scholarly journals In Silico Prediction of Horizontal Gene Transfer Events in Lactobacillus bulgaricus and Streptococcus thermophilus Reveals Protocooperation in Yogurt Manufacturing

2009 ◽  
Vol 75 (12) ◽  
pp. 4120-4129 ◽  
Author(s):  
Mengjin Liu ◽  
Roland J. Siezen ◽  
Arjen Nauta
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Cluster ◽  
In Silico ◽  
Bacterial Species ◽  
Streptococcus Thermophilus ◽  
Starter Cultures ◽  
Lactobacillus Helveticus ◽  
Lactobacillus Bulgaricus ◽  
Genetic Level

ABSTRACT Lactobacillus bulgaricus and Streptococcus thermophilus, used in yogurt starter cultures, are well known for their stability and protocooperation during their coexistence in milk. In this study, we show that a close interaction between the two species also takes place at the genetic level. We performed an in silico analysis, combining gene composition and gene transfer mechanism-associated features, and predicted horizontally transferred genes in both L. bulgaricus and S. thermophilus. Putative horizontal gene transfer (HGT) events that have occurred between the two bacterial species include the transfer of exopolysaccharide (EPS) biosynthesis genes, transferred from S. thermophilus to L. bulgaricus, and the gene cluster cbs-cblB(cglB)-cysE for the metabolism of sulfur-containing amino acids, transferred from L. bulgaricus or Lactobacillus helveticus to S. thermophilus. The HGT event for the cbs-cblB(cglB)-cysE gene cluster was analyzed in detail, with respect to both evolutionary and functional aspects. It can be concluded that during the coexistence of both yogurt starter species in a milk environment, agonistic coevolution at the genetic level has probably been involved in the optimization of their combined growth and interactions.

In silico prediction of horizontal gene transfer in Streptococcus thermophilus

2011 ◽  
Vol 193 (4) ◽  
pp. 287-297 ◽  
Author(s):  
Catherine Eng ◽  
Annabelle Thibessard ◽  
Morten Danielsen ◽  
Thomas Bovbjerg Rasmussen ◽  
Jean-François Mari ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
In Silico ◽  
Streptococcus Thermophilus ◽  
In Silico Prediction

Effects of different starter cultures on the ripening characteristics of Golot cheese

2020 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Hayriye Sekban ◽  
Zekai Tarakci
Keyword(s):  
Positive Impact ◽  
Starter Culture ◽  
Control Sample ◽  
Streptococcus Thermophilus ◽  
Sensory Properties ◽  
Starter Cultures ◽  
Lactobacillus Helveticus ◽  
Lactobacillus Bulgaricus ◽  
Content Type ◽  
Positive Effects

Purpose The purpose of this study was to investigate the chemical, textural and sensory properties of some starter cultures fruit-added Golot cheese. Design/methodology/approach Six types of Golot cheeses were produced in this study. While the control sample contained no starter cultures, five different starter culture combinations (GS1: Streptococcus thermophilus, Lactococcus lactis subsp. cremoris, L. lactis subsp. lactis and Lactobacillus bulgaricus; GS2: S. thermophilus and L. bulgaricus; GS3: S. thermophilus; GS4: S. thermophilus and Lactobacillus helveticus; and GS5: S. thermophilus, L. lactis subsp. cremoris and L. lactis subsp. lactis) were applied to the other cheese samples using an immersion technique. Then, all cheeses were vacuum-packed and ripened at 4 ± 1°C for three months and their chemical, biochemical, sensory and textural analyses were performed on the 2nd, 15th, 30th, 60th and 90th days of ripening. Findings Results indicated that generally starter cultures have positive effects on the chemical, biochemical and sensory properties of Golot cheese. Considering the final values, the addition of starter cultures enhanced the ripening index of Golot cheeses (8.4%–9.2%), except the GS3 (7.4%), compared to the control (8.1%). At the end of the ripening period, meltability values of GS4 (16.5 mm) cultured cheeses were higher than those of other cultured cheeses (13.0–15.5 mm) and control cheese (14.5 mm). While lipolysis values were low in fresh cheese, it increased during ripening. Overall, GS3 (2.46 acid degree value [ADV]) and GS4 (2.40 ADV) had the highest lipolysis rate, while GS1 (2.14 ADV) had the lowest (p = 0.07). Electrophoretograms indicated that the highest fragmentation of α- and ß-casein occurred in GS5 (48.43%) and GS1 (44.24%), respectively. Also, GS5 was the most appreciated and preferred cheese in terms of sensory. Regarding texture, hardness, cohesiveness, adhesiveness, springiness and gumminess values were determined to be statistically important in terms of ripening time and cheese variety (p < 0.01). Originality/value Consequently, all starters had a positive impact on Golot cheese samples and among all S. thermophilus and L. helveticus starter were determined to be the most applicable one considering ripening, texture, sensory and melting properties.

