Host Species Affects Bacterial Evenness, but Not Diversity: Comparison of Fecal Bacteria of Cows and Goats Offered the Same Diet

Multi-omics reveals the effects of dietary supplementation with Bupleuri radix branch powder on gut microbiota and lipid metabolism: insights into gut microbial-muscle interactions

Improving livestock growth and raising the quality of livestock products have attracted much attention owing to the market's growing need for livestock products. Bupleuri Radix branches powder (BR) has a variety of health characteristics, but its effects on ruminant growth and animal product quality are still uncertain. This study explored the effects of BR on growth performance, health status, gut microbiota, and muscle lipid metabolism of Shaanxi fine-wool sheep (SFS), and examined the interaction between gut microbiota and lipid metabolism through correlation analysis. The results indicated that BR can regulate the immune function, intestinal VFAs, and enzyme activity of FSF by improving the gut microbiota, thereby affecting its muscle lipid metabolism. The lipid metabolite TG showed a strong positive correlation with the gut microbes Bacteroides and Fibrobacter, while Phosphatidylethanolamine and Phosphatidyl serine (PE and PS) showed a significant negative correlation with Fibrobacter. The above results indicate that gut microbiota and lipid metabolites interact with each other. BR has the effects of promoting SFS growth, improving body health, and improving meat quality. These findings offer new insights into improve animal growth performance and livestock product quality in modern farming.

IMPORTANCE

Enhancing livestock growth performance and improving meat quality are important guidelines for the development of the current animal husbandry industry; thus, we explored a comprehensive study of Bupleuri Radix (BR) on growth performance, gut microbiology, and muscle lipid metabolism in Shaanxi fine-wool sheep (SFS). Our research has found that BR could improve the growth performance of SFS and meat quality by affecting gut microbes. This study provides new solutions to improve the economic efficiency of animal husbandry.

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.

Effects of yeast culture and oxalic acid supplementation on in vitro nutrient disappearance, rumen fermentation, and bacterial community composition

Hemicellulose is an important polysaccharide in ruminant nutrition, but it has not been studied as thoroughly as cellulose. Further research is needed to explore supplements that can improve its digestibility and ruminal buffering effects. Our previous research demonstrated the efficacy of oxalic acid (OA) as an essential nutrient in yeast culture (YC) for improving rumen fermentation performance. Consequently, we conducted in vitro rumen digestion experiments to examine the effects of YC and OA on rumen fermentation and bacterial composition. Two diets containing different levels of hemicellulose were formulated: diet 1 with 10.3% and diet 2 with 17% hemicellulose. Three levels of YC (0.00, 0.625, and 1.25 g/kg) and three doses of OA (0.0, 0.4, and 0.8 g/kg, DM) were added into each diet with a 3 × 3 factorial design. A comprehensive assessment was conducted on a total of 18 experimental treatments at fermentation periods of 0, 6, 12, 24, and 48 h. In the first experiment (diet 1), the supplementation of YC, OA, and their interaction significantly increased in vitro DM disappearance (IVDMD) and NDF disappearance (IVNDFD; p < 0.001). In the second experiment (diet 2), the supplementation of OA and the interaction between YC and OA (p < 0.001) increased IVDMD and IVCPD, but had no significant effects on IVNDFD. The interactions of YC and OA significantly increased ammonia nitrogen (p < 0.001). The production of acetic acid, propionic acid, and total volatile fatty acids (TVFA), and pH levels were significantly higher in treatments supplemented with YC and OA (p < 0.001). YC and OA in both diets significantly altered the rumen bacterial community leading to increased Shannon and Simpson diversity indices (p < 0.001). In both diets, OA supplementation significantly increased the relative abundance of the phylum Bacteroidetes and Prevotella genus. The result also showed a positive correlation between the Prevotella and Selenomonas genera with IVDMD, IVNDFD, propionic acid, and TVFA production, suggesting that these dominant bacteria enhanced nutrient disappearance in the rumen. In conclusion, adding YC and OA resulted in modifications to the bacterial community's composition and diversity, and improved nutrient disappearance. These changes indicate improved rumen fermentation efficiency, which is promising for future in vivo studies.

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.

