Soon Kyeong Kwon

Evolutionary architecture of the infant-adapted group of Bifidobacterium species associated with the probiotic function

Bifidobacteria, often associated with the gastrointestinal tract of animals, are well known for their roles as probiotics. Among the dozens of Bifidobacterium species, Bifidobacterium bifidum, B. breve, and B. longum are the ones most frequently isolated from the feces of infants and known to help the digestion of human milk oligosaccharides. To investigate the correlation between the metabolic properties of bifidobacteria and their phylogeny, we performed a phylogenomic analysis based on 452 core genes of forty-four completely sequenced Bifidobacterium species. Results show that a major evolutionary event leading to the clade of the infant-adapted species is linked to carbohydrate metabolism, but it is not the only factor responsible for the adaptation of bifidobacteria to the gut. The genome of B. longum subsp. infantis, a typical bifidobacterium in the gut of breast-fed infants, encodes proteins associated with several kinds of species-specific metabolic pathways, including urea metabolism and biosynthesis of riboflavin and lantibiotics. Our results demonstrate that these metabolic features, which are associated with the probiotic function of bifidobacteria, are species-specific and highly correlate with their phylogeny.

Complete genome sequence of the probiotic bacterium Bifidobacterium breve KCTC 12201BP isolated from a healthy infant

We present the completely sequenced genome of Bifidobacterium breve CBT BR3, which was isolated from the feces of a healthy infant. The 2.43-Mb genome contains several kinds of genetic factors associated with health promotion of the human host such as oligosaccharide-degrading genes and vitamin-biosynthetic genes.

Genome sequence of the marine flavobacterium Croceitalea dokdonensis DOKDO 023 that contains proton- and sodium-pumping rhodopsins

Bacteroidetes are considered as efficient degraders of the high-molecular-weight particulate organic matter that is present in the marine environment. Here, we report the first genome sequence of the genus Croceitalea that belongs to Flavobacteriia. Gratifying the reputation, the genome of Croceitalea dokdonensis DOKDO 023 encodes many hydrolytic enzymes for utilizing biopolymers, mainly polysaccharides and proteins. The genome also harbors two genes for microbial rhodopsins, proteorhodopsin and a recently discovered sodium pump. This research provides a genetic basis for better understanding of Croceitalea, as well as insights into the strategies adapted by a rhodopsin-containing photoheterotroph to thrive in the marine environment.

Genome information of Maribacter dokdonensis DSW-8 and comparative analysis with other Maribacter genomes.

Maribacter dokdonensis DSW-8 was isolated from the seawater off Dokdo in Korea. To investigate the genomic features of this marine bacterium, we sequenced its genome and analyzed the genomic features. After de novo assembly and gene prediction, 16 contigs totaling 4,434,543 bp (35.95% G+C content) in size were generated and 3,835 protein-coding sequences, 36 transfer RNAs, and 6 ribosomal RNAs were detected. In the genome of DSW-8, genes encoding the proteins associated with gliding motility, molybdenum cofactor biosynthesis, and utilization of several kinds of carbohydrates were identified. To analyze the genomic relationships among Maribacter species, we compared publically available Maribacter genomes, including that of M. dokdonensis DSW-8. A phylogenomic tree based on 1,772 genes conserved among the eight Maribacter strains showed that Maribacter speices isolated from seawater are distinguishable from species originating from algal blooms. Comparison of the gene contents using COG and subsystem databases demonstrated that the relative abundance of genes involved in carbohydrate metabolism are higher in seawater-originating strains than those of algal blooms. These results indicate that the genomic information of Maribacter species reflects the characteristics of their habitats and provides useful information for carbon utilization of marine flavobacteria.

Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5

Bacteria in the genus Polaribacter, belonging to the family Flavobacteriaceae, are typically isolated from marine environments. Polaribacter dokdonensis DSW-5, the type strain of the species, is a Gram-negative bacterium isolated from the East Sea of Korea. Whole genome shotgun sequencing was performed with the HiSeq 2000 platform and paired-end reads were generated at 188-fold coverage. The sequencing reads were assembled into two contigs with a total length of 3.08 Mb. The genome sequences of DSW-5 contain 2,776 proteincoding sequences and 41 RNA genes. Comparison of average nucleotide identities among six available Polaribacteria genomes including DSW-5 suggested that the DSW-5 genome is most similar to that of Polaribacter sp. MED152, which is a proteorhodopsin-containing marine bacterium. A phylogenomic analysis of the six Polaribacter strains and 245 Flavobacteriaceae bacteria confirmed a close relationship of the genus Polaribacter with Tenacibaculum and Kordia. DSW-5’s genome has a gene encoding proteorhodopsin and genes encoding 85 enzymes belonging to carbohydrate-active enzyme families and involved in polysaccharide degradation, which may play important roles in energy metabolism of the bacterium in the marine ecosystem. With genes for 238 CAZymes and 203 peptidases, DSW-5 has a relatively high number of degrading enzymes for its genome size suggesting its characteristics as a free-living marine heterotroph.

Genome sequence of Escherichia coli NCCP15653, a group D strain isolated from a diarrhea patient

BackgroundPathogenic strains in Escherichia coli can be divided into several pathotypes according to their virulence features. Among them, uropathogenic E. coli causes most of the urinary tract infections and has a genotype distinct from other virulent strains of E. coli. In this study, we sequenced and analyzed the genome of E. coli NCCP15653 isolated from the feces of a diarrhea patient in 2007 in South Korea.ResultsA phylogenetic tree based on MLST showed that NCCP15653 belongs to the D group of E. coli and located in the lineage containing strains ST2747, UMN026 and 042. In the genome of NCCP15653, genes encoding major virulence factors of uropathogenic E. coli were detected. They include type I fimbriae, hemin uptake proteins, iron/manganese transport proteins, yersiniabactin siderophore proteins, type VI secretion proteins, and hemolysin. On the other hand, genes encoding AslA, OmpA, and the K1 capsule, which are virulence factors associated with invasion of neonatal meningitis-causing E. coli, were also present, while a gene encoding CNF-1 protein, which is a cytotoxic necrotizing factor 1, was not detected.ConclusionsThrough the genome analysis of NCCP15653, we report an example of a genome of chimeric pathogenic properties. The gene content of NCCP15653, a group D strain, demonstrates that it could be both uropathogenic E. coli and neonatal meningitis-causing E. coli. Our results suggest the dynamic nature of plastic genomes in pathogenic strains of E. coli.

Genome sequences of the Shiga-like toxin-producing Escherichia coli NCCP15655 and NCCP15656

BackgroundVirulence genes can spread among commensal bacteria through horizontal gene transfer. The bacterium with novel virulence factors may pose a severe threat to public health because of the absence of a management system unlike known pathogens. Especially, when a pathogenic bacterium acquires a new kind of virulence genes, it tends to exhibit stronger virulence. In this study, we analyzed the genomes of the two strains of Escherichia coli that were isolated from the feces of patients with diarrhea and produce Shiga-like toxin.ResultsPhylogenetic analysis of conserved genes and average nucleotide identity values of the draft genome sequences indicate that strains NCCP15655 and NCCP15656, isolated from diarrhea patients, belong to the B1 group of E. coli and form a sister clade with strain E24377A. However, the proportion the genes belonging to the subsystem category “phages, prophages, transposable elements, plasmids” and “virulence, disease and defense” are higher than E24377A. Indeed, in their genomes, genes encoding Shiga toxin type 1, Shiga toxin type 2, and type 1 fimbriae were detected. Moreover, a plasmid encoding hemolysin and entropathogenic E. coli secreted protein C was identified in both genomes.ConclusionsThrough the genome analysis of NCCP15655 and NCCP15656, we identified two types of Shiga-like toxin genes that could be responsible for the manifestation of the diarrhea symptom. However, the LEE island, which is one of the major virulence factors of enterohemorrhagic E. coli, was not detected and they are most similar with non-Shiga-like toxin-producing E. coli at the genomic level. NCCP15655 and NCCP15656 will be good examples of Shiga-like toxin-producing E. coli whose genomes are not as similar with typical enterohemorrhagic E. coli as non-Shiga-like toxin-producing E. coli.