ArticlePLoS computational biology2014
Defining the estimated core genome of bacterial populations using a Bayesian decision model.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
34 citing papers in PubMed, 68 citations in OpenAlex.
- Comparative metagenomics using pan-metagenomic graphs.bioRxiv : the preprint server for biology · 2025Article
- Genomic Characterization and Antimicrobial Resistance Profile ofAntibiotics (Basel, Switzerland) · 2025Article
- CELEBRIMBOR: core and accessory genes from metagenomes.Bioinformatics (Oxford, England) · 2024Article
- Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure.Microbial genomics · 2024Article
- A core genome multi-locus sequence typing scheme forMicrobial genomics · 2024Article
- Exploring the biosynthetic gene clusters in Brevibacterium: a comparative genomic analysis of diversity and distribution.BMC genomics · 2023Article
- Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY.Cell reports · 2023Article
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- Helicobacter pylori treatment in the post-antibiotics era-searching for new drug targets.Applied microbiology and biotechnology · 2020Review
- PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.PLoS computational biology · 2020Article
- A Core Genome Multilocus Sequence Typing Scheme forFrontiers in microbiology · 2020Article
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- Identification of Streptococcus pneumoniae by a real-time PCR assay targeting SP2020.Scientific reports · 2019Article
- Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.Frontiers in microbiology · 2019Article
- Effect of Vaccination on Pneumococci Isolated from the Nasopharynx of Healthy Children and the Middle Ear of Children with Otitis Media in Iceland.Journal of clinical microbiology · 2018Article
- Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak.International journal of food microbiology · 2018Article
- Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome-Wide Typing of Clostridium difficile.Journal of clinical microbiology · 2018Article
- Genome Sequencing Reveals a Large and Diverse Repertoire of Antimicrobial Peptides.Frontiers in microbiology · 2018Article
- Genetic Diversity ofFrontiers in genetics · 2018Article
- Core Genome Multilocus Sequence Typing Scheme for Stable, Comparative Analyses of Campylobacter jejuni and C. coli Human Disease Isolates.Journal of clinical microbiology · 2017Article
Corrections and comments
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Authors and funding
13 authors at 6 institutions in 3 countries.
Funding
Abstract
The bacterial core genome is of intense interest and the volume of whole genome sequence data in the public domain available to investigate it has increased dramatically. The aim of our study was to develop a model to estimate the bacterial core genome from next-generation whole genome sequencing data and use this model to identify novel genes associated with important biological functions. Five bacterial datasets were analysed, comprising 2096 genomes in total. We developed a Bayesian decision model to estimate the number of core genes, calculated pairwise evolutionary distances (p-distances) based on nucleotide sequence diversity, and plotted the median p-distance for each core gene relative to its genome location. We designed visually-informative genome diagrams to depict areas of interest in genomes. Case studies demonstrated how the model could identify areas for further study, e.g. 25% of the core genes with higher sequence diversity in the Campylobacter jejuni and Neisseria meningitidis genomes encoded hypothetical proteins. The core gene with the highest p-distance value in C. jejuni was annotated in the reference genome as a putative hydrolase, but further work revealed that it shared sequence homology with beta-lactamase/metallo-beta-lactamases (enzymes that provide resistance to a range of broad-spectrum antibiotics) and thioredoxin reductase genes (which reduce oxidative stress and are essential for DNA replication) in other C. jejuni genomes. Our Bayesian model of estimating the core genome is principled, easy to use and can be applied to large genome datasets. This study also highlighted the lack of knowledge currently available for many core genes in bacterial genomes of significant global public health importance.
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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.