Yasuhiro Date

Nitrogen removal performance using anaerobic ammonium oxidation at low temperatures

An anaerobic ammonium oxidation (anammox) process for ammonia-rich wastewater treatment has not been reported at temperatures below 15 degrees C. This study used a gel carrier with entrapped anammox bacteria to obtain a stable nitrogen removal performance at low temperatures. In a continuous feeding test, a high nitrogen conversion rate (6.2 kg N m(-3) day(-1)) was confirmed at 32 degrees C. Nitrogen removal activity decreased gradually with decreasing operation temperature; however, it still occurred at 6 degrees C. Nitrogen conversion rates at 22 and 6.3 degrees C were 2.8 and 0.36 kg N m(-3) day(-1), respectively. Moreover, the stability of anammox activity below 20 degrees C was confirmed for more than 130 days. In batch experiments, anammox gel carriers were characterized with respect to temperature. The optimum temperature for anammox bacteria was found to be 37 degrees C. Furthermore, it was clear that the temperature dependence changed at about 28 degrees C. The apparent activation energy in the temperature range from 22 to 28 degrees C was calculated as 93 kJ mol(-1), and that in the range from 28 to 37 degrees C was 33 kJ mol(-1). This value agrees with the result of a continuous feeding test (94 kJ mol(-1), between 6 and 22 degrees C). The nitrogen removal performance demonstrated at the low temperatures used in this study will open the door for the application of anammox processes to many types of industrial wastewater treatment.

Strengthening of the intestinal epithelial tight junction by Bifidobacterium bifidum

Epithelial barrier dysfunction has been implicated as one of the major contributors to the pathogenesis of inflammatory bowel disease. The increase in intestinal permeability allows the translocation of luminal antigens across the intestinal epithelium, leading to the exacerbation of colitis. Thus, therapies targeted at specifically restoring tight junction barrier function are thought to have great potential as an alternative or supplement to immunology‐based therapies. In this study, we screened Bifidobacterium, Enterococcus, and Lactobacillus species for beneficial microbes to strengthen the intestinal epithelial barrier, using the human intestinal epithelial cell line (Caco‐2) in an in vitro assay. Some Bifidobacterium and Lactobacillus species prevented epithelial barrier disruption induced by TNF‐α, as assessed by measuring the transepithelial electrical resistance (TER). Furthermore, live Bifidobacterium species promoted wound repair in Caco‐2 cell monolayers treated with TNF‐α for 48 h. Time course 1H‐NMR‐based metabonomics of the culture supernatant revealed markedly enhanced production of acetate after 12 hours of coincubation of B. bifidum and Caco‐2. An increase in TER was observed by the administration of acetate to TNF‐α‐treated Caco‐2 monolayers. Interestingly, acetate‐induced TER‐enhancing effect in the coculture of B. bifidum and Caco‐2 cells depends on the differentiation stage of the intestinal epithelial cells. These results suggest that Bifidobacterium species enhance intestinal epithelial barrier function via metabolites such as acetate.

Microbial diversity of anammox bacteria enriched from different types of seed sludge in an anaerobic continuous-feeding cultivation reactor.

Enrichment of anammox bacteria from three types of seed sludge, sewage, digester, and nitrification sludges, was conducted using a nonwoven fabric carrier for immobilizing the anammox bacteria, and the microbial diversity of the enriched anammox culture was investigated. About four months later, simultaneous removals of ammonium and nitrite, and production of a small amount of nitrate, which is unique to the anammox reaction, were observed in all 3 sludge reactors. Results of 16S rRNA gene analysis indicated that anammox bacteria were cultivated and diversified in each sludge type. Moreover, the microbial diversity of anammox bacteria was higher in the enriched culture from sewage sludge compared to the other two types of seed sludge. Bacillus sp. coexisted in the anammox culture cultivated from sewage sludge. These results suggest that differences in the anammox community in the enriched culture were caused by differences in the type of seed sludge.

