GenBank as a source to monitor and analyze Host-Microbiome data.

ABSTRACT:

Motivation

Microbiome datasets are often constrained by sequencing limitations. GenBank is the largest collection of publicly available DNA sequences, which is maintained by the National Center of Biotechnology Information (NCBI). The metadata of GenBank records are a largely understudied resource and may be uniquely leveraged to access the sum of prior studies focused on microbiome composition. Here, we developed a computational pipeline to analyze GenBank metadata, containing data on hosts, microorganisms and their place of origin. This work provides the first opportunity to leverage the totality of GenBank to shed light on compositional data practices that shape how microbiome datasets are formed as well as examine host-microbiome relationships.

Results

The collected data

SUBMITTER: Ramanan V 

PROVIDER: S-EPMC9438952 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature