Assessment of microbiome changes after rumen transfaunation: implications on improving feed efficiency in beef cattle

Ruminal-buccal microbiota transmission and their diagnostic roles in subacute rumen acidosis in dairy goats

BACKGROUND

Subacute rumen acidosis (SARA) is a common metabolic disorder in ruminants that disrupts the rumen microbiome and animal health, but diagnosis is challenging due to subtle symptoms and invasive testing requirements. This study explores the potential of the buccal (oral) microbiome as a diagnostic indicator for SARA, hypothesizing an interaction with the rumen microbiome.

RESULTS

The study involved 47 dairy goats, including 11 on a control diet and 36 on high-concentrate diets with increasing rumen-degradable starch. Animals were grouped based on dietary exposure and ruminal pH: Control, Low-RDS Tolerance/SARA (LRDST/LRDSS), and High-RDS Tolerance/SARA (HRDST/HRDSS). Transcriptomics of rumen epithelium showed heightened inflammatory pathway gene expression in SARA-susceptible goats compared to controls and tolerant groups. Alpha diversity of ruminal bacteria showed lower Shannon diversity in HRDSS goats compared to HRDST whereas buccal bacteria displayed significantly lower Chao1 diversity in LRDSS goats compared to HRDST. Beta diversity analyses revealed distinct patterns between SARA-affected goats and healthy controls in both ruminal and buccal microbiomes. Prevotellaceae_UCG-003 emerged as a candidate biomarker, with reduced abundance in SARA-susceptible goats in both rumen and buccal samples. Machine learning classifiers achieved high accuracy in distinguishing SARA-susceptible goats using this genus (rumen AUC = 0.807; buccal AUC = 0.779). Source tracking analysis illustrated diminished cross-population of bacteria from the buccal to rumen (2.86% to 0.25%) and vice versa (8.59% to 1.17%), signifying compromised microbial interchange in SARA-affected goats. A microbiota transplant experiment verified SARA microbiota's ability to induce pH decline, escalate inflammation-related gene expression (MAPK10, IL17B, FOSB, SPP1), disrupt microbial transfer, and reduce Prevotellaceae_UCG-003 in recipients.

CONCLUSION

Our findings highlight SARA's dual impact on ruminal and buccal microbiota, exacerbating epithelial inflammation gene expression. Shifts in the buccal microbiome, specifically reductions in Prevotellaceae_UCG-003, mirror ruminal changes and can be influenced by inter-compartmental bacterial transmission, thereby offering a non-invasive diagnostic approach for SARA.

Effects of chili straw on rumen fermentation, meat quality, amino acid and fatty acid contents, and rumen bacteria diversity in sheep

Crop residues have shown promise as non-conventional feed sources to enhance animal health and growth. This study evaluated the effects of chili straw (CS) on rumen fermentation, meat quality, amino and fatty acid composition, and rumen microbial diversity in sheep. Fifty F1 Dorper×Hu lambs (29.58 ± 2.06 kg) were randomly assigned to five groups, fed pelleted feed with 0%, 5%, 10%, 15%, or 20% CS over a 63-day period, including a 7-day pre-test. Post-trial, rumen fluid was sampled to assess fermentation and microbial profiles, and slaughter performance and meat quality were evaluated. Key findings include: (1) No significant differences were observed in rumen pH, NH3-N, or acetic acid-to-propionic acid ratio across groups (P > 0.05). (2) Rumen microbial diversity indices did not vary significantly between groups (P > 0.05), though the relative abundance of Firmicutes and Proteobacteria increased, and Bacteroidota decreased in CS-fed groups, with specific genus-level changes. (3) Carcass weight decreased in the CS20% group (P < 0.01). (4) Cooking loss decreased in CS10%, 15%, and 20% groups (P < 0.05), and meat redness increased in CS15% and 20% groups (P < 0.01). (5) Saturated fatty acids decreased, while the PUFA/SFA ratio and amino acid profiles, including sulfur-containing amino acids (SAA), dibasic amino acids (DAA), essential amino acids (EAA), and total amino acids (TAA), increased with CS, with a significant rise in Gly content in the CS15% group (P < 0.05). In conclusion, incorporating CS into lamb diets can enhance meat quality without adversely affecting rumen fermentation, with recommended levels between 10% and 15%.

Invited review: Ruminal acidosis and its definition-A critical review

Ruminal acidosis occurs as a continuum of disorders, stemming from ruminal dysbiosis and disorders of metabolism, of varying severity. The condition has a marked temporal dynamic expression, resulting in cases expressing quite different rumen concentrations of VFA, lactic acid, ammonia, and rumen pH over time. Clinical ruminal acidosis is an important condition of cattle and subclinical ruminal acidosis (SRA) is very prevalent in many dairy populations, with estimates between 10% and 26% of cows in early lactation. Estimates of the duration of a case suggest that the lactational incidence of the condition may be as high as 500 cases per 100 cows in the first 100 d of lactation. Historical confusion about the etiology and pathogenesis of ruminal acidosis led to definitions that are not fit for purpose, as acidic ruminal conditions solely characterized by ruminal pH determination at a single point fail to reflect the complexity of the condition. Use of a model based on integrated ruminal measures, including VFA, ammonia, lactic acid, and pH, for evaluating ruminal acidosis is fit for purpose, as indicated by meeting postulates for assessing metabolic disease, but requires a method to simplify application in the field. Although it is likely that this model, which we have termed the Bramley acidosis model (BAM), will be refined, the critical value in the model is that it demonstrates that ruminal acidosis is much more than ruminal pH. Disease, milk yield, and milk composition are more associated with the BAM than rumen pH alone. Two single VFA, propionate and valerate, are sensitive and specific for SRA, especially when compared with rumen pH. Even with the use of such a model, astute evaluations of the condition, whether in experimental or field circumstances, will be aided by ancillary measures that can be used in parallel or in series to enhance diagnosis and interpretation. Sensing methods, including rumination detection, behavior, milk analysis, and passive analysis of rumen function, have the potential to improve the detection of SRA; however, these may advance more rapidly if SRA is defined more broadly than by ruminal pH alone.

Multi-omics revealed the mechanism of feed efficiency in sheep by the combined action of the host and rumen microbiota

This study was conducted to investigate potential regulatory mechanisms of feed efficiency (FE) in sheep by linking rumen microbiota with its host by the multi-omics analysis. One hundred and ninety-eight hybrid female sheep (initial body weight = 30.88 ± 4.57 kg; 4-month-old) were selected as candidate sheep. Each test sheep was fed in an individual pen for 60 days, and the residual feed intake (RFI) was calculated. The ten candidate sheep with the highest RFI were divided into the Low-FE group, and the ten with the lowest RFI were divided into the High-FE group, all selected for sample collection. The RFI, average daily gain and average daily feed intake were highly significantly different between the two experimental groups (P < 0.05). Compared with Low-FE group, the insulin-like growth factor-1 and very low-density lipoprotein in serum and the propionate in rumen significantly increased in High-FE group (P < 0.01), but the acetate:propionate ratio in rumen significantly decreased in High-FE group (P = 0.034). Metagenomics revealed Selenomonas ruminantium, Selenomonas sp. and Faecalibacterium prausnitzi i were key bacteria, and increased abundance of the genes encoding the enzymes for cellulose degradation and production of propionate in High-FE group. The results of proteomics and section showed the rumen papilla length (P < 0.001) and expression of carbonic anhydrase and Na+/K+-ATPase were significantly higher in High-FE group (P < 0.05). On the other hand, the acetyl-CoA content significantly increased in the liver of High-FE group (P = 0.002). The relative expression levels of insulin-like growth factor-1 and apolipoprotein A4 genes were significantly up-regulated in the liver of High-FE group (P < 0.01), but relative expression level of monoacylglycerol O-acyltransferase 3 gene was significantly down-regulated (P = 0.037). These findings provide the mechanism by which the collaborative interaction between rumen microbiota fermentation and host uptake and metabolism of fermentation products impacts feed efficiency traits in sheep.

Compendium of 5810 genomes of sheep and goat gut microbiomes provides new insights into the glycan and mucin utilization

BACKGROUND

Ruminant gut microbiota are critical in ecological adaptation, evolution, and nutrition utilization because it regulates energy metabolism, promotes nutrient absorption, and improves immune function. To study the functional roles of key gut microbiota in sheep and goats, it is essential to construct reference microbial gene catalogs and high-quality microbial genomes database.

RESULTS

A total of 320 fecal samples were collected from 21 different sheep and goat breeds, originating from 32 distinct farms. Metagenomic deep sequencing and binning assembly were utilized to construct a comprehensive microbial genome information database for the gut microbiota. We successfully generated the largest reference gene catalogs for gut microbiota in sheep and goats, containing over 162 million and 82 million nonredundant predicted genes, respectively, with 49 million shared nonredundant predicted genes and 1138 shared species. We found that the rearing environment has a greater impact on microbial composition and function than the host's species effect. Through subsequent assembly, we obtained 5810 medium- and high-quality metagenome-assembled genomes (MAGs), out of which 2661 were yet unidentified species. Among these MAGs, we identified 91 bacterial taxa that specifically colonize the sheep gut, which encode polysaccharide utilization loci for glycan and mucin degradation.

CONCLUSIONS

By shedding light on the co-symbiotic microbial communities in the gut of small ruminants, our study significantly enhances the understanding of their nutrient degradation and disease susceptibility. Our findings emphasize the vast potential of untapped resources in functional bacterial species within ruminants, further expanding our knowledge of how the ruminant gut microbiota recognizes and processes glycan and mucins. Video Abstract.

