Jiyoung Kim

Microbial community and metabolomic comparison of irritable bowel syndrome faeces

Human health relies on the composition of microbiota in an individual’s gut and the synthesized metabolites that may alter the gut environment. Gut microbiota and faecal metabolites are involved in several gastrointestinal diseases. In this study, 16S rRNA-specific denaturing gradient gel electrophoresis and quantitative PCR analysis showed that the mean similarity of total bacteria was significantly different (P<0.001) in faecal samples from patients with irritable bowel syndrome (IBS; n = 11) and from non-IBS (nIBS) patients (n = 8). IBS subjects had a significantly higher diversity of total bacteria, as measured by the Shannon index (H′) (3.36<H′<4.37, P = 0.004), Bacteroidetes and lactobacilli; however, less diversity was observed for Bifidobacter (1.7< H′<3.08, P<0.05) and Clostridium coccoides (0.9< H′<2.98, P = 0.007). In this study, no significant difference was found in total bacterial quantity (P>0.05). GC/MS-based multivariate analysis delineated the faecal metabolites of IBS from nIBS samples. Elevated levels of amino acids (alanine and pyroglutamic acid) and phenolic compounds (hydroxyphenyl acetate and hydroxyphenyl propionate) were found in IBS. These results were highly correlated with the abundance of lactobacilli and Clostridium, which indicates an altered metabolism rate associated with these gut micro-organisms. A higher diversity of Bacteroidetes and Lactobacillus groups in IBS faecal samples also correlated with the respective total quantity. In addition, these changes altered protein and carbohydrate energy metabolism in the gut.

Correlation between Antioxidative Activities and Metabolite Changes during Cheonggukjang Fermentation

Liquid chromatography mass spectrometry and multivariate analysis were employed to investigate the correlation between fermentation time-dependent metabolite changes in cheonggukjang, a traditional fermented soybean product, and changes in its antioxidant activity over 72 h. The metabolite patterns were clearly distinguished not by strains but by fermentation time, into patterns I (0–12 h), II (12–24 h), and III (24–72 h), which appeared as distinct clusters on principal component analysis. The compounds that significantly contributed to patterns I, II, and III were soyasaponins, isoflavonoid derivatives, and isoflavonoid aglycons respectively. Partial least square analysis for metabolite to antioxidant effects showed correlations between the ferric reducing/antioxidant power (FRAP) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay during 24–36 h, and 2,2′-azinobis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) test and total phenol content (TPC) during 36–72 h. Compared with the strong negative correlations of glucosylated-isoflavonoids with DPPH, ABTS and TPC during fermentation, the isoflavonoid aglycon displayed strong positive correlations with these compounds during fermentation.

cdc-25.2, a C. elegans ortholog of cdc25, is required to promote oocyte maturation

Cdc25 is an evolutionarily conserved protein phosphatase that promotes progression through the cell cycle. Some metazoans have multiple isoforms of Cdc25, which have distinct functions and different expression patterns during development. C. elegans has four cdc-25 genes. cdc-25.1 is required for germline mitotic proliferation. To determine if the other members of the cdc-25 family also contribute to regulation of cell division in the germ line, we examined phenotypes of loss-of-function mutants of the other cdc-25 family genes. We found that cdc-25.2 is also essential for germline development. cdc-25.2 homozygous mutant hermaphrodites exhibited sterility as a result of defects in oogenesis: mutant oocytes were arrested as endomitotic oocytes that were not fertilized successfully. Spermatogenesis and male germline development were not affected. Through genetic interaction studies, we found that CDC-25.2 functions upstream of maturation-promoting factor containing CDK-1 and CYB-3 to promote oocyte maturation by counteracting function of WEE-1.3. We propose that cdc-25 family members function as distinct but related cell cycle regulators to control diverse cell cycles in C. elegans germline development.

GC-MS based metabolite profiling of rice Koji fermentation by various fungi.

In this study, Aspergillus kawachii, Aspergillus oryzae, and Rhizopus sp., were utilized for rice Koji fermentation, and the metabolites were analyzed in a time-dependent manner by gas chromatography-mass spectrometry. On Principal Component Analysis, the metabolite patterns were clearly distinguished based on the fungi species. This approach revealed that the quantities of glucose, galactose, and glycerol gradually increased as a function of fermentation time in all trials rice Koji fermentation. The time-dependent changes of these metabolites showed significant increases in glucose in the A. oryzae-treated rice, and in glycerol and galactose in the A. kawachii-treated rice. In addition, glycolysis-related enzyme activities were correlated with the changes in these metabolites. The results indicate that time-dependent metabolite production has the potential to be a valuable tool in selecting inoculant fungi and the optimal fermentation time for rice koji.

Effect of fermented soybean product (Cheonggukjang) intake on metabolic parameters in mice fed a high-fat diet.

As a nontargeted metabolomics approach, we investigated changes in the plasma metabolite levels in a mouse model of obesity induced by a high-fat diet and fermented soybean product diet. We analyzed the plasma samples by using ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). In the present study, the animals were divided into four groups according to the diet type; normal fat diet control group (ND), high-fat diet control group (HD), high-fat diet plus 30% cooked soybean power (HD + S), and high-fat diet plus 30% 72-h fermented Cheonggukjang powder (HD + CGJ). To examine the changes in plasma metabolite levels because of high-fat diet feeding, total cholesterol and triglyceride levels were measured. Total cholesterol and triglyceride levels were lower in the HD + S and HD + CGJ groups than in the ND group. According to partial least-squares discriminant analysis (PLS-DA), major metabolites contributing to the discrimination between each group were assigned as lipid metabolites in plasma, e.g., lyso-phosphatidylcholines and phosphatidylcholines. Therefore, diets containing soy-based food products, which are rich sources of isoflavonoids, might be helpful for controlling the lipid metabolism under high-fat diet conditions.

