Determination of microbial diversity in meju,fermented cooked soya beans,using nested PCR‐denaturing gradient gel electrophoresis

Aims: To identify the microbiota in meju, fermented cooked soya beans, that may directly affect the microbial communities of Korean fermented soya bean foods. Methods and Results: Using conventional bacterial 16S rDNA, bacilli‐specific 16S rDNA or fungi 18S rDNA‐specific primers, PCR products were amplified through a series of PCRs using the DNA extracted from ten meju samples. The amplicons were analysed using denaturing gradient gel electrophoresis (DGGE), which showed that Enterococcus durans was commonly detected in nine of ten meju samples. Bacillus subtilis was shown to be the major strain of bacilli in the samples tested. Based on the DGGE analysis of fungi in meju, we determined that Absidia corymbifera, Aspergillus sp. and Candida rugosa were the main fungi in the tested samples. Conclusions: A variety of bacterial and fungal micro‐organisms were identified in meju samples, in addition to the micro‐organisms already known to be present. Significance and Impact of the Study: This is the first report showing the differences and similarities in the populations of micro‐organisms in meju samples using nested PCR‐DGGE, a culture‐independent method. The results may be applicable to the development of improved meju, in which the indigenous micro‐organisms required for fermentation can be standardized.     

Two’s company,three’s a crowd: Exploring how host–parasite–microbiota interactions may influence disease susceptibility and conservation of wildlife

A large body of research has demonstrated that host‐associated microbiota—the archaeal, bacterial, fungal and viral communities residing on and inside organisms—are critical to host health (Cho & Blaser, 2012). Although the vast majority of these studies focus on humans or model organisms in laboratory settings (Pascoe, Hauffe, Marchesi, & Perkins, 2017), they nevertheless provide important conceptual evidence that the disruption of host‐associated microbial communities (termed “dysbiosis”) among wild animals may reduce host fitness and survival under natural environmental conditions. Among the myriad of environmental factors capable of inducing dysbiosis among wild animals (Trevelline, Fontaine, Hartup, & Kohl, 2019), parasitic infections represent a potentially potent, yet poorly understood, factor influencing microbial community dynamics and animal health. The study by DeCandia et al. in this issue of Molecular Ecology is a rare example of a host–parasite–microbiota interaction that impacts the health, survival and conservation of a threatened wild animal in its natural habitat. Using culture‐independent techniques, DeCandia et al. found that the presence of an ectoparasitic mite (Otodectes cynotis) in the ear canal of the Santa Catalina Island fox (Urocyon littoralis catalinae) was associated with significantly reduced ear canal microbial diversity, with the opportunistic pathogen Staphylococcus pseudintermedius dominating the community. These findings suggest that parasite‐induced inflammation may contribute to the formation of ceruminous gland tumours in this subspecies of Channel Island fox. As a rare example of a host–parasite–microbiota interaction that may mediate a lethal disease in a population of threatened animals, their study provides an excellent example of how aspects of disease ecology can be integrated into studies of host‐associated microbiota to advance conservation science and practice.     

Diversity and dynamics of bacteriocins from human microbiome

Human commensal microbiota are an important determinant of health and disease of the host. Different human body sites harbour different bacterial microbiota, bacterial communities that maintain a stable balance. However, many of the factors influencing the stabilities of bacterial communities associated with humans remain unknown. In this study, we identified putative bacteriocins produced by human commensal microbiota. Bacteriocins are peptides or proteins with antimicrobial activity that contribute to the stability and dynamics of microbial communities. We employed bioinformatic analyses to identify putative bacteriocin sequences in metagenomic sequences obtained from different human body sites. Prevailing bacterial taxa of the putative bacteriocins producers matched the most abundant organisms in each human body site. Remarkably, we found that samples from different body sites contain different density of putative bacteriocin genes, with the highest in samples from the vagina, the airway, and the oral cavity and the lowest in those from gut. Inherent differences of different body sites thus influence the density and types of bacteriocins produced by commensal bacteria. Our results suggest that bacteriocins play important roles to allow different bacteria to occupy several human body sites, and to establish a long‐term commensal relationship with human hosts.     

