scholarly journals Subtelomeres are fast-evolving regions of the Streptomyces linear chromosome

2021 ◽  
Author(s):  
Jean-Noël Lorenzi ◽  
Olivier Lespinet ◽  
Pierre Leblond ◽  
Annabelle Thibessard
Keyword(s):  
Central Region ◽  
Bacterial Population ◽  
Core Genome ◽  
Rapid Evolution ◽  
Linear Chromosome ◽  
Content Type ◽  
Link Type ◽  
New Information ◽  
Genetic Pool ◽  
Core Genes

Streptomycespossess a large linear chromosome (6–12 Mb) consisting of a conserved central region flanked by variable arms covering several megabases. In order to study the evolution of the chromosome across evolutionary times, a representative panel ofStreptomycesstrains and species (125) whose chromosomes are completely sequenced and assembled was selected. The pan-genome of the genus was modelled and shown to be open with a core-genome reaching 1018 genes. The evolution ofStreptomyceschromosome was analysed by carrying out pairwise comparisons, and by monitoring indexes measuring the conservation of genes (presence/absence) and their synteny along the chromosome. Using the phylogenetic depth offered by the chosen panel, it was possible to infer that within the central region of the chromosome, the core-genes form a highly conserved organization, which can reveal the existence of an ancestral chromosomal skeleton. Conversely, the chromosomal arms, enriched in variable genes evolved faster than the central region under the combined effect of rearrangements and addition of new information from horizontal gene transfer. The genes hosted in these regions may be localized there because of the adaptive advantage that their rapid evolution may confer. We speculate that (i) within a bacterial population, the variability of these genes may contribute to the establishment of social characters by the production of ‘public goods’ (ii) at the evolutionary scale, this variability contributes to the diversification of the genetic pool of the bacteria.

scholarly journals Yersinia artesiana sp. nov., Yersinia proxima sp. nov., Yersinia alsatica sp. nov., Yersina vastinensis sp. nov., Yersinia thracica sp. nov. and Yersinia occitanica sp. nov., isolated from humans and animals

2020 ◽  
Vol 70 (10) ◽  
pp. 5363-5372 ◽  
Author(s):  
Anne-Sophie Le Guern ◽  
Cyril Savin ◽  
Hilde Angermeier ◽  
Sylvie Brémont ◽  
Dominique Clermont ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Type Strain ◽  
Core Genome ◽  
Novel Species ◽  
Reference Laboratory ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Approach ◽  
Core Genes

Thirty-three Yersinia strains previously characterized by the French Yersinia National Reference Laboratory (YNRL) and isolated from humans and animals were suspected to belong to six novel species by a recently described core genome multilocus sequence typing scheme. These strains and five additional strains from the YNRL were characterized using a polyphasic taxonomic approach including a phylogenetic analysis based on 500 core genes, determination of average nucleotide identity (ANI), determination of DNA G+C content and identification of phenotypic features. Phylogenetic analysis confirmed that the 38 studied strains formed six well-demarcated clades. ANI values between these clades and their closest relatives were <94.7 % and ANI values within each putative novel species were >97.5 %. Distinctive biochemical characteristics were identified in five out of the six novel species. All of these data demonstrated that the 38 strains belong to six novel species of the genus Yersinia : Yersinia artesiana sp. nov., type strain IP42281T (=CIP 111845T=DSM 110725T); Yersinia proxima sp. nov., type strain IP37424T (=CIP 111847T=DSM 110727T); Yersinia alsatica sp. nov., type strain IP38850T (=CIP 111848T=DSM 110726T); Yersinia vastinensis sp. nov., type strain IP38594T (=CIP 111844T=DSM 110738T); Yersinia thracica sp. nov., type strain IP34646T (=CIP 111842T=DSM 110736T); and Yersinia occitanica sp. nov., type strain IP35638T (=CIP 111843T=DSM 110739T).

scholarly journals Heterogeneity among estimates of the core genome and pan-genome in different pneumococcal populations