A mutation of cdc-25.1 causes defects in germ cells but not in somatic tissues in C. elegans

By screening C. elegans mutants for severe defects in germline proliferation, we isolated a new loss-of-function allele of cdc-25.1, bn115. bn115 and another previously identified loss-of-function allele nr2036 do not exhibit noticeable cell division defects in the somatic tissues but have reduced numbers of germ cells and are sterile, indicating that cdc-25.1 functions predominantly in the germ line during postembryonic development, and that cdc-25.1 activity is probably not required in somatic lineages during larval development. We analyzed cell division of germ cells and somatic tissues in bn115 homozygotes with germline-specific anti-PGL-1 immunofluorescence and GFP transgenes that express in intestinal cells, in distal tip cells, and in gonadal sheath cells, respectively. We also analyzed the expression pattern of cdc-25.1 with conventional and quantitative RT-PCR. In the presence of three other family members of cdc-25 in C. elegans defects are observed only in the germ line but not in the somatic tissues in cdc-25.1 single mutants, and cdc-25.1 is expressed predominantly, if not exclusively, in the germ line during postembryonic stages. Our findings indicate that the function of cdc-25.1 is unique in the germ line but likely redundant with other members in the soma.

Lysophospholipid profile in serum and liver by high-fat diet and tumor induction in obesity-resistant BALB/c mice

OBJECTIVE Our previous study revealed that chronic consumption of a high-fat diet (HFD) stimulates colon cancer progression in obesity-resistant BALB/c mice. The aim of the present study was to investigate the significant alteration of metabolites caused by tumor progression and an HFD in the serum and liver in the same mouse model. METHODS Male BALB/c mice were fed either a control diet or a HFD for 20.5 wk. The syngeneic CT26 colon carcinoma cells were injected into the right rear flank of mice after 16 wk of feeding. Metabolites in serum and liver samples were analyzed by ultra-performance liquid chromatography-quadrupole-time-of-flight-mass spectrometry-based metabolomics. RESULTS HFD feeding and tumor injection induced changes in the choline-containing phospholipids, namely, phosphatidylcholines and lysophosphatidylcholines (lysoPCs), and lysophosphatidylethanolamines in the serum and liver. The majority of these metabolite changes were due to HFD feeding (11 in sera and 5 in livers) rather than tumors (3 in sera and 1 in livers). CONCLUSION The HFD- and tumor-related metabolite alterations of phospholipids, especially lysoPCs, in the liver and serum of obesity-resistant mice, suggesting that the lysoPCs are potential biomarkers for the chronic consumption of HFD in nonobese individuals.

Influence of iron regulation on the metabolome of Cryptococcus neoformans.

Iron is an essential nutrient for virtually all organisms and acts as a cofactor for many key enzymes of major metabolic pathways. Furthermore, iron plays a critical role in pathogen-host interactions. In this study, we analyzed metabolomic changes associated with iron availability and the iron regulatory protein Cir1 in a human fungal pathogen Cryptococcus neoformans. Our metabolite analysis revealed that Cir1 influences the glycolytic pathway, ergosterol biosynthesis and inositol metabolism, which require numerous iron-dependent enzymes and play important roles in pathogenesis and antifungal sensitivity of the fungus. Moreover, we demonstrated that increased cellular iron content and altered gene expression in the cir1 mutant contributed to metabolite changes. Our study provides a new insight into iron regulation and the role of Cir1 in metabolome of C. neoformans.

A Correlation between Antioxidant Activity and Metabolite Release during the Blanching of Chrysanthemum coronarium L.

Liquid chromatography tandem mass spectrometry (LCMS/MS)-based metabolite profiling was applied to elucidate the correlation between metabolite release and antioxidant activity during water blanching of Chrysanthemum coronarium L. (CC). Some major metabolites showing differences between fresh CC and blanched CC (BCC) were selected by principal component analysis (PCA) and partial least-square discriminate analysis (PLS-DA) loading plots, and were identified as dicaffeoylquinic acid (DCQA), succinoyl-DCQA, and acetylmycosinol. By PLS regression analysis of the correlation between antioxidant components and effects, candidate antioxidative metabolites were predicted due to strong positive correlations with DCQA and succinoyl-DCQA, and by a relatively weak positive correlation with acetylmycosinol.

Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli

YmfB from Escherichia coli is the Nudix hydrolase involved in the metabolism of thiamine pyrophosphate, an important compound in primary metabolism and a cofactor of many enzymes. In addition, it hydrolyzes (d)NTPs to (d)NMPs and inorganic orthophosphates in a stepwise manner. The structures of YmfB alone and in complex with three sulfates and two manganese ions determined by X-ray crystallography, when compared with the structures of other Nudix hydrolases such as MutT, Ap4Aase and DR1025, provide insight into the unique hydrolysis mechanism of YmfB. Mass-spectrometric analysis confirmed that water attacks the terminal phosphates of GTP and GDP sequentially. Kinetic analysis of binding-site mutants showed that no individual residue is absolutely required for catalytic activity, suggesting that protein residues do not participate in the deprotonation of the attacking water. Thermodynamic integration calculations show that a hydroxyl ion bound to two divalent metal ions attacks the phosphate directly without the help of a nearby catalytic base.