ArticleGenome research2013
Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 63 citations in OpenAlex.
- Exploring the oral microbiome: from traditional techniques to advanced omics and databases.Antonie van Leeuwenhoek · 2026Review
- Role of CRISPR-Cas systems in periodontal disease pathogenesis and potential for periodontal therapy: A review.Molecular oral microbiology · 2025Review
- Comparative analysis ofMicrobiology spectrum · 2024Article
- Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research.FEMS microbiology reviews · 2023Review
- Genetic Characterization and Phylogenetic Analysis of Fasciola Species Isolated From Yaks on Qinghai-Tibet Plateau, China.Frontiers in veterinary science · 2022Article
- Porphyromonas gingivalis outside the oral cavity.Odontology · 2022Review
- Machine Learning-Based Single Cell and Integrative Analysis Reveals That Baseline mDC Predisposition Correlates With Hepatitis B Vaccine Antibody Response.Frontiers in immunology · 2021Article
- Beyond the pan-genome: current perspectives on the functional and practical outcomes of the distributed genome hypothesis.Biochemical Society transactions · 2020Review
- Insights into the dynamics between viruses and their hosts in a hot spring microbial mat.The ISME journal · 2020Article
- Virulence of the Pathogen Porphyromonas gingivalis Is Controlled by the CRISPR-Cas Protein Cas3.mSystems · 2020Article
- The apical root canal system microbial communities determined by next-generation sequencing.Scientific reports · 2020Article
- Single-Cell Genomics and the Oral Microbiome.Journal of dental research · 2020Review
- Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults.Frontiers in immunology · 2020Observational
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- High-throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations.Molecular ecology resources · 2019Review
- Metagenomic of clinically diseased and healthy broiler affected with respiratory disease complex.Data in brief · 2018Article
- Review
- Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.BMC genomics · 2018Article
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Corrections and comments
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Authors and funding
21 authors at 4 institutions in 2 countries.
Funding
Abstract
Although biofilms have been shown to be reservoirs of pathogens, our knowledge of the microbial diversity in biofilms within critical areas, such as health care facilities, is limited. Available methods for pathogen identification and strain typing have some inherent restrictions. In particular, culturing will yield only a fraction of the species present, PCR of virulence or marker genes is mainly focused on a handful of known species, and shotgun metagenomics is limited in the ability to detect strain variations. In this study, we present a single-cell genome sequencing approach to address these limitations and demonstrate it by specifically targeting bacterial cells within a complex biofilm from a hospital bathroom sink drain. A newly developed, automated platform was used to generate genomic DNA by the multiple displacement amplification (MDA) technique from hundreds of single cells in parallel. MDA reactions were screened and classified by 16S rRNA gene PCR sequence, which revealed a broad range of bacteria covering 25 different genera representing environmental species, human commensals, and opportunistic human pathogens. Here we focus on the recovery of a nearly complete genome representing a novel strain of the periodontal pathogen Porphyromonas gingivalis (P. gingivalis JCVI SC001) using the single-cell assembly tool SPAdes. Single-cell genomics is becoming an accepted method to capture novel genomes, primarily in the marine and soil environments. Here we show for the first time that it also enables comparative genomic analysis of strain variation in a pathogen captured from complex biofilm samples in a healthcare facility.
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Registered trials
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.