2017 ◽  
Author(s):  
Andries J van Tonder ◽  
James E Bray ◽  
Keith A Jolley ◽  
Sigríður J Quirk ◽  
Gunnsteinn Haraldsson ◽  
...  
Keyword(s):  
Bacterial Population ◽  
Core Genome ◽  
Bacterial Species ◽  
Essential Point ◽  
Genetic Lineages ◽  
The Core ◽  
Pan Genome ◽  
Single Dataset ◽  
Genomic Regions ◽  
Core Genes

AbstractBackgroundUnderstanding the structure of a bacterial population is essential in order to understand bacterial evolution, or which genetic lineages cause disease, or the consequences of perturbations to the bacterial population. Estimating the core genome, the genes common to all or nearly all strains of a species, is an essential component of such analyses. The size and composition of the core genome varies by dataset, but our hypothesis was that variation between different collections of the same bacterial species should be minimal. To test this, the genome sequences of 3,121 pneumococci recovered from healthy individuals in Reykjavik (Iceland), Southampton (United Kingdom), Boston (USA) and Maela (Thailand) were analysed.ResultsThe analyses revealed a ‘supercore’ genome (genes shared by all 3,121 pneumococci) of only 303 genes, although 461 additional core genes were shared by pneumococci from Reykjavik, Southampton and Boston. Overall, the size and composition of the core genomes and pan-genomes among pneumococci recovered in Reykjavik, Southampton and Boston were very similar, but pneumococci from Maela were distinctly different. Inspection of the pan-genome of Maela pneumococci revealed several >25 Kb sequence regions that were homologous to genomic regions found in other bacterial species.ConclusionsSome subsets of the global pneumococcal population are highly heterogeneous and thus our hypothesis was rejected. This is an essential point of consideration before generalising the findings from a single dataset to the wider pneumococcal population.

scholarly journals Proposal to reclassify Streptobacillus hongkongensis into a novel genus as Pseudostreptobacillus hongkongensis gen. nov., comb. nov.

2020 ◽  
Vol 70 (4) ◽  
pp. 2366-2368 ◽  
Author(s):  
Tobias Eisenberg ◽  
Stefanie P. Glaeser ◽  
Jochen Blom ◽  
Peter Kämpfer
Keyword(s):  
Type Species ◽  
Core Genome ◽  
Housekeeping Genes ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Protein Coding ◽  
Content Type ◽  
Phenotypic Differences ◽  
Link Type ◽  
The 16S Rrna Gene

The reclassification of Streptobacillus hongkongensis as Pseudostreptobacillus hongkongensis gen. nov., comb. nov. is proposed because of the separate phylogenetic position on the basis of the 16S rRNA gene sequence phylogeny, the combined analysis of the three protein-coding housekeeping genes groEL, gyrB and recA and a core genome sequence phylogeny to all other Streptobacillus species that is supported by phenotypic differences. The species Pseudostreptobacillus hongkongensis is the type species of the genus. The type strain is HKU33T, JCM 18691T, NCTC 13659T, DSM 26322T.

scholarly journals Evaluation of whole-genome sequencing-based subtyping methods for the surveillance of Shigella spp. and the confounding effect of mobile genetic elements in long-term outbreaks

2021 ◽  
Vol 7 (11) ◽  
Author(s):  
Isabelle Bernaquez ◽  
Christiane Gaudreau ◽  
Pierre A. Pilon ◽  
Sadjia Bekal
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Type Species ◽  
Core Genome ◽  
Outbreak Detection ◽  
Whole Genome ◽  
Content Type ◽  
Link Type ◽  
Interpretation Criteria

