Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data

Short-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly feasible. We demonstrate that whole bacterial chromosomes can be obtained from an enriched community, by application of MinION sequencing to a sample from an EBPR bioreactor, producing 6 Gb of sequence that assembles into multiple closed bacterial chromosomes. We provide a simple pipeline for processing such data, which includes a new approach to correcting erroneous frame-shifts. Advances in long-read sequencing technology and corresponding algorithms will allow the routine extraction of whole chromosomes from environmental samples, providing a more detailed picture of individual members of a microbiome.

• Publication year

  2019

• Venue

  Microbiome

• Publication date

  2019-01-04

• Fields of study

  Biology, Medicine, Computer Science, Environmental Science

• Identifiers
  DOI 10.1186/s40168-019-0665-yPMID 30992083PMCID 6469205
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

  2017cited by this paper
• Completing bacterial genome assemblies with multiplex MinION sequencing

  2017cited by this paper
• Minimap2: pairwise alignment for nucleotide sequences

  2017cited by this paper
• MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs

  2017cited by this paper
• The language of geometry: Fast comprehension of geometrical primitives and rules in human adults and preschoolers

  2017cited by this paper
• Shotgun metagenomics, from sampling to analysis

  2017cited by this paper
• The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

  2016cited by this paper
• MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

  2016cited by this paper
• Erratum to: The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

  2016cited by this paper
• Fast and accurate de novo genome assembly from long uncorrected reads

  2016cited by this paper
• Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system

  2016cited by this paper
• Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

  2016cited by this paper
• Erratum to: The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

  2016cited by this paper
• MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

  2015cited by this paper
• Bandage: interactive visualization of de novo genome assemblies

  2015cited by this paper
• metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data

  2015cited by this paper
• Expanding our view of genomic diversity in Candidatus Accumulibacter clades.

  2015cited by this paper
• CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

  2015cited by this paper
• Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics

  2015cited by this paper
• Prokka: rapid prokaryotic genome annotation

  2014cited by this paper
• Fast and sensitive protein alignment using DIAMOND

  2014cited by this paper
• Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

  2014cited by this paper
• Low acetate concentrations favor polyphosphate-accumulating organisms over glycogen-accumulating organisms in enhanced biological phosphorus removal from wastewater.

  2013cited by this paper
• The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

  2012cited by this paper
• An Alternate Algorithm for (3x3) Median Filtering of Digital Images

  2012cited by this paper
• Structure, Function and Diversity of the Healthy Human Microbiome

  2012cited by this paper
• SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

  2012cited by this paper
• Adaptive seeds tame genomic sequence comparison.

  2011cited by this paper
• Abundance and ecophysiology of Defluviicoccus spp., glycogen-accumulating organisms in full-scale wastewater treatment processes.

  2007cited by this paper
• Obtaining highly enriched cultures of Candidatus Accumulibacter phosphates through alternating carbon sources.

  2006cited by this paper
• Recovery of an environmental Chlamydia strain from activated sludge by co-cultivation with Acanthamoeba sp.

  2005cited by this paper
• GenBank

  2004cited by this paper
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

  1997cited by this paper

• Phylogenetic analysis reveals diversity in glycan biosynthesis in "Candidatus Accumulibacter".

  2026cites this paper
• Comparative transcription profiles of Candidatus Accumulibacter and Propionivibrio under phosphate limitation in sequencing batch reactors

  2025cites this paper
• MMonitor for real-time monitoring of microbial communities using long reads

  2025cites this paper
• Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition.

  2025cites this paper
• MMonitor: Software for Real-Time Monitoring of Microbial Communities Using Long Reads

  2025cites this paper
• Sensitive and error-tolerant annotation of protein-coding DNA with BATH

  2024cites this paper
• Sensitive and error-tolerant annotation of protein-coding DNA with BATH

  2024cites this paper
• Two new clades recovered at high temperatures provide novel phylogenetic and genomic insights into Candidatus Accumulibacter

  2024cites this paper
• Highly accurate metagenome-assembled genomes from human gut microbiota using long-read assembly, binning, and consolidation methods

  2024cites this paper
• Temporal Dynamics and Contribution of Phage Community to the Prevalence of Antibiotic Resistance Genes in a Full-Scale Sludge Anaerobic Digestion Plant.

