Functional phylotyping approach for assessing intraspecific diversity of Ruminococcus albus within the rumen microbiome
Functional phylotyping approach for assessing intraspecific diversity of Ruminococcus albus within the rumen microbiome
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DOI：
10.1093/femsle/fnu047
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发表时间：
2015-02-01
影响因子：
2.1
通讯作者：
Lamed, Raphael
中科院分区：
文献类型：
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作者：
Grinberg, Inna Rozman;Yin, Guohua;Lamed, Raphael
白色瘤胃球菌是瘤胃中的一种重要的纤维素分解菌。白瘤胃球菌缺乏经典的纤维素酶体复合物，但它具有独特的家族37碳水化合物结合模块（CBM 37），该模块整合到多种碳水化合物活性酶中。我们开发了一种潜在的分子工具，用于R.基于cel48A基因中的可变区，cel48A在该细菌的所有已知菌株中编码CBM 37相关家族48糖苷水解酶的单拷贝。从4个牛的瘤胃宏基因组样品中扩增cel48A基因的片段，并对其丰度和多样性进行了评估。对所获得的序列的分析揭示了在所有四只动物中多种功能性cel 48A类型的共存。这些包括与R相同或相似的序列。白色分离株（参考菌株），以及几个新的序列。优势的cel48A类型在动物之间变化。该方法可用于R.在宏基因组样本中发现了白色。scaC是一个已知的R. flavefaciens，我们提出了一套两个种特异性标记的Ruminocococci分型在草食动物瘤胃。
Ruminococcus albus, a cellulolytic bacterium, is a critical member of the rumen community. Ruminococcus albus lacks a classical cellulosome complex, but it possesses a unique family 37 carbohydrate-binding module (CBM37), which is integrated into a variety of carbohydrate-active enzymes. We developed a potential molecular tool for functional phylotyping of the R. albus population in the rumen, based on a variable region in the cel48A gene. cel48A encodes a single copy of the CBM37-associated family 48 glycoside hydrolase in all known strains of this bacterium. A segment of the cel48A gene was amplified from rumen metagenomic samples of four bovines, and its abundance and diversity were evaluated. Analysis of the obtained sequences revealed the co-existence of multiple functional phylotypes of cel48A in all four animals. These included sequences identical or similar to those of R. albus isolates (reference strains), as well as several novel sequences. The dominant cel48A type varied among animals. This method can be used for detection of intraspecific diversity of R. albus in metagenomic samples. Together with scaC, a previously reported gene marker for R. flavefaciens, we present a set of two species-specific markers for phylotyping of Ruminococci in the herbivore rumen.