Environmental filtering increases with elevation for the assembly of gut microbiota in wild pikas

Despite their important roles in host nutrition, metabolism and adaptability, the knowledge on how the mammalian gut microbial community assemble is relatively scanty, especially regarding the ecological mechanisms that govern microbiota along environmental gradients. To address this, we surveyed the diversity, function and ecological processes of gut microbiota in the wild plateau pika, Ochotona curzoniae, along the elevational gradient from 3106 to 4331 m on ‘the Roof of the World’—Qinghai-Tibet Plateau. The results indicated that the alpha, beta and functional diversity of gut microbiota significantly increased with elevation, and elevation significantly explained the variations in the gut microbial communities, even after controlling for geographical distance, host sex and body weight. Some gene functions (e.g. nitrogen metabolism and protein kinases) associated with metabolism were enriched in the high-altitude pikas. Null model and phylogenetic analysis suggest that the relative contributions of environmental filtering responsible for local gut communities increased with elevation. In addition, deterministic processes dominated gut microbial communities in the high-altitude (more than 3694 m) pikas, while the percentages of stochastic and deterministic processes were very close in the low-altitude (3106 and 3580 m) pikas. The observed mechanisms that influence pika gut microbiota assembly and function seemed to be mainly mediated by the internal gut environment and by the external environmental pressure (i.e. lower temperature) in the harsh high-altitude environment. These findings enhance our understanding of gut microbiota assembly patterns and function in wild mammals from extreme harsh environments.     

Altitudinal variation of the gut microbiota in wild house mice

The maintenance of oxygen homeostasis in the gut is critical for the maintenance of a healthy gut microbiota. However, few studies have explored how the concentration of atmospheric oxygen affects the gut microbiota in natural populations. High‐altitude environments provide an opportunity to study the potential effects of atmospheric oxygen on the composition and function of the gut microbiota. Here, we characterized the caecal microbial communities of wild house mice (Mus musculus domesticus) in two independent altitudinal transects, one in Ecuador and one in Bolivia, from sea level to nearly 4,000 m. First, we found that differences in altitude were associated with differences in the gut microbial community after controlling for the effects of body mass, diet, reproductive status and population of origin. Second, obligate anaerobes tended to show a positive correlation with altitude, while all other microbes tended to show a negative correlation with altitude. These patterns were seen independently in both transects, consistent with the expected effects of atmospheric oxygen on gut microbes. Prevotella was the most‐enriched genus at high elevations in both transects, consistent with observations in high‐altitude populations of pikas, ruminants and humans, and also consistent with observations of laboratory mice exposed to hypoxic conditions. Lastly, the renin–angiotensin system, a recently proposed microbiota‐mediated pathway of blood pressure regulation, was the top predicted metagenomic pathway enriched in high altitudes in both transects. These results suggest that high‐altitude environments affect the composition and function of the gut microbiota in wild mammals.     

Seasonal variation in structure and function of gut microbiota in Pomacea canaliculata

Gut microbiota is associated with host health and its environmental adaption, influenced by seasonal variation. Pomacea canaliculata is one of the world''s 100 worst invasive alien species. Here, we used high‐throughput sequencing of the 16S rRNA gene to analyze the seasonal variation of gut microbiota of P. canaliculata. The results suggested that the predominant gut microbial phyla of P. canaliculata included Firmicutes and Proteobacteria, which helped digest plant food and accumulate energy. The gut microbiota of P. canaliculata in summer group showed the highest diversity, whereas the winter group possessed the lowest, probably due to the shortage of food resources of P. canaliculata in winter. Principal coordinate analysis analysis based on unweighted unifrac and weighted unifrac indicated that the composition of gut microbiota of P. canaliculata significantly varied across seasons. Bacteroidetes tended to be enriched in summer by linear discriminant analysis effect size analysis. Actinobacteria and Cyanobacteria were extremely abundant in autumn, while Fusobacteria and Cetobacterium enriched in winter. In conclusion, the structure of the gut microbiota of P. canaliculata was significantly different among seasons, which was beneficial to the environment adaptation and the digestion and metabolism of food during different periods.     

