小柯机器人

美国斯坦福大学Dylan Dodd，Michael A. Fischbach和荷兰瓦赫宁根大学Marnix H. Medema共同合作，近期取得重要工作进展。他们研究开发了gutSMASH算法，可以预测人体肠道微生物群的特化初级代谢途径。相关研究成果2023年2月13日在线发表于《自然—生物技术》杂志上。

据介绍，肠道微生物群产生数百个小分子，其中许多调节宿主生理。尽管研究人员已努力确定次级代谢产物的生物合成基因，但肠道微生物组的化学输出主要由初级代谢产物组成。

研究人员介绍了用于识别初级代谢基因簇的gutSMASH算法，并使用它系统地描述了肠道微生物组代谢，在4240个高质量微生物基因组中识别了19890个基因簇。研究人员发现门之间的路径分布存在显著差异，反映了不同的能量捕获策略。这些数据解释了短链脂肪酸生产的分类差异，并提出了每个分类单元的特征代谢生态位。对荷兰人群队列中1135名个体的分析表明，血浆和粪便中微生物组来源的代谢产物水平几乎与相应代谢基因的宏基因组丰度完全无关，这表明了通路特异性基因调节和代谢产物通量的关键作用。

总之，这项工作是理解细菌分类群对微生物组化学作用作出贡献的起点。

附：英文原文

Title: gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota

Author: Pascal Andreu, Victria, Augustijn, Hannah E., Chen, Lianmin, Zhernakova, Alexandra, Fu, Jingyuan, Fischbach, Michael A., Dodd, Dylan, Medema, Marnix H.

Issue&Volume: 2023-02-13

Abstract: The gut microbiota produce hundreds of small molecules, many of which modulate host physiology. Although efforts have been made to identify biosynthetic genes for secondary metabolites, the chemical output of the gut microbiome consists predominantly of primary metabolites. Here we introduce the gutSMASH algorithm for identification of primary metabolic gene clusters, and we used it to systematically profile gut microbiome metabolism, identifying 19,890 gene clusters in 4,240 high-quality microbial genomes. We found marked differences in pathway distribution among phyla, reflecting distinct strategies for energy capture. These data explain taxonomic differences in short-chain fatty acid production and suggest a characteristic metabolic niche for each taxon. Analysis of 1,135 individuals from a Dutch population-based cohort shows that the level of microbiome-derived metabolites in plasma and feces is almost completely uncorrelated with the metagenomic abundance of corresponding metabolic genes, indicating a crucial role for pathway-specific gene regulation and metabolite flux. This work is a starting point for understanding differences in how bacterial taxa contribute to the chemistry of the microbiome.

DOI: 10.1038/s41587-023-01675-1

Source: https://www.nature.com/articles/s41587-023-01675-1

Nature Biotechnology：《自然—生物技术》，创刊于1996年。隶属于施普林格·自然出版集团，最新IF：68.164
官方网址：https://www.nature.com/nbt/
投稿链接：https://mts-nbt.nature.com/cgi-bin/main.plex