Phages of dairy bacteria

In Silico Evidence of the Multifunctional Features of Lactiplantibacillus pentosus LPG1, a Natural Fermenting Agent Isolated from Table Olive Biofilms

In recent years, there has been a growing interest in obtaining probiotic bacteria from plant origins. This is the case of Lactiplantibacillus pentosus LPG1, a lactic acid bacterial strain isolated from table olive biofilms with proven multifunctional features. In this work, we have sequenced and closed the complete genome of L. pentosus LPG1 using both Illumina and PacBio technologies. Our intention is to carry out a comprehensive bioinformatics analysis and whole-genome annotation for a further complete evaluation of the safety and functionality of this microorganism. The chromosomic genome had a size of 3,619,252 bp, with a GC (Guanine-Citosine) content of 46.34%. L. pentosus LPG1 also had two plasmids, designated as pl1LPG1 and pl2LPG1, with lengths of 72,578 and 8713 bp (base pair), respectively. Genome annotation revealed that the sequenced genome consisted of 3345 coding genes and 89 non-coding sequences (73 tRNA and 16 rRNA genes). Taxonomy was confirmed by Average Nucleotide Identity analysis, which grouped L. pentosus LPG1 with other sequenced L. pentosus genomes. Moreover, the pan-genome analysis showed that L. pentosus LPG1 was closely related to the L. pentosus strains IG8, IG9, IG11, and IG12, all of which were isolated from table olive biofilms. Resistome analysis reported the absence of antibiotic resistance genes, whilst PathogenFinder tool classified the strain as a non-human pathogen. Finally, in silico analysis of L. pentosus LPG1 showed that many of its previously reported technological and probiotic phenotypes corresponded with the presence of functional genes. In light of these results, we can conclude that L. pentosus LPG1 is a safe microorganism and a potential human probiotic with a plant origin and application as a starter culture for vegetable fermentations.

Virulent Phages Isolated from a Smear-Ripened Cheese Are Also Detected in Reservoirs of the Cheese Factory

Smear-ripened cheeses host complex microbial communities that play a crucial role in the ripening process. Although bacteriophages have been frequently isolated from dairy products, their diversity and ecological role in such this type of cheese remain underexplored. In order to fill this gap, the main objective of this study was to isolate and characterize bacteriophages from the rind of a smear-ripened cheese. Thus, viral particles extracted from the cheese rind were tested through a spot assay against a collection of bacteria isolated from the same cheese and identified by sequencing the full-length small subunit ribosomal RNA gene. In total, five virulent bacteriophages infecting Brevibacterium aurantiacum, Glutamicibacter arilaitensis, Leuconostoc falkenbergense and Psychrobacter aquimaris species were obtained. All exhibit a narrow host range, being only able to infect a few cheese-rind isolates within the same species. The complete genome of each phage was sequenced using both Nanopore and Illumina technologies, assembled and annotated. A sequence comparison with known phages revealed that four of them may represent at least new genera. The distribution of the five virulent phages into the dairy-plant environment was also investigated by PCR, and three potential reservoirs were identified. This work provides new knowledge on the cheese rind viral community and an overview of the distribution of phages within a cheese factory.

Comparative genomics and in silico gene evaluation involved in the probiotic potential of Bifidobacterium longum 51A

The Bifidobacterium longum 5^1A strain of isolated from feces of a healthy child, has demonstrated probiotic properties by in vivo and in vitro studies, which may be assigned to its production of metabolites such as acetate. Thus, through the study of comparative genomics, the present work sought to identify unique genes that might be related to the production of acetate. To perform the study, the DNA strain was sequenced using Illumina HiSeq technology, followed by assembly and manual curation of coding sequences. Comparative analysis was performed including 19 complete B. longum genomes available in Genbank/NCBI. In the phylogenetic analysis, the CECT 7210 and 157F strains of B. longum subsp. infantis aggregated within the subsp. longum cluster, suggesting that their taxonomic classification should be reviewed. The strain 5^1A of B. longum has 26 unique genes, six of which are possibly related to carbohydrate metabolism and acetate production. The phosphoketolase pathway from B. longum 5^1A showed a difference in acetyl-phosphate production. This result seems to corroborate the analysis of their unique genes, whose presence suggests the strain may use different sources of carbohydrates that allow a greater production of acetate and consequently offer benefits to the host health.

Application of CRISPR-Cas9 gene editing for congenital heart disease

Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR-Cas9) is an ancient prokaryotic defense system that precisely cuts foreign genomic DNA under the control of a small number of guide RNAs. The CRISPR-Cas9 system facilitates efficient double-stranded DNA cleavage that has been recently adopted for genome editing to create or correct inherited genetic mutations causing disease. Congenital heart disease (CHD) is generally caused by genetic mutations such as base substitutions, deletions, and insertions, which result in diverse developmental defects and remains a leading cause of birth defects. Pediatric CHD patients exhibit a spectrum of cardiac abnormalities such as septal defects, valvular defects, and abnormal chamber development. CHD onset occurs during the prenatal period and often results in early lethality during childhood. Because CRISPR-Cas9-based genome editing technology has gained considerable attention for its potential to prevent and treat diseases, we will review the CRISPR-Cas9 system as a genome editing tool and focus on its therapeutic application for CHD.

