Space, time and captivity: quantifying the factors influencing the fecal microbiome of an alpine ungulate

The Alpine ibex (Capra ibex) gut microbiome, seasonal dynamics, and potential application in lignocellulose bioconversion

Aiming to shed light on the biology of wild ruminants, we investigated the gut microbiome seasonal dynamics of the Alpine ibex (Capra ibex) from the Central Italian Alps. Feces were collected in spring, summer, and autumn during non-invasive sampling campaigns. Samples were analyzed by 16S rRNA amplicon sequencing, shotgun metagenomics, as well as targeted and untargeted metabolomics. Our findings revealed season-specific compositional and functional profiles of the ibex gut microbiome that may allow the host to adapt to seasonal changes in available forage, by fine-tuning the holobiont catabolic layout to fully exploit the available food. Besides confirming the importance of the host-associated microbiome in providing the phenotypic plasticity needed to buffer dietary changes, we obtained species-level genome bins and identified minimal gut microbiome community modules of 11-14 interacting strains as a possible microbiome-based solution for the bioconversion of lignocellulose to high-value compounds, such as volatile fatty acids.

Effect of Garlic Straw with Silage Corn Stalks on Hu Sheep Rumen Fermentation and Microbial Community In Vitro

Garlic, an important economic crop, provides nutrient-rich straw. When appropriately balanced with silage corn stalks, it is a high-quality forage resource. However, studies on the impact of garlic straw with silage corn stalks on Hu sheep's digestive metabolism and rumen microbiota are scarce. In this study, different addition ratios of garlic straw and silage corn stalks were utilized for in vitro experiments. We designed six experimental groups (CON, G0, G20, G40, G60, G80, and G100) based on varying ratios of garlic straw to silage corn stalks. Rumen microbiota was analyzed through 16S rRNA sequencing. Nutrient composition analysis indicated that garlic straw's relative feeding value (RFV) closely resembled that of silage corn stalks. After 24 h of fermentation, dry matter digestibility and in vitro gas production significantly increased, reaching peak values at a 60% addition ratio. Furthermore, volatile fatty acids (VFAs) such as acetic, propionic, and butyric acid exhibited elevated contents, with the highest yields observed at 60% inclusion. At the genus level, Prevotella, Rikenellaceae RC9 gut group, and Succiniclasticum were identified as the dominant bacterial groups. The gas production test showed a significant decrease in the G80 group compared to others. Microbial analysis revealed a higher abundance of Prevotella in G80 compared to G20, offering valuable insights for reducing greenhouse gas emissions from ruminant animals. Finally, this study predicted the impact of garlic straw with silage corn stalks' addition on Hu sheep's metabolic pathways and biological functions of the rumen microbiota. This research highlights the potential for effectively utilizing garlic straw as a feed resource for Hu sheep and proposes a rational proportion for combining garlic straw with silage corn stalks.

"Get the best out of what comes in" - adaptation of the microbiota of chamois (Rupicapra rupicapra) to seasonal forage availability in the Bavarian Alps

As an inhabitant of the Alps, chamois are exposed to significant climatic changes throughout the year and are also strongly confronted with changing forage availability. Besides horizontal and vertical migratory movements as an adaptation, it undergoes physiological transformations and dynamic changes in the ruminal microbiota. The following study used 48 chamois of different ages and genders to investigate to which extent the ingested food plants, the resulting crude nutrients in the rumen (reticulorumen) contents, and the bacterial microbiota in the rumen and their fermentation products were influenced by the changes over the seasons. Very little is known about the microbiota of wild ruminants, and many bacterial taxa could only be determined to certain taxonomic levels in this study. However, adapted microbiota reflects the significant changes in the ingested forage and the resulting crude nutrients. For some taxa, our results indicated potential functional relationships. In addition, 15 genera were identified, representing almost 90% of the relative abundance, forming the central part of the microbial community throughout the year. The successful and flexible adaptation of chamois is reflected in the chamois rumen's nutrient and microbial profile. This is also the first study that analyzes the microbiota of the chamois using rumen samples and considers the microbiota in a seasonal comparison.

