Gut microbial communities of American pikas ( O chotona princeps ): Evidence for phylosymbiosis and adaptations to novel diets

Review: Mechanism of herbivores synergistically metabolizing toxic plants through liver and intestinal microbiota

Interspecific interactions are central to ecological research. Plants produce toxic plant secondary metabolites (PSMs) as a defense mechanism against herbivore overgrazing, prompting their gradual adaptation to toxic substances for tolerance or detoxification. P450 enzymes in herbivore livers bind to PSMs, whereas UDP-glucuronosyltransferase and glutathione S-transferase increase the hydrophobicity of the bound PSMs for detoxification. Intestinal microorganisms such as Bacteroidetes metabolize cellulase and other macromolecules to break down toxic components. However, detoxification is an overall response of the animal body, necessitating coordination among various organs to detoxify ingested PSMs. PSMs undergo detoxification metabolism through the liver and gut microbiota, evidenced by increased signaling processes of bile acids, inflammatory signaling molecules, and aromatic hydrocarbon receptors. In this context, we offer a succinct overview of how metabolites from the liver and gut microbiota of herbivores contribute to enhancing metabolic PSMs. We focused mainly on elucidating the molecular communication between the liver and gut microbiota involving endocrine, immune, and metabolic processes in detoxification. We have also discussed the potential for future alterations in the gut of herbivores to enhance the metabolic effects of the liver and boost the detoxification and metabolic abilities of PSMs.

Effects of dietary nutrients of the gut microbiota in the long-tailed dwarf hamster (Cricetulus longicaudatus)

Gut microbiota is a key factor in maintaining the dietary and metabolic homeostasis of small mammals. To explore the effect of diet on the gut microbiota of the long-tailed dwarf hamster (Cricetulus longicaudatus), 16S rDNA high-throughput sequencing combined with bioinformatics analysis was used to investigate the succession process of the gut microbiota and effects of different nutrients on the composition and function of the gut microbiota. The results showed that diet structure can significantly influence the composition and function of the gut microbiota, as well as the health of animals. The highest relative abundance of Firmicutes, and the simplest co-occurrence network occurred in the wild. Whereas the relative abundance of Bacteroidetes is higher and the most complex network structure was observed after 35 days of same feeding. Compared to the other four groups, the relative abundance of Firmicutes in the wheat + peanuts (WP) group was the highest after 35 days of different feeding, and the highest relative abundance of Bacteroidetes occurred in the wheat-only (WH) group. Bacteroidetes exhibit carbohydrate degradation activity, and Firmicutes are strongly associated with fat uptake. We also found a significant positive correlation between Lactobacillus and body weight, indicating that Lactobacillus plays a crucial role in modulating fat intake and weight management. This study provides empirical evidence to facilitate the understanding of the co-evolutionary dynamics between C. longicaudatus and their gut microbiota and establishes a theoretical foundation for utilizing gut microbiota in rodent control.

Retrospective review of the pathology of American pikas

American pikas (Ochotona princeps) are small lagomorphs that live in mountainous talus areas of western North America. Studies on the histopathology of American pikas are limited. We summarize here the clinical histories, and gross and histologic findings of 12 American pikas, including 9 captive (wild-caught) and 3 wild animals. Death was often attributed to stress (transport, handling, anesthesia) with few-to-no premonitory clinical signs. Infection was the cause of death in 2 cases: 1 had bacterial pyogranulomatous dermatitis, cellulitis, and lymphadenitis with sepsis; the other case had oomycete-induced necrotizing colitis. Incidental parasitic infections included sarcocystosis, nematodosis (oxyurids), and ectoparasitism. Most animals with adequate nutritional status had periportal hepatic lipidosis; this finding was absent in all animals with adipose atrophy, and it is possible that periportal hepatic lipidosis is non-pathologic in American pikas. Three cases had myocardial necrosis that was considered the cause of death; the cause of necrosis was not determined, but it may have been caused by stress or vitamin E-selenium deficiency. Esophageal hyperkeratosis was noted in animals with a history of anorexia and negative energy balance; accumulation of esophageal keratin can result from lack of mucosal abrasion by ingesta. Several histologic findings that are likely normal in American pikas include splenic extramedullary hematopoiesis, thymic tissue in adults, and Clostridium sp. in the enteric lumen.

Geographical distribution and species variation of gut microbiota in small rodents from the agro-pastoral transition ecotone in northern China

The gut microbiota of rodents is essential for survival and adaptation and is susceptible to various factors, ranging from environmental conditions to genetic predispositions. Nevertheless, few comparative studies have considered the contribution of species identity and geographic spatial distance to variations in the gut microbiota. In this study, a random sampling survey encompassing four rodent species (Apodemus agrarius, Cricetulus barabensis, Tscherskia triton and Rattus norvegicus) was conducted at five sites in northern China's farming-pastoral ecotone. Through a cross-factorial comparison, we aimed to discern whether belonging to the same species or sharing the same capture site predominantly influences the composition of gut microbiota. Notably, the observed variations in microbiome composition among these four rodent species match the host phylogeny at the family level but not at the species level. The gut microbiota of these four rodent species exhibited typical mammalian characteristics, predominantly characterized by the Firmicutes and Bacteroidetes phyla. As the geographic distance between populations increased, the number of shared microbial taxa among conspecific populations decreased. We observed that within a relatively small geographical range, even different species exhibited convergent α-diversity due to their inhabitation within the same environmental microbial pool. In contrast, the composition and structure of the intestinal microbiota in the allopatric populations of A. agrarius demonstrated marked differences, similar to those of C. barabensis. Additionally, geographical environmental elements exhibited significant correlations with diversity indices. Conversely, host-related factors had minimal influence on microbial abundance. Our findings indicated that the similarity of the microbial compositions was not determined primarily by the host species, and the location of the sampling explained a greater amount of variation in the microbial composition, indicating that the local environment played a crucial role in shaping the microbial composition.

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.

16S rRNA gene-based meta-analysis of the reptile gut microbiota reveals environmental effects, host influences and a limited core microbiota

An animal's gut microbiota plays an important role in host health, reproduction and digestion. However, many studies focus on only a few individuals or a single species, limiting our ability to recognize emergent patterns across a wider taxonomic grouping. Here, we compiled and reanalysed published 16S rRNA gene sequence data for 745 gut microbiota samples from 91 reptile species using a uniform bioinformatics pipeline to draw broader conclusions about the taxonomy of the reptile gut microbiota and the forces shaping it. Our meta-analysis revealed the significant differences in alpha- and beta-diversity across host order, environment, diet, habitat and conservation status, with host diet and order contributing the most to these differences. We identified the principal bacterial phyla present in the reptile gut microbiota as Bacteroidota, Proteobacteria (mostly Gamma class), and Firmicutes, and detected the bacterial genus Bacteroides in most reptile individuals, thus representing a putative 'core' microbiota. Our study provides novel insights into key drivers of the reptile gut microbiota, highlights existing knowledge gaps and lays the groundwork for future research on these fascinating hosts and their associated microbes.

Phylosymbiosis: The Eco-Evolutionary Pattern of Insect-Symbiont Interactions

Insects harbor diverse assemblages of bacterial and fungal symbionts, which play crucial roles in host life history. Insects and their various symbionts represent a good model for studying host-microbe interactions. Phylosymbiosis is used to describe an eco-evolutionary pattern, providing a new cross-system trend in the research of host-associated microbiota. The phylosymbiosis pattern is characterized by a significant positive correlation between the host phylogeny and microbial community dissimilarities. Although host-symbiont interactions have been demonstrated in many insect groups, our knowledge of the prevalence and mechanisms of phylosymbiosis in insects is still limited. Here, we provide an order-by-order summary of the phylosymbiosis patterns in insects, including Blattodea, Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera. Then, we highlight the potential contributions of stochastic effects, evolutionary processes, and ecological filtering in shaping phylosymbiotic microbiota. Phylosymbiosis in insects can arise from a combination of stochastic and deterministic mechanisms, such as the dispersal limitations of microbes, codiversification between symbionts and hosts, and the filtering of phylogenetically conserved host traits (incl., host immune system, diet, and physiological characteristics).

