摘要
出身背景
人类肠道微生物组与健康和疾病有关。然而，它在来自非洲等不同人群的健康成年人中的作用尚不清楚。我们将揭示拉各斯州健康的农村和城市约鲁巴人肠道微生物组的作用。
方法论
从农村（n = 10） 和城市（n = 10） 参与者。使用ZR粪便DNA MiniPrep提取粪便DNA™ D6010和在Illumina Miseq平台上进行的宏基因组下一代测序。分别使用同源群簇（COG）和综合抗生素耐药性数据库（CARD）工具进行功能作用预测和抗生素耐药性基因（ARGs）。使用主成分分析（PCA）推断表型和COG丰度之间的潜在联系。
后果
我们从肠道微生物中发现了12类（城市）和11类（农村）COG蛋白质。E类蛋白质表示氨基酸运输和代谢，是城市受访者所独有的，主要由5-烯醇丙酮酸莽草酸-3-磷酸合成酶（45%）和天冬酰胺合成酶（30%）组成，这意味着高蛋白饮食。在两组中均发现S类。COG蛋白质家族显示，在农村受访者的碳水化合物丰富饮食中，存在外-β-1,3-葡聚糖酶（31%）、丙酮酸脱羧酶和硫胺素焦磷酸所需酶（22%）。此外，在两者中都发现了与假设功能相关的未表征蛋白质。城市人群的COG蛋白与女性、BMI（体重指数）和BP（血压）聚集在一起，而农村人群则与身高、BMI和BP聚集在一起。CARD分析显示，两组中的ARG（城市90%；农村10%）均为大肠杆菌16S rRNA（rrsB）突变，对链霉素具有耐药性，基因变体模型A523C n/a对氨基糖苷类抗生素具有耐药性。
结论
这项研究定义了来自城市和农村受访者肠道微生物的蛋白质类别，并强调了与假设和未知功能相关的未表征蛋白质的存在。预测角色之间的差异似乎是由饮食、临床和社会人口因素驱动的。在城市人群中观察到的ARGs丰度较高，这对抗生素耐药性的传播造成了严重的公共卫生问题。
Abstract
Background
The human gut microbiome is implicated in health and disease. Yet, its functions in healthy adults from a divergent population like those seen in Africa are quite unclear. We set to reveal the roles of the gut microbiome of a healthy rural and urban Yoruba population of Lagos State.

Methodology
Sociodemographic and clinical data, and fecal samples were obtained from rural (n = 10) and urban (n = 10) participants. fecal DNA extraction was done using ZR Fecal DNA MiniPrep™ D6010 and metagenomic next generation sequencing performed on Illumina Miseq platform. Functional roles prediction and antibiotics resistance genes (ARGs) were done using the Clusters of Orthologous Groups (COG) and Comprehensive Antibiotic Resistance Database (CARD) tools, respectively. The potential link between phenotypes and COG abundance were inferred using principal component analysis (PCA).

Results
We found 12 (urban) and 11 (rural) COG classes of proteins from the gut microbes. Class E protein which denotes amino acid transport and metabolism was unique to urban respondents and was dominated by 5-enolpyruvylshikimate-3-phosphate synthase (45%) and asparagine synthase (30%), implying a high protein-based diet. Class S was found in both groups. COG families of proteins revealed the presence of exo-beta-1,3-glucanase (31%), pyruvate-decarboxylase, and thiamine pyrophosphate-requiring enzymes (22%) among the rural respondents’ indicative of carbohydrate-rich diets. In addition, uncharacterized protein linked to hypothetical functions was found in both. The COG proteins clustered with female sex, BMI (body mass index) and BP (blood pressure) for urban while for the rural populace, it clustered with height, BMI, and BP. CARD analysis showed ARGs in both groups (urban 90%; rural 10%) and all were Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to streptomycin with gene variant model A523C n/a to aminoglycoside antibiotics.

Conclusion
The study defined the classes of proteins from gut microbes of urban and rural respondents and highlighted the presence of uncharacterized proteins linked to hypothetical and unknown functions. Differences seen among the predicted roles appear to be driven by diet, clinical and sociodemographic factors. The higher abundance of ARGs observed in the urban population poses a serious public health concern with regards to the spread of antibiotic resistance.

https://www.sciencedirect.com/science/article/pii/S2468227622003507