Isolation of a Novel Phage with Activity against Streptococcus mutans Biofilms

peer-reviewedStreptococcus mutans is one of the principal agents of caries formation mainly, because of its ability to form biofilms at the tooth surface. Bacteriophages (phages) are promising antimicrobial agents that could be used to prevent or treat caries formation by S. mutans. The aim of this study was to isolate new S. mutans phages and to characterize their antimicrobial properties. A new phage, ɸAPCM01, was isolated from a human saliva sample. Its genome was closely related to the only two other available S. mutans phage genomes, M102 and M102AD. ɸAPCM01 inhibited the growth of S. mutans strain DPC6143 within hours in broth and in artificial saliva at multiplicity of infections as low as 2.5x10-5. In the presence of phage ɸAPCM01 the metabolic activity of a S. mutans biofilm was reduced after 24 h of contact and did not increased again after 48 h, and the live cells in the biofilm decreased by at least 5 log cfu/ml. Despite its narrow host range, this newly isolated S. mutans phage exhibits promising antimicrobial properties

A long and abundant non-coding RNA in Lactobacillus salivarius

Lactobacillus salivarius, found in the intestinal microbiota of humans and animals, is studied as an example of the sub-dominant intestinal commensals that may impart benefits upon their host. Strains typically harbour at least one megaplasmid that encodes functions contributing to contingency metabolism and environmental adaptation. RNA sequencing (RNA-seq) transcriptomic analysis of L. salivarius strain UCC118 identified the presence of a novel unusually abundant long non-coding RNA (lncRNA) encoded by the megaplasmid, and which represented more than 75 % of the total RNA-seq reads after depletion of rRNA species. The expression level of this 520 nt lncRNA in L. salivarius UCC118 exceeded that of the 16S rRNA, it accumulated during growth, was very stable over time and was also expressed during intestinal transit in a mouse. This lncRNA sequence is specific to the L. salivarius species; however, among 45 L. salivarius genomes analysed, not all (only 34) harboured the sequence for the lncRNA. This lncRNA was produced in 27 tested L. salivarius strains, but at strain-specific expression levels. High-level lncRNA expression correlated with high megaplasmid copy number. Transcriptome analysis of a deletion mutant lacking this lncRNA identified altered expression levels of genes in a number of pathways, but a definitive function of this new lncRNA was not identified. This lncRNA presents distinctive and unique properties, and suggests potential basic and applied scientific developments of this phenomenon

Three New Escherichia coli Phages from the Human Gut Show Promising Potential for Phage Therapy

peer-reviewedWith the emergence of multi-drug resistant bacteria the use of bacteriophages (phages) is gaining renewed interest as promising anti-microbial agents. The aim of this study was to isolate and characterize phages from human fecal samples. Three new coliphages, ɸAPCEc01, ɸAPCEc02 and ɸAPCEc03, were isolated. Their phenotypic and genomic characteristics, and lytic activity against biofilm, and in combination with ciprofloxacin, were investigated. All three phages reduced the growth of E. coli strain DPC6051 at multiplicity of infection (MOI) between 10−3 and 105. A cocktail of all three phages completely inhibited the growth of E. coli. The phage cocktail also reduced biofilm formation and prevented the emergence of phage-resistant mutants which occurred with single phage. When combined with ciprofloxacin, phage alone or in cocktail inhibited the growth of E. coli and prevented the emergence of resistant mutants. These three new phages are promising biocontrol agents for E. coli infections

The Complete Genome of Propionibacterium freudenreichii CIRM-BIA1T, a Hardy Actinobacterium with Food and Probiotic Applications

Background: Propionibacterium freudenreichii is essential as a ripening culture in Swiss-type cheeses and is also considered for its probiotic use [1]. This species exhibits slow growth, low nutritional requirements, and hardiness in many habitats. It belongs to the taxonomic group of dairy propionibacteria, in contrast to the cutaneous species P. acnes. The genome of the type strain, P. freudenreichii subsp. shermanii CIRM-BIA1 (CIP 103027T), was sequenced with an 11-fold coverage. Methodology/Principal Findings: The circular chromosome of 2.7 Mb of the CIRM-BIA1 strain has a GC-content of 67% and contains 22 different insertion sequences (3.5% of the genome in base pairs). Using a proteomic approach, 490 of the 2439 predicted proteins were confirmed. The annotation revealed the genetic basis for the hardiness of P. freudenreichii, as the bacterium possesses a complete enzymatic arsenal for de novo biosynthesis of aminoacids and vitamins (except panthotenate and biotin) as well as sequences involved in metabolism of various carbon sources, immunity against phages, duplicated chaperone genes and, interestingly, genes involved in the management of polyphosphate, glycogen and trehalose storage. The complete biosynthesis pathway for a bifidogenic compound is described, as well as a high number of surface proteins involved in interactions with the host and present in other probiotic bacteria. By comparative genomics, no pathogenicity factors found in P. acnes or in other pathogenic microbial species were identified in P. freudenreichii, which is consistent with the Generally Recognized As Safe and Qualified Presumption of Safety status of P. freudenreichii. Various pathways for formation of cheese flavor compounds were identified: the Wood-Werkman cycle for propionic acid formation, amino acid degradation pathways resulting in the formation of volatile branched chain fatty acids, and esterases involved in the formation of free fatty acids and esters. Conclusions/Significance: With the exception of its ability to degrade lactose, P. freudenreichii seems poorly adapted to dairy niches. This genome annotation opens up new prospects for the understanding of the P. freudenreichii probiotic activity