Microbiological analysis of conjunctival secretion in anophthalmic cavity,contralateral eye and ocular prosthesis of patients with maxillofacial abnormalities

The purpose of this study was to identify and analyse the micro‐organisms present in the conjunctival secretion in anophthalmic cavities of wearers of ocular prostheses, as well as on the prostheses used by them, correlating them with the microbiota of the contralateral eye. Nine patients with maxillofacial abnormalities, wearers of an acrylic resin ocular prosthesis participated in the study. Collections of conjunctival secretions and biofilm were performed on the prosthesis, anophthalmic cavity and contralateral eye for the mycological and bacterial analyses. The data were submitted to statistical analysis, performing a Kendall correlation test to identify the correlation between the collection site and the identified micro‐organism (P < 0·05). It was verified that the most prevalent micro‐organisms were the Staphylococcus aureus and Staphylococcus epidermidis, independent of the collection site, and that negative cultures for fungi were encountered in 85·2% of collections, independent of the region. It was not possible to establish a correlation among the types of micro‐organisms and the collection sites.

Significance and Impact of the Study

Some evidence suggests that the surface roughness of ocular prostheses can influence interactions with micro‐organisms, with greater prejudicial consequences, such as the establishment of biofilms, which could lead to infections. Thus, it becomes extremely important to identify the micro‐organisms present on the acrylic surfaces of ocular prostheses, as well as the microbiota of the anophthalmic cavity and contralateral eye of wearers of the same, so that subsequent control measures promote the homeostatic maintenance of the ocular region.     

Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses

Different factors may modulate the gut microbiota of animals. In any particular environment, diet, genetic factors and human influences can shape the bacterial communities residing in the gastrointestinal tract. Metagenomic approaches have significantly expanded our knowledge on microbiota dynamics inside hosts, yet cultivation and isolation of bacterial members of these complex ecosystems may still be necessary to fully understand interactions between bacterial communities and their host. A dual approach, involving culture‐independent and ‐dependent techniques, was used here to decipher the microbiota communities that inhabit the gastro intestinal tract of free‐range, broiler and feral chickens. In silico analysis revealed the presence of a core microbiota that is typical of those animals that live in different geographical areas and that have limited contact with humans. Anthropic influences guide the metabolic potential and the presence of antibiotic resistance genes of these different bacterial communities. Culturomics attempts, based on different cultivation conditions, were applied to reconstruct in vitro the microbiota of feral chickens. A unique strain collection representing members of the four major phyla of the poultry microbiota was assembled, including bacterial strains that are not typically retrieved from the chicken gut.     

Stochastically reduced communities—Microfluidic compartments as model and investigation tool for soil microorganism growth in structured spaces

Microbial community in soil is a complex and dynamic system. Using traditional culture experiments it is difficult to model the stochastic distribution of single organisms of microbial communities in the soil pore's structure. Droplet‐based micro‐segmented flow technique allows the transfer of the principle of stochastic confinement of stochastically reduced communities from soil micro pores into nanoliter droplets. Microfluidics was applied for the investigation and comparison of soil samples from ancient mining areas by highly resolved concentration‐dependent screenings. As results, the generation, incubation, and in situ optical characterization of nanoliter droplets of suspensions of unknown soil microbial communities allowed the identification of different response characteristics toward heavy metal exposition. The investigations proved the high potential of microfluidics for investigations of soil microbial communities. It may be in the future helpful to detect bacteria and consortia with special biosorption characteristics, which could be useful for the development of biological accumulation and detoxification strategies.     

Genotype and rhizobium inoculation modulate the assembly of soybean rhizobacterial communities

Rhizosphere bacterial communities are vital for plants, yet the composition of rhizobacterial communities and the complex interactions between roots and microbiota, or between microbiota, are largely unknown. In this study, we investigated the structure and composition of rhizobacterial communities in two soybean cultivars and their recombinant inbred lines contrasting in nodulation through 16S rRNA amplicon sequencing in two years of field trials. Our results demonstrate that soybean plants are able to select microbes from bulk soils at the taxonomic and functional level. Soybean genotype significantly influenced the structure of rhizobacterial communities and resulted in dramatically different co‐occurrence networks of rhizobacterial communities between different genotypes of soybean plants. Furthermore, the introduction of exogenous rhizobia through inoculation altered soybean rhizobacterial communities in genotype‐dependent manner. Rhizobium inoculation not only stimulated the proliferation of potential beneficial microbes but also increased connections in rhizobacterial networks and changed the hub microbes, all of which led to the association of distinctive bacterial communities. Taken together, we demonstrated that the assembly of soybean rhizobacterial communities was determined by both genotype and the introduction of exogenous rhizobia. These findings bolster the feasibility of root microbiome engineering through inoculation of specific microbial constituents.     