Fecal microbiota of the synanthropic golden jackal (Canis aureus)

The golden jackal (Canis aureus), is a medium canid carnivore widespread throughout the Mediterranean region and expanding into Europe. This species thrives near human settlements and is implicated in zoonoses such as rabies. This study explores for the first time, the golden jackal fecal microbiota. We analyzed 111 fecal samples of wild golden jackals using 16S rRNA amplicon sequencing the connection of the microbiome to animal characteristics, burden of pathogens and geographic and climate characteristics. We further compared the fecal microbiota of the golden jackal to the black-backed jackal and domestic dog. We found that the golden jackal fecal microbiota is dominated by the phyla Bacteroidota, Fusobacteriota and Firmicutes. The golden jackal fecal microbiota was associated with different variables, including geographic region, age-class, exposure to rabies oral vaccine, fecal parasites and toxoplasmosis. A remarkable variation in the relative abundance of different taxa was also found associated with different variables, such as age-class. Linear discriminant analysis effect size (LEfSe) analysis found abundance of specific taxons in each region, Megasphaera genus in group 1, Megamonas genus in group 2 and Bacteroides coprocola species in group 3. We also found a different composition between the fecal microbiota of the golden jackal, blacked-backed jackal and the domestic dog. Furthermore, LEfSe analysis found abundance of Fusobacterium and Bacteroides genera in the golden jackal, Clostridia class in blacked-backed jackal and Megamonas genus in domestic dog. The golden jackal fecal microbiota is influenced by multiple factors including host traits and pathogen burden. The characterization of the microbiota of this thriving species may aid in mapping its spread and proximity to human settlements. Moreover, understanding the jackal microbiota could inform the study of potential animal and human health risks and inform control measures.

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.

Benzoic Acid Metabolism and Lipopolysaccharide Synthesis of Intestinal Microbiome Affects the Health of Ruminants under Free-Range and Captive Mode

It is urgent to explore new ways to protect endangered wild animals and develop sustainable animal husbandry on the Qinghai–Tibet Plateau due to its fragile ecological environment. Ruminants, raised in captivity and free-range, have important niches in the Plateau and are the best models to analyze the effects of different feeding modes on their health. In this study, two ruminants, yaks and goats in free-range and captive modes, respectively, were selected to study the relationship between gut microbes and ruminant health. The results showed that the gut microbial diversity of free-range ruminants was higher than those of captive ruminants. Principal co-ordinates analysis (PCoA) showed that there were significant differences in the gut microbial communities in different breeding modes. Both the captive ruminants enriched the Succinivibrionaceae family, which had a strong potential to synthesize lipopolysaccharide, and the low exercise amount of the captive animals was significantly related to this function. Meanwhile, free-range ruminants enriched Oscillospiraceae, which had the potential to degrade benzoic acid, and this potential had a significant positive correlation with resistance to parasitic infections. We offer other possibilities, such as adding benzoic acid to feed or increasing the exercise time of captive ruminants to make them healthier.

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.

Distinct gut microbiomes in two polar bear subpopulations inhabiting different sea ice ecoregions

Gut microbiomes were analyzed by 16S rRNA gene metabarcoding for polar bears (Ursus maritimus) from the southern Beaufort Sea (SB), where sea ice loss has led to increased use of land-based food resources by bears, and from East Greenland (EG), where persistent sea ice has allowed hunting of ice-associated prey nearly year-round. SB polar bears showed a higher number of total (940 vs. 742) and unique (387 vs. 189) amplicon sequence variants and higher inter-individual variation compared to EG polar bears. Gut microbiome composition differed significantly between the two subpopulations and among sex/age classes, likely driven by diet variation and ontogenetic shifts in the gut microbiome. Dietary tracer analysis using fatty acid signatures for SB polar bears showed that diet explained more intrapopulation variation in gut microbiome composition and diversity than other tested variables, i.e., sex/age class, body condition, and capture year. Substantial differences in the SB gut microbiome relative to EG polar bears, and associations between SB gut microbiome and diet, suggest that the shifting foraging habits of SB polar bears tied to sea ice loss may be altering their gut microbiome, with potential consequences for nutrition and physiology.

