Seasonal dynamics of diet-gut microbiota interaction in adaptation of yaks to life at high altitude

Alterations in the diversity and composition of the fecal microbiota of domestic yaks (Bos grunniens) with pasture alteration-induced diarrhea

Diarrhea is a common issue in domestic yaks (Bos grunniens) that can occur with pasture alterations and significantly impacts growth performance. Previous research has examined the microbiota of diarrhetic yaks; however, the structural changes in gut bacterial community and microbial interactions in yaks with grassland alteration-induced diarrhea remain poorly understood. To explore variations in gut microbiota homeostasis among yaks suffering from diarrhea, fecal microbiota diversity and composition were analyzed using 16 S rRNA amplicon sequencing. Gut fecal microbiota diversity was lower in diarrhetic yaks than in non-diarrhetic yaks. Furthermore, the bacterial community composition (including that of Proteobacteria and Actinobacteria) in the feces of diarrhetic yaks displayed significant alterations. Co-occurrence network analysis further underscored the compromised intestinal flora stability in yaks with diarrhea relative to that in non-diarrhetic yaks. Interestingly, the abundance of beneficial bacteria, such as Lachnospiraceae_AC2044_group and Lachnospiraceae_NK4A136_group, were decreased in yaks with diarrhea, and the reductions were negatively correlated with the fecal water content. Collectively, these findings indicate that diminished microbial stability and increased abundance of certain bacteria in the gut may contribute to diarrhea occurrence in yaks.

Comparative analysis of energy homeostasis regulation at different altitudes in Hengduan Mountain of red-backed vole, Eothenomys miletus, during high-fat diet acclimation: examining gut microbial and physiological interactions

The study aimed to explore the similarities and differences in gut microorganisms and their functions in regulating body mass in Eothenomys miletus across different altitudes in the Hengduan Mountains when exposed to a high-fat diet. Eothenomys miletus specimens were gathered from Dali (DL) and Xianggelila (XGLL) in Yunnan Province, China, and categorized into control, high-fat (1 week of high-fat diet), and re-feeding groups (1 week of high-fat diet followed by 2 weeks of standard food). The analysis utilized 16S rRNA sequencing to assess the diversity and structure of intestinal microbial communities in E. miletus. The investigation focused on the impact of high-fat diet consumption and different altitudes on gut microbial diversity, structure, and physiological markers. Results revealed that a high-fat diet influenced the beta diversity of gut microorganisms in E. miletus, leading to variations in microbial community structure between the two regions with different altitudes. High-fat food significantly affected body mass, white adipose tissue mass, triglycerides, and leptin levels, but not food intake. Specific intestinal microorganisms were observed in the high-fat groups, aiding in food digestion and being enriched in particular flora. In particular, microbial genera like Lactobacillus and Hylemonella were enriched in the high-fat group of DL. The enriched microbiota in the control group was associated with plant polysaccharide and cellulose decomposition. Following a high-fat diet, gut microbiota adapted to support lipid metabolism and energy supply, while upon re-feeding, the focus shifted back to cellulose digestion. These findings suggested that alterations in gut microbial composition, alongside physiological markers, play a vital role in adaptation of E. miletus to the diverse habitats of the Hengduan Mountains at varying altitudes.

Seasonal dynamics of intestinal microbiota in juvenile Chinese mitten crab (Eriocheir sinensis) in the Yangtze Estuary

Introduction

In this study, the seasonal differences in the intestinal microbiota of Chinese mitten crab (Eriocheir sinensis) larvae were investigated at different sites in the intertidal zone of the Yangtze River Estuary.

Methods

16S rRNA high-throughput sequencing technology was used to compare and analyze the microbial community structure in the intestines of juvenile crab from different seasons.

Results

The results showed that the main microbial phyla in all seasons and sites were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, which accounted for 97.1% of the total microbiota. Composition analysis revealed that the relative abundance of Proteobacteria decreased from summer to winter at each station, whereas Bacteroidetes showed the opposite trend. Alpha diversity analysis showed that species richness increased from summer to winter at the upstream site (P < 0.05), but decreased at the downstream site (P < 0.05), with no significant differences observed in other comparisons. Biomarker species analysis showed that juvenile crab exhibited a more specialized microbial community in summer compared with autumn and winter. Co-occurrence network analysis revealed that microbial interaction network complexity was lower in autumn compared with summer and autumn. Functional prediction analysis showed that the microbial community only exhibited seasonal differences in amino acid biosynthesis, cofactor, prosthetic group, electron carrier, and vitamin biosynthesis, aromatic compound degradation, nucleotide and nucleoside degradation, and tricarboxylic acid cycle pathways.

Discussion

The results indicated that the microbiota did not significantly differ among sites, and seasonal variation was a main factor influencing the differences in intestinal microbiota of Chinese mitten juvenile crab. Moreover, the microbial community was more complex in summer compared with autumn and winter.

Linking growth performance and carcass traits with enterotypes in Muscovy ducks

OBJECTIVE

Enterotypes (ETs) are the clustering of gut microbial community structures, which could serve as indicators of growth performance and carcass traits. However, ETs have been sparsely investigated in waterfowl. The objective of this study was to identify the ileal ETs and explore the correlation of the ETs with growth performance and carcass traits in Muscovy ducks.

METHODS

A total of 200 Muscovy ducks were randomly selected from a population of 5,000 ducks at 70-day old, weighed and slaughtered. The growth performance and carcass traits, including body weight, dressed weight and evidenced weight, dressed percentage, percentage of apparent yield, breast muscle weight, leg muscle weight, percentage of leg muscle and percentage of breast muscle, were determined. The contents of ileum were collected for the isolation of DNA and 16S rRNA gene sequencing. The ETs were identified based on the 16S rRNA gene sequencing data and the correlation of the ETs with growth performance and carcass traits was performed by Spearman correlation analysis.

RESULTS

Three ETs (ET1, ET2, and ET3) were observed in the ileal microbiota of Muscovy ducks with significant differences in number of features and α-diversity among these ETs (p<0.05). Streptococcus, Candida Arthritis, and Bacteroidetes were the presentative genus in ET1 to ET3, respectively. Correlation analysis revealed that Lactococcus and Bradyrhizobium were significantly correlated with percentage of eviscerated yield and leg muscle weight (p<0.05) while ETs were found to have a close association with percentage of eviscerated yield, leg muscle weight, and percentage of leg muscle in Muscovy ducks. However, the growth performance of ducks with different ETs did not show significant difference (p>0.05). Lactococcus were found to be significantly correlated with leg muscle weight, dressed weight, and percentage of eviscerated yield.

CONCLUSION

Our findings revealed a substantial variation in carcass traits associated with ETs in Muscovy ducks. It is implied that ETs might have the potential to serve as a valuable biomarker for assessing duck carcass traits. It would provide novel insights into the interaction of gut microbiota with growth performance and carcass traits of ducks.

The Conservation Implications of the Gut Microbiome for Protecting the Critically Endangered Gray Snub-Nosed Monkey (Rhinopithecus brelichi)

The gut microbiota plays a crucial role in regulating energy metabolism, facilitating nutrient absorption, and supporting immune function, thereby assisting the host in adapting to seasonal dietary changes. Here, we compare the gut microbiome composition of wild gray snub-nosed monkeys during winter (from October to December) and spring (from January to March) to understand differences in seasonal nutrient intake patterns. Snub-nosed monkeys are foregut fermenters and consume difficult-to-digest carbohydrates and lichen. To examine the digestive adaptations of gray snub-nosed monkeys, we collected 14 fresh fecal samples for DNA analysis during the winter and spring. Based on 16S rRNA sequencing, metagenomic sequencing, and functional metagenomic analyses, we identified that Firmicutes, Actinobacteria, Verrucomicrobia, and Bacteroidetes constitute a keystone bacterial group in the gut microbiota during winter and spring and are responsible for degrading cellulose. Moreover, the transition in dietary composition from winter to spring was accompanied by changes in gut microbiota composition, demonstrating adaptive responses to varying food sources and availability. In winter, the bacterial species of the genera Streptococcus were found in higher abundance. At the functional level, these bacteria are involved in fructose and mannose metabolism and galactose metabolism c-related pathways, which facilitate the breakdown of glycogen, starch, and fiber found in fruits, seeds, and mature leaves. During spring, there was an increased abundance of bacteria species from the Prevotella and Lactobacillus genera, which aid the digestion of protein-rich buds. Combined, these findings reveal how the gut microbiota adjusts to fluctuations in energy balance and nutrient intake across different seasons in this critically endangered species. Moreover, we also identified Pseudomonas in two samples; the presence of potential pathogens within the gut could pose a risk to other troop members. Our findings highlight the necessity of a conservation plan that focuses on protecting vegetation and implementing measures to prevent disease transmission for this critically endangered species.

Grazing decreases net ecosystem carbon exchange by decreasing shrub and semi-shrub biomass in a desert steppe

Livestock grazing can strongly determine how grasslands function and their role in the carbon cycle. However, how ecosystem carbon exchange responds to grazing and the underlying mechanisms remain unclear. We measured ecosystem carbon fluxes to explore the changes in carbon exchange and their driving mechanisms under different grazing intensities (CK, control; HG, heavy grazing; LG, light grazing; MG, moderate grazing) based on a 16-year long-term grazing experimental platform in a desert steppe. We found that grazing intensity influenced aboveground biomass during the peak growing season, primarily by decreasing shrubs and semi-shrubs and perennial forbs. Furthermore, grazing decreased net ecosystem carbon exchange by decreasing aboveground biomass, especially the functional group of shrubs and semi-shrubs. At the same time, we found that belowground biomass and soil ammonium nitrogen were the driving factors of soil respiration in grazed systems. Our study indicates that shrubs and semi-shrubs are important factors in regulating ecosystem carbon exchange under grazing disturbance in the desert steppe, whereas belowground biomass and soil available nitrogen are important factors regulating soil respiration under grazing disturbance in the desert steppe; this results provide deeper insights for understanding how grazing moderates the relationships between soil nutrients, plant biomass, and ecosystem CO2 exchange, which provide a theoretical basis for further grazing management.

