Metagenomics Reveals the Diversity and Taxonomy of Carbohydrate-Active Enzymes and Antibiotic Resistance Genes in Suancai Bacterial Communities

Abstract

Suancai, as a traditional fermented food in China with reputed health benefits, has piqued global attention for many years. In some circumstances, the microbial-driven fermentation may confer health (e.g., probiotics) or harm (e.g., antibiotic resistance genes) to the consumers. To better utilize beneficial traits, a deeper comprehension of the composition and functionality of the bacterial species harboring enzymes of catalytically active is required. On the other hand, ingestion of fermented food increases the likelihood of microbial antibiotic resistance genes (ARGs) spreading in the human gastrointestinal tract. Besides, the diversity and taxonomic origin of ARGs in suancai are little known. In our study, a metagenomic approach was employed to investigate distribution structures of CAZymes and ARGs in main bacterial species in suancai. Functional annotation using the CAZy database identified a total of 8796 CAZymes in metagenomic data. A total of 83 ARGs were detected against the CARD database. The most predominant ARG category is multidrug-resistant genes. The ARGs of antibiotic efflux mechanism are mostly in Proteobacteria. The resistance mechanism of ARGs in Firmicutes is primarily antibiotic inactivation, followed by antibiotic efflux. Due to the abundance of species with different ARGs, strict quality control including microbial species, particularly those with lots of ARGs, is vital for decreasing the risk of ARG absorption via consumption. Ultimately, we significantly widen the understanding of suancai microbiomes by using metagenomic sequencing to offer comprehensive information on the microbial functional potential (including CAZymes and ARGs content) of household suancai.

The resistome of the food chain: A One Health perspective

“…(Yasir et al, 2022). Song et al (2022) also reported that the majority of ARGs found in suancai (traditional cabbage pickle) were linked to Pseudomonas, the main genus in raw vegetables. Therefore, it is imperative to implement hygienic handling practices and maintain a clean processing environment to prevent the spread of ARGs and protect the health of consumers.…”

“…Lactic acid bacteria are the predominant species in most fermented vegetables (Liu et al., 2023 ; Yasir et al., 2022 ), with a low abundance of ARGs (Yasir et al., 2022 ). Several metagenomic studies have shown that ARGs related to lincosamides, aminoglycosides, tetracyclines and multidrug resistance are some of the most abundant ARGs in fermented vegetables (Liu et al., 2023 ; Song et al., 2022 ; Yasir et al., 2022 ). Indeed, high levels of ARGs found on fermented vegetables were associated with bacteria related to improper storage and handling of fermented foods, or linked to cross‐contamination from processing environments or equipment, such as in the case of Klebsiella sp.…”