Microbial consortia including methanotrophs: some benefits of living together

With the progress of biotechnological research and improvements made in bioprocessing with pure cultures, microbial consortia have gained recognition for accomplishing biological processes with improved effectiveness. Microbes are indispensable tool in developing bioprocesses for the production of bioenergy and biochemicals while utilizing renewable resources due to technical, economic and environmental advantages. They communicate with specific cohorts in close proximity to promote metabolic cooperation. Use of positive microbial associations has been recognized widely, especially in food industries and bioremediation of toxic compounds and waste materials. Role of microbial associations in developing sustainable energy sources and substitutes for conventional fuels is highly promising with many commercial prospects. Detoxification of chemical contaminants sourced from domestic, agricultural and industrial wastes has also been achieved through microbial catalysis in pure and co-culture systems. Methanotrophs, the sole biological sink of greenhouse gas methane, catalyze the methane monooxygenasemediated oxidation of methane to methanol, a high energy density liquid and key platform chemical to produce commodity chemical compounds and their derivatives. Constructed microbial consortia have positive effects, such as improved biomass, biocatalytic potential, stability etc. In a methanotroph-heterotroph consortium, non-methanotrophs provide key nutrient factors and alleviate the toxicity from the culture. Non-methanotrophic organisms biologically stimulate the growth and activity of methanotrophs via production of growth stimulators. However, methanotrophs in association with co-cultured microorganisms are in need of further exploration and thorough investigation to study their interaction mode and application with improved effectiveness.

Biodiversity and Classification of Phages Infecting Lactobacillus brevis

Lactobacillus brevis is a lactic acid bacterium that is known as a food and beverage spoilage organism, and more specifically as a beer-spoiler. Phages of L. brevis have been described, but very limited data is available regarding temperate phages of L. brevis. Temperate phages may exert benefits to the host, while they may also be employed to combat beer spoilage. The current study reports on the incidence of prophage sequences present in nineteen distinct L. brevis genomes. Prophage induction was evaluated using mitomycin C exposure followed by genome targeted-PCR, electron microscopy and structural proteome analysis. The morphological and genome sequence analyses revealed significant diversity among L. brevis prophages, which appear to be dominated by members of the Myoviridae phage family. Based on this analysis, we propose a classification of L. brevis phages into five groups.

Molecular, physiological and phylogenetic traits of Lactococcus 936-type phages from distinct dairy environments

Bacteriophage infection of Lactococcus species can cause serious disruption of dairy fermentation processes. The most common isolates from the dairy environment are Siphoviridae lytic 936-type phages. To gain specific knowledge about this group of phages in Polish dairies, we examined 90 isolates from 8 different locations. Based on restriction fragment length polymorphism analysis, coupled with physiological and molecular studies, the isolated phages were divided into 8 distinct groups. Whole-genome sequencing of single representatives from each phage group provided data about their biology and genetic composition. The phages present an overall conserved genome organization. High sequence homology to another Polish isolate, Lactococcus phage bIBB29, indicates their close phylogenetic relatedness to this strain. Such similarity may be suggestive of a general genome conservation among phages persisting in Polish dairies. Comparative genome analyses with other 936-type phages revealed several discriminative traits, including the presence and position of HNH endonuclease genes, varying number of orfs in the early gene region, and a putative TpeX gene. Interestingly, host range of the sequenced phages was restricted to L. lactis subsp. lactis biovar. diacetylactis strains. The results provide new data regarding phages present in the Polish dairy environment and permit analysis of their biology, genome composition and relatedness to other Lactococcus 936-type phages.

Current Trends and Potential Applications of Microbial Interactions for Human Welfare

For a long time, it was considered that interactions between microbes are only inhibitory in nature. However, latest developments in research have demonstrated that within our environment, several classes of microbes exist which produce different products upon interaction and thus embrace a wider scope of useful and potentially valuable aspects beyond simple antibiosis. Therefore, the current review explores different types of microbial interactions and describes the role of various physical, chemical, biological, and genetic factors regulating such interactions. It further explains the mechanism of action of biofilm formation and role of secondary metabolites regulating bacteria-fungi interaction. Special emphasis and focus is placed on microbial interactions which are important in medicine, food industry, agriculture, and environment. In short, this review reveals the recent contributions of microbial interaction for the benefit of mankind.

Selective Inactivation of Bacteriophage in the Presence of Bacteria by Use of Ground Rh-Doped SrTiO3 Photocatalyst and Visible Light

Bacteriophage (denoted as phage) infection in the bacterial fermentation industry is a major problem, leading to the loss of fermented products such as alcohol and lactic acid. Currently, the prevention of phage infection is limited to biological approaches, which are difficult to apply in an industrial setting. Herein, we report an alternative chemical approach using ground Rh-doped SrTiO₃ (denoted as g-STO:Rh) as a visible-light-driven photocatalyst. The g-STO:Rh showed selective inactivation of phage without bactericidal activity when irradiated with visible light (λ > 440 nm). After inactivation, the color of g-STO:Rh changed from gray to purple, suggesting that the Rh valence state partially changed from 3+ to 4+ induced by photocatalysis, as confirmed by diffuse reflectance spectroscopy. To study the effect of the Rh⁴⁺ ion on phage inactivation under visible-light irradiation, the survival rate of phage for g-STO:Rh was compared to that for ground Rh,Sb-codoped SrTiO₃ (denoted as g-STO:Rh,Sb), where the change of Rh valence state from 3+ to 4+ is almost suppressed under visible-light irradiation due to charge compensation by the Sb⁵⁺ ion. Only g-STO:Rh effectively inactivated phage, which indicated that Rh⁴⁺ ion induced by photocatalysis particularly contributed to phage inactivation under visible-light irradiation. These results suggested that g-STO:Rh has potential as an antiphage material in bacterial fermentation.

