The Microbiome of Animals: Implications for Conservation Biology

Microbial DNA extraction method for avian feces and preen oil from diverse species

As DNA sequencing technology continues to rapidly improve, studies investigating the microbial communities of host organisms (i.e., microbiota) are becoming not only more popular but also more financially accessible. Across many taxa, microbiomes can have important impacts on organismal health and fitness. To evaluate the microbial community composition of a particular microbiome, microbial DNA must be successfully extracted. Fecal samples are often easy to collect and are a good source of gut microbial DNA. Additionally, interest in the avian preen gland microbiome is rapidly growing, due to the importance of preen oil for many aspects of avian life. Microbial DNA extractions from avian fecal and preen oil samples present multiple challenges, however. Here, we describe a modified PrepMan Ultra Sample Preparation Reagent microbial DNA extraction method that is less expensive than other commonly used methodologies and is highly effective for both fecal and preen oil samples collected from a broad range of avian species. We expect our method will facilitate microbial DNA extractions from multiple avian microbiome reservoirs, which have previously proved difficult and expensive. Our method therefore increases the feasibility of future studies of avian host microbiomes.

Selection for stress tolerance and longevity in Drosophila melanogaster have strong impacts on microbiome profiles

There is experimental evidence that microbiomes have a strong influence on a range of host traits. Understanding the basis and importance of symbiosis between host and associated microorganisms is a rapidly developing research field, and we still lack a mechanistic understanding of ecological and genetic pressures affecting host-microbiome associations. Here Drosophila melanogaster lines from a large-scale artificial selection experiment were used to investigate whether the microbiota differ in lines selected for different stress resistance traits and longevity. Following multiple generations of artificial selection all selection regimes and corresponding controls had their microbiomes assessed. The microbiome was interrogated based on 16S rRNA sequencing. We found that the microbiome of flies from the different selection regimes differed markedly from that of the unselected control regime, and microbial diversity was consistently higher in selected relative to control regimes. Several common Drosophila bacterial species showed differentially abundance in the different selection regimes despite flies being exposed to similar environmental conditions for two generations prior to assessment. Our findings provide strong evidence for symbiosis between host and microbiomes but we cannot reveal whether the interactions are adaptive, nor whether they are caused by genetic or ecological factors.

Microbiome and epigenetic variation in wild fish with low genetic diversity

Non-genetic sources of phenotypic variation, such as the epigenome and the microbiome, could be important contributors to adaptive variation for species with low genetic diversity. However, little is known about the complex interaction between these factors and the genetic diversity of the host, particularly in wild populations. Here, we examine the skin microbiome composition of two closely-related mangrove killifish species with different mating systems (self-fertilising and outcrossing) under sympatric and allopatric conditions. This allows us to partition the influence of the genotype and the environment on their microbiome and (previously described) epigenetic profiles. We find the diversity and community composition of the skin microbiome are strongly shaped by the environment and, to a lesser extent, by species-specific influences. Heterozygosity and microbiome alpha diversity, but not epigenetic variation, are associated with the fluctuating asymmetry of traits related to performance (vision) and behaviour (aggression). Our study identifies that a proportion of the epigenetic diversity and microbiome differentiation is unrelated to genetic variation, and we find evidence for an associative relationship between microbiome and epigenetic diversity in these wild populations. This suggests that both mechanisms could potentially contribute to variation in species with low genetic diversity.

Microbiome composition and presence of cultivable commensal groups of Southern Tamanduas (Tamandua tetradactyla) varies with captive conditions

Southern Tamanduas (Tamandua tetradactyla) belong to the specialized placental myrmecophages. There is not much information about their intestinal microbiome. Moreover, due to their food specialization, it is difficult to create an adequate diet under breeding conditions. Therefore, we used 16S rDNA amplicon sequencing to analyze the fecal microbiome of captive Southern Tamanduas from four locations in the Czech Republic and evaluated the impact of the incoming diet and facility conditions on microbiome composition. Together with the microbiome analysis, we also quantified and identified cultivable commensals. The anteater fecal microbiome was dominated by the phyla Bacillota and Bacteroidota, while Pseudomonadota, Spirochaetota, and Actinobacteriota were less abundant. At the taxonomic family level, Lachnospiraceae, Prevotellaceae, Bacteroidaceae, Oscillospiraceae, Erysipelotrichaceae, Spirochaetaceae, Ruminococcaceae, Leuconostocaceae, and Streptococcaceae were mainly represented in the fecal microbiome of animals from all locations. Interestingly, Lactobacillaceae dominated in the location with a zoo-made diet. These animals also had significantly lower diversity of gut microbiome in comparison with animals from other locations fed mainly with a complete commercial diet. Moreover, captive conditions of analyzed anteater included other factors such as the enrichment of the diet with insect-based products, probiotic interventions, the presence of other animals in the exposure, which can potentially affect the composition of the microbiome and cultivable microbes. In total, 63 bacterial species from beneficial commensal to opportunistic pathogen were isolated and identified using MALDI-TOF MS in the set of more than one thousand selected isolates. Half of the detected species were present in the fecal microbiota of most animals, the rest varied across animals and locations.

Variable effects of captivity on microbiomes in populations of IUCN-endangered Blanding's turtles (Emydoidea blandingii)

AIMS

Microbiome composition is increasingly considered in species reintroduction efforts and may influence survival and reproductive success. Many turtle species are threatened by anthropogenic pressures and are frequently raised in captivity for reintroduction efforts, yet little is known about turtle microbiome composition in either wild or captive settings. Here, we investigated trends in microbiome composition of captive and wild IUCN-endangered Blanding's turtles (Emydoidea blandingii).

METHODS AND RESULTS

We amplified and sequenced the V4 region of the 16S rDNA locus from plastron, cloaca, and water samples of wild E. blandingii adults and two populations of captive E. blandingii juveniles being raised for headstarting. Plastron, cloaca, and water-associated microbiomes differed strongly from each other and were highly variable among captive sites and between captive and wild sites. Across plastron, cloaca, and water-associated microbial communities, microbial diversity changed over time, but not in a predictable direction between captive sites. Plastron beta diversity correlated with growth rate in captive samples, indicating that external microbiomes may correlate with individual fitness.

CONCLUSIONS

Our results indicate that external and internal microbiomes vary between captive and wild turtles and may reflect differences in fitness of captive-raised individuals.

Rusa deer microbiota: the importance of preliminary data analysis for meaningful diversity comparisons

The microbiome is an important consideration for the conservation of endangered species. Studies provided evidence of the effect of behavior and habitat change on the microbiota of wild animals and reported various inferences. It indicates the complexity of factors influencing microbiota diversity, including incomplete sampling procedures. Data abnormality may arise due to the procedures warranting preliminary analysis, such as rarefaction, before downstream analysis. This present study demonstrated the effect of data rarefaction and aggregation on the comparison of wild rusa deer's gut microbial diversity. Eighty-five feces samples were collected from 11 deer populations inhabiting three national parks in Java and Bali islands. Using the Illumina Nova-Seq platform, fragments of 16s rRNA gene were sequenced, and raw data of 51,389 reads corresponding to 2 domains, 22 phyla, 45 classes, 83 orders, 182 families, and 460 genera of bacteria were obtained. Data rarefaction was applied at two different library sizes (minimum and fixed) and aggregation (11 populations into 3 research sites) to investigate its effect on the microbial diversity comparison. There are significant differences in alpha diversity between populations, but not research sites, at all library sizes of rarefaction. A similar finding is also found in beta diversity. Moreover, data rarefaction and aggregation result in different values of the diversity metrics. This present study shows that statistical analysis remains a substantial concern in microbiome studies applied to conservation biology. It suggests reporting a more detailed data normalization in microbiome studies as an inherent control of suboptimal sampling, particularly when involving feces.