  2024cites this paper
• Assessing viral metagenomics for the diagnosis of acute undifferentiated fever in returned travellers: a multicenter cohort study.

  2024cites this paper
• Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2

  2023cites this paper
• Integrated genomics provides insights for the evolution of the polyphosphate accumulation trait of Ca. Accumulibacter

  2023cites this paper
• CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter.

  2023cites this paper
• Recovery and Analysis of Long-Read Metagenome-Assembled Genomes.

  2023cites this paper
• Integrated genomics provides insights into the evolution of the polyphosphate accumulation trait of Ca. Accumulibacter

  2023cites this paper
• Candidatus Accumulibacter use fermentation products for enhanced biological phosphorus removal.

  2023cites this paper
• Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes

  2023cites this paper
• Strategies and tools in illumina and nanopore‐integrated metagenomic analysis of microbiome data

  2023cites this paper
• Metagenomic analysis reveals indole signaling effect on microbial community in sequencing batch reactors: Quorum sensing inhibition and antibiotic resistance enrichment.

  2023cites this paper
• DIAMOND +  MEGAN Microbiome Analysis.

  2023cites this paper
• MAIRA: Protein-based Analysis of MinION Reads on a Laptop.

  2023cites this paper
• Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group

  2023cites this paper
• Microorganisms as bio‐filters to mitigate greenhouse gas emissions from high‐altitude permafrost revealed by nanopore‐based metagenomics

  2022influential citation
• Comparative Genomics of Members of the Genus Defluviicoccus With Insights Into Their Ecophysiological Importance

  2022cites this paper
• Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing

  2022cites this paper
• Diversity and Ecophysiology of the Genus OLB8 and Other Abundant Uncultured Saprospiraceae Genera in Global Wastewater Treatment Systems

  2022cites this paper
• Designing a synthetic microbial community devoted to biological control: The case study of Fusarium wilt of banana

  2022cites this paper
• Hybrid metagenome assemblies link carbohydrate structure with function in the human gut microbiome

  2022cites this paper
• Arthrobacter polaris sp. nov., a new cold-adapted member of the family Micrococcaceae isolated from Antarctic fellfield soil.

  2022cites this paper
• Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by ‘Candidatus Formimonas warabiya’ strain DCMF

  2022cites this paper
• Systematic whole-genome sequencing reveals an unexpected diversity among actinomycetoma pathogens and provides insights into their antibacterial susceptibilities

  2022cites this paper
• Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets

  2022cites this paper
• BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies

  2022cites this paper
• Exploration of the Potential Relationship Between Gut Microbiota Remodeling Under the Influence of High-Protein Diet and Crohn’s Disease

  2022cites this paper
• Novel canine high-quality metagenome-assembled genomes, prophages and host-associated plasmids provided by long-read metagenomics together with Hi-C proximity ligation

  2022cites this paper
• Oxford Nanopore R10.4 long-read sequencing enables near-perfect bacterial genomes from pure cultures and metagenomes without short-read or reference polishing

  2021cites this paper
• Is Oxford Nanopore sequencing ready for analyzing complex microbiomes?

  2021influential citation
• The microbiome and host mucosal interactions in urinary tract diseases

  2021cites this paper
• Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes

  2021cites this paper
• Recent advances in understanding the ecophysiology of enhanced biological phosphorus removal.

