title: Metagenome-assembled genome: SRP300315_co1_34
organism: uncultured Candidatus Saccharibacteria bacterium
description: This sample represents a Third Party Annotation (TPA) Metagenome-assembled genome assembled from the metagenomic runs SRR13355620,SRR13355622 of study SRP300315.
attributes.tag: ENA first public
attributes.value: 2024-12-11
attributes.tag: INSDC center name
attributes.value: CMR
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: SRP300315_co1_34
attributes.tag: assembly quality
attributes.value: Many fragments with little to no review of assembly other than reporting of standard assembly statistics
attributes.tag: assembly software
attributes.value: metaSPAdes;3.15.4;default
attributes.tag: binning parameters
attributes.value: coverage and kmer
attributes.tag: binning software
attributes.value: MetaBAT2;2.15;default
attributes.tag: broad-scale environmental context
attributes.value: aquatic
attributes.tag: collection date
attributes.value: 2018-02-15
attributes.tag: completeness score
attributes.value: 89.24
attributes.tag: completeness software
attributes.value: CheckM2;1.0.2;default
attributes.tag: contamination score
attributes.value: 0.82
attributes.tag: environmental medium
attributes.value: aquatic
attributes.tag: geographic location (country and/or sea)
attributes.value: Cyprus
attributes.tag: geographic location (latitude)
attributes.value: 35.150243
attributes.tag: geographic location (longitude)
attributes.value: 33.391634
attributes.tag: investigation type
attributes.value: metagenome-assembled genome
attributes.tag: isolation_source
attributes.value: wastewater metagenome
attributes.tag: local environmental context
attributes.value: wastewater biome
attributes.tag: metagenomic source
attributes.value: wastewater metagenome
attributes.tag: project name
attributes.value: Antibiotic resistance is an emerging global issue of utmost importance. Wastewater treatment plants are considered evolutionary hotspots for microbial multi-drug resistance of strains with known pathogenic potential, gradually depriving the arsenal of chemotherapeutic weapons. Membrane bioreactors (MBR) are good alternatives to conventional activated sludge (CAS) systems in reducing the load of antibiotic resistance genes (ARGs) and pathogens in treated effluents. So far, limited information is available regarding the removal of pathogens and ARGs, based mainly on bench-scale experimental setups. To this end, the performance of two full-scale urban wastewater treatment plants (UWTPs), a membrane bioreactor (MBR) and a conventional activated sludge (CAS) system, were investigated for the removal and ecological correlations of putative pathogenic bacteria, antibiotic resistance genes (ARGs), biocide resistance genes (BRGs) and mobile genetic elements (MGEs), using a shotgun metagenomic approach. Total prokaryotic, eukaryotic and viral marker genes in the influent and effluent of the two full-scale systems were also analyzed. Vertical (along the treatment line) and horizontal (between UWTPs) comparisons determined the efficiency of the two systems. Correlation tests revealed links between identified putative pathogens and: (i) ARGs/BRGs/MGEs, denoting associations of clinical importance and inferring potential roles of MGEs in pathogen dispersal (ii) bacteriophages/protists/ predatory bacteria defining specific and significant predator-prey interactions, for the homeostasis of the engineered systems. A strong decline in the abundance of pathogen-containing taxa and ARGs was observed in the MBR-treated effluents compared with the CAS-treated ones. MBR treatment favored ARGs associated with the commonly found in urban wastewater triclosan or antimicrobials of natural occurrence like streptothricin. On the other hand, CAS effluents contained a diverse set of ARGs associated with antibiotics of clinical importance. The conducted correlation tests showed that: (i) opportunistic pathogens like Clostridia and Nocardia may be developing resistance against first-line treatments in the tested environments and (ii) that bacteriophages play an important role in controlling bacterial populations in such systems and thus may be considered as a natural mechanism for pathogen-specific removal in UWTPs. Overall, our findings reinforce the capacity of MBR systems of retaining pathogenic loads, hence reducing the potential health risks associated with the release or reuse of treated wastewaters.
attributes.tag: sample derived from
attributes.value: SAMN17167484,SAMN17167482
attributes.tag: sample name
attributes.value: SRP300315_co1_34
attributes.tag: scientific_name
attributes.value: uncultured Candidatus Saccharibacteria bacterium
attributes.tag: sequencing method
attributes.value: Illumina HiSeq 2500
attributes.tag: taxonomic identity marker
attributes.value: multi-marker approach