The Bacterial Microbiome of the Coral Skeleton Algal Symbiont Ostreobium Shows Preferential Associations and Signatures of Phylosymbiosis

Ostreobium, the major algal symbiont of the coral skeleton, remains understudied despite extensive research on the coral holobiont. The enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment, allowing stronger associations with the algae. Here, we describe the bacterial communities associated with cultured strains of 5 Ostreobium clades using 16S rRNA sequencing. We shed light on their likely physical associations by comparative analysis of three datasets generated to capture (1) all algae associated bacteria, (2) enriched tightly attached and potential intracellular bacteria, and (3) bacteria in spent media. Our data showed that while some bacteria may be loosely attached, some tend to be tightly attached or potentially intracellular. Although colonised with diverse bacteria, Ostreobium preferentially associated with 34 bacterial taxa revealing a core microbiome. These bacteria include known nitrogen cyclers, polysaccharide degraders, sulphate reducers, antimicrobial compound producers, methylotrophs, and vitamin B12 producers. By analysing co-occurrence networks of 16S rRNA datasets from Porites lutea and Paragoniastrea australensis skeleton samples, we show that the Ostreobium-bacterial associations present in the cultures are likely to also occur in their natural environment. Finally, our data show significant congruence between the Ostreobium phylogeny and the community composition of its tightly associated microbiome, largely due to the phylosymbiotic signal originating from the core bacterial taxa. This study offers insight into the Ostreobium microbiome and reveals preferential associations that warrant further testing from functional and evolutionary perspectives.

Species-Level Taxonomic Characterization of Uncultured Core Gut Microbiota of Plateau Pika

Rarely has the vast diversity of bacteria on Earth been profiled, particularly on inaccessible plateaus. These uncultured microbes, which are also known as "microbial dark matter," may play crucial roles in maintaining the ecosystem and are linked to human health, regarding pathogenicity and prebioticity. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is a keystone species in the maintenance of ecological balance. We used a combination of full-length 16S rRNA amplicon sequencing, shotgun metagenomics, and metabolomics to elucidate the species-level community structure and the metabolic potential of the gut microbiota of the plateau pika. Using a full-length 16S rRNA metataxonomic approach, we clustered 618 (166 ± 35 per sample) operational phylogenetic units (OPUs) from 105 plateau pika samples and assigned them to 215 known species, 226 potentially new species, and 177 higher hierarchical taxa. Notably, 39 abundant OPUs (over 60% total relative abundance) are found in over 90% of the samples, thereby representing a "core microbiota." They are all classified as novel microbial lineages, from the class to the species level. Using metagenomic reads, we independently assembled and binned 109 high-quality, species-level genome bins (SGBs). Then, a precise taxonomic assignment was performed to clarify the phylogenetic consistency of the SGBs and the 16S rRNA amplicons. Thus, the majority of the core microbes possess their genomes. SGBs belonging to the genus Treponema, the families Muribaculaceae, Lachnospiraceae, and Oscillospiraceae, and the order Eubacteriales are abundant in the metagenomic samples. In addition, multiple CAZymes are detected in these SGBs, indicating their efficient utilization of plant biomass. As the most widely connected metabolite with the core microbiota, tryptophan may relate to host environmental adaptation. Our investigation allows for a greater comprehension of the composition and functional capacity of the gut microbiota of the plateau pika. IMPORTANCE The great majority of microbial species remain uncultured, severely limiting their taxonomic characterization and biological understanding. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is considered to be the keystone species in the maintenance of ecological stability. We comprehensively investigated the gut microbiota of the plateau pika via a multiomics endeavor. Combining full-length 16S rRNA metataxonomics, shotgun metagenomics, and metabolomics, we elucidated the species-level taxonomic assignment of the core uncultured intestinal microbiota of the plateau pika and revealed their correlation to host nutritional metabolism and adaptation. Our findings provide insights into the microbial diversity and biological significance of alpine animals.

On Holobionts, Holospecies, and Holoniches: the Role of Microbial Symbioses in Ecology and Evolution

My goal in writing this is to increase awareness of the roles played by microbial symbionts in eukaryote ecology and evolution. Most eukaryotes host one or more species of symbiotic microorganisms, including prokaryotes and fungi. Many of these have profound impacts on the biology of their hosts. For example, microbial symbionts may expand the niches of their hosts, cause rapid adaptation of the host to the environment and re-adaptation to novel conditions via symbiont swapping, facilitate speciation, and fundamentally alter our concept of the species. In some cases, microbial symbionts and multicellular eukaryote hosts have a mutual dependency, which has obvious conservation implications. Hopefully, this contribution will stimulate a reevaluation of important ecological and evolutionary concepts including niche, adaptation, the species, speciation, and conservation of multicellular eukaryotes.

Anthropogenic disturbance promotes the diversification of antibiotic resistance genes and virulence factors in the gut of plateau pikas (Ochotona curzoniae)

The prevalence and transmission of antibiotic resistance genes (ARGs) and virulence factors (VFs) pose a great threat to public health. The importance of pollution in determining the occurrence of ARGs and VFs in wildlife is poorly understood. Using a metagenomic approach, this study investigates the composition and functional pathways of bacteria, ARGs, and VFs in the gut microbiome of Plateau pikas in regions of medical pollution (MPR), heavy tourist traffic (HTR), and no contamination (NCR). We found that the abundance of probiotic genera (Clostridium, Eubacterium, Faecalibacterium, and Roseburia) were significantly lower in the HTR. The metabolic pathways of replication and repair in the endocrine and nervous systems were significantly enriched in the MPR, whereas endocrine and metabolic diseases were significantly enriched in the NCR. The Shannon and Gini–Simpson α-diversity indices of ARGs were highest in the HTR, and there were significant differences in β-diversity among the three regions. The resistance of ARGs to glycopeptide antibiotics increased significantly in the MPR, whereas the ARGs for aminocoumarins increased significantly in the HTR. The diversity of mobile genetic elements (MGEs) was significantly higher in the MPR than in other regions. We observed a strong positive correlation between ARGs and pathogenic bacteria, and the network structure was the most complex in the MPR. There were significant differences in the β-diversity of VFs among the three regions. Medical pollution led to significant enrichment of fibronectin-binding protein and PhoP, whereas tourism-related pollution (in the HTR) led to significant enrichment of LPS and LplA1. Our study indicates that environmental pollution can affect the structure and function of gut microbes and disseminate ARGs and VFs via horizontal transmission, thereby posing a threat to the health of wild animals.

The influence of species identity and geographic locations on gut microbiota of small rodents

Although the correlation between gut microbiota, species identity and geographic locations has long attracted the interest of scientists, to what extent species identity and geographic locations influence the gut microbiota assemblages in granivorous rodents needs further investigation. In this study, we performed a survey of gut microbial communities of four rodent species (Apodemus agrarius, A. peninsulae, Tamias sibiricus and Clethrionomys rufocanus) distributed in two areas with great distance (> 600 km apart), to assess if species identity dominates over geographic locations in shaping gut microbial profiles using 16S rRNA gene sequencing. We found that gut microbiota composition varied significantly across host species and was closely correlated with host genetics. We identified strong species identity effects on gut microbial composition, with a comparatively weaker signal of geographic provenance on the intestinal microbiota. Specifically, microbiota of one species was on average more similar to that of conspecifics living in separate sites than to members of a closely related species living in the same location. Our study suggests that both host genetics and geographical variations influence gut microbial diversity of four rodent species, which merits further investigation to reveal the patterns of phylogenetic correlation of gut microbial community assembly in mammals across multiple habitats.

Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium

BACKGROUND

Many animals live in intimate associations with a species-rich microbiome. A key factor in maintaining these beneficial associations is fidelity, defined as the stability of associations between hosts and their microbiota over multiple host generations. Fidelity has been well studied in terrestrial hosts, particularly insects, over longer macroevolutionary time. In contrast, little is known about fidelity in marine animals with species-rich microbiomes at short microevolutionary time scales, that is at the level of a single host population. Given that natural selection acts most directly on local populations, studies of microevolutionary partner fidelity are important for revealing the ecological and evolutionary processes that drive intimate beneficial associations within animal species.

RESULTS

In this study on the obligate symbiosis between the gutless marine annelid Olavius algarvensis and its consortium of seven co-occurring bacterial symbionts, we show that partner fidelity varies across symbiont species from strict to absent over short microevolutionary time. Using a low-coverage sequencing approach that has not yet been applied to microbial community analyses, we analysed the metagenomes of 80 O. algarvensis individuals from the Mediterranean and compared host mitochondrial and symbiont phylogenies based on single-nucleotide polymorphisms across genomes. Fidelity was highest for the two chemoautotrophic, sulphur-oxidizing symbionts that dominated the microbial consortium of all O. algarvensis individuals. In contrast, fidelity was only intermediate to absent in the sulphate-reducing and spirochaetal symbionts with lower abundance. These differences in fidelity are likely driven by both selective and stochastic forces acting on the consistency with which symbionts are vertically transmitted.

CONCLUSIONS

We hypothesize that variable degrees of fidelity are advantageous for O. algarvensis by allowing the faithful transmission of their nutritionally most important symbionts and flexibility in the acquisition of other symbionts that promote ecological plasticity in the acquisition of environmental resources. Video Abstract.

