Grasslands Research Centre, AgResearch Limited, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand.
Appl Environ Microbiol. 2010 Apr;76(7):2058-66. doi: 10.1128/AEM.02580-09. Epub 2010 Jan 29.
Homoacetogens produce acetate from H(2) and CO(2) via the Wood-Ljungdahl pathway. Some homoacetogens have been isolated from the rumen, but these organisms are expected to be only part of the full diversity present. To survey the presence of rumen homoacetogens, we analyzed sequences of formyltetrahydrofolate synthetase (FTHFS), a key enzyme of the Wood-Ljungdahl pathway. A total of 275 partial sequences of genes encoding FTHFS were PCR amplified from rumen contents of a cow, two sheep, and a deer. Phylogenetic trees were constructed using these FTHFS gene sequences and the translated amino acid sequences, together with other sequences from public databases and from novel nonhomoacetogenic bacteria isolated from the rumen. Over 90% of the FTHFS sequences fell into 34 clusters defined with good bootstrap support. Few rumen-derived FTHFS sequences clustered with sequences of known homoacetogens. Conserved residues were identified in the deduced FTHFS amino acid sequences from known homoacetogens, and their presence in the other sequences was used to determine a "homoacetogen similarity" (HS) score. A homoacetogen FTHFS profile hidden Markov model (HoF-HMM) was used to assess the homology of rumen and homoacetogen FTHFS sequences. Many clusters had low HS scores and HoF-HMM matches, raising doubts about whether the sequences originated from homoacetogens. In keeping with these findings, FTHFS sequences from nonhomoacetogenic bacterial isolates grouped in these clusters with low scores. However, sequences that formed 10 clusters containing no known isolates but representing 15% of our FTHFS sequences from rumen samples had high HS scores and HoF-HMM matches and so could represent novel homoacetogens.
产乙酸菌通过 Wood-Ljungdahl 途径利用 H(2) 和 CO(2) 生成乙酸。一些产乙酸菌已经从瘤胃中分离出来,但这些生物预计只是存在的全部多样性的一部分。为了调查瘤胃产乙酸菌的存在,我们分析了甲酸四氢叶酸合成酶 (FTHFS) 的序列,这是 Wood-Ljungdahl 途径的关键酶。从一头牛、两只绵羊和一只鹿的瘤胃液中用 PCR 扩增了总共 275 个编码 FTHFS 的基因的部分序列。使用这些 FTHFS 基因序列和翻译的氨基酸序列以及来自公共数据库和从瘤胃中分离的新型非产乙酸菌的其他序列构建了系统发育树。超过 90%的 FTHFS 序列落入了 34 个具有良好自举支持的聚类中。很少有来自瘤胃的 FTHFS 序列与已知产乙酸菌的序列聚类。在已知产乙酸菌的推导 FTHFS 氨基酸序列中鉴定出保守残基,并在其他序列中存在这些残基,以确定“产乙酸菌相似性”(HS)得分。产乙酸菌 FTHFS 隐马尔可夫模型 (HoF-HMM) 用于评估瘤胃和产乙酸菌 FTHFS 序列的同源性。许多聚类具有较低的 HS 得分和 HoF-HMM 匹配,这使人怀疑这些序列是否来自产乙酸菌。与这些发现一致的是,来自非产乙酸菌分离株的 FTHFS 序列在这些聚类中得分较低。然而,形成 10 个聚类的序列没有已知的分离株,但代表了我们从瘤胃样本中获得的 FTHFS 序列的 15%,具有较高的 HS 得分和 HoF-HMM 匹配,因此可能代表新的产乙酸菌。