Generation of Current Vortex by Spin Current in Rashba Systems.

Employing unbiased large-scale time-dependent density-matrix renormalization-group simulations, we demonstrate the generation of a charge-current vortex via spin injection in the Rashba system. The spin current is polarized perpendicular to the system plane and injected from an attached antiferromagnetic spin chain. We discuss the conversion between spin and orbital angular momentum in the current vortex that occurs because of the conservation of the total angular momentum and the spin-orbit interaction. This is in contrast to the spin Hall effect, in which the angular-momentum conservation is violated. Finally, we predict the electromagnetic field that accompanies the vortex with regard to possible future experiments.

Valley-Dependent Spin Transport in Monolayer Transition-Metal Dichalcogenides.

We study valley-dependent spin transport theoretically in monolayer transition-metal dichalcogenides in which a variety of spin and valley physics are expected because of spin-valley coupling. The results show that the spins are valley-selectively excited with appropriate carrier doping and valley polarized spin current (VPSC) is generated. The VPSC leads to the spin-current Hall effect, transverse spin accumulation originating from the Berry curvature in momentum space. The results indicate that spin excitations with spin-valley coupling lead to both valley and spin transport, which is promising for future low-consumption nanodevice applications.

Long-term colonization exceeding six years from early infancy of Bifidobacterium longum subsp. longum in human gut.

BACKGROUND: The importance of the gut microbiota at the early stage of life and their longitudinal effect on host health have recently been well investigated. In particular, Bifidobacterium longum subsp. longum, a common component of infant gut microbiota, appears in the gut shortly after birth and can be detected there throughout an individual's lifespan. However, it remains unclear whether this species colonizes in the gut over the long term from early infancy. Here, we investigated the long-term colonization of B. longum subsp. longum by comparing the genotypes of isolates obtained at different time points from individual subjects. Strains were isolated over time from the feces of 12 subjects followed from early infancy (the first six months of life) up to childhood (approximately six years of age). We also considered whether the strains were transmitted from their mothers' perinatal samples (prenatal feces and postnatal breast milk). RESULTS: Intra-species diversity of B. longum subsp. longum was observed in some subjects' fecal samples collected in early infancy and childhood, as well as in the prenatal fecal samples of their mothers. Among the highlighted strains, several were confirmed to colonize and persist in single individuals from as early as 90 days of age for more than six years; these were classified as long-term colonizers. One of the long-term colonizers was also detected from the corresponding mother's postnatal breast milk. Quantitative polymerase chain reaction data suggested that these long-term colonizers persisted in the subjects' gut despite the existence of the other predominant species of Bifidobacterium. CONCLUSIONS: Our results showed that several strains belonging to B. longum subsp. longum colonized in the human gut from early infancy through more than six years, confirming the existence of long-term colonizers from this period. Moreover, the results suggested that these strains persisted in the subjects' gut while co-existing with the other predominant bifidobacterial species. Our findings also suggested the importance of microbial-strain colonization in early infancy relative to their succession and showed the possibility that probiotics targeting infants might have longitudinal effects. TRIAL REGISTRATION: TRN: ISRCTN25216339 . Date of registration: 11/03/2016. Prospectively registered.

Quantitative detection of viable Bifidobacterium bifidum BF-1 cells in human feces by using propidium monoazide and strain-specific primers.

