Convergence of gut microbiomes in myrmecophagous mammals

The gut microbiome of Madagascar's lemurs from forest fragments in the central highlands

The gut microbiome is now understood to play essential roles in host nutrition and health and has become a dominant research focus in primatology. Over the past decade, research has clarified the evolutionary traits that govern gut microbiome structure across species and the ecological traits that further influence consortia within them. Nevertheless, we stand to gain resolution by sampling hosts in understudied habitats. We focus on the lemurs of Madagascar's central highlands. Madagascar's highlands have a deep history as heterogeneous grassland-forest mosaics, but due to significant anthropogenic modification, have long been overlooked as lemur habitat. We collected fecal samples from Verreaux's sifakas (Propithecus verreauxi), common brown lemurs (Eulemur fulvus), and Goodman's mouse lemurs (Microcebus lehilahytsara) inhabiting two protected areas in the highlands and used amplicon sequencing to determine gut microbiome diversity and membership. As expected, the lemurs harbored distinct gut consortia tuned to their feeding strategies. Mouse lemurs harbored abundant Bifidobacterium and Alloprevotella that are implicated in gum metabolism, sifakas harbored abundant Lachnospiraceae that are implicated in leaf-fiber metabolism, and brown lemurs harbored diverse consortia with abundant WCBH1-41 that could be associated with frugivory in harsh seasons and habitats. Within brown lemurs, a suite of bacteria varied between seed-packed and leaf-packed feces, a proxy for dietary intakes, collected from the same group over days. Our results underscore the evolutionary and ecological factors that govern primate gut microbiomes. More broadly, we showcase the forests of Madagascar's central highlands as rich habitat for future research of lemur ecology and evolution.

Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices

Comparative approaches in animal gut microbiome research have revealed patterns of phylosymbiosis, dietary and physiological convergences, and environment-host interactions. However, most large-scale comparative studies, especially those that are highly cited, have focused on mammals, and efforts to integrate comparative approaches with existing ecological frameworks are lacking. While mammals serve as useful model organisms, developing generalised principles of how animal gut microbiomes are shaped and how these microbiomes interact bidirectionally with host ecology and evolution requires a more complete sampling of the animal kingdom. Here, we provide an overview of what past comparative studies have taught us about the gut microbiome, and how community ecology theory may help resolve certain contradictions in comparative gut microbiome research. We explore whether certain hypotheses are supported across clades, and how the disproportionate focus on mammals has introduced potential bias into gut microbiome theory. We then introduce a methodological solution by which public gut microbiome data of understudied hosts can be compiled and analysed in a comparative context. Our aggregation and analysis of 179 studies shows that generating data sets with rich host diversity is possible with public data and that key gut microbes associated with mammals are widespread across the animal kingdom. We also show the effects that sample size and taxonomic rank have on comparative gut microbiome studies and that results of multivariate analyses can vary significantly with these two parameters. While challenges remain in developing a universal model of the animal gut microbiome, we show that existing ecological frameworks can help bring us one step closer to integrating the gut microbiome into animal ecology and evolution.

Differences and correlation analysis of feeding habits and intestinal microbiome in Schizopygopsis microcephalus and Ptychobarbus kaznakovi in the upper reaches of Yangtze River

Background

The intestinal microbiota has co-evolved with the host to establish a stable and adaptive microbial community that is essential for maintaining host health and facilitating food digestion. Food selection is a critical factor influencing variations in gut microbial composition, shaping gut microbiome communities, and determining the ecological niches of fish.

Methods

In this study, high-throughput amplicon sequencing of 16S rRNA and 18S rRNA was utilized to compare the dietary and gut microbial differences between Schizopygopsis microcephalus and Ptychobarbus kaznakovi, both collected from the same sites in the Tuotuo River and Tongtian River, which are tributaries of the Yangtze River. We compared the microbial community structure, diet composition, and diversity between the two fish species using various analytical methods, including LefSe, α-diversity and β-diversity analyses. Additionally, we constructed co-occurrence networks to determine their correlations.

Results and discussion

The alpha diversity results indicated that S. microcephalus exhibited higher intestinal microbiota and feeding diversity compared to P. kaznakovi. Furthermore, the beta diversity results revealed significant differences in both intestinal microbiota and eukaryotic communities between the two species. The dominant bacterial phyla in both S. microcephalus and P. kaznakovi included Proteobacteria, Firmicutes, Actinobacteriota, Chloroflexi, and Verrucomicrobiota; however, Firmicutes was significantly more abundant in P. kaznakovi (P = 0.006), while Actinobacteriota was significantly higher (P = 0.019) in S. microcephalus at the phylum level. The primary food sources for S. microcephalus and P. kaznakovi were identified as Streptophyta (54.41%, 77.50%) and Cercozoa (8.67%, 1.94%), with Bacillariophyta (25.65%) was also the main food of constituting a major component of the diet for S. microcephalus. These differences suggested that S. microcephalus and P. kaznakovi occupy distinct dietary niches. To further explore the relationship between gut microbiota and feeding habits, we identified significant correlations between various food components and the gut microbial community through co-occurrence networks. This study enhances our understanding of the co-evolution and co-adaptation between host gut microbiota and feeding behaviors in sympatric fish species.

Impacts of host phylogeny, diet, and geography on the gut microbiome of rodents

Mammalian gut microbial communities are thought to play a variety of important roles in health and fitness, including digestion, metabolism, nutrition, immune response, behavior, and pathogen protection. Gut microbiota diversity among hosts is strongly shaped by diet as well as phylogenetic relationships among hosts. Although various host factors may influence microbial community structure, the relative contribution may vary depending on several variables, such as taxonomic scales of the species studied, dietary patterns, geographic location, and gut physiology. The present study focused on 12 species of rodents representing 3 rodent families and 3 dietary guilds (herbivores, granivores, and omnivores) to evaluate the influence of host phylogeny, dietary guild and geography on microbial diversity and community composition. Colon samples were examined from rodents that were collected from 7 different localities in Texas and Oklahoma which were characterized using 16S rRNA gene amplicon sequencing targeting the V1-V3 variable regions. The microbiota of colon samples was largely dominated by the family Porphyromonadaceae (Parabacteriodes, Coprobacter) and herbivorous hosts harbored richer gut microbial communities than granivores and omnivores. Differential abundance analysis showed significant trends in the abundance of several bacterial families when comparing herbivores and granivores to omnivores, however, there were no significant differences observed between herbivores and granivores. The gut microbiotas displayed patterns consistent with phylosymbiosis as host phylogeny explained more variation in gut microbiotas (34%) than host dietary guilds (10%), and geography (3%). Overall, results indicate that among this rodent assemblage, evolutionary relatedness is the major determinant of microbiome compositional variation, but diet and to a lesser extent geographic provenance are also influential.

Comparative Metagenomic Analysis of the Gut Microbiota of Captive Pangolins: A Case Study of Two Species

Pangolins, one of the most trafficked mammals, face significant health challenges in captivity, including digestive disorders and immune dysfunctions. These issues are closely linked to alterations in their gut microbiota, which play vital roles in the host metabolism, immunity, and overall health. This study investigated the differences in the gut microbiota composition and function between two pangolin species, Chinese pangolins (Manis pentadactyla) and Malayan pangolins (Manis javanica), under identical captive conditions to better understand their ecological adaptability and health implications. Using metagenomic sequencing, fecal samples from eight adult captive pangolins were analyzed, including four male Malayan pangolins and three male and one female Chinese pangolins. Comparative analyses of the alpha and beta diversities, microbial community structure, and functional profiles were performed. Both species harbored gut microbiota dominated by Firmicutes, Bacteroidetes, and Proteobacteria. However, the Chinese pangolins exhibited higher microbial diversity (Shannon index, p = 0.042; Simpson index, p = 0.037) and lower relative abundance of Proteobacteria compared with the Malayan pangolins. A functional analysis revealed significant differences in the metabolic pathways, where the Chinese pangolins demonstrated a higher potential for fiber degradation, whereas the Malayan pangolins exhibited elevated levels of antibiotic resistance genes and pathogenic taxa, such as Escherichia coli. These findings suggest that captivity duration and environmental stress likely contribute to the observed differences, with the Malayan pangolins experiencing greater dysbiosis due to longer captivity periods. This study provides valuable insights into the role of gut microbiota in pangolin health and offers a foundation for improving conservation strategies and captive care protocols.

Social, environmental, and developmental factors affect the microbiota of barn owls (Tyto alba) in a cross-fostering experiment

BACKGROUND

Species host diverse microbial communities that can impact their digestion and health, which has led to much interest in understanding the factors that influence their microbiota. We studied the developmental, environmental, and social factors that influence the microbiota of nestling barn owls (Tyto alba) through a partial cross-fostering experiment that manipulated the social and nest environment of the nestlings. We then examined the nestling microbiota before and three weeks after the exchange of nestlings between nests, along with the microbiota of the adults at the nest and nestlings in unmanipulated nests.

RESULTS

We found that nestlings had higher bacterial diversity and different bacterial communities than adults. The microbiota of nestlings was more like that of their mothers than their fathers, but the similarity to the father tended to increase with the amount of time the father was in close proximity to the nest, as measured from movement data. Cross-fostered offspring had higher bacterial diversity and greater changes in bacterial community composition over time than control offspring. Cross-fostering led the microbiota of the nestlings in the experiment to converge on similar bacterial communities. The microbiota of nestling owls therefore rapidly changed along with alterations to their social and nest environments.

CONCLUSIONS

These results highlight the dynamic nature of the microbiota during early development and that social interactions can shape microbial communities.

Sniffing out morphological convergence in the turbinal complex of myrmecophagous placentals

The length of the snout in mammals has important evolutionary consequences for the functional systems housed within the rostrum. However, whether increased snout lengths lead to expanded olfactory performance has rarely been examined. Here, we investigate inner rostral function among 10 species of myrmecophagous (ant- and/or termite-eating) placental mammals and 10 closely related species. We use nondestructive computed tomography scanning methods to characterize inner rostral function based on the underlying morphology of the turbinal bones in the nasal cavity. Three approaches were chosen to address this question, including the quantification of functional turbinal surface area, the quantification of functional turbinal three-dimensional complexity, and geometric morphometrics. By including non-model species from several different mammalian orders, we were able to extend the discussion surrounding turbinal homologies to comparisons across mammals. Our results show no increased olfactory function in all myrmecophagous species relative to their sister taxa, which suggests that there is no trade-off for increased olfactory capabilities in myrmecophagous species with elongated snouts. We found no evidence of convergence in turbinal morphology among all five myrmecophagous lineages. However, we found evidence of morphological convergence in the turbinals between the giant armadillo and the aardvark, suggesting a more complex interplay between the evolution of turbinal morphology and ecological correlates. While myrmecophagy alone may not be a strong enough ecological signal to overcome phylogenetic and developmental constraints, we suggest that this might be the case at the intersection of this dietary specialization with a primarily underground lifestyle where odorants may be difficult to detect.

Host diet drives gut microbiome convergence between coral reef fishes and mammals

Animal gut microbiomes are critical to host physiology and fitness. The gut microbiomes of fishes-the most abundant and diverse vertebrate clade-have received little attention relative to other clades. Coral reef fishes, in particular, make up a wide range of evolutionary histories and feeding ecologies that are likely associated with gut microbiome diversity. The repeated evolution of herbivory in fishes and mammals also allows us to examine microbiome similarity in relationship to diet across the entire vertebrate tree of life. Here, we generate a large coral reef fish gut microbiome dataset (n = 499 samples, 19 species) and combine it with a diverse aggregation of public microbiome data (n = 447) to show that host diet drives significant convergence between coral reef fish and mammalian gut microbiomes. We demonstrate that this similarity is largely driven by carnivory and herbivory and that herbivorous and carnivorous hosts exhibit distinct microbial compositions across fish and mammals. We also show that fish and mammal gut microbiomes share prominent microbial taxa, including Ruminoccocus spp. and Akkermansia spp., and predicted metabolic pathways. Despite the major evolutionary and ecological differences between fishes and mammals, our results reveal that their gut microbiomes undergo similar dietary selective pressures. Thus, diet, in addition to phylosymbiosis must be considered even when comparing the gut microbiomes of distantly related hosts.

Diet components associated with specific bacterial taxa shape overall gut community compositions in omnivorous African viverrids

Gut bacterial communities provide flexibility to hosts during dietary changes. Despite the increasing number of studies exploring the associations between broader dietary guilds of mammalian hosts and their gut bacteria, it is generally unclear how diversity and variability in consumed diets link to gut bacterial taxa in wild non-primate mammals, particularly in omnivores. Here, we contribute to filling this gap by exploring consumed diets and gut bacterial community compositions with metabarcoding of faecal samples for two African mammals, Civettictis civetta and Genetta spp., from the family Viverridae. For each individual sample, we characterised bacterial communities and identified dietary taxa by sequencing vertebrate, invertebrate and plant markers. This led us to establish diet compositions that diverged from what has previously been found from visual identification methods. Specifically, while the two genera have been categorised into the same dietary guild, we detected more animal dietary items than plant items in C. civetta, while in Genetta spp., we observed the opposite. We further found that individuals with similar diets have similar gut bacterial communities within both genera. This association tended to be driven by specific links between dietary items and gut bacterial genera, rather than communities as a whole, implying diet-driven selection for specific gut microbes in individual wild hosts. Our findings underline the importance of molecular tools for improving characterisations of omnivorous mammalian diets and highlight the opportunities for simultaneously disentangling links between diets and gut symbionts. Such insights can inform robustness and flexibility in host-microbe symbioses to dietary change associated with seasonal and habitat changes.

Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification

The acquisition of microbial symbionts enables animals to rapidly adapt to and exploit novel ecological niches, thus significantly enhancing the evolutionary fitness and success of their hosts. However, the dynamics of host-microbe interactions and their evolutionary implications remain largely underexplored in marine invertebrates. Crabs of the family Sesarmidae (Crustacea: Brachyura) are dominant inhabitants of mangrove forests and are considered keystone species there. Their rapid diversification, particularly after adopting a plant-feeding lifestyle, is believed to have been facilitated by symbiotic gut microbes, enabling successful colonization of intertidal and terrestrial environments. To investigate the patterns and mechanisms shaping the microbial communities and the role of microbes in the evolution of Sesarmidae, we characterized and compared the gut microbiome compositions across 43 crab species from Sesarmidae and other mangrove-associated families using 16S metabarcoding. We found that the gut microbiome assemblages in crabs are primarily determined by host identity, with a secondary influence from environmental factors such as microhabitat and sampling location, and to a lesser extent influenced by biological factors such as sex and gut region. While patterns of phylosymbiosis (i.e. when microbial community relationships recapitulate the phylogeny of their hosts) were consistently observed in all beta-diversity metrics analysed, the strength of phylosymbiosis varied across crab families. This suggests that the bacterial assemblages in each family were differentially shaped by different degrees of host filtering and/or other evolutionary processes. Notably, Sesarmidae displayed signals of cophylogeny with its core gut bacterial genera, which likely play crucial functional roles in their hosts by providing lignocellulolytic enzymes, essential amino acids, and fatty acids supplementation. Our results support the hypothesis of microbial contribution to herbivory and terrestrialization in mangrove crabs, highlighting the tight association and codiversification of the crab holobiont.

Association of maternal genetics with the gut microbiome and eucalypt diet selection in captive koalas

Background

Koalas, an Australian arboreal marsupial, depend on eucalypt tree leaves for their diet. They selectively consume only a few of the hundreds of available eucalypt species. Since the koala gut microbiome is essential for the digestion and detoxification of eucalypts, their individual differences in the gut microbiome may lead to variations in their eucalypt selection and eucalypt metabolic capacity. However, research focusing on the relationship between the gut microbiome and differences in food preferences is very limited. We aimed to determine whether individual and regional differences exist in the gut microbiome of koalas as well as the mechanism by which these differences influence eucalypt selection.

Methods

Foraging data were collected from six koalas and a total of 62 feces were collected from 15 koalas of two zoos in Japan. The mitochondrial phylogenetic analysis was conducted to estimate the mitochondrial maternal origin of each koala. In addition, the 16S-based gut microbiome of 15 koalas was analyzed to determine the composition and diversity of each koala's gut microbiome. We used these data to investigate the relationship among mitochondrial maternal origin, gut microbiome and eucalypt diet selection.

Results and Discussion

This research revealed that diversity and composition of the gut microbiome and that eucalypt diet selection of koalas differs among regions. We also revealed that the gut microbiome alpha diversity was correlated with foraging diversity in koalas. These individual and regional differences would result from vertical (maternal) transmission of the gut microbiome and represent an intraspecific variation in koala foraging strategies. Further, we demonstrated that certain gut bacteria were strongly correlated with both mitochondrial maternal origin and eucalypt foraging patterns. Bacteria found to be associated with mitochondrial maternal origin included bacteria involved in fiber digestion and degradation of secondary metabolites, such as the families Rikenellaceae and Synergistaceae. These bacteria may cause differences in metabolic capacity between individual and regional koalas and influence their eucalypt selection.

Conclusion

We showed that the characteristics (composition and diversity) of the gut microbiome and eucalypt diet selection of koalas differ by individuals and regional origins as we expected. In addition, some gut bacteria that could influence eucalypt foraging of koalas showed the relationships with both mitochondrial maternal origin and eucalypt foraging pattern. These differences in the gut microbiome between regional origins may make a difference in eucalypt selection. Given the importance of the gut microbiome to koalas foraging on eucalypts and their strong symbiotic relationship, future studies should focus on the symbiotic relationship and coevolution between koalas and the gut microbiome to understand individual and regional differences in eucalypt diet selection by koalas.

Critical complex network structures in animal gastrointestinal tract microbiomes

BACKGROUND

Living things from microbes to their hosts (plants, animals and humans) interact with each other, and their relationships may be described with complex network models. The present study focuses on the critical network structures, specifically the core/periphery nodes and backbones (paths of high-salience skeletons) in animal gastrointestinal microbiomes (AGMs) networks. The core/periphery network (CPN) mirrors nearly ubiquitous nestedness in ecological communities, particularly dividing the network as densely interconnected core-species and periphery-species that only sparsely linked to the core. Complementarily, the high-salience skeleton network (HSN) mirrors the pervasive asymmetrical species interactions (strictly microbial species correlations), particularly forming heterogenous pathways in AGM networks with both "backbones" and "rural roads" (regular or weak links). While the cores and backbones can act as critical functional structures, the periphery nodes and weak links may stabilize network functionalities through redundancy.

