Exploring Microbial Functional Biodiversity at the Protein Family Level-From Metagenomic Sequence Reads to Annotated Protein Clusters

Overview

Journal Front Bioinform

Specialty Biology

Date 2023 Mar 24

PMID 36959975

Authors

Fotis A Baltoumas

Evangelos Karatzas

David Paez-Espino

Nefeli K Venetsianou

Eleni Aplakidou

Anastasis Oulas

Robert D Finn

Sergey Ovchinnikov

Evangelos Pafilis

Nikos C Kyrpides

Georgios A Pavlopoulos

Affiliations

Soon will be listed here.

Abstract

Metagenomics has enabled accessing the genetic repertoire of natural microbial communities. Metagenome shotgun sequencing has become the method of choice for studying and classifying microorganisms from various environments. To this end, several methods have been developed to process and analyze the sequence data from raw reads to end-products such as predicted protein sequences or families. In this article, we provide a thorough review to simplify such processes and discuss the alternative methodologies that can be followed in order to explore biodiversity at the protein family level. We provide details for analysis tools and we comment on their scalability as well as their advantages and disadvantages. Finally, we report the available data repositories and recommend various approaches for protein family annotation related to phylogenetic distribution, structure prediction and metadata enrichment.

Citing Articles

Visualizing metagenomic and metatranscriptomic data: A comprehensive review.

Aplakidou E, Vergoulidis N, Chasapi M, Venetsianou N, Kokoli M, Panagiotopoulou E Comput Struct Biotechnol J. 2024; 23:2011-2033.

PMID: 38765606 PMC: 11101950. DOI: 10.1016/j.csbj.2024.04.060.

Unraveling the functional dark matter through global metagenomics.

Pavlopoulos G, Baltoumas F, Liu S, Selvitopi O, Camargo A, Nayfach S Nature. 2023; 622(7983):594-602.

PMID: 37821698 PMC: 10584684. DOI: 10.1038/s41586-023-06583-7.

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