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.

Differences in Fecal Microbiome and Antimicrobial Resistance between Captive and Free-Range Sika Deer under the Same Exposure of Antibiotic Anthelmintics

This study aimed to compare the fecal microbiome and antimicrobial resistance between captive and free-range sika deer with the same exposure to antibiotic anthelmintics. The taxonomic differences mainly involved significant changes in the dominant phyla, genera, and species. Linear discriminant analysis effect size (LEfSe) analysis revealed that 22 taxa were significantly different between the two groups. The KEGG analysis showed that the fecal microbiome metabolic function, and all level 2 categories in metabolism had higher abundance in the free-range deer. Based on the carbohydrate-active enzyme (CAZy) database analysis, glycoside hydrolases and carbohydrate-binding modules showed remarkable differences between the two groups. Regarding antibiotic resistance, tetQ and lnuC dominated the antibiotic resistance ontology (ARO) terms, and tetracycline and lincosamide resistance dominated the antimicrobial resistance patterns. Furthermore, the lnuC, ErmF, and tetW/N/W AROs and lincosamide resistance showed higher abundance in the captive deer, suggesting that captivity may yield more serious resistance issues because of the differences in greenfeed diet, breeding density, and/or housing environment. The results also revealed important associations between the phylum Proteobacteria, genus Prevotella, and major antibiotic resistance genes. Although the present study was a pilot study with a limited sample size that was insufficient control for some potential factors, it serves as the metagenomic study on the microbial communities and antimicrobial resistance in sika deer.

IMPORTANCE We used a metagenomic approach to investigate whether and how captive and free-range impact the microbial communities and antimicrobial resistance in sika deer. The results provide solid evidence of the significant impacts on the microbial composition and function in captive and free-range sika deer. Interestingly, although the sika deer had the same exposure to antibiotic anthelmintics, the antimicrobial resistances were affected by the breeding environment.

The effects of captivity on the microbiome of the endangered Comal Springs riffle beetle (Heterelmis comalensis)

The gut microbiome is affected by host intrinsic factors, diet and environment, and strongly linked to host's health. Although fluctuations of microbiome composition are normal, some are due to changes in host environmental conditions. When species are moved into captive environments for conservation, education or rehabilitation, these new conditions can influence a change in gut microbiome composition. Here, we compared the microbiomes of wild and captive Comal Springs riffle beetles (Heterelmis comalensis) by using amplicon sequencing of the 16S rRNA gene. We found that the microbiome of captive beetles was more diverse than wild beetle microbiomes. We identified 24 amplicon sequence variants (ASVs) with relative abundances significantly different between the wild and captive beetles. Many of the ASVs overrepresented in captive beetle microbiomes belong to taxa linked to nitrogen-rich environments. This is one of the first studies comparing the effects of captivity on the microbiome of an endangered insect species. Our findings provide valuable information for future applications in the management of captive populations of H. comalensis.

Gut microbiome composition predicts summer core range size in two divergent ungulates

The gut microbiome of animals vary by age, diet, and habitat, and directly influences an individual's health. Similarly, variation in home ranges is linked to feeding strategies and fitness. Ungulates (hooved mammals) exhibit species-specific microbiomes and habitat use patterns. We combined gut microbiome and movement data to assess relationships between space use and the gut microbiome in a specialist and a generalist ungulate. We GPS radiocollared 24 mountain goats (Oreamnos americanus) and 34 white-tailed deer (Odocoileus virginianus), collected fecal samples, and conducted high-throughput sequencing of the 16S rRNA gene. We generated gut diversity metrics and key bacterial ratios. Our research question centred around the idea that larger Firmicutes to Bacteroidetes ratios confer body size or fat advantages that allow for larger home ranges, and relationships of disproportionate habitat use are stronger in the habitat specialist mountain goat. Firmicutes to Bacteroidetes ratios were positively correlated with core range area in both species. Mountain goats exhibited a negative relationship between gut diversity and proportional use of treed areas and escape terrain, and no relationships were detected in the habitat generalist white-tailed deer. This is the first study to relate range size to the gut microbiome in wild ungulates and is an important proof of concept that advances the information that can be gleaned from non-invasive sampling.