From bench to bed and back again: phage therapy of childhood Escherichia coli diarrhea

Over the last 20 years, the Nestlé Research Center in Switzerland and the International Center for Diarrhoeal Diseases Research in Bangladesh have explored the efficacy of alternative biological agents for the treatment of diarrheal diseases. This paper reviews the work of this collaborative effort, particularly on Escherichia coli phage therapy (PT), and discusses the development of the project, starting with the isolation of T4-like coliphages from the stool of diarrhea patients, their pilot plant amplification and purification, and the constitution and testing of a cocktail of T4-like phages in mice. A series of phase I clinical trials has demonstrated the safety of PT. Oral phage given without protection survived gastric passage and was recovered in the feces. Oral T4 phage cocktail was then tested in parallel to a commercial phage product in a phase II randomized, placebo-controlled single-center trial in Bangladeshi children hospitalized with acute E. coli diarrhea. It was found that oral phage did not perform better than the current standard of care by oral rehydration/zinc treatment. Furthermore, fecal E. coli pathogen titers were low and mixed infections were found to be frequent. Microbiota analysis showed a correlation between diarrhea and increased levels of Streptococcus, which raises fundamental questions on the causative agent of diarrhea that may explain PT clinical failure.

Bacteriophage Therapy: Advances in Formulation Strategies and Human Clinical Trials

Recently, a number of phage therapy phase I and II safety trials have been concluded, showing no notable safety concerns associated with the use of phage. Though hurdles for efficient treatment remain, these trials hold promise for future phase III clinical trials. Interestingly, most phage formulations used in these clinical trials are straightforward phage suspensions, and not much research has focused on the processing of phage cocktails in specific pharmaceutical dosage forms. Additional research on formulation strategies and the stability of phage-based drugs will be of key importance, especially with phage therapy advancing toward phase III clinical trials.

Genomic Diversity of Phages Infecting Probiotic Strains of Lactobacillus paracasei

Strains of the Lactobacillus casei group have been extensively studied because some are used as probiotics in foods. Conversely, their phages have received much less attention. We analyzed the complete genome sequences of five L. paracasei temperate phages: CL1, CL2, iLp84, iLp1308, and iA2. Only phage iA2 could not replicate in an indicator strain. The genome lengths ranged from 34,155 bp (iA2) to 39,474 bp (CL1). Phages iA2 and iLp1308 (34,176 bp) possess the smallest genomes reported, thus far, for phages of the L. casei group. The GC contents of the five phage genomes ranged from 44.8 to 45.6%. As observed with many other phages, their genomes were organized as follows: genes coding for DNA packaging, morphogenesis, lysis, lysogeny, and replication. Phages CL1, CL2, and iLp1308 are highly related to each other. Phage iLp84 was also related to these three phages, but the similarities were limited to gene products involved in DNA packaging and structural proteins. Genomic fragments of phages CL1, CL2, iLp1308, and iLp84 were found in several genomes of L. casei strains. Prophage iA2 is unrelated to these four phages, but almost all of its genome was found in at least four L. casei strains. Overall, these phages are distinct from previously characterized Lactobacillus phages. Our results highlight the diversity of L. casei phages and indicate frequent DNA exchanges between phages and their hosts.

A virulent phage infecting Lactococcus garvieae, with homology to Lactococcus lactis phages

A new virulent phage belonging to the Siphoviridae family and able to infect Lactococcus garvieae strains was isolated from compost soil. Phage GE1 has a prolate capsid (56 by 38 nm) and a long noncontractile tail (123 nm). It had a burst size of 139 and a latent period of 31 min. Its host range was limited to only two L. garvieae strains out of 73 tested. Phage GE1 has a double-stranded DNA genome of 24,847 bp containing 48 predicted open reading frames (ORFs). Putative functions could be assigned to only 14 ORFs, and significant matches in public databases were found for only 17 ORFs, indicating that GE1 is a novel phage and its genome contains several new viral genes and encodes several new viral proteins. Of these 17 ORFs, 16 were homologous to deduced proteins of virulent phages infecting the dairy bacterium Lactococcus lactis, including previously characterized prolate-headed phages. Comparative genome analysis confirmed the relatedness of L. garvieae phage GE1 to L. lactis phages c2 (22,172 bp) and Q54 (26,537 bp), although its genome organization was closer to that of phage c2. Phage GE1 did not infect any of the 58 L. lactis strains tested. This study suggests that phages infecting different lactococcal species may have a common ancestor.

Bacteriophage application restores ethanol fermentation characteristics disrupted by Lactobacillus fermentum

BACKGROUND

Contamination of corn mash by lactic acid bacteria (LAB) reduces the efficiency of the ethanol fermentation process. The industry relies heavily on antibiotics for contamination control and there is a need to develop alternative methods. The goals of this study were to determine the diversity and abundance of bacteria contaminating commercial ethanol fermentations, and to evaluate the potential of anti-LAB bacteriophages in controlling production losses.

RESULTS

Bacterial populations in 27 corn mash samples collected from nine different commercial plants were determined by pyrosequencing of 16S rRNA amplicons. The results showed that the most abundant bacteria (>50 % of total population) in 24 of the 27 samples included LAB genera such as Lactobacillus, Streptococcus, Lactococcus, Weissella, Enterococcus, and Pediococcus. Lactobacillus was identified as the most prevalent genus at all fermentation stages in all plants, accounting for between 2.3 and 93.7 % of each population and constituting the major genus (>50 %) in nine samples from five plants and the most abundant genus in five other samples. Lactobacillus species, including L. delbrueckii, L. fermentum, L. mucosae, and L. reuteri were the most well-represented species. Two bacteriophages that target L. fermentum strains from ethanol plants, vB_LfeS_EcoSau and vB_LfeM_EcoInf (EcoSau and EcoInf), were isolated and characterized as a siphophage and a myophage, respectively. Analysis of the 31,703 bp genome of EcoSau revealed its similarity to the P335-like phage group, and the 106,701 bp genome of phage EcoInf was determined to be a novel phage type despite its distant relationship to the SPO1-like phages. Addition of phages EcoSau and EcoInf to L. fermentum-contaminated corn mash fermentation models restored the yields of ethanol and reduced levels of residual glucose, lactic acid, and acetic acid to that comparable to the infection-free control.