Many public health laboratories across the world have implemented whole-genome sequencing (WGS) for the surveillance and outbreak detection of foodborne pathogens. PulseNet-affiliated laboratories have determined that most single-strain foodborne outbreaks are contained within 0–10 multi-locus sequence typing (MLST)-based allele differences and/or core genome single-nucleotide variants (SNVs). In addition to being a food- and travel-associated outbreak pathogen, most Shigella spp. cases occur through continuous person-to-person transmission, predominantly involving men who have sex with men (MSM), leading to long-term and recurrent outbreaks. Continuous transmission patterns coupled to genetic evolution under antibiotic treatment pressure require an assessment of existing WGS-based subtyping methods and interpretation criteria for cluster inclusion/exclusion. An evaluation of 4 WGS-based subtyping methods [SNVPhyl, coreMLST, core genome MLST (cgMLST) and whole-genome MLST (wgMLST)] was performed on 9 foodborne-, travel- and MSM-related retrospective outbreaks from a collection of 91 Shigella flexneri and 232  Shigella sonnei isolates to determine the methods’ epidemiological concordance, discriminatory power, robustness and ability to generate stable interpretation criteria. The discriminatory powers were ranked as follows: coreMLST<SNVPhyl<cgMLST<wgMLST (range: 0.970–1.000). The genetic differences observed for non-MSM-related Shigella spp. outbreaks respect the standard 0–10 allele/SNV guideline; however, mobile genetic element (MGE)-encoded loci caused inflated genetic variation and discrepant phylogenies for prolonged MSM-related S. sonnei outbreaks via wgMLST. The S. sonnei correlation coefficients of wgMLST were also the lowest at 0.680, 0.703 and 0.712 for SNVPhyl, coreMLST and cgMLST, respectively. Plasmid maintenance, mobilization and conjugation-associated genes were found to be the main source of genetic distance inflation in addition to prophage-related genes. Duplicated alleles arising from the repeated nature of IS elements were also responsible for many false cg/wgMLST differences. The coreMLST approach was shown to be the most robust, followed by SNVPhyl and wgMLST for inter-laboratory comparability. Our results highlight the need for validating species-specific subtyping methods based on microbial genome plasticity and outbreak dynamics in addition to the importance of filtering confounding MGEs for cluster detection.

Microbe Profile: Buchnera aphidicola: ancient aphid accomplice and endosymbiont exemplar

Microbiology ◽  
2021 ◽  
Vol 167 (12) ◽  
Author(s):  
Nancy A. Moran
Keyword(s):  
Type Species ◽  
Rapid Evolution ◽  
Essential Amino Acids ◽  
Aphid Species ◽  
Buchnera Aphidicola ◽  
Content Type ◽  
Link Type ◽  
Phylogenetic Reconstructions ◽  
Gene Acquisition ◽  
Conserved Gene

Buchnera aphidicola is an obligate endosymbiont of aphids that cannot be cultured outside of hosts. It exists as diverse strains in different aphid species, and phylogenetic reconstructions show that it has been maternally transmitted in aphids for >100 million years. B. aphidicola genomes are highly reduced and show conserved gene order and no gene acquisition, but encoded proteins undergo rapid evolution. Aphids depend on B. aphidicola for biosynthesis of essential amino acids and as an integral part of embryonic development. How B. aphidicola populations are regulated within hosts remains little known.

scholarly journals Development and Application of a Core Genome Multilocus Sequence Typing Scheme for the Health Care-Associated Pathogen Pseudomonas aeruginosa

2020 ◽  
Vol 58 (9) ◽  
Author(s):  
Richard A. Stanton ◽  
Gillian McAllister ◽  
Jonathan B. Daniels ◽  
Erin Breaker ◽  
Nicholas Vlachos ◽  
...  
Keyword(s):  
Health Care ◽  
Pseudomonas Aeruginosa ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Health Care Environment ◽  
Content Type ◽  
Health Care Associated Infections ◽  
Opportunistic Human Pathogen ◽  
The Stability ◽  
Core Genes

ABSTRACT Pseudomonas aeruginosa is an opportunistic human pathogen that frequently causes health care-associated infections (HAIs). Due to its metabolic diversity and ability to form biofilms, this Gram-negative nonfermenting bacterium can persist in the health care environment, which can lead to prolonged HAI outbreaks. We describe the creation of a core genome multilocus sequence typing (cgMLST) scheme to provide a stable platform for the rapid comparison of P. aeruginosa isolates using whole-genome sequencing (WGS) data. We used a diverse set of 58 complete P. aeruginosa genomes to curate a set of 4,440 core genes found in each isolate, representing ∼64% of the average genome size. We then expanded the alleles for each gene using 1,991 contig-level genome sequences. The scheme was used to analyze genomes from four historical HAI outbreaks to compare the phylogenies generated using cgMLST to those of other means (traditional MLST, pulsed-field gel electrophoresis [PFGE], and single-nucleotide variant [SNV] analysis). The cgMLST scheme provides sufficient resolution for analyzing individual outbreaks, as well as the stability for comparisons across a variety of isolates encountered in surveillance studies, making it a valuable tool for the rapid analysis of P. aeruginosa genomes.

