Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.

The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in “omic” data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent “omics” approaches continue to revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.

ABSTRACTFeed-efficient animals have lower production costs and reduced environmental impact. Given that rumen microbial fermentation plays a pivotal role in host nutrition, the premise that rumen microbiota may contribute to host feed efficiency is gaining momentum. Since diet is a major factor in determining rumen community structure and fermentation patterns, we investigated the effect of divergence in phenotypic residual feed intake (RFI) on ruminal community structure of beef cattle across two contrasting diets. PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) were performed to profile the rumen bacterial population and to quantify the ruminal populations ofEntodiniumspp., protozoa,Fibrobacter succinogenes,Ruminococcus flavefaciens,Ruminococcus albus,Prevotella brevis, the genusPrevotella, and fungi in 14 low (efficient)- and 14 high (inefficient)-RFI animals offered a low-energy, high-forage diet, followed by a high-energy, low-forage diet. Canonical correspondence and Spearman correlation analyses were used to investigate associations between physiological variables and rumen microbial structure and specific microbial populations, respectively. The effect of RFI on bacterial profiles was influenced by diet, with the association between RFI group and PCR-DGGE profiles stronger for the higher forage diet. qPCR showed thatPrevotellaabundance was higher (P< 0.0001) in inefficient animals. A higher (P< 0.0001) abundance ofEntodiniumandPrevotellaspp. and a lower (P< 0.0001) abundance ofFibrobacter succinogeneswere observed when animals were offered the low-forage diet. Thus, differences in the ruminal microflora may contribute to host feed efficiency, although this effect may also be modulated by the diet offered.

The objective of this study was to examine the effect of level and duration of feeding of an n-3 PUFA-enriched fish oil (FO) supplement in combination with soybean oil (SO) on the transcriptional regulation of Delta(9)-desaturase gene expression in bovine muscle. Beef bulls (n = 40) were assigned to 1 of 4 iso-lipid and isonitrogenous concentrate diets fed for ad libitum intake for a 100-d finishing period. Concentrates were supplemented with one of the following: 1) 6% SO (CON); 2) 6% SO + 1% FO (FO1); 3) 6% SO + 2% FO (FO2); or 4) 8% palmitic acid for the first 50 d and 6% SO + 2% FO for the second 50 d [FO2(50)]. Samples of LM were harvested and concentrations of fatty acids were measured. Total RNA was isolated and the gene expression of Delta(9)-desaturase was determined. The mRNA expression of putative regulators of Delta(9)-desaturase gene expression, sterol regulatory element binding protein-1c (SREBP-1c) and peroxisome proliferator activated receptor-alpha (PPAR-alpha), were also measured in the CON and FO2 groups. Expression of mRNA for Delta(9)-desaturase was decreased (P < 0.05) 2.6-, 4.4-, and 4.9-fold in FO1, FO2(50), and FO2 compared with CON, respectively. Expression of Delta(9)-desaturase mRNA tended to be reduced (P = 0.09) by increasing FO from 1 to 2%, but was not affected by duration of supplementation (P > 0.24). Expression of mRNA for SREBP-1c was decreased 2-fold in FO2 compared with CON (P < 0.05), whereas expression of PPAR-alpha was not affected (P > 0.30). There was a positive relationship between Delta(9)-desaturase and SREBP-1c gene expression (P < 0.01), but the expression of both genes was negatively related to tissue concentrations of n-3 PUFA (P < 0.05) and positively related to concentration of n-6 PUFA (P < 0.01). Simultaneous enhancement of tissue concentrations of CLA and n-3 PUFA concentrations in bovine muscle may be hindered by negative interactions between n-3 PUFA and Delta(9)-desaturase gene expression, possibly mediated through reduced expression of SREBP-1c.

Many microbes in complex competitive environments share genes for acquiring and utilising nutrients, questioning whether niche specialisation exists and if so, how it is maintained. We investigated the genomic signatures of niche specialisation in the rumen microbiome, a highly competitive, anaerobic environment, with limited nutrient availability determined by the biomass consumed by the host. We generated individual metagenomic libraries from 14 cows fed an ad libitum diet of grass silage and calculated functional isoform diversity for each microbial gene identified. The animal replicates were used to calculate confidence intervals to test for differences in diversity of functional isoforms between microbes that may drive niche specialisation. We identified 153 genes with significant differences in functional isoform diversity between the two most abundant bacterial genera in the rumen (Prevotella and Clostridium). We found Prevotella possesses a more diverse range of isoforms capable of degrading hemicellulose, whereas Clostridium for cellulose. Furthermore, significant differences were observed in key metabolic processes indicating that isoform diversity plays an important role in maintaining their niche specialisation. The methods presented represent a novel approach for untangling complex interactions between microorganisms in natural environments and have resulted in an expanded catalogue of gene targets central to rumen cellulosic biomass degradation.