Dynamics and diversity of microbial community succession during fermentation of Suan yu, a Chinese traditional fermented fish, determined by high throughput sequencing

Zang, Jinhong; Xu, Yanshun; Xia, Wenshui; Yu, Dawei; Gao, Pei; Jiang, Qixing; Yang, Fang

doi:10.1016/j.foodres.2018.05.076

Cited by 130 publications

(72 citation statements)

References 61 publications

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“…Dynamic changes to α-diversity indices indicated that the fungal diversity of Panxian ham fluctuated greatly during processing, while bacterial diversity tended to continually decrease ( Table 1). Similar trends have been reported during the Suan yu, a fermentation process for Chinese traditional fermented fish; Zang et al (2018) suggested that chitin (a characteristic component of the fungal cell wall) may be responsible for these results, providing a certain protection against environmental stress. Microbiota structural changes were analyzed using NMDS and PCoA based on Binary-Jaccard distances to evaluate variation and similarity (Figures 3C,D).…”

Section: Abundance and Diversity Of Bacterial And Fungal Microorganismssupporting

confidence: 77%

Combined Application of High-Throughput Sequencing and Metabolomics Reveals Metabolically Active Microorganisms During Panxian Ham Processing

et al. 2020

Front. Microbiol.

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Panxian ham, a traditional Chinese dry-cured ham, is protected by national geographical indication. Similar to other fermented foods, the microbial population of dry-cured ham is pivotal to taste and flavor formation. This study aimed to establish the relationship between microorganisms and metabolites during the spontaneous fermentation of Panxian ham. Multivariate analysis based on metabolomics data revealed that continuous metabolic changes occurred during the entire fermentation process, with the most significant changes occurring in the initial stage of ripening. Thirty-one significantly different metabolites (SDMs) were identified as discriminant factor, and pathway analysis suggested that these metabolites were involved in 30 pathways, including alanine, aspartate, and glutamate metabolism; glycine, serine, and threonine metabolism; and arginine and proline metabolism. Microbial community analysis using the Illumina MiSeq platform indicated that the bacterial community was more complex than the fungal community, and their succession regulation differed during processing. At the genus level, 11 bacteria and five fungi were identified as core microbes, of which Staphylococcus was the dominant bacteria and Debaryomyces and Aspergillus were the dominant fungi. Further, statistical redundancy analysis (RDA) indicated that Staphylococcus, Debaryomyces, and Chromohalobacter promoted the production of amino and fatty acids; Cobetia and Aspergillus were associated with sugar metabolism, and Kushneria, Penicillium, and Yamadazyma were closely related with organic acids. These findings provide fundamental knowledge regarding the metabolically active microorganisms in Panxian ham, helping industrial processors to develop effective strategies for standardizing quality parameters.

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Section: Abundance and Diversity Of Bacterial And Fungal Microorganismssupporting

confidence: 77%

Combined Application of High-Throughput Sequencing and Metabolomics Reveals Metabolically Active Microorganisms During Panxian Ham Processing

et al. 2020

Front. Microbiol.

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“…These discrepancies may be due to the shortcoming of the length of the sequencing fragment (average length 249.41 bp), and the limitation of the database's classification . Notably, similar phenomena have appeared in some published reports, indicating that there are still deficiencies in the field. Besides, according to culture studies, the number of LAB was at a high level, whereas the relative abundance of LAB was far lower than than that of Bacillus .…”

Section: Discussionmentioning

confidence: 99%

Evaluation of bacterial and fungal communities during the fermentation of Baixi sufu, a traditional spicy fermented bean curd

Wan

Liu

et al. 2019

J Sci Food Agric

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BACKGROUND: Baixi sufu (BS) is a traditional Chinese spicy fermented bean curd manufactured with a natural starter.In this study, the bacterial and fungal communities during BS fermentation were determined by culture and by the culture-independent method of high-throughput sequencing (HTS). Correlation analyses were performed to select the microorganisms potentially contributing to this fermentation. RESULTS: During the fermentation of BS, 162 bacterial and 97 fungal strains were isolated and identified, and a total of 268 314 bacterial and 287 844 fungal high-quality sequences were analyzed. In general, lactic acid bacteria (LAB), especially Enterococcus and Lactococcus, were dominant in the early stage of fermentation, and spore-forming bacteria, especially Bacillus spp., became the predominant bacteria by the end of fermentation. Geotrichum, Mortierella, and unclassified Ascomycota, were the major fungal populations, which could not be detected in the final product. Correlation analyses indicated that Enterococcus, Bacillus, Geotrichum, and unclassified Ascomycota correlated significantly and positively with amino nitrogen. However, due to the sporulation characteristics of Bacillus, they may have little effect on BS ripening. The presence of Bifidobacterium spp. in sufu is reported for the first time, but the excessive counts of the Bacillus cereus group (>10 5 CFU g −1 ) indicate a potential hazard to consumers.CONCLUSION: The profiles obtained from this study will contribute to the development of autochthonous starter cultures to control BS fermentation, and may lead to the development of novel strategies to shorten the fermentation time of sufu products.