Microbiology is the basis of sustainable agriculture: an opinion

Agricultural microbiology is presented as a synthetic research field responsible for knowledge transfer from general microbiology and microbial ecology to the agricultural biotechnologies. The major goal of agricultural microbiology is a comprehensive analysis of symbiotic micro‐organisms (bacteria, fungi) interacting with agriculturally important plants and animals: here we have focussed on plants. In plants, interactions with micro‐organisms are diverse, ranging from two‐partite symbioses (e.g. legume–rhizobia N₂‐fixing nodular symbioses or arbuscular mycorrhiza) to multipartite endophytic and epiphytic (root‐associated, phyllosphere) communities. Two‐partite symbioses provide the clearest models for addressing genetic cooperation between partners, resulting in the formation of super‐organism genetic systems, which are responsible for host productivity. Analysis of these systems has now been extended considerably by using the approaches of metagenomics, which allow the dissection of taxonomic/population structures and the metabolic/ecological functions of microbial communities, which have resulted from the adaptation of free‐living, soil microflora in the endosymbiotic niches. Both beneficial (nutritional, defensive, regulatory) and antagonistic (biocontrol) functions expressed by symbiotic microbes towards their hosts are the potential subjects of effective agronomic use. A fundamental knowledge of the genetics, molecular biology, ecology and evolution of symbiotic interactions could enable the development of microbe‐based sustainable agriculture. This could achieve: (a) an improvement of major adaptive functions and productivity in crop plants by manipulating their microbial cohabitants; (b) partial or even full substitution of ecologically hazardous agrochemicals (mineral fertilizers, pesticides) by microbial preparations; (c) a decrease in the cost and an improvement of the quality of agricultural products.     

Microbiome alterations in HIV infection a review

Recent developments in molecular techniques have allowed researchers to identify previously uncultured organisms, which has propelled a vast expansion of our knowledge regarding our commensal microbiota. Interest in the microbiome specific to HIV grew from earlier findings suggesting that bacterial translocation from the intestines is the cause of persistent immune activation despite effective viral suppression with antiretroviral therapy (ART). Studies of SIV infected primates have demonstrated that Proteobacteria preferentially translocate and that mucosal immunity can be restored with probiotics. Pathogenic SIV infection results in a massive expansion of the virome, whereas non‐pathogenic SIV infection does not. Human HIV infected cohorts have been shown to have microbiota distinctive from that of HIV negative controls and efforts to restore the intestinal microbiome via probiotics have often had positive results on host markers. The microbiota of the genital tract may play a significant role in acquisition and transmission of HIV. Modification of commensal microbial communities likely represents an important therapeutic adjunct to treatment of HIV. Here we review the literature regarding human microbiome in HIV infection.     

Sex-specific asymmetry within the cloacal microbiota of the striped plateau lizard, <Emphasis Type="Italic">Sceloporus virgatus</Emphasis>

The structure and diversity of microbial communities in wild vertebrate populations remain poorly understood, but are expected to have important consequences for individual survival and reproductive success. For instance, recent work has demonstrated that cloacal microbe assemblages of wild birds are related to the phenotypic quality of the host. To contribute to this field of study, we examined the composition and diversity of the cloacal microbiota of free-ranging striped plateau lizards, Sceloporus virgatus, using 16s rRNA-based culture independent techniques. Our dataset, generated from cloacal swabs of six males and six females, and based on twenty five 16s rRNA clones from each sample, revealed (i) low overall microbial diversity, (ii) a striking sex asymmetry in microbial community composition with males displaying cloacal microbiota more typical of gastrointestinal residents found in other organisms, while females display only gammaproteobacterial phylotypes, (iii) a significant sex difference in microbial community structure, with females having significantly lower microbial diversity and richness than do males, and (iv) that the diversity of the female microbial community is negatively correlated to her ectoparasitic mite load. It is not yet clear if the female-specific paucity of cloacal microbial diversity is due to host function or microbe-microbe interactions, or whether the relationship to female mite load is causal, however these findings are expected to have relevance to the species’ life history and ecology. Although the diversity of microbiota from humans, mice, birds, zebrafish, and invertebrates is widely investigated, this is one of only a few reports in the literature describing the cloacal microbiota of a wild vertebrate, and is perhaps the first report for wild reptiles that utilizes culture-independent techniques.     