Comparative research of intestinal microbiota diversity and body mass regulation in Eothenomys miletus from different areas of Hengduan mountain regions

In order to investigate the effects of different areas on intestinal bacterial diversity and body mass regulation in Eothenomys miletus from Hengduan mountain regions, and to explore the community structure and diversity of intestinal microflora and their role in body mass regulation. E. miletus was collected from five areas including Deqin (DQ), Xianggelila (XGLL), Lijiang (LJ), Jianchuan (JC), and Dali (DL), we used 16S rRNA sequencing technology combined with physiological and morphological methods to study the intestinal microbiota diversity, abundance and community structure of the intestinal bacteria in winter, and to explore the influence of geographical factors, physiological indicators including food intake, resting metabolic rate (RMR), non-shivering thermogenesis (NST), neuropeptide Y (NPY), Agouti-Related Protein (AgRP), proopiomelanocortin (POMC), cocaine and amphetamine regulated transcription peptide (CART), and morphological indicators including body mass, body length and other nine indicators on the intestinal microflora diversity in E. miletus. The results showed that there were significant differences in metabolic indexes such as RMR, NST, NPY, AgRP, and morphological indexes such as body length, tail length and ear length among the five regions. Bacterial community in intestinal tract of E. miletus mainly includes three phyla, of which Firmicutes is the dominant phyla, followed by Bacteroidetes and Tenericutes. At the genus level, the dominant bacterial genera were S24-7(UG), Clostridiales (UG), and Lachnospiraceae (UG), etc. α diversity of intestinal microorganisms in DL and JC were significantly different from that in the other three regions. Genera of intestinal microorganisms in DL and JC were also the most. Moreover, Bacteroides, Ruminococcus, and Treponema could affect energy metabolism in E. miletus, which were closely related to the environment in which they lived. All of these results indicated that different areas in Hengduan Mountain had certain effects on the structure of intestinal microbial community in E. miletus, which were responded positively to changes in food abundance and other environmental factors. Furthermore, Firmicutes and Bacteroidetes play an important role in the body mass regulation in E. miletus.

Alteration of Gut Microbiota of a Food-Storing Hibernator, Siberian Chipmunk Tamias sibiricus

Hibernation represents a state of fasting because hibernators cease eating in the torpid periods. Therefore, food deprivation during hibernation is expected to modify the gut microbiota of host. However, there are few reports of gut microbiota in food-storing hibernators that feed during the interbout arousals. Here we collected fecal samples of Siberian chipmunk T. sibiricus to character and examine changes in the gut microbiota at various stages relative to hibernation: pre-hibernation, early-hibernation, mid-hibernation, late-hibernation, and post-hibernation. Compared to the pre-hibernation state, alpha-diversity of gut microbiota was significantly increased during the interbout arousal periods. In addition, beta-diversity of the fecal communities from pre-hibernation and interbout arousal periods grouped together, and post-hibernation gut microbiota resembled the counterpart at late-hibernation. Hibernation significantly decreased the relative abundance of Firmicutes but increased Bacteroidetes, reflecting a shift of microbiota toward taxa in favor of host-derived substrates. The increased abundance of Ruminococcaceae_UCG-014, Lactobacillus, and Christensenellaceae_R-7_group in gut microbiota may help the chipmunks reduce intestinal inflammation and then maintain healthy bowel during hibernation. KEGG pathway indicated that hibernation altered the metabolic function of gut microflora of T. sibiricus. Our study provides evidence that the gut microbiota of food-storing hibernators, despite feeding during the interbout arousals, shows similar response to hibernation that has well documented in fat-storing counterparts, suggesting the potential for a core gut microbiota during hibernation of mammals. Importantly, these results will broaden our understanding of the effects of hibernation on gut microbiota of mammal hibernators.

Phylosymbiotic Structures of the Microbiota in Mollitrichosiphum tenuicorpus (Hemiptera: Aphididae: Greenideinae)

Aphids harbor an array of symbionts that provide hosts with ecological benefits. Microbial community assembly generally varies with respect to aphid species, geography, and host plants. However, the influence of host genetics and ecological factors on shaping intraspecific microbial community structures has not been fully understood. In the present study, using Illumina sequencing of the V3 - V4 hypervariable region of the 16S rRNA gene, we characterized the microbial compositions associated with Mollitrichosiphum tenuicorpus from different regions and plants in China. The primary symbiont Buchnera aphidicola and the secondary symbiont Arsenophonus dominated the microbial flora in M. tenuicorpus. Ordination analyses and statistical tests suggested that geography and aphid genetics primarily contributed to the variation in the microbiota of M. tenuicorpus. We further confirmed the combined effect of aphid genetics and geography on shaping the structures of symbiont and secondary symbiont communities. Moreover, the significant correlation between aphid genetic divergence and symbiont community dissimilarity provides evidence for intraspecific phylosymbiosis in natural systems. Our study helped to elucidate the eco-evolutionary relationship between symbiont communities and aphids within one given species.

Eco-Evolutionary Dynamics of the Human-Gut Microbiota Symbiosis in a Changing Nutritional Environment

The operational harmony between living beings and their circumstances, their ever-changing environment, is a constitutive condition of their existence. Nutrition and symbiosis are two essential aspects of this harmony. Disruption of the symbiosis between host and gut microbiota, the so-called dysbiosis, as well as the inadequate diet from which it results, contribute to the etiology of immunometabolic disorders. Research into the development of these diseases is highly influenced by our understanding of the evolutionary roots of metabolic functioning, thereby considering that chronic non-communicable diseases arise from an evolutionary mismatch. However, the lens has been mostly directed toward energy availability and metabolism, but away from our closest environmental factor, the gut microbiota. Thus, this paper proposes a narrative thread that places symbiosis in an evolutionary perspective, expanding the traditional framework of humans’ adaptation to their food environment.

Significant effects of host dietary guild and phylogeny in wild lemur gut microbiomes

Mammals harbor diverse gut microbiomes (GMs) that perform critical functions for host health and fitness. Identifying factors associated with GM variation can help illuminate the role of microbial symbionts in mediating host ecological interactions and evolutionary processes, including diversification and adaptation. Many mammals demonstrate phylosymbiosis-a pattern in which more closely-related species harbor more similar GMs-while others show overwhelming influences of diet and habitat. Here, we generated 16S rRNA sequence data from fecal samples of 15 species of wild lemurs across southern Madagascar to (1) test a hypothesis of phylosymbiosis, and (2) test trait correlations between dietary guild, habitat, and GM diversity. Our results provide strong evidence of phylosymbiosis, though some closely-related species with substantial ecological niche overlap exhibited greater GM similarity than expected under Brownian motion. Phylogenetic regressions also showed a significant correlation between dietary guild and UniFrac diversity, but not Bray-Curtis or Jaccard. This discrepancy between beta diversity metrics suggests that older microbial clades have stronger associations with diet than younger clades, as UniFrac weights older clades more heavily. We conclude that GM diversity is predominantly shaped by host phylogeny, and that microbes associated with diet were likely acquired before evolutionary radiations within the lemur families examined.

Adapting to Novel Environments Together: Evolutionary and Ecological Correlates of the Bacterial Microbiome of the World's Largest Cavefish Diversification (Cyprinidae, Sinocyclocheilus)

The symbiosis between a host and its microbiome is essential for host fitness, and this association is a consequence of the host’s physiology and habitat. Sinocyclocheilus, the largest cavefish diversification of the world, an emerging multi-species model system for evolutionary novelty, provides an excellent opportunity for examining correlates of host evolutionary history, habitat, and gut-microbial community diversity. From the diversification-scale patterns of habitat occupation, major phylogenetic clades (A–D), geographic distribution, and knowledge from captive-maintained Sinocyclocheilus populations, we hypothesize habitat to be the major determinant of microbiome diversity, with phylogeny playing a lesser role. For this, we subject environmental water samples and fecal samples (representative of gut-microbiome) from 24 Sinocyclocheilus species, both from the wild and after being in captivity for 6 months, to bacterial 16S rRNA gene profiling using Illumina sequencing. We see significant differences in the gut microbiota structure of Sinocyclocheilus, reflective of the three habitat types; gut microbiomes too, were influenced by host-related factors. There is no significant association between the gut microbiomes and host phylogeny. However, there is some microbiome related structure at the clade level, with the most geographically distant clades (A and D) being the most distinct, and the two overlapping clades (B and C) showing similarities. Microbes inhabiting water were not a cause for significant differences in fish-gut microbiota, but water quality parameters were. Transferring from wild to captivity, the fish microbiomes changed significantly and became homogenized, signifying plastic changes and highlighting the importance of environmental factors (habitat) in microbiome community assembly. The core microbiome of this group, at higher taxonomic scale, resembled that of other teleost fishes. Our results suggest that divergent natural environments giving rise to evolutionary novelties underlying host adaptations, also includes the microbiome of these fishes.

