Comparative genomic and biochemical analyses identify a collagen galactosylhydroxylysyl glucosyltransferase from Acanthamoeba polyphaga mimivirus.

Humans and Acanthamoeba polyphaga mimivirus share numerous homologous genes, including collagens and collagen-modifying enzymes. To explore this homology, we performed a genome-wide comparison between human and mimivirus using DELTA-BLAST (Domain Enhanced Lookup Time Accelerated BLAST) and identified 52 new putative mimiviral proteins that are homologous with human proteins. To gain functional insights into mimiviral proteins, their human protein homologs were organized into Gene Ontology (GO) and REACTOME pathways to build a functional network. Collagen and collagen-modifying enzymes form the largest subnetwork with most nodes. Further analysis of this subnetwork identified a putative collagen glycosyltransferase R699. Protein expression test suggested that R699 is highly expressed in Escherichia coli, unlike the human collagen-modifying enzymes. Enzymatic activity assay and mass spectrometric analyses showed that R699 catalyzes the glucosylation of galactosylhydroxylysine to glucosylgalactosylhydroxylysine on collagen using uridine diphosphate glucose (UDP-glucose) but no other UDP-sugars as a sugar donor, suggesting R699 is a mimiviral collagen galactosylhydroxylysyl glucosyltransferase (GGT). To facilitate further analysis of human and mimiviral homologous proteins, we presented an interactive and searchable genome-wide comparison website for quickly browsing human and Acanthamoeba polyphaga mimivirus homologs, which is available at RRID Resource ID: SCR_022140 or https://guolab.shinyapps.io/app-mimivirus-publication/ .

Identification and Characterization of Cancer-Associated Fibroblast Subpopulations in Lung Adenocarcinoma.

Cancer-associated fibroblasts (CAFs) reside within the tumor microenvironment, facilitating cancer progression and metastasis via direct and indirect interactions with cancer cells and other stromal cell types. CAFs are composed of heterogeneous subpopulations of activated fibroblasts, including myofibroblastic, inflammatory, and immunosuppressive CAFs. In this study, we sought to identify subpopulations of CAFs isolated from human lung adenocarcinomas and describe their transcriptomic and functional characteristics through single-cell RNA sequencing (scRNA-seq) and subsequent bioinformatics analyses. Cell trajectory analysis of combined total and THY1 + CAFs revealed two branching points with five distinct branches. Based on Gene Ontology analysis, we denoted Branch 1 as "immunosuppressive", Branch 2 as "neoantigen presenting", Branch 4 as "myofibroblastic", and Branch 5 as "proliferative" CAFs. We selected representative branch-specific markers and measured their expression levels in total and THY1 + CAFs. We also investigated the effects of these markers on CAF activity under coculture with lung cancer cells. This study describes novel subpopulations of CAFs in lung adenocarcinoma, highlighting their potential value as therapeutic targets.

ZEB1-regulated lnc-Nr2f1 promotes the migration and invasion of lung adenocarcinoma cells.

Numerous long non-coding RNAs (lncRNAs) are differentially expressed in cancer cells compared with normal cells and are involved in tumor progression and metastasis. Metastasis is initiated by the epithelial-to-mesenchymal transition (EMT) process, which can also be regulated by lncRNAs. Given that ZEB1 is an important transcription factor inducing EMT, we screened lncRNAs controlled by ZEB1 using RNA sequencing in murine lung adenocarcinoma cells. Among several lncRNAs regulated by ZEB1, we selected lnc-Nr2f1. Lnc-Nr2f1 is upregulated by ZEB1 and TGF-ß, a potent EMT signal. Growth, migration, and invasion of lung adenocarcinoma cells were decreased after lnc-Nr2f1 knockdown and increased after lnc-Nr2f1 overexpression. Interestingly, lnc-Nr2f1 was transcriptionally controlled by NR2F1, a transcription factor that is transcribed in the antisense direction. NR2F1 was also upregulated and positively correlated with ZEB1, forming a ZEB1/NR2F1/lnc-Nr2f1 axis. Lnc-Nr2f1, in turn, promoted Twist2 transcription through direct binding to its genomic DNA region. Collectively, lnc-Nr2f1 was upregulated by ZEB1 and NR2F1, and promoted migration and invasion of lung adenocarcinoma cells via TWIST2 regulation.

