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...     

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.     

Host and environmental influences on the gut bacterial community of carabid beetles in distinct paddy fields

The relationship between the gut bacterial communities of carabid beetles and their habitats holds implications for understanding ecological dynamics. This study examined the gut bacterial communities of two carabid beetle species, Chlaenius pallipes and Pheropsophus jessoensis, in terraced and flat paddy fields. Differences in gut bacterial communities were evident at the species level and were based on habitat. Specifically, P. jessoensis had a greater presence of Firmicutes and Proteobacteria in terraced fields but more Actinobacteria in flatland fields. In comparison, C. pallipes consistently showed high levels of Firmicutes in both habitats. These differences were reflected at class and genus levels, emphasizing the role of host specificity in shaping gut microbiota. Alpha diversity metrics indicated that P. jessoensis hosted a more diverse bacterial community than C. pallipes. Terraced fields, however, showed slightly reduced diversity in P. jessoensis, suggesting environmental effects on microbial populations. Beta diversity analysis using Bray–Curtis distances differentiated the bacterial communities of the two beetles. Multivariate analysis of variance reinforced these findings. Insights from the Sloan neutral model indicate that environmental factors predominantly influence bacterial community assembly through stochastic processes. Functionally, metabolism was highlighted, indicating the role of gut bacteria in beetle metabolic processes. Notably, energy metabolism varied between field types, revealing environmental effects on gut bacterial functions. This study offers in-depth insights into interactions between host-specific and environmental factors influencing gut bacterial communities of carabid beetles, contributing to a broader understanding of microbial ecology and the roles of environment and host in microbiota dynamics.     

Exploring the gut microbiota composition of Indian major carp,rohu (Labeo rohita), under diverse culture conditions

Gut microbiota of freshwater carps are often investigated for their roles in nutrient absorption, enzyme activities and probiotic properties. However, little is known about core microbiota, assembly pattern and the environmental influence on the gut microbiota of the Indian major carp, rohu. The gut microbial composition of rohu reared in different culture conditions was analysed by 16S rRNA amplicon sequencing. There was variation on gut microbial diversity and composition. A significant negative correlation between dissolved oxygen content (DO) and alpha diversity was observed, thus signifying DO content as one of the key environmental factors that regulated the diversity of rohu gut microbial community. A significant positive correlation was observed between phosphate concentration and abundance of Actinobacteria in different culture conditions. Two phyla, Proteobacteria and Actinobacteria along with OTU750868 (Streptomyces) showed significant (p < 0.05) differences in their abundance among all culture conditions. The Non-metric multidimensional scaling ordination (NMDS) analysis using Bray-Curtis distances, showed the presence of unique gut microbiota in rohu compared to other herbivorous fish. Based on niche breadth, 3 OTUs were identified as core generalists, persistent across all the culture conditions whereas the specialists dominated in the rohu gut microbiota assembly. Co-occurrence network analysis revealed positive interaction within core members while mutual exclusion between core and non-core members. Predicted microbiota function revealed that different culture conditions affected the metabolic capacity of gut microbiota of rohu. The results overall indicated the significant effect of different rearing environments on gut microbiota structure, assembly and inferred community function of rohu which might be useful for effective manipulation of gut microbial communities of rohu to promote better health and growth under different husbandry settings.     

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).     

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.     

Diversity of diazotrophic gut inhabitants of pikas (Ochotonidae) revealed by PCR-DGGE analysis

