- bongori strains. - bongori strains so far reported. - This novel T6SS resembled the SPI-19 T6SS of the warm-blooded host infecting Salmonella Subgroup I lineages. - Human salmonellosis is primarily caused by Salmonella Subgroup I lineages but may occasionally be elicited also by bacteria of the other. - 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - 1 Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin 150081, China Full list of author information is available at the end of the article. - revelation of the genetic differences among the S. - Consequently, the previous species became serovars of the only Salmonella species, Salmonella enterica [24]. - Later, Subgroup V regained the scientific name of Salmonella bongori based on its greater genetic divergence from all other subgroups [25]. - bongori, but the precise phylogenetic rela- tionships of the bacteria among the serotypes and the phyletic status within each of the serotypes remain largely unclear.. - RKS3044, which is one of the Salmonella Reference Col- lection C strains kindly provided by Dr. - bongori strains that had different antigenic formulae or were isolated from cold-blooded hosts. - bongori strains have diverged into distinct lineages and, interestingly, strain RKS3044 had a novel cluster of T6SS-associated genes. - Genomic comparisons of the completely sequenced S.. - bongori strains: RKS3044 representing a warm-blooded host pathogen. - bongori strains (Additional file 3: Table S1). - Table 1 General characteristics of the complete S. - bongori strains (see Additional file 3: Table S1) in comparison with rep- resentative strains of the other Salmonella subgroups (Additional file 5: Table S3). - common to the 26 analyzed strains and constructed a phylogenetic tree. - bongori strains had similar genetic distances from one another as those seen among the Subgroup I strains (Fig. - bongori strains RKS3044 and N268–08 had a genetic distance between them similar to that as between S. - bongori strains RKS3044 and N268–08.. - bongori strains into clear-cut phylogenetic clusters. - To evaluate the phylogenetic significance of the demon- strated genetic separation among the S. - i.e., to determine whether the genetic divergence might be clear-cut (i.e., making the lineages clearly discrete) or continuous (i.e., showing a spectrum of gradual or con- tinuous genetic differences without clear cut-offs among the “lineages. - we detected the percentages of the hom- ologous genes that share identical nucleotide sequences (zero nucleotide degeneracy) between the bacteria (Add- itional file 2: Figure S2 and Additional file 6: Table S4).. - bongori strains into three groups: high, from 85 to 100% (e.g., between N268–08 and BCW_1557 or CATO-2016, between NCTC12419 and SA19983605 or BCW_1556, etc. - low, lower than 20% and mostly around 10% (the majority of the ana- lyzed S. - typhi, which are highly cohesive as members of the same phylogenetic cluster [19]. - the “medium” group resembles bacteria between S. - the “low” group resembles bacteria between most Salmonella Subgroup I serotypes like S. - bongori strains that had the percentages between 35 and 85%, probably because the number of S.. - bongori strains analyzed here was not large enough to. - cover sufficient ranges of the genetic divergence, al- though our previous work has demonstrated that the. - pullorum [16], is indicative of phylogenetic divergence of the compared bacteria into distinct species.. - nih.gov), we identified most of the previously reported S.. - bongori virulence genes in RKS3044 strain, except some of the genes encoding T3SS effector proteins (Additional file 7: Table S5). - bongori strains but absent in RKS3044 are indicated by capital letters from A to O. - 2 Phylogenetic tree of the Salmonella strains. - The phylogenetic tree was constructed by genes common to the 26 Salmonella strains representing Salmonella subgroups I, II, IIIa, IIIb, and V. - 4b), with structural similarity to the T6SS in SPI-19 (T6SS SPI-19 ) of. - To assess the evolutionary relationships of the T6SSs in RKS3044 with those in closely related bacteria, we con- structed a phylogenetic tree on concatenated TssB and TssC protein sequences of T6SS novel and T6SS SPI-22 of RKS3044 and those from selected E. - bongori RKS3044 and S. - RKS3044 and the other S. - bongori strains form distinct phylogenetic lineages. - bongori strains and conducted sys- tematic comparisons among the bacteria, focusing on its genomic location and degeneration patterns. - bongori lineages and the divergence patterns were consistent with the phylogenetic clustering of the bacteria, suggesting that the lineages have di- verged into different phylogenetic and ecological posi- tions for long evolutionary times, so they do not have much chances to freely exchange their genetic materials (Additional file 10: Table S8).. - genomic sequence amelioration patterns we proposed the Adopt-Adapt model