Multi-Omics Analysis Reveals the Regulatory Mechanism of Probiotics on the Growth Performance of Fattening Sheep

Probiotics have been proven to improve the growth performance of livestock and poultry. The aim of this experiment was to investigate the effects of probiotic supplementation on the growth performance; rumen and intestinal microbiota; rumen fluid, serum, and urine metabolism; and rumen epithelial cell transcriptomics of fattening meat sheep. Twelve Hu sheep were selected and randomly divided into two groups. They were fed a basal diet (CON) or a basal diet supplemented with 1.5 × 108 CFU/g probiotics (PRB). The results show that the average daily weight gain, and volatile fatty acid and serum antioxidant capacity concentrations of the PRB group were significantly higher than those of the CON group (p < 0.05). Compared to the CON group, the thickness of the rumen muscle layer in the PRB group was significantly decreased (p < 0.01); the thickness of the duodenal muscle layer in the fattening sheep was significantly reduced; and the length of the duodenal villi, the thickness of the cecal and rectal mucosal muscle layers, and the thickness of the cecal, colon, and rectal mucosal layers (p < 0.05) were significantly increased. At the genus level, the addition of probiotics altered the composition of the rumen and intestinal microbiota, significantly upregulating the relative abundance of Subdivision5_genera_incertae_sedis and Acinetobacter in the rumen microbiota, and significantly downregulating the relative abundance of Butyrivibrio, Saccharofermentans, and Fibrobacter. The relative abundance of faecalicoccus was significantly upregulated in the intestinal microbiota, while the relative abundance of Coprococcus, Porphyromonas, and Anaerobacterium were significantly downregulated (p < 0.05). There were significant differences in the rumen, serum, and urine metabolites between the PRB group and the CON group, with 188, 138, and 104 metabolites (p < 0.05), mainly affecting pathways such as vitamin B2, vitamin B3, vitamin B6, and a series of amino acid metabolisms. The differential genes in the transcriptome sequencing were mainly enriched in protein modification regulation (especially histone modification), immune function regulation, and energy metabolism. Therefore, adding probiotics improved the growth performance of fattening sheep by altering the rumen and intestinal microbiota; the rumen, serum, and urine metabolome; and the transcriptome.

Inoculation of Newborn Lambs with Ruminal Solids Derived from Adult Goats Reprograms the Development of Gut Microbiota and Serum Metabolome and Favors Growth Performance

Microbial transplantation in early life was a strategy to optimize the health and performance of livestock animals. This study aimed to investigate the effect of active ruminal solids microorganism supplementation on newborn lamb gut microbiota and serum metabolism. Twenty-four Youzhou dark newborn lambs were randomly divided into three groups: (1) newborn lambs fed with sterilized goat milk inoculated with sterilized normal saline (CON), supernatant from ruminal solids (SRS), or autoclaved supernatant from ruminal solids (ASRS). Results showed that SRS increased gut bacterial richness and community, downregulating the Firmicutes/Bacteroidetes ratio, and increased the abundance of some probiotics (Bacteroidetes, Spirochaetota, and Fibrobacterota), while reducing the abundance of Fusobacteriota, compared to the CON group. SRS also improved the plasma metabolic function, such as arachidonic acid metabolism, primary bile acid biosynthesis, and tryptophan metabolism and then actively promoted the levels of ALP and HLD. Our study indicated that inoculation with active ruminal solids significantly affected the intestinal microbial communities and metabolic characteristics, and these changes can improve the growing health of the newborn lamb. These findings provided an experimental and theoretical basis for the application of ruminal solid-attached microorganisms in the nutritional management of lambs reared for human consumption.

Comparative analysis of functional diversity of rumen microbiome in bison and beef heifers

IMPORTANCE

Ruminants play a key role in the conversion of cellulolytic plant material into high-quality meat and milk protein for humans. The rumen microbiome is the driver of this conversion, yet there is little information on how gene expression within the microbiome impacts the efficiency of this conversion process. The current study investigates gene expression in the rumen microbiome of beef heifers and bison and how transplantation of ruminal contents from bison to heifers alters gene expression. Understanding interactions between the host and the rumen microbiome is the key to developing informed approaches to rumen programming that will enhance production efficiency in ruminants.

Compound enzyme preparation supplementation improves the production performance of goats by regulating rumen microbiota

Enzyme preparation is one of the widely used additives in ruminant production. However, a suitable method of adding compound enzyme preparation (CEP) to the feeds is still lacking. This study investigated the effect of adding CEP on the diet of goats. Twenty 4-month-old Boer goats were randomly assigned to four groups. The dietary treatments contained different CEPs (Saccharomyces cerevisiae cells, cellulase, xylanase, β-glucanase amylase, and protease) at the concentrations of 0, 0.25, 0.50, and 0.75 g/kg of feed provided for a period of 56 days. Adding CEP in goat feed significantly increased average daily gain (ADG) during the entire test period. The oxidative indices, hormones, and immune cells did not differ significantly among the different groups. CEP significantly increased the content of total volatile fatty acids measured at the end of the experiment on day 56 of the final normal feeding phase. 16S rDNA sequencing revealed that CEP increased the abundance of Ruminococcaceae in the rumen and g__norank_f__Eubacterium_coprostanoligenes_group, Oscillibacter g__unclassified_f__Ruminococcaceae, and g__unclassified_o__Oscillospirales in fecal matter collected on day 56 of the final normal feeding phase. However, CEP decreased the abundance of unclassified_f__Lachnospiraceae, norank_f__UCG-010, Butyrivibrio, and Saccharofermentans in the rumen. The abundance of Ruminococcaceae in the rumen and propionic acid was positively correlated with ADG. Function prediction showed that carbon fixation, carbohydrate digestion and absorption pathways were significantly enriched in rumen microbiota in the treatment group. The findings indicated that supplementation with 0.5 g CEP/kg of feed for 56 days significantly improves the production performance of goats without adverse health effects. KEY POINTS: • Feeding with compound enzyme preparation for 56 days significantly improved the productive performance but did not affect the antioxidative capacity and immunity of goats. • Supplementing compound enzyme preparation in diet could increase the relative abundance of Ruminococcus to increase the levels of short-chain fatty acids produced. • The most appropriate supplemental amount of compound enzyme preparation per kilogram of the diet was 0.5 g.

Multi-breed host rumen epithelium transcriptome and microbiome associations and their relationship with beef cattle feed efficiency

Understanding host-microbial interactions in the rumen and its influence on desirable production traits may lead to potential microbiota manipulation or genetic selection for improved cattle feed efficiency. This study investigated the host transcriptome and its correlation with the rumen archaea and bacteria differential abundance of two pure beef cattle breeds (Angus and Charolais) and one composite beef hybrid (Kinsella) divergent for residual feed intake (RFI; low-RFI vs. high-RFI). Using RNA-Sequencing of rumen tissue and 16S rRNA gene amplicon sequencing, differentially expressed genes (FDR ≤ 0.05, |log2(Fold-change) >|2) and differentially abundant (p-value < 0.05) archaea and bacteria amplicon sequence variants (ASV) were determined. Significant correlations between gene expression and ASVs (p-value < 0.05) were determine using Spearman correlation. Interesting associations with muscle contraction and the modulation of the immune system were observed for the genes correlated with bacterial ASVs. Potential functional candidate genes for feed efficiency status were identified for Angus (CCL17, CCR3, and CXCL10), Charolais (KCNK9, GGT1 and IL6), and Kinsella breed (ESR2). The results obtained here provide more insights regarding the applicability of target host and rumen microbial traits for the selection and breeding of more feed efficient beef cattle.

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

Background

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

Results

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

Conclusion

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

Fermented Total Mixed Ration Alters Rumen Fermentation Parameters and Microbiota in Dairy Cows

This study aimed to determine changes and interactions of ruminal microbiota and chemical parameters in dairy cows fed FTMR. Twelve multiparous Holstein dairy cows (Body weight = 616 ± 13.4 kg; day in milk = 106 ± 7.55 d; and parity = 2.31 ± 0.49; mean ± standard deviation) were divided randomly into two treatments depending on the day in milk, milk production, and parity. The two treatments were: (1) total mixed ration (TMR) and (2) FTMR. Illumina MiSeq sequencing was used to explore the changes in the ruminal microbiota. The results revealed that the bacterial and fungal diversity of the FTMR group were significantly higher than the TMR group. The predominant microbiota phyla in the bacteria and fungi showed significant differences between TMR and FTMR, as follows: Verrucomicrobia (p = 0.03) and Tenericutes (p = 0.01), Ascomycota (p = 0.04) and Basidiomycota (p = 0.04). The dominant bacterial genera in the bacteria, fungi, protozoan, and archaea that showed significant differences between TMR and FTMR were Unclassified_Bacteroidales (p = 0.02), Unclassified_RFP12 (p = 0.03), Candida (p = 0.0005), Bullera (p = 0.002), Cryptococcus (p = 0.007), and Ostracodinium (p = 0.01). LefSe analysis was performed to reveal the biomarker genera of the rumen microbiota community (bacteria, fungi, protozoan, and archaea) in the TMR and FTMR were the genera Shuttleworthia, Ruminococcus, Cryptococcus, Mycosphaerella, Bullera, Candida, and Ostracodinium. NH3-N concentration (p < 0.0001), total VFA concentration (p = 0.003), and molar proportion in total VFA of acetate (p = 0.01) were higher for the cows fed FTMR compared with the cows fed the TMR. Several bacterial genera showed significant correlations with rumen fermentation parameters. The genus Unclassified_Bacteroidales and Bullera were positively correlated with total volatile fatty acids (VFA) and acetate, whereas Candida and Ostracodinium showed negative correlations. Meanwhile, propionate was positively correlated with Candida and negatively correlated with Bullera. The PICRUSt functional profile prediction indicated that the xenobiotics biodegradation and metabolism, the lipid, amino acid, terpenoids, and polyketides metabolisms of the FTMR group were significantly higher than that of the TMR group. The results imply that FTMR can increase lipid and amino acid metabolism, and modulate the rumen microbiome and improve ruminal fermentation.