Effect of the Interaction between Dietary Patterns and the Gastric Microbiome on the Risk of Gastric Cancer.

We aimed to observe the combined effects of Gaussian graphical model (GGM)-derived dietary patterns and the gastric microbiome on the risk of gastric cancer (GC) in a Korean population. The study included 268 patients with GC and 288 healthy controls. Food intake was assessed using a 106-item semiquantitative food frequency questionnaire. GGMs were applied to derive dietary pattern networks. 16S rRNA gene sequencing was performed using DNA extracted from gastric biopsy samples. The fruit pattern network was inversely associated with the risk of GC for the highest vs. lowest tertiles in the total population (odds ratio (OR): 0.47; 95% confidence interval (CI): 0.28-0.77; p for trend = 0.003) and in females (OR: 0.38; 95% CI: 0.17-0.83; p for trend = 0.021). Males who had a low microbial dysbiosis index (MDI) and high vegetable and seafood pattern score showed a significantly reduced risk of GC (OR: 0.44; 95% CI: 0.22-0.91; p-interaction = 0.021). Females who had a low MDI and high dairy pattern score showed a significantly reduced risk of GC (OR: 0.23; 95% CI: 0.07-0.76; p-interaction = 0.018). Our novel findings revealed that vegetable and seafood pattern might interact with dysbiosis to attenuate the risk of GC in males, whereas the dairy pattern might interact with dysbiosis to reduce the GC risk in females.

Cancer-associated fibroblasts activated by miR-196a promote the migration and invasion of lung cancer cells.

Fibroblasts in the tumor microenvironment, known as cancer-associated fibroblasts (CAFs), promote the migration, invasion, and metastasis of cancer cells when they are activated through diverse processes, including post-transcriptional regulation by microRNAs (miRNAs). To identify the miRNAs that regulate CAF activation, we used NanoString to profile miRNA expression within normal mouse lung fibroblasts (LFs) and CAFs. Based on NanoString profiling, miR-196a was selected as a candidate that was up-regulated in CAFs. miR-196a-overexpressed LFs (LF-196a) promoted the migration and invasion of lung cancer cells in co-culture systems (Transwell migration and spheroid invasion assays). ANXA1 was confirmed as a direct target of miR-196a, and adding back ANXA1 to LF-196a restored the cancer cell invasion promoted by miR-196a. miR-196a increased CCL2 secretion in fibroblasts, and that was suppressed by ANXA1. Furthermore, blocking CCL2 impeded cancer spheroid invasion. In lung adenocarcinoma patients, high miR-196a expression was associated with poor prognosis. Collectively, our results suggest that CAF-specific miR-196a promotes lung cancer progression in the tumor microenvironment via ANXA1 and CCL2 and that miR-196a will be a good therapeutic target or biomarker in lung adenocarcinoma.

Long Non-Coding RNAs as Regulators of Interactions between Cancer-Associated Fibroblasts and Cancer Cells in the Tumor Microenvironment.

Long non-coding RNAs (lncRNAs) regulate diverse physiological and pathological processes via post-transcriptional, post-translational, and epigenetic mechanisms. They are also involved in tumor initiation, progression, and metastasis by functioning as key players in the tumor microenvironment. Cancer-associated fibroblasts (CAFs) promote tumor initiation, progression, metastasis, drug resistance, and immunosuppression, which can be modulated by lncRNAs. LncRNAs regulate the intrinsic properties of CAFs or cancer cells intracellularly or function extracellularly through exosomal secretion. In-depth studies on the mechanisms of lncRNA functions will enable their clinical use as diagnosis/prognosis markers and therapeutic targets in cancer treatment.

Identification of Novel microRNA Prognostic Markers Using Cascaded Wx, a Neural Network-Based Framework, in Lung Adenocarcinoma Patients.

The evolution of next-generation sequencing technology has resulted in a generation of large amounts of cancer genomic data. Therefore, increasingly complex techniques are required to appropriately analyze this data in order to determine its clinical relevance. In this study, we applied a neural network-based technique to analyze data from The Cancer Genome Atlas and extract useful microRNA (miRNA) features for predicting the prognosis of patients with lung adenocarcinomas (LUAD). Using the Cascaded Wx platform, we identified and ranked miRNAs that affected LUAD patient survival and selected the two top-ranked miRNAs (miR-374a and miR-374b) for measurement of their expression levels in patient tumor tissues and in lung cancer cells exhibiting an altered epithelial-to-mesenchymal transition (EMT) status. Analysis of miRNA expression from tumor samples revealed that high miR-374a/b expression was associated with poor patient survival rates. In lung cancer cells, the EMT signal induced miR-374a/b expression, which, in turn, promoted EMT and invasiveness. These findings demonstrated that this approach enabled effective identification and validation of prognostic miRNA markers in LUAD, suggesting its potential efficacy for clinical use.

