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Lookup NU author(s): Professor Hans-Peter Klenk
This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
© 2022 The AuthorsThe phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%–50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences.
Author(s): Seshadri R, Roux S, Huber KJ, Wu D, Yu S, Udwary D, Call L, Nayfach S, Hahnke RL, Pukall R, White JR, Varghese NJ, Webb C, Palaniappan K, Reimer LC, Sarda J, Bertsch J, Mukherjee S, Reddy TBK, Hajek PP, Huntemann M, Chen I-MA, Spunde A, Clum A, Shapiro N, Wu Z-Y, Zhao Z, Zhou Y, Evtushenko L, Thijs S, Stevens V, Eloe-Fadrosh EA, Mouncey NJ, Yoshikuni Y, Whitman WB, Klenk H-P, Woyke T, Goker M, Kyrpides NC, Ivanova NN
Publication type: Article
Publication status: Published
Journal: Cell Genomics
Year: 2022
Volume: 2
Issue: 12
Print publication date: 14/12/2022
Online publication date: 11/11/2022
Acceptance date: 16/10/2022
Date deposited: 05/01/2023
ISSN (electronic): 2666-979X
Publisher: Cell Press
URL: https://doi.org/10.1016/j.xgen.2022.100213
DOI: 10.1016/j.xgen.2022.100213
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