Research on safety and compliance of imported microbial inoculants using high-throughput sequencing

Antibiotic Resistance Characterization and Molecular Characteristics of Enterococcus Species Isolated from Combination Probiotic Preparations in China

Enterococci can act as reservoirs for antibiotic-resistant genes that are potentially at risk of being transferred to other bacteria that inhabit in the gastrointestinal tract. The aim of this study was to determine the phenotypic and molecular characteristics of antibiotic-resistant enterococci isolated from probiotic preparations. In total, we isolated 15 suspected Enterococcus species from 5 compound probiotics, which were identified by 16S rDNA as 12 Enterococcus faecium and 3 Enterococcus faecalis. Determination of antimicrobial susceptibility by the microdilution broth method showed widespread resistance to sulfamethoxazole (100%), norfloxacin (99.3%), azithromycin (99.3%), gentamicin (86.7%), and chloramphenicol (20%). Whole genome sequencing of five resistant strains revealed that all had circular DNA chromosomes and that E. faecium J-1-A to J-4-A contained a plasmid, while E. faecalis J-5-A did not. The results of the resistance gene analysis revealed that each strain contained approximately 30 resistance genes, with the antibiotic resistance genes and the multidrug resistance efflux pump genes mdtG, lmrC, and lmrD detected in all strains. The chloramphenicol resistance genes ykkC and ykkD were first identified in E. faecalis. And there were 21, 19, 21, 21, and 29 virulence factors involved in strains, respectively. Further analysis of the gene islands (GIs) revealed that each strain contained more than 10 GIs. The above results confirm the existence of hidden dangers in the safety of probiotics and remind us to carefully select probiotic preparations containing enterococcal strains to avoid the potential spread of resistance and pathogenicity.

Harnessing Native Bacillus spp. for Sustainable Wheat Production

The genus Bacillus has been widely applied in contemporary agriculture as an environmentally-friendly biological agent. However, the real effect of commercial Bacillus-based fertilizers and pesticides varies immensely in the field. To harness Bacillus for efficient wheat production, we reviewed the diversity, functionality, and applicability of wheat-associated native Bacillus for the first time. Our main findings are: (i) Bacillus spp. inhabit the rhizosphere, root, stem, leaf, and kernel of wheat; (ii) B. subtilis and B. velezensis are the most widely endophytic species that can be isolated from both below and aboveground tissues; (iii) major functions of these representative strains are promotion of plant growth and alleviation of both abiotic and biotic stresses in wheat; (iv) stability and effectiveness are 2 major challenges during field application; (v) a STVAE pipeline that includes 5 processes, namely, Screen, Test, Validation, Application, and Evaluation, has been proposed for the capture and refinement of wheat-associated Bacillus spp. In particular, this review comprehensively addresses possible solutions, concerns, and criteria during the development of native Bacillus-based inoculants for sustainable wheat production.

High-Throughput Sequencing as a Tool for the Quality Control of Microbial Bioformulations for Agriculture

Microbial bioformulations, due to their positive impact on the growth and development of plants, as well as the absence of harmful effects on the environment and humans, have a vast potential for mass introduction into agriculture. Assessing the quality of bioformulations, especially complex ones, is a difficult task. In this study, we show that high-throughput sequencing can be an effective tool for the quality control and safety of microbial bioformulations. By the method of high-throughput sequencing on the MiSeq platform, we studied 20 samples of commercially available microbial bioformulations. In parallel with this, bioformulations were studied by classical microbiological methods. The analysis showed the presence of extraneous undeclared bacterial genera by the manufacturer. Only 10% of the bioformulations fully corresponded to the commercial composition, and another 10% of the bioformulations did not contain the bacteria declared by the manufacturer in their composition at all. The bacterial composition of 80% of the bioformulations partially corresponded to the composition indicated on the package. The most frequent microbial bioformulations contaminants were Enterococcus, Lactobacillaceae, Klebsiella, Escherichia-Shigella and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. Universal methods for the quality control of bioformulations are needed. The advantages of high-throughput sequencing for the evaluation of bioformulations are considered in this work.