scholarly journals Novel Variants of Streptococcus thermophilus Bacteriophages Are Indicative of Genetic Recombination among Phages from Different Bacterial Species

2016 ◽  
Vol 83 (5) ◽  
Author(s):  
Paula Szymczak ◽  
Thomas Janzen ◽  
Ana Rute Neves ◽  
Witold Kot ◽  
Lars H. Hansen ◽  
...  
Keyword(s):  
Genetic Recombination ◽  
Genetic Relationships ◽  
Bacterial Species ◽  
Streptococcus Thermophilus ◽  
Starter Cultures ◽  
Sequencing Analysis ◽  
Content Type ◽  
Novel Variants ◽  
Positive Results

ABSTRACT Bacteriophages are the main cause of fermentation failures in dairy plants. The majority of Streptococcus thermophilus phages can be divided into either cos- or pac-type phages and are additionally characterized by examining the V2 region of their antireceptors. We screened a large number of S. thermophilus phages from the Chr. Hansen A/S collection, using PCR specific for the cos- or pac-type phages, as well as for the V2 antireceptor region. Three phages did not produce positive results with the assays. Analysis of phage morphologies indicated that two of these phages, CHPC577 and CHPC926, had shorter tails than the traditional S. thermophilus phages. The third phage, CHPC1151, had a tail size similar to those of the cos- or pac-type phages, but it displayed a different baseplate structure. Sequencing analysis revealed the genetic similarity of CHPC577 and CHPC926 with a subgroup of Lactococcus lactis P335 phages. Phage CHPC1151 was closely related to the atypical S. thermophilus phage 5093, homologous with a nondairy streptococcal prophage. By testing adsorption of the related streptococcal and lactococcal phages to the surface of S. thermophilus and L. lactis strains, we revealed the possibility of cross-interactions. Our data indicated that the use of S. thermophilus together with L. lactis, extensively applied for dairy fermentations, triggered the recombination between phages infecting different bacterial species. A notable diversity among S. thermophilus phage populations requires that a new classification of the group be proposed. IMPORTANCE Streptococcus thermophilus is a component of thermophilic starter cultures commonly used for cheese and yogurt production. Characterizing streptococcal phages, understanding their genetic relationships, and studying their interactions with various hosts are the necessary steps for preventing and controlling phage attacks that occur during dairy fermentations.

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 Identification of isolated or mixed strains from long reads: a challenge met on Streptococcus thermophilus using a MinION sequencer

2021 ◽  
Vol 7 (11) ◽  
Author(s):  
Grégoire Siekaniec ◽  
Emeline Roux ◽  
Téo Lemane ◽  
Eric Guédon ◽  
Jacques Nicolas
Keyword(s):  
Memory Management ◽  
Bacterial Species ◽  
Streptococcus Thermophilus ◽  
Bacterial Strains ◽  
Content Type ◽  
Long Reads ◽  
Detailed Classification ◽  
Long Read ◽  
Identification Of Bacteria

This study aimed to provide efficient recognition of bacterial strains on personal computers from MinION (Nanopore) long read data. Thanks to the fall in sequencing costs, the identification of bacteria can now proceed by whole genome sequencing. MinION is a fast, but highly error-prone sequencing device and it is a challenge to successfully identify the strain content of unknown simple or complex microbial samples. It is heavily constrained by memory management and fast access to the read and genome fragments. Our strategy involves three steps: indexing of known genomic sequences for a given or several bacterial species; a request process to assign a read to a strain by matching it to the closest reference genomes; and a final step looking for a minimum set of strains that best explains the observed reads. We have applied our method, called ORI, on 77 strains of Streptococcus thermophilus . We worked on several genomic distances and obtained a detailed classification of the strains, together with a criterion that allows merging of what we termed ‘sibling’ strains, only separated by a few mutations. Overall, isolated strains can be safely recognized from MinION data. For mixtures of several non-sibling strains, results depend on strain abundance.

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 Genomic Characterization of VIM Metallo-β-Lactamase-Producing Alcaligenes faecalis from Gaza, Palestine

2017 ◽  
Vol 61 (11) ◽  
Author(s):  
Nahed Al Laham ◽  
Kalyan D. Chavda ◽  
Astrid V. Cienfuegos-Gallet ◽  
Barry N. Kreiswirth ◽  
Liang Chen
Keyword(s):  
Bacterial Species ◽  
Alcaligenes Faecalis ◽  
Gram Negative Bacteria ◽  
Sequencing Analysis ◽  
Large Hospital ◽  
Content Type ◽  
Next Generation Sequencing Analysis ◽  
Genomic Characterization ◽  
Generation Sequencing

