Genome-resolved insight into the reservoir of antibiotic resistance genes in aquatic microbial community

Abstract

Aquatic microbial communities are an important reservoir of antibiotic resistance genes (ARGs). However, distribution and diversity of different ARG categories in environmental microbes with different ecological strategies is not yet well studied. Despite the potential exposure of the southern part of the Caspian Sea to the release of antibiotics, little is known about its natural resistome profile. We used a combination of Hidden Markov model (HMM), homology alignment and a deep learning approach for comprehensive screening of the diversity and distribution of ARGs in the Caspian Sea metagenomes at genome resolution. Detected ARGs were classified into five antibiotic resistance categories including prevention of access to target (44%), modification/protection of targets (30%), direct modification of antibiotics (22%), stress resistance (3%), and metal resistance (1%). The 102 detected ARG containing metagenome-assembled genomes of the Caspian Sea were dominated by representatives of Acidimicrobiia, Gammaproteobacteria, and Actinobacteria classes. Comparative analysis revealed that the highly abundant, oligotrophic, and genome streamlined representatives of taxa Acidimicrobiia and Actinobacteria modify the antibiotic target via mutation to develop antibiotic resistance rather than carrying extra resistance genes. Our results help with understanding how the encoded resistance categories of each genome are aligned with its ecological strategies.

Niche-aware metagenomic screening for enzyme methioninase illuminates its contribution to metabolic syntrophy

“…We used a methionine gamma-lyase (i. e., methioninase) Hidden Markov Model (HMM) from TIGRFAM (TIGR01328) as the search input to screen an extensive set of bacterial and archaeal genome assemblies (33,469 bacterial and archaeal genome assemblies) via the Annotree database (version 1.2.0, with taxonomy based on R95 GTDB release) [28]. We also used TIGR01328 to screen predicted open reading frames from the assembled depth profile metagenomes of the Caspian Sea [25], [29] as well as 1278 metageomes assembled genomes (MAGs) and 114 single-cell amplified genomes (SAGs) of the Fennoscandian Shield Genomic Database (FSGD) [27] for putative methioninases.…”

“…The confirmed methioninase sequence of the Caspian Sea branches together with other methioninases recovered from representatives of phylum Proteobacteria. Comparing this sequence against metagenome assembled genomes (MAGs) reconstructed from the Caspian Sea metagenomes [29] returns 100% sequence identity and full query coverage with a protein in the MAG casp40-mb.126 (GenBank assembly accession GCA_027618555.1). The taxonomic affiliation of this MAG based on GTDB is assigned to the phylum Proteobacteria (class Gammaproteobacteria , order Pseudomonadales , family Porticoccaceae , genus HTCC2207, and species HTCC2207 sp002382445) reiterating its close relation with other proteobacterial methioninases.…”

CARPDM: cost-effective antibiotic resistome profiling of metagenomic samples using targeted enrichment

“…Attractive monitoring targets are environments such as wastewater, a fertile ground for genetic exchange between bacteria [5] that provides a snapshot of ARG prevalence in the community (14)(15)(16)(17)(18)(19)(20). Natural environments such as soils, rivers, and farms are known reservoirs of ARGs, many with the potential to mobilize into pathogens (21)(22)(23)(24)(25). Finally, profiling the resistome of human and animal microbiomes allows us to identify critical determinants in the spread of resistance within and between these two groups (26,27).…”

Bacteriological Evaluation of Surface and Groundwater used for Domestic Purposes in Ibadan

“…Ensuring access to safe drinking water is of paramount importance for both rural and urban populations in order to mitigate health risks [6]. It is now common knowledge that natural ecosystems are reservoirs of antibiotic resistant genes, particularly domestic water bodies that receive industrial, hospital and animal waste [7].…”