Characterisation of the bacterial community in the gastrointestinal tracts of elk (Cervus canadensis)

A taste of wilderness: supplementary feeding of red deer (Cervus elaphus) increases individual bacterial microbiota diversity but lowers abundance of important gut symbionts

The gut microbiome plays a crucial role in the health and well-being of animals. It is especially critical for ruminants that depend on this bacterial community for digesting their food. In this study, we investigated the effects of management conditions and supplemental feeding on the gut bacterial microbiota of red deer (Cervus elaphus) in the Bavarian Forest National Park, Germany. Fecal samples were collected from free-ranging deer, deer within winter enclosures, and deer in permanent enclosures. The samples were analyzed by high-throughput sequencing of the 16 S rRNA gene. The results showed that the gut bacterial microbiota differed in diversity, abundance, and heterogeneity within and between the various management groups. Free-ranging deer exhibited lower alpha diversity compared with deer in enclosures, probably because of the food supplementation available to the animals within the enclosures. Free-living individuals also showed the highest beta diversity, indicating greater variability in foraging grounds and plant species selection. Moreover, free-ranging deer had the lowest abundance of potentially pathogenic bacterial taxa, suggesting a healthier gut microbiome. Winter-gated deer, which spent some time in enclosures, exhibited intermediate characteristics between free-ranging and all-year-gated deer. These findings suggest that the winter enclosure management strategy, including supplementary feeding with processed plants and crops, has a significant impact on the gut microbiome composition of red deer. Overall, this study provides important insights into the effects of management conditions, particularly winter enclosure practices, on the gut microbiome of red deer. Understanding these effects is crucial for assessing the potential health implications of management strategies and highlights the value of microbiota investigations as health marker.

Fecal and vaginal microbiota of vaccinated and non-vaccinated pregnant elk challenged with Brucella abortus

Introduction

Brucella abortus is the causative agent of brucellosis in cattle and in humans, resulting in economic losses in the agricultural sector and representing a major threat to public health. Elk populations in the American Northwest are reservoirs for this bacterium and transmit the agent to domestic cattle herds. One potential strategy to mitigate the transmission of brucellosis by elk is vaccination of elk populations against B. abortus; however, elk appear to be immunologically distinct from cattle in their responses to current vaccination strategies. The differences in host response to B. abortus between cattle and elk could be attributed to differences between the cattle and elk innate and adaptive immune responses. Because species-specific interactions between the host microbiome and the immune system are also known to affect immunity, we sought to investigate interactions between the elk microbiome and B. abortus infection and vaccination.

Methods

We analyzed the fecal and vaginal microbial communities of B. abortus-vaccinated and unvaccinated elk which were challenged with B. abortus during the periparturient period.

Results

We observed that the elk fecal and vaginal microbiota are similar to those of other ruminants, and these microbial communities were affected both by time of sampling and by vaccination status. Notably, we observed that taxa representing ruminant reproductive tract pathogens tended to increase in abundance in the elk vaginal microbiome following parturition. Furthermore, many of these taxa differed significantly in abundance depending on vaccination status, indicating that vaccination against B. abortus affects the elk vaginal microbiota with potential implications for animal reproductive health.

Discussion

This study is the first to analyze the vaginal microbiota of any species of the genus Cervus and is also the first to assess the effects of B. abortus vaccination and challenge on the vaginal microbiome.

Metabolic changes before and after weaning in Dezhou donkey foals in relation to gut microbiota