Feeding Drosophila gut microbiomes from young and old flies modifies the microbiome

It is becoming increasingly evident that the myriad of microbes in the gut, within cells and attached to body parts (or roots of plants), play crucial roles for the host. Although this has been known for decades, recent developments in molecular biology allow for expanded insight into the abundance and function of these microbes. Here we used the vinegar fly, Drosophila melanogaster, to investigate fitness measures across the lifetime of flies fed a suspension of gut microbes harvested from young or old flies, respectively. Our hypothesis was that flies constitutively enriched with a 'Young microbiome' would live longer and be more agile at old age (i.e. have increased healthspan) compared to flies enriched with an 'Old microbiome'. Three major take home messages came out of our study: (1) the gut microbiomes of young and old flies differ markedly; (2) feeding flies with Young and Old microbiomes altered the microbiome of recipient flies and (3) the two different microbial diets did not have any effect on locomotor activity nor lifespan of the recipient flies, contradicting our working hypothesis. Combined, these results provide novel insight into the interplay between hosts and their microbiomes and clearly highlight that the phenotypic effects of gut transplants and probiotics can be complex and unpredictable.

Opportunities and challenges with transitioning to non-lethal sampling of wild fish for microbiome research

The microbial communities of fish are considered an integral part of maintaining the overall health and fitness of their host. Research has shown that resident microbes reside on various mucosal surfaces, such as the gills, skin, and gastrointestinal tract, and play a key role in various host functions, including digestion, immunity, and disease resistance. A second, more transient group of microbes reside in the digesta, or feces, and are primarily influenced by environmental factors such as the host diet. The vast majority of fish microbiome research currently uses lethal sampling to analyse any one of these mucosal and/or digesta microbial communities. The present paper discusses the various opportunities that non-lethal microbiome sampling offers, as well as some inherent challenges, with the ultimate goal of creating a sound argument for future researchers to transition to non-lethal sampling of wild fish in microbiome research. Doing so will reduce animal welfare and population impacts on fish while creating novel opportunities to link host microbial communities to an individual's behavior and survival across space and time (e.g., life-stages, seasons). Current lethal sampling efforts constrain our ability to understand the mechanistic ecological consequences of variation in microbiome communities in the wild. Transitioning to non-lethal sampling will open new frontiers in ecological and microbial research.

A first characterization of the microbiota-resilience link in swine

BACKGROUND

The gut microbiome plays a crucial role in understanding complex biological mechanisms, including host resilience to stressors. Investigating the microbiota-resilience link in animals and plants holds relevance in addressing challenges like adaptation of agricultural species to a warming environment. This study aims to characterize the microbiota-resilience connection in swine. As resilience is not directly observable, we estimated it using four distinct indicators based on daily feed consumption variability, assuming animals with greater intake variation may face challenges in maintaining stable physiological status. These indicators were analyzed both as linear and categorical variables. In our first set of analyses, we explored the microbiota-resilience link using PERMANOVA, α-diversity analysis, and discriminant analysis. Additionally, we quantified the ratio of estimated microbiota variance to total phenotypic variance (microbiability). Finally, we conducted a Partial Least Squares-Discriminant Analysis (PLS-DA) to assess the classification performance of the microbiota with indicators expressed in classes.

RESULTS

This study offers four key insights. Firstly, among all indicators, two effectively captured resilience. Secondly, our analyses revealed robust relationship between microbial composition and resilience in terms of both composition and richness. We found decreased α-diversity in less-resilient animals, while specific amplicon sequence variants (ASVs) and KEGG pathways associated with inflammatory responses were negatively linked to resilience. Thirdly, considering resilience indicators in classes, we observed significant differences in microbial composition primarily in animals with lower resilience. Lastly, our study indicates that gut microbial composition can serve as a reliable biomarker for distinguishing individuals with lower resilience.

CONCLUSION

Our comprehensive analyses have highlighted the host-microbiota and resilience connection, contributing valuable insights to the existing scientific knowledge. The practical implications of PLS-DA and microbiability results are noteworthy. PLS-DA suggests that host-microbiota interactions could be utilized as biomarkers for monitoring resilience. Furthermore, the microbiability findings show that leveraging host-microbiota insights may improve the identification of resilient animals, supporting their adaptive capacity in response to changing environmental conditions. These practical implications offer promising avenues for enhancing animal well-being and adaptation strategies in the context of environmental challenges faced by livestock populations. Video Abstract.

CHARACTERIZATION OF THE FUNGAL MICROBIOTA IN THE NOSTRILS AND RECTUM OF AMAZONIAN MANATEES (TRICHECHUS INUNGUIS) FROM A REHABILITATION PROGRAM IN BRAZIL

The present study characterized the filamentous and yeast-like fungal microbiota of the nasal cavity and rectum of Amazonian manatees (Trichechus inunguis) undergoing rehabilitation at the Laboratory of Aquatic Mammals, National Institute of Amazonian Research, Manaus, Amazonas, and determined the antifungal susceptibility of these organisms. Nasal and rectal swabs were collected from 22 calves and three juveniles. The samples were seeded in Sabouraud agar supplemented with chloramphenicol 10%, incubated at 26°C, and observed daily for up to 7 d. The growth of different filamentous and yeast-like fungi was observed among the two anatomical sites. Filamentous fungi were categorized by macro- and microscopic characteristics of the colonies. Representatives of each group were selected for molecular identification based on the internal transcribed spacer region. Yeast identification was performed using MALDI-TOF MS and molecular analyses. Thirteen genera of filamentous fungi and six genera of yeasts were isolated and identified. The dominant filamentous species were Fusarium spp., Aspergillus spp., and Cochliobolus lunatus in the nostril samples and Aspergillus melleus in the rectal samples. Candida was the dominant genus among the identified yeasts at both anatomical sites. In the antifungal susceptibility test, 28 isolates showed resistance to fluconazole (78%), itraconazole (39%), and nystatin (42%). The knowledge of fungal microbiota composition of Amazonian manatees provides information that assists in monitoring the health status of individuals maintained in captivity, as these organisms can behave either as opportunists or as primary pathogens. Moreover, the composition and resistance of these organisms may vary among different rehabilitation institutions or different time frames of search, reinforcing the importance of constant in loco surveillance of these microorganisms. This study provides new perspectives on the fungal diversity in the microbiota of manatees and supports future studies concerning the clinical and epidemiological aspects and the impacts of these agents on the health of Amazonian manatees undergoing rehabilitation.

Turtle species and ecology drive carapace microbiome diversity in three seasonally interconnected wetland habitats

Different species of freshwater turtles exhibit primary behaviours ranging from aerial basking to benthic bottom-walking, cycle between wet and dry conditions at different time intervals, and undertake short-distance overland movements between aquatic habitats. These behaviours in turn may impact the accumulation of microbes on external shell surfaces of turtles and provide novel niches for differentiation of microbial communities. We assessed microbial diversity using 16S and 18S rRNA metabarcoding on carapace surfaces of six species of freshwater turtles residing in three adjacent and seasonally interconnected wetland habitats in southeast Oklahoma (United States). Communities were highly diverse, with nearly 4200 prokaryotic and 500 micro-eukaryotic amplicon sequence variants recovered, and included taxa previously reported as common or differentially abundant on turtle shells. The 16S rRNA alpha diversity tended to be highest for two species of benthic turtles, while 18S rRNA alpha diversity was highest for two basking and one shallow-water benthic species. Beta diversity of communities was more strongly differentiated by turtle species than by collection site, and ordination patterns were largely reflective of turtle species' primary habits (i.e. benthic, basking, or benthic-basking). Our data support that freshwater turtles could play a role in microbial ecology and evolution in freshwater habitats and warrant additional exploration including in areas with high native turtle diversity and inter-habitat turtle movements.

Fecal and skin microbiota of two rescued Mediterranean monk seal pups during rehabilitation

IMPORTANCE

This study showed that during the rehabilitation of two rescued Mediterranean monk seal pups (Monachus monachus), the skin and fecal bacterial communities showed similar succession patterns between the two individuals. This finding means that co-housed pups share their microbiomes, and this needs to be considered in cases of infection outbreaks and their treatment. The housing conditions, along with the feeding scheme and care protocols, including the admission of antibiotics as prophylaxis, probiotics, and essential food supplements, resulted in bacterial communities with no apparent pathogenic bacteria. This is the first contribution to the microbiome of the protected seal species of M. monachus and contributes to the animal's conservation practices through its microbiome.