How microbiomes can help inform conservation: landscape characterisation of gut microbiota helps shed light on additional population structure in a specialist folivore

BACKGROUND

The koala (Phascolarctos cinereus), an iconic yet endangered specialised folivore experiencing widespread decline across Australia, is the focus of many conservation programs. Whilst animal translocation and progressive conservation strategies such as faecal inoculations may be required to bring this species back from the brink of extinction, insight into the variation of host-associated gut microbiota and the factors that shape this variation are fundamental for their success. Despite this, very little is known about the landscape variability and factors affecting koala gut microbial community dynamics. We used large scale field surveys to evaluate the variation and diversity of koala gut microbiotas and compared these diversity patterns to those detected using a population genetics approach. Scat samples were collected from five locations across South East Queensland with microbiota analysed using 16S rRNA gene amplicon sequencing.

RESULTS

Across the landscape koala gut microbial profiles showed large variability, with location having a large effect on bacterial community composition and bacterial diversity. Certain bacteria were found to be significantly differentially abundant amongst locations; koalas from Noosa showed a depletion in two bacterial orders (Gastranaerophilales and Bacteroidales) which have been shown to provide beneficial properties to their host. Koala gut microbial patterns were also not found to mirror population genetic patterns, a molecular tool often used to design conservation initiatives.

CONCLUSIONS

Our data shows that koala gut microbiotas are extremely variable across the landscape, displaying complex micro- and macro- spatial variation. By detecting locations which lack certain bacteria we identified koala populations that may be under threat from future microbial imbalance or dysbiosis. Additionally, the mismatching of gut microbiota and host population genetic patterns exposed important population structure that has previously gone undetected across South East Queensland. Overall, this baseline data highlights the importance of integrating microbiota research into conservation biology in order to guide successful conservation programs such as species translocation and the implementation of faecal inoculations.

Effect of Geography and Captivity on Scat Bacterial Communities in the Imperiled Channel Island Fox

With developing understanding that host-associated microbiota play significant roles in individual health and fitness, taking an interdisciplinary approach combining microbiome research with conservation science is increasingly favored. Here we establish the scat microbiome of the imperiled Channel Island fox (Urocyon littoralis) and examine the effects of geography and captivity on the variation in bacterial communities. Using high throughput 16S rRNA gene amplicon sequencing, we discovered distinct bacterial communities in each island fox subspecies. Weight, timing of the sample collection, and sex contributed to the geographic patterns. We uncovered significant taxonomic differences and an overall decrease in bacterial diversity in captive versus wild foxes. Understanding the drivers of microbial variation in this system provides a valuable lens through which to evaluate the health and conservation of these genetically depauperate foxes. The island-specific bacterial community baselines established in this study can make monitoring island fox health easier and understanding the implications of inter-island translocation clearer. The decrease in bacterial diversity within captive foxes could lead to losses in the functional services normally provided by commensal microbes and suggests that zoos and captive breeding programs would benefit from maintaining microbial diversity.

Seasonal Dietary Shifts Alter the Gut Microbiota of Avivorous Bats: Implication for Adaptation to Energy Harvest and Nutritional Utilization

Plasticity in the microbial community composition and function can permit the host to adapt to ecological, environmental, and physiological changes. Much of the information on the gut microbiota-host relationship to date derives from studies of laboratory model organisms, while little is known concerning wild animals and their ecological relevance to gut microbes. It is also unclear how microbial community composition and activity adapt to changes in diet and energy, nutritional requirements, and utilization induced by dietary expansion from invertebrates to vertebrates. The great evening bat (Ia io) is both an insectivore and an avivore (that is, a bird-eater), and thus provides an opportunity to investigate the diet-host-microbiota-physiology relationship. Here, we investigated this relationship by using 16S rRNA amplicon sequencing and functional prediction in adult males of I. io. We found that gut microbial diversity was similar, while microbial community structures were significantly different between insectivorous and avivorous diets. Moreover, increases in the relative abundance of Firmicutes and the Firmicutes-to-Bacteroidetes ratio, changes in carbohydrate and nucleotide metabolism, and a decrease in Pseudomonas were associated with higher energy demands for hunting birds and with fat storage for entering hibernation and migration. These findings demonstrated that seasonal dietary shifts drive a significant change in the composition and function of gut microbiomes, thereby facilitating adaptation to the challenging avian dietary niche in bats. These results suggest that the gut microbial communities can constantly respond to alterations in diets, potentially facilitating the diversity of wild animal dietary niches, and enhance our understanding of the diet-host-microbiota-physiology relationship. IMPORTANCE The coevolution between the host and its gut microbes can promote an animal's adaptation to its specific ecological niche and changes in energy and nutritional requirements. This study focused on an avivorous bat, the great evening bat (Ia io), to investigate how seasonal dietary shifts affect the gut microbial composition and function, thereby facilitating adaptation to an avian diet. We found that seasonal dietary shifts driving a significant change in the composition and function of gut microbiomes in I. io were associated with higher energy demands for hunting birds and fat storage for entering hibernation and migration. Our study provides novel insight into the role of gut bacteria in generating ecological diversity and flexibility in wild mammals. The results are valuable for clarifying the complicated host-microbiota-physiology relationship in a dietary niche expansion context.

Seasonal Dietary Shifts Alter the Gut Microbiota of Avivorous Bats: Implication for Adaptation to Energy Harvest and Nutritional Utilization

Plasticity in the microbial community composition and function can permit the host to adapt to ecological, environmental, and physiological changes. Much of the information on the gut microbiota-host relationship to date derives from studies of laboratory model organisms, while little is known concerning wild animals and their ecological relevance to gut microbes. It is also unclear how microbial community composition and activity adapt to changes in diet and energy, nutritional requirements, and utilization induced by dietary expansion from invertebrates to vertebrates. The great evening bat (Ia io) is both an insectivore and an avivore (that is, a bird-eater), and thus provides an opportunity to investigate the diet-host-microbiota-physiology relationship. Here, we investigated this relationship by using 16S rRNA amplicon sequencing and functional prediction in adult males of I. io. We found that gut microbial diversity was similar, while microbial community structures were significantly different between insectivorous and avivorous diets. Moreover, increases in the relative abundance of Firmicutes and the Firmicutes-to-Bacteroidetes ratio, changes in carbohydrate and nucleotide metabolism, and a decrease in Pseudomonas were associated with higher energy demands for hunting birds and with fat storage for entering hibernation and migration. These findings demonstrated that seasonal dietary shifts drive a significant change in the composition and function of gut microbiomes, thereby facilitating adaptation to the challenging avian dietary niche in bats. These results suggest that the gut microbial communities can constantly respond to alterations in diets, potentially facilitating the diversity of wild animal dietary niches, and enhance our understanding of the diet-host-microbiota-physiology relationship.

IMPORTANCE The coevolution between the host and its gut microbes can promote an animal’s adaptation to its specific ecological niche and changes in energy and nutritional requirements. This study focused on an avivorous bat, the great evening bat (Ia io), to investigate how seasonal dietary shifts affect the gut microbial composition and function, thereby facilitating adaptation to an avian diet. We found that seasonal dietary shifts driving a significant change in the composition and function of gut microbiomes in I. io were associated with higher energy demands for hunting birds and fat storage for entering hibernation and migration. Our study provides novel insight into the role of gut bacteria in generating ecological diversity and flexibility in wild mammals. The results are valuable for clarifying the complicated host-microbiota-physiology relationship in a dietary niche expansion context.

Experimental validation of small mammal gut microbiota sampling from faeces and from the caecum after death

Data on the gut microbiota (GM) of wild animals are key to studies on evolutionary biology (host-GM interactions under natural selection), ecology and conservation biology (GM as a fitness component closely connected to the environment). Wildlife GM sampling often requires non-invasive techniques or sampling from dead animals. In a controlled experiment profiling microbial 16S rRNA in 52 house mice (Mus musculus) from eight families and four genetic backgrounds, we studied the effects of live- and snap-trapping on small mammal GM and evaluated the suitability of microbiota from non-fresh faeces as a proxy for caecal GM. We compared CM from individuals sampled 16-18 h after death with those in live traps and caged controls, and caecal and faecal GM collected from mice in live-traps. Sampling delay did not affect GM composition, validating data from fresh cadavers or snap-trapped animals. Animals trapped overnight displayed a slight but significant difference in GM composition to the caged controls, though the change only had negligible effect on GM diversity, composition and inter-individual divergence. Hence, the trapping process appears not to bias GM profiling. Despite their significant difference, caecal and faecal microbiota were correlated in composition and, to a lesser extent, diversity. Both showed congruent patterns of inter-individual divergence following the natural structure of the dataset. Thus, the faecal microbiome represents a good non-invasive proxy of the caecal microbiome, making it suitable for detecting biologically relevant patterns. However, care should be taken when analysing mixed datasets containing both faecal and caecal samples.

