Microbiome and Metabolomics Reveal the Effects of Different Feeding Systems on the Growth and Ruminal Development of Yaks

Succession of rumen microbiota and metabolites across different reproductive periods in different sheep breeds and their impact on the growth and development of offspring lambs

BACKGROUND

The microbiota and metabolites in the gastrointestinal tracts of female animals at different reproductive periods are very important to the growth, development, and health of themselves and their offspring. However, the changes in the gastrointestinal microbiota and metabolites throughout reproductive period of different sheep breeds and their effects on the growth and development of offspring lambs are still unclear. Hence, this study presents an assessment of the reproductive hormone levels, immune levels, rumen microbiota, and metabolites in Hu sheep and Suffolk ewes at different reproductive periods and their effects on the growth and development of offspring lambs.

RESULTS

Hu sheep and Suffolk during non-pregnancy, pregnancy, and lactation were used as the research objects to determine reproductive and immune indexes of ewes at different periods, analyze rumen microbiome and metabolome, and track the growth performance and development of offspring lambs. The results showed that the reproductive hormone and immune levels of Hu sheep and Suffolk underwent adaptive changes across different reproductive periods. Compared with non-pregnancy, the microbial energy metabolism and lipid metabolism function decreased during Hu sheep pregnancy, and energy metabolism function decreased during lactation. In Suffolk, energy metabolism, glycan biosynthesis, and metabolism function were enhanced during pregnancy, and the metabolism of cofactors and vitamins was enhanced during lactation. Prevotella increased in Suffolk during pregnancy and lactation (P < 0.05) and was positively correlated with the birth weight and body size of the lambs (P < 0.05). Moreover, the abundances of Butyrivibrio and Rikenellaceae_RC9_gut_group during pregnancy were positively correlated with the intestinal immunity of the offspring lambs (P < 0.05), thereby regulating the intestinal immunity level of the lambs. Metabolomic analysis revealed that the protein digestion, absorption, and amino acid metabolism of Hu sheep were enhanced during pregnancy, which provided amino acids for the growth and development of pregnant ewes and fetuses and was significantly correlated with the birth weight, body size, and intestinal immunity of lambs (P < 0.05). Simultaneously, there was an increase in acetate and propionate during the pregnancy and lactation period of both Hu sheep and Suffolk, providing energy for ewes during reproductive period. Moreover, the microbiota during the lactation period was significantly correlated with the milk quality and lambs daily gain (P < 0.05).

CONCLUSIONS

This study revealed the characteristic succession changes in the rumen microbiota and its metabolites at different reproductive periods in sheep breeds and their regulation of reproductive hormone and immune levels and identified their potential effects on the growth and development of offspring lambs. The findings provide valuable insights into the health and feeding management of different sheep breeds during the reproductive stage. Video Abstract.

Comparative Analysis of Gut Bacterial Diversity in Wild and Domestic Yaks on the Qinghai-Tibetan Plateau

The gut microbiota is a diverse and complex population, and it has a key role in the host's health and adaptability to the environment. The present study investigated the fecal bacterial community of wild grazing (WG) and domestic grazing (DG) yaks on natural grazing pastures, analyzing the gut microbiota using 16S rRNA sequencing to assess bacterial diversity. A total of 48 yak fecal samples were selected from two different grazing habitats. The DG group had more crude proteins and non-fiber carbohydrates. The WG group had more OM, insoluble dietary fiber such as NDF, ADF, ether extract, and TC. There were 165 and 142 unique operational taxonomic units (OTUs) in the WG and DG groups, respectively. Shannon index analysis revealed a higher bacterial diversity in the WG group than in the DG group. At the phylum level, Firmicutes were the dominant bacterial taxa in both groups. The relative abundance of Firmicutes in the WG group was higher than in the DG group. At the family level, the WG group had a significantly higher abundance of Ruminococcaceae (p < 0.001) and Rikenellaceae (p < 0.001) than the DG group. The abundances of Alloprevotella and Succinivibrio were more pronounced in the DG group than in the WG group at the genus level. This study presents a novel understanding of the bacterial communities of ruminants and their potential applications for livestock production.

Integrating 16S rRNA Sequencing and LC-MS-Based Metabolomics to Evaluate the Effects of Dietary Crude Protein on Ruminal Morphology, Fermentation Parameter and Digestive Enzyme Activity in Tibetan Sheep

The dietary crude protein level could affect ruminal fermentation parameters and the microflora of ruminants. The present study's aim was to investigate the effects of different protein level diets on ruminal morphology, fermentation parameters, digestive enzyme activity, microflora and metabolites of Tibetan sheep. Ninety weaned lambs (initial weight of 15.40 ± 0.81 kg, 2 months old) were selected and randomly divided into three groups (six pens/treatment, five rams/pen). Dietary treatments were formulated with 13.03% (high protein, HP), 11.58% (moderate protein, MP) and 10.20% (low protein, LP), respectively. Compared with LP, both papillae length and papillae width were significantly promoted in HP and MP (p < 0.05). The concentrations of ammonia nitrogen, total VFAs, propionic acids and butyric acids in HP were significantly increased compared to those in MP and LP (p < 0.05). The activities of protease and α-amylase in HP were significantly greater than those of LP (p < 0.05). For the ruminal microbial community, higher proportions of phylum Prevotella 1 and Succiniclasticum and genus Rikenellaceae RC9 gut group and Ruminococcus 1 were observed in HP (p < 0.05). A total of 60 differential metabolites (DMs) (28 up, 32 down) between HP and MP; 73 DMs (55 up, 18 down) between HP and LP; and 65 DMs (49 up, 16 down) between MP and LP were identified. Furthermore, four pathways of the biosynthesis of unsaturated fatty acids, tryptophan metabolism, bile secretion and ABC transporters were significantly different (p < 0.05). The abundance of phylum Prevotella 1 was negatively associated with stearic acid and palmitic acid but positively associated with the taurine. The abundance of genus Ruminococcus 1 was negatively associated with stearic acid, oleic acid, erucic acid, Indole-3-acetamide and palmitic acid but positively associated with 6-hydroxymelatonin. In conclusion, a 13.03% CP level improved ruminal morphology, fermentation parameters and digestive enzyme activities through modulating the microbial community and regulating metabolism in Tibetan sheep.

Disrupted Microbiota of Colon Results in Worse Immunity and Metabolism in Low-Birth-Weight Jinhua Newborn Piglets

The Jinhua pig is well known in China due to its delicious meat. However, because of large litter size, low birth weight always happens. This experiment used this breed as a model to research bacterial evidence leading to growth restriction and provide a possible solution linked to probiotics. In this experiment, the differences in organs indexes, colonic morphology, short chain fatty acid (SCFA) concentrations, microbiome, and transcriptome were detected between piglets in the standard-birth-weight group (SG) and low-birth-weight group (LG) to find potential evidence leading to low birth weight. We found that LG piglets had a lower liver index (p < 0.05), deeper colonic crypt depth (p < 0.05), fewer goblet cells (p < 0.05), and more inflammatory factor infiltration. In addition, differentially expressed genes (DEGs) were mainly enriched in B-cell immunity and glucose metabolism, and LG piglets had lower concentrations of SCFAs, especially butyrate and isobutyrate (p < 0.05). Finally, most of the significantly differentially abundant microbes were fewer in LG piglets, which affected DEG expressions and SCFA concentrations further resulting in worse energy metabolism and immunity. In conclusion, colonic disrupted microbiota may cause worse glucose metabolism, immunity, and SCFA production in LG piglets, and beneficial microbes colonized in SG piglets may benefit these harmful changes.

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.

Enhancing Rumen Fermentation and Bacteria Community in Sika Deer (Cervus nippon) through Varying Levels of Dragon Fruit Peel Polyphenolic Extract: An In Vitro Study

The aim of this study is to investigate the effect of dragon fruit peel polyphenolic extract (DFPE) on gas production, rumen fermentation, and bacterial communities in sika deer using an in vitro technique. Three treatments with different DFPE levels (DFPE0, base diet; DFPE5, base diet + 5 mg/g DFPE; DFPE10, base diet + 10 mg/g DFPE, respectively; n = 6) were implemented. The phenolic composition of DFPE, gas production (GP), ammonia nitrogen (NH3-N), volatile fatty acid (VFA), and bacteria communities was evaluated after 24 h of incubation. The results showed that GP and NH3-N were reduced by DFPE supplementation. Total VFA, isovaleric acid, and valeric acid were increased (p < 0.05) by the addition of DFPE. No changes (p > 0.05) were observed in pH, acetic acid, propionic acid, isobutyric acid, butyric acid, and the ratio of acetic acid to propionic acid. Additionally, the alpha indexes, including Sobs, Shannon, and Ace, were increased by DFPE supplementation. Moreover, at the phylum level, DFPE supplementation increased (p = 0.01) Bacteroidota but reduced (p < 0.01) Firmicutes. At the genus level, compared to DFPE0, the DFPE10 had increased relative abundances of Rikenellaceae_RC9_gut_group (p < 0.01), norank_f_Muribaculaceae (p = 0.01), Lachnospiraceae_NK3A20_group (p < 0.01), Christensenellaceae_R-7_group (p < 0.01), and NK4A214_group (p < 0.01), decreased relative abundances of Streptococcus (p < 0.01), Oribacterium (p = 0.01), and Enterococcus (p < 0.01). Compared to DFPE0, DFPE5 had no change (p > 0.05) in all bacteria at the genus level except for decreased relative abundance of Enterococcus (p < 0.01). These results indicated that DFPE may be able to be used as a feed additive to enhance fermentation parameters and improve ruminal bacteria communities in Sika deer.