CONCLUSIONS

This study provides detailed insight into the microbiota contaminating commercial ethanol fermentations, and highlights the abundance of LAB, especially L. delbrueckii, L. fermentum, L. mucosae, and L. reuteri, in the process. This study suggests that phages with broad coverage of major LAB species can be applied directly to corn mash for antibiotic-free control of contamination in the ethanol fermentation industry.

Functional analysis of the N-terminal region of endolysin Lyb5 encoded by Lactobacillus fermentum bacteriophage φPYB5

Lactobacillus fermentum temperate bacteriophage φPYB5 uses endolysin Lyb5 and holin Hyb5 to burst the host cell. Previous results showed that expression of Lyb5 in Escherichia coli caused host cell lysis slowly, leading us to suppose that Lyb5 could pass the cytoplasmic membrane partly. In this work, the function of a putative signal peptide (SPLyb5) at the N-terminal of Lyb5 was investigated. In E. coli, the cell adopted a spherical shape during induction of Lyb5 protein, while morphological changes were not observed during expression of the SPLyb5 truncation, indicating that the SPLyb5 motif may serve as a functional signal peptide. However, SPLyb5 was not proteolytically cleaved at the predicted site during the translocation of Lyb5, and the expressed Lyb5 protein appeared in the cytoplasm, cytoplasmic membrane and periplasm fractions with the same molecular mass. Similar results were obtained using Lactococcus lactis as a host to express Lyb5. These results indicated that SPLyb5 could direct Lyb5 to the periplasm in a membrane-tethered form, and then release it as a soluble active enzyme into the periplasm. In addition, SPLyb5 could also drive the fused NucleaseB protein to the extracytoplasm environment in E. coli as well as in L. lactis. We proposed that in Gram-negative and Gram-positive hosts SPLyb5 acted as a signal-anchor-release domain, which was firstly identified here by experimental evidences in lactic acid bacteria phages. The application of signal-anchor-release domain for endolysin export in bacteriophages infecting Gram-positive and Gram-negative hosts was discussed.

Phage-mediated transfer of a dextranase gene in Lactobacillus sanfranciscensis and characterization of the enzyme

While phages of lactobacilli are extensively studied with respect to their structure and role in the dairy environment, knowledge about phages in bacteria residing in sourdough fermentation is limited. Based on the previous finding that the Lactobacillus sanfranciscensis phage EV3 carries a putative dextranase gene (dex), we have investigated the distribution of similar dex(+) phages in L. sanfranciscensis, the chance of gene transfer and the properties of the dextranase encoded by phage EV3. L. sanfranciscensis H2A (dex(-)), originally isolated from a wheat sourdough, expressed a Dex(+) phenotype upon infection with EV3. The dextranase gene was isolated from the transductant and heterologously expressed in Escherichia coli. The gene encoded a protein of 801 amino acids with a calculated molecular weight (Mw) of 89.09 kDa and a calculated pI of 5.62. Upon purification aided by a 6-His tag, enzyme kinetic parameters were determined. The Km value was 370 mM, and the Vmax was calculated in about 16 μmol of glucose released from dextran by 1 mg of enzyme in 1 min in a buffer solution at pH 5.0. The optimum conditions were 60 °C and pH 4.5. The enzyme retained its activity for >3h at 60 °C and exhibited only 40% activity at 30 °C; the highest homology of 72% was found to a dextranase gene from Lactobacillus fermentum phage φPYB5. Within 25 L. sanfransiscensis isolates tested, the strain 4B5 carried a similar prophage encoding a dextranase gene. Our data suggest a phage-mediated transfer of dextranase genes in the sourdough environment resulting in superinfection-resistant L. sanfranciscensis Dex(+) strains with a possible ecological advantage in dextran-containing sourdoughs.

PsasM2I, a type II restriction-modification system in Pseudomonas savastanoi pv. savastanoi: differential distribution of carrier strains in the environment and the evolutionary history of homologous RM systems in the Pseudomonas syringae complex

A type II restriction-modification system was found in a native plasmid of Pseudomonas savastanoi pv. savastanoi MLLI2. Functional analysis of the methyltransferase showed that the enzyme acts by protecting the DNA sequence CTGCAG from cleavage. Restriction endonuclease expression in recombinant Escherichia coli cells resulted in mutations in the REase sequence or transposition of insertion sequence 1A in the coding sequence, preventing lethal gene expression. Population screening detected homologous RM systems in other P. savastanoi strains and in the Pseudomonas syringae complex. An epidemiological survey carried out by sampling olive and oleander knots in two Italian regions showed an uneven diffusion of carrier strains, whose presence could be related to a selective advantage in maintaining the RM system in particular environments or subpopulations. Moreover, carrier strains can coexist in the same orchards, plants, and knot tissues with non-carriers, revealing unexpected genetic variability on a very small spatial scale. Phylogenetic analysis of the RM system and housekeeping gene sequences in the P. syringae complex demonstrated the ancient acquisition of the RM systems. However, the evolutionary history of the gene complex also showed the involvement of horizontal gene transfer between related strains and recombination events.