Weaning is undoubtedly one of the most crucial stages in the growth and development of all mammalian animals, including donkey foals. Weaning is a dynamic and coordinated process of the body, which is closely associated with the health, nutrition, and metabolism of the host. Many studies have shown that the intestinal microbiota and serum metabolites of mammals exhibit different changes during lactation, weaning, and postweaning. However, the alterations in serum metabolites in donkey foals before and postweaning and the correlation between serum metabolites and intestinal microbiota are largely unknown. This study is based on the fecal 16S rRNA and serum metabolomes of Dezhou donkey foals. In total, 10 samples (fecal and serum) were collected during the following three stages: before weaning (F.M.1), during weaning (F.M.3), and postweaning (F.M.6). To study the alterations in intestinal microflora, serum metabolites, and their correlation before and postweaning. We found that with the growth and weaning progress of donkey foals, the intestinal microbiota of donkey foals underwent obvious changes, and the diversity of fecal bacteria increased (Chao1 and Shannon indexes). The main intestinal microbial flora of donkey foals include Bacteroides and Firmicutes. We found many microbiota that are associated with immunity and digestion in the postweaning group, such as Verrucomicrobiales, Clostridia, Oscillospiraceae, Akkermansia, and Rikenellaceae, which can be considered microbial markers for the transition from liquid milk to solid pellet feed. Clostridia and Oscillospiraceae can produce organic acids, including butyric acid and acetic acid, which are crucial for regulating the intestinal microecological balance of donkeys. Furthermore, the metabolome showed that the serum metabolites enriched before and postweaning were mainly related to arachidonic acid metabolism and riboflavin metabolism. Riboflavin was associated with the development of the small intestine and affected the absorption of the small intestine. We also found that the changes in the gut microbiome of the foals were significantly correlated with changes in serum metabolites, including lysophosphatidylcholine (LPC; 12,0) and positively correlated with Lachnoclostridium and Roseburia. To summarize, this study provides theoretical data for the changes in the intestinal microbiome and serum metabolism during the entire weaning period of donkey foals.

Gut microbiome biogeography in reindeer supersedes millennia of ecological and evolutionary separation

Ruminants are dependent on their gut microbiomes for nutrient extraction from plant diets. However, knowledge about the composition, diversity, function, and spatial structure of gut microbiomes, especially in wild ruminants, is limited, largely because analysis has been restricted to faeces or the rumen. In two geographically separated reindeer subspecies, 16S rRNA gene amplicon sequencing revealed strong spatial structuring, and pronounced differences in microbial diversity of at least 33 phyla across the stomach, small intestine, and large intestine (including faeces). The main structural feature was the Bacteroidota to Firmicutes ratio, which declined from the stomach to the large intestine, likely reflecting functional adaptation. Metagenome shotgun sequencing also revealed highly significant structuring in the relative occurrence of carbohydrate-active enzymes (CAZymes). CAZymes were enriched in the rumen relative to the small and large intestines. Interestingly, taxonomic diversity was highest in the large intestine, suggesting an important and understudied role for this organ. Despite the two study populations being separated by an ocean and six millennia of evolutionary history, gut microbiome structuring was remarkably consistent. Our study suggests a strong selection for gut microbiome biogeography along the gastrointestinal tract in reindeer subspecies.

Exploring the digesta- and mucosa-associated microbial community dynamics in the rumen and hindgut of goats from birth to adult

Recently, the relationship between the goat host and its gastrointestinal microbiome has emerged as a hallmark of host-microbiota symbiosis, which was indispensable for the proper physiological function that convert the plant biomass to livestock products. However, little integrative information about the establishment of gastrointestinal microflora in goats exists. Herein, we characterized the colonizing process of the bacterial community in the digesta and mucosa of the rumen, cecum, and colon of the cashmere goat from birth to adulthood to compare its spatiotemporal difference via 16S rRNA gene sequencing. A total of 1,003 genera belonging to 43 phyla were identified. Principal coordinate analysis unveiled the similarity of microbial community between or within each age group increased and gradually developed toward mature whatever in digesta or mucosa. In the rumen, the composition of the bacterial community in digesta differed significantly from in mucosa across age groups; whereas in the hindgut, there was a high similarity of bacterial composition between the in digesta and mucosa in each age group before weaning, while the bacterial community structure differed markedly between these two types of samples after weaning. Taxonomic analysis indicated that 25 and 21 core genera coexisted in digesta and mucosa of the rumen and hindgut, respectively; but their abundances differed considerably by GIT region and/or age. In digesta, as goats aged, a lower abundance of Bacillus was observed with higher abundances of Prevotella 1 and Rikenellaceae RC9 in the rumen; while in the hindgut, the genera Escherichia-Shigella, Variovorax, and Stenotrophomonas decreased and Ruminococcaceae UCG-005, Ruminococcaceae UCG-010, and Alistipes increased with age increased. In mucosa, the rumen showed microbial dynamics with increases of Butyrivibrio 2 and Prevotellaceae UCG-001 and decreases of unclassified_f_Pasteurellaceae; while the genera Treponema 2 and Ruminococcaceae UCG-010 increased and Escherichia-Shigella decreased in the hindgut as goats aged. These results shed light on the colonization process of microbiota in the rumen and hindgut, which mainly include the initial, transit, and mature phases. Furthermore, there is a significant difference in the microbial composition between in digesta and mucosa, and both these exhibit a considerable spatiotemporal specificity.

