Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota.
Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota.
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DOI：
10.1038/s41522-023-00392-6
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发表时间：
2023-05-11
影响因子：
9.2
通讯作者：
Ventura, Marco
中科院分区：
文献类型：
--
作者：
Lugli, Gabriele Andrea;Mancabelli, Leonardo;Milani, Christian;Fontana, Federico;Tarracchini, Chiara;Alessandri, Giulia;van Sinderen, Douwe;Turroni, Francesca;Ventura, Marco
在婴儿期，肠道微生物区系的发育是建立微生物-宿主相互作用的关键过程，这种相互作用可能持续整个成年期，并被认为影响宿主健康。为了充分了解这种相互作用的复杂性，有必要评估新生儿肠道微生物区系的多样性及其相关的微生物动力学和与健康和疾病有关的关系。为了探索人类生命最初3年的微生物生物多样性，对10,935个鸟枪式元基因组数据集进行了分类和功能分类。婴儿间微生物种类分布揭示了8个主要的婴儿群落状态类型(ICSTs)，其中17个细菌类群占主导地位，其分布与地理来源和婴儿健康状况相对应。总共从元基因组数据中重建了2390个优势分类群的染色体序列，并与44,987个公开可用基因组相结合，追踪不同婴儿群体中微生物种群亚种(PS)的分布，揭示了ICST之间多菌株共存的模式。最后，基于元基因组和元转录的代谢图谱的实施突出了肠道微生物区系的不同酶表达模式，使我们能够深入了解新生儿肠道微生物区系相互作用的机制方面。后基因组学和后转录组学数据之间的比较突显了如何通过采用两种测序方法并可能辅以代谢组学方法来研究像人类肠道这样的复杂环境。虽然元基因组分析对微生物分类非常有用，旨在揭示推动微生物区系平衡的关键因素，但使用这些数据来解释微生物区系的功能并不总是合理的。
During infancy, gut microbiota development is a crucial process involved in the establishment of microbe–host interactions which may persist throughout adulthood, and which are believed to influence host health. To fully understand the complexities of such interactions, it is essential to assess gut microbiota diversity of newborns and its associated microbial dynamics and relationships pertaining to health and disease. To explore microbial biodiversity during the first 3 years of human life, 10,935 shotgun metagenomic datasets were taxonomically and functionally classified. Microbial species distribution between infants revealed the presence of eight major Infant Community State Types (ICSTs), being dominated by 17 bacterial taxa, whose distribution was shown to correspond to the geographical origin and infant health status. In total, 2390 chromosomal sequences of the predominant taxa were reconstructed from metagenomic data and used in combination with 44,987 publicly available genomes to trace the distribution of microbial Population Subspecies (PS) within the different infant groups, revealing patterns of multistrain coexistence among ICSTs. Finally, implementation of a metagenomic- and metatranscriptomic-based metabolic profiling highlighted different enzymatic expression patterns of the gut microbiota that allowed us to acquire insights into mechanistic aspects of health-gut microbiota interplay in newborns. Comparison between metagenomic and metatranscriptomic data highlights how a complex environment like the human gut must be investigated by employing both sequencing methodologies and possibly supplemented with metabolomics approaches. While metagenomic analyses are very useful for microbial classification aimed at unveiling key players driving microbiota balances, using these data to explain functionalities of the microbiota is not always warranted.
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影响因子：
4.3
作者：
Mallick H;Rahnavard A;McIver LJ;Ma S;Zhang Y;Nguyen LH;Tickle TL;Weingart G;Ren B;Schwager EH;Chatterjee S;Thompson KN;Wilkinson JE;Subramanian A;Lu Y;Waldron L;Paulson JN;Franzosa EA;Bravo HC;Huttenhower C
通讯作者：
Huttenhower C
DOI：
10.1093/bioinformatics/btr490
发表时间：
2011-11-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Howe EA;Sinha R;Schlauch D;Quackenbush J
通讯作者：
Quackenbush J
影响因子：
28.3
作者：
Gibson, Molly K.;Wang, Bin;Ahmadi, Sara;Burnham, Carey-Ann D.;Tarr, Phillip I.;Warner, Barbara B.;Dantas, Gautam
通讯作者：
Dantas, Gautam
DOI：
10.1073/pnas.1002601107
发表时间：
2010-06-29
影响因子：
11.1
作者：
Dominguez-Bello, Maria G.;Costello, Elizabeth K.;Knight, Rob
通讯作者：
Knight, Rob
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.