Transition from traditional high-fiber to Western diets in urbanizing communities of Sub-Saharan Africa is associated with increased risk of non-communicable diseases (NCD), exemplified by colorectal cancer (CRC) risk. To investigate how urbanization gives rise to microbial patterns that may be amenable by dietary intervention, we analyzed diet intake, fecal 16 S bacteriome, virome, and metabolome in a cross-sectional study in healthy rural and urban Xhosa people (South Africa). Urban Xhosa individuals had higher intakes of energy (urban: 3,578 ± 455; rural: 2,185 ± 179 kcal/d), fat and animal protein. This was associated with lower fecal bacteriome diversity and a shift from genera favoring degradation of complex carbohydrates (e.g., Prevotella) to taxa previously shown to be associated with bile acid metabolism and CRC. Urban Xhosa individuals had higher fecal levels of deoxycholic acid, shown to be associated with higher CRC risk, but similar short-chain fatty acid concentrations compared with rural individuals. Fecal virome composition was associated with distinct gut bacterial communities across urbanization, characterized by different dominant host bacteria (urban: Bacteriodota; rural: unassigned taxa) and variable correlation with fecal metabolites and dietary nutrients. Food and skin microbiota samples showed compositional differences along the urbanization gradient. Rural-urban dietary transition in South Africa is linked to major changes in the gut microbiome and metabolome. Further studies are needed to prove cause and identify whether restoration of specific components of the traditional diet will arrest the accelerating rise in NCDs in Sub-Saharan Africa.

在撒哈拉以南非洲的城市化社区中，从传统高纤维饮食向西方饮食的转变与非传染性疾病（NCD）风险增加相关，例如结直肠癌（CRC）风险。为了调查城市化如何产生可通过饮食干预进行调节的微生物模式，我们在健康农村和城市科萨人（南非）的一项横断面研究中分析了饮食摄入量、粪便 16S 细菌组、病毒组和代谢组。城市科萨人的能量摄入量较高（城市：3,578 ± 455；农村：2,185 ± 179 kcal/d）、脂肪和动物蛋白。这与粪便细菌多样性较低以及从有利于复合碳水化合物降解的属（例如普雷沃氏菌）向先前显示与胆汁酸代谢和结直肠癌相关的分类群的转变有关。城市科萨人粪便中的脱氧胆酸水平较高，这与较高的结直肠癌风险相关，但与农村人相比，短链脂肪酸浓度相似。粪便病毒组组成与城市化过程中不同的肠道细菌群落相关，其特征是不同的优势宿主细菌（城市：拟杆菌；农村：未分配的分类单元）以及与粪便代谢物和膳食营养素的可变相关性。食物和皮肤微生物群样本显示出沿城市化梯度的组成差异。南非城乡饮食转变与肠道微生物组和代谢组的重大变化有关。需要进一步的研究来证明原因并确定恢复传统饮食的特定成分是否会阻止撒哈拉以南非洲非传染性疾病的加速增长。