Uncovering differences in the composition and function of phage communities and phage-bacterium interactions in raw soy sauce
IntroductionAlthough 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.MethodsThis study determined the diversity, taxonomic composition, and predicted function of phage...
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Frontiers Media S.A.
2023-12-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1328158/full |
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| author | Guiliang Tan Shaohan Qi Yi Wang Xueyan Li Xiangli Li Mei Li Lin Li Lichao Zhao Min Hu |
| author_facet | Guiliang Tan Shaohan Qi Yi Wang Xueyan Li Xiangli Li Mei Li Lin Li Lichao Zhao Min Hu |
| author_sort | Guiliang Tan |
| collection | DOAJ |
| description | IntroductionAlthough 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.MethodsThis 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 discussionThese 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. |
| first_indexed | 2024-03-08T18:55:15Z |
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| issn | 1664-302X |
| language | English |
| last_indexed | 2024-03-08T18:55:15Z |
| publishDate | 2023-12-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Microbiology |
| spelling | doaj.art-c508a20452214fff8debde774bea57b82023-12-28T13:54:42ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-12-011410.3389/fmicb.2023.13281581328158Uncovering differences in the composition and function of phage communities and phage-bacterium interactions in raw soy sauceGuiliang Tan0Shaohan Qi1Yi Wang2Xueyan Li3Xiangli Li4Mei Li5Lin Li6Lichao Zhao7Min Hu8School of Material Science and Food Engineering, University of Electronic Science and Technology of China, Zhongshan Institute, Zhongshan, ChinaCollege of Food Science, South China Agricultural University, Guangzhou, Guangdong, ChinaSchool of Material Science and Food Engineering, University of Electronic Science and Technology of China, Zhongshan Institute, Zhongshan, ChinaSchool of Material Science and Food Engineering, University of Electronic Science and Technology of China, Zhongshan Institute, Zhongshan, ChinaSchool of Health Industry, Zhongshan Torch Polytechnic, Zhongshan, ChinaSchool of Material Science and Food Engineering, University of Electronic Science and Technology of China, Zhongshan Institute, Zhongshan, ChinaSchool of Material Science and Food Engineering, University of Electronic Science and Technology of China, Zhongshan Institute, Zhongshan, ChinaCollege of Food Science, South China Agricultural University, Guangzhou, Guangdong, ChinaSchool of Environmental Science and Engineering, Changzhou University, Changzhou, ChinaIntroductionAlthough 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.MethodsThis 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 discussionThese 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.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1328158/fullraw soy saucephage diversity and functionsphage-host associationmetagenome-assembled genomeauxiliary metabolic genes |
| spellingShingle | Guiliang Tan Shaohan Qi Yi Wang Xueyan Li Xiangli Li Mei Li Lin Li Lichao Zhao Min Hu Uncovering differences in the composition and function of phage communities and phage-bacterium interactions in raw soy sauce Frontiers in Microbiology raw soy sauce phage diversity and functions phage-host association metagenome-assembled genome auxiliary metabolic genes |
| title | Uncovering differences in the composition and function of phage communities and phage-bacterium interactions in raw soy sauce |
| title_full | Uncovering differences in the composition and function of phage communities and phage-bacterium interactions in raw soy sauce |
| title_fullStr | Uncovering differences in the composition and function of phage communities and phage-bacterium interactions in raw soy sauce |
| title_full_unstemmed | Uncovering differences in the composition and function of phage communities and phage-bacterium interactions in raw soy sauce |
| title_short | Uncovering differences in the composition and function of phage communities and phage-bacterium interactions in raw soy sauce |
| title_sort | uncovering differences in the composition and function of phage communities and phage bacterium interactions in raw soy sauce |
| topic | raw soy sauce phage diversity and functions phage-host association metagenome-assembled genome auxiliary metabolic genes |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1328158/full |
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