Comparative genomics of Lactobacillus species as bee symbionts and description of Lactobacillus bombintestini sp. nov., isolated from the gut of Bombus ignitus.

The Lactobacillus genus is widely used for fermentation of plant materials and dairy products. These species are typically found in highly specialized environments, with the bee gut serving as one of the niche locations in which Lactobacillus is detected. Lactobacillus species isolated from the bee gut and bee-related habitats were phylogenetically classified into three distinct groups, Lactobacillus kunkeei, Firm-4, and Firm-5. The L. kunkeei group was clearly differentiated from other members of the Lactobacillus buchneri group isolated from non-bee habitats. In comparison with non-bee members of the L. buchneri group, three bee-symbiotic Lactobacillus groups had a small-sized genome with low G + C content and showed a sharp reduction in the number of genes involved in energy production, carbohydrate transport and metabolism, and amino acid transport and metabolism. In addition, all three groups lacked the mutY gene, which encodes A/G-specific adenine glycosylase. The phylogenetic dendrogram based on the presence or absence of 1,199 functional genes indicated that these bee-symbiotic groups experienced convergent evolution. The occurrence of convergent evolution is thought to stem from the three bee-symbiotic groups sharing a similar habitat, i.e., the bee gut. The causative factor underlying genomic reduction was postulated to be mutY, which was absent in all three groups. Here, a novel strain, BHWM-4T, isolated from the gut of Bombus ignites was studied using polyphasic taxonomy and classified as a new member of the L. kunkeei group. The strain was Gram-positive, facultative anaerobic, and rod-shaped. The 16S ribosomal RNA gene sequence and genome analysis revealed that strain BHWM-4T was clustered into the L. kunkeei group, forming a compact cluster with L. kunkeei and Lactobacillus apinorum. Biochemical, chemotaxonomic, and genotypic data of strain BHWM-4T supports the proposal of a novel species, Lactobacillus bombintestini sp. nov., whose type strain is BHWM-4T (= KACC 19317 = NBRC 113067T).

Xylanimonas allomyrinae sp. nov. isolated from the gut of larva of Allomyrina dichotoma, reclassification of Xylanibacterium ulmi as Xylanimonas ulmi comb. nov. and Xylanimicrobium pachnodae as Xylanimonas pachnodae comb. nov., and emendation of the genus Xylanimonas.

A bacterium that was Gram-staining-positive, facultatively anaerobic, non-motile, rod- or filamentous-shaped, designated as strain 2JSPR-7T, was isolated from a gut of larvae of Allomyrina dichotoma which were raised at the National Institute of Agricultural Sciences, Wanju-gun, Republic of Korea. 2JSPR-7T had the highest 16S rRNA gene sequence similarity to Xylanibacterium ulmi XIL08T (98.1 %), Xylanimicrobium pachnodae NBRC 107786T (97.8 %) and Xylanimonas cellulosilytica DSM 15894T (97.5 %). Optimum growth conditions were at 28-30 °C, pH 7-8 and 0 % salt concentration. The cellular fatty acids mainly consisted of anteiso-C15 : 0, C14 : 0 and C16 : 0. The polar lipids were diphosphatidylglycerol, four unidentified phospholipids and two unidentified glycophospholipids. The major menaquinones were MK-8(H4) and MK-9(H4). The peptidoglycan structure was suggested to be the type A3α (A11.14) l-Lys-l-Ser with the presence of d-Ala, l-Ala, d-Glu, l-Ser and l-Lys. Whole cell sugars were rhamnose, ribose and glucose. The DNA G+C content was 72.7 mol%. We encountered difficulty in selecting a suitable genus to accommodate strain 2JSPR-7T from any of the genera Xylanimonas, Xylanimicrobium and Xylanibacterium based on the polyphasic approach including phylogenetic and phenotypic characterization. Therefore, it is proposed to combine the genera Xylanimicrobium and Xylanibacterium with the genus Xylanimonas considering the priority of publication and to classify strain 2JSPR-7T in the genus as Xylanimonas allomyrinae sp. nov. The type strain of the novel species is 2JSPR-7T (=KACC 19330T=NBRC 113052T). In addition, the description of the genus Xylanimonas is emended, and Xylanibacterium ulmi and Xylanimicrobium pachnodae are reclassified as Xylanimonas ulmi comb. nov. and Xylanimonas pachnodae comb. nov., respectively.

