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Many prokaryotes harbor the adaptive CRISPR-Cas system, which stores small nucleotide fragments from previous invasions of nucleic acids via viruses or plasmids. This molecular archive blocks further invaders carrying identical or similar nucleotide sequences. However, very few of these systems have been experimentally confirmed to be active in gut bacteria. Here, we experimentally demonstrate that the type I-C CRISPR-Cas system of the prevalent gut bacterium Eggerthella lenta can specifically target and cleave foreign DNA in vitro by using a plasmid transformation assay. We also show that the CRISPR-Cas system acquires new immunities (spacers) from the genome of a virulent E. lenta phage using traditional phage-assays in vitro but also in vivo using gnotobiotic (GB) mice. An increased number of spacer acquisition events were observed when E. lenta was exposed to a low multiplicity of infection in vitro, and three phage genes were found to contain protospacer hotspots. Interestingly, much less new spacer acquisitions were detected in vivo than in vitro. Longitudinal analysis of phage-bacteria interactions showed sustained coexistence in the gut of GB mice, with phage abundance being approximately one log higher than the bacteria. Our findings show that while the type I-C CRISPR-Cas system is active in vitro and in vivo, a highly virulent phage in vitro was still able co-exist with its bacterial host in vivo. Taken altogether, our results suggest that the CRISPR-Cas defense system of E. lenta provides only partial immunity in the gut.

The complete genome sequence of the virulent bacteriophage PMBT3, isolated on the proteolytic Pseudomonas grimontii strain MBTL2-21, showed no significant similarity to other known phage genome sequences, making this phage the first reported to infect a strain of P. grimontii. Electron microscopy revealed PMBT3 to be a member of the family Siphoviridae, with notably long and flexible whiskers. The linear, double-stranded genome of 87,196 bp has a mol% G+C content of 60.4 and contains 116 predicted protein-encoding genes. A putative tellurite resistance (terB) gene, originally reported to occur in the genome of a bacterium, was detected in the genome of phage PMBT3.

Background: Clostridium perfringens is a well known swine pathogen. C. perfringens type A is considered the causative agent of enteric diseases in neonatal and weaned piglets. Phage therapy using C. perfringens phages in vivo has previously proved effective. Materials and Methods: Pig fecal samples were used to isolate phages, with Clostridium perfringens type A as host. Complete genome sequencing, comparative genomics, a proteome analysis and electron microscopy were used to characterize the phage. Results: Clostridium phage Susfortuna has a double-stranded DNA genome of 19,046 bp with a G+C% content of 29.2, inverted terminal repeats and 28 predicted coding sequences (CDSs). Putative functions could not be assigned to most of the CDSs (64.3%). Transmission electron microscopy of phage Susfortuna revealed an isometric head and a short protruding tail stub resembling the structure of the Podoviridae family. A proteome analysis of phage Susfortuna identified seven structural proteins, but only one could be assigned with a putative function. Conclusions: Based on the morphology, the inverted terminal repeats and the small genome size, phage Susfortuna belongs to subfamily Picovirinae within the Podoviridae family in the order Caudovirales. Together with C. perfringens bacteriophage CPD7, phage Susfortuna represent a new genus of bacteriophages with very limited DNA sequence similarity to other known C. perfringens phages. Despite the limited DNA sequence similarity, the gene synteny among putative structural genes of phage Susfortuna is conserved among several C. perfringens bacteriophages belonging to the Podoviridae family indicating a common ancestor.

