Comparison of the bacterial communities in feces from wild versus housed sables (Martes zibellina) by high-throughput sequence analysis of the bacterial 16S rRNA gene

The comparison of gut microbiota between wild and captive Asian badgers (Meles leucurus) under different seasons

The gut microbiota plays an important role in the immunology, physiology and growth and development of animals. However, currently, there is a lack of available sequencing data on the gut microbiota of Asian badgers. Studying the gut microbiota of Asian badgers could provide fundamental data for enhancing productivity and immunity of badgers' breeding, as well as for the protection of wild animals. In this study, we first characterized the composition and structure of the gut microbiota in the large intestines of wild and captive Asian badgers during summer and winter by sequencing the V3-V4 region of the 16S ribosomal RNA gene. A total of 9 dominant phyla and 12 genera among the bacterial communities of the large intestines exhibited significant differences. Our results showed that Firmicutes and Proteobacteria were the most predominant in both wild and captive badgers, regardless of the season. Romboutsia, Streptococcus and Enterococcus may represent potential sources of zoonoses, warranting further attention and study. Our findings indicated that the diversity and availability of food resources were the most important influencing factors on the gut microbiota of Asian badgers, providing fundamental data for the protection and conservation of wild animals. Variation in the gut microbiota due to season, age and sex in both wild and captive Asian badgers should be considered in future research directions. Furthermore, combined multi-omics studies could provide more information for wild animal conservation, and enhancing our understanding of the molecular mechanism between the microbiota and host.

Effects of ex situ conservation on diversity and function of the gut microbiota of the Tibetan wild ass (Equus kiang)

Ex situ conservation is the main method for the protection of endangered wildlife. To explore the effect of ex situ conservation on the gut microbiota of the kiang (Equus kiang), metagenomic sequencing combined with bioinformatics analysis was used to investigate the composition and function of the gut microbiota of the kiang. The results showed that ex situ conservation not only protected wildlife, but also affected the composition and function of gut microbiota, as well as the health of animals. In the zoo, the ratio of the relative abundance of Firmicutes to that of Bacteroidetes (F/B) is higher, clusters of potentially pathogenic bacteria (such as Catonella, Catonella, and Mycoplasma) are more numerous, the abundance of resistance genes is higher, and the abundance of metabolic functions is increased. The dynamic changes of the gut microbiota also played an important role in the nutritional absorption, energy metabolism, and environmental adaptation of the kiang. Improving the rearing environment and increasing food diversity play important roles for increasing the diversity of gut microbiota, reducing the spread of potentially pathogenic bacteria, and reducing diseases. In the wild, especially in winter and in food-deficient areas, food supplementation can enhance the gut microbial homeostasis of wild animals and reduce the impact of crises. In depth studies of the gut microbial function of wildlife have important implications for improving ex situ conservation.

Comparative analysis of the fecal microbiota of healthy and injured common kestrel (Falco tinnunculus) from the Beijing Raptor Rescue Center

The gut microbiota is a complex ecosystem that interacts with many other factors to affect the health and disease states of the host. The common kestrel (Falco tinnunculus) is protected at the national level in China. However, the available sequencing data of the gut microbiota from the feces of wild common kestrels, especially for being rescued individuals by professional organization, remains limited. In the present study, we characterized the fecal bacterial communities of healthy and injured common kestrels, and compared the structure of their fecal microbiota by analyzing the V3-V4 region of the 16S rRNA gene using high-throughput sequencing technology with the Illumina MiSeq platform. We found that Firmicutes, Proteobacteria and Actinobacteria were the most predominant phyla in common kestrels. Further, the beta diversity analysis showed that changes in gut microbes were associated with injuries to the common kestrel. The Bacteroides/Firmicutes ratio was significantly lower in the injured group. At the genus level, Glutamicibacter showed significant difference in the two groups. The aim of our current study was to characterize the basic bacterial composition and community structure in the feces of healthy common kestrels, and then compare the differences in the fecal microbiota between healthy and injured individuals. Patescibacteria, Spirochaetes, and Glutamicibacter may be studied as potential biomarkers for certain diseases in raptors. The results could provide the basic data for additional research on the fecal microbiota of common kestrels and contribute to the rescue of wild raptors in the future.

