Comparison of Rumen Fermentation Parameters and Microbiota of Yaks From Different Altitude Regions in Tibet, China

Survey of the fecal microbiota of indigenous small ruminants living in different areas of Guizhou

Introduction

Gut microbiota are associated with the health and performance of ruminant species, and they are affected by altitude, host genetics, and sex. However, there has been little research on comparing the fecal microbiota of indigenous small ruminants such as sheep and goats in Guizhou province, China. In the present study, we revealed the effect of altitude, genetics, and sex on fecal microbiota profiles and enterotypes in indigenous small ruminants of Guizhou province, China.

Methods

Fecal samples were collected from Hei and Qianbei Ma goats and Weining sheep in the Chinese province of Guizhou. 16S rRNA gene sequencing targeting the V3-V4 region was performed using the Illumina MiSeq platform. Sequences were processed using QIIME2, and the qualified sequences were processed using the plugin DADA2 to generate amplicon sequence variants (ASVs). The statistical analysis was performed using R studio.

Results

The fecal microbial profile was found to vary by herd (influenced by genetics/altitude) and sex. All samples were categorized into two enterotypes. The first enterotype is dominated by UCG-005, and the second enterotype is dominated by the Christensenellaceae_R-7_group, which may be highly driven by the host's genetics (breed). The predicted functional profiles of the fecal microbiota were also assigned to two clusters that corresponded exactly to the enterotypes. Cluster 1 of the functional profiling was characterized by biosynthesis pathways, and cluster 2 was characterized by energy metabolism pathways.

Discussion

Our findings may provide new insights into the fecal microbial community and enterotypes in small ruminants by herds, offering clues for understanding the mechanisms by which the fecal microbiota contribute to divergent host phenotypes in indigenous small ruminants in Guizhou.

Altitude-dependent metabolite biomarkers reveal the mechanism of plateau pika adaptation to high altitudes

The harsh environment in the Tibetan plateau, the highest place in the world, poses thermoregulatory challenges and hypoxic stress to animals. The impacts of plateau environment on animal physiology and reproduction include external factors such as strong ultraviolet radiation and low temperature, and internal factors such as animal metabolites and gut microbiota. However, it remains unclear how plateau pika adapt to high altitudes through the combination of serum metabolites and gut microbiota. To this end, we captured 24 wild plateau pikas at the altitudes of 3400, 3600, or 3800 m a.s.l. in a Tibetan alpine grassland. Using the machine learning algorithms (random forest), we identified five biomarkers of serum metabolites indicative of the altitudes, that is, dihydrotestosterone, homo-l-arginine, alpha-ketoglutaric-acid, serotonin, and threonine, which were related to body weight, reproduction, and energy metabolism of pika. Those metabolic biomarkers were positively correlated with Lachnospiraceae_ Agathobacter, Ruminococcaceae, or Prevotellaceae_Prevotella, suggesting the close relationship between metabolites and gut microbiota. By identifying the metabolic biomarkers and gut microbiota analysis, we reveal the mechanisms of adaptation to high altitudes in plateau pika.

Comparative Analysis of Rumen Microbiota Composition in Dairy Cows with Simple Indigestion and Healthy Cows

Simple indigestion in cows leads to substantial economic losses in the dairy industry. Despite ongoing efforts, an effective treatment for this issue remains elusive. Previous studies have emphasized the vital role of rumen microbes in maintaining ruminant health. To deepen our comprehension of the intricate interplay between rumen microbiota and simple indigestion, we undertook a study involving the analysis of rumen fluid from eight cows with simple indigestion and ten healthy cows. Additionally, we collected data pertaining to milk production, rumination behavior, and rumen characteristics. The results showed that cows with simple indigestion displayed significantly lower milk yield, reduced rumination duration, and weakened rumen contraction when contrasted with the healthy cows (p < 0.05). However, no significant difference in microbiota α-diversity emerged (p > 0.05). Principal coordinate analysis (PCoA) illuminated substantial variations in rumen microbial structure among the two groups (p < 0.05). Further analysis spotlighted distinctive bacteria in the rumen of the cows with indigestion, including Allisonella, Synergistes, Megasphaera, Clostridium_XIVb, Campylobacter, and Acidaminococcus. In contrast, Coraliomargarita, Syntrophococcus, and Coprococcus are the dominant bacterial genera in the rumen of healthy dairy cows. Importantly, these key bacterial genera also dominated the overarching microbial interaction network. The observation suggests that changes in the abundance of these dominant bacterial genera potentially underlie the principal etiology of cows with simple indigestion. The present findings can provide insights into simple indigestion prevention and treatment in dairy cows.

