Genomics of Atlantic Forest Mycobacteriaceae strains unravels a mobilome diversity with a novel integrative conjugative element and plasmids harbouring T7SS

Abstract

Mobile genetic elements (MGEs) are agents of bacterial evolution and adaptation. Genome sequencing provides an unbiased approach that has revealed an abundance of MGEs in prokaryotes, mainly plasmids and integrative conjugative elements. Nevertheless, many mobilomes, particularly those from environmental bacteria, remain underexplored despite their representing a reservoir of genes that can later emerge in the clinic. Here, we explored the mobilome of the Mycobacteriaceae family, focusing on strains from Brazilian Atlantic Forest soil. Novel Mycolicibacterium and Mycobacteroides strains were identified, with the former ones harbouring linear and circular plasmids encoding the specialized type-VII secretion system (T7SS) and mobility-associated genes. In addition, we also identified a T4SS-mediated integrative conjugative element (ICEMyc226) encoding two T7SSs and a number of xenobiotic degrading genes. Our study uncovers the diversity of the Mycobacteriaceae mobilome, providing the evidence of an ICE in this bacterial family. Moreover, the presence of T7SS genes in an ICE, as well as plasmids, highlights the role of these mobile genetic elements in the dispersion of T7SS.

Comprehensive in silico survey of the Mycolicibacterium mobilome reveals an as yet underexplored diversity

“…The study of these elements is the starting point for understanding the dynamics of gene flow within a bacterial community and how it affects its diversity and density [7]. These genetic entities include DNA elements such as integrons, plasmids, integrative conjugative elements, insertion sequences, bacteriophages and transposons that can mobilize and integrate into the host genome [2,8].…”

“…Moreover, despite several reports of Mycolicibacterium genomes [15][16][17][18][19][20][21][22][23][24][25][26], these studies rarely survey plasmids among their contigs. Thus, only a few plasmids have been reported in this genus, mainly from unrecognized genomes [2,14,[27][28][29][30]. Despite the reclassification of Mycobacterium, some Mycobacterium sp.…”

“…Most species in the family Mycobacteriaceae belong to the genera Mycobacterium (slowly growing mycobacteria), which includes several human pathogens, and Mycolicibacterium (rapidly growing mycobacteria), saprophyte organisms that mainly comprise environmental species and opportunistic pathogens [ 1 ]. Although the family Mycobacteriaceae has a huge diversity of species, its mobilome is underexplored [ 2 ].…”

A plasmid network from the gut microbiome of semi-isolated human groups reveals unique and shared metabolic and virulence traits

“…Beyond that, we are aware that our study has biases and limitations, for example, the plasmid identification that is based on the current plasmid markers in the databases. However, different studies have successfully carried out bioinformatic analysis of sequences and addressed them to plasmids, mainly when the plasmids were in vitro isolated from the strains 51 , 52 . The semi-isolated groups may harbor plasmid markers that have not yet been characterized and this may have resulted in the general lack of relaxase, MPF, and oriT sequences identified.…”

Conjugative transfer of naturally occurring plasmid in Mycolicibacterium sp

“…In addition, in another Mycolicibacterium sp. lineage, no plasmids were identified (Morgado and Vicente, 2020). So, to contribute with experimental evidence of conjugation in this bacterial family, analyzing the conjugative capability of these natural plasmids, we performed conjugation tests using these wild Mycolicibacterium strains carrying plasmids as donors and a wild Mycolicibacterium as the recipient.…”