scholarly journals Looking for the X Factor in Bacterial Pathogenesis: Association of orfX-p47 Gene Clusters with Toxin Genes in Clostridial and Non-Clostridial Bacterial Species

Toxins ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 19 ◽  
Author(s):  
Maria B. Nowakowska ◽  
François P. Douillard ◽  
Miia Lindström
Keyword(s):  
Gene Cluster ◽  
In Silico ◽  
Botulinum Neurotoxin ◽  
Bacterial Species ◽  
Gene Clusters ◽  
Bacterial Pathogenesis ◽  
Toxin Gene ◽  
Toxin Complex ◽  
Analytical Tools ◽  
Bacillus Isolate

The botulinum neurotoxin (BoNT) has been extensively researched over the years in regard to its structure, mode of action, and applications. Nevertheless, the biological roles of four proteins encoded from a number of BoNT gene clusters, i.e., OrfX1-3 and P47, are unknown. Here, we investigated the diversity of orfX-p47 gene clusters using in silico analytical tools. We show that the orfX-p47 cluster was not only present in the genomes of BoNT-producing bacteria but also in a substantially wider range of bacterial species across the bacterial phylogenetic tree. Remarkably, the orfX-p47 cluster was consistently located in proximity to genes coding for various toxins, suggesting that OrfX1-3 and P47 may have a conserved function related to toxinogenesis and/or pathogenesis, regardless of the toxin produced by the bacterium. Our work also led to the identification of a putative novel BoNT-like toxin gene cluster in a Bacillus isolate. This gene cluster shares striking similarities to the BoNT cluster, encoding a bont/ntnh-like gene and orfX-p47, but also differs from it markedly, displaying additional genes putatively encoding the components of a polymorphic ABC toxin complex. These findings provide novel insights into the biological roles of OrfX1, OrfX2, OrfX3, and P47 in toxinogenesis and pathogenesis of BoNT-producing and non-producing bacteria.

scholarly journals An Evolutionary Link between Natural Transformation and CRISPR Adaptive Immunity

mBio ◽  
2012 ◽  
Vol 3 (5) ◽  
Author(s):  
Peter Jorth ◽  
Marvin Whiteley
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Bacterial Diversity ◽  
Natural Transformation ◽  
Bacterial Species ◽  
Comparative Genomic ◽  
Content Type ◽  
Immune Systems ◽  
Adaptive Immune ◽  
Adaptive Immune Systems

