Bacteriophage-insensitive mutants for high quality Crescenza manufacture

Phage defence loci of Streptococcus thermophilus-tip of the anti-phage iceberg?

Bacteria possess (bacterio)phage defence systems to ensure their survival. The thermophilic lactic acid bacterium, Streptococcus thermophilus, which is used in dairy fermentations, harbours multiple CRISPR-Cas and restriction and modification (R/M) systems to protect itself against phage attack, with limited reports on other types of phage-resistance. Here, we describe the systematic identification and functional analysis of the phage resistome of S. thermophilus using a collection of 27 strains as representatives of the species. In addition to CRISPR-Cas and R/M systems, we uncover nine distinct phage-resistance systems including homologues of Kiwa, Gabija, Dodola, defence-associated sirtuins and classical lactococcal/streptococcal abortive infection systems. The genes encoding several of these newly identified S. thermophilus antiphage systems are located in proximity to the genetic determinants of CRISPR-Cas systems thus constituting apparent Phage Defence Islands. Other phage-resistance systems whose encoding genes are not co-located with genes specifying CRISPR-Cas systems may represent anchors to identify additional Defence Islands harbouring, as yet, uncharacterised phage defence systems. We estimate that up to 2.5% of the genetic material of the analysed strains is dedicated to phage defence, highlighting that phage-host antagonism plays an important role in driving the evolution and shaping the composition of dairy streptococcal genomes.

Selection and characterization of spontaneous phage-resistant mutant of Limosilactobacillus fermentum

Phage infection remains a major cause of fermentation failures in the dairy industry. The development of phage-resistant mutants of important fermentation strains is an effective measure used to address phage-related issues. This study employed the secondary culture method to screen for spontaneous phage-resistant mutants from the phage sensitive strain Limosilactobacillus fermentum IMAU32646 (L. fermentum IMAU32646). The phenotypic characteristics, technological attributes, probiotic characterization, adsorption characteristics and mutant genes were investigated. The results showed that the mutant strain displayed a high degree of phage-resistance and stability. The mutant strain produced more lactic acid during fermentation than the sensitive strain, while maintaining identical cell structure and morphologies. The mutant strain exhibited superior tolerance to acid and bile salts compared to the sensitive strain. Furthermore, the adsorption rate of phage LFP01 on the mutant strain was significantly lower than that of the sensitive strain. Following genome re-sequencing analysis showed that adsorption interference and blocked DNA injection were responsible for its phage-resistance. These results may provide a new strategy for avoiding phage contamination and industrial application of phage-resistant strains with good characteristics.

Tn5 Transposon-based Mutagenesis for Engineering Phage-resistant Strains of Escherichia coli BL21 (DE3)

Escherichia coli is a preferred strain for recombinant protein production, however, it is often plagued by phage infection during experimental studies and industrial fermentation. While the existing methods of obtaining phage-resistant strains by natural mutation are not efficient enough and time-consuming. Herein, a high-throughput method by combining Tn5 transposon mutation and phage screening was used to produce Escherichia coli BL21 (DE3) phage-resistant strains. Mutant strains PR281-7, PR338-8, PR339-3, PR340-8, and PR347-9 were obtained, and they could effectively resist phage infection. Meanwhile, they had good growth ability, did not contain pseudolysogenic strains, and were controllable. The resultant phage-resistant strains maintained the capabilities of producing recombinant proteins since no difference in mCherry red fluorescent protein expression was found in phage-resistant strains. Comparative genomics showed that PR281-7, PR338-8, PR339-3, and PR340-8 mutated in ecpE, nohD, nrdR, and livM genes, respectively. In this work, a strategy was successfully developed to obtain phage-resistant strains with excellent protein expression characteristics by Tn5 transposon mutation. This study provides a new reference to solve the phage contamination problem.

