Campbell, D. E. | bioRxiv Science

bioRxiv2020

Discovering the Molecular Determinants of Phaeobacter inhibens susceptibility to Phaeobacter phage MD18

Bacteriophage technologies have immense potential as antibiotic therapies and in genetic engineering. Understanding the mechanisms that bacteriophages implement to infect their hosts will allow researchers to manipulate these systems and adapt them to specific bacterial targets. Here, we isolated a bacteriophage capable of infecting the marine alphaproteobacterium Phaeobacter inhibens and dissected its mechanism of infection. Phaeobacter phage MD18, a novel species of bacteriophage isolated in Woods Hole, MA, exhibits potent lytic ability against P. inhibens and appears to be of the Siphoviridae morphotype. Consistent with this finding, the sequence of the MD18 revealed significant similarity to another siphophage, the recently discovered Roseobacter phage DSS3P8. We incubated MD18 with a library of barcoded P. inhibens transposon insertion mutants and identified 22 genes that appear to be required for phage predation of this host. Network analysis of these genes using genomic position, GO term enrichment, and protein associations reveals that these genes are enriched for roles in assembly of a type IV pilus (T4P) and regulators of cellular morphology. Our results suggest that T4P serve as receptors for a novel marine virus that targets P. inhibens. ImportanceBacteriophages are useful non-antibiotic therapeutics for bacterial infections as well as threats to industries utilizing bacterial agents. This study identifies Phaeobacter phage MD18, the first documented phage of Phaeobacter inhibens, a bacterium with promising use as a probiotic for aquatic farming industries. Genomic analysis suggests that the P haeobacter phage MD18 has evolved to enhance its replication in P. inhibens by adopting favorable tRNA genes as well as through genomic sequence adaptation to resemble host codon usage. Lastly, a high-throughput analysis of P. inhibens transposon insertion mutants identifies genes that modulate host susceptibility to phage MD18 and implicates the type IV pilus as the likely receptor recognized for adsorption. This study marks the first characterization of the relationship between P. inhibens and an environmentally sampled phage, which informs our understanding of natural threats to the bacterium and may promote the development of novel phage technologies for genetic manipulation of this host.

microbiology↗

bioRxiv2020

Infection with novel Bacteroides phage BV01 alters host transcriptome and bile acid metabolism in a common human gut microbe

The bacterial genus Bacteroides is among the most abundant and common taxa in the human gut, yet little is known about the phages infecting the group. Bacteroides phage BV01 (BV01) was identified as a prophage integrated on the chromosome of its host, Bacteroides vulgatus ATCC 8482. Phage BV01 is actively produced, and infects susceptible B. vulgatus hosts in the mouse gut. Infection with BV01 causes a generalized repression of the B. vulgatus transcriptome, downregulating 103 transcripts and upregulating only 12. Integration of BV01 disrupts the promoter sequence of a downstream gene encoding a putative tryptophan-rich sensory protein (tspO). Deletion of tspO and subsequent RNAseq analysis revealed that more than half of the differentially-regulated transcripts are shared with the BV01 lysogen, suggesting the transcriptomic response to BV01 is linked to tspO. Among these differentially-regulated transcripts are two encoding bile salt hydrolases. Bile acid deconjugation assays show that BV01 represses its hosts ability to hydrolyze bile acids in a tspO-dependent manner. Analysis of 256 published healthy human gut metagenomes suggests that phage integration adjacent to B. vulgatus-like tspO genes is rare within an individual, but common among humans. Finally, this work proposes a novel phage family that includes BV01, the Salyersviridae, whose host range spans the Bacteroides and is detectable in human-associated samples. Together, these findings highlight the importance of phage-host interactions to our understanding of how gut microbes sense and interact with their environment. IMPORTANCEThe links between human disease and the gut microbiome are numerous. Most mechanisms by which most gut microbes and their activities change and impact human health remain elusive. Phages, viruses that infect bacteria, are hypothesized to play a central role in modulating both community dynamics and functional activities. Here we have characterized an active prophage, BV01, which infects a pervasive and abundant human gut-associated species. BV01 infection alters its hosts transcriptional profile including its metabolism of bile acids, molecules implicated in mediating health and disease states in the gut. This highlights that prophages and other components of the variable genome should not be overlooked in bacterial genomes because they may dramatically alter host phenotypes. Furthermore, BV01 represents a new family of phages infecting human gut symbionts, providing a foundation for future investigations of phage-host interactions in these clinically-relevant but underexplored hosts.

microbiology↗