The gastrointestinal microbiome of browsing goats (Capra hircus)

Despite the growing interest in the ruminants' gastrointestinal tract (GIT) microbiomes' ability to degrade plant materials by animal husbandry and industrial sectors, only a few studies addressed browsing ruminants. The present work describes the taxonomic and functional profile of the bacterial and archaeal communities from five different gastrointestinal sections (rumen, omasum-abomasum, jejunum, cecum and colon) of browsing Capra hircus, by metabarcoding using 16S rRNA genes hypervariable regions. The bacterial communities across the GITs are mainly composed of Bacillota and Bacteroidota. Prevotella was the leading bacterial group found in the stomachs, Romboutsia in the jejuna, and Rikenellaceae_RC9_gut_group, Bacteroides, UCG-010_ge, UCG-005, and Alistipes in large intestines. The archaeal communities in the stomachs and jejuna revealed to be mainly composed of Methanobrevibacter, while in the large intestines its dominance is shared with Methanocorpusculum. Across the GITs, the main metabolic functions were related to carbohydrate, amino acid, and energy metabolisms. Significant differences in the composition and potential biological functions of the bacterial communities were observed among stomachs, jejuna and large intestines. In contrast, significant differences were observed among stomachs and jejuna verse large intestines for archaeal communities. Overall different regions of the GIT are occupied by different microbial communities performing distinct biological functions. A high variety of glycoside hydrolases (GHs) indispensable for degrading plant cell wall materials were predicted to be present in all the GIT sections.

Gastrointestinal Biogeography of Luminal Microbiota and Short-Chain Fatty Acids in Sika Deer (Cervus nippon)

The gut microbiota of sika deer has been widely investigated, but the spatial distribution of symbiotic microbes among physical niches in the gastrointestinal tract remains to be established. While feces are the most commonly used biological samples in these studies, the accuracy of fecal matter as a proxy of the microbiome at other gastrointestinal sites is as yet unknown. In the present study, luminal contents obtained along the longitudinal axis of deer gastrointestinal tract (rumen, reticulum, omasum, abomasum, small intestine, cecum, colon, and rectum) were subjected to 16S rRNA gene sequencing for profiling of the microbial composition, and samples from the rumen, small intestine, and cecum were subjected to metabolomic analysis to evaluate short-chain fatty acid (SCFA) profiles. Prevotella bacteria were the dominant gastric core microbes, while Christensenellaceae_R-7_group was predominantly observed in the intestine. While the eight gastrointestinal sites displayed variations in microbial diversity, abundance, and function, they could be clustered into stomach, small intestine, and large intestine segments, and the results further highlighted a specific microbial niche of the small intestine. SCFA levels in the rumen, small intestine, and cecum were significantly different, with Bacteroidetes and Spirochaetes were shown to play a critical role in SCFA production. Finally, the rectal microbial composition was significantly correlated with colonic and cecum communities but not those of the small intestine and four gastric sites. Quantification of the compositions and biogeographic relationships between gut microbes and SCFAs in sika deer should provide valuable insights into the interactions contributing to microbial functions and metabolites. IMPORTANCE Feces or specific segments of the gastrointestinal tract (in particular, the rumen) were sampled to explore the gut microbiome. The gastrointestinal biogeography of the luminal microbiota in ruminants, which is critical to guide accurate sampling for different purposes, is poorly understood at present. The microbial community of the rectal sample (as a proxy of fecal sample) showed higher correlation with those of other large intestinal sites relative to the small intestine or stomach, suggesting that the microbial composition is specifically shaped by the unique physiological characteristics of different gastrointestinal niches. In addition, significant differences in microbiomes and SCFAs were observed among the different gastrointestinal sites.