Gut microbiome adaptation to extreme cold winter in wild plateau pika (Ochotona curzoniae) on the Qinghai-Tibet Plateau

The Qinghai-Tibet Plateau is a harsh environment characterized by low temperature, high altitude and hypoxia, although some native mammals may adapt well to the extreme climate. However, how animal gut microbial community structure and function adapt to extreme cold climates is not well understood. Plateau pika (Ochotona curzoniae) is an ideal animal model with which to study the effects of climate change on host adaptation by studing intestinal microorganisms. Here, we used 16S rRNA sequencing technology combined with physiological methods to investigate plateau pika gut microbiota in summer and winter. Due to limited diet resources, the pikas in winter have a lower ability of degradation and fermentation for plant-based food (reduced cellulase activity and total short-chain fatty acids) by decreasing gut microbial diversity and some functional microbes, such as fiber-degrading bacteria Oscillospira and Treponema. Metagenomic prediction showed that most of those gene functions associated with metabolism (e.g. energy metabolism and lipid metabolism) were less abundant in winter, implying that the plateau pika slows diet fermentation and weakens energy requirements in the cold season. Our results have significance for explaining the mechanism of wild plateau mammals adapting to a high-altitude cold environment from the perspective of gut microbiome.

Shades of grey: host phenotype dependent effect of urbanization on the bacterial microbiome of a wild mammal

BACKGROUND

Host-associated microbiota are integral to the ecology of their host and may help wildlife species cope with rapid environmental change. Urbanization is a globally replicated form of severe environmental change which we can leverage to better understand wildlife microbiomes. Does the colonization of separate cities result in parallel changes in the intestinal microbiome of wildlife, and if so, does within-city habitat heterogeneity matter? Using 16S rRNA gene amplicon sequencing, we quantified the effect of urbanization (across three cities) on the microbiome of eastern grey squirrels (Sciurus carolinensis). Grey squirrels are ubiquitous in rural and urban environments throughout their native range, across which they display an apparent coat colour polymorphism (agouti, black, intermediate).

RESULTS

Grey squirrel microbiomes differed between rural and city environments; however, comparable variation was explained by habitat heterogeneity within cities. Our analyses suggest that operational taxonomic unit (OTU) community structure was more strongly influenced by local environmental conditions (rural and city forests versus human built habitats) than urbanization of the broader landscape (city versus rural). The bacterial genera characterizing the microbiomes of built-environment squirrels are thought to specialize on host-derived products and have been linked in previous research to low fibre diets. However, despite an effect of urbanization at fine spatial scales, phylogenetic patterns in the microbiome were coat colour phenotype dependent. City and built-environment agouti squirrels displayed greater phylogenetic beta-dispersion than those in rural or forest environments, and null modelling results indicated that the phylogenetic structure of urban agouti squirrels did not differ greatly from stochastic expectations.

CONCLUSIONS

Squirrel microbiomes differed between city and rural environments, but differences of comparable magnitude were observed between land classes at a within-city scale. We did not observe strong evidence that inter-environmental differences were the result of disparate selective pressures. Rather, our results suggest that microbiota dispersal and ecological drift are integral to shaping the inter-environmental differences we observed. However, these processes were partly mediated by squirrel coat colour phenotype. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide a useful free-living system with which to study how host genetics mediate environment x microbiome interactions.

Environment and host species identity shape gut microbiota diversity in sympatric herbivorous mammals

The previous studies have reported that the mammalian gut microbiota is a physiological consequence; nonetheless, the factors influencing its composition and function remain unclear. In this study, to evaluate the contributions of the host and environment to the gut microbiota, we conducted a sequencing analysis of 16S rDNA and shotgun metagenomic DNA from plateau pikas and yaks, two sympatric herbivorous mammals, and further compared the sequences in summer and winter. The results revealed that both pikas and yaks harboured considerably more distinct communities between summer and winter. We detected the over-representation of Verrucomicrobia and Proteobacteria in pikas, and Archaea and Bacteroidetes in yaks. Firmicutes and Actinobacteria, associated with energy-efficient acquisition, significantly enriched in winter. The diversity of the microbial community was determined by the interactive effects between the host and season. Metagenomic analysis revealed that methane-metabolism-related pathway of yaks was significantly enriched in summer, while some pathogenic pathways were more abundant in pikas. Both pikas and yaks had a higher capacity for lipid degradation in winter. Pika and yak shared more OTUs when food shortage occurred in winter, and this caused a convergence in gut microbial composition and function. From winter to summer, the network module number increased from one to five in pikas, which was different in yaks. Our study demonstrates that the host is a dominant factor in shaping the microbial communities and that seasonality promotes divergence or convergence based on dietary quality across host species identity.

Host specificity of the gut microbiome

Developing general principles of host-microorganism interactions necessitates a robust understanding of the eco-evolutionary processes that structure microbiota. Phylosymbiosis, or patterns of microbiome composition that can be predicted by host phylogeny, is a unique framework for interrogating these processes. Identifying the contexts in which phylosymbiosis does and does not occur facilitates an evaluation of the relative importance of different ecological processes in shaping the microbial community. In this Review, we summarize the prevalence of phylosymbiosis across the animal kingdom on the basis of the current literature and explore the microbial community assembly processes and related host traits that contribute to phylosymbiosis. We find that phylosymbiosis is less prevalent in taxonomically richer microbiomes and hypothesize that this pattern is a result of increased stochasticity in the assembly of complex microbial communities. We also note that despite hosting rich microbiomes, mammals commonly exhibit phylosymbiosis. We hypothesize that this pattern is a result of a unique combination of mammalian traits, including viviparous birth, lactation and the co-evolution of haemochorial placentas and the eutherian immune system, which compound to ensure deterministic microbial community assembly. Examining both the individual and the combined importance of these traits in driving phylosymbiosis provides a new framework for research in this area moving forward.

Gut microbiota of frugo-folivorous sifakas across environments

Background

Captive animals, compared to their wild counterparts, generally harbor imbalanced gut microbiota owing, in part, to their altered diets. This imbalance is particularly striking for folivores that fundamentally rely on gut microbiota for digestion, yet rarely receive sufficient dietary fiber in captivity. We examine the critically endangered Coquerel’s sifaka (Propithecus coquereli), an anatomically specialized, rather than facultative, folivore that consumes a seasonal frugo-folivorous diet in the wild, but is provisioned predominantly with seasonal foliage and orchard vegetables in captivity. Using amplicon and metagenomic sequencing applied to fecal samples collected from two wild and one captive population (each comprising multiple groups), we clarify how dietary variation underlies the perturbational effect of captivity on the structure and function of this species’ gut microbiota.

Results

The gut microbiota of wild sifakas varied by study population, most notably in community evenness and in the abundance of diet-associated microbes from Prevotellaeceae and Lachnospiraceae. Nevertheless, the differences among wild subjects were minor compared to those evident between wild and captive sifakas: Unusually, the consortia of captive sifakas were the most diverse, but lacked representation of endemic Bacteroidetes and metagenomic capacity for essential amino-acid biosynthesis. Instead, they were enriched for complex fiber metabolizers from the Firmicutes phylum, for archaeal methanogens, and for several metabolic pathways putatively linked to plant fiber and secondary compound metabolism.

Conclusions

The relatively minor differences in gut microbial structure and function between wild sifaka populations likely reflect regional and/or temporal environmental variability, whereas the major differences observed in captive conspecifics, including the loss of endemic microbes, but gain in low-abundance taxa, likely reflect imbalanced or unstable consortia. Indeed, community perturbation may not necessarily entail decreased community diversity. Moreover, signatures of greater fiber degradation indicate that captive sifakas consume a more fibrous diet compared to their wild counterparts. These results do not mirror those typically reported for folivores and herbivores, suggesting that the direction and strength of captivity-induced ‘dysbiosis’ may not be universal across species with similar feeding strategies. We propose that tailored, species-specific dietary interventions in captivity, aimed at better approximating naturally foraged diets, could functionally ‘rewild’ gut microbiota and facilitate successful management of diverse species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00093-5.

Patterns of Microbiome Variation Among Infrapopulations of Permanent Bloodsucking Parasites

While interspecific variation in microbiome composition can often be readily explained by factors such as host species identity, there is still limited knowledge of how microbiomes vary at scales lower than the species level (e.g., between individuals or populations). Here, we evaluated variation in microbiome composition of individual parasites among infrapopulations (i.e., populations of parasites of the same species living on a single host individual). To address this question, we used genome-resolved and shotgun metagenomic data of 17 infrapopulations (balanced design) of the permanent, bloodsucking seal louse Echinophthirius horridus sampled from individual Saimaa ringed seals Pusa hispida saimensis. Both genome-resolved and read-based metagenomic classification approaches consistently show that parasite infrapopulation identity is a significant factor that explains both qualitative and quantitative patterns of microbiome variation at the intraspecific level. This study contributes to the general understanding of the factors driving patterns of intraspecific variation in microbiome composition, especially of bloodsucking parasites, and has implications for understanding how well-known processes occurring at higher taxonomic levels, such as phylosymbiosis, might arise in these systems.

Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales

The gut microbiota is critical for host function. Among mammals, host phylogenetic relatedness and diet are strong drivers of gut microbiota structure, but one factor may be more influential than the other. Here, we used 16S rRNA gene sequencing to determine the relative contributions of host phylogeny and host diet in structuring the gut microbiotas of 11 herbivore species from 5 families living sympatrically in southwest Kenya. Herbivore species were classified as grazers, browsers, or mixed-feeders and dietary data (% C4 grasses in diet) were compiled from previously published sources. We found that herbivore gut microbiotas were highly species-specific, and that host taxonomy accounted for more variation in the gut microbiota (30%) than did host dietary guild (10%) or sample month (8%). Overall, similarity in the gut microbiota increased with host phylogenetic relatedness (r = 0.74) across the 11 species of herbivores, but among 7 closely related Bovid species, dietary %C4 grass values more strongly predicted gut microbiota structure (r = 0.64). Additionally, within bovids, host dietary guild explained more of the variation in the gut microbiota (17%) than did host species (12%). Lastly, while we found that the gut microbiotas of herbivores residing in southwest Kenya converge with those of distinct populations of conspecifics from central Kenya, fine-scale differences in the abundances of bacterial amplicon sequence variants (ASVs) between individuals from the two regions were also observed. Overall, our findings suggest that host phylogeny and taxonomy strongly structure the gut microbiota across broad host taxonomic scales, but these gut microbiotas can be further modified by host ecology (i.e., diet, geography), especially among closely related host species.

The Gut Microbial Composition Is Species-Specific and Individual-Specific in Two Species of Estrildid Finches, the Bengalese Finch and the Zebra Finch

Microbial communities residing in the gastrointestinal tracts of animals have profound impacts on the physiological processes of their hosts. In humans, host-specific and environmental factors likely interact together to shape gut microbial communities, resulting in remarkable inter-individual differences. However, we still lack a full understanding of to what extent microbes are individual-specific and controlled by host-specific factors across different animal taxa. Here, we document the gut microbial characteristics in two estrildid finch species, the Bengalese finch (Lonchura striata domestica) and the zebra finch (Taeniopygia guttata) to investigate between-species and within-species differences. We collected fecal samples from breeding pairs that were housed under strictly controlled environmental and dietary conditions. All individuals were sampled at five different time points over a range of 120 days covering different stages of the reproductive cycle. We found significant species-specific differences in gut microbial assemblages. Over a period of 3 months, individuals exhibited unique, individual-specific microbial profiles. Although we found a strong individual signature in both sexes, within-individual variation in microbial communities was larger in males of both species. Furthermore, breeding pairs had more similar microbial profiles, compared to randomly chosen males and females. Our study conclusively shows that host-specific factors contribute structuring of gut microbiota.

Microbiome and environment explain the absence of correlations between consumers and their diet in Bornean microsnails

Classical ecological theory posits that species partition resources such that each species occupies a unique resource niche. In general, the availability of more resources allows more species to co-occur. Thus, a strong relationship between communities of consumers and their resources is expected. However, correlations may be influenced by other layers in the food web, or by the environment. Here we show, by studying the relationship between communities of consumers (land snails) and individual diets (from seed plants), that there is in fact no direct, or at most a weak but negative, relationship. However, we found that the diversity of the individual microbiome positively correlates with both consumer community diversity and individual diet diversity in three target species. Moreover, these correlations were affected by various environmental variables, such as anthropogenic activity, habitat island size, and a possibly important nutrient source, guano runoff from nearby caves. Our results suggest that the microbiome and the environment explain the absence of correlations between diet and consumer community diversity. Hence, we advocate that microbiome inventories are routinely added to any community dietary analysis, which our study shows can be done with relatively little extra effort. Our approach presents the tools to quickly obtain an overview of the relationships between consumers and their resources. We anticipate our approach to be useful for ecologists and environmentalists studying different communities in a local food web.

Environmental gradients of selection for an alpine-obligate bird, the white-tailed ptarmigan (Lagopus leucura)

The warming climate will expose alpine species adapted to a highly seasonal, harsh environment to novel environmental conditions. A species can shift their distribution, acclimate, or adapt in response to a new climate. Alpine species have little suitable habitat to shift their distribution, and the limits of acclimation will likely be tested by climate change in the long-term. Adaptive genetic variation may provide the raw material for species to adapt to this changing environment. Here, we use a genomic approach to describe adaptive divergence in an alpine-obligate species, the white-tailed ptarmigan (Lagopus leucura), a species distributed from Alaska to New Mexico, across an environmentally variable geographic range. Previous work has identified genetic structure and morphological, behavioral, and physiological differences across the species' range; however, those studies were unable to determine the degree to which adaptive divergence is correlated with local variation in environmental conditions. We used a genome-wide dataset generated from 95 white-tailed ptarmigan distributed throughout the species' range and genotype-environment association analyses to identify the genetic signature and environmental drivers of local adaptation. We detected associations between multiple environmental gradients and candidate adaptive loci, suggesting ptarmigan populations may be locally adapted to the plant community composition, elevation, local climate, and to the seasonality of the environment. Overall, our results suggest there may be groups within the species' range with genetic variation that could be essential for adapting to a changing climate and helpful in guiding conservation action.

Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters

Studies of microbiome variation in wildlife often emphasize host physiology and diet as proximate selective pressures acting on host-associated microbiota. In contrast, microbial dispersal and ecological drift are more rarely considered. Using amplicon sequencing, we characterized the bacterial microbiome of adult female (n = 86) Sable Island horses (Nova Scotia, Canada) as part of a detailed individual-based study of this feral population. Using data on sampling date, horse location, age, parental status, and local habitat variables, we contrasted the ability of spatiotemporal, life history, and environmental factors to explain microbiome diversity among Sable Island horses. We extended inferences made from these analyses with both phylogeny-informed and phylogeny-independent null modelling approaches to identify deviations from stochastic expectations. Phylogeny-informed diversity measures were correlated with spatial and local habitat variables, but null modelling results suggested that heterogeneity in ecological drift, rather than differential selective pressures acting on the microbiome, was responsible for these correlations. Conversely, phylogeny-independent diversity measures were best explained by host spatial and social structure, suggesting that taxonomic composition of the microbiome was shaped most strongly by bacterial dispersal. Parental status was important but correlated with measures of β-dispersion rather than β-diversity (mares without foals had lower alpha diversity and more variable microbiomes than mares with foals). Our results suggest that between host microbiome variation within the Sable Island horse population is driven more strongly by bacterial dispersal and ecological drift than by differential selective pressures. These results emphasize the need to consider alternative ecological processes in the study of microbiomes.

Mechanisms governing avian phylosymbiosis: Genetic dissimilarity based on neutral and MHC regions exhibits little relationship with gut microbiome distributions of Galápagos mockingbirds

The gut microbiome of animals, which serves important functions but can also contain potential pathogens, is to varying degrees under host genetic control. This can generate signals of phylosymbiosis, whereby gut microbiome composition matches host phylogenetic structure. However, the genetic mechanisms that generate phylosymbiosis and the scale at which they act remain unclear. Two non-mutually exclusive hypotheses are that phylosymbiosis is driven by immunogenetic regions such as the major histocompatibility complex (MHC) controlling microbial composition, or by spatial structuring of neutral host genetic diversity via founder effects, genetic drift, or isolation by distance. Alternatively, associations between microbes and host phylogeny may be generated by their spatial autocorrelation across landscapes, rather than the direct effects of host genetics. In this study, we collected MHC, microsatellite, and gut microbiome data from separate individuals belonging to the Galápagos mockingbird species complex, which consists of four allopatrically distributed species. We applied multiple regression with distance matrices and Bayesian inference to test for correlations between average genetic and microbiome similarity across nine islands for which all three levels of data were available. Clustering of individuals by species was strongest when measured with microsatellite markers and weakest for gut microbiome distributions, with intermediate clustering of MHC allele frequencies. We found that while correlations between island-averaged gut microbiome composition and both microsatellite and MHC dissimilarity existed across species, these relationships were greatly weakened when accounting for geographic distance. Overall, our study finds little support for large-scale control of gut microbiome composition by neutral or adaptive genetic regions across closely related bird phylogenies, although this does not preclude the possibility that host genetics shapes gut microbiome at the individual level.