We developed a PCR-based method to detect and quantify viable Bifidobacterium bifidum BF-1 cells in human feces. This method (PMA-qPCR) uses propidium monoazide (PMA) to distinguish viable from dead cells and quantitative PCR using a BF-1-specific primer set designed from the results of randomly amplified polymorphic DNA analysis. During long-term culture (10 days), the number of viable BF-1 cells detected by counting the number of CFU on modified MRS agar, by measuring the ATP contents converted to CFU, and by using PMA-qPCR decreased from about 10(10) to 10(6) cells/ml; in contrast, the total number of (viable and dead) BF-1 cells detected by counting 4',6-diamidino-2-phenylindolee (DAPI)-stained cells and by using qPCR without PMA and reverse transcription-qPCR remained constant. The number of viable BF-1 cells in fecal samples detected by using PMA-qPCR was highly and significantly correlated with the number of viable BF-1 cells added to the fecal samples, within the range of 10(5.3) to 10(10.3) cells/g feces (wet weight) (r > 0.99, P < 0.001). After 12 healthy subjects ingested 10(10.3) to 10(11.0) CFU of BF-1 in a fermented milk product daily for 28 days, 10(4.5 ± 1.5) (mean ± standard deviation [SD]) BF-1 CFU/g was detected in fecal samples by using strain-specific selective agar; in contrast, 10(6.2 ± 0.4) viable BF-1 cells/g were detected by using PMA-qPCR, and a total of 10(7.6 ± 0.7) BF-1 cells/g were detected by using qPCR without PMA. Thus, the number of viable BF-1 cells detected by PMA-qPCR was about 50 times higher (P < 0.01) than that detected by the culture-dependent method. We conclude that strain-specific PMA-qPCR can be used to quickly and accurately evaluate viable BF-1 in feces.

Characterization of Bifidobacterium kashiwanohense that utilizes both milk- and plant-derived oligosaccharides.

Bifidobacteria are prominent members of the human gut microbiota throughout life. The ability to utilize milk- and plant-derived carbohydrates is important for bifidobacterial colonization of the infant and adult gut. The Bifidobacterium catenulatum subspecies kashiwanohense (B. kashiwanohense) was originally isolated from infant feces. However, only a few strains have been described, and the characteristics of this subspecies have been poorly investigated. Here, we characterized genotypes and phenotypes of 23 B. kashiwanohense-associated strains, including 12 newly sequenced isolates. Genome-based analysis clarified the phylogenetic relationship between these strains, revealing that only 13 strains are genuine B. kashiwanohense. We defined specific marker sequences and investigated the worldwide prevalence of B. kashiwanohense based on metagenome data. This revealed that not only infants but also adults and weaning children harbor this subspecies in the gut. Most B. kashiwanohense strains utilize long-chain xylans and possess genes for extracellular xylanase (GH10), arabinofuranosidase and xylosidase (GH43), and ABC transporters that contribute to the utilization of xylan-derived oligosaccharides. We also confirmed that B. kashiwanohense strains utilize short- and long-chain human milk oligosaccharides and possess genes for fucosidase (GH95 and GH29) and specific ABC transporter substrate-binding proteins that contribute to the utilization of a wide range of human milk oligosaccharides. Collectively, we found that B. kashiwanohense strains utilize both plant- and milk-derived carbohydrates and identified key genetic factors that allow them to assimilate various carbohydrates.

Bacterial production of the tunicate-derived antitumor cyclic depsipeptide didemnin B.

Natural products obtained from marine invertebrates such as sponges and tunicates are attractive sources of drugs. However, a critical obstacle in the development of these compounds is the problem of supply. In most cases, neither chemical synthesis nor mariculture of invertebrates is economically feasible. Due to structural similarities, many marine natural products are suspected to be produced by associated microorganisms. A favorable strategy for the production of such compounds is to use culturable microorganisms. Here we report that didemnin B, a tunicate-derived depsipeptide, has been isolated from a culturable bacterium, Tistrella mobilis YIT 12409.

Direct measurement of stool consistency by texture analyzer and calculation of reference value in Belgian general population.

Stool consistency is evaluated mainly in reference to indirect indicators such as water content or the appearance of stool forms using Bristol Stool Form Scale (BSFS). Methods of measurement are limited. We thus aimed to develop a simple protocol for direct measurement of stool consistency using the TA.XTExpress Texture Analyser (Stable Micro Systems Ltd.). We developed a protocol which enables mechanical quantification of the gram-force against a cylindrical probe (ø 6 mm) pushed into the stool surface at 2.0 mm/s to 5 mm depth. The consistency of 252 stools collected from 40 healthy Belgians was evaluated by the direct method and by the indirect indicators (water content and BSFS) for comparison. The log-transformed stool consistency values measured by the texture analyzer had a negative linear correlation with the stool water contents (rrm = - 0.781) with homoscedastic variance, suggesting the appropriateness of the new protocol. They showed a similar correlation with the BSFS, but with a large variance in the consistency values of normal stool forms. This correlation was much smaller for BSFS scored by subjects (rrm = - 0.587) than by experts (rrm = - 0.789), collectively indicating BSFS as a rough indicator of stool consistency susceptible to subjective bias despite its effectiveness in clinical use. The optimized direct method using the texture analyzer enables the accurate quantification of stool consistency, which facilitates understanding of the intestinal environment and function and thus may enhance the value of the stool as a predictor of human health.