ABSTRACT Carbapenemase-producing Gram-negative bacteria (CP-GNB) have increasingly spread worldwide, and different families of carbapenemases have been identified in various bacterial species. Here, we report the identification of five VIM metallo-β-lactamase-producing Alcaligenes faecalis isolates associated with a small outbreak in a large hospital in Gaza, Palestine. Next-generation sequencing analysis showed bla VIM-2 is harbored by a chromosomal genomic island among three strains, while bla VIM-4 is carried by a novel plasmid in two strains.

scholarly journals Metaproteomics Analysis Reveals the Adaptation Process for the Chicken Gut Microbiota

2013 ◽  
Vol 80 (2) ◽  
pp. 478-485 ◽  
Author(s):  
Yue Tang ◽  
Anthony Underwood ◽  
Adriana Gielbert ◽  
Martin J. Woodward ◽  
Liljana Petrovska
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
High Throughput Sequencing ◽  
Bacterial Species ◽  
Abundant Species ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Content Type ◽  
Chicken Gut Microbiota

ABSTRACTThe animal gastrointestinal tract houses a large microbial community, the gut microbiota, that confers many benefits to its host, such as protection from pathogens and provision of essential metabolites. Metagenomic approaches have defined the chicken fecal microbiota in other studies, but here, we wished to assess the correlation between the metagenome and the bacterial proteome in order to better understand the healthy chicken gut microbiota. Here, we performed high-throughput sequencing of 16S rRNA gene amplicons and metaproteomics analysis of fecal samples to determine microbial gut composition and protein expression. 16 rRNA gene sequencing analysis identifiedClostridiales,Bacteroidaceae, andLactobacillaceaespecies as the most abundant species in the gut. For metaproteomics analysis, peptides were generated by using the Fasp method and subsequently fractionated by strong anion exchanges. Metaproteomics analysis identified 3,673 proteins. Among the most frequently identified proteins, 380 proteins belonged toLactobacillusspp., 155 belonged toClostridiumspp., and 66 belonged toStreptococcusspp. The most frequently identified proteins were heat shock chaperones, including 349 GroEL proteins, from many bacterial species, whereas the most abundant enzymes were pyruvate kinases, as judged by the number of peptides identified per protein (spectral counting). Gene ontology and KEGG pathway analyses revealed the functions and locations of the identified proteins. The findings of both metaproteomics and 16S rRNA sequencing analyses are discussed.

scholarly journals Unleashing natural competence inLactococcus lactisby induction of the competence regulator ComX

2017 ◽  
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 ◽  
Competence Gene ◽  
Gene Sets ◽  
Novel Traits ◽  
Derivatives Of

AbstractIn biotechnological work horses likeStreptococcus thermophilusandBacillus subtilisnatural competence can be induced, which facilitates genetic manipulation of these microbes. However, in strains of the important dairy starterLactococcus lactisnatural competence has not been established to date. However,in silicoanalysis of complete genome sequences of 43L. lactisstrains revealed complete late-competence gene-sets in 2L. lactissubspeciescremorisstrains (KW2 and KW10) and 8L. lactissubspecieslactisstrains, 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 regulatorcomXinL. lactissubsp.lactisKF147 resulted in the induction of expression of the canonical competence regulon, and elicited a state of natural competence in this strain. By contrast,comXexpression inL. lactisNZ9000, predicted to encode an incomplete competence gene-set, failed to induce natural competence. Moreover, mutagenesis of thecomEA-ECoperon in strain KF147, abolished thecomXdriven natural competence, underpinning the involvement of the competence machinery. Finally, introduction of nisin-induciblecomXexpression intonisRK-harboring derivatives of strains IL1403 and KW2 allowed the induction of natural competence also in these strains, expanding this phenotype to otherL. lactisstrains of both subspecies.Significance statementSpecific 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 speciesLactococcus lactisare 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 Cell Wall Glycans Mediate Recognition of the Dairy BacteriumStreptococcus thermophilusby Bacteriophages

2018 ◽  
Vol 84 (23) ◽  
Author(s):  
Paula Szymczak ◽  
Sérgio Raposo Filipe ◽  
Gonçalo Covas ◽  
Finn Kvist Vogensen ◽  
Ana Rute Neves ◽  
...  
Keyword(s):  
Cell Wall ◽  
Cell Surface ◽  
Streptococcus Thermophilus ◽  
Starter Cultures ◽  
Host Recognition ◽  
Structured Illumination ◽  
Sequencing Data ◽  
Structured Illumination Microscopy ◽  
Content Type ◽  
Type Phage

ABSTRACTReceptors on the cell surfaces of bacterial hosts are essential during the infection cycle of bacteriophages. To date, the phage receptors of the industrial relevant dairy starter bacteriumStreptococcus thermophilusremain elusive. Thus, we set out to identify cell surface structures that are involved in host recognition by dairy streptococcal phages. Five industrialS. thermophilusstrains sensitive to different phages (pactype,costype, and the new type 987), were selected to generate spontaneous bacteriophage-insensitive mutants (BIMs). Of these, approximately 50% were deselected as clustered regularly interspaced short palindromic repeat (CRISPR) mutants, while the other pool was further characterized to identify receptor mutants. On the basis of genome sequencing data, phage resistance in putative receptor mutants was attributed to nucleotide changes in genes encoding glycan biosynthetic pathways. Superresolution structured illumination microscopy was used to visualize the interactions betweenS. thermophilusand its phages. The phages were either regularly distributed along the cells or located at division sites of the cells. The cell wall structures mediating the latter type of phage adherence were further analyzed via phenotypic and biochemical assays. Altogether, our data suggested that phage adsorption toS. thermophilusis mediated by glycans associated with the bacterial cell surface. Specifically, thepac-type phage CHPC951 adsorbed to polysaccharides anchored to peptidoglycan, while the 987-type phage CHPC926 recognized exocellular polysaccharides associated with the cell surface.IMPORTANCEStreptococcus thermophilusis widely used in starter cultures for cheese and yoghurt production. During dairy fermentations, infections of bacteria with bacteriophages result in acidification failures and a lower quality of the final products. An understanding of the molecular factors involved in phage-host interactions, in particular, the phage receptors in dairy bacteria, is a crucial step for developing better strategies to prevent phage infections in dairy plants.

scholarly journals Whole-Genome Sequencing Analysis of Salmonella enterica Serovar Enteritidis Isolates in Chile Provides Insights into Possible Transmission between Gulls, Poultry, and Humans

2016 ◽  
Vol 82 (20) ◽  
pp. 6223-6232 ◽  
Author(s):  
Magaly Toro ◽  
Patricio Retamal ◽  
Sherry Ayers ◽  
Marlen Barreto ◽  
Marc Allard ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Genetic Relationships ◽  
The United States ◽  
Interspecies Transmission ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Content Type ◽  
Published Evidence ◽  
Trace Back ◽  
The World

ABSTRACTSalmonella entericasubsp.entericaserotype Enteritidis is a major cause of human salmonellosis worldwide; however, little is known about the genetic relationships betweenS. Enteritidis clinical strains andS. Enteritidis strains from other sources in Chile. We compared the whole genomes of 30S. Enteritidis strains isolated from gulls, domestic chicken eggs, and humans in Chile, to investigate their phylogenetic relationships and to establish their relatedness to international strains. Core genome multilocus sequence typing (cgMLST) analysis showed that only 246/4,065 shared loci differed among these Chilean strains, separating them into two clusters (I and II), with cluster II being further divided into five subclusters. One subcluster (subcluster 2) contained strains from all surveyed sources that differed at 1 to 18 loci (of 4,065 loci) with 1 to 18 single-nucleotide polymorphisms (SNPs), suggesting interspecies transmission ofS. Enteritidis in Chile. Moreover, clusters were formed by strains that were distant geographically, which could imply that gulls might be spreading the pathogen throughout the country. Our cgMLST analysis, using otherS. Enteritidis genomes available in the National Center for Biotechnology Information (NCBI) database, showed thatS. Enteritidis strains from Chile and the United States belonged to different lineages, which suggests thatS. Enteritidis regional markers might exist and could be used for trace-back investigations.IMPORTANCEThis study highlights the importance of gulls in the spread ofSalmonellaEnteritidis in Chile. We revealed a close genetic relationship between some human and gullS. Enteritidis strains (with as few as 2 of 4,065 genes being different), and we also found that gull strains were present in clusters formed by strains isolated from other sources or distant locations. Together with previously published evidence, this suggests that gulls might be spreading this pathogen between different regions in Chile and that some of those strains have been transmitted to humans. Moreover, we discovered that ChileanS. Enteritidis strains clustered separately from most ofS. Enteritidis strains isolated throughout the world (in the GenBank database) and thus it might be possible to distinguish the geographical origins of strains based on specific genomic features. This could be useful for trace-back investigations of foodborne illnesses throughout the world.

