Neglectibacter timonensis gen. nov., sp. nov. and Scatolibacter rhodanostii gen. nov., sp. nov., two anaerobic bacteria isolated from human stool samples.


Journal

Archives of microbiology
ISSN: 1432-072X
Titre abrégé: Arch Microbiol
Pays: Germany
ID NLM: 0410427

Informations de publication

Date de publication:
21 Dec 2021
Historique:
received: 22 06 2021
accepted: 15 11 2021
revised: 12 11 2021
entrez: 21 12 2021
pubmed: 22 12 2021
medline: 24 12 2021
Statut: epublish

Résumé

Strains Marseille-P2265

Identifiants

pubmed: 34932147
doi: 10.1007/s00203-021-02712-w
pii: 10.1007/s00203-021-02712-w
doi:

Substances chimiques

DNA, Bacterial 0
Fatty Acids 0
RNA, Ribosomal, 16S 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

45

Informations de copyright

© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.

Références

Anani H, Abou Abdallah R, Chelkha N et al (2019) Draft genome and description of Merdibacter massiliensis gen.nov., sp. nov., a new bacterium genus isolated from the human ileum. Sci Rep 9:7931. https://doi.org/10.1038/s41598-019-44343-8
doi: 10.1038/s41598-019-44343-8 pubmed: 31138831 pmcid: 6538751
Aramaki T, Blanc-Mathieu R, Endo H et al (2020) KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36:2251–2252. https://doi.org/10.1093/bioinformatics/btz859
doi: 10.1093/bioinformatics/btz859 pubmed: 31742321
Auch AF, von Jan M, Klenk H-P, Göker M (2010) Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genom Sci 2:117–134. https://doi.org/10.4056/sigs.531120
doi: 10.4056/sigs.531120
Bankevich A, Nurk S, Antipov D et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021
doi: 10.1089/cmb.2012.0021 pubmed: 22506599 pmcid: 3342519
Bessis S, Ndongo S, Lagier J-C et al (2016) ‘Neglecta timonensis’ gen. nov., sp. nov., a new human-associated species. New Microbes New Infect 13:13–14. https://doi.org/10.1016/j.nmni.2016.05.016
doi: 10.1016/j.nmni.2016.05.016 pubmed: 27358741 pmcid: 4917392
Chaplin AV, Sokolova SR, Shcherbakova VA et al (2020) Hydrogeniiclostidium mannosilyticum gen. nov., sp. nov. isolated from human faeces. Int J Syst Evol Microbiol 70:1210–1216. https://doi.org/10.1099/ijsem.0.003900
doi: 10.1099/ijsem.0.003900 pubmed: 32122456
Diakite A, Dubourg G, Dione N et al (2020) Optimization and standardization of the culturomics technique for human microbiome exploration. Sci Rep 10:9674. https://doi.org/10.1038/s41598-020-66738-8
doi: 10.1038/s41598-020-66738-8 pubmed: 32541790 pmcid: 7295790
Dione N, Sankar SA, Lagier J-C et al (2016) Genome sequence and description of Anaerosalibacter massiliensis sp. nov. New Microbes New Infect 10:66–76. https://doi.org/10.1016/j.nmni.2016.01.002
doi: 10.1016/j.nmni.2016.01.002 pubmed: 4753391 pmcid: 4753391
Drancourt M, Bollet C, Carlioz A et al (2000) 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol 38:3623–3630
doi: 10.1128/JCM.38.10.3623-3630.2000
Kanehisa M, Furumichi M, Tanabe M et al (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 45:D353–D361. https://doi.org/10.1093/nar/gkw1092
doi: 10.1093/nar/gkw1092 pubmed: 27899662
Kim M, Oh H-S, Park S-C, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351. https://doi.org/10.1099/ijs.0.059774-0
doi: 10.1099/ijs.0.059774-0 pubmed: 24505072 pmcid: 24505072
Kim B-C, Seung Jeon B, Kim S et al (2015) Caproiciproducens galactitolivorans gen. nov., sp. nov., a bacterium capable of producing caproic acid from galactitol, isolated from a wastewater treatment plant. Int J Syst Evol Microbiol 65:4902–4908. https://doi.org/10.1099/ijsem.0.000665
doi: 10.1099/ijsem.0.000665 pubmed: 26474980
Kim D, Park S, Chun J (2021) Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 59:476–480. https://doi.org/10.1007/s12275-021-1154-0
doi: 10.1007/s12275-021-1154-0 pubmed: 33907973
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120. https://doi.org/10.1007/BF01731581
doi: 10.1007/BF01731581 pubmed: 7463489 pmcid: 7463489
Konstantinidis KT, Tiedje JM (2005) Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187:6258–6264. https://doi.org/10.1128/JB.187.18.6258-6264.2005
doi: 10.1128/JB.187.18.6258-6264.2005 pubmed: 16159757 pmcid: 16159757
Kumar S, Stecher G, Li M et al (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096
doi: 10.1093/molbev/msy096 pubmed: 29722887 pmcid: 29722887
Lagier J-C, Armougom F, Million M et al (2012) Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 18:1185–1193. https://doi.org/10.1111/1469-0691.12023
doi: 10.1111/1469-0691.12023 pubmed: 23033984 pmcid: 23033984
Lagier J-C, Hugon P, Khelaifia S et al (2015a) The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev 28:237–264. https://doi.org/10.1128/CMR.00014-14
doi: 10.1128/CMR.00014-14 pubmed: 4284300 pmcid: 4284300
Lagier J-C, Khelaifia S, Azhar EI et al (2015b) Genome sequence of Oceanobacillus picturae strain S1, an halophilic bacterium first isolated in human gut. Stand Genom Sci. https://doi.org/10.1186/s40793-015-0081-2
doi: 10.1186/s40793-015-0081-2
Lagkouvardos I, Pukall R, Abt B et al (2016) The mouse intestinal bacterial collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nat Microbiol 1:16131. https://doi.org/10.1038/nmicrobiol.2016.131
doi: 10.1038/nmicrobiol.2016.131 pubmed: 27670113
Lee I, Ouk Kim Y, Park S-C, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103. https://doi.org/10.1099/ijsem.0.000760
doi: 10.1099/ijsem.0.000760 pubmed: 26585518 pmcid: 26585518
Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60. https://doi.org/10.1186/1471-2105-14-60
doi: 10.1186/1471-2105-14-60
Page AJ, Cummins CA, Hunt M et al (2015) Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31:3691–3693. https://doi.org/10.1093/bioinformatics/btv421
doi: 10.1093/bioinformatics/btv421 pubmed: 26198102 pmcid: 4817141
Price MN, Dehal PS, Arkin AP (2010) FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5:e9490. https://doi.org/10.1371/journal.pone.0009490
doi: 10.1371/journal.pone.0009490 pubmed: 2835736 pmcid: 2835736
Rossi-Tamisier M, Benamar S, Raoult D, Fournier P-E (2015) Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species. Int J Syst Evol Microbiol 65:1929–1934. https://doi.org/10.1099/ijs.0.000161
doi: 10.1099/ijs.0.000161 pubmed: 25736410
Sasser M (2006) Bacterial identification by gas chromatographic analysis of fatty acids methyl esters (GC-FAME)
Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to Imagej: 25 years of image analysis. Nat Methods 9:671–675. https://doi.org/10.1038/nmeth.2089
doi: 10.1038/nmeth.2089 pubmed: 22930834 pmcid: 5554542
Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. https://doi.org/10.1093/bioinformatics/btu153
doi: 10.1093/bioinformatics/btu153
Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 44:846–849. https://doi.org/10.1099/00207713-44-4-846
doi: 10.1099/00207713-44-4-846
Tindall BJ, Rosselló-Móra R, Busse H-J et al (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249–266. https://doi.org/10.1099/ijs.0.016949-0
doi: 10.1099/ijs.0.016949-0 pubmed: 19700448
Zgheib R, Anani H, Raoult D, Fournier P-E (2020) Draft genome sequence of Salirhabdus euzebyi strain Q1438. Microbiol Resour Announc. https://doi.org/10.1128/MRA.00246-20
doi: 10.1128/MRA.00246-20 pubmed: 32354978 pmcid: 7193933

Auteurs

Rita Zgheib (R)

Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.
UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, Aix Marseille Université, Marseille, France.

Ahmad Ibrahim (A)

Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.
UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille Université, Marseille, France.

Hussein Anani (H)

Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.
UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, Aix Marseille Université, Marseille, France.

Sokhna Ndongo (S)

Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.
UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille Université, Marseille, France.

Melhem Bilen (M)

Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA, USA.

Nicholas Armstrong (N)

Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.

Magali Richez (M)

Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.

Didier Raoult (D)

Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.
UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille Université, Marseille, France.
Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.

Pierre-Edouard Fournier (PE)

Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France. pierre-edouard.fournier@univ-amu.fr.
UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, Aix Marseille Université, Marseille, France. pierre-edouard.fournier@univ-amu.fr.

Articles similaires

Genome, Chloroplast Phylogeny Genetic Markers Base Composition High-Throughput Nucleotide Sequencing

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female
Humans United States Aged Cross-Sectional Studies Medicare Part C

Classifications MeSH