Seasonal and geographical differences in the ruminal microbial and chloroplast composition of sika deer (Cervus nippon) in Japan

To understand the nutritional status of culled wild sika deer (Cervus nippon), we compared the ruminal microbes of deer living in habitats differing in food composition (Nagano winter, Nagano spring, and Hokkaido winter) using next-generation sequencing. Twenty-nine sika deer were sampled. Alpha and beta diversity metrics determined via 16S and 18S rRNA amplicon-seq analysis showed compositional differences. Prevotella, Entodinium, and Piromyces were the dominant genera of bacteria, fungi and protozoa, respectively. Moreover, 66 bacterial taxa, 44 eukaryotic taxa, and 46 chloroplastic taxa were shown to differ significantly among the groups by the linear discriminant analysis effect size (LEfSe) technique. Total RNA-seq analysis yielded 397 significantly differentially expressed transcripts (q < 0.05), of which 48 (q < 0.01) were correlated with the bacterial amplicon-seq results (Pearson correlation coefficient > 0.7). The ruminal microbial composition corresponded with the presence of different plants because the amplicon-seq results indicated that chloroplast from broadleaf trees and Stramenopiles-Alveolates-Rhizaria (SAR) were enriched in Nagano, whereas chloroplast from graminoids, Firmicutes and the dominant phylum of fungi were enriched in Hokkaido. These results could be related to the severe snow conditions in Hokkaido in winter and the richness of plants with leaves and acorns in Nagano in winter and spring. The findings are useful for understanding the nutritional status of wild sika deer.

Non-invasive monitoring of multiple wildlife health factors by fecal microbiome analysis

Fecal microbial biomarkers represent a less invasive alternative for acquiring information on wildlife populations than many traditional sampling methodologies. Our goal was to evaluate linkages between fecal microbiome communities in Rocky Mountain elk (Cervus canadensis) and four host factors including sex, age, population, and physical condition (body-fat). We paired a feature-selection algorithm with an LDA-classifier trained on elk differential bacterial abundance (16S-rRNA amplicon survey) to predict host health factors from 104 elk microbiomes across four elk populations. We validated the accuracy of the various classifier predictions with leave-one-out cross-validation using known measurements. We demonstrate that the elk fecal microbiome can predict the four host factors tested. Our results show that elk microbiomes respond to both the strong extrinsic factor of biogeography and simultaneously occurring, but more subtle, intrinsic forces of individual body-fat, sex, and age-class. Thus, we have developed and described herein a generalizable approach to disentangle microbiome responses attributed to multiple host factors of varying strength from the same bacterial sequence data set. Wildlife conservation and management presents many challenges, but we demonstrate that non-invasive microbiome surveys from scat samples can provide alternative options for wildlife population monitoring. We believe that, with further validation, this method could be broadly applicable in other species and potentially predict other measurements. Our study can help guide the future development of microbiome-based monitoring of wildlife populations and supports hypothetical expectations found in host-microbiome theory.

Gastrointestinal Tract and Dietary Fiber Driven Alterations of Gut Microbiota and Metabolites in Durco × Bamei Crossbred Pigs

Gastrointestinal tract and dietary fiber (DF) are known to influence gut microbiome composition. However, the combined effect of gut segment and long-term intake of a high fiber diet on pig gut microbiota and metabolite profiles is unclear. Here, we applied 16S rRNA gene sequencing and untargeted metabolomics to investigate the effect of broad bean silage on the composition and metabolites of the cecal and jejunal microbiome in Durco × Bamei crossbred pigs. Twenty-four pigs were allotted to four graded levels of DF chow, and the content of jejunum and cecum were collected. Our results demonstrated that cecum possessed higher α-diversity and abundance of Bacteroidetes, unidentified Ruminococcaceae compared to jejunum, while jejunum possessed higher abundance of Lactobacillus, Streptococcus. DF intake significantly altered diversity of the bacterial community. The abundance of Bacteroidetes and Turicibacter increased with the increase of DF in cecum and jejunum respectively. Higher concentrations of amino acids and conjugated bile acids were detected in the jejunum, whereas free bile acids and fatty acids were enriched in the cecum. The concentrations of fatty acids, carbohydrate metabolites, organic acids, 2-oxoadipic acid, and succinate in cecum were higher in the high DF groups. Overall, the results indicate that the composition of bacteria and the microbiota metabolites were distinct in different gut segments. DF had a significant influence on the bacterial composition and structure in the cecum and jejunum, and that the cecal metabolites may further affect host health, growth, and slaughter performance.