Expression of EEF1A1 Is Associated with Prognosis of Patients with Colon Adenocarcinoma.

BACKGROUND: The prognostic role of the translational factor, elongation factor-1 alpha 1 (EEF1A1), in colon cancer is unclear. OBJECTIVES: The present study aimed to investigate the expression of EEF1A in tissues obtained from patients with stage II and III colon cancer and analyze its association with patient prognosis. METHODS: A total of 281 patients with colon cancer who underwent curative resection were analyzed according to EEF1A1 expression. RESULTS: The five-year overall survival in the high-EEF1A1 group was 87.7%, whereas it was 65.6% in the low-EEF1A1 expression group (hazard ratio (HR) 2.47, 95% confidence interval (CI) 1.38-4.44, p = 0.002). The five-year disease-free survival of patients with high EEF1A1 expression was 82.5%, which was longer than the rate of 55.4% observed for patients with low EEF1A1 expression (HR 2.94, 95% CI 1.72-5.04, p < 0.001). Univariate Cox regression analysis indicated that age, preoperative carcinoembryonic antigen level, adjuvant treatment, total number of metastatic lymph nodes, and EEF1A1 expression level were significant prognostic factors for death. In multivariate analysis, expression of EEF1A1 was an independent prognostic factor associated with death (HR 3.01, 95% CI 1.636-5.543, p < 0.001). EEF1A1 expression was also an independent prognostic factor for disease-free survival in multivariate analysis (HR 2.54, 95% CI 1.459-4.434, p < 0.001). CONCLUSIONS: Our study demonstrated that high expression of EEF1A1 has a favorable prognostic effect on patients with colon adenocarcinoma.

Lactococcus allomyrinae sp. nov., isolated from gut of larvae of Allomyrina dichotoma.

Strain 1JSPR-7T, a facultatively anaerobic bacterium isolated from the gut of larvae of Allomyrina dichotoma raised in Wanju-gun, Republic of Korea, was characterized using a polyphasic approach. Comparative analysis of 16S rRNA gene and rpoB gene sequences showed that strain 1JSPR-7T fell within the genus Lactococcus, forming a compact cluster with the type strain of four subspecies of Lactococcus lactis and Lactococcus taiwanensis. The 16S rRNA gene sequence of strain 1JSPR-7T revealed the highest homology with L. lactissubsp. lactis JCM 5805T (97.3 %) and L. lactissubsp. hordniae NBRC 100931T (97.1 %), and the rpoB gene sequence showed the highest similarity to L. lactissubsp. cremoris DSM 20069T (91.4 %) and L. lactissubsp. tructae L105T (91.4 %). The average nucleotide identity and digital DNA-DNA hybridization values indicated that strain 1JSPR-7T was a novel species of the genus Lacococcus. The major fatty acids (>10 % of the total fatty acids) were summed feature 7 (unknown 18.846, C19 : 1ω6c and/or C19 : 0cyclo ω10c), C16 : 0 and C14 : 0, and the predominant menaquinone was MK-8 with MK-7 as a minor one. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and three unidentified glycolipids with diphosphatidylglycerol as the major one. The cell-wall peptidoglycan was of the A4α type with an interpeptide bridge comprising l-Lys-d-Asp. The DNA G+C content based on the whole genome sequences was 37.4 mol%. Based on the data obtained, strain 1JSPR-7T represents a novel species of the genus Lactococcus, for which the name Lactococcusallomyrinae sp. nov. is proposed. The type strain is 1JSPR-7T (=KACC 19319T=NBRC 113068T).

Paenibacillus nuruki sp. nov., isolated from Nuruk, a Korean fermentation starter.

