ArticleMicrobiome2018
Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes.
Article in Microbiome, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 123 citations in OpenAlex.
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- Strain-level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
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- Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria.ISME communications · 2025Article
- Microbial communities associated with marine sponges from diverse geographic locations harbor biosynthetic novelty.Applied and environmental microbiology · 2024Article
- The oral-gut microbiome axis in health and disease.Nature reviews. Microbiology · 2024Review
- Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes.FEMS microbiology reviews · 2024Review
- Metabolic activities of marine ammonia-oxidizing archaea orchestrated by quorum sensing.mLife · 2024Article
- Genomic representativeness and chimerism in large collections of SAGs and MAGs of marine prokaryoplankton.Microbiome · 2024Article
- dna2bit: high performance genomic distance estimation software for microbial genome analysis.Frontiers in microbiology · 2024Article
- Identification of closely related species inFrontiers in microbiology · 2024Article
- Bacterial single-cell transcriptomics: Recent technical advances and future applications in dentistry.The Japanese dental science review · 2023Review
- Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years.Nature communications · 2023Article
- Baseline metagenome-assembled genome (MAG) data of Sikkim hot springs from Indian Himalayan geothermal belt (IHGB) showcasing its potential CAZymes, and sulfur-nitrogen metabolic activity.World journal of microbiology & biotechnology · 2023Article
- Trait biases in microbial reference genomes.Scientific data · 2023Article
- Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes.Science advances · 2023Article
- Comprehensive insights on environmental adaptation strategies in Antarctic bacteria and biotechnological applications of cold adapted molecules.Frontiers in microbiology · 2023Review
- Integrated Analysis of Gut Microbiome and Lipid Metabolism in Mice Infected with Carbapenem-ResistantMetabolites · 2022Article
Corrections and comments
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Authors and funding
11 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundProkaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.
resultsWe compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs.
conclusionsThe strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.
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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.