coupling with bacterial community structure, suggesting that trophic ecology is unlikely to be the main driver of the infection-associated microbiome signal. Although causal directionality cannot be inferred, our results reveal measurable and consistent microbiome restructuring associated with Sarbecovirus detection in a natural reservoir host and highlight the potential of microbiome profiling for monitoring wildlife disease processes.

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.

The female reproductive tract harbors complex microbial communities that may influence reproductive success. In previous work using 16S rRNA gene sequencing, we identified bacterial taxa in the vagina and uterus of beef cattle associated with pregnancy outcomes, but taxonomic resolution and functional inference was limited. Here we used shotgun metagenomic sequencing to characterize the taxonomic composition, functional potential, and antimicrobial resistome of vaginal and uterine microbiomes at the time of artificial insemination (AI) in cows that subsequently became pregnant or remained open. Vaginal (pregnant n = 54; open n = 7) and uterine (pregnant, n = 41; open, n = 9) samples were collected prior to AI. Microbial community structure did not differ between pregnancy outcome groups in either anatomical site (PERMANOVA; P > 0.05). However, cows that remained open showed significantly greater species-level richness and diversity in the vaginal microbiome (P < 0.05). No diversity differences were observed in the uterine microbiome. In contrast, significant differences were detected between anatomical sites, with distinct dominant taxa and functional profiles. Vaginal microbiomes were enriched in pathways related to genetic information processing, whereas uterine microbiomes exhibited greater representation of metabolic pathways. A total of 105 ARGs spanning 11 antimicrobial classes were identified, with tetracycline resistance genes [tet(Q), tet(W), and tet(M)] predominating, and blaTEM-116 more abundant in the uterine microbiome. Overall, while vaginal and uterine microbiomes were compositionally and functionally distinct, no robust pregnancy-associated taxonomic or functional signatures were detected, likely reflecting limited statistical power and challenges inherent to low-biomass metagenomic datasets. IMPORTANCEUnderstanding the role of the reproductive tract microbiome in fertility could improve reproductive efficiency in cattle. We used shotgun metagenomic sequencing to characterize the taxonomic composition, functional potential, and antimicrobial resistome of vaginal and uterine microbiomes at the time of artificial insemination in cows that subsequently became pregnant or remained open. Using paired samples from the same animals, we directly compared microbial communities between the upper and lower reproductive tract to identify shared and site-specific features. Although no distinct microbial signatures associated with pregnancy outcomes were detected, this may reflect limited statistical power and low microbial biomass inherent to these samples. Despite these challenges, our study provides high-resolution insights into the composition, functional potential, and resistome of bovine reproductive microbiomes and highlights important technical considerations for studying low-biomass microbial ecosystems.

Spotty Liver Disease (SLD) is an acute bacterial infection of layer chickens in production, caused by Campylobacter hepaticus, and occurs most frequently in barn-housed and free-range systems. The disease is characterized by a sharp decline in egg production and increased mortality. The hallmark pathological feature is 1-2 mm white to grey necrotic foci distributed across the liver surface. Despite its growing economic impact on commercial poultry, the molecular mechanisms underlying host responses to C. hepaticus infection remain poorly understood. To address this gap, we performed a comprehensive transcriptome analysis of liver tissue from chickens naturally infected with SLD compared to uninfected controls. High-throughput transcriptome sequencing, yielding 9,277 differentially expressed genes (DEG), of which 3,063 were upregulated and 6,214 were downregulated. Functional pathway enrichment analysis revealed significant alterations in immune and metabolic processes associated with SLD pathophysiology. Infected chickens exhibited significant activation of immune response pathways, particularly cytokine-cytokine receptor interactions involving interleukins IL-22, IL-21, and IL-6, along with enhanced cell signaling, and cell adhesion. Among the individual genes, C1QTNF1 and the adhesion molecule gene ADGRD1 were notably overexpressed, indicating enhanced inflammatory activity. In contrast, core hepatic metabolic functions were profoundly reduced, as evidenced by downregulation of oxidative phosphorylation, fatty acid metabolism, iron ion binding, and heme binding pathways. A marked increase in serum amyloid A gene (SAA) expression further confirmed robust acute-phase responses and compromised liver function during infection. Together, these findings demonstrate a complex interplay between inflammatory activation and metabolic dysregulation during SLD. The strong upregulation of acute-phase proteins and pro-inflammatory cytokines demonstrates the hosts vigorous attempt to combat bacterial infection, whereas the concurrent suppression of essential metabolic pathways reflects the pathological consequences of SLD. This study provides a transcriptomic characterization of host responses to C. hepaticus infection, offering insights into SLD pathogenesis and potential avenues for targeted intervention.

