Genomic and Proteomic Characterization of Bacteriophage BH1 Spontaneously Released from Probiotic Lactobacillus rhamnosus Pen

Abstract

Lactobacillus rhamnosus Pen is a human endogenous strain used for the production of probiotic formula, which is effective in the prevention of antibiotic-associated diarrhoea. Our study showed that this probiotic strain releases bacteriophage BH1 without the addition of any inducing agent. Our research revealed that phage BH1 has a circular genome with a length of 40721 nt and a GC content of 44.8%. The genome of phage BH1 possesses 57 open reading frames which could be divided into functional modules associated with DNA packaging, morphogenesis, lysis, integration, genetic switch, and replication. In spite of similarity in morphology and genomic organization, comparative analysis revealed substantial genetic diversity and mosaic genomic architecture among phages described for the Lactobacillus casei group. Additionally, qPCR and ddPCR analysis confirmed earlier microscopic observations indicating that L. rhamnosus Pen liberates bacteriophage particles during growth. This occurs spontaneously, and is not a result of external inducing factors. For samples collected after 4 and 24 h of L. rhamnosus Pen culture, the number of attB and attP copies increased 2.5 and 12 times, respectively. This phenomenon, by introducing resistance to other phages or enhancing the biofilm-forming capabilities, may increase the survivability of microorganisms in their natural ecological niche. Conversely, spontaneous phage induction may be an important virulence factor for bacteria, posing a potential threat for the human host.

Occurrence and genetic diversity of prophage sequences identified in the genomes of L. casei group bacteria

“…It is worth noting that within the described study, a bacteriophage (R23.1) was isolated that had a genome of only 14.5 kb in which 22 ORFs were detected. This bacteriophage showed no genetic similarity with bacteriophages previously described for L. rhamnosus species 5 , 13 , 31 . Of great interest is the enormous variation between the prophage sequences detected for the species studied.…”

“…Lysogeny is a common phenomenon in bacteria of the genus Lactobacillus, including those belonging to the L. casei group 5 – 8 . Bacteria of this group, as a result of reclassification of the genus Lactobacillus, now belong to the genus Lacticaseibacillus , which includes 17 species including Lacticaseibacillus casei , Lacticaseibacillus paracasei and Lacticaseibacillus rhamnosus, traditionally considered as the L. casei group .…”

“…Considering that these bacteria are used in many industrial processes, the potential for induction and lysis would bring about negative consequences for the industries in which they are used 8 . On the other hand, many studies indicate that lysogenic phages have a benign nature, and do not cause complete lysis of bacterial cultures even when induced 5 , 9 , 10 . The process of stimulating the life cycle itself, resulting in the formation of phage particles, can be caused by environmental factors, such as changes in pH and temperature, poor nutrient availability, or exposure to reactive oxygen species and antibiotics 4 , 11 , 12 .…”

Genome and Pangenome Analysis of Lactobacillus hilgardii FLUB—A New Strain Isolated from Mead

“…Ochman and Davalos [ 33 ] have noted that there is no space for large amounts of pseudogenes in the genomes of free-living bacteria, and so they are removed by effective selection. Three regularly interspaced short palindromic repeats (CRISPR) were found in the whole genome sequence (WGS): one located on the circular chromosomal sequence CDS (3,071,102 bp, locus 2,452,162–2,459,226, with a prediction of genes of csn2, cas2, cas1, cas9), and two on plasmids 2 (37,669 bp, locus 425–582) and 4 (6896 bp, locus 5201–5303), indicating that L. hilgardii FLUB may acquire resistance to phage infection [ 34 , 35 ]. In this article, we wanted to identify the characteristics of L. hilgardii FLUB that may be associated with its evolutionary success in adapting to the new habitat provided by mead.…”

Exoproteome Analysis of Antagonistic Interactions between the Probiotic Bacteria Limosilactobacillus reuteri LR1 and Lacticaseibacillus rhamnosus F and Multidrug Resistant Strain of Klebsiella pneumonia

“…While the majority of phage-encoded genes are repressed during lysogeny, moron loci are often highly expressed and can provide a competitive advantage to the host [57]. Interestingly, the secretion of individual prophage genes was previously reported for L. rhamnosus LRB [58], while L. rhamnosus Pen can spontaneously release entire phage particles that were proposed to increase the survivability of microorganism in their natural ecological niche [59].…”