Neumann Anthony P, McCormick Caroline A, Suen Garret
Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA.
Environ Microbiol. 2017 Sep;19(9):3768-3783. doi: 10.1111/1462-2920.13878. Epub 2017 Aug 24.
The genus Fibrobacter contains cellulolytic bacteria originally isolated from the rumen. Culture-independent investigations have since identified Fibrobacter populations in the gastrointestinal tracts of numerous hindgut-fermenting herbivores, but their physiology is poorly characterized due to few representative axenic cultures. To test the hypothesis that novel Fibrobacter diversity exists in hindgut fermenters, we performed culturing and 16S rRNA gene amplicon sequencing on samples collected from phylogenetically diverse herbivorous hosts. Using a unique approach for recovering axenic Fibrobacter cultures, we isolated 45 novel strains from 11 different hosts. Full-length 16S rRNA gene sequencing of these isolates identified nine discrete phylotypes (cutoff = 0.03%) among them, including several that were only isolated from hindgut-fermenting hosts, and four previously unrepresented by axenic cultures. Our phylogenetic analysis indicated that six of the phylotypes are more closely related to previously described subspecies of Fibrobacter succinogenes, while the remaining three were more closely related to F. intestinalis. Culture-independent bacterial community profiling confirmed that most isolates were representative of numerically dominant phylotypes in their respective samples and strengthened the association of certain phylotypes with either ruminants or hindgut-fermenters. Despite considerable phylogenetic diversity observed among the Fibrobacter strains isolated here, phenotypic characterization suggests a conserved specialization for growth on cellulose.
纤维杆菌属包含最初从瘤胃中分离出的纤维素分解菌。此后，不依赖培养的研究在众多后肠发酵食草动物的胃肠道中鉴定出了纤维杆菌种群，但由于代表性的纯培养物较少，它们的生理学特征了解甚少。为了验证后肠发酵动物中存在新型纤维杆菌多样性这一假设，我们对从系统发育上不同的食草宿主收集的样本进行了培养和16S rRNA基因扩增子测序。我们采用一种独特的方法来获得纤维杆菌纯培养物，从11个不同宿主中分离出45株新菌株。对这些分离株进行全长16S rRNA基因测序，在其中鉴定出9个不同的系统型（截止值 = 0.03%），包括几个仅从后肠发酵宿主中分离出的系统型，以及4个以前没有纯培养物代表的系统型。我们的系统发育分析表明，其中6个系统型与先前描述的琥珀酸纤维杆菌亚种关系更密切，而其余3个与肠道纤维杆菌关系更密切。不依赖培养的细菌群落分析证实，大多数分离株代表了各自样本中数量占优势的系统型，并加强了某些系统型与反刍动物或后肠发酵动物的关联。尽管在此分离出的纤维杆菌菌株之间观察到了相当大的系统发育多样性，但表型特征表明它们在纤维素上生长具有保守的专一性。