Gene functions of the Ambystoma altamirani skin microbiome vary across space and time but potential antifungal genes are widespread and prevalent

Amphibian skin microbiomes can play a critical role in host survival against emerging diseases by protecting their host against pathogens. While a plethora of biotic and abiotic factors have been shown to influence the taxonomic diversity of amphibian skin microbiomes it remains unclear whether functional genomic diversity varies in response to temporal and environmental factors. Here we applied a metagenomic approach to evaluate whether seasonality, distinct elevations/sites, and pathogen presence influenced the functional genomic diversity of the A. altamirani skin microbiome. We obtained a gene catalogue of 92 107 nonredundant annotated genes and a set of 50 unique metagenome assembled genomes (MAGs). Our analysis showed that genes linked to general and potential antifungal traits significantly differed across seasons and sampling locations at different elevations. Moreover, we found that the functional genomic diversity of A. altamirani skin microbiome differed between B. dendrobatidis infected and not infected axolotls only during winter, suggesting an interaction between seasonality and pathogen infection. In addition, we identified the presence of genes and biosynthetic gene clusters (BGCs) linked to potential antifungal functions such as biofilm formation, quorum sensing, secretion systems, secondary metabolite biosynthesis, and chitin degradation. Interestingly genes linked to these potential antifungal traits were mainly identified in Burkholderiales and Chitinophagales MAGs. Overall, our results identified functional traits linked to potential antifungal functions in the A. altamirani skin microbiome regardless of variation in the functional diversity across seasons, elevations/sites, and pathogen presence. Our findings suggest that potential antifungal traits found in Burkholderiales and Chitinophagales taxa could be related to the capacity of A. altamirani to survive in the presence of Bd, although further experimental analyses are required to test this hypothesis.

Bat-associated microbes: Opportunities and perils, an overview

The potential biotechnological uses of bat-associated bacteria are discussed briefly, indicating avenues for biotechnological applications of bat-associated microbes. The uniqueness of bats in terms of their lifestyle, genomes and molecular immunology may predispose bats to act as disease reservoirs. Molecular phylogenetic analysis has shown several instances of bats harbouring the ancestral lineages of bacterial (Bartonella), protozoal (Plasmodium, Trypanosoma cruzi) and viral (SARS-CoV2) pathogens infecting humans. Along with the transmission of viruses from bats, we also discuss the potential roles of bat-associated bacteria, fungi, and protozoan parasites in emerging diseases. Current evidence suggests that environmental changes and interactions between wildlife, livestock, and humans contribute to the spill-over of infectious agents from bats to other hosts. Domestic animals including livestock may act as intermediate amplifying hosts for bat-origin pathogens to transmit to humans. An increasing number of studies investigating bat pathogen diversity and infection dynamics have been published. However, whether or how these infectious agents are transmitted both within bat populations and to other hosts, including humans, often remains unknown. Metagenomic approaches are uncovering the dynamics and distribution of potential pathogens in bat microbiomes, which might improve the understanding of disease emergence and transmission. Here, we summarize the current knowledge on bat zoonoses of public health concern and flag the gaps in the knowledge to enable further research and allocation of resources for tackling future outbreaks.

Diversity of gut microbiome in Rocky Mountainsnail across its native range

The animal gut microbiome is often a key requirement for host nutrition, digestion, and immunity, and can shift in relation to host geography and environmental factors. However, ecological drivers of microbiome community assembly across large geographic ranges have rarely been examined in invertebrates. Oreohelix strigosa (Rocky Mountainsnail) is a widespread land snail found in heterogeneous environments across the mountainous western United States. It is ideally suited for biogeography studies due to its broad distribution, low migration, and low likelihood of passive transport via other animals. This study aims to uncover large-scale geographic shifts in the composition of O. strigosa gut microbiomes by using 16S rRNA gene sequencing on samples from across its native range. Additionally, we elucidate smaller-scale microbiome variation using samples collected only within Colorado. Results show that gut microbiomes vary significantly across broad geographic ranges. Several possible ecological drivers, including soil and vegetation composition, habitat complexity, habitat type, and human impact, collectively explained 27% of the variation across Coloradan O. strigosa gut microbiomes. Snail gut microbiomes show more similarity to vegetation than soil microbiomes. Gut microbial richness was highest in the rocky habitats and increased significantly in the most disturbed habitats (low complexity, high human impact), potentially indicating signs of dysbiosis in the snails' gut microbiomes. These small-scale environmental factors may be driving changes in O. strigosa gut microbiome composition seen across large-scale geography. This knowledge will also help us better understand how microbial associations influence species survival in diverse environments and aid wildlife conservation efforts.

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

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

Toxicity effects of pesticides based on zebrafish (Danio rerio) models: Advances and perspectives

Pesticides inevitably enter aquatic environments, posing potential risks to organisms. The common aquatic model organism, zebrafish (Danio rerio), are widely used to evaluate the toxicity of pesticides. In this review, we searched the Web of Science database for articles published between 2012 and 2022, using the keywords "pesticide", "zebrafish", and "toxicity", retrieving 618 publications. Furthermore, we described the main pathways by which pesticides enter aquatic environments and the fate of their residues in these environments. We systematically reviewed the toxicity effects of pesticides on zebrafish, including developmental toxicity, endocrine-disrupting effects, reproductive toxicity, neurotoxicity, immunotoxicity, and genotoxicity. Importantly, we summarized the latest research progress on the toxicity mechanism of pesticides to zebrafish based on omics technologies, including transcriptomics, metabolomics, and microbiomics. Finally, we discussed future research prospects, focusing on the combined exposure of multiple pollutants including pesticides, the risk of multigenerational exposure to pesticides, and the chronic toxicity of aquatic nanopesticides. This review provides essential data support for ecological risk assessments of pesticides in aquatic environments, and has implications for water management in the context of pesticide pollution.

Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing

Asian elephant (Elephas maximus) is the national symbol of Thailand and linked to Thai history and culture for centuries. The elephant welfare improvement is one of the major components to achieve sustainable captive management. Microbiome inhabiting digestive tracts have been shown with symbiotic relations to host health. This work provided high-resolution microbiome profiles of 32 captive elephants at a species level by utilizing full-length 16S rRNA gene nanopore sequencing. Eleven common uncultured bacterial species were found across elephants fed with solid food including uncultured bacterium Rikenellaceae RC9 gut group, Kiritimatiellae WCHB1-41, Phascolarctobacterium, Oscillospiraceae NK4A214 group, Christensenellaceae R-7 group, Oribacterium, Oscillospirales UCG-010, Lachnospiraceae, Bacteroidales F082, uncultured rumen Rikenellaceae RC9 gut group, and Lachnospiraceae AC2044 group. We observed microbiome shifts along the age classes of baby (0-2 years), juvenile (2-10 years), and adult (> 10 years). Interestingly, we found distinct microbiome profiles among adult elephants fed with a local palm, Caryota urens, as a supplement. Potential beneficial microbes have been revealed according to the age classes and feed diets. The retrieved microbiome data could be provided as good baseline microbial profiles for monitoring elephant health, suggesting further studies towards dietary selection suitable for each age class and the use of local supplementary diets.

Conserved core microbiota in managed and free-ranging Loxodonta africana elephants

The gut microbiota plays a crucial role in animal health and homeostasis, particularly in endangered species conservation. This study investigated the fecal microbiota composition of European captive-bred African savanna elephants (Loxodonta africana) housed in French zoos, and compared it with wild African savanna elephants. Fecal samples were collected and processed for DNA extraction and amplicon sequencing of the 16S rRNA gene. The analysis of α and β diversity revealed significant effects of factors such as diet, daily activity, and institution on microbiota composition. Specifically, provision of branches as part of the diet positively impacted microbiota diversity. Comparative analyses demonstrated distinct differences between captive and wild elephant microbiomes, characterized by lower bacterial diversity and altered co-occurrence patterns in the captive population. Notably, specific taxa were differentially abundant in captive and wild elephants, suggesting the influence of the environment on microbiota composition. Furthermore, the study identified a core association network shared by both captive and wild elephants, emphasizing the importance of certain taxa in maintaining microbial interactions. These findings underscore the impact of environment and husbandry factors on elephant gut microbiota, highlighting the benefits of dietary enrichment strategies in zoos to promote microbiome diversity and health. The study contributes to the broader understanding of host-microbiota interactions and provides insights applicable to conservation medicine and captive animal management.

