Chinese urbanization

Researchers determine whether Chinese urbanization changes their gut microbiomes to resemble the microbiomes of the urbanized American population.

The transition from rural to urban lifestyles witnessed in many parts of the developing world is accompanied by changes in the living environment, diet, and physical activity. Changes in diet are known to be associated with changes in the microbiome, which is the community or collection of microorganisms found in the gut.1,2 Furthermore, changes in the microbiome are known to be associated with inflammatory bowel disease, obesity, diabetes, and cancer.3-6 However, a comprehensive understanding of the effects of lifestyle changes on the microbiome is lacking. A study was carried out recently to determine if rapid Chinese urbanization changes the microbiome significantly.

Comparisons Between Urban and Rural Populations

The study, carried out in the Hunan province of China, examined differences in the microbiomes of 20 recently urbanized and 20 rural individuals. The results of the study were published in the journal Microbiome in September 2017.7 The participants were between 18 and 65 years of age, had lived in the same area for at least two years, were not pregnant or lactating, did not have cancer, had not been exposed to arsenic, or used antibiotics in the preceding 3 months. Fasting blood samples, as well as urine and fecal samples, were collected from the participants twice at a two-week interval. Researchers also collected information on probiotic and antibiotic use, glucose and insulin levels, and fat intake.

Comparing Data to American Microbiomes

They then analyzed samples for the presence of various metabolites, a process known as metabolic profiling. Additionally, the fecal samples were used to sequence the V4 hypervariable region of 16S ribosomal RNA as well as whole genomes. The sequence data was used to identify and classify the microorganisms present in the fecal samples as well as the genes and proteins present and their corresponding functions. The sequence data were also analyzed to determine the presence of antibiotic resistance genes and virulence factors. Virulence factors are proteins produced by disease-causing microorganisms that help them successfully invade and colonize the host or evade the host’s immune system. The data were also compared to the data obtained from the Human Microbiome Project, which studied the microbiomes of healthy American subjects.

Significant Differences between Rural and Urban Groups

The study found significant differences in the microbial populations between the rural and urban groups. Urbanization resulted in the loss of microbial diversity, and among the microorganisms lost were viruses and archaebacteria. More specifically, 60 species, 44 genera, 71 families, 35 orders, 21 classes, 9 phyla, and 3 domains were found to be significantly different between the two groups with the urbanized individuals losing most of these taxonomic groups. The study also found that those microbial groups that were more prevalent in urban individuals were more likely to be present in the urbanized American population.

Genes for Antibiotic Resistance More Abundant in Urban Samples

Notably, genes that conferred antibiotic resistance were more abundant in the urban samples, even though antibiotic use during the preceding 6 months was not different in the two groups. The results indicate that pathogenic strains of Escherichia coli and Shigella harboring antibiotic resistance genes and virulence factors tend to colonize the gut with urbanization. Earlier studies have indicated links between the virulence factors harbored by pathogenic E. coli and Crohn’s disease and cancer. The results of this study underline the need for a further examination of the links between urbanization, changes in the microbiome, and disease. They also imply that antibiotics may not be as efficacious in urban settings as in rural ones.

As for the results of metabolic profiling, while the metabolomes did not differ in terms of diversity between the rural and urban groups, they differed in terms of composition. Sixteen metabolites were found to vary significantly with rural versus urban status; of these, 10 metabolites were involved in carbohydrate, lipid, and energy metabolism, indicating that these changes may be a consequence of adopting a Western diet.

Results Should be Validated in a Larger Sample Size

One strength of the study is that the comparison was carried out between groups people living in neighboring geographical locations, and therefore, is not influenced by factors such as ethnicity, geography, and regional dietary variations. A notable limitation is the small sample size; the results need to be validated using a larger group of individuals. Overall, the study points to a strong link between urbanization and gut dysbiosis and underlines the need for further studies to understand its relationship with chronic diseases.

Written by Usha B. Nair, Ph.D.


1) Walker AW, Ince J, Duncan SH, et al. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J. 2011 Feb;5(2):220-30. doi: 10.1038/ismej.2010.118. Epub 2010 Aug 5. PubMed PMID: 20686513; PubMed Central PMCID: PMC3105703.
2) David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014 Jan 23;505(7484):559-63. doi: 10.1038/nature12820. Epub 2013 Dec 11. PubMed PMID: 24336217; PubMed Central PMCID: PMC3957428.
3) Qin J, Li Y, Cai Z, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012 Oct 4;490(7418):55-60. doi: 10.1038/nature11450. Epub 2012 Sep 26. PubMed PMID: 23023125.
4) Arthur JC, Gharaibeh RZ, Mühlbauer M, Perez-Chanona E, Uronis JM, McCafferty J, Fodor AA, Jobin C. Microbial genomic analysis reveals the essential role of inflammation in bacteria-induced colorectal cancer. Nat Commun. 2014 Sep 3;5:4724. doi: 10.1038/ncomms5724. PubMed PMID: 25182170; PubMed Central PMCID: PMC4155410.
5) Kostic AD, Xavier RJ, Gevers D. The microbiome in inflammatory bowel disease:  current status and the future ahead. Gastroenterology. 2014 May;146(6):1489-99. doi: 10.1053/j.gastro.2014.02.009. Epub 2014 Feb 19. Review. PubMed PMID: 24560869; PubMed Central PMCID: PMC4034132.
6) Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature. 2009 Jan 22;457(7228):480-4. doi: 10.1038/nature07540. Epub 2008 Nov 30. PubMed PMID: 19043404; PubMed Central PMCID: PMC2677729.
7) Winglee K, Howard AG, Sha W, Gharaibeh RZ, Liu J, Jin D, Fodor AA, Gordon-Larsen P. Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes. Microbiome. 2017 Sep 15;5(1):121. doi: 10.1186/s40168-017-0338-7. PubMed PMID: 28915922; PubMed Central PMCID: PMC5603068.

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