美国加州大学伯克利分校Jillian F. Banfield团队开发出新方法可从宏基因组学数据中分析群体的微生物多样性。相关论文于2021年1月18日在线发表在《自然—生物技术》杂志上。

研究人员报道了inStrain这个程序，该程序使用宏基因组配对读取来分析整个基因组中的群体内遗传多样性（微生物多样性），并以一种具有微生物多样性意识的方式比较微生物群体，从而大大提高了以现有方法为基准的基因组比较的准确性。

研究人员使用inStrain对来自新生早产儿的超过1,000个粪便基因组进行了分析，并发现同胞双胞胎比不相关的婴儿共享更多的菌株，尽管同卵双胞胎与兄弟同胞共享的菌株不多。剖宫产出生的婴儿所携带的克雷伯菌具有比通过阴道分娩的婴儿更高的核苷酸多样性，这可能反映了从医院而不是母亲的微生物群所获取而来。

在单个婴儿中表现出多样性的基因组位点包括在其他婴儿之间发现的变异，这可能反映了来自医院相关来源的多种微生物接触。inStrain可以应用于任何宏基因组数据集，从而进行微观多样性分析和严格的菌株比较。

据了解，同一物种的共存微生物细胞通常表现出遗传变异，这会影响表型，包括从营养偏好到致病性。

附：英文原文

Title: inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains

Author: Matthew R. Olm, Alexander Crits-Christoph, Keith Bouma-Gregson, Brian A. Firek, Michael J. Morowitz, Jillian F. Banfield

Issue&Volume: 2021-01-18

Abstract: Coexisting microbial cells of the same species often exhibit genetic variation that can affect phenotypes ranging from nutrient preference to pathogenicity. Here we present inStrain, a program that uses metagenomic paired reads to profile intra-population genetic diversity (microdiversity) across whole genomes and compares microbial populations in a microdiversity-aware manner, greatly increasing the accuracy of genomic comparisons when benchmarked against existing methods. We use inStrain to profile >1,000 fecal metagenomes from newborn premature infants and find that siblings share significantly more strains than unrelated infants, although identical twins share no more strains than fraternal siblings. Infants born by cesarean section harbor Klebsiella with significantly higher nucleotide diversity than infants delivered vaginally, potentially reflecting acquisition from hospital rather than maternal microbiomes. Genomic loci that show diversity in individual infants include variants found between other infants, possibly reflecting inoculation from diverse hospital-associated sources. inStrain can be applied to any metagenomic dataset for microdiversity analysis and rigorous strain comparison. A metagenome analysis tool identifies microbial strains within and between populations.

DOI: 10.1038/s41587-020-00797-0

Source: https://www.nature.com/articles/s41587-020-00797-0