高原鼠兔肠道微生物中丰富及稀有类群的季节性特征

气候及食物是驱动植食性小哺乳动物肠道菌群产生季节性变化的重要因素。然而,此类研究很少涉及肠道丰富及稀有微生物类群。本文以高原鼠兔（Ochotona curzoniae）为对象,通过16S rRNA基因测序和分析,探讨丰富及稀有肠道微生物类群的结构组成、多样性指数及功能在春、夏、秋、冬四季的变化特征。结果显示,丰富类群对菌群主要门和功能的季节性变异贡献大于稀有类群,稀有类群对菌群OTU和alpha多样性的变异贡献大于丰富类群。丰富类群和稀有类群的香农指数均在冬季显著高于其他季节;丰富类群的ACE指数在秋季显著低于其他季节,而稀有类群的ACE指数则在冬季显著高于春季和夏季。丰富类群中拟杆菌门（Bacteroidetes）的相对丰度在冬季和秋季显著高于春季和夏季,但在稀有类群中,夏季和秋季的相对丰度显著高于冬季和春季。丰富类群中氨基酸代谢通路的相对丰度在冬季显著高于春季和夏季,而在稀有类群中,其相对丰度在春季显著高于夏季和秋季。气温、降水量和植被中的营养物质与肠道菌群中丰富类群和稀有类群的变化均显著相关,环境变量对丰富类群和稀有类群变化的总解释率分别为18%（气温：3%;降水：4%;植被营养成分：10%;联合：1%）和9%（气温：1%;降水：2%;植被营养成分：5%;联合：1%）。以上结果表明肠道微生物中的丰富和稀有类群具有不同的分布模式和季节性特征,二者对整体菌群变异的贡献存在差异,环境因素更多地影响丰富类群,反映了肠道微生物不同类群对季节变化响应的非一致性。本研究增进了我们对哺乳动物肠道菌群季节性变化过程及环境适应性的认识。     

Gut microbiota of invasive bullfrog tadpoles responds more rapidly to temperature than a noninvasive congener

Environmental temperature can alter the composition, diversity, and function of ectothermic vertebrate gut microbial communities, which may result in negative consequences for host physiology, or conversely, increase phenotypic plasticity and persistence in harsh conditions. The magnitude of either of these effects will depend on the length of time animals are exposed to extreme temperatures, and how quickly the composition and function of the gut microbiota can respond to temperature change. However, the temporal effects of temperature on gut microbiota are currently unknown. Here, we investigated the length of time required for increased temperature to alter the composition of gut bacterial communities in tadpoles of two frog species, the green frog, Lithobates clamitans, and its congener, the globally invasive American bullfrog, L. catesbeianus. We also explored the potential functional consequences of these changes by comparing predicted metagenomic profiles across temperature treatments at the last experimental time point. Bullfrog‐associated microbial communities were more plastic than those of the green frog. Specifically, bullfrog communities were altered by increased temperature within hours, while green frog communities took multiple days to exhibit significant changes. Further, over ten times more bullfrog bacterial functional pathways were temperature‐dependent compared to the green frog. These results support our hypothesis that bullfrog gut microbial communities would respond more rapidly to temperature change, potentially bolstering their ability to exploit novel environments. More broadly, we have revealed that even short‐term increases in environmental temperature, expected to occur frequently under global climate change, can alter the gut microbiota of ectothermic vertebrates.     

Intestinal microbiota composition in fishes is influenced by host ecology and environment

The digestive tracts of vertebrates are colonized by complex assemblages of micro-organisms, collectively called the gut microbiota. Recent studies have revealed important contributions of gut microbiota to vertebrate health and disease, stimulating intense interest in understanding how gut microbial communities are assembled and how they impact host fitness (Sekirov et al. 2010). Although all vertebrates harbour a gut microbiota, current information on microbiota composition and function has been derived primarily from mammals. Comparisons of different mammalian species have revealed intriguing associations between gut microbiota composition and host diet, anatomy and phylogeny (Ley et al. 2008b). However, mammals constitute <10% of all vertebrate species, and it remains unclear whether similar associations exist in more diverse and ancient vertebrate lineages such as fish. In this issue, Sullam et al. (2012) make an important contribution toward identifying factors determining gut microbiota composition in fishes. The authors conducted a detailed meta-analysis of 25 bacterial 16S rRNA gene sequence libraries derived from the intestines of different fish species. To provide a broader context for their analysis, they compared these data sets to a large collection of 16S rRNA gene sequence data sets from diverse free-living and host-associated bacterial communities. Their results suggest that variation in gut microbiota composition in fishes is strongly correlated with species habitat salinity, trophic level and possibly taxonomy. Comparison of data sets from fish intestines and other environments revealed that fish gut microbiota compositions are often similar to those of other animals and contain relatively few free-living environmental bacteria. These results suggest that the gut microbiota composition of fishes is not a simple reflection of the micro-organisms in their local habitat but may result from host-specific selective pressures within the gut (Bevins & Salzman 2011).     

Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota

To explain differences in gut microbial communities we must determine how processes regulating microbial community assembly (colonization, persistence) differ among hosts and affect microbiota composition. We surveyed the gut microbiota of threespine stickleback (Gasterosteus aculeatus) from 10 geographically clustered populations and sequenced environmental samples to track potential colonizing microbes and quantify the effects of host environment and genotype. Gut microbiota composition and diversity varied among populations. These among-population differences were associated with multiple covarying ecological variables: habitat type (lake, stream, estuary), lake geomorphology and food- (but not water-) associated microbiota. Fish genotype also covaried with gut microbiota composition; more genetically divergent populations exhibited more divergent gut microbiota. Our results suggest that population level differences in stickleback gut microbiota may depend more on internal sorting processes (host genotype) than on colonization processes (transient environmental effects).     

海拔高度对青藏高原放牧牦牛肠道菌群多样性的影响

[背景]肠道菌群与宿主健康及环境适应性密切相关,牦牛为青藏高原特有的草食性反刍动物,不同海拔高度如何影响牦牛肠道菌群组成及肠道菌群在牦牛适应高海拔生境中的作用尚不清楚.[目的]探究青藏高原放牧牦牛肠道菌群多样性及其与海拔高度间的关系.[方法]采集青海省玛沁县(海拔4220 m)和乐都县(2745 m)2个海拔高度放牧牦...     

Comparative analysis of Korean human gut microbiota by barcoded pyrosequencing

Human gut microbiota plays important roles in harvesting energy from the diet, stimulating the proliferation of the intestinal epithelium, developing the immune system, and regulating fat storage in the host. Characterization of gut microbiota, however, has been limited to western people and is not sufficiently extensive to fully describe microbial communities. In this study, we investigated the overall composition of the gut microbiota and its host specificity and temporal stability in 20 Koreans using 454-pyrosequencing with barcoded primers targeting the V1 to V3 region of the bacterial 16S rRNA gene. A total of 303,402 high quality reads covered each sample and 8,427 reads were analyzed on average. The results were compared with those of individuals from the USA, China and Japan. In general, microbial communities were dominated by five previously identified phyla: Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Proteobacteria. UPGMA cluster analysis showed that the species composition of gut microbiota was host-specific and stable over the duration of the test period, but the relative abundance of each member fluctuated. 43 core Korean gut microbiota were identified by comparison of sequences from each individual, of which 15 species level phylotypes were related to previously-reported butyrate-producing bacteria. UniFrac analysis revealed that human gut microbiota differed between countries: Korea, USA, Japan and China, but tended to vary less between individual Koreans, suggesting that gut microbial composition is related to internal and external characteristics of each country member such as host genetics and diet styles.     

Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats

Host ecological factors and external environmental factors are known to influence the structure of gut microbial communities, but few studies have examined the impacts of environmental changes on microbiotas in free‐ranging animals. Rapid land‐use change has the potential to shift gut microbial communities in wildlife through exposure to novel bacteria and/or by changing the availability or quality of local food resources. The consequences of such changes to host health and fitness remain unknown and may have important implications for pathogen spillover between humans and wildlife. To better understand the consequences of land‐use change on wildlife microbiotas, we analyzed long‐term dietary trends, gut microbiota composition, and innate immune function in common vampire bats (Desmodus rotundus) in two nearby sites in Belize that vary in landscape structure. We found that vampire bats living in a small forest fragment had more homogenous diets indicative of feeding on livestock and shifts in microbiota heterogeneity, but not overall composition, compared to those living in an intact forest reserve. We also found that irrespective of sampling site, vampire bats which consumed relatively more livestock showed shifts in some core bacteria compared with vampire bats which consumed relatively less livestock. The relative abundance of some core microbiota members was associated with innate immune function, suggesting that future research should consider the role of the host microbiota in immune defense and its relationship to zoonotic infection dynamics. We suggest that subsequent homogenization of diet and habitat loss through livestock rearing in the Neotropics may lead to disruption to the microbiota that could have downstream impacts on host immunity and cross‐species pathogen transmission.     