RESULTS

Here, we build and analyze 36 pairs of CPN/HSN for the AGMs based on 4903 gastrointestinal-microbiome samples containing 473,359 microbial species collected from 318 animal species covering all vertebrate and four major invertebrate classes. The network analyses were performed at host species, order, class, phylum, kingdom scales and diet types with selected and comparative taxon pairs. Besides diet types, the influence of host phylogeny, measured with phylogenetic (evolutionary) timeline or "age", were integrated into the analyses. For example, it was found that the evolutionary trends of three primary microbial phyla (Bacteroidetes/Firmicutes/Proteobacteria) and their pairwise abundance-ratios in animals do not mirror the patterns in modern humans phylogenetically, although they are consistent in terms of diet types.

CONCLUSIONS

Overall, the critical network structures of AGMs are qualitatively and structurally similar to those of the human gut microbiomes. Nevertheless, it appears that the critical composition (the three phyla of Bacteroidetes, Firmicutes, and Proteobacteria) in human gut microbiomes has broken the evolutionary trend from animals to humans, possibly attributable to the Anthropocene epoch and reflecting the far-reaching influences of agriculture and industrial revolution on the human gut microbiomes. The influences may have led to the deviations between modern humans and our hunter-gather ancestors and animals.

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.

Evolution and conservation genetics of pangolins

Pangolins (Pholidota, Manidae) are classified as an evolutionarily distinct and globally endangered mammal due to their unique morphology (nail-like scales and a myrmecophagous diet) and being the victim of heavy poaching and worldwide trafficking. As such, pangolins serve as a textbook example for studying the special phenotypic evolutionary adaptations and conservation genetics of an endangered species. Recent years have demonstrated significant advancements in the fields of molecular genetics and genomics, which have translated to a series of important research achievements and breakthroughs concerning the evolution and conservation genetics of pangolins. This review comprehensively presents the hitherto advances in phylogeny, adaptive evolution, conservation genetics, and conservation genomics that are related to pangolins, which will provide an ample understanding of their diversity, molecular adaptation mechanisms, and evolutionary potentials. In addition, we highlight the priority of investigating species/population diversity among pangolins and suggest several avenues of research that are highly relevant for future pangolin conservation.

Analysis of twelve genomes of the bacterium Kerstersia gyiorum from brown-throated sloths (Bradypus variegatus), the first from a non-human host

Kerstersia gyiorum is a Gram-negative bacterium found in various animals, including humans, where it has been associated with various infections. Knowledge of the basic biology of K. gyiorum is essential to understand the evolutionary strategies of niche adaptation and how this organism contributes to infectious diseases; however, genomic data about K. gyiorum is very limited, especially from non-human hosts. In this work, we sequenced 12 K. gyiorum genomes isolated from healthy free-living brown-throated sloths (Bradypus variegatus) in the Parque Estadual das Fontes do Ipiranga (São Paulo, Brazil), and compared them with genomes from isolates of human origin, in order to gain insights into genomic diversity, phylogeny, and host specialization of this species. Phylogenetic analysis revealed that these K. gyiorum strains are structured according to host. Despite the fact that sloth isolates were sampled from a single geographic location, the intra-sloth K. gyiorum diversity was divided into three clusters, with differences of more than 1,000 single nucleotide polymorphisms between them, suggesting the circulation of various K. gyiorum lineages in sloths. Genes involved in mobilome and defense mechanisms against mobile genetic elements were the main source of gene content variation between isolates from different hosts. Sloth-specific K. gyiorum genome features include an IncN2 plasmid, a phage sequence, and a CRISPR-Cas system. The broad diversity of defense elements in K. gyiorum (14 systems) may prevent further mobile element flow and explain the low amount of mobile genetic elements in K. gyiorum genomes. Gene content variation may be important for the adaptation of K. gyiorum to different host niches. This study furthers our understanding of diversity, host adaptation, and evolution of K. gyiorum, by presenting and analyzing the first genomes of non-human isolates.

Comparative Analysis of Gut Microbiomes in Laboratory Chinchillas, Ferrets, and Marmots: Implications for Pathogen Infection Research

Gut microbes play a vital role in the health and disease of animals, especially in relation to pathogen infections. Chinchillas, ferrets, and marmots are commonly used as important laboratory animals for infectious disease research. Here, we studied the bacterial and fungal microbiota and discovered that chinchillas had higher alpha diversity and a higher abundance of bacteria compared to marmots and ferrets by using the metabarcoding of 16S rRNA genes and ITS2, coupled with co-occurrence network analysis. The dominant microbes varied significantly among the three animal species, particularly in the gut mycobiota. In the ferrets, the feces were dominated by yeast such as Rhodotorula and Kurtzmaniella, while in the chinchillas, we found Teunomyces and Penicillium dominating, and Acaulium, Piromyces, and Kernia in the marmots. Nevertheless, the dominant bacterial genera shared some similarities, such as Clostridium and Pseudomonas across the three animal species. However, there were significant differences observed, such as Vagococcus and Ignatzschineria in the ferrets, Acinetobacter and Bacteroides in the chinchillas, and Bacteroides and Cellvibrio in the marmots. Additionally, our differential analysis revealed significant differences in classification levels among the three different animal species, as well as variations in feeding habitats that resulted in distinct contributions from the host microbiome. Therefore, our data are valuable for monitoring and evaluating the impacts of the microbiome, as well as considering potential applications.

Fine-scale geographic difference of the endangered Big-headed Turtle (Platysternon megacephalum) fecal microbiota, and comparison with the syntopic Beale's Eyed Turtle (Sacalia bealei)

BACKGROUND

Studies have elucidated the importance of gut microbiota for an organism, but we are still learning about the important influencing factors. Several factors have been identified in helping shape the microbiome of a host, and in this study we focus on two factors-geography and host. We characterize the fecal microbiota of the Big-headed Turtle (Platysternon megacephalum) and compare across a relatively fine geographic scale (three populations within an 8-km radius) and between two syntopic hosts (P. megacephalum and Sacalia bealei). Both species are endangered, which limits the number of samples we include in the study. Despite this limitation, these data serve as baseline data for healthy, wild fecal microbiotas of two endangered turtle species to aid in conservation management.

RESULTS

For geography, the beta diversity of fecal microbiota differed between the most distant sites. The genus Citrobacter significantly differs between sites, which may indicate a difference in food availability, environmental microbiota, or both. Also, we identify the common core microbiome for Platysternon across Hong Kong as the shared taxa across the three sites. Additionally, beta diversity differs between host species. Since the two species are from the same site and encounter the same environmental microbiota, we infer that there is a host effect on the fecal microbiota, such as diet or the recruitment of host-adapted bacteria. Lastly, functional analyses found metabolism pathways (KEGG level 1) to be the most common, and pathways (KEGG level 3) to be statistically significant between sites, but statistically indistinguishable between species at the same site.

CONCLUSIONS

We find that fecal microbiota can significantly differ at a fine geographic scale and between syntopic hosts. Also, the function of fecal microbiota seems to be strongly affected by geographic site, rather than species. This study characterizes the identity and function of the fecal microbiota of two endangered turtle species, from what is likely their last remaining wild populations. These data of healthy, wild fecal microbiota will serve as a baseline for comparison and contribute to the conservation of these two endangered species.

Gut diazotrophs in lagomorphs are associated with season but not altitude and host phylogeny

Invertebrates such as termites feeding on nutrient-poor substrate receive essential nitrogen by biological nitrogen fixation of gut diazotrophs. However, the diversity and composition of gut diazotrophs of vertebrates such as Plateau pikas living in nutrient-poor Qinghai-Tibet Plateau remain unknown. To fill this knowledge gap, we studied gut diazotrophs of Plateau pikas (Ochotona curzoniae) and its related species, Daurian pikas (Ochotona daurica), Hares (Lepus europaeus) and Rabbits (Oryctolagus cuniculus) by high-throughput amplicon sequencing methods. We analyzed whether the gut diazotrophs of Plateau pikas are affected by season, altitude, and species, and explored the relationship between gut diazotrophs and whole gut microbiomes. Our study showed that Firmicutes, Spirochaetes, and Euryarchaeota were the dominant gut diazotrophs of Plateau pikas. The beta diversity of gut diazotrophs of Plateau pikas was significantly different from the other three lagomorphs, but the alpha diversity did not show a significant difference among the four lagomorphs. The gut diazotrophs of Plateau pikas were the most similarly to that of Rabbits, followed by Daurian pikas and Hares, which was inconsistent with gut microbiomes or animal phylogeny. The dominant gut diazotrophs of the four lagomorphs may reflect their living environment and dietary habits. Season significantly affected the alpha diversity and abundance of dominant gut diazotrophs. Altitude had no significant effect on the gut diazotrophs of Plateau pikas. In addition, the congruence between gut microbiomes and gut diazotrophs was low. Our results proved that the gut of Plateau pikas was rich in gut diazotrophs, which is of great significance for the study of ecology and evolution of lagomorphs.