The microbiome shifts throughout the gastrointestinal tract of Bradford cattle in the Pampa biome

A deep understanding of the cattle gastrointestinal microbiome is crucial to selective breeding high-efficiency animals that produce more and generate less environmental damage. Here we performed the taxonomic identification of Bacterial and Archaeal communities using high throughput 16SrRNA gene sequencing from critical compartments of the gastrointestinal tract of Bradford cattle raised in a natural grassland in the Pampa biome, Brazil. We analyzed 110 samples, including saliva, ruminal fluid, and feces from 36 months old Bradford heifers (weighing on average 343 ± 30 kg by the sampling time). To reduce unexpected variation and confounders, we selected the animals from the same breed, submitted them to the same food source, and collected the samples for three consecutive years from different animals in the same season. Our main goal was to analyze the microbial shifts throughout the gastrointestinal tract to reference future works proposing management strategies and interventions to improve animal nutrition and increase production in the Pampa Biome. To accomplish our objective, we accessed the microbial community differences in groups with a high and low weight gain controlling for food ingestion and quality of grazed pasture. Few taxa were shared among the samples. About 40% of the phyla and 60% of the genera were unique from saliva samples, and 12.4% of the microbial genera were uniquely found in feces. All samples shared only 36.1% of phyla and 7.5% of genera. Differences in microbial diversity and taxa counts were observed. The ruminal fluid presented the lowest microbial richness, while saliva and feces presented the highest microbial richness. On the other hand, saliva and feces also presented more distinct communities between themselves when compared with ruminal samples. Our data showed that the saliva microbiome is not representative of the rumen microbiome and should not be used as an easy-to-collect sample for studies about the rumen microbiome.

Assessment of effectiveness of deworming options in recently weaned beef cattle utilizing different anthelmintic programs in the southeast

This study evaluated the effects of three different anthelmintic strategies on animal performance and anthelmintic effectiveness in weaned calves during a 42-d preconditioning period. The study was conducted at four locations over 2 yr and included a total of 797 recently weaned spring-born calves (initial BW 260 ± 37.7 kg). At the start of each year, at each location, calves were weaned and randomly assigned to one of four treatments: 1) oxfendazole (ORAL); 2) transdermal eprinomectin (POUR); 3) both anthelmintic treatments (BOTH); and 4) the control (CONT) group who did not receive treatment. Anthelmintic was applied per the manufacturer recommendation, the transdermal eprinomectin was administered at 1 mL per 10 kg and oxfendazole was administered orally at 1 mL per 50 kg. Weights were measured at the start of the study (day 0) and again at the end of the preconditioning phase (day 42). Fecal samples were collected at the start of the study prior to treatment application (day 0) and again on day 14. Rumen fluid was collected at the start of the study prior to treatment (day 0) and again on day 6. There were treatment effects for all performance metrics (P < 0.001). All treatments had greater weight gain and value of weight gained (P < 0.024), and all three strategies did not differ from each other (P > 0.420). On day 0, there were no (P = 0.795) treatment effects detected for fecal eggs per gram (EPG) counts. On day 14, there were (P < 0.001) treatment effects for EPG counts with feces from CONT calves containing greater (P < 0.014) EPG than feces from treated calves. EPG in feces from BOTH calves did not differ (P > 0.123) from the other two treated groups and feces from POUR calves tended (P = 0.052) to contain greater EPG counts than feces from ORAL calves. Volatile fatty acids were similar across treatments on days 0 and 6 (P > 0.115). Butyrate tended (P = 0.063) to be lower in ORAL on day 6. These results suggest that using eprinomectin and oxfendazole in combination was an effective strategy for reducing EPG and improving performance during a 42-d preconditioning phase.

Transmission of the gut microbiome in cohousing goats and pigs

Social interaction facilitates the horizontal transmission of the microbiota between different individuals. However, little is known about the level of microbiota transmission in different livestock animals and different digestive tracts. The Hainan black goat and Wuzhishan pig are typical tropical local breeds on Hainan Island in China. Thus, we sampled and analyzed the gut microbiome in Hainan black goats (cecum and rumen) and Wuzhishan pigs (cecum) to study horizontal transmission by rearing them in the same pen (six goats and six pigs) or separate pens (nine goats and nine pigs). De novo assembly and binning recovered 3,262 strain-level and 2,488 species-level metagenome-assembled genomes (MAGs) using ∼1.3 Tb sequencing data. Of these MAGs, 1,856 MAGs were identified as novel strain. Compared with goats living in separate pens, social interaction in the same pen promotes community homogeneity in the rumen microbiome (P < 0.05) and the cecum microbiome (P < 0.05), respectively. Notably, approximately 7.08% (231/3262) of the gut microbial population could transmit during cohousing, 12 strains only in inter-species transmission, versus 190 strains only in intra-species transmission, and 10 strains only in foregut and hindgut transmission. In addition, the social contact group has high transmitted strain abundance, which is correlated with community composition. This study provided a new insight into the influence of social interaction on the animal gut microbiota.

Ruminal Microbiota Determines the High-Fiber Utilization of Ruminants: Evidence from the Ruminal Microbiota Transplant

The rumen, which contains a series of prokaryotes and eukaryotes with high abundance, determines the high ability to degrade complex carbohydrates in ruminants. Using 16S rRNA gene sequencing, we compared the ruminal microbiota of dairy goats with that in the foregut and colon of mice and found more Bacteroides identified in the rumen, which helps ruminants to utilize plant-derived polysaccharides, cellulose, and other structural carbohydrates. Furthermore, high-fiber diets did not significantly increase intestinal fiber-degrading bacteria in mice, but did produce higher levels of ruminal fiber-degrading bacteria in dairy goats. Through rumen microbe transplantation (RMT), we found that rumen-derived fiber-degrading bacteria can colonize the intestines of mice to exert their fiber-degrading function, but their colonization efficiency is affected by diet. Additionally, the colonization of these fiber-degrading bacteria in the colon may involve higher content of butyrate in the colon, protecting the colonic epithelial barrier and promoting energy metabolism. Overall, the fiber degradation function of rumen bacteria through RMT was verified, and our results provide new insights into isolating the functional and beneficial fiber-degrading bacteria in the rumen, providing a theoretical basis for the role of dietary fiber in intestinal health. IMPORTANCE Ruminants have a powerful progastric digestive system that converts structural carbohydrates into nutrients useful to humans. It is well known that this phenomenon is due to the fact that the rumen of ruminants is a natural microbial fermenter, which can ferment structural carbohydrates such as cellulose and hemicellulose and transform them into volatile fatty acids to supply energy for host. However, monogastric animals have an inherent disadvantage in utilizing fiber, so screening rumen-derived fiber-degrading bacteria as a fermentation strain for biological feed is needed in an attempt at improving the fiber digestibility of monogastric animals. In this study, a ruminal microbiota transplant experiment from goats to mice proves that ruminal microbiota could serve as a key factor in utilization of high-fiber diets and provides a new perspective for the development of probiotics with fiber degradation function from the rumen and the importance of the use of prebiotics during the intake of probiotics.

An Age Effect of Rumen Microbiome in Dairy Buffaloes Revealed by Metagenomics

Age is an important factor in shaping the gut microbiome. However, the age effect on the rumen microbial community for dairy buffaloes remains less explored. Using metagenomics, we examined the microbial composition and functions of rumen microbiota in dairy Murrah buffaloes of different ages: Y (1 year old), M (3−5 years old), E (6−8 years old), and O (>9 years old). We found that Bacteroidetes and Firmicutes were the predominant phyla, with Prevotella accounting for the highest abundance at the genus level. The proportion of Bacteroides and Methanobrevibacter significantly increased with age, while the abundance of genus Lactobacillus significantly decreased with age (LDA > 3, p < 0.05). Most differed COG and KEGG pathways were enriched in Y with carbohydrate metabolism, while older buffaloes enriched more functions of protein metabolism and the processing of replication and repair (LDA > 2, p < 0.05). Additionally, the functional contribution analysis revealed that the genera Prevotella and Lactobacillus of Y with more functions of CAZymes encoded genes of glycoside hydrolases and carbohydrate esterases for their roles of capable of metabolizing starch and sucrose-associated oligosaccharide enzyme, hemicellulase, and cellulase activities than the other three groups (LDA > 2, p < 0.05), thus affecting the 1-year-old dairy buffalo rumen carbohydrate metabolism. This study provides comprehensive dairy buffalo rumen metagenome data and assists in manipulating the rumen microbiome for improved dairy buffalo production.

Expressions of resistome is linked to the key functions and stability of active rumen microbiome

BACKGROUND

The resistome describes the array of antibiotic resistant genes (ARGs) present within a microbial community. Recent research has documented the resistome in the rumen of ruminants and revealed that the type and abundance of ARGs could be affected by diet and/or antibiotic treatment. However, most of these studies only assessed ARGs using metagenomics, and expression of the resistome and its biological function within the microbiome remains largely unexplored.