Yaks Are Dependent on Gut Microbiota for Survival in the Environment of the Qinghai Tibet Plateau

The yak (Poephagus grunniens) has evolved unique adaptations to survive the harsh environment of the Qinghai-Tibetan Plateau, while their gut microorganisms play a crucial role in maintaining the health of the animal. Gut microbes spread through the animal population not only by horizontal transmission but also vertically, which enhances microbial stability and inheritance between generations of the population. Homogenization of gut microbes in different animal species occurs in the same habitat, promoting interspecies coexistence. Using the yak as a model animal, this paper discusses the adaptive strategies under extreme environments, and how the gut microbes of the yak circulate throughout the Tibetan Plateau system, which not only affects other plateau animals such as plateau pikas, but can also have a profound impact on the health of people. By examining the relationships between yaks and their gut microbiota, this review offers new insights into the adaptation of yaks and their ecological niche on the Qinghai-Tibetan plateau.

Tibetan terrestrial and aquatic ecosystems collapsed with cryosphere loss inferred from sedimentary ancient metagenomics

Glacier and permafrost shrinkage and land-use intensification threaten mountain wildlife and affect nature conservation strategies. Here, we present paleometagenomic records of terrestrial and aquatic taxa from the southeastern Tibetan Plateau covering the last 18,000 years to help understand the complex alpine ecosystem dynamics. We infer that steppe-meadow became woodland at 14 ka (cal BP) controlled by cryosphere loss, further driving a herbivore change from wild yak to deer. These findings weaken the hypothesis of top-down control by large herbivores in the terrestrial ecosystem. We find a turnover in the aquatic communities at 14 ka, transitioning from glacier-related (blue-green) algae to abundant nonglacier-preferring picocyanobacteria, macrophytes, fish, and otters. There is no evidence for substantial effects of livestock herding in either ecosystem. Using network analysis, we assess the stress-gradient hypothesis and reveal that root hemiparasitic and cushion plants are keystone taxa. With ongoing cryosphere loss, the protection of their habitats is likely to be of conservation benefit on the Tibetan Plateau.

High-Energy Supplemental Feeding Shifts Gut Microbiota Composition and Function in Red Deer (Cervus elaphus)

Winter supplemental feeding (SF) is commonly used to improve the survival of captive wildlife. To investigate the impact of winter supplementation on the gut microbiota of wildlife, we assessed changes in the gut microbiota of red deer (Cervus elaphus) during the supplementary and non-supplementary feeding (NSF) groups using 16S rRNA sequencing technology. We found no significant differences in the diversity of the gut microbiota between SF and NSF except for the Simpson's index. However, the relative abundance of Bacteroidetes, Lentisphaerae, and Proteobacteria in the gut microbiota was significantly higher during SF. Further, genera such as Intestinimonas, Rikenella, Lawsonibacter, Muribaculum, and Papillibacter were more abundant during SF. Beta diversity analysis showed significant differences between SF and NSF. The microbes detected during SF were primarily associated with lipid metabolism, whereas those detected during NSF were linked to fiber catabolism. High-energy feed affects the gut microbial composition and function in red deer. During SF, the gut microbes in red deer were enriched in microorganisms associated with butyrate and lipid metabolism, such as R. microfusus, M. intestinale, and Papillibacter cinnamivorans. These gut microbes may be involved in ameliorating obesity associated with high-energy diets. In summary, SF is a reasonable and effective management strategy.

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.

Microbial Metagenomes and Host Transcriptomes Reveal the Dynamic Changes of Rumen Gene Expression, Microbial Colonization and Co-Regulation of Mineral Element Metabolism in Yaks from Birth to Adulthood

Yaks are the main pillar of plateau animal husbandry and the material basis of local herdsmen's survival. The level of mineral elements in the body is closely related to the production performance of yaks. In this study, we performed a comprehensive analysis of rumen epithelial morphology, transcriptomics and metagenomics to explore the dynamics of rumen functions, microbial colonization and functional interactions in yaks from birth to adulthood. Bacteria, eukaryotes, archaea and viruses colonized the rumen of yaks from birth to adulthood, with bacteria being the majority. Bacteroidetes and Firmicutes were the dominant phyla in five developmental stages, and the abundance of genus Lactobacillus and Fusobacterium significantly decreased with age. Glycoside hydrolase (GH) genes were the most highly represented in five different developmental stages, followed by glycosyltransferases (GTs) and carbohydrate-binding modules (CBMs), where the proportion of genes coding for CBMs increased with age. Integrating host transcriptome and microbial metagenome revealed 30 gene modules related to age, muscle layer thickness, nipple length and width of yaks. Among these, the MEmagenta and MEturquoise were positively correlated with these phenotypic traits. Twenty-two host genes involved in transcriptional regulation related to metal ion binding (including potassium, sodium, calcium, zinc, iron) were positively correlated with a rumen bacterial cluster 1 composed of Alloprevotella, Paludibacter, Arcobacter, Lactobacillus, Bilophila, etc. Therefore, these studies help us to understand the interaction between rumen host and microorganisms in yaks at different ages, and further provide a reliable theoretical basis for the development of feed and mineral element supplementation for yaks at different ages.

Cold exposure, gut microbiota and health implications: A narrative review

Temperature has been recognized as an important environmental factor affecting the composition and function of gut microbiota (GM). Although research on high-temperature impacts has been well studied, knowledge about the effect of cold exposure on GM remains limited. This narrative review aims to synthesize the latest scientific findings on the impact of cold exposure on mammalian GM, and its potential health implications. Chronic cold exposure could disrupt the α-diversity and the composition of GM in both experimental animals and wild-living hosts. Meanwhile, cold exposure could impact gut microbial metabolites, such as short-chain fatty acids. We also discussed plausible biological pathways and mechanisms by which cold-induced changes may impact host health, including metabolic homeostasis, fitness and thermogenesis, through the microbiota-gut-brain axis. Intriguingly, alterations in GM may provide a tool for favorably modulating the host response to the cold temperature. Finally, current challenges and future perspectives are discussed, emphasizing the need for translational research in humans. GM could be manipulated by utilizing nutritional strategies, such as probiotics and prebiotics, to deal with cold-related health issues and enhance well-being in populations living or working in cold environments.

Microbial community composition in the dung of five sympatric European herbivore species

The dung microbiome is a complex system that is highly influenced by species and diet. This study characterized the dung bacterial and fungal communities of five herbivore species inhabiting the National Park Zuid-Kennemerland, the Netherlands. The five selected herbivore species were rabbit (Oryctolagus cuniculus L.), cow (Bos taurus L.), horse (Equus ferus caballus L.), fallow deer (Dama dama L.), and European bison (Bison bonasus L.). We explored the effects of distinct digestive physiology (ruminants vs. non-ruminants) and diverse dietary preferences on the microbial community composition of herbivore dung. Firmicutes and Bacteroidetes were dominant bacterial phyla in the dung of all five herbivore species, and Ascomycota was the predominant fungal phylum. Verrucomicrobiota and Mucoromycota were more present in horse dung and Proteobacteria were more abundant in rabbit dung than the three ruminant dung types. There were few significant differences in the microbial community structure among the three ruminant dung types. The alpha and beta diversity of dung microbial communities significantly differed between ruminants and non-ruminants, especially in bacterial communities. Based on MetaCyc pathways, we found that the primary functions of bacteria in herbivore dung were focused on biosynthesis, various super pathways, and degradation, with a few differences between ruminant and non-ruminant dung. FUNGuild analysis showed that horse dung had more saprotrophic fungi, while the fungi in fallow deer dung had more symbiotrophic properties, with the fungal functions of bison, cow, and rabbit dung somewhere in between. There was also a correlation between microbial community and nutrient composition of the substrate in herbivore dung. Understanding the dung microbial community composition of these herbivore species can enrich the database of mammalian gut microbiomes for studying the mechanisms of microbial community variation while preparing for exploring a new perspective to study the impact of herbivores on ecosystems through dung deposition.

The maturity, humus content, and microbial metabolic function of sheep manure compost on the Qinghai-Tibet Plateau can be significantly improved by reducing the moisture content

The Qinghai-Tibet Plateau (QTP) is characterized by an extreme hypoxia, which may lead to lack of sufficient oxygen for compost production, and thus seriously affecting the compost quality. The moisture content (MC) has a direct effect on the oxygen content of composting pile. At present, the research on the optimum moisture content of compost production on the QTP is still lacking. This study aimed to investigate the influences of MC on fermentation quality of sheep manure composting on the QTP and to further analyze the changes of microbial metabolic function and enzyme activity under different MC. Composting experiment with low MC (45%) and conventional MC (60%) was conducted in both summer and autumn. The results showed that the composting efficiency of 45% MC was better than 60% in both seasons, which was mainly manifested as longer high-temperature period (summer:16 d vs 14 d, autumn: 7 d vs 2 d), higher germination index (summer:136.1% vs 128.6%, autumn:103.5% vs 81.2%), and more humus synthesis (summer:159.8 g/kg vs 151.2 g/kg, autumn:136.1 k/kg vs 115.5 k/kg). The 45% MC can improve microbial metabolism, including increasing the abundance of functional genes involved in carbohydrate metabolism, amino acid metabolism, and nucleotide metabolism and improving the activities of cellulase, β-glucosidase, protease, polyphenol oxidase, and peroxidase. In conclusion, 45% MC can improve the fermentation efficiency and products quality of sheep manure compost on QTP.

