Identifying active rumen epithelial associated bacteria and archaea in beef cattle divergent in feed efficiency using total RNA-seq

Rumen DNA virome and its relationship with feed efficiency in dairy cows

BACKGROUND

The rumen harbors a diverse virome that interacts with other microorganisms, playing pivotal roles in modulating metabolic processes within the rumen environment. However, the characterization of rumen viruses remains incomplete, and their association with production traits, such as feed efficiency (FE), has not been documented. In this study, rumen fluid from 30 Chinese Holstein dairy cows was analyzed using next-generation sequencing (NGS) and High-Fidelity (HiFi) sequencing to elucidate the rumen DNA virome profile and uncover potential viral mechanisms influencing FE.

RESULTS

Integrated NGS and HiFi sequencing enhanced the length, completeness, and resolution of viral operational taxonomic units (vOTUs) compared to NGS. A total of 6,922 vOTUs were identified, including 4,716 lytic and 1,961 temperate vOTUs. At the family level, lytic viruses were predominantly from Siphoviridae (30.35%) and Schitoviridae (23.93%), while temperate viruses were primarily Siphoviridae (67.21%). The study annotated 2,382 auxiliary metabolic genes (AMGs), comprising 1,752 lytic virus-associated AMGs across 51 functional categories and 589 temperate virus-associated AMGs across 29 categories. Additionally, 2,232 vOTU-host metagenome-assembled genome (hMAG) linkages were predicted, with Firmicutes_A (33.60%) and Bacteroidota (33.24%) being the most prevalent host phyla. Significant differences in viral populations were observed between high and low FE groups across multiple taxonomic levels (P < 0.05). Two pathways were proposed to explain how rumen viruses might modulate FE: (1) Lytic viruses could lyse beneficial host bacteria linked to favorable cattle phenotypes, such as vOTU1836 targeting Ruminococcaceae, resulting in diminished organic acid production and consequently lower FE; (2) AMG-mediated host metabolism modulation, exemplified by GT2 carried by vOTU0897, which may enhance Lachnospiraceae fermentation capacity, increasing organic acid production and thereby improving FE.

CONCLUSIONS

This study constructed a comprehensive rumen DNA virome profile for Holstein dairy cows, elucidating the structural and functional complexity of rumen viruses, the roles of AMGs, and vOTU-hMAG linkages. The integration of these data offers novel insights into the mechanisms by which rumen viruses may regulate nutrient utilization, potentially influencing FE in dairy cows. Video Abstract.

- Invited Review - Translational gut microbiome research for strategies to improve beef cattle production sustainability and meat quality

Advanced and innovative breeding and management of meat-producing animals are needed to address the global food security and sustainability challenges. Beef production is an important industry for securing animal protein resources in the world and meat quality significantly contributes to the economic values and human needs. Improvement of cattle feed efficiency has become an urgent task as it can lower the environmental burden of methane gas emissions and the reduce the consumption of human edible cereal grains. Cattle depend on their symbiotic microbiome and its activity in the rumen and gut to maintain growth and health. Recent developments in high-throughput omics analysis (metagenome, metatranscriptome, metabolome, metaproteome and so on) have made it possible to comprehensively analyze microbiome, hosts and their interactions and to define their roles in affecting cattle biology. In this review, we focus on the relationships among gut microbiome and beef meat quality, feed efficiency, methane emission as well as host genetics in beef cattle, aiming to determine the current knowledge gaps for the development of the strategies to improve the sustainability of beef production.

Initial timing of alfalfa hay supplementation manipulates blood parameters, rumen gene expression, and epithelial microbiota in pre-weaning lambs