土壤动物肠道微生物多样性研究进展

随着分子生物学技术方法的快速发展,动物肠道微生物已成为医学、动物生理学与微生物生态学等研究领域热点。土壤动物种类繁多,分布广泛,其作为陆地生态系统重要组分,是驱动生态系统功能的关键因子。土壤动物体内的微生物由于与宿主长期共存,在与宿主协同进化中形成了丰富多样的群落结构,能够影响土壤动物本身的健康,进而介导土壤动物生态功能的实现。近些年,土壤动物肠道微生物工作方兴未艾,日渐得到重视。总结了四个部分内容：1)首先总结了土壤动物肠道微生物多样性领域的研究现状,该领域年发文量逐年增长,且近十年增长快速。土壤模式生物肠道微生物多样性研究较多且更为深入。土壤动物肠道微生物多样性组成与驱动机制、共存机制及群落构建的理论研究是该领域前沿;2)进而展示了土壤动物肠道微生物多样性组成和研究方法,土壤动物肠道菌群组成以变形菌门、厚壁菌门、放线菌门和拟杆菌门为主。早期工作基于传统分离培养,近年来新一代测序技术推动了该领域发展;3)接着关注了土壤动物肠道微生物的生态学功能,总体上体现在肠道微生物能帮助宿主分解食物基质、参与营养利用、影响寿命和繁殖及提高宿主免疫能力,且其能够影响土壤动物的气体排放及介导其对生态系...     

Kinship,inbreeding and fine‐scale spatial structure influence gut microbiota in a hindgut‐fermenting tortoise

Herbivorous vertebrates rely on complex communities of mutualistic gut bacteria to facilitate the digestion of celluloses and hemicelluloses. Gut microbes are often convergent based on diet and gut morphology across a phylogenetically diverse group of mammals. However, little is known about microbial communities of herbivorous hindgut‐fermenting reptiles. Here, we investigate how factors at the individual level might constrain the composition of gut microbes in an obligate herbivorous reptile. Using multiplexed 16S rRNA gene sequencing, we characterized the faecal microbial community of a population of gopher tortoises (Gopherus polyphemus) and examined how age, genetic diversity, spatial structure and kinship influence differences among individuals. We recovered phylotypes associated with known cellulolytic function, including candidate phylum Termite Group 3, suggesting their importance for gopher tortoise digestion. Although host genetic structure did not explain variation in microbial composition and community structure, we found that fine‐scale spatial structure, inbreeding, degree of relatedness and possibly ontogeny shaped patterns of diversity in faecal microbiomes of gopher tortoises. Our findings corroborate widespread convergence of faecal‐associated microbes based on gut morphology and diet and demonstrate the role of spatial and demographic structure in driving differentiation of gut microbiota in natural populations.     

Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity

Animals harbour diverse communities of symbiotic bacteria, which differ dramatically among host individuals. This heterogeneity poses an immunological challenge: distinguishing between mutualistic and pathogenic members of diverse and host‐specific microbial communities. We propose that Major Histocompatibility class II (MHC) genotypes contribute to recognition and regulation of gut microbes, and thus, MHC polymorphism contributes to microbial variation among hosts. Here, we show that MHC IIb polymorphism is associated with among‐individual variation in gut microbiota within a single wild vertebrate population of a small fish, the threespine stickleback. We sampled stickleback from Cedar Lake, on Vancouver Island, and used next‐generation sequencing to genotype the sticklebacks’ gut microbiota (16S sequencing) and their MHC class IIb exon 2 sequences. The presence of certain MHC motifs was associated with altered relative abundance (increase or decrease) of some microbial Families. The effect sizes are modest and entail a minority of microbial taxa, but these results represent the first indication that MHC genotype may affect gut microbiota composition in natural populations (MHC‐microbe associations have also been found in a few studies of lab mice). Surprisingly, these MHC effects were frequently sex‐dependent. Finally, hosts with more diverse MHC motifs had less diverse gut microbiota. One implication is that MHC might influence the efficacy of therapeutic strategies to treat dysbiosis‐associated disease, including the outcome of microbial transplants between healthy and diseased patients. We also speculate that macroparasite‐driven selection on MHC has the potential to indirectly alter the host gut microbiota, and vice versa.     