ABSTRACTNatural transformation by competent bacteria is a primary means of horizontal gene transfer; however, evidence that competence drives bacterial diversity and evolution has remained elusive. To test this theory, we used a retrospective comparative genomic approach to analyze the evolutionary history ofAggregatibacter actinomycetemcomitans, a bacterial species with both competent and noncompetent sister strains. Through comparative genomic analyses, we reveal that competence is evolutionarily linked to genomic diversity and speciation. Competence loss occurs frequently during evolution and is followed by the loss of clustered regularly interspaced short palindromic repeats (CRISPRs), bacterial adaptive immune systems that protect against parasitic DNA. Relative to noncompetent strains, competent bacteria have larger genomes containing multiple rearrangements. In contrast, noncompetent bacterial genomes are extremely stable but paradoxically susceptible to infective DNA elements, which contribute to noncompetent strain genetic diversity. Moreover, incomplete noncompetent strain CRISPR immune systems are enriched for self-targeting elements, which suggests that the CRISPRs have been co-opted for bacterial gene regulation, similar to eukaryotic microRNAs derived from the antiviral RNA interference pathway.IMPORTANCEThe human microbiome is rich with thousands of diverse bacterial species. One mechanism driving this diversity is horizontal gene transfer by natural transformation, whereby naturally competent bacteria take up environmental DNA and incorporate new genes into their genomes. Competence is theorized to accelerate evolution; however, attempts to test this theory have proved difficult. Through genetic analyses of the human periodontal pathogenAggregatibacter actinomycetemcomitans, we have discovered an evolutionary connection between competence systems promoting gene acquisition and CRISPRs (clustered regularly interspaced short palindromic repeats), adaptive immune systems that protect bacteria against genetic parasites. We show that competentA. actinomycetemcomitansstrains have numerous redundant CRISPR immune systems, while noncompetent bacteria have lost their CRISPR immune systems because of inactivating mutations. Together, the evolutionary data linking the evolution of competence and CRISPRs reveals unique mechanisms promoting genetic heterogeneity and the rise of new bacterial species, providing insight into complex mechanisms underlying bacterial diversity in the human body.

scholarly journals Acquisition of Beta-Lactamase by Neisseria meningitidis through Possible Horizontal Gene Transfer

2018 ◽  
Vol 62 (9) ◽  
Author(s):  
Eva Hong ◽  
Ala-Eddine Deghmane ◽  
Muhamed-Kheir Taha
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genome Sequencing ◽  
Meningococcal Disease ◽  
Bacterial Species ◽  
Whole Genome ◽  
Beta Lactamase ◽  
Content Type ◽  
Beta Lactamases ◽  
Lactamase Gene

ABSTRACT We report the detection in France of a beta-lactamase-producing invasive meningococcal isolate. Whole-genome sequencing of the isolate revealed a ROB-1-type beta-lactamase gene that is frequently encountered in Haemophilus influenzae, suggesting horizontal transfer between isolates of these bacterial species. Beta-lactamases are exceptional in meningococci, with no reports for more than 2 decades. This report is worrying, as the expansion of such isolates may jeopardize the effective treatment against invasive meningococcal disease.

Yeasts as Primary Contaminants in Yogurts Produced Commercially in Lagos, Nigeria

1987 ◽  
Vol 50 (3) ◽  
pp. 193-198 ◽  
Author(s):  
MINABELEMA DUBLIN GREEN ◽  
STELLA N. IBE
Keyword(s):  
Streptococcus Thermophilus ◽  
Maximum Growth ◽  
Starter Cultures ◽  
Lactobacillus Bulgaricus ◽  
Contamination Level ◽  
Psychrotrophic Bacteria ◽  
Retail Outlets ◽  
Candida Lusitaniae ◽  
Aspergillus Sp ◽  
Initial Contamination

Yogurt samples purchased from a dairy industry, retail outlets, and hawkers in Lagos, Nigeria, were plated on potato dextrose agar containing 100 μg of chloramphenicol/ml and found to contain Candida lusitaniae, C krusei, C rugosa, Kluveromyces fragilis, and Saccharomyces cerevisiae as the primary yeast contaminants. Sixty-seven percent of the samples had yeast counts in the range of 104–106 cfu/ml. C. lusitaniae, K. fragilis and C. krusei had the highest counts and occurrence of 65, 48 and 51%, respectively, in 100 random yogurt samples. C. lusitaniae attained the highest count in yogurts stored at 10°C and C. krusei in those at 30°C. Ninety percent of the samples had less than 10 coliforms or staphylococci per ml, whereas 20% had over 103 psychrotrophic bacteria per ml. Molds of Aspergillus sp. and Neurospora sp. were isolated mainly from the strawberry-fluid yogurt. The starter cultures, Lactobacillus bulgaricus and Streptococcus thermophilus, were present in the ratio of 1:1 and reached maximum growth levels of 107 to 108 cfu/ml after 4 to 8 d of storage at 10°C, whereas the yeast continued to increase beyond this level by the 12th day. The extent of contamination observed suggests high initial contamination level and improper refrigeration of yogurts marketed.

