Alterations of the microbiome are linked to increasingly common diseases such as obesity, allergy, and inflammatory bowel disease. Post-industrial lifestyles are thought to contribute to the gut microbiome alterations that cause or aggravate these diseases. Comparing communities across the industrialization spectrum can reveal associations between gut microbiome alterations and lifestyle and health, and help pinpoint which specific aspect of the post-industrial lifestyle is linked to microbiome alterations. Here, we compare the gut microbiomes of 60 mother and infant pairs from rural and urban areas of Senegal over two time points. We find that urban mothers, who were more frequently overweight, had different gut microbiome compositions than rural mothers, showing an expansion of Lachnospiraceae and Enterobacter. Urban infants, on the other hand, showed a delayed gut microbiome maturation and a higher susceptibility to infectious diseases. Thus, we identify new microbiome features associated with industrialization, whose association with disease may be further investigated.