Lactobacillus odoratitofui sp. nov., isolated from stinky tofu brine.

Three Gram-positive-staining strains isolated from fermented stinky tofu brine were rod-shaped, non-motile, asporogenous, facultatively anaerobic, heterofermentative and did not exhibit catalase activity. Comparative analyses of 16S rRNA, rpoA and pheS gene sequences demonstrated that the novel strains were members of the genus Lactobacillus. On the basis of 16S rRNA gene sequence similarity, the type strains of Lactobacillus collinoides (98.6 %), Lactobacillus paracollinoides (98.6 %) and Lactobacillus similis (99.6 %) were the closest neighbours. However, DNA-DNA reassociation values with these strains were less than 10 %. The phenotypic and genotypic features demonstrated that these isolates represent a novel species of the genus Lactobacillus, for which the name Lactobacillus odoratitofui sp. nov. is proposed. The type strain is YIT 11304(T) (=JCM 15043(T) =BCRC 17810(T) =DSM 19909(T)).

Identification and quantification of Lactobacillus casei strain Shirota in human feces with strain-specific primers derived from randomly amplified polymorphic DNA.

Lactobacillus casei strain Shirota (LcS) has been used in the production of fermented milk products for many years and is one of the most intensively studied probiotics. To evaluate the ability of LcS to proliferate in human intestines after it has been ingested, we developed a PCR-based method to identify and quantify LcS using an LcS-specific primer set (pLcS) derived from a randomly amplified polymorphic DNA (RAPD) analysis. We confirmed the high specificity of the pLcS primer set in 167 bacterial strains (57 strains of L. casei and 110 other strains of bacteria commonly isolated from human feces). The method's ability to identify LcS matched that of an ELISA using a monoclonal antibody and a RAPD analysis in a representative sample of colonies cultured from human feces. The detection limit of quantitative PCR (qPCR) using pLcS was 10(4.6) per gram of feces. The number of LcS in feces detected with qPCR was highly and significantly correlated with the number of LcS added to fecal samples within the range of 10(4.6) to 10(9.6) per gram feces (r(2)=0.999, P<0.001). After 14 healthy subjects ingested 10(11.0) CFU of LcS daily for 7 days, 10(9.1+/-0.5) LcS g(-1) (mean+/-S.D.) was detected in the fecal samples of all subjects by qPCR, and 10(8.0+/-0.9) CFU g(-1) was detected by culture; these values were significantly different (P<0.001, paired t-test). After the subjects stopped ingesting LcS, fecal LcS counts obtained with both methods decreased daily. The values produced by the 2 methods might have differed because of an overestimation in the PCR analysis due to the presence of dead LcS cells or an underestimation in the culture system due to the use of selective culture media; however, dead LcS cells can also be beneficial as immunomodulators. We confirmed that qPCR with an LcS-specific primer set was a rapid and accurate method for determining the total amount of LcS in feces including dead or less active cells which could not be detected by culture method.

Ethnic diversity of gut microbiota: species characterization of Bacteroides fragilis group and genus Bifidobacterium in healthy Belgian adults, and comparison with data from Japanese subjects.