High-throughput DNA metabarcoding for determining the gut microbiome of captive critically endangered Malayan tiger (Pantheratigrisjacksoni) during fasting

The Malayan tiger (Pantheratigrisjacksoni) is a critically endangered species native to the Malaysian Peninsula. To imitate wild conditions where tigers do not hunt every day, numerous wildlife sanctuaries do not feed their tigers daily. However, the effects of fasting on the gut microbiota of captive Malayan tigers remains unknown. This study aimed to characterise the gut microbiota of captive Malayan tigers by comparing their microbial communities during fasting versus normal feeding conditions. This study was conducted at the Melaka Zoo, Malaysian Peninsula and involved Malayan tigers fasted every Monday. In total, ten faecal samples of Malayan tiger, two of Bengal tiger (outgroup) and four of lion (outgroup) were collected and analysed for metabarcoding targeting the 16S rRNA V3-V4 region. In total, we determined 14 phyla, 87 families, 167 genera and 53 species of gut microbiome across Malayan tiger samples. The potentially harmful bacterial genera found in this study included Fusobacterium, Bacteroides, Clostridium sensu stricto 1, Solobacterium, Echerichiashigella, Ignatzschineria and Negativibacillus. The microbiome in the fasting phase had a higher composition and was more diverse than in the feeding phase. The present findings indicate a balanced ratio in the dominant phyla, reflecting a resetting of the imbalanced gut microbiota due to fasting. These findings can help authorities in how to best maintain and improve the husbandry and health of Malayan tigers in captivity and be used for monitoring in ex-situ veterinary care unit.

Combining 16S rRNA Sequencing and Metabolomics Data to Decipher the Interactions between Gut Microbiota, Host Immunity, and Metabolites in Diarrheic Young Small Ruminants

Diarrhea is associated with gut microbiota, immunity, and metabolic alterations in goat kids and lambs. This study used 28 lambs (11 healthy and 17 diarrheic) and 20 goat kids (10 healthy and 10 diarrheic) to investigate the association between diarrhea occurrence and changes in gut microbiota, metabolism, and immunity in goat kids and lambs. The results revealed that Firmicutes, Proteobacteria, and Bacteroidetes were the dominant phyla in goat kids and lambs. In addition, Enterobacteriaceae and Lachnospiraceae families were identified in both diarrheic goat kids and lambs. Furthermore, functional prediction of microbiota showed that it was involved in cell motility and cancer pathways. The identified differential metabolites were implicated in the bile secretion pathway. Lambs had significant differences in immunoglobulin G (IgG), immunoglobulin M (IgM), interleukin-1β (IL-1β), and tumor necrosis factor-alpha (TNF-α) compared to goat kids. IgG and IL-1β were positively correlated to Patescibacteria, Clostridiaceae, and unclassified_Muribaculaceae in both diarrheic goat kids and lambs. In addition, weighted gene co-expression network analysis (WGCNA) revealed that the MEgreen module was positively associated with IgG, IgM, IL-1β, TNF-α, and triglyceride (TG). In conclusion, our results characterized the gut microbiota, metabolism, and immune status of lambs and goat kids suffering from diarrhea.

Feeding hempseed cake alters the bovine gut, respiratory and reproductive microbiota

A growing number of studies have investigated the feasibility of utilizing hemp by-products as livestock feedstuffs; however, their impact on livestock microbiomes remains unexplored. Here, we evaluated the effects of feeding hempseed cake on the gastrointestinal, respiratory, and reproductive microbiota in beef heifers. Angus-crossbred heifers (19-months old, initial body weight = 494 ± 10 kg [SE]) were fed a corn-based finishing diet containing 20% hempseed cake as a substitute for 20% corn dried distillers' grains with solubles (DM basis; Control; n = 16/group) for 111 days until slaughter. Ruminal fluid and deep nasopharyngeal swabs (days 0, 7, 42, 70 and 98), and vaginal and uterine swabs (at slaughter) were collected, and the microbiota assessed using 16S rRNA gene sequencing. Diet affected the community structure of the ruminal (d 7-98; 0.06 ≤ R² ≤ 0.12; P < 0.05), nasopharyngeal (d 98; R² = 0.18; P < 0.001), and vaginal (R² = 0.06; P < 0.01) microbiota. Heifers fed hempseed cake had increased microbial diversity in the rumen, reduced microbial richness in the vagina, and greater microbial diversity and richness in the uterus. In addition to the distinct microbial communities in the rumen, nasopharynx, vagina and uterus, we identified 28 core taxa that were shared (≥ 60% of all samples) across these sampling locations. Feeding hempseed cake appeared to alter the bovine gut, respiratory and reproductive microbiota. Our results suggest that future research aiming to evaluate the use of hemp by-products in livestock diet should consider their impact on animal microbiome and microbiome mediated animal health and reproductive efficiency. Our findings also highlight the need for research evaluating the impact of hemp-associated food and personal care products on the human microbiome.