Novel microbiota Mesosutterella faecium sp. nov. has a protective effect against inflammatory bowel disease

A novel Gram-negative, obligate anaerobe, non-motile, flagella-lacking, catalase- and oxidase-negative, coccobacilli-shaped bacterial strain designated AGMB02718T was isolated from swine feces. The 16S rRNA gene analysis indicated that strain AGMB02718T belonged to the genus Mesosutterella with the highest similarity to M. multiformis 4NBBH2T (= DSM 106860T) (sequence similarity of 96.2%), forming a distinct phylogenetic lineage. Its growth occurred at 25-45°C (optimal 37°C) and in 0.5-1% NaCl (optimal 0.5%). Strain AGMB02718T was asaccharolytic and contained menaquinone 6 (MK-6) and methylmenaquinone 6 (MMK-6) as the predominant respiratory quinones. The major cellular fatty acids in the isolate were C18:1ω9c and C16:0. Based on the whole-genome sequencing analysis, strain AGMB02718T had a 2,606,253 bp circular chromosome with a G + C content of 62.2%. The average nucleotide identity value between strain AGMB02718T and M. multiformis 4NBBH2T was 72.1%, while the digital DNA-DNA hybridization value was 20.9%. Interestingly, genome analysis suggested that strain AGMB02718T possessed a low-toxicity lipopolysaccharide (LPS) because the genome of the isolate does not include lpxJ and lpxM genes for Kdo2-Lipid A (KLA) assembly, which confers high toxicity to LPS. Moreover, in vitro macrophage stimulation assay confirmed that AGMB02718T produced LPS with low toxicity. Because the low-toxicity LPS produced by the Sutterellaceae family is involved in regulating host immunity and low-toxicity LPS-producing strains can help maintain host immune homeostasis, we evaluated the anti-inflammatory activity of strain AGMB02718T against inflammatory bowel disease (IBD). As a result, strain AGMB02718T was able to prevent the inflammatory response in a dextran sulfate sodium (DSS)-induced colitis model. Therefore, this strain represents a novel species of Mesosutterella that has a protective effect against DSS-induced colitis, and the proposed name is Mesosutterella faecium sp. nov. The type strain is AGMB02718T (=GDMCC 1.2717T = KCTC 25541T).

Anti-obesity activity of human gut microbiota Bacteroides stercoris KGMB02265

Obesity is a global health threat that causes various complications such as type 2 diabetes and nonalcoholic fatty liver disease. Gut microbiota is closely related to obesity. In particular, a higher Firmicutes to Bacteroidetes ratio has been reported as a biomarker of obesity, suggesting that the phylum Bacteroidetes may play a role in inhibiting obesity. Indeed, the genus Bacteroides was enriched in the healthy subjects based on metagenome analysis. In this study, we determined the effects of Bacteroides stercoris KGMB02265, a species belonging to the phylum Bacteroidetes, on obesity both in vitro and in vivo. The cell-free supernatant of B. stercoris KGMB02265 inhibited lipid accumulation in 3T3-L1 preadipocytes, in which the expression of adipogenic marker genes was repressed. In vivo study showed that the oral administration of B. stercoris KGMB02265 substantially reduced body weight and fat weight in high-fat diet induced obesity in mice. Furthermore, obese mice orally administered with B. stercoris KGMB02265 restored glucose sensitivity and reduced leptin and triglyceride levels. Taken together, our study reveals that B. stercoris KGMB02265 has anti-obesity activity and suggests that it may be a promising candidate for treating obesity.

