Gut, oral and skin microbiome of Indian patrilineal families reveal perceptible association with age

Diptaraj S Chaudhari,Dhiraj M Agarwal,Akshay H Gaike,Ulhas K Patil,Parmeshwar Jadhav,Ashish Bavdekar,Yogesh S Shouche,Dattatray Mongad,Devika Bhalerao,Sanjay K Juvekar,Dhiraj P Dhotre,Himangi Lubree,Sundeep Salvi,Vilas P Sinkar

doi:10.1038/s41598-020-62195-5

Abstract

The human microbiome plays a key role in maintaining host homeostasis and is influenced by age, geography, diet, and other factors. Traditionally, India has an established convention of extended family arrangements wherein three or more generations, bound by genetic relatedness, stay in the same household. In the present study, we have utilized this unique family arrangement to understand the association of age with the microbiome. We characterized stool, oral and skin microbiome of 54 healthy individuals from six joint families by 16S rRNA gene-based metagenomics. In total, 69 (1.03%), 293 (2.68%) and 190 (8.66%) differentially abundant OTUs were detected across three generations in the gut, skin and oral microbiome, respectively. Age-associated changes in the gut and oral microbiome of patrilineal families showed positive correlations in the abundance of phyla Proteobacteria and Fusobacteria, respectively. Genera Treponema and Fusobacterium showed a positive correlation with age while Granulicatella and Streptococcus showed a negative correlation with age in the oral microbiome. Members of genus Prevotella illustrated high abundance and prevalence as a core OTUs in the gut and oral microbiome. In conclusion, this study highlights that precise and perceptible association of age with microbiome can be drawn when other causal factors are kept constant.

Highlights

Aging is an extremely complex, perpetual, progressive and multifactorial process resulting in decreased physiologic functions of all the organ systems[1]
India has an established convention of the joint family system, which is an extended family arrangement consisting of three or more generations living in the same household structure bound by genetic relatedness[29,30]
Four samples (St.D1004, St.D301, St.S610 and St.S612) were removed from further analysis due to lower sequencing depth. Bacterial phyla such as Bacteroidetes (49.3%), Firmicutes (41.6%), Proteobacteria (5.7%), Actinobacteria (2.18%) and Tenericutes (0.4%) were highly dominant and constituted ~99% of the total gut microbiome

Summary

Introduction

Aging is an extremely complex, perpetual, progressive and multifactorial process resulting in decreased physiologic functions of all the organ systems[1]. Studies have suggested that the complex and diverse communities of microbes that inhabit the gut vary through different stages of an individual’s life[5] Many of these alterations are harmless and natural, while some of the alterations can have an important effect on overall homeostasis[6]. The Indian population provides a unique opportunity to understand age-related changes in the human microbiome. We provide a comprehensive analysis of the human microbiome from the gut, oral and skin ecosystems from 54 healthy subjects belonging to six different patrilineally related three generation families staying together in rural Indian settings. 16S rRNA gene amplicon sequencing-based microbiome analysis performed to investigate the age-related changes in the gut, skin and oral microbiome of Endogamous Agriculturist Indian (EAI) sub-population Other microbiome contributing factors were harmonized and age was the only distinguishing factor. 16S rRNA gene amplicon sequencing-based microbiome analysis performed to investigate the age-related changes in the gut, skin and oral microbiome of Endogamous Agriculturist Indian (EAI) sub-population

Methods

Results

Conclusion