A systematic review of the microbial community in taiassuids: a One Health approach

Collared and white-lipped peccaries are sympatric and are distributed in most of South America and in the humid tropical forests of Mexico and Central America. Historically, these species have been used as a source of protein by traditional and/or indigenous human communities, but currently they have been used for legal consumption in different countries. Thus, there has been greater interaction between these wild species and domestic animals and humans, enabling microbial interactions between different niches. The present study presents a systematic review of the literature on the microbial community of collared peccaries and white-lipped peccaries distributed throughout the world, focusing on experimental studies related to the detection of microorganisms as well as the prevalence of the animal species and its characterization of the studied population, in situ or ex situ. Seventy-two studies were selected, mainly in South American countries, related to different species of microorganisms isolated or serologically detected (viruses, bacteria, fungi, and parasites), either as microbiota, pathogens or commensals, many of which are of zoonotic interest, such as Leptospira, Toxoplasma, Brucella, among others. Therefore, these wild mammals are characterized as sentinel agents of anthropic action and require the implementation of studies in relation to their contribution to the spread of microorganisms, being a potential source of amplification and transmission of pathogens.

Inter-comparison of marine microbiome sampling protocols

Research on marine microbial communities is growing, but studies are hard to compare because of variation in seawater sampling protocols. To help researchers in the inter-comparison of studies that use different seawater sampling methodologies, as well as to help them design future sampling campaigns, we developed the EuroMarine Open Science Exploration initiative (EMOSE). Within the EMOSE framework, we sampled thousands of liters of seawater from a single station in the NW Mediterranean Sea (Service d'Observation du Laboratoire Arago [SOLA], Banyuls-sur-Mer), during one single day. The resulting dataset includes multiple seawater processing approaches, encompassing different material-type kinds of filters (cartridge membrane and flat membrane), three different size fractionations (>0.22 µm, 0.22-3 µm, 3-20 µm and >20 µm), and a number of different seawater volumes ranging from 1 L up to 1000 L. We show that the volume of seawater that is filtered does not have a significant effect on prokaryotic and protist diversity, independently of the sequencing strategy. However, there was a clear difference in alpha and beta diversity between size fractions and between these and "whole water" (with no pre-fractionation). Overall, we recommend care when merging data from datasets that use filters of different pore size, but we consider that the type of filter and volume should not act as confounding variables for the tested sequencing strategies. To the best of our knowledge, this is the first time a publicly available dataset effectively allows for the clarification of the impact of marine microbiome methodological options across a wide range of protocols, including large-scale variations in sampled volume.

Influence of scat ageing on the gut microbiome: how old is too old?

BACKGROUND

The study of the host-microbiome by the collection of non-invasive samples has the potential to become a powerful tool for conservation monitoring and surveillance of wildlife. However, multiple factors can bias the quality of data recovered from scats, particularly when field-collected samples are used given that the time of defecation is unknown. Previous studies using scats have shown that the impact of aerobic exposure on the microbial composition is species-specific, leading to different rates of change in microbial communities. However, the impact that this aging process has on the relationship between the bacterial and fungal composition has yet to be explored. In this study, we measured the effects of time post-defecation on bacterial and fungal compositions in a controlled experiment using scat samples from the endangered koala (Phascolarctos cinereus).

RESULTS

We found that the bacterial composition remained stable through the scat aging process, while the fungal composition did not. The absence of an increase in facultative anaerobes and the stable population of obligate anaerobic bacteria were likely due to our sampling from the inner portion of the scat. We report a cluster of fungal taxa that colonises scats after defecation which can dilute the genetic material from the autochthonous mycoflora and inhibit recovery.

CONCLUSION

We emphasize the need to preserve the integrity of scat samples collected in the wild and combat the effects of time and provide strategies for doing so.

Influence of native and exotic plant diet on the gut microbiome of the Gray's Malayan stick insect, Lonchodes brevipes

Herbivorous insects require an active lignocellulolytic microbiome to process their diet. Stick insects (phasmids) are common in the tropics and display a cosmopolitan host plant feeding preference. The microbiomes of social insects are vertically transmitted to offspring, while for solitary species, such as phasmids, it has been assumed that microbiomes are acquired from their diet. This study reports the characterization of the gut microbiome for the Gray's Malayan stick insect, Lonchodes brevipes, reared on native and introduced species of host plants and compared to the microbiome of the host plant and surrounding soil to gain insight into possible sources of recruitment. Clear differences in the gut microbiome occurred between insects fed on native and exotic plant diets, and the native diet displayed a more species-rich fungal microbiome. While the findings suggest that phasmids may be capable of adapting their gut microbiome to changing diets, it is uncertain whether this may lead to any change in dietary efficiency or organismal fitness. Further insight in this regard may assist conservation and management decision-making.

Keady M, Lim HC. Honey bees and bumble bees occupying the same landscape have distinct gut microbiomes and amplicon sequence variant-level responses to infections

The gut microbiome of bees is vital for the health of their hosts. Given the ecosystem functions performed by bees, and the declines faced by many species, it is important to improve our understanding of the amount of natural variation in the gut microbiome, the level of sharing of bacteria among co-occurring species (including between native and non-native species), and how gut communities respond to infections. We conducted 16S rRNA metabarcoding to discern the level of microbiome similarity between honey bees (Apis mellifera, N = 49) and bumble bees (Bombus spp., N = 66) in a suburban-rural landscape. We identified a total of 233 amplicon sequence variants (ASVs) and found simple gut microbiomes dominated by bacterial taxa belonging to Gilliamella, Snodgrassella, and Lactobacillus. The average number of ASVs per species ranged from 4.00-15.00 (8.79 ± 3.84, mean ± SD). Amplicon sequence variant of one bacterial species, G. apicola (ASV 1), was widely shared across honey bees and bumble bees. However, we detected another ASV of G. apicola that was either exclusive to honey bees, or represented an intra-genomic 16S rRNA haplotype variant in honey bees. Other than ASV 1, honey bees and bumble bees rarely share gut bacteria, even ones likely derived from outside environments (e.g., Rhizobium spp., Fructobacillus spp.). Honey bee bacterial microbiomes exhibited higher alpha diversity but lower beta and gamma diversities than those of bumble bees, likely a result of the former possessing larger, perennial hives. Finally, we identified pathogenic or symbiotic bacteria (G. apicola, Acinetobacter sp. and Pluralibacter sp.) that associate with Trypanosome and/or Vairimorpha infections in bees. Such insights help to determine bees' susceptibility to infections should gut microbiomes become disrupted by chemical pollutants and contribute to our understanding of what constitutes a state of dysbiosis.

Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes

Microorganisms are ubiquitous in nature and form complex community networks to survive in various environments. This community structure depends on numerous factors like nutrient availability, abiotic factors like temperature and pH as well as microbial composition. Categorising accessible biomes according to their habitats would help in understanding the complexity of the environment-specific communities. Owing to the recent improvements in sequencing facilities, researchers have started to explore diverse microbiomes rapidly and attempts have been made to study microbial crosstalk. However, different metagenomics sampling, preprocessing, and annotation methods make it difficult to compare multiple studies and hinder the recycling of data. Huge datasets originating from these experiments demand systematic computational methods to extract biological information beyond microbial compositions. Further exploration of microbial co-occurring patterns across the biomes could help us in designing cross-biome experiments. In this review, we catalogue databases with system-specific microbiomes, discussing publicly available common databases as well as specialised databases for a range of microbiomes. If the new datasets generated in the future could maintain at least biome-specific annotation, then researchers could use those contemporary tools for relevant and bias-free analysis of complex metagenomics data.