RESULTS

We characterized the pools of ARGs (resistome) and their activities in the rumen of 48 beef cattle belonging to three breeds (Angus, Charolais, Kinsella composite hybrid), using shotgun metagenomics and metatranscriptomics. Sixty (including 20 plasmid-associated) ARGs were expressed which accounted for about 30% of the total number of ARGs (187) identified in metagenomic datasets, with tetW and mefA exhibiting the highest level of expression. In addition, the bacterial hosts of 17 expressed ARGs were identified. The active resistome was less diverse in Kinsella composite hybrid than Angus, however, expression of ARGs did not differ among breeds. Although not associated with feed efficiency, the total abundance of expressed ARGs was positively correlated with metabolic pathways and 'attenuation values' (a measurement of stability) of the active rumen microbiome, suggesting that ARGs expression influences the stability and functionality of the rumen microbiome. Moreover, Ruminococcus spp., Prevotella ruminicola, Muribaculaceae spp. and Collinsella aerofaciens were all identified as hosts of expressed ARGs, possibly promoting the dominance of these carbohydrate degraders within the rumen microbiome.

CONCLUSIONS

Findings from this study provide new insight into the active rumen resistome in vivo, which may inform strategies to limit the spread of ubiquitously found ARGs from the rumen to the broader environment without negatively impacting the key functional outcomes of the rumen microbiome.

Feedomics provides bidirectional omics strategies between genetics and nutrition for improved production in cattle

Increasing the efficiency and sustainability of cattle production is an effective way to produce valuable animal proteins for a growing human population. Genetics and nutrition are the 2 major research topics in selecting cattle with beneficial phenotypes and developing genetic potentials for improved performance. There is an inextricable link between genetics and nutrition, which urgently requires researchers to uncover the underlying molecular mechanisms to optimize cattle production. Feedomics integrates a range of omic techniques to reveal the mechanisms at different molecular levels related to animal production and health, which can provide novel insights into the relationships of genes and nutrition/nutrients. In this review, we summarized the applications of feedomics techniques to reveal the effect of genetic elements on the response to nutrition and investigate how nutrients affect the functional genome of cattle from the perspective of both nutrigenetics and nutrigenomics. We highlighted the roles of rumen microbiome in the interactions between host genes and nutrition. Herein, we discuss the importance of feedomics in cattle nutrition research, with a view to ensure that cattle exhibit the best production traits for human consumption from both genetic and nutritional aspects.

Effects of Altitude on the Digestion Performance, Serum Antioxidative Characteristics, Rumen Fermentation Parameters, and Rumen Bacteria of Sanhe Heifers

The production efficiency of dairy cows is affected by altitude, with lower efficiency reported at higher altitudes. However, only a few studies have investigated the digestion performance, serum antioxidative characteristics, rumen fermentation performance, and rumen bacteria of Sanhe heifers at different altitudes. Therefore, in this study, we explored the effects of altitude on these aspects of Sanhe heifers. We evaluated the effects of altitude on the apparent digestibility of nutrients, serum antioxidative characteristics, rumen fermentation parameters, and rumen bacteria in Sanhe heifers. Twenty Sanhe heifers from the same herd and managed with the same practice were used. However, the heifers were from two regions in China: 10 were fed in Hulunbuir City, Inner Mongolia Autonomous Region (119°57'E, 47°17'N; approximately 700 m altitude, named LA) and 10 were fed in Lhasa City, Tibet Autonomous Region (91°06'E, 29°36'N; approximately 3,750 m altitude, named HA). The dry matter intake (DMI), average daily gain (ADG), and DMI/ADG ratio were higher (p < 0.05) in LA than in HA heifers, whereas the apparent total tract digestibility of dry matter, ether extract, and crude proteins were higher (p < 0.05) in the HA group. Compared with LA heifers, the HA heifers showed decreased (p < 0.05) serum concentrations of superoxide dismutase and glutathione peroxidase and increased serum concentration of hydrogen peroxide (p < 0.05). Altitude did not significantly affect the volatile fatty acid concentration in the rumen, but HA presented a lower acetate-to-propionate ratio than LA. The 16S rRNA gene sequencing data showed that altitude significantly affected the rumen microbial composition. At the phylum level, the HA heifers presented a lower relative abundance of Actinobacteria (p < 0.05) and higher relative abundance of Spirochaetae (p < 0.05) than the LA heifers. The correlation analysis revealed that the operational taxonomic units belonging to the genus Prevotella_1 were correlated (p < 0.05) with altitude and DMI. The results indicate that altitude can influence the apparent digestibility of nutrients, serum antioxidant capacity, rumen fermentation, and rumen bacteria composition of Sanhe heifers. The study provides insights into the adaptation mechanism of Sanhe heifers to high-altitude areas.

Translational multi-omics microbiome research for strategies to improve cattle production and health

Cattle microbiome plays a vital role in cattle growth and performance and affects many economically important traits such as feed efficiency, milk/meat yield and quality, methane emission, immunity and health. To date, most cattle microbiome research has focused on metataxonomic and metagenomic characterization to reveal who are there and what they may do, preventing the determination of the active functional dynamics in vivo and their causal relationships with the traits. Therefore, there is an urgent need to combine other advanced omics approaches to improve microbiome analysis to determine their mode of actions and host-microbiome interactions in vivo. This review will critically discuss the current multi-omics microbiome research in beef and dairy cattle, aiming to provide insights on how the information generated can be applied to future strategies to improve production efficiency, health and welfare, and environment-friendliness in cattle production through microbiome manipulations.

Microbiome-metabolomics analysis of the effects of decreasing dietary crude protein content on goat rumen mictobiota and metabolites

Objective

The objective of this study was to investigate the effects of decreasing dietary crude protein content on rumen fermentation, mictobiota, and metabolites in goats.

Methods

In an 84-day feeding trial, a total of twelve male Anhui white goat kids with initial body weight 15.9±1.13 kg were selected and randomly classified into two groups, feeding a normal crude protein diet (14.8% CP, NCP) or a low crude protein diet (12.0% CP, LCP). At the end of the experimental trial (on day 84), six animals were randomly selected from each group and were slaughtered to collect rumen fluid samples for the analysis of rumen fermentation parameters, microbiome, and metabolome.

Results

The concentrations of ammonia-nitrogen, total volatile fatty acid, acetate, and propionate were decreased (p<0.05) in the LCP group in comparison with those in the NCP group. The abundances of genera Prevotella, Campylobacter, Synergistetes, and TG5, which were associated with nitrogen metabolism, were lower (p<0.05) in the LCP group compared with those in the NCP group. The levels of 78 metabolites (74 decreased, 4 increased) in the rumen fluid were altered (p<0.05) by the treatment. Most of the ruminal metabolites that showed decreased levels in the LCP group were substrates for microbial protein synthesis. Metabolic pathway analysis showed that vitamin B6 metabolism was significantly different (p<0.05) in rumen fluid between the two treatments.

Conclusion

Decreased dietary protein level inhibited rumen fermentation through microbiome and metabolome shifts in goat kids. These results enhance our understanding of ruminal bacteria and metabolites of goat fed a low protein diet.

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

Rumen microbiota are closely linked to feed utilization and environmental adaptability of ruminants. At present, little is known about the influence of different extreme environments on the rumen microbiota of yaks. In this study, 30 ruminal fluid samples from 30 healthy female yaks (average 280 kg of BW) in 5-8 years of life were collected from three regions in Tibet, China, and compared by gas chromatography and high-throughput sequencing. Results showed that propionic acid, butyric acid, and total volatile fatty acids were significantly (p < 0.05) higher, while microbial abundance and diversity were significantly (p < 0.05) lower, in the Nagqu (4,500 m altitude) compared with the Xigatse (4,800 m altitude) and Lhasa (3,800 m altitude) regions. Principal coordinate analysis revealed significant (p < 0.05) differences in rumen microbial composition of yaks from different regions. Specifically, Bacteroidetes and Firmicutes were identified by linear discriminant analysis effect size (LDA > 3) as being the signature phyla for Xigatse and Nagqu regions, respectively. In addition, the relative abundance of Rikenellaceae_RC9_gut_group, Quinella, Prevotellaceae_UCG-003, Lachnospiraceae_NK3A20_group, Papillibacter, Ruminococcaceae_UCG-010, Prevotellaceae_NK3B31_group, and Ruminococcaceae_UCG-005 correlated with altitude and rumen fermentation parameters (p < 0.05). Finally, the predicted function of rumen microbiota was found to differ between regions (p < 0.05). In summary, our results reveal that regions located at different altitudes influence microbiota composition and fermentation function of yaks' rumen. The present findings can provide mechanistic insights on yak adaptation to high altitudes and improve the feeding efficiency of these animals in extreme regions.

Gut Microbiota Implications for Health and Welfare in Farm Animals: A Review

Simple Summary

Farm animal health and welfare have been paid increasing concern in the world, which is generally assessed by the measurements of physical health, immune response, behavior, and physiological indicators, such as stress-related hormone, cortisone, and norepinephrine. Gut microbiota as a “forgotten organ” has been reported for its great influence on the host phenotypes through the immune, neural, and endocrine pathways to affect the host health and behavior. In addition, fecal microbiota transplantation as a novel approach is applied to regulating the composition and function of the recipient farm animals. In this review, we summarized recent studies that gut microbiota influenced health, immunity, behavior, and stress response, as well as the progress of fecal microbiota transplantation in farm animals. The review will provide new insights into the measurement of farm animal health and welfare concerning gut microbiota, and the implication of fecal microbiota transplantation to improve productivity, health, and welfare. Above all, this review suggests that gut microbiota is a promising field to evaluate and improve animal welfare.