Intensive feeding alters the rumen microbiota and its fermentation parameters in natural grazing yaks

Introduction

Amidst the challenging environmental conditions characterized by low oxygen levels and cold temperatures on the plateau, alterations in nutrient supply emerge as pivotal factors influencing the survival and reproduction of yaks. Intensive feeding stands out as a substantial mechanism for nutrient provision, initiating discernible changes in the host's rumen flora. Within the extreme natural conditions prevailing in the plateau area of northwest Yunnan, China, there exists a con-strained comprehension of the variations in rumen microflora, fermentation parameters, and growth responses exhibited by yaks subjected to intensive feeding.

Methods

This study employs 16S rRNA and ITS sequencing methods to scrutinize the rumen flora of yaks engaged in both natural grazing (G) and intensive feeding (F) on the plateau.

Results

The outcomes unveil that, during the severe winter season, yaks adeptly modulate the abundance and diversity of rumen flora in response to dietary modifications under intensive feeding, aiming to optimize the efficient utilization of dietary fiber and energy. Principal Coordinate Analysis (PCoA) illustrates a substantial alteration in the rumen microbial community of naturally grazing yaks when exposed to intensive feeding. The natural grazing group manifests a higher prevalence of Firmicutes and Bacteroidetes, while the intensive feeding group exhibits heightened levels of Prevotella in the rumen. The Rikenellaceae _ RC9 _ gut_ group, associated with mycobacteria, prevails more abundantly in the natural grazing setting. PICRUSt2 analysis indicates that intensive feeding induces bacterial gene overexpression linked to protein metabolism. Rumen fungi showcase heightened diversity under intensification. Intensive feeding results in an augmented abundance of non-fiber-degrading bacteria and semi-fiber-degrading bacteria, accompanied by elevated concentrations of Volatile Fatty Acids (VFA).

Discussion

These findings yield novel insights into the shifts in the rumen microflora of yaks acclimated to intensive feeding in high-altitude environments, provide an important reference for the nutritional regulation of supplemental feeding of natural grazing yaks in the cold season, ultimately contributing to their enhanced growth.

Multi-omics analyses reveal rumen microbes and secondary metabolites that are unique to livestock species

Ruminant livestock, including cattle, sheep, goats, and camels, possess a distinctive digestive system with complex microbiota communities critical for feed conversion and secondary metabolite production, including greenhouse gases. Yet, there is limited knowledge regarding the diversity of rumen microbes and metabolites benefiting livestock physiology, productivity, climate impact, and defense mechanisms across ruminant species. In this study, we utilized metataxonomics and metabolomics data from four evolutionarily distinct livestock species, which had fed on diverse plant materials like grass, shrubs, and acacia trees, to uncover the unique signature microbes and secondary metabolites. We established the presence of a distinctive anaerobic fungus called Oontomyces in camels, while cattle exhibited a higher prevalence of unique microbes like Psychrobacter, Anaeromyces, Cyllamyces, and Orpinomyces. Goats hosted Cleistothelebolus, and Liebetanzomyces was unique to sheep. Furthermore, we identified a set of conserved core microbes, including Prevotella, Rickenellaceae, Cladosporium, and Pecoramyces, present in all the ruminants, irrespective of host genetics and dietary composition. This underscores their indispensable role in maintaining crucial physiological functions. Regarding secondary metabolites, camel's rumen is rich in organic acids, goat's rumen is rich in alcohols and hydrocarbons, sheep's rumen is rich in indoles, and cattle's rumen is rich in sesquiterpenes. Additionally, linalool propionate and terpinolene were uniquely found in sheep rumen, while valencene was exclusive to cattle. This may suggest the existence of species-specific microbes and metabolites that require host rumen-microbes' environment balance. These results have implications for manipulating the rumen environment to target specific microbes and secondary metabolite networks, thereby enhancing livestock productivity, resilience, reducing susceptibility to vectors, and environmentally preferred livestock husbandry.IMPORTANCERumen fermentation, which depends on feed components and rumen microbes, plays a crucial role in feed conversion and the production of various metabolites important for the physiological functions, health, and environmental smartness of ruminant livestock, in addition to providing food for humans. However, given the complexity and variation of the rumen ecosystem and feed of these various livestock species, combined with inter-individual differences between gut microbial communities, how they influence the rumen secondary metabolites remains elusive. Using metagenomics and metabolomics approaches, we show that each livestock species has a signature microbe(s) and secondary metabolites. These findings may contribute toward understanding the rumen ecosystem, microbiome and metabolite networks, which may provide a gateway to manipulating rumen ecosystem pathways toward making livestock production efficient, sustainable, and environmentally friendly.

Rumen fermentation and microbiota in Shami goats fed on condensed tannins or herbal mixture

BACKGROUND

Phytochemical compounds can modify the rumen microbiome and improve rumen fermentation. This study evaluated the impact of supplementation with tannin and an herbal mixture containing ginger (Zingiber officinale), garlic (Allium sativum), Artemisia (Artemisia vulgaris), and turmeric (Curcuma longa) on the rumen fermentation and microbiota, and histology of rumen tissue of goats. Eighteen Shami male goats were divided into three groups (n = 6): non-supplemented animals fed the basal diet (C, control); animals fed basal diet and supplemented with condensed tannin (T); and animals fed basal diet and supplemented with herbal mixture (HM). Each animal received a basal diet composed of Alfalfa hay and a concentrate feed mixture.

RESULTS

Group HM revealed higher (P < 0.05) rumen pH, total volatile fatty acids (VFA), acetic, propionic, isobutyric, butyric, isovaleric, and valeric. Principal Co-ordinate analysis (PCoA) showed that rumen microbial communities in the control group and supplemented groups were distinct. The supplementation increased (P < 0.05) the relative abundances of phylum Bacteroidota and Proteobacteria and declined (P < 0.05) Firmicutes and Fibrobacterota. Additionally, the dominant genus Prevotella and Rikenellaceae RC9 gut group were increased (P < 0.05) and the family Ruminococcaceae was declined (P < 0.05) due to the supplementation. The supplementation decreased (P < 0.05) the archaeal genus Methanobrevibacter and increased (P < 0.05) Candidatus Methanomethylophilus. Tannin supplementation in T group shortened the rumen papillae.

CONCLUSIONS

The results revealed that the herbal mixture might be used to alter the rumen microbiota to improve rumen fermentation.

Bacterial community and diversity in the rumen of 11 Mongolian cattle as revealed by 16S rRNA amplicon sequencing

Through microorganism in the rumen of ruminant, plant fiber can be converted to edible food such as meat and milk. Ruminants had a rich and complex microbial community within the rumen, and the bacteria comprised the dominant proportion of the ruminal microbes. High-throughput sequencing offered a viable solution for the study of rumen microbes. In this study, rumen fluid samples were taken from 11 cattle from Inner Mongolian, the DNA of 11 rumen fluid samples were extracted and bacterial amplicons of the V4 regions of 16S rRNA were subjected to Illumina sequencing. More than 90,000 raw reads and 60,000 effect Tags per sample were obtained. 28,122 operational taxonomic units (OTUs) were observed from 11 samples, in average 2557 ± 361 OTUs for each sample. Bacteroidetes (44.41 ± 7.31%), Firmicutes (29.07 ± 3.78%), and Proteobacteria (7.18 ± 5.63%) were the dominant phyla among the bacteria of rumen, accounting for 82%. At the genus level, the highest relative abundance was Prevotella. Their functions were predicted using the Kyoto Encyclopedia of Genes and Genomes (KEGG). The results showed that they included metabolism, genetic information processing, environmental information processing and cellular processes. It explored the bacterial community diversity and composition of the rumen of Mongolian cattle. On the whole, our research showed that there was a high diversity as well as rich bacterial flora function of rumen bacteria in Mongolian cattle. Meanwhile, these findings provided information for further studies on the relationship between the community, diversity, functions of rumen bacteria and the nutritional physiological functions of the host.

