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Skin Microbiomes of Megacity Dwellers More Fragile Than Those in Smaller Urban Areas

NEW YORK (GenomeWeb) – The skin microbiomes of people living in megacities are more fragile than those of people living in smaller urban areas.

Skin diseases like atopic dermatitis are more common among people who live in large urban locations, leading Woo Jun Sul at Chung-Ang University in South Korea and his colleagues to suspect that the skin microbiomes of people in megacities might differ from those of people in smaller cities.

They collected microbial skin samples from more than 200 healthy women living in one of two megacities or one of three smaller cities in China for 16S ribosomal RNA gene amplicon sequencing. Clustering analysis grouped the skin microbiomes of megacity-dwelling women apart from the others, and further analyses suggested that how microbial communities are assembled differs between the two types of urban areas. Additionally, microbial networks among megacity skin microbiomes were more tenuous, which the researchers said could influence the incidence of skin diseases there.

"An individual's residential environment and lifestyle have a significant impact on the formation process of skin microbiome," the researchers wrote in their paper, which was published today in Science Advances.

Sul and his colleagues collected skin swabs from the cheeks of 231 healthy women. Of these, 83 women lived in the megacities of Beijing or Guangzhou — each with a population of more than 10 million people — while 148 lived in the smaller, but still large, cities of Hohot, Xi'an, or Kunming. All the participants had been living in the same city for at least five years.

Sequencing 16S rRNA gene amplicons from these samples uncovered four prominent skin microbiome phyla — Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes — that accounted for 90 percent of the microbiome.

Still, the researchers noted heterogeneity among the samples. Principal coordinates analysis clustered megacity and non-megacity samples separately, a grouping confirmed by random forest analysis. Samples from non-megacities also had greater inter-individual variation than samples from megacities, and non-megacity samples harbored a higher overall number of OTUs.

Sul and his colleagues applied three different approaches to examine whether there were differences in how microbial communities are assembled by city type.

They first calculated β diversity, a measure of compositional variation, among the samples by comparing the communities they observed against what they'd expect to see based on a neutral model that assumes community assembly is random. In this approach, a β diversity deviation close to zero reflects that neutral model, while a higher or lower value indicates a niche-based community assembly process. A niche-based model assumes different species occupy different niches due to either environmental factors or interspecific competition.

Here, the researchers reported that the β-null deviation pattern was higher in megacities as compared to non-megacities, indicating that a more niche-based process occurs in megacities.

Likewise, using a phylogenetic diversity theory approach, the researchers also assessed community assembly processes. This method relies on summing the branch lengths of phylogenetic trees and examining the edge-length abundance distribution to gauge metacommunities' phylogenetic structure. Again, they compared their observed communities to what would be expected under a null model to find that niche-based processes affect the skin microbiomes from all five cities.

Lastly, through a dominance test that compares the occurrence frequency and mean relative abundance of bacterial taxa in observed microbiomes with predicted models, they similarly found that microbiomes collected in Beijing, Guangzhou, and Kunming more closely resembled niche-based models, as compared to Xi'an and Hohhot microbiomes. This suggested to the researchers that neutral process have less of a role in microbiome assembly processes in megacities than in smaller cities.

Network analysis of the skin microbiomes also uncovered that megacity-derived samples had lower network density than non-megacity samples. Additionally, the analysis indicated that non-megacity samples had more complex microbial network structures. This suggested to the researchers that the megacity microbiomes are more fragile, and that this fragility could contribute to skin disease in those regions.