Comparative analysis and characterization of the gut microbiota of four farmed snakes from southern China

Snowflake: visualizing microbiome abundance tables as multivariate bipartite graphs

Current visualizations in microbiome research rely on aggregations in taxonomic classifications or do not show less abundant taxa. We introduce Snowflake: a new visualization method that creates a clear overview of the microbiome composition in collected samples without losing any information due to classification or neglecting less abundant reads. Snowflake displays every observed OTU/ASV in the microbiome abundance table and provides a solution to include the data's hierarchical structure and additional information obtained from downstream analysis (e.g., alpha- and beta-diversity) and metadata. Based on the value-driven ICE-T evaluation methodology, Snowflake was positively received. Experts in microbiome research found the visualizations to be user-friendly and detailed and liked the possibility of including and relating additional information to the microbiome's composition. Exploring the topological structure of the microbiome abundance table allows them to quickly identify which taxa are unique to specific samples and which are shared among multiple samples (i.e., separating sample-specific taxa from the core microbiome), and see the compositional differences between samples. An R package for constructing and visualizing Snowflake microbiome composition graphs is available at https://gitlab.com/vda-lab/snowflake.

Fecal and oral microbiome analysis of snakes from China reveals a novel natural emerging disease reservoir

Introduction

The gastrointestinal tract and oral cavity of animal species harbor complex microbial communities, the composition of which is indicative of the behavior, co-evolution, diet, and immune system of the host.

Methods

This study investigated the microbial composition in snakes from varying altitudinal ranges by assessing the fecal and oral bacterial communities in Protobothrops mucrosquamatus, Elaphe dione, and Gloydius angusticeps from Sichuan Province, China, using metagenomic sequencing.

Results and discussion

It was revealed that Bacteroidetes, Proteobacteria, Firmicutes, and Fusobacteria were the core microbial phyla in fecal samples across all three species, while Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes were the core microbial phyla in oral samples across all three species. Notably, the dominance of Armatimonadetes was documented for the first time in the feces of all three species. Comparative analysis of the microbiomes of the three species indicated distinct microbiological profiles between snakes living at low- and high-altitude regions. Furthermore, 12 to 17 and 22 to 31 bacterial pathogens were detected in the oral and fecal samples, respectively, suggesting that snakes may serve as a novel reservoir for emerging diseases. Overall, this study provides a comparative analysis of the fecal and oral microbiomes in three snake species. Future investigations are anticipated to further elucidate the influence of age, genetics, behavior, diet, environment, ecology, and evolution on the gut and oral microbial communities of snakes.

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.

Comparisons of the Oral Microbiota from Seven Species of Wild Venomous Snakes in Taiwan Using the High-Throughput Amplicon Sequencing of the Full-Length 16S rRNA Gene

A venomous snake's oral cavity may harbor pathogenic microorganisms that cause secondary infection at the wound site after being bitten. We collected oral samples from 37 individuals belonging to seven species of wild venomous snakes in Taiwan, including Naja atra (Na), Bungarus multicinctus (Bm), Protobothrops mucrosquamatus (Pm), Trimeresurus stejnegeri (Ts), Daboia siamensis (Ds), Deinagkistrodon acutus (Da), and alpine Trimeresurus gracilis (Tg). Bacterial species were identified using full-length 16S rRNA amplicon sequencing analysis, and this is the first study using this technique to investigate the oral microbiota of multiple Taiwanese snake species. Up to 1064 bacterial species were identified from the snake's oral cavities, with 24 pathogenic and 24 non-pathogenic species among the most abundant ones. The most abundant oral bacterial species detected in our study were different from those found in previous studies, which varied by snake species, collection sites, sampling tissues, culture dependence, and analysis methods. Multivariate analysis revealed that the oral bacterial species compositions in Na, Bm, and Pm each were significantly different from the other species, whereas those among Ts, Ds, Da, and Tg showed fewer differences. Herein, we reveal the microbial diversity in multiple species of wild snakes and provide potential therapeutic implications regarding empiric antibiotic selection for wildlife medicine and snakebite management.