Composition and function of the Galapagos penguin gut microbiome vary with age, location, and a putative bacterial pathogen

Microbial colonization plays a direct role in host health. Understanding the ecology of the resident microbial community for a given host species is thus an important step for detecting population vulnerabilities like disease. However, the idea of integrating microbiome research into conservation is still relatively new, and wild birds have received less attention in this field than mammals or domesticated animals. Here we examine the composition and function of the gut microbiome of the endangered Galapagos penguin (Spheniscus mendiculus) with the goals of characterizing the normal microbial community and resistome, identifying likely pathogens, and testing hypotheses of structuring forces for this community based on demographics, location, and infection status. We collected fecal samples from wild penguins in 2018 and performed 16S rRNA gene sequencing and whole genome sequencing (WGS) on extracted DNA. 16S sequencing revealed that the bacterial phyla Fusobacteria, Epsilonbacteraeota, Firmicutes, and Proteobacteria dominate the community. Functional pathways were computed from WGS data, showing genetic functional potential primarily focused on metabolism-amino acid metabolism, carbohydrate metabolism, and energy metabolism are the most well-represented functional groups. WGS samples were each screened for antimicrobial resistance, characterizing a resistome made up of nine antibiotic resistance genes. Samples were screened for potential enteric pathogens using virulence factors as indicators; Clostridium perfringens was revealed as a likely pathogen. Overall, three factors appear to be shaping the alpha and beta diversity of the microbial community: penguin developmental stage, sampling location, and C. perfringens. We found that juvenile penguins have significantly lower alpha diversity than adults based on three metrics, as well as significantly different beta diversity. Location effects are minimal, but one site has significantly lower Shannon diversity than the other primary sites. Finally, when samples were grouped by C. perfringens virulence factors, we found dramatic changes in beta diversity based on operational taxonomic units, protein families, and functional pathways. This study provides a baseline microbiome for an endangered species, implicates both penguin age and the presence of a potential bacterial pathogen as primary factors associated with microbial community variance, and reveals widespread antibiotic resistance genes across the population.

Current levels of microplastic pollution impact wild seabird gut microbiomes

Microplastics contaminate environments worldwide and are ingested by numerous species, whose health is affected in multiple ways. A key dimension of health that may be affected is the gut microbiome, but these effects are relatively unexplored. Here, we investigated if microplastics are associated with changes in proventricular and cloacal microbiomes in two seabird species that chronically ingest microplastics: northern fulmars and Cory's shearwaters. The amount of microplastics in the gut was significantly correlated with gut microbial diversity and composition: microplastics were associated with decreases in commensal microbiota and increases in (zoonotic) pathogens and antibiotic-resistant and plastic-degrading microbes. These results illustrate that environmentally relevant microplastic concentrations and mixtures are associated with changes in gut microbiomes in wild seabirds.

A parasitic nematode induces dysbiosis in susceptible but not resistant gastropod hosts

Animals’ gut microbiomes affect a wide array of biological processes including immunity and protection from pathogens. However, how the microbiome changes due to infection by parasites is still largely unknown, as is how the microbiome changes in hosts that differ in their susceptibility to parasites. To investigate this, we exposed two slug species of differing susceptibility to the parasitic nematode Phasmarhabditis hermaphrodita (Deroceras reticulatum is highly susceptible and Ambigolimax valentianus resistant to the nematode) and profiled the gut microbiota after 7 and 14 days. Before infection, both slug species’ microbiota was dominated by similar bacterial genera: Pseudomonas (by far the most abundant), Sphingobacterium, Pedobacter, Chryseobacterium, and Flavobacterium. In the resistant host A. valentianus, there was no significant change in the bacterial genera after infection, but in D. reticulatum, the bacterial profile changed, with a decrease in the abundance of Pseudomonadaceae and an increase in the abundance of Flavobacteriaceae and Sphingobacteriaceae after 7 days postinfection. This suggests nematode infection causes dysbiosis in hosts that are susceptible to infection, but the microbiome of resistant species remains unaltered. In summary, the regulation of the immune system is tightly linked with host survival, and nematode infection can alter the microbiome structure.

First insights into the gut microbiomes and the diet of the Littorina snail ecotypes, a recently emerged marine evolutionary model

Microbes can play a prominent role in the evolution of their hosts, facilitating adaptation to various environments and promoting ecological divergence. The Wave and Crab ecotypes of the intertidal snail Littorina saxatilis is an evolutionary model of rapid and repeated adaptation to environmental gradients. While patterns of genomic divergence of the Littorina ecotypes along the shore gradients have been extensively studied, their microbiomes have been so far overlooked. The aim of the present study is to start filling this gap by comparing gut microbiome composition of the Wave and Crab ecotypes using metabarcoding approach. Since Littorina snails are micro-grazers feeding on the intertidal biofilm, we also compare biofilm composition (i.e. typical snail diet) in the crab and wave habitats. In the results, we found that bacterial and eukaryotic biofilm composition varies between the typical habitats of the ecotypes. Further, the snail gut bacteriome was different from outer environments, being dominated by Gammaproteobacteria, Fusobacteria, Bacteroidia and Alphaproteobacteria. There were clear differences in the gut bacterial communities between the Crab and the Wave ecotypes as well as between the Wave ecotype snails from the low and high shores. These differences were both observed in the abundances and in the presence of different bacteria, as well as at different taxonomic level, from bacterial OTU's to families. Altogether, our first insights show that Littorina snails and their associated bacteria are a promising marine system to study co-evolution of the microbes and their hosts, which can help us to predict the future for wild species in the face of rapidly changing marine environments.

The role of Drosophila microbiota in gut homeostasis and immunity

The gut epithelia of virtually all animals harbor complex microbial communities that play an important role in maintaining immune and cellular homeostasis. Gut microbiota have evolutionarily adapted to the host gut environment, serving as key regulators of intestinal stem cells to promote a healthy gut barrier and modulate epithelial self-renewal. Disruption of these populations has been associated with inflammatory disorders or cancerous lesions of the intestine. However, the molecular mechanisms controlling gut-microbe interactions are only partially understood due to the high diversity and biologically dynamic nature of these microorganisms. This article reviews the current knowledge on Drosophila gut microbiota and its role in signaling pathways that are crucial for the induction of distinct homeostatic and immune responses. Thanks to the genetic tractability of Drosophila and its cultivable and simple microbiota, this association model offers new efficient tools for investigating the crosstalk between a host and its microbiota while providing a framework for a better understanding of the ecological and evolutionary roles of the microbiome.

The skin microbiota of the axolotl Ambystoma altamirani is highly influenced by metamorphosis and seasonality but not by pathogen infection

BACKGROUND

Microbiomes have been increasingly recognized as major contributors to host health and survival. In amphibians, bacterial members of the skin microbiota protect their hosts by inhibiting the growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). Even though several studies describe the influence of biotic and abiotic factors over the skin microbiota, it remains unclear how these symbiotic bacterial communities vary across time and development. This is particularly relevant for species that undergo metamorphosis as it has been shown that host physiology and ecology drastically influence diversity of the skin microbiome.

RESULTS

We found that the skin bacterial communities of the axolotl A. altamirani are largely influenced by the metamorphic status of the host and by seasonal variation of abiotic factors such as temperature, pH, dissolved oxygen and conductivity. Despite high Bd prevalence in these samples, the bacterial diversity of the skin microbiota did not differ between infected and non-infected axolotls, although relative abundance of particular bacteria were correlated with Bd infection intensity.

CONCLUSIONS

Our work shows that metamorphosis is a crucial process that shapes skin bacterial communities and that axolotls under different developmental stages respond differently to environmental seasonal variations. Moreover, this study greatly contributes to a better understanding of the factors that shape amphibian skin microbiota, especially in a largely underexplored group like axolotls (Mexican Ambystoma species).

Host diet shapes functionally differentiated gut microbiomes in sympatric speciation of blind mole rats in Upper Galilee, Israel

The gut microbiome is important for host nutrient metabolism and ecological adaptation. However, how the gut microbiome is affected by host phylogeny, ecology and diet during sympatric speciation remain unclear. Here, we compare and contrast the gut microbiome of two sympatric blind mole rat species and correlate them with their corresponding host phylogeny, ecology soil metagenomes, and diet to determine how these factors may influence their gut microbiome. Our results indicate that within the host microbiome there is no significant difference in community composition, but the functions between the two sympatric species populations vary significantly. No significant correlations were found between the gut microbiome differentiation and their corresponding ecological soil metagenomes and host phylogeny. Functional enrichment analysis suggests that the host diets may account for the functional divergence of the gut microbiome. Our results will help us understand how the gut microbiome changes with corresponding ecological dietary factors in sympatric speciation of blind subterranean mole rats.