The composition of the human gut microbiota is related to host health, and it is thought that dietary habits may play a role in shaping this composition. Here, we examined the population size and prevalence of six predominant bacterial genera and the species compositions of genus Bifidobacterium (g-Bifid) and Bacteroides fragilis group (g-Bfra) in 42 healthy Belgian adults by quantitative PCR (qPCR) over a period of one month. The population sizes and prevalence of these bacteria were basically stable throughout the study period. The predominant g-Bifid species were Bifidobacterium adolescentis and Bifidobacterium longum ss. longum, and the predominant g-Bfra species were Bacteroides vulgatus, Bacteroides uniformis, and Bacteroides ovatus. The Belgian gut microbiota data were then compared with gut microbiota data from 46 Japanese subjects collected according to the same protocol (Matsuki et al., Appl. Environ. Microbiol. 70, 167-173, 2004). The population size and prevalence of Bifidobacterium catenulatum group were significantly lower in the Belgian gut microbiota than in the Japanese gut microbiota (P < 0.001); however, the population size and prevalence of g-Bifid did not differ. This species-level qPCR analysis will be helpful for investigating the diversity of gut microbiota among ethnic groups.

Development and evaluation of a real-time quantitative PCR assay for detection and enumeration of yeasts of public health interest in dairy products.

Yeast contamination is a problem in the food industry as a cause of spoilage. Moreover, various species of yeasts are known to be capable of causing opportunistic infections in humans. We have developed a real-time quantitative PCR (qPCR) assay to directly detect and quantify nine emerging opportunistic yeast species (Candida albicans, Candida glabrata, Candida parapsilosis, Candida tropicalis, Clavispora lusitaniae, Filobasidiella neoformans, Issatchenkia orientalis, Trichosporon asahii, and Trichosporon jirovecii) in dairy product samples. We designed six primer pairs, conserved sequences of the variable D1/D2 domains of the 26S rRNA gene, to detect the yeasts and demonstrated their specificity. The qPCR assay could accurately quantify emerging opportunistic yeasts in an artificially contaminated dairy product. qPCR with the primer pairs we designed, was very sensitive and will allow producers to enumerate contaminating yeasts and identify whether they are opportunistic pathogens, in only 4 to 5h. This assay can easily be extended to other food items and to a variety of food-monitoring initiatives.

Bifidobacterium mongoliense sp. nov., from airag, a traditional fermented mare's milk product from Mongolia.

Two novel micro-organisms, designated strains YIT 10443(T) and YIT 10738, were isolated from airag, a traditional fermented mare's milk from Mongolia. The two strains were Gram-positive-staining, non-motile, asporogenous, catalase-negative, facultatively anaerobic rods of various shapes. Comparative analyses of 16S rRNA and ClpC ATPase (clpC) gene sequences and the presence of fructose-6-phosphate phosphoketolase (F6PPK) demonstrated that the novel strains were members of the genus Bifidobacterium. On the basis of 16S rRNA gene sequence similarity, the type strains of Bifidobacterium minimum (96.6 %) and Bifidobacterium psychraerophilum (95.7 %) were the closest neighbours of the novel strains, and DNA-DNA reassociation values with these strains were found to be lower than 15 %. The phenotypic and genotypic features demonstrated that the two strains represent a single, novel Bifidobacterium species, for which the name Bifidobacterium mongoliense sp. nov. is proposed. The type strain is YIT 10443(T) (=JCM 15461(T) =DSM 21395(T)).

Lactobacillus kisonensis sp. nov., Lactobacillus otakiensis sp. nov., Lactobacillus rapi sp. nov. and Lactobacillus sunkii sp. nov., heterofermentative species isolated from sunki, a traditional Japanese pickle.

Thirty six Gram-positive, rod-shaped, non-spore-forming, non-motile bacterial strains were isolated from the non-salted pickle solution used in producing sunki products, a traditional Japanese pickle. The novel strains were discriminated and separated into four groups by amplified fragment length polymorphism profiling, and by analysis based on recA gene sequences. The strains were classified into four species groups belonging to the Lactobacillus buchneri species group, which consists of L. buchneri, Lactobacillus diolivorans, Lactobacillus hilgardii, Lactobacillus kefiri, Lactobacillus parabuchneri and Lactobacillus parakefiri. The phenotypic and genotypic features of the four groups demonstrated that they represented four novel species, for which the names Lactobacillus kisonensis sp. nov. (type strain YIT 11168(T)=NRIC 0741(T)=JCM 15041(T)=DSM 19906(T)), Lactobacillus otakiensis sp. nov. (type strain YIT 11163(T)=NRIC 0742(T)=JCM 15040(T)=DSM 19908(T)), Lactobacillus rapi sp. nov. (type strain YIT 11204(T)=NRIC 0743(T)=JCM 15042(T)=DSM 19907(T)) and Lactobacillus sunkii sp. nov. (type strain YIT 11161(T)=NRIC 0744(T)=JCM 15039(T)=DSM 19904(T)) are proposed.

