ArticleNPJ biofilms and microbiomes2021
Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing.
Article in NPJ biofilms and microbiomes, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 45 citations in OpenAlex.
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- Genomic mining of Vibrio parahaemolyticus highlights prevalence of antimicrobial resistance genes and new genetic markers associated with AHPND and tdh + /trh + genotypes.BMC genomics · 2024Article
- The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies.Microbial genomics · 2024Article
- Dancing the Nanopore limbo - Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction.BMC genomics · 2023Article
- Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing.Genome research · 2023Article
- Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources.Microorganisms · 2023Article
- Strategies and tools in illumina and nanopore-integrated metagenomic analysis of microbiome data.iMeta · 2023Review
- History of the Study of the GenusInternational journal of molecular sciences · 2022Review
- Two New Species of Filamentous Sulfur Bacteria of the GenusMicroorganisms · 2022Article
- Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter.Environmental microbiology · 2022Article
- Recovery of High Quality Metagenome-Assembled Genomes From Full-Scale Activated Sludge Microbial Communities in a Tropical Climate Using Longitudinal Metagenome Sampling.Frontiers in microbiology · 2022Article
- Comparative Genomics of Members of the GenusFrontiers in microbiology · 2022Article
- The evolution of bacterial genome assemblies - where do we need to go next?Microbiome research reports · 2022Article
- Co-selective Pressure of Cadmium and Doxycycline on the Antibiotic and Heavy Metal Resistance Genes in Ditch Wetlands.Frontiers in microbiology · 2022Article
Corrections and comments
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Authors and funding
13 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes from complex microbial communities. Using long read data (ONT MinION) obtained from an ensemble of activated sludge enrichment bioreactors we recover 22 closed or complete genomes of community members, including several species known to play key functional roles in wastewater bioprocesses, specifically microbes known to exhibit the polyphosphate- and glycogen-accumulating organism phenotypes (namely Candidatus Accumulibacter and Dechloromonas, and Micropruina, Defluviicoccus and Candidatus Contendobacter, respectively), and filamentous bacteria (Thiothrix) associated with the formation and stability of activated sludge flocs. Additionally we demonstrate the recovery of close to 100 circularised plasmids, phages and small microbial genomes from these microbial communities using long read assembled sequence. We describe methods for validating long read assembled genomes using their counterpart short read metagenome-assembled genomes, and assess the influence of different correction procedures on genome quality and predicted gene quality. Our findings establish the feasibility of performing long read metagenome-assembled genome recovery for both chromosomal and non-chromosomal replicons, and demonstrate the value of parallel sampling of moderately complex enrichment communities to obtaining high quality reference genomes of key functional species relevant for wastewater bioprocesses.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.