scholarly journals Reclassification of genus Izhakiella into the family Erwiniaceae based on phylogenetic and genomic analyses

2020 ◽  
Vol 70 (5) ◽  
pp. 3541-3546 ◽  
Author(s):  
Lingmin Jiang ◽  
Dexin Wang ◽  
Ji-Sun Kim ◽  
Ju Huck Lee ◽  
Dae-Hyuk Kim ◽  
...  
Keyword(s):  
Type Species ◽  
Housekeeping Gene ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Conserved Signature Indels ◽  
The Family ◽  
Taxonomical Classification ◽  
Core Genes

The genus Izhakiella was established and designated as a member of the family Enterobacteriaceae in 2016. Although the taxonomical classification of most members in this family has been relatively resolved after two reclassifications in 2016 and 2017, the classification of the genus Izhakiella remains ambiguous. In this study, a polyphasic approach was used to provide evidence supporting the fact that the genus Izhakiella should no longer be considered a member of Enterobacteriaceae and proposes its reclassification into the family Erwiniaceae . The phylogenetic tree of type species in the families Enterobacteriaceae and Erwiniaceae based on the sequences of the 16S rRNA gene, rpoB housekeeping gene, and the whole-genome comprising the 92 core genes revealed that the genus Izhakiella forms a phylogenetic lineage within the family Erwiniaceae . The average nucleotide identity (ANI) value of the type species with genus Izhakiella was found to be higher for the family Erwiniaceae than that for the family Enterobacteriaceae . Notably, 12 conserved signature indels (CSIs) that are exclusively shared among the Erwiniaceae clade members were found in the type strains of the genus Izhakiella . Based on these analyses, this study suggests the reclassification of I. capsodis and I. australiensis into the family Erwiniaceae .

Collimonas silvisoli sp. nov. and Collimonas humicola sp. nov., two novel species isolated from forest soil

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Jiali Li ◽  
Mingkai Pan ◽  
Xianjiao Zhang ◽  
Yang Zhou ◽  
Guang-Da Feng ◽  
...  
Keyword(s):  
Forest Soil ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
Type Strains ◽  
Core Genes

Three aerobic, Gram-stain-negative, non-motile and rod-shaped bacteria, designated strains RXD178T, RXD172-2 and RLT1W51T, were isolated from two forest soil samples of Nanling National Nature Reserve in Guangdong Province, PR China. Phylogenetic analyses based on 16S rRNA gene sequences and 92 core genes showed that they belonged to the genus Collimonas , and were most closely related to four validly published species with similarities ranging from 99.4 to 98.2 %. The genomic DNA G+C contents of strains RXD178T, RXD172-2 and RLT1W51T were 57.1, 59.5 and 59.4 mol%, respectively. The genome-derived average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the novel strains and closely related type species were below 37.90 and 89.34 %, respectively. Meanwhile, the ANI and dDDH values between strains RXD172-2 and RLT1W51T were 98.27 and 83.50 %, respectively. The three novel strains contained C16 : 0, C17 : 0 cyclo and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) as the major fatty acids, and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) comprised a relative higher proportion in strain RXD178T than in other strains. Both strains RXD172-2 and RLT1W51T had phosphatidylglycerol (PG), phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG) and an unidentified aminophospholipid (APL) as the main polar lipids while only PE and APL were detected in strain RXD178T. Ubiquinone 8 was the predominant quinone. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic analyses, strain RXD178T should be considered as representing one novel species within the genus Collimonas and strains RXD172-2 and RLT1W51T as another one, for which the names Collimonas silvisoli sp. nov. and Collimonas humicola sp. nov. are proposed, with RXD178T (=GDMCC 1.1925T=KACC 21987T) and RLT1W51T (=GDMCC 1.1923T=KACC 21985T) as the type strains, respectively.