Differences in the luminal and mucosal gut microbiomes and metabolomes of oriental rat snake (Ptyas mucosus)

Previous studies regarding the gastrointestinal biogeography of microbiomes generally focused on longitudinal comparisons, whereas few studies have compared luminal and mucosal microbiomes. Investigations of the snake gut microbiome have attracted interest because of the unique digestive physiology and hibernation behavior, but adequate sampling methods must be developed. Here, we used an omics approach combining 16S rRNA gene sequencing with untargeted metabolomics to profile the luminal and mucosal gut microbiomes and metabolomes in oriental rat snakes, with the goal of revealing the heterogeneity and co-occurrence at these sites. The α-diversity of the gut microbiome was significantly higher at mucosal sites than at luminal sites. Microbial composition also differed according to sampling site, with significant differences in the abundances of dominant phyla and genera, as well as β-diversity clustering and distribution. Metabolome profiling revealed differences that were mainly related to cholinergic substances and nucleic acids. Analysis of variations in Kyoto Encyclopedia of Genes and Genomes functions of microbes and metabolites showed that the mucosal microbiome was more frequently involved in genetic information processing and cellular processes, whereas the luminal microbiome generally participated in metabolic regulation. Notably, we found a greater abundance of the opportunistic pathogen genus Escherichia-Shigella at luminal sites and higher levels of the lipid-regulator metabolite fenfluramine at mucosal sites. Despite the extensive differences between the two sampling sites, the results revealed similarities in terms of amplicon sequence variant composition and dominant core microbes. This pilot exploration of luminal and mucosal microbiomes and metabolites provides key insights to guide future research. KEY POINTS: • Snake luminal and mucosal microbiota was distinct in composition and function. • Metabolome profiling revealed differences related to different metabolites. • The pathogenic microbes are more likely to colonize the gut lumina.

Dietary and Sexual Correlates of Gut Microbiota in the Japanese Gecko, Gekko japonicus (Schlegel, 1836)

Numerous studies have demonstrated that multiple intrinsic and extrinsic factors shape the structure and composition of gut microbiota in a host. The disorder of the gut microbiota may trigger various host diseases. Here, we collected fecal samples from wild-caught Japanese geckos (Gekko japonicus) and captive conspecifics fed with mealworms (mealworm-fed geckos) and fruit flies (fly-fed geckos), aiming to examine the dietary and sexual correlates of the gut microbiota. We used 16S rRNA gene sequencing technology to determine the composition of the gut microbiota. The dominant phyla with a mean relative abundance higher than 10% were Verrucomicrobiota, Bacteroidota, and Firmicutes. Gut microbial community richness and diversity were higher in mealworm-fed geckos than in wild geckos. Neither community evenness nor beta diversity of gut microbiota differed among wild, mealworm-fed, and fly-fed geckos. The beta rather than alpha diversity of gut microbiota was sex dependent. Based on the relative abundance of gut bacteria and their gene functions, we concluded that gut microbiota contributed more significantly to the host's metabolic and immune functions. A higher diversity of gut microbiota in mealworm-fed geckos could result from higher chitin content in insects of the order Coleoptera. This study not only provides basic information about the gut microbiota of G. japonicus but also shows that gut microbiota correlates with dietary habits and sex in the species.

Comparative Study of the Gut Microbiota Community between the Farmed and Wild Mastacembelus armatus (Zig-Zag Eel)

