Non-targeted detection of the microbial composition using high-throughput sequencing
Microbial inoculants are widely used in wastewater treatment, soil remediation and biological control. However, imported microbial inoculants increase the risk of biosafety by unknown transboundary alien species. Microbial inoculants composition was commonly identified by phenotypic culture, which is time-consuming and labor intense with occasionally false negative results provided, and can only be tested for a specific species. High-throughput sequencing (HTS), known for its non-targeted detection of unknown species composition in samples, is suitable for composition consistency identification and biosafety analysis of imported microbial inoculants. The applicability of HTS method for microflora distribution was verified in microbial inoculants for environmental protection and then applicated in imported microbial inoculants. Both Illumina and Nanopore based HTS methods identified same dominant bacterial species successfully in the imported microbial inoculants. The main component bacterial species were Bacillus subtilis, Bacillus amyloliquefaciens, Bacillus licheniformis, and Enterococcus faecium, and further confirmed with traditional methods. Our results indicated that HTS processes the application potential to identify the active ingredients of microbial inoculants and can prevent the invasion of unknown organisms.