Exposing the secrets of two well-known Lactobacillus casei phages, J-1 and PL-1, by genomic and structural analysis

Bacteriophage J-1 was isolated in 1965 from an abnormal fermentation of Yakult using Lactobacillus casei strain Shirota, and a related phage, PL-1, was subsequently recovered from a strain resistant to J-1. Complete genome sequencing shows that J-1 and PL-1 are almost identical, but PL-1 has a deletion of 1.9 kbp relative to J-1, resulting in the loss of four predicted gene products involved in immunity regulation. The structural proteins were identified by mass spectrometry analysis. Similarly to phage A2, two capsid proteins are generated by a translational frameshift and undergo proteolytic processing. The structure of gene product 16 (gp16), a putative tail protein, was modeled based on the crystal structure of baseplate distal tail proteins (Dit) that form the baseplate hub in other Siphoviridae. However, two regions of the C terminus of gp16 could not be modeled using this template. The first region accounts for the differences between J-1 and PL-1 gp16 and showed sequence similarity to carbohydrate-binding modules (CBMs). J-1 and PL-1 GFP-gp16 fusions bind specifically to Lactobacillus casei/paracasei cells, and the addition of l-rhamnose inhibits binding. J-1 gp16 exhibited a higher affinity than PL-1 gp16 for cell walls of L. casei ATCC 27139 in phage adsorption inhibition assays, in agreement with differential adsorption kinetics observed for both phages in this strain. The data presented here provide insights into how Lactobacillus phages interact with their hosts at the first steps of infection.

Complete Genome Sequences of Four Novel Lactococcus lactis Phages Distantly Related to the Rare 1706 Phage Species

Lactoccocus lactis is a Gram-positive bacterium widely used in the dairy industry in the production of an array of cheeses and other fermented milk products. Here, we describe the sequencing and genome annotations of a set of four phages virulent to L. lactis and exhibiting similarities to phage 1706.

Bacteriophages and Their Derivatives as Biotherapeutic Agents in Disease Prevention and Treatment

The application of bacteriophages for the elimination of pathogenic bacteria has received significantly increased attention world-wide in the past decade. This is borne out by the increasing prevalence of bacteriophage-specific conferences highlighting significant and diverse advances in the exploitation of bacteriophages. While bacteriophage therapy has been associated with the Former Soviet Union historically, since the 1990s, it has been widely and enthusiastically adopted as a research topic in Western countries. This has been justified by the increasing prevalence of antibiotic resistance in many prominent human pathogenic bacteria. Discussion of the therapeutic aspects of bacteriophages in this review will include the uses of whole phages as antibacterials and will also describe studies on the applications of purified phage-derived peptidoglycan hydrolases, which do not have the constraint of limited bacterial host-range often observed with whole phages.

The genome of the Lactobacillus sanfranciscensis temperate phage EV3

BACKGROUND

Bacteriophages infection modulates microbial consortia and transduction is one of the most important mechanism involved in the bacterial evolution. However, phage contamination brings food fermentations to a halt causing economic setbacks. The number of phage genome sequences of lactic acid bacteria especially of lactobacilli is still limited. We analysed the genome of a temperate phage active on Lactobacillus sanfranciscensis, the predominant strain in type I sourdough fermentations.

RESULTS

Sequencing of the DNA of EV3 phage revealed a genome of 34,834 bp and a G + C content of 36.45%. Of the 43 open reading frames (ORFs) identified, all but eight shared homology with other phages of lactobacilli. A similar genomic organization and mosaic pattern of identities align EV3 with the closely related Lactobacillus vaginalis ATCC 49540 prophage. Four unknown ORFs that had no homologies in the databases or predicted functions were identified. Notably, EV3 encodes a putative dextranase.

CONCLUSIONS

EV3 is the first L. sanfranciscensis phage that has been completely sequenced so far.

Genomic impact of CRISPR immunization against bacteriophages

CRISPR (clustered regularly interspaced short palindromic repeats) together with cas (CRISPR-associated) genes form the CRISPR–Cas immune system, which provides sequence-specific adaptive immunity against foreign genetic elements in bacteria and archaea. Immunity is acquired by the integration of short stretches of invasive DNA as novel ‘spacers’ into CRISPR loci. Subsequently, these immune markers are transcribed and generate small non-coding interfering RNAs that specifically guide nucleases for sequence-specific cleavage of complementary sequences. Among the four CRISPR–Cas systems present in Streptococcus thermophilus, CRISPR1 and CRISPR3 have the ability to readily acquire new spacers following bacteriophage or plasmid exposure. In order to investigate the impact of building CRISPR-encoded immunity on the host chromosome, we determined the genome sequence of a BIM (bacteriophage-insensitive mutant) derived from the DGCC7710 model organism, after four consecutive rounds of bacteriophage challenge. As expected, active CRISPR loci evolved via polarized addition of several novel spacers following exposure to bacteriophages. Although analysis of the draft genome sequence revealed a variety of SNPs (single nucleotide polymorphisms) and INDELs (insertions/deletions), most of the in silico differences were not validated by Sanger re-sequencing. In addition, two SNPs and two small INDELs were identified and tracked in the intermediate variants. Overall, building CRISPR-encoded immunity does not significantly affect the genome, which allows the maintenance of important functional properties in isogenic CRISPR mutants. This is critical for the development and formulation of sustainable and robust next-generation starter cultures with increased industrial lifespans.