Background: Soft rot Pectobacteriaceae includes the genera Pectobacterium and Dickeya, which are important plant pathogens being responsible for diseases in a wide range of plant species, with potatoes as the main group. Both genera cause pre- and postharvest losses of potatoes, resulting in huge economic losses linked with the soft rot diseases. Materials and Methods: Organic waste was used to isolate phages, with Pectobacterium carotovorum subsp. carotovorum DSM 30170 as host. Complete genome sequencing, comparative genomics, and electron microscopy were used to characterize the phage. An adsorption assay was used to estimate adsorption rate. Twenty-three strains from the genera Pectobacterium and Dickeya were used to examine the host range of the phage. Results: Pectobacterium phage Jarilo represents a novel genus of bacteriophages within the family Autographiviridae, order Caudovirales. Jarilo possesses a double-stranded DNA genome of 40557 bp with a G+C% content of 50.08% and 50 predicted open reading frames. Gene synteny and products seem to be partly conserved between Pectobacterium phage Jarilo and Enterobacteria phage T7, but limited nucleotide similarity is found between Jarilo and other phages within the family Autographiviridae. The adsorption rate of phage Jarilo increased continuously for 1 h upon infection. Phage Jarilo was not able to infect any strains of P. carotovorum and Dickeya tested with the exception of the P. carotovorum strain used for isolation. However, phage Jarilo infected 10 of 16 Pectobacterium atrosepticum strains tested. Conclusion: We propose Pectobacterium phage Jarilo as the first member of a new genus of bacteriophages within the family Autographiviridae, order Caudovirales, displaying a broad host range within the genera of Pectobacterium.

Gut microbiome (GM) composition and function are linked to human health and disease, and routes for manipulating the GM have become an area of intense research. Due to its high treatment efficacy, the use of fecal microbiota transplantation (FMT) is generally accepted as a promising experimental treatment for patients suffering from GM imbalances (dysbiosis), e.g. caused by recurrent Clostridioides difficile infections (rCDI). Mounting evidence suggests that bacteriophages (phages) play a key role in successful FMT treatment by restoring the dysbiotic bacterial GM. As a refinement to FMT, removing the bacterial component of donor feces by sterile filtration, also referred to as fecal virome transplantation (FVT), decreases the risk of invasive infections caused by bacteria. However, eukaryotic viruses and prophage-encoded virulence factors remain a safety issue. Recent in vivo studies show how cascading effects are initiated when phage communities are transferred to the gut by e.g. FVT, which leads to changes in the GM composition, host metabolome, and improve host health such as alleviating symptoms of obesity and type-2-diabetes (T2D). In this review, we discuss the promises and limitations of FVT along with the perspectives of using FVT to treat various diseases associated with GM dysbiosis.

Ultraviolet C (UVC) radiation is a widely used technology for the disinfection of surfaces, air flows, water and other liquids. Although extensive research has been conducted on the UV tolerance of bacteriophages used as surrogates for waterborne viruses, limited information is available on phages relevant to food processing. Phages of dairy starters may reach high numbers in dairy facilities and cause fermentation failure with great economic losses for the dairy industry. Here, the UV tolerance of virulent phages, belonging to the 936-group (Skunavirus) of Lactococcus lactis subsp. diacetylactis F7/2, was assessed, employing both host infectivity loss and qPCR assays. A highly heat-tolerant phage (P680) and a less heat-tolerant phage (P008) were exposed to UV radiation at 265 nm (UVC), 285 nm (UVB) and 365 nm (UVA), respectively, in an aqueous suspension, using UV Light-Emitting-Diodes (LEDs) in a static set-up. UVC at 265 nm achieved the highest total inactivation, leading to a 4 log10 reduction of the phage titer at a UV dose of 327 and 164 mJ/cm2 for P680 and P008, respectively. UVB at 285 nm achieved similar inactivation levels, while UVA at 365 nm did not cause major reductions. Phages were also suspended in yoghurt serum of pH 5.5 and pH 7.0 and exposed to UVC radiation at 265 nm. The heat-tolerant phage P680 was more UV tolerant for all wavelengths, matrices and pH values tested. A higher aggregation degree together with less DNA damage was observed for both phages at pH 5.5, especially for phage P680, indicating a UV light-shielding effect. Interestingly, there were indications of some phage survivors exhibiting higher UV tolerance on re-exposure, pointing out a need for further investigation. Our results show that UV LEDs emitting at 265 nm and 285 nm are efficient in reducing the phage population significantly, but also underline that 936-type phages are relatively UV resistant. A further understanding of the main factors influencing UV efficiency could enable future use of the UV technology as an alternative or complement to thermal treatment for phage inactivation.