Cultivated and wild fish of the same species may exhibit different characteristics, such as in their flavor, growth and development. In some wild fish species, reproductive functions may even be retarded when wild individuals are moved into cultivated conditions. The gut microbiota may be one of the reasons for these phenomena as they have been reported to play an important role in host growth and development, as well as in normal reproductive functioning. Here, we used Mastacembelus armatus (zig-zag eel), a freshwater fish which shows anormal reproductive function in cultivated conditions, as a model to comparatively study the diversity, structure and function of gut microbiota in cultivated and wild groups by analyzing the 16S rRNA sequence of each group's microbiota. The results showed that Proteobacteria and Firmicutes were the dominant phyla in the gut microbiota of wild (accounting for 45.8% and 20.3% of the total number of Proteobacteria and Firmicutes, respectively) and farmed (accounting for 21.4% and 75.6% of the total number of Proteobacteria and Firmicutes, respectively) zig-zag eel. Wild zig-zag eels (Shannon = 3.56; Chao = 583.08; Ace = 579.18) had significantly higher alpha diversity than those in cultivated populations (Shannon = 2.09; Chao = 85.45; Ace = 86.14). A significant difference in the community structure of the gut microbiota was found between wild and cultivated populations. The wild zig-zag eel showed a high abundance of functional pathways in metabolism, genetic information processing and organismal system function. These results suggested that the diversity and function of gut microbiota in zig-zag eel were correlated with their diet and habitat conditions, which indicated that the management of cultivated populations should mimic the wild diet and habitat to improve the productivity and quality of farmed zig-zag eel.

CAZyme from gut microbiome for efficient lignocellulose degradation and biofuel production

Over-exploitation and energy security concerns of the diminishing fossil fuels is a challenge to the present global economy. Further, the negative impact of greenhouse gases released using conventional fuels has led to the need for searching for alternative biofuel sources with biomass in the form of lignocellulose coming up as among the potent candidates. The entrapped carbon source of the lignocellulose has multiple applications other than biofuel generation under the biorefinery approach. However, the major bottleneck in using lignocellulose for biofuel production is its recalcitrant nature. Carbohydrate Active Enzymes (CAZymes) are enzymes that are employed for the disintegration and consumption of lignocellulose biomass as the carbon source for the production of biofuels and bio-derivatives. However, the cost of enzyme production and their stability and catalytic efficiency under stressed conditions is a concern that hinders large-scale biofuel production and utilization. Search for novel CAZymes with superior activity and stability under industrial condition has become a major research focus in this area considering the fact that the most conventional CAZymes has low commercial viability. The gut of plant-eating herbivores and other organisms is a potential source of CAZyme with high efficiency. The review explores the potential of the gut microbiome of various organisms in the production of an efficient CAZyme system and the challenges in using the biofuels produced through this approach as an alternative to conventional biofuels.

Novel Sources of Bioactive Molecules: Gut Microbiome of Species Routinely Exposed to Microorganisms

Simple Summary

The majority of antibiotics available in the market are produced by bacteria isolated from soil. However, the low-hanging fruit has been picked; hence, there is a need to mine bacteria from unusual sources. With this in mind, it is important to note that animals and pests, such as cockroaches, snake, crocodiles, water monitor lizards, etc., come across pathogenic bacteria regularly, yet flourish in contaminated environments. These species must have developed methods to defend themselves against pathogens. Besides the immunity they may confer, bacteria associated with animals/pests may offer a potential source of novel antibacterial agents. This paper discusses the current knowledge of bacteria isolated from land and marine animals with antibacterial properties and proposes untapped sources for the isolation of bacteria to mine potentially novel antibiotic molecules.

Abstract

The development of novel bioactive molecules is urgently needed, especially with increasing fatalities occurring due to infections by bacteria and escalating numbers of multiple-drug-resistant bacteria. Several lines of evidence show that the gut microbiome of cockroaches, snakes, crocodiles, water monitor lizards, and other species may possess molecules that are bioactive. As these animals are routinely exposed to a variety of microorganisms in their natural environments, it is likely that they have developed methods to counter these microbes, which may be a contributing factor in their persistence on the planet for millions of years. In addition to the immune system, the gut microbiota of a host may thwart colonization of the gastro-intestine by pathogenic and/or foreign microorganisms through two mechanisms: (i) production of molecules with antibacterial potential targeting foreign microorganisms, or (ii) production of molecules that trigger host immunity targeting foreign microorganisms that penetrate the host. Herein, we discuss and deliberate on the current literature examining antibacterial activities that stem from the gut bacteria of animals such as crocodiles, cockroaches, and water monitor lizards, amongst other interesting species, which likely encounter a plethora of microorganisms in their natural environments. The overall aim is to unveil a potential library of novel bioactive molecules for the benefit of human health and for utilization against infectious diseases.