The present study aimed to investigate the impact of initiating alfalfa supplementation at either 14 d or 42 d of age on growth performance, blood parameters, rumen tissue gene expression, and epithelial microbiota in pre-weaning lambs. A total of 42 seven-day-old male Hu lambs (3.88 ± 0.92 kg) were selected for this study. After 7 d of adjustment period, 6 lambs were slaughtered at 14 d of age to establish a baseline control. The remaining 36 lambs were randomly allocated to 2 treatment groups, every 3 lambs were considered a unit, including fed milk replacer, starter pellets, and either alfalfa hay fed at 14 (EAF) or 42 d of age (LAF). Body weight and feed intake were recorded for lamb until 70 d of age. Blood samples, rumen tissue samples, and epithelial microbiota samples were collected from the lambs at 42, 56, and 70 d of age. The results indicated that average daily gain, starter intake, and total dry matter intake were greater in the EAF group compared to the LAF group from 14 to 42 d of age (P < 0.01), but no significant differences from 43 to 70 d of age or during the entire trial. Treatment and age interactively affected the alfalfa intake (P = 0.02) from 43 to 70 d of age. The concentration of serum immunoglobulin A (IgA) (P < 0.01) and the expression of the rumen gene insulin-like growth factor-1 (P < 0.01) were greater in the EAF group compared to the LAF group at 42 d of age. Furthermore, the concentrations of alkaline phosphatase (P = 0.03), albumin (P < 0.01), total protein (P = 0.03), urea (P = 0.04), lipopolysaccharide (P < 0.01), β-hydroxybutyric acid (P = 0.02), interleukin-1β (IL-1β) (P < 0.01), IL-4 (P < 0.01), and tumor necrosis factor-α (P < 0.01) were affected by age. The abundance of Prevotella was lower (P < 0.05), whereas Megasphaera (P < 0.05) was greater in the EAF group compared to the LAF group at 42 d of age. The early addition of alfalfa promotes rumen epithelial microbiota colonization. In conclusion, this study demonstrated that alfalfa provision at 14 d of age promotes growth performance in lambs, but this effect disappeared at 43 to 70 d of age. Moreover, provision of alfalfa at 14 d of age enhances the immune response, promotes rumen tissue cell proliferation, and affects dynamical changes of rumen epithelial microbiota. Meanwhile, our findings showed that the rumen undergoes significant physiological challenges during the transition from a liquid diet to a solid diet.

Evolving understanding of rumen methanogen ecophysiology

Production of methane by methanogenic archaea, or methanogens, in the rumen of ruminants is a thermodynamic necessity for microbial conversion of feed to volatile fatty acids, which are essential nutrients for the animals. On the other hand, methane is a greenhouse gas and its production causes energy loss for the animal. Accordingly, there are ongoing efforts toward developing effective strategies for mitigating methane emissions from ruminant livestock that require a detailed understanding of the diversity and ecophysiology of rumen methanogens. Rumen methanogens evolved from free-living autotrophic ancestors through genome streamlining involving gene loss and acquisition. The process yielded an oligotrophic lifestyle, and metabolically efficient and ecologically adapted descendants. This specialization poses serious challenges to the efforts of obtaining axenic cultures of rumen methanogens, and consequently, the information on their physiological properties remains in most part inferred from those of their non-rumen representatives. This review presents the current knowledge of rumen methanogens and their metabolic contributions to enteric methane production. It also identifies the respective critical gaps that need to be filled for aiding the efforts to mitigate methane emission from livestock operations and at the same time increasing the productivity in this critical agriculture sector.

Effects of rearing mode on gastro-intestinal microbiota and development, immunocompetence, sanitary status and growth performance of lambs from birth to two months of age

BACKGROUND

Artificial rearing system, commonly used in prolific sheep breeds, is associated to increased mortality and morbidity rates before weaning, which might be linked to perturbations in digestive tract maturation, including microbiota colonization. This study evaluated the effect of rearing mode (mothered or artificially reared) on the establishment of the rumen and intestinal microbiome of lambs from birth to weaning. We also measured immunological and zootechnical parameters to assess lambs' growth and health. GIT anatomy as well as rumen and intestinal epithelium gene expression were also analysed on weaned animals to assess possible long-term effects of the rearing practice.

RESULTS

Total VFA concentrations were higher in mothered lambs at 2 months of age, while artificially-reared lambs had lower average daily gain, a more degraded sanitary status and lower serum IgG concentration in the early growth phase. Metataxonomic analysis revealed higher richness of bacterial and eukaryote populations in mothered vs. artificially-reared lambs in both Rumen and Feces. Beta diversity analysis indicated an evolution of rumen and fecal bacterial communities in mothered lambs with age, not observed in artificially-reared lambs. Important functional microorganisms such as the cellulolytic bacterium Fibrobacter succinogenes and rumen protozoa did not establish correctly before weaning in artificially-reared lambs. Enterobacteriaceae and Escherichia coli were dominant in the fecal microbiota of mothered lambs, but main E. coli virulence genes were not found differential between the two groups, suggesting they are commensal bacteria which could exert a protective effect against pathogens. The fecal microbiota of artificially-reared lambs had a high proportion of lactic acid bacteria taxa. No difference was observed in mucosa gene expression in the two lamb groups after weaning.