scholarly journals Multiple holins contribute to extracellular DNA release in Pseudomonas aeruginosa biofilms

Microbiology ◽  
2021 ◽  
Author(s):  
Amelia L. Hynen ◽  
James J. Lazenby ◽  
George M. Savva ◽  
Laura C. McCaughey ◽  
Lynne Turnbull ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Type Species ◽  
Extracellular Polymeric Substances ◽  
Bacterial Population ◽  
Extracellular Dna ◽  
Bacterial Biofilms ◽  
Content Type ◽  
Link Type ◽  
Dna Release ◽  
Biofilm Development

Bacterial biofilms are composed of aggregates of cells encased within a matrix of extracellular polymeric substances (EPS). One key EPS component is extracellular DNA (eDNA), which acts as a ‘glue’, facilitating cell–cell and cell–substratum interactions. We have previously demonstrated that eDNA is produced in Pseudomonas aeruginosa biofilms via explosive cell lysis. This phenomenon involves a subset of the bacterial population explosively lysing, due to peptidoglycan degradation by the endolysin Lys. Here we demonstrate that in P. aeruginosa three holins, AlpB, CidA and Hol, are involved in Lys-mediated eDNA release within both submerged (hydrated) and interstitial (actively expanding) biofilms, albeit to different extents, depending upon the type of biofilm and the stage of biofilm development. We also demonstrate that eDNA release events determine the sites at which cells begin to cluster to initiate microcolony formation during the early stages of submerged biofilm development. Furthermore, our results show that sustained release of eDNA is required for cell cluster consolidation and subsequent microcolony development in submerged biofilms. Overall, this study adds to our understanding of how eDNA release is controlled temporally and spatially within P. aeruginosa biofilms.

scholarly journals Symbiosis islands of Loteae-nodulating Mesorhizobium comprise three radiating lineages with concordant nod gene complements and nodulation host-range groupings

2020 ◽  
Vol 6 (9) ◽  
Author(s):  
Benjamin J. Perry ◽  
John T. Sullivan ◽  
Elena Colombi ◽  
Riley J.T. Murphy ◽  
Joshua P. Ramsay ◽  
...  
Keyword(s):  
Host Range ◽  
Soil Bacteria ◽  
Evolutionary Relationship ◽  
Broad Host Range ◽  
Content Type ◽  
Regulatory Motifs ◽  
Integrative And Conjugative Elements ◽  
Link Type ◽  
Group I ◽  
Core Genes

Mesorhizobium is a genus of soil bacteria, some isolates of which form an endosymbiotic relationship with diverse legumes of the Loteae tribe. The symbiotic genes of these mesorhizobia are generally carried on integrative and conjugative elements termed symbiosis islands (ICESyms). Mesorhizobium strains that nodulate Lotus spp. have been divided into host-range groupings. Group I (GI) strains nodulate L. corniculatus and L. japonicus ecotype Gifu, while group II (GII) strains have a broader host range, which includes L. pedunculatus. To identify the basis of this extended host range, and better understand Mesorhizobium and ICESym genomics, the genomes of eight Mesorhizobium strains were completed using hybrid long- and short-read assembly. Bioinformatic comparison with previously sequenced mesorhizobia genomes indicated host range was not predicted by Mesorhizobium genospecies but rather by the evolutionary relationship between ICESym symbiotic regions. Three radiating lineages of Loteae ICESyms were identified on this basis, which correlate with Lotus spp. host-range grouping and have lineage-specific nod gene complements. Pangenomic analysis of the completed GI and GII ICESyms identified 155 core genes (on average 30.1 % of a given ICESym). Individual GI or GII ICESyms carried diverse accessory genes with an average of 34.6 % of genes unique to a given ICESym. Identification and comparative analysis of NodD symbiotic regulatory motifs – nod boxes – identified 21 branches across the NodD regulons. Four of these branches were associated with seven genes unique to the five GII ICESyms. The nod boxes preceding the host-range gene nodZ in GI and GII ICESyms were disparate, suggesting regulation of nodZ may differ between GI and GII ICESyms. The broad host-range determinant(s) of GII ICESyms that confer nodulation of L. pedunculatus are likely present amongst the 53 GII-unique genes identified.

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