Characterization of the Gut Microbiota in Six Geographical Populations of Chinese Rhesus Macaques (Macaca mulatta), Implying an Adaptation to High-Altitude Environment

Exploring the population interaction of Przewalski's gazelle (Procapra przewalskii) based on the variations in gut microbiota across diverse geographic populations

The differences in gut microbiota among different populations, to a certain extent, reflect the degree of interaction between individuals within populations. To assess the interaction levels among several small populations of Przewalski's gazelle (Procapra przewalskii) (n = 105, from seven different regions) based on differences in gut microbiota, we used the closely related Tibetan gazelle (P. picticaudata) (n = 52, from seven different regions) as a control. We then compared the gut microbial communities between different populations of the two species using high-throughput sequencing of the 16S rRNA gene. The results showed that within a 100 km geographical distance, the intergroup differences in relative abundance of dominant bacteria, α-diversity, β-diversity, and functional metabolism abundance were higher or significantly higher in Przewalski's gazelle (narrowly distributed species) compared to the Tibetan gazelle (widely distributed species). Additionally, the proportion of shared OTUs between groups in Przewalski's gazelle was significantly lower than in Tibetan gazelle (p < 0.05). Additionally, neutral community model results also showed lower dispersal limitation in the Tibetan gazelle compared to Przewalski's gazelle. Therefore, based on the above results, we comprehensively speculate that the spatial interaction degree of Przewalski's gazelle in different habitat patches is relatively low. This study, starting from the perspective of gut microbiota, adopts a non-genetic perspective or method to assess whether there is, or to what extent there is, close interaction between species populations.

Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia

BACKGROUND

Scavenging indigenous village chickens play a vital role in sub-Saharan Africa, sustaining the livelihood of millions of farmers. These chickens are exposed to vastly different environments and feeds compared to commercial chickens. In this study, we analysed the caecal microbiota of 243 Ethiopian village chickens living in different altitude-dependent agro-ecologies.

RESULTS

Differences in bacterial diversity were significantly correlated with differences in specific climate factors, topsoil characteristics, and supplemental diets provided by farmers. Microbiota clustered into three enterotypes, with one particularly enriched at high altitudes. We assembled 9977 taxonomically and functionally diverse metagenome-assembled genomes. The vast majority of these were not found in a dataset of previously published chicken microbes or in the Genome Taxonomy Database.

CONCLUSIONS

The wide functional and taxonomic diversity of these microbes highlights their importance in the local adaptation of indigenous poultry, and the significant impacts of environmental factors on the microbiota argue for further discoveries in other agro-ecologies. Video Abstract.

The gut microbial differences between pre-released and wild red deer: Firmicutes abundance may affect wild adaptation after release

Insufficient density of red deer has affected the stability of forest ecosystems and the recovery of large carnivores (represented by Amur tiger). Conservation translocations from captivity to the wild has become an important way to restore the red deer populations. However, the difference in gut microbes between pre-release and wild red deer may affect the feeding adaptability of red deer after release. In this study, we clarified the differences in gut microbes between pre-released and wild red deer and screened the key gut microbes of the red deer involved in feeding by using metagenomic sequencing and feeding analysis. The results showed that the microbial difference between pre-released and wild red deer was mainly related to Firmicutes represented by Eubacteriales and Clostridia, and Firmicutes abundance in pre-released red deer (68.23%) was significantly lower than that of wild red deer (74.91%, p < 0.05). The expression of microbial metabolic pathways in pre-released red deer were significantly lower than those in wild red deer (p < 0.05), including carbohydrate metabolism, amino acid metabolism, glycan biosynthesis and metabolism, etc. The combinations of Firmicutes were significantly positively correlated with the intake of plant fiber and carbohydrate (p < 0.05), and were key microbes to help red deer deal with wild plant resources. Additionally, the combinations of Firmicutes represented by Eubacteriales and Clostridia lacking in pre-released red deer contributed the most to expression of microbial metabolic pathways (importance > 1), showing a significant positive correlation (p < 0.05). This study indicates that high abundance of Firmicutes is an important guarantee for red deer to adapt to the wild feeding environment, which provides critical implications for the recovery of red deer populations and the protection of endangered ungulates.

Diet components associated with specific bacterial taxa shape overall gut community compositions in omnivorous African viverrids

Gut bacterial communities provide flexibility to hosts during dietary changes. Despite the increasing number of studies exploring the associations between broader dietary guilds of mammalian hosts and their gut bacteria, it is generally unclear how diversity and variability in consumed diets link to gut bacterial taxa in wild non-primate mammals, particularly in omnivores. Here, we contribute to filling this gap by exploring consumed diets and gut bacterial community compositions with metabarcoding of faecal samples for two African mammals, Civettictis civetta and Genetta spp., from the family Viverridae. For each individual sample, we characterised bacterial communities and identified dietary taxa by sequencing vertebrate, invertebrate and plant markers. This led us to establish diet compositions that diverged from what has previously been found from visual identification methods. Specifically, while the two genera have been categorised into the same dietary guild, we detected more animal dietary items than plant items in C. civetta, while in Genetta spp., we observed the opposite. We further found that individuals with similar diets have similar gut bacterial communities within both genera. This association tended to be driven by specific links between dietary items and gut bacterial genera, rather than communities as a whole, implying diet-driven selection for specific gut microbes in individual wild hosts. Our findings underline the importance of molecular tools for improving characterisations of omnivorous mammalian diets and highlight the opportunities for simultaneously disentangling links between diets and gut symbionts. Such insights can inform robustness and flexibility in host-microbe symbioses to dietary change associated with seasonal and habitat changes.

Metagenomics Analysis Reveals the Composition and Functional Differences of Fecal Microbiota in Wild, Farm, and Released Chinese Three-Keeled Pond Turtles (Mauremys reevesii)

The intestine of living organisms harbors different microbiota associated with the biological functioning and health of the host and influences the process of ecological adaptation. Here, we studied the intestinal microbiota's composition and functional differences using 16S rRNA and metagenomic analysis in the wild, farm, and released Chinese three-keeled pond turtle (Mauremys reevesii). At the phylum level, Bacteroidota dominated, followed by Firmicutes, Fusobacteriota, and Actinobacteriota in the wild group, but Chloroflexi was more abundant in the farm and released groups. Moreover, Chryseobacterium, Acinetobacter, Comamonas, Sphingobacterium, and Rhodobacter were abundant in the released and farm cohorts, respectively. Cetobacterium, Paraclostridium, Lysobacter, and Leucobacter showed an abundance in the wild group. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed that the relative abundance of most pathways was significantly higher in the wild turtles (carbohydrate metabolism, lipid metabolism, metabolism of cofactors, and vitamins). The comprehensive antibiotic resistance database (CARD) showed that the antibiotic resistance gene (ARG) subtype macB was the most abundant in the farm turtle group, while tetA was higher in the wild turtles, and srpYmcr was higher in the released group. Our findings shed light on the association between the intestinal microbiota of M. reevesii and its habitats and could be useful for tracking habitats to protect and conserve this endangered species.

High-altitude-induced alterations in intestinal microbiota

In high-altitude environments characterized by low pressure and oxygen levels, the intestinal microbiota undergoes significant alterations. Whether individuals are subjected to prolonged exposure or acute altitude changes, these conditions lead to shifts in both the diversity and abundance of intestinal microbiota and changes in their composition. While these alterations represent adaptations to high-altitude conditions, they may also pose health risks through certain mechanisms. Changes in the intestinal microbiota induced by high altitudes can compromise the integrity of the intestinal mucosal barrier, resulting in gastrointestinal dysfunction and an increased susceptibility to acute mountain sickness (AMS). Moreover, alterations in the intestinal microbiota have been implicated in the induction or exacerbation of chronic heart failure. Targeted modulation of the intestinal microbiota holds promise in mitigating high-altitude-related cardiac damage. Dietary interventions, such as adopting a high-carbohydrate, high-fiber, low-protein, and low-fat diet, can help regulate the effects of intestinal microbiota and their metabolic byproducts on intestinal health. Additionally, supplementation with probiotics, either through dietary sources or medications, offers a means of modulating the composition of the intestinal microbiota. These interventions may offer beneficial effects in preventing and alleviating AMS following acute exposure to high altitudes.

Impact of high-altitude acclimatization and de-acclimatization on the intestinal microbiota of rats in a natural high-altitude environment

Introduction

Intestinal microorganisms play an important role in the health of both humans and animals, with their composition being influenced by changes in the host's environment.

Methods

We evaluated the longitudinal changes in the fecal microbial community of rats at different altitudes across various time points. Rats were airlifted to high altitude (3,650 m) and acclimatized for 42 days (HAC), before being by airlifted back to low altitude (500 m) and de-acclimatized for 28 days (HADA); meanwhile, the control group included rats living at low altitude (500 m; LA). We investigated changes in the gut microbiota at 12 time points during high-altitude acclimatization and de-acclimatization, employing 16S rRNA gene sequencing technology alongside physiological indices, such as weight and daily autonomous activity time.

Results

A significant increase in the Chao1 index was observed on day 14 in the HAC and HADA groups compared to that in the LA group, indicating clear differences in species richness. Moreover, the principal coordinate analysis revealed that the bacterial community structures of HAC and HADA differed from those in LA. Long-term high-altitude acclimatization and de- acclimatization resulted in the reduced abundance of the probiotic Lactobacillus. Altitude and age significantly influenced intestinal microbiota composition, with changes in ambient oxygen content and atmospheric partial pressure being considered key causal factors of altitude-dependent alterations in microbiota composition. High-altitude may be linked to an increase in anaerobic bacterial abundance and a decrease in non-anaerobic bacterial abundance.