Dairy propionibacteria as human probiotics: A review of recent evidence

Probiotics have been the subject of intensive research, mainly focusing on bifidobacteria and lactic acid bacteria. However, there is evidence that dairy propionibacteria also display probiotic properties, which as yet have been underestimated. The aim of this paper is to review recent data which report probiotic characteristics of dairy propionibacteria and to distinctly organise them based on the experimental strategy employed: ranked from in vitro evidence to in vivo trials, which is a new approach. In addition to the selection criteria for probiotics in areas such as food safety, technological and digestive stress tolerance, many potential health benefits have been described which include modulation of microbiota and metabolic activity in the gut, modulation of intestinal motility and absorption, impact on intestinal inflammation, modulation of the immune system and potential modulation of risk factors for cancer development. The robust nature of dairy propionibacteria towards technological stresses should allow their future use in various fermented probiotic foods. Among the probiotic properties of dairy propionibacteria described in the literature, some of these properties are different from those reported for bifidobacteria and lactic acid bacteria. However, supplementation with dairy propionibacteria in randomised, placebo-controlled, double-blind human trials has mainly involved mixtures of propionibacteria with probiotic bacteria from other genera. Clinical studies involving the use of dairy propionibacteria alone are lacking. Such studies will allow the specifically observed health benefits to be attributed to dairy propionibacteria. This, in turn, will allow the investigation of the synergistic effects with other probiotic bacteria or beneficial food components

Role of the β-glucan surface polysaccharide in Propionibacterium freudenreichii: physiological and immunomodulatory properties

P. freudenreichii (PF) is a Gram + species, with the GRAS (Generally Recognized As Safe) status in the USA and a Qualified Presumption of Safety (QPS) status in Europe. It is widely consumed by humans because it is an essential ripening culture in Swiss type cheeses (Emmental, Leerdammer®…), and also as a probiotic in food supplement (Propio-Fidus®). Recently, PF was shown to produce a (1→3, 1→2)-β-D-glucan polysaccharide. A single gene (named gtf) is responsible for the biosynthesis of this surface polysaccharide, that has been immunodetected for 30% of the 100 strains of PF tested. Here we investigated the role(s) of this β-D-glucan

Role of the β-glucan surface polysaccharide in Propionibacterium freudenreichii: physiological and immunomodulatory properties

P. freudenreichii (PF) is a Gram + species, with the GRAS (Generally Recognized As Safe) status in the USA and a Qualified Presumption of Safety (QPS) status in Europe. It is widely consumed by humans because it is an essential ripening culture in Swiss type cheeses (Emmental, Leerdammer®…), and also as a probiotic in food supplement (Propio-Fidus®). Recently, PF was shown to produce a (1→3, 1→2)-β-D-glucan polysaccharide. A single gene (named gtf) is responsible for the biosynthesis of this surface polysaccharide, that has been immunodetected for 30% of the 100 strains of PF tested. Here we investigated the role(s) of this β-D-glucan

Multiplex PCR for rapid identification of major lactic acid bacteria genera in cider and other fermented foods

Lactobacillus, Pediococcus, Oenococcus and Leuconostoc are the main Lactic Acid Bacteria (LAB) genera present in cider as they are able to survive this hostile environment. LAB play a significant role in cider quality, for example in the process of malolactic fermentation, even though they can also be involved in spoilage of cider (production of biogenic amines, exopolysaccharides, off-flavours…). In this context a better monitoring of the fermentation process is a matter of interest to guarantee cider quality. In the present study, we designed a genus-specific multiplex PCR for a rapid and simultaneous detection of the four main LAB genera involved in cider production. This multiplex PCR worked equally with purified genomic DNA of bacterial isolates and with colonies directly picked from agar plates. This new PCR method was also successfully extended to wine and dairy isolates, and thus constitutes an effective tool to quickly identify LAB associated with fermented foods. Moreover, many biodiversity studies would also benefit from this fast, cheap and reliable identification method