Community-wide analysis of microbial genome sequence signatures.
Community-wide analysis of microbial genome sequence signatures.
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DOI：
10.1186/gb-2009-10-8-r85
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发表时间：
2009
期刊：
影响因子：
12.3
通讯作者：
Banfield JF
中科院分区：
文献类型：
--
作者：
Dick GJ;Andersson AF;Baker BJ;Simmons SL;Thomas BC;Yelton AP;Banfield JF
基因组签名用于从酸性生物膜微生物群落元基因组数据集中识别和聚类序列，揭示关于低丰度群落成员的信息。对培养微生物的DNA序列分析揭示了全基因组、特定类群的核苷酸组成特征，称为基因组签名。这些特征对于理解基因组进化和在元基因组序列片段分类中的潜在应用具有深远的意义。然而，关于基因组签名在自然微生物群落中的分布或环境因素在多大程度上塑造它们，人们知之甚少。我们分析了来自两个嗜酸生物膜群落的元基因组序列数据，包括为九个古菌、三个细菌和许多相关病毒重建的复合基因组，以及来自菌株变种和低丰度生物的数千个未分配的片段。基因组签名，以四核苷酸频率的形式通过紧急自组织映射图进行分析，从所有具有50%到60%平均氨基酸同一性的已知种群中分离出序列，并揭示了与低丰度生物和假定的质粒相对应的先前未知的基因组簇。签名在全基因组范围内普遍存在。由于翻译选择或蛋白质对细胞内(pH~5)和细胞外(pH~1)环境的适应导致的基因组内差异相对于基因组间差异较小，因此簇被解决。我们发现，这些基因组特征源于多种影响，但主要通过密码子组成来表现，我们认为这是基因组特有的突变偏向的结果。一个重要的结论是，共同的环境压力和共同进化的生物体之间的相互作用不会掩盖酸性矿山废水社区的基因组签名。因此，基因组签名可用于将序列片段分配给种群，如果元基因组学要提供对微生物群落功能的生态和生化洞察，这是一个基本的先决条件。
Genome signatures are used to identify and cluster sequences de novo from an acid biofilm microbial community metagenomic dataset, revealing information about the low-abundance community members. Analyses of DNA sequences from cultivated microorganisms have revealed genome-wide, taxa-specific nucleotide compositional characteristics, referred to as genome signatures. These signatures have far-reaching implications for understanding genome evolution and potential application in classification of metagenomic sequence fragments. However, little is known regarding the distribution of genome signatures in natural microbial communities or the extent to which environmental factors shape them. We analyzed metagenomic sequence data from two acidophilic biofilm communities, including composite genomes reconstructed for nine archaea, three bacteria, and numerous associated viruses, as well as thousands of unassigned fragments from strain variants and low-abundance organisms. Genome signatures, in the form of tetranucleotide frequencies analyzed by emergent self-organizing maps, segregated sequences from all known populations sharing < 50 to 60% average amino acid identity and revealed previously unknown genomic clusters corresponding to low-abundance organisms and a putative plasmid. Signatures were pervasive genome-wide. Clusters were resolved because intra-genome differences resulting from translational selection or protein adaptation to the intracellular (pH ~5) versus extracellular (pH ~1) environment were small relative to inter-genome differences. We found that these genome signatures stem from multiple influences but are primarily manifested through codon composition, which we propose is the result of genome-specific mutational biases. An important conclusion is that shared environmental pressures and interactions among coevolving organisms do not obscure genome signatures in acid mine drainage communities. Thus, genome signatures can be used to assign sequence fragments to populations, an essential prerequisite if metagenomics is to provide ecological and biochemical insights into the functioning of microbial communities.
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影响因子：
56.9
作者：
DeLong, EF;Preston, CM;Karl, DM
通讯作者：
Karl, DM
影响因子：
56.9
作者：
Andersson, Anders F.;Banfield, Jillian F.
通讯作者：
Banfield, Jillian F.
影响因子：
56.9
作者：
Béjà, O;Aravind, L;DeLong, EF
通讯作者：
DeLong, EF
影响因子：
4.1
作者：
Abe, Takashi;Sugawara, Hideaki;Ikemura, Toshimichi
通讯作者：
Ikemura, Toshimichi
DOI：
10.1073/pnas.93.12.5854
发表时间：
1996-06-11
影响因子：
11.1
作者：
Blaisdell, BE;Campbell, AM;Karlin, S
通讯作者：
Karlin, S