Kozo Asano

Are Uncultivated Bacteria Really Uncultivable

Many strategies have been used to increase the number of bacterial cells that can be grown from environmental samples but cultivation efficiency remains a challenge for microbial ecologists. The difficulty of cultivating a fraction of bacteria in environmental samples can be classified into two non-exclusive categories. Bacterial taxa with no cultivated representatives for which appropriate laboratory conditions necessary for growth are yet to be identified. The other class is cells in a non-dividing state (also known as dormant or viable but not culturable cells) that require the removal or addition of certain factors to re-initiate growth. A number of strategies, from simple to high throughput techniques, are reviewed that have been used to increase the cultivation efficiency of environmental samples. Some of the underlying mechanisms that contribute to the success of these cultivation strategies are described. Overall this review emphasizes the need of researchers to first understand the factors that are hindering cultivation to identify the best strategies to improve cultivation efficiency.

Catellatospora, a New Genus of the Actinomycetales

Two species of the new genus Catellatospora, belonging to the “actinoplanates” group, are described under the names Catellatospora citrea sp. nov. and Catellatospora ferruginea sp. nov. The organisms of this genus are aerobic and produce nonfragmenting vegetative hyphae and no true aerial mycelium. Short chains of nonmotile spores emerge singly or in tufts from the vegetative hyphae on the surface of agar media. The organisms have meso-diaminopimelic and 3-hydroxydiaminopimelic acids and glycine in the cell walls (a type II cell wall); xylose and arabinose (a pattern D whole-cell sugar); and phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides but not phosphatidylcholine (a type PII phospholipid pattern). The major menaquinones in C. citrea and C. ferruginea are MK-9 (H4) and MK-10 (H8), respectively. The guanine-plus-cytosine content of the deoxyribonucleic acids ranges from 70.9 to 71.5 mol%. The type strain of type species C. citrea is strain IFO 14495T (6183-ET), and the type strain of C. ferruginea is strain IFO 14496T (6257-CT).

Modulation of Rat Cecal Microbiota by Administration of Raffinose and Encapsulated Bifidobacterium breve

ABSTRACT To investigate the effects of administration of raffinose and encapsulated Bifidobacterium breve JCM 1192T cells on the rat cecal microbiota, in a preclinical synbiotic study groups of male WKAH/Hkm Slc rats were fed for 3 weeks with four different test diets: basal diet (group BD), basal diet supplemented with raffinose (group RAF), basal diet supplemented with encapsulated B. breve (group CB), and basal diet supplemented with both raffinose and encapsulated B. breve (group RCB). The bacterial populations in cecal samples were determined by fluorescence in situ hybridization (FISH) and terminal restriction fragment length polymorphism (T-RFLP). B. breve cells were detected only in the RCB group and accounted for about 6.3% of the total cells as determined by FISH analysis. B. breve was also detected only in the RCB group by T-RFLP analysis. This was in contrast to the CB group, in which no B. breve signals were detected by either FISH or T-RFLP. Increases in the sizes of the populations of Bifidobacterium animalis, a Bifidobacterium indigenous to the rat, were observed in the RAF and RCB groups. Principal-component analysis of T-RFLP results revealed significant alterations in the bacterial populations of rats in the RAF and RCB groups; the population in the CB group was similar to that in the control group (group BD). To the best of our knowledge, these results provide the first clear picture of the changes in the rat cecal microbiota in response to synbiotic administration.