Imbalance of Gastrointestinal Microbiota in the Pathogenesis of Helicobacter pylori‐Associated Diseases

The development of new nucleotide sequencing techniques and advanced bioinformatics tools has opened the field for studying the diversity and complexity of the gastrointestinal microbiome independent of traditional cultural methods. Owing largely to the gastric acid barrier, the human stomach was long thought to be sterile. The discovery of Helicobacter pylori, the gram‐negative bacterium that infects upwards of 50% of the global population, has started a major paradigm shift in our understanding of the stomach as an ecologic niche for bacteria. Recent sequencing analysis of gastric microbiota showed that H. pylori was not alone and the interaction of H. pylori with those microorganisms might play a part in H. pylori‐associated diseases such as gastric cancer. In this review, we summarize the available literature about the changes of gastrointestinal microbiota after H. pylori infection in humans and animal models, and discuss the possible underlying mechanisms including the alterations of the gastric environment, the secretion of hormones and the degree of inflammatory response. In general, information regarding the composition and function of gastrointestinal microbiome is still in its infancy, future studies are needed to elucidate whether and to what extent H. pylori infection perturbs the established microbiota. It is assumed that clarifying the role of gastrointestinal communities in H. pylori‐associated diseases will provide an opportunity for translational application as a biomarker for the risk of serious H. pylori diseases and perhaps identify specific organisms for therapeutic eradication.     

Ecosystem productivity is associated with bacterial phylogenetic distance in surface marine waters

Understanding the link between community diversity and ecosystem function is a fundamental aspect of ecology. Systematic losses in biodiversity are widely acknowledged but the impact this may exert on ecosystem functioning remains ambiguous. There is growing evidence of a positive relationship between species richness and ecosystem productivity for terrestrial macro‐organisms, but similar links for marine micro‐organisms, which help drive global climate, are unclear. Community manipulation experiments show both positive and negative relationships for microbes. These previous studies rely, however, on artificial communities and any links between the full diversity of active bacterial communities in the environment, their phylogenetic relatedness and ecosystem function remain hitherto unexplored. Here, we test the hypothesis that productivity is associated with diversity in the metabolically active fraction of microbial communities. We show in natural assemblages of active bacteria that communities containing more distantly related members were associated with higher bacterial production. The positive phylogenetic diversity–productivity relationship was independent of community diversity calculated as the Shannon index. From our long‐term (7‐year) survey of surface marine bacterial communities, we also found that similarly, productive communities had greater phylogenetic similarity to each other, further suggesting that the traits of active bacteria are an important predictor of ecosystem productivity. Our findings demonstrate that the evolutionary history of the active fraction of a microbial community is critical for understanding their role in ecosystem functioning.     

Dissecting the Rhizosphere complexity: The truffle-ground study case

The word Rhizosphere describes the part of the soil which is immediately adjacent to and affected by plant roots. This is a very dynamic environment where plants, soil and microorganisms interact. The plant releases, in addition to biologically active substances, nutritive substances (exudates), which create a privileged habitat for many microbial populations. The same microbes that live in the rhizosphere may be useful for the plant. Interest in this fascinating environment has increased over the years. However, our knowledge of the biology and diversity of microbial populations in the rhizosphere is still limited, because it has always been linked to traditional culture-based techniques. These methods, which only allow the study of cultured microorganisms, do not allow the majority of the organisms existing in nature to be characterized. Over the last few years, this limitation has been overcome through the introduction of methodologies that are independent of culture techniques. This different approach, which has revolutionized scientific research, is known as metagenomics. In this review, the rhizosphere environment is considered with particular attention to the fungal and symbiotic organisms, which populate it. The new environmental genomic techniques and how these have been applied to the study of the various environments and the rhizosphere are described. Finally, a specific rhizosphere, a truffle-ground, is described as our study case.      

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.     

How do microbiota associated with an invasive seaweed vary across scales?