Lactobacillus capillatus sp. nov., a motile bacterium isolated from stinky tofu brine.

Three Gram-positive, catalase-negative, motile, rod-shaped bacteria were isolated from fermented stinky tofu brine. These strains, designated YIT 11306(T), YIT 11317 and YIT 11318, were discriminated from five isolates on the basis of randomly amplified polymorphic DNA profiles. They produced l-lactic acid as the main end product from glucose without gas formation, synthesized dextran from sucrose and hydrolysed aesculin. Ammonia was not produced from arginine. Comparative 16S rRNA gene sequence analysis demonstrated that the novel isolates were members of the genus Lactobacillus. Based on levels of 16S rRNA gene sequence similarity, the three novel strains were related most closely to the type strains of Lactobacillus mali (97.2 %) and Lactobacillus satsumensis (96.8 %). However, levels of DNA-DNA relatedness between the novel isolates and the type strains of L. mali and L. satsumensis were less than 10 %. The phenotypic and genotypic data demonstrate that the three strains represent a single novel species of the genus Lactobacillus, for which the name Lactobacillus capillatus sp. nov. is proposed. The type strain is YIT 11306(T) (=JCM 15044(T)=BCRC 17811(T)=DSM 19910(T)).

Lactobacillus durianis Leisner et al. 2002 is a later heterotypic synonym of Lactobacillus vaccinostercus Kozaki and Okada 1983.

The taxonomic status of the species Lactobacillus durianis and Lactobacillus vaccinostercus is briefly summarized and experimental evidence concerning their similarity is presented. Highly similar 16S rRNA gene sequences (99.8 % similarity over 1,523 bp), partial recA gene sequences (99.5 % similarity over 600 bp) and partial hsp60 gene sequences (99.1 % similarity over 924 bp) suggest that the two species are closely related. Moreover, a high DNA-DNA binding level (87 %) and similar genomic DNA G+C contents (41-44 mol% for both species) as well as similar biochemical characteristics support the evidence that they constitute a single species. Consequently, according to Rules 38 and 42 of the Bacteriological Code, the name Lactobacillus vaccinostercus, the oldest legitimate name, must be maintained and the name Lactobacillus durianis should be considered a later heterotypic synonym.

Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces.

16S rRNA gene-targeted group-specific primers were designed and validated for specific detection and quantification of the Clostridium leptum subgroup and the Atopobium cluster. To monitor the predominant bacteria in human feces by real-time PCR, we used these specific primers together with four sets of group-specific primers for the Clostridium coccoides group, the Bacteroides fragilis group, Bifidobacterium, and Prevotella developed in a previous study (T. Matsuki, K. Watanabe, J. Fujimoto, Y. Miyamoto, T. Takada, K. Matsumoto, H. Oyaizu, and R. Tanaka, Appl. Environ. Microbiol. 68:5445-5451, 2002). Examination of DNA extracted from the feces of 46 healthy adults showed that the C. coccoides group was present in the greatest numbers (log10 10.3 +/- 0.3 cells per g [wet weight] [average +/- standard deviation]), followed by the C. leptum subgroup (log10 9.9 +/- 0.7 cells per g [wet weight]), the B. fragilis group (log10 9.9 +/- 0.3 cells per g [wet weight]), Bifidobacterium (log10 9.4 +/- 0.7 cells per g [wet weight]), and the Atopobium cluster (log10 9.3 +/- 0.7 cells per g [wet weight]). These five bacterial groups were detected in all 46 volunteers. Prevotella was found in only 46% of the subjects at a level of log10 9.7 +/- 0.8 cells per g (wet weight). Examination of changes in the population and the composition of the intestinal flora for six healthy adults over an 8-month period revealed that the composition of the flora of each volunteer remained stable throughout the test period.