Invasive Amphibian Gut Microbiota and Functions Shift Differentially in an Expanding Population but Remain Conserved Across Established Populations

Studies of laboratory animals demonstrate extensive variation of host gut microbiomes and their functional capabilities across populations, but how does anthropogenic change impact the microbiomes of non-model species? The anthropogenic movement of species to novel environments can drastically alter animals' microbiomes; however, factors that shape invasive species gut microbiota during introduction remain relatively unexplored. Through 16S amplicon sequencing on guttural toad (Sclerophrys gutturalis) faecal samples, we determine that residence time does not impact microbiome variation between source and introduced populations. The youngest population (~ 20 years in Cape Town) has the most distinct microbiome and associated functional capabilities, whereas longer residence times (~ 100 years in Réunion and Mauritius) produce less divergent microbial compositional, phylogenetic, and predicted functional diversity and differential abundance from source populations (Durban). Additionally, we show extensive variation of microbial and functional diversity, as well as differential abundance patterns in an expanding introduced population (Cape Town) between core and periphery sites. Contrasting previous studies, we suggest that introduction pathways might be an important factor impacting host microbial divergence. These findings also imply that the microbiome can diverge in accordance with host population dynamics.

Gut microbial ecology of Philippine gekkonids: ecoevolutionary effects on microbiome compositions

Given the rapidly changing landscapes of habitats across the globe, a sound understanding of host-associated microbial communities and the ecoevolutionary forces that shape them is needed to assess general organismal adaptability. Knowledge of the symbiotic endogenous microbiomes of most reptilian species worldwide remains limited. We sampled gut microbiomes of geckos spanning nine species and four genera in the Philippines to (i) provide baseline data on gut microbiota in these host species, (ii) test for significant associations between host phylogenetic relationships and observed microbial assemblages, potentially indicative of phylosymbiosis, and (iii) identify correlations between multiple ecoevolutionary factors (e.g. species identity, habitat tendencies, range extents, and maximum body sizes) and gut microbiomes in Philippine gekkonids. We recovered no significant association between interspecific host genetic distances and observed gut microbiomes, providing limited evidence for phylosymbiosis in this group. Philippine gekkonid microbiomes were associated most heavily with host species identity, though marked variation among conspecifics at distinct sampling sites indicates that host locality influences gut microbiomes as well. Interestingly, individuals grouped as widespread and microendemic regardless of host species identity displayed significant differences in alpha and beta diversity metrics examined, likely driven by differences in rare OTU presence between groups. These results provide much needed insight in host-associated microbiomes in wild reptiles and the ecoevolutionary forces that structure such communities.

The cloacal microbiome of a cavity-nesting raptor, the lesser kestrel (Falco naumanni)

Background

Microbial communities are found on any part of animal bodies exposed to the environment, and are particularly prominent in the gut, where they play such a major role in the host metabolism and physiology to be considered a "second genome". These communities, collectively known as "microbiome", are well studied in humans and model species, while studies on wild animals have lagged behind. This is unfortunate, as different studies suggested the central role of the gut microbiome in shaping the evolutionary trajectories of species and their population dynamics. Among bird species, only few descriptions of raptor gut microbiomes are available, and mainly carried out on captive individuals.

Objectives

In this study, we aimed at improving the knowledge of raptor microbiomes by providing the first description of the gut microbiome of the lesser kestrel (Falco naumanni), a cavity-nesting raptor.

Results

The gut microbiome of the lesser kestrel was dominated by Actinobacteria (83.9%), Proteobacteria (8.6%) and Firmicutes (4.3%). We detected no differences in microbiome composition between males and females. Furthermore, the general composition of the microbiome appears similar to that of phylogenetically distant cavity-nesting species.

Conclusions

Our results broaden the knowledge of raptor gut microbial communities and let us hypothesize that the distinct nest environment in terms of microclimate and presence of organic material from previous breeding attempts, to which cavity-nesting species that reuse the nest are exposed, might be an important driver shaping microbiomes.

Sustained Drought, but Not Short-Term Warming, Alters the Gut Microbiomes of Wild Anolis Lizards

As rising temperatures threaten biodiversity across the globe, tropical ectotherms are thought to be particularly vulnerable due to their narrow thermal tolerance ranges. Nevertheless, physiology-based models highlighting the vulnerability of tropical organisms rarely consider the contributions of their gut microbiota, even though microbiomes influence numerous host traits, including thermal tolerance. We combined field and lab experiments to understand the response of the slender anole lizard (Anolis apletophallus) gut microbiome to climatic shifts of various magnitude and duration. First, to examine the effects of long-term climate warming in the wild, we transplanted lizards from the mainland Panama to a series of warmer islands in the Panama Canal and compared their gut microbiome compositions after three generations of divergence. Next, we mimicked the effects of a short-term "heat-wave" by using a greenhouse experiment and explored the link between gut microbiome composition and lizard thermal physiology. Finally, we examined variation in gut microbiomes in our mainland population in the years both before and after a naturally occurring drought. Our results suggest that slender anole microbiomes are surprisingly resilient to short-term warming. However, both the taxonomic and predicted functional compositions of the gut microbiome varied by sampling year across all sites, suggesting that the drought may have had a regional effect. We provide evidence that short-term heat waves may not substantially affect the gut microbiota, while more sustained climate anomalies may have effects at broad geographic scales. IMPORTANCE As climate change progresses, it is crucial to understand how animals will respond to shifts in their local environments. One component of this response involves changes in the microbial communities living in and on host organisms. These "microbiomes" can affect many processes that contribute to host health and survival, yet few studies have measured changes in the microbiomes of wild organisms experiencing novel climatic conditions. We examined the effects of shifting climates on the gut microbiome of the slender anole lizard (Anolis apletophallus) by using a combination of field and laboratory studies, including transplants to warm islands in the Panama Canal. We found that slender anole microbiomes remain stable in response to short-term warming but may be sensitive to sustained climate anomalies, such as droughts. We discuss the significance of these findings for a species that is considered highly vulnerable to climate change.

Fungal signatures of oral disease reflect environmental degradation in a facultative avian scavenger

Degradation of natural ecosystems increases the risk of infections in wildlife due to microbiota dysbiosis. However, little is known about its influence on the development of fungal communities in predators and facultative avian scavengers. We evaluated the incidence of oral disease in wild nestling black kites (Milvus migrans) under contrasting environmental degradation conditions, and explored their oral fungal patterns using molecular methods and multivariate analysis. Oral lesions were found in 36.8% of the 38 nestlings examined in an anthropogenically altered habitat (southeastern Madrid, Spain), but in none of the 105 nestlings examined in a well-conserved natural area (Doñana National Park, Spain). In a subsample of 48 black kites, the composition of the oral fungal community differed among symptomatic nestlings from Madrid (SM) and asymptomatic nestlings from Madrid (AM) and Doñana (AD). Opportunistic fungal pathogens (e.g., Fusarium incarnatum-equiseti species complex, Mucor spp., Rhizopus oryzae) were more prevalent in SM and AM than in AD. Hierarchical clustering and principal component analyses revealed that fungal patterns were distinct between both study areas, and that anthropogenic and natural environmental factors had a greater impact on them than oral disease. Fungal signatures associated with anthropogenic and natural stresses harbored some taxa that could be used to flag oral infection (F. incarnatum-equiseti species complex and Alternaria), indicate environmental degradation (Alternaria) or provide protective benefits in degraded environments (Trichoderma, Epicoccum nigrum and Sordaria). Co-occurrence associations between potentially beneficial and pathogenic fungi were typical of AM and AD, hinting at a possible role in host health. This study shows that early-life exposure to highly degraded environments induces a shift towards a higher prevalence of pathogenic species in the oral cavity of black kites, favoring oral disease. Furthermore, our findings suggest potential ecological applications of the monitoring of oral mycobiome as a bioindication of oral disease and environmental degradation.

