Metatranscriptomics reveals the gene functions and metabolic properties of the major microbial community during Chinese Sichuan Paocai fermentation

Xiao, Muyan; Huang, Tao; Xu, Yang; Peng, Zhen; Liu, Zhanggen; Guan, Qianqian; Xie, Mingyong; Xiong, Tao

doi:10.1016/j.fm.2020.103573

Cited by 38 publications

(14 citation statements)

References 37 publications

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“…Metatranscriptome analysis has been used for the investigation of functional and taxonomic dynamics in fermented foods such as hard cheese ( Quijada et al, 2022 ), camembert cheese ( Lessard et al, 2014 ), liquor starter ( Huang et al, 2017 ), pao cai ( Xiao et al, 2021 ), and kimchi ( Jung et al, 2013 ). The transcriptomes of USM in the kimchi sample were compared with those of the NM using metatranscriptomic analysis with the SEED subsystem ( Figure 2 ; Supplementary Table 3 ).…”

Section: Resultsmentioning

confidence: 99%

Metatranscriptomic and metataxonomic insights into the ultra-small microbiome of the Korean fermented vegetable, kimchi

Lee

Yoon²,

Dang³

et al. 2022

Front. Microbiol.

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Presently, pertinent information on the ultra-small microbiome (USM) in fermented vegetables is still lacking. This study analyzed the metatranscriptome and metataxonome for the USM of kimchi. Tangential flow filtration was used to obtain a USM with a size of 0.2 μm or less from kimchi. The microbial diversity in the USM was compared with that of the normal microbiome (NM). Alpha diversity was higher in the USM than in NM, and the diversity of bacterial members of the NM was higher than that of the USM. At the phylum level, both USM and NM were dominated by Firmicutes. At the genus level, the USM and NM were dominated by Lactobacillus, Leuconostoc, and Weissella, belonging to lactic acid bacteria. However, as alpha diversity is higher in the USM than in the NM, the genus Akkermansia, belonging to the phylum Verrucomicrobia, was detected only in the USM. Compared to the NM, the USM showed a relatively higher ratio of transcripts related to “protein metabolism,” and the USM was suspected to be involved with the viable-but-nonculturable (VBNC) state. When comparing the sub-transcripts related to the “cell wall and capsule” of USM and NM, USM showed a proportion of transcripts suspected of being VBNC. In addition, the RNA virome was also identified, and both the USM and NM were confirmed to be dominated by pepper mild mottle virus (PMMoV). Additionally, the correlation between metataxonome and metatranscriptome identified USM and NM was estimated, however, only limited correlations between metataxonome and metatranscriptome were estimated. This study provided insights into the relationship between the potential metabolic activities of the USM of kimchi and the NM.

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Section: Resultsmentioning

confidence: 99%

Metatranscriptomic and metataxonomic insights into the ultra-small microbiome of the Korean fermented vegetable, kimchi

Lee

Yoon²,

Dang³

et al. 2022

Front. Microbiol.

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“…Moreover, Weissella , as the dominant bacteria during the entire fermentation ( Figure 4 B), showed a positive correlation with umami and sweet amino acids, consistent with previous observations [ 16 ]. In particular, brown sugar was added during the manufacture of Yibin Yacai, and sucrose is its main ingredient, which is preferentially favored by microbes as carbon source [ 8 ], thus generating FAAs through the tricarboxylic acid cycle under aminopeptidase and transaminase secreted by microbes [ 30 ].…”

Section: Resultsmentioning

confidence: 99%

“…In Yibin Yacai, Halomonas and Bacillus were found as the dominant bacteria, while Saccharomycetales and Debaryomyces were the major fungi [ 6 , 7 ]. Microbes play a crucial role in the unique flavor formation of fermented vegetables; thus, the inoculation of a pure strain as a starter becomes one of the main methods to improve the quality of fermented vegetables [ 8 , 9 ]. Some microbial communities are positively correlated with the good quality of fermented products [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

Impact of Inoculating with Indigenous Bacillus marcorestinctum YC-1 on Quality and Microbial Communities of Yibin Yacai (Fermented Mustard) during the Fermentation Process