scholarly journals A Cryptic Non-Inducible Prophage Confers Phage-Immunity on the Streptococcus thermophilus M17PTZA496

Viruses ◽  
2018 ◽  
Vol 11 (1) ◽  
pp. 7 ◽  
Author(s):  
Vinícius da Silva Duarte ◽  
Sabrina Giaretta ◽  
Stefano Campanaro ◽  
Laura Treu ◽  
Andrea Armani ◽  
...  
Keyword(s):  
Mitomycin C ◽  
Defense Mechanisms ◽  
Large Subunit ◽  
Bacterial Species ◽  
Dairy Industry ◽  
Model Organism ◽  
Streptococcus Thermophilus ◽  
Starter Cultures ◽  
Economic Losses ◽  
Important Species

Streptococcus thermophilus is considered one of the most important species for the dairy industry. Due to their diffusion in dairy environments, bacteriophages can represent a threat to this widely used bacterial species. Despite the presence of a CRISPR-Cas system in the S. thermophilus genome, some lysogenic strains harbor cryptic prophages that can increase the phage-host resistance defense. This characteristic was identified in the dairy strain S. thermophilus M17PTZA496, which contains two integrated prophages 51.8 and 28.3 Kb long, respectively. In the present study, defense mechanisms, such as a lipoprotein-encoding gene and Siphovirus Gp157, the last associated to the presence of a noncoding viral DNA element, were identified in the prophage M17PTZA496 genome. The ability to overexpress genes involved in these defense mechanisms under specific stressful conditions, such as phage attack, has been demonstrated. Despite the addition of increasing amounts of Mitomycin C, M17PTZA496 was found to be non-inducible. However, the transcriptional activity of the phage terminase large subunit was detected in the presence of the antagonist phage vB_SthS-VA460 and of Mitomycin C. The discovery of an additional immune mechanism, associated with bacteriophage-insensitive strains, is of utmost importance, for technological applications and industrial processes. To our knowledge, this is the first study reporting the capability of a prophage integrated into the S. thermophilus genome expressing different phage defense mechanisms. Bacteriophages are widespread entities that constantly threaten starter cultures in the dairy industry. In cheese and yogurt manufacturing, the lysis of Streptococcus thermophilus cultures by viral attacks can lead to huge economic losses. Nowadays S. thermophilus is considered a well-stablished model organism for the study of natural adaptive immunity (CRISPR-Cas) against phage and plasmids, however, the identification of novel bacteriophage-resistance mechanisms, in this species, is strongly desirable. Here, we demonstrated that the presence of a non-inducible prophage confers phage-immunity to an S. thermophilus strain, by the presence of ltp and a viral noncoding region. S. thermophilus M17PTZA496 arises as an unconventional model to study phage resistance and potentially represents an alternative starter strain for dairy productions.

scholarly journals Unleashing Natural Competence in Lactococcus lactis by Induction of the Competence Regulator ComX

2017 ◽  
Vol 83 (20) ◽  
Author(s):  
Joyce Mulder ◽  
Michiel Wels ◽  
Oscar P. Kuipers ◽  
Michiel Kleerebezem ◽  
Peter A. Bron
Keyword(s):  
Lactococcus Lactis ◽  
Genetic Manipulation ◽  
Bacterial Species ◽  
Streptococcus Thermophilus ◽  
Starter Cultures ◽  
Natural Competence ◽  
Content Type ◽  
Competence Gene ◽  
Gene Sets ◽  
Novel Traits