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

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

Multi-omics revealed the effects of dietary energy levels on the rumen microbiota and metabolites in yaks under house-feeding conditions

Yak (Bos grunniens) is a unique large ruminant species in the Qinghai-Tibetan Plateau (QTP). Changing the energy levels of their rations can significantly improve their growth performance. Therefore, studying the effects of dietary energy levels on the rumen microflora and metabolites of yak is crucial for enhancing the development of the yak industry. Currently, there is a lack of understanding regarding the impact of feeding energy diets on rumen fermentation parameters, microbial functions, and metabolites. This study was designed to determine the appropriate energy level for feeding yak. Three test diets with metabolizable energy levels of 7.57 MJ/kg, 9.44 MJ/kg, and 11.9 MJ/kg were used and the concentration of volatile fatty acids (VFA) in rumen fluid was measured. The microbial communities, functions, and metabolites in yaks were studied by 16S rRNA sequencing, metagenome, and LC-MS non-targeted metabolomics to investigate the relationships among rumen fermentation parameters, microbial diversity, and metabolites. Ration energy levels significantly affect total VFA, acetate, propionate, butyrate, iso-valerate, valerate, and acetate/propionate (p < 0.05). At the phylum level, the dominant phyla in all three treatment groups were Bacteroidota, Firmicutes, and Actinobacteriota. At the genus level, the abundance of the unclassified_o__Bacteroidales, norank_f_Muribaculaceae, Lachnospiraceae_NK4A136_group, and Family _XIII_AD3011_group showed significant differences (p < 0.05) and were significantly correlated with differential metabolites screened for phosphatidylcholine [PC(16:0/0:0), PC(18:3/0:0)], uridine 3'-monophosphate, and adenosine monophosphate, etc. CAZymes family analysis showed that GHs and CEs differed significantly among the three groups. In addition, differential metabolites were mainly enriched in the pathways of lipid metabolism, nucleotide metabolism, and biosynthesis of other secondary metabolites, and the concentrations of differential metabolites were correlated with microbial abundance. In summary, this study analyzed the effects of ration energy levels on rumen microorganisms and metabolites of yaks and their relationships. The results provided a scientific basis for the selection of dietary energy for yaks in the house feeding period in the future.

Linking active rectal mucosa-attached microbiota to host immunity reveals its role in host-pathogenic STEC O157 interactions

The rectal-anal junction (RAJ) is the major colonization site of Shiga toxin-producing Escherichia coli (STEC) O157 in beef cattle, leading to transmission of this foodborne pathogen from farms to food chains. To date, there is limited understanding regarding whether the mucosa-attached microbiome has a profound impact on host-STEC interactions. In this study, the active RAJ mucosa-attached microbiota and its potential role in host immunity-STEC commensal interactions were investigated using RAJ mucosal biopsies collected from calves orally challenged with two STEC O157 strains with or without functional stx2a (stx2a+ or stx2a-). The results revealed that shifts of microbial diversity, topology, and assembly patterns were subjected to stx2a production post-challenge and Paeniclostridium and Gallibacterium were the keystone taxa for both microbial interactions and assembly. Additional mucosal transcriptome profiling showed stx2a-dependent host immune responses (i.e. B- and T-cell signaling and antigen processing and presentation) post-challenge. Further integrated analysis revealed that mucosa-attached beneficial microbes (i.e. Provotella, Faecalibacterium, and Dorea) interacted with host immune genes pre-challenge to maintain host homeostasis; however, opportunistic pathogenic microbes (i.e. Paeniclostridium) could interact with host immune genes after the STEC O157 colonization and interactions were stx2a-dependent. Furthermore, predicted bacterial functions involved in pathogen (O157 and Paeniclostridium) colonization and metabolism were related to host immunity. These findings suggest that during pathogen colonization, host-microbe interactions could shift from beneficial to opportunistic pathogenic bacteria driven and be dependent on the production of particular virulence factors, highlighting the potential regulatory role of mucosa-attached microbiota in affecting pathogen-commensal host interactions in calves with STEC O157 infection.

The Effects of Composite Alkali-Stored Spent Hypsizygus marmoreus Substrate on Carcass Quality, Rumen Fermentation, and Rumen Microbial Diversity in Goats

The objective of this study was to investigate the effects of composite alkali-stored spent Hypsizygus marmoreus substrate (SHMS) on carcass quality, rumen fermentation, and rumen microbial diversity in goats. Twenty-four 6-month-old Chuanzhong black goats with similar body weights (20 ± 5 kg) were selected and randomly divided into four groups (n = 6 per group) and received four treatments: 0% (control group, CG); 20% (low-addition group, LG); 30% (moderate-addition group, MG); and 40% (high-addition group, HG) of SHMS-replaced silage corn and oat hay. The experiment lasted for 74 days (including a 14 d adaptation period and a 60 d treatment period). The results of this study showed that MG and HG significantly improved the marble score of goat meat (p < 0.05). The flesh color score significantly increased in each group (p < 0.05). The fat color scores significantly increased in LG and MG (p < 0.05). There were no significant effects on the pH value or shear force of the longissimus dorsi in each group (p > 0.05). The cooking loss in MG was higher than that in CG (p < 0.05). The histidine and tyrosine contents in each group of muscles significantly increased (p < 0.05), with no significant effect on fatty acids (p > 0.05). The rumen pH of MG significantly decreased (p < 0.05), while the total volatile fatty acids (TVFAs) and ammoniacal nitrogen (NH3-N) increased by 44.63% and 54.50%, respectively. The addition of the SHMS altered both the alpha and beta diversities of the rumen microbiota and significant differences in the composition and structure of the four microbial communities. The dominant bacterial phylum in each group were Firmicutes and Bacteroidetes, with Prevotella 1 as the dominant bacterial genus. Correlation analysis revealed that rumen bacteria are closely related to the animal carcass quality and rumen fermentation. In the PICRUSt prediction, 21 significantly different pathways were found, and the correlation network showed a positive correlation between the Prevotella 1 and 7 metabolic pathways, while the C5-branched dibasic acid metabolism was positively correlated with nine bacteria. In summary, feeding goats with an SHMS diet can improve the carcass quality, promote rumen fermentation, and alter the microbial structure. The research results can provide a scientific reference for the utilization of SHMS as feed in the goat industry.

Effects of dietary supplementation of a blend of Saccharomyces cerevisiae, multiple live probiotic bacteria, and their fermentation products on performance, health, and rumen bacterial community of newly weaned beef steers during a 56-d receiving period

We examined the effects of a blend of Saccharomyces cerevisiae, multiple live probiotic bacteria, and their fermentation products on performance, health, and the ruminal bacterial community of newly weaned beef steers during a 56-d receiving period. Forty newly weaned Angus crossbred steers (221 ± 25.6 kg BW; 180 ± 17 d of age) were stratified by body weight (BW) into four pens (10 steers per pen) such that each pen had a similar average BW at the beginning of the experiment. The pens were randomly assigned to receive a corn silage basal diet (CON; n = 20) or the basal diet supplemented with 9 g/steer/d of PRO feed additive (PRO; n = 20). The PRO additive is a blend of S. cerevisiae and the fermentation products of Enterococcus faecium, Bacillus licheniformis, B. subtilis, Lactobacillus animalis, and Propionibacterium freudenreichii. The DMI and water consumed were monitored using the GrowSafe intake nodes and custom flow meters, respectively. BWs were recorded weekly to calculate average daily gain (ADG). Before morning feeding, 10 mL of blood was taken from each steer on days 0-7, and thereafter weekly for analyses of immune cells, plasma glucose, and NEFAs. On day 56, rumen fluid samples (200 mL each) were collected from all the steers for microbiome analysis. Over the 56-d receiving period, the supplemental PRO had no effects on DMI, water intake, or ADG. However, compared to CON, beef steers fed supplemental PRO tended to have greater ADG (P = 0.08) and BW (P = 0.07) during the first 14 d of the study. There was a treatment × day interaction (P ≤ 0.05) for WBC, neutrophils and monocytes over the 56 d such that beef steers fed supplemental PRO had lower blood concentrations on certain days during the first 7 d after weaning, indicating reduced inflammation or stress response. The results of the rumen microbiome analysis revealed that the relative abundance of complex fiber degrading or obligate proton-reducing bacterial genera such as Bacteroides, Ruminococcus gauvreauii group, Desulfovibrio, Syntrophococcus, and Acetitomaculum were greater (P ≤ 0.05) in beef steers fed supplemental PRO compared to CON. This study demonstrated that dietary supplementation of PRO improved the growth performance, reduced stress or inflammatory response during the initial days after weaning, and altered the ruminal bacterial community toward increased relative abundance of bacterial genera associated with improved rumen function.

