Uncovering differences in the composition and function of phage communities and phage-bacterium interactions in raw soy sauce

Guiliang Tan; Shaohan Qi; Yi Wang; Xueyan Li; Xiangli Li; Mei Li; Lin Li; Lichao Zhao; Min Hu

doi:10.3389/fmicb.2023.1328158

Uncovering differences in the composition and function of phage communities and phage-bacterium interactions in raw soy sauce

Front Microbiol. 2023 Dec 22:14:1328158. doi: 10.3389/fmicb.2023.1328158. eCollection 2023.

Authors

Guiliang Tan¹, Shaohan Qi², Yi Wang¹, Xueyan Li¹, Xiangli Li³, Mei Li¹, Lin Li¹, Lichao Zhao², Min Hu⁴

Affiliations

¹ School of Material Science and Food Engineering, University of Electronic Science and Technology of China, Zhongshan Institute, Zhongshan, China.
² College of Food Science, South China Agricultural University, Guangzhou, Guangdong, China.
³ School of Health Industry, Zhongshan Torch Polytechnic, Zhongshan, China.
⁴ School of Environmental Science and Engineering, Changzhou University, Changzhou, China.

Abstract

Introduction: Although the composition and succession of microbial communities in soy sauce fermentation have been well-characterized, the understanding of phage communities in soy sauce remains limited.

Methods: This study determined the diversity, taxonomic composition, and predicted function of phage communities and the phage-host interactions in two types of raw soy sauce (Cantonese-type fermentation, NJ; Japanese-type fermentation, PJ) using shotgun metagenomics.

Results and discussion: These two raw soy sauces showed differences in phage composition (121 viral operational taxonomic units (vOTUs) in NJ and 387 vOTUs in PJ), with a higher abundance of the family Siphoviridae (58.50%) in the NJ phage community and a higher abundance of Myoviridae (33.01%) in PJ. Auxiliary metabolic functional annotation analyses showed that phages in the raw soy sauces mostly encoded genes with unknown functions (accounting for 66.33% of COG profiles), but the NJ sample contained genes mostly annotated to conventional functions related to carbohydrate metabolism (0.74%) and lipid metabolism (0.84%), while the PJ sample presented a higher level of amino acid metabolism functions (0.12%). Thirty auxiliary metabolism genes (AMGs) were identified in phage genomes, which were associated with carbohydrate utilization, cysteine and methionine metabolism, and aspartic acid biosynthesis for the host. To identify phage-host interactions, 30 host genomes (affiliated with 22 genera) were also recruited from the metagenomic dataset. The phage-host interaction analysis revealed a wide range of phage hosts, for which a total of 57 phage contigs were associated with 17 host genomes, with Shewanella fodinae and Weissella cibaria infected by the most phages. This study provides a comprehensive understanding of the phage community composition, auxiliary metabolic functions, and interactions with hosts in two different types of raw soy sauce.

Keywords: auxiliary metabolic genes; metagenome-assembled genome; phage diversity and functions; phage-host association; raw soy sauce.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the Natural Science Foundation of Guangdong Province (Grant No. 2022A1515012158), the National Science Foundation of China (Grant No. 41977138), the Construction Project of Teaching Quality and Teaching Reform in Guangdong Province (Grant No. SJD202001), the General University Project of Guangdong Provincial Department of Education (Grant Nos. 2021KCXTD070 and 2021ZDZX4072), the Key Project of Social Welfare and Basic Research of Zhongshan City (Grant No. 2020B2010), and the start-up fund from the Zhongshan Institute at the University of Electronic Science and Technology in China (Grant No. 419YKQN12).