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在泛基因组分析中,人类鼻腔相关物种的代谢能力高度保守。

Metabolic capabilities are highly conserved among human nasal-associated species in pangenomic analyses.

作者信息

Tran Tommy H, Escapa Isabel F, Roberts Ari Q, Gao Wei, Obawemimo Abiola C, Segre Julia A, Kong Heidi H, Conlan Sean, Kelly Matthew S, Lemon Katherine P

机构信息

Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA.

The Forsyth Institute (Microbiology), Cambridge, MA, USA.

出版信息

bioRxiv. 2024 Aug 27:2023.06.05.543719. doi: 10.1101/2023.06.05.543719.

Abstract

species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of are often positively associated with health. Among the most common human nasal species are , , and . To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the metabolic capabilities of 87 distinct human nasal strain genomes: 31 from Botswana and 56 from the USA. had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution spanning Africa and North America. All species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent versus accessory genome of each species indicating limited strain-level variability in metabolic capacity. Based on prevalence data, at least two species likely coexist in the nasal microbiota of 82% of adults. So, it was surprising that core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the USA clade of lacked genes for assimilatory sulfate reduction present in most of the strains in the Botswana clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.

摘要

在人类整个生命周期的鼻腔微生物群中,这些物种在全球范围内普遍存在。此外,以这些物种相对丰度较高为特征的鼻腔微生物群谱通常与健康呈正相关。人类鼻腔中最常见的这些物种包括[具体物种1]、[具体物种2]和[具体物种3]。为了深入了解这四个物种的功能,我们确定了基因组、系统发育基因组和泛基因组特性,并估计了87个不同的人类鼻腔[物种名称]菌株基因组的代谢能力:其中31个来自博茨瓦纳,56个来自美国。[具体物种1]有与局部菌株传播一致的地理上不同的进化枝,而其他物种的一些菌株有跨越非洲和北美的广泛地理分布。所有物种都有相似的基因组和泛基因组结构。分配到所有COG代谢类别的基因簇在每个物种的持久基因组与附属基因组中均有过度表达,这表明代谢能力在菌株水平上的变异性有限。根据流行率数据,至少两种[具体物种名称]物种可能共存于82%的成年人鼻腔微生物群中。因此,令人惊讶的是,这四个物种的核心代谢能力高度保守,表明物种水平的代谢变异有限。引人注目的是,[具体物种1]美国进化枝中的菌株缺乏在博茨瓦纳进化枝的大多数菌株以及其他研究物种中存在的同化硫酸盐还原基因,这表明同化硫酸盐还原在地理上最近出现了丧失。总体而言,代谢能力的最小物种和菌株变异性意味着共存的菌株占据不同代谢生态位的能力可能有限。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e091/11423123/1cc88cd13196/nihpp-2023.06.05.543719v2-f0001.jpg

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