A Gram-stain-positive, rod-shaped, non-endospore-forming motile by means of peritrichous flagella, facultatively anaerobic bacterium designated TI45-13arT was isolated from Nuruk, a Korean traditional Makgeolli fermentation starter. It grew at 4-35°C (optimum, 28-30°C), pH 5.0-9.0 (optimum, pH 7.0) and NaCl concentrations up to 5% (w/v). Phylogenetic trees generated using 16S rRNA gene sequences revealed that strain TI45-13arT belonged to the genus Paenibacillus and showed the highest sequence similarities with Paenibacillus kyungheensis DCY88T (98.5%), Paenibacillus hordei RH-N24T (98.4%) and Paenibacillus nicotianae YIM h-19T (98.1%). The major fatty acid was anteiso-C15:0. The DNA G+C content was 39.0 mol%, and MK-7 was the predominant isoprenoid quinone. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified glycolipids, and one unidentified aminoglycolipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid. On the basis of polyphasic taxonomy study, it was suggested that strain TI45-13arT represents a novel species within the genus Paenibacillus for which the name Paenibacillus nuruki sp. nov. is proposed. The type strain was TI45-13arT (= KACC 18728T = NBRC 112013T).

Weissella cryptocerci sp. nov., isolated from gut of the insect Cryptocercus kyebangensis.

A taxonomic study of a Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, catalase-negative bacterium, isolated from the gut of an insect, Cryptocercus kyebangensis collected from the mountainous area of Seoraksan, Yangyang-gun, Republic of Korea, was conducted. Its 16S rRNA gene sequence showed high similarity values to Weissella ghanensis LMG 24286T (95.9 %), Weissella beninensis 2L24P13T (95.9 %), Weissella fabalis M75T (95.7 %) and Weissella fabaria 257T (95.7 %). The phylogenetic tree indicated that the novel organism formed a cluster with W. ghanensis LMG 24286T, W. beninensis 2L24P13T, W. fabalis M75T and W. fabaria 257T. The G+C content was 41.1 mol% on the basis of the whole-genome sequence. Polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, two unidentified aminophospholipids, one unidentified phospholipid and four unidentified lipids. The major cellular fatty acids were C18 : 1 ω9c, C16 : 0, C14 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and summed feature 8 (C16 : 1 ω7c and/or C16 : 1 ω6c). The cell-wall peptidoglycan was of A4α type with the interpeptide bridge of Gly-d-Glu. Based on these results, strain 26KH-42T could be classified as a novel species of the genus Weissella, for which the name Weissellacryptocerci sp. nov. is proposed. The type strain is 26KH-42T (=KACC 18423T=NBRC 113066T).

QKI, a miR-200 target gene, suppresses epithelial-to-mesenchymal transition and tumor growth.

The microRNA-200 (miR-200) family plays a major role in specifying epithelial phenotype by preventing expression of the transcription repressors ZEB1 and ZEB2, which are well-known regulators of the epithelial-to-mesenchymal transition (EMT) in epithelial tumors including oral squamous cell carcinoma (OSCC). Here, we elucidated whether miR-200 family members control RNA-binding protein quaking (QKI), a newly identified tumor suppressor that is regulated during EMT. We predicted that miR-200a and miR-200b could recognize QKI 3'-UTR by analyzing TargetScan and The Cancer Genome Atlas head and neck squamous cell carcinoma (HNSCC) dataset. Forced expression of miR-200b/a/429 inhibited expression of ZEB1/2 and decreased cell migration in OSCC cell lines CAL27 and HSC3. QKI expression was also suppressed by miR-200 overexpression, and the 3'-UTR of QKI mRNA was directly targeted by miR-200 in luciferase reporter assays. Interestingly, shRNA-mediated knockdown of QKI led to pronounced EMT and protumor effects in both in vitro and in vivo studies of OSCC. Furthermore, high expression of QKI protein is associated with favorable prognosis in surgically resected HNSCC and lung adenocarcinoma. In conclusion, QKI increases during EMT and is targeted by miR-200; while, it suppresses EMT and tumorigenesis. We suggest that QKI and miR-200 form a negative feedback loop to maintain homeostatic responses to EMT-inducing signals.

MiR-34a and miR-34b/c have distinct effects on the suppression of lung adenocarcinomas.