Response of rumen fermentation and microbiota to dietary supplementation of sodium selenite and bio-nanostructured selenium in lactating Barki sheep

Dietary selenium (Se) sources affects the structure of the rumen microbial community and rumen fermentation. This study evaluated the effects of sodium selenite (SS) and bio-nanostructured selenium (SeNSM) on rumen fermentation and structure of rumen microbial community of lactating Barki ewes. Twenty one lactating Barki ewes were assigned into three groups based on their body weight and milk yield. The experiment lasted for 50 days, whenever, the control group was fed basal diet; group SS received basal diets plus sodium selenite as inorganic source of Se; and group SeNSM received basal diet plus organic selenium bio-nanostructured. Ruminal pH and volatile Fatty Acids (VFA) was lower (P < 0.05) in SeNSM group compared to control. Principle Coordinate Analysis separated the microbial communities into three clusters based on feeding treatment. The bacterial community was dominated by phylum Bacteroidetes and Firmicutes that were affected (P < 0.05) by Se sources. Specifically Bacteriodetes was higher (P < 0.05) in SS and SeNSM groups; and Firmicutes was higher (P < 0.05) in the control group. Moreover, the predominant bacterial genera were Prevotella, Rikenellaceae RC9 gut group, Unclassified_Bacteroidales, which were higher (P < 0.05) in SeNSM group. The methanogenic community belonged to phylum Euryarchaeota and was significantly decreased (P < 0.05) by Se supplementation. Principal component analysis based on rumen fermentation parameters, and relative abundances of bacteria and methanogens revealed three distinct clusters. These findings suggest that Se supplementation affected the relative abundances of dominant bacterial groups, declined rumen methanogens and SeNSM supplementation showed some positive impacts on some fibrolytic bacteria.

New insights into the genetic predisposition of brucellosis and its effect on the gut and vaginal microbiota in goats

Goats contribute significantly to the global food security and industry. They constitute a main supplier of meat and milk for large proportions of people in Egypt and worldwide. Brucellosis is a zoonotic infectious disease that causes a significant economic loss in animal production. A case-control genome-wide association analysis (GWAS) was conducted using the infectious status of the animal as a phenotype. The does that showed abortion during the last third period of pregnancy and which were positive to both rose bengal plate and serum tube agglutination tests, were considered as cases. Otherwise, they were considered as controls. All animals were genotyped using the Illumina 65KSNP BeadChip. Additionally, the diversity and composition of vaginal and fecal microbiota in cases and controls were investigated using PCR-amplicone sequencing of the V4 region of 16S rDNA. After applying quality control criteria, 35,818 markers and 66 does were available for the GWAS test. The GWAS revealed a significantly associated SNP (P = 5.01 × 10-7) located on Caprine chromosome 15 at 29 megabases. Four other markers surpassed the proposed threshold (P = 2.5 × 10-5). Additionally, fourteen genomic regions accounted for more than 0.1% of the variance explained by all genome windows. Corresponding markers were located within or in close vicinity to several candidate genes, such as ARRB1, RELT, ATG16L2, IGSF21, UBR4, ULK1, DCN, MAPB1, NAIP, CD26, IFIH1, NDFIP2, DOK4, MAF, IL2RB, USP18, ARID5A, ZAP70, CNTN5, PIK3AP1, DNTT, BLNK, and NHLRC3. These genes play important roles in the regulation of immune responses to the infections through several biological pathways. Similar vaginal bacterial community was observed in both cases and controls while the fecal bacterial composition and diversity differed between the groups (P < 0.05). Faeces from the control does showed a higher relative abundance of the phylum Bacteroidota compared to cases (P < 0.05), while the latter showed more Firmicutes, Spirochaetota, Planctomycetota, and Proteobacteria. On the genus level, the control does exhibited higher abundances of Rikenellaceae RC9 gut group and Christensenellaceae R-7 group (P < 0.05), while the infected does revealed higher Bacteroides, Alistipes, and Prevotellaceae UCG-003 (P < 0.05). This information increases our understanding of the genetics of the susceptibility to Brucella in goats and may be useful in breeding programs and selection schemes that aim at controlling the disease in livestock.

Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle

The biological mechanisms underlying meat quality remain unclear. Currently, many studies report that the gastrointestinal microbiota is essential for animal growth and performance. However, it is uncertain which bacterial species are specifically associated with the meat quality traits. In this study, 16S rDNA and metagenomic sequencing were performed to explore the composition and function of microbes in various gastrointestinal segments of Tan sheep and Dorper sheep, as well as the relationship between microbiota and meat quality (specifically, the fatty acid content of the muscle). In the ruminal, duodenal, and colonic microbiome, several bacteria were uniquely identified in respective breeds, including Agrobacterium tumefaciens, Bacteroidales bacterium CF, and several members of the family Oscillospiraceae. The annotation of GO, KEGG, and CAZYme revealed that these different bacterial species were linked to the metabolism of glucose, lipids, and amino acids. Additionally, our findings suggested that 16 microbial species may be essential to the content of fatty acids in the muscle, especially C12:0 (lauric acid). 4 bacterial species, including Achromobacter xylosoxidans, Mageeibacillus indolicus, and Mycobacterium dioxanotrophicus, were positively correlated with C12:0, while 13 bacteria, including Methanobrevibacter millerae, Bacteroidales bacterium CF, and Bacteroides coprosuis were negatively correlated with C12:0. In a word, this study provides a basic data for better understanding the interaction between ruminant gastrointestinal microorganisms and the meat quality traits of hosts.

Astragalus additive in feed improved serum immune function, rumen fermentation and the microbiota structure of early-weaned lambs

AIM

The purpose of this study was to determine the mechanism of Astragalus activity on the immune function, rumen microbiota structure, and rumen fermentation of early-weaned lambs.

METHODS AND RESULTS

Thirty healthy early-weaned lambs with similar body weights (17.42 ± 2.02 kg) were selected for the feeding experiment. The control group (KB) was fed a basal diet, and the Astragalus group (HQ) was fed 0.3% Astragalus additive on the basis of a basic diet. The formal trial period was 60 days. The results showed that the concentrations of blood immunoglobulin A (IgA) and immunoglobulin M (IgM) in the HQ group were significantly higher than those in the KB group (P < 0.05). Compared with the KB group, the concentrations of acetic acid, butyric acid, and total volatile fatty acids (VFAs) in the HQ group were higher (P < 0.01). The expression levels of the rumen epithelial-related genes MCT1, MCT4, NHE2, and ZO1 in the Astragalus group were significantly higher than those in the KB group (P < 0.05). 16S rRNA analysis showed that at the phylum level, Bacteroidetes in the HQ group significantly increased (P < 0.01); at the genus level, Prevotella (P < 0.01) and Succiniclasticum (P < 0.01) in the HQ group were found at significantly higher abundances than those in the KB group, and the results of microbiota gene and function prediction showed that "energy metabolism," "glycan biosynthesis and metabolic" pathways were significantly enriched in the HQ group (P < 0.05).

CONCLUSION

As a feed additive, Astragalus can improve the immunity of early-weaned lambs, the structure of the rumen microbiota of lambs, and the fermentation capacity of the rumen.

Effects of different feeding systems on ruminal fermentation, digestibility, methane emissions, and microbiota of Hanwoo steers

This study evaluates how different feeding systems impact ruminal fermentation, methane production, and microbiota of Hanwoo steers native to Korea. In a replicated 2 × 2 crossover design over 29 days per period, eight Hanwoo steers (507.1 ± 67.4 kg) were fed twice daily using a separate feeding (SF) system comprising separate concentrate mix and forage or total mixed rations (TMR) in a 15:85 ratio. The TMR-feeding group exhibited a considerable neutral detergent fiber digestibility increase than the SF group. However, ruminal fermentation parameters and methane production did not differ between two feeding strategies. In addition, TMR-fed steers expressed elevated Prevotellaceae family, Christensenellaceae R-7 group, and an unidentified Veillonellaceae family genus abundance in their rumen, whereas SF-fed steers were rich in the Rikenellaceae RC9 gut group, Erysipelotrichaceae UCG-004, and Succinivibrio. Through linear regression modeling, positive correlations were observed between the Shannon Diversity Index and the SF group's dry matter intake and methane production. Although feeding systems do not affect methane production, they can alter ruminal microbes. These results may guide future feeding system investigations or ruminal microbiota manipulations as a methane-mitigation practice examining different feed ingredients.

