Metatranscriptome analysis of lactic acid bacteria during kimchi fermentation with genome-probing microarrays

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Viruses are recognized as the most abundant biological components on Earth, and they regulate the structure of microbial communities in many environments. In soil and marine environments, microorganisminfecting phages are the most common type of virus. Although several types of bacteriophage have been isolated from fermented foods, little is known about the overall viral assemblages (viromes) of these environments. In this study, metagenomic analyses were performed on the uncultivated viral communities from three fermented foods, fermented shrimp, kimchi, and sauerkraut. Using a high-throughput pyrosequencing technique, a total of 81,831, 70,591 and 69,464 viral sequences were obtained from fermented shrimp, kimchi and sauerkraut, respectively. Moreover, 37 to 50% of these sequences showed no significant hit against sequences in public databases. There were some discrepancies between the prediction of bacteriophages hosts via homology comparison and bacterial distribution, as determined from 16S rRNA gene sequencing. These discrepancies likely reflect the fact that the viral genomes of fermented foods are poorly represented in public databases. Double-stranded DNA viral communities were amplified from fermented foods by using a linker-amplified shotgun library. These communities were dominated by bacteriophages belonging to the viral order Caudovirales (i.e., Myoviridae, Podoviridae, and Siphoviridae). This study indicates that fermented foods contain less complex viral communities than many other environmental habitats, such as seawater, human feces, marine sediment, and soil.

Section: Resultsmentioning

confidence: 99%

Metagenomic Analysis of the Viral Communities in Fermented Foods

Park

Kim

Abell

et al. 2011

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“…Although these culture-independent approaches can estimate species richness within a kimchi microbial community, they are unable to resolve the true genotypic diversity, because diversity of 16S rRNA gene sequences may not correlate well with genotypic and phenotypic diversity (60). Thus, although progress made using 16S RNA gene analysis and culture-based methods has been significant, current understanding of kimchi microbiology is piecemeal and has significant limitations regarding community dynamics and function during fermentation (12,28,38).…”

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confidence: 99%

Metagenomic Analysis of Kimchi, a Traditional Korean Fermented Food

Jung

Lee

Kim

et al. 2011

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399

268

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, and Weissella. 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, the Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 and Lactobacillus sakei subsp. sakei 23K 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 to Leuconostoc mesenteroides and Lactobacillus genes. 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.

“…However, starter cultures have been developed in order to better control the fermentation and thus improve quality, safety, and shelf life of the fermented product (15,16,20,24). Several LAB species have been identified as likely contributors in kimchi fermentations, including species of the genera Leuconostoc, Lactobacillus, Lactococcus, Pediococcus, and Weissella (6,18,19,32,35,36,[38][39][40][41]51,53,57). Weissella species isolated from kimchi include Weissella confusa, Weissella kimchii, and Weissella koreensis.…”

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confidence: 99%

Novel Podoviridae Family Bacteriophage Infecting Weissella cibaria Isolated from Kimchi

Kleppen

Holo

Jeon

et al. 2012

bThe first complete genome sequence of a phage infecting Weissella cibaria (Weissella kimchii) is presented. The bacteriophage YS61 was isolated from kimchi, a Korean fermented vegetable dish. Bacteriophages are recognized as a serious problem in industrial fermentations; however, YS61 differed from many virulent phages associated with food fermentations since it was difficult to propagate and was very susceptible to resistance development. Sequence analysis revealed that YS61 resembles Podoviridae of the subfamily Picovirinae. Within the subfamily Picovirinae, the 29-like phages have been extensively studied, and their terminal protein-primed DNA replication is well characterized. Our data strongly suggest that YS61 also replicates by a protein-primed mechanism. Weissella phage YS61 is, however, markedly different from members of the Picovirinae with respect to genome size and morphology. Picovirinae are characterized by small (approximately 20-kb) genomes which contrasts with the 33,594-bp genome of YS61. Based on electron microscopy analysis, YS61 was classified as a member of the Podoviridae of morphotype C2, similar to the 29-like phages, but its capsid dimensions are significantly larger than those reported for these phages. The novelty of YS61 was also emphasized by the low number of open reading frames (ORFs) showing significant similarity to database sequences. We propose that the bacteriophage YS61 should represent a new subfamily within the family Podoviridae. Kimchi, a traditional Korean dish, is manufactured by fermentation of vegetables such as Chinese cabbage and radish. Hundreds of kimchi varieties are produced by the addition of different seasonings, such as scallions, powdered chili peppers, garlic, ginger, and fermented seafood. Lactic acid produced during fermentation contributes to preservation and gives kimchi its characteristic sour taste. Proper ripening and preservation are ensured by a 2 to 5% (wt/vol) salt content and anaerobic fermentation at low temperatures. Kimchi is traditionally prepared by spontaneous fermentation by lactic acid bacteria (LAB) indigenous to the vegetable ingredients. However, starter cultures have been developed in order to better control the fermentation and thus improve quality, safety, and shelf life of the fermented product (15,16,20,24). Several LAB species have been identified as likely contributors in kimchi fermentations, including species of the genera Leuconostoc, Lactobacillus, Lactococcus, Pediococcus, and Weissella (6,18,19,32,35,36,[38][39][40][41]51,53,57). Weissella species isolated from kimchi include Weissella confusa, Weissella kimchii, and Weissella koreensis. These bacteria are abundant late in the fermentation process and can continue to grow during storage at low temperatures (Ϫ1°C). Weissella species have thus been associated with the excessive acidic taste of overripened kimchi products. The species Weissella kimchii, first described in 2002 (19), was reclassified as Weissella cibaria in 2004 (9, 23).The kimchi fermentation process is ch...