Complete Genome Sequence of the Industrial Fast-Acidifying Strain Streptococcus thermophilus N4L (original) (raw)
Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus
Nature Biotechnology, 2004
The lactic acid bacterium Streptococcus thermophilus is widely used for the manufacture of yogurt and cheese. This dairy species of major economic importance is phylogenetically close to pathogenic streptococci, raising the possibility that it has a potential for virulence. Here we report the genome sequences of two yogurt strains of S. thermophilus. We found a striking level of gene decay (10% pseudogenes) in both microorganisms. Many genes involved in carbon utilization are nonfunctional, in line with the paucity of carbon sources in milk. Notably, most streptococcal virulence-related genes that are not involved in basic cellular processes are either inactivated or absent in the dairy streptococcus. Adaptation to the constant milk environment appears to have resulted in the stabilization of the genome structure. We conclude that S. thermophilus has evolved mainly through loss-of-function events that remarkably mirror the environment of the dairy niche resulting in a severely diminished pathogenic potential.
Genomic Analysis of Dairy Starter Culture Streptococcus thermophilus MTCC 5461
Journal of Microbiology and Biotechnology, 2013
The lactic acid bacterium Streptococcus thermophilus is widely used as a starter culture for the production of dairy products. Whole-genome sequencing is expected to utilize the genetic basis behind the metabolic functioning of lactic acid bacterium (LAB), for development of their use in biotechnological and probiotic applications. We sequenced the whole genome of Streptococcus thermophilus MTCC 5461, the strain isolated from a curd source, by 454 GS-FLX titanium and Ion Torrent PGM. We performed comparative genome analysis using the local BLAST and RDP for 16S rDNA comparison and by the RAST server for functional comparison against the published genome sequence of Streptococcus thermophilus CNRZ 1066. The whole genome size of S. thermophilus MTCC 5461 is of 1.73 Mb size with a GC content of 39.3%. Streptococcal virulence-related genes are either inactivated or absent in the strain. The genome possesses coding sequences for features important for a probiotic organism such as adhesion, acid tolerance, bacteriocin production, and lactose utilization, which was found to be conserved among the strains MTCC 5461 and CNRZ 1066. Biochemical analysis revealed the utilization of 17 sugars by the bacterium, where the presence of genes encoding enzymes involved in metabolism for 16 of these 17 sugars were confirmed in the genome. This study supports the facts that the strain MTCC 5461 is nonpathogenic and harbors essential features that can be exploited for its probiotic potential.
The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2
Standards in genomic sciences, 2017
Streptococcus thermophilus ACA-DC 2 is a newly sequenced strain isolated from traditional Greek yogurt. Among the 14 fully sequenced strains of S. thermophilus currently deposited in the NCBI database, the ACA-DC 2 strain has the smallest chromosome, containing 1,731,838 bp. The annotation of its genome revealed the presence of 1,850 genes, including 1,556 protein-coding genes, 70 RNA genes and 224 potential pseudogenes. A large number of pseudogenes were identified. This was also accompanied by the absence of pathogenic features suggesting evolution of strain ACA-DC 2 through genome decay processes, most probably due to adaptation to the milk ecosystem. Analysis revealed the existence of one complete lactose-galactose operon, several proteolytic enzymes, one exopolysaccharide cluster, stress response genes and four putative antimicrobial peptides. Interestingly, one CRISPR-cas system and one orphan CRISPR, both carrying only one spacer, were predicted indicating low activity or ina...
Frontiers in Microbiology, 2017
Lactic acid bacteria play increasingly important roles in the food industry. Streptococcus thermophilus KLDS 3.1003 strain was isolated from traditional yogurt in Inner Mongolia, China. It has shown high antimicrobial activity against selected foodborne and vaginal pathogens. In this study, we investigated and analyzed its complete genome sequence. The S. thermophilus KLDS 3.1003 genome comprise of a 1,899,956 bp chromosome with a G+C content of 38.92%, 1,995 genes, and 6 rRNAs. With the exception of S. thermophilus M17TZA496, S. thermophilus KLDS 3.1003 has more tRNAs (amino acid coding genes) compared to some S. thermophilus strains available on the National Centre for Biotechnology Information database. MG-RAST annotation showed that this strain has 317 subsystems with most genes associated with amino acid and carbohydrate metabolism. This strain also has a unique EPS gene cluster containing 23 genes, and may be a mixed dairy starter culture. This information provides more insight into the molecular basis of its potentials for further applications in the dairy and allied industries.
Current Science
Genomic analysis of Streptococcus thermophilus strain MTCC 5460, an isolate from market dahi (curd), revealed particular gene features that contributed towards its adaptation to a dairy-specific niche. The genome comprising 1.6 Mb, encoding 1809 genes, revealed the presence of genes involved in lactose/ galactose utilization; well-developed proteolytic system including cell envelop proteinases and several transporters; and bacteriocin synthesis and competence proteins involved in defence mechanism, which help prevent food spoilage. The genome comprised genes for stress resistance property of the strain, contributing to its gut endurance and gene encoding formation of aroma compounds. Unlike pathogenic streptococci, genes for virulence property were absent in the genome. Overall, the study revealed features within the genome that enabled the organism to survive in a gastric environment and assisted in its interaction with the host microbiota and mucosa, thus, validating the strain as a potent functional dairy starter and a promising candidate for potential probiotic applications.
Genome Sequences of Four Italian Streptococcus thermophilus Strains of Dairy Origin
Genome Announcements, 2014
This report describes the genome sequences of four Streptococcus thermophilus strains, namely, TH982, TH985, TH1477, and 1F8CT, isolated from different dairy environments from the Campania and the Veneto regions in Italy. These data are aimed at increasing the genomic information available on this species, which is of paramount importance for the dairy industry.