A novel Lactobacillus delbrueckii bacteriophage PMBT4 was isolated from the Nigerian fermented milk product nono. The phage possesses a long and thin, non-contractile tail and an isometric head, indicating that it belongs to the Siphoviridae family. A neck passage structure (`collar`), previously hypothesized to be encoded by two genes located in the Lactobacillus delbrueckii phage LL-K insertion sequence (KIS) element, as well as in two additional Lb. delbrueckii phages Ld17 and Ld25A, could also be observed on an estimated 1-5% of phage particles by transmission electron microscopy. However, neither mapping of high throughput sequencing data to KIS element genes from Lb. delbrueckii phages LL-K, Ld17 and Ld25A nor PCR amplification of the KIS element genes could corroborate the presence of these genes in the PMBT4 genome. The PMBT4 genome consists of 31,399 bp with a mol% GC content of 41.6 and exhibits high (95-96%) sequence homologies to Lb. delbrueckii phages c5, Ld3, Ld25A and Ld17, which assigned PMBT4 as a new member of this genus, i.e. the Cequinquevirus genus.

Yeasts are eukaryotic microorganisms which have a long history in the biotechnology of food production, as they have been used since centuries in bread-making or in the production of alcoholic beverages such as wines or beers. Relative to this importance, a lot of research has been devoted to the study of yeasts involved in making these important products. The role of yeasts in other fermentations in association with other microorganisms - mainly lactic acid bacteria - has been relatively less studied, and often it is not clear if yeasts occurring in such fermentations are contaminants with no role in the fermentation, spoilage microorganisms or whether they actually serve a technological or functional purpose. Some knowledge is available for yeasts used as starter cultures in fermented raw sausages or in the production of acid curd cheeses. This review aimed to summarize the current knowledge on the taxonomy, the presence and potential functional or technological roles of yeasts in traditional fermented plant, dairy, fish and meat fermentations.

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome. ispartof: NATURE MICROBIOLOGY vol:4 issue:10 pages:1727-1736 ispartof: location:England status: published

Exudative epidermitis (EE), also known as greasy pig disease, is one of the most frequent skin diseases affecting piglets. Zoonotic infections in human occur. EE is primarily caused by virulent strains of Staphylococcus (S.) hyicus. Generally, antibiotic treatment of this pathogen is prone to decreasing success, due to the incremental development of multiple resistances of bacteria against antibiotics. Once approved, bacteriophages might offer interesting alternatives for environmental sanitation or individualized treatment, subject to the absence of virulence and antimicrobial resistance genes. However, genetic characterization of bacteriophages for S. hyicus has, so far, been missing. Therefore, we investigated a piglet raising farm with a stock problem due to EE. We isolated eleven phages from the environment and wash water of piglets diagnosed with the causative agent of EE, i.e., S. hyicus. The phages were morphologically characterized by electron microscopy, where they appeared Siphoviridae-like. The genomes of two phages were sequenced on a MiSeq instrument (Illumina), resulting in the identification of a new virulent phage, PITT-1 (PMBT8), and a temperate phage, PITT-5 (PMBT9). Sequencing of three host bacteria (S. hyicus) from one single farm revealed the presence of two different strains with genes coding for two different exfoliative toxin genes, i.e., exhA (2 strains) and exhC (1 strain). The exhC-positive S. hyicus strain was only weakly lysed by most lytic phages. The occurrence of different virulent S. hyicus strains in the same outbreak limits the prospects for successful phage treatment and argues for the simultaneous use of multiple and different phages attacking the same host.