ABSTRACT In biotechnological workhorses like Streptococcus thermophilus and Bacillus subtilis, natural competence can be induced, which facilitates genetic manipulation of these microbes. However, in strains of the important dairy starter Lactococcus lactis, natural competence has not been established to date. However, in silico analysis of the complete genome sequences of 43 L. lactis strains revealed complete late competence gene sets in 2 L. lactis subsp. cremoris strains (KW2 and KW10) and at least 10 L. lactis subsp. lactis strains, including the model strain IL1403 and the plant-derived strain KF147. The remainder of the strains, including all dairy isolates, displayed genomic decay in one or more of the late competence genes. Nisin-controlled expression of the competence regulator comX in L. lactis subsp. lactis KF147 resulted in the induction of expression of the canonical competence regulon and elicited a state of natural competence in this strain. In contrast, comX expression in L. lactis NZ9000, which was predicted to encode an incomplete competence gene set, failed to induce natural competence. Moreover, mutagenesis of the comEA-EC operon in strain KF147 abolished the comX-driven natural competence, underlining the involvement of the competence machinery. Finally, introduction of nisin-inducible comX expression into nisRK-harboring derivatives of strains IL1403 and KW2 allowed the induction of natural competence in these strains also, expanding this phenotype to other L. lactis strains of both subspecies. IMPORTANCE Specific bacterial species are able to enter a state of natural competence in which DNA is taken up from the environment, allowing the introduction of novel traits. Strains of the species Lactococcus lactis are very important starter cultures for the fermentation of milk in the cheese production process, where these bacteria contribute to the flavor and texture of the end product. The activation of natural competence in this industrially relevant organism can accelerate research aiming to understand industrially relevant traits of these bacteria and can facilitate engineering strategies to harness the natural biodiversity of the species in optimized starter strains.

scholarly journals Yogurt Produced by Novel Natural Starter Cultures Improves Gut Epithelial Barrier In Vitro

2020 ◽  
Vol 8 (10) ◽  
pp. 1586 ◽  
Author(s):  
Nikola Popović ◽  
Emilija Brdarić ◽  
Jelena Đokić ◽  
Miroslav Dinić ◽  
Katarina Veljović ◽  
...  
Keyword(s):  
Dairy Product ◽  
Starter Culture ◽  
Streptococcus Thermophilus ◽  
Starter Cultures ◽  
Added Value ◽  
Lactobacillus Bulgaricus ◽  
Intestinal Epithelial ◽  
Beneficial Effects ◽  
Health Promoting

Yogurt is a traditional fermented dairy product, prepared with starter cultures containing Streptococcus thermophilus and Lactobacillus bulgaricus that has gained widespread consumer acceptance as a healthy food. It is widely accepted that yogurt cultures have been recognized as probiotics, due to their beneficial effects on human health. In this study, we have characterized technological and health-promoting properties of autochthonous strains S. thermophilus BGKMJ1-36 and L. bulgaricus BGVLJ1-21 isolated from artisanal sour milk and yogurt, respectively, in order to be used as functional yogurt starter cultures. Both BGKMJ1-36 and BGVLJ1-21 strains have the ability to form curd after five hours at 42 °C, hydrolyze αs1-, β-, and κ- casein, and to show antimicrobial activity toward Listeria monocytogenes. The strain BGKMJ1-36 produces exopolysaccharides important for rheological properties of the yogurt. The colonies of BGKMJ1-36 and BGVLJ1-21 strains that successfully survived transit of the yogurt through simulated gastrointestinal tract conditions have been tested for adhesion to intestinal epithelial Caco-2 cells. The results reveal that both strains adhere to Caco-2 cells and significantly upregulate the expression of autophagy-, tight junction proteins-, and anti-microbial peptides-related genes. Hence, both strains may be interesting for use as a novel functional starter culture for production of added-value yogurt with health-promoting properties.

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