Effects of fermented herbal tea residue on meat quality, rumen fermentation parameters and microbes of black goats

Herbal tea residue (HTR) is generally considered to be a reusable resource which has still retains considerable proportion of nutrients and active substances. This study aimed to investigate the effects of substitution of whole corn silage with fermented herbal tea residue (FHTR) on meat quality, serum indices, rumen fermentation, and microbes in Chuanzhong black goats. Twenty-two female Chuanzhong black goats (4 months old) with similar weight (9.55 ± 0.95 kg) were selected and randomly divided into two groups. FHTR was used to replace 0% (CON group) and 30% (FHTR group) of whole corn silage in the diets and fed as a total mixed ration (TMR) for Chuanzhong black goats. The adaptation feeding period was 7 days, and the experimental period was 35 days. Results illustrated that the FHTR group had higher value of a* and concentrations of DM and CP and lower rate of water loss (P < 0.05) than the CON group. For the serum indices, goats fed with 30% FHTR had higher (P < 0.05) concentration of CR on day 35. For rumen fermentation, the pH and ratio of acetic acid/propionic acid (AA/PA) in the FHTR group were significantly lower than those in the CON group (P < 0.05). In addition, we studied the goats's rumen microbial community composition and found that the dominant phyla were Firmicutes, Bacteroidetes,and Tenericutes; and the dominant genera were Quinella, Candidatus_Saccharimonas, and Saccharofermentans. There was a significant difference in the beta diversity of the rumen microbiota between groups (P < 0.05). To sum up, the addition of FHTR can affect the meat quality, serum indices, improved rumen fermentation by adjusted the diversity and function of the rumen microbiota.

Yeast Peptides Improve the Intestinal Barrier Function and Alleviate Weaning Stress by Changing the Intestinal Microflora Structure of Weaned Lambs

Early weaning stress in lambs leads to decreased feed intake, damage to intestinal morphology, changes in the microbial flora structure, and subsequent complications. Yeast peptides are antimicrobial peptides with anti-inflammatory, antioxidant, and bacteriostasis effects. To study the effects of yeast peptides on relieving weaning stress in lambs, 54 lambs were randomly divided into three groups: ewe-reared (ER), yeast-peptide-treated (AP), and early-weaned (EW) lambs. The body weight and dry matter intake did not significantly differ among all groups. After weaning, the daily gain and feed conversion rate decreased significantly (p < 0.01), but AP showed an upward trend. In the EW group, immunoglobulin (Ig) levels changed significantly post-weaning (IgG decreased; IgA and IgM increased); the villi shortened, the crypt depth increased, and the villi height/crypt depth decreased (p < 0.001). The abundance and diversity of microflora among all groups were not significantly different. A column coordinate analysis showed significant differences in the intestinal microbial structure between the AP and EW groups. Lactobacillus, Aeriscardovia, Ruminosaceae_UCG-014, and Catenisphaera may play key roles in alleviating weaning stress in lambs. Our study provides new clues for alleviating weaning stress in lambs by describing the influence of yeast peptides on the intestinal microflora during weaning.

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.

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.

Dynamic changes in fecal microbiota in donkey foals during weaning: From pre-weaning to post-weaning

Introduction

A better understanding of the microbiota community in donkey foals during the weaning transition is a prerequisite to optimize gut function and improve feed efficiency. The objective of the present study was to investigate the dynamic changes in fecal microbiota in donkey foals from pre-to post-weaning period.

