Bioenergetic mapping of ‘healthy microbiomes’ via compound processing potential imprinted in gut and soil metagenomes

作者：Craig Liddicoat, Robert A. Edwards, Michael J. Roach, Jake M. Robinson, Kiri Joy Wallace, Andrew D. Barnes, Joel E. Brame, Anna Heintz‐Buschart, Timothy R. Cavagnaro, Elizabeth A. Dinsdale, Michael P. Doane, Nico Eisenhauer, Grace Mitchell, Bibishan Rai, Sunita A. Ramesh, Martin F. Breed · 发表于：The Science of The Total Environment · 年份：2024 · DOI：10.1016/j.scitotenv.2024.173543 · 被引用次数：9 · 研究领域：Gut microbiota and health、Metabolomics and Mass Spectrometry Studies、Bioinformatics and Genomic Networks

Despite mounting evidence of their importance in human health and ecosystem functioning, the definition and measurement of 'healthy microbiomes' remain unclear. More advanced knowledge exists on health associations for compounds used or produced by microbes. Environmental microbiome exposures (especially via soils) also help shape, and may supplement, the functional capacity of human microbiomes. Given the synchronous interaction between microbes, their feedstocks, and micro-environments, with functional genes facilitating chemical transformations, our objective was to examine microbiomes in terms of their capacity to process compounds relevant to human health. Here we integrate functional genomics and biochemistry frameworks to derive new quantitative measures of in silico potential for human gut and environmental soil metagenomes to process a panel of major compound classes (e.g., lipids, carbohydrates) and selected biomolecules (e.g., vitamins, short-chain fatty acids) linked to human health. Metagenome functional potential profile data were translated into a universal compound mapping 'landscape' based on bioenergetic van Krevelen mapping of function-level meta-compounds and corresponding functional relative abundances, reflecting imprinted genetic capacity of microbiomes to metabolize an array of different compounds. We show that measures of 'compound processing potential' associated with human health and disease (examining atherosclerotic cardiovascular disease, colorec...