Isolation, characterization and utilization of starter cultures for the development of wheyghurt drink

2013 ◽  
Vol 115 (8) ◽  
pp. 1169-1186 ◽  
Author(s):  
Muhammad Saeed ◽  
Faqir Muhammad Anjum ◽  
Moazzam Rafiq Khan ◽  
Muhammad Issa Khan ◽  
Muhammad Nadeem
Keyword(s):  
Starter Culture ◽  
Streptococcus Thermophilus ◽  
Starter Cultures ◽  
Organoleptic Evaluation ◽  
Content Type ◽  
Overall Acceptability ◽  
Minimum Score ◽  
Good Nutrition ◽  
Sensory Parameters ◽  
And Storage

PurposeWhey products have conventionally been professed as a means of reducing ingredient costs. The authentic benefits of adding whey products are the enhanced worth resulting from flavor, texture and nutritional improvements as well as nutraceutical or health‐enhancing payback. Therefore, the present study aims to isolate and characterize suitable starter cultures for the production of wheyghurt drink.Design/methodology/approachKeeping in view all the benefits of yoghurt technology this study was planned to isolate the starter cultures and optimize the conditions for the production of wheyghurt drink. The starter cultures (Lactobacillus delbruceckii ssp. Bulgaricus and Streptococcus thermophilus) were isolated from the yoghurt and further characterized on the basis of their morphological and biochemical characteristics. The wheyghurt drink prepared from starter cultures with varying starter culture concentrations (1, 1.5, 2 and 2.5 percent) was analyzed for the physicochemical and sensory characteristics to explore the potential of wheyghurt drink.FindingsDuring storage, color, flavor, taste and overall acceptability were affected significantly. But the interaction between treatments and storage was found non‐significant to all the sensory parameters. At zero day maximum score (7.40) for overall acceptability was recorded for T3 and minimum score (5.60) was awarded to T4. After five, ten and 15 days of storage, judges observed a slight decline in overall acceptability in all wheyghurt drink samples. Hence it was concluded that wheyghurt drink sample T3 obtained maximum scores regarding the organoleptic evaluation and remained the best.Practical implicationsThe key to growth is a continuous evaluation and modification of the product to match consumer expectations. Currently there are many apparent benefits that result from incorporating selected whey products into yogurt formulas. The starter cultures for the production of fermented whey products are not presently produced in Pakistan and are imported for industrial use. The use of LAB as starter culture may help to improve the quality and shelf life of the whey products.Originality/valueThe research is useful for food manufacturers in order to develop functional food products for consumers. Understanding consumer needs and preferences is critical to successful product development and enhancing marketing values of a product. Nutritionally improved foods, such as wheyghurt over the conventional counterpart, will be highly successful in the marketplace. Consumers will prefer such kinds of foods because they are more conscious about their health and such foods provide them with what they desire, i.e. health benefits with good nutrition.

scholarly journals Implications of Genome-Based Discrimination between Clostridium botulinum Group I and Clostridium sporogenes Strains for Bacterial Taxonomy

2015 ◽  
Vol 81 (16) ◽  
pp. 5420-5429 ◽  
Author(s):  
Michael R. Weigand ◽  
Angela Pena-Gonzalez ◽  
Timothy B. Shirey ◽  
Robin G. Broeker ◽  
Maliha K. Ishaq ◽  
...  
Keyword(s):  
Clostridium Botulinum ◽  
Bacterial Species ◽  
Phylogenetic Reconstruction ◽  
Bacterial Taxonomy ◽  
Clostridium Sporogenes ◽  
Content Type ◽  
Group I ◽  
Taxonomic Organization ◽  
Different Strains

ABSTRACTTaxonomic classification ofClostridium botulinumis based on the production of botulinum neurotoxin (BoNT), while closely related, nontoxic organisms are classified asClostridium sporogenes. However, this taxonomic organization does not accurately mirror phylogenetic relationships between these species. A phylogenetic reconstruction using 2,016 orthologous genes shared among strains ofC. botulinumgroup I andC. sporogenesclearly separated these two species into discrete clades which showed ∼93% average nucleotide identity (ANI) between them. Clustering of strains based on the presence of variable orthologs revealed 143C. sporogenesclade-specific genetic signatures, a subset of which were further evaluated for their ability to correctly classify a panel of presumptiveC. sporogenesstrains by PCR. Genome sequencing of severalC. sporogenesstrains lacking these signatures confirmed that they clustered withC. botulinumstrains in a core genome phylogenetic tree. Our analysis also identifiedC. botulinumstrains that containedC. sporogenesclade-specific signatures and phylogenetically clustered withC. sporogenesstrains. The genome sequences of twobont/B2-containing strains belonging to theC. sporogenesclade contained regions with similarity to abont-bearing plasmid (pCLD), while two different strains belonging to theC. botulinumclade carriedbont/B2on the chromosome. These results indicate thatbont/B2was likely acquired byC. sporogenesstrains through horizontal gene transfer. The genome-based classification of these species used to identify candidate genes for the development of rapid assays for molecular identification may be applicable to additional bacterial species that are challenging with respect to their classification.

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