Comparative genomic and functional analysis of 100 Lactobacillus rhamnosus strains and their comparison with strain GG

Lactobacillus rhamnosus is a lactic acid bacterium that is found in a large variety of ecological habitats, including artisanal and industrial dairy products, the oral cavity, intestinal tract or vagina. To gain insights into the genetic complexity and ecological versatility of the species L. rhamnosus, we examined the genomes and phenotypes of 100 L. rhamnosus strains isolated from diverse sources. The genomes of 100 L. rhamnosus strains were mapped onto the L. rhamnosus GG reference genome. These strains were phenotypically characterized for a wide range of metabolic, antagonistic, signalling and functional properties. Phylogenomic analysis showed multiple groupings of the species that could partly be associated with their ecological niches. We identified 17 highly variable regions that encode functions related to lifestyle, i.e. carbohydrate transport and metabolism, production of mucus-binding pili, bile salt resistance, prophages and CRISPR adaptive immunity. Integration of the phenotypic and genomic data revealed that some L. rhamnosus strains possibly resided in multiple niches, illustrating the dynamics of bacterial habitats. The present study showed two distinctive geno-phenotypes in the L. rhamnosus species. The geno-phenotype A suggests an adaptation to stable nutrient-rich niches, i.e. milk-derivative products, reflected by the alteration or loss of biological functions associated with antimicrobial activity spectrum, stress resistance, adaptability and fitness to a distinctive range of habitats. In contrast, the geno-phenotype B displays adequate traits to a variable environment, such as the intestinal tract, in terms of nutrient resources, bacterial population density and host effects.

Some bacterial species are specialists and adapted to a single niche, while others are generalists and able to grow in various environmental conditions. Lactobacillus rhamnosus is a generalist and its members can often be found in different human cavities but also in various artisanal and industrial dairy products. To gain insights into the genetic complexity and ecological versatility of this species, we collected 100 L. rhamnosus strains from different niches. Genomic and functional analysis of these revealed a dichotomy within the species that reflected its adaptation to particular niches. The variable regions identified in the L. rhamnosus genome encode lifestyle traits that allowed us to demonstrate that some L. rhamnosus isolates possibly resided in multiple habitats. Our work brings valuable data on the ecological dynamics and adaptability of the species and provides a basis for a model explaining the ecology of L. rhamnosus in an anthropocentric perspective. Finally, we observed that a set of pheno-genomic markers, i.e. CRISPR oligotyping or carbohydrate metabolism, would be sufficient and among the best ways to differentiate the L. rhamnosus strains, providing a general approach to select the highest diversity in these and other bacterial species.

Phage inhibition of Escherichia coli in ultrahigh-temperature-treated and raw milk

Escherichia coli can contaminate raw milk during the milking process or via environmental contamination in milk-processing facilities. Three bacteriophages, designated EC6, EC9, and EC11, were investigated for their ability to inhibit the growth of three strains of E. coli in ultrahigh-temperature (UHT) treated and raw bovine milk. A cocktail of the three phages completely inhibited E. coli ATCC 25922 and E. coli O127:H6 in UHT milk at 25 °C and under refrigeration temperatures (5-9 °C). The phage cocktail produced similar results in raw milk; however, E. coli ATCC 25922 and O127:H6 in raw milk controls also declined to below the level of detection at both temperatures. This observation indicated that competition by the raw milk microbiota might have contributed to the decline in viable E. coli cells. A cocktail containing EC6 and EC9 completely inhibited E. coli O5:H-, an enterohemorrhagic strain, in UHT milk at both temperatures. In raw milk, the phage cocktail initially inhibited growth of E. coli O5:H- but regrowth occurred following incubation for 9 h at 25 °C and 144 h at 5-9 °C. In contrast to the other E. coli strains, O5:H- was not inhibited in the raw milk controls. This study demonstrates that bacteriophages are effective biocontrol agents against E. coli host strains in UHT and raw bovine milk at various storage temperatures.

Cluster J mycobacteriophages: intron splicing in capsid and tail genes

Bacteriophages isolated on Mycobacterium smegmatis mc²155 represent many distinct genomes sharing little or no DNA sequence similarity. The genomes are architecturally mosaic and are replete with genes of unknown function. A new group of genomes sharing substantial nucleotide sequences constitute Cluster J. The six mycobacteriophages forming Cluster J are morphologically members of the Siphoviridae, but have unusually long genomes ranging from 106.3 to 117 kbp. Reconstruction of the capsid by cryo-electron microscopy of mycobacteriophage BAKA reveals an icosahedral structure with a triangulation number of 13. All six phages are temperate and homoimmune, and prophage establishment involves integration into a tRNA-Leu gene not previously identified as a mycobacterial attB site for phage integration. The Cluster J genomes provide two examples of intron splicing within the virion structural genes, one in a major capsid subunit gene, and one in a tail gene. These genomes also contain numerous free-standing HNH homing endonuclease, and comparative analysis reveals how these could contribute to genome mosaicism. The unusual Cluster J genomes provide new insights into phage genome architecture, gene function, capsid structure, gene mobility, intron splicing, and evolution.

Characterization of the genome of the dairy Lactobacillus helveticus bacteriophage {Phi}AQ113

The complete genomic sequence of the dairy Lactobacillus helveticus bacteriophage ΦAQ113 was determined. Phage ΦAQ113 is a Myoviridae bacteriophage with an isometric capsid and a contractile tail. The final assembled consensus sequence revealed a linear, circularly permuted, double-stranded DNA genome with a size of 36,566 bp and a G+C content of 37%. Fifty-six open reading frames (ORFs) were predicted, and a putative function was assigned to approximately 90% of them. The ΦAQ113 genome shows functionally related genes clustered together in a genome structure composed of modules for DNA replication/regulation, DNA packaging, head and tail morphogenesis, cell lysis, and lysogeny. The identification of genes involved in the establishment of lysogeny indicates that it may have originated as a temperate phage, even if it was isolated from natural cheese whey starters as a virulent phage, because it is able to propagate in a sensitive host strain. Additionally, we discovered that the ΦAQ113 phage genome is closely related to Lactobacillus gasseri phage KC5a and Lactobacillus johnsonii phage Lj771 genomes. The phylogenetic similarities between L. helveticus phage ΦAQ113 and two phages that belong to gut species confirm a possible common ancestral origin and support the increasing consideration of L. helveticus as a health-promoting organism.