Comparative Analyses of the Fecal Microbiome of Five Wild Black-Billed Capercaillie (Tetrao parvirostris) Flocks

Black-billed capercaillie (Tetrao parvirostris) was listed as a first-class state-protected animal because it was endangered in China (Category I). This study is the first to examine the diversity and composition of T. parvirostris gut microbiome in the wild. We collected fecal samples from five black-billed capercaillie flock roosting sites (each 20 km apart) in one day. Thirty fecal samples were sequenced with 16S rRNA gene amplicons on the Illumina HiSeq platform. This study is the first to analyze the fecal microbiome composition and diversity of black-billed capercaillie in the wild. At the phylum level, Camplyobacterota, Bacillota, Cyanobacteria, Actinomycetota, and Bacteroidota were the most abundant in the fecal microbiome of black-billed capercaillie. At the genus level, unidentified Chloroplast, Escherichia-Shigella, Faecalitalea, Bifidobacterium, and Halomonas were the dominant genera. Based on alpha and beta diversity analyses, we found no significant differences in the fecal microbiome between five flocks of black-billed capercaillie. Protein families: genetic information processing; protein families: signaling and cellular processes, carbohydrate metabolism; protein families: metabolism and energy metabolism are the main predicted functions of the black-billed capercaillie gut microbiome through the PICRUSt2 method. This study reveals the composition and structure of the fecal microbiome of the black-billed capercaillie under wild survival conditions, and this study provides scientific data for the comprehensive conservation of the black-billed capercaillie.

Comparison of fecal microbiota of SPF and non-SPF Beagle dogs

Microbial colonization of animal intestine impacts host metabolism and immunity. The study was aimed to investigate the diversity of the intestinal microflora in specific pathogen free (SPF) and non-SPF Beagle dogs of different ages by direct sequencing analysis of the 16S rRNA gene. Stool samples were collected from four non-SPF and four SPF healthy Beagle dogs. From a total of 792 analyzed Operation taxonomic units, four predominant bacterial phyla were identified: Firmicutes (75.23%), Actinobacteria (10.98%), Bacteroidetes (9.33%), and Proteobacteria (4.13%). At the genus level, Streptococcus, Lactobacillus, and Bifidobacterium were dominated. Among which, Alloprevotella, Prevotella_9, and Faecalibacterium were presented exclusively in non-SPF beagles, with potentially anti-inflammatory capability, which could protect non-SPF beagles from complex microbial environment. The number and diversity of intestinal flora for non-SPF Beagle dogs were the highest at birth and gradually decreased with growth, whereas the results for the SPF beagle samples were the opposite, with the number and diversity of intestinal microbiota gradually increases as beagles grow. In a nutshell, the microbial complexity of the rearing environment can enrich the gut microbiota of beagles, many of which are anti-inflammatory microbiota with the potential to increase the adaptability of the animal to the environment. However, the gut microbiota of SPF beagles was more sensitive to environmental changes than that of non-SPF beagles. This study is of great significance for understanding the bionomics of intestinal microflora in non-SPF and SPF beagles, improving the experimental accuracy in scientific research.