Collinsella urealyticum sp. nov., a urease-positive bacterial strain isolated from swine faeces

A novel actinobacterial strain, designated AGMB00827^T, was isolated from swine faeces. Strain AGMB00827^T was obligately anaerobic, Gram-stain-positive, non-motile, non-spore-forming and rod-shaped bacterium. Comparative analyses based on the 16S rRNA gene and whole genome sequence revealed that strain AGMB00827^T was affiliated to the genus Collinsella, and was most closely related to Collinsella vaginalis Marseille-P2666^T (= KCTC 25056^T). Biochemical analysis showed strain AGMB00827^T was negative for catalase and oxidase. Interestingly, strain AGMB00827^T possessed urease activity, which was determined by traditional methods (API test and Christensen's urea medium), unlike related strains. Furthermore, the major cellular fatty acids (> 10%) of the isolate were C_18:1 ω9c, C_16:0, C_16:0 DMA and C_18:2 ω9,12c DMA. Based on the whole genome sequence analysis, the DNA G + C content of strain AGMB00827^T was 52.3%, and the genome size and numbers of rRNA and tRNA genes were 1,945,251 bp, 3 and 46, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between strain AGMB00827^T and C. vaginalis KCTC 25056 ^T were 71.0 and 23.2%, respectively. Additionally, the genome analysis revealed that strain AGMB00827^T possesses urease gene cluster including ureABC and ureDEFG while the related strains do not have those genes, which is consistent with the urease activity. On the basis of polyphasic taxonomic approach, strain AGMB00827^T represents a novel species within the genus Collinsella, for which the name Collinsella urealyticum sp. nov. is proposed. The type strain is AGMB00827^T (= KCTC 25287^T = GDMCC 1.2724^T).

Parabacteroides faecalis sp. nov. Isolated from Swine Faeces

A Gram-negative, obligate anaerobic, non-motile, non-spore-forming, rod-shaped bacterial strain designated AGMB00274^T was isolated from swine faeces. An 16S rRNA gene analysis indicated that strain AGMB00274^T belonged to the genus Parabacteroides, with the highest similarity to Parabacteroides johnsonii (P. johnsonii) DSM 18315^T (sequence similarity of 94.9%). The genome size of strain AGMB00274^T was 4,308,683 bp, with a DNA G+C content of 42.5 mol%. The biochemical analysis of strain AGMB00274^T showed that it was positive for gelatin hydrolysis and α-fucosidase, but negative for the acid production from D-glucose, D-mannitol, D-maltose, salicin, glycerol, D-cellobiose, D-mannose, D-melezitose, D-sorbitol, D-trehalose, and negative for α-arabinosidase, glutamic acid decarboxylase, and pyroglutamic acid arylamidase. The dominant cellular fatty acids (> 10%) of the isolate were anteiso-C_{15: 0} (23.2%), iso-C_{15: 0} (16.6%), C_{18: 1} ω9c (16.4%), summed feature 11 (iso-C_{17: 0} 3-OH and/or C_{18: 2} DMA) (12.5%), and C_{16: 0} (11.3%). The major respiratory quinones of strain AGMB00274^T were MK-9 (55.4%) and MK-10 (44.6%). The major polar lipid was phosphatidylethanolamine. Based on phylogenetic, genetic, physiological, and chemotaxonomic analyses, as a novel species of the genus Parabacteroides, strain AGMB00274^T was proposed with the name Parabacteroides faecalis sp. nov. The type strain used was AGMB00274^T (= KCTC 25286^T = GDMCC 1.2742^T).

Cell-Free Supernatant of Odoribacter splanchnicus Isolated From Human Feces Exhibits Anti-colorectal Cancer Activity

The gut microbiota (GM) has been shown to be closely associated with the development of colorectal cancer (CRC). However, the involvement of GM is CRC has mainly been demonstrated by metagenomic profiling studies showing the compositional difference between the GM of healthy individuals and that of CRC patients and not by directly studying isolated gut microbes. Thus, to discover novel gut microbes involved in CRC, we isolated the GM from the feces of healthy individuals and evaluated its anti-CRC activity in vitro and in vivo. After GM isolation, cell-free supernatants (CFSs) were prepared from the isolated gut microorganisms to efficiently screen a large amount of the GM for anti-proliferative ability in vitro. Our results showed that the CFSs of 21 GM isolates had anti-proliferative activity against human colon cancer HCT 116 cells. Of these 21 GM isolates, GM07 was chosen for additional study because it had the highest anti-cancer activity against mouse colon cancer CT 26 cells in vitro and was further evaluated in a CT 26 allograft mouse model in vivo. GM07 was identified as Odoribacter splanchnicus through phylogenetic analysis based on 16S rRNA gene sequencing. Further investigation determined that the CFS of O. splanchnicus (OsCFS) induced anti-proliferative activity via apoptosis, but not cell cycle arrest. Moreover, GC/MS analysis suggested that the putative active molecule in OsCFS is malic acid. Finally, in the CRC mouse model, peri-tumoral injection of OsCFS significantly decreased CRC formation, compared to the control group. Altogether, these findings will provide valuable information for the discovery of potential probiotic candidates that inhibit CRC.