Comparing the gut microbiota of Sichuan golden monkeys across multiple captive and wild settings: roles of anthropogenic activities and host factors

BACKGROUND

Captivity and artificial food provision are common conservation strategies for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). Anthropogenic activities have been reported to impact the fitness of R. roxellana by altering their gut microbiota, a crucial indicator of animal health. Nevertheless, the degree of divergence in gut microbiota between different anthropogenically-disturbed (AD) R. roxellana and their counterparts in the wild has yet to be elucidated. Here, we conducted a comparative analysis of the gut microbiota across nine populations of R. roxellana spanning China, which included seven captive populations, one wild population, and another wild population subject to artificial food provision.

RESULTS

Both captivity and food provision significantly altered the gut microbiota. AD populations exhibited common variations, such as increased Bacteroidetes and decreased Firmicutes (e.g., Ruminococcus), Actinobacteria (e.g., Parvibacter), Verrucomicrobia (e.g., Akkermansia), and Tenericutes. Additionally, a reduced Firmicutes/Bacteroidetes ratiosuggested diminished capacity for complex carbohydrate degradation in captive individuals. The results of microbial functional prediction suggested that AD populations displayed heightened microbial genes linked to vitamin and amino acid metabolism, alongside decreased genes associated antibiotics biosynthesis (e.g., penicillin, cephalosporin, macrolides, and clavulanic acid) and secondary metabolite degradation (e.g., naphthalene and atrazine). These microbial alterations implied potential disparities in the health status between AD and wild individuals. AD populations exhibited varying degrees of microbial changes compared to the wild group, implying that the extent of these variations might serve as a metric for assessing the health status of AD populations. Furthermore, utilizing the individual information of captive individuals, we identified associations between variations in the gut microbiota of R. roxellana and host age, as well as pedigree. Older individuals exhibited higher microbial diversity, while a closer genetic relatedness reflected a more similar gut microbiota.

CONCLUSIONS

Our aim was to assess how anthropogenic activities and host factors influence the gut microbiota of R. roxellana. Anthropogenic activities led to consistent changes in gut microbial diversity and function, while host age and genetic relatedness contributed to interindividual variations in the gut microbiota. These findings may contribute to the establishment of health assessment standards and the optimization of breeding conditions for captive R. roxellana populations.

Available sulfur and phosphorus transformation mechanism and functional microorganisms during sheep manure composting on Qinghai-Tibet Plateau under two moisture contents

Understanding the mechanisms of sulfur and phosphorus transformation during composting is important for improving compost fertility. This study aims to investigate the microbial mechanism of available sulfur and phosphorus transformation during sheep manure composting under different moisture contents (45%: M45 and 60%: M60) on the Qinghai-Tibet Plateau using metagenomics technology. The results showed that the final available sulfur and phosphorus contents of M45 were 11% and 13% higher than those of M60, respectively. M45 enhanced sulfur oxidation, sulfate reduction, and thiosulfate disproportionation. These steps were significantly positively correlated with available sulfur, and Pseudomonas, Thermobifida, Luteimonas, Brevibacterium, Planifilum, and Xinfangfangia were the main participants. Available phosphorus was significantly positively correlated with polyphosphate degradation and inorganic P solubilization, and the main participants in these steps were Luteimonas, Brachybacterium, Corynebacterium, Jeotgalicoccus, Microbacterium, Streptomyces, and Pseudoxanthomonas. These findings reveal the microbial mechanisms of available and phosphorus transformation during composting at two moisture contents.

Linkages between rumen microbiome, host, and environment in yaks, and their implications for understanding animal production and management

Livestock on the Qinghai-Tibetan Plateau is of great importance for the livelihood of the local inhabitants and the ecosystem of the plateau. The natural, harsh environment has shaped the adaptations of local livestock while providing them with requisite eco-services. Over time, unique genes and metabolic mechanisms (nitrogen and energy) have evolved which enabled the yaks to adapt morphologically and physiologically to the Qinghai-Tibetan Plateau. The rumen microbiota has also co-evolved with the host and contributed to the host's adaptation to the environment. Understanding the complex linkages between the rumen microbiota, the host, and the environment is essential to optimizing the rumen function to meet the growing demands for animal products while minimizing the environmental impact of ruminant production. However, little is known about the mechanisms of host-rumen microbiome-environment linkages and how they ultimately benefit the animal in adapting to the environment. In this review, we pieced together the yak's adaptation to the Qinghai-Tibetan Plateau ecosystem by summarizing the natural selection and nutritional features of yaks and integrating the key aspects of its rumen microbiome with the host metabolic efficiency and homeostasis. We found that this homeostasis results in higher feed digestibility, higher rumen microbial protein production, higher short-chain fatty acid (SCFA) concentrations, and lower methane emissions in yaks when compared with other low-altitude ruminants. The rumen microbiome forms a multi-synergistic relationship among the rumen microbiota services, their communities, genes, and enzymes. The rumen microbial proteins and SCFAs act as precursors that directly impact the milk composition or adipose accumulation, improving the milk or meat quality, resulting in a higher protein and fat content in yak milk and a higher percentage of protein and abundant fatty acids in yak meat when compared to dairy cow or cattle. The hierarchical interactions between the climate, forage, rumen microorganisms, and host genes have reshaped the animal's survival and performance. In this review, an integrating and interactive understanding of the host-rumen microbiome environment was established. The understanding of these concepts is valuable for agriculture and our environment. It also contributes to a better understanding of microbial ecology and evolution in anaerobic ecosystems and the host-environment linkages to improve animal production.

Gut microbiota reflect adaptation of cave-dwelling tadpoles to resource scarcity

Gut microbiota are significant to the host's nutrition and provide a flexible way for the host to adapt to extreme environments. However, whether gut microbiota help the host to colonize caves, a resource-limited environment, remains unknown. The nonobligate cave frog Oreolalax rhodostigmatus completes its metamorphosis within caves for 3-5 years before foraging outside. Their tadpoles are occasionally removed from the caves by floods and utilize outside resources, providing a contrast to the cave-dwelling population. For both cave and outside tadpoles, the development-related reduction in their growth rate and gut length during prometamorphosis coincided with a shift in their gut microbiota, which was characterized by decreased Lactobacillus and Cellulosilyticum and Proteocatella in the cave and outside individuals, respectively. The proportion of these three genera was significantly higher in the gut microbiota of cave-dwelling individuals compared with those outside. The cave-dwellers' gut microbiota harbored more abundant fibrolytic, glycolytic, and fermentative enzymes and yielded more short-chain fatty acids, potentially benefitting the host's nutrition. Experimentally depriving the animals of food resulted in gut atrophy for the individuals collected outside the cave, but not for those from inside the cave. Imitating food scarcity reproduced some major microbial features (e.g. abundant Proteocatella and fermentative genes) of the field-collected cave individuals, indicating an association between the cave-associated gut microbiota and resource scarcity. Overall, the gut microbiota may reflect the adaptation of O. rhodostigmatus tadpoles to resource-limited environments. This extends our understanding of the role of gut microbiota in the adaptation of animals to extreme environments.

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.

Moderate altitude exposure impacts host fasting blood glucose and serum metabolome by regulation of the intestinal flora

Moderate altitude exposure has shown beneficial effects on diabetes incidence but the underlying mechanisms are not understood. Our study aimed to investigate how the human gut microbiome impacted the serum metabolome and associated with glucose homeostasis in healthy Chinese individuals upon moderate-altitude exposure. Faecal microbiome composition was assessed using shotgun metagenomic sequencing. Serum metabolome was acquired by untargeted metabolomics technology, and amino acids (AAs) and propionic acid in serum were quantified by targeted metabolomics technology. The results indicated that the moderate-altitude exposed individuals presented lowered fasting blood glucose (FBG) and propionic acid, increased circulating L-Glutamine but decreased L-Glutamate and L-Valine, which correlated with enriched Bacteroidetes and decreased Proteobacteria. Additionally, the silico causality associations among gut microbiota, serum metabolome and host FBG were analyzed by mediation analysis. It showed that increased Bacteroides ovatus (B. ovatus) and decreased Escherichia coli (E. coli) were identified as the main antagonistic species driving the association between L-Glutamate and FBG in silico causality. Furthermore, the high-fat diet (HFD) fed mice subjected to faecal microbiota transplantation (FMT) were applied to validate the cause-in-fact effects of gut microbiota on the beneficial glucose response. We found that microbiome in the moderate-altitude exposed donor could predict the extent of the FBG response in recipient mice, which showed lowered FBG, L-Glutamate and Firmicutes/Bacteroidetes ratio. Our findings suggest that moderate-altitude exposure targeting gut microbiota and circulating metabolome, may pave novel avenues to counter dysglycemia.

