Phage ecology has attracted increasing attention in recent years. Fermented foods have rich and diverse microbial communities, which are not only the creators of the unique flavors in food, but also good hosts for bacteriophages. However, at present, much is known about the bacterial and fungal communities and their functions in fermented foods, but little is known about the bacteriophages that inhabit the bacteria. This article reviews recent findings on phage diversity in fermented foods, highlighting how these organisms influence and relate to the dynamics of microbial communities in fermented foods. The application of bacteriophages in fermented food is also discussed, which will help to better control the food fermentation process in the future and promote its further development by the food industry.

Ganoderma species are widely distributed in the world with high diversity. Some species are considered to be pathogenic fungi while others are used as traditional medicine in Asia. In this study, we sequenced and assembled four Ganoderma complete mitogenomes, including G. subamboinense s118, G. lucidum s37, G. lingzhi s62, and G. lingzhi s74. The sizes of the four mitogenomes ranged from 50,603 to 73,416 bp. All Ganoderma specimens had a full set of core protein-coding genes (PCGs), and the rps3 gene of Ganoderma species was detected to be under positive or relaxed selection. We found that the non-conserved PCGs, which encode RNA polymerases, DNA polymerases, homing endonucleases, and unknown functional proteins, are dynamic within and between Ganoderma species. Introns were thought to be the main contributing factor in Ganoderma mitogenome size variation (p < 0.01). Frequent intron loss/gain events were detected within and between Ganoderma species. The mitogenome of G. lucidum s26 gained intron P637 in the cox3 gene compared with the other two G. lucidum mitogenomes. In addition, some rare introns in Ganoderma were detected in distinct Basidiomycetes, indicating potential gene transfer events. Comparative mitogenomic analysis revealed that gene arrangements also varied within and between Ganoderma mitogenomes. Using maximum likelihood and Bayesian inference methods with a combined mitochondrial gene dataset, phylogenetic analyses generated identical, well-supported tree topologies for 71 Agaricomycetes species. This study reveals intraspecific and interspecific variations of the Ganoderma mitogenomes, which promotes the understanding of the origin, evolution, and genetic diversity of Ganoderma species.

In this study, we used combined transcriptomics and metabolomics to analyze the H. mutabilis cultivar’s genetic and physiological mechanisms during three flower color transition periods (from white to pink, then from pink to red) within the span of one day. As a result, 186 genes were found to be significantly increased with the deepening of the H. mutabilis flower color; these genes were mainly involved in the expression of peroxidase 30, zinc finger protein, phosphate transporter PHO1, etc. In contrast, 298 genes were significantly downregulated with the deepening of H. mutabilis flower color, including those involved in the expression of probable O-methyltransferase 3, copper binding protein 9, and heat stress transcription factor A-6b. Some genes showed differential expression strategies as the flower color gradually darkened. We further detected 19 metabolites that gradually increased with the deepening of the H. mutabilis flower color, including L-isoleucine, palmitic acid, L-methionine, and (+)-7-isonitrobenzene. The content of the metabolite hexadecanedioate decreased with the deepening of the H. mutabilis flower color. Combined transcriptomics and metabolomics revealed that the metabolic pathways, including those related to anthocyanin biosynthesis, cysteine and methionine metabolism, and sulfur metabolism, appear to be closely related to H. mutabilis flower color transition. This study served as the first report on the genetic and physiological mechanisms of short-term H. mutabilis flower color transition and will promote the molecular breeding of ornamental cultivars of H. mutabilis.