Amplicon-based functional prediction of microbial communities

Anish Tamang; Mohit Swarnkar; Pawan Kumar; Dinesh Kumar; Shiv Shanker Pandey; Vipin Hallan

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Amplicon-based functional prediction of microbial communities

AT Anish Tamang

MS Mohit Swarnkar

PK Pawan Kumar

DK Dinesh Kumar

SP Shiv Shanker Pandey

VH Vipin Hallan

This method is extracted from research article: Microbiol Spectr, Oct 2023

Endomicrobiome of in vitro and natural plants deciphering the endophytes-associated secondary metabolite biosynthesis in Picrorhiza kurrooa, a Himalayan medicinal herb

DOI: 10.1128/spectrum.02279-23

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To predict the metabolic pathways associated with the bacterial communities, Phylogenetic investigation of communities by reconstruction of unobserved state (PICRUSt2) software was utilized (177). Based on the database of Kyoto Encyclopedia of Genes and Genome (KEGG) and evolutionary genealogy of genes (EggNOG), the KEGG orthology (KO) was predicted based on the OTU matrix, along with abundance was also obtained. EC number involved in the possible secondary metabolite biosynthesis was manually categorized based on the KEGG database.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

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