Peptoniphilus faecalis sp. nov., isolated from swine faeces

An obligately anaerobic, Gram-positive, non-motile, coccus-shaped bacterial strain designated AGMB00490^T was isolated from swine faeces. 16S rRNA gene sequence-based phylogenetic analysis indicated that the isolate belongs to the genus Peptoniphilus and that the most closely related species is Peptoniphilus gorbachii WAL 10418^T (=KCTC 5947^T, 97.22 % 16S rRNA gene sequence similarity). Whole genome sequence analysis determined that the DNA G+C content of strain AGMB00490^T was 31.2 mol% and moreover that the genome size and numbers of tRNA and rRNA genes were 2 129 517 bp, 34 and 10, respectively. Strain AGMB00490^T was negative for oxidase and urease; positive for catalase, indole production, arginine arylamidase, leucine arylamidase, tyrosine arylamidase and histidine arylamidase; and weakly positive for phenylalanine arylamidase and glycine arylamidase. The major cellular fatty acids (>10 %) of the isolate were determined to be C_16 : 0 and C_18 : 1 ω9c. Strain AGMB00490^T produced acetic acid as a major end product of metabolism. Accordingly, phylogenetic, physiologic and chemotaxonomic analyses revealed that strain AGMB00490^T represents a novel species for which the name Peptoniphilus faecalis sp. nov. is proposed. The type strain is AGMB00490^T (=KCTC 15944^T=NBRC 114159^T).

Sutterella faecalis sp. nov., isolated from human faeces

An obligately anaerobic, Gram-stain-negative, non-motile, non-spore-forming, and coccobacilli-shaped bacterial strain, designated KGMB03119^T, was isolated from human faeces from a Korean. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the genus Sutterella and most closely related to Sutterlla wadsworthensis KCTC 15691^T (96.8% 16S rRNA gene sequence similarity). The DNA G + C content of strain KGMB03119^T was 58.3 mol% as determined from its whole genome sequence. Strain KGMB03119^T was asaccharolytic, catalase-positive, oxidase- and urease-negative. Furthermore, the isolate was positive for alkaline phosphatase, leucine arylamidase, acid phosphatase, arginine arylamidase, alanine arylamidase, and glycine arylamidase. The major cellular fatty acids (> 10%) of the isolate were C_18:1ω9c and C_16:0. Methylmenaquinone-5 (MMK-5, 100%) was the predominant isoprenoid quinone in the isolate. Based on the phylogenetic, physiological, and chemotaxonomic characteristics, strain KGMB03119^T represents a novel species, for which the name Sutterella faecalis sp. nov. is proposed. The type strain is KGMB03119^T (= KCTC 15823^T = NBRC 114254^T).

Activation of the Transducers of Unfolded Protein Response in Plants

Maintenance of homeostasis of the endoplasmic reticulum (ER) ensures the balance between loading of nascent proteins and their secretion. Certain developmental conditions or environmental stressors affect protein folding causing ER stress. The resultant ER stress is mitigated by upregulating a set of stress-responsive genes in the nucleus modulating the mechanism of the unfolded protein response (UPR). In plants, the UPR is mediated by two major pathways; by the proteolytic processing of bZIP17/28 and by the IRE1-mediated splicing of bZIP60 mRNA. Recent studies have shown the involvement of plant-specific NAC transcription factors in UPR regulation. The molecular mechanisms activating plant-UPR transducers are only recently being unveiled. This review focuses on important structural features involved in the activation of the UPR transducers like bZIP17/28/60, IRE1, BAG7, and NAC017/062/089/103. Also, we discuss the activation of the UPR pathways, including BAG7-bZIP28 and IRE1-bZIP60, in detail, together with the NAC-TFs, which adds a new paradigm to the plant UPR.