Discussion

In this study, the hypobaric hypoxic conditions at high-altitude increased the abundance of anaerobes, while reducing the abundance of probiotics; these changes in bacterial community structure may, ultimately, affect host health. Overall, gaining a comprehensive understanding of the intestinal microbiota alterations during high-altitude acclimatization and de-acclimatization is essential for the development of effective prevention and treatment strategies to better protect the health of individuals traveling between high- and low-altitude areas.

Distinct Gut Microbial Enterotypes and Functional Dynamics in Wild Striped Field Mice (Apodemus agrarius) across Diverse Populations

Rodents, including the striped field mouse (Apodemus agrarius), play vital roles in ecosystem functioning, with their gut microbiota contributing significantly to various ecological processes. Here, we investigated the structure and function of 94 wild A. agrarius individuals from 7 geographic populations (45°57' N, 126°48' E; 45°87' N, 126°37' E; 45°50' N, 125°31' E; 45°59' N, 124°37' E; 46°01' N, 124°88' E; 46°01' N, 124°88' E; 46°01' N, 124°88' E), revealing two distinct enterotypes (Type1 and Type2) for the first time. Each enterotype showed unique microbial diversity, functions, and assembly processes. Firmicutes and Bacteroidetes dominated, with a significant presence of Lactobacillus and Muribaculaceae. Functional analysis highlighted metabolic differences, with Type1 emphasizing nutrient processing and Type2 showing higher energy production capacity. The analysis of the neutral model and the null model revealed a mix of stochastic (drift and homogenizing dispersal) and deterministic processes (homogenous selection) that shape the assembly of the microbiota, with subtle differences in the assembly processes between the two enterotypes. Correlation analysis showed that elevation and BMI were associated with the phylogenetic turnover of microbial communities, suggesting that variations in these factors may influence the composition and diversity of the gut microbiota in A. agrarius. Our study sheds light on gut microbial dynamics in wild A. agrarius populations, highlighting the importance of considering ecological and physiological factors in understanding host-microbiota interactions.

Altered microbiota, antimicrobial resistance genes, and functional enzyme profiles in the rumen of yak calves fed with milk replacer

IMPORTANCE

Yaks, as ruminants inhabiting high-altitude environments, possess a distinct rumen microbiome and are resistant to extreme living conditions. This study investigated the microbiota, resistome, and functional gene profiles in the rumen of yaks fed milk or milk replacer (MR), providing insights into the regulation of the rumen microbiome and the intervention of antimicrobial resistance in yaks through dietary methods. The abundance of Prevotella members increased significantly in response to MR. Tetracycline resistance was the most predominant. The rumen of yaks contained multiple antimicrobial resistance genes (ARGs) originating from different bacteria, which could be driven by MR, and these ARGs displayed intricate and complex interactions. MR also induced changes in functional genes. The enzymes associated with fiber degradation and butyrate metabolism were activated and showed close correlations with Prevotella members and butyrate concentration. This study allows us to deeply understand the ruminal microbiome and ARGs of yaks and their relationship with rumen bacteria in response to different milk sources.

Gut diazotrophs in lagomorphs are associated with season but not altitude and host phylogeny

Invertebrates such as termites feeding on nutrient-poor substrate receive essential nitrogen by biological nitrogen fixation of gut diazotrophs. However, the diversity and composition of gut diazotrophs of vertebrates such as Plateau pikas living in nutrient-poor Qinghai-Tibet Plateau remain unknown. To fill this knowledge gap, we studied gut diazotrophs of Plateau pikas (Ochotona curzoniae) and its related species, Daurian pikas (Ochotona daurica), Hares (Lepus europaeus) and Rabbits (Oryctolagus cuniculus) by high-throughput amplicon sequencing methods. We analyzed whether the gut diazotrophs of Plateau pikas are affected by season, altitude, and species, and explored the relationship between gut diazotrophs and whole gut microbiomes. Our study showed that Firmicutes, Spirochaetes, and Euryarchaeota were the dominant gut diazotrophs of Plateau pikas. The beta diversity of gut diazotrophs of Plateau pikas was significantly different from the other three lagomorphs, but the alpha diversity did not show a significant difference among the four lagomorphs. The gut diazotrophs of Plateau pikas were the most similarly to that of Rabbits, followed by Daurian pikas and Hares, which was inconsistent with gut microbiomes or animal phylogeny. The dominant gut diazotrophs of the four lagomorphs may reflect their living environment and dietary habits. Season significantly affected the alpha diversity and abundance of dominant gut diazotrophs. Altitude had no significant effect on the gut diazotrophs of Plateau pikas. In addition, the congruence between gut microbiomes and gut diazotrophs was low. Our results proved that the gut of Plateau pikas was rich in gut diazotrophs, which is of great significance for the study of ecology and evolution of lagomorphs.

Coping with extremes: Alternations in diet, gut microbiota, and hepatic metabolic functions in a highland passerine

In wild animals, diet and gut microbiota interactions are critical moderators of metabolic functions and are highly contingent on habitat conditions. Challenged by the extreme conditions of high-altitude environments, the strategies implemented by highland animals to adjust their diet and gut microbial composition and modulate their metabolic substrates remain largely unexplored. By employing a typical human commensal species, the Eurasian tree sparrow (Passer montanus, ETS), as a model species, we studied the differences in diet, digestive tract morphology and enzyme activity, gut microbiota, and metabolic energy profiling between highland (the Qinghai-Tibet Plateau, QTP; 3230 m) and lowland (Shijiazhuang, Hebei; 80 m) populations. Our results showed that highland ETSs had enlarged digestive organs and longer small intestinal villi, while no differences in key digestive enzyme activities were observed between the two populations. The 18S rRNA sequencing results revealed that the dietary composition of highland ETSs were more animal-based and less plant-based than those of the lowland ones. Furthermore, 16S rRNA sequencing results suggested that the intestinal microbial communities were structurally segregated between populations. PICRUSt metagenome predictions further indicated that the expression patterns of microbial genes involved in material and energy metabolism, immune system and infection, and xenobiotic biodegradation were strikingly different between the two populations. Analysis of liver metabolomics revealed significant metabolic differences between highland and lowland ETSs in terms of substrate utilization, as well as distinct sex-specific alterations in glycerophospholipids. Furthermore, the interplay between diet, liver metabolism, and gut microbiota suggests a dietary shift resulting in corresponding changes in gut microbiota and metabolic functions. Our findings indicate that highland ETSs have evolved to optimize digestion and absorption, rely on more protein-rich foods, and possess gut microbiota tailored to their dietary composition, likely adaptive physiological and ecological strategies adopted to cope with extreme highland environments.

Diversity of gut microbiome in Rocky Mountainsnail across its native range

The animal gut microbiome is often a key requirement for host nutrition, digestion, and immunity, and can shift in relation to host geography and environmental factors. However, ecological drivers of microbiome community assembly across large geographic ranges have rarely been examined in invertebrates. Oreohelix strigosa (Rocky Mountainsnail) is a widespread land snail found in heterogeneous environments across the mountainous western United States. It is ideally suited for biogeography studies due to its broad distribution, low migration, and low likelihood of passive transport via other animals. This study aims to uncover large-scale geographic shifts in the composition of O. strigosa gut microbiomes by using 16S rRNA gene sequencing on samples from across its native range. Additionally, we elucidate smaller-scale microbiome variation using samples collected only within Colorado. Results show that gut microbiomes vary significantly across broad geographic ranges. Several possible ecological drivers, including soil and vegetation composition, habitat complexity, habitat type, and human impact, collectively explained 27% of the variation across Coloradan O. strigosa gut microbiomes. Snail gut microbiomes show more similarity to vegetation than soil microbiomes. Gut microbial richness was highest in the rocky habitats and increased significantly in the most disturbed habitats (low complexity, high human impact), potentially indicating signs of dysbiosis in the snails' gut microbiomes. These small-scale environmental factors may be driving changes in O. strigosa gut microbiome composition seen across large-scale geography. This knowledge will also help us better understand how microbial associations influence species survival in diverse environments and aid wildlife conservation efforts.

Gut Microbiome Profiling of the Endangered Southern Greater Glider (Petauroides volans) after the 2019-2020 Australian Megafire

Studying the gut microbiome can provide valuable insights into animal health and inform the conservation management of threatened wildlife. Gut microbiota play important roles in regulating mammalian host physiology, including digestion, energy metabolism and immunity. Dysbiosis can impair such physiological processes and compromise host health, so it is essential that the gut microbiome be considered in conservation planning. The southern greater glider (Petauroides volans) is an endangered arboreal marsupial that faced widespread habitat fragmentation and population declines following the 2019-2020 Australian bushfire season. This study details baseline data on the gut microbiome of this species. The V3-V4 region of the 16S rRNA gene was amplified from scats collected from individuals inhabiting burnt and unburnt sites across southeastern Australia and sequenced to determine bacterial community composition. Southern greater glider gut microbiomes were characterised by high relative abundances of Firmicutes and Bacteroidota, which is consistent with that reported for other marsupial herbivores. Significant differences in gut microbial diversity and community structure were detected among individuals from different geographic locations. Certain microbiota and functional orthologues were also found to be significantly differentially abundant between locations. The role of wildfire in shaping southern greater glider gut microbiomes was shown, with some significant differences in the diversity and abundance of microbiota detected between burnt and unburnt sites. Overall, this study details the first data on greater glider (Petauroides) gut microbiomes, laying the foundation for future studies to further explore relationships between microbial community structure, environmental stressors and host health.