  2021cites this paper
• DIAMOND+MEGAN: Fast and Easy Taxonomic and Functional Analysis of Short and Long Microbiome Sequences

  2021influential citation
• High molecular weight DNA extraction strategies for long‐read sequencing of complex metagenomes

  2021cites this paper
• Current State and Future Directions of Genetics and Genomics of Endophytic Fungi for Bioprospecting Efforts

  2021cites this paper
• Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing

  2021cites this paper
• Surveillance of potential pathogens and antibiotic resistance in wastewater and surface water from Boston, USA and Vellore, India using long-read metagenomic sequencing

  2021cites this paper
• Influence of Extraction Solvent on Nontargeted Metabolomics Analysis of Enrichment Reactor Cultures Performing Enhanced Biological Phosphorus Removal (EBPR)

  2021cites this paper
• Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces

  2021cites this paper
• Linking carbohydrate structure with function in the human gut microbiome using hybrid metagenome assemblies

  2021cites this paper
• Prospects for multi-omics in the microbial ecology of water engineering.

  2021cites this paper
• Phylogenetic context using phylogenetic outlines

  2021influential citation
• Parallel algorithm for the unsupervised binning of metagenomic sequences

  2021cites this paper
• Novel canine high-quality metagenome-assembled genomes, prophages, and host-associated plasmids by long-read metagenomics together with Hi-C proximity ligation

  2021cites this paper
• Unearthing Shifts in Microbial Communities Across a Soil Disturbance Gradient

  2021cites this paper
• Recovery of High Quality Metagenome-Assembled Genomes From Full-Scale Activated Sludge Microbial Communities in a Tropical Climate Using Longitudinal Metagenome Sampling

  2021cites this paper
• proovframe: frameshift-correction for long-read (meta)genomics

  2021cites this paper
• Finding the right fit: A comprehensive evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data

  2021cites this paper
• Microbial Phylogenetic Context Using Phylogenetic Outlines

  2021influential citation
• Strategies for Abiotic Stress Management in Plants Through Soil Rhizobacteria 

  2021cites this paper
• Metagenomic Sequencing of Multiple Soil Horizons and Sites in Close Vicinity Revealed Novel Secondary Metabolite Diversity

  2021cites this paper
• Predominant Biphenyl Dioxygenase From Legacy Polychlorinated Biphenyl (PCB)-Contaminated Soil Is a Part of Unusual Gene Cluster and Transforms Flavone and Flavanone

  2021cites this paper
• BugSplit: highly accurate taxonomic binning of metagenomic assemblies enables genome-resolved metagenomics

  2021cites this paper
• Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis

  2021cites this paper
• Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing

  2021cites this paper
• metaFlye: scalable long-read metagenome assembly using repeat graphs

  2020cites this paper
• Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors

  2020cites this paper
• Genomic analysis of dibenzofuran-degrading Pseudomonas veronii strain Pvy reveals its biodegradative versatility

  2020cites this paper
• Long-Read Metagenomics to Retrieve High-Quality Metagenome-Assembled Genomes from Canine Feces

  2020cites this paper
• High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies

  2020cites this paper
• MAIRA- real-time taxonomic and functional analysis of long reads on a laptop

  2020cites this paper
• Comparative genome analysis proposes three new Aureobasidium species isolated from grape juice.

  2020cites this paper
• Responses of Exogenous Bacteria to Soluble Extracellular Polymeric Substances in Wastewater: A Mechanistic Study and Implications on Bioaugmentation.

  2020cites this paper
• Analysis procedures for assessing recovery of high quality, complete, closed genomes from Nanopore long read metagenome sequencing

  2020cites this paper
• Recycling the Interspecific Relations with Epithelial Cells: Bacteria and Cancer Metabolic Symbiosis.

  2020cites this paper
• Development of a dynamic feeding strategy for continuous-flow aerobic granulation and nitrogen removal in a modified airlift loop reactor for municipal wastewater treatment.

  2020cites this paper
• Accurate and complete genomes from metagenomes

  2019cites this paper
• Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads

  2019cites this paper
• Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes

  2019cites this paper