ArticleMicrobiome2021
Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy.
Article in Microbiome, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 1 of them a synthesis that pooled it.
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Who cites it
34 citing papers in PubMed, 1 synthesis or guideline pooled it, 71 citations in OpenAlex.
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- Nanopore Environmental Analysis.JACS Au · 2025Review
- Soil warming increases the active antibiotic resistome in the gut of invasive giant African snails.Microbiome · 2025Article
- Longitudinal dynamics and cross-domain interactions of eukaryotic populations in wastewater treatment plants.The ISME journal · 2025Article
- High-throughput single-cell sequencing of activated sludge microbiome.Environmental science and ecotechnology · 2025Article
- Analysis of metagenomic data.Nature reviews. Methods primers · 2025Article
- Advances in lasso peptide discovery, biosynthesis, and function.Trends in genetics : TIG · 2024Review
- The increase of particle size shifts the biogeochemical cycle functions of mineral-associated microorganisms and weakens the mineral-associated organic carbon sink in mangrove soils.Applied and environmental microbiology · 2024Article
- Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system.Microbiome · 2024Article
- Metatranscriptomics-guided genome-scale metabolic reconstruction reveals the carbon flux and trophic interaction in methanogenic communities.Microbiome · 2024Article
- Dirammox-dominated microbial community for biological nitrogen removal from wastewater.Applied microbiology and biotechnology · 2024Article
- Corallococcus caeni sp. nov., a novel myxobacterium isolated from activated sludge.Archives of microbiology · 2024Article
- Advancing metagenome-assembled genome-based pathogen identification: unraveling the power of long-read assembly algorithms in Oxford Nanopore sequencing.Microbiology spectrum · 2024Article
- Effects of operational parameters on bacterial communities in Hong Kong and global wastewater treatment plants.mSystems · 2024Article
- BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis.Nature communications · 2024Article
- Draft genome sequences ofMicrobiology resource announcements · 2024Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLong-read sequencing has shown its tremendous potential to address genome assembly challenges, e.g., achieving the first telomere-to-telomere assembly of a gapless human chromosome. However, many issues remain unresolved when leveraging error-prone long reads to characterize high-complexity metagenomes, for instance, complete/high-quality genome reconstruction from highly complex systems.
resultsHere, we developed an iterative haplotype-resolved hierarchical clustering-based hybrid assembly (HCBHA) approach that capitalizes on a hybrid (error-prone long reads and high-accuracy short reads) sequencing strategy to reconstruct (near-) complete genomes from highly complex metagenomes. Using the HCBHA approach, we first phase short and long reads from the highly complex metagenomic dataset into different candidate bacterial haplotypes, then perform hybrid assembly of each bacterial genome individually. We reconstructed 557 metagenome-assembled genomes (MAGs) with an average N50 of 574 Kb from a deeply sequenced, highly complex activated sludge (AS) metagenome. These high-contiguity MAGs contained 14 closed genomes and 111 high-quality (HQ) MAGs including full-length rRNA operons, which accounted for 61.1% of the microbial community. Leveraging the near-complete genomes, we also profiled the metabolic potential of the AS microbiome and identified 2153 biosynthetic gene clusters (BGCs) encoded within the recovered AS MAGs.
conclusionOur results established the feasibility of an iterative haplotype-resolved HCBHA approach to reconstruct (near-) complete genomes from highly complex ecosystems, providing new insights into "complete metagenomics". The retrieved high-contiguity MAGs illustrated that various biosynthetic gene clusters (BGCs) were harbored in the AS microbiome. The high diversity of BGCs highlights the potential to discover new natural products biosynthesized by the AS microbial community, aside from the traditional function (e.g., organic carbon and nitrogen removal) in wastewater treatment. Video Abstract.
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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.