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A novel, strictly anaerobic, gram-negative, segmented filamentous bacterium strain AGMB03513T, was isolated from the faeces of a 5-month-old pig. Phylogenetic analysis based on the 16S rRNA gene indicated that the isolate was a member of the family Lachnospiraceae, and the closest strain was Anaerostipes butyraticus. Strain AGMB03513T formed a lineage within the genus Anaerostipes and was closely related to A. butyraticus DSM 22094 T (= KCTC 15125 T, 95.8%), Anaerostipes hadrus DSM 3319 T (= KCTC 15606 T, 95.5%), Anaerostipes caccae DSM 14662 T (= KCTC 15019 T, 94.0%), and Anaerostipes rhamnosivorans DSM 26241 T (= KCTC 15316 T, 93.4%). Strain AGMB03513T grew at temperatures between 30 and 45 °C, within a pH range of 7.0–9.0, and in medium containing up to 1.5% NaCl. Cells were found to utilise d-glucose, d-mannitol, d-lactose, d-saccharose, d-maltose, d-xylose, l-arabinose, d-mannose, and d-sorbitol, and acetate was identified as the major end product of metabolism. The major components of the cellular fatty acids were C12:0, C16:0, and C18:0. In addition, the bacterium contained meso-diaminopimelic acid in the cell wall. According to the comparative analysis of the whole genome sequence, the DNA G + C content of strain AGMB03513 was 37.0 mol%. In addition, Average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridisation (dDDH) values were obtained in comparisons of strain AGMB03513T with reference strains of species in the genus Anaerostipes. ANI values were found to be between 71.0 and 75.7%, AAI values between 66.6 and 73.2%, and dDDH values between 19.5 and 21.4%. All the data were below the threshold range for species determination. Based on phenotypic, phylogenetic, biochemical, chemotaxonomic, and genomic characteristics, we considered it reasonable to assign a novel species status to strain AGMB03513T, for which we propose the name Anaerostipes faecalis sp. nov. The type strain is AGMB03513T (= KCTC 25020 T = NBRC 114896 T).

Cancer cells are a major source of enzymes that modify collagen to create a stiff, fibrotic tumor stroma. High collagen lysyl hydroxylase 2 (LH2) expression promotes metastasis and is correlated with shorter survival in lung adenocarcinoma (LUAD) and other tumor types. LH2 hydroxylates lysine (Lys) residues on fibrillar collagen’s amino- and carboxy-terminal telopeptides to create stable collagen cross-links. Here, we show that electrostatic interactions between the LH domain active site and collagen determine the unique telopeptidyl lysyl hydroxylase (tLH) activity of LH2. However, CRISPR/Cas-9-mediated inactivation of tLH activity does not fully recapitulate the inhibitory effect of LH2 knock out on LUAD growth and metastasis in mice, suggesting that LH2 drives LUAD progression, in part, through a tLH-independent mechanism. Protein homology modeling and biochemical studies identify an LH2 isoform (LH2b) that has previously undetected collagen galactosylhydroxylysyl glucosyltransferase (GGT) activity determined by a loop that enhances UDP-glucose-binding in the GLT active site and is encoded by alternatively spliced exon 13 A. CRISPR/Cas-9-mediated deletion of exon 13 A sharply reduces the growth and metastasis of LH2b-expressing LUADs in mice. These findings identify a previously unrecognized collagen GGT activity that drives LUAD progression., Guo et al. determine the molecular basis of collagen lysyl hydroxylase 2 (LH2) substrate specificity. They further show that LH2 also functions as a collagen glucosyltransferase to promote lung cancer progression.

Bacillus cereus can cause blood infections (i.e., sepsis). Its early detection is very important for treating patients. However, an antibody with high binding affinity to B. cereus is not currently available. Bacteriophage cell wall-binding domain (CBD) has strong and specific binding affinity to B. cereus. Here, we report the improvement in the sensitivity of an ATP bioluminescence assay for B. cereus detection using CBD-conjugated magnetic nanoparticles (CBDMNPs). The assay was able to detect as few as 10 colony forming units (CFU) per mL and 103 CFU per mL in buffer and blood. CBD-MNPs did not show any cross-reactivity with other microorganisms. These results demonstrate the feasibility of the ATP assay for the detection of B. cereus.