The effect of early colonized gut microbiota on the growth performance of suckling lambs

The early colonized gut microbiota during the newborn period has been reported to play important roles in the health and immunity of animals; however, whether they can affect the growth performance of suckling lambs is still unclear. In this study, a total of 84 newborn lambs were assigned into LF-1 (top 15%), LF-2 (medium 70%), and LF-3 (bottom 15%) groups according to their average body weight gain at 30 days of age. Fecal samples of lambs (LF) as well as feces (MF), vagina (VAG), colostrum (COL), teat skin (TEAT) samples of ewes, and the air sediment (AIR) in the delivery room were collected 72 h after birth, and then the 16S rRNA gene was sequenced on the Illumina MiSeq platform. The results showed that the early colonized gut microbiota had a significant effect on the growth performance of suckling lambs with alpha and beta diversity (p < 0.05), and we observed that the contribution of early colonized bacteria on the growth performance of lambs increased with age (from BW30 at 25.35% to BW45 at 31.10%; from ADG30 at 33.02% to ADG45 at 39.79% by measuring the relative effects of factors that influence growth performance). The early colonized gut microbiota of suckling lambs with high growth performance was similar to that in VAG, MF, and AIR (p < 0.05). With the RandomForest machine learning algorithm, we detected 11, 11, 6, and 4 bacterial taxa at the genus level that were associated with BW30, BW45, ADG30, and ADG45 of suckling lambs, respectively, and the correlation analysis showed that Butyricicoccus, Ruminococcus_gnavus_group, Ruminococcaceae_Other, and Fusobacterium could significantly affect the growth performance (BW30, BW45, ADG30, and ADG45) of suckling lambs (p < 0.05). In conclusion, the early colonized gut microbiota could significantly affect the growth performance of suckling lambs, and targeting the early colonized gut microbiota might be an alternative strategy to improve the growth performance of suckling lambs.

Ruminal and feces metabolites associated with feed efficiency, water intake and methane emission in Nelore bulls

The objectives of this study were twofold: (1) to identify potential differences in the ruminal and fecal metabolite profiles of Nelore bulls under different nutritional interventions; and (2) to identify metabolites associated with cattle sustainability related-traits. We used different nutritional interventions in the feedlot: conventional (Conv; n = 26), and by-product (ByPr, n = 26). Thirty-eight ruminal fluid and 27 fecal metabolites were significantly different (P < 0.05) between the ByPr and Conv groups. Individual dry matter intake (DMI), residual feed intake (RFI), observed water intake (OWI), predicted water intake (WI), and residual water intake (RWI) phenotypes were lower (P < 0.05) in the Conv group, while the ByPr group exhibited lower methane emission (ME) (P < 0.05). Ruminal fluid dimethylamine was significantly associated (P < 0.05) with DMI, RFI, FE (feed efficiency), OWI and WI. Aspartate was associated (P < 0.05) with DMI, RFI, FE and WI. Fecal C22:1n9 was significantly associated with OWI and RWI (P < 0.05). Fatty acid C14:0 and hypoxanthine were significantly associated with DMI and RFI (P < 0.05). The results demonstrated that different nutritional interventions alter ruminal and fecal metabolites and provided new insights into the relationship of these metabolites with feed efficiency and water intake traits in Nelore bulls.

Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing

Asian elephant (Elephas maximus) is the national symbol of Thailand and linked to Thai history and culture for centuries. The elephant welfare improvement is one of the major components to achieve sustainable captive management. Microbiome inhabiting digestive tracts have been shown with symbiotic relations to host health. This work provided high-resolution microbiome profiles of 32 captive elephants at a species level by utilizing full-length 16S rRNA gene nanopore sequencing. Eleven common uncultured bacterial species were found across elephants fed with solid food including uncultured bacterium Rikenellaceae RC9 gut group, Kiritimatiellae WCHB1-41, Phascolarctobacterium, Oscillospiraceae NK4A214 group, Christensenellaceae R-7 group, Oribacterium, Oscillospirales UCG-010, Lachnospiraceae, Bacteroidales F082, uncultured rumen Rikenellaceae RC9 gut group, and Lachnospiraceae AC2044 group. We observed microbiome shifts along the age classes of baby (0-2 years), juvenile (2-10 years), and adult (> 10 years). Interestingly, we found distinct microbiome profiles among adult elephants fed with a local palm, Caryota urens, as a supplement. Potential beneficial microbes have been revealed according to the age classes and feed diets. The retrieved microbiome data could be provided as good baseline microbial profiles for monitoring elephant health, suggesting further studies towards dietary selection suitable for each age class and the use of local supplementary diets.

Single-cell transcriptome and metagenome profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants

The rumen undergoes developmental changes during maturation. To characterize this understudied dynamic process, we profiled single-cell transcriptomes of about 308,000 cells from the rumen tissues of sheep and goats at 17 time points. We built comprehensive transcriptome and metagenome atlases from early embryonic to rumination stages, and recapitulated histomorphometric and transcriptional features of the rumen, revealing key transitional signatures associated with the development of ruminal cells, microbiota, and core transcriptional regulatory networks. In addition, we identified and validated potential cross-talk between host cells and microbiomes and revealed their roles in modulating the spatiotemporal expression of key genes in ruminal cells. Cross-species analyses revealed convergent developmental patterns of cellular heterogeneity, gene expression, and cell-cell and microbiome-cell interactions. Finally, we uncovered how the interactions can act upon the symbiotic rumen system to modify the processes of fermentation, fiber digestion, and immune defense. These results significantly enhance understanding of the genetic basis of the unique roles of rumen.

Differences in serum metabolome profile explain individual variation in growth performance of young goats

High growth rates and body weight are important traits of young dairy goats that can shorten generation intervals, improve animal performance, and increase economic benefits. In the present study, ninety-nine, 6-month-old, female goats were fed with the same diet and kept under the same management condition. The ten goats with highest average daily gain (ADG, HADG, 135.27 ± 4.59 g/d) and ten goats with lowest ADG (LADG, 87.74 ± 3.13 g/d) were selected to identify the key serum metabolites associated with ADG, and to investigate the relationships of serum metabolome profiles with digestive tract microbiota. The results showed that a total of 125 serum metabolites were significantly different between HADG and LADG. Of these, 43 serum metabolites were significantly higher levels in HADG, including D-ornithine, l-glutamine, L-histidine, carnosine, LysoPC (16:1(9Z)/0:0), DCTP and hydroxylysine, while, 82 serum metabolites were significantly higher levels in LADG, including P-salicylic acid and deoxycholic acid 3-glucuronide. Pathway analysis indicated that these different metabolites were mainly involved in amino acid and lipid metabolism. Furthermore, Spearman's rank correlation analysis revealed that these differential serum metabolites were correlated with ADG and ADG-related bacteria. Notably, serum hydroxylysine and L-histidine could be used as biomarkers for distinguishing HADG and LADG goats, with an accuracy of >92.0%. SIGNIFICANCE: Our study confirms that individual microbiota and metabolic differences contribute to the variations of growth rate in young goats. Some serum metabolites may be useful in improving the growth performance of young goats, which provides directions for developing further nutritional regulation in the goat industry to achieve healthy feeding and efficiency enhancement.

Multi-omics revealed the long-term effect of ruminal keystone bacteria and the microbial metabolome on lactation performance in adult dairy goats

BACKGROUND

The increased growth rate of young animals can lead to higher lactation performance in adult goats; however, the effects of the ruminal microbiome on the growth of young goats, and the contribution of the early-life rumen microbiome to lifelong growth and lactation performance in goats has not yet been well defined. Hence, this study assessed the rumen microbiome in young goats with different average daily gains (ADG) and evaluated its contribution to growth and lactation performance during the first lactation period.

RESULTS

Based on monitoring of a cohort of 99 goats from youth to first lactation, the 15 highest ADG (HADG) goats and 15 lowest ADG (LADG) goats were subjected to rumen fluid microbiome and metabolome profiling. The comparison of the rumen metagenome of HADG and LADG goats revealed that ruminal carbohydrate metabolism and amino acid metabolism function were enhanced in HADG goats, suggesting that the rumen fluid microbiome of HADG goats has higher feed fermentation ability. Co-occurrence network and correlation analysis revealed that Streptococcus, Candidatus Saccharimonans, and Succinivibrionaceae UCG-001 were significantly positively correlated with young goats' growth rates and some HADG-enriched carbohydrate and protein metabolites, such as propionate, butyrate, maltoriose, and amino acids, while several genera and species of Prevotella and Methanogens exhibited a negative relationship with young goats' growth rates and correlated with LADG-enriched metabolites, such as rumen acetate as well as methane. Additionally, some functional keystone bacterial taxa, such as Prevotella, in the rumen of young goats were significantly correlated with the same taxa in the rumen of adult lactation goats. Prevotella also enriched the rumen of LADG lactating goats and had a negative effect on rumen fermentation efficiency in lactating goats. Additional analysis using random forest machine learning showed that rumen fluid microbiota and their metabolites of young goats, such as Prevotellaceae UCG-003, acetate to propionate ratio could be potential microbial markers that can potentially classify high or low ADG goats with an accuracy of prediction of > 81.3%. Similarly, the abundance of Streptococcus in the rumen of young goats could be predictive of milk yield in adult goats with high accuracy (area under the curve 91.7%).