Phase variation is a common mechanism for creating phenotypic heterogeneity of surface structures in bacteria important for niche adaptation. In Campylobacter, phase variation occurs by random variation in hypermutable homonucleotide 7–11 G (polyG) tracts. To elucidate how phages adapt to phase-variable hosts, we study Fletchervirus phages infecting Campylobacter dependent on a phase-variable receptor. Our data demonstrate that Fletcherviruses mimic their host and encode hypermutable polyG tracts, leading to phase-variable expression of two of four receptor-binding proteins. This creates phenotypically diverse phage populations, including a sub-population that infects the bacterial host when the phase-variable receptor is not expressed. Such population dynamics of both phage and host promote co-existence in a shared niche. Strikingly, we identify polyG tracts in more than 100 phage genera, infecting more than 70 bacterial species. Future experimental work may confirm phase variation as a widespread strategy for creating phenotypically diverse phage populations., Cell Reports, 35 (10), ISSN:2666-3864, ISSN:2211-1247

Background: Bacterial soft rot caused by members of the soft rot Pectobacteriaceae afflicts plant production of both vegetable and ornamental crops. Recent outbreaks highlight Dickeya sp. in the etiology of this disease in potatoes. Since there is a lack of control strategies for these diseases, alternative approaches have been suggested, including the use of biological control mediated by bacteriophages (phages). However, phages infecting many of these members are still undiscovered or poorly described. Materials and Methods: Two phages targeting Dickeya dadantii subsp. dadantii (NCPPB 4097) were isolated from household organic waste and purified. They were then further characterized using whole-genome sequencing and comparative genomics, transmission electron microscopy, latent period and burst size. Results: Dickeya phage Sucellus displayed Siphovirus morphology and had a genome of 39,826 bp with very limited similarity to any previously described phages. Dickeya phage Amaethon had a Podovirus morphology with a genome comprising 41,436 bp and limited similarity to phages in the Kafuna genus. The phages exhibited burst sizes of app. 94 and 240 virions per cell with latent periods of 91 and 86 minutes for Sucellus and Amaethon, respectively. While both phages had similar adsorption efficiencies and latent periods, the rise periods for the two phages diverged markedly, highlighting an odd growth pattern. Conclusions: Together, the two phages isolated here expand the known diversity of phages infecting the important plant pathogen D. dadantii. As they both share limited similarity to previously described groups of phages, they likely constitute novel genera within their respective groups.

International audience; Background:Pseudomonas syringae are ubiquitous epiphytic plant pathogens infecting a wide range of important agricultural plant species. Bacteriophages has been proposed as biocontrol agents against plant pathogens, however, in order to utilize this approach, a deeper understanding of phage diversity and phage-host interactions is required.Materials and Methods: Phages targeting P. syringae GAW0113 were isolated from organic waste samples. Three distinct phage isolates were purified and subjected to whole-genome sequencing, comparative genomics, transmission electron microscopy and host-range assay using a wide selection of diverse P. syringae isolates.Results: The three phage isolates, Pseudomonas phage Bertil, Misse, and Strit, were shown to have podovirus morphology with a short tail stub and isometric head. They had double-stranded DNA ranging from 41,342 to 41,374 bp in size comprising 50–51 open reading frames. The three phage genomes were highly similar and genomic comparison analyses showed that they all belong to the Autographiviridae family of the order Caudovirales. All three phages were shown to have a narrow host-range.Conclusions: The three phages were shown to share morphological and genomic features with other phages in the Autographiviridae family, however, based on the limited nucleotide similarity we propose that the phages constitute a novel genus. All three phages were found to infect multiple strains of P. syringae covering several phylogroups.

