Flavobacterium bizetiae sp. nov., isolated from diseased freshwater fish in Canada at the end of the 1970s DOI Open Access
Estelle Mühle,

Chloé Abry,

Priscilla Leclerc

et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2020, Volume and Issue: 71(1)

Published: Nov. 30, 2020

Genome sequence analysis of two strains collected in Canada at the end 1970s and deposited 1998 Collection de l’Institut Pasteur has led to taxonomic description a novel fish-associated species genus Flavobacterium . Both strains, CIP 105534 T 105535, were yellow-pigmented, Gram-stain-negative, non-spore-forming rod-shaped bacteria that exhibited gliding motility. They grew aerobically temperature range from 5 30 °C with optimal growth 25 on trypticase soy or Reasoner's 2A agar but they did not grow marine agar. Their major fatty acid profiles similar, consisting iso-C 15 : 0 , C 16 1 ω7 c and/or 2-OH (shown as summed feature 3), 3-OH, 17 3-OH The polyamine was sym -homospermidine. Phosphatidylethanolamine and, most notably, ornithine-containing lipid OL2 unidentified aminophospholipid APL1 polar lipids. A yellow pigment spot visible after chromatographic analysis. predominant respiratory quinone MK-6. G+C content genomes 34 mol% their size around 5.8 Mb. Comparison 16S rRNA gene sequences those closely related type showed high levels relatedness collinsii pectinovorum All average nucleotide identity (ANI) digital DNA–DNA hybridization values estimated against publicly available genome assemblies lower than 90 %, respectively. Phylogenetic, phenotypic chemotaxonomic data indicated represent for which name bizetiae sp. nov. is proposed. strain (=LMG 1342 ). unique ability F. use melibiose sole source carbon could provide simple test discriminate its closest relatives.

Language: Английский

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph DOI Creative Commons
Guillaume Gautreau, Adelme Bazin,

Mathieu Gachet

et al.

PLoS Computational Biology, Journal Year: 2020, Volume and Issue: 16(3), P. e1007732 - e1007732

Published: March 19, 2020

The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms occurrence a given species. These usually lack multivariate statistical models infer the partitions optimal number classes don't account genome organization. We introduce graph structure model pangenomes which nodes represent edges genomic neighborhood. Our method, named PPanGGOLiN, using an Expectation-Maximization algorithm based on Bernoulli Mixture Model coupled with Markov Random Field. This approach takes into topology presence/absence genes persistent, cloud, one or several shell partitions. By analyzing partitioned pangenome graphs isolate genomes from 439 species metagenome-assembled 78 species, we demonstrate that our method is effective estimating persistent genome. Interestingly, it shows key element understand dynamics, presumably because reflects how present at intermediate frequencies drive adaptation its proportion independent size. graph-based proposed by PPanGGOLiN useful depict overall diversity thousands strains compact provides basis very large scale genomics. software freely available https://github.com/labgem/PPanGGOLiN.

Language: Английский

Citations

167
Diversity and functional landscapes in the microbiota of animals in the wild DOI Creative Commons
Doron Levin, Neta Raab, Yishay Pinto

et al.

Science, Journal Year: 2021, Volume and Issue: 372(6539)

Published: March 25, 2021

Animals in the wild are able to subsist on pathogen-infected and poisonous food show immunity various diseases. These may be due their microbiota, yet we have a poor understanding of animal microbial diversity function. We used metagenomics analyze gut microbiota more than 180 species wild, covering diverse classes, feeding behaviors, geographies, traits. Using de novo metagenome assembly, constructed functionally annotated database 5000 genomes, comprising 1209 bacterial which 75% unknown. The composition, diversity, functional content exhibit associations with taxonomy, diet, activity, social structure, life span. identify animals as largely untapped resource for discovery therapeutics biotechnology applications.

Language: Английский

Citations

155
Pan-drug resistance and hypervirulence in a human fungal pathogen are enabled by mutagenesis induced by mammalian body temperature DOI
Jingjing Huang, Pengjie Hu, Leixin Ye

et al.

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(7), P. 1686 - 1699

Published: June 19, 2024

Language: Английский

Citations

19
A Klebsiella pneumoniae ST307 outbreak clone from Germany demonstrates features of extensive drug resistance, hypermucoviscosity, and enhanced iron acquisition DOI Creative Commons
Stefan E. Heiden, Nils–Olaf Hübner,

Jürgen A. Bohnert

et al.

Genome Medicine, Journal Year: 2020, Volume and Issue: 12(1)

Published: Dec. 1, 2020

Abstract Background Antibiotic-resistant Klebsiella pneumoniae are a major cause of hospital- and community-acquired infections, including sepsis, liver abscess, pneumonia, driven mainly by the emergence successful high-risk clonal lineages. The K. sequence type (ST) 307 lineage has appeared in several different parts world after first being described Europe 2008. From June to October 2019, we recorded an outbreak extensively drug-resistant ST307 four medical facilities north-eastern Germany. Methods Here, investigated these isolates those from subsequent cases same facilities. We performed whole-genome sequencing study phylogenetics, microevolution, plasmid transmission, as well phenotypic experiments growth curves, hypermucoviscosity, siderophore secretion, biofilm formation, desiccation resilience, serum survival, heavy metal resistance for in-depth characterization this clone. Results Phylogenetics suggest homogenous phylogram with sub-clades containing either only one patient or originating patients, suggesting inter-patient transmission. identified three large plasmids, carrying NDM-1, CTX-M-15, OXA-48, which likely donated other STs even bacterial species (e.g., Enterobacter cloacae ) within clinical settings. Several chromosomally plasmid-encoded, hypervirulence-associated virulence factors yersiniabactin, metabolite transporter, aerobactin, genes) were addition. While growth, comparable control strains, results secretion hypermucoviscosity revealed superiority clone, similar archetypical, hypervirulent strain (hvKP1). Conclusions combination extensive drug virulence, partly conferred through “mosaic” both antibiotic features, demonstrates serious public health implications.