Transmission mode and dispersal traits correlate with host specificity in mammalian gut microbes

Different host species associate with distinct gut microbes in mammals, a pattern sometimes referred to as phylosymbiosis. However, the processes shaping this host specificity are not well understood. One model proposes that barriers to microbial transmission promote specificity by limiting microbial dispersal between hosts. This model predicts that specificity levels measured across microbes is correlated to transmission mode (vertical vs. horizontal) and individual dispersal traits. Here, we leverage two large publicly available gut microbiota data sets (1490 samples from 195 host species) to test this prediction. We found that host specificity varies widely across bacteria (i.e., there are generalist and specialist bacteria) and depends on transmission mode and dispersal ability. Horizontally-like transmitted bacteria equipped with traits that facilitate switches between host (e.g., tolerance to oxygen) were found to be less specific (more generalist) than microbes without those traits, for example, vertically-like inherited bacteria that are intolerant to oxygen. Altogether, our findings are compatible with a model in which limited microbial dispersal abilities foster host specificity.

The effect of host admixture on wild house mouse gut microbiota is weak when accounting for spatial autocorrelation

The question of how interactions between the gut microbiome and vertebrate hosts contribute to host adaptation and speciation is one of the major problems in current evolutionary research. Using bacteriome and mycobiome metabarcoding, we examined how these two components of the gut microbiota vary with the degree of host admixture in secondary contact between two house mouse subspecies (Mus musculus musculus and M. m. domesticus). We used a large data set collected at two replicates of the hybrid zone and model-based statistical analyses to ensure the robustness of our results. Assuming that the microbiota of wild hosts suffers from spatial autocorrelation, we directly compared the results of statistical models that were spatially naive with those that accounted for spatial autocorrelation. We showed that neglecting spatial autocorrelation can strongly affect the results and lead to misleading conclusions. The spatial analyses showed little difference between subspecies, both in microbiome composition and in individual bacterial lineages. Similarly, the degree of admixture had minimal effects on the gut bacteriome and mycobiome and was caused by changes in a few microbial lineages that correspond to the common symbionts of free-living house mice. In contrast to previous studies, these data do not support the hypothesis that the microbiota plays an important role in host reproductive isolation in this particular model system.

Gut microbiota in the short-beaked echidna (Tachyglossus Aculeatus) shows stability across gestation

Indigenous gut microbial communities (microbiota) play critical roles in health and may be especially important for the mother and fetus during pregnancy. Monotremes, such as the short-beaked echidna, have evolved to lay and incubate an egg, which hatches in their pouch where the young feeds. Since both feces and eggs pass through the cloaca, the fecal microbiota of female echidnas provides an opportunity for vertical transmission of microbes to their offspring. Here, we characterize the gut/fecal microbiome of female short-beaked echidnas and gain a better understanding of the changes that may occur in their microbiome as they go through pregnancy. Fecal samples from four female and five male echidnas were obtained from the Currumbin Wildlife Sanctuary in Queensland and sequenced to evaluate bacterial community structure. We identified 25 core bacteria, most of which were present in male and female samples. Genera such as Fusobacterium, Bacteroides, Escherichia-Shigella, and Lactobacillus were consistently abundant, regardless of sex or gestation stage, accounting for 58.00% and 56.14% of reads in male and female samples, respectively. The echidna microbiome remained stable across the different gestation stages, though there was a significant difference in microbiota composition between male and female echidnas. This study is the first to describe the microbiome composition of short-beaked echidnas across reproductive phases and allows the opportunity for this novel information to be used as a metric of health to aid in the detection of diseases triggered by microbiota dysbiosis.

Convergence of gut microbiota in myrmecophagous amphibians

The gut microbiome composition of terrestrial vertebrates is known to converge in response to common specialized dietary strategies, like leaf-eating (folivory) or ant- and termite-eating (myrmecophagy). To date, such convergence has been studied in mammals and birds, but has been neglected in amphibians. Here, we analysed 15 anuran species (frogs and toads) representing five Neotropical families and demonstrated the compositional convergence of the gut microbiomes of distantly related myrmecophagous species. Specifically, we found that the gut microbial communities of bufonids and microhylids, which have independently evolved myrmecophagy, were significantly more similar than expected based on their hosts' evolutionary divergence. Conversely, we found that gut microbiome composition was significantly associated with host evolutionary history in some cases. For instance, the microbiome composition of Xenohyla truncata, one of the few known amphibians that eat fruits, was not different from those of closely related tree frogs with an arthropod generalist diet. Bacterial taxa overrepresented in myrmecophagous species relative to other host families include Paludibacter, Treponema, and Rikenellaceae, suggesting diet-mediated selection and prey-to-predator transmission likely driving the observed compositional convergence. This study provides a basis for examining the roles of the gut microbiome in host tolerance and sequestration of toxic alkaloids from ants and termites.

Core gut microbes Cloacibacterium and Aeromonas associated with different gastropod species could be persistently transmitted across multiple generations

BACKGROUND

Studies on the gut microbiota of animals have largely focused on vertebrates. The transmission modes of commensal intestinal bacteria in mammals have been well studied. However, in gastropods, the relationship between gut microbiota and hosts is still poorly understood. To gain a better understanding of the composition of gut microbes and their transmission routes in gastropods, a large-scale and long-term experiment on the dynamics and transmission modes of gut microbiota was conducted on freshwater snails.

RESULTS

We analyzed 244 microbial samples from the digestive tracts of freshwater gastropods and identified Proteobacteria and Bacteroidetes as dominant gut microbes. Aeromonas, Cloacibacterium, and Cetobacterium were identified as core microbes in the guts, accounting for over 50% of the total sequences. Furthermore, both core bacteria Aeromonas and Cloacibacterium, were shared among 7 gastropod species and played an important role in determining the gut microbial community types of both wild and cultured gastropods. Analysis of the gut microbiota at the population level, including wild gastropods and their offspring, indicated that a proportion of gut microbes could be consistently vertically transmitted inheritance, while the majority of the gut microbes resulted from horizontal transmission. Comparing cultured snails to their wild counterparts, we observed an increasing trend in the proportion of shared microbes and a decreasing trend in the number of unique microbes among wild gastropods and their offspring reared in a cultured environment. Core gut microbes, Aeromonas and Cloacibacterium, remained persistent and dispersed from wild snails to their offspring across multiple generations. Interestingly, under cultured environments, the gut microbiota in wild gastropods could only be maintained for up to 2 generations before converging with that of cultured snails. The difference observed in gut bacterial metabolism functions was associated with this transition. Our study also demonstrated that the gut microbial compositions in gastropods are influenced by developmental stages and revealed the presence of Aeromonas and Cloacibacterium throughout the life cycle in gastropods. Based on the dynamics of core gut microbes, it may be possible to predict the health status of gastropods during their adaptation to new environments. Additionally, gut microbial metabolic functions were found to be associated with the adaptive evolution of gastropods from wild to cultured environments.

CONCLUSIONS

Our findings provide novel insights into the dynamic processes of gut microbiota colonization in gastropod mollusks and unveil the modes of microbial transmission within their guts. Video Abstract.

The role of diet and host species in shaping the seasonal dynamics of the gut microbiome

The gut microbiome plays an important role in the health and fitness of hosts. While previous studies have characterized the importance of various ecological and evolutionary factors in shaping the composition of the gut microbiome, most studies have been cross-sectional in nature, ignoring temporal variation. Thus, it remains unknown how these same factors might affect the stability and dynamics of the gut microbiome over time, resulting in variation across the tree of life. Here, we used samples collected in each of four seasons for three taxa: the herbivorous southern white rhinoceros (Ceratotherium simum simum, n = 5); the carnivorous Sumatran tiger (Panthera tigris sumatrae, n = 5); and the red panda (Ailurus fulgens, n = 9), a herbivorous carnivore that underwent a diet shift in its evolutionary history from carnivory to a primarily bamboo-based diet. We characterize the variability of the gut microbiome among these three taxa across time to elucidate the influence of diet and host species on these dynamics. Altogether, we found that red pandas exhibit marked seasonal variation in their gut microbial communities, experiencing both high microbial community turnover and high variation in how individual red panda's gut microbiota respond to seasonal changes. Conversely, while the gut microbiota of rhinoceros change throughout the year, all individuals respond in the same way to seasonal changes. Tigers experience relatively low levels of turnover throughout the year, yet the ways in which individuals respond to seasonal transitions are highly varied. We highlight how the differences in microbiome richness and network connectivity between these three species may affect the level of temporal stability in the gut microbiota across the year.

Metagenomics uncovers dietary adaptations for chitin digestion in the gut microbiota of convergent myrmecophagous mammals

IMPORTANCE

Myrmecophagous mammals are specialized in the consumption of ants and/or termites. They do not share a direct common ancestor and evolved convergently in five distinct placental orders raising questions about the underlying adaptive mechanisms involved and the relative contribution of natural selection and phylogenetic constraints. Understanding how these species digest their prey can help answer these questions. More specifically, the role of their gut microbial symbionts in the digestion of the insect chitinous exoskeleton has not been investigated in all myrmecophagous orders. We generated 29 new gut metagenomes from nine myrmecophagous species to reconstruct more than 300 bacterial genomes in which we identified chitin-degrading enzymes. Studying the distribution of these chitinolytic bacteria among hosts revealed both shared and specific bacteria between ant-eating species. Overall, our results highlight the potential role of gut symbionts in the convergent dietary adaptation of myrmecophagous mammals and the evolutionary mechanisms shaping their gut microbiota.

