Application of denaturing gradient gel electrophoresis to microbial diversity analysis in Chinese Douchi

Chen, Tingtao; Jiang, Shuying; Xiong, Shunqiang; Wang, Mengjuan; Zhu, Daochen; Wei, Hua

doi:10.1002/jsfa.5604

Cited by 44 publications

(37 citation statements)

References 23 publications

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“…In the RDA ordination plot, one OTU ( Staphylococcus ) was enriched in koji making, while one OTU ( Corynebacterium ) was enriched in fermentation. Differences in microbiota could reflect differences in the environments of the two stages, and indicate a marked transition between steps [55,36,56]. In this regard, Montal et al .…”

Section: Resultsmentioning

confidence: 99%

“…The influence of the molecular ecology and culturing method on the diversity, composition and dynamics of the microbial community have been investigated using cell cultures, colony counting, denaturing gradient gel electrophoresis [9,10], temperature gradient gel electrophoresis [11–13], microarray [14] and length heterogeneity polymerase chain reaction [15,16]. However, a complete understanding of the microbial community remains elusive [17].…”

Section: Introductionmentioning

confidence: 99%

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High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation

Yang

2016

PLoS ONE

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Douchi is a type of Chinese traditional fermented food that is an important source of protein and is used in flavouring ingredients. The end product is affected by the microbial community present during fermentation, but exactly how microbes influence the fermentation process remains poorly understood. We used an Illumina MiSeq approach to investigate bacterial and fungal community diversity during both douchi-koji making and fermentation. A total of 181,443 high quality bacterial 16S rRNA sequences and 221,059 high quality fungal internal transcribed spacer reads were used for taxonomic classification, revealing eight bacterial and three fungal phyla. Firmicutes, Actinobacteria and Proteobacteria were the dominant bacterial phyla, while Ascomycota and Zygomycota were the dominant fungal phyla. At the genus level, Staphylococcus and Weissella were the dominant bacteria, while Aspergillus and Lichtheimia were the dominant fungi. Principal coordinate analysis showed structural separation between the composition of bacteria in koji making and fermentation. However, multivariate analysis of variance based on unweighted UniFrac distances did identify distinct differences (p <0.05), and redundancy analysis identified two key genera that are largely responsible for the differences in bacterial composition between the two steps. Staphylococcus was enriched in koji making, while Corynebacterium was enriched in fermentation. This is the first investigation to integrate douchi fermentation and koji making and fermentation processes through this technological approach. The results provide insight into the microbiome of the douchi fermentation process, and reveal a structural separation that may be stratified by the environment during the production of this traditional fermented food.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation

Yang

2016

PLoS ONE

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“…As a powerful tool, denaturing gradient gel electrophoresis (DGGE) is based on the direct analysis of DNA extracted from the microbial environment, allowing us to recover the full diversity of the enriching bacteria and to characterize the predominant bacteria in the culture at the species level (Chen et al, 2012), and had been widely applied to monitor the microbial diversity in soil, polluted water, fermented food, wines and animal intestinal tracts. And the combination of viable cell count and DGGE will better evaluate the effect of RA on the intestinal microbiota.…”

Section: Introductionmentioning

confidence: 99%

The Effects of Rebaudioside A on Microbial Diversity in Mouse Intestine

Chen

Dong

et al. 2014

FSTR

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Rebaudioside A (RA), a natural high potency sweetener, is isolated from the leaves of the Stevia rebaudiana plant, and has potential for wide use in our diet today. To investigate the effect of RA on the changes of microbial diversity in animal intestinal tract, the viable cell count and denaturing gradient gel electrophoresis (DGGE) method were used to monitor the microbial number and species in vivo, and before that, we also evaluated its influence on the growth of some selected bacteria in vitro. Our results indicated that the RA had little or no effect on the growth of E. coli O157 H7, S. typhimurium, L. monocytogenes and B. longum, while could promote the growth of L. plantarum and inhibit that of S. aureus in vitro; moreover, the viable cell count and DGGE results confirmed that the RA posed little pressure on the composition of total bacteria, enterobacteria and lactobacilli in vivo. In conclusion, RA posed little pressure on the growth and the composition of microbes, suggesting it is safe for gut microbes.

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“…DGGE was performed on 8% (w/v) polyacrylamide gels in running buffer containing 1 × TAE (20 mmol L −1 Tris, 10 mmol L −1 acetate, 0.5 mmol L −1 EDTA (pH 8.0)) and a denaturing gradient of 35–65% urea and formamide (Sigma) for bacteria, enterobacteria and lactobacilli (where 100% is defined as 7 mol L −1 urea and 40% (v/v) formamide). Electrophoresis was conducted under 80 V at 60 °C for 16 h. DNA bands in gels were visualized by silver staining …”

Section: Methodsmentioning

confidence: 99%

“…Although culture‐dependent methods had been proven to be useful and quite successful in a wide range of microbiological applications, they could only be used to monitor the bacterial groups growing on selective media, and might not always truly reflect the microbial composition of the actual situation . As a powerful tool, denaturing gradient gel electrophoresis (DGGE) is based on the direct analysis of DNA extracted from the microbial environment and requires no cell cultivation, allowing us to recover the full diversity of the enriching bacteria and to characterize the predominant bacteria in the culture at the species level .…”

Section: Introductionmentioning

confidence: 99%

The beneficial effect of exopolysaccharides from Bifidobacterium bifidum WBIN03 on microbial diversity in mouse intestine

Chen

et al. 2013

J. Sci. Food Agric.

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Application of denaturing gradient gel electrophoresis to microbial diversity analysis in Chinese Douchi

Cited by 44 publications

References 23 publications

High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation

High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation

The Effects of Rebaudioside A on Microbial Diversity in Mouse Intestine

The beneficial effect of exopolysaccharides from Bifidobacterium bifidum WBIN03 on microbial diversity in mouse intestine

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