Phages are generally considered species- or even strain-specific, yet polyvalent phages are able to infect bacteria from different genera. Here, we characterize the novel polyvalent phage S144, a member of the Loughboroughvirus genus. By screening 211 Enterobacteriaceae strains, we found that phage S144 forms plaques on specific serovars of Salmonella enterica subsp. enterica and on Cronobacter sakazakii. Analysis of phage resistant mutants suggests that the O-antigen of lipopolysaccharide is the phage receptor in both bacterial genera. The S144 genome consists of 53,628 bp and encodes 80 open reading frames (ORFs), but no tRNA genes. In total, 32 ORFs coding for structural proteins were confirmed by ESI-MS/MS analysis, whereas 45 gene products were functionally annotated within DNA metabolism, packaging, nucleotide biosynthesis and phage morphogenesis. Transmission electron microscopy showed that phage S144 is a myovirus, with a prolate head and short tail fibers. The putative S144 tail fiber structure is, overall, similar to the tail fiber of phage Mu and the C-terminus shows amino acid similarity to tail fibers of otherwise unrelated phages infecting Cronobacter. Since all phages in the Loughboroughvirus genus encode tail fibers similar to S144, we suggest that phages in this genus infect Cronobacter sakazakii and are polyvalent Funding: This research was funded by Danish AgriFish Agency of Ministry of Environment and Food, grant number 34009-14-0873. Acknowledgments: We thank Mark van Raaij for his advice (CNB–CSIC, Madrid, Spain) and John E. Olsen (Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark), Anne Elsser-Gravesen (ISI Food Protection, Århus, Denmark) and Yinghua Xiao (Arla Foods, Århus, Denmark) for providing bacterial strains used in the determination of phage host range. Angela Back (Max Rubner-Institut) is acknowledged for her technical assistance with the electron microscopy

Phages are generally considered species- or even strain-specific, yet polyvalent phages are able to infect bacteria from different genera. Here, we characterize the novel polyvalent phage S144, a member of the Loughboroughvirus genus. By screening 211 Enterobacteriaceae strains, we found that phage S144 forms plaques on specific serovars of Salmonella enterica subsp. enterica and on Cronobacter sakazakii. Analysis of phage resistant mutants suggests that the O-antigen of lipopolysaccharide is the phage receptor in both bacterial genera. The S144 genome consists of 53,628 bp and encodes 80 open reading frames (ORFs), but no tRNA genes. In total, 32 ORFs coding for structural proteins were confirmed by ESI-MS/MS analysis, whereas 45 gene products were functionally annotated within DNA metabolism, packaging, nucleotide biosynthesis and phage morphogenesis. Transmission electron microscopy showed that phage S144 is a myovirus, with a prolate head and short tail fibers. The putative S144 tail fiber structure is, overall, similar to the tail fiber of phage Mu and the C-terminus shows amino acid similarity to tail fibers of otherwise unrelated phages infecting Cronobacter. Since all phages in the Loughboroughvirus genus encode tail fibers similar to S144, we suggest that phages in this genus infect Cronobacter sakazakii and are polyvalent.

International audience; Streptococcus thermophilus is a lactic acid bacterium commonly used for the manufacture of yogurt and specialty cheeses. Virulent phages represent a major risk for milk fermentation processes worldwide, as they can inactivate the added starter bacterial cells, leading to low-quality fermented dairy products. To date, four genetically distinct groups of phages infecting S. thermophilus have been described. Here, we describe a fifth group. Phages P738 and D4446 are virulent siphophages that infect a few industrial strains of S. thermophilus. The genomes of phages P738 and D4446 were sequenced and found to contain 34,037 and 33,656 bp as well as 48 and 46 open reading frames, respectively. Comparative genomic analyses revealed that the two phages are closely related to each other but display very limited similarities to other S. thermophilus phages. In fact, these two novel S. thermophilus phages share similarities with streptococcal phages of nondairy origin, suggesting that they emerged recently in the dairy environment.IMPORTANCE Despite decades of research and adapted antiphage strategies such as CRISPR-Cas systems, virulent phages are still a persistent risk for the milk fermentation industry worldwide, as they can cause manufacturing failures and alter product quality. Phages P738 and D4446 are novel virulent phages that infect the foodgrade Gram-positive bacterial species Streptococcus thermophilus. These two related viruses represent a fifth group of S. thermophilus phages, as they are significantly distinct from other known S. thermophilus phages. Both phages share similarities with phages infecting nondairy streptococci, suggesting their recent emergence and probable coexistence in dairy environments. These findings highlight the necessity of phage surveillance programs as the phage population evolves in response to the application of antiphage strategies.