The gut microbiota influence many aspects of their hosts health and physiology including the digestion of food, and food intake in turn influences the composition of the gut microbiome. However, the ways in which food can alter the behavior of intestinal bacteria remain largely unknown, due in large part to the difficulty of assessing behavior in situ. Larval zebrafish provide a model for addressing this gap because of their optical transparency and their ability to be prepared germ-free and then associated with specific microbial species. Using light sheet fluorescence microscopy to visualize bacteria inside the intestines of live zebrafish larvae, we examine the properties of two commensal strains with markedly different physical characteristics. One is a zebrafish-commensal Enterobacter species that forms large aggregates in unfed larvae, and the other is a pathobiont Vibrio species that is motile and planktonic. Following host consumption of rotifers, a common food, Enterobacter clusters disintegrate into motile individuals. Vibrio remains planktonic in fed larvae but decreases the activity of its Type VI Secretion System, leading to a strong decrease in damage to host tissue. Our results reveal that feeding can have major impacts on bacterial behavior that should be considered in models of normal gut microbiome dynamics as well as pathogenesis.

Animal-associated bacteria (microbiomes) can have important effects on host phenotypes and fitness. Microbiomes can also vary across individuals in ways that depend on host genotype and environment. Temperature is an especially important environmental factor that can affect the microbiome in a way that depends on host genotype and affects organismal fitness. Thermal stress, in particular, can have dramatic effects on animal microbiomes, including dysbiosis and immune dysregulation. However, most previous work on extreme temperature effects has focused on heat stress. To investigate how low temperatures affect the microbiome of a warm-adapted animal, we characterized the bacterial communities associated with house fly (Musca domestica) males raised at cool (18{degrees}C) and warm (29{degrees}C) temperatures. We sampled two distinct genotypes in these experimental flies, each of which is associated with a particular thermal environment (warm or cool). We contrasted our experimental results with the microbiomes we characterized in wild house flies from two collection sites with different large animals present. We found that temperature has a much stronger effect on the house fly microbiome than the host genotype in our experimental flies. Consistent with the strong environmental effects in our experiment, we found that wild house fly microbiomes differed between the two collection sites. Despite these environmental effects on the house fly microbiome, we did not detect evidence for dysbiosis associated with either cool or warm temperatures. We therefore conclude that the environment has more of an effect on the house fly microbiome than host genotype, but dysbiosis does not occur within the temperature range we considered.

Microbial residents of ectothermic hosts are exposed to variations in temperature that have the potential to impact their physiology and the host-microbe symbiotic relationship. In this experimental warming study, laboratory populations of American cockroaches (Periplaneta americana) were kept at a baseline low room temperature of 20-22{degrees}C or a high temperature of 30{degrees}C for two weeks. We quantified bacterial load and performed high-throughput 16S rRNA gene sequencing to assess the hindgut microbiomes response to a near 10{degrees}C shift in environmental temperature. We report modest impacts of temperature on cockroach gut microbiome composition. The high temperature treatment induced increases in the relative abundance of Proteobacteria and Euryarchaeota phyla as well as the Lactobacillaceae and Enterococcaceae families. We also observed increased interindividual variability. There were no significant differences in the dominant Bacteroidota or Firmicutes phyla and no significant losses or reductions in taxa or bacterial load, respectively. This suggests that the gut community of American cockroaches is largely resilient to prolonged increases in temperature and has implications for the cockroach to withstand the impacts of climate change. ImportanceInsects, as with most animals, often harbor microbial symbionts that play an essential role in host health and nutrition. As insects are ectotherms, these microbial symbionts are subject to the same temperature fluctuations as their hosts, potentially impacting host temperature responses. Here, we demonstrate that the American cockroach (Periplaneta americana) gut microbiome exhibits only modest changes following an [~]10{degrees}C increase in environmental temperature. This contrasts with studies in other insects, whose microbiota were highly responsive to temperature variation. This work illustrates that the microbiota of insects may vary in their sensitivity to long-term temperature shifts, providing a more comprehensive understanding of potential variability in insect responses to climate change.