Possibilities and limits for using the gut microbiome to improve captive animal health

Because of its potential to modulate host health, the gut microbiome of captive animals has become an increasingly important area of research. In this paper, we review the current literature comparing the gut microbiomes of wild and captive animals, as well as experiments tracking the microbiome when animals are moved between wild and captive environments. As a whole, these studies report highly idiosyncratic results with significant differences in the effect of captivity on the gut microbiome between host species. While a few studies have analyzed the functional capacity of captive microbiomes, there has been little research directly addressing the health consequences of captive microbiomes. Therefore, the current body of literature cannot broadly answer what costs, if any, arise from having a captive microbiome in captivity. Addressing this outstanding question will be critical to determining whether it is worth pursuing microbial manipulations as a conservation tool. To stimulate the next wave of research which can tie the captive microbiome to functional and health impacts, we outline a wide range of tools that can be used to manipulate the microbiome in captivity and suggest a variety of methods for measuring the impact of such manipulation preceding therapeutic use. Altogether, we caution researchers against generalizing results between host species given the variability in gut community responses to captivity and highlight the need to understand what role the gut microbiome plays in captive animal health before putting microbiome manipulations broadly into practice.

Recent progress in research on the gut microbiota and highland adaptation on the Qinghai-Tibet Plateau

Microbial communities that inhabit the host's intestine influence many aspects of the host's health and bear the adaptive potential to alterations in harsh environments and diets. The Qinghai-Tibet Plateau represents one of the harshest environments in the world. Preliminary progress has been made in identifying the communities of gut microbes in Indigenous Tibetans and non-human animals. However, due to the complexity of microbial communities, the effects of gut microbes on the host's health and high-plateau adaptation remain unexplained. Herein, we review the latest progress in identifying factors affecting the gut microbiota of native Tibetans and non-human animals and highlight the complex interactions between the gut microbiota, health and highland adaptation, which provides a basis for exploring the correlations between the gut microbiota and clinical indexes in native highland residents and travellers, as well as developing microbiota-based strategies to mitigate health risks for tourists and treatments for mountain sickness during high-altitude travel in the future.

Habitat environmental factors influence intestinal microbial diversity of the short-faced moles (Scaptochirus moschata)

The short-faced moles (Scaptochirus moschata) are unique Chinese mammal that live in burrows for life. They have complex ecological adaptation mechanisms to adapt to perennial underground life. Intestinal microbes play an important role in the ecological adaptation of wild animals. The gut microbiota diversity and its function in short-faced moles’ ecological adaptation is a scientific issue worth exploring. In this study, the Illumina HiSeq sequencing platform was used to sequence the V3-V4 hypervariable regions of the 16S rRNA genes of 22 short-faced moles’ intestinal samples to study the composition and functional structure of their intestinal microbiota. The results showed that in the short-faced moles’ intestine, there are four main phyla, Firmicutes, Proteobacteria, Actinobacteria and Bacteroidete. At the family level, Peptostreptococcaceae and Enterobacteriaceae have the highest abundance. At the genus level, Romboutsia is the genus with the highest microbial abundance. According to the KEGG database, the main functions of short-faced mole gut microbes are metabolism, genetic information processing, environmental information processing, and cellular processes. The function of short-faced mole intestinal microbiota is suitable for its long-term burrowing life. No gender difference is found in the composition and function of the short-faced mole intestinal microbiota. There are significant differences in the composition and functional structure of the short-faced mole gut microbiota between samples collected from different habitats. We conferred that this is related to the different environment factors in which they live, especially to the edaphic factors.

Habitat Elevation Shapes Microbial Community Composition and Alter the Metabolic Functions in Wild Sable (Martes zibellina) Guts

In recent decades, wild sable (Carnivora Mustelidae Martes zibellina) habitats, which are often natural forests, have been squeezed by anthropogenic disturbances such as clear-cutting, tilling and grazing. Sables tend to live in sloped areas with relatively harsh conditions. Here, we determine effects of environmental factors on wild sable gut microbial communities between high and low altitude habitats using Illumina Miseq sequencing of bacterial 16S rRNA genes. Our results showed that despite wild sable gut microbial community diversity being resilient to many environmental factors, community composition was sensitive to altitude. Wild sable gut microbial communities were dominated by Firmicutes (relative abundance 38.23%), followed by Actinobacteria (30.29%), and Proteobacteria (28.15%). Altitude was negatively correlated with the abundance of Firmicutes, suggesting sable likely consume more vegetarian food in lower habitats where plant diversity, temperature and vegetation coverage were greater. In addition, our functional genes prediction and qPCR results demonstrated that energy/fat processing microorganisms and functional genes are enriched with increasing altitude, which likely enhanced metabolic functions and supported wild sables to survive in elevated habitats. Overall, our results improve the knowledge of the ecological impact of habitat change, providing insights into wild animal protection at the mountain area with hash climate conditions.