Oxygen enrichment protects against intestinal damage and gut microbiota disturbance in rats exposed to acute high-altitude hypoxia

Acute high-altitude hypoxia can lead to intestinal damage and changes in gut microbiota. Sustained and reliable oxygen enrichment can resist hypoxic damage at high altitude to a certain extent. However, it remains unclear whether oxygen enrichment can protect against gut damage and changes in intestinal flora caused by acute altitude hypoxia. For this study, eighteen male Sprague-Dawley rats were divided into three groups, control (NN), hypobaric hypoxic (HH), and oxygen-enriched (HO). The NN group was raised under normobaric normoxia, whereas the HH group was placed in a hypobaric hypoxic chamber simulating 7,000 m for 3 days. The HO group was exposed to oxygen-enriched air in the same hypobaric hypoxic chamber as the HH group for 12 h daily. Our findings indicate that an acute HH environment caused a fracture of the crypt structure, loss of epithelial cells, and reduction in goblet cells. Additionally, the structure and diversity of bacteria decreased in richness and evenness. The species composition at Phylum and Genus level was characterized by a higher ratio of Firmicutes and Bacteroides and an increased abundance of Lactobacillus with the abundance of Prevotellaceae_NK3B31_group decreased in the HH group. Interestingly, after oxygen enrichment intervention, the intestinal injury was significantly restrained. This was confirmed by an increase in the crypt depth, intact epithelial cell morphology, increased relative density of goblet cells, and higher evenness and richness of the gut microbiota, Bacteroidetes and Prevotellaceae as the main microbiota in the HO group. Finally, functional analysis showed significant differences between the different groups with respect to different metabolic pathways, including Amino acid metabolism, energy metabolism, and metabolism. In conclusion, this study verifies, for the first time, the positive effects of oxygen enrichment on gut structure and microbiota in animals experiencing acute hypobaric hypoxia.

Synergistic Responses of Tibetan Sheep Rumen Microbiota, Metabolites, and the Host to the Plateau Environment

Plateau adaptation in animals involves genetic mechanisms as well as coevolutionary mechanisms of the microbiota and metabolome of the animal. Therefore, the characteristics of the rumen microbiome and metabolome, transcriptome, and serum metabolome of Tibetan sheep at different altitudes (4500 m, 3500 m, and 2500 m) were analyzed. The results showed that the rumen differential metabolites at 3500 m and 4500 m were mainly enriched in amino acid metabolism, lipid metabolism, and carbohydrate metabolism, and there was a significant correlation with microbiota. The differentially expressed genes and metabolites at middle and high altitudes were coenriched in asthma, arachidonic acid metabolism, and butanoate and propanoate metabolism. In addition, the serum differential metabolites at 3500 m and 4500 m were mainly enriched in amino acid metabolism, lipid metabolism, and metabolism of xenobiotics by cytochrome P450, and they were also related to microbiota. Further analysis revealed that rumen metabolites accounted for 7.65% of serum metabolites. These common metabolites were mainly enriched in metabolic pathways and were significantly correlated with host genes (p < 0.05). This study found that microbiota, metabolites, and epithelial genes were coenriched in pathways related to lipid metabolism, energy metabolism, and immune metabolism, which may be involved in the regulation of Tibetan sheep adaptation to plateau environmental changes.

Comparative analysis of gut microbiota between common (Macaca fascicularis fascicularis) and Burmese (M. f. aurea) long-tailed macaques in different habitats

The environment has an important effect on the gut microbiota-an essential part of the host's health-and is strongly influenced by the dietary pattern of the host as these together shape the composition and functionality of the gut microbiota in humans and other animals. This study compared the gut microbiota of Macaca fascicularis fascicularis and M. f. aurea in mangrove and island populations using 16S rRNA gene sequencing on a nanopore platform to investigate the effect of the environment and/or diet. The results revealed that the M. f. fascicularis populations that received anthropogenic food exhibited a higher richness and evenness of gut microbiota than the M. f. aurea populations in different habitats. Firmicutes and Bacteroidetes were the two most abundant bacterial phyla in the gut microbiota of both these subspecies; however, the relative abundance of these phyla was significantly higher in M. f. aurea than in M. f. fascicularis. This variation in the gut microbiota between the two subspecies in different habitats mostly resulted from the differences in their diets. Moreover, the specific adaptation of M. f. aurea to different environments with a different food availability had a significant effect on their microbial composition.

Evaluation of Gut Microbiota Stability and Flexibility as a Response to Seasonal Variation in the Wild François' Langurs (Trachypithecus francoisi) in Limestone Forest

The coevolution between gut microbiota and the host markedly influences the digestive strategies of animals to cope with changes in food sources. We have explored the compositional structure and seasonal variation in the gut microbiota of François' langur in a limestone forest in Guangxi, southwest China, using 16S rRNA sequencing. Our results demonstrated that Firmicutes and Bacteroidetes were the dominant phyla in langurs, followed by Oscillospiraceae, Christensenellaceae, and Lachnospiraceae at the family level. The top five dominant phyla did not show significant seasonal variations, and only 21 bacterial taxa differed at the family level, indicating stability in gut the microbiota possibly with respect to foraging for several dominant plants and high-leaf feeding by the langurs. Moreover, rainfall and minimum humidity are important factors affecting the gut microbiota of the langurs, but they explain few changes in bacterial taxa. The activity budget and thyroid hormone levels of the langurs did not differ significantly between seasons, indicating that these langurs did not respond to seasonal changes in food by regulating behavior or reducing metabolism. The present study indicates that the gut microbiota's structure is related to digestion and energy absorption of these langurs, providing new perspectives on their adaptation to limestone forests. IMPORTANCE François' langur is a primate that particularly lives in karst regions. The adaptation of wild animals to karst habitats has been a hot topic in behavioral ecology and conservation biology. In this study, gut microbiota, behavior, and thyroid hormone data were integrated to understand the interaction of the langurs and limestone forests from the physiological response, providing basic data for assessing the adaptation of the langurs to the habitats. The responses of the langurs to environmental changes were explored from the seasonal variations in gut microbiota, which would help to further understand the adaptive strategies of species to environmental changes.

Maternal transfer of resorcinol-bis(diphenyl)-phosphate perturbs gut microbiota development and gut metabolism of offspring in rats

Resorcinol-bis(diphenyl)-phosphate (RDP), an emerging organophosphate flame retardant, is increasingly used as a primary alternative for decabromodiphenyl ether and is frequently detected in global environmental matrices. However, the long-term effects of its exposure to humans remain largely unknown. To investigate its intergenerational transfer capacity and health risks, female Sprague Dawley rats were orally exposed to RDP from the beginning of pregnancy to the end of the lactation period. The RDP content, gut microbiota homeostasis, and metabolic levels were determined. RDP accumulation occurred in the livers of maternal rats and offspring and increased with exposure time. 16S rRNA gene sequencing showed that exposure to RDP during pregnancy and/or lactation significantly disrupted gut microbiota homeostasis, as evidenced by decreased abundance and diversity. In particular, the abundance of Turicibacter, Adlercreutzia, and YRC22 decreased, correlating significantly with glycollipic metabolism. This finding was consistent with the reduced levels of short-chain fatty acids, the crucial gut microbial metabolites. Meanwhile, RDP exposure resulted in changes in gut microbiome-related metabolism. Nine critical overlapping KEGG metabolic pathways were identified, and the levels of related differential metabolites decreased. Our results suggest that the significant adverse impacts of RDP on gut microbiota homeostasis and metabolic function may increase the long-term risks related to inflammation, obesity, and metabolic diseases.

Seasonal dietary shifts alter the gut microbiota of a frugivorous lizard Teratoscincus roborowskii (Squamata, Sphaerodactylidae)

Seasonal dietary shifts in animals are important strategies for ecological adaptation. An increasing number of studies have shown that seasonal dietary shifts can influence or even determine the composition of gut microbiota. The Turpan wonder gecko, Teratoscincus roborowskii, lives in extreme desert environments and has a flexible dietary shift to fruit-eating in warm seasons. However, the effect of such shifts on the gut microbiota is poorly understood. In this study, 16S rRNA sequencing and LC-MS metabolomics were used to examine changes in the gut microbiota composition and metabolic patterns of T. roborowskii. The results demonstrated that the gut microbes of T. roborowskii underwent significant seasonal changes, and the abundance of phylum level in autumn was significantly higher than spring, but meanwhile, the diversity was lower. At the family level, the abundance and diversity of the gut microbiota were both higher in autumn. Firmicutes, Bacteroidetes, and Proteobacteria were the dominant gut microbes of T. roborowskii. Verrucomicrobia and Proteobacteria exhibited dynamic ebb and flow patterns between spring and autumn. Metabolomic profiling also revealed differences mainly related to the formation of secondary bile acids. The pantothenate and CoA biosynthesis, and lysine degradation pathways identified by KEGG enrichment symbolize the exuberant metabolic capacity of T. roborowskii. Furthermore, strong correlations were detected between metabolite types and bacteria, and this correlation may be an important adaptation of T. roborowskii to cope with dietary shifts and improve energy acquisition. Our study provides a theoretical basis for exploring the adaptive evolution of the special frugivorous behavior of T. roborowskii, which is an important progress in the study of gut microbes in desert lizards.

Exploring the elevation dynamics of rumen bacterial communities in Barn feeding cattle from 900 to 3,600 meters by full-length 16S sequencing

The diversity and abundance of rumen microorganisms serve as indicators not only of the host's digestive and metabolic capacity but also of its health status. The complex microbial communities in the rumen are influenced to varying degrees by environmental adaptability. In this study, we collected 24 rumen fluid samples from 24 healthy male cattle in three regions of Yunnan, China. Using 16S rRNA amplicon sequencing data analysis, we examined the variations in rumen microorganisms among cattle fed at altitudes of 900 m, 1800 m, and 3,600 m. Altitude-related environmental factors did not surpass phylogeny as the main driving force behind the convergent evolution of yellow cattle rumen microbiome composition. However, they did have an impact on the alpha diversity of the rumen microbiome and the coevolution of the core microbiome. The change in altitude noticeably influenced the diversity and richness of the rumen microbiota, highlighting the environmental effect of altitude. As altitude increased, there was an observed increase in the abundance of Firmicutes and Bacteroidetes, while the abundance of ruminal Proteobacteria and Kiritimatiellaeota decreased. Importantly, at the genus level, the core genus exhibited distinct dynamic changes as altitude increased. Ruminants exhibit the ability to adapt their gut type in accordance with altitude, thereby optimizing energy utilization, especially in high-altitude settings. These discoveries offer valuable insights into the coevolution of host-microbe interactions during ruminant adaptation to various altitudinal environments.