Centrohelid heliozoans are a monophyletic group of free-living, ubiquitous, predatory protists widely distributed in aquatic and soil ecosystems. Centrohelids are known as cytotrophic protists that feed on bacteria, algae, and small unicellular eukaryotes. While algal and chloroplast symbioses have been documented in this group, their bacterial associations remain largely unexplored. In this study, we characterize the bacterial communities associated with centrohelids isolated from freshwater habitats using full-length 16S rRNA PacBio sequencing. Amplicon sequencing revealed 5 phyla, 6 classes, and 58 genera in the bacterial communities associated with seven centrohelid isolates. Alphaproteobacteria, Bacteroidia, and Gammaproteobacteria were the most abundant classes, while Arcicella, Sphingobium, Pseudomonas, Sphingomonas, Azospirillum, Shinella, Flavobacterium, Variovorax, and Rhodococcus were the most abundant genera. Notably, Arcicella, Variovorax, Sphingobium, and Pseudomonas constituted the core microbiome. Unexpectedly, we detected bacteria known as opportunistic pathogens, providing the first evidence that centrohelids may serve as environmental reservoirs for bacteria with pathogenic potential (e.g., Acidovorax, Acinetobacter, Anaerococcus, Bosea, Corynebacterium, Escherichia, Moraxella, Mycobacterium, Prevotella, Pseudomonas, Ralstonia, and Sphingomonas). In addition, this study provides the first evidence of Rickettsiaceae associations with centrohelids. IMPORTANCEThis study reveals that centrohelid heliozoans, ubiquitous microbial predators, harbor diverse and host-specific bacterial communities. Critically, we show they can serve as environmental reservoirs for bacteria with pathogenic potential, a role previously overlooked outside of model protist groups. These findings expand our understanding of pathogen ecology, suggesting that a wider range of protists may contribute to the persistence and dispersal of opportunistic pathogens in aquatic ecosystems.

Bilophila wadsworthia is a gut pathobiont implicated in dysbiosis-driven inflammation, yet its pathogenic mechanisms remain poorly investigated. Here, we evaluated the suitability of Galleria mellonella larvae as an in vivo model to study B. wadsworthia infection. Two infection routes were compared: oral inoculation to mimic gastrointestinal colonization and hemolymph injection to model systemic infection. Oral challenge had minimal impact on larval health, whereas hemolymph injection caused marked morbidity, including reduced mobility, impaired cocoon formation, and progressive melanization, indicating that access to the circulatory system is required for overt disease. Infection required live bacteria, with B. wadsworthia capable of intracellular replication within hemocytes, leading to transient depletion of circulating immune cells followed by compensatory hemocyte proliferation. These findings reveal tight coupling between bacterial proliferation and host immune dynamics. Comparison with other sulfidogenic bacteria suggests that Bilophila pathogenicity is likely to involve host-specific interactions. Overall, our results establish G. mellonella as a practical and ethically favorable model to investigate B. wadsworthia virulence, host-pathogen interactions, and mechanisms relevant to gut-associated infection.

Microbial diversity remains largely unexplored across environments and scales, notably because at local scales many microbial taxa exist under a dormant state. Microbial biogeography is shaped by edaphic and ecological drivers, and shifts in microbial community composition are frequently associated with host community structure and health. Nontuberculous mycobacteria represent a striking example of environmental microorganisms with opportunistic pathogenic potential. Unfortunately, data on their diversity, distribution, and ecological interactions in aquatic environments remain limited. However, understanding competition for niche space and the role of abiotic and biotic factors shaping their biogeography is crucial for predicting disease emergence and transmission. Here we aimed at i) identifying microhabitat abiotic and biotic drivers influencing their distribution, ii) assessing the predictability of their diversity and distribution across continents, and iii) examining potential exclusion or associations between pathogenic and nonpathogenic mycobacterial species. By deploying an eDNA-based metabarcoding approach from freshwater samples collected in urban and rural sites in French Guiana and Cote dIvoire, we have boosted our understanding of environmental mycobacteria ecology by highlighting the influence of habitat type, abiotic factors, and microbial interactions on mycobacterial distribution. In addition, the detection of pathogenic species further highlighted the importance of environmental reservoirs in mycobacterial disease transmission.

The cattle rumen microbiota represents a highly complex and dynamic ecosystem, whose organization and connection to host phenotypes are of the highest importance to food security and the environment. In this study, we analyzed the rumen microbiota, from 2,492 cattle belonging to five different breeds and production systems across five countries, categorizing them into microbial co-abundance groups referred to as Ruminosignatures. We identified twelve distinct Ruminosignatures, including two that were consistently observed across all populations and were dominated by the genus Prevotella and UBA2810. Additional Ruminosignatures showed breed-and diet-specific patterns and collectively explained 96-99% of the variance in rumen microbial composition. The abundances of several Ruminosignatures were associated with methane emissions and feed efficiency, and were influenced by host genetics, with heritability estimates ranging from 0.09 to 0.51. The Ruminosignature dominated by UAB2810 was negatively associated with methane emissions across all datasets and positively linked to feed efficiency in Holstein from Italy and crossbred from Ireland. Additionally, the type of production system affects both the occurrence of Ruminosignatures and their impact on host phenotypes, emphasizing the need for context-specific approaches to modulate the rumen microbiome. Overall, our results offer new perspectives on the assembly of ruminal microbes and underscore the potential of the Ruminosignatures framework for microbiome-informed precision agriculture and breeding initiatives aimed at enhancing feed efficiency and minimizing the environmental impact of cattle farming.

