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Background  The gut microbiota composition is known to be influenced by a myriad of factors including the host genetic profile and a number of environmental influences. Here, we focus on the environmental influence of cohabitation on the gut microbiota as well as whether these environmentally influenced microorganisms are associated with cardiometabolic and inflammatory burden. We perform this by investigating the gut microbiota composition of various groups of related individuals including cohabitating monozygotic (MZ) twin pairs, non-cohabitating MZ twin pairs and spouse pairs.    Results  A stronger correlation between alpha diversity was found in cohabitating MZ twins (45 pairs, r = 0.64,  p  = 2.21 × 10 − 06 ) than in non-cohabitating MZ twin pairs (121 pairs, r = 0.42,  p  = 1.35 × 10 − 06 ). Although the correlation of alpha diversity did not attain significance between spouse pairs (42 pairs, r = 0.23,  p  = 0.15), the correlation was still higher than those in the 209 unrelated pairs (r = − 0.015,  p  = 0.832). Bray-Curtis (BC) dissimilarity metrics showed cohabitating MZ twin pairs had the most similar gut microbiota communities which were more similar than the BC values of non-cohabitating MZ twins (empirical  p -value = 0.0103), cohabitating spouses (empirical p-value = 0.0194), and pairs of unrelated non-cohabitating individuals (empirical p-value< 0.00001). There was also a significant difference between the BC measures from the spouse pairs and those from the unrelated non-cohabitating individuals (empirical  p -value< 0.00001). Intraclass correlation coefficients were calculated between the various groups of interest and the results indicate the presence of OTUs with an environmental influence and one OTU that appeared to demonstrate genetic influences. One of the OTUs (Otu0190) was observed to have a significant association with both the cardiometabolic and inflammatory burden scores (p’s < 0.05).    Conclusions  Through the comparison of the microbiota contents of MZ twins with varying cohabitation status and spousal pairs, we showed evidence of environmentally influenced OTUs, one of which had a significant association with cardiometabolic and inflammatory burden scores.

Cohabitation is associated with a greater resemblance in gut microbiota which can impact cardiometabolic and inflammatory risk