Diazotrophic gut symbionts are considered to act as nitrogen providers for their hosts, as was shown for various termite species. Although the diet of lagomorphs, like pikas or rabbits, is very poor in nitrogen and energy, their fecal matter contains 30–40% of protein. Since our hypothesis was that pikas maintained a diazotrophic consortium in their gastrointestinal tract, we conducted the first investigation of microbial diversity in pika guts. We obtained gut samples from animals of several Ochotona species, O. hyperborea (Northern pika), O. mantchurica (Manchurian pika), and O. dauurica (Daurian pika), in order to retrieve and compare the nitrogen-fixing communities of different pika species. The age and gender of the animals were taken into consideration. We amplified 320-bp long fragments of the nifH gene using the DNA extracted directly from the colon and cecum samples of pika’s gut, resolved them by DGGE, and performed phylogenetic reconstruction of 51 sequences obtained from excised bands. No significant difference was detected between the nitrogen-fixing gut inhabitants of different pika species. NifH sequences fell into two clusters. The first cluster contained the sequences affiliated with NifH Cluster I (Zehr et al., 2003) with similarity to Sphingomonas sp., Bradyrhizobium sp., and various uncultured bacteria from soil and rhizosphere. Sequences from the second group were related to Treponema sp., Fibrobacter succinogenes, and uncultured clones from the guts of various termites and belonged to NifH Cluster III. We suggest that diazotrophic organisms from the second cluster are genuine endosymbionts of pikas and provide nitrogen for further synthesis processes thus allowing these animals not to be short of protein.     

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.     

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...     

Metaproteomic strategies and applications for gut microbial research

The human intestine hosts various complex microbial communities that are closely associated with multiple health and disease processes. Determining the composition and function of these microbial communities is critical to unveil disease mechanisms and promote human health. Recently, meta-omic strategies have been developed that use high-throughput techniques to provide a wealth of information, thus accelerating the study of gut microbes. Metaproteomics is a newly emerged analytical approach that aims to identify proteins on a large scale in complex environmental microbial communities (e.g., the gut microbiota). This review introduces the recent analytical strategies and applications of metaproteomics, with a focus on advances in gut microbiota research, including a discussion of the limitations and challenges of these approaches.

     

Deterministic Assembly of Complex Bacterial Communities in Guts of Germ-Free Cockroaches

The gut microbiota of termites plays important roles in the symbiotic digestion of lignocellulose. However, the factors shaping the microbial community structure remain poorly understood. Because termites cannot be raised under axenic conditions, we established the closely related cockroach Shelfordella lateralis as a germ-free model to study microbial community assembly and host-microbe interactions. In this study, we determined the composition of the bacterial assemblages in cockroaches inoculated with the gut microbiota of termites and mice using pyrosequencing analysis of their 16S rRNA genes. Although the composition of the xenobiotic communities was influenced by the lineages present in the foreign inocula, their structure resembled that of conventional cockroaches. Bacterial taxa abundant in conventional cockroaches but rare in the foreign inocula, such as Dysgonomonas and Parabacteroides spp., were selectively enriched in the xenobiotic communities. Donor-specific taxa, such as endomicrobia or spirochete lineages restricted to the gut microbiota of termites, however, either were unable to colonize germ-free cockroaches or formed only small populations. The exposure of xenobiotic cockroaches to conventional adults restored their normal microbiota, which indicated that autochthonous lineages outcompete foreign ones. Our results provide experimental proof that the assembly of a complex gut microbiota in insects is deterministic.     

Spatiotemporal successions of shrimp gut microbial colonization: high consistency despite distinct species pool

Aquatic animals encounter suites of novel planktonic microbes during their development. Although hosts have been shown to exert strong selection on their gut microbiota from surrounding environment, to what extent and the generality that the gut microbiota and the underlying ecological processes are affected by biotic and abiotic variations are largely unclear. Here, these concerns were explored by coupling spatiotemporal data on gut and rearing water bacterial communities with environmental variables over shrimp life stages at spatially distant locations. Shrimp gut microbiotas significantly changed mirroring their development, as evidenced by gut bacterial signatures of shrimp life stage contributing 95.5% stratification accuracy. Shrimp sourced little (2.6%–15.8%) of their gut microbiota from their rearing water. This microbial resistance was reflected by weak compositional differences between shrimp farming spatially distinct locations where species pools were distinct. Consistently, the assembly of shrimp gut microbiota was not adequately explained by the rearing water variables and bacterial community, but rather by host-age-associated biotic features. The successions of shrimp gut microbiota were droved by replacement (βsim), rather than by nestedness (βnes), while those of bacterioplankton communities were equally governed by replacement and nestedness. Our study highlights how shrimp gut bacterial community assembly is coupled to their development, rearing species pool, and that the successional pattern of host-associated communities is differed from that of free-living bacteria.     