The Impact of Host Genotype, Intestinal Sites and Probiotics Supplementation on the Gut Microbiota Composition and Diversity in Sheep

Three sampling strategies with a 16s rRNA high-throughput sequencing and gene expression assay (by RT-PCR) were designed, to better understand the host and probiotics effect on gut microbiota in sheep. Sampling: (1) colon contents and back-fat tissues from small-tailed Han sheep (SHS), big-tailed Hulun Buir sheep (BHBS), and short-tailed Steppe sheep (SHBS) (n = 12, 14, 12); (2) jejunum, cecum and colon contents, and feces from Tan sheep (TS, n = 6); (3) feces from TS at 4 time points (nonfeeding, 30 and 60 feeding days, and stop feeding 30 days) with probiotics supplementation (n = 7). The results indicated SHS had the highest Firmicutes abundance, the thinnest back-fat, and the lowest expression of C/EBPβ, C/EBPδ, ATGL, CFD, and SREBP1. Some bacteria orders and families could be potential biomarkers for sheep breeds with a distinct distribution of bacterial abundance, implying the host genotype is predominant in shaping unique microbiota under a shared environment. The microbiota diversity and Bifidobacterial populations significantly changed after 60 days of feeding but restored to its initial state, with mostly colonies, after 30 days ceased. The microbiota composition was greatly different between the small and large intestines, but somewhat different between the large intestine and feces; feces may be reliable for studying large intestinal microbiota in ruminants.

Effects of supplemental feeding on the fecal bacterial communities of Rocky Mountain elk in the Greater Yellowstone Ecosystem

Supplemental feeding of wildlife is a common practice often undertaken for recreational or management purposes, but it may have unintended consequences for animal health. Understanding cryptic effects of diet supplementation on the gut microbiomes of wild mammals is important to inform conservation and management strategies. Multiple laboratory studies have demonstrated the importance of the gut microbiome for extracting and synthesizing nutrients, modulating host immunity, and many other vital host functions, but these relationships can be disrupted by dietary perturbation. The well-described interplay between diet, the microbiome, and host health in laboratory and human systems highlights the need to understand the consequences of supplemental feeding on the microbiomes of free-ranging animal populations. This study describes changes to the gut microbiomes of wild elk under different supplemental feeding regimes. We demonstrated significant cross-sectional variation between elk at different feeding locations and identified several relatively low-abundance bacterial genera that differed between fed versus unfed groups. In addition, we followed four of these populations through mid-season changes in supplemental feeding regimes and demonstrated a significant shift in microbiome composition in a single population that changed from natural forage to supplementation with alfalfa pellets. Some of the taxonomic shifts in this population mirrored changes associated with ruminal acidosis in domestic livestock. We discerned no significant changes in the population that shifted from natural forage to hay supplementation, or in the populations that changed from one type of hay to another. Our results suggest that supplementation with alfalfa pellets alters the native gut microbiome of elk, with potential implications for population health.

Individual and Site-Specific Variation in a Biogeographical Profile of the Coyote Gastrointestinal Microbiota

Most knowledge of the vertebrate gut microbiota comes from fecal samples; due to difficulties involved in sample collection, the upper intestinal microbiota is poorly understood in wild animals despite its potential to inform broad interpretations about host-gut microbe relationships under natural conditions. Here, we used 16S rRNA gene sequencing to characterize the microbiota of wild coyotes (Canis latrans) along the gastrointestinal tract, including samples from the duodenum, jejunum, ileum, caecum, ascending and descending colon, and feces. We used this intestinal profile to (1) quantify how intestinal site and individual identity interact to shape the microbiota in an uncontrolled setting, and (2) evaluate whether the fecal microbiota adequately represent other intestinal sites. Microbial communities in the large intestine were distinct from those in the small intestine, with higher diversity and a greater abundance of anaerobic taxa. Within each of the small and large intestine, individual identity explained significantly more among-sample variation than specific intestinal sites, revealing the importance of individual variation in the microbiota of free-living animals. Fecal samples were not an adequate proxy for studying upper intestinal environments, as they contained only half the amplicon sequence variants (ASVs) present in the small intestine at three- to four-fold higher abundances. Our study is a unique biogeographical investigation of the microbiota using free-living mammals rather than livestock or laboratory organisms and provides a foundational understanding of the gastrointestinal microbiota in a wild canid.