Asaccharobacter celatus gen. nov., sp. nov., isolated from rat caecum

An obligately anaerobic and equol-producing bacterium, designated strain do03T, was isolated from the caecal content of a rat. Cells were Gram-positive, non-spore-forming rods. The results from a phylogenetic analysis based on 16S rRNA gene sequences showed that strain do03T formed a separate line of descent in the phylogenetic cluster of the family Coriobacteriaceae. The strain was unable to metabolize glucose or other carbohydrates as sole carbon sources; growth was enhanced in the presence of arginine. The cell wall contained meso-diaminopimelic acid. The major fatty acid was C18 : 1cis9 (54.0 %). The strain had one unidentified predominant (91.9 %) quinone that was not menaquinone, methylmenaquinone, demethylmenaquinone, ubiquinone or rhodoquinone. The DNA G+C content was 63 mol%. The data presented in this work show that strain do03T differs from members of the related recognized genera Eggerthella and Denitrobacterium at both the phylogenetic and phenotypic level. Therefore, the strain constitutes a novel genus and species, for which the name Asaccharobacter celatus gen. nov., sp. nov. is proposed. The type strain of the type species is do03T (=JCM 14811T=DSM 18785T=AHU 1763T).

Phylogenetic analysis of bacteria preserved in a permafrost ice wedge for 25,000 years

ABSTRACT Phylogenetic analysis of bacteria preserved within an ice wedge from the Fox permafrost tunnel was undertaken by cultivation and molecular techniques. The radiocarbon age of the ice wedge was determined. Our results suggest that the bacteria in the ice wedge adapted to the frozen conditions have survived for 25,000 years.

The Molecular Phylogeny of the Genus Rhizopus Based on rDNA Sequences

In order to establish the molecular phylogeny of the genus Rhizopus, three molecules of the ribosomal RNA-encoding DNA (rDNA), complete 18S, internal transcribed spacer (ITS)1-5.8S-ITS2, and 28S D1/D2 regions of all the species of the genus were sequenced. Phylogenetic trees showed three major clusters corresponding to the three groups in the current morphological taxonomy, microsporus-group, stolonifer-group, and R. oryzae. R. stolonifer var. lyococcos was clustered independently from the major clusters. R. schipperae clustered differently in all trees. Strains of R. sexualis had multiple ITS sequences. A. rouxii clustered with R. oryzae. These results indicate the possibility of molecular identification of species groups using rDNA sequencing. Reclassification of the genus might be appropriate.

Purification and characterization of phytase from Klebsiella pneumoniae 9-3B

Phytase, an enzyme that catalyzes the hydrolysis of phytate, was purified from Klebsiella pneumoniae 9-3B. The isolate was preferentially selected in a medium which contains phytate as a sole carbon and phosphate source. Phytic acid was utilized for growth and consequently stimulated phytase production. Phytase production was detected throughout growth and the highest phytase production was observed at the onset of stationary phase. The purification scheme including ion exchange chromatography and gel filtration resulted in a 240 and 2077 fold purification of the enzyme with 2% and 15% recovery of the total activity for liberation of inorganic phosphate and inositol, respectively. The purified phytase was a monomeric protein with an estimated molecular weight of 45kDa based on size exclusion chromatography and SDS-PAGE analyses. The phytase has an optimum pH of 4.0 and optimum temperature of 50°C. The phytase activity was slightly stimulated by Ca(2+) and EDTA and inhibited by Zn(2+) and Fe(2+). The phytase exhibited broad substrate specificity and the K(m) value for phytate was 0.04mM. The enzyme completely hydrolyzed myo-inositol hexakisphosphate (phytate) to myo-inositol and inorganic phosphate. The properties of the enzyme prove that it is a good candidate for the hydrolysis of phytate for industrial applications.

Soybean β51–63 peptide stimulates cholecystokinin secretion via a calcium-sensing receptor in enteroendocrine STC-1 cells

