Optimization of the DGGE band identification method

Fermentation and the microbial community of Japanese koji and miso: A review

Miso is a well-known traditional Japanese fermented food, with a characteristic savory flavor and aroma, known predominately as the seasoning in miso soup. Miso production involves a two-stage fermentation, where first a mold, such as Aspergillus oryzae, is inoculated onto a substrate to make koji. A subsequent fermentation, this time by bacteria and yeast, occurs when the koji is added to a salt and soybean mash, with the miso left to ferment for up to 2 years. The microbial community of miso is considered essential to the development of the unique taste, texture, and nutritional profile of miso. Despite the importance of microorganisms in the production of miso, very little research has been undertaken to characterize and describe the microbial process. In this review, we provide an overview of the two-stage fermentation process, describe what is currently known about the microbial communities involved and consider any potential health benefits associated with the consumption of miso, along with food safety concerns. As the popularity of miso continues to expand globally and is produced under new environmental conditions, understanding the microbiological processes involved will assist to ensure that global production of miso is safe as well as delicious.

PCR denaturing gradient gel electrophoresis as a useful method to identify of intestinal bacteria flora in Haemaphysalis flava ticks

Ticks are blood-sucking ectoparasites of great medical and veterinary significance that can transmit bacteria, protozoa, fungi and viruses, causing a variety of human and animal diseases worldwide. In the present study, the intestinal bacterial flora associated with Haemaphysalis flava ticks in different developmental stages were analyzed using polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE). Eleven distinct DGGE bands were found using PCR-DGGE method. Sequences analyses indicated that they belonged to Bacillus cereus, Candidatus rickettsia, Erwinia sp., Klebsiella pneumoniae, Pectobacterium carotovorum, Pseudomonas aeruginosa, Rickettsia peacockii, Rickettsia helvetica, Rickettsia slovaca, Staphylococcus simulans and Uncultured bacterium clone. Our find that the K. pneumoniae and P. aeruginosa isolates were presented in all H. flava ticks in different developmental stages. The present results indicated that zoonotic pathogens are present in H. flava ticks in Henan province, China. To our knowledge, this is the first report on intestinal bacterial flora associated with H. flava ticks in China.

Identification of intestinal bacterial flora in Rhipicephalus microplus ticks by conventional methods and PCR-DGGE analysis

In this study, we have analyzed the intestinal microbial flora associated with Rhipicephalus microplus ticks using both culture-dependent and independent methods based on PCR and denaturing gradient gel electrophoresis (PCR-DGGE). The R. microplus ticks were collected from cattle and goats in Jiangxi, Hunan and Guizhou Provinces of China. Three distinct strains of bacteria were isolated using culture-dependent methods: Staphylococcus simulans, Bacillus subtilis and Bacillus flexus strain. Nineteen distinct DGGE bands were found using PCR-DGGE analysis, and their search for identity shows that they belonged to Rickettsiaceae, Xanthomonadaceae, Coxiella sp., Ehrlichia sp., Pseudomonas sp., Ehrlichia sp., Orphnebius sp., Rickettsia peacockii, Bacillus flexus. Rickettsia peacockii and Coxiella genus were the dominant strain of the R. microplus ticks from cattle, Pseudomonas sp. and B. flexus strain were the most common species in all tick samples from goats. Ehrlichia canis were detected only in R. microplus ticks from Yongshun area in Hunan Province. The results indicate that the intestinal microbial diversity of R. microplus ticks was influenced by tick hosts and local differences in the sampling location and these two aspects may affect transmission of pathogen to humans and animals.

Adhesion forces and composition of planktonic and adhering oral microbiomes

The oral microbiome consists of a planktonic microbiome residing in saliva and an adhering microbiome (the biofilm adhering to oral hard and soft tissues). Here we hypothesized that possible differences in microbial composition of the planktonic and adhering oral microbiome on teeth can be related to the forces by which different bacterial species are attracted to the tooth surface. The relative presence of 7 oral bacterial species in saliva and biofilm collected from 10 healthy human volunteers was determined twice in each volunteer by denaturing-gradient-gel electrophoresis. Analysis of both microbiomes showed complete separation of the planktonic from the adhering oral microbiome. Next, adhesion forces of corresponding bacterial strains with saliva-coated enamel surfaces were measured by atomic force microscopy. Species that were found predominantly in the adhering microbiome had significantly higher adhesion forces to saliva-coated enamel (-0.60 to -1.05 nN) than did species mostly present in the planktonic microbiome (-0.40 to -0.55 nN). It is concluded that differences in composition of the planktonic and the adhering oral microbiome are due to small differences in the forces by which strains adhere to saliva-coated enamel, providing an important step in understanding site- and material-specific differences in the composition of biofilms in the oral cavity.

Authentication of official Da-huang by sequencing and multiplex allele-specific PCR of a short maturase K gene

Rhubarb (official Da-huang) is an important medicinal herb in Asia. Many adulterants of official Da-huang have been discovered in Chinese markets in recent years, which has resulted in adverse effects in medicinal treatment. Here, novel molecular markers based on a short maturase K (matK) gene were developed for authenticating official Da-huang. This study showed that all the species from official Da-huang were clustered together in one clade in the polygenetic trees based on short matK. Two highly conserved single nucleotide polymorphisms of short matK were mined in the species from official Da-huang. Based on these polymophisms, four improved specific primers of official Da-huang were successfully developed that generated reproducible specific bands. These results suggest that the short matK sequence can be considered as a favorable candidate for distinguishing official Da-huang from its adulterants. The established multiplex allele-specific PCR was determined to be simple and accurate and may serve as a preferable tool for authentication of official Da-huang. In addition, we suggest that short-sized specific bands be developed to authenticate materials used in traditional Chinese medicine.