QMRA of beach water by Nanopore sequencing-based viability-metagenomics absolute quantification

Yang, Yu; Deng, Yu; Shi, Xianghui; Liu, Lei; Yin, Xiaole; Zhao, Wanwan; Li, Shuxian; Yang, Chao; Zhang, Tong

doi:10.1016/j.watres.2023.119858

Cited by 12 publications

(4 citation statements)

References 45 publications

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“…In summary, given the growing interest in incorporating long reads into metagenomics, along with anticipated improvements in sequencing depth and more comprehensive databases, we believe that Melon will not only prove useful in taxonomic profiling but also pave the way for a wide range of applications, e.g., absolute quantification [46].…”

Section: Discussionmentioning

confidence: 99%

“…Short and long reads of Bacillus amyloliquefaciens (Gram-positive) and Pseudomonas alloputida (Gram-negative), were collected from a previous study [46]. Short reads were quality-controlled with fastp v0.23.4 [59], while long reads were processed with Porechop v0.2.4 [60] (‘--discard middle’) and nanoq v0.10.0 [61] (‘--min-qual 10 --min-len 1000’).…”

Section: Methodsmentioning

confidence: 99%

“…ARG copies were determined by mapping filtered reads to the SARG v3.2.1-F [70] database using the frame-shift alignment mode of DIAMOND (same configuration and post-filtering as before, but with '--id 75' for removal of spurious hits, see section "Selection of universal and single-copy marker genes"). Hits were excluded if their predicted ARG families were flagged as multidrug, since multidrug efflux pumps have a broad range of substrates that are not necessarily specific to antibiotics [46]. ARG abundances, expressed as "ARG copies per cell" (assuming one genome copy per cell), were calculated by dividing the estimated ARG copies by the total genome copies.…”

Section: Estimation Of Genome Copies Mean Genome Sizes and Arg Abunda...mentioning

confidence: 99%

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Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes

Xi,

Yin,

Shi

et al. 2023

Preprint

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Long-read sequencing holds great potential for characterizing complex microbial communities, yet taxonomic profiling tools designed specifically for long reads remain lacking. Here we introduce Melon, a novel marker-based taxonomic profiler that capitalizes on the unique attributes of long reads. Melon employs a two-stage classification scheme to reduce computational time and is equipped with an expectation-maximization-based post-correction module to handle ambiguous reads. Melon achieves superior performance compared to other existing tools in both mock and simulated samples. Using wastewater metagenomic samples, we demonstrate the applicability of Melon by showing it is capable in providing reliable estimates of overall genome copies, and species-level taxonomic profiles.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Estimation Of Genome Copies Mean Genome Sizes and Arg Abunda...mentioning

confidence: 99%

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Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes

Xi,

Yin,

Shi

et al. 2023

Preprint

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“…The framework identified 73 high‐risk ARG groups, of which 35 were included in the WHO list of high clinical concern 27 . For the risk assessment at specific sites like beach water, quantitative microbial risk assessment using viability‐resolved metagenomic methods integrating risk evaluation of pathogens and ARGs may help us conduct a holistic microbial risk assessment and guide risk management to control antibiotic resistance 28 .…”

Section: Establishing Framework Of Risk Assessmentmentioning

confidence: 99%

Roadmap to tackle antibiotic resistance in the environment under the One Health framework

Li,

Zhang

2023

mLife

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Antibiotic resistance has been recognized as a major challenge worldwide for humans. “One Health” has been recognized as a key concept for containment of antibiotic resistance. Under the framework, the role of the environment in the development of antibiotic resistance genes (ARGs) has become increasingly obvious. Despite numerous efforts, response to antibiotic resistance is considered to be inadequate, which is probably due to the lack of a clear roadmap. Here, we propose a “One Health” roadmap to combat antibiotic resistance in the environment through (1) understanding environmental resistome. The environmental gene pool has long been recognized as the single largest reservoir of both known and novel ARGs. (2) Standardizing ARG quantification. Systematic joint efforts based on standardized quantification are urgently needed to understand the true tempospatial profiles of the environmental resistome. (3) Identifying mechanisms of resistome development. Horizontal gene transfer and co‐selection have been recognized as the two main mechanisms contributing to the environmental resistome. (4) Establishing a risk‐assessment framework. The first critical step for large‐scale cost‐effective targeted ARG management in the environment is the risk assessment to identify the priority ARGs for control. (5) Formulating regulatory standards. By correlating the environmental ARG profile with public health, we may identify the indicator ARGs that can be integrated into current environmental quality standards. (6) Developing control strategies. Systematic analysis of available control technologies is required to identify the most feasible ones to curtail the spread of ARGs in the environment. The proposed roadmap under the “One Health” framework provides a guide to tackle antibiotic resistance in the environment.

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Two-year Monitoring of Microbiological Water Quality in Small Water Supply Systems: Implications for Microbial Risk Management

Zeng,

Nakanishi,

Itoh

2024

Environmental Management

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QMRA of beach water by Nanopore sequencing-based viability-metagenomics absolute quantification

Cited by 12 publications

References 45 publications

Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes

Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes

Roadmap to tackle antibiotic resistance in the environment under the One Health framework

Two-year Monitoring of Microbiological Water Quality in Small Water Supply Systems: Implications for Microbial Risk Management

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