Small and equipped: the rich repertoire of antibiotic resistance genes in Candidate Phyla Radiation genomes

Abstract

Microbes belonging to Candidate Phyla Radiation (CPR) have joined the tree of life as a new unique branch, thanks to the intensive application of metagenomics and advances of sequencing technologies. Despite their ultra-small size, reduced genome and metabolic pathways which mainly depend on symbiotic/exo-parasitic relationship with their bacterial host, CPR microbes are abundant and ubiquitous in almost all environments and are consequently survivors in highly competitive circumstances within microbial communities. They have been eventually identified by 16S rRNA analysis and represent more than 26% of microbial diversity. CPR microbes were able to survive in this context, although their defence mechanisms and phenotypic characteristic remain, however, poorly explored. Here, we conducted a thorough in-silico analysis on 4,062 CPR genomes to test whether these ultrasmall microorganisms might encode for antibiotic resistance (AR)-like enzymes. We used an adapted AR screening criteria with an exhaustive consensus database and complementary steps conferring their resistance functions. We conclude by reporting the surprising discovery of rich reservoir of divergent AR-like genes (n= 30,545 HITs, mean=7.5 HITs/genome [0-41] encoding for 89 AR enzymes, distributed across the 13 CPR phyla, and associated with 14 different chemical classes of antimicrobials. However, most HITs found (93.6%) were linked to glycopeptide, beta-lactams, macrolide-lincosamide-streptogramin, tetracycline and aminoglycoside resistance. Moreover, a distinct AR profile was discerned between the microgenomates group and Candidatus Parcubacteria, and between each of them and other CPR phyla. CPR cells seem to be active players during microbial competitive interactions and are well-equipped for the microbial combat in different habitats, supporting their natural survival/persistence and continued existence.

Adapted Protocol for Saccharibacteria Cocultivation: Two New Members Join the Club of Candidate Phyla Radiation

“…We did not find any nonribosomal peptide synthetase/polyketide synthase (NRPS/PKS) clusters or insertion sequences in either genome. In addition, according to Maatouk et al, we applied the same adapted strategy to predict the antibiotic resistance genes in these genomes ( 15 ). “ Ca .…”

“…Likewise, we found resistance genes for glycopeptide, tetracycline, and macrolides-lincosamides-streptogramin in the “ Ca . Minimicrobia vallesae” genome ( 15 ). Finally, for the pilus secretion systems, we found type II, IV, and VI pilus secretion systems in both genomes and type I in “ Ca .…”

“…Proteomes were predicted with BLASTp (E value of 0.001, minimum coverage and identity of 70% and 30%, respectively) against the Cluster of Orthologous Groups database ( 41 ). Antibiotic resistance genes were then predicted using the adapted strategy for CPR that was recently described in Maatouk et al ( 15 ). Similarly, we looked for the presence of NRPS-PKS using BLASTp against the Non-Ribosomal Peptide and Polyketide Synthase PURified (NRPPUR) database ( 42 ) In addition, in order to detect lateral sequence transfers between our species and their host (presence of transposon/integron), a screening for IS sequences was performed by BLASTn and BLASTp against the ISfinder online tool ( 43 ).…”

“…Analysis of the genomes available in the NCBI (National Centre for Biotechnology Information) database has led to the prediction of certain phenotypic characteristics unique to this group of microbes. These characteristics include antibiotic resistance ( 15 ), their natural resistance to bacteriophage despite the absence of the CRISPR viral defense in their genomes, which is due to the lack of viral receptors in their cell membrane ( 16 ), and the presence of different proteins involved in quorum-sensing phenomena and cell-cell communication ( 17 ). None of these characteristics, however, have yet been confirmed in vitro.…”

Glacier-fed stream biofilms harbour diverse resistomes and biosynthetic gene clusters

“…Although Patescibacteria have been identified in oligotrophic environments [57,58] with carbon and/or nutrient limitations similar to those observed for GFSs, it is plausible that their ability to survive with minimal biosynthetic and metabolic pathways may indeed depend on the expression of BGCs and AMR. At the time of writing, a preprint by Maatouk et al [59], described the presence of ARGs across publicly available CPR bacterial genomes.…”