Activation of the Transducers of Unfolded Protein Response in Plants

Maintenance of homeostasis of the endoplasmic reticulum (ER) ensures the balance between loading of nascent proteins and their secretion. Certain developmental conditions or environmental stressors affect protein folding causing ER stress. The resultant ER stress is mitigated by upregulating a set of stress-responsive genes in the nucleus modulating the mechanism of the unfolded protein response (UPR). In plants, the UPR is mediated by two major pathways; by the proteolytic processing of bZIP17/28 and by the IRE1-mediated splicing of bZIP60 mRNA. Recent studies have shown the involvement of plant-specific NAC transcription factors in UPR regulation. The molecular mechanisms activating plant-UPR transducers are only recently being unveiled. This review focuses on important structural features involved in the activation of the UPR transducers like bZIP17/28/60, IRE1, BAG7, and NAC017/062/089/103. Also, we discuss the activation of the UPR pathways, including BAG7-bZIP28 and IRE1-bZIP60, in detail, together with the NAC-TFs, which adds a new paradigm to the plant UPR.

RNA Chaperone Function of a Universal Stress Protein in Arabidopsis Confers Enhanced Cold Stress Tolerance in Plants

The physiological function of Arabidopsis thaliana universal stress protein (AtUSP) in plant has remained unclear. Thus, we report here the functional role of the Arabidopsis universal stress protein, AtUSP (At3g53990). To determine how AtUSP affects physiological responses towards cold stress, AtUSP overexpression (AtUSP OE) and T-DNA insertion knock-out (atusp, SALK_146059) mutant lines were used. The results indicated that AtUSP OE enhanced plant tolerance to cold stress, whereas atusp did not. AtUSP is localized in the nucleus and cytoplasm, and cold stress significantly affects RNA metabolism such as by misfolding and secondary structure changes of RNA. Therefore, we investigated the relationship of AtUSP with RNA metabolism. We found that AtUSP can bind nucleic acids, including single- and double-stranded DNA and luciferase mRNA. AtUSP also displayed strong nucleic acid-melting activity. We expressed AtUSP in RL211 Escherichia coli, which contains a hairpin-loop RNA structure upstream of chloramphenicol acetyltransferase (CAT), and observed that AtUSP exhibited anti-termination activity that enabled CAT gene expression. AtUSP expression in the cold-sensitive Escherichia coli (E. coli) mutant BX04 complemented the cold sensitivity of the mutant cells. As these properties are typical characteristics of RNA chaperones, we conclude that AtUSP functions as a RNA chaperone under cold-shock conditions. Thus, the enhanced tolerance of AtUSP OE lines to cold stress is mediated by the RNA chaperone function of AtUSP.

Multicentre study of the safety of laparoscopic subtotal gastrectomy for gastric cancer in the elderly

BACKGROUND

The aim of this study was to assess the safety and short-term value of laparoscopic gastrectomy in the elderly with gastric cancer compared with a younger cohort.

METHODS

Data on all patients with gastric cancer undergoing laparoscopic gastrectomy at ten institutions in Korea between May 1998 and December 2005 were collected. Patients under the age of 45 years and those undergoing total gastrectomy, proximal gastrectomy and pylorus-preserving gastrectomy were excluded. An analysis of clinicopathological data for patients aged 45-69 years (average-age group) and those aged 70 years or more (elderly group) was undertaken.

RESULTS

Co-morbidity was more common and postoperative hospital stay was longer in elderly patients. Pre-existing pulmonary and cardiovascular disease in the elderly contributed to respiratory dysfunction and intraperitoneal complications respectively. Tumour size and location, stage, methods of reconstruction and the number of combined operations were similar in the two groups. There were no significant differences in postoperative morbidity or mortality.

