Hiroshi Habe

National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan

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Publications (116)248.29 Total impact

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    ABSTRACT: In biological wastewater treatment, municipal wastewater sometimes undergoes unexpected changes in physicochemical parameters, such as organic carbon concentration. The aim of this study was to understand how microbial communities in activated sludge in a membrane bioreactor (MBR) adapt to high organic loading and maintain their degradation ability during reactor operation. A pilot-scale MBR was operated for 19 days. On day 8, the concentration of organic matter in the synthetic wastewater increased from 450 to 900 mg chemical oxygen demand (COD)/L. Even under conditions of high organic loading, COD removal rates were high, ranging from 85.3 to 91.4%. High-throughput sequencing of 16S rRNA genes revealed that microbial communities changed drastically with increased organic loading. After day 8, Aquabacterium- and Azospira-related operational taxonomic units (OTUs) belonging to the class β-proteobacteria became dominant; this potentially enhanced the degradation of organic substances and decreased activated sludge microbial diversity. Due to the use of dissolved oxygen (DO) for degradation of organic substances, DO levels in the reactor decreased. This led to an increase in a subset of OTUs related to not only aerobic but also anaerobic bacteria, e.g., those in the class Clostridia. During this period, anaerobic microorganisms may have contributed to the degradation of organic substances to maintain MBR performance. On the other hand, high-throughput sequencing also made it possible to identify yet-to-be cultured or minor microorganisms affiliated with the candidate phylogenetic division SR1 and ammonia-oxidizing archaea in activated sludge.
    No preview · Article · Nov 2015 · Journal of Bioscience and Bioengineering
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    ABSTRACT: Microbiota activators (MAs) have been used to improve the reactor performances of biological wastewater treatment processes. In this study, to remove ammonium (NH4+) accumulated during the pre-operation of a pilot-scale membrane bioreactor (MBR) under high-organic-loading conditions, an MA was added to the MBR system and the resulting changes in reactor performances and microbial communities were monitored for 12 days. The NH4+ concentrations in the sludge and effluent decreased (from 427 to 246 mg/L in the sludge (days 1–9)), and mixed liquor suspended solid increased (from 6,793 to 11,283 mg/L (days 1–12)) after the addition of MA. High-throughput Illumina sequencing of 16S rRNA genes revealed that the microbial community structure changed along with the NH4+ removal resulting from the MA addition. In particular, the relative abundance of an Acidovorax-related operational taxonomic unit (OTU) increased significantly, accounting for approximately 50% of the total microbial population at day 11. In contrast, the ammonia-oxidizing bacteria and archaea showed low abundances (<0.05%), and no anaerobic ammonia oxidizers were detected. These results suggested that the Acidovorax-related OTU was mainly involved in the NH4+ removal in the MBR, probably due to its ammonia-assimilating metabolism.
    Full-text · Article · Sep 2015 · The Journal of General and Applied Microbiology
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    ABSTRACT: Nineteen levulinic acid (LA)-utilizing bacteria were isolated from environmental samples. Following examination of the use of 80 g/L LA by some isolated strains, Brevibacterium epidermidis LA39-2 consumed 62.6 g/L LA following 8 days incubation. The strain also utilized both 90 and 100 g/L LA, with consumption ratio of 84.3 and 53.3%, respectively, after 10 days incubation.
    No preview · Article · Apr 2015 · Bioscience Biotechnology and Biochemistry
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    ABSTRACT: The yeast Starmerella bombicola NBRC10243 is an excellent producer of sophorolipids (SLs) from various feedstocks. Here, we report the draft genome sequence of S. bombicola NBRC10243. Analysis of the sequence may provide insight into the properties of this yeast that make it superior for use in the production of functional glycolipids and biomolecules, leading to the further development of S. bombicola NBRC10243 for industrial applications.
    Preview · Article · Mar 2015 · Genome Announcements
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    ABSTRACT: Levulinic acid (LA) is a platform chemical derived from cellulosic biomass, and the expansion of LA utilization as a feedstock is important for production of a wide variety of chemicals. To investigate the potential of LA as a substrate for microbial conversion to chemicals, we isolated and identified LA-utilizing bacteria. Among the six isolated strains, Pseudomonas sp. LA18T and Rhodococcus hoagie LA6W degraded up to 70g/L LA in a high-cell-density system. The maximal accumulation of acetic acid by strain LA18T and propionic acid by strain LA6W was 13.6g/L and 9.1g/L, respectively, after a 4-day incubation. Another isolate, Burkholderia stabilis LA20W, produced trehalose extracellularly in the presence of 40g/L LA to approximately 2g/L. These abilities to produce useful compounds supported the potential of microbial LA conversion for future development and cellulosic biomass utilization. Copyright © 2014 Elsevier Ltd. All rights reserved.
    No preview · Article · Nov 2014 · Bioresource Technology
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    ABSTRACT: To produce l-glyceric acid (l-GA) from dl-GA, microbial resolution was investigated using newly isolated bacterial strains capable of enantiospecific degradation of d-GA. Strains GA3R and GA72P, identified as Serratia and Pseudomonas species, respectively, exhausted d-GA within 72 h, resulting in production of l-GA with enantiomeric purity ≥89%.
    No preview · Article · Nov 2014 · Journal of Bioscience and Bioengineering
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    ABSTRACT: Here we report the 3.7-Mb draft genome sequence of Acetobacter tropicalis NBRC16470T, which can produce optically pure d-glyceric acid (d-GA; 99% enantiomeric excess) from raw glycerol feedstock derived from biodiesel fuel production processes. FOOTNOTES Address correspondence to Hiroshi Habe, hiroshi.habe{at}aist.go.jp. Citation Koike H, Sato S, Morita T, Fukuoka T, Habe H. 2014. Draft genome sequence of Acetobacter tropicalis type strain NBRC16470, a producer of optically pure d-glyceric acid. Genome Announc. 2(6):e01329-14. doi:10.1128/genomeA.01329-14. Received 12 November 2014. Accepted 13 November 2014. Published 18 December 2014. Copyright © 2014 Koike et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
    Preview · Article · Nov 2014 · Genome Announcements
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    ABSTRACT: The basidiomycetous yeast Pseudozyma antarctica is known as a producer of industrial enzymes and the extracellular glycolipids, mannosylerythritol lipids. Here, we report the draft genome sequence of the type strain JCM10317. The draft genome assembly has a size of 18.1 Mb and a G+C content of 60.9%, and it consists of 197 scaffolds.
    Preview · Article · Sep 2014 · Genome Announcements
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    ABSTRACT: Gluconobacter oxydans IFO12528 is able to produce glyceric acid (GA) from glycerol through the action of a membrane-bound alcohol dehydrogenase (mADH), which is required for GA production. To determine whether membrane-bound aldehyde dehydrogenase (mALDH) also plays a role in GA production in G. oxydans, we constructed an aldH-disrupted mutant of G. oxydans (ΔaldH). ΔaldH was unable to produce acetic acid from ethanol, but was able to produce GA at a level approximately half that of the wildtype strain, suggesting the involvement of another ALDH in GA production. We also investigated the enantiomeric composition of GA produced by the IFO12528 and ΔaldH strains. No difference in GA composition was evident in the ΔaldH mutant, with ~73% d-GA enantiomeