The J. Craig Venter Institute, Rockville, Maryland, United States of America.
PLoS One. 2012;7(11):e48289. doi: 10.1371/journal.pone.0048289. Epub 2012 Nov 7.
A combination of Sanger and 454 sequences of small subunit rRNA loci were used to interrogate microbial diversity in the bovine rumen of 12 cows consuming a forage diet. Observed bacterial species richness, based on the V1-V3 region of the 16S rRNA gene, was between 1,903 to 2,432 species-level operational taxonomic units (OTUs) when 5,520 reads were sampled per animal. Eighty percent of species-level OTUs were dominated by members of the order Clostridiales, Bacteroidales, Erysipelotrichales and unclassified TM7. Abundance of Prevotella species varied widely among the 12 animals. Archaeal species richness, also based on 16S rRNA, was between 8 and 13 OTUs, representing 5 genera. The majority of archaeal OTUs (84%) found in this study were previously observed in public databases with only two new OTUs discovered. Observed rumen fungal species richness, based on the 18S rRNA gene, was between 21 and 40 OTUs with 98.4-99.9% of OTUs represented by more than one read, using Good's coverage. Examination of the fungal community identified numerous novel groups. Prevotella and Tannerella were overrepresented in the liquid fraction of the rumen while Butyrivibrio and Blautia were significantly overrepresented in the solid fraction of the rumen. No statistical difference was observed between the liquid and solid fractions in biodiversity of archaea and fungi. The survey of microbial communities and analysis of cross-domain correlations suggested there is a far greater extent of microbial diversity in the bovine rumen than previously appreciated, and that next generation sequencing technologies promise to reveal novel species, interactions and pathways that can be studied further in order to better understand how rumen microbial community structure and function affects ruminant feed efficiency, biofuel production, and environmental impact.
本研究采用 Sanger 和 454 测序技术，对 12 头采食饲粮的奶牛瘤胃内的微生物多样性进行了研究。基于 16S rRNA 基因 V1-V3 区，当每个动物的测序读长为 5520 时，观察到的细菌物种丰富度在 1903 到 2432 个种水平操作分类单元（OTUs）之间。80%的种水平 OTUs 由梭菌目（Clostridiales）、拟杆菌目（Bacteroidales）、真杆菌目（Erysipelotrichales）和未分类的 TM7 成员组成。12 个动物中普雷沃氏菌属（Prevotella）的丰度差异很大。基于 16S rRNA 的古菌物种丰富度在 8 到 13 个 OTUs 之间，代表 5 个属。本研究中发现的大多数古菌 OTUs（84%）之前在公共数据库中已经观察到，仅发现了 2 个新的 OTUs。基于 18S rRNA 基因，瘤胃液真菌物种丰富度在 21 到 40 个 OTUs 之间，Good 覆盖率为 98.4-99.9%的 OTUs 有超过一个读长代表。对真菌群落的分析确定了许多新的群组。在瘤胃液的液体部分，普雷沃氏菌属（Prevotella）和坦纳氏菌属（Tannerella）过度表达，而丁酸弧菌属（Butyrivibrio）和布劳特氏菌属（Blautia）在瘤胃液的固体部分显著过度表达。在古菌和真菌的生物多样性方面，液体和固体部分之间没有观察到统计学差异。微生物群落的调查和跨域相关性分析表明，奶牛瘤胃中的微生物多样性比以前认为的要广泛得多，下一代测序技术有望揭示新的物种、相互作用和途径，可以进一步研究，以更好地了解瘤胃微生物群落结构和功能如何影响反刍动物的饲料效率、生物燃料生产和环境影响。