Comparison of Gut Microbiota Diversity Between Captive and Wild Tokay Gecko (Gekko gecko)

Captive animals and wild animals may exhibit different characteristics due to the heterogeneity of their living environments. The gut microbiota play an important role in the digestion and absorption, energy metabolism, immune regulation, and physiological health of the host. However, information about the gut microbiota of captive and wild Gekko gecko is currently limited. To determine the difference in gut microbiota community composition, diversity, and structure between captive and wild geckos, we used the Illumina miseq platform to conduct high-throughput sequencing and bioinformatics analysis of the v3–v4 hypervariable region of 16S rRNA in 54 gecko samples. Our results showed that Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria were the dominant gut microbiota phyla of the gecko. The dominant genera comprised mainly Pseudomonas, Burkholderia-caballeronia-paraburkholderia, Ralstonia, Romboutsia, and Bacteroides. Captive geckos had significantly higher alpha diversity and potential pathogenic bacteria than wild populations. Moreover, significant differences in beta diversity of gut microbiota were observed between two populations. Functional prediction analysis showed that the relative abundance of functional pathways of wild geckos was more higher in metabolism, genetic information processing and organismal system function than those in captive geckos. Total length significantly affected gut microbial community (R² = 0.4527, p = 0.001) and explained 10.45% of the total variation for gut microbial community variance between two groups. These results may be related to differences in diet and living environment between two populations, suggesting that the management of captive populations should mimic wild environments to the greatest extent possible to reduce the impact on their gut microbiota.

Comparative study on gut microbiota in three Anura frogs from a mountain stream

Composition and diversity in gut microbiota are impacted by a wide variety of factors. The similarity of gut microbiota in related or sympatric species has been gaining recent traction. Here, 16S rRNA gene sequencing technology was employed to study the gut microbiota of three sympatric frog species, namely Odorrana tormota, O. graminea, and Amolops wuyiensis. In these three frog species, the most abundant phylum was Proteobacteria, followed by Bacteroidetes, Verrucomicrobia, and Firmicutes. The most abundant family was Burkholderiaceae in three species. The most dominant genera were Burkholderia, Caballeronia, and Paraburkholderia with the highest relative abundance in O. tormota, O. graminea, and A. wuyiensis, respectively. No differences were observed in alpha diversity indexes among the three frog species. However, bacterial similarity of gut microbiota was significantly different between O. tormota and A. wuyiensis and between O. graminea and A. wuyiensis. Metabolism‐related gene function was predominantly enriched in the gut microbiota of the three evaluated frog species. From these findings, that the relative abundance of the gut microbiota and predicted gene functions differed in three species, we conclude that there were significant differences in the gut microbiota of the three species. Similar alpha diversity and interspecific bacterial similarity in the gut might be related to bacterial transmission among the three Anura frogs evaluated in this study.

Gut microbiome-immune system interaction in reptiles

Reptiles are ectothermic amniotes in a world dominated by endotherms. Reptiles originated more than 300 million years ago and they often dwell in polluted environments which may expose them to pathogenic micro-organisms, radiation and/or heavy metals. Reptiles also possess greater longevity and may live much longer than similar-sized land mammals, for example, turtles, tortoises, crocodiles and tuatara are long-lived reptiles living up to 100 years or more. Many recent studies have emphasized the pivotal role of the gut microbiome on its host; thus, we postulated that reptilian gut microbiome and/or its metabolites and the interplay with their robust immune system may contribute to their longevity and overall hardiness. Herein, we discuss the composition of the reptilian gut microbiome, immune system-gut microbiome cross-talk, antimicrobial peptides, reptilian resistance to infectious diseases and cancer, ageing, as well the current knowledge of the genome and epigenome of these remarkable species. Preliminary studies have demonstrated that microbial gut flora of reptiles such as crocodiles, tortoises, water monitor lizard and python exhibit remarkable anticancer and antibacterial properties, as well as comprise novel gut bacterial metabolites and antimicrobial peptides. The underlying mechanisms between the gut microbiome and the immune system may hold clues to developing new therapies overall for health, and possible extrapolation to exploit the ancient defence systems of reptiles for Homo sapiens benefit.