Gut microbiome signatures of extreme environment adaption in Tibetan pig

Tibetan pigs (TPs) can adapt to the extreme environments in the Tibetan plateau implicated by their self-genome signals, but little is known about roles of the gut microbiota in the host adaption. Here, we reconstructed 8210 metagenome-assembled genomes from TPs (n = 65) living in high-altitude and low-altitude captive pigs (87 from China-CPs and 200 from Europe-EPs) that were clustered into 1050 species-level genome bins (SGBs) at the threshold of 95% average nucleotide identity. 73.47% of SGBs represented new species. The gut microbial community structure analysis based on 1,048 SGBs showed that TPs was significantly different from low-altitude captive pigs. TP-associated SGBs enabled to digest multiple complex polysaccharides, including cellulose, hemicellulose, chitin and pectin. Especially, we found TPs showed the most common enrichment of phyla Fibrobacterota and Elusimicrobia, which were involved in the productions of short- and medium-chain fatty acids (acetic acid, butanoate and propanoate; octanomic, decanoic and dodecanoic acids), as well as in the biosynthesis of lactate, 20 essential amino acids, multiple B vitamins (B1, B2, B3, B5, B7 and B9) and cofactors. Unexpectedly, Fibrobacterota solely showed powerful metabolic capacity, including the synthesis of acetic acid, alanine, histidine, arginine, tryptophan, serine, threonine, valine, B2, B5, B9, heme and tetrahydrofolate. These metabolites might contribute to host adaptation to high-altitude, such as energy harvesting and resistance against hypoxia and ultraviolet radiation. This study provides insights into understanding the role of gut microbiome played in mammalian high-altitude adaptation and discovers some potential microbes as probiotics for improving animal health.

Captivity restructures the gut microbiota of François' langurs (Trachypithecus francoisi)

Gut microbiota is crucial to primate survival. Data on the gut microbiota of captive and wild animals can provide a physiological and ecological basis for the conservation of rare and endangered species. To study the effect of captivity on the gut microbiota, we examine the difference in the gut microbiota composition between captive and wild Francois' langurs (Trachypithecus francoisi), using 16S rRNA sequencing technology. The results showed that the composition of the gut microbiota of captive and wild langurs was characterized by Firmicutes (51.93 ± 10.07% vs. 76.15 ± 8.37%) and Bacteroidetes (32.43 ± 10.00% vs. 4.82 ± 1.41%) at the phylum level and was characterized by Oscillospiraceae (15.80 ± 5.19% vs. 30.21 ± 4.87%) at the family level. The alpha diversity of gut microbiota in captive langurs was higher than those in wild, such as the Shannon index (4.45 ± 0.33 vs. 3.98 ± 0.19, P < 0.001) and invSimpson index (35.11 ± 15.63 vs. 19.02 ± 4.87, P < 0.001). Principal coordinates analysis (PCoA) results showed significant differences in the composition of gut microbiota between captive and wild langurs at both the phylum and family levels (weight UniFrac algorithm, phylum level: R² = 0.748, P = 0.001; family level: R² = 0.685, P = 0.001). The relative abundance of Firmicutes (51.93 ± 10.07%) in captive langurs was lower than that of wild langurs (76.15 ± 8.37%), and the relative abundance of Bacteroidetes (32.43 ± 10.00%) in captive langurs was higher than that of wild (4.82 ± 1.41%). Our study concludes that dietary composition could be a crucial determinant in shaping the gut microbiota of langurs because more fiber-rich foods used by the wild langurs could increase the abundance of Firmicutes, and more simple carbohydrate-rich foods consumed by the captive langurs increase the abundance of Bacteroidetes. We highlight the importance of captivity on the gut microbiota and the need to consider the gut microbiota in animal provision.

Metagenome and metabolome insights into the energy compensation and exogenous toxin degradation of gut microbiota in high-altitude rhesus macaques (Macaca mulatta)

There have been many reports on the genetic mechanism in rhesus macaques (RMs) for environmental adaptation to high altitudes, but the synergistic involvement of gut microbiota in this adaptation remains unclear. Here we performed fecal metagenomic and metabolomic studies on samples from high- and low-altitude populations to assess the synergistic role of gut microbiota in the adaptation of RMs to high-altitude environments. Microbiota taxonomic annotation yielded 7471 microbiota species. There were 37 bacterial species whose abundance was significantly enriched in the high-altitude populations, 16 of which were previously reported to be related to the host's dietary digestion and energy metabolism. Further functional gene enrichment found a stronger potential for gut microbiota to synthesize energy substrate acetyl-CoA using CO₂ and energy substrate pyruvate using oxaloacetate, as well as a stronger potential to transform acetyl-CoA to energy substrate acetate in high-altitude populations. Interestingly, there were no apparent differences between low-altitude and high-altitude populations in terms of genes enriched in the main pathways by which the microbiota consumed the three energy substrates, and none of the three energy substrates were detected in the fecal metabolites. These results strongly suggest that gut microbiota plays an important energy compensatory role that helps RMs to adapt to high-altitude environments. Further functional enrichment after metabolite source analysis indicated the abundance of metabolites related to the degradation of exogenous toxins was also significantly higher in high-altitude populations, which suggested a contributory role of gut microbiota to the degradation of exogenous toxins in wild RMs adapted to high-altitude environments.

Gut microbiota of skywalker hoolock gibbons (Hoolock tianxing) from different habitats and in captivity: Implications for gibbon health

The gut microbiota plays an integral role in the metabolism and immunity of animal hosts, and provides insights into the health and habitat assessment of threatened animals. The skywalker hoolock gibbon (Hoolock tianxing) is a newly described gibbon species, and is considered an endangered species. Here, we used 16S rRNA amplicon sequencing to describe the fecal bacterial community of skywalker hoolock gibbons from different habitats and in captivity. Fecal samples (n = 5) from two captive gibbons were compared with wild populations (N = 6 gibbons, n = 33 samples). At the phylum level, Spirochetes, Proteobacteria, Firmicutes, Bacteroidetes dominated in captive gibbons, while Firmicutes, Bacteroidetes, and Tenericutes dominated in wild gibbons. At the genus level, captive gibbons were dominated by Treponema-2, followed by Succinivibrio and Cerasicoccus, while wild gibbons were dominated by Anaeroplasma, Prevotellaceae UCG-001, and Erysipelotrichaceae UCG-004. Captive rearing was significantly associated with lower taxonomic alpha-diversity, and different relative abundance of some dominant bacteria compared to wild gibbons. Predicted Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that captive gibbons have significantly lower total pathway diversity and higher relative abundance of bacterial functions involved in "drug resistance: antimicrobial" and "carbohydrate metabolism" than wild gibbons. This study reveals the potential influence of captivity and habitat on the gut bacterial community of gibbons and provides a basis for guiding the conservation management of captive populations.

Molecular characteristics and pathogenicity of a Tibet-origin mutant avian leukosis virus subgroup J isolated from Tibetan chickens in China

Tibetan chicken is found in China Tibet (average altitude; ˃4500 m). However, little is known about avian leukosis virus subgroup J (ALV-J) found in Tibetan chickens. ALV-J is a typical alpharetrovirus that causes immunosuppression and myelocytomatosis and thus seriously affects the development of the poultry industry. In this study, Tibet-origin mutant ALV-J was isolated from Tibetan chickens and named RKZ-1-RKZ-5. A Myelocytomatosis outbreak occurred in a commercial Tibetan chicken farm in Shigatse of Rikaze, Tibet, China, in March 2022. About 20% of Tibetan chickens in the farm showed severe immunosuppression, and mortality increased to 5.6%. Histopathological examination showed typical myelocytomas in various tissues. Virus isolation and phylogenetic analysis demonstrated that ALV-J caused the disease. Gene-wide phylogenetic analysis showed the RKZ isolates were the original strains of the previously reported Tibetan isolates (TBC-J4 and TBC-J6) (identity; 94.5% to 94.9%). Furthermore, significant nucleotide mutations and deletions occurred in the hr1 and hr2 hypervariable regions of gp85 gene, 3'UTR, Y Box, and TATA Box of 3'LTR. Pathogenicity experiments demonstrated that the viral load, viremia, and viral shedding level were significantly higher in RKZ-1-infected chickens than in NX0101-infected chickens. Notably, RKZ-1 caused more severe cardiopulmonary damage in SPF chickens. These findings prove the origin of Tibet ALV-J and provide insights into the molecular characteristics and pathogenic ability of ALV-J in the plateau area. Therefore, this study may provide a basis for ALV-J prevention and eradication in Tibet.