No evidence for phylosymbiosis in western chipmunk species

Phylosymbiosis refers to a congruent pattern between the similarity of microbiomes of different species and the branching pattern of the host phylogeny. Phylosymbiosis has been detected in a variety of vertebrate and invertebrate hosts, but has only been assessed in geographically isolated populations. We tested for phylosymbiosis in eight (sub)species of western chipmunks with overlapping ranges and ecological niches; we used a nuclear (Acrosin) and a mitochondrial (CYTB) phylogenetic marker because there are many instances of mitochondrial introgression in chipmunks. We predicted that similarity among microbiomes increases with: (1) increasing host mitochondrial relatedness, (2) increasing host nuclear genome relatedness and (3) decreasing geographic distance among hosts. We did not find statistical evidence supporting phylosymbiosis in western chipmunks. Furthermore, in contrast to studies of other mammalian microbiomes, similarity of chipmunk microbiomes is not predominantly determined by host species. Sampling site explained most variation in microbiome composition, indicating an important role of local environment in shaping microbiomes. Fecal microbiomes of chipmunks were dominated by Bacteroidetes (72.2%), followed by Firmicutes (24.5%), which is one of the highest abundances of Bacteroidetes detected in wild mammals. Future work will need to elucidate the effects of habitat, ecology and host genomics on chipmunk microbiomes.

Gut microbiomes of sympatric Amazonian wood-eating catfishes (Loricariidae) reflect host identity and little role in wood digestion

Neotropical wood-eating catfishes (family Loricariidae) can occur in diverse assemblages with multiple genera and species feeding on the same woody detritus. As such, they present an intriguing system in which to examine the influence of host species identity on the vertebrate gut microbiome as well as to determine the potential role of gut bacteria in wood digestion. We characterized the gut microbiome of two co-occurring catfish genera and four species: Panaqolus albomaculatus, Panaqolus gnomus, Panaqolus nocturnus, and Panaque bathyphilus, as well as that of submerged wood on which they feed. The gut bacterial community did not significantly vary across three gut regions (proximal, mid, distal) for any catfish species, although interspecific variation in the gut microbiome was significant, with magnitude of interspecific difference generally reflecting host phylogenetic proximity. Further, the gut microbiome of each species was significantly different to that present on the submerged wood. Inferring the genomic potential of the gut microbiome revealed that the majority of wood digesting pathways were at best equivalent to and more often depleted or nonexistent within the catfish gut compared to the submerged wood, suggesting a minimal role for the gut microbiome in wood digestion. Rather, these fishes are more likely reliant on fiber degradation performed by microbes in the environment, with their gut microbiome determined more by host identity and phylogenetic history.

Spatial variation in diet-microbe associations across populations of a generalist North American carnivore

Generalist species, by definition, exhibit variation in niche attributes that promote survival in changing environments. Increasingly, phenotypes previously associated with a species, particularly those with wide or expanding ranges, are dissolving and compelling greater emphasis on population-level characteristics. In the present study, we assessed spatial variation in diet characteristics, gut microbiome and associations between these two ecological traits across populations of coyotes Canis latrans. We highlight the influence of the carnivore community in shaping these relationships, as the coyote varied from being an apex predator to a subordinate, mesopredator across sampled populations. We implemented a scat survey across three distinct coyote populations in Michigan, USA. We used carbon (δ¹³ C) and nitrogen (δ¹⁵ N) isotopic values to reflect consumption patterns and trophic level, respectively. Corresponding samples were also paired with 16S rRNA sequencing to describe the microbial community and correlate with isotopic values. Although consumption patterns were comparable, we found spatial variation in trophic level among coyote populations. Specifically, δ¹⁵ N was highest where coyotes were the apex predator and lowest where coyotes co-occurred with grey wolves Canis lupus. The gut microbial community exhibited marked spatial variation across populations with the lowest operational taxonomic units diversity found where coyotes occurred at their lowest trophic level. Bacteriodes and Fusobacterium dominated the microbiome and were positively correlated across all populations. We found no correlation between δ¹³ C and microbial community attributes. However, positive associations between δ¹⁵ N and specific microbial genera increased as coyotes ascended trophic levels. Coyotes provide a model for exploring implications of niche plasticity because they are a highly adaptable, wide-ranging omnivore. As coyotes continue to vary in trophic position and expand their geographic range, we might expect increased divergence within their microbial community, changes in physiology and alterations in behaviour.

Geographical separation and physiology drive differentiation of microbial communities of two discrete populations of the bat Leptonycteris yerbabuenae

In this paper, we explore how two discrete and geographically separated populations of the lesser long-nosed bat (Leptonycteris yerbabuenae)-one in central and the other in the Pacific region of Mexico-differ in their fecal microbiota composition. Considering the microbiota-host as a unity, in which extrinsic (as food availability and geography) or intrinsic factors (as physiology) play an important role in the microbiota composition, we would expect differentiation in the microbiota of two geographically separated populations. The Amplicon Sequences Variants (ASVs) of the V4 region of the 16s rRNA gene from 68 individuals were analyzed using alpha and beta diversity metrics. We obtained a total of 11 566 (ASVs). The bacterial communities in the Central and Pacific populations had a diversity of 6,939 and 4,088 ASVs, respectively, sharing a core microbiota of 539 ASVs accounting for 75% of the relative abundance, suggesting stability over evolutionary time. The Weighted UniFrac metrics tested by a PERMANOVA showed that lactating and pregnant females had significant beta diversity differences in the two populations compared with other reproductive stages. This could be a consequence of the increased energy requirements of these physiological stages, more than the variation due to geographical separation. In contrast, a positive correlation of the observed ASVs of fecal microbiota with the observed ASVs of plastids related to the diet was observed in the juveniles and adults, suggesting that in these physiological stages an extrinsic factor as the diet shapes the microbiota composition. The results provide a baseline for future studies of the microbiome in these two wild populations of the lesser long-nosed bat, the main pollinator of the Agaves from which the beverages tequila and mezcal are made.

Ecological and evolutionary mechanisms underlying patterns of phylosymbiosis in host-associated microbial communities

Phylosymbiosis, where similarities in host-associated microbial communities recapitulate the phylogeny of their hosts, is a newly recognized yet pervasive pattern in the field of host-microbe interactions. While phylosymbiosis has been documented across many systems, we still have a poor understanding of the mechanisms that underlie this emergent pattern. Host selection of the microbiome is a widely cited mechanism, yet other basic ecological and evolutionary processes (dispersal, drift and diversification) may also be at play. This paper discusses the roles that each of these processes and their interactions may play in yielding phylosymbiotic signals across hosts. Finally, this paper will identify open questions and methods that are required to better understand the relative contributions of these basic processes to phylosymbiosis. Given that phylosymbiosis has been shown to relate to functional components of host fitness, understanding the processes that contribute to these patterns will be important for our understanding of the ecology and evolution of host-microbe interactions. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Phylosymbiosis across Deeply Diverging Lineages of Omnivorous Cockroaches (Order Blattodea)

The gut microbiome is shaped by both host diet and host phylogeny. However, separating the relative influence of these two factors over long periods of evolutionary time is often difficult. We conducted a 16S rRNA gene amplicon-based survey of the gut microbiome from 237 individuals and 19 species of omnivorous cockroaches from the order Blattodea. The order Blattodea represents an ancient lineage of insects that emerged over 300 million years ago, have a diverse gut microbiota, and have a typically gregarious lifestyle. All cockroaches shared a broadly similar gut microbiota, with 66 microbial families present across all species and 13 present in every individual examined. Although our network analysis of the cockroach gut microbiome showed a large amount of connectivity, we demonstrated that gut microbiota cluster strongly by host species. We conducted follow-up tests to determine if cockroaches exhibit phylosymbiosis, or the tendency of host-associated microbial communities to parallel the phylogeny of related host species. Across the full data set, gut microbial community similarity was not found to correlate with host phylogenetic distance. However, a weak but significant phylosymbiotic signature was observed using the matching cluster metric, which allows for localized changes within a phylogenetic tree that are more likely to occur over long evolutionary distances. This finding suggests that host phylogeny plays a large role in structuring the cockroach gut microbiome over shorter evolutionary distances and a weak but significant role in shaping the gut microbiome over extended periods of evolutionary time.IMPORTANCE The gut microbiome plays a key role in host health. Therefore, it is important to understand the evolution of the gut microbiota and how it impacts, and is impacted by, host evolution. In this study, we explore the relationship between host phylogeny and gut microbiome composition in omnivorous, gregarious cockroaches within the Blattodea order, an ancient lineage that spans 300 million years of evolutionary divergence. We demonstrate a strong relationship between host species identity and gut microbiome composition and found a weaker but significant role for host phylogeny in determining microbiome similarity over extended periods of evolutionary time. This study advances our understanding of the role of host phylogeny in shaping the gut microbiome over different evolutionary distances.