STUDY OF THE BIOTECHNOLOGICAL POTENTIAL OF SELECTED LACTIC ACID BACTERIA CULTURES

Fermenting microflora has been selected by biotechnological activity markers, with various methodological approaches used, namely: directional selection, selection of bacteriophage-insensitive mutants, protoplast regeneration. The experimental data show a significant biotechnological potential of the selected lactic acid bacteria. They are characterized by high milk-clotting activity and yield, the ability to form aromatic compounds and/or viscous components, excellent organoleptic qualities of clots fermented by them, antago-nistic activity against pathogenic and opportunistic pathogenic microorganisms, and phage-resistance to species-specific virulent phages. The collection of industrial microorganisms of Institute of Food Resources of National Academy of Agrarian Sciences (IFR NAAS) has been supplemented with new bioactive strains, in particular, the species Streptococcus thermophilus, Lactobacillus acidophilus, Lactoba-cillus rhamnosus and Lactococcus lactis. Four bacterial compositions have been created. Three of them (Iprovit-LB-R; Iprovit-LB-A, and Iprovit-ST) are supposed to be used as functional enrichers for dry foodstuffs or as biologically active supplements. The bacterial prepara-tion Iprovit-Bifidolux is a universal composition. It can be introduced both as a fermenting culture for milk fermentation and as an enricher for dry and liquid foodstuffs. Biotechnologies for the production of dry bacterial preparations on the basis of selected strains have been field-proven at the State Research Enterprise of Starter Cultures that belongs to the IFR NAAS. The data on a wide range of clinical and therapeutic effects of the bacterial preparation Iprovit-Bifidolux allow recommending it for manufacturing functional foods.

Generation of Bacteriophage-Insensitive Mutants of Streptococcus thermophilus via an Antisense RNA CRISPR-Cas Silencing Approach

Predation of starter lactic acid bacteria such as Streptococcus thermophilus by bacteriophages is a persistent and costly problem in the dairy industry. CRISPR-mediated bacteriophage insensitive mutants (BIMs), while straightforward to generate and verify, can quickly be overcome by mutant phages. The aim of this study was to develop a tool allowing the generation of derivatives of commercial S. thermophilus strains which are resistant to phage attack through a non-CRISPR-mediated mechanism, with the objective of generating BIMs exhibiting stable resistance against a range of isolated lytic S. thermophilus phages. To achieve this, standard BIM generation was complemented by the use of the wild-type (WT) strain which had been transformed with an antisense mRNA-generating plasmid (targeting a crucial CRISPR-associated [cas] gene) in order to facilitate the generation of non-CRISPR-mediated BIMs. Phage sensitivity assays suggest that non-CRISPR-mediated BIMs exhibit some advantages compared to CRISPR-mediated BIMs derived from the same strain.IMPORTANCE The outlined approach reveals the presence of a powerful host-imposed barrier for phage infection in S. thermophilus Considering the detrimental economic consequences of phage infection in the dairy processing environment, the developed methodology has widespread applications, particularly where other methods may not be practical or effective in obtaining robust, phage-tolerant S. thermophilus starter strains.

In vivo efficacy of single phage versus phage cocktail in resolving burn wound infection in BALB/c mice

Klebsiella pneumoniae is one of the most predominant pathogens associated with burn wound infections, causing considerable morbidity and mortality. The indiscriminate usage of antibiotics has led to the development of resistant strains, which have contributed towards the inefficacy of antibiotics. Phage therapy is a promising alternative to hinder the progression of pathogenic bacteria. However, phage bacterial resistance is already well known but the use of phage cocktails can overcome this drawback. The aim of the study was to evaluate the therapeutic efficacy of monophage (Kpn1, Kpn2, Kpn3, Kpn4 and Kpn5) in comparison to phage cocktail in resolving the course of burn wound infection in mice. Although, animals receiving monophage therapy exhibited efficacy in resolving the course of infection but phage cocktail was highly effective in arresting the entire infection process (bacterial load, wound contraction, skin myeloperoxidase activity, collagen formation and histopathological analysis). In comparison to untreated control mice, a significant reduction in bacterial load to 4.32, 4.64, 4.42, 4.11 and 4.27 log CFU/ml in Kpn1, Kpn2, Kpn3 Kpn4 and Kpn5 treated animals was obtained respectively was on peak day (3rd day). However, the group receiving phage cocktail (group 7) showed maximum reduction in bacterial load in the skin tissue. The bacterial load was significantly reduced to 3.01 log CFU/ml on peak day. This accounts for a significant reduction of 6 log cycles (p < 0.01) as compared to that of untreated control animals where a peak of 8.81 log CFU/ml was seen followed by steady decrease thereafter. Thus, phage cocktail gave maximum protection against burn wound infection by K. pneumoniae B5055. Compared to any single phage, phage cocktail significantly checked the emergence of resistant mutants. Hence this approach can serve as an effective strategy in treating Klebsiella mediated burn wound infections in individuals who do not respond to conventional antibiotic therapy.