Methane produced by methanogenic archaea in ruminants contributes significantly to anthropogenic greenhouse gas emissions. The host genetic link controlling microbial methane production is unknown and appropriate genetic selection strategies are not developed. We used sire progeny group differences to estimate the host genetic influence on rumen microbial methane production in a factorial experiment consisting of crossbred breed types and diets. Rumen metagenomic profiling was undertaken to investigate links between microbial genes and methane emissions or feed conversion efficiency. Sire progeny groups differed significantly in their methane emissions measured in respiration chambers. Ranking of the sire progeny groups based on methane emissions or relative archaeal abundance was consistent overall and within diet, suggesting that archaeal abundance in ruminal digesta is under host genetic control and can be used to genetically select animals without measuring methane directly. In the metagenomic analysis of rumen contents, we identified 3970 microbial genes of which 20 and 49 genes were significantly associated with methane emissions and feed conversion efficiency respectively. These explained 81% and 86% of the respective variation and were clustered in distinct functional gene networks. Methanogenesis genes (e.g. mcrA and fmdB) were associated with methane emissions, whilst host-microbiome cross talk genes (e.g. TSTA3 and FucI) were associated with feed conversion efficiency. These results strengthen the idea that the host animal controls its own microbiota to a significant extent and open up the implementation of effective breeding strategies using rumen microbial gene abundance as a predictor for difficult-to-measure traits on a large number of hosts. Generally, the results provide a proof of principle to use the relative abundance of microbial genes in the gastrointestinal tract of different species to predict their influence on traits e.g. human metabolism, health and behaviour, as well as to understand the genetic link between host and microbiome.

BackgroundMethane represents 16 % of total anthropogenic greenhouse gas emissions. It has been estimated that ruminant livestock produce ca. 29 % of this methane. As individual animals produce consistently different quantities of methane, understanding the basis for these differences may lead to new opportunities for mitigating ruminal methane emissions. Metagenomics is a powerful new tool for understanding the composition and function of complex microbial communities. Here we have applied metagenomics to the rumen microbial community to identify differences in the microbiota and metagenome that lead to high- and low-methane-emitting cattle phenotypes.MethodsFour pairs of beef cattle were selected for extreme high and low methane emissions from 72 animals, matched for breed (Aberdeen-Angus or Limousin cross) and diet (high or medium concentrate). Community analysis was carried out by qPCR of 16S and 18S rRNA genes and by alignment of Illumina HiSeq reads to the GREENGENES database. Total genomic reads were aligned to the KEGG genes databasefor functional analysis.ResultsDeep sequencing produced on average 11.3 Gb per sample. 16S rRNA gene abundances indicated that archaea, predominantly Methanobrevibacter, were 2.5× more numerous (P = 0.026) in high emitters, whereas among bacteria Proteobacteria, predominantly Succinivibrionaceae, were 4-fold less abundant (2.7 vs. 11.2 %; P = 0.002). KEGG analysis revealed that archaeal genes leading directly or indirectly to methane production were 2.7-fold more abundant in high emitters. Genes less abundant in high emitters included acetate kinase, electron transport complex proteins RnfC and RnfD and glucose-6-phosphate isomerase. Sequence data were assembled de novo and over 1.5 million proteins were annotated on the subsequent metagenome scaffolds. Less than half of the predicted genes matched matched a domain within Pfam. Amongst 2774 identified proteins of the 20 KEGG orthologues that correlated with methane emissions, only 16 showed 100 % identity with a publicly available protein sequence.ConclusionsThe abundance of archaeal genes in ruminal digesta correlated strongly with differing methane emissions from individual animals, a finding useful for genetic screening purposes. Lower emissions were accompanied by higher Succinovibrionaceae abundance and changes in acetate and hydrogen production leading to less methanogenesis, as similarly postulated for Australian macropods. Large numbers of predicted protein sequences differed between high- and low-methane-emitting cattle. Ninety-nine percent were unknown, indicating a fertile area for future exploitation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2032-0) contains supplementary material, which is available to authorized users.

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The nutritional and immunological importance of colostrum for the survival and development of the neonatal pig are reviewed. The pig is born with low body energy stores and devoid of serum immunoglobulins. Colostrum provides the piglet with both energy and maternal antibodies but its fat and protein composition is very variable. Colostrum is very digestible, and both colostral energy and nitrogen (N) are retained with a very high efficiency. Colostrum production by the sow assessed from the weight gain of the litter from birth to 24 h of age is very variable (from 1900 to 5300 g). There is no clear effect of litter size or parity, suggesting that colostrum production is a characteristic of the sow. Within a litter, colostrum consumption by the individual piglets varies considerably. It is independent of birth order, but related positively to birth weight and negatively to litter size. Other factors influencing colostrum consumption, including cold stress, premature birth and birth hypoxia, are discussed. Because of the epitheliochorial nature of the porcine placenta, the new-born piglet must acquire maternal immunoglobulin G (IgG) from ingested colostrum for passive immune protection until the immune system of the piglet becomes fully developed. Colostrum IgG concentrations in milk vary widely between individual sows both in initial concentration and in the rate at which concentrations decline during the first 24 h of life. The piglet can only absorb intact IgG prior to gut closure, which occurs in the first 24 h of life and is induced by intakes of colostrum which are insufficient to maintain piglet live-weight. As a result, the amounts of intact IgG absorbed by the piglet vary widely. The effects of colostrum consumption on neonatal survival are discussed. Consumption of colostrum in amounts sufficient to meet the energy requirement of the piglet is a major determinant for survival. Since most neonatal losses occur in the first 2 days of life, before acquisition of a maternal IgG for immune protection becomes important for survival, piglet serum IgG concentration does not correlate well with early survival but is important in later resistance to disease challenge. It is concluded that colostrum production is a good marker for the maternal quality of the sow. Future research should focus on the ability of the sow to produce more colostrum and on the possible delayed effects of passive immunisation on the health and performance of piglet at weaning and later in life.

BackgroundThe emergence and spread of antimicrobial resistance is the most urgent current threat to human and animal health. An improved understanding of the abundance of antimicrobial resistance genes and genes associated with microbial colonisation and pathogenicity in the animal gut will have a major role in reducing the contribution of animal production to this problem. Here, the influence of diet on the ruminal resistome and abundance of pathogenicity genes was assessed in ruminal digesta samples taken from 50 antibiotic-free beef cattle, comprising four cattle breeds receiving two diets containing different proportions of concentrate.ResultsTwo hundred and four genes associated with antimicrobial resistance (AMR), colonisation, communication or pathogenicity functions were identified from 4966 metagenomic genes using KEGG identification. Both the diversity and abundance of these genes were higher in concentrate-fed animals. Chloramphenicol and microcin resistance genes were dominant in samples from forage-fed animals (P < 0.001), while aminoglycoside and streptomycin resistances were enriched in concentrate-fed animals. The concentrate-based diet also increased the relative abundance of Proteobacteria, which includes many animal and zoonotic pathogens. A high ratio of Proteobacteria to (Firmicutes + Bacteroidetes) was confirmed as a good indicator for rumen dysbiosis, with eight cases all from concentrate-fed animals. Finally, network analysis demonstrated that the resistance/pathogenicity genes are potentially useful as biomarkers for health risk assessment of the ruminal microbiome.ConclusionsDiet has important effects on the complement of AMR genes in the rumen microbial community, with potential implications for human and animal health.Electronic supplementary materialThe online version of this article (10.1186/s40168-017-0378-z) contains supplementary material, which is available to authorized users.