BackgroundNon-invasive methods to colonize intact gut microbiota populations with specific bacterial species are useful for experimental studies that advance our understanding of this commensal microbial population in health and disease. Within the gut microbiota, the anaerobic muciniphile Akkermansia muciniphila has many established health benefits. We report the development of a new voluntary feeding protocol for non-invasive administration of bacteria into the intestine and use it to characterize the early life colonization of the intestinal tract by A. muciniphila. ResultsMice were voluntarily fed a human strain of A. muciniphila (MucT/BAA-835) in the week after weaning, whereupon they consistently and rapidly ingested the bacterium. At this developmental period, conventionally housed mice were rapidly colonized by human A. muciniphila that persisted until at least 8 weeks of age. In mice that contained a dysbiotic gut microbiota that lack endogenous A. muciniphila, voluntary feeding with human A. muciniphila similarly led to rapid and stable colonization. Colonization was similar in female and male mice. Also, in conventionally housed mice there was incomplete colonization of the intestinal tract with endogenous A. muciniphila between 3 - 4 weeks of age, which enabled its competitive exclusion by human A. muciniphila that was orally delivered. ConclusionsThese findings establish a new and non-invasive approach for colonizing the intestinal tract with commensal microbes that provides information on the early life colonization of the gut microbiota with A. muciniphila.

AbstractBeneficial associations between bobtail squids (Cephalopoda: Sepiolidae) and Vibrio bacteria encompass a unique association where symbionts are obtained environmentally from the surrounding environment. Vibrio symbionts are susceptible to a number of ecological pressures such as protozoan grazing whilst in their free-living state. Impacts of grazing have several consequences for symbiosis characteristics such as biofilm formation, a trait crucial for survival both in and outside the squid. Therefore, in order to ascertain how biotic factors such as grazing in the environment effect symbiotic success, two V. fischeri strains, ES114 and ETBB1-C were experimentally evolved in separate biofilm grazing experiments with the amoeba, Acanthamoeba castellanii and ciliate Tetrahymena pyriformis. Both ES114 and ETBB1-C biofilms were evolved up to 50 generations through serial passaging. At 50 generations, ES114 biofilms displayed variability in response to predation by both predators, whereas ETBB1-C biofilms were more stable across generations of grazing. A. castellanii decreased in population numbers when co-inoculated with ETBB1-C, whereas T. pyriformis increased in numbers with biofilm growth. Growth of V. fischeri biofilms in the presence of grazers such as T. pyriformis has an important role in inducing biofilm growth by acting as a chaperone for recycling nutrients back into the environment. Additionally, V. fischeri colonization fitness in the host was dependent on which grazer was used to evolve the biofilms. Such variation in response by V. fischeri to different types of predation demonstrates the versatility of this symbiont in its free living state and has subsequent impacts on the eventual association with squids. ImportanceThis manuscript demonstrates the importance of biotic factors (such as protozoan grazing) in the environment that effect host colonization in a beneficial symbiosis. Using an experimental evolution approach, this work demonstrates how symbiotic biofilms can adapt to pressures such as grazing that subsequently influences the ability to colonize its invertebrate host.

Parasites occur in every ecosystem, although their dispersal is often constrained by the availability of hosts or vectors. Here, we explore how variation in parasite life history traits, particularly transmission strategy, may influence their distributions. Specifically, we test whether a variety of parasites ad-here to the rules of island biogeography, and whether their distributions vary with transmission strategy. We utilised broad-spectrum parasite detection from existing Whole Genome Sequence (WGS) data to characterise parasites with varying transmission strategies from the blood of a passerine bird, the silvereye (Zosterops lateralis), sampled across 25 islands in the South Pacific and from five of the states in mainland Australia. Overall, parasite richness was higher on mainland Australia compared to islands and decreased with distance of islands from the Australian continent. However, these patterns were dependent on transmission strategy. For parasites transmitted by flying insect vectors, richness decreased on islands compared to the mainland. However, increasing isolation from the mainland among islands had little further impact. On the other hand, richness of directly transmitted parasites and those requiring another intermediate host declined sharply with increasing distance from the mainland. While islands may act as an initial barrier to colonisation for parasites relying on flying insect vectors, their highly dispersive vectors may subsequently reduce the impact of increasing isolation distance on richness. Our work underscores the importance of considering parasite life-histories and their transmission strategies for understanding the processes that shape parasite communities on islands.