FARAO: the flexible all-round annotation organizer

Hammarén, Rickard; Pal, Chandan; Bengtsson‐Palme, Johan

doi:10.1093/bioinformatics/btw499

Cited by 6 publications

(3 citation statements)

References 17 publications

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“…The six-frame translations were also scanned against Pfam (47) using HMMER (using defined trusted thresholds, the “--cut_tc” option). All annotations were added to a FARAO annotation database (48). Lists of annotated integron regions were then produced by querying the FARAO database with different criteria.…”

Section: Methodsmentioning

confidence: 99%

Microbial retention and resistances in stormwater quality improvement devices treating road runoff

Liguori

Rommel

Bengtsson‐Palme

et al. 2021

Preprint

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Current knowledge about the microbial communities inhabiting the stormwater quality improvement devices (SQIDs) for road runoff is scarce. However, as a bioactive compound of these systems, microbes can facilitate water quality improvement through the biodegradation or precipitation of dissolved contaminants. On the other hand, these contaminants may select for stress resistant opportunistic microbial strains, which are discharged into surface waters or groundwater. In this study, the microbial community of two SQIDs with different design were analyzed to determine the microbial load, retention, composition, and mobile resistance genes in the filter media and the microbial composition in the treated runoff. The bacterial abundance of the SQIDs was relatively stable over time in effluent water samples. Although the microbes were replaced by new taxa in the effluent, there was no major retention of cells or microbial genera. The communities were influenced both by seasonality and by the SQID design. The heavy metal content of the SQIDs was correlated to intl1 and distinct microbial groups. The filter media led to an enrichment and subsequent discharge of Intl1 gene cassettes carrying several heavy metal and multidrug resistance genes (e.g. czrA, czcA, silP, mexW and mexI). Overall, the results suggest that different engineering designs affect the bacterial communities of the SQIDs, and subsequently influence the microbial community and the genes released with the treated water.

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Section: Methodsmentioning

confidence: 99%

Microbial retention and resistances in stormwater quality improvement devices treating road runoff

Liguori

Rommel

Bengtsson‐Palme

et al. 2021

Preprint

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“…To estimate how the differences in ability to assemble ARGs by different tools affect the downstream results, we performed ARG quantification. First, the Illumina reads were mapped to each assembly using bowtie2 v2.3.5.1 (Langmead and Salzberg 2012) and the coverage was estimated for all full and truncated ARG hits (minimum 95% identity and 80% coverage) on the assembled contigs using the FARAO (Hammarén et al 2016) estimate_coverage function with -c 0 flag estimating coverage per all bases across the feature:…”

Section: Evaluation Using Long-reads Referencementioning

confidence: 99%

Metagenomic assemblies tend to break around antibiotic resistance genes

Abramova,

Karkman,

Bengtsson-Palme

2023

Preprint

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BackgroundAssembly of metagenomic samples can provide essential information about the mobility potential and taxonomic origin of antibiotic resistance genes (ARGs), and inform interventions to prevent further spread of resistant bacteria. However, ARGs typically occur in multiple genomic contexts across different species, representing a considerable challenge for the assembly process. Usually, this results in many fragmented contigs of unclear origin, complicating the risk assessment of ARG detections. To systematically investigate the impact of this issue on detection, quantification and contextualization of ARGs, we evaluated the performance of different assembly approaches, including genomic-, metagenomic- and transcriptomic-specialized assemblers. We quantified recovery and accuracy rates of each tool for ARGs both fromin silicospiked metagenomic samples as well as real samples sequenced using both long- and short-read sequencing technologies.ResultsThe results revealed that none of the investigated tools can accurately capture genomic contexts present in samples of high complexity. The transcriptomic assembler Trinity showed a better performance in terms of reconstructing longer and fewer contigs matching unique genomic contexts, which can be beneficial for deciphering the taxonomic origin of ARGs. The currently commonly used metagenomic assembly tools metaSPAdes and MEGAHIT were able to identify the ARG repertoire but failed to fully recover the diversity of genomic contexts present in a sample. On top of that, in a complex scenario MEGAHIT produced very short contigs, which can lead to considerable underestimation of the resistome in a given sample.ConclusionsOur study shows that metaSPAdes and Trinity would be the preferable tools in terms of accuracy to recover correct genomic contexts around ARGs in metagenomic samples characterized by uneven coverages. Overall, the inability of assemblers to reconstruct long ARG-containing contigs has impacts on ARG quantification, suggesting that directly mapping reads to an ARG database might be necessary, at least as a complementary strategy, to get accurate ARG abundance and diversity measures.

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“…The six-frame translations were also scanned against Pfam (47) using HMMER (using defined trusted thresholds, the "--cut_tc" option). All annotations were added to a FARAO annotation database (48). Lists of annotated integron regions were then produced by querying the FARAO database with different criteria.…”

Section: Intl1 Gene Analysismentioning

confidence: 99%

Microbial retention and resistances in stormwater quality improvement devices treating road runoff

et al. 2021

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Current knowledge about the microbial communities that occur in in urban road runoff is scarce. Road runoff of trafficked roads can be heavily polluted and is treated by stormwater quality improvement devices (SQIDs). However, microbes may influence the treatment process of these devices or could lead to stress resistant opportunistic microbial strains. In this study, the microbial community in the influent, effluent and the filter materials for the removal of dissolved heavy metals of two different SQIDs were analyzed to determine the microbial load, retention, composition, and mobile resistance genes. Although the microbes were replaced by new taxa in the effluent, there was no major retention of microbial genera. Further, the bacterial abundance of the SQIDs effluent was relatively stable over time. The heavy metal content correlated with intl1 and with microbial genera. The filter media itself was enriched with Intl1 gene cassettes, carrying several heavy metal and multidrug resistance genes (e.g. czrA, czcA, silP, mexW and mexI), indicating that this is a hot spot for horizontal gene transfer. Overall, the results shed light on road runoff microbial communities, and pointed to distinct bacterial communities within the SQIDs, which subsequently influence the microbial community and the genes released with the treated water.

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FARAO: the flexible all-round annotation organizer

Cited by 6 publications

References 17 publications

Microbial retention and resistances in stormwater quality improvement devices treating road runoff

Microbial retention and resistances in stormwater quality improvement devices treating road runoff

Metagenomic assemblies tend to break around antibiotic resistance genes

Microbial retention and resistances in stormwater quality improvement devices treating road runoff

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