Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.
Department of Medicine and Surgery, University of Parma, Parma, Italy.
NPJ Biofilms Microbiomes. 2023 May 11;9(1):25. doi: 10.1038/s41522-023-00392-6.
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.
在婴儿期，肠道微生物群的发展是一个关键过程，涉及到微生物与宿主相互作用的建立，这些相互作用可能会持续到成年期，并被认为会影响宿主的健康。为了充分理解这些相互作用的复杂性，评估新生儿的肠道微生物多样性及其与健康和疾病相关的微生物动态和关系至关重要。为了探索人类生命的前三年的微生物多样性，对 10935 个 shotgun 宏基因组数据集进行了分类学和功能分类。婴儿之间微生物物种的分布揭示了存在八种主要的婴儿群落状态类型（ICSTs），由 17 种细菌类群主导，其分布与地理起源和婴儿健康状况相对应。总共从宏基因组数据中重建了主要类群的 2390 个染色体序列，并与 44987 个公开可用的基因组结合使用，以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，实施基于宏基因组和宏转录组的代谢物分析，突出了肠道微生物群的不同酶表达模式，使我们能够深入了解新生儿健康-肠道微生物群相互作用的机制方面。宏基因组和宏转录组数据的比较突出了像人类肠道这样复杂的环境必须通过同时使用测序方法并可能补充代谢组学方法进行研究。虽然宏基因组分析对于揭示驱动微生物群平衡的关键因素的微生物分类非常有用，但使用这些数据来解释微生物群的功能并不总是合理的。