First Report of Culturable Skin Bacteria in Melanophryniscus admirabilis (Admirable Redbelly Toad)

Melanophryniscus admirabilis is a small toad, critically endangered with a microendemic distribution in the Atlantic Forest in southern Brazil. The amphibian skin microbiome is considered one of the first lines of defense against pathogenic infections, such as Batrachochytrium dendrobatidis (Bd). The knowledge of skin amphibian microbiomes is important to numerous fields, including species conservation, detection, and quantification of environmental changes and stressors. In the present study, we investigated, for the first time, cultivable bacteria in the skin of wild M. admirabilis, and detected Bd fungus by nested polymerase chain reaction (PCR) technique. Skin swab samples were collected from 15 wild M. admirabilis, and the isolation of bacteria was performed by means of different culture strategies. A total of 62 bacterial isolates being Bacillus (n = 22; 34.48%), Citrobacter (n = 10; 16.13%), and Serratia (n = 12; 19.35%) were more frequently isolated genera. Interestingly, all skin samples tested were Bd negative. Some bacterial genera identified in our study might be acting in a synergic relationship and protecting them against the Bd fungus. In addition, these bacteria may play an essential role in maintaining this species in an environment modulated by anthropic actions. This first report of skin cultivable bacteria from M. admirabilis natural population improves our knowledge of skin amphibian microbiomes, contributing to a better understanding of their ecology and how this species has survived in an environment modulated by anthropic action.

Microbiome Research as an Effective Driver of Success Stories in Agrifood Systems – A Selection of Case Studies

Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describe products, methodologies, applications, tools, and processes that created an economic and societal impact. Additionally, they cover a broad range of fields within the agrifood chain: the management of diseases and putative pathogens; the use of microorganism as soil fertilizers and plant strengtheners; the investigation of the microbial dynamics occurring during food fermentation; the presence of microorganisms and/or genes associated with hazards for animal and human health (e.g., mycotoxins, spoilage agents, or pathogens) in feeds, foods, and their processing environments; applications to improve HACCP systems; and the identification of novel probiotics and prebiotics to improve the animal gut microbiome or to prevent chronic non-communicable diseases in humans (e.g., obesity complications). The microbiomes of soil, plants, and animals are pivotal for ensuring human and environmental health and this review highlights the impact that microbiome applications have with this regard.

Characterising the Gut Microbiomes in Wild and Captive Short-Beaked Echidnas Reveals Diet-Associated Changes

The gut microbiome plays a vital role in health and wellbeing of animals, and an increasing number of studies are investigating microbiome changes in wild and managed populations to improve conservation and welfare. The short-beaked echidna (Tachyglossus aculeatus) is an iconic Australian species, the most widespread native mammal, and commonly held in zoos. Echidnas are cryptic animals, and much is still unknown about many aspects of their biology. Furthermore, some wild echidna populations are under threat, while echidnas held in captivity can have severe gastric health problems. Here, we used citizen science and zoos to collect echidna scats from across Australia to perform the largest gut microbiome study on any native Australian animal. Using 16S rRNA gene metabarcoding of scat samples, we characterised and compared the gut microbiomes of echidnas in wild (n = 159) and managed (n = 44) populations, which were fed four different diets. Wild echidna samples were highly variable, yet commonly dominated by soil and plant-fermenting bacteria, while echidnas in captivity were dominated by gut commensals and plant-fermenting bacteria, suggesting plant matter may play a significant role in echidna diet. This work demonstrates significant differences between zoo held and wild echidnas, as well as managed animals on different diets, revealing that diet is important in shaping the gut microbiomes in echidnas. This first analysis of echidna gut microbiome highlights extensive microbial diversity in wild echidnas and changes in microbiome composition in managed populations. This is a first step towards using microbiome analysis to better understand diet, gastrointestinal biology, and improve management in these iconic animals.

Gut microbiome of century-old snail specimens stable across time in preservation

BACKGROUND

Museum biological specimens provide a unique means of gathering ecological information that spans wide temporal ranges. Museum specimens can also provide information on the microbial communities that persist within the host specimen. Together, these provide researchers valuable opportunities to study long-term trends and mechanisms of microbial community change. The effects of decades-long museum preservation on host-microbial communities have not been systematically assessed. The University of Colorado's Museum of Natural History has densely sampled Oreohelix strigosa (Rocky Mountainsnail) for the past century; many are preserved in ethanol, which provides an excellent opportunity to explore how the microbiome changes across time in preservation.

RESULTS

We used 16S rRNA (ribosomal ribonucleic acid) gene amplicon sequencing to examine Oreohelix strigosa gut microbiomes from museum specimens across a 98-year range, as well as within short-term preservation treatments collected in 2018. Treatment groups included samples extracted fresh, without preservation; samples starved prior to extraction; and samples preserved for 1 month, 6 months, and 9 months. General microbiome composition was similar across all years. Sample groups belonging to specific years, or specific short-term treatments, showed unique associations with select bacterial taxa. Collection year was not a significant predictor of microbial richness, though unpreserved short-term treatments showed significantly higher richness than preserved treatments. While the year was a significant factor in microbiome composition, it did not explain much of the variation across samples. The location was a significant driver of community composition and explained more of the variability.

CONCLUSIONS

This study is the first to examine animal host-associated microbiome change across a period of nearly one century. Generally, geographic location was a greater factor in shaping gut microbiome composition, rather than a year collected. Consistent patterns across this temporal range indicate that historic specimens can answer many ecological questions surrounding the host-associated microbiome. Video Abstract.

Anthropogenic Disturbance Impacts Gut Microbiome Homeostasis in a Malagasy Primate

Increasing anthropogenic disturbances in Madagascar are exerting constrains on endemic Malagasy lemurs and their habitats, with possible effects on their health and survival. An important component of health is the gut microbiome, which might be disrupted by various stressors associated with environmental change. We have studied the gut microbiome of gray-brown mouse lemurs (Microcebus griseorufus), one of the smallest Malagasy primates and an important model of the convergent evolution of diseases. We sampled two sites: one situated in a national park and the other consisting of a more disturbed site around human settlement. We found that more intense anthropogenic disturbances indeed disrupted the gut microbiome of this lemur species marked by a reduction in bacterial diversity and a shift in microbial community composition. Interestingly, we noted a decrease in beneficial bacteria (i.e., members of the Bacteroidaceae family) together with a slight increase in disease-associated bacteria (i.e., members of the Veillonellaceae family), and alterations in microbial metabolic functions. Because of the crucial services provided by the microbiome to pathogen resistance and host health, such negative alterations in the gut microbiome of mouse lemurs inhabiting anthropogenically disturbed habitats might render them susceptible to diseases and ultimately affecting their survival in the shrinking biodiversity seen in Madagascar. Gut microbiome analyses might thus serve as an early warning signal for pending threats to lemur populations.

Do amino and fatty acid profiles of pollen provisions correlate with bacterial microbiomes in the mason bee Osmia bicornis?

Bee performance and well-being strongly depend on access to sufficient and appropriate resources, in particular pollen and nectar of flowers, which constitute the major basis of bee nutrition. Pollen-derived microbes appear to play an important but still little explored role in the plant pollen-bee interaction dynamics, e.g. through affecting quantities and ratios of important nutrients. To better understand how microbes in pollen collected by bees may affect larval health through nutrition, we investigated correlations between the floral, bacterial and nutritional composition of larval provisions and the gut bacterial communities of the solitary megachilid bee Osmia bicornis. Our study reveals correlations between the nutritional quality of pollen provisions and the complete bacterial community as well as individual members of both pollen provisions and bee guts. In particular pollen fatty acid profiles appear to interact with specific members of the pollen bacterial community, indicating that pollen-derived bacteria may play an important role in fatty acid provisioning. As increasing evidence suggests a strong effect of dietary fatty acids on bee performance, future work should address how the observed interactions between specific fatty acids and the bacterial community in larval provisions relate to health in O. bicornis. This article is part of the theme issue 'Natural processes influencing pollinator health: from chemistry to landscapes'.