Abstract

In the past few decades, farm animal health and welfare have been paid increasing concern worldwide. Farm animal health and welfare are generally assessed by the measurements of physical health, immune response, behavior, and physiological indicators. The gut microbiota has been reported to have a great influence on host phenotypes, possibly via the immune processes, neural functions, and endocrine pathways, thereby influencing host phenotypes. However, there are few reviews regarding farm animals’ health and welfare status concerning the gut microbiota. In this point of view, (1) we reviewed recent studies showing that gut microbiota (higher alpha diversity, beneficial composition, and positive functions) effectively influenced health characteristics, immunity, behaviors, and stress response in farm animals (such as pigs, chickens, and cows), which would provide a novel approach to measure and evaluate the health status and welfare of farm animals. In addition, fecal microbiota transplantation (FMT) as one of the methods can modulate the recipient individual’s gut microbiota to realize the expected phenotype. Further, (2) we highlighted the application of FMT on the improvement of the production performance, the reduction in disease and abnormal behavior, as well as the attenuation of stress in farm animals. It is concluded that the gut microbiota can be scientifically used to assess and improve the welfare of farm animals. Moreover, FMT may be a helpful strategy to reduce abnormal behavior and improve stress adaption, as well as the treatment of disease for farm animals. This review suggests that gut microbiota is a promising field to evaluate and improve animal welfare.

Amino acids metabolism by rumen microorganisms: Nutrition and ecology strategies to reduce nitrogen emissions from the inside to the outside

For the ruminant animal industry, the emission of nitrogenous substances, such as nitrous oxide (N₂O) and ammonia (NH₃), not only challenges environmental sustainability but also restricts its development. The metabolism of proteins and amino acids by rumen microorganisms is a key factor affecting nitrogen (N) excretion in ruminant animals. Rumen microorganisms that affect N excretion mainly include three types: proteolytic and peptidolytic bacteria (PPB), ureolytic bacteria (UB), and hyper-ammonia-producing bacteria (HAB). Microbes residing in the rumen, however, are influenced by several complex factors, such as diet, which results in fluctuations in the rumen metabolism of proteins and amino acids and ultimately affects N emission. Combining feed nutrition strategies (including ingredient adjustment and feed additives) and ecological mitigation strategies of N₂O and NH₃ in industrial practice can reduce the emission of nitrogenous pollutants from the ruminant breeding industry. In this review, the characteristics of the rumen microbial community related to N metabolism in ruminants were used as the metabolic basis. Furthermore, an effective strategy to increase N utilisation efficiency in combination with nutrition and ecology was reviewed to provide an inside-out approach to reduce N emissions from ruminants.

A review of the resistome within the digestive tract of livestock

Antimicrobials have been widely used to prevent and treat infectious diseases and promote growth in food-production animals. However, the occurrence of antimicrobial resistance poses a huge threat to public and animal health, especially in less developed countries where food-producing animals often intermingle with humans. To limit the spread of antimicrobial resistance from food-production animals to humans and the environment, it is essential to have a comprehensive knowledge of the role of the resistome in antimicrobial resistance (AMR), The resistome refers to the collection of all antimicrobial resistance genes associated with microbiota in a given environment. The dense microbiota in the digestive tract is known to harbour one of the most diverse resistomes in nature. Studies of the resistome in the digestive tract of humans and animals are increasing exponentially as a result of advancements in next-generation sequencing and the expansion of bioinformatic resources/tools to identify and describe the resistome. In this review, we outline the various tools/bioinformatic pipelines currently available to characterize and understand the nature of the intestinal resistome of swine, poultry, and ruminants. We then propose future research directions including analysis of resistome using long-read sequencing, investigation in the role of mobile genetic elements in the expression, function and transmission of AMR. This review outlines the current knowledge and approaches to studying the resistome in food-producing animals and sheds light on future strategies to reduce antimicrobial usage and control the spread of AMR both within and from livestock production systems.

Exogenous Fecal Microbial Transplantation Alters Fearfulness, Intestinal Morphology, and Gut Microbiota in Broilers

Fecal microbiota transplantation (FMT) documented transplanting a donor fecal sample to a receipt individual for a desired physiologic effect. However, whether the gut microbiota construction, intestinal maturation, and behavioral plasticity are modulated by FMT during the early life of broilers is waiting for verification. To evaluate the role of transfer of fecal microbiota from aged broilers donor (BD) to another individual, 96 birds were equally divided into a check (CK, control) group and a broiler recipient (BR) group. FMT was conducted daily from 5 to 12 days of age to determine the future impact on body weight, behavior, intestinal development, and gut microbiota. Results indicated that fearfulness in the CK group was higher than the BR group in both the behavioral tests (p < 0.05). The muscularis mucosa, thickness of muscle layer, and thickness of serous membrane layer in the BR group were higher compared with those of the CK group in the jejunum (p < 0.05). In the gut microbiota, Shannon diversity showed no difference, while beta diversity presented a difference in principal coordination analysis (PCoA) between the CK and BR groups. At the phylum level, the relative abundance of Lentisphaerae in the CK group was lower than the BR (p = 0.052) and BD (p = 0.054) groups. The relative abundance of Tenericutes in the BD group was higher than that in the CK and BR groups (p < 0.05). At the genus level, Megamonas in the CK group was higher than the BR (p = 0.06) and BD (p < 0.05) groups. In the BR group, the functional capabilities of microbial communities analyzed by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were increased in the glutamatergic synapse and N-glycan biosynthesis pathways in comparison with the CK and BD groups (p < 0.05). Some characteristics of gut microbiota in the donor chickens could be transferred to recipient chickens by FMT. In conclusion, exogenous FMT as a probiotic-like administration might be an efficient way to improve the physiology and behavior of chickens. Notably, the role of microbiota for various individuals and periods remains undefined, and the mechanism of microbiota on behaviors still needs further investigation.

The potential for mitigation of methane emissions in ruminants through the application of metagenomics, metabolomics, and other -OMICS technologies

Ruminant supply chains contribute 5.7 gigatons of CO_2-eq per annum, which represents approximately 80% of the livestock sector emissions. One of the largest sources of emission in the ruminant sector is methane (CH₄), accounting for approximately 40% of the sectors total emissions. With climate change being a growing concern, emphasis is being put on reducing greenhouse gas emissions, including those from ruminant production. Various genetic and environmental factors influence cattle CH₄ production, such as breed, genetic makeup, diet, management practices, and physiological status of the host. The influence of genetic variability on CH₄ yield in ruminants indicates that genomic selection for reduced CH₄ emissions is possible. Although the microbiology of CH₄ production has been studied, further research is needed to identify key differences in the host and microbiome genomes and how they interact with one another. The advancement of “-omics” technologies, such as metabolomics and metagenomics, may provide valuable information in this regard. Improved understanding of genetic mechanisms associated with CH₄ production and the interaction between the microbiome profile and host genetics will increase the rate of genetic progress for reduced CH₄ emissions. Through a systems biology approach, various “-omics” technologies can be combined to unravel genomic regions and genetic markers associated with CH₄ production, which can then be used in selective breeding programs. This comprehensive review discusses current challenges in applying genomic selection for reduced CH₄ emissions, and the potential for “-omics” technologies, especially metabolomics and metagenomics, to minimize such challenges. The integration and evaluation of different levels of biological information using a systems biology approach is also discussed, which can assist in understanding the underlying genetic mechanisms and biology of CH₄ production traits in ruminants and aid in reducing agriculture’s overall environmental footprint.

Data of bacterial community dynamics resulting from total rumen content exchange in beef cattle

OBJECTIVES

Extensive efforts have been made to characterize the rumen microbiome under various conditions. However, few studies have addressed the long-term impacts of ruminal microbiome dysbiosis and the extent of host control over microbiome stability. These data can also inform host-microbial symbioses. The objective was to develop preliminary data to measure the changes that occur in the rumen bacterial communities following a rumen content exchange to understand the effects major perturbations may impart upon the rumen microbiome, which may be host-driven.

DATA DESCRIPTION

We report here an initial rumen content exchange between two SimAngus (Simmental/Angus) non-pregnant, non-lactating cows of ~ 6 years of age weighing 603.4 ± 37.5 kg. To measure bacterial community succession and acclimation following the exchange, rumen content was collected via rumen cannula at the beginning of the study immediately prior to and following the rumen content exchange, and weekly for 12 weeks. The V4 hypervariable region of the 16S rRNA gene was targeted for DNA sequencing and bacterial analysis. Over 12 weeks, numerous genera and diversity varied, before partial return to pre-exchange metrics. These preliminary data help support potential host control for the rumen microbiome, aiding in efforts to define bovine host-microbe relationships.

Potential Use of Gut Microbiota Composition as a Biomarker of Heat Stress in Monogastric Species: A Review

Simple Summary

Heat stress is a significant environmental challenge faced by food animal production worldwide because of its adverse effects on animal performance and productivity. Trillions of microorganisms living in the gut are essential for host health by participating in various digestive, immune, and metabolic activities. At the same time, they are known to be sensitive to changes in the surrounding environment. The present review summarizes current research progress of how the gut microbial community responds to elevated ambient heat in monogastric animal species and discusses the use of the gut microbiota composition as a potential indicator for heat stress.

Abstract

Heat stress is a current challenge for livestock production, and its impact could dramatically increase if global temperatures continue to climb. Exposure of agricultural animals to high ambient temperatures and humidity would lead to substantial economic losses because it compromises animal performance, productivity, health, and welfare. The gut microbiota plays essential roles in nutrient absorption, energy balance, and immune defenses through profound symbiotic interactions with the host. The homeostasis of those diverse gut microorganisms is critical for the host’s overall health and welfare status and also is sensitive to environmental stressors, like heat stress, reflected in altered composition and functionality. This article aims to summarize the research progress on the interactions between heat stress and gut microbiome and discuss the potential use of the gut microbiota composition as a biomarker of heat stress in monogastric animal species. A comprehensive understanding of the gut microbiota’s role in responding to or regulating physiological activities induced by heat stress would contribute to developing mitigation strategies.

