Winglee Kathryn, Fodor Anthony A
Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA.
Nutr Diet Suppl. 2015;7:69-76. doi: 10.2147/NDS.S62362. Epub 2015 Oct 7.
The gut microbiome performs many crucial functions for the human host, but the molecular mechanisms by which host, microbe and diet interact to mediate health and disease are only starting to be revealed. Here we review the literature on how changes in the diet affect the microbiome. A number of studies have shown that within a geographic region, different diets (such as vegan vs. omnivore) are associated with differences in a modest number of taxa but do not reliably produce radical differences within the gut microbial community. In contrast, studies that look across continents consistently find profoundly different microbial communities between Westernized and traditional populations, although it remains unclear to what extent diet or other differences in lifestyle drive these distinct microbial community structures. Furthermore, studies that place subjects on controlled short term experimental diets have found the resulting alterations to the gut microbial community to generally be small in scope, with changes that do not overcome initial individual differences in microbial community structure. These results emphasize that the human gut microbial community is relatively stable over time. In contrast, short term changes in diet can cause large changes in metabolite profiles, including metabolites processed by the gut microbial community. These results suggest that commensal gut microbes have a great deal of genetic plasticity and can activate different metabolic pathways independent of changes to microbial community composition. Thus, future studies of the how diet impacts host health via the microbiome may wish to focus on functional assays such as transcriptomics and metabolomics, in addition to 16S rRNA and whole-genome metagenome shotgun analyses of DNA. Taken together, the literature is most consistent with a model in which the composition of the adult gut microbial community undergoes modest compositional changes in response to altered diet but can nonetheless respond very rapidly to dietary changes via up- or down-regulation of metabolic pathways that can have profound and immediate consequences for host health.
肠道微生物群对人类宿主发挥着许多关键功能，但宿主、微生物和饮食相互作用以介导健康与疾病的分子机制才刚刚开始被揭示。在此，我们综述了关于饮食变化如何影响微生物群的文献。许多研究表明，在一个地理区域内，不同的饮食（如纯素食与杂食）与少数分类群的差异有关，但并不能可靠地在肠道微生物群落中产生根本性差异。相比之下，跨大陆的研究一致发现，西方化人群和传统人群之间的微生物群落存在显著差异，尽管饮食或其他生活方式差异在多大程度上驱动了这些独特的微生物群落结构尚不清楚。此外，将受试者置于受控短期实验饮食的研究发现，由此导致的肠道微生物群落变化通常范围较小，这些变化并未克服微生物群落结构最初的个体差异。这些结果强调，人类肠道微生物群随着时间的推移相对稳定。相比之下，饮食的短期变化会导致代谢物谱的巨大变化，包括由肠道微生物群处理的代谢物。这些结果表明，共生肠道微生物具有很大的遗传可塑性，并且可以独立于微生物群落组成的变化激活不同的代谢途径。因此，未来关于饮食如何通过微生物群影响宿主健康的研究，除了对DNA进行16S rRNA和全基因组宏基因组鸟枪法分析外，可能还希望关注转录组学和代谢组学等功能分析。综上所述，现有文献最符合这样一种模型：成年肠道微生物群落的组成会因饮食改变而发生适度的组成变化，但仍可通过上调或下调对宿主健康有深远和直接影响的代谢途径，对饮食变化做出非常迅速的反应。