Three miR-34 family members (miR-34a, miR-34b, and miR-34c) are clustered on two different chromosomal loci, Mir34a and Mir34b/c. These miRNAs have identical seed sequences, which are predicted to target the same set of genes. However, miR-34a and miR-34c have different sets of negatively correlated genes in lung adenocarcinoma data from The Cancer Genome Atlas. Therefore, we hypothesized that the individual miR-34 family members, which are tumor suppressive miRNAs, would have varying effects on lung tumorigenesis. To show this, we overexpressed each miR-34 cluster in murine lung cancer cells. MiR-34b/c enhanced cancer cell attachment and suppressed cell growth and invasion compared with miR-34a. In a syngeneic mouse model, both miR-34a and miR-34b/c blocked lung metastasis. However, miR-34b/c suppressed tumor growth more than miR-34a. MiR-34b/c also decreased the expression of mesenchymal markers (Cdh2 and Fn1) and increased the expression of epithelial markers (Cldn3, Dsp, and miR-200) to a greater degree than miR-34a. These results imply that miR-34b and miR-34c inhibit epithelial-to-mesenchymal transition. Furthermore, knockout of all three miR-34 members promoted mutant Kras-driven lung tumor progression in mice. Similarly, lung adenocarcinoma patients with higher miR-34a/b/c levels had better survival rates than did those with lower levels. In summary, we suggest that miR-34b and miR-34c are more effective tumor suppressors than miR-34a.

Urinary Exosomal and cell-free DNA Detects Somatic Mutation and Copy Number Alteration in Urothelial Carcinoma of Bladder.

Urothelial bladder carcinoma (UBC) is characterized by a large number of genetic alterations. DNA from urine is a promising source for liquid biopsy in urological malignancies. We aimed to assess the availability of cell-free DNA (cfDNA) and exosomal DNA (exoDNA) in urine as a source for liquid biopsy in UBC. We included 9 patients who underwent surgery for UBC and performed genomic profiling of tumor samples and matched urinary cfDNA and exoDNA. For mutation analysis, deep sequencing was performed for 9 gene targets and shallow whole genome sequencing (sWGS) was used for the detection of copy number variation (CNV). We analyzed whether genetic alteration in tumor samples was reflected in urinary cfDNA or exoDNA. To measure the similarity between copy number profiles of tumor tissue and urinary DNA, the Pearson's correlation coefficient was calculated. We found 17 somatic mutations in 6 patients. Of the 17 somatic mutations, 14 and 12 were identified by analysis of cfDNA and exoDNA with AFs of 56.2% and 65.6%, respectively. In CNV analysis using sWGS, although the mean depth was 0.6X, we found amplification of MDM2, ERBB2, CCND1 and CCNE1, and deletion of CDKN2A, PTEN and RB1, all known to be frequently altered in UBC. CNV plots of cfDNA and exoDNA showed a similar pattern with those from the tumor samples. Pearson's correlation coefficients of tumor vs. cfDNA (0.481) and tumor vs. exoDNA (0.412) were higher than that of tumor vs. normal (0.086). We successfully identified somatic mutations and CNV in UBC using urinary cfDNA and exoDNA. Urinary exoDNA could be another source for liquid biopsy. Also, CNV analysis using sWGS is an alternative strategy for liquid biopsy, providing data from the whole genome at a low cost.

Lifestyle Factors and Bowel Preparation for Screening Colonoscopy.

PURPOSE: The quality of bowel preparation is a major determinant of the quality of colonoscopy. This study evaluated lifestyle factors, including usual dietary style, associated with bowel preparation. METHODS: This retrospective study evaluated 1,079 consecutive subjects who underwent complete colonoscopy from December 2012 to April 2014 at National Cancer Center of Korea. Questionnaires on bowel preparation were completed by the subjects, with the quality of bowel preparation categorized as optimal (excellent or good) or suboptimal (fair, poor or inadequate). Lifestyle factors associated with bowel preparation were analyzed. RESULTS: The 1,079 subjects included 680 male (63.0%) and 399 female patietns (37.0%), with a mean age of 49.6 ± 8.32 years. Bowel preparation was categorized as optimal in 657 subjects (60.9%) and as suboptimal in 422 (39.1%). Univariate analyses showed no differences between groups in lifestyle factors, such as regular exercise, alcohol intake, smoking, and dietary factor. Body mass index (BMI) > 25 kg/m2 was the only factor associated with suboptimal bowel preparation on both the univariate (P = 0.007) and the multivariate (odds ratio, 1.437; 95% confidence interval, 1.104-1.871; P = 0.007) analyses. CONCLUSION: Most lifestyle factors, including dietary patterns, exercise, alcohol intake and smoking, were not associated with suboptimal bowel preparation in Koreans. However, BMI > 25 kg/m2 was independently associated with suboptimal bowel preparation. More intense preparation regimens before colonoscopy can be helpful in subjects with BMI > 25 kg/m2.