To date, Certrevirus is one of two genera of bacteriophage (phage), with phages infecting Pectobacterium atrosepticum, an economically important phytopathogen that causes potato blackleg and soft rot disease. This study provides a detailed description of Pectobacterium phage CB7 (vB_PatM_CB7), which specifically infects P. atrosepticum. Host range, morphology, latent period, burst size and stability at different conditions of temperature and pH were examined. Analysis of its genome (142.8 kbp) shows that the phage forms a new species of Certrevirus, sharing sequence similarity with other members, highlighting conservation within the genus. Conserved elements include a putative early promoter like that of the Escherichia coli sigma70 promoter, which was found to be shared with other genus members. A number of dissimilarities were observed, relating to DNA methylation and nucleotide metabolism. Some members do not have homologues of a cytosine methylase and anaerobic nucleotide reductase subunits NrdD and NrdG, respectively. Furthermore, the genome of CB7 contains one of the largest numbers of homing endonucleases described in a single phage genome in the literature to date, with a total of 23 belonging to the HNH and LAGLIDADG families. Analysis by RT-PCR of the HNH homing endonuclease residing within introns of genes for the large terminase, DNA polymerase, ribonucleotide reductase subunits NrdA and NrdB show that they are splicing competent. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) was also performed on the virion of CB7, allowing the identification of 26 structural proteins&mdash, 20 of which were found to be shared with the type phages of the genera of Vequintavirus and Seunavirus. The results of this study provide greater insights into the phages of the Certrevirus genus as well as the subfamily Vequintavirinae.

Bacteria of Lactobacillus sp. are very useful to humans. However, the biology and genomic diversity of their (bacterio)phage enemies remains understudied. Knowledge on Lactobacillus phage diversity should broaden to develop efficient phage control strategies. To this end, organic waste samples were screened for phages against two wine-related Lactobacillus plantarum strains. Isolates were shotgun sequenced and compared against the phage database and each other by phylogenetics and comparative genomics. The new isolates had only three distant relatives from the database, but displayed a high overall degree of genomic similarity amongst them. The latter allowed for the use of one isolate as a representative to conduct transmission electron microscopy and structural protein sequencing, and to study phage adsorption and growth kinetics. The microscopy and proteomics tests confirmed the observed diversity of the new isolates and supported their classification to the family Siphoviridae and the proposal of the new phage genus “Silenusvirus”.

The lactobacilli associated with a fermented goat milk product from Tajikistan were isolated to characterize their technological properties and antibiotic resistances in order to assess their suitability for development as starter cultures. In this study, twenty three strains were identified by 16S rRNA sequencing as typical dairy-associated lactic acid bacterial strains, i.e. L. plantarum, L. pentosus, L. delbrueckii, L. helveticus and L. paracasei strains. These strains were generally susceptible to most antibiotics tested in this study and this allowed a selection of strains as safe starters. The draft genomes of four representative strains were sequenced and the number of contigs of the four assembled genomes ranged from 51 to 245 and the genome sizes ranged from 1.75 to 3.24 Mbp. These representative strains showed differences in their growth behavior and pH reducing abilities in in vitro studies. The co-inoculation of these Lactobacillus spp. strains together with a yeast Kluyveromyces marxianus MBT-5698, or together with the yeast and an additional Streptococcus thermophilus MBT-2, led to a pH reduction to 3.4 after 48 h. Only in the case of fermentation inoculated with the co-culture, the viscosity of the milk increased noticeably. In contrast, fermentations with single strains did not lead to gelation of the milk and to decrease the pH after 24h. The results of this study provide a comprehensive understanding of the predominant lactobacilli related to Tajikistan fermented milk products.

