LogMPIE, pan-India profiling of the human gut microbiome using 16S rRNA sequencing

Abstract

The “Landscape Of Gut Microbiome - Pan-India Exploration”, or LogMPIE study, is the first large-scale, nationwide record of the Indian gut microbiome. The primary objective of the study was to identify and map the Indian gut microbiome baseline. This observational study was conducted across 14 geographical locations in India. Enrolled subjects were uniformly distributed across geographies (north, east, west and south) and body mass index (obese and non-obese). Furthermore, factors influencing the microbiome, such as age and physical activity, were also considered in the study design. The LogMPIE study recorded data from 1004 eligible subjects and reported 993 unique microorganisms across the Indian microbiome diaspora. The data not only map the Indian gut microbiome baseline but also function as a useful resource to study, analyse and identify signatures characterizing the physiological dispositions of the subjects. Furthermore, they provide insight into the unique features describing the Indian microbiome. The data are open and may be accessed from the European Nucleotide Archive (ENA) portal of the European Bioinformatics Institute (https://www.ebi.ac.uk/ena/data/view/PRJEB25642).

Gut microbiota features of the geographically diverse Indian population

“…The detailed the subject data is described in the original article reporting the LogMPIE study (Dubey et al , 2018). Briefly, the study reported microbial profile of 1004 Indian individuals residing in 14 cities different cities.…”

“…The data analysed in this study was obtained from figshare (Dubey et al , 2018). Detailed information on sample collection and processing for DNA extraction, 16S rRNA gene amplification and sequencing are provided in the original publication (Dubey et al , 2018). Here, some key points are described.…”

“…DNA extraction was done using the QiaAmp DNA Stool Mini Kit (Qiagen, Hilden, Germany). Two primer pairs one of V3 and one for V4 hypervariable region of the 16S rRNA gene was used for amplification (Milani et al , 2013, Dubey et al , 2018). The sequencing was done Ion S5 System (Thermo Fisher Scientific, Carlsbad, CA, USA).…”

“…The relative abundance microbial profiling data and metadata were obtained from (Dubey et al , 2018)(https://doi.org/10.6084/m9.figshare.c.4147079.v1). The taxonomy was corrected to make it compatible with read _ phyloseq function of microbiome R package (Lahti & Shetty, 2018).…”

“…The raw sequencing files are made available by the authors at European nucleotide archive (ENA) under the primary accession code, PRJEB25642, and secondary accession code, ERP07577 (Dubey et al , 2018). The codes used for the analysis done in this manuscript will be made available at the following GitHub repository (https://github.com/microsud/Indian-gut-microbiota).…”