Ottowia oryzae sp. nov., isolated from Andong sikhye, a Korean traditional rice beverage.

A Gram-stain-negative, non-spore-forming, non-motile, short-rod-shaped bacterial strain, designated KADR8-3T, isolated from Andong sikhye in Andong-si, Gyeongsangbuk-do, Republic of Korea, was characterized using a polyphasic approach. On the basis of morphological, genetic and chemotaxonomic characteristics, it was determined to belong to the genus Ottowia. The phylogenetic similarity based on the 16S rRNA gene sequences indicated the strain formed a clade with Ottowia beijingensis GCS-AN-3T, Ottowia thiooxydans DSM 14619T, Ottowia pentelensis RB3-7T and 'Ottowia shaoguanensis' J5-66T, showing the highest similarity to O. beijingensis GCS-AN-3T (96.3 %). The major fatty acids were C16 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The predominant respiratory quinone was Q-8. The polar lipids present were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, two unidentified aminolipids and two unidentified lipids. The genomic DNA G+C content was 66.80 mol%. These results supported that strain KADR8-3T was clearly distinguishable from its closely related species and represents a novel species of the genus Ottowia, for which the name Ottowia oryzae is proposed. The type strain is KADR8-3T (=KACC 19325T=NBRC 113109T).

Paenibacillus solanacearum sp. nov., isolated from rhizosphere soil of a tomato plant.

The taxonomic position of a bacterial strain designated T16R-228T, isolated from a rhizosphere soil sample of a tomato plant collected from a farm in Buyeo, Chungcheongnam-do, Republic of Korea, was determined using a polyphasic approach. On the basis of morphological, genetic and chemotaxonomic characteristics, it was determined to belong to the genus Paenibacillus. It was an aerobic, Gram-stain-positive, non-motile, catalase-negative, oxidase-negative rod with peritrichous flagella. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, hydroxyl- phosphatidylethanolamine and one unidentified polar lipid. Menaquiones were MK-7. Predominant cellular fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. DNA G+C content was 56.8 mol%. The phylogenetic tree constructed based on the 16S rRNA gene sequences showed the strain formed a clade with P. mucilaginosus VKPM B-7519T, P. edaphicus T7T, P. ehimensis KCTC 3748T, P. koreensis YC300T, P. tianmuensis B27T and P. elgii SD17T, showing the highest sequence similarity with P. mucilaginosus VKPM B-7519T (96.5 %). The polyphasic data supported that strain T16R-228T was clearly distinguished from its closely related species and represents a novel species of the genus Paenibacillus for which the name Paenibacillus solanacearum is proposed. The type strain is T16R-228T (=KACC 18654T=NBRC 111896T).

Terrimonas terrae sp. nov., isolated from the rhizosphere of a tomato plant.

A yellow, aerobic, Gram-stain-negative, non-motile, rod-shaped and non-flagellated bacterial strain, designated T16R-129T, was isolated from the rhizosphere of a tomato plant collected at a farm located on Buyeo-gun of Chungcheongnam-do, South Korea. Strain T16R-129T grew at 15-40 °C and pH 7.0-9.0, and did not require NaCl for growth. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain T16R-129T clustered with members of the genus Terrimonas, and it shared highest similarity with Terrimonas arctica R9-86T (96.1 %), Terrimonas pekingensis QHT (95.9 %), Terrimonas lutea DYT (94.9 %), Terrimonas crocea M1-33108T (95.4 %) and Terrimonas rhizosphaerae CR94T (95.3 %). The major isoprenoid quinone was menaquinone 7 (MK-7). The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The polar lipids of strain T16R-129T were phosphatidylethanolamine, two unidentified aminolipids, two unidentified aminophospholipids and five unidentified polar lipids. The G+C content of the genomic DNA was 46.0 mol%. On the basis of data from this polyphasic taxonomic study, strain T16R-129T represents a novel species in the genus Terrimonas, for which the name Terrimonas terrae sp. nov. is proposed; the type strain is T16R-129T (=KACC 18787T=JCM 31603T).