Unprecedented Diversity of Lactococcal Group 936 Bacteriophages Revealed by Amplicon Sequencing of the Portal Protein Gene

Variants of a putative baseplate wedge protein extend the host range of Pseudomonas phage K8

BACKGROUND

Narrow host range is a major limitation for phage applications, but phages can evolve expanded host range through adaptations in the receptor-binding proteins.

RESULTS

Here, we report that Pseudomonas phage K8 can evolve broader host range and higher killing efficiency at the cost of virion stability. Phage K8 host range mutant K8-T239A carries a mutant version of the putative baseplate wedge protein GP075, termed GP075m. While phage K8 adsorbs to hosts via the O-specific antigen of bacterial LPS, phage K8-T239A uses GP075m to also bind the bacterial core oligosaccharide, enabling infection of bacterial strains resistant to K8 infection due to modified O-specific antigens. This mutation in GP075 also alters inter-protein interactions among phage proteins, and reduces the stability of phage particles to environmental stressors like heat, acidity, and alkalinity. We find that a variety of mutations in gp075 are widespread in K8 populations, and that the gp075-like genes are widely distributed among the domains of life.

CONCLUSION

Our data show that a typical life history tradeoff occurs between the stability and the host range in the evolution of phage K8. Reservoirs of viral gene variants may be widely present in phage communities, allowing phages to rapidly adapt to any emerging environmental stressors. Video Abstract.

Genomics and Geographic Diversity of Bacteriophages Associated With Endosymbionts in the Guts of Workers and Alates of Coptotermes Species (Blattodea: Rhinotermitidae)

Subterranean termites depend nutritionally on their gut microbiota, which includes protozoa as well as taxonomically and functionally diverse bacteria. Our previous metavirome study revealed a high diversity and novel families of bacteriophages in the guts of Coptotermes formosanus workers from New Orleans, Louisiana, United States. Two assembled bacteriophage genomes (Phages TG-crAlp-04 and 06, family Podoviridae) existed in all colonies and showed similarity to a prophage (ProJPt-Bp1) previously sequenced from a bacterial endosymbiont (Candidatus Azobacteroides pseudotrichonymphae, CAP) of protozoa in the gut of a termite species of the genus Prorhinotermes from Taiwan. In this study the genomes of Phage TG-crAlp-04 and 06 were subjected to detailed functional annotation. Both phage genomes contained conserved genes for DNA packaging, head and tail morphogenesis, and phage replication. Approximately 30% of the amino acid sequences derived from genes in both genomes matched to those of ProJPt-Bp1 phage or other phages from the crAss-like phage group. No integrase was identified; the lack of a lysogeny module is a characteristic of crAss-like phages. Primers were designed to sequence conserved genes of the two phages and their putative host bacterium (CAP) to detect their presence in different termite species from native and introduced distribution ranges. Related strains of the host bacterium were found across different termite genera and geographic regions. Different termite species had separate CAP strains, but intraspecific geographical variation was low. These results together with the fact that CAP is an important intracellular symbiont of obligate cellulose-digesting protozoa, suggest that CAP is a core gut bacterium and co-evolved across several subterranean termite species. Variants of both crAss-like phages were detected in different Coptotermes species from the native and introduced range, but they did not differentiate by species or geographic region. Since similar phages were detected in different termite species, we propose the existence of a core virome associated with core bacterial endosymbionts of protozoa in the guts of subterranean termites. This work provides a strong basis for further study of the quadripartite relationship of termites, protozoa, bacteria, and bacteriophages.

Viruses in fermented foods: are they good or bad? Two sides of the same coin

The emergence of Coronavirus disease 2019 as a global pandemic has increased popular concerns about diseases caused by viruses. Fermented foods containing high loads of viable fungi and bacteria are potential sources for virus contamination. The most common include viruses that infect bacteria (bacteriophage) and yeasts reported in fermented milks, sausages, vegetables, wine, sourdough, and cocoa beans. Recent molecular studies have also associated fermented foods as vehicles for pathogenic human viruses. Human noroviruses, rotavirus, and hepatitis virus have been identified in different fermented foods through multiple routes. No severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) virus or close members were found in fermented foods to date. However, the occurrence/persistence of other pathogenic viruses reveals a potential vulnerability of fermented foods to SARS-CoV-2 contamination. On the other side of the coin, some bacteriophages are being suggested for improving the fermentation process and food safety, as well as owing potential probiotic properties in modern fermented foods. This review will address the diversity and characteristics of viruses associated with fermented foods and what has been changed after a short introduction to the most common next-generation sequencing platforms. Also, the risk of SARS-CoV-2 transmission via fermented foods and preventive measures will be discussed.

Metataxonomic and metagenomic approaches for the study of undefined strain starters for cheese manufacture

Undefined strain starters are used for the production of many traditional and artisanal cheeses. Composition of undefined starters depends on several factors, and the diversity in strains and species significantly affects cheese quality and features. Culture-dependent approaches have long been used for the microbial profiling and functionalities of undefined cultures but underestimate their diversity due to culturability biases. Recently, culture-independent methods, based on high-throughput sequencing (HTS), have been preferred, with a significant boost in resolution power and sensitivity level. Amplicon targeted (AT) metagenomics, based on 16S rRNA sequencing, returned a larger microbiota diversity at genus and, sometimes, at species levels for artisanal starters of several PDO cheeses, but was inappropriate for populations with high strain diversity, and other gene targets were tested in AT approaches. Shotgun metagenomics (total DNA) and metatranscriptomics (total RNA), although are more powerful in depicting diversity and functionality of undefined cultures, have been rarely applied because of some limitations (e.g., high costs and laboriousness, need for bioinformatics skills). The advantages of HTS technologies are undoubted, but some hurdles need to be still overcame (e.g., resolution power, discrepancy between active and inactive cells, robust analytic pipelines, cost and time reduction for integrated approaches) so that HTS become routinary and convenient for defining complexity, microbial interactions (including host-phage relationships) and evolution in cheeses of undefined starters.