Harnessing the strategy of metagenomics for exploring the intestinal microecology of sable (Martes zibellina), the national first-level protected animal

Sable (Martes zibellina), a member of family Mustelidae, order Carnivora, is primarily distributed in the cold northern zone of Eurasia. The purpose of this study was to explore the intestinal flora of the sable by metagenomic library-based techniques. Libraries were sequenced on an Illumina HiSeq 4000 instrument. The effective sequencing data of each sample was above 6000 M, and the ratio of clean reads to raw reads was over 98%. The total ORF length was approximately 603,031, equivalent to 347.36 Mbp. We investigated gene functions with the KEGG database and identified 7140 KEGG ortholog (KO) groups comprising 129,788 genes across all of the samples. We selected a subset of genes with the highest abundances to construct cluster heat maps. From the results of the KEGG metabolic pathway annotations, we acquired information on gene functions, as represented by the categories of metabolism, environmental information processing, genetic information processing, cellular processes and organismal systems. We then investigated gene function with the CAZy database and identified functional carbohydrate hydrolases corresponding to genes in the intestinal microorganisms of sable. This finding is consistent with the fact that the sable is adapted to cold environments and requires a large amount of energy to maintain its metabolic activity. We also investigated gene functions with the eggNOG database; the main functions of genes included gene duplication, recombination and repair, transport and metabolism of amino acids, and transport and metabolism of carbohydrates. In this study, we attempted to identify the complex structure of the microbial population of sable based on metagenomic sequencing methods, which use whole metagenomic data, and to map the obtained sequences to known genes or pathways in existing databases, such as CAZy, KEGG, and eggNOG. We then explored the genetic composition and functional diversity of the microbial community based on the mapped functional categories.

Marsupial Gut Microbiome

The study of the gut microbiome in threatened wildlife species has enormous potential to improve conservation efforts and gain insights into host-microbe coevolution. Threatened species are often housed in captivity, and during this process undergo considerable changes to their gut microbiome. Studying the gut microbiome of captive animals therefore allows identification of dysbiosis and opportunities for improving management practices in captivity and for subsequent translocations. Manipulation of the gut microbiome through methods such as fecal transplant may offer an innovative means of restoring dysbiotic microbiomes in threatened species to provide health benefits. Finally, characterization of the gut microbiome (including the viral components, or virome) provides important baseline health information and may lead to discovery of significant microbial pathogens. Here we summarize our current understanding of microbiomes in Australian marsupial species.

Age, Gender, and Feeding Environment Influence Fecal Microbial Diversity in Spotted Hyenas (Crocuta crocuta)

Fecal microbes play an important role in the survival and health of wild animals. Spotted hyena (Crocuta crocuta) is one of the representative carnivores in Africa. In this study, we examined the fecal microflora of spotted hyena by conducting high-throughput sequencing of the fecal microbial 16S rRNA gene V3-V4 high mutation region. The effects of age, sex, and feeding environment on the fecal microbiota of spotted hyenas were determined. The results showed that the core bacteria phyla of spotted hyenas fecal microbiota include Firmicutes (at an average relative abundance of 53.93%), Fusobacteria (19.56%), Bacteroidetes (11.40%), Actinobacteria (5.78%), and Proteobacteria (3.26%), etc. Age, gender, and feeding environment all had important effects on the fecal microbiota of spotted hyenas, among which feeding environment might be the most significant. The abundance of the Firmicutes in the adult group was significantly higher than that in the juvenile group, whereas the abundance of Fusobacteria, Bacteroidetes, and Proteobacteria were significantly lower than that in the juvenile group. The abundance of Lachnospiraceae and Ruminococcaceae in the female group was significantly higher than that in the male group. There were significant differences between the fecal microbial communities of Jinan group and Weihai group, and microbes from the phyla Firmicutes and Synergistetes were representative species associated with the difference.