Thermal inactivation of highly heat-stable Lactococcus lactis phages P680 and P1532 of the 936 group and P635 of the c2 group was investigated in a pilot-plant pasteurizer after suspension of the phages in raw milk (107 pfu/ml). The heat-sensitive reference phage P008 was tested as a control. The titers of the phages P008 and P635 decreased ≥99.99% after heating for 32 s at 75 °C and 80 °C, respectively. To achieve a similar inactivation of ≥99.99%, phages P680 and P1532 had to be treated for 39 s at temperatures of 95 °C and 97.5 °C, respectively. D- and z-values for thermal inactivation were calculated for each of the phages. When comparing thermal inactivation data of phages in the pilot-plant pasteurizer obtained in this study with literature data on phage heat inactivation in stainless-steel test tubes in a water bath, the pilot-plant pasteurizer was notably more efficient.

To investigate the notion that starter cultures can be a reservoir of bacteriophages (phages) in the dairy environment, strains of three DL-starters (undefined mesophilic mixed-strain starters containing Lactococcus lactis subsp. lactis biovar. diacetylactis and Leuconostoc species) were selected and induced by mitomycin C, and the whole starters were induced spontaneously as well as by mitomycin C. Frequency of induction of 17%, 26% and 12% was estimated among the isolates of the three starters, with majority of the induced phages mostly showing morphological similarity to known P335 phages, and with a fraction of them showing atypical features. Sequences of P335 quasi-species phages were found to be the most frequent entities in almost all metaviromes derived from the induced lysates. However, sequences of Slavirus phages (previously 936 phages) were emerged as the predominant entities following spontaneous induction of one of the starters, suggesting a phage-carrier state. Sequences of other phages such as 949,1706, C2virus (previously c2 phages) and Leuconostoc species could also be observed but with a lower relative frequency. Taken together, the majority of the P335 quasi-species phages could represent the induced viral community of the starters and the remaining phase groups mainly represent the background ambient viral community.

Campylobacter phage vB_CjeM_Los1 was recently isolated from a slaughterhouse in the Republic of Ireland using the host Campylobacter jejuni subsp. jejuni PT14, and full-genome sequencing and annotation were performed. The genome was found to be 134,073 bp in length and to contain 169 predicted open reading frames. Transmission electron microscopy images of vB_CjeM_Los1 revealed that it belongs to the family Myoviridae, with tail fibres observed in both extended and folded conformations, as seen in T4. The genome size and morphology of vB_CjeM_Los1 suggest that it belongs to the genus Cp8virus, and seven other Campylobacter phages with similar size characteristics have also been fully sequenced. In this work, comparative studies were performed in relation to genomic rearrangements and conservation within each of the eight genomes. None of the eight genomes were found to have undergone internal rearrangements, and their sequences retained more than 98% identity with one another despite the widespread geographical distribution of each phage. Whole-genome phylogenetics were also performed, and clades were shown to be representative of the differing number of tRNAs present in each phage. This may be an indication of lineages within the genus, despite their striking homology.

Lactobacilli are involved in fermentation of milk-, plant-, or meat-based food products. They metabolize hexose sugars to lactic acid during fermentation, leading to a decrease in the pH. This preservative effect contributes to the digestibility of the raw material and improves the organo leptic properties of the product. Food fermentations are widely utilized in modern food production, with lactobacilli as defined starter cultures, specifically in the production of fermented raw sausages or milk products.

A Gram-stain-negative, rod-shaped Proteobacteria isolate, MBT G8648T, was obtained from an acid curd cheese called Quargel. The isolate was moderately salt tolerant and motile, with numerous peritrichous flagella. The 16S rRNA gene sequence analysis indicated that the strain belongs to the genus Halomonas , with 98.42 % 16S rRNA gene sequence similarity with Halomonas titanicae BH1T as nearest related neighbour. Further comparative sequence analysis of secA and gyrB genes, as well as physiological and biochemical tests, revealed that this bacterium formed a taxon well-separated from its nearest neighbours and other established Halomonas species. Thus, the strain represents a new species, for which the name Halomonas nigrificans sp. nov. is proposed, with strain MBT G8648T (=LMG 29097T =DSM 105749T) as type strain.