MAP, Johne's disease and the microbiome; current knowledge and future considerations

Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne's disease in ruminants. As an infectious disease that causes reduced milk yields, effects fertility and, eventually, the loss of the animal, it is a huge financial burden for associated industries. Efforts to control MAP infection and Johne's disease are complicated due to difficulties of diagnosis in the early stages of infection and challenges relating to the specificity and sensitivity of current testing methods. The methods that are available contribute to widely used test and cull strategies, vaccination programmes also in place in some countries. Next generation sequencing technologies have opened up new avenues for the discovery of novel biomarkers for disease prediction within MAP genomes and within ruminant microbiomes. Controlling Johne's disease in herds can lead to improved animal health and welfare, in turn leading to increased productivity. With current climate change bills, such as the European Green Deal, targeting livestock production systems for more sustainable practices, managing animal health is now more important than ever before. This review provides an overview of the current knowledge on genomics and detection of MAP as it pertains to Johne's disease.

Aspergillus oryzae and Aspergillus niger Co-Cultivation Extract Affects In Vitro Degradation, Fermentation Characteristics, and Bacterial Composition in a Diet-Specific Manner

AOAN may provide enzymes to improve the digestibility of feeds and enhance rumen fermentation. This study determined the effects of AOAN on digestibility, fermentation characteristics, and bacterial composition using in vitro gas recording fermentation system. A total of 30 mg of AOAN was supplemented into 500 mg of TMR, corn silage, oat hay, and alfalfa hay. Fermentation parameters and bacterial communities were determined after 48 h fermentation, and digestibility was determined after 7, 24, 30, and 48 h fermentation. Gas production and dry matter (DM), crude protein (CP), neutral detergent fiber (NDF), and acid detergent fiber (ADF) digestibility were significantly increased by AOAN supplementation at 48 h (p < 0.05), except for digestibility of CP of the TMR (p > 0.05). AOAN increased starch digestibility in corn silage (p < 0.05) and tended to increase that in TMR (0.05 < p < 0.10). AOAN supplementation increased total volatile fatty acid production (p < 0.05). The molar proportions of acetate and acetate to propionate ratio of oat hay and alfalfa hay were increased (p < 0.05). The 16S rRNA analysis revealed that the microbial richness of TMR and oat hay, and microbial evenness of TMR were increased (p < 0.05). AOAN did not affect the α diversity, β diversity, and bacterial composition of the corn silage. The relative abundance of Prevotella was increased and Ruminococcus was decreased in TMR, oat hay, and alfalfa hay. In conclusion, results suggest that AOAN has the potential to improve the utilization of diets differently, including providing enzymes with changing microbiota (TMR, oat hay, and alfalfa hay) or providing enzymes alone (corn silage).

The Comparative Analysis of the Ruminal Bacterial Population in Reindeer (Rangifer tarandus L.) from the Russian Arctic Zone: Regional and Seasonal Effects

Simple Summary

The reindeer (Rangifer tarandus) is a unique ruminant that lives in arctic areas characterized by severe living conditions. Low temperatures and a scarce diet containing a high proportion of hard-to-digest components have contributed to the development of several adaptations that allow reindeer to have a successful existence in the Far North region. These adaptations include the microbiome of the rumen—a digestive organ in ruminants that is responsible for crude fiber digestion through the enzymatic activity of microorganisms. In this study, research was conducted on the ruminal microbiome of reindeer of the Nenets breed living in various climatic zones of the Russian Arctic (in the Yamalo-Nenetski Autonomous District and Nenetski Autonomous District. The impacts of the habitat, season of the year, sex, and age factors on the rumen microbiome were investigated. As a result, it was found that significant differences in the reindeer ruminal microbiome composition are associated with the region of habitat and change of seasons that the reindeer are exposed to. The distinctions mainly come down to different ratios of bacteria involved in the metabolism of volatile fatty acids and cellulose decomposition in the rumen, which is apparently a reflection of the different plant components in the diet in different regions and seasons.

Abstract

The reindeer (Rangifer tarandus L.) is a unique animal inhabitant of arctic regions. Low ambient temperatures and scant diets (primarily, lichens) have resulted in different evolutional adaptations, including the composition of the ruminal microbiota. In the study presented here, the effects of seasonal and regional aspects of the composition of the ruminal microbiota in reindeer (Nenets breed, 38 animals) were studied (wooded tundra from the Yamalo-Nenetski Autonomous District (YNAD) vs. from the Nenetski Autonomous District (NAD)). The ruminal content of calves (n = 12) and adult animals (n = 26, 15 males and 11 females) was sampled in the summer (n = 16) and winter seasons (n = 22). The composition of the ruminal microbial population was determined by the V3–V4 16S rRNA gene region sequencing. It was found that the population was dominated by Bacteroidetes and Firmicutes phyla, followed by Spirochaetes and Verrucomicrobia. An analysis of the community using non-metric multidimensional scaling and Bray–Curtis similarity metrics provided evidence that the most influential factors affecting the composition of ruminal microbiota are the region (p = 0.001) and season (p = 0.001); heat map analysis revealed several communities that are strongly affected by these two factors. In the summer season, the following communities were significantly larger compared to in the winter season: Coriobactriaceae, Erysipelothrihaceae, and Mycoplasmataceae. The following communities were significantly larger in the winter season compared to in summer: Paraprevotellaceae, Butyrivibrio spp., Succiniclasticum spp., Coprococcus spp., Ruminococcus spp., and Pseudobutyrivibrio spp. In NAD (tundra), the following communities were significantly larger in comparison to YNAD (wooded tundra): Verrucomicrobia (Verruco-5), Anaerolinaceae, PeHg47 Planctomycetes, cellulolytic Lachnospiraceae, and Succiniclasticum spp. The following bacterial groups were significantly larger in YNAD in comparison to NAD: cellulolytic Ruminococaceae, Dehalobacteriaceae, Veillionelaceae, and Oscilospira spp. The significant differences in the ruminal microbial population were primarily related to the ingredients of diets, affected by region and season. The summer-related increases in the communities of certain pathogens (Mycoplasmataceae, Fusobacterium spp., Porphyromonas endodentalis) were found. Regional differences were primarily related to the ratio of the species involved in ruminal cellulose degradation and ruminal fatty acids metabolism; these differences reflect the regional dissimilarities in botanical diet ingredients.

Strategies to improve the efficiency of beef cattle production

Globally, there are approximately one billion beef cattle, and compared with poultry and swine, beef cattle have the poorest conversion efficiency of feed to meat. However, these metrics fail to consider that beef cattle produce high-quality protein from feeds that are unsuitable for other livestock species. Strategies to improve the efficiency of beef cattle are focusing on operational and breeding management, host genetics, functional efficiency of rumen and respiratory microbiomes, and the structure and composition of feed. These strategies must also consider the health and immunity of the herd as well as the need for beef cattle to thrive in a changing environment. Genotyping can identify hybrid vigor with positive consequences for animal health, productivity, and environmental adaptability. The role of microbiome–host interactions is key in efficient nutrient digestion and host health. Microbial markers and gene expression patterns within the rumen microbiome are being used to identify hosts that are efficient at fibre digestion. Plant breeding and processing are optimizing the feed value of both forages and concentrates. Strategies to improve the efficiency of cattle production are a prerequisite for the sustainable intensification needed to satisfy the future demand for beef.

Effects of king grass and sugarcane top in the absence or presence of exogenous enzymes on the growth performance and rumen microbiota diversity of goats

In the present study, the feasibility of sugarcane top (ST) application in the goat's diet was evaluated. A total of 20 goats were randomly divided into four groups. The dietary treatments were set as follows: animals were fed with king grass (KG), KG with exogenous enzymes (KGE), ST, and ST with exogenous enzymes (STE). The animals were given free access to feed and water. After 15 days of adaptation and 60 days of the experiment, the growth performance, plasma parameters, and rumen microbiota of goats were assessed. The results showed that the KG, ST, and exogenous enzyme supplement had no significant effects on the growth performance and plasma parameters. The diet affected the rumen microbiota diversity and structure, and the alpha and beta diversity in the animals fed with ST were dramatically greater compared with the animals fed with KG. The abundances of Proteobacteria, Cyanobacteria, and Elusimicrobia were significantly decreased in the animals fed with KG or KGE, while the abundances of Firmicutes and Euryarchaeota were significantly higher in the animals fed with KG or KGE. Furthermore, the microbial communities were also different at the genus level. Moreover, the exogenous enzymes had a slight effect on rumen microbiota. Linear discriminant analysis effect size (LEfSe) analysis showed that the greatest differences were found in bacterial taxa, and these specific taxa could be used as biomarkers to distinguish rumen microbiota. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) functional profile prediction indicated that the dietary treatments of ST and KG could also alter the gene expression pattern in nutrient and energy metabolism, as well as replication and repair of genetic information pathways. Collectively, the dietary treatments of KG and ST in the absence or presence of exogenous enzymes had similar effects on the growth performance and plasma parameters of goats. Besides, the KG and ST diets could affect the rumen microbiota community and function of goats. Therefore, ST could be used as a promising alternative feed resource for ruminants without the addition of exogenous enzymes in tropical regions.