Rumen bacterial cluster identification and its influence on rumen metabolites and growth performance of young goats

Enterotypes, which are defined as bacterial clusters in the gut microbiome, have been found to have a close relationship to host metabolism and health. However, this concept has never been used in the rumen, and little is known about the complex biological relationships between ruminants and their rumen bacterial clusters. In this study, we used young goats (n = 99) as a model, fed them the same diet, and analyzed their rumen microbiome and corresponding bacterial clusters. The relationships between the bacterial clusters and rumen fermentation and growth performance in the goats were further investigated. Two bacterial clusters were identified in all goats: the P-cluster (dominated by genus Prevotella, n = 38) and R-cluster (dominated by Ruminococcus, n = 61). Compared with P-cluster goats, R-cluster goats had greater growth rates, concentrations of propionate, butyrate, and 18 free amino acids¸ and proportion of unsaturated fatty acids, but lower acetate molar percentage, acetate to propionate ratio, and several odd and branched chain and saturated fatty acids in rumen fluid (P < 0.05). Several members of Firmicutes, including Ruminococcus, Oscillospiraceae NK4A214 group, and Christensenellaceae R-7 group were significantly higher in the R-cluster, whereas Prevotellaceae members, such as Prevotella and Prevotellaceae UCG-003, were significantly higher in P-cluster (P < 0.01). Co-occurrence networks showed that R-cluster enriched bacteria had significant negative correlations with P-cluster enriched bacteria (P < 0.05). Moreover, we found the concentrations of propionate, butyrate and free amino acids, and the proportions of unsaturated fatty acids were positively correlated with R-cluster enriched bacteria (P < 0.05). The concentrations of acetate, acetate to propionate ratio, and the proportion of odd and branched chain and saturated fatty acids were positively correlated with P-cluster enriched bacteria (P < 0.05). Overall, our results indicated that rumen bacterial clusters can influence rumen fermentation and growth performance of young goats, which may shed light on modulating the rumen microbiome in early life to improve the growth performance of ruminant animals.

Dietary habits of pastoralists on the Tibetan plateau are influenced by remoteness and economic status

In general, dietary habits of pastoralists are livestock-derived, but are also influenced by external food sources under globalization. We hypothesized that dietary habits of pastoralists would be influenced by their remoteness, and that changes from the traditional diet would result in deviations in the local ecological chain. To test this hypothesis, we determined the δ13C and δ15N values of soil, plants, and hair of animals and pastoralists (n = 885). The δ13C value in human hair reflects the proportions of protein originating from C3 and C4 plants; whereas, the δ15N value reflects the proportions of protein derived from plants and animals, with higher values indicating a greater consumption of meat. The isotopic signatures enabled us to estimate the variation in dietary habits of pastoralists across a socio-economic gradient of easily accessible to remote areas on the Tibetan plateau, and to determine the trophic transfer of the isotopes along an ecological chain. The trophic magnification factor (TMF) evaluated the trophic transfer of δ15N in the soil-plants-animals-pastoralists ecological chain. The high δ15N values in soil and plants were not recovered in animals and pastoralists in easily accessible and developed areas, indicating the use of external feed and food resources, and that they deviated from the ecological chain. The mean δ13C (-22.0 ‰) and δ15N values (6.9 ‰) of pastoralists indicated diets consisting mainly of local C3 plants and animal products. However, pastoralists in remote areas relied more on meat protein and on the local ecological chain than pastoralists in easily accessible areas, as their δ15N values and trophic magnification factor of δ15N in the ecological chain were greater. In addition to remoteness, per capita GDP influenced dietary changes in pastoralists, with richer pastoralists consuming more external food. We concluded that dietary changes of pastoralists in the easily accessible areas were due to external food resources and alterations in the local ecological chain of animals and plant-based foods available to the pastoralists.

Prickly Ash Seeds improve immunity of Hu sheep by changing the diversity and structure of gut microbiota

Prickly Ash Seeds (PAS), as a traditional Chinese medicinal herb, have pharmacological effects such as anti-asthma, anti-thrombotic, and anti-bacterial, but their impact on gut microbiota is still unclear. This study used a full-length 16 s rRNA gene sequencing technique to determine the effect of adding PAS to the diet on the structure and distribution of gut microbiota in Hu sheep. All lambs were randomly divided into two groups, the CK group was fed with a basal ration, and the LZS group was given a basal diet with 3% of PAS added to the ration. The levels of inflammatory factors (IL-10, IL-1β, and TNF-α) in intestinal tissues were measured by enzyme-linked immunosorbent assay (ELISA) for Hu sheep in the CK and LZS group. The results indicate that PAS can increase the diversity and richness of gut microbiota, and can affect the community composition of gut microbiota. LEfSe analysis revealed that Verrucomicrobiota, Kiritimatiella, WCHB 41, and uncultured_rumen_bacterium were significantly enriched in the LZS group. KEGG pathway analysis found that LZS was significantly higher than the CK group in the Excretory system, Folding, sorting and degradation, and Immune system pathways (p < 0.05). The results of ELISA assay showed that the level of IL-10 was significantly higher in the LZS group than in the CK group (p < 0.05), and the levels of TNF-α and IL-1β were significantly higher in the CK group than in the LZS group (p < 0.05). LEfSe analysis revealed that the dominant flora in the large intestine segment changed from Bacteroidota and Gammaproteobacteria to Akkermansiaceae and Verrucomicrobiae after PAS addition to Hu sheep lambs; the dominant flora in the small intestine segment changed from Lactobacillales and Aeriscardovia to Kiritimatiellae and WCHB1 41. In conclusion, the addition of PAS to sheep diets can increase the number and types of beneficial bacteria in the intestinal tract, improve lamb immunity, and reduce intestinal inflammation. It provides new insights into healthy sheep production.

Stochastic Processes Derive Gut Fungi Community Assembly of Plateau Pikas (Ochotona curzoniae) along Altitudinal Gradients across Warm and Cold Seasons

Although fungi occupy only a small proportion of the microbial community in the intestinal tract of mammals, they play important roles in host fat accumulation, nutrition metabolism, metabolic health, and immune development. Here, we investigated the dynamics and assembly of gut fungal communities in plateau pikas inhabiting six altitudinal gradients across warm and cold seasons. We found that the relative abundances of Podospora and Sporormiella significantly decreased with altitudinal gradients in the warm season, whereas the relative abundance of Sarocladium significantly increased. Alpha diversity significantly decreased with increasing altitudinal gradient in the warm and cold seasons. Distance-decay analysis showed that fungal community similarities were significantly and negatively correlated with elevation. The co-occurrence network complexity significantly decreased along the altitudinal gradients as the total number of nodes, number of edges, and degree of nodes significantly decreased. Both the null and neutral model analyses showed that stochastic or neutral processes dominated the gut fungal community assembly in both seasons and that ecological drift was the main ecological process explaining the variation in the gut fungal community across different plateau pikas. Homogeneous selection played a weak role in structuring gut fungal community assembly during the warm season. Collectively, these results expand our understanding of the distribution patterns of gut fungal communities and elucidate the mechanisms that maintain fungal diversity in the gut ecosystems of small mammals.

Combined network analysis and interpretable machine learning reveals the environmental adaptations of more than 10,000 ruminant microbial genomes

Background

The ruminant gastrointestinal contains numerous microbiomes that serve a crucial role in sustaining the host's productivity and health. In recent times, numerous studies have revealed that variations in influencing factors, including the environment, diet, and host, contribute to the shaping of gastrointestinal microbial adaptation to specific states. Therefore, understanding how host and environmental factors affect gastrointestinal microbes will help to improve the sustainability of ruminant production systems.

Results

Based on a graphical analysis perspective, this study elucidates the microbial topology and robustness of the gastrointestinal of different ruminant species, showing that the microbial network is more resistant to random attacks. The risk of transmission of high-risk metagenome-assembled genome (MAG) was also demonstrated based on a large-scale survey of the distribution of antibiotic resistance genes (ARG) in the microbiota of most types of ecosystems. In addition, an interpretable machine learning framework was developed to study the complex, high-dimensional data of the gastrointestinal microbial genome. The evolution of gastrointestinal microbial adaptations to the environment in ruminants were analyzed and the adaptability changes of microorganisms to different altitudes were identified, including microbial transcriptional repair.

Conclusion

Our findings indicate that the environment has an impact on the functional features of microbiomes in ruminant. The findings provide a new insight for the future development of microbial resources for the sustainable development in agriculture.

Species variations in the gut microbiota of captive snub-nosed monkeys

Introduction

Snub-nosed monkeys are species in danger of extinction due to habitat fragmentation and human activities. Captivity has been suggested as an Auxiliary Conservation Area (ASA) strategy. However, little is known about the adaptation of different species of snub-nosed monkeys to captive environments.

Methods

This study compared the gut microbiota between Rhinopithecus bieti, R. brelichi, and R. roxellana under identical captive conditions to provide insights for improving captive conservation strategies.

Results

The results showed that these three Rhinopithecus species shared 80.94% of their Operational Taxonomic Unit (OTU), indicating high similarity in gut microbiota composition. The predominant phyla were Firmicutes and Bacteroidetes for all three Rhinopithecus species, but differences were observed in diversity, characteristic bacterial communities, and predicted function. Significant enrichment of cellulolytic families, including Ruminococcaceae, Clostridiales vadinBB60 group, Christensenellaceae, and Erysipelotrichaceae, and pathways involved in propionate and butyrate metabolism in the gut of R. bieti suggested that it may have a superior dietary fiber utilization capacity. In contrast, Bacteroidetes, Ruminoccaceae, and Trichospiraceae were more abundant in R. brelichi and R. roxellana, and were associated with saccharide and glycan metabolic pathways. Moreover, R. brelichi and R. roxellana also had higher similarity in microbiota composition and predicted function.

