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. 2023 Oct 6;26(11):108136.
doi: 10.1016/j.isci.2023.108136. eCollection 2023 Nov 17.

Urbanization associates with restricted gut microbiome diversity and delayed maturation in infants

Francesco Morandini  1 , Kevin Perez  2 , Loic Brot  3   4 , Sidy Mohammed Seck  5 , Laurence Tibère  6 , Jean-Pierre Grill  4 , Enguerran Macia  7   8 , Philippe Seksik  3   4   9
Affiliations

Urbanization associates with restricted gut microbiome diversity and delayed maturation in infants

Francesco Morandini et al. iScience. .

Abstract

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.

Keywords: Developmental biology; Microbiology; Microbiome.

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Conflict of interest statement

P.S. declares financial support for scientific works from Biocodex, MSD, Takeda, Janssen, and Sandoz, and consultant fees from Abbvie, Merk, MSD, Gilead, Pfizer, Sandoz, Janssen, and Fresenius Kabi.

Figures

None
Graphical abstract
Figure 1
Figure 1
Design of the study and phylum-level gut microbiome composition of the study groups (A) Design of the study. (B) Proportions of most common phyla for mothers and infants at both time points. One bar corresponds to one individual. Individuals have been ordered by decreasing proportion of Firmicutes.
Figure 2
Figure 2
Factors affecting gut microbiome diversity and composition in mothers (A) Comparison of alpha diversity (Chao1) between rural and urban mothers at multiple time points. (B) Correlation between time since delivery and alpha diversity in mothers (Chao1). (C) Effect of Entamoeba coli parasitism in mothers, separated by rural/urban and time point. (D) Variables explaining beta diversity (Aitchison) between mothers ranked by effect size. (. = p < 0.1, ∗ = p < 0.05, ∗∗ = p < 0.01, ∗∗∗ = p < 0.001). (E) PCoA of Aitchison beta diversity, showing clustering of Entamoeba coli + mothers. Group centroids are included as a visual aid. (F) Associations between genera abundance in mothers and rural/urban environment, Entamoeba coli parasitism, and time since delivery.
Figure 3
Figure 3
Factors affecting gut microbiome diversity and composition in infants (A) Comparison of alpha diversity (Chao1) between rural and urban infants at multiple time points. (B) Variables explaining beta diversity (Aitchison) between infants ranked by effect size. (. = p < 0.1, ∗ = p < 0.05, ∗∗ = p < 0.01, ∗∗∗ = p < 0.001) (C) PCoA of Aitchison beta diversity, showing a maturation trajectory from newborn (T1) to adult microbiome. Group centroids are included as a visual aid. (D) UnifracW beta diversity between adults and infants by group. (E) Associations between genera abundance in infants and rural/urban environment, infant age, and the interaction of environment and age.
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