Impact of feeding regimens on the composition of gut microbiota and metabolite profiles of plasma and feces from Mongolian sheep

Mongolian sheep are an indigenous ruminant raised for wool and meat production in China. The gut microbial community plays an important role in animal performance and metabolism. The objective of this study was to investigate the effects of two feeding regimens on the diversity and composition of gut microbiota and metabolite profiles of feces and plasma from Mongolian sheep. A total of 20 Mongolian sheep were assigned to one of two feeding regimens: free grazing (FG) and barn confinement (BC). When samples were collected, the average live weights of the sheep were 31.28 ± 1.56 kg and 34.18 ± 1.87 kg for the FG and BC groups, respectively. At the genus level, the FG group showed higher levels of Bacteroides, RC9_gut_group, Alistipes, Phocaeicola, Barnesiella, and Oscillibacter, and lower levels of Succinivibrio, Treponema, and Prevotella, compared to the BC group. The butyric acid content in feces was lower in the FG group (P > 0.05). Higher levels of palmitic acid, oleic acid, alpha-linolenic acid, L-carnitine, L-citrulline, and L-histidine, and lower levels of L-tyrosine, L-phenylalanine, and L-kynurenine were found in the plasma of the FG sheep. Moreover, there were substantial associations between several gut microbiota genera and alterations in feces and plasma metabolites especially those involved in the metabolism of butyric acid, linolenic acid, and L-tyrosine. Feeding regimens can not only influence the composition of gut microbiota, but also alter metabolic homeaostasis in sheep.

Characterization and Comparison of Microbiota in the Gastrointestinal Tracts of the Goat (Capra hircus) During Preweaning Development

Bacterial communities in gastrointestinal tracts (GIT) play an important role in animal health and performance. Despite its importance, little information is available on the establishment of microbial populations in the goat GIT or on changes occurring during early development. Therefore, this study investigated the bacterial community dynamics of the rumen, duodenum, jejunum, ileum, cecum, and colon in 15 goats at five developmental stages (0, 14, 28, 42, and 56 days old) by using 16S rDNA sequencing and quantitative real-time PCR technology. 940 genera were found to belong to 44 phyla distributed along the GIT. As a whole, the microbial richness and diversity showed a clear increasing trend as the kids aged and alpha diversity differed significantly among GIT compartments mainly occurring at middle day ages (14 and 28 days). Principal coordinate analysis indicated that the bacterial community displayed distinct temporal and spatial specificity along the GIT in preweaning goats. As kids aged, the phylum Firmicutes was replaced by Bacteroidetes in rumen, whereas Proteobacteria in the large intestine was displaced by Firmicutes. The phylum Proteobacteria was mainly present in the small intestine in older animals. In the rumen, taxa, such as Bacillus and Lactococcus decreased and Prevotella, Treponema, Ruminococcus, and unclassified Prevotellaceae increased with the age of kids. Furthermore, a lower proportion of taxa, such as Lactobacillus and Bacteroides was observed with higher abundances of both Christensenellaceae_R_7 and Ruminococcus in duodenum and jejunum in older animals. In the large intestine, the microbiota displayed taxonomic dynamics with increases of Ruminococcaceae UCG 005, unclassified Lachnospiraceae, Barnesiella, and Blautia as kids aged. Predicted pathway analysis suggested that genes involved in amino acid metabolism, and translation were abundant in both rumen and duodenum, while genes involved in membrane transport and carbohydrate metabolism were enriched in the large intestine. These results indicate that both the microbial colonization process and potential function exert a temporal-spatial specificity throughout the GIT of goats. This study provides new insight into the temporal dynamics of GIT microbiota development during preweaning and will aid to develop strategies for improving animal health and downstream production.