Discussion

In conclusion, the results demonstrate that host species are associated with the composition and function of the gut microbiota in snub-nosed monkeys. Thus, host species should be considered when formulating nutritional strategies and disease surveillance in captive snub-nosed monkeys.

Effects of turning frequency on fermentation efficiency and microbial community metabolic function of sheep manure composting on the Qinghai-Tibet Plateau

This study explored the effects of turning frequency on fermentation efficiency and microbial metabolic function of sheep manure composting on the Qinghai-Tibet Plateau (QTP). Five treatments with different turning frequencies were set up in this study: turning every 1 day (T1), 2 days (T2), 4 days (T3), 6 days (T4), and 8 days (T5). Results showed that the high temperature period for T1 and T5 lasted only 4 days, while that for T2-T4 lasted more than 8 days. The germination index of T1 and T5 was lower than 80%, while that of T2-T4 was 100.6%, 97.8%, and 88.6%, respectively. This study further predicted the microbial metabolic function of T2-T4 using the bioinformatics tool PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) and determining the activities of various functional enzymes. The results showed that carbohydrate metabolism, protein metabolism, and nucleotide metabolism were the main metabolic pathways of microorganisms, and that T2 increased the abundance of functional genes of these metabolic pathways. The activities of protease, cellulase, and peroxidase in T2 and T3 were higher than those in T4, and the effect of T2 was more significant. In conclusion, turning once every 2 days can improve the quality of sheep manure compost on the QTP.

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.

Comparative study of the gut microbiota in three captive Rhinopithecus species

BACKGROUND

Snub-nosed monkeys are highly endangered primates and their population continues to decline with the habitat fragmentation. Artificial feeding and breeding is an important auxiliary conservation strategy. Studies have shown that changes and imbalances in the gut microbiota often cause gastrointestinal problems in captive snub-nosed monkeys. Here, we compare the gut microbiota composition, diversity, and predicted metabolic function of three endangered species of snub-nosed monkeys (Rhinopithecus bieti, R. brelichi, and R. roxellana) under the same captive conditions to further our understanding of the microbiota of these endangered primates and inform captive conservation strategies. 16 S rRNA gene sequencing was performed on fecal samples from 15 individuals (R. bieti N = 5, R. brelichi N = 5, R. roxellana N = 5).

RESULTS

The results showed that the three Rhinopithecus species shared 24.70% of their amplicon sequence variants (ASVs), indicating that the composition of the gut microbiota varied among the three Rhinopithecus species. The phyla Firmicutes and Bacteroidetes represented 69.74% and 18.45% of the core microbiota. In particular, analysis of microbiota diversity and predicted metabolic function revealed a profound impact of host species on the gut microbiota. At the genus level, significant enrichment of cellulolytic genera including Rikenellaceae RC9 gut group, Ruminococcus, Christensenellaceae R7 group, UCG 004 from Erysipelatoclostridiaceae, and UCG 002 and UCG 005 from Oscillospiraceae, and carbohydrate metabolism including propionate and butyrate metabolic pathways in the gut of R. bieti indicated that R. bieti potentially has a stronger ability to use plant fibers as energy substances. Bacteroides, unclassified Muribaculaceae, Treponema, and unclassified Eubacterium coprostanoligenes group were significantly enriched in R. brelichi. Prevotella 9, unclassified Lachnospiraceae, and unclassified UCG 010 from Oscillospirales UCG 010 were significantly enriched in R. roxellana. Among the predicted secondary metabolic pathways, the glycan biosynthesis and metabolism had significantly higher relative abundance in the gut of R. brelichi and R. roxellana than in the gut of R. bieti. The above results suggest that different Rhinopithecus species may have different strategies for carbohydrate metabolism. The Principal coordinate analysis (PCoA) and Unweighted pair-group method with arithmetic mean (UPGMA) clustering tree revealed fewer differences between the gut microbiota of R. brelichi and R. roxellana. Correspondingly, no differences were detected in the relative abundances of functional genes between the two Rhinopithecus species.

CONCLUSION

Taken together, the study highlights that host species have an effect on the composition and function of the gut microbiota of snub-nosed monkeys. Therefore, the host species should be considered when developing nutritional strategies and investigating the effects of niche on the gut microbiota of snub-nosed monkeys.

Comparative analysis of the gut bacteria of the relict gull (Larus Relictus) and black-necked grebe (Podiceps Nigricollis) in Erdos Relic Gull National Nature Reserve in Inner Mongolia, China

The gut microbiota promotes host health by maintaining homeostasis and enhancing digestive efficiency. The gut microflora in wild birds affects host physiological characteristics, nutritional status, and stress response. The relict gull (Larus Relictus, a Chinese national first-class protected species) and the black-necked grebe (Podiceps Nigricollis, a secondary protected species) bred in the Ordos Relic Gull National Nature Reserve share similar feeding habits and living environments but are distantly related genetically. To explore the composition and differences in the gut microbiota of these two key protected avian species in Erdos Relic Gull National Nature Reserve and provide a basis for their protection, 16S rRNA gene high-throughput sequencing was performed and the gut microbial diversity and composition of the relict gull (L. Relictus) and black-necked grebe (P. Nigricollis) was characterized. In total, 445 OTUs (operational taxonomic units) were identified and classified into 15 phyla, 22 classes, 64 orders, 126 families, and 249 genera. Alpha diversity analysis indicates that the gut microbial richness of the relict gull is significantly lower than that of the black-necked grebe. Gut microbe composition differs significantly between the two species. The most abundant bacterial phyla in these samples were Proteobacteria, Firmicutes, Fusobacteria, and Bacteroidetes. The prominent phylum in the relict gull was Proteobacteria, whereas the prominent phylum in the black-necked grebe was Firmicutes. The average relative abundance of the 17 genera identified was greater than 1%. The dominant genus in the relict gull was Escherichia-Shigella, whereas Halomonas was dominant in the black-necked grebe. Microbial functional analyses indicate that environmental factors exert a greater impact on relict gulls than on black-necked grebes. Compared with the relict gull, the black-necked grebe was able to use food more efficiently to accumulate its nutrient requirements, and the gut of the relict gull harbored more pathogenic bacteria, which may be one reason for the decline in the relict gull population, rendering it an endangered species. This analysis of the gut microbial composition of these two wild avian species in the same breeding grounds is of great significance, offers important guidance for the protection of these two birds, especially relict gulls, and provides a basis for understanding the propagation of related diseases.

Characteristics of glucose and lipid metabolism and the interaction between gut microbiota and colonic mucosal immunity in pigs during cold exposure

BACKGROUND

Cold regions have long autumn and winter seasons and low ambient temperatures. When pigs are unable to adjust to the cold, oxidative damage and inflammation may develop. However, the differences between cold and non-cold adaptation regarding glucose and lipid metabolism, gut microbiota and colonic mucosal immunological features in pigs are unknown. This study revealed the glucose and lipid metabolic responses and the dual role of gut microbiota in pigs during cold and non-cold adaptation. Moreover, the regulatory effects of dietary glucose supplements on glucose and lipid metabolism and the colonic mucosal barrier were evaluated in cold-exposed pigs.

RESULTS

Cold and non-cold-adapted models were established by Min and Yorkshire pigs. Our results exhibited that cold exposure induced glucose overconsumption in non-cold-adapted pig models (Yorkshire pigs), decreasing plasma glucose concentrations. In this case, cold exposure enhanced the ATGL and CPT-1α expression to promote liver lipolysis and fatty acid oxidation. Meanwhile, the two probiotics (Collinsella and Bifidobacterium) depletion and the enrichment of two pathogens (Sutterella and Escherichia-Shigella) in colonic microbiota are not conducive to colonic mucosal immunity. However, glucagon-mediated hepatic glycogenolysis in cold-adapted pig models (Min pigs) maintained the stability of glucose homeostasis during cold exposure. It contributed to the gut microbiota (including the enrichment of the Rikenellaceae RC9 gut group, [Eubacterium] coprostanoligenes group and WCHB1-41) that favored cold-adapted metabolism.

CONCLUSIONS

The results of both models indicate that the gut microbiota during cold adaptation contributes to the protection of the colonic mucosa. During non-cold adaptation, cold-induced glucose overconsumption promotes thermogenesis through lipolysis, but interferes with the gut microbiome and colonic mucosal immunity. Furthermore, glucagon-mediated hepatic glycogenolysis contributes to glucose homeostasis during cold exposure.