Host genetic background rather than diet-induced gut microbiota shifts of sympatric black-necked crane, common crane and bar-headed goose

Introduction

Gut microbiota of wild birds are affected by many factors, and host genetic background and diet are considered to be two important factors affecting their structure and function.

Methods

In order to clarify how these two factors influence the gut microbiota, this study selected the sympatric and closely related and similar-sized Black-necked Crane (Grus nigricollis) and Common Crane (Grus grus), as well as the distantly related and significantly different-sized Bar-headed Goose (Anser indicus). The fecal samples identified using sanger sequencing as the above three bird species were subjected to high-throughput sequencing of rbcL gene and 16S rRNA gene to identify the feeding types phytophagous food and gut microbiota.

Results

The results showed significant differences in food diversity between black-necked cranes and Common Cranes, but no significant differences in gut microbiota, Potatoes accounted for approximately 50% of their diets. Bar-headed Geese mainly feed on medicinal plants such as Angelica sinensis, Alternanthera philoxeroides, and Ranunculus repens. Black-necked cranes and Common Cranes, which have a high-starch diet, have a similar degree of enrichment in metabolism and synthesis functions, which is significantly different from Bar-headed Geese with a high-fiber diet. The differences in metabolic pathways among the three bird species are driven by food. The feeding of medicinal plants promotes the health of Bar-headed Geese, indicating that food influences the functional pathways of gut microbiota. Spearman analysis showed that there were few gut microbiota related to food, but almost all metabolic pathways were related to food.

Conclusion

The host genetic background is the dominant factor determining the composition of the microbiota. Monitoring the changes in gut microbiota and feeding types of wild birds through bird feces is of great reference value for the conservation of other endangered species.

Phylogenetic signal in gut microbial community rather than in rodent metabolic traits

Host phylogeny and environment have all been implicated in shaping the gut microbiota and host metabolic traits of mammals. However, few studies have evaluated phylogeny-associated microbial assembly and host metabolic plasticity concurrently, and their relationships on both short-term and evolutionary timescales. We report that the branching order of a gut microbial dendrogram was nearly congruent with phylogenetic relationships of seven rodent species, and this pattern of phylosymbiosis was intact after diverse laboratory manipulations. Laboratory rearing, diet or air temperature (Ta) acclimation induced alterations in gut microbial communities, but could not override host phylogeny in shaping microbial community assembly. A simulative heatwave reduced core microbiota diversity by 26% in these species, and led to an unmatched relationship between the microbiota and host metabolic phenotypes in desert species. Moreover, the similarity of metabolic traits across species at different Tas was not correlated with phylogenetic distance. These data demonstrated that the gut microbial assembly showed strong concordance with host phylogeny and may be shaped by environmental variables, whereas host metabolic traits did not seem to be linked with phylogeny.

Effects of plant-derived protein and rapeseed oil on growth performance and gut microbiomes in rainbow trout

BACKGROUND

Rainbow trout (Oncorhynchus mykiss) is becoming popular with the increased demand for fish protein. However, the limited resources and expense of fish meal and oil have become restrictive factors for the development of the rainbow trout related industry. To solve this problem, plant-derived proteins and vegetable oils have been developed as alternative resources. The present study focuses on evaluating the effects of two experimental diets, FMR (fish meal replaced with plant-derived protein) and FOR (fish oil replaced with rapeseed oil), through the alteration of the gut microbiota in triploid rainbow trout. The commercial diet was used in the control group (FOM).

RESULTS

Amplicon sequencing of the 16S and 18S rRNA genes was used to assess the changes in gut bacteria and fungi. Our analysis suggested that the α-diversity of both bacteria and fungi decreased significantly in the FMR and FOR groups, and β-diversity was distinct between FOM/FMR and FOM/FOR based on principal coordinate analysis (PCoA). The abundance of the Planctomycetota phylum increased significantly in the FMR group, while that of Firmicutes and Bacteroidetes decreased. We also found that the fungal phylum Ascomycota was significantly increased in the FMR and FOR groups. At the genus level, we found that the abundance of Citrobacter was the lowest and that of pathogenic Schlesneria, Brevundimonas, and Mycoplasma was highest in the FMR and FOR groups. Meanwhile, the pathogenic fungal genera Verticillium and Aspergillus were highest in the FMR and FOR groups. Furthermore, canonical correspondence analysis (CCA) and network analysis suggested that the relatively low-abundance genera, including the beneficial bacteria Methylobacterium, Enterococcus, Clostridium, Exiguobacterium, Sphingomonas and Bacteroides and the fungi Papiliotrema, Preussia, and Stachybotrys, were positively correlated with plant protein or rapeseed oil. There were more modules that had the above beneficial genera as the hub nodes in the FMR and FOR groups.

CONCLUSIONS

Our study suggested that the FMR and FOR diets could affect the gut microbiome in rainbow trout, which might offset the effects of the dominant and pathogenic microbial genera. This could be the underlying mechanism of explaining why no significant difference was observed in body weight between the different groups.

Analysis of the Intestinal and Faecal Bacterial Microbiota of the Cervidae Family Using 16S Next-Generation Sequencing: A Review

The Cervidae family has a wide distribution due to its adaptation to numerous ecological environments, which allows it to develop a diverse microbial community in its digestive tract. Recently, research has focused on the taxonomic composition and functionality of the intestinal and faecal microbiota of different cervid species worldwide, as well as their microbial diversity and variation under different associated factors such as age, sex, diet, distribution, and seasonal variation. In addition, there is special interest in knowing how cervids act as reservoirs of zoonotic pathogenic microorganisms, which represent a threat to public health. This review provides a synthesis of the growing field of microbiota determination in cervids worldwide, focusing on intestinal and faecal samples using 16S next-generation sequencing. It also documents factors influencing microbial diversity and composition, the microorganisms reported as pathogenic/zoonotic, and the perspectives regarding the conservation of these species. Knowing the interactions between bacteria and cervid health can drive management and conservation strategies for these species and help develop an understanding of their evolutionary history and the interaction with emerging disease-causing microorganisms.

Comparative Histology and Histochemistry of the Parotid Gland and Mandibular Gland in the Lowland Tapir (Tapirus terrestris Perissodactyla) and Aardvark (Orycteropus afer Tubulidentata)

In terrestrial mammals, the parotid and mandibular glands secrete different types of saliva into the oral cavity. Both glands were obtained from two female lowland tapirs (Tapirus terrestris) and one female aardvark (Orycteropus afer) from the Wroclaw Zoological Garden (Poland) and examined by light microscopy (hematoxylin and eosin, mucicarmine, periodic acid-Schiff, Alcian blue pH 1.0, Alcian blue pH 2.5, Alcian blue pH 2.5/PAS, and Hale's dialysed iron). Both the parotid glands observed in the lowland tapir and aardvark were compound alveolar serous secretory units, and in both species, the secretion was composed of neutral and acidic mucopolysaccharides (sialo and sulfated mucins). However, in both the lowland tapir and aardvark, a histological examination found the stroma of the mandibular gland was divided into very large lobes by poorly marked connective tissue. While many interlobar and striated ducts were found in the aardvark, very few were found in the lowland tapir. The mandibular gland was a branched tubular (mucous secretion) type in the lowland tapir, but it was a branched tubuloalveolar (mucous-serous) type in the aardvark. In all tested glands, the secretion was composed of neutral mucopolysaccharides, acid-sulfated mucosubstances, and sialomucins.

Molecular mechanisms of adaptive evolution in wild animals and plants

Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.

Food provisioning results in functional, but not compositional, convergence of the gut microbiomes of two wild Rhinopithecus species: Evidence of functional redundancy in the gut microbiome

The consumption of similar diets has led to the convergence of gut microbial compositions and functions across phylogenetically distinct animals. However, given the functional redundancy in gut microbiomes, it remains unclear whether synchrony occurs in their functions only and not in their composition, even within phylogenetically close animals consuming a similar diet. In this study, we collected fresh fecal samples from a Rhinopithecus roxellana population in April 2021 (before food provisioning) and June and December 2021 (after food provisioning) and used high-throughput sequencing methods (full-length 16S rRNA gene sequencing and metagenomes) to investigate changes in the gut microbiome due to food provisioning. Combining the results from our previous studies on a wild Rhinopithecus bieti population, we found that the artificial food provisions (e.g., apples, carrots, and peanuts) affected the gut microbiome, and synchrony occurred only in its functions and antibiotic resistance gene community in both Rhinopithecus species, reflecting its ecological functional redundancy. Given the current findings (e.g., depletion in probiotic microbes, dysbiosis in the gut microbial community, and changes in the antibiotic resistance gene profile), anthropogenic disturbances (e.g., food provisioning) would have potential negative effects on host health. Therefore, human activity in animal conservation should be rethought from the standpoint of gut microbial diversity.