We previously demonstrated that intraduodenal administration of an arginine-rich beta 51-63 peptide in soybean beta-conglycinin suppresses food intake via cholecystokinin (CCK) secretion in rats. However, the cellular mechanisms by which the beta 51-63 peptide induces CCK secretion remain to be clarified. In the present study, we examined whether the extracellular calcium-sensing receptor (CaR) mediates beta 51-63-induced CCK secretion in murine CCK-producing enteroendocrine cell line STC-1. CCK secretion and changes in intracellular Ca(2+) concentration in response to beta 51-63 peptide were measured in STC-1 cells under various extracellular Ca(2+) concentrations and after treatment with a CaR antagonist. Intracellular Ca(2+) concentrations in response to beta 51-63 peptide and extracellular Ca(2+) were also measured in CaR-expressing human embryonic kidney (HEK-293) cells. The beta 51-63 peptide induced CCK secretion and intracellular Ca(2+) mobilization in STC-1 cells under normal (1.2mM) extracellular Ca(2+) conditions in a dose-dependent manner. These responses to beta 51-63 peptide were reduced by the removal of intra- or extracellular Ca(2+) but enhanced by increasing extracellular Ca(2+) concentrations. Intracellular Ca(2+) mobilization induced by extracellular Ca(2+) was also increased by the pretreatment with beta 51-63 peptide. Treatment with a specific CaR antagonist (NPS2143) inhibited beta 51-63-induced CCK secretion and intracellular Ca(2+) mobilization. In addition, HEK-293 cells transfected with CaR acquired sensitivity to the beta 51-63 peptide. From these results, we conclude that CaR is the beta 51-63 peptide sensor responsible for the stimulation of CCK secretion in enteroendocrine STC-1 cells.

Insect’s intestinal organ for symbiont sorting

Significance In general, animals have a mouth for feeding, an anus for defecation, and a gut connecting them for digestion and absorption. However, we discovered that the stinkbug’s gut is functionally disconnected in the middle by a previously unrecognized organ for symbiont sorting, which blocks food fluid and nonsymbiotic bacteria but selectively allows passing of a specific bacterial symbiont. Though very tiny and inconspicuous, the organ governs the configuration and specificity of stinkbug gut symbiosis, wherein the posterior gut region is devoid of food flow, populated by a specific bacterial symbiont, and transformed into an isolated organ for symbiosis. Mutant analyses showed that the symbiont’s flagellar motility is needed for passing the host organ, highlighting intricate host–symbiont interactions underpinning the symbiont sorting process. Symbiosis has significantly contributed to organismal adaptation and diversification. For establishment and maintenance of such host–symbiont associations, host organisms must have evolved mechanisms for selective incorporation, accommodation, and maintenance of their specific microbial partners. Here we report the discovery of a previously unrecognized type of animal organ for symbiont sorting. In the bean bug Riptortus pedestris, the posterior midgut is morphologically differentiated for harboring specific symbiotic bacteria of a beneficial nature. The sorting organ lies in the middle of the intestine as a constricted region, which partitions the midgut into an anterior nonsymbiotic region and a posterior symbiotic region. Oral administration of GFP-labeled Burkholderia symbionts to nymphal stinkbugs showed that the symbionts pass through the constricted region and colonize the posterior midgut. However, administration of food colorings revealed that food fluid enters neither the constricted region nor the posterior midgut, indicating selective symbiont passage at the constricted region and functional isolation of the posterior midgut for symbiosis. Coadministration of the GFP-labeled symbiont and red fluorescent protein-labeled Escherichia coli unveiled selective passage of the symbiont and blockage of E. coli at the constricted region, demonstrating the organ’s ability to discriminate the specific bacterial symbiont from nonsymbiotic bacteria. Transposon mutagenesis and screening revealed that symbiont mutants in flagella-related genes fail to pass through the constricted region, highlighting that both host’s control and symbiont’s motility are involved in the sorting process. The blocking of food flow at the constricted region is conserved among diverse stinkbug groups, suggesting the evolutionary origin of the intestinal organ in their common ancestor.

Breeding of Brewing Yeast Producing a Large Amount of β-Phenylethyl Alcohol and β-Phenylethyl Acetate

β-Phenylethyl alcohol and β-phenylethyl acetate have rose-like flavors and are very important aroma components of higher boiling points in various alcoholic beverages. β- to obtain mutants producing more of these components, the authors succeeded in obtaining mutants producing a large quantity of β- phenylethyl alcohol and its acetate using phenylalanine analogues and in producing sake with a characteristic flavor property