Temporal Variations in the Gut Microbiota of the Globally Endangered Sichuan Partridge (Arborophila rufipectus): Implications for Adaptation to Seasonal Dietary Change and Conservation

Host-associated microbiotas are known to influence host health by aiding digestion, metabolism, nutrition, physiology, immune function, and pathogen resistance. Although an increasing number of studies have investigated the avian microbiome, there is a lack of research on the gut microbiotas of wild birds, especially endangered pheasants. Owing to the difficulty of characterizing the dynamics of dietary composition, especially in omnivores, how the gut microbiotas of birds respond to seasonal dietary changes remains poorly understood. The Sichuan partridge (Arborophila rufipectus) is an endangered pheasant species with a small population endemic to the mountains of southwest China. Here, 16S rRNA sequencing and Tax4Fun were used to characterize and compare community structure and functions of the gut microbiota in the Sichuan partridges across three critical periods of their annual life cycle (breeding, postbreeding wandering, and overwintering). We found that the microbial communities were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Cyanobacteria throughout the year. Diversity of the gut microbiotas was highest during postbreeding wandering and lowest during the overwintering periods. Seasonal dietary changes and reassembly of the gut microbial community occurred consistently. Composition, diversity, and functions of the gut microbiota exhibited diet-associated variations, which might facilitate host adaptation to diverse diets in response to environmental shifts. Moreover, 28 potential pathogenic genera were detected, and their composition differed significantly between the three periods. Investigation of the wild bird gut microbiota dynamics has enhanced our understanding of diet-microbiota associations over the annual life cycle of birds, aiding in the integrative conservation of this endangered bird. IMPORTANCE Characterizing the gut microbiotas of wild birds across seasons will shed light on their annual life cycle. Due to sampling difficulties and the lack of detailed dietary information, studies on how the gut microbiota adapts to seasonal dietary changes of wild birds are scarce. Based on more detailed dietary composition, we found a seasonal reshaping pattern of the gut microbiota of Sichuan partridges corresponding to their seasonal dietary changes. The variation in diet and gut microbiota potentially facilitated the diversity of dietary niches of this endangered pheasant, revealing a seasonal diet-microbiota association across the three periods of the annual cycle. In addition, identifying a variety of potentially pathogenic bacterial genera aids in managing the health and improving survival of Sichuan partridges. Incorporation of microbiome research in the conservation of endangered species contributes to our comprehensive understanding the diet-host-microbiota relationship in wild birds and refinement of conservation practices.

Insights into autotrophic carbon fixation strategies through metagonomics in the sediments of seagrass beds

Seagrass beds contributes up to 10% ocean carbon storage. Carbon fixation in seagrass bed greatly affect global carbon cycle. Currently, six carbon fixation pathways are widely studied: Calvin, reductive tricarboxylic acid (rTCA), Wood-Ljungdahl (WL), 3-hydroxypropionate (3HP), 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) and dicarboxylate/4-hydroxybutyrate (DC/4-HB). Despite the knowledges about carbon fixation increase, the carbon fixation strategies in seagrass bed sediment remain unexplored. We collected seagrass bed sediment samples from three sites with different characteristics in Weihai, a city in Shandong, China. The carbon fixation strategies were investigated through metagenomics. The results exhibited that five pathways were present, of which Calvin and WL were the most dominant. The community structure of microorganisms containing the key genes of these pathways were further analyzed, and those dominant microorganisms with carbon fixing potential were revealed. Phosphorus significantly negatively corelated with those microorganisms. This study provides an insight into the strategies of carbon fixation in seagrass bed sediments.

Identification of Candidate Genes Associated with Yak Body Size Using a Genome-Wide Association Study and Multiple Populations of Information

Yaks have evolved several breeds or genetic resources owing to their geographical and ecological environment, and investigating the genetic construction of body size among breeds is key for breeding. Here, a genome-wide association study (GWAS) was performed for five body size traits in 31 yak breeds and genetic resources. The information from clustering individuals according to their habitats was used for kinship grouping in the compressed mixed linear model (CMLM). We named this approach the pCMLM method. A total of 3,584,464 high-quality single nucleotide polymorphisms (SNPs) were obtained, and six markers were found to be significantly associated with height by pCMLM. Four candidate genes, including FXYD6, SOHLH2, ADGRB2, and OSBPL6, were identified. Our results show that when CMLM cannot identify optimal clustering groups, pCMLM can provide sufficient associated results based on population information. Moreover, this study provides basic information on the gene localization of quantitative traits of body size among yak breeds.

Gut Microbiome Variation Along A Lifestyle Gradient Reveals Threats Faced by Asian Elephants

The gut microbiome is closely related to host nutrition and health. However, the relationships between gut microorganisms and host lifestyle are not well characterized. In the absence of confounding geographic variation, we defined clear patterns of variation in the gut microbiomes of Asian elephants (AEs) in the Wild Elephant Valley, Xishuangbanna, China, along a lifestyle gradient (fully captive, semicaptive, semiwild, and purely wild). A phylogenetic analysis using the 16S rRNA gene sequences highlighted that the microbial diversity decreased as the degree of captivity increased. Furthermore, the results showed that the bacterial taxon WCHB1-41_c was significantly affected by lifestyle gradient variations. Quantitative real-time PCR revealed a paucity of genes related to butyrate production in the microbiome of AEs with a pure wild lifestyle, which may be due to the increased environmental unfavorable factors. Overall, these results demonstrate the distinct gut microbiome characteristics among AEs with a gradient of lifestyles and provide a basis for designing strategies to improve the well-being or conservation of this important animal species.

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.

Fermented cottonseed and rapeseed meals outperform soybean meal in improving performance, rumen fermentation, and bacterial composition in Hu sheep

Background

This study examined the effects of substituting cottonseed meal (CSM) or rapeseed meal (RSM) for soybean meal (SBM) on Hu sheep performance, rumen fermentation, and bacterial composition. 51 four-month-old indigenous male Hu sheep with starting body weights of 22.51 ± 2.84 kg and similar origins were randomly assigned to three treatments; (1) non-fermented total mixed ration (TMR) with SBM (CK), (2) fermented TMR containing CSM (F-CSM group), and (3) fermented TMR containing RSM (F-RSM group).

Results

The three groups’ intake of dry matter differed significantly (p &lt; 0.05). In terms of average daily gain, the F-RSM group outperformed the CK and F-CSM groups (p &lt; 0.05). The pH of the rumen was substantially lower in the CK group than in the F-CSM and F-RSM groups (p &lt; 0.05), and the F-CSM group had greater amounts of volatile fatty acids (VFA) than the F-RSM and CK groups. In comparison to the CK group, the microbial crude protein yield was significantly higher in the F-CSM and F-RSM groups (p &lt; 0.05). The F-CSM group significantly outperformed the F-RSM group of pepsin and cellulose enzyme activity (p &lt; 0.05). The relative abundance of Bacteroidetes was greater in the CK and F-RSM groups compared to the F-CSM group (p &lt; 0.05). In comparison to the other groups, Firmicutes were less abundant in the CK group (p &lt; 0.05). Prevotella was present in a higher relative abundance in the F-CSM and F-RSM groups than in the CK group (p &lt; 0.05). Prevotella was greater in relative abundance in the F-CSM and F-RSM groups than in the CK group (p &lt; 0.05). The relative abundances of Veillonellaceae_UCG-001 and Lachnospiraceae_XPB1014 correlated with rumen butyric acid content and NH3-N content (p &lt; 0.05). Gene function prediction revealed that replacing SBM with F-CSM or F-RSM in the diet of Hu sheep can promote glycan biosynthesis and metabolism.

Conclusion

The replacement of F-CSM and F-RSM for SBM has an influence on the richness and diversity of rumen bacteria at the phylum and genus levels. Replacement of SBM with F-CSM increased VFA yield and further promoted the performance of Hu sheep.

Shift of Feeding Strategies from Grazing to Different Forage Feeds Reshapes the Rumen Microbiota To Improve the Ability of Tibetan Sheep (Ovis aries) To Adapt to the Cold Season

The dynamics of ruminant-rumen microbiome symbiosis associated with feeding strategies in the cold season were examined. Twelve pure-grazing adult Tibetan sheep (Ovis aries) (18 months old; body weight, 40 ± 0.23 kg) were transferred from natural pasture to two indoor feedlots and fed either a native-pasture diet (NPF group) or an oat hay diet (OHF group) (n = 6 per treatment), and then the flexibility of rumen microbiomes to adapt to these compositionally different feeding strategies was examined. Principal-coordinate analysis and similarity analysis indicated that the rumen bacterial composition correlated with altered feeding strategies. Microbial diversity was higher in the grazing group than in those fed with native pasture and an oat hay diet (P < 0.05). The dominant microbial phyla were Bacteroidetes and Firmicutes, and the core bacterial taxa comprised mostly (42.49% of shared operational taxonomic units [OTUs]) Ruminococcaceae (408 taxa), Lachnospiraceae (333 taxa), and Prevotellaceae (195 taxa), which were relatively stable across different treatments. Greater relative abundances of Tenericutes at the phylum level, Pseudomonadales at the order level, Mollicutes at the class level, and Pseudomonas at the genus level were observed in a grazing period than in the other two treatments (NPF and OHF) (P < 0.05). In the OHF group, due to the high nutritional quality of the forage, Tibetan sheep can produce high concentrations of short-chain fatty acids (SCFAs) and NH3-N by increasing the relative abundances of key bacteria in the rumen, such as Lentisphaerae, Negativicutes, Selenomonadales, Veillonellaceae, Ruminococcus 2, Quinella, Bacteroidales RF16 group, and Prevotella 1, to aid in nutrients degradation and energy utilization. The levels of beneficial bacteria were increased by the oat hay diet; these microbiotas are likely to help improve and maintain host health and metabolic ability in Tibetan sheep to adapt to cold environments. The rumen fermentation parameters were significantly influenced by feeding strategy in the cold season (P < 0.05). Overall, the results of this study demonstrate the strong effect of feeding strategies on the rumen microbiota of Tibetan sheep, which provided a new idea for the nutrition regulation of Tibetan sheep grazing in the cold season on the Qinghai-Tibetan Plateau. IMPORTANCE During the cold season, like other high-altitude mammals, Tibetan sheep have to adapt their physiological and nutritional strategies, as well as the structure and function of their rumen microbial community, to the seasonal variation of lower food availability and quality. This study focused on the changes and adaptability in the rumen microbiota of Tibetan sheep when they adapted from grazing to a high-efficiency feeding strategy during the cold season by analyzing the rumen microbiota of Tibetan sheep raised under the different management systems, and it shows the linkages among the rumen core and pan-bacteriomes, nutrient utilization, and rumen short-chain fatty acids. The findings from this study suggest that the feeding strategies potentially contribute to variations in the pan-rumen bacteriome, together with the core bacteriome. Fundamental knowledge on the rumen microbiomes and their roles in nutrient utilization furthers our understanding of how rumen microbial adaptation to harsh environments may function in hosts. The facts obtained from the present trial clarified the possible mechanisms of the positive effects of feeding strategy on nutrient utilization and rumen fermentation in harsh environments.