Diet and high altitude strongly drive convergent adaptation of gut microbiota in wild macaques, humans, and dogs to high altitude environments

Animal gut microbiota plays an indispensable role in host adaptation to different altitude environments. At present, little is known about the mechanism of animal gut microbiota in host adaptation to high altitude environments. Here, we selected wild macaques, humans, and dogs with different levels of kinship and intimate relationships in high altitude and low altitude environments, and analyzed the response of their gut microbiota to the host diet and altitude environments. Alpha diversity analysis found that at high altitude, the gut microbiota diversity of wild macaques with more complex diet in the wild environments is much higher than that of humans and dogs with simpler diet (p < 0.05), and beta diversity analysis found that the UniFrac distance between humans and dogs was significantly lower than between humans and macaques (p < 0.05), indicating that diet strongly drive the convergence of gut microbiota among species. Meanwhile, alpha diversity analysis found that among three subjects, the gut microbiota diversity of high altitude population is higher than that of low altitude population (ACE index in three species, Shannon index in dog and macaque and Simpson index in dog, p < 0.05), and beta diversity analysis found that the UniFrac distances among the three subjects in the high altitude environments were significantly lower than in the low altitude environments (p < 0.05). Additionally, core shared ASVs analysis found that among three subjects, the number of core microbiota in high altitude environments is higher than in low altitude environments, up to 5.34 times (1,105/207), and the proportion and relative abundance of the core bacteria types in each species were significantly higher in high altitude environments than in low altitude environments (p < 0.05). The results showed that high altitude environments played an important role in driving the convergence of gut microbiota among species. Furthermore, the neutral community model trial found that the gut microbiota of the three subjects was dispersed much more at high altitude than at low altitude, implying that the gut microbiota convergence of animals at high altitudes may be partly due to the microbial transmission between hosts mediated by human activities.

Gut microbiota of white-headed black langurs (Trachypithecus leucocephalus) in responses to habitat fragmentation

The white-headed black langur (Trachypithecus leucocephalus) is exclusively distributed in the karst forests and is critically endangered owing to habitat fragmentation. Gut microbiota can provide physiological data for a comprehensive study of the langur's response to human disturbance in the limestone forest; to date, data on spatial variations in the langurs' gut microbiota are limited. In this study, we examined intersite variations in the gut microbiota of white-headed black langurs in the Guangxi Chongzuo White-headed Langur National Nature Reserve, China. Our results showed that langurs in the Bapen area with a better habitat had higher gut microbiota diversity. In the Bapen group, the Bacteroidetes (13.65% ± 9.73% vs. 4.75% ± 4.70%) and its representative family, Prevotellaceae, were significantly enriched. In the Banli group, higher relative abundance of Firmicutes (86.30% ± 8.60% vs. 78.85% ± 10.35%) than the Bapen group was observed. Oscillospiraceae (16.93% ± 5.39% vs. 16.13% ± 3.16%), Christensenellaceae (15.80% ± 4.59% vs. 11.61% ± 3.60%), and norank_o__Clostridia_UCG-014 (17.43% ± 6.64% vs. 9.78% ± 3.83%) were increased in comparison with the Bapen group. These intersite variations in microbiota diversity and composition could be accounted for by differences in food resources caused by fragmentation. Furthermore, compared with the Banli group, the community assembly of gut microbiota in the Bapen group was influenced by more deterministic factors and had a higher migration rate, but the difference between the two groups was not significant. This might be attributed to the serious fragmentation of the habitats for both groups. Our findings highlight the importance of gut microbiota response for the integrity of wildlife habitats and the need in using physiological indicators to study the mechanisms by which wildlife responds to human disturbances or ecological variations.

Assembly of novel microbial genomes from gut metagenomes of rhesus macaque (Macaca mulatta)

Rhesus macaque (RM, Macaca mulatta), as an important model animal, commonly suffers from chronic diarrheal disease, challenging the breeding of RMs. Gut microbiomes play key roles in maintaining intestinal health of RMs. However, it is still unclear about more features of gut microbiome as responsible for intestinal health of RMs. In this study, we performed de novo assembly of metagenome-assembled genomes (MAGs) based on fecal metagenomes from chronic diarrheal RMs and asymptomatic individuals. In total of 731 non-redundant MAGs with at least 80% completeness were reconstructed in this study. More than 97% MAGs were novel genomes compared with more than 250,000 reference genomes. MAGs of Campylobacter and Helicobacteraceae from RM guts mainly carried flagella-associated virulence genes and chemotaxis-associated virulence genes, which might mediate motility and adhesion of bacteria. Comparing to MAGs of Campylobacter from humans, distributions and functions of these MAGs of Campylobacter from RMs exhibited significant differences. Most members of Bacteroidota, Spirochaetota, Helicobacteraceae, Lactobacillaceae and Anaerovibrio significantly decreased in guts of chronic diarrhea RMs. More than 92% MAGs in this study were not contained in 2,985 MAGs previously reported from other 22 non-human primates (NHPs), expanding the microbial diversity in guts of NHPs. The distributions and functions of gut microbiome were prominently influenced by host phylogeny of NHPs. Our results could help to more clearly understand about the diversity and function of RMs gut microbiome.

Distribution of bacteria in different regions of the small intestine with Zanthoxylum bungeanum essential oil supplement in small-tailed Han sheep

Zanthoxylum bungeanum essential oil (EOZB) as an extract of Zanthoxylum bungeanum has a range of pharmacological effects such as antibacterial, anti-inflammatory, and antioxidant. However, there were no relevant studies on the regulation of gut microbes by EOZB in ruminants. In this study, the effects of different doses of EOZB on the structure and distribution of microorganisms in the small intestine of small-tailed Han sheep (STH) were investigated by 16s rRNA gene sequencing technique. We found that with the intervention of EOZB. The differential bacteria of duodenal at the phylum level were Firmicutes, Bacteroidetes, Tenericutes and Proteobacteria, and genus level differential bacteria were Prevotella 1, Ruminococcus 2 and Eubacterium coprostanoligenes group. The differential bacteria of jejunal at the phylum level were Firmicutes, Bacteroidetes, Tenericutes and Proteobacteria, and genus level differential bacteria were Prevotella 1, Rikenellaceae RC9 gut group, Christensenellaceae R-7 group, Ruminococcaceae UCG-014, Saccharofermentans, Ruminococcaceae NK4A214 group and Prevotellaceae UCG-001. The differential bacteria of ileal at the phylum level were Firmicutes, Bacteroidetes and Tenericutes, and genus level differential bacteria were Prevotella 1, Christensenellaceae R-7 group, Romboutsia and Ruminococcaceae UCG-014. In addition, at the same dose of EOZB, the five most abundant genera of bacteria varied in different regions of the small intestine. Among them, the abundance of Prevotella 1, Christensenellacea R-7 group and Ruminococcus 2 in ALW group was the highest in jejunum, duodenum and ileum, respectively. The abundance of Prevotella 1, Christensenellacea R-7 group and Rikenellacea RC9 gut group in BLW group was the highest in duodenum, jejunum and ileum, respectively. The abundance of Prevotella 1, Christensenellacea R-7 group and Ruminococcaeae NK4A214 group in CLW group was the highest in jejunum, duodenum and ileum, respectively. The abundance of Prevotella 1, Ruminococcus 2 and Ruminococcus NK4A214 groups in DLW group was the highest in jejunum, duodenum and ileum, respectively. Differential bacteria formed under the regulation of EOZB are associated with the digestion and absorption of nutrients and the state of intestinal health in the host. This study is the first to investigate the effect of EOZB on the distribution and structure of bacteria in the small intestine of STH. The results of the study enriched the structure and distribution of bacteria in the small intestine of ruminants and provided new insights into the future application of herbal medicine in ruminant production. Additionally, it provides a theoretical basis for the selection of probiotic bacteria for ruminants and the development and application of microecological preparations.

A Catalog of over 5,000 Metagenome-Assembled Microbial Genomes from the Caprinae Gut Microbiota

Most microbiome studies regarding the ruminant digestive tract have focused on the rumen microbiota, whereas only a few studies were performed on investigating the gut microbiota of ruminants, which limits our understanding of this important component. Herein, the gut microbiota of 30 Caprinae animals (sheep and goats) from six provinces in China was characterized using ultradeep (>100 Gbp per sample) metagenome shotgun sequencing. An inventory of Caprinae gut microbial species containing 5,046 metagenomic assembly genomes (MAGs) was constructed. Particularly, 2,530 of the genomes belonged to uncultured candidate species. These genomes largely expanded the genomic repository of the current microbes in the Caprinae gut. Several enzymes and biosynthetic gene clusters encoded by these Caprinae gut species were identified. In summary, our study extends the gut microbiota characteristics of Caprinae and provides a basis for future studies on animal production and animal health. IMPORTANCE We constructed a microbiota catalog containing 5,046 MAGs from Caprinae gut from six regions of China. Most of the MAGs do not overlap known databases and appear to be potentially new species. We also characterized the functional spectrum of these MAGs and analyzed the differences between different regions. Our study enriches the understanding of taxonomic, functional, and metabolic diversity of Caprinae gut microbiota. We are confident that the manuscript will be of utmost interest to a wide range of readers and be widely applied in future research.

Analysis of the gut microbiome in obese native Tibetan children living at different altitudes: A case-control study

Objective

To explore the relationship between intestinal flora and obesity in Tibetan children at different altitudes.

Methods

Using16S rRNA gene sequencing results and blood lipid metabolism indexes to study the characteristics of the intestinal flora present in faeces and changes in blood lipid metabolism in obese children in Tibet who reside at different altitudes and to study correlations between blood lipid metabolism indicators and the intestinal flora composition.