The objective of the present study was to analyze host-phage adsorption of bacteriophages infecting Escherichia coli O157:H7 and the other E. coli strains. Out of 55 coliphage strains, we selected seven coliphages infectious only to 23 E. coli O157 and seven other coliphages of broad specificity to E. coli O157:H7 and other 61 E. coli. Escherichia coli O157-specific phages and the broadly specific phages all belonged to the Siphoviridae and Myoviridae family, respectively. Escherichia coli O157-specific phages infected E. coli O157:H7, but not E. coli O157:H7△rfaL, deletion mutant of O-antigen ligase gene for lipopolysaccharide. Five coliphages among the broadly specific phages infected E. coli O103, but not E. coli O103△rfaG, deletion mutant of the glycosyltransferase gene. E. coli O157:H7-specific phages among Siphoviridae recognized O-antigen of E. coli O157, but the broadly specific coliphages of Myoviridae may recognize O-antigen and/or a part of the lipopolysaccharide core as an adsorption site in various E. coli. The receptor of the two coliphage groups interacts with some part of lipopolysaccharide, and the tail morphology of the coliphages may be related to their adsorption to and recognition of a different part of lipopolysaccharide. In particular, specificity of E. coli O157:H7-specific phages carrying the long tail of Siphoviridae for O-antigen as a receptor seems to be high.

Korean fermented foods are known to be beneficial for human health. Bacterial community studies have been conducted to figure out what roles the bacteria used to ferment these foods play in food fermentation. The metagenomic approach identifies both culturable and unculturable bacterial compositions, but this technique is limited in its ability to accurately determine the bacterial species from short 16S rRNA PCR products. In this study, we revisited the culture-dependent method using a relatively large number of bacterial isolates in an attempt to overcome the problem of bacterial identification, accepting that the unculturable bacterial population in each fermented food would be undetectable. Eight Korean fermented foods including kimchi, jeotgal, and meju were collected, and 1589 fermenting bacterial strains were randomly isolated. Bacteria were grouped by banding pattern using arbitrary-primed (AP) PCR prior to bacterial identification and sorted into 219 groups; 351 strains were not grouped because there was no identical AP-PCR band pattern. 16S rRNA sequence analysis identified the bacterial compositions of the fermented foods. As dominant genera, Lactobacillus and Leuconostoc strains were detected in four kimchi samples, Staphylococcus in three jeotgal samples, and Enterococcus and Bacillus in the meju sample. Interestingly, S. Equorum was most dominant in saeu-jeotgal, indicating that it is halophilic and may enhance the fermentation flavor. Further comparative analysis of this study with previous metagenomic results revealed that bacterial communities in fermented foods are highly similar at the genus level but often differ at the species level. This bacterial community study is useful for understanding the roles and functional properties of fermenting bacteria in the fermentation process of Korean fermented foods.

Amylosucrase (AS), a glucosyltransferase of the glycoside hydrolase 13 family, does not require a nucleotide-activated sugar as a glucosyl-donor. A gene (drpas) of Deinococcus radiopugnans encoding a putative AS was identified and cloned for characterization. The amino acid sequence revealed that drpas exhibited 76 and 74% identities with AS genes from D. geothermalis and D. radiodurans, respectively. Recombinant DRpAS exhibited AS activities. The ratios of hydrolysis, polymerization, and isomerization reactions were 5.8:82.7:11.5 at 40°C. The DRpAS was highly thermostable and produced more polymerization products than AS from D. radiodurans although the optimum growth temperature of both strains is 30°C.

Due to the emergence of antibiotic-resistant strains, bacteriophages are considered to be an alternative approach for the control of pathogens. In this study, the bacteriophages BPS10C and BPS13 were isolated and characterized to investigate their ability to control food-borne pathogenic Bacillus cereus. Phage BPS13 exhibited slightly higher host lysis activity compared with phage BPS10C. In addition, phage BPS13 exhibited greater stability under various pH and temperature conditions. To extend our knowledge of the lysis of B. cereus by these phages, their genomes were completely sequenced and analyzed, revealing that these phage genomes encode endolysin and two tail lysins, which are likely involved in host lysis and invasion mechanisms, respectively. These lysis-related proteins may increase the bactericidal activities of these phages, suggesting that they may be good candidates for the potential control of B. cereus.

The sequential organ failure assessment (SOFA) score is easy to calculate and has been well validated as an outcome predictor in critically ill adult patients. However, its use in children has been limited, mainly because of differences in basal reference levels of serum creatinine. Data include 87 patients requiring continuous renal replacement therapy (CRRT) between January 2005 and July 2011. We modified the SOFA score by excluding the renal component to an extrarenal SOFA score, based on the assumption that CRRT may mitigate the renal effect on outcome and investigated the utility in predicting outcome with comparison with pediatric risk of mortality (PRISM) III, pediatric logistic organ dysfunction (PELOD), and SOFA scores. Results showed that 95.4 % (n = 83) had multiple organ dysfunction syndrome with an overall mortality of 50.6 %. The extrarenal SOFA score at CRRT initiation and ≥20 % fluid overload were significantly associated with mortality. In comparison with the predictive power of various scoring systems, the extrarenal SOFA score showed the largest area under the receiver operating characteristic curve (extrarenal SOFA 0.774, SOFA 0.770, PRISM III 0.660, and PELOD 0.650). The extrarenal SOFA score may be a useful prognostic marker in critically ill children treated with CRRT.

