Populations of Select Cultured and Uncultured Bacteria in the Rumen of Sheep and the Effect of Diets and Ruminal Fractions

[摘要] The objective of this study was to assess the importance of select cultured and uncultured bacteria in the rumen by quantifying their populations and the effect of diets and ruminal fractions. Full-length 16S rRNA gene (rrs) sequences were recovered from rumen samples using specific primers designed from partial sequences recovered previously. Five uncultured bacterial operational taxonomic units (OTUs) were quantified using specific quantitative PCR (qPCR) in fractionated ruminal samples from sheep fed either hay alone or hay plus corn. SpeciesFibrobacter succinogenes,Ruminococcus albus,R. flavefaciens,Ruminobacter amylophilus,Selenomonas ruminantium, andMitsuokella multacidaand generaButyrivibrioandPrevotellawere also quantified as comparison. The full-lengthrrssequence improved taxonomic assignments of partialrrssequences. GenusPrevotellahad the greatest abundance. Of the three major cultured cellulolytic species,R. flavefacienswas most abundant, followed byR. albusandF. succinogenes. The five uncultured bacterial OTUs, classified to genusAcetivibrio, genusAllobaculum, familyRuminococcaceae, orderClostridiales, or classClostridia, had abundance comparable to that of the above species of genera exceptPrevotella. Corn supplementation and fractions affected distribution of the rumen bacteria, but to a limited extent. When compared to the qPCR data, sequence frequencies in therrsclone libraries tended to overestimate the abundance of the bacteria represented. This study showed that abundance and population dynamics of uncultured bacteria can be quantified by specific qPCR, which complements the results ofrrsclone libraries. This study also revealed that some uncultured bacteria might be as important as some of the well-characterized bacteria in the rumen. The approach used should be applicable to assess the abundance and potential importance of uncultured bacteria in other environments.

[学科分类] 微生物学和免疫学