of bacterial speci- ation, with the “adopted” lateral genes diverting the dir- ection of evolution and the ensuing genomic sequence amelioration for “adaptation” to accept the adopted genes and become increasingly fit to the new niche, e.g., a new host or environment . - bongori strains to identify the hypothesized unique set of laterally adopted genes and adaptive sequence amelioration events in RKS3044 and to determine whether genetic boundaries might have been formed between RKS3044 and other S. - bongori strains.. - bongori RKS3044 and other sequenced S. - bongori strains to reveal their pos- sible genomic differences. - We found that RKS3044 shared most of the virulence genes with the previously sequenced S. - bongori strains and also lacked SPI-2, but on the other hand contained a novel T6SS (T6SS novel ) encoded in a new SPI (SPI- RKS3044) identified in this study. - RKS3044 and conducted comparisons with the other sequenced S. - As NCTC12419 and SA19983065 belong to the same serotype (66:z41. - bon- gori might be similar to that of Salmonella Subgroup I lineages, in which most serotypes are monophyletic and the monophyletic serotypes correspond to natural species [6]. - Notably, there are usually broad windows be- tween the “high” and “low” percentages (higher than 70% vs lower than 20%, without intermediates between 70 and 20%, with rare exceptions which would make the allelic distance an applicable parameter to define and delineate bacteria into natural species. - bongori consist of discrete phylogenetic groups corre- sponding to the individual serotypes, which are equivalent. - bongori strains have a T6SS in SPI-22, strain RKS3044 has an add- itional T6SS in SPI- RKS3044. - As the SPI-22 T6SS in RKS3044 is defective but the SPI-RKS3044 T6SS resem- bles the functional SPI-19 T6SS of the warm-blooded host infecting Salmonella Subgroup I lineages, it is possible that acquisition of the SPI-19-like T6SS might have facilitated the evolution of a branch of S. - These findings provide new support to the model of bacterial speciation to become pathogens.. - Eventually, we verified the correctness of the finished genome by PFGE based on cleavage data of XbaI, AvrII and SpeI.. - The graph- ical circular map of the S. - The phylogenetic trees of the genomes and T6SS loci were structured using the Neighbor-Joining method [50] in MEGA6 [51] by 1000 bootstrap replicates. - Graphical map of the S. - Genomic comparison among the Salmonella bongori strains. - Additional file 3: Table S1. - bongori strains used for genomic comparisons in this study.. - Additional file 4: Table S2. - Additional file 5: Table S3. - Percentages of homologous genes that share identical nucleotide sequences between pairs of the bacteria compared.. - Additional file 7: Table S5. - bongori strains RKS3044 and NCTC12419.. - Additional file 8: Table S6. - Additional file 9: Table S7. - The funding bodies played no roles in the design of the study. - 47) to the White-Kauffmann-Le Minor scheme. - Evolutionary genetic relationships of clones of Salmonella serovars that cause human typhoid and other enteric fevers.. - Molecular genetic relationships of the salmonellae. - Evolution of Salmonella nomenclature: a critical note. - Endemic presence of Salmonella bongori 48:z35:- causing enteritis in children in Sicily. - Genome Sequence of Salmonella bongori Strain N268 – 08 [corrected]. - The XbaI-BlnI-CeuI genomic cleavage map of Salmonella enteritidis shows an inversion relative to Salmonella typhimurium LT2. - Genomic cleavage map of Salmonella typhi Ty2. - Differential degeneration of the ACTAGT sequence among Salmonella: a reflection of distinct nucleotide amelioration patterns during bacterial divergence. - On the serology of the Salmonella group. - A simplification of the serologic diagnosis of Salmonella cultures. - Designation of Salmonella enterica sp. - rev., as the type and only species of the genus Salmonella. - Rearrangements in the genome of the bacterium Salmonella typhi. - Genome Sequence of Salmonella bongori Strain N268 – 08. - Salmonella bongori provides insights into the evolution of the salmonellae. - Genomic analysis of the type VI secretion systems in Pseudomonas spp.: novel clusters and putative effectors uncovered. - Determining divergence times of the major kingdoms of living organisms with a protein clock.. - The XbaI-BlnI-CeuI genomic cleavage map of Salmonella paratyphi B. - The XbaI-BlnI-CeuI genomic cleavage map of Salmonella typhimurium LT2 determined by double digestion, end labelling, and pulsed-field gel electrophoresis. - The evolving genome of Salmonella enterica serovar Pullorum. - Contribution of the type VI secretion system encoded in SPI-19 to chicken colonization by Salmonella enterica serotypes Gallinarum and Enteritidis. - I-CeuI reveals conservation of the genome of independent strains of Salmonella typhimurium
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