The Gut Microbiome of 54 Mammalian Species

The gut microbiome plays a critical role in many aspects of host life, and the microbial community composition is heavily influenced by the prevailing conditions in the gut environment. Community composition has been suggested to have large implications for conservation efforts, and gut health has become of interest for optimizing animal care in captivity. In this study, we explore the gut microbiome of a wide range of animals in the context of conservation biology. The composition of the gut microbial community of 54 mammalian animal species was investigated using 16S rRNA gene amplicon sequencing. The composition of the gut microbiota clearly reflects diet and the structure of the gastrointestinal system, and it is to a certain degree more similar between closely related animals. Specific clusters of taxa were observed across animals of the same species, diet, and gut morphology. The microbiota retained regardless of captivity status is hypothesized to cover important symbiotic relationships with the host, while the remaining part reflects the artificial living conditions and can therefore be used as a future tool for conservation biologists. For five animal species (giraffes, horses, baboons, elephants, and zebras), it was possible to compare the microbiota of wild and captive individuals. Differences were observed in the proportion of microbiota detected between wild and captive specimens of the same animal species. We propose that the gut microbiota harbours important species, which can potentially serve as indicators for the well-being of the animal and the effect of living in captivity.

Egg microbiota is the starting point of hatchling gut microbiota in the endangered yellow-spotted Amazon river turtle

Establishment and development of gut microbiota during vertebrates' early life are likely to be important predictors of health and fitness. Host-parental and host-environment interactions are essential to these processes. In oviparous reptiles whose nests represent a source of the parent's microbial inocula, the relative role of host-selection and stochastic environmental factors during gut microbial assemblage remains unknown. We sampled eggs incubated in artificial nests as well as hatchlings and juveniles (up to 30 days old) of the yellow-spotted Amazon river turtle (Podocnemis unifilis) developing in tubs filled with river water. We examined the relative role of the internal egg microbiota and the abiotic environment on hatchling and juvenile turtle's cloacal microbiota assemblages during the first 30 days of development. A mean of 71% of ASVs in hatched eggs could be traced to the nest environmental microbiota and in turn a mean of 77% of hatchlings' cloacal ASVs were traced to hatched eggs. Between day 5 and 20 of juvenile turtle's development, the river water environment plays a key role in the establishment of the gut microbiota (accounting for a mean of 13%-34.6% of cloacal ASVs) and strongly influences shifts in microbial diversity and abundance. After day 20, shifts in gut microbiota composition were mainly driven by host-selection processes. Therefore, colonization by environmental microbiota is key in the initial stages of establishing the host's gut microbiota which is subsequently shaped by host-selection processes. Our study provides a novel quantitative understanding of the host-environment interactions during gut microbial assemblage of oviparous reptiles.

Population bottlenecks constrain host microbiome diversity and genetic variation impeding fitness

It is becoming increasingly clear that microbial symbionts influence key aspects of their host’s fitness, and vice versa. This may fundamentally change our thinking about how microbes and hosts interact in influencing fitness and adaptation to changing environments. Here we explore how reductions in population size commonly experienced by threatened species influence microbiome diversity. Consequences of such reductions are normally interpreted in terms of a loss of genetic variation, increased inbreeding and associated inbreeding depression. However, fitness effects of population bottlenecks might also be mediated through microbiome diversity, such as through loss of functionally important microbes. Here we utilise 50 Drosophila melanogaster lines with different histories of population bottlenecks to explore these questions. The lines were phenotyped for egg-to-adult viability and their genomes sequenced to estimate genetic variation. The bacterial 16S rRNA gene was amplified in these lines to investigate microbial diversity. We found that 1) host population bottlenecks constrained microbiome richness and diversity, 2) core microbiomes of hosts with low genetic variation were constituted from subsets of microbiomes found in flies with higher genetic variation, 3) both microbiome diversity and host genetic variation contributed to host population fitness, 4) connectivity and robustness of bacterial networks was low in the inbred lines regardless of host genetic variation, 5) reduced microbial diversity was associated with weaker evolutionary responses of hosts in stressful environments, and 6) these effects were unrelated to Wolbachia density. These findings suggest that population bottlenecks reduce hologenomic variation (combined host and microbial genetic variation). Thus, while the current biodiversity crisis focuses on population sizes and genetic variation of eukaryotes, an additional focal point should be the microbial diversity carried by the eukaryotes, which in turn may influence host fitness and adaptability with consequences for the persistence of populations.

It is becoming increasingly clear that organisms and the microbes that live on or in them–their microbiome–affect each other in profound ways that we are just beginning to understand. For instance, a diverse microbiome can help maintain metabolic functions or fight pathogens causing diseases. A disrupted microbiome may be especially critical for animals and plants that occur in low numbers because of threats from e.g. human exploitation or climate change, as they may already suffer from genetic challenges such as inbreeding and reduced evolutionary potential. The importance of such a reduction in population size, called a bottleneck, on the microbial diversity and the potential interactive effects on host health remains unexplored. Here we experimentally test these associations by investigating the microbiomes of 50 inbred or non-inbred populations of vinegar flies. We found that restricting the population size constrain the host’s genetic variation and simultaneously decreases the diversity of the microbiome that they harbor, and that both effects were detrimental to host fitness. The microbial communities in inbred host populations were less robust than in their non-inbred counterparts, suggesting that we should increasingly consider the microbiome diversity, which may ultimately influence the health and persistence of threatened species.

Genomics and Informatics, Conjoined Tools Vital for Understanding and Protecting Plant Health

Genomics' impact on crop production continuously expands. The number of sequenced plant and microbial species and strains representing diverse populations of individual species rapidly increases thanks to the advent of next-generation sequencing technologies. Their genomic blueprints revealed candidate genes involved in various functions and processes crucial for crop health and helped in understanding how the sequenced organisms have evolved at the genome level. Functional genomics quickly translates these blueprints into a detailed mechanistic understanding of how such functions and processes work and are regulated; this understanding guides and empowers efforts to protect crops from diverse biotic and abiotic threats. Metagenome analyses help identify candidate microbes crucial for crop health and uncover how microbial communities associated with crop production respond to environmental conditions and cultural practices, presenting opportunities to enhance crop health by judiciously configuring microbial communities. Efficient conversion of disparate types of massive genomics data into actionable knowledge requires a robust informatics infrastructure supporting data preservation, analysis, and sharing. This review starts with an overview of how genomics came about and has quickly transformed life science. We illuminate how genomics and informatics can be applied to investigate various crop health-related problems using selected studies. We end the review by noting why community empowerment via crowdsourcing is crucial to harnessing genomics to protect global food and nutrition security without continuously expanding the environmental footprint of crop production.

Research Progress of the Gut Microbiome in Hybrid Fish

Fish, including hybrid species, are essential components of aquaculture, and the gut microbiome plays a vital role in fish growth, behavior, digestion, and immune health. The gut microbiome can be affected by various internal and/or external factors, such as host development, diet, and environment. We reviewed the effects of diet and dietary supplements on intestinal microorganisms in hybrid fish and the difference in the gut microbiome between the hybrid and their hybrids that originate. Then, we summarized the role of the gut microbiome in the speciation and ecological invasion of hybrid fish. Finally, we discussed possible future studies on the gut microbiome in hybrid fish, including the potential interaction with environmental microbiomes, the effects of the gut microbiome on population expansion, and fish conservation and management.

Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea)

The Asian clam Corbicula fluminea (Family: Cyneridae) has aggressively invaded freshwater habitats worldwide, resulting in dramatic ecological changes and declines of native bivalves such as freshwater mussels (Family: Unionidae), one of the most imperiled faunal groups. Despite increases in our knowledge of invasive C. fluminea biology, little is known of how intrinsic and extrinsic factors, including co-occurring native species, influence its microbiome. We investigated the gut bacterial microbiome across genetically differentiated populations of C. fluminea in the Tennessee and Mobile River Basins in the Southeastern United States and compared them to those of six co-occurring species of native freshwater mussels. The gut microbiome of C. fluminea was diverse, differed with environmental conditions and varied spatially among rivers, but was unrelated to host genetic variation. Microbial source tracking suggested that the gut microbiome of C. fluminea may be influenced by the presence of co-occurring native mussels. Inferred functions from 16S rRNA gene data using PICRUST2 predicted a high prevalence and diversity of degradation functions in the C. fluminea microbiome, especially the degradation of carbohydrates and aromatic compounds. Such modularity and functional diversity of the microbiome of C. fluminea may be an asset, allowing to acclimate to an extensive range of nutritional sources in invaded habitats, which could play a vital role in its invasive success.