CONCLUSION

Although elderly patients had greater co-morbidity, laparoscopic gastrectomy was a safe treatment for gastric cancer in this age group.

Apoptosis induced by human Fas-associated factor 1, hFAF1, requires its ubiquitin homologous domain, but not the Fas-binding domain

FAF1 is a Fas-binding protein without typical death domain. Instead, FAF1 has several domains found in proteins of ubiquitination pathway. Transient overexpression of hFAF1 in BOSC23 cells caused membrane blebbing and cell body condensation which were characteristics of apoptosis. Subsequent analysis revealed that overexpression of hFAF1 induced nuclear condensation, appearance of phosphatidylserines in the outer leaflet of the cellular membrane, and caspase 3 activation. The apoptotic potential of hFAF1 required downstream ubiquitin homologous domain (UB2) and adjacent nuclear localization signal but not the Fas-binding domain. Our data showed that mere intrinsic overexpression of hFAF1 initiated apoptosis in the absence of any extrinsic death signal in BOSC23 cells.

Interaction of Daxx, a Fas binding protein, with sentrin and Ubc9

Sentrin is a ubiquitin-like protein that can covalently modify cellular proteins, and is a Fas binding protein that protects cells against anti-Fas induced cell death. However, the mechanism by which sentrin exerts its effect upon Fas-mediated apoptosis is not well known. Thus, this study examined the interaction of sentrin with Daxx. Sentrin interacted with Daxx but not with FADD when analyzed by yeast two-hybrid assay. In vitro translated Daxx bound to GST-sentrin fusion protein. FLAG-sentrin fusion protein was also coimmunoprecipitated with Daxx in BOSC23 cells. Also, Daxx interacted with Ubc9, an essential protein as a key conjugating enzyme. Amino acids 625-740 of Daxx, known as Fas binding region, was also mapped as sentrin and Ubc9 binding region. Colocalization of Fas, sentrin, and Ubc9 binding regions suggests the importance of that region upon the regulation of Daxx. Our data also demonstrated that sentrin could homooligomerize by protein-protein interaction.

Human Fas associated factor 1, hFAF1, gene maps to chromosome band 1p32

Human Fas associated factor 1 protein (hFAF1) is involved in the positive regulation of Fas signaling even though it can not initiate the signal for itself. By chromosomal assignment using somatic cell hybrids (CASH), the hFAF1 gene was located on human chromosome 1 between markers D1S443 and D1S197. The hFAF1 gene was mapped to human chromosome band 1p32 by FISH utilizing a genomic PAC clone containing the gene. In genomic Southern analysis using hFAF1 cDNA as a probe, several bands appeared in three different restriction enzyme digestions. The single band appearance in FISH analysis compared to several bands in Southern blots implies that the hFAF1 gene would be rather big or that an additional hFAF1 gene isotype(s) might be present in close vicinity.

Identification and characterization of human Fas associated factor 1, hFAF1

We have identified and characterized a cDNA encoding human Fas associated factor 1 (hFAF1) cDNA and a shorter form of hFAF1 cDNA [hFAF1(s)] with a 456 bp internal in-frame deletion from a human HeLa cDNA library. The nucleotide sequences of hFAF1 and hFAF1(s) were identical except for the deletion. GST-hFAF1 fusion protein bound to the in vitro translation product of Fas. The N-terminal region (amino acid 1 approximately 201) including the upstream ubiquitin homology domain of hFAF1 could bind with the death domain of Fas unlike that of qFAF1 whose binding region with Fas could not be determined. However hFAF1 did not bind to the death domain of Fas mutant, lpr(cg). hFAF1 was expressed abundantly in testis, skeletal muscle, and heart as 2.8 kb mRNA. Polyclonal antibody against hFAF1 detected 74 kD protein, a deduced protein size from the ORF and 40 kD protein in some cell lines.