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。     

A brief history of Great Basin pikas

Aim Within the past few decades, seven of the 25 historically described populations of American pikas (Ochotona princeps) in the Great Basin of arid western North America appear to have become extinct. In this paper, the prehistoric record for pikas in the Great Basin is used to place these losses in deeper historical context. Location The Great Basin, or area of internal drainage, of the western United States. Methods The location, elevation, and age of all reported prehistoric Great Basin specimens of American pikas were extracted from the literature. Elevations of extinct pika populations were arrayed through time, and latitudes and longitudes of those populations used to determine changing distances of those populations from the nearest extant populations. Results The average elevation of now‐extinct Great Basin pika populations during the late Wisconsinan (c. 40,000–10,000 radiocarbon years ago) and early Holocene (c. 10,000–7500 years ago) was 1750 m. During the hot and dry middle Holocene (c. 7500–4500 years ago), the average elevation of these populations rose 435 m, to 2168 m. All prehistorically known late Holocene (c. 4500–200 years ago) populations in the Great Basin are from mountain ranges that currently support populations of this animal, but historic period losses have caused the average elevation of pika populations to rise an additional 152 m. The total elevational increase, from the late Wisconsinan and early Holocene to today, has been 783 m. As lower elevation pika populations were lost, their distribution increasingly came to resemble its modern form. During the late Wisconsinan, now‐extinct pika populations were located an average of 170 km from the nearest extant population. By the late Holocene, this distance had declined to 30 km. Main conclusions Prehistoric alterations in the distribution of pika population in the Great Basin were driven by climate change and attendant impacts on vegetation. Today, Great Basin pikas contend with both climate change and anthropogenic impacts and thus may be on the brink of extinction.     

Marked seasonal variation in the wild mouse gut microbiota

Recent studies have provided an unprecedented view of the microbial communities colonizing captive mice; yet the host and environmental factors that shape the rodent gut microbiota in their natural habitat remain largely unexplored. Here, we present results from a 2-year 16 S ribosomal RNA gene sequencing-based survey of wild wood mice (Apodemus sylvaticus) in two nearby woodlands. Similar to other mammals, wild mice were colonized by 10 bacterial phyla and dominated by the Firmicutes, Bacteroidetes and Proteobacteria. Within the Firmicutes, the Lactobacillus genus was most abundant. Putative bacterial pathogens were widespread and often abundant members of the wild mouse gut microbiota. Among a suite of extrinsic (environmental) and intrinsic (host-related) factors examined, seasonal changes dominated in driving qualitative and quantitative differences in the gut microbiota. In both years examined, we observed a strong seasonal shift in gut microbial community structure, potentially due to the transition from an insect- to a seed-based diet. This involved decreased levels of Lactobacillus, and increased levels of Alistipes (Bacteroidetes phylum) and Helicobacter. We also detected more subtle but statistically significant associations between the gut microbiota and biogeography, sex, reproductive status and co-colonization with enteric nematodes. These results suggest that environmental factors have a major role in shaping temporal variations in microbial community structure within natural populations.     

Semi-captive Przewalski's gazelles cope with winter adversity by adjusting their gut bacterial communities

The intestinal microbiota plays an important role in the digestion and absorption of nutrients in animals. To address the challenge of conservation, many endangered wildlife are kept in captive or semi-captive conditions. Numerous studies have been conducted on the intestinal microbiota of captive animals, but little information is available on the intestinal microbiota of semi-captive animals, such as Przewalski's gazelle (Procapra przewalskii), which is an endangered ungulate species only distributed around Qinghai Lake in China. In this study, we used high-throughput sequencing methods to analyze the gut bacterial community of semi-captive Przewalski's gazelles during summer and winter. There were differences in the gut bacterial community composition between the 2 seasons, with higher bacterial diversity in winter. Deterministic processes dominated the bacterial community assembly in both seasons. There was a greater influence of heterogeneous selection in winter compared to summer, suggesting that there was more intestinal environmental filtering and selection on shaping the gut bacterial community during winter. There were more potential probiotic bacteria and fewer potential pathogens in winter compared to summer. Overall, stronger heterogeneous selection in winter might enhance gut selection for potential probiotic bacteria and filter out potential pathogens in Przewalski's gazelles, allowing them to adapt to the harsh living conditions in winter. Our study clarified that seasonal fluctuations trigger shifts in bacterial communities, which have potential benefits for Przewalski's gazelles. These results could provide valuable information for managing semi-captive populations and for future wild releases of Przewalski's gazelles.     