Ruminal Degradation of Rumen-Protected Glucose Influences the Ruminal Microbiota and Metabolites in Early-Lactation Dairy Cows

Rumen-protected glucose (RPG) plays an important role in alleviating the negative energy balance of dairy cows. This study used a combination of rumen microbes 16S and metabolomics to elucidate the changes of rumen microbial composition and rumen metabolites of different doses of RPG's rumen degradation part in early-lactation dairy cows. Twenty-four multiparous Holstein cows in early lactation were randomly allocated to control (CON), low-RPG (LRPG), medium-RPG (MRPG), or high-RPG (HRPG) groups in a randomized block design. The cows were fed a basal total mixed ration diet with 0, 200, 350, and 500 g of RPG per cow per day, respectively. Rumen fluid samples were analyzed using Illumina MiSeq sequencing and ultrahigh-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. MRPG supplementation increased bacterial richness and diversity, including increasing the relative abundance of cellulolytic bacteria, such as Ruminococcus, Lachnospiraceae_NK3A20_group, Ruminiclostridium, and Lachnospiraceae_UCG-008 MRPG significantly increased the concentrations of acetate, propionate, butyrate, and total volatile fatty acid in the rumen. Ruminal fluid metabolomics analysis showed that RPG supplementation could significantly regulate the synthesis of amino acids digested by protozoa in the rumen. Correlation analysis of the ruminal microbiome and metabolome revealed some potential relationships between major bacterial abundance and metabolite concentrations. Our analysis found that RPG supplementation of different doses can change the diversity of microorganisms in the rumen and affect the rumen fermentation pattern and microbial metabolism and that a daily supplement of 350 g of RPG might be the ideal dose.IMPORTANCE Dairy cows in early lactation are prone to a negative energy balance because their dry matter intake cannot meet the energy requirements of lactation. Rumen-protected glucose is used as an effective feed additive to alleviate the negative energy balance of dairy cows in early lactation. However, one thing that is overlooked is that people often think that rumen-protected glucose is not degraded in the rumen, thus ignoring its impact on the microorganisms in the rumen environment. Our investigation and previous experiments have found that rumen-protected glucose is partially degraded in the rumen. However, there are few reports on this subject. Therefore, we conducted research on this problem and found that rumen-protected glucose supplementation at 350 g/day can promote the development and metabolism of rumen flora. This provides a theoretical basis for the extensive application of rumen bypass glucose at a later stage.

Ruminal microbiota-host interaction and its effect on nutrient metabolism

Rumen microbiota has a close and intensive interaction with the ruminants. Microbiota residing in the rumen digests and ferments plant organic matters into nutrients that are subsequently utilized by the host, making ruminants a unique group of animals that can convert plant materials indigestible by humans into high-quality animal protein as meat and milk. Many studies using meta-omics technologies have demonstrated the relationships between rumen microbiome and animal phenotypes associated with nutrient metabolism. Recently, the causality and physiological mechanisms underpinning the host-microbiota interactions have attracted tremendous research interest among researchers. This review discusses the host-microbiota interactions and the factors affecting these interactions in ruminants and provides a summary of the advances in research on animal husbandry. Understanding the microbiota composition, the functions of key bacteria, and the host-microbiota interaction is crucial for the development of knowledge-based strategies to enhance animal productivity and host health.

The Horse Gut Microbiome Responds in a Highly Individualized Manner to Forage Lignification

Although contributions of the equine gut microbiome to forage utilization are well recognized, the impact of alfalfa (Medicago sativa L.) lignification on the equine gut microbiome remains unknown; thus, we characterized microbial communities in the equine gut when feeding reduced lignin (RL) and conventional (CON) alfalfa hays to adult stock-type horses. Dietary treatments were fed to six horses in a crossover study. Experimental periods consisted of a 9-day dietary adaptation phase followed by a 5-day total fecal collection phase, during which horses were housed in individual box stalls and manure was removed on a continuous 24-hour basis. At 12-hour intervals, manure was mixed, frozen, and processed for V4, 16S rRNA amplicon MiSeq sequencing. Reduced lignin alfalfa did not shift microbiome composition equally across all horses; however, each subject's microbiome responded to hay lignin content in an individualized manner, mostly, in terms of beta diversity. Amplicon sequence variants affiliated to Akkermansia, Fibrobacter succinogenes, Treponema, and Paludibacter fluctuated significantly when RL alfalfa was fed, with abundance patterns unique to each horse. Horse-specific associations between individual gut microbiome traits and characteristics of the digested CON or RL alfalfa were also observed, mainly in regards to dry matter digestibility and mean fecal particle size. These results indicate that the horse gut microbiome responds in an individualized manner to changes in the amount of acid detergent lignin in alfalfa hay, potentially impacting several feed digestibility characteristics. The implications of these horse-specific responses to hay lignification, for metabolic health and performance, remain to be elucidated.

Cross Inoculation of Rumen Fluid to Improve Dry Matter Disappearance and Its Effect on Bacterial Composition Using an in vitro Batch Culture Model

Environmental pressures of ruminant production could be reduced by improving digestive efficiency. Previous in vivo attempts to manipulate the rumen microbial community have largely been unsuccessful probably due to the influencing effect of the host. Using an in vitro consecutive batch culture technique, the aim of this study was to determine whether manipulation was possible once the bacterial community was uncoupled from the host. Two cross inoculation experiments were performed. Rumen fluid was collected at time of slaughter from 11 Holstein-Friesian steers from the same herd for Experiment 1, and in Experiment 2 were collected from 11 Charolais cross steers sired by the same bull and raised on a forage only diet on the same farm from birth. The two fluids that differed most in their in vitro dry matter disappearance (IVDMD; “Good,” “Bad”) were selected for their respective experiment. The fluids were also mixed (1:1, “Mix”) and used to inoculate the model. In Experiment 1, the mixed rumen fluid resulted in an IVDMD midway between that of the two rumen fluids from which it was made for the first 24 h batch culture (34, 29, 20 g per 100 g DM for the Good, Mix, and Bad, respectively, P < 0.001) which was reflected in fermentation parameters recorded. No effect of cross inoculation was seen for Experiment 2, where the Mix performed most similarly to the Bad. In both experiments, IVDMD increased with consecutive culturing as the microbial population adapted to the in vitro conditions and differences between the fluids were lost. The improved performance with each consecutive batch culture was associated with reduced bacterial diversity. Increases in the genus Pseudobutyrivibrio were identified, which may be, at least in part, responsible for the improved digestive efficiency observed, whilst Prevotella declined by 50% over the study period. It is likely that along with host factors, there are individual factors within each community that prevent other microbes from establishing. Whilst we were unable to manipulate the bacterial community, uncoupling the microbiota from the host resulted in changes in the community, becoming less diverse with time, likely due to environmental heterogeneity, and more efficient at digesting DM.

Temporal changes in the fecal bacterial community in Holstein dairy calves from birth through the transition to a solid diet

The development of a robust microbiome is critical to the health of dairy calves, but relatively little is known about the progression of the microbiome through the weaning transition. In this study, fecal samples were obtained from ten female Holstein calves at 6 timepoints between 2–13 weeks of age. Calves were fed acidified milk until weaning at 8 weeks old and had access to starter grain throughout the study. Fecal samples were extracted for genomic DNA, PCR-amplified for the V1-V2 region of the 16S rRNA bacterial gene, sequenced on the Illumina MiSeq platform, and analyzed using the QIIME2 pipeline. Bacterial richness, estimated by number of observed species, and bacterial diversity, estimated by Shannon diversity index, both differed significantly between timepoints and both increased over time (P <0.05), with the largest increases occurring during weaning. Weighted and unweighted UniFrac analysis showed significant differences (P <0.05) between bacterial communities across timepoints; betadisper analysis revealed that the microbiomes of individual calves became more similar with time. Throughout the study, Firmicutes was the dominant phylum, followed by Bacteroidetes. Thirteen bacterial genera were found to be significantly influenced by time, including Faecalibacterium, Clostridium, unclassified S24-7, Collinsella, Sharpea, and Treponema. Unclassified Ruminococcaceae was the most prevalent genus at timepoints 1, 3, 5, and 6, but different amplicon sequence variants were detected at each timepoint suggesting the presence of different species of Ruminococcaceae at different times. Bacteroides was the most prevalent genus at timepoint 2, and Prevotella was most prevalent at timepoint 4. Our results indicate that there is considerable variation in the calf microbiome pre-weaning, but the microbial community stabilizes and becomes similar to the adult microbiome at weaning. Further studies to describe the phylogeny and functionality of core microbiota through the weaning transition are needed to improve health and reduce diarrhea in the neonatal period.

Investigating temporal microbial dynamics in the rumen of beef calves raised on two farms during early life

Manipulation of the rumen microorganisms during early life has emerged as a promising strategy for persistent improvement of nutrient utilisation and lowering of enteric methanogenesis. However, limited understanding of the dynamics of rumen microbial colonisation has prevented the identification of the optimum timeframe for such interventions. The present study used DNA amplicon sequencing of the 16S rRNA gene to assess bacterial and archaeal dynamics in the rumen digesta of beef calves raised on two farms from birth through to post-weaning. The colonisation patterns of both communities were influenced by age (P < 0.05) and farm of origin (P < 0.05). The bacterial community exhibited an age-wise progression during the first month of life which appeared to be partly related to diet, and settled by day 21, indicating that this may mark the boundary of a timeframe for intervention. The archaeal community appeared less sensitive to age/diet than bacteria in the first month of life but was more sensitive to farm environment. These data show that ruminal microbial composition during early life is driven by calf age, diet and local environment, and provide important fundamental information concerning the ontogeny of the rumen microbiota from birth.

Contribution of influent rivers affected by different types of pollution to the changes of benthic microbial community structure in a large lake

As a microbial group in watershed ecosystems, the bacterial community is a sensitive indicator of external environmental fluctuations. However, the effects of different sources of exogenous pollution on the diversity and structure of bacterial communities in inflow rivers and lakes have not been studied in depth. In this study, we used 16S rRNA gene sequencing technology to study the diversity and composition of bacterial communities in rivers affected by different types of pollution. The results showed that the composition of the bacterial communities in rivers with different exogenous pollution sources was different. For example, the genus Arenimonas, which belongs to the Gamma-proteobacteria, is extensively enriched in IDPR (industrially and domestically polluted rivers) and ADPR (agriculturally and domestically polluted rivers) (KW, p < 0.05), while the genus Micromonospora is a more unique genus found in APR (agriculturally polluted rivers). When exploring the topology and classification characteristics of river microbial symbiosis models, it was found that the bacterial community symbiosis network is divided into six modules under different exogenous pollution regimes, and the nodes in the different modules perform different functions, such as the IDPR-dominated module I. In the network, the relatively abundant the genus Flavobacterium and the genus Nitrospira are the key factors driving the nitrogen cycle in the watershed where the samples were collected. In addition, our research indicates that communities in lake environments may be more susceptible to disturbances of various physiological or functional redundancies, thus retaining their original community structure. Overall, this study emphasizes that adaptive changes in the bacterial community structure of the sediments in the catchment and the occurrence of interactions are responses to different exogenous pollution sources.