Comparison of the gut microbiota composition between the wild and captive Tibetan wild ass (Equus kiang)

Aims

The gut microbiota has a great effect on the health and nutrition of the host. Manipulation of the intestinal microbiota may improve animal health and growth performance. The objectives of our study were to characterize the faecal microbiota between wild and captive Tibetan wild asses and discuss the differences and their reasons.

Methods and Results

Through high‐throughput sequencing of the 16S rRNA V4‐V5 region, we studied the gut microbiota composition and structure of Tibetan wild asses in winter, and analysed the differences between wild and captive groups. The results showed that the most common bacterial phylum in Tibetan wild ass faeces samples was Bacteroidetes, while the phylum Firmicutes was dominant in captive Tibetan wild ass faecal samples. The relative abundance of Firmicutes, Tenericutes and Spirochaetes were significantly higher (P < 0·01) than in the wild groups.

Conclusions

Captivity reduces intestinal microbial diversity, evenness and operational taxonomic unit number due to the consumption of industrial food, therefore, increasing the risk of disease prevalence and affecting the health of wildlife.

Significance and Impact of the Study

We studied the effect of the captive environment on intestinal micro‐organisms. This article provides a theoretical basis for the ex‐situ conservation of wild animals in the future.

The microbiota in the intestinal and respiratory tracts of naked mole-rats revealed by high-throughput sequencing

Background

The naked mole-rat (NMR, Heterocephalus glaber) is being bred as a novel laboratory animal due to its unique biological characteristics, including longevity, cancer resistance, hypoxia tolerance, and pain insensitivity. It is expected that differences exist between the microbiota of wild NMRs and that of NMRs in an artificial environment. Overall, the effect of environment on changes in the NMR microbiota remains unknown. In an attempt to understand the microbiota composition of NMRs in captivity, variability in the microbiota of the intestinal and respiratory tracts of two groups of NMRs was assessed under two conditions.

Results

The results obtained by high-throughput sequencing revealed significant differences at the phylum, class, order, family and genus levels in the microbiota between the two groups of NMRs examined (first group in conventional environment, second group in barrier environment). For the trachea, 24 phyla and 533 genera and 26 phyla and 733 genera were identified for the first and second groups of animals. Regarding the cecum, 23 phyla and 385 genera and 25 phyla and 110 genera were identified in the microbiota of first and second groups of animals. There were no obvious differences between females and males or young and adult animals.

Conclusions

Our results suggest that the intestinal and respiratory tract NMR microbiota changed during captivity, which may be related to the transition to the breeding environment. Such changes in the microbiota of NMRs may have an effect on the original characteristics, which may be the direction of further research studies.

Fecal bacterial communities of wild-captured and stranded green turtles (Chelonia mydas) on the Great Barrier Reef