Geography and elevation as drivers of cloacal microbiome assemblages of a passerine bird distributed across Sulawesi, Indonesia

BACKGROUND

Empirical field studies allow us to view how ecological and environmental processes shape the biodiversity of our planet, but collecting samples in situ creates inherent challenges. The majority of empirical vertebrate gut microbiome research compares multiple host species against abiotic and biotic factors, increasing the potential for confounding environmental variables. To minimize these confounding factors, we focus on a single species of passerine bird found throughout the geologically complex island of Sulawesi, Indonesia. We assessed the effects of two environmental factors, geographic Areas of Endemism (AOEs) and elevation, as well as host sex on the gut microbiota assemblages of the Sulawesi Babbler, Pellorneum celebense, from three different mountains across the island. Using cloacal swabs, high-throughput-amplicon sequencing, and multiple statistical models, we identified the core microbiome and determined the signal of these three factors on microbial composition.

RESULTS

The five most prevalent bacterial phyla within the gut microbiome of P. celebense were Proteobacteria (32.6%), Actinobacteria (25.2%), Firmicutes (22.1%), Bacteroidetes (8.7%), and Plantomycetes (2.6%). These results are similar to those identified in prior studies of passeriform microbiomes. Overall, microbiota diversity decreased as elevation increased, irrespective of sex or AOE. A single ASV of Clostridium was enriched in higher elevation samples, while lower elevation samples were enriched with the genera Perlucidibaca (Family Moraxellaceae), Lachnoclostridium (Family Lachnospiraceae), and an unidentified species in the Family Pseudonocardiaceae.

CONCLUSIONS

While the core microbiota families recovered here are consistent with other passerine studies, the decreases in diversity as elevation increases has only been seen in non-avian hosts. Additionally, the increased abundance of Clostridium at high elevations suggests a potential microbial response to lower oxygen levels. This study emphasizes the importance of incorporating multiple statistical models and abiotic factors such as elevation in empirical microbiome research, and is the first to describe an avian gut microbiome from the island of Sulawesi.

A glance at the gut microbiota and the functional roles of the microbes based on marmot fecal samples

Research on the gut microbiota, which involves a large and complex microbial community, is an important part of infectious disease control. In China, few studies have been reported on the diversity of the gut microbiota of wild marmots. To obtain full details of the gut microbiota, including bacteria, fungi, viruses and archaea, in wild marmots, we have sequenced metagenomes from five sample-sites feces on the Hulun Buir Grassland in Inner Mongolia, China. We have created a comprehensive database of bacterial, fungal, viral, and archaeal genomes and aligned metagenomic sequences (determined based on marmot fecal samples) against the database. We delineated the detailed and distinct gut microbiota structures of marmots. A total of 5,891 bacteria, 233 viruses, 236 fungi, and 217 archaea were found. The dominant bacterial phyla were Firmicutes, Proteobacteria, Bacteroidetes, and Actinomycetes. The viral families were Myoviridae, Siphoviridae, Phycodnaviridae, Herpesviridae and Podoviridae. The dominant fungi phyla were Ascomycota, Basidiomycota, and Blastocladiomycota. The dominant archaea were Biobacteria, Omoarchaea, Nanoarchaea, and Microbacteria. Furthermore, the gut microbiota was affected by host species and environment, and environment was the most important factor. There were 36,989 glycoside hydrolase genes in the microbiota, with 365 genes homologous to genes encoding β-glucosidase, cellulase, and cellulose β-1,4-cellobiosidase. Additionally, antibiotic resistance genes such as macB, bcrA, and msbA were abundant. To sum up, the gut microbiota of marmot had population diversity and functional diversity, which provides a basis for further research on the regulatory effects of the gut microbiota on the host. In addition, metagenomics revealed that the gut microbiota of marmots can degrade cellulose and hemicellulose.

Factors shaping the gut microbiome of five species of lizards from different habitats

Background

Host-gut microbiota interactions are complex and can have a profound impact on the ecology and evolution of both counterparts. Several host traits such as systematics, diet and social behavior, and external factors such as prey availability and local environment are known to influence the composition and diversity of the gut microbiota.

Methods

In this study, we investigate the influence of systematics, sex, host size, and locality/habitat on gut microbiota diversity in five lizard species from two different sites in Portugal: Podarcis bocagei and Podarcis lusitanicus, living in syntopy in a rural area in northern Portugal (Moledo); the invasive Podarcis siculus and the native Podarcis virescens, living in sympatry in an urbanized environment (Lisbon); and the invasive Teira dugesii also living in an urban area (Lisbon). We also infer the potential microbial transmission occurring between species living in sympatry and syntopy. To achieve these goals, we use a metabarcoding approach to characterize the bacterial communities from the cloaca of lizards, sequencing the V4 region of the 16S rRNA.

Results

Habitat/locality was an important factor explaining differences in gut bacterial composition and structure, with species from urbanized environments having higher bacterial diversity. Host systematics (i.e., species) influenced gut bacterial community structure only in lizards from the urbanized environment. We also detected a significant positive correlation between lizard size and gut bacterial alpha-diversity in the invasive species P. siculus, which could be due to its higher exploratory behavior. Moreover, estimates of bacterial transmission indicate that P. siculus may have acquired a high proportion of local microbiota after its introduction. These findings confirm that a diverse array of host and environmental factors can influence lizards' gut microbiota.

Evaluating a potential model to analyze the function of the gut microbiota of the giant panda

To contribute to the conservation of endangered animals, the utilization of model systems is critical to analyze the function of their gut microbiota. In this study, the results of a fecal microbial transplantation (FMT) experiment with germ-free (GF) mice receiving giant panda or horse fecal microbiota showed a clear clustering by donor microbial communities in GF mice, which was consistent with the results of blood metabolites from these mice. At the genus level, FMT re-established approximately 9% of the giant panda donor microbiota in GF mice compared to about 32% for the horse donor microbiota. In line with this, the difference between the panda donor microbiota and panda-mice microbiota on whole-community level was significantly larger than that between the horse donor microbiota and the horse-mice microbiota. These results were consistent with source tracking analysis that found a significantly higher retention rate of the horse donor microbiota (30.9%) than the giant panda donor microbiota (4.0%) in GF mice where the microbiota remained stable after FMT. Further analyzes indicated that the possible reason for the low retention rate of the panda donor microbiota in GF mice was a low relative abundance of Clostridiaceae in the panda donor microbiota. Our results indicate that the donor microbiota has a large effect on GF mice microbiota after FMT.

Quantifying (non)parallelism of gut microbial community change using multivariate vector analysis

Parallel evolution of phenotypic traits is regarded as strong evidence for natural selection and has been studied extensively in a variety of taxa. However, we have limited knowledge of whether parallel evolution of host organisms is accompanied by parallel changes of their associated microbial communities (i.e., microbiotas), which are crucial for their hosts' ecology and evolution. Determining the extent of microbiota parallelism in nature can improve our ability to identify the factors that are associated with (putatively adaptive) shifts in microbial communities. While it has been emphasized that (non)parallel evolution is better considered as a quantitative continuum rather than a binary phenomenon, quantitative approaches have rarely been used to study microbiota parallelism. We advocate using multivariate vector analysis (i.e., phenotypic change vector analysis) to quantify direction and magnitude of microbiota changes and discuss the applicability of this approach for studying parallelism, and we compiled an R package for multivariate vector analysis of microbial communities ('multivarvector'). We exemplify its use by reanalyzing gut microbiota data from multiple fish species that exhibit parallel shifts in trophic ecology. We found that multivariate vector analysis results were largely consistent with other statistical methods, parallelism estimates were not affected by the taxonomic level at which the microbiota is studied, and parallelism might be stronger for gut microbiota function compared to taxonomic composition. This approach provides an analytical framework for quantitative comparisons across host lineages, thereby providing the potential to advance our capacity to predict microbiota changes. Hence, we emphasize that the development and application of quantitative measures, such as multivariate vector analysis, should be further explored in microbiota research in order to better understand the role of microbiota dynamics during their hosts' adaptive evolution, particularly in settings of parallel evolution.

Screening for Volatile α-Unsaturated Ester-Producing Yeasts from the Feces of Wild Animals in South Africa

α-unsaturated esters are fruity-aromatic compounds which are largely spread in the volatilome of many different fruits, but they are rarely found in the volatilome of yeasts. The yeast S. suaveolens has been recently shown to produce relatively high amounts of α-unsaturated esters and it appears to be an interesting model for the production of these compounds. This study aimed to isolate new α-unsaturated ester-producing yeasts by focusing on strains displaying a similar metabolism to S. suaveolens. While the production of α-unsaturated esters by S. suaveolens is believed to be closely related to its ability to grow on media containing branched-chain amino acids (isoleucine, leucine and valine) as the sole carbon source (ILV⁺ phenotype), in this study, an original screening method was developed that selects for yeast strains displaying ILV⁺ phenotypes and is able to produce α-unsaturated esters. Among the 119 yeast strains isolated from the feces of 42 different South African wild animal species, 43 isolates showed the ILV⁺ phenotype, among which 12 strains were able to produce α-unsaturated esters. Two interesting α-unsaturated esters were detected in two freshly isolated strains, both identified as Galactomyces candidus. These new esters were detected neither in the volatilome of the reference strain S. suaveolens, nor in any other yeast species previously studied for their aroma production. This work demonstrated the efficiency of an original method to rapidly screen for α-unsaturated ester-producing yeasts. In addition, it demonstrated that wild animal feces are interesting resources to isolate novel strains producing compounds with original aromas.

