Identification of Huge Phages from Wastewater Metagenomes

Megaphages are bacteriophages (i.e., phages) with exceptionally large genomes that are ecosystem cosmopolitans, infect various bacterial hosts, and have been discovered across various metagenomic datasets globally. To date, almost all megaphages have evaded cultivation, with only phage G being in active culture for over 50 years. We examined with multiomics this five decades long cultivated history from nine different laboratories with five different lab variants to the modern era. In this work, we resolved the five complete phage G genomes, the particle proteome,de novomethylome, and used artificial intelligence (AI) to annotate the genome of phage G. Phage G is one of the largest phages with a size of >0.6 µm, about half the width of the host cell, and a 499 kbp, non-permuted, linear genome that has, uniquely among known phages, two pairs of ends. Its closest known relative is Moose phage W30-1 which was metagenomically assembled without cultivation from a moose rumen sample. Phage G has >650 protein-coding open reading frames (ORFs), with >65% being hypothetical proteins with no known function, with the rest of the genome geared towards nucleic acid replication (e.g., helicases, polymerases, endonucleases) and are structural in nature (e.g., capsid, tail, portal, terminase). The genome encodes a 35 kbp stretch with 66 ORFs without any known functional homology, a cryptic genomic region that is roughly the size of phage lambda. Phage G has an expansive repertoire of auxiliary metabolic genes (AMGs) acquired from its bacterial host, including aphoH,ftsZ,UvsX/RecA-like, gyrA, gyrB,andDHFR. Furthermore, AMGs discovered in phage G could manipulate host sporulation (sspD, RsfA, spoK) and antiviral escape genes (e.g., anti-CBass nuclease and Anti-Pycsar protein). Phage proteomics found >15% of the protein ORFs were present in either the wild-type or mutant variants of phage G, including genes involved in replication (e.g.,UvsX/RecA-like), host sporulation, as well as structural genes (e.g., capsid, tail, portal). The methylome of phage G was localized to the cryptic region with limited functional homology, with supervised machine learning (i.e., HMMs) was unable to resolve this region, but was resolved with protein structural AI. This cryptic region was a hot spot for methylation at 32%, where many of the functions of the ORF are still unknown. Our study represents a doorway into the complexity of the genomic repertoire of the only cultivated megaphage, highlighting five decades of continuous cultivation for the first time.

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Recent Progress in Terrestrial Biota Derived Antibacterial Agents for Medical Applications

Vladkova,

Smani,

Martinov

et al. 2024

Molecules

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Conventional antibiotic and multidrug treatments are becoming less and less effective and the discovery of new effective and safe antibacterial agents is becoming a global priority. Returning to a natural antibacterial product is a relatively new current trend. Terrestrial biota is a rich source of biologically active substances whose antibacterial potential has not been fully utilized. The aim of this review is to present the current state-of-the-art terrestrial biota-derived antibacterial agents inspired by natural treatments. It summarizes the most important sources and newly identified or modified antibacterial agents and treatments from the last five years. It focuses on the significance of plant- animal- and bacteria-derived biologically active agents as powerful alternatives to antibiotics, as well as the advantages of utilizing natural antibacterial molecules alone or in combination with antibiotics. The main conclusion is that terrestrial biota-derived antibacterial products and substances open a variety of new ways for modern improved therapeutic strategies. New terrestrial sources of known antibacterial agents and new antibacterial agents from terrestrial biota were discovered during the last 5 years, which are under investigation together with some long-ago known but now experiencing their renaissance for the development of new medical treatments. The use of natural antibacterial peptides as well as combinational therapy by commercial antibiotics and natural products is outlined as the most promising method for treating bacterial infections. In vivo testing and clinical trials are necessary to reach clinical application.

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Identification of Huge Phages from Wastewater Metagenomes

Cited by 3 publications

References 104 publications

Genomic mapping of wastewater bacteriophage may predict potential bacterial pathogens infecting the community

Genomic mapping of wastewater bacteriophage may predict potential bacterial pathogens infecting the community

Unlocking the genomic repertoire of a cultivated megaphage

Recent Progress in Terrestrial Biota Derived Antibacterial Agents for Medical Applications

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