Quantitative PCR with 16S rRNA-gene-targeted species-specific primers for analysis of human intestinal bifidobacteria.

A highly sensitive quantitative PCR detection method has been developed and applied to the distribution analysis of human intestinal bifidobacteria by combining real-time PCR with Bifidobacterium genus- and species-specific primers. Real-time PCR detection of serially diluted DNA extracted from cultured bifidobacteria was linear for cell counts ranging from 10(6) to 10 cells per PCR assay. It was also found that the method was applicable to the detection of Bifidobacterium in feces when it was present at concentrations of >10(6) cells per g of feces. Concerning the distribution of Bifidobacterium species in intestinal flora, the Bifidobacterium adolescentis group, the Bifidobacterium catenulatum group, and Bifidobacterium longum were found to be the three predominant species by examination of DNA extracted from the feces of 46 healthy adults. We also examined changes in the population and composition of Bifidobacterium species in human intestinal flora of six healthy adults over an 8-month period. The results showed that the composition of bifidobacterial flora was basically stable throughout the test period.

Development of 16S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces.

For the detection and identification of predominant bacteria in human feces, 16S rRNA-gene-targeted group-specific primers for the Bacteroides fragilis group, Bifidobacterium, the Clostridium coccoides group, and Prevotella were designed and evaluated. The specificity of these primers was confirmed by using DNA extracted from 90 species that are commonly found in the human intestinal microflora. The group-specific primers were then used for identification of 300 isolates from feces of six healthy volunteers. The isolates were clearly identified as 117 isolates of the B. fragilis group, 22 isolates of Bifidobacterium, 65 isolates of the C. coccoides group, and 17 isolates of Prevotella, indicating that 74% of the isolates were identified with the four pairs of primers. The remaining 79 isolates were identified by 16S ribosomal DNA sequence analysis and consisted of 40 isolates of Collinsella, 24 isolates of the Clostridium leptum subgroup, and 15 isolates of disparate clusters. In addition, qualitative detection of these bacterial groups was accomplished without cultivation by using DNA extracted from the fecal samples. The goal for this specific PCR technique is to develop a procedure for quantitative detection of these bacterial groups, and a real-time quantitative PCR for detection of Bifidobacterium is now being investigated (T. Requena, J. Burton, T. Matsuki, K. Munro, M. A. Simon, R. Tanaka, K. Watanabe, and G. W. Tannock, Appl. Environ. Microbiol. 68:2420-2427, 2002). Therefore, the approaches used to detect and identify predominant bacteria with the group-specific primers described here should contribute to future studies of the composition and dynamics of the intestinal microflora.

Degradation of estrogens by Rhodococcus zopfii and Rhodococcus equi isolates from activated sludge in wastewater treatment plants.

We have isolated four strains of Rhodococcus which specifically degrade estrogens by using enrichment culture of activated sludge from wastewater treatment plants. Strain Y 50158, identified as Rhodococcus zopfii, completely and rapidly degraded 100 mg of 17beta-estradiol, estrone, estriol, and ethinyl estradiol/liter, as demonstrated by thin-layer chromatography and gas chromatography-mass spectrometry analyses. Strains Y 50155, Y 50156, and Y 50157, identified as Rhodococcus equi, showed degradation activities comparable with that of Y 50158. Using the random amplified polymorphism DNA fingerprinting test, these three strains were confirmed to have been derived from different sources. R. zopfii Y 50158, which showed the highest activity among these four strains, revealed that the strain selectively degraded 17beta-estradiol during jar fermentation, even when glucose was used as a readily utilizable carbon source in the culture medium. Measurement of estrogenic activities with human breast cancer-derived MVLN cells showed that these four strains each degraded 100 mg of 17beta-estradiol/liter to 1/100 of the specific activity level after 24 h. It is thus suggested that these strains degrade 17beta-estradiol into substances without estrogenic activity.