Mycoplasmataceae dominate microbial community differences between gut regions in mammals with a simple gut architecture

Faunivorous mammals with simple guts are thought to rely primarily on endogenously produced enzymes to digest food, in part because they lack fermentation chambers for facilitating mutualistic interactions with microbes. However, variation in microbial community composition along the length of the gastrointestinal tract has yet to be assessed in faunivorous species with simple guts. We tested for differences in bacterial taxon abundances and community compositions between the small intestines and colons of 26 individuals representing four species of shrew in the genus Crocidura. We sampled these hosts from a single locality on Sulawesi Island, Indonesia, to control for potential geographic and temporal variation. Bacterial community composition differed significantly between the two gut regions and members of the family Mycoplasmataceae contributed substantially to these differences. Three operational taxonomic units (OTUs) of an unclassified genus in this family were more abundant in the small intestine, whereas 1 OTU of genus Ureaplasma was more abundant in the colon. Species of Ureaplasma encode an enzyme that degrades urea, a metabolic byproduct of protein catabolism. Additionally, a Hafnia–Obesumbacterium OTU, a genus known to produce chitinase in bat gastrointestinal tracts, was also more abundant in the colon compared to the small intestine. The presence of putative chitinase- and urease-producing bacteria in shrew guts suggests mutualisms with microorganisms play a role in facilitating the protein-rich, faunivorous diets of simple gut mammals.

Convergent evolution of the gut microbiome in marine carnivores

The gut microbiome can help the host adapt to a variety of environments and is affected by many factors. Marine carnivores have unique habitats in extreme environments. The question of whether marine habitats surpass phylogeny to drive the convergent evolution of the gut microbiome in marine carnivores remains unanswered. In the present study, we compared the gut microbiomes of 16 species from different habitats. Principal component analysis (PCA) and principal coordinate analysis (PCoA) separated three groups according to their gut microbiomes: marine carnivores, terrestrial carnivores, and terrestrial herbivores. The alpha diversity and niche breadth of the gut microbiome of marine carnivores were lower than those of the gut microbiome of terrestrial carnivores and terrestrial herbivores. The gut microbiome of marine carnivores harbored many marine microbiotas, including those belonging to the phyla Planctomycetes, Cyanobacteria, and Proteobacteria, and the genus Peptoclostridium. Collectively, these results revealed that marine habitats drive the convergent evolution of the gut microbiome of marine carnivores. This study provides a new perspective on the adaptive evolution of marine carnivores.

Foraging Burrow Site Selection and Diet of Chinese Pangolins, Chandragiri Municipality, Nepal

The Chinese pangolin (Manis pentadactyla) is a myrmecophagous, nocturnal mammal species that occurs in forests, agricultural lands, and grasslands. It is critically endangered due to illegal hunting and habitat loss. Characterizing the Chinese pangolin’s habitat and diet could improve our knowledge of the conditions necessary for species persistence; however, limited information is available. We investigated the habitat and diet of Chinese pangolins in the Chandragiri Municipality, Kathmandu, Nepal from November 2021−March 2022. We identified foraging burrows within plots established along 20 transects, collected scats opportunistically at these burrows, and used a generalized linear model to assess the site-level habitat characteristics related to burrow occurrence. We recorded 88 foraging burrows which occurred in forests with 50−75% canopy closure at 1500−1700 m elevation with 20−40° slopes. The probability of detecting a Chinese pangolin foraging burrow was greater with the increasing slope gradient and decreased with increasing distance to agricultural lands and ant nests or termite mounds. The analysis of 10 scats revealed that Aphaenogastersymthiesii, Camponotus sp., Monomorium sp., and Pheidole sp. were the dominant ant prey species; no termites were detected. Baseline data from this study could be used for ex-situ conservation and the captive breeding of Chinese pangolins as well as aiding site-specific management plans in Nepal.

Global landscape of gut microbiome diversity and antibiotic resistomes across vertebrates

Multiple factors influence gut microbiome diversity in vertebrate hosts. Most previous studies have only investigated specific factors and certain host species or taxa. However, a comprehensive assessment of the relative contributions of individual factors towards gut microbial diversity within a broader evolutionary context remains lacking. Here, 2202 16S rRNA gene sequencing samples of gut bacterial communities collected from 452 host species across seven classes were analyzed together to understand the factors broadly affecting vertebrate gut microbiomes across hosts with different diets, threatened status, captivity status, and habitat environmental factors. Among wild vertebrates, diet was most significantly associated with gut microbiome alpha diversity, while host phylogeny and diet were significantly associated with beta diversity, consistent with a previous study. Host threatened status and habitat environmental factors (e.g., geography and climate) were also associated with gut bacterial community beta diversity. Subsequent ecological modeling revealed a strong association between stochastic assembly processes and patterns of gut bacterial diversity among free-ranging vertebrates. In addition, metagenomic analysis of gut microbiomes from 62 captive vertebrates and sympatric humans revealed similar diversity and resistome profiles despite differences in host phylogeny, diet, and threatened status. These results thus suggest that captivity diminishes the effects of host phylogeny, diet, and threatened status on the diversity of vertebrate gut bacterial communities. The most overrepresented antibiotic resistant genes (ARGs) observed in these samples are involved in resistance to β-lactams, aminoglycosides, and tetracycline. These results also revealed potential horizontal transfers of ARGs between captive animals and humans, thereby jointly threatening public health and vertebrate conservation. Together, this study provides a comprehensive overview of the diversity and resistomes of vertebrate gut microbiomes. These combined analyses will help guide future vertebrate conservation via the rational manipulation of microbial diversity and reducing antibiotic usage.

Gut microbiome modulation mediated by probiotics: Positive impact on growth and health status of Labeo rohita

The current study was targeted to determine the effect of probiotics on the growth, physiology, and gut microbiology of Labeo rohita fingerlings. One hundred and twenty fishes were divided into four dietary groups, each in triplicate for a feeding trial of 90 days. These treatments included T0 (control, basal diet) used as the reference, and three probiotic-supplemented diets represented as Tbc (Bacillus cereus), Tgc (Geotrichum candidum), and Tmc (B. cereus and G. candidum). The probiotics were supplemented at a level of 1 × 109 CFU/g feed. Fishes nurtured on probiotic-added diet showed significantly high physiological improvement (p < 0.05) in terms of growth, feed utilization capacity, hematological profile, and digestive enzymes as compared to control. The fish were subjected to a challenge test after a 90-day feeding trial. The Tmc exhibited maximum fish growth when challenged by Staphylococcus aureus and showed fish survival when compared to control, in which fish mortality was examined. Fish gut microbial composition was modulated by probiotic treatments, especially in Tgc and Tmc as compared to control. The absence of opportunistic pathogens such as Staphylococcus saprophyticus and Sporobolomyces lactosus and detection of lower levels of Trichosporon and Cryptococcus in treated groups indicate the gut modulation driven by applied probiotics. The G. candidum QAUGC01 was retrieved in yeast metagenomics data, which might be due to the production of polyamines by them that facilitated adherence and consequent persistence. In conclusion, it can be suggested that the probiotic-supplemented diet could enhance fish growth and feed efficiency through community modulation and digestive enzymes, which could be a milestone in local aquaculture.

Investigation of Gut Bacterial Communities of Asian Citrus Psyllid (Diaphorina citri) Reared on Different Host Plants

Simple Summary

Diaphorina citri is a crucial natural vector of the Huanglongbing pathogen, which has devastated the citrus industry. The host plant is a critical factor that affects insect biology and its symbiont abundance. However, little is known about how host plants affect the bacterial community located in D. citri. In this work, the guts of five different host-plant-feeding populations (i.e., Citrus reticulata cv. Shatangju, Citrus poonensis cv. Ponkan, Murraya paniculata (orange jasmine), Citrus limon (lemon), and Citrus sinensis (navel orange)) were analyzed for bacterial communities by next-generation sequencing. The dominant phylum was Proteobacteria. The most common and abundant bacterial genera in D. citri were Wolbachia, Escherichia-Shigella, and Candidatus Profftella, but their relative abundance varied among the different host plant groups. There were obvious differences in the gut microbiota among the different hosts, and the gut microbe diversity was the highest in the ponkan-feeding population, while the lowest was in the Shatangju-feeding population. Overall, our findings indicate that the host plant can significantly affect the gut microbial community of D. citri. This result can provide new insights into the co-adaptation of D. citri and its symbionts.

Abstract

Diaphorina citri Kuwayama (Hemiptera: Liviidae) can cause severe damage to citrus plants, as it transmits Candidatus Liberibacter spp., a causative agent of Huanglongbing disease. Symbiotic bacteria play vital roles in the ecology and biology of herbivore hosts, thereby affecting host growth and adaptation. In our research, the effects of Rutaceous plants (i.e., Citrus reticulata cv. Shatangju, Citrus poonensis cv. Ponkan, Murraya paniculata (orange jasmine), Citrus limon (lemon), and Citrus sinensis (navel orange)) on the gut microbiota (GM) and microbial diversity of D. citri adults were investigated by 16S rRNA high-throughput sequencing. It was found that Proteobacteria dominated the GM communities. The gut microbe diversity was the highest in the ponkan-feeding population, and the lowest in the Shatangju-feeding population. The NMDS analysis revealed that there were obvious differences in the GM communities among the different hosts. PICRUSt function prediction indicated significant differences in host function, and those pathways were crucial for maintaining population reproduction, growth, development, and adaptation to environmental stress in D. citri. Our study sheds new light on the interactions between symbionts, herbivores, and host plants and expands our knowledge on host adaptation related to GM in D. citri.

