Metagenome-assembled genomes reveal Pseudogracilibacillus amylolyticus sp. nov., a functional uncultured microorganism in high-temperature Daqu

Chinese Baijiu, a traditional distilled spirit with profound historical and cultural significance, is renowned for its intricate flavor profiles and persistent aftertaste. The unique fermentation process of Baijiu, characterized by natural inoculation and open fermentation, not only imparts its distinctive sensory attributes but also introduces significant complexity and variability due to the involvement of diverse microbial consortia (Jin et al., 2017; Liu and Sun, 2018; Xu et al., 2022). The microbiota associated with Baijiu fermentation is diverse, and only a fraction of the community has been characterized, posing challenges to the elucidation and regulation of the brewing process (Wang et al., 2017).

The influence of environmental microbiota on the Baijiu fermentation ecosystem is profound. These microorganisms, originating from the production environment during open fermentation, play a critical role in shaping the microbial community structure and, ultimately, the quality of the final product (Li et al., 2011). Daqu, a pivotal starter culture in Baijiu production, harbors a complex microbial community dominated by spore-forming bacteria, particularly members of the genus Bacillus, which occupy a key ecological niche (Hu et al., 2021; Zou et al., 2018). The relative abundance and functional dominance of these spore-forming bacteria underscore their pivotal role in the fermentation dynamics (Li et al., 2011; Wang et al., 2017; Wu et al., 2013). The taxonomic classification of species from the genus Bacillus remains an active area of investigation, with novel species and strains continually being identified through advanced molecular phylogenetic techniques, reflecting the dynamic nature of microbial systematics (Ash et al., 1991; Dunlap et al., 2016; Gupta et al., 2020; Liu et al., 2015). Furthermore, the contribution of unculturable microorganisms to Baijiu fermentation is increasingly recognized, as they are hypothesized to significantly influence community metabolism and, consequently, the flavor and aroma profiles of the final product (He et al., 2019; Hu et al., 2021; Li et al., 2011; Liu and Sun, 2018; Wang et al., 2017; Whitman and Venter, 2024).

Metagenomic technologies have revolutionized our ability to characterize the complex microbial communities in traditional Baijiu fermentation. By analyzing Daqu samples at the genomic level, these studies have uncovered remarkable genetic diversity while simultaneously identifying novel taxonomic clades (He et al., 2019; Wu et al., 2013). During a comprehensive genomic analysis of high-temperature Daqu, three yet-uncultivated bacterial genomes belonging to the genus Pseudogracilibacillus (A3–12A_bin_9TS, M2–6-2A_bin_27 and M2–7-9A_bin_18) were discovered. Phylogenetic reconstruction, average nucleotide identity (ANI) and average amino acid identity (AAI) analyses revealed that these genomes exhibit high intragroup similarity while displaying significant divergence from previously described species within the genus Pseudogracilibacillus. Collectively, these results suggest that the three genomes represent a novel taxon within the Pseudogracilibacillus lineage. Functional annotation of the encoded genetic content with the KEGG database revealed that this taxon exhibits multimodal metabolic versatility, demonstrating amylolytic activity within the Daqu fermentation matrix and aromatic compound catabolic capacity, suggesting its putative role in flavor-active metabolite biosynthesis. In accordance with the standardized guidelines for taxonomic classification (O'Brien, Luo O'brien and Luo, 2023, Orr et al., 2022, Whitman et al., 2022, Whitman and Venter, 2024), we formally propose the name Pseudogracilibacillus amylolyticus sp. nov.

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