Complete Genome Sequence of Streptococcus thermophilus KLDS 3.1003, A Strain with High Antimicrobial Potential against Foodborne and Vaginal Pathogens

Evivie, Smith Etareri; Li, Bailiang; Xiuyun, Ding; Meng, Yao; Yu, Shangfu; Jincheng, Du; Xu, Min; Li, Wan; Da, Jin; Gui-cheng, Huo; Liu, Fei

doi:10.3389/fmicb.2017.01238

Cited by 16 publications

(12 citation statements)

References 31 publications

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“…Interestingly, only strains JIM 8232, GABA, and NCTC12958 T were found to carry a gene encoding a putative galactofuranosyl-transferase. Finally, genes implicated in the polymerization and translocation of the EPS repeating units have been also identified in all EPS clusters, as reported previously for S. thermophilus strains (Goh et al, 2011;Wu et al, 2014;Cui et al, 2017;Evivie et al, 2017).…”

Section: Biosynthesis Of Epssupporting

confidence: 68%

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: Biosynthesis Of Epssupporting

confidence: 68%

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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“…Brasca et al (2016) investigated 191 S. thermophilus strains isolated from different origins, and only a total of 20 strains (10%) harbored the gadB gene. Among all the strains investigated in this study apart from CS5, CS9, CS18, and CS20 strains, only seven strains ( Supplementary Table S1) were found to contain gadB gene, including B59671, APC151, GABA, KLDS_3.1003, TH1435, ND03, and ACA-DC 2 (Sun et al, 2011;Treu et al, 2014;Alexandraki et al, 2017;Evivie et al, 2017;Linares et al, 2017;Renye et al, 2017). In these seven strains, the GABA synthesis ability of only a few strains was evaluated.…”

Section: Analysis Of γ-Aminobutyric Acid Productionmentioning

confidence: 89%

Genome Analysis and Physiological Characterization of Four Streptococcus thermophilus Strains Isolated From Chinese Traditional Fermented Milk

Cui

Zhang

et al. 2020

Front. Microbiol.

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Streptococcus thermophilus plays important roles in the dairy industry and is widely used as a dairy starter in the production of fermented dairy products. The genomes of S. thermophilus strains CS5, CS9, CS18, and CS20 from fermented milk in China were sequenced and used for biodiversity analysis. In the present study, the phylogenetic analysis of all 34 S. thermophilus genomes publicly available including these four strains reveals that the phylogenetic reconstruction does not match geographic distribution as strains isolated from the same continent are not even clustered on the nearby branches. The core and variable genes were also identified, which vary among strains from 0 to 202. CS9 strain contained 127 unique genes from a variety of distantly related species. It was speculated that CS9 had undergone horizontal gene transfer (HGT) during the long evolutionary process. The safety evaluation of these four strains indicated that none of them contains antibiotic resistance genes and that they are all sensitive to multiple antibiotics. In addition, the strains do not contain any pathogenic virulence factors or plasmids and thus can be considered safe. Furthermore, these strains were investigated in terms of their technological properties including milk acidification, exopolysaccharide (EPS) and γ-aminobutyric acid (GABA) production, and in vitro survival capacity in the gastrointestinal tract. CS9 possesses a special eps gene cluster containing significant traces of HGT, while the eps gene clusters of CS5, CS18, and CS20 are almost the same. The monosaccharide compositional analysis indicated that crude EPS-CS5, EPS-CS9, EPS-CS18, and EPS-CS20 contain similar monosaccharide compositions with different ratios. Furthermore, CS9 was one of a few GABA-producing strains that could ferment glutamate to produce GABA, which is beneficial for improving the acid tolerance of the strain. CS18 has the most potential for the production of fermented food among these four strains because of its fast growth rate, rapid acidifying capacity, and stronger acid and bile salt resistance capacity. This study focused on the genome analysis of the four new S. thermophilus strains to investigate the diversity of strains and provides a reference for selecting excellent strains by use of the genome data.

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“…SOAPnuke and SMRT analysis 2.3.0 software were performed to filter the raw data ( Chin et al, 2013 ). RS_HGAP Assembly3 in SMRT analysis v2.3.0 was employed to assemble the clean Pacbio subreads ( Evivie et al, 2017 ). Then, the assembled fragments were further aligned and corrected with HiSeq clean data using SOAPaligner 2.21, and were further scaffolded and checked to produce a circular chromosome using SSPACE-LongRead ( Khaleque et al, 2017 ).…”

Section: Methodsmentioning

confidence: 99%

Genomic Characterization and Probiotic Potency of Bacillus sp. DU-106, a Highly Effective Producer of L-Lactic Acid Isolated From Fermented Yogurt

Tian

Liang

et al. 2018

Front. Microbiol.

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Bacillus sp. DU-106, a newly isolated member of Bacillus cereus group, exhibits the predominant ability to produce L-lactic acid. The probiotic potency of test strain revealed its survivability at acidic pH, bile salts and viability in simulated gastric juice in vitro. The acute oral toxicity test indicated its no toxicity to laboratory mice in vivo. We further determined the complete genome of strain DU-106 to understand genetic basis as a potential probiotic. It has a circular chromosome and three plasmids for a total genome 5,758,208 bp in size with a G + C content of 35.10%. Genes associated with lactate synthesis were found in the DU-106 genome. We also annotated various stress-related, bile salt resistance, and adhesion-related domains in this strain, which likely provide support in exerting probiotic action by enabling adhesion to host epithelial cells and survival under gastrointestinal tract. Moreover, strain DU-106 genome lacks the virulence genes encodes cereulide synthetase, enterotoxin FM, and cytotoxin K. These phenotypic and genomic probiotic potencies facilitate its potential candidate as probiotic starter in food industry.

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Complete Genome Sequence of Streptococcus thermophilus KLDS 3.1003, A Strain with High Antimicrobial Potential against Foodborne and Vaginal Pathogens

Cited by 16 publications

References 31 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

Genome Analysis and Physiological Characterization of Four Streptococcus thermophilus Strains Isolated From Chinese Traditional Fermented Milk

Genomic Characterization and Probiotic Potency of Bacillus sp. DU-106, a Highly Effective Producer of L-Lactic Acid Isolated From Fermented Yogurt

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