Bacteriophages for managing Shigella in various clinical and non-clinical settings

The control of shigellosis in humans enjoys a prominent position in the history of bacteriophage therapy. d’Herelle first demonstrated the efficacy of phage therapy by curing 4 patients of shigellosis, and several subsequent studies confirmed the ability of phages to reduce Shigella based infection. Shigella spp continue to cause millions of illnesses and deaths each year and the use of phages to control the disease in humans and the spread of the bacteria within food and water could point the way forward to the effective management of an infectious disease with global influence.

Identification of the receptor-binding protein in lytic Leuconostoc pseudomesenteroides bacteriophages

Two phages, P793 and ΦLN04, sharing 80.1% nucleotide sequence identity but having different strains of Leuconostoc pseudomesenteroides as hosts, were selected for identification of the host determinant gene. Construction of chimeric phages leading to the expected switch in host range identified the host determinant genes as ORF21P793/ORF23ΦLN04. The genes are located in the tail structural module and have low sequence similarity at the distal end.

Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system

Bacteria and archaea have evolved an adaptive, heritable immune system that recognizes and protects against viruses or plasmids. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences, called 'spacers' into its CRISPR system. Spacers in the CRISPR system provide a record of the history of bacteria and phage coevolution. We use a physical model to study the dynamics of this coevolution as it evolves stochastically over time. We focus on the impact of mutation and recombination on bacteria and phage evolution and evasion. We discuss the effect of different spacer deletion mechanisms on the coevolutionary dynamics. We make predictions about bacteria and phage population growth, spacer diversity within the CRISPR locus, and spacer protection against the phage population.

CRISPR-mediated adaptive immune systems in bacteria and archaea

Effective clearance of an infection requires that the immune system rapidly detects and neutralizes invading parasites while strictly avoiding self-antigens that would result in autoimmunity. The cellular machinery and complex signaling pathways that coordinate an effective immune response have generally been considered properties of the eukaryotic immune system. However, a surprisingly sophisticated adaptive immune system that relies on small RNAs for sequence-specific targeting of foreign nucleic acids was recently discovered in bacteria and archaea. Molecular vaccination in prokaryotes is achieved by integrating short fragments of foreign nucleic acids into a repetitive locus in the host chromosome known as a CRISPR (clustered regularly interspaced short palindromic repeat). Here we review the mechanisms of CRISPR-mediated immunity and discuss the ecological and evolutionary implications of these adaptive defense systems.

On the nature of mycobacteriophage diversity and host preference

The complete genome sequences of over 220 mycobacteriophages reveal them to be highly diverse, with numerous types sharing little or no nucleotide sequence identity with each other. We have determined the preferences of these phages for Mycobacterium tuberculosis and for other strains of Mycobacterium smegmatis, and find there is a correlation between genome type (cluster, subcluster, singleton) and host range. For many of the phages, expansion of host range occurs at relatively high frequencies, and we describe several examples in which host constraints occur at early stages of infection (adsorption or DNA injection), and phages have the ability to expand their host range through mutations in tail genes. We present a model in which phage diversity is a function of both the ability of phages to rapidly adapt to new hosts and the richness of the diversity of the bacterial population from which those phages are isolated.

The highly dynamic CRISPR1 system of Streptococcus agalactiae controls the diversity of its mobilome

Clustered regularly interspaced short palindromic repeats (CRISPR) confer immunity against mobile genetic elements (MGEs) in prokaryotes. Streptococcus agalactiae, a leading cause of neonatal infections contains in its genome two CRISPR/Cas systems. We show that type 1-C CRISPR2 is present in few strains but type 2-A CRISPR1 is ubiquitous. Comparative sequence analysis of the CRISPR1 spacer content of 351 S. agalactiae strains revealed that it is extremely diverse due to the acquisition of new spacers, spacer duplications and spacer deletions that witness the dynamics of this system. The spacer content profile mirrors the S. agalactiae population structure. Transfer of a conjugative transposon targeted by CRISPR1 selected for spacer rearrangements, suggesting that deletions and duplications pre-exist in the population. The comparison of protospacers located within MGE or the core genome and protospacer-associated motif-shuffling demonstrated that the GG motif is sufficient to discriminate self and non-self and for spacer selection and integration. Strikingly more than 40% of the 949 different CRISPR1 spacers identified target MGEs found in S. agalactiae genomes. We thus propose that the S. agalactiae type II-A CRISPR1/Cas system modulates the cohabitation of the species with its mobilome, as such contributing to the diversity of MGEs in the population.

Bioinformatic Analysis of Prophage Endolysins and Endolysin-Like Genes from the Order Lactobacillales

Endolysins belonging to the group of peptigoglycan hydrolases, which are able to cleave peptidoglycan in bacterial cell walls, become an extensively studied group of enzymes. Thanks to their narrow target specificity and low probability of resistance they are considered to be an appropriate alternative to conventional antibiotics. The present paper concerns the occurrence of endolysin and endolysin-like genes in genomes of bacteria belonging to the order Lactobacillales. Using bioinformatic programmes we compared and analysed protein sequences of catalytic and cell wall binding (CWB) domains of these enzymes, their preferred combinations, their phylogenetic relationship and potential occurence of natural "domain shuffling". The existence of this phenomenon in selected group of enzymes was confirmed only in limited range, so we assume that the natural trend is the distribution of "well-tried" combinations of catalytic and CWB domains of endolysin genes as a whole.