CONCLUSIONS

The rearing mode influences gastrointestinal microbiota and health-associated parameters in offspring in early life: rumen maturation was impaired in artificially-reared lambs which also presented altered sanitary status and higher risk of gut dysbiosis. The first month of age is thus a critical period where the gastrointestinal tract environment and microbiota are particularly unstable and special care should be taken in the management of artificially fed newborn ruminants.

Breed and ruminal fraction effects on bacterial and archaeal community composition in sheep

While the breed of cattle can impact on the composition and structure of microbial communities in the rumen, breed-specific effects on rumen microbial communities have rarely been examined in sheep. In addition, rumen microbial composition can differ between ruminal fractions, and be associated with ruminant feed efficiency and methane emissions. In this study, 16S rRNA amplicon sequencing was used to investigate the effects of breed and ruminal fraction on bacterial and archaeal communities in sheep. Solid, liquid and epithelial rumen samples were obtained from a total of 36 lambs, across 4 different sheep breeds (Cheviot (n = 10), Connemara (n = 6), Lanark (n = 10) and Perth (n = 10)), undergoing detailed measurements of feed efficiency, who were offered a nut based cereal diet ad-libitum supplemented with grass silage. Our results demonstrate that the feed conversion ratio (FCR) was lowest for the Cheviot (most efficient), and highest for the Connemara breed (least efficient). In the solid fraction, bacterial community richness was lowest in the Cheviot breed, while Sharpea azabuensis was most abundant in the Perth breed. Lanark, Cheviot and Perth breeds exhibited a significantly higher abundance of epithelial associated Succiniclasticum compared to the Connemara breed. When comparing ruminal fractions, Campylobacter, Family XIII, Mogibacterium, and Lachnospiraceae UCG-008 were most abundant in the epithelial fraction. Our findings indicate that breed can impact the abundance of specific bacterial taxa in sheep while having little effect on the overall composition of the microbial community. This finding has implications for genetic selection breeding programs aimed at improving feed conversion efficiency of sheep. Furthermore, the variations in the distribution of bacterial species identified between ruminal fractions, notably between solid and epithelial fractions, reveals a rumen fraction bias, which has implications for sheep rumen sampling techniques.

Differential carbon utilization enables co-existence of recently speciated Campylobacteraceae in the cow rumen epithelial microbiome

The activities of different microbes in the cow rumen have been shown to modulate the host's ability to utilize plant biomass, while the host-rumen interface has received little attention. As datasets collected worldwide have pointed to Campylobacteraceae as particularly abundant members of the rumen epithelial microbiome, we targeted this group in a subset of seven cows with meta- and isolate genome analysis. We show that the dominant Campylobacteraceae lineage has recently speciated into two populations that were structured by genome-wide selective sweeps followed by population-specific gene import and recombination. These processes led to differences in gene expression and enzyme domain composition that correspond to the ability to utilize acetate, the main carbon source for the host, at the cost of inhibition by propionate. This trade-off in competitive ability further manifests itself in differential dynamics of the two populations in vivo. By exploring population-level adaptations that otherwise remain cryptic in culture-independent analyses, our results highlight how recent evolutionary dynamics can shape key functional roles in the rumen microbiome.

Distinctive roles between rumen epimural and content bacterial communities on beef cattle feed efficiency: A combined analysis

Rumen content-associated (RC) and epithelial tissue-attached (RT) bacterial communities are composed of different phylotypes and play distinctive roles. This study aimed to compare the composition of the RT and RC bacterial communities of steers differing in feed efficiency. The microbiota of RT and RC samples collected from sixteen beef steers with high or low residual feed intake (RFI) were analyzed through sequencing of partial 16S rRNA gene amplicons. Bacteroidetes, Proteobacteria and Firmicutes were the predominant phyla and Prevotella was the most abundant genus in both RC and RT bacterial communities. In total, 19 OTUs of the RC samples and 19 OTUs of the RT samples were differentially abundant (DA) between H-RFI and l-RFI steers. Among them, a common DA OTU belonged to Prevotella genus was identified in both RC and RT samples, making it the potential key microbial marker for indicating feed efficiency of steers. The co-occurrence of the DA OTUs among RT and RC samples suggest the importance of these two communities function as a complete system in influencing host feed efficiency.