Environmental changes affect the assembly of soil bacterial community primarily by mediating stochastic processes

Both ‘species fitness difference’‐based deterministic processes, such as competitive exclusion and environmental filtering, and ‘species fitness difference’‐independent stochastic processes, such as birth/death and dispersal/colonization, can influence the assembly of soil microbial communities. However, how both types of processes are mediated by anthropogenic environmental changes has rarely been explored. Here we report a novel and general pattern that almost all anthropogenic environmental changes that took place in a grassland ecosystem affected soil bacterial community assembly primarily through promoting or restraining stochastic processes. We performed four experiments mimicking 16 types of environmental changes and separated the compositional variation of soil bacterial communities caused by each environmental change into deterministic and stochastic components, with a recently developed method. Briefly, because the difference between control and treatment communities is primarily caused by deterministic processes, the deterministic change was quantified as (mean compositional variation between treatment and control) – (mean compositional variation within control). The difference among replicate treatment communities is primarily caused by stochastic processes, so the stochastic change was estimated as (mean compositional variation within treatment) – (mean compositional variation within control). The absolute of the stochastic change was greater than that of the deterministic change across almost all environmental changes, which was robust for both taxonomic and functional‐based criterion. Although the deterministic change may become more important as environmental changes last longer, our findings showed that changes usually occurred through mediating stochastic processes over 5 years, challenging the traditional determinism‐dominated view.     

The Colonization Dynamics of the Gut Microbiota in Tilapia Larvae

The gut microbiota of fish larvae evolves fast towards a complex community. Both host and environment affect the development of the gut microbiota; however, the relative importance of both is poorly understood. Determining specific changes in gut microbial populations in response to a change in an environmental factor is very complicated. Interactions between factors are difficult to separate and any response could be masked due to high inter-individual variation even for individuals that share a common environment. In this study we characterized and quantified the spatio-temporal variation in the gut microbiota of tilapia larvae, reared in recirculating aquaculture systems (RAS) or active suspension tanks (AS). Our results showed that variation in gut microbiota between replicate tanks was not significantly higher than within tank variation, suggesting that there is no tank effect on water and gut microbiota. However, when individuals were reared in replicate RAS, gut microbiota differed significantly. The highest variation was observed between individuals reared in different types of system (RAS vs. AS). Our data suggest that under experimental conditions in which the roles of deterministic and stochastic factors have not been precisely determined, compositional replication of the microbial communities of an ecosystem is not predictable.     

Are you what you eat? A highly transient and prey‐influenced gut microbiome in the grey house spider Badumna longinqua

Stable core microbial communities have been described in numerous animal species and are commonly associated with fitness benefits for their hosts. Recent research, however, highlights examples of species whose microbiota are transient and environmentally derived. Here, we test the effect of diet on gut microbial community assembly in the spider Badumna longinqua. Using 16S rRNA gene amplicon sequencing combined with quantitative PCR, we analyzed diversity and abundance of the spider's gut microbes, and simultaneously characterized its prey communities using nuclear rRNA markers. We found a clear correlation between community similarity of the spider's insect prey and gut microbial DNA, suggesting that microbiome assembly is primarily diet‐driven. This assumption is supported by a feeding experiment, in which two types of prey—crickets and fruit flies—both substantially altered microbial diversity and community similarity between spiders, but did so in different ways. After cricket consumption, numerous cricket‐derived microbes appeared in the spider's gut, resulting in a rapid homogenization of microbial communities among spiders. In contrast, few prey‐associated bacteria were detected after consumption of fruit flies; instead, the microbial community was remodelled by environmentally sourced microbes, or abundance shifts of rare taxa in the spider's gut. The reshaping of the microbiota by both prey taxa mimicked a stable core microbiome in the spiders for several weeks post feeding. Our results suggest that the spider's gut microbiome undergoes pronounced temporal fluctuations, that its assembly is dictated by the consumed prey, and that different prey taxa may remodel the microbiota in drastically different ways.