Results

The results showed the following. (a) The triglyceride (TG) and low-density lipoprotein cholesterol (LDL-C) levels in the obesity groups were higher than those in the normal-weight groups, and those in the high-altitude obesity groups were lower than those in the low-altitude obesity groups. (b) The 16S rRNA gene sequencing results showed that altitude affected the composition and relative abundance of the gut microbiota. These parameters were basically the same among the low-altitude groups, while they were significantly lower in the high-altitude groups than in the low-altitude groups. (c) Groups that lived at different altitudes and had different body weights had different dominant bacterial genera. Megamonas was closely related to obesity, and its relative abundance in the low-altitude groups was higher than that in the high-altitude groups. Prevotella was associated with altitude, and its relative abundance in the high-altitude groups was higher than that in the low-altitude groups. In addition, Prevotella elicited changes in the abundance of Escherichia-Shigella. The lower prevalence of obesity and incidence of intestinal inflammation in those living at high altitudes were related to the abundance of Prevotella. (d) There were correlations between the gut microbiota composition and lipid metabolism indicators. The abundance of Romboutsia was positively correlated with TG and LDL-C levels but negatively correlated with high-density lipoprotein cholesterol (HDL-C) levels. The abundance of Akkermansia was negatively correlated with LDL-C levels, and the abundance of Blautia was negatively correlated with body mass index (BMI) and LDL-C levels.

Conclusions

The intestinal flora diversity varied by body weight and altitude, with lower diversity in those at higher altitudes and with lower body weights. Prevotella likely plays a role in suppressing obesity at high altitudes.

Effect of Homo-Fermentative Lactic Acid Bacteria Inoculants on Fermentation Characteristics and Bacterial and Fungal Communities in Alfalfa Silage

We evaluated the effects of a homo-fermentative lactic acid bacteria (homo-LAB) inoculant on the fermentation and microbial communities of alfalfa ensiled at two dry matter (DM) contents of 38 and 46% DM. At both DMs, alfalfa was treated or not with an inoculant containing Pediococcus acidilactici, Enterococcus faecium and Lactobacillus plantarum at a targeted application rate of 165,000 cfu/g of fresh weight and stored for 3, 30 and 60 days. Treatment with the inoculant resulted in a lower drop in pH and, in general, higher lactic acid and lower acetic acid when applied to medium DM silage. For the four most abundant microbial genera, increased abundances of Bacteroides and Lactobacillus (p < 0.05), as well as decreased abundances of Muribaculaceae were observed in high DM and inoculated silages. The abundance of Prevotellaceae-UCG-001 was lower in medium DM control silages than in high DM control silages. Inoculation and DM affected abundances of Vishniacozyma (p < 0.05). Increased abundances of Vishniacozyma, as well as decreased abundances of Leucosporidium were observed in medium DM-inoculated silages. Changes in the relative abundance (RA) of the main populations of bacteria and yeasts did explain the fermentation and nutrition differences among treatments.

Diet-induced microbial adaptation process of red deer (Cervus elaphus) under different introduced periods

Insufficient prey density is a major factor hindering the recovery of the Amur tiger (Panthera tigris altaica), and to effectively restore the Amur tiger, red deer (Cervus elaphus) was released into the Huangnihe National Nature Reserve of Northeast China as the main reinforcement. Differences in feeding and synergistic changes caused by the intestinal microbial communities could impact the adaptation of wildlife following reintroductions into field environments. We analyzed the foraging changes in shaping the intestinal microbial community of the red deer after being released to the Huangnihe National Nature Reserve and screened the key microbial flora of the red deer when processing complex food resources. The feeding and intestinal microbial communities of the red deer were analyzed by plant Deoxyribonucleic acid (DNA) barcoding sequencing and 16S rRNA high-throughput sequencing, respectively. The results showed that there were significant differences in food composition between wild and released groups [released in 2019 (R2): n = 5; released in 2021 (R0): n = 6]; the wild group fed mainly on Acer (31.8%) and Abies (25.6%), R2 fed mainly on Betula (44.6%), R0 had not formed a clear preferred feeding pattern but had certain abilities to process and adapt to natural foods. Firmicutes (77.47%) and Bacteroides (14.16%) constituted the main bacterial phylum of red deer, of which, the phylum Firmicutes was the key species of the introduced red deer for processing complex food resources (p < 0.05). The wild release process significantly changed the intestinal microbial structure of the red deer, making it integrate into the wild red deer. The period since release into the wild may be a key factor in reshaping the structure of the microbial community. This study suggested that the intestinal microbial structure of red deer was significantly different depending on how long since captive deer has been translocated. Individuals that have lived in similar environments for a long time will have similar gut microbes. This is the adaption process of the wildlife to natural environment after wild release, taking into account the gut microbes, and the feeding changes in shaping microbial communities can help introduced red deer match complex food resources and novel field environments.

Alterations in gut microbiota and metabolites associated with altitude-induced cardiac hypertrophy in rats during hypobaric hypoxia challenge

The gut microbiota is involved in host responses to high altitude. However, the dynamics of intestinal microecology and their association with altitude-related illness are poorly understood. Here, we used a rat model of hypobaric hypoxia challenge to mimic plateau exposure and monitored the gut microbiome, short-chain fatty acids (SCFAs), and bile acids (BAs) over 28 d. We identified weight loss, polycythemia, and pathological cardiac hypertrophy in hypoxic rats, accompanied by a large compositional shift in the gut microbiota, which is mainly driven by the bacterial families of Prevotellaceae, Porphyromonadaceae, and Streptococcaceae. The aberrant gut microbiota was characterized by increased abundance of the Parabacteroides, Alistipes, and Lactococcus genera and a larger Bacteroides to Prevotella ratio. Trans-omics analyses showed that the gut microbiome was significantly correlated with the metabolic abnormalities of SCFAs and BAs in feces, suggesting an interaction network remodeling of the microbiome-metabolome after the hypobaric hypoxia challenge. Interestingly, the transplantation of fecal microbiota significantly increased the diversity of the gut microbiota, partially inhibited the increased abundance of the Bacteroides and Alistipes genera, restored the decrease of plasma propionate, and moderately ameliorated cardiac hypertrophy in hypoxic rats. Our results provide an insight into the longitudinal changes in intestinal microecology during the hypobaric hypoxia challenge. Abnormalities in the gut microbiota and microbial metabolites contribute to the development of high-altitude heart disease in rats.

Pesticide thiram exposure alters the gut microbial diversity of chickens

Thiram is a major dithiocarbamate pesticide commonly found in polluted field crops, feed, and rivers. Environmental thiram exposure has been demonstrated to cause angiogenesis and osteogenesis disorders in chickens, but information regarding thiram influences on gut microbiota, apoptosis, and autophagy in chickens has been insufficient. Here, we explored the effect of thiram exposure on gut microbiota, apoptosis, and autophagy of chickens. Results demonstrated that thiram exposure impaired the morphology and structure of intestinal and liver tissues. Moreover, thiram exposure also triggered liver apoptosis and autophagy. The gut microbiota in chickens exposed to thiram exhibited a significant decline in alpha diversity, accompanied by significant shifts in taxonomic compositions. Bacterial taxonomic analysis indicated that thiram exposure causes a significant reduction in the levels of eight genera, as well as a significant increase in the levels of two phyla and 10 genera. Among decreased bacterial genera, seven genera even cannot be observed in the thiram-induced chickens. In summary, this study demonstrated that thiram exposure not only dramatically altered the gut microbial diversity and composition but also induced liver apoptosis and autophagy in chickens. Importantly, this study also conveyed a key message that the dysbiosis of gut microbiota may be one of the major pathways for thiram to exert its toxic effects.

The Association between Gut Microbiome Diversity and Composition and Heat Tolerance in Cattle

Cattle are raised around the world and are frequently exposed to heat stress, whether in tropical countries or in regions with temperate climates. It is universally acknowledged that compared to those in temperate areas, the cattle breeds developed in tropical and subtropical areas have better heat tolerance. However, the underlying mechanism of heat tolerance has not been fully studied, especially from the perspective of intestinal microbiomics. The present study collected fecal samples of cattle from four representative climatic regions of China, namely, the mesotemperate (HLJ), warm temperate (SD), subtropical (HK), and tropical (SS) regions. Then, the feces were analyzed using high-throughput 16S rRNA sequencing. The results showed that with increasing climatic temperature from HLJ to SS, the abundance of Firmicutes increased, accompanied by an increasing Firmicutes to Bacteroidota ratio. Proteobacteria showed a trend of reduction from HLJ to SS. Patescibacteria, Chloroflexi, and Actinobacteriota were particularly highest in SS for adapting to the tropical environment. The microbial phenotype in the tropics was characterized by an increase in Gram-positive bacteria and a decrease in Gram-negative bacteria, aerobic bacteria, and the forming of_biofilms. Consistently, the functional abundances of organismal systems and metabolism were decreased to reduce the material and energy demands in a hot environment. Genetic information processing and information storage and processing may be how gut flora deals with hot conditions. The present study revealed the differences in the structure and function of gut microbes of cattle from mesotemperate to tropical climates and provided an important reference for future research on the mechanism of heat tolerance regulated by the gut microbiota and a potential microbiota-based target to alleviate heat stress.

Main Factors Influencing the Gut Microbiota of Datong Yaks in Mixed Group

Simple Summary

This study examined the differences and similarities in gut microbial diversity and ecological assembly processes of Datong yaks, including domestic males and females and wild males, which were fed together on the Qinghai-Tibet Plateau in a mixed group. The results revealed that mixed grouping could influence the gut microbiota of these three groups of yaks and improve the gut microbial diversity of domestic females. The findings of this study can help to understand the effects of mixed grouping on the gut microbiota of livestock on the Qinghai-Tibet Plateau and improve the production of Datong yaks.