Diet and gut microbiome enterotype are associated at the population level in African buffalo

Studies in humans and laboratory animals link stable gut microbiome “enterotypes” with long-term diet and host health. Understanding how this paradigm manifests in wild herbivores could provide a mechanistic explanation of the relationships between microbiome dynamics, changes in dietary resources, and outcomes for host health. We identify two putative enterotypes in the African buffalo gut microbiome. The enterotype prevalent under resource-abundant dietary regimes, regardless of environmental conditions, has high richness, low between- and within-host beta diversity, and enrichment of genus Ruminococcaceae-UCG-005. The second enterotype, prevalent under restricted dietary conditions, has reduced richness, elevated beta diversity, and enrichment of genus Solibacillus. Population-level gamma diversity is maintained during resource restriction by increased beta diversity between individuals, suggesting a mechanism for population-level microbiome resilience. We identify three pathogens associated with microbiome variation depending on host diet, indicating that nutritional background may impact microbiome-pathogen dynamics. Overall, this study reveals diet-driven enterotype plasticity, illustrates ecological processes that maintain microbiome diversity, and identifies potential associations between diet, enterotype, and disease.

There are stable relationships between diet and microbiome in humans and lab animals. A study on African buffalo finds that diet influences microbiome variation and enterotype formation. Three pathogens may associate with microbiome depending on host diet, suggesting nutrition impacts relationships between gut microbiome and host health.

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.

Toward Best Practice in Livestock Microbiota Research: A Comprehensive Comparison of Sample Storage and DNA Extraction Strategies

Understanding the roles of microorganisms in the animal gastrointestinal microenvironment is highly important for the development of effective strategies to manage and manipulate these microbial communities. In order to guide future animal gut microbiota research projects and standardization efforts, we have conducted a systematic comparison of 10 currently used sample preservation and DNA extraction approaches for pig and chicken microbiota samples and quantified their effects on bacterial DNA yield, quality, integrity, and on the resulting sequence-based bacterial composition estimates. The results showed how key stages of conducting a microbiota study, including the sample storage and DNA extraction, can substantially affect DNA recovery from the microbial community, and therefore, biological interpretation in a matrix-dependent manner. Our results highlight the fact that the influence of storage and extraction methods on the resulting microbial community structure differed by sample type, even within the same species. As the effects of these technical steps are potentially large compared with the real biological variability to be explained, standardization is crucial for accelerating progress in the area of livestock microbiota research. This study provided a framework to assist future animal gut microbiota research projects and standardization efforts.

Anthropogenic interferences lead to gut microbiome dysbiosis in Asian elephants and may alter adaptation processes to surrounding environments

Human activities interfere with wild animals and lead to the loss of many animal populations. Therefore, efforts have been made to understand how wildlife can rebound from anthropogenic disturbances. An essential mechanism to adapt to environmental and social changes is the fluctuations in the host gut microbiome. Here we give a comprehensive description of anthropogenically induced microbiome alterations in Asian elephants (n = 30). We detected gut microbial changes due to overseas translocation, captivity and deworming. We found that microbes belonging to Planococcaceae had the highest contribution in the microbiome alterations after translocation, while Clostridiaceae, Spirochaetaceae and Bacteroidia were the most affected after captivity. However, deworming significantly changed the abundance of Flavobacteriaceae, Sphingobacteriaceae, Xanthomonadaceae, Weeksellaceae and Burkholderiaceae. These findings may provide fundamental ideas to help guide the preservation tactics and probiotic replacement therapies of a dysbiosed gut microbiome in Asian elephants. More generally, these results show the severity of anthropogenic activities at the level of gut microbiome, altering the adaptation processes to new environments and the subsequent capability to maintain normal physiological processes in animals.