The Bacillus cereus group phages infecting B. cereus, B. anthracis, and B. thuringiensis (Bt) have been studied at the molecular level and, recently, at the genomic level to control the pathogens B. cereus and B. anthracis and to prevent phage contamination of the natural insect pesticide Bt. A comparative phylogenetic analysis has revealed three different major phage groups with different morphologies (Myoviridae for group I, Siphoviridae for group II, and Tectiviridae for group III), genome size (group I > group II > group III), and lifestyle (virulent for group I and temperate for group II and III). A subsequent phage genome comparison using a dot plot analysis showed that phages in each group are highly homologous, substantiating the grouping of B. cereus phages. Endolysin is a host lysis protein that contains two conserved domains: a cell-wall-binding domain (CBD) and an enzymatic activity domain (EAD). In B. cereus sensu lato phage group I, four different endolysin groups have been detected, according to combinations of two types of CBD and four types of EAD. Group I phages have two copies of tail lysins and one copy of endolysin, but the functions of the tail lysins are still unknown. In the B. cereus sensu lato phage group II, the B. anthracis phages have been studied and applied for typing and rapid detection of pathogenic host strains. In the B. cereus sensu lato phage group III, the B. thuringiensis phages Bam35 and GIL01 have been studied to understand phage entry and lytic switch regulation mechanisms. In this review, we suggest that further study of the B. cereus group phages would be useful for various phage applications, such as biocontrol, typing, and rapid detection of the pathogens B. cereus and B. anthracis and for the prevention of phage contamination of the natural insect pesticide Bt.

For molecular study of marine bacteria Pseudoalteromonas phenolica using bacteriophage, a novel bacteriophage, TW1, belonging to the family Siphoviridae, was isolated, and its genome was completely sequenced and analyzed. The phage TW1 genome consists of 39,940-bp-length double-stranded DNA with a GC content of 40.19 %, and it was predicted to have 62 open reading frames (ORFs), which were classified into functional groups, including phage structure, packaging, DNA metabolism, regulation, and additional function. The phage life style prediction using PHACTS showed that it may be a temperate phage. However, genes related to lysogeny and host lysis were not detected in the phage TW1 genome, indicating that annotation information about P. phenolica phages in the genome databases may not be sufficient for the functional prediction of their encoded proteins. This is the first report of a P. phenolica-infecting phage, and this phage genome study will provide useful information for further molecular research on P. phenolica and its phage, as well as their interactions.

Bacillus cereus causes food poisoning, resulting in vomiting and diarrhea, due to production of enterotoxins. As a means of controlling this food-borne pathogen, the virulent bacteriophage B4 was isolated and characterized. Bacterial challenge assays showed that phage B4 effectively inhibited growth of members of the B. cereus group as well as B. subtilis, and growth inhibition persisted for over 20 h. One-step growth analysis also revealed the host lysis activity of phage B4, with relatively short eclipse/latent times (10/15 min) and a large burst size (>200 PFU). The complete genome of phage B4, containing a 162-kb DNA with 277 ORFs, was analyzed. The endolysin encoded by the phage B4 genome accounts for the cell lysis activity of this phage. These results suggest that phage B4 has potential as a biological agent to control B. cereus propagation.

Bacteriophage chi is a well-known phage that infects pathogens such as E. coli, Salmonella, and Serratia via bacterial flagella. To further understand its host-phage interaction and infection mechanism via host flagella, the genome was completely sequenced and analyzed. The phage genome contains 59,407-bp-length DNA with a GC content of 56.51 %, containing 75 open reading frames (ORFs) with no tRNA genes. Its annotation and functional analysis revealed that chi is evolutionarily very closely related to Enterobacter phage Enc34 and Providencia phage Redjac. However, most of the annotated genes encode hypothetical proteins, indicating that further genomic study of phage chi is required to elucidate the bacterial-flagellum-targeting infection mechanism of phage chi.

Two anion receptors 1 and 2 with a nitrophenyl group as a signaling group and urea/thiourea as a binding group were synthesized and their anion binding abilities were examined. The receptor 1 formed the hydrogen-bonded complex with various anions except fluoride. However, the receptor 2 immediately formed deprotonated receptor with various anions. Therefore, they operated based on a hydrogen bonding and an acid–base equilibrium. In addition, the receptor 1 proved to be an efficient and selective naked-eye detector for the fluoride ion.