Abstract

The Datong yak (Bos grunniens) is the first artificial breed of yaks in the world and has played an important role in the improvement of domestic yak quality on the Qinghai-Tibet Plateau. The Datong yak breeding farm in the Qinghai province of China is the main place for the breeding and feeding of Datong yaks. It hosts domestic Datong yaks and wild male yaks, mainly in mixed groups. Different managements have different effects on livestock. The gut microbiota is closely related to the health and immunity of Datong yaks, and mixed grouping can affect the composition and diversity of the gut microbiota of Datong yaks. To reveal the effects of mixed grouping on the gut microbiota of Datong yaks and wild yaks and identify the main dominant factors, we compared the gut microbial diversities of domestic males and females and wild males based on 16S rRNA V3–V4 regions using fresh fecal samples. The data showed significant differences in the gut microbial diversity of these three groups, and the α-diversity was the highest in wild males. Different factors influence the gut microbiota, and the main influencing factors were different in different groups, including sex differences, host genetics, and physical interactions. We also compared ecological assembly processes in the three groups. The results showed that mixed grouping contributed to the improvement of gut microbial diversity in domestic females. Our study provides effective and feasible suggestions for the feeding and management of the Datong yaks.

Seasonal and Soil Microbiota Effects on the Adaptive Strategies of Wild Goitered Gazelles Based on the Gut Microbiota

Seasonal variation in extreme environments is a threat to endangered species. The gut microbiota is important in the adaptive strategies of wild herbivores, and herbivores will contact the soil microbiota when they are feeding. However, there are no studies about the effects of soil microbiota on the gut microbiota of wild herbivores. Understanding the seasonal adaptive strategies of wild herbivores based on their gut microbiota and the effects of soil microbiota on the herbivorous gut microbiota is indispensable for making optimal conservation recommendations. To address those issues, we compared the diversity and functions of gut microbiota in goitered gazelles between winter and summer with a non-invasive fecal sampling method from the Qaidam Basin based on 16S rRNA V3–V4 regions. The data showed that seasonal variations caused the significant changes in gut microbiota at α-and β-diversity levels. The main gut microbial function was “Metabolism.” It showed significant seasonal changes. The goitered gazelles adapted to the seasonal changes by increasing the relative abundance of Firmicutes, Christensenellaceae, Bacteroides and the function about “Metabolism” in the winter to improve the adaptability. We also compared the effects of soil microbiota on the gut microbiota between winter and summer, covering source tracking analysis and the seasonal differences in ecological assembly processes. The contribution of soil microbiota on the gut microbiota of goitered gazelles was 5.3095% and 15.6347% in winter and summer, respectively, which was greater than on species of animals living underground. Seasonal variation also influenced the ecological processes of microbiota both in the gut and soil. Due to the differences in environments, the ecological processes between fecal microbiota and soil microbiota showed significant differences, and they were dominated by stochastic processes and deterministic processes, respectively. The soil microbiota has contributed to the gut microbiota, but not a decisive factor. Our research laid the foundation on the seasonal and soil microbiota effects on the adaptive strategies of goitered gazelles, and is the first study to explain the soil microbiota influence on the gut microbiota of wild herbivores.

Comparative Analysis of Gut Microbial Composition and Functions in Przewalski's Gazelle (Procapra przewalskii) From Various Habitats

Gut microbiota of mammals participates in host nutrient metabolism and plays an important role in host adaptation to the environment. Herein, to understand the relationship between environment differences and the composition and abundance of the gut microbiota of Przewalski's gazelle (Procapra przewalskii) in almost all its habitats, high throughput sequencing of the 16S rRNA gene was used to compared the characteristics of the gut microbiota based on total 120 fecal samples. The results showed that Przewalski's gazelle exhibited different characteristics of microbiota diversity in different habitats. The Jiangxigou Rescue Station (JX), Nongchang (NC), and Ganzihe and Haergai townships (GH) groups had a relatively high microbiota diversity, while the Niaodao scenic area (ND) group had the lowest diversity. This finding seemed to follow a similar pattern of change in the population of Przewalski's gazelle. Bacteroidetes and Actinobacteria were the phyla with significant differences, especially between the Wayu township (WY) and the other groups. The difference in the microbiota mainly included the Ruminococcaceae UCG-005, Christensenellaceae R-7 group, and Bacteroidaceae and was enriched in the ND, WY, and other regions. We speculated that the difference in the gut microbiota was due to a difference in environmental characteristics, particularly the food resources that the host can obtain. We speculated that a similar microbiome has important functions for species survival and represents the evolutionary commonality of Przewalski's gazelle, while a different microbiome plays an important role in the adaptation of Przewalski's gazelle to a different environment. The results of this study illustrate how the same species adapts to different environments from the perspective of gut microbiota plasticity and therefore are of great significance for the protection and restoration of the population of this species.

Acute exposure to simulated high-altitude hypoxia alters gut microbiota in mice

Gut microbiota bears adaptive potential to different environments, but little is known regarding its responses to acute high-altitude exposure. This study aimed to evaluate the microbial changes after acute exposure to simulated high-altitude hypoxia. C57BL/6 J mice were divided into hypoxia and normoxia groups. The hypoxia group was exposed to a simulated altitude of 5500 m for 24 h above sea level. The normoxia group was maintained in low altitude of 10 m above sea level. Colonic microbiota was analyzed using 16S rRNA V4 gene sequencing. Compared with the normoxia group, Shannon, Simpson and Akkermansia were significantly increased, while Firmicutes-to-Bacteroidetes ratio and Bifidobacterium were significantly decreased in the hypoxia group. The hypoxia group exhibited lower mobile element containing and higher potentially pathogenic and stress-tolerant phenotypes than those in the normoxia group. Functional analysis indicated that environmental information processing was significantly lower, metabolism, cellular processes and organismal systems were significantly higher in the hypoxia group than those in the normoxia group. In conclusion, acute exposure to simulated high-altitude hypoxia alters gut microbiota diversity and composition, which may provide a potential target to alleviate acute high-altitude diseases.

Diet and feeding behavior of a group of high-altitude rhesus macaques: high adaptation to food shortages and seasonal fluctuations

Diet and feeding behavior data are crucial to a deep understanding of the behavioral response and adaptation of primates to a high-altitude environment. From August 2019 to June 2021, we collected data on the feeding behavior of a high-altitude rhesus macaque Macaca mulatta group from Yajiang County, Western Sichuan Plateau, which has an altitude of over 3,500 m. The results showed that feeding (33.0 ± 1.8%) and moving (28.3 ± 2.6%) were the dominant behavior of rhesus macaques. Macaques ate 193 food items, comprising 11 food categories from 90 species. Our study found that plant roots (30.9±30.1%) and young leaves (28.0±33.1%) were the main foods eaten by macaques. The preferred foods of rhesus macaques were young leaves, fruits and seeds, and the consumption of these items was positively correlated with its food availability. When the availability of preferred foods was low, macaques took plant roots, barks and fallen leaves as fallback foods. In particular, roots were a dominant food item in winter, and this way of feeding became a key survival strategy. Our results suggest that, facing the relative scarcity and strong seasonal fluctuations of food resources in high-altitude habitat, macaques adopt active foraging strategies, relying on a variety of food species and adjusting flexibly their food choices based on food availability, which may help to maximize the energy efficiency of high-altitude macaques.

Altitude-adaption of gut microbiota in Tibetan chicken

Low oxygen levels and extremely cold weather in high-altitude environments requires more energy intake to maintain body temperature in animals. However, little is known about the characteristics of cecal and ileac microbiota in Tibetan chicken and how the high and low altitude environments affect the gut microbiota communities in Tibetan chicken. In the present study, In the present study, Tibetan chickens (Group HA, 3572 m, 578.5 Pa) and their introduced flatland counterparts (Group LA, 580 m, 894.6 Pa) in the cecum and ileum to identify the possible bacterial species that are helpful for their host in environmental adaption. High-throughput sequencing was used to sequence the V3 to V4 hypervariable regions of the bacterial 16S rRNA gene. By comparing the gut microbial diversity of HA chicken with that of LA, the results indicated that the microbial diversity of the cecum and ileum in group HA was significantly lower (P < 0.05) than those in group LA. The cecum microbiome maintained higher population diversity and richness than the ileum (P < 0.05). Four phyla Firmicutes, Bacterioidetes, Actinobacteria, and Proteobacteria were dominant in two groups. Interestingly, there were significant differences in abundance ratio among the four groups (P < 0.05). The predominant bacteria in HA and LA ileum belong to Proteobacteria and Firmicutes, whereas in cecum, Bacterioidetes and Actinobacteria were predominant in both groups (P < 0.05). Correlation analysis showed that Sporosarcina, Enterococcus, and Lactococcus were strongly related to air pressure, and Peptoclostridium and Ruminococcaceae_UCG-014 are related to altitude and gut microbiota of LA group was influenced by altitude, while HA group affected by air pressure. Meanwhile, the Ruminococcus-torques-group was negatively correlated with the relative abundance of Paenibacillus, and positive correlated with those of other microorganisms. Furthermore, HA has higher abundance of microbiota involved in energy and glycan biosynthesis metabolism pathway, while LA has higher abundance of microbiota involved in membrane transport, signal transduction, and xenobiotics biodegradation and metabolism. Generally, our results suggested that the composition and diversity of gut microbes changed after Tibetan chickens were introduced to the plain. Tibetan chicken may adapt to new environment via reshaping the gut microbiota. Gut microbes may contribute to the host adaption to high altitude environments by increasing host energy and glycan biosynthesis.