Green turtles (Chelonia mydas) are endangered marine herbivores that break down food particles, primarily sea grasses, through microbial fermentation. However, the microbial community and its role in health and disease is still largely unexplored. In this study, we investigated and compared the fecal bacterial communities of eight wild-captured green turtles to four stranded turtles in the central Great Barrier Reef regions that include Bowen and Townsville. We used high-throughput sequencing analysis targeting the hypervariable V1-V3 regions of the bacterial 16S rRNA gene. At the phylum level, Firmicutes predominated among wild-captured green turtles, followed by Bacteroidetes and Proteobacteria. In contrast, Proteobacteria (Gammaproteobacteria) was the most significantly dominant phylum among all stranded turtles, followed by Bacteroidetes and Firmicutes. In addition, Fusobacteria was also significantly abundant in stranded turtles. No significant differences were found between the wild-captured turtles in Bowen and Townsville. At the family level, the core bacterial community consisted of 25 families that were identified in both the wild-captured and stranded green turtles, while two unique sets of 14 families each were only found in stranded or wild-captured turtles. The predominance of Bacteroides in all groups indicates the importance of these bacteria in turtle gut health. In terms of bacterial diversity and richness, wild-captured green turtles showed a higher bacterial diversity and richness compared with stranded turtles. The marked differences in the bacterial communities between wild-captured and stranded turtles suggest the possible dysbiosis in stranded turtles in addition to potential causal agents.

Comparison of the gut microbiota composition between wild and captive sika deer (Cervus nippon hortulorum) from feces by high-throughput sequencing

The gut microbiota is characterized as a complex ecosystem that has effects on health and diseases of host with the interactions of many other factors together. Sika deer is the national level for the protection of wild animals in China. The available sequencing data of gut microbiota from feces of wild sika deer, especially for Cervus nippon hortulorum in Northeast China, are limited. Here, we characterized the gastrointestinal bacterial communities of wild (7 samples) and captive (12 samples) sika deer from feces, and compared their gut microbiota by analyzing the V4 region of 16S rRNA gene using high-throughput sequencing technology on the Illumina Hiseq platform [corrected]. Firmicutes (77.624%), Bacteroidetes (18.288%) and Tenericutes (1.342%) were the most predominant phyla in wild sika deer. While in captive sika deer, Firmicutes (50.710%) was the dominant phylum, followed by Bacteroidetes (31.996%) and Proteobacteria (4.806%). A total of 9 major phyla, 22 families and 30 genera among gastrointestinal bacterial communities showed significant differences between wild and captive sika deer. The specific function and mechanism of Tenericutes in wild sika deer need further study. Our results indicated that captive sika deer in farm had higher fecal bacterial diversity than the wild. Abundance and quantity of diet source for sika deer played crucial role in shaping the composition and structure of gut microbiota.

Unexplored Archaeal Diversity in the Great Ape Gut Microbiome

Archaea are habitual residents of the human gut flora but are detected at substantially lower frequencies than bacteria. Previous studies have indicated that each human harbors very few archaeal species. However, the low diversity of human-associated archaea that has been detected could be due to the preponderance of bacteria in these communities, such that relatively few sequences are classified as Archaea even when microbiomes are sampled deeply. Moreover, the universal prokaryotic primer pair typically used to interrogate microbial diversity has low specificity to the archaeal domain, potentially leaving vast amounts of diversity unobserved. As a result, the prevalence, diversity, and distribution of archaea may be substantially underestimated. Here we evaluate archaeal diversity in gut microbiomes using an approach that targets virtually all known members of this domain. Comparing microbiomes across five great ape species allowed us to examine the dynamics of archaeal lineages over evolutionary time scales. These analyses revealed hundreds of gut-associated archaeal lineages, indicating that upwards of 90% of the archaeal diversity in the human and great ape gut microbiomes has been overlooked. Additionally, these results indicate a progressive reduction in archaeal diversity in the human lineage, paralleling the decline reported for bacteria. IMPORTANCE Our findings show that Archaea are a habitual and vital component of human and great ape gut microbiomes but are largely ignored on account of the failure of previous studies to realize their full diversity. Here we report unprecedented levels of archaeal diversity in great ape gut microbiomes, exceeding that detected by conventional 16S rRNA gene surveys. Paralleling what has been reported for bacteria, there is a vast reduction of archaeal diversity in humans. Our study demonstrates that archaeal diversity in the great ape gut microbiome greatly exceeds that reported previously and provides the basis for further studies on the role of archaea in the gut microbiome.