The association of prokaryotic antiviral systems and symbiotic phage communities in drinking water microbiomes

Abstract

Prokaryotic antiviral systems are important mediators for prokaryote-phage interactions, which have significant implications for the survival of prokaryotic community. However, the prokaryotic antiviral systems under environmental stress are poorly understood, limiting the understanding of microbial adaptability. Here, we systematically investigated the profile of the prokaryotic antiviral systems at the community level and prokaryote-phage interactions in the drinking water microbiome. Chlorine disinfectant was revealed as the main ecological driver for the difference in prokaryotic antiviral systems and prokaryote-phage interactions. Specifically, the prokaryotic antiviral systems in the microbiome exhibited a higher abundance, broader antiviral spectrum, and lower metabolic burden under disinfectant stress. Moreover, significant positive correlations were observed between phage lysogenicity and enrichment of antiviral systems (e.g., Type IIG and IV restriction-modification (RM) systems, and Type II CRISPR-Cas system) in the presence of disinfection, indicating these antiviral systems might be more compatible with lysogenic phages and prophages. Accordingly, there was a stronger prokaryote-phage symbiosis in disinfected microbiome, and the symbiotic phages carried more auxiliary metabolic genes (AMGs) related to prokaryotic adaptability as well as antiviral systems, which might further enhance prokaryote survival in drinking water distribution systems. Overall, this study demonstrates that the prokaryotic antiviral systems had a close association with their symbiotic phages, which provides novel insights into prokaryote-phage interactions and microbial environmental adaptation.

Comprehensive Analysis of Antiphage Defense Mechanisms: Serovar-Specific Patterns

“…A recent pangenome analysis has unveiled various new systems within bact nomes, some of which elucidate novel defense mechanisms at the population le These bacterial defense systems pose challenges to the effectiveness of phage app The thorough characterization of phage defense systems, along with their potentia backs, is essential for the deeper comprehension of the hurdles in practical phag cation and for the advancement of phage technology. Of the 151 antiphage systems today, 24 were found in the investigated Leptospira strains (Figure 5) [28].…”

“…The thorough characterization of phage defense systems, along with their potential drawbacks, is essential for the deeper comprehension of the hurdles in practical phage application and for the advancement of phage technology. Of the 151 antiphage systems known today, 24 were found in the investigated Leptospira strains (Figure 5) [28]. The functional subunits of R-M systems include methyltransferase (MTas transfers a methyl group from the S-adenosyl methionine (SAM) donor molecul sine or adenine in the DNA, along with the corresponding restriction endo (REase).…”

“…The thorough characterization of phage defense systems, along with their potential drawbacks, is essential for the deeper comprehension of the hurdles in practical phage application and for the advancement of phage technology. Of the 151 antiphage systems known today, 24 were found in the investigated Leptospira strains ( Figure 5 ) [ 28 ].…”

Uncovering differences in the composition and function of phage communities and phage-bacterium interactions in raw soy sauce

“…Six phages (ctg182745, ctg307755, ctg321052, ctg328091, ctg409955, and ctg98054) were found to possess gene DNMT1 encoding DNA (cytosine-5)-methyltransferase 1 (EC:2.1.1.37), which was involved in organic nitrogen metabolism (cysteine and methionine metabolism). The gene DNMT1 was also detected in phage genomes in drinking water distribution systems (Huang et al, 2023). In addition, one contig (ctg409955) was found to carry the gene asnB (Figure 4B), which is also associated with organic nitrogen metabolism.…”

New drinking water genome catalog identifies a globally distributed bacterial genus adapted to disinfected drinking water systems

“…For instance, studies have shown enrichment of functional traits (e.g., necrotrophy) in a treatment and disinfection strategy-specific manner [13][14][15][16] . Metagenomics has also helped identify pathogenic traits 15 and antibiotic resistant genes 17,18 and further elucidated the prevalence of phages 4 and anti-phage defense mechanisms 19 which can impact microbial community dynamics. Recently, Liu et al (2024) 15 conducted a meta-analysis involving reconstruction and consolidation of metagenome assembled genomes (MAGs) from multiple drinking water metagenomes.…”