CONCLUSIONS

This study identified the keystone bacterial taxa that influence carbohydrate and amino acid metabolic functions and shape the rumen fluid microbiota in the rumen of adult animals. Keystone bacteria and their effects on rumen fluid microbiota and metabolome composition during early life can lead to higher lactation performance in adult ruminants. These findings suggest that the rumen microbiome together with their metabolites in young ruminants have long-term effect on feed efficiency and animal performance. The fundamental knowledge may allow us to develop advanced methods to manipulate the rumen microbiome and improve production efficiency of ruminants. Video Abstract.

From the perspective of rumen microbiome and host metabolome, revealing the effects of feeding strategies on Jersey Cows on the Tibetan Plateau

Background

Previous studies have discussed the effects of grazing and house feeding on yaks during the cold season when forage is in short supply, but there is limited information on the effects of these feeding strategies on Jersey cows introduced to the Tibetan Plateau. The objective of this study was to use genomics and metabolomics analyses to examine changes in rumen microbiology and organism metabolism of Jersey cows with different feeding strategies.

Methods

We selected 12 Jersey cows with similar body conditions and kept them for 60 days under grazing (n = 6) and house-feeding (n = 6) conditions. At the end of the experiment, samples of rumen fluid and serum were collected from Jersey cows that had been fed using different feeding strategies. The samples were analyzed for rumen fermentation parameters, rumen bacterial communities, serum antioxidant and immunological indices, and serum metabolomics. The results of the study were examined to find appropriate feeding strategies for Jersey cows during the cold season on the Tibetan plateau.

Results

The results of rumen fermentation parameters showed that concentrations of acetic acid, propionic acid, and ammonia nitrogen in the house-feeding group (Group B) were significantly higher than in the grazing group (Group G) (P < 0.05). In terms of the rumen bacterial community 16S rRNA gene, the Chao1 index was significantly higher in Group G than in Group B (P = 0.038), while observed species, Shannon and Simpson indices were not significantly different from the above-mentioned groups (P > 0.05). Beta diversity analysis revealed no significant differences in the composition of the rumen microbiota between the two groups. Analysis of serum antioxidant and immune indices showed no significant differences in total antioxidant capacity between Group G and Group B (P > 0.05), while IL-6, Ig-M , and TNF-α were significantly higher in Group G than in Group B (P < 0.05). LC-MS metabolomics analysis of serum showed that a total of 149 major serum differential metabolites were found in Group G and Group B. The differential metabolites were enriched in the metabolic pathways of biosynthesis of amino acids, protein digestion and absorption, ABC transporters, aminoacyl-tRNA biosynthesis, mineral absorption, and biosynthesis of unsaturated fatty acids. These data suggest that the house-feeding strategy is more beneficial to improve the physiological state of Jersey cows on the Tibetan Plateau during the cold season when forages are in short supply.

Effects of organic and inorganic copper on cecal microbiota and short-chain fatty acids in growing rabbits

Introduction

Copper (Cu) is an essential trace element for the growth of rabbits. This study aimed to investigate the effects of different Cu sources on intestinal microorganisms and short-chain fatty acids (SCFAs) in growing rabbits.

Methods

The experimental animals were randomly divided into four experimental groups, each group comprised eight replicates, with six rabbits (half male and half female) per replicate. And they were fed diets was composed by mixing the basal diet with 20 mg/kg Cu from one of the two inorganic Cu (cupric sulfate and dicopper chloride trihydroxide) or two organic Cu (cupric citrate and copper glycinate). Cecal contents of four rabbits were collected from four experimental groups for 16S rDNA gene amplification sequencing and gas chromatography analysis.

Results

Our results indicate that the organic Cu groups were less variable than the inorganic Cu groups. Compared with the inorganic Cu groups, the CuCit group had a significantly higher relative abundance of Rikenella Tissierella, Lachnospiraceae_NK3A20_group, Enterococcus, and Paeniclostridium, while the relative abundance of Novosphingobium and Ruminococcus were significantly lower (p < 0.05). The SCFAs level decreased in the organic Cu groups than in the inorganic Cu groups. Among the SCFAs, the butyric acid level significantly decreased in the CuCit group than in the CuSO₄ and CuCl₂ groups. The relative abundance of Rikenella and Turicibacter genera was significantly negatively correlated with the butyric acid level in the CuCit group compared with both inorganic Cu groups. These results revealed that the organic Cu (CuCit) group had an increased abundance of Rikenella, Enterococcus, Lachnospiraceae_NK3A20_group, and Turicibacter genera in the rabbit cecum.

Discussion

In summary, this study found that organic Cu and inorganic Cu sources had different effects on cecal microbiota composition and SCFAs in rabbits. The CuCit group had the unique higher relative abundance of genera Rikenella and Lachnospiraceae_NK3A20_group, which might be beneficial to the lower incidence of diarrhea in rabbits.

Comparison of Fecal Antimicrobial Resistance Genes in Captive and Wild Asian Elephants

The Asian elephant (Elephas maximus) is a flagship species of tropical rainforests, and it has generated much concern. In this case, the gut bacterial communities of captive and wild Asian elephants are particularly noteworthy. We aim to compare the differences in bacterial diversity and antibiotic resistance gene (ARG) subtypes in fecal samples of Asian elephants from different habitats, which may affect host health. Analyses reveal that differences in the dominant species of gut bacteria between captive and wild Asian elephants may result in significant differences in ARGs. Network analysis of bacterial communities in captive Asian elephants has identified potentially pathogenic species. Many negative correlations in network analysis suggest that different food sources may lead to differences in bacterial communities and ARGs. Results also indicate that the ARG levels in local captive breeding of Asian elephants are close to those of the wild type. However, we found that local captive elephants carry fewer ARG types than their wild counterparts. This study reveals the profile and relationship between bacterial communities and ARGs in different sources of Asian elephant feces, providing primary data for captive breeding and rescuing wild Asian elephants.

Effects of forage type on the rumen microbiota, growth performance, carcass traits, and meat quality in fattening goats

Forages fed to goats influence ruminal microbiota, and further contribute to affect growth performance, meat quality and its nutritional composition. Our objective for current study was to investigate the effects of different forages on growth performance, carcass traits, meat nutritional composition, rumen microflora, and the relationships between key bacteria and amino acids and fatty acids in the longissimus dorsi and semimembranosus muscles of goats. Boer crossbred goats were separately fed commercial concentrate diet supplemented with Hemarthria altissima (HA), Pennisetum sinese (PS), or forage maize (FG), and then slaughtered 90 days after the beginning of the experiment. Growth performances did not vary but carcass traits of dressing percentage, semi-eviscerated slaughter percentage, and eviscerated slaughter percentage displayed significant difference with the treatment studied. Meats from goats fed forage maize, especially semimembranosus muscles are rich in essential amino acids, as well as an increase in the amount of beneficial fatty acids. Our 16S rRNA gene sequencing results showed that the Firmicutes, Bacteroidetes, and Proteobacteria were the most dominant phyla in all groups but different in relative abundance. Further, the taxonomic analysis and linear discriminant analysis effect size (LEfSe) identified the specific taxa that were differentially represented among three forage treatments. The spearman's correlation analysis showed that rumen microbiota was significantly associated with the goat meat nutritional composition, and more significant positive correlations were identified in semimembranosus muscles when compared with longissimus dorsi muscles. More specifically, the lipid metabolism-related bacteria Rikenellaceae_RC9_gut_group showed positively correlated with meat amino acid profile, while genera Oscillospiraceae_UCG-005 were positively correlated with fatty acid composition. These bacteria genera might have the potential to improve nutritional value and meat quality. Collectively, our results showed that different forages alter the carcass traits, meat nutritional composition, and rumen microflora in fattening goats, and forage maize induced an improvement in its nutritional value.

Effects of dietary crude protein levels in the concentrate supplement after grazing on rumen microbiota and metabolites by using metagenomics and metabolomics in Jersey-yak

Introduction

The crude protein level in the diet will affect the fermentation parameters, microflora, and metabolites in the rumen of ruminants. It is of great significance to study the effect of crude protein levels in supplementary diet on microbial community and metabolites for improving animal growth performance. At present, the effects of crude protein level in supplementary diet on rumen fermentation parameters, microbial community, and metabolites of Jersey-Yak (JY) are still unclear.