Communities are shaped by scale dependent processes. To study the diversity and variation of microbial communities across scales, the invasive and widespread seaweed Agarophyton vermiculophyllum presents a unique opportunity. We characterized pro‐ and eukaryotic communities associated with this holobiont across its known distribution range, which stretches over the northern hemisphere. Our data reveal that community composition and diversity in the holobiont vary at local but also larger geographic scales. While processes acting at the local scale (i.e., within population) are the main structuring drivers of associated microbial communities, changes in community composition also depend on processes acting at larger geographic scales. Interestingly, the largest analysed scale (i.e., native and non‐native ranges) explained variation in the prevalence of predicted functional groups, which could suggest a functional shift in microbiota occurred over the course of the invasion process. While high variability in microbiota at the local scale supports A. vermiculophyllum to be a generalist host, we also identified a number of core taxa. These geographically independent holobiont members imply that cointroduction of specific microbiota may have additionally promoted the invasion process.     

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.     

Metacommunity theory for transmission of heritable symbionts within insect communities

Microbial organisms are ubiquitous in nature and often form communities closely associated with their host, referred to as the microbiome. The microbiome has strong influence on species interactions, but microbiome studies rarely take interactions between hosts into account, and network interaction studies rarely consider microbiomes. Here, we propose to use metacommunity theory as a framework to unify research on microbiomes and host communities by considering host insects and their microbes as discretely defined “communities of communities” linked by dispersal (transmission) through biotic interactions. We provide an overview of the effects of heritable symbiotic bacteria on their insect hosts and how those effects subsequently influence host interactions, thereby altering the host community. We suggest multiple scenarios for integrating the microbiome into metacommunity ecology and demonstrate ways in which to employ and parameterize models of symbiont transmission to quantitatively assess metacommunity processes in host‐associated microbial systems. Successfully incorporating microbiota into community‐level studies is a crucial step for understanding the importance of the microbiome to host species and their interactions.     

Relocation,high‐latitude warming and host genetic identity shape the foliar fungal microbiome of poplars

Micro‐organisms associated with plants and animals affect host fitness, shape community structure and influence ecosystem properties. Climate change is expected to influence microbial communities, but their reactions are not well understood. Host‐associated micro‐organisms are influenced by the climate reactions of their hosts, which may undergo range shifts due to climatic niche tracking, or may be actively relocated to mitigate the effects of climate change. We used a common‐garden experiment and rDNA metabarcoding to examine the effect of host relocation and high‐latitude warming on the complex fungal endophytic microbiome associated with leaves of an ecologically dominant boreal forest tree (Populus balsamifera L.). We also considered the potential effects of poplar genetic identity in defining the reactions of the microbiome to the treatments. The relocation of hosts to the north increased the diversity of the microbiome and influenced its structure, with results indicating enemy release from plausible pathogens. High‐latitude warming decreased microbiome diversity in comparison with natural northern conditions. The warming also caused structural changes, which made the fungal communities distinct in comparison with both low‐latitude and high‐latitude natural communities, and increased the abundance of plausible pathogens. The reactions of the microbiome to relocation and warming were strongly dependent on host genetic identity. This suggests that climate change effects on host–microbiome systems may be mediated by the interaction of environmental factors and the population genetic processes of the hosts.     

Impact of Next Generation Sequencing Techniques in Food Microbiology

Understanding the Maxam-Gilbert and Sanger sequencing as the first generation, in recent years there has been an explosion of newly-developed sequencing strategies, which are usually referred to as next generation sequencing (NGS) techniques. NGS techniques have high-throughputs and produce thousands or even millions of sequences at the same time. These sequences allow for the accurate identification of microbial taxa, including uncultivable organisms and those present in small numbers. In specific applications, NGS provides a complete inventory of all microbial operons and genes present or being expressed under different study conditions. NGS techniques are revolutionizing the field of microbial ecology and have recently been used to examine several food ecosystems. After a short introduction to the most common NGS systems and platforms, this review addresses how NGS techniques have been employed in the study of food microbiota and food fermentations, and discusses their limits and perspectives. The most important findings are reviewed, including those made in the study of the microbiota of milk, fermented dairy products, and plant-, meat- and fish-derived fermented foods. The knowledge that can be gained on microbial diversity, population structure and population dynamics via the use of these technologies could be vital in improving the monitoring and manipulation of foods and fermented food products. They should also improve their safety.     

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.