室内饲养对高原鼠兔肠道微生物群落构建过程的影响

群落生态构建过程是近年来微生物群落生态学的研究热点。室内饲养可引起肠道菌群的剧烈变化,这种改变是否会影响群落的构建过程,一直未见报道。本文以高原鼠兔(Ochotona curzoniae)为对象,采用16S rRNA测序技术,探讨室内饲养和野生高原鼠兔肠道微生物群落在结构、功能以及群落构建过程等方面的差异。结果表明,在繁殖季节,室内饲养组的群落多样性指数和均匀度指数均显著低于野外组;群落丰度指数和群落覆盖度指数在非繁殖季节显著高于繁殖季节。拟杆菌门(Bacteroidetes)在室内饲养组显著富集,而厚壁菌门(Firmicute)和浮霉菌门(Planctomycetes)在野外组显著富集;在野外组,Epsilonbacteraeota和软壁菌门(Tenericutes)在繁殖季节显著富集。菌群功能分析显示,室内饲养组与野生组在细胞通讯和心血管疾病通路存在显著差异;野外组繁殖季节与非繁殖季节肠道菌群功能在氨基酸代谢、碳水化合物代谢和脂质代谢等通路存在显著差异。中性模型拟合结果表明,室内饲养明显降低了菌群构建的随机过程。野外组生理状态也会降低菌群构建的随机性。本研究证明室内饲养和宿主生理状...     

Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits

The gastrointestinal tract harbors a complex and diverse microbiota that has an important role in host metabolism. Microbial diversity is influenced by a combination of environmental and host genetic factors and is associated with several polygenic diseases. In this study we combined next-generation sequencing, genetic mapping, and a set of physiological traits of the BXD mouse population to explore genetic factors that explain differences in gut microbiota and its impact on metabolic traits. Molecular profiling of the gut microbiota revealed important quantitative differences in microbial composition among BXD strains. These differences in gut microbial composition are influenced by host-genetics, which is complex and involves many loci. Linkage analysis defined Quantitative Trait Loci (QTLs) restricted to a particular taxon, branch or that influenced the variation of taxa across phyla. Gene expression within the gastrointestinal tract and sequence analysis of the parental genomes in the QTL regions uncovered candidate genes with potential to alter gut immunological profiles and impact the balance between gut microbial communities. A QTL region on Chr 4 that overlaps several interferon genes modulates the population of Bacteroides, and potentially Bacteroidetes and Firmicutes-the predominant BXD gut phyla. Irak4, a signaling molecule in the Toll-like receptor pathways is a candidate for the QTL on Chr15 that modulates Rikenellaceae, whereas Tgfb3, a cytokine modulating the barrier function of the intestine and tolerance to commensal bacteria, overlaps a QTL on Chr 12 that influence Prevotellaceae. Relationships between gut microflora, morphological and metabolic traits were uncovered, some potentially a result of common genetic sources of variation.     

Proteomics,human gut microbiota and probiotics

The various bacterial communities associated with humans have many functions and the gut microbiota has a major role in the host. Bacterial imbalance in the gut, known as dysbiosis, has therefore been linked to several diseases. Probiotics, that is, microbial strains that have beneficial effects on the host, are thought to benefit this intestinal ecosystem. Hence, knowledge of the gut microbiota composition and an understanding of its functionalities are of interest. Recently, efforts have focused on developing new high-throughput techniques for studying microbial cells and complex communities. Among them, proteomics is increasingly being used. The purpose of this article is to focus on the recent development of this technology and its usefulness in analyzing the human gut ecosystem and probiotic strains.     