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“…The amplification system included 0.3 μM of each primer, 40–60 ng template DNA, 1 μL KOD-FX-Neo (TOYOBO, Osaka, Japan), 1 × buffer and 0.4 mM dNTPs. The amplification conditions were 95°C for 5 min, followed by 15 cycles of 95°C for 1 min, 50°C for 1 min, and 72°C for 1 min, and a final step at 72°C for 7 min ( Zang et al, 2018 ). The amplification products were mixed with VAHTS DNA clean beads (Vazyme, Nanjing, China) for purification, and further amplified by solexa PCR using 0.25 μM of each primer (MPPI-a and MPPI-b), 10 μL purified amplification products, and 1 × Phusion (NEB, Ipswich, Massachusetts).…”

Section: Methodsmentioning

confidence: 99%

“…The amplification products were mixed with VAHTS DNA clean beads (Vazyme, Nanjing, China) for purification, and further amplified by solexa PCR using 0.25 μM of each primer (MPPI-a and MPPI-b), 10 μL purified amplification products, and 1 × Phusion (NEB, Ipswich, Massachusetts). The solexa PCR conditions were 98°C for 30 s, followed by 10 cycles of 98°C for 10 s, 65°C for 30 s, and 72°C for 30 s, and a final step at 72°C for 7 min ( Zang et al, 2018 ). The solexa PCR products were used for DNA library construction after quantification by Qubit 2.0 (Thermo Fisher Scientific, Waltham, MA, United States), mix 1:1 by mass, and DNA gel extraction.…”

Section: Methodsmentioning

confidence: 99%

Profiling of Fungal Diversity and Fermentative Yeasts in Traditional Chinese Xiaoqu

2020

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To increase the safety and quality of baijiu and rice wine in China, controlling the use of traditional Xiaoqu by studying the beneficial yeasts present has recently been considered. The fungal diversity of six Chinese Xiaoqu including five traditional and one commercial samples was investigated to screen fermentative yeasts with low yields of higher alcohols. A high throughput sequencing approach detected fifteen fungal species with relative abundance higher than 1%, and displayed dissimilarities of fungal diversity among Xiaoqu samples. The 15 fungal species were composed of 11 filamentous fungi with Rhizopus arrhizus as the most common specie and four yeast species, containing Hyphopichia burtonii , Saccharomyces cerevisiae , Saccharomycopsis fibuligera , and Saccharomycopsis malanga . Classic culture-dependent approaches, including 5.8S-ITS-RFLP analysis and D1/D2 sequencing of the 26S rRNA gene, identified nine yeast species in the five traditional Chinese Xiaoqu . In addition to the four yeast species also detected by high throughput sequencing approach, the other five yeast species isolated were Clavispora lusitaniae , Cryptococcus neoformans , Komagataella pastoris , Trichosporon asahii , and Wickerhamomyces anomalus . Further micro-fermentations of rice wine were performed using 19 single yeast isolates, and after the fermentation of rice wine, higher alcohols and ethanol were analyzed by gas chromatography. Two yeast strains, Saccharomyces cerevisiae FBKL2.8022 and Wickerhamomyces anomalus FBKL2.8023, were found to have low yields of higher alcohols and could produce 11.70%vol and 7.10%vol ethanol separately. This study for the first time, to the best of our knowledge, explored the fungal resources in traditional Xiaoqu from different regions of Guizhou, China. The screened S. cerevisiae and W. anomalus strains could be used to establish specific starters to promote the standardization of the production of baijiu and rice wine.

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Dynamics and diversity of microbial community succession during fermentation of Suan yu, a Chinese traditional fermented fish, determined by high throughput sequencing

Cited by 130 publications

References 61 publications

Combined Application of High-Throughput Sequencing and Metabolomics Reveals Metabolically Active Microorganisms During Panxian Ham Processing

Combined Application of High-Throughput Sequencing and Metabolomics Reveals Metabolically Active Microorganisms During Panxian Ham Processing

Evaluation of bacterial and fungal communities during the fermentation of Baixi sufu, a traditional spicy fermented bean curd

Profiling of Fungal Diversity and Fermentative Yeasts in Traditional Chinese Xiaoqu

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