Methods

A total of 27 fecal samples of donkey foals were collected in the rectum before morning feeding at pre-weaning (30 days of age, PreW group, n = 9), dur-weaning (100 days of age, DurW group, n = 9) and post-weaning (170 days of age, PostW group, n = 9) period. The 16S rRNA amplicon sequencing were employed to indicate the microbial changes during the weaning period.

Results

In the present study, the cessation of breastfeeding gradually and weaning onto plant-based feeds increased the microbial diversity and richness, with a higher Shannon, Ace, Chao and Sobs index in DurW and PostW than in PreW (p < 0.05). The predominant bacterial phyla in donkey foal feces were Firmicutes (>50.5%) and Bacteroidota (>29.5%), and the predominant anaerobic fungi and archaea were Neocallimastigomycota and Euryarchaeota. The cellulolytic related bacteria including phylum Firmicutes, Spirochaetota and Fibrobacterota and genus norank_f_F082, Treponema, NK4A214_group, Lachnospiraceae_AC2044_group and Streptococcus were increased from pre-to post-weaning donkey foals (p < 0.05). Meanwhile, the functions related to the fatty acid biosynthesis, carbohydrate metabolism and amino acid biosynthesis were significantly enriched in the fecal microbiome in the DurW and PostW donkeys. Furthermore, the present study provided the first direct evidence that the initial colonization and establishment of anaerobic fungi and archaea in donkey foals began prior to weaning. The relative abundance of Orpinomyces were the highest in DurW donkey foals among the three groups (p < 0.01). In terms of archaea, the abundance of Methanobrevibacter were higher in PreW than in DurW and PostW (p < 0.01), but the abundance of Methanocorpusculum were significantly increased in DurW and PostW compared to PreW donkey foals (p < 0.01).

Discussion

Altogether, the current study contributes to a comprehensive understanding of the development of the microbiota community in donkey foals from pre-to post-weaning period, which may eventually result in an improvement of the digestion and feed efficiency in donkeys.

The gastrointestinal microbiome of browsing goats (Capra hircus)

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

Dietary Concentrate-to-Forage Ratio Affects Rumen Bacterial Community Composition and Metabolome of Yaks

Changes in dietary composition affect the rumen microbiota in ruminants. However, information on the effects of dietary concentrate-to-forage ratio changes on yak rumen bacteria and metabolites is limited. This study characterized the effect of three different dietary concentrate-to-forage ratios (50:50, C50 group; 65:35, C65 group; 80:20, C80 group) on yak rumen fluid microbiota and metabolites using 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC-MS) analyses. Rumen fermentation parameters and the abundance of rumen bacteria were affected by changes in the dietary concentrate-to-forage ratio, and there was a strong correlation between them. At the genus level, higher relative abundances of norank_f__F082, NK4A214_group, Lachnospiraceae_NK3A20_group, Acetitomaculum, and norank_f__norank_o__Clostridia_UCG-014 were observed with a high dietary concentrate-to-forage ratio (P < 0.05). Combined metabolomic and enrichment analyses showed that changes in the dietary concentrate-to-forage ratio significantly affected rumen metabolites related to amino acid metabolism, protein digestion and absorption, carbohydrate metabolism, lipid metabolism, and purine metabolism. Compared with the C50 group, 3-methylindole, pantothenic acid, D-pantothenic acid, and 20-hydroxy-leukotriene E4 were downregulated in the C65 group, while spermine and ribose 1-phosphate were upregulated. Compared to the C50 group, Xanthurenic acid, tyramine, ascorbic acid, D-glucuronic acid, 6-keto-prostaglandin F1a, lipoxin B4, and deoxyadenosine monophosphate were upregulated in the C80 group, while 3-methylindole and 20-hydroxy-leukotriene E4 were downregulated. All metabolites (Xanthurenic acid, L-Valine, N-Acetyl-L-glutamate 5-semialdehyde, N-Acetyl-L-glutamic acid, Tyramine, 6-Keto-prostaglandin F1a, Lipoxin B4, Xanthosine, Thymine, Deoxyinosine, and Uric acid) were upregulated in the C80 group compared with the C65 group. Correlation analysis of microorganisms and metabolites provided new insights into the function of rumen bacteria, as well as a theoretical basis for formulating more scientifically appropriate feeding strategies for yak.