ArticleBMC microbiology2017
First gene-ontology enrichment analysis based on bacterial coregenome variants: insights into adaptations of Salmonella serovars to mammalian- and avian-hosts.
Article in BMC microbiology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed, 27 citations in OpenAlex.
- Long-read methylome analysis of Oleidesulfovibrio alaskensis G20 biofilm under copper stress.Scientific reports · 2025Article
- For Someone, You Are the Whole World: Host-Specificity ofInternational journal of molecular sciences · 2023Article
- Tell me if you prefer bovine or poultry sectors and I'll tell you who you are: Characterization ofFrontiers in microbiology · 2023Article
- Review
- A retrospective and regional approach assessing the genomic diversity ofNAR genomics and bioinformatics · 2022Article
- A European-wide dataset to uncover adaptive traits of Listeria monocytogenes to diverse ecological niches.Scientific data · 2022Article
- Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks.BMC genomics · 2022Article
- Article
- The Spatiotemporal Dynamics and Microevolution Events That Favored the Success of the Highly Clonal Multidrug-Resistant MonophasicFrontiers in microbiology · 2021Article
- Comparative phenotypic, genotypic and genomic analyses of Bacillus thuringiensis associated with foodborne outbreaks in France.PloS one · 2021Article
- First Report on the Finding ofPathogens (Basel, Switzerland) · 2020Article
- Dynamics of mobile genetic elements of Listeria monocytogenes persisting in ready-to-eat seafood processing plants in France.BMC genomics · 2020Article
- Genome-wide microsatellite characteristics of five human Plasmodium species, focusing on Plasmodium malariae and P. ovale curtisi.Parasite (Paris, France) · 2020Article
- Phylogeography and Genetic Diversity ofFrontiers in microbiology · 2020Article
- Source Attribution Study of SporadicFrontiers in microbiology · 2020Article
- Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale.BMC genomics · 2019Article
- The speciation and hybridization history of the genusMicrobial genomics · 2019Article
- Large-Scale Genomic Analyses and Toxinotyping ofFrontiers in microbiology · 2019Article
- Biofilm Formation ofFrontiers in microbiology · 2019Article
- A Simple and Robust Statistical Method to Define Genetic Relatedness of Samples Related to Outbreaks at the Genomic Scale - Application to RetrospectiveFrontiers in microbiology · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
backgroundMany of the bacterial genomic studies exploring evolution processes of the host adaptation focus on the accessory genome describing how the gains and losses of genes can explain the colonization of new habitats. Consequently, we developed a new approach focusing on the coregenome in order to describe the host adaptation of Salmonella serovars.
methodsIn the present work, we propose bioinformatic tools allowing (i) robust phylogenetic inference based on SNPs and recombination events, (ii) identification of fixed SNPs and InDels distinguishing homoplastic and non-homoplastic coregenome variants, and (iii) gene-ontology enrichment analyses to describe metabolic processes involved in adaptation of Salmonella enterica subsp. enterica to mammalian- (S. Dublin), multi- (S. Enteritidis), and avian- (S. Pullorum and S. Gallinarum) hosts.
resultsThe 'VARCall' workflow produced a robust phylogenetic inference confirming that the monophyletic clade S. Dublin diverged from the polyphyletic clade S. Enteritidis which includes the divergent clades S. Pullorum and S. Gallinarum (i). The scripts 'phyloFixedVar' and 'FixedVar' detected non-synonymous and non-homoplastic fixed variants supporting the phylogenetic reconstruction (ii). The scripts 'GetGOxML' and 'EveryGO' identified representative metabolic pathways related to host adaptation using the first gene-ontology enrichment analysis based on bacterial coregenome variants (iii).
conclusionsWe propose in the present manuscript a new coregenome approach coupling identification of fixed SNPs and InDels with regards to inferred phylogenetic clades, and gene-ontology enrichment analysis in order to describe the adaptation of Salmonella serovars Dublin (i.e. mammalian-hosts), Enteritidis (i.e. multi-hosts), Pullorum (i.e. avian-hosts) and Gallinarum (i.e. avian-hosts) at the coregenome scale. All these polyvalent Bioinformatic tools can be applied on other bacterial genus without additional developments.
Indexed as
Identifiers
What OpenQuestion holds
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.