How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes

Exploring the mechanisms of maintaining microbial community structure is important to understand biofilm development or microbiota dysbiosis. In this paper, we propose a functional gene-based composition prediction(FCP) model to predict the population structure composition within a microbial community. The model predicts the community composition well in both a low-complexity community as acid mine drainage(AMD) microbiota, and a complex community as human gut microbiota. Furthermore, we define community structure shaping(CSS) genes as functional genes crucial for shaping the microbial community. We have identified CSS genes in AMD and human gut microbiota samples with FCP model and find that CSS genes change with the conditions. Compared to essential genes for microbes, CSS genes are significantly enriched in the genes involved in mobile genetic elements, cell motility, and defense mechanisms, indicating that the functions of CSS genes are focused on communication and strategies in response to the environment factors. We further find that it is the minority, rather than the majority, which contributes to maintaining community structure. Compared to health control samples, we find that some functional genes associated with metabolism of amino acids, nucleotides, and lipopolysaccharide are more likely to be CSS genes in the disease group. CSS genes may help us to understand critical cellular processes and be useful in seeking addable gene circuitries to maintain artificial self-sustainable communities. Our study suggests that functional genes are important to the assembly of microbial communities.     

Proteomics, human gut microbiota and probiotics

The various bacterial communities associated with humans have many functions and the gut microbiota has a major role in the host. Bacterial imbalance in the gut, known as dysbiosis, has therefore been linked to several diseases. Probiotics, that is, microbial strains that have beneficial effects on the host, are thought to benefit this intestinal ecosystem. Hence, knowledge of the gut microbiota composition and an understanding of its functionalities are of interest. Recently, efforts have focused on developing new high-throughput techniques for studying microbial cells and complex communities. Among them, proteomics is increasingly being used. The purpose of this article is to focus on the recent development of this technology and its usefulness in analyzing the human gut ecosystem and probiotic strains.     

Diet drives convergent evolution of gut microbiomes in bamboo-eating species

Gut microbiota plays a critical role in host physiology and health. The coevolution between the host and its gut microbes facilitates animal adaptation to its specific ecological niche. Multiple factors such as host diet and phylogeny modulate the structure and function of gut microbiota. However, the relative contribution of each factor in shaping the structure of gut microbiota remains unclear. The giant(Ailuropoda melanoleuca) and red(Ailurus styani) pandas belong to different families of order Carnivora. They have evolved as obligate bamboo-feeders and can be used as a model system for studying the gut microbiome convergent evolution. Here, we compare the structure and function of gut microbiota of the two pandas with their carnivorous relatives using 16S rRNA and metagenome sequencing. We found that both panda species share more similarities in their gut microbiota structure with each other than each species shares with its carnivorous relatives. This indicates that the specialized herbivorous diet rather than host phylogeny is the dominant driver of gut microbiome convergence within Arctoidea.Metagenomic analysis revealed that the symbiotic gut microbiota of both pandas possesses a high level of starch and sucrose metabolism and vitamin B12 biosynthesis. These findings suggest a diet-driven convergence of gut microbiomes and provide new insight into host-microbiota coevolution of these endangered species.     

Comparative metagenomics analysis reveals how the diet shapes the gut microbiota in several small mammals

The gut microbiomes of the host are large and complex communities, which helps to maintain homeostasis, improves digestive efficiency, and promotes the development of the immune system. The small mammals distributed in Sichuan Province are the most popular species for biodiversity research in Southwest China. However, the effects of different diets on the structure and function of the gut microbial community of these small mammals are poorly understood. In this study, whole‐metagenome shotgun sequencing has been used to analyze the composition and functional structures of the gut microbiota of seven small mammals in Laojunshan National Nature Reserve, Sichuan Province, China. Taxonomic classification revealed that the most abundant phyla in the gut of seven small mammals were Bacteroides, Proteobacteria, and Firmicutes. Moreover, Hafnia, Lactobacillus, and Yersinia were the most abundant genus in the gut microbiomes of these seven species. At the functional level, we annotated a series of KEGG functional pathways, six Cazy categories, and 46,163 AROs in the gut microbiomes of the seven species. Comparative analysis found that the difference in the gut microbiomes between the Soricidea and Muridae concentrated on the increase in the F/B (Firmicutes/Bacteroides) ratio in the Soricidea group, probably driven by the high‐fat and ‐calorie digestive requirements due to their insectivorous diet. The comparative functional profiling revealed that functions related to metabolism and carbohydrates were significantly more abundant in Muridae group, which may be attributed to their high carbohydrate digestion requirements caused by their herbivorous diet. These data suggested that different diets in the host may play an important role in shaping the gut microbiota, and lay the foundation for teasing apart the influences of heritable and environmental factors on the evolution of gut microbial communities.