Survey of rumen microbiota of domestic grazing yak during different growth stages revealed novel maturation patterns of four key microbial groups and their dynamic interactions

BACKGROUND

The development and maturation of rumen microbiota across the lifetime of grazing yaks remain unexplored due to the varied lifestyles and feed types of yaks as well as the challenges of obtaining samples. In addition, the interactions among four different rumen microbial groups (bacteria, archaea, fungi and protozoa) in the rumen of yak are not well defined. In this study, the rumen microbiota of full-grazing yaks aged 7 days to 12 years old was assessed to determine the maturation patterns of these four microbial groups and the dynamic interactions among them during different growth stages.

RESULTS

The rumen microbial groups (bacteria, archaea, protozoa and fungi) varied through the growth of yaks from neonatal (7 days) to adult (12 years), and the bacterial and archaeal groups were more sensitive to changes in growth stages compared to the two eukaryotic microbial groups. The age-discriminatory taxa within each microbial group were identified with the random forest model. Among them, Olsenella (bacteria), Group 10 sp., belonging to the family Methanomassiliicoccaceae (archaea), Orpinomyces (fungi), and Dasytricha (protozoa) contributed the most to discriminating the age of the rumen microbiota. Moreover, we found that the rumen archaea reached full maturation at 5 approximately years of age, and the other microbial groups matured between 5 and 8 years of age. The intra-interactions patterns and keystone species within each microbial group were identified by network analysis, and the inter-interactions among the four microbial groups changed with growth stage. Regarding the inter-interactions among the four microbial groups, taxa from bacteria and protozoa, including Christensenellaceae R-7 group, Prevotella 1, Trichostomatia, Ruminococcaceae UCG-014 and Lachnospiraceae, were the keystone species in the network based on betweenness centrality scores.

CONCLUSIONS

This study depicted a comprehensive view of rumen microbiota changes in different growth stages of grazing yaks. The results revealed the unique microbiota maturation trajectory and the intra- and inter-interactions among bacteria, archaea, fungi and protozoa in the rumen of grazing yaks across the lifetime of yaks. The information obtained in this study is vital for the future development of strategies to manipulate rumen microbiota in grazing yaks for better growth and performance in the harsh Qinghai-Tibetan Plateau ecosystem.

The Role of the Gut Microbiome in Cattle Production and Health: Driver or Passenger?

Ruminant production systems face significant challenges currently, driven by heightened awareness of their negative environmental impact and the rapidly rising global population. Recent findings have underscored how the composition and function of the rumen microbiome are associated with economically valuable traits, including feed efficiency and methane emission. Although omics-based technological advances in the last decade have revolutionized our understanding of host-associated microbial communities, there remains incongruence over the correct approach for analysis of large omic data sets. A global approach that examines host/microbiome interactions in both the rumen and the lower digestive tract is required to harness the full potential of the gastrointestinal microbiome for sustainable ruminant production. This review highlights how the ruminant animal production community may identify and exploit the causal relationships between the gut microbiome and host traits of interest for a practical application of omic data to animal health and production.

A meta-analysis of the bovine gastrointestinal tract microbiota

The bovine gastrointestinal (GI) tract microbiota has important influences on animal health and production. Presently, a large number of studies have used high-throughput sequencing of the archaeal and bacteria 16S rRNA gene to characterize these microbiota under various experimental parameters. By aggregating publically available archaeal and bacterial 16S rRNA gene datasets from 52 studies we were able to determine taxa that are common to nearly all microbiota samples from the bovine GI tract as well as taxa that are strongly linked to either the rumen or feces. The methanogenic genera Methanobrevibacter and Methanosphaera were identified in nearly all fecal and rumen samples (> 99.1%), as were the bacterial genera Prevotella and Ruminococcus (≥ 92.9%). Bacterial genera such as Alistipes, Bacteroides, Clostridium, Faecalibacterium and Escherichia/Shigella were associated with feces and Fibrobacter, Prevotella, Ruminococcus and Succiniclasticum with the rumen. As expected, individual study strongly affected the bacterial community structure, however, fecal and rumen samples did appear separated from each other. This meta-analysis provides the first comparison of high-throughput sequencing 16S rRNA gene datasets generated from the bovine GI tract by multiple studies and may serve as a foundation for improving future microbial community research with cattle.

Review: Ruminal microbiome and microbial metabolome: effects of diet and ruminant host

The rumen contains a great diversity of prokaryotic and eukaryotic microorganisms that allow the ruminant to utilize ligno-cellulose material and to convert non-protein nitrogen into microbial protein to obtain energy and amino acids. However, rumen fermentation also has potential deleterious consequences associated with the emissions of greenhouse gases, excessive nitrogen excreted in manure and may also adversely influence the nutritional value of ruminant products. While several strategies for optimizing the energy and nitrogen use by ruminants have been suggested, a better understanding of the key microorganisms involved and their activities is essential to manipulate rumen processes successfully. Diet is the most obvious factor influencing the rumen microbiome and fermentation. Among dietary interventions, the ban of antimicrobial growth promoters in animal production systems has led to an increasing interest in the use of plant extracts to manipulate the rumen. Plant extracts (e.g. saponins, polyphenol compounds, essential oils) have shown potential to decrease methane emissions and improve the efficiency of nitrogen utilization; however, there are limitations such as inconsistency, transient and adverse effects for their use as feed additives for ruminants. It has been proved that the host animal may also influence the rumen microbial population both as a heritable trait and through the effect of early-life nutrition on microbial population structure and function in adult ruminants. Recent developments have allowed phylogenetic information to be upscaled to metabolic information; however, research effort on cultivation of microorganisms for an in-depth study and characterization is needed. The introduction and integration of metagenomic, transcriptomic, proteomic and metabolomic techniques is offering the greatest potential of reaching a truly systems-level understanding of the rumen; studies have been focused on the prokaryotic population and a broader approach needs to be considered.

The day-to-day stability of the ruminal and fecal microbiota in lactating dairy cows

In this study, we examined differences between the microbiota of the ruminal fluid (DR) and feces (DF) from five lactating dairy cows over three consecutive days using 16S rRNA gene sequence-based analysis. Results showed significant differences between the microbial communities of the DR and DF. In particular, the relative abundance of the phyla Firmicutes and Actinobacteria was significantly lower (q < 0.001) in DR compared with DF, while the relative abundance of Bacteroidetes was significantly higher in DF than that of DR (q < 0.001). A significantly higher relative abundance of the genera Bifidobacterium, 5-7N15, Clostridium, Epulopiscium, SMB53, Turicibacter, Dorea, Roseburia, and Akkermansia was observed in the DF, while a higher relative abundance of the genera Prevotella, Butyrivibrio, CF231, RFN20, and Succiniclasticum was observed in the DR. A further analysis using the functional prediction program PICRUSt showed that sequences belonging to the 5-7N15, Akkermansia, Bifidobacterium, Clostridium, Dorea, Epulopiscium, Roseburia, and Turicibacter were significantly and positively correlated with glycan biosynthesis and metabolism, while CF231, Prevotella, RFN20, and Succiniclasticum were significantly and positively correlated with amino acid, lipid, carbohydrate, other amino acid, cofactors, and vitamins metabolism. No significant differences were observed across the three consecutive days in either the DR or DF ecosystems, with no significant differences in the diversity or abundance at the phylum and genus levels suggested that there is a limited day-to-day variability in the gut microbiota.

Synchrony Degree of Dietary Energy and Nitrogen Release Influences Microbial Community, Fermentation, and Protein Synthesis in a Rumen Simulation System

Synchrony of energy and nitrogen release in rumen has been proposed to maximize ruminal microbial fermentation. However, the information regarding bacterial community composition and its metabolism under a higher or lower degree of synchronization is limited. In our study, a 0 to 6 h post-feeding infusion (first half infusion, FHI), 6 to 12 h post-feeding infusion (second half infusion, SHI), and 0 to 12 h post-feeding infusion (continuous infusion, CI) of maltodextrin were used to simulate varying degrees of synchronization of energy and nitrogen release in a rumen simulation system. In addition, the bacterial community, metabolite, enzyme activity, and microbial protein synthesis (MPS) were evaluated. Compared with the FHI and CI, the relative abundance of Fibrobacter, Ruminobacter, BF311, and CF231 decreased in the SHI, but that of Klebsiella and Succinivibrio increased in the SHI. The NH₃-N and branched-chain volatile fatty acids were significantly higher, but propionate content and activities of glutamate dehydrogenase (GDH) and alanine dehydrogenase were significantly lower in the SHI than those in the FHI and CI. The SHI had lower MPS and less efficiency of MPS than the FHI and CI, which indicated that the SHI had a lower degree of synchronization. Correlation analysis showed that MPS was positively related to GDH activity and relative abundance of Fibrobacter but negatively related to NH₃-N and relative abundance of Klebsiella. Therefore, a higher degree of synchronization of energy and nitrogen release increased MPS partly via influencing the bacterial community, metabolism, and enzyme activities of ammonia assimilation in the in vitro fermenters.