Novel microbial syntrophies identified by longitudinal metagenomics
Novel microbial syntrophies identified by longitudinal metagenomics
复制标题
通过纵向宏基因组学鉴定的新型微生物互养体
DOI：
10.1101/2021.07.05.451125
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发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Raguideau S
中科院分区：
文献类型：
--
作者：
Raguideau S
识别微生物群落中的物种相互作用以及其与群落功能的关系是一个关键挑战。为了应对这一挑战，我们在此提供了广泛的基因组解析纵向数据集和相关元数据。我们每周收集微生物群落样本，并记录工业甲烷生产厌氧消化反应器一年的运行条件。这使我们能够恢复 2240 个去复制的宏基因组组装基因组 (dMAG)，以及它们的覆盖动态和功能注释，从中推断出功能性状。在这些 dMAG 中，1910 个是新物种，其中 22 个代表新目和纲。产甲烷菌群落预计将由产甲烷菌和产生其底物的互养体之间的互养和其他关联构成牢固的结构。我们通过搜索具有高度相关时间序列的产甲烷和非产甲烷 dMAG 对，鉴定了 450 个潜在的互养 dMAG。潜在共养生物的基因组富含氧化还原酶和糖转运基因，并且它们与产甲烷菌的关联存在强烈的分类学信号。特别值得注意的是，我们发现深古细菌与热原体和热球菌类的产甲烷菌特异性相关。在多个反应器中很少观察到相同的互养关联，这表明互养可能是兼性的，物种内的特定菌株仅有时而不一定总是与相同的产甲烷伙伴形成互养关联。所呈现的结果表明，纵向宏基因组学是识别微生物群落中的物种及其相互作用的非常有价值的方法。一句话总结微生物群落的纵向研究识别新物种并预测它们的相互作用和在群落功能中的作用。
Identifying species interactions in a microbial community and how this relates to community function is a key challenge. Towards addressing this challenge, we present here an extensive genome-resolved, longitudinal dataset and associated metadata. We collected weekly samples of microbial communities and recorded operating conditions from industrial methane producing anaerobic digestion reactors for a year. This allowed us to recover 2240 dereplicated metagenome assembled genomes (dMAGs), together with their coverage dynamics and functional annotations from which functional traits were inferred. Of these dMAGs, 1910 were novel species, with 22 representing novel orders and classes. Methanogenic communities are expected to be strongly structured by syntrophic and other associations between the methanogens and syntrophs that produce their substrates. We identified 450 potential syntrophic dMAGs by searching for pairs of methanogenic and non-methanogenic dMAGs that had highly correlated time-series. Genomes of potential syntrophs were enriched for oxidoreductases and sugar transport genes and there was a strong taxonomic signal in their associations with methanogens. Of particular note, we found that Bathyarchaeiea associated specifically with methanogens from the Thermoplasmata, and Thermococci classes. Same syntrophic associations were only rarely observed across multiple reactors, suggesting that syntrophies might be facultative, with particular strains within a species forming syntrophic associations only sometimes and not necessarily always with the same methanogenic partner. The presented results show that longitudinal metagenomics is a highly valuable approach for identifying species and their interactions in microbial communities.One Sentence SummaryLongitudinal study of microbial communities identifies novel species and predicts their interactions and role in community function.
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影响因子：
15.5
作者：
Danczak RE;Johnston MD;Kenah C;Slattery M;Wrighton KC;Wilkins MJ
通讯作者：
Wilkins MJ
影响因子：
9.2
作者：
Sierocinski, Pawel;Milferstedt, Kim;Buckling, Angus
通讯作者：
Buckling, Angus
影响因子：
56.9
作者：
Evans, Paul N.;Parks, Donovan H.;Tyson, Gene W.
通讯作者：
Tyson, Gene W.
DOI：
10.1099/ijs.0.000065
发表时间：
2015-04-01
影响因子：
2.8
作者：
Jablonski, Slawomir;Rodowicz, Pawel;Lukaszewicz, Marcin
通讯作者：
Lukaszewicz, Marcin
PhyMet2：用于产甲烷菌系统发育和代谢分析的数据库和工具包
影响因子：
3.3
作者：
Burdukiewicz Michał;Przemysław Gagat;Sławomir Jabłoński;J. Chilimoniuk;M. Gaworski;P. Mackiewicz;Łukaszewicz Marcin
通讯作者：
Łukaszewicz Marcin