An introduction to phylosymbiosis

Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of a new, cross-system trend in host-associated microbiomes. Defining phylosymbiosis as 'microbial community relationships that recapitulate the phylogeny of their host', we review the relevant literature and data in the last decade, emphasizing frequently used methods and regular patterns observed in analyses. Quantitative support for phylosymbiosis is provided by statistical methods evaluating higher microbiome variation between host species than within host species, topological similarities between the host phylogeny and microbiome dendrogram, and a positive association between host genetic relationships and microbiome beta diversity. Significant degrees of phylosymbiosis are prevalent, but not universal, in microbiomes of plants and animals from terrestrial and aquatic habitats. Consistent with natural selection shaping phylosymbiosis, microbiome transplant experiments demonstrate reduced host performance and/or fitness upon host-microbiome mismatches. Hybridization can also disrupt phylosymbiotic microbiomes and cause hybrid pathologies. The pervasiveness of phylosymbiosis carries several important implications for advancing knowledge of eco-evolutionary processes that impact host-microbiome interactions and future applications of precision microbiology. Important future steps will be to examine phylosymbiosis beyond bacterial communities, apply evolutionary modelling for an increasingly sophisticated understanding of phylosymbiosis, and unravel the host and microbial mechanisms that contribute to the pattern. This review serves as a gateway to experimental, conceptual and quantitative themes of phylosymbiosis and outlines opportunities ripe for investigation from a diversity of disciplines.

Gut microbiota of provisioned and wild rhesus macaques (Macaca mulatta) living in a limestone forest in southwest Guangxi, China

The gut microbiota plays an important role in animal health and is strongly affected by the environment. Captivity and human source food have been shown to influence drastically the gut microbiota composition and function of wild animals. Therefore, in the present study, the gut microbiota of provisioned and wild populations of limestone-living rhesus macaques (Macaca mulatta) were compared using high-throughput 16S rRNA sequencing and bioinformatic analyses. The results indicated that provisioned macaques had a higher microbial richness than wild macaques, but there was no significant difference in the evenness of the gut microbiota between the two populations. Provisioned macaques also showed a higher abundance of Firmicutes and a lower abundance of Bacteroidetes than wild macaques. Functional analysis revealed that wild macaques had enriched microbial pathways involved in glycan biosynthesis and metabolism, transport and catabolism, and the digestive and endocrine systems, while provisioned macaques were richer in pathways associated with signaling molecules and interaction, neurodegenerative diseases. These differences were likely due to modification of the gut microbiota of the provisioned macaques to enable the digestion of new foods.

Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea

How the microbiome interacts with hosts across evolutionary time is poorly understood. Data sets including many host species are required to conduct comparative analyses. Here, we analyzed 142 intestinal microbiome samples from 92 birds belonging to 74 species from Equatorial Guinea, using the 16S rRNA gene. Using four definitions for microbial taxonomic units (97%OTU, 99%OTU, 99%OTU with singletons removed, ASV), we conducted alpha and beta diversity analyses. We found that raw abundances and diversity varied between the data sets but relative patterns were largely consistent across data sets. Host taxonomy, diet and locality were significantly associated with microbiomes, at generally similar levels using three distance metrics. Phylogenetic comparative methods assessed the evolutionary relationship between the microbiome as a trait of a host species and the underlying bird phylogeny. Using multiple ways of defining "microbiome traits", we found that a neutral Brownian motion model did not explain variation in microbiomes. Instead, we found a White Noise model (indicating little phylogenetic signal), was most likely. There was some support for the Ornstein-Uhlenbeck model (that invokes selection), but the level of support was similar to that of a White Noise simulation, further supporting the White Noise model as the best explanation for the evolution of the microbiome as a trait of avian hosts. Our study demonstrated that both environment and evolution play a role in the gut microbiome and the relationship does not follow a neutral model; these biological results are qualitatively robust to analytical choices.

Host-associated microbiomes are predicted by immune system complexity and climate

BACKGROUND

Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacterial communities have the potential to elucidate global-scale patterns of microbial community structure and function. It is possible that host surface-associated (external) microbiomes respond more strongly to variations in environmental factors, whereas internal microbiomes are more tightly linked to host factors.

RESULTS

Here, we use the dataset from the Earth Microbiome Project and accumulate data from 50 additional studies totaling 654 host species and over 15,000 samples to examine global-scale patterns of bacterial diversity and function. We analyze microbiomes from non-captive hosts sampled from natural habitats and find patterns with bioclimate and geophysical factors, as well as land use, host phylogeny, and trophic level/diet. Specifically, external microbiomes are best explained by variations in mean daily temperature range and precipitation seasonality. In contrast, internal microbiomes are best explained by host factors such as phylogeny/immune complexity and trophic level/diet, plus climate.

CONCLUSIONS

Internal microbiomes are predominantly associated with top-down effects, while climatic factors are stronger determinants of microbiomes on host external surfaces. Host immunity may act on microbiome diversity through top-down regulation analogous to predators in non-microbial ecosystems. Noting gaps in geographic and host sampling, this combined dataset represents a global baseline available for interrogation by future microbial ecology studies.

Schistosomiasis Vector Snails and Their Microbiota Display a Phylosymbiosis Pattern

Planorbidae snails are the intermediate host for the trematode parasite of the Schistosoma genus, which is responsible for schistosomiasis, a disease that affects both humans and cattle. The microbiota for Schistosoma has already been described as having an effect on host/parasite interactions, specifically through immunological interactions. Here, we sought to characterize the microbiota composition of seven Planorbidae species and strains. Individual snail microbiota was determined using 16S ribosomal DNA amplicon sequencing. The bacterial composition was highly specific to the host strain with limited interindividual variation. In addition, it displayed complete congruence with host phylogeny, revealing a phylosymbiosis pattern. These results were confirmed in a common garden, suggesting that the host highly constrains microbial composition. This study presents the first comparison of bacterial communities between several intermediate snail hosts of Schistosoma parasites, paving the way for further studies on the understanding of this tripartite interaction.

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition

Microbial communities are increasingly recognized as crucial for animal health. However, our understanding of how microbial communities are structured across wildlife populations is poor. Mechanisms such as interspecific associations are important in structuring free-living communities, but we still lack an understanding of how important interspecific associations are in structuring gut microbial communities in comparison with other factors such as host characteristics or spatial proximity of hosts. Here, we ask how gut microbial communities are structured in a population of North American moose Alces alces. We identify key microbial interspecific associations within the moose gut and quantify how important they are relative to key host characteristics, such as body condition, for predicting microbial community composition. We sampled gut microbial communities from 55 moose in a population experiencing decline due to a myriad of factors, including pathogens and malnutrition. We examined microbial community dynamics in this population utilizing novel graphical network models that can explicitly incorporate spatial information. We found that interspecific associations were the most important mechanism structuring gut microbial communities in moose and detected both positive and negative associations. Models only accounting for associations between microbes had higher predictive value compared to models including moose sex, evidence of previous pathogen exposure or body condition. Adding spatial information on moose location further strengthened our model and allowed us to predict microbe occurrences with ~90% accuracy. Collectively, our results suggest that microbial interspecific associations coupled with host spatial proximity are vital in shaping gut microbial communities in a large herbivore. In this case, previous pathogen exposure and moose body condition were not as important in predicting gut microbial community composition. The approach applied here can be used to quantify interspecific associations and gain a more nuanced understanding of the spatial and host factors shaping microbial communities in non-model hosts.

Parallel changes in gut microbiome composition and function during colonization, local adaptation and ecological speciation

The processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from the repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we use three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.

Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species (Sciurus aberti and S. niger) living in sympatry

Microbiota inhabiting the gastrointestinal (GI) tract of animals has important impacts on many host physiological processes. Although host diet is a major factor influencing the composition of the gut micro-organismal community, few comparative studies have considered how differences in diet influence community composition across the length of the GI tract. We used 16S sequencing to compare the microbiota along the length of the GI tract in Abert's (Sciurus aberti) and fox squirrels (S. niger) living in the same habitat. While fox squirrels are generalist omnivores, the diet of Abert's squirrels is unusually high in plant fiber, particularly in winter when they extensively consume fiber-rich inner bark of ponderosa pine (Pinus ponderosa). Consistent with previous studies, microbiota of the upper GI tract of both species consisted primarily of facultative anaerobes and was less diverse than that of the lower GI tract, which included mainly obligate anaerobes. While we found relatively little differentiation between the species in the microbiota of the upper GI tract, the community composition of the lower GI tract was clearly delineated. Notably, the Abert's squirrel lower GI community was more stable in composition and enriched for microbes that play a role in the degradation of plant fiber. In contrast, overall microbial diversity was higher in fox squirrels. We hypothesize that these disparities reflect differences in diet quality and diet breadth between the species.