Kimchi, a traditional food in the Korean culture, is made from vegetables by fermentation. In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation process. Metagenomic DNA was extracted from kimchi samples obtained periodically and was sequenced using a 454 GS FLX Titanium system, which yielded a total of 701,556 reads, with an average read length of 438 bp. Phylogenetic analysis based on 16S rRNA genes from the metagenome indicated that the kimchi microbiome was dominated by members of three genera:Leuconostoc,Lactobacillus, andWeissella. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates, which was supported by the detection of mannitol, lactate, acetate, and ethanol as fermentation products. When the metagenomic reads were mapped onto the database of completed genomes, theLeuconostoc mesenteroidessubsp.mesenteroidesATCC 8293 andLactobacillus sakeisubsp.sakei23K genomes were highly represented. These same two genera were confirmed to be important in kimchi fermentation when the majority of kimchi metagenomic sequences showed very high identity toLeuconostoc mesenteroidesandLactobacillusgenes. Besides microbial genome sequences, a surprisingly large number of phage DNA sequences were identified from the cellular fractions, possibly indicating that a high proportion of cells were infected by bacteriophages during fermentation. Overall, these results provide insights into the kimchi microbial community and also shed light on fermentation processes carried out broadly by complex microbial communities.

The ease of genetic manipulation, low cost, rapid growth and number of previous studies have made Escherichia coli one of the most widely used microorganism species for producing recombinant proteins. In this post-genomic era, challenges remain to rapidly express and purify large numbers of proteins for academic and commercial purposes in a high-throughput manner. In this review, we describe several state-of-the-art approaches that are suitable for the cloning, expression and purification, conducted in parallel, of numerous molecules, and we discuss recent progress related to soluble protein expression, mRNA folding, fusion tags, post-translational modification and production of membrane proteins. Moreover, we address the ongoing efforts to overcome various challenges faced in protein expression in E. coli , which could lead to an improvement of the current system from trial and error to a predictable and rational design.

Purpose.: The aims of our study were to compare the ocular microbial communities of humans with and without blepharitis in an attempt to elucidate which microorganisms may cause blepharitis. Methods.: Bacterial 16S rRNA genes of eyelash and tear samples from seven blepharitis patients and four healthy controls were sequenced using a pyrosequencing method, and their bacterial community structures were compared bioinformatically. Results.: Phylotypic analysis demonstrated that eyelash and tear samples had highly diverse bacterial communities with many previously undescribed bacteria. Bacterial communities in eyelash samples from subjects with blepharitis were less diverse than those from healthy controls, while the bacterial communities of tear subjects with blepharitis were more diverse than those of healthy subjects. Statistical analyses using UniFrac and a principle coordinate analysis showed that the bacterial communities of tear samples from subjects with blepharitis were well clustered, regardless of individual, while the bacterial communities of all eyelash samples and healthy tear samples were not well clustered due to high interpersonal variability. Bioinformatic analysis revealed that Propionibacterium, Staphylococcus, Streptophyta, Corynebacterium, and Enhydrobacter were the common ocular bacteria. An increase of Staphylococcus, Streptophyta, Corynebacterium, and Enhydrobacter, and a decrease of Propionibacterium were observed from blepharitis subjects, in terms of the relative abundances. Conclusions.: Higher abundances of Streptophyta, Corynebacterium, and Enhydrobacter in blepharitis subjects suggested that human blepharitis might be induced by the infestations of pollens, dusts, and soil particles. These results will provide valuable information for the prevention and treatment of human blepharitis based on ocular microbial flora.