Zhong

Zou

Zheng

et al. 2022

Foods

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Bacillus species play an important role in improving the quality of some fermented foods and are also one of the dominant bacteria in Yibin Yacai (fermented mustard). However, little is known about their effects on the quality of Yibin Yacai. Here, the effect of Bacillus marcorestinctum YC-1 on the quality and microbial communities of Yibin Yacai during the fermentation process was investigated. Results indicated that the inoculation of Bacillus marcorestinctum YC-1 promoted the growth of Weissella spp. and Lactobacillus spp. and inhibited the growth of pathogens, accelerating the synthesis of free amino acids and organic acids and the degradation of nitrite. Furthermore, inoculating Yibin Yacai with YC-1 could effectively enhance the synthesis of alcohols and terpenoids in yeasts, thus producing more linalool, terpinen-4-ol, and α-muurolen in Yibin Yacai, and endowing it with pleasant floral, fruity, woody, and spicy aromas. These findings reveal that the inoculation of B. marcorestinctum YC-1 can improve the quality and safety of Yibin Yacai by changing microbial communities as fermentation proceeds.

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“…It reaches the maximum at 180 days, which may be related to the abundance of LAB (25). Much evidence shows that the function of carbohydrate metabolism is mainly assigned to LAB in the vegetable fermentation process, and carbohydrate metabolism contributes to the survival of LAB in various environments (26)(27)(28). The metabolism of carbohydrates through glycolytic and citrate cycle pathways can produce acids and substrates for amino acid metabolism, as well as some by-products (29).…”

Section: Analysis Of Enrichment Of Metabolic Pathwaysmentioning

confidence: 99%

Effects of post-fermentation on the flavor compounds formation in red sour soup

Zhou¹,

Zhou²,

He³

et al. 2022

Front. Nutr.

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Red Sour Soup (RSS) is a traditional fermented food in China. After two rounds of fermentation, sour soup has a mellow flavor. However, the microbial composition and flavor formation processes in post-fermentation in RSS are unclear. This study investigates the bacteria composition of RSS during the post-fermentation stage (0–180 days) using high-throughput sequencing. The results show that lactic acid bacteria (LAB) are dominant during the post-fermentation process, and their abundance gradually increases with fermentation time. Additionally, gas chromatography-mass spectrometry was used to detect volatile flavor compounds in the post-fermentation process. Seventy-seven volatile flavor compounds were identified, including 24 esters, 14 terpenes, 9 aromatic hydrocarbons, 9 alkanes, 6 heterocyclic compounds, 3 alcohols, 3 acids, 3 ketones, 2 phenols, 2 aldehydes, 1 amine, and 1 other. Esters and aromatic hydrocarbons are the main volatile compounds in RSS during the post-fermentation process. Orthogonal partial least squares screening and correlation analysis derived several significant correlations, including 48 pairs of positive correlations and 19 pairs of negative correlations. Among them, Acetobacter spp., Clostridium spp. and Sporolactobacillus spp. have 15, 14, 20 significant correlation pairs, respectively, and are considered the most important bacterial genera post-fermentation. Volatile substances become abundant with increasing fermentation time. LAB are excessive after more than 120 days but cause a drastic reduction in volatile ester levels. Thus, the post-fermentation time should be restricted to 120 days, which retains the highest concentrations of volatile esters in RSS. Overall, these findings provide a theoretical basis to determine an optimal post-fermentation time duration, and identify essential bacteria for manufacturing high-quality starter material to shorten the RSS post-fermentation processing time.

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Metatranscriptomics reveals the gene functions and metabolic properties of the major microbial community during Chinese Sichuan Paocai fermentation

Cited by 38 publications

References 37 publications

Metatranscriptomic and metataxonomic insights into the ultra-small microbiome of the Korean fermented vegetable, kimchi

Metatranscriptomic and metataxonomic insights into the ultra-small microbiome of the Korean fermented vegetable, kimchi

Impact of Inoculating with Indigenous Bacillus marcorestinctum YC-1 on Quality and Microbial Communities of Yibin Yacai (Fermented Mustard) during the Fermentation Process

Effects of post-fermentation on the flavor compounds formation in red sour soup

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