What Dominates in Shaping Human Gut Microbiota?

By Maryna Mullerman ‘20

Figure 1. An environment’s genetic makeup dominates over a host’s genetic makeup in determining the microbial composition in the human gut.

The human microbiome is thought to be shaped by many factors. Daphna Rothschild and researchers from Weizmann Institute of Science in Israel attempted to find the most important   determinant for the microbial composition of the human gut. They compared genetic and environmental factors that were thought to influence gut composition and utilized statistical measures to analyze them.

The study recruited 1046 healthy Israeli individuals with various ancestries and similar living environments. Each participant completed a questionnaire regarding his or her lifestyle, nutrition, medical history, lactose consumption, and ancestry. Each volunteer was genotyped – the DNA sequence was determined. Their stool samples were analyzed using metagenome-sequencing and 16S rRNA genes sequencing, which provide information about a sample’s bacterial composition. The researchers searched for relationships between genetic ancestry, single nucleotide polymorphisms (SNPs) and β-diversity, the microbial community diversity among various environments. Moreover, they analyzed the data from 2,252 twins from a TwinsUK cohort for gut microbiome heritability. The study used microbiome and human genetics to predict the phenotypes and introduced b2 microbiome-association index that represented the overall association between them. The microbiome data was used to predict human traits such as body mass index (BMI) and cholesterol level. The study was later replicated with the cohort of 836 from the north Netherlands (LLD cohort) to consolidate the results and establish clear patters.

There was a lack of association between microbiome composition and host genetic ancestry. There was no strong association with individual SNPs, and the mean heritability of microbiome taxa was less than 2 percent. However, more than 20 percent of microbiome β-diversity was impacted by environmental factors such as diet. There was a significant resemblance among the gut populations among genetically unrelated participants within a household.

The study’s results suggested that the environment primarily determined human microbiome composition. Individuals within a household possessed similar bacteria. The researchers successfully demonstrated that microbiome data could be used to supplement genetic information in predicting human traits. The study could be improved by providing pre-determined cohort sample sizes. The techniques utilized in the study could be used to improve clinical practices among people of different backgrounds.



  1. D. Rothschild, et. al., Environment dominates over host genetics in shaping human gut microbiota. Nature 555, 210-215 (2018). doi: 10.1038/nature25973.
  2. Image retrieved from: https://www.google.com/search?safe=active&as_st=y&hl=en&tbs=sur%3Afmc&tbm=isch&sa=1&ei=vLKlWvqvBcqHggeY0ZnYAQ&q=microbes+gut&oq=microbes+gut&gs_l=psy-ab.3..0i8i30k1l3j0i24k1.48978.49493.0.49706.….0…1c.1.64.psy-ab..0.4.519…0j0i67k1j0i30k1.0.t7ek-4n4Y8s#imgrc=vD5s0BmcT0uHOM

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