Study of Streptococcus thermophilus population on a world-wide and historical collection by a new MLST scheme

Delorme, Christine; Legravet, Nicolas; Jamet, Emmanuel; Hoarau, Caroline; Bolotin, Alexandre; El-Sharoud, Walid; Darwish, Mohamed Samir; Renault, Pierre

doi:10.1016/j.ijfoodmicro.2016.11.016

Cited by 20 publications

(31 citation statements)

References 58 publications

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“…This may suggest a more stringent selection of core proteins during our analysis. Despite the fact that several different strains were analyzed in our study and the study by Delorme et al (2017), phylogenetic clustering of strains exhibited similarities supporting more or less the distinction we propose between cluster A and B strains and the subgroups observed within them. Differences in the topology of the two phylogenetic trees can be attributed to the different dataset of genomes analyzed as well as the different methods employed to construct the trees.…”

Section: Pan/core Genome Analysis and Phylogenomicssupporting

confidence: 79%

“…These subgroups include strains ASCC 1275, DGCC 7710, KLDS SM, MN-BM-A02, and ND07 (subgroup AI), MN-BM-A01 and MN-ZLW-002 (subgroup AII), LMD-9 and SMQ-301 (subgroup AIII), APC151 and ND03 (subgroup AIV), and finally CNRZ1066, CS8, EPS, and S9 (subgroup BI) (Figures 2, 3). As already mentioned, core genome phylogeny was also previously performed in a dataset of 25 S. thermophilus strains employing genomes sequenced to a variable degree of completeness (Delorme et al, 2017). In this study 1,311 core proteins were reported.…”

Section: Pan/core Genome Analysis and Phylogenomicsmentioning

confidence: 99%

“…Original studies used typing techniques like random amplification of polymorphic DNA-PCR (RAPD-PCR) or pulsed-field gel electrophoresis (PFGE), while more recent ones used multilocus sequence typing (MLST) (Moschetti et al, 1998;Giraffa et al, 2001;Mora et al, 2002;Ercolini et al, 2005;Delorme et al, 2010Delorme et al, , 2017Yu et al, 2015). Application of MLST in S. thermophilus had to be optimized to increase discriminating power, given the fact that the species may exhibit limited genetic variability (Delorme et al, 2017). In this study the authors reported 116 sequence types and the existence of groups of strains based on phylogenetic analysis of concatenated sequences of housekeeping genes.…”

Section: Introductionmentioning

confidence: 99%

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Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species

et al. 2019

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Streptococcus thermophilus is a major starter for the dairy industry with great economic importance. In this study we analyzed 23 fully sequenced genomes of S. thermophilus to highlight novel aspects of the evolution, biology and technological properties of this species. Pan/core genome analysis revealed that the species has an important number of conserved genes and that the pan genome is probably going to be closed soon. According to whole genome phylogeny and average nucleotide identity (ANI) analysis, most S. thermophilus strains were grouped in two major clusters (i.e., clusters A and B). More specifically, cluster A includes strains with chromosomes above 1.83 Mbp, while cluster B includes chromosomes below this threshold. This observation suggests that strains belonging to the two clusters may be differentiated by gene gain or gene loss events. Furthermore, certain strains of cluster A could be further subdivided in subgroups, i.e., subgroup I (ASCC 1275, DGCC 7710, KLDS SM, MN-BM-A02, and ND07), II (MN-BM-A01 and MN-ZLW-002), III (LMD-9 and SMQ-301), and IV (APC151 and ND03). In cluster B certain strains formed one distinct subgroup, i.e., subgroup I (CNRZ1066, CS8, EPS, and S9). Clusters and subgroups observed for S. thermophilus indicate the existence of lineages within the species, an observation which was further supported to a variable degree by the distribution and/or the architecture of several genomic traits. These would include exopolysaccharide (EPS) gene clusters, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)-CRISPR associated (Cas) systems, as well as restriction-modification (R-M) systems and genomic islands (GIs). Of note, the histidine biosynthetic cluster was found present in all cluster A strains (plus strain NCTC12958 T) but was absent from all strains in cluster B. Other loci related to lactose/galactose catabolism and urea metabolism, aminopeptidases, the majority of amino acid and peptide transporters, as well as amino acid biosynthetic pathways

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Section: Pan/core Genome Analysis and Phylogenomicssupporting

confidence: 79%

Section: Pan/core Genome Analysis and Phylogenomicsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species

et al. 2019

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“…However, studies have suggested that the fruit pathogen Pseudomonas syringae pv. acitinidiae 36,37 and the environmental Streptococcus thermophuilis 38 have regional phylogenies. These results are in line with the findings of this study.…”