The Epithelia-Specific Membrane Trafficking Factor AP-1B Controls Gut Immune Homeostasis in Mice

BACKGROUND & AIMS Epithelial cells that cover the intestinal mucosal surface maintain immune homeostasis and tolerance in the gastrointestinal tract. However, little is known about the molecular mechanisms that regulate epithelial immune functions. Epithelial cells are distinct in that they are highly polarized; this polarity is, at least in part, established by the epithelium-specific polarized sorting factor adaptor protein (AP)-1B. We investigated the role of AP-1B-mediated protein sorting in the maintenance of gastrointestinal immune homeostasis. METHODS The role of AP-1B in intestinal immunity was examined in AP-1B-deficient mice (Ap1m2(-/-)) by monitoring their phenotypes, intestinal morphology, and epithelial barrier functions. AP-1B-mediated protein sorting was examined in polarized epithelial cells from AP-1B knockdown and Ap1m2(-/-) mice. RESULTS Ap1m2(-/-) mice developed spontaneous chronic colitis, characterized by accumulation of interleukin-17A-producing, T-helper 17 cells. Deficiency of AP-1B caused epithelial immune dysfunction, such as reduced expression of antimicrobial proteins and impaired secretion of immunoglobulin A. These defects promoted intestinal dysbiosis and increased bacterial translocation within the mucosa. Importantly, AP-1B deficiency led to mistargeting of a subset of basolateral cytokine receptors to the apical plasma membrane in a polarized epithelial cell line and in colonic epithelial cells from mice. AP1M2 expression was reduced significantly in colonic epithelium samples from patients with Crohns disease. CONCLUSIONS AP-1B is required for proper localization of a subset of cytokine receptors in polarized epithelial cells, which allows them to respond to cytokine signals from underlying lamina propria cells. The AP-1B-mediated protein sorting machinery is required for maintenance of immune homeostasis and prevention of excessive inflammation.

Comparative metabolomic and ionomic approach for abundant fishes in estuarine environments of Japan

Environmental metabolomics or ionomics is widely used to characterize the effects of environmental stressors on the health of aquatic organisms. However, most studies have focused on liver and muscle tissues of fish, and little is known about how the other organs are affected by environmental perturbations and effects such as metal pollutants or eutrophication. We examined the metabolic and mineral profiles of three kinds of abundant fishes in estuarine ecosystem, yellowfin goby, urohaze-goby, and juvenile Japanese seabass sampled from Tsurumi River estuary, Japan. Multivariate analyses, including nuclear magnetic resonance-based metabolomics and inductively coupled plasma optical emission spectrometry-based ionomics approaches, revealed that the profiles were clustered according to differences among body tissues rather than differences in body size, sex, and species. The metabolic and mineral profiles of the muscle and fin tissues, respectively, suggest that these tissues are most appropriate for evaluating environmental perturbations. Such analyses will be highly useful in evaluating the environmental variation and diversity in aquatic ecosystems.

SpinCouple: Development of a Web Tool for Analyzing Metabolite Mixtures via Two-Dimensional J-Resolved NMR Database

A new Web-based tool, SpinCouple, which is based on the accumulation of a two-dimensional (2D) (1)H-(1)H J-resolved NMR database from 598 metabolite standards, has been developed. The spectra include both J-coupling and (1)H chemical shift information; those are applicable to a wide array of spectral annotation, especially for metabolic mixture samples that are difficult to label through the attachment of (13)C isotopes. In addition, the user-friendly application includes an absolute-quantitative analysis tool. Good agreement was obtained between known concentrations of 20-metabolite mixtures versus the calibration curve-based quantification results obtained from 2D-Jres spectra. We have examined the web tool availability using nine series of biological extracts, obtained from animal gut and waste treatment microbiota, fish, and plant tissues. This web-based tool is publicly available via http://emar.riken.jp/spincpl.

Integrated Analysis of Seaweed Components during Seasonal Fluctuation by Data Mining Across Heterogeneous Chemical Measurements with Network Visualization

Biological information is intricately intertwined with several factors. Therefore, comprehensive analytical methods such as integrated data analysis, combining several data measurements, are required. In this study, we describe a method of data preprocessing that can perform comprehensively integrated analysis based on a variety of multimeasurement of organic and inorganic chemical data from Sargassum fusiforme and explore the concealed biological information by statistical analyses with integrated data. Chemical components including polar and semipolar metabolites, minerals, major elemental and isotopic ratio, and thermal decompositional data were measured as environmentally responsive biological data in the seasonal variation. The obtained spectral data of complex chemical components were preprocessed to isolate pure peaks by removing noise and separating overlapping signals using the multivariate curve resolution alternating least-squares method before integrated analyses. By the input of these preprocessed multimeasurement chemical data, principal component analysis and self-organizing maps of integrated data showed changes in the chemical compositions during the mature stage and identified trends in seasonal variation. Correlation network analysis revealed multiple relationships between organic and inorganic components. Moreover, in terms of the relationship between metal group and metabolites, the results of structural equation modeling suggest that the structure of alginic acid changes during the growth of S. fusiforme, which affects its metal binding ability. This integrated analytical approach using a variety of chemical data can be developed for practical applications to obtain new biochemical knowledge including genetic and environmental information.