Language: Английский

Citations

122
A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy ofKlebsiella pneumoniaeStrains DOI Creative Commons
Mélanie Hennart, Julien Guglielmini, Sébastien Bridel

et al.

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(7)

Published: June 14, 2022

Abstract Sublineages (SLs) within microbial species can differ widely in their ecology and pathogenicity, precise definition is important basic research for industrial or public health applications. Widely accepted strategies to define SLs are currently missing, which confuses communication population biology epidemiological surveillance. Here, we propose a broadly applicable genomic classification nomenclature approach bacterial strains, using the prominent threat Klebsiella pneumoniae as model. Based on 629-gene core genome multilocus sequence typing (cgMLST) scheme, devised dual barcoding system that combines multilevel single linkage (MLSL) clustering life identification numbers (LINs). Phylogenetic analyses of >7,000 sequences captured structure discontinuities, were used guide 10 infraspecific genetic dissimilarity thresholds. The 7-gene (MLST) was mapped onto MLSL (threshold: 190 allelic mismatches) clonal group 43) identifiers backwards compatibility. taxonomy publicly accessible through community-curated platform (https://bigsdb.pasteur.fr/klebsiella), also enables external users’ identification. proposed strain two phylogenetically informative barcode systems provide full stability (LIN codes) nomenclatural continuity with previous (MLSL). This species-specific strategy strains should contribute unify global cross-sector collaborative knowledge emergence microevolution pathogens.

Language: Английский

Citations

59
Pseudoalteromonas holothuriae sp. nov., isolated from the sea cucumber Holothuria forskali DOI

Marion Yvin,

Estelle Mühle, O. Chesneau

et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2025, Volume and Issue: 75(2)

Published: Feb. 25, 2025

Two motile bacterial strains, designated as cfHf56-1 T and SW 252, were isolated from the coelomic fluid of Holothuria forskali surrounding seawater at animal sampling site, respectively. The sea cucumber was collected in Glénan archipelago (Brittany, France). Strains 252 Gram-stain-negative, non-spore-forming rod-shaped bacteria. Colonies made on marine agar plates brown color. pH temperature ranges for growth 7–8 18–30 °C, respectively, broth. major fatty acids 16 : 1 cis9 0. Phylogenetic analyses evidenced that both strains belong to a novel species genus Pseudoalteromonas . closely related type caenipelagi , byunsanensis amylolytica, with 75–78 % ANI 19–21 dDDH values. In this context, (= CIP 111854 = CECT 30642 ) is considered strain which name holothuriae sp. nov. proposed. genome characterized by size 5.1 Mbp G+C content 40.5%.

Language: Английский

Citations

1
Corynebacterium rouxii sp. nov., a novel member of the diphtheriae species complex DOI Creative Commons
Edgar Badell, Mélanie Hennart, Carla Rodrigues

et al.

Research in Microbiology, Journal Year: 2020, Volume and Issue: 171(3-4), P. 122 - 127

Published: Feb. 28, 2020

A group of six clinical isolates previously identified as Corynebacterium diphtheriae biovar Belfanti, isolated from human cutaneous or peritoneum infections and one dog, were characterized by genomic sequencing, biochemical analysis MALDI-TOF mass spectrometry. The negative for the diphtheria toxin gene. Phylogenetic analyses showed that (including FRC0190T) are clearly demarcated C. diphtheriae, belfantii, ulcerans pseudotuberculosis. average nucleotide identity FRC0190T with NCTC11397T was 92.6%, 91.8% belfantii FRC0043T. subsp. lausannense strain CHUV2995T appeared to be a later heterotypic synonym (ANI, 99.3%). Phenotyping data revealed an atypical heterogeneous intermediate maltose fermentation reaction isolates. spectrometry differentiated new other taxa presence specific spectral peaks. rpoB sequences atypical, maltose-negative Belfanti described two cats in USA. We propose name rouxii sp. nov. novel group, (= CIP 111752T = DSM 110354T) type strain.

Language: Английский

Citations

61
Phages against Noncapsulated Klebsiella pneumoniae: Broader Host range, Slower Resistance DOI Creative Commons
Marta Lourenço, Lisa Osbelt,

Virginie Passet

et al.

Microbiology Spectrum, Journal Year: 2023, Volume and Issue: 11(4)

Published: June 20, 2023

Klebsiella pneumoniae (Kp) is an ecologically generalist bacterium as well opportunistic pathogen that responsible for hospital-acquired infections and a major contributor to the global burden of antimicrobial resistance. In last decades, limited advances have been made in use virulent phages alternatives or complements antibiotics are used treat Kp infections.

Language: Английский

Citations

19
Genetic basis for the biodegradation of a polyether-polyurethane-acrylic copolymer by a landfill microbial community inferred by metagenomic deconvolution analysis DOI
Ayixón Sánchez‐Reyes, Itzel Gaytán,

Julián Pulido-García

et al.

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 881, P. 163367 - 163367

Published: April 10, 2023

Language: Английский

Citations

13
Corynebacterium ramonii sp. nov., a novel toxigenic member of the Corynebacterium diphtheriae species complex DOI Creative Commons
Chiara Crestani, Gabriele Arcari, Annie Landier

et al.

Research in Microbiology, Journal Year: 2023, Volume and Issue: 174(7), P. 104113 - 104113

Published: Aug. 10, 2023

Language: Английский

Citations

12