Section: Discussionmentioning

confidence: 99%

Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering

Ahrenfeldt

Waisi

Loft

et al. 2020

Sci Rep

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Knowledge about the difference in the global distribution of pathogens and non-pathogens is limited. Here, we investigate it using a multi-sample metagenomics phylogeny approach based on short-read metagenomic sequencing of sewage from 79 sites around the world. For each metagenomic sample, bacterial template genomes were identified in a non-redundant database of whole genome sequences. Reads were mapped to the templates identified in each sample. Phylogenetic trees were constructed for each template identified in multiple samples. The countries from which the samples were taken were grouped according to different definitions of world regions. For each tree, the tendency for regional clustering was determined. Phylogenetic trees representing 95 unique bacterial templates were created covering 4 to 71 samples. Varying degrees of regional clustering could be observed. The clustering was most pronounced for environmental bacterial species and human commensals, and less for colonizing opportunistic pathogens, opportunistic pathogens and pathogens. No pattern of significant difference in clustering between any of the organism classifications and country groupings according to income were observed. our study suggests that while the same bacterial species might be found globally, there is a geographical regional selection or barrier to spread for individual clones of environmental and human commensal bacteria, whereas this is to a lesser degree the case for strains and clones of human pathogens and opportunistic pathogens. One of the basic dogma in microbiology has for almost a century been that we for microorganisms consider that "everything is everywhere but the environment selects" 1,2. A large number of papers about the global transmission events of bacterial clones have been published, including descriptions of emergence and spread of specific clones of Vibrio cholera, MRSA, Escherichia coli, Clostridium difficile 3-6 and many other bacterial pathogens. The main focus has been on pathogenic clones and virtually nothing is known about the global phylogeny of commensal species and clones. The gut microbiota has so far mainly been studied in relation to diet, use of medication and diseases 7,8 , mostly within countries 9 and in some studies between countries 10,11. These studies have looked at the species or genera composition of the microbiota and the interaction between species, while virtually no details on within species phylogeny have been investigated. The same has been the case for environmental bacteria; there are numerous projects, which have sequenced the metagenome of different niches 12 , but not with much focus on the importance of geographical locations or within species phylogeny. Almost all studies into the within species phylogeny of bacterial species have been conducted using whole genome sequencing of single cultivated isolates. A recent metagenomic study where DNA was isolated both directly from faeces and from isolates cultured from the faeces, demonstrated that most pairs of isolates and metageno...

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“…Unlike the more studied genera of amoeba Acanthamoeba and Entamoeba, which tend to have more defined and constrained dispersal routes, the MLST analysis for N. perurans did not reveal fine scale resolution of population structure [13,18]. When the BURST analysis was considered, the evidence for highly genetically different geographic populations based on changes in conserved genes was further diminished.…”

Section: Discussionmentioning

confidence: 77%

Multilocus Sequence Typing (MLST) and Random Polymorphic DNA (RAPD) Comparisons of Geographic Isolates of Neoparamoeba perurans, the Causative Agent of Amoebic Gill Disease

et al. 2019

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Neoparamoba perurans, is the aetiological agent of amoebic gill disease (AGD), a disease that affects farmed Atlantic salmon worldwide. Multilocus sequence typing (MLST) and Random Amplified Polymorphic DNA (RAPD) are PCR-based typing methods that allow for the highly reproducible genetic analysis of population structure within microbial species. To the best of our knowledge, this study represents the first use of these typing methods applied to N. perurans with the objective of distinguishing geographical isolates. These analyses were applied to a total of 16 isolates from Australia, Canada, Ireland, Scotland, Norway, and the USA. All the samples from Australia came from farm sites on the island state of Tasmania. Genetic polymorphism among isolates was more evident from the RAPD analysis compared to the MLST that used conserved housekeeping genes. Both techniques consistently identified that isolates of N. perurans from Tasmania, Australia were more similar to each other than to the isolates from other countries. While genetic differences were identified between geographical isolates, a BURST analysis provided no evidence of a founder genotype. This suggests that emerging outbreaks of AGD are not due to rapid translocation of this important salmonid pathogen from the same area.

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Study of Streptococcus thermophilus population on a world-wide and historical collection by a new MLST scheme

Cited by 20 publications

References 58 publications

Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species

Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species

Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering

Multilocus Sequence Typing (MLST) and Random Polymorphic DNA (RAPD) Comparisons of Geographic Isolates of Neoparamoeba perurans, the Causative Agent of Amoebic Gill Disease

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