Methods

The purpose of this experiment was to study the appropriate crude protein level in the diet of JY. The rumen fermentation indexes (volatile fatty acids and pH) were determined by supplementary diets with crude protein levels of 15.16 and 17.90%, respectively, and the microbial community and metabolites of JYs were analyzed by non-target metabonomics and metagenome sequencing technology, and the changes of rumen fermentation parameters, microbial flora, and metabolites in the three groups and their interactions were studied.

Results and Discussion

The crude protein level in the supplementary diet had significant effects on pH, valeric acid, and the ratio of acetic acid to propionic acid (p < 0.05). The protein level had no significant effect on the dominant microflora at the phylum level (p > 0.05), and all three groups were Bacteroides and Firmicutes. The results of metabolite analysis showed that the crude protein level of supplementary diet significantly affected the metabolic pathways such as Bile secretion and styrene degradation (p < 0.05), and there were different metabolites between the LP group and HP group, and these different metabolites were related to the dominant microbial to some extent. To sum up, in this experiment, the effects of crude protein level in supplementary diet on rumen microorganisms and metabolites of JY and their relationship were studied, which provided the theoretical basis for formulating a more scientific and reasonable supplementary diet in the future.

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.

The gas production, ruminal fermentation parameters, and microbiota in response to Clostridium butyricum supplementation on in vitro varying with media pH levels

The aim of this study was to investigate the gas production (GP), dry matter disappearance (DMD), fermentation parameters, and rumen microbiota in response to Clostridium butyricum (CB) supplementation in batch culture using a high forage substrate. The doses of CB were supplemented at 0 (Control), 0.5 × 10⁶, 1 × 10⁶, and 2 × 10⁶  CFU/bottle, respectively, at either media pH 6.0 or pH 6.6. The 16S rRNA gene sequencing was used to detect the microbiota of fermentation culture in control and 1 × 10⁶  CFU/bottle after 24 h of incubation. The results showed that the GP (p < 0.001), DMD (p = 0.008), total volatile fatty acid (VFA) concentration (p < 0.001), acetate to propionate ratio (p < 0.001), and NH₃-N concentration (p < 0.001) were greater at media pH 6.6 than pH 6.0. Furthermore, the linearly increased DMD (pH 6.0, p = 0.002; pH 6.6, p < 0.001) and quadratically increased butyrate proportion (pH 6.0, p = 0.076; pH 6.6, p < 0.053) and NH₃-N concentration (pH 6.0, p = 0.003; pH 6.6, p = 0.014) were observed with increasing doses of CB. The Alpha diversity indexes of OTU number and Chao1 were higher (p = 0.045) at media pH 6.6 than pH 6.0, but they were not affected by CB supplementation. The PCoA analysis (unweighted uniFrac) demonstrated that the clustering of the bacterial microbiota of control and CB were distinctly separated from each other at media pH 6.0. At the phylum level, the abundance of Bacteroidota (p < 0.001) decreased, whereas that of Firmicutes (p = 0.026) increased when the media pH was elevated from 6.0 to 6.6. Supplementation of CB increased relative abundances of Rikenellaceae_RC9_gut_group (p = 0.002), Christensenellaceae_R-7_group (p < 0.001), and NK4A214_group (p = 0.002) at genus level. Interactions between media pH and CB addition were observed for bacteria at both phylum and genus levels. These results indicated that increasing the media pH level and CB supplementation increased in vitro rumen digestibility, and altered the ruminal fermentation pattern (by media pH) and microbiota.

Comparison of rumen bacterial communities between yaks (Bos grunniens) and Qaidam cattle (Bos taurus) fed a low protein diet with different energy levels

The yak (Bos grunniens), an indigenous bovine on the Qinghai-Tibetan plateau (QTP), is reported to digest low quality forage to a greater extent and to require less protein and energy for maintenance than the introduced Qaidam cattle (Bos taurus). Ruminal bacteria play a major role in feed degradation, and therefore, we hypothesized that ruminal bacteria composition would differ between yaks and cattle, and confer an advantage to yaks for poor quality diets. To test our hypothesis, we determined the ruminal bacteria profiles, rumen fermentation parameters, and enzyme activities in these bovine species consuming a low-protein diet differing in energy level. Six castrated yaks (155 ± 5.8 kg) and 6 castrated Qaidam cattle (154 ± 8.0 kg) were used in two concurrent 4 × 4 Latin square designs with 2 additional animals of each species in each period. The animals were offered a low-protein diet of 70.4 g/kg dry matter (DM) and one of four metabolizable energy levels, namely 6.62, 8.02, 9.42, and 10.80 MJ/kg. Ruminal pH, concentrations of ammonia-N and total volatile fatty acids (VFAs), the molar proportion of acetate, and the ratio of acetate to propionate (A:P) were greater (P < 0.05), whereas the molar proportion of propionate was lesser (P = 0.043) in yaks than in cattle. With increasing dietary energy level, ruminal pH, the molar proportion of acetate and the ratio of A:P decreased linearly (P < 0.05), whereas, the concentration of total VFAs, molar proportions of propionate, butyrate, iso-butyrate, and iso-valerate and concentration of ammonia-N increased linearly (P < 0.05). The relative abundance (RA) of Firmicutes increased linearly (P < 0.01), whereas, the RA of Bacteroidetes decreased linearly (P < 0.001) with increasing energy level in both bovine species. The RAs of Prevotella and Rikenellaceae_RC9_gut_group decreased linearly (P < 0.05) with increasing energy level in both yaks and cattle. The RAs of fibrolytic (e.g., Rikenellaceae_RC9_gut_group), and H2-incorporating (e.g., Quinella) bacteria were greater (P < 0.05) in yaks than in cattle. We concluded that the two bovines differ in ruminal bacterial profiles and rumen fermentation parameters, and confer an advantage to yaks over cattle in consuming a low protein diet with differing energy level.

Changes in the rumen microbiota community in ketosis cows during propylene glycol treatment

Ketosis, a common metabolic disorder in dairy cattle, occurs during early lactation and leads to higher concentrations of non-esterified fatty acids (NEFAs) and β-hydroxybutyrate (BHBA), and is generally believed to be caused by excessive negative energy balance (NEB). Propylene glycol (PG), a gluconeogenic precursor, has been proved to promote gluconeogenesis and alleviate NEB. Oral administration of PG is widely considered one of the most effective therapeutic options for treating ketosis. Thus, in this study, we assessed the effects of PG on rumen microbiota via 16S rDNA analysis. The results show that one dose (500 mL) of PG treatment could rapidly reduce the blood BHBA level in ketosis cows by increasing the level and proportion of propionate in the rumen. Meanwhile, PG also had certain effects on the rumen bacterial community. Compared with before treatment, the relative abundances of Prevotella, Succinivibrionaceae_UCG-001 and Prevotellaceae_UCG-001 increased significantly, while those of Christensenellaceae_R-7_group, Butyrivibrio and Saccharofermentans significantly decreased. LEfSe analysis revealed that after PG treatment, only Rikenellaceae_RC9_gut_group was enriched in the rumen fluid at the genus level. In conclusion, the present study indicates that ketosis is accompanied by alterations in the rumen microbiota community. PG treatment changes the composition of rumen microbiota to a healthier state and contributes to rapid recovery from ketosis. These results support the usage of PG for treating such metabolic diseases that challenge high-yield cows due to their minimized cost and maximized safety without any adverse events.

Characteristics of Bacterial Microbiota in Different Intestinal Segments of Aohan Fine-Wool Sheep

The microbial community performs vital functions in the intestinal system of animals. Modulation of the gut microbiota structure can indirectly or directly affect gut health and host metabolism. Aohan fine-wool sheep grow in semi-desert grasslands in China and show excellent stress tolerance. In this study, we amplified 16S rRNA gene to investigate the dynamic distribution and adaptability of the gut microbiome in the duodenum, jejunum, ileum, cecum, colon, and rectum of seven Aohan fine-wool sheep at 12 months. The results showed that the microbial composition and diversity of the ileum and the large intestine (collectively termed the hindgut) were close together, and the genetic distance and functional projections between them were similar. Meanwhile, the diversity index results revealed that the bacterial richness and diversity of the hindgut were significantly higher than those of the foregut. We found that from the foregut to the hindgut, the dominant bacteria changed from Proteobacteria to Bacteroidetes. In LEfSe analysis, Succiniclasticum was found to be significantly abundant bacteria in the foregut and was involved in succinic acid metabolism. Ruminococcaceae and Caldicoprobacteraceae were significantly abundant in hindgut, which can degrade cellulose polysaccharides in the large intestine and produce beneficial metabolites. Moreover, Coriobacteriaceae and Eggthellaceae are involved in flavonoid metabolism and polyphenol production. Interestingly, these unique bacteria have not been reported in Mongolian sheep or other sheep breeds. Collectively, the gut microbiota of Aohan fine-wool sheep is one of the keys to adapting to the semi-desert grassland environment. Our results provide new insights into the role of gut microbiota in improving stress tolerance and gut health in sheep.

