Insights into the bacterial, fungal, and phage communities and volatile profiles in different types of Daqu

Daqu has a rich and diverse microbiota, giving them a suitable biotope for phages. However, the absolute abundances of bacteria and fungi, as well as the phage community characteristics in Daqu, remain unclear. In this study, the microbiota absolute abundance, indigenous phage composition and function, and volatile compound profiles of high-temperature Daqu (HTDQ), medium-temperature Daqu (MTDQ), and low-temperature Daqu (LTDQ) were investigated. Absolute microbiota quantification revealed that there were significant variations in microbial composition and absolute abundance across three types of Daqu. The absolute abundances of the top 30 bacterial genera in LTDQ, MTDQ, and HTDQ were 6.0 × 105, 5.3 × 104, 1.4 × 105 copies/ng DNA, while the top 30 fungal genera had 8.5 × 107, 2.1 × 106, and 6.2 × 105 copies/ng DNA, respectively. LTDQ were enriched in Pantoea, Staphylococcus, and Saccharomycopsis; MTDQ were dominated by Saccharopolyspora, Staphylococcus, Saccharomycopsis, and Aspergillus; HTDQ were dominated by Saccharopolyspora, Bacillus, Byssochlamys, and Saccharomycopsis. Volatile profile analysis revealed that LTDQ, MTDQ, and HTDQ comprised 68, 68, and 75 compounds, respectively, with 39 compounds shared by the three types. Fourteen volatile compounds were identified as highly discriminative features among three types of Daqu, which were closely related to Saccharopolyspora, Thermoactinomyces, Kroppenstedtia, Byssochlamys, and Thermomyces. Metaviromics indicated that Genomoviridae, Mimiviridae and Siphoviridae, and Parvoviridae were the dominant viruses in LTDQ, MTDQ, and HTDQ, respectively. The hosts of phages in Daqu mainly included Lactobacillus, Enterobacter, Pantoea, Bacillus, Pediococcus, and Staphylococcus. Phages may prey on numerous microbes living on Daqu via pathways such as genetic information processing, signaling and cellular processes, and replication and repair. This study highlights the use of absolute quantification to avoid misjudgment of differential taxa in comparative microbiome analysis and provides new insights into the phage community and function in Daqu.