Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.

Twenty-eight bacteriophages infecting the local host Bacillus pumilus BL-8 were isolated, purified, and characterized. Nine genomes were sequenced, of which six were annotated and are the first of this host submitted to the public record. The 28 phages were divided into two groups by sequence and morphological similarity, yielding 27 cluster BpA phages and 1 cluster BpB phage, which is a BL-8 prophage. Most of the BpA phages have a host range restricted to distantly related strains, B. pumilus and B. simplex, reflecting the complexities of Bacillus taxonomy. Despite isolation over wide geographic and temporal space, the six cluster BpA phages share most of their 23 functionally annotated protein features and show a high degree of sequence similarity, which is unique among phages of the Bacillus genera. This is the first report of B. pumilus phages since 1981.

The industrial and small-scale processing of plant-based food materials is associated with by-products that may have a negative impact on the environment but could add value to bread-based products. The bioactivity of plant-based food by-products, their impact on the properties of functional bread, and their bioavailability/bioaccessibility leading to potential health effects when consumed was reviewed. Plant-based food by-products which may be added to bread include rice bran, wheat bran, corn bran, grape pomace/seed extract, tomato seed/skin, and artichoke stems/leaves. These by-products contain high concentrations of bioactive compounds, including phenolics, bioactive peptides, and arabinoxylan. Pre-treatment procedures, including fermentation and thermal processing, impact the properties of plant-based by-products. In most cases, bread formulated with flour from plant-based by-products demonstrated increased fibre and bioactive compound contents. In terms of the sensory and nutritional acceptability of bread, formulations with an average of 5% flour from plant-based by-products produced bread with acceptable sensory properties. Bread enriched with plant-based by-products demonstrated enhanced bioavailability and bioaccessibility and favourable bioactive properties in human blood, although long-term studies are warranted. There is a need to investigate the bioactive properties of other underutilised plant-based by-products and their potential application in bread as a sustainable approach towards improving food and nutrition security.

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