Intestinal Microbial Diversity of Free-Range and Captive Yak in Qinghai Province

BACKGROUND

The gut microbiome is a large and complex organic assemblage with subtle and close relationships with the host. This symbiotic mechanism is important for the health and adaptability of the host to the environment. Compared with other ruminants, there are few studies on yak intestinal microbes. The study of the gut microbiota of the yak will help us better understand the correlation between the microbiota and the environmental adaptability of the host. In this study, we adapted 16S rDNA sequencing technology to investigate the diversity and composition of the intestinal microbial community in free-range yaks and captive yaks living on the Qinghai-Tibet Plateau (QTP).

RESULTS

Sequencing results showed that the intestinal microbial community diversity was significantly different between free-range yaks and captive yaks. Firmicutes and Bacteroidetes were the dominant bacteria in both free-range and captive yaks. However, there were differences between the microbes of the two analyzed feeding styles in different classification levels. Compared with the captive type, free-range yaks had a higher abundance of Ruminococcaceae, Eubacteriaceae, Desulfovibrionaceae, Elusimicrobium, and Oscillibacter, while the abundance of Succinivibrionaceae, Clostridiales, Lachnospiraceae, Prevotellaceae, Roseburia, and Barnesiella was relatively low. The feeding method may be the key factor for the formation of intestinal flora differences in yaks, while altitude did not significantly affect Qinghai yak.

CONCLUSIONS

In this study, we used 16S rDNA sequencing technology to investigate the composition of intestinal flora in free-range and captive yaks living on the QTP. The exploration of dietary factors can provide a theoretical basis for scientifically and rationally breeding yaks and provides a new direction for the development of prebiotics and microecological agents.

Fermented Wheat Bran Polysaccharides Intervention Alters Rumen Bacterial Community and Promotes Rumen Development and Growth Performance in Lambs

There is growing interest in the utilization of plant polysaccharides for the modulation of the rumen bacterial community and enhancement of growth performance in ruminants. Fermented wheat bran polysaccharides (FWBPs), plant polysaccharides, have been shown to improve the growth performance of lambs, but little is known about their effect on rumen bacteria. The aim of this study was to investigate the effects of FWBPs supplementation to milk replacer (MR) on the growth performance, blood metabolites, weight and morphology of rumen, rumen fermentation, and rumen bacterial community which were investigated in lambs. Twelve 1.5-month-old crossbred lambs (Dorper × Small-tailed Han Sheep) with an initial body weight (BW) of 11.38 ± 0.19 kg were randomly divided into two groups, namely, the control group and FWBPs group. Compared with the control group, the FWBPs group had a higher average daily weight gain and serum total protein concentrations, and a lower feed: gain ratio. A tendency of increase in final BW and carcass BW was also observed. Administration of FWBPs increased the ruminal papillae width and ruminal butyrate proportion and decreased the concentration of ammonia nitrogen and the proportion of isobutyrate and isovalerate. In addition, the epithelial cell thickness had an increased trend in the FWBPs group. High-throughput sequencing data showed that the relative abundance of Lachnospiraceae_NK3A20_group and Solobacterium was enhanced by FWBP treatment; meanwhile, the relative abundance of NK4A214_group, Megasphaera, and Treponema showed a tendency to be higher than that of the control group. Furthermore, Spearman's correlation analysis revealed that the relative abundances of NK4A214_group, Treponema, and Lachnospiraceae_NK3A20_group were positively correlated with butyrate proportion. Collectively, FWBPs supplementation to MR on lambs altered the rumen bacterial community, promoted rumen development, and improved growth performance.

Establishment of Immortalized Yak Ruminal Epithelial Cell Lines by Lentivirus-Mediated SV40T and hTERT Gene Transduction

Yak is a unique species of cattle that is adapted to the harsh natural environment of the Qinghai-Tibet Plateau. Research on the function of the yak rumen is limited to animal experiments, and the cell molecular mechanism is very limited. The high cost of isolation and culture of adult yak rumen epithelial cells (YRECs), low success rate, and limited cell life limit the scope of long-term physiological functions and nutrient absorption mechanisms of yak rumen epithelium in vitro studies. This study aimed to explore the isolation and immortal culture methods of primary YRECs and establish a new cell line model for studying cell molecular mechanisms. The human telomerase reverse transcriptase gene (hTERT) and simian virus 40 large T antigen (SV40T) were transferred into primary YDECs using mammalian gene expression lentiviral vectors. The immortalized cell line (SV40T-YREC-hTERT) retains the morphological and functional characteristics of primary cells. The epithelial cell marker protein cytokeratin 18 of the immortalized cell lines was positive, and the cell proliferation and karyotype were normal. The SV40T and hTERT genes were successfully transferred into immortalized cell lines and maintained high expression. Simultaneously, the immortalized cell lines had normal function of short-chain fatty acid (SCFA) transport and absorption, and the immortalized yak rumen epithelial cell lines were successfully established. In addition, the transepithelial electrical resistance value gradually increased with culture time, and the permeability of epithelial cells decreased by culturing epithelial cells in Transwell culture chambers. Transmission electron microscopy demonstrated the submicroscopic structure of cells in the integrity barrier model and established the YREC barrier model in vitro.

Comparison of the Intestinal Structure and Intestinal Microbiome between Two Geographically Isolated Populations of Culter alburnus

Geographical populations of Culter alburnus inhabiting different regions of China present substantial differences in their reproduction and development characters. This study compared the intestinal structures, digestive enzyme activities, and intestinal microbiomes in the Xingkai (XK) Lake and the Dianshan (DS) Lake populations of C. alburnus collected in two isolated and contrasting river systems. We wanted to discover whether the intestinal structure and functional divergence were formed in the two populations due to adaptive evolution caused by geographical isolation. Our study indicated that higher intestinal villi, thicker intestinal mucosa layer and intestinal muscle layer, and significantly higher activity of α-amylase were identified in the XK population. Moreover, quite different intestinal microbiomes were presented in the two populations, with the higher abundance of Bacteroidetes and Firmicutes in the XK population. The significantly different intestinal microbiome in the XK population was functionally enriched in carbohydrate, lipid, and amino acid metabolism by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Our findings indicated that substantial adaptative divergence in the intestinal structures and intestine microbiomes was formed in the two populations due to long-term geographical isolation, which may have strongly affected the digestion and absorption ability of the XK population compared with the DS population.

Serum Biochemical Parameters, Rumen Fermentation, and Rumen Bacterial Communities Are Partly Driven by the Breed and Sex of Cattle When Fed High-Grain Diet

Hybridization in bovines is practiced with the main aim of improving production performance, which may imply the microbial variations in the rumen from the parental breed cross to their progeny. Besides, the interactions of offspring breed with sex in terms of rumen bacteria are not clear. This study aims to evaluate the variations in rumen bacterial communities in different breeds and sexes, and the correlations among fattening performance, serum biochemical parameters, and rumen fermentation. Forty-two 19.2 ± 0.67-month-old beef cattle (390 ± 95 kg of initial body weight) comprising two genetic lines (Yiling and Angus × Yiling) and two sexes (heifers and steers) were raised under the same high-grain diet for 120 d. On the last two days, blood samples were collected from each animal via the jugular vein before morning feeding for analyzing serum biochemical parameters; rumen fluid samples were obtained via esophageal intubation 2 h after morning feeding for analyzing rumen fermentation parameters and bacterial communities. The results show that both breed and sex had a certain impact on fattening performance, serum biochemical parameters, and rumen fermentation. No differences in the diversity and structure of rumen bacterial communities were observed. Significant interactions (p < 0.05) of breed and sex were observed for Succinivibrionaceae UCG-002 and Prevotellaceae UCG-001. The relative abundances of the Rikenellaceae RC9 gut group, Prevotellaceae UCG-003, and Succinivibrio were different (p < 0.05) between breeds. Heifers had a higher (p = 0.008) relative abundance of the Rikenellaceae RC9 gut group than steers. Correlation analysis showed a significant relationship (p < 0.05) of rumen bacteria with serum biochemical parameters, rumen pH, and rumen fermentation patterns. Additionally, only two genera, Prevotellaceae UCG-003 and Prevotellaceae UCG-001, had positive correlations with feed efficiency. In conclusion, serum biochemical parameters, rumen fermentation, and rumen bacterial communities are partly driven by the breed and sex of cattle fed a high-grain diet.