Comparative Analysis of Gut Microbiota Between Healthy and Diarrheic Horses

Increasing evidence reveals the importance of gut microbiota in animals for regulating intestinal homeostasis, metabolism, and host health. The gut microbial community has been reported to be closely related to many diseases, but information regarding diarrheic influence on gut microbiota in horses remains scarce. This study investigated and compared gut microbial changes in horses during diarrhea. The results showed that the alpha diversity of gut microbiota in diarrheic horses decreased observably, accompanied by obvious shifts in taxonomic compositions. The dominant bacterial phyla (Firmicutes, Bacteroidetes, Spirochaetes, and Kiritimatiellaeota) and genera (uncultured_bacterium_f_Lachnospiraceae, uncultured_bacterium_f_p-251-o5, Lachnospiraceae_AC2044_group, and Treponema_2) in the healthy and diarrheic horses were same regardless of health status but different in abundances. Compared with the healthy horses, the relative abundances of Planctomycetes, Tenericutes, Firmicutes, Patescibacteria, and Proteobacteria in the diarrheic horses were observably decreased, whereas Bacteroidetes, Verrucomicrobia, and Fibrobacteres were dramatically increased. Moreover, diarrhea also resulted in a significant reduction in the proportions of 31 genera and a significant increase in the proportions of 14 genera. Taken together, this study demonstrated that the gut bacterial diversity and abundance of horses changed significantly during diarrhea. Additionally, these findings also demonstrated that the dysbiosis of gut microbiota may be an important driving factor of diarrhea in horses.

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.

The gut bacterial microbiome of Nile tilapia (Oreochromis niloticus) from lakes across an altitudinal gradient

Background

Microorganisms inhabiting the gut play a significant role in supporting fundamental physiological processes of the host, which contributes to their survival in varied environments. Several studies have shown that altitude affects the composition and diversity of intestinal microbial communities in terrestrial animals. However, little is known about the impact of altitude on the gut microbiota of aquatic animals. The current study examined the variations in the gut microbiota of Nile tilapia (Oreochromis niloticus) from four lakes along an altitudinal gradient in Ethiopia by using 16S rDNA Illumina MiSeq high-throughput sequencing.

Results

The results indicated that low-altitude samples typically displayed greater alpha diversity. The results of principal coordinate analysis (PCoA) showed significant differences across samples from different lakes. Firmicutes was the most abundant phylum in the Lake Awassa and Lake Chamo samples whereas Fusobacteriota was the dominant phylum in samples from Lake Hashengie and Lake Tana. The ratio of Firmicutes to Bacteroidota in the high-altitude sample (Lake Hashengie, altitude 2440 m) was much higher than the ratio of Firmicutes to Bacteroidota in the low altitude population (Lake Chamo, altitude 1235 m). We found that the relative abundances of Actinobacteriota, Chloroflexi, Cyanobacteria, and Firmicutes were negatively correlated with altitude, while Fusobacteriota showed a positive association with altitude. Despite variability in the abundance of the gut microbiota across the lakes, some shared bacterial communities were detected.

Conclusions

In summary, this study showed the indirect influence of altitude on gut microbiota. Altitude has the potential to modulate the gut microbiota composition and diversity of Nile tilapia. Future work will be needed to elucidate the functional significance of gut microbiota variations based on the geographical environment.

Significance and impact of the study

Our study determined the composition and diversity of the gut microbiota in Nile tilapia collected from lakes across an altitude gradient. Our findings greatly extend the baseline knowledge of fish gut microbiota in Ethiopian lakes that plays an important role in this species sustainable aquaculture activities and conservation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02496-z.

Metabolic Alternations During Gestation in Dezhou Donkeys and the Link to the Gut Microbiota

The maternal intestinal microbial community changes dramatically during pregnancy and plays an important role in animal growth, metabolism, immunity and reproduction. However, our understanding of microbiota compositional dynamics during the whole pregnancy period in donkey is incomplete. This study was carried out to evaluate gut microbiota alterations as well as the correlation with serum biochemical indices, comparing pregnant donkeys to non-pregnant donkeys. A total of 18 pregnant (including EP, early-stage pregnancy; MP, middle-stage pregnancy and LP, late-stage pregnancy) and six non-pregnant (C as a control) donkey blood samples and rectum contents were collected. The results showed that pregnant donkeys had higher microbial richness than non-pregnant donkeys and that the lowest microbial diversity occurred at the EP period. Moreover, the relative abundances of the families Clostridiaceae and Streptococcaceae were significantly higher in the EP group (p < 0.05) than that in the C and MP groups, while the relative abundances of the families Lachnospiraceae and Rikenellaceae were significantly lower in the EP group (p < 0.05) than that in the C group. The predicted microbial gene functions related to the inflammatory response and apoptosis, such as Staphylococcus aureus infection, the RIG-1-like receptor signaling pathway and apoptosis, were mainly enriched in EP. Furthermore, pregnant donkeys had higher glucose levels than non-pregnant donkeys, especially at EP period. EP donkeys had lower triglyceride, total protein and albumin levels but higher malondialdehyde, interleukin 1β, interleukin 6 and tumor necrosis factor-α levels than those in the C and MP groups. Additionally, there were strong correlations between inflammatory cytokine levels and the relative abundances of genera belonging to the Clostridiaceae and Streptococcaceae families. This is the first comparative study performed in donkeys that indicates that pregnancy status (especially in the early pregnancy period) alters the gut microbiota composition, which was correlated with serum biochemical parameters. These results could provide useful information for improving the reproductive management in Dezhou donkeys.

Integration of intestinal microbiota and metabonomics to elucidate different alleviation impacts of non-saponification and saponification astaxanthin pre-treatment on paracetamol-induced oxidative stress in rats

Intestinal microbiota and metabonomics were integrated to investigate the efficiency of non-saponification or saponification astaxanthin (N-Asta or S-Asta) derived from Penaeus sinensis by-products on alleviating paracetamol (PCM)-induced oxidative stress. Pre-treatment with N-Asta or S-Asta for 14 days restored the cellular morphology of the intestine and increased glutathione (GSH) levels under PCM overdose in rats. However, S-Asta displayed higher adsorption than that of N-Asta. PCM overdose reduced the richness and diversity of intestinal microbiota in the model group. Comparably, N-Asta or S-Asta pre-treatment increased the Actinobacteria abundance. Increased phyla Bacteroidetes and Verrucomicrobia were only found in the S-Asta-pre-treated group. At the genus level, N-Asta pre-treatment increased Lactobacillus and Parasutterella abundance, whereas S-Asta pre-treatment elevated Bacteroidales_S24-7_group_norank and Ruminococcaceae_uncultured. Compared to the control and model groups, remarkable increases of fecal short-chain fatty acids were detected in both N-Asta and S-Asta pre-treatment groups, suggesting the contribution of N-Asta and S-Asta adsorption to SCFA-producing bacteria enrichment. Furthermore, the genera of Ruminococcaceae_uncultured, Ruminiclostridium_9, Ruminococcaceae_unclassified and Ruminococcus_1 showed high correlations with propionic acid, isobutyric acid, butyric acid, isovaleric acid and valeric acid increases in the S-Asta pre-treated group. Seventeen plasma biomarker metabolites in more than 10 metabolic pathways were responsible for the difference between the N-Asta and S-Asta pre-treated groups. Metabolites GSH, retinol, all-trans-Retinoic acid and taurine related to antioxidant activities were significantly accumulated in the S-Asta pre-treated group, while increasing taurocholic acid levels associated with the anti-inflammatory activity was found in the N-Asta-pre-treated group. Therefore, N-Asta and S-Asta could have potential applications in counterbalancing intestinal flora and metabolite disturbances by overdose chemical induction.

Environmental hexavalent chromium exposure induces gut microbial dysbiosis in chickens

Hexavalent chromium [Cr (VI)] is a hazardous heavy metal that pollutes soil, water and crops. Moreover, its prolonged exposure can harm the gastrointestinal system, liver and respiratory tract in different species, but knowledge regarding Cr (VI) influence on gut microbiota in chickens remains scarce. Therefore, this study was performed to investigate the impact of Cr (VI) on gut microbiota in chickens. Results revealed that the gut microbiota in Cr (VI)-induced chickens exhibited a distinct reduction in alpha diversity, accompanied by significant shifts in microbial composition. Specifically, Firmicutes and Bacteroidetes were the most dominant phyla in the control chickens, whereas Firmicutes and Actinobacteria were observed to be predominant in the Cr (VI)-induced populations. Moreover, the types and relative abundances of predominant bacterial genus in control and Cr (VI)-induced chickens were also different. Bacterial taxonomic analysis revealed that the relative abundances of 3 phyla and 7 genera obviously increased, whereas 8 phyla and 30 genera dramatically decreased during Cr (VI) induction. Among them, 1 phylum (Deferribacteres) and 5 genera (Butyricicoccus, Butyricimonas, Intestinimonas, Lachnospiraceae_FCS020_group and Ruminococcaceae_V9D2013_group) even could not be found in the gut microbial community of Cr (VI)-induced chickens. Taken together, our study indicated that the long-term exposure to Cr (VI) dramatically alter the gut microbial diversity and composition in chickens. Notably, it represents a breakthrough in understanding the impact of Cr (VI) on the intestinal microbiota of chickens.

Seasonal diets supersede host species in shaping the distal gut microbiota of Yaks and Tibetan sheep

Yaks and Tibetan sheep are important and renowned livestock of the Qinghai-Tibetan Plateau (QTP). Both host genetics and environmental factors can shape the composition of gut microbiota, however, there is still no consensus on which is the more dominant factor. To investigate the influence of hosts and seasons on the gut microbiome diversity component, we collected fecal samples from yaks and Tibetan sheep across different seasons (summer and winter), during which they consumed different diets. Using 16S rRNA sequencing, principal component analysis (PCoA) data showed that PCo1 explained 57.4% of the observed variance (P = 0.001) and clearly divided winter samples from summer ones, while PCo2 explained 7.1% of observed variance (P = 0.001) and mainly highlighted differences in host species. Cluster analysis data revealed that the gut microbiota composition displayed a convergence caused by season and not by genetics. Further, we profiled the gut microbial community and found that the more dominant genera in yak and Tibetan sheep microbiota were influenced by seasonal diets factors rather than genetics. This study therefore indicated that seasonal diet can trump host genetics even at higher taxonomic levels, thus providing a cautionary note for the breeding and management of these two species.