Cangene Gold Medal Award Lecture — Genomic analysis and modification ofBurkholderia cepaciacomplex bacteriophages1This article is based on a presentation by Dr. Karlene Lynch at the 61st Annual Meeting of the Canadian Society of Microbiologists in St. John’s, Newfoundland and Labrador, on 21 June 2011. Dr. Lynch was the recipient of the 2011 Cangene Gold Medal as the Canadian Graduate Student Microbiologist of the Year, an annual award sponsored by Cangene Corporation intended to recognize excellence in graduate research

The Burkholderia cepacia complex (Bcc) is a group of 17 Gram-negative predominantly environmental bacterial species that cause potentially fatal opportunistic infections in cystic fibrosis (CF) patients. Although its prevalence in these individuals is lower than that of Staphylococcus aureus and Pseudomonas aeruginosa , the Bcc remains a serious problem in the CF community because of the pathogenicity, transmissibility, and inherent antibiotic resistance of these organisms. An alternative treatment for Bcc infections that is currently being developed is phage therapy, the clinical use of viruses that infect bacteria. To assess the suitability of individual phage isolates for therapeutic use, the complete genome sequences of a panel of Bcc‐specific phages were determined and analyzed. These sequences encode a broad range of proteins with a gradient of relatedness to phage and bacterial gene products from Burkholderia and other genera. The majority of these phages were found not to encode virulence factors, and despite their predominantly temperate nature, a proof-of-principle experiment has shown that they may be modified to a lytic form. Both the genomic characterization and subsequent engineering of Bcc‐specific phages are fundamental to the development of an effective phage therapy strategy for these bacteria.

Safety assessment of Bifidobacterium longum JDM301 based on complete genome sequences

AIM

To assess the safety of Bifidobacterium longum (B. longum) JDM301 based on complete genome sequences.

METHODS

The complete genome sequences of JDM301 were determined using the GS 20 system. Putative virulence factors, putative antibiotic resistance genes and genes encoding enzymes responsible for harmful metabolites were identified by blast with virulence factors database, antibiotic resistance genes database and genes associated with harmful metabolites in previous reports. Minimum inhibitory concentration of 16 common antimicrobial agents was evaluated by E-test.

RESULTS

JDM301 was shown to contain 36 genes associated with antibiotic resistance, 5 enzymes related to harmful metabolites and 162 nonspecific virulence factors mainly associated with transcriptional regulation, adhesion, sugar and amino acid transport. B. longum JDM301 was intrinsically resistant to ciprofloxacin, amikacin, gentamicin and streptomycin and susceptible to vancomycin, amoxicillin, cephalothin, chloramphenicol, erythromycin, ampicillin, cefotaxime, rifampicin, imipenem and trimethoprim-sulphamethoxazol. JDM301 was moderately resistant to bacitracin, while an earlier study showed that bifidobacteria were susceptible to this antibiotic. A tetracycline resistance gene with the risk of transfer was found in JDM301, which needs to be experimentally validated.

CONCLUSION

The safety assessment of JDM301 using information derived from complete bacterial genome will contribute to a wider and deeper insight into the safety of probiotic bacteria.

CRISPR: new horizons in phage resistance and strain identification

Bacteria have been widely used as starter cultures in the food industry, notably for the fermentation of milk into dairy products such as cheese and yogurt. Lactic acid bacteria used in food manufacturing, such as lactobacilli, lactococci, streptococci, Leuconostoc, pediococci, and bifidobacteria, are selectively formulated based on functional characteristics that provide idiosyncratic flavor and texture attributes, as well as their ability to withstand processing and manufacturing conditions. Unfortunately, given frequent viral exposure in industrial environments, starter culture selection and development rely on defense systems that provide resistance against bacteriophage predation, including restriction-modification, abortive infection, and recently discovered CRISPRs (clustered regularly interspaced short palindromic repeats). CRISPRs, together with CRISPR-associated genes (cas), form the CRISPR/Cas immune system, which provides adaptive immunity against phages and invasive genetic elements. The immunization process is based on the incorporation of short DNA sequences from virulent phages into the CRISPR locus. Subsequently, CRISPR transcripts are processed into small interfering RNAs that guide a multifunctional protein complex to recognize and cleave matching foreign DNA. Hypervariable CRISPR loci provide insights into the phage and host population dynamics, and new avenues for enhanced phage resistance and genetic typing and tagging of industrial strains.

Bacteriophages as twenty-first century antibacterial tools for food and medicine

Antibiotic-resistant bacteria are an increasing source of concern in all environments in which these drugs have been used. More stringent regulations have led to a slow but sure decrease in antibiotic use in the food industry worldwide, but have also stimulated the search for alternative antibacterial agents. In medicine, the number of people infected with pan-resistant bacteria is driving research to develop new treatments. Within these contexts, studies on the use of bacteriophages in both medicine and the food industry have recently flourished. This renewed interest has coincided with the demonstration that these viruses are involved in geochemical cycles, revolutionizing our vision of their ecological role on our planet. Bacteriophages have co-evolved with bacteria for billions of years and retain the ability to infect bacteria efficiently. They are undoubtedly one of the best potential sources of new solutions for the management of undesirable bacteria.

Pili and flagella biology, structure, and biotechnological applications

Bacteria and Archaea expose on their outer surfaces a variety of thread-like proteinaceous organelles with which they interact with their environments. These structures are repetitive assemblies of covalently or non-covalently linked protein subunits, organized into filamentous polymers known as pili ("hair"), flagella ("whips") or injectisomes ("needles"). They serve different roles in cell motility, adhesion and host invasion, protein and DNA secretion and uptake, conductance, or cellular encapsulation. Here we describe the functional, morphological and genetic diversity of these bacterial filamentous protein structures. The organized, multi-copy build-up and/or the natural function of pili and flagella have lead to their biotechnological application as display and secretion tools, as therapeutic targets or as molecular motors. We review the documented and potential technological exploitation of bacterial surface filaments in light of their structural and functional traits.