Characterization of Microbial Communities from the Alimentary Canal of Typhaea stercorea (L.) (Coleoptera: Mycetophagidae)

Simple Summary

Hairy fungus beetle, Typhaea stercorea, is a secondary post-harvest pest of stored grains that thrives by feeding on mytoxigenic fungi. Bacterial communities residing in the alimentary canal of most insects contribute to their host’s development. While there are many examples, little is known about the role of bacterial communities in the alimentary canal of T. stercorea. The objectives of this study were to (1) characterize the microbial communities residing in T. stercorea and (2) compare the microbial compositions of field-collected and laboratory-reared populations. In this study, we were able to identify bacterial communities that possess mycolytic properties and track mark changes in the microbiota profiles associated with development. The genus Pseudomonas was enriched in T. stercorea larvae compared to adults. Furthermore, field-collected T. sterocrea adults had a lower species richness than both larva and adult laboratory-reared T. sterocrea. Moreover, the gut microbial compositions of field-collected and laboratory-reared populations were vastly different. Overall, our results suggest that the environment and physiology can shift the microbial composition in the alimentary canal of T. stercorea.

Abstract

The gut microbiomes of symbiotic insects typically mediate essential functions lacking in their hosts. Here, we describe the composition of microbes residing in the alimentary canal of the hairy fungus beetle, Typhaea stercorea (L.), at various life stages. This beetle is a post-harvest pest of stored grains that feeds on fungi and serves as a vector of mycotoxigenic fungi. It has been reported that the bacterial communities found in most insects’ alimentary canals contribute to nutrition, immune defenses, and protection from pathogens. Hence, bacterial symbionts may play a key role in the digestive system of T. stercorea. Using 16S rRNA amplicon sequencing, we examined the microbiota of T. stercorea. We found no difference in bacterial species richness between larvae and adults, but there were compositional differences across life stages (PERMANOVA:pseudo-F_(8,2) = 8.22; p = 0.026). The three most abundant bacteria found in the alimentary canal of the larvae and adults included Pseudomonas (47.67% and 0.21%, respectively), an unspecified genus of the Enterobacteriaceae family (46.60 % and 90.97%, respectively), and Enterobacter (3.89% and 5.75%, respectively). Furthermore, Pseudomonas spp. are the predominant bacteria in the larval stage. Our data indicated that field-collected T. stercorea tended to have lower species richness than laboratory-reared beetles (Shannon: H = 5.72; p = 0.057). Furthermore, the microbial communities of laboratory-reared insects resembled one another, whereas field-collected adults exhibited variability (PERMANOVA:pseudo-F_(10,3) = 4.41; p = 0.006). We provide evidence that the environment and physiology can shift the microbial composition in the alimentary canal of T. stercorea.

Habitat and Host Species Drive the Structure of Bacterial Communities of Two Neotropical Trap-Jaw Odontomachus Ants : Habitat and Host Species Drive the Structure of Bacterial Communities of Two Neotropical Trap-Jaw Odontomachus Ants

Ants have long been known for their associations with other taxa, including macroscopic fungi and symbiotic bacteria. Recently, many ant species have had the composition and function of their bacterial communities investigated. Due to its behavioral and ecological diversity, the subfamily Ponerinae deserves more attention regarding its associated microbiota. Here, we used the V4 region of the 16S rRNA gene to characterize the bacterial communities of Odontomachus chelifer (ground-nesting) and Odontomachus hastatus (arboreal), two ponerine trap-jaw species commonly found in the Brazilian savanna ("Cerrado") and Atlantic rainforest. We investigated habitat effects (O. chelifer in the Cerrado and the Atlantic rainforest) and species-specific effects (both species in the Atlantic rainforest) on the bacterial communities' structure (composition and abundance) in two different body parts: cuticle and gaster. Bacterial communities differed in all populations studied. Cuticular communities were more diverse, while gaster communities presented variants common to other ants, including Wolbachia and Candidatus Tokpelaia hoelldoblerii. Odontomachus chelifer populations presented different communities in both body parts, highlighting the influence of habitat type. In the Atlantic rainforest, the outcome depended on the body part targeted. Cuticular communities were similar between species, reinforcing the habitat effect on bacterial communities, which are mainly composed of environmentally acquired taxa. Gaster communities, however, differed between the two Odontomachus species, suggesting species-specific effects and selective filters. Unclassified Firmicutes and uncultured Rhizobiales variants are the main components accounting for the observed differences. Our study indicates that both host species and habitat act synergistically, but to different degrees, to shape the bacterial communities in these Odontomachus species.

High-Altitude Drives the Convergent Evolution of Alpha Diversity and Indicator Microbiota in the Gut Microbiomes of Ungulates

Convergent evolution is an important sector of evolutionary biology. High-altitude environments are one of the extreme environments for animals, especially in the Qinghai Tibet Plateau, driving the inquiry of whether, under broader phylogeny, high-altitude factors drive the convergent evolution of Artiodactyla and Perissodactyla gut microbiomes. Therefore, we profiled the gut microbiome of Artiodactyla and Perissodactyla at high and low altitudes using 16S rRNA gene sequencing. According to cluster analyses, the gut microbiome compositions of high-altitude Artiodactyla and Perissodactyla were not grouped together and were far from those of low-altitude Artiodactyla and Perissodactyla. The Wilcoxon’s test in high-altitude ungulates showed significantly higher Sobs and Shannon indices than in low-altitude ungulates. At the phylum level, Firmicutes and Patescibacteria were significantly enriched in the gut microbiomes of high-altitude ungulates, which also displayed a higher Firmicutes/Bacteroidetes value than low-altitude ungulates. At the family level, Ruminococcaceae, Christensenellaceae, and Saccharimonadaceae were significantly enriched in the gut microbiomes of high-altitude ungulates. Our results also indicated that the OH and FH groups shared two significantly enriched genera, Christensenellaceae_R_7_group and Candidatus_Saccharimonas. These findings indicated that a high altitude cannot surpass the order level to drive the convergent evolution of ungulate gut microbiome composition but can drive the convergent evolution of alpha diversity and indicator microbiota in the gut microbiome of ungulates. Overall, this study provides a novel perspective for understanding the adaptation of ungulates to high-altitude environments.

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.

Patterns of Microbiome Composition Vary Across Spatial Scales in a Specialist Insect

Microbial communities associated with animals vary based on both intrinsic and extrinsic factors. Of many possible determinants affecting microbiome composition, host phylogeny, host diet, and local environment are the most important. How these factors interact across spatial scales is not well understood. Here, we seek to identify the main influences on microbiome composition in a specialist insect, the western corn rootworm (WCR; Diabrotica virgifera virgifera), by analyzing the bacterial communities of adults collected from their obligate host plant, corn (Zea mays), across several geographic locations and comparing the patterns in communities to its congeneric species, the northern corn rootworm (NCR; Diabrotica barberi). We found that bacterial communities of WCR and NCR shared a portion of their bacterial communities even when collected from disparate locations. However, within each species, the location of collection significantly influenced the composition of their microbiome. Correlations of geographic distance between sites with WCR bacterial community composition revealed different patterns at different spatial scales. Community similarity decreased with increased geographic distance at smaller spatial scales (~25 km between the nearest sites). At broad spatial scales (>200 km), community composition was not correlated with distances between sites, but instead reflected the historical invasion path of WCR across the United States. These results suggest bacterial communities are structured directly by dispersal dynamics at small, regional spatial scales, while landscape-level genetic or environmental differences may drive community composition across broad spatial scales in this specialist insect.

Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom

Archaea are common constituents of the gut microbiome of humans, ruminants, and termites but little is known about their diversity and abundance in other animals. Here, we analyse sequencing and quantification data of archaeal and bacterial 16S rRNA genes from 250 species of animals covering a large taxonomic spectrum. We detect the presence of archaea in 175 animal species belonging to invertebrates, fish, amphibians, birds, reptiles and mammals. We identify five dominant gut lineages, corresponding to Methanobrevibacter, Methanosphaera, Methanocorpusculum, Methanimicrococcus and "Ca. Methanomethylophilaceae". Some archaeal clades, notably within Methanobrevibacter, are associated to certain hosts, suggesting specific adaptations. The non-methanogenic lineage Nitrososphaeraceae (Thaumarchaeota) is frequently present in animal samples, although at low abundance, but may have also adapted to the gut environment. Host phylogeny, diet type, fibre content, and intestinal tract physiology are major drivers of the diversity and abundance of the archaeome in mammals. The overall abundance of archaea is more influenced by these factors than that of bacteria. Methanogens reducing methyl-compounds with H2 can represent an important fraction of the overall methanogens in many animals. Together with CO2-reducing methanogens, they are influenced by diet and composition of gut bacteria. Our results provide key elements toward our understanding of the ecology of archaea in the gut, an emerging and important field of investigation.