Taxonomy, not locality, influences the cloacal microbiota of two nearctic colubrids: a preliminary analysis

BACKGROUND

The gut microbiota is an emerging frontier in wildlife research and its importance to vertebrate health and physiology is becoming ever more apparent. Reptiles, in particular snakes, have not received the same attention given to other vertebrates and the composition of their wild gut microbiome remains understudied. The primary goal of this work was to describe the cloacal microbiota of two Colubrids, the Eastern Gartersnake (Thamnophis sirtalis sirtalis) and the Northern Watersnake (Nerodia sipedon sipedon), and if their cloacal microbiota differed as well as if it did between a wetland and upland population of the former species.

METHODS AND RESULTS

We utilized next-generation sequencing of cloacal swabs-a non-destructive proxy for the gut microbiota. The cloacal microbiome of Eastern Gartersnakes (N = 9) was like those of other snakes being comprised of Proteobacteria, Bacteroidetes, and Firmicutes, while that of Northern Watersnakes (N = 6) was dominated by Tenericutes. Seven microbial operational taxonomic units (OTUs), all members of Proteobacteria, were shared among all individuals and were indicative of a core microbiome in Eastern Gartersnakes, but these OTUs were not particularly relevant to Northern Watersnakes. The latter had greater OTU richness than did Eastern Gartersnakes, and habitat did not have any apparent effect on the microbial community composition in Eastern Gartersnakes.

CONCLUSIONS

Our findings suggest host taxonomy to be a determining factor in the cloacal microbiota of snakes and that Tenericutes are associated with aquatic habitats. This is the first report to examine the cloacal microbiome of these species and provides a useful foundation for future work to build upon.

Parasites, Drugs and Captivity: Blastocystis-Microbiome Associations in Captive Water Voles

(1) Background: Blastocystis is a microbial eukaryote inhabiting the gastrointestinal tract of a broad range of animals including humans. Several studies have shown that the organism is associated with specific microbial profiles and bacterial taxa that have been deemed beneficial to intestinal and overall health. Nonetheless, these studies are focused almost exclusively on humans, while there is no similar information on other animals. (2) Methods: Using a combination of conventional PCR, cloning and sequencing, we investigated presence of Blastocystis along with Giardia and Cryptosporidium in 16 captive water voles sampled twice from a wildlife park. We also characterised their bacterial gut communities. (3) Results: Overall, alpha and beta diversities between water voles with and without Blastocystis did not differ significantly. Differences were noted only on individual taxa with Treponema and Kineothrix being significantly reduced in Blastocystis positive water voles. Grouping according to antiprotozoal treatment and presence of other protists did not reveal any differences in the bacterial community composition either. (4) Conclusion: Unlike human investigations, Blastocystis does not seem to be associated with specific gut microbial profiles in water voles.

Venomous Snakes Reveal Ecological and Phylogenetic Factors Influencing Variation in Gut and Oral Microbiomes

The gastrointestinal tract (GIT) of vertebrates contains a series of organs beginning with the mouth and ending with the anus or cloacal opening. Each organ represents a unique environment for resident microorganisms. Due to their simple digestive anatomy, snakes are good models for studying microbiome variation along the GIT. Cloacal sampling captures the majority of the microbial diversity found in the GIT of snakes—yet little is known about the oral microbiota of snakes. Most research on the snake mouth and gut microbiota are limited to studies of a single species or captive-bred individuals. It therefore remains unclear how a host’s life history, diet, or evolutionary history correlate with differences in the microbial composition within the mouths and guts of wild snakes. We sampled the mouth and gut microbial communities from three species of Asian venomous snakes and utilized 16S rRNA microbial inventories to test if host phylogenetic and ecological differences correlate with distinct microbial compositions within the two body sites. These species occupy three disparate habitat types: marine, semi-arboreal, and arboreal, our results suggest that the diversity of snake mouth and gut microbial communities correlate with differences in both host ecology and phylogeny.