Effects of Two Feeding Patterns on Growth Performance, Rumen Fermentation Parameters, and Bacterial Community Composition in Yak Calves

The health of young ruminants is highly dependent on early rumen microbial colonization. In this study, the effects of milk replacer on growth performance, rumen fermentation, and the rumen microflora in yak calves were evaluated. Sixty yak calves (body weight = 22.5 ± 0.95 kg, age = 30 ± 1 d) were assigned to the CON group (breastfed) or TRT group (milk replacer fed) and evaluated over 120 d. At 120 d, ruminal fluid samples were collected from 14 calves and then conducted for rumen fermentation and microbiota analyses. There was no difference in growth performance; however, calf survival was higher in the TRT group than in the CON group. The concentration of total volatile fatty acids and the molar proportion of butyric acid and lactic acid were increased with milk replacer feed in the TRT group (p < 0.05), but iso-valeric acid concentration was highest in the CON group (p < 0.05). Firmicutes and Bacteroidetes were the most dominant phyla in the CON and TRT groups, respectively. In the TRT group, Bacteroidetes, Prevotellaceae, Bacteroidia, Bacteroidetes, and Prevotella_1 were the dominant flora in the rumen of calves. The relative abundances of various taxa were correlated with rumen fermentation parameters; the relative abundance of Quinella and iso-butyrate levels were positively correlated (r = 0.57). The relative abundances of the Christensenellaceae_R-7_group and A/P were positively correlated (r = 0.57). In summary, milk replacer is conducive to the development of the rumen microflora, the establishment of rumen fermentation function, and the implementation of early weaning in yaks.

Microbial Enterotypes Shape the Divergence in Gut Fermentation, Host Metabolism, and Growth Rate of Young Goats

Enterotypes can be useful tools for studying the gut microbial community landscape, which is thought to play a crucial role in animal performance. However, few studies have been carried out to identify enterotypes and their associations with growth performance in young goats. In this study, two enterotypes were categorized in 76 goats: cluster 1 (n = 39) and cluster 2 (n = 37). Compared to cluster 2, cluster 1 had greater growth rates, the concentrations of acetate, propionate, valerate, and total volatile fatty acids (VFA) in the gut. Several serum glycolipid metabolism parameters, including glucose, total cholesterol, high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C), were also increased in cluster 1, while serum IgG was decreased in cluster 1. Using α-diversity analysis, we found a microbiome with lower richness and diversity in cluster 1. Some gut bacteria, including Succinivibrio and several members of the Prevotellaceae family, were enriched in cluster 1, while Christensenellaceae R-7 group, Romboutsia, and Clostridium sensu stricto 1 were enriched in cluster 2. A co-occurrence network analysis revealed that the differential interaction patterns existed in two enterotypes, and microbial function prediction suggested that some nutrient metabolism-related pathways, including amino acid biosynthesis and starch and sucrose metabolism, were enriched in cluster 1. Furthermore, a correlation analysis showed that enterotype-related bacteria were closely correlated with gut fermentation, serum biochemistry, and growth rate. Overall, our data provide a new perspective for understanding enterotype characteristics in goats, offering insights into important microbial interaction mechanisms for improving the growth performance of ruminant animals. IMPORTANCE The intricate relationships between a host animal and its resident gut microbiomes provide opportunities for dealing with energy efficiency and production challenges in the livestock industry. Here, we applied the enterotype concept to the gut microbiome in young goats and found that it can be classified into two enterotypes which are apparently associated with divergences in gut fermentation, blood biochemistry, and goat growth rates. The microbial co-occurrence networks and function predictions differed between the two enterotypes, suggesting that the formation of host phenotype may be modified by different bacterial features and complex bacterial interactions. The characteristics of enterotypes related to growth performance in young goats may enable us to improve long-term production performance in goat industry by modulating the gut microbiome during early life.

Seasonal Changes in the Structure and Function of Gut Microbiota in the Muskrat (Ondatra zibethicus)

The gut microbiota plays a crucial role in the nutrition, metabolism, and immune function of the host animal. The muskrat (Ondatra zibethicus) is a typical seasonal breeding animal. The present study performed a metagenomic analysis of cecum contents from muskrats in the breeding and non-breeding seasons. The results indicated that the breeding muskrats and non-breeding muskrats differed in gut microbiota structure and function. During the breeding season, the relative abundance of phylum Bacteroidetes, genus Prevotella, and genus Alistipes increased, while the relative abundance of phylum Firmicutes and phylum Actinobacteria decreased. The muskrat gut microbiota was enriched in the metabolism-related pathways, especially amino acid and vitamin metabolism, and genetically related metabolites in the breeding season. We presumed that the muskrat gut microbiota might seasonally change to secure reproductive activity and satisfy the metabolic demands of different seasons. This study could explore potential mechanisms by which gut microbiota affects reproduction. Moreover, this study may provide a new theoretical basis for the management of muskrat captive breeding.

The cecal ecosystem is a great contributor to intramuscular fat deposition in broilers

Intramuscular fat (IMF) content is a meat quality trait of major economic importance in animal production. Emerging evidence has demonstrated that meat quality can be improved by regulating the gut microbiota. However, the organization and ecological properties of the gut microbiota and its relationship with the IMF content remain unclear in chickens. Here, we investigated the microbial communities of 206 cecal samples from broilers with excellent meat quality. We noted that the cecal microbial ecosystem obtained from hosts reared under the same management and dietary conditions showed clear compositional stratification. Two enterotypes, in which the ecological properties, including diversity and interaction strengths, were significantly different, described the microbial composition pattern. Compared with enterotype 2, enterotype 1, distinguished by the Clostridia_vadinBB60_group, had a higher fat deposition, although no discrepancy was found in growth performance and meat yield. A moderate correlation was observed in the IMF content between 2 muscle tissues, despite the IMF content of thigh muscle was 42.76% greater than that of breast muscle. Additionally, the lower abundance of cecal vadinBE97 was related to higher IMF levels in both muscle tissues. Although vadinBE97 accounted for 0.40% of the total abundance of genera in the cecum, it exhibited significant and positive correlations with other genera (accounting for 25.3% of the tested genera). Our results highlight important insights into the cecal microbial ecosystem and its association with meat quality. Microbial interactions should be carefully considered when developing approaches to improve the IMF content by regulating the gut microbiota in broilers.

Food provisioning results in functional, but not compositional, convergence of the gut microbiomes of two wild Rhinopithecus species: Evidence of functional redundancy in the gut microbiome

The consumption of similar diets has led to the convergence of gut microbial compositions and functions across phylogenetically distinct animals. However, given the functional redundancy in gut microbiomes, it remains unclear whether synchrony occurs in their functions only and not in their composition, even within phylogenetically close animals consuming a similar diet. In this study, we collected fresh fecal samples from a Rhinopithecus roxellana population in April 2021 (before food provisioning) and June and December 2021 (after food provisioning) and used high-throughput sequencing methods (full-length 16S rRNA gene sequencing and metagenomes) to investigate changes in the gut microbiome due to food provisioning. Combining the results from our previous studies on a wild Rhinopithecus bieti population, we found that the artificial food provisions (e.g., apples, carrots, and peanuts) affected the gut microbiome, and synchrony occurred only in its functions and antibiotic resistance gene community in both Rhinopithecus species, reflecting its ecological functional redundancy. Given the current findings (e.g., depletion in probiotic microbes, dysbiosis in the gut microbial community, and changes in the antibiotic resistance gene profile), anthropogenic disturbances (e.g., food provisioning) would have potential negative effects on host health. Therefore, human activity in animal conservation should be rethought from the standpoint of gut microbial diversity.

Microbiome variation correlates with the insecticide susceptibility in different geographic strains of a significant agricultural pest, Nilaparvata lugens

Microbiome-mediated insecticide resistance is an emerging phenomenon found in insect pests. However, microbiome composition can vary by host genotype and environmental factors, but how these variations may be associated with insecticide resistance phenotype remains unclear. In this study, we compared different field and laboratory strains of the brown planthopper Nilaparvata lugens in their microbiome composition, transcriptome, and insecticide resistance profiles to identify possible patterns of correlation. Our analysis reveals that the abundances of core bacterial symbionts are significantly correlated with the expression of several host detoxifying genes (especially NlCYP6ER1, a key gene previously shown involved in insecticides resistance). The expression levels of these detoxifying genes correlated with N. lugens insecticide susceptibility. Furthermore, we have identified several environmental abiotic factors, including temperature, precipitation, latitude, and longitude, as potential predictors of symbiont abundances associated with expression of key detoxifying genes, and correlated with insecticide susceptibility levels of N. lugens. These findings provide new insights into how microbiome-environment-host interactions may influence insecticide susceptibility, which will be helpful in guiding targeted microbial-based strategies for insecticide resistance management in the field.

