Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life
Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life
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DOI：
10.1186/2049-2618-1-30
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发表时间：
2013-01-01
期刊：
影响因子：
15.5
通讯作者：
Banfield, Jillian F.
中科院分区：
文献类型：
--
作者：
Brown, Christopher T.;Sharon, Itai;Banfield, Jillian F.
背景：与成人相比，早产儿肠道的个体微生物多样性较低，但个体间的微生物多样性较高。基于先前的16S rRNA基因调查，预计来自该环境的许多物种与先前在人类微生物群中检测到的物种相似。然而，基因组的新奇和代谢变异的菌株在婴儿gut.Results中发现的水平仍然相对unexplored：研究的稳定性和功能的早产儿肠道的早期微生物定植，9粪便样本，在第三周的生命早产男婴通过剖腹产。宏基因组序列被组装并分箱成接近完整的和部分的基因组，使得能够对微生物群落进行菌株水平的基因组分析。我们重建了11个接近完整的和6个部分的细菌基因组，这些基因组代表了微生物群落的关键成员。其中12个基因组与参考基因组具有>90%的推定直系同源氨基酸同一性。一个特别新的基因组的组装的人工管理导致了第一个基本上完整的基因组序列（在三个片段中，由于重复而无法确定其顺序）为Varibaculum cambriense（菌株Dora），这是一种与脓肿形成有关的医学相关物种。在研究期间，微生物群落经历了组成的转变，其中专性厌氧菌（发酵菌）超过大肠杆菌作为最丰富的物种。其他物种保持稳定，可能是由于它们能够厌氧呼吸或通过发酵生长，以及它们能够耐受氧气水平的波动。对V. cambriense的代谢预测表明，与微生物群落的其他成员一样，这种生物能够处理各种糖底物，并在厌氧呼吸期间利用多种不同的电子受体。放线菌科内的基因组比较揭示了呼吸代谢和motility.Conclusions相关的重要差异：基于基因组的分析提供了直接的洞察菌株特异性的潜力，厌氧呼吸，并产生了第一个基因组的属Varibaculum。重要的是，这些从头组装的基因组与密切相关的分离基因组的比较支持宏基因组学方法的准确性。在一个星期的时间内，早期肠道微生物群落过渡到一个社会具有较高的代表性专性厌氧菌，强调在殖民化过程中的分类和代谢不稳定性。
Background: The premature infant gut has low individual but high inter-individual microbial diversity compared with adults. Based on prior 16S rRNA gene surveys, many species from this environment are expected to be similar to those previously detected in the human microbiota. However, the level of genomic novelty and metabolic variation of strains found in the infant gut remains relatively unexplored.Results: To study the stability and function of early microbial colonizers of the premature infant gut, nine stool samples were taken during the third week of life of a premature male infant delivered via Caesarean section. Metagenomic sequences were assembled and binned into near-complete and partial genomes, enabling strain-level genomic analysis of the microbial community. We reconstructed eleven near-complete and six partial bacterial genomes representative of the key members of the microbial community.Twelve of these genomes share >90% putative ortholog amino acid identity with reference genomes. Manual curation of the assembly of one particularly novel genome resulted in the first essentially complete genome sequence (in three pieces, the order of which could not be determined due to a repeat) for Varibaculum cambriense (strain Dora), a medically relevant species that has been implicated in abscess formation. During the period studied, the microbial community undergoes a compositional shift, in which obligate anaerobes (fermenters) overtake Escherichia coli as the most abundant species. Other species remain stable, probably due to their ability to either respire anaerobically or grow by fermentation, and their capacity to tolerate fluctuating levels of oxygen. Metabolic predictions for V. cambriense suggest that, like other members of the microbial community, this organism is able to process various sugar substrates and make use of multiple different electron acceptors during anaerobic respiration. Genome comparisons within the family Actinomycetaceae reveal important differences related to respiratory metabolism and motility.Conclusions: Genome-based analysis provided direct insight into strain-specific potential for anaerobic respiration and yielded the first genome for the genus Varibaculum. Importantly, comparison of these de novo assembled genomes with closely related isolate genomes supported the accuracy of the metagenomic methodology. Over a one-week period, the early gut microbial community transitioned to a community with a higher representation of obligate anaerobes, emphasizing both taxonomic and metabolic instability during colonization.