Curing piglets from diarrhea and preparation of a healthy microbiome with Bacillus treatment for industrial animal breeding

High-throughput farming of animals for an essential purpose such as large scale health and production of hogs is a challenge for the food industry in the modern world. The problem is that the breeding of livestock for fast growth or high yields of meat is often associated with illness and microbial infection that develop under the breeding conditions. Piglet diarrhea is most common pig disease, leading to heavy mortality and thereby economic loss. We proved that chemical drugs can relieve the symptoms of diarrhea in ill piglets, but they do not treat the underlying cause, i.e. significantly altered bacterial gut flora. Using Illumina sequencing of fecal DNA, we showed that the bacterial gut flora of piglets treated with antibiotics remain close to the ill conditions. However, using Illumina sequencing of fecal DNA from piglets treated with a specific Bacillus (Bacillus subtilis Y-15, B. amyloliquefaciens DN6502 and B. licheniformis SDZD02) demonstrated the efficiency of natural bioproducts not only on curing diarrhea, but also on beneficial bacteria to re-establish in the piglet gut. We therefore propose a new natural “medicine” to be explored by the world farm animal agriculture industry, particularly for sustainable improvement of swine livestock production and health.

The gut bacterial microbiota of sea turtles differs between geographically distinct populations

The microbiota of metazoans can be influenced by a variety of factors including diet, environment and genetics. In this study we sampled multiple populations from 2 host species that do not overlap in distribution, in order to test whether their bacterial microbiotas are species-specific or more variable. Intestinal swabs were collected from loggerhead turtles originating from Florida, USA, and Queensland, Australia, as well as from flatback turtles from Crab Island, Queensland, and Port Hedland, Western Australia. We then manually extracted bacterial DNA and used 16S rRNA sequencing to explore bacterial microbial community composition and structure. Our investigation showed that the bacterial microbiota of sea turtles is heavily influenced by geography, with loggerhead turtles originating from the USA and Australia harbouring significantly different bacterial microbial populations in terms of composition. Similarly, we also found that flatback turtles from Crab Island had significantly less diverse microbiotas, with a predominance of the bacterial phylum Firmicutes, in comparison to their genetically similar counterparts from Port Hedland. Factors that may explain these observed differences between populations include host genetics, differences in foraging habitat quality and differences in migratory distance (and thus durations of inappetence) between foraging and breeding grounds. The mechanisms by which these factors may influence bacterial microbial composition of sea turtle gastrointestinal tracts warrants further investigation. The results of this study highlight the importance of interpreting microbiota data of wild animals in the context of geography.

Microbial symbiosis and coevolution of an entire clade of ancient vertebrates: the gut microbiota of sea turtles and its relationship to their phylogenetic history

Background

The microbiota plays a critical role in host homeostasis and has been shown to be a major driving force in host evolution. However, our understanding of these important relationships is hampered by a lack of data for many species, and by significant gaps in sampling of the evolutionary tree. In this investigation we improve our understanding of the host-microbiome relationship by obtaining samples from all seven extant species of sea turtle, and correlate microbial compositions with host evolutionary history.

Results

Our analysis shows that the predominate phyla in the microbiota of nesting sea turtles was Proteobacteria. We also demonstrate a strong relationship between the bacterial phyla SR1 and sea turtle phylogeny, and that sea turtle microbiotas have changed very slowly over time in accordance with their similarly slow phenotypic changes.

Conclusions

This is one of the most comprehensive microbiota studies to have been performed in a single clade of animals and further improves our knowledge of how microbial populations have influenced vertebrate evolution.