Polymorphism analysis of the CYP1A1 locus in Koreans: presence of the solitary m2 allele

This study determined the complete genotype and the frequencies of all four mutations [T6235C (m1), A4889G (m2), T5639C (m3) and C4887A (m4)] of the CYP1A1 from 48 healthy Koreans and 17 Korean lung cancer patients. The mutations were analyzed by polymerase chain reaction (PCR)/restriction fragment length polymorphism (RFLP) and single stand conformation polymorphism (SSCP) simultaneously in order to improve accuracy as well as to screen for possible new alleles. Previously, the m2 mutation has always been linked to the m1 mutation. Also, the m1m2 double mutant allele (*2B) was thought to have a positive correlation with lung cancer susceptibility. Here we report the presence of the solitary m2 mutant allele without the m1 mutation (m1+m2) for the first time. This would be an evidence to support the theory of intragenic recombination in the CYP1A1 locus. The m1 mutation frequencies of healthy Koreans and lung cancer patients were 38.5% and 29.4%, respectively. The m2 mutation frequencies of healthy Koreans and lung cancer patients were 25.0% and 14.7%, respectively. Unlike the case for both Japanese and Caucasian lung cancer patients, neither m1 nor m2 mutations were overrepresented in Korean lung cancer patients. The m2 mutation frequency in Korean patients was significantly higher than those for Caucasians (2.7%) and the Japanese (19.8%). The African-American specific m3 mutation and m4 mutation found in Caucasians were not discovered in this study. The CYP1A1 allele with novel mutation was also not present.

Mutation analysis of CYP2D6 locus in the Korean population: identification of rare poor metabolizer alleles at the nucleotide level

The CYP2D6 loci of one hundred and eight genetically unrelated Koreans were analyzed. The G1934A mutation which causes aberrant splicing, thereby producing nonfunctional enzymes and is responsible for 70% of poor metabolizer (PM) phenotype among Caucasians, was found in three heterozygous individuals. The mutation frequency of Koreans at 1934 (1.5%) was one thirteenth of that of Caucasians (20.7%). Such a low mutation frequency could be the major genetic explanation for rare PMs in Koreans. A substitution allele of Gly169-Arg(G1846A) which also produces a nonfunctional enzyme was detected in one heterozygous individual. This PM allele has been reported only in Chinese but not in Caucasians. This is the first report which demonstrates the presence of CYP2D6 PM alleles at the nucleotide level in Koreans. No base changes were detected at 1795, 2637, and 3023 whose mutations would also make nonfunctional enzymes. Individuals with two nonfunctional alleles are thereby expected to be PMs phenotypically and were not detected in this study. Mutant alleles with Arg296-Cys(C2938T) and Ser476-Thr(G4268C) substitutions known to reduce enzyme activity and with silent mutations at 1749 were studied; mutation frequencies were 17.9%, 64.7%, and 66%, respectively. The mutation frequency at 2938 was especially reduced by half when compared to that of Caucasians (32.4%).

Absence of p15INK4B and p16INK4A gene alterations in primary cervical carcinoma tissues and cell lines with human papillomavirus infection

OBJECTIVE

Alterations of the p15INK4B and p16INK4A gene which are separated by 25 kb on chromosome 9p21 have been reported in various tumor-derived cell lines and primary tumors, but the role of these genes in cervical cancer is unknown. To determine the frequency of deletions and point mutations of these genes in human cervical cancer, we examined for alterations of the p15INK4B and p16INK4A genes in cervical carcinomas.

METHODS

We examined 57 primary tumors and matched normal tissues and 3 cervical cancer-derived cell lines. All the tumor tissues and cell lines were human papillomavirus (HPV) positive. Deletions or point mutations of exon 2 of the pINK4B gene and exons 1, 2, and 3 of the p16INK3A gene were examined by polymerase chain reaction and direct sequencing, respectively.

RESULTS

Our data indicate no evidence for intragenic homozygous deletion or point mutation in the primary cervical cancer tissues or cancer-derived cell lines.

CONCLUSION

Deletions or point mutations in the p15INK4B or p16INK4A gene may not be required for the development of HPV-positive cervical cancer or for establishment of cervical cancer cell lines.