Food Microbiology, 2017
Eight Streptococcus thermophilus strains of dairy origin isolated in Italy were chosen to investigate autochthonous bacterial diversity in this important technological species. In the present study a comparative analysis of all the 17 S. thermophilus genomes publicly available was performed to identify the core and the variable genes, which vary among strains from 196 to 265. Additionally, correlation between the isolation site and the genetic distance was investigated at genomic level. Results highlight that the phylogenetic reconstruction differs from the geographical strain distribution. Moreover, strain M17PTZA496 has a genome of 2.15 Mbp, notably larger than that of the others, determined by lateral gene transfer (including phage-mediated incorporation) and duplication events. Important technological characters, such as growth kinetics, bacteriocin production, acidification kinetics and surface adhesion capability were studied in all the Italian strains. Results indicate a wide range of variability in adhesion properties that significantly clustered strains into four groups. Genomic differences among strains in relation to these characters were identified but a clear correlation between genotype and phenotype was not always found since most of the genomic modifications arise from single nucleotide polymorphisms. This research represents a step forward in the identification of strains-specific functions in Streptococcus thermophilus and it
Scientific Reports, 2014
Streptococcus thermophilus ASCC 1275 (ST 1275), a typical dairy starter bacterium, yields the highest known amount (,1,000 mg/L) of exopolysaccharide (EPS) in milk among the species of S. thermophilus. The addition of this starter in milk fermentation exhibited texture modifying properties for fermented dairy foods such as yogurt and cheese in the presence of EPS as its important metabolite. In this genomic study, a novel eps gene cluster for EPS assembly of repeating unit has been reported. It contains two-pair epsC-epsD genes which are assigned to determine the chain length of EPS. This also suggests this organism produces two types of EPSs-capsular and ropy EPS, as observed in our previous studies. Additionally, ST 1275 appears to exhibit effective proteolysis system and sophisticated stress response systems to stressful conditions, and has the highest number of four separate CRISPR/Cas loci. These features may be conducive to milk adaptation of this starter and against undesirable bacteriophage infections which leads to failure of milk fermentation. Insights into the genome of ST 1275 suggest that this strain may be a model high EPS-producing dairy starter. C onventional dairy starter bacteria including Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus and Lactococcus lactis have a long history of use in the home-made and modern manufacture of fermented dairy foods, i.e., yogurt and cheese 1,2. These dairy starters are able to ferment milk lactose to produce lactic acid which decreases the pH to 4.5 , 4.7 resulting in the coagulation of milk proteins 3,4. Among these important conventional starters, S. thermophilus is a non-pathogenic and homofermentative facultative anaerobe, which is used for the manufacture of yogurt and certain types of cheese. There has been an increasing interest in using a novel EPS-producing S. thermophilus for enhancing functionalities of yogurt and cheeses 5-9. Until April 2014, six strains of S. thermophilus have been fully sequenced and their whole-genome sequence data are released in the NCBI Genome database 10-14. Comparative genome analysis of dairy S. thermophilus suggests that their proteolytic activity, nitrogen metabolism, sugar utilization and transporter systems play crucial roles for their adaptation to milk environments 7,12,15. In addition to the ''generally recognized as safe'' status of dairy S. thermophilus through loss-of function events such as decay and loss of virulence determinants during evolution, both lateral gene transfer (LGT) and natural competence contribute to the shaping of S. thermophilus genome. This kind of evolution results in diverse metabolic activities and gives new functionalities to dairy foods 10,16. Common features of dairy S. thermophilus include rapid acidification of milk, acid tolerance, bacteriocin synthesis, lactose utilization, production of formic and folic acids, innate and adaptive immunity, bacteriophage resistance, and most importantly, exopolysaccharide (EPS) biosynthesis 7,15. These features are important for dairy S. thermophilus as starter bacterium for its applications in milk fermentation. Extracellular polysaccharide, also known as exopolysaccharide (EPS), produced by lactic acid bacteria (LAB) including S. thermophilus is generally regarded as a food-grade as it is naturally produced 5,8,9. EPS may be secreted into the medium as ropy EPS, or may be attached to cell surface of the microorganism in the form of capsular EPS 8. EPS has been reported to improve the viscosity and texture of yogurt and some cheeses, and to prevent syneresis in yogurt 5,8,17-21. Moreover, EPS produced by dairy LAB is able to replace chemically modified starches or milk fat in commercial yogurt, especially set-type yogurt, to give considerable rheological effects, mouthfeel, and creaminess to fermented milk products 5,20,21. Certain EPSs have also been reported to have some important
FEMS Microbiology Reviews, 2005
Streptococcus thermophilus is a major dairy starter used for the manufacture of yoghurt and cheese. The access to three genome sequences, comparative genomics and multilocus sequencing analyses suggests that this species recently emerged and is still undergoing a process of regressive evolution towards a specialised bacterium for growth in milk. Notably, S. thermophilus has maintained a well-developed nitrogen metabolism whereas its sugar catabolism has been subjected to a high level of degeneracy due to a paucity of carbon sources in milk. Furthermore, while pathogenic streptococci are recognised for a high capacity to expose proteins at their cell surface in order to achieve cell adhesion or to escape the host immune system, S. thermophilus has nearly lost this unique feature as well as many virulence-related functions. Although gene decay is obvious in S. thermophilus genome evolution, numerous small genomic islands, which were probably acquired by horizontal gene transfer, comprise important industrial phenotypic traits such as polysaccharide biosynthesis, bacteriocin production, restriction-modification systems or oxygen tolerance.
Frontiers in Microbiology, 2019
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