Insular holobionts: persistence and seasonal plasticity of the Balearic wall lizard (Podarcis lilfordi) gut microbiota

Background

Integrative studies of animals and associated microbial assemblages (i.e., the holobiont) are rapidly changing our perspectives on organismal ecology and evolution. Insular vertebrates provide ideal natural systems to understand patterns of host-gut microbiota coevolution, the resilience and plasticity these microbial communities over temporal and spatial scales, and ultimately their role in the host ecological adaptation.

Methods

Here we used the endemic Balearic wall lizard Podarcis lilfordi to dissect the drivers of the microbial diversity within and across host allopatric populations/islets. By focusing on three extensively studied populations/islets of Mallorca (Spain) and fecal sampling from individually identified lizards along two years (both in spring and autumn), we sorted out the effect of islet, sex, life stage, year and season on the microbiota composition. We further related microbiota diversity to host genetics, trophic ecology and expected annual metabolic changes.

Results

All the three populations showed a remarkable conservation of the major microbial taxonomic profile, while carrying their unique microbial signature at finer level of taxonomic resolution (Amplicon Sequence Variants (ASVs)). Microbiota distances across populations were compatible with both host genetics (based on microsatellites) and trophic niche distances (based on stable isotopes and fecal content). Within populations, a large proportion of ASVs (30-50%) were recurrently found along the four sampling dates. The microbial diversity was strongly marked by seasonality, with no sex effect and a marginal life stage and annual effect. The microbiota showed seasonal fluctuations along the two sampled years, primarily due to changes in the relative abundances of fermentative bacteria (mostly families Lachnospiraceae and Ruminococcaceae), without any major compositional turnover.

Conclusions

These results support a large resilience of the major compositional aspects of the P. lilfordi gut microbiota over the short-term evolutionary divergence of their host allopatric populations (<10,000 years), but also indicate an undergoing process of parallel diversification of the both host and associated gut microbes. Predictable seasonal dynamics in microbiota diversity suggests a role of microbiota plasticity in the lizards' metabolic adaptation to their resource-constrained insular environments. Overall, our study supports the need for longitudinal and integrative studies of host and associated microbes in natural systems.

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.

Comparison of coated and uncoated trace elements on growth performance, apparent digestibility, intestinal development and microbial diversity in growing sheep

The suitable supplement pattern affects the digestion and absorption of trace minerals by ruminants. This study aimed to compare the effects of coated and uncoated trace elements on growth performance, apparent digestibility, intestinal development and microbial diversity in growing sheep. Thirty 4-month-old male Yunnan semi-fine wool sheep were randomly assigned to three treatments (n = 10) and fed with following diets: basal diet without adding exogenous trace elements (CON), basal diet plus 400 mg/kg coated trace elements (CTE, the rumen passage rate was 65.87%) and basal diet plus an equal amount of trace elements in uncoated form (UTE). Compared with the CON group, the average daily weight gain and apparent digestibility of crude protein were higher (P < 0.05) in the CTE and UTE groups, while there was no difference between the CTE and UTE groups. The serum levels of selenium, iodine and cobalt were higher (P < 0.05) in the CTE and UTE groups than those in the CON group, the serum levels of selenium and cobalt were higher (P < 0.05) in the CTE group than those in the UTE group. Compared with the CON and UTE groups, the villus height and the ratio of villus height to crypt depth in duodenum and ileum were higher (P < 0.05) in the CTE groups. The addition of trace minerals in diet upregulated most of the relative gene expression of Ocludin, Claudin-1, Claudin-2, ZO-1, and ZO-2 in the duodenum and jejunum and metal ion transporters (FPN1 and ZNT4) in small intestine. The relative abundance of the genera Christensenellaceae R-7 group, Ruminococcus 1, Lachnospiraceae NK3A20 group, and Ruminococcaceae in ileum, and Ruminococcaceae UCG-014 and Lactobacillus in colon was higher in the CTE group that in the CON group. These results indicated that dietary trace mineral addition improved the growth performance and intestinal development, and altered the structure of intestinal bacteria in growing sheep. Compared to uncoated form, offering trace mineral elements to sheep in coated form had a higher absorption efficiency, however, had little effect on improving growth performance of growing sheep.

Simulated seasonal diets alter yak rumen microbiota structure and metabolic function

Yak is the only ruminant on the Qinghai-Tibetan Plateau that grazes year-round. Although previous research has shown that yak rumen microbiota fluctuates in robust patterns with seasonal foraging, it remains unclear whether these dynamic shifts are driven by changes in environment or nutrient availability. The study examines the response of yak rumen microbiota (bacteria, fungi, and archaea) to simulated seasonal diets, excluding the contribution of environmental factors. A total of 18 adult male yaks were randomly divided into three groups, including a nutrition stress group (NSG, simulating winter pasture), a grazing simulation group (GSG, simulating warm season pasture), and a supplementation group (SG, simulating winter pasture supplemented with feed concentrates). Volatile fatty acids (VFAs) profiling showed that ruminal acetate, propionate and total VFA contents were significantly higher (p < 0.05) in GSG rumen. Metagenomic analysis showed that Bacteroidetes (53.9%) and Firmicutes (37.1%) were the dominant bacterial phyla in yak rumen across dietary treatments. In GSG samples, Actinobacteriota, Succinivibrionaceae_UCG-002, and Ruminococcus albus were the most abundant, while Bacteroides was significantly more abundant in NSG samples (p < 0.05) than that in GSG. The known fiber-degrading fungus, Neocallimastix, was significantly more abundant in NSG and SG samples, while Cyllamyces were more prevalent in NSG rumen than in the SG rumen. These findings imply that a diverse consortium of microbes may cooperate in response to fluctuating nutrient availability, with depletion of known rumen taxa under nutrient deficiency. Archaeal community composition showed less variation between treatments than bacterial and fungal communities. Additionally, Orpinomyces was significantly positively correlated with acetate levels, both of which are prevalent in GSG compared with other groups. Correlation analysis between microbial taxa and VFA production or between specific rumen microbes further illustrated a collective response to nutrient availability by gut microbiota and rumen VFA metabolism. PICRUSt and FUNGuild functional prediction analysis indicated fluctuation response of the function of microbial communities among groups. These results provide a framework for understanding how microbiota participate in seasonal adaptations to forage availability in high-altitude ruminants, and form a basis for future development of probiotic supplements to enhance nutrient utilization in livestock.

Highland adaptation of birds on the Qinghai-Tibet Plateau via gut microbiota

Highland birds evolve multiple adaptive abilities to cope with the harsh environments; however, how they adapt to the high-altitude habitats via the gut microbiota remains understudied. Here we integrated evidences from comparative analysis of gut microbiota to explore the adaptive mechanism of black-necked crane, a typical highland bird in the Qinghai-Tibet Plateau. Firstly, the gut microbiota diversity and function was compared among seven crane species (one high-altitude species and six low-altitude species), and then among three populations of contrasting altitudes for the black-necked crane. Microbiota community diversity in black-necked crane was significantly lower than its low-altitude relatives, but higher microbiota functional diversity was observed in black-necked crane, suggesting that unique bacteria are developed and acquired due to the selection pressure of high-altitude environments. The functional microbial genes differed significantly between the low- and high-altitude black-necked cranes, indicating that altitude significantly impacted microbial communities' composition and structure. Adaptive changes in microbiota diversity and function are observed in response to high-altitude environments. These findings provide us a new insight into the adaptation mechanism to the high-altitude environment for birds via the gut microbiota. KEY POINTS: • The diversity and function of gut microbiota differed significantly between the low- and high-altitude crane species. • Black-necked crane adapts to the high-altitude environment via specific gut microbiota. • Altitude significantly impacted microbial communities' composition and structure.

Increased availability of preferred food and decreased foraging costs from degraded grasslands lead to rodent pests in the Qinghai-Tibet Plateau

The increased population density of rodent species during ongoing grassland degradation further deteriorates its conditions. Understanding the effects of grassland degradation on rodent feeding habits is of great value for optimizing grassland management strategies. In this study, lightly degraded (LD), moderately degraded (MD), severely degraded (SD), and reseeded grassland (RG) were selected and their plant resources and soil physical properties were investigated. In addition, the study used ITS2 barcode combined with the Illumina MiSeq sequencing method to analyze the food composition and proportion of plateau zokors in different grassland conditions. The results showed that, with grassland degradation, plant biomass decreased, but the relative proportion of forbs increased (LD: 32.05 ± 3.89%; MD: 28.97 ± 2.78%; SD: 49.16 ± 4.67% and RG: 10.93 ± 1.53%). Forbs were the main food of the plateau zokor, accounting for more than 90% of their diet, and the animal had a clear preference for Potentilla species; the soil compaction of feeding habits showed a decreasing trend in the 10–25 cm soil layer, suggesting a decreased foraging cost. Nutritional analysis showed that the stomach content of crude protein in zokors feeding on MD grassland was significantly higher than that of animals feeding on the other grassland types. Structural equation modeling showed that soil physical properties and the relative biomass of forbs had significant (P &lt; 0.05) and extremely significant (P &lt; 0.001) impacts on the population density of plateau zokors, with direct impact contribution rates of 0.20 and 0.63. As the severity of grassland degradation increased, although the aboveground and underground biomass of the plants decreased, the proportion of food preferred by the plateau zokor increased, and the corresponding changes in the feeding environment resulted in decreased foraging energy expenditure, thereby increasing the suitability of the degraded grassland for the plateau zokor. Compared with degraded grassland, the food diversity and evenness of zokors increased, the food niche width enlarged, and the proportion of weeds decreased in RG, which increased the difficulty of obtaining food. Reseeding in grassland management is therefore an effective way to control plateau zokors.