Metabolic Sequences of Anaerobic Fermentation on Glucose-Based Feeding Substrates Based on Correlation Analyses of Microbial and Metabolite Profiling

Degradation processes in various biomasses are managed by complex metabolic dynamics created by diverse and extensive interactions and competition in microbial communities and their environments. It is important to develop visualization methods to provide a birds-eye view when characterizing the entire sequential metabolic process in an environmental ecosystem. Here, we describe an approach for the visualization of the metabolic sequences in anaerobic fermentation ecosystems, characterizing the entire metabolic dynamics using a combination of microbial community profiles and metabolic profiles. By evaluating their time-dependent variation, we found that microbial community profiles and metabolite production processes were characteristically affected by the feeding of different glucose-based substrates (glucose, starch, cellulose), although the compositions of the major microbial community and the metabolites detected were likely to be similar in all experiments. This combinatorial approach to variation in microbial communities and metabolic profiles was used successfully to visualize metabolic sequences in anaerobic fermentation ecosystems, in addition to mining candidate microbiota for cellulose degradation. Thus, this approach provides a powerful tool for visualizing and evaluating metabolic sequences within the biomass degradation process in an environmental ecosystem. This is the first report to visualize the entire metabolic dynamic in an anaerobic fermentation ecosystem as metabolic sequences.

Noninvasive analysis of metabolic changes following nutrient input into diverse fish species, as investigated by metabolic and microbial profiling approaches

An NMR-based metabolomic approach in aquatic ecosystems is valuable for studying the environmental effects of pharmaceuticals and other chemicals on fish. This technique has also contributed to new information in numerous research areas, such as basic physiology and development, disease, and water pollution. We evaluated the microbial diversity in various fish species collected from Japan’s coastal waters using next-generation sequencing, followed by evaluation of the effects of feed type on co-metabolic modulations in fish-microbial symbiotic ecosystems in laboratory-scale experiments. Intestinal bacteria of fish in their natural environment were characterized (using 16S rRNA genes) for trophic level using pyrosequencing and noninvasive sampling procedures developed to study the metabolism of intestinal symbiotic ecosystems in fish reared in their environment. Metabolites in feces were compared, and intestinal contents and feed were annotated based on HSQC and TOCSY using SpinAssign and network analysis. Feces were characterized by species and varied greatly depending on the feeding types. In addition, feces samples demonstrated a response to changes in the time series of feeding. The potential of this approach as a non-invasive inspection technique in aquaculture is suggested.

Differences in Cellulosic Supramolecular Structure of Compositionally Similar Rice Straw Affect Biomass Metabolism by Paddy Soil Microbiota

Because they are strong and stable, lignocellulosic supramolecular structures in plant cell walls are resistant to decomposition. However, they can be degraded and recycled by soil microbiota. Little is known about the biomass degradation profiles of complex microbiota based on differences in cellulosic supramolecular structures without compositional variations. Here, we characterized and evaluated the cellulosic supramolecular structures and composition of rice straw biomass processed under different milling conditions. We used a range of techniques including solid- and solution-state nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy followed by thermodynamic and microbial degradability characterization using thermogravimetric analysis, solution-state NMR, and denaturing gradient gel electrophoresis. These measured data were further analyzed using an “ECOMICS” web-based toolkit. From the results, we found that physical pretreatment of rice straw alters the lignocellulosic supramolecular structure by cleaving significant molecular lignocellulose bonds. The transformation from crystalline to amorphous cellulose shifted the thermal degradation profiles to lower temperatures. In addition, pretreated rice straw samples developed different microbiota profiles with different metabolic dynamics during the biomass degradation process. This is the first report to comprehensively characterize the structure, composition, and thermal degradation and microbiota profiles using the ECOMICS toolkit. By revealing differences between lignocellulosic supramolecular structures of biomass processed under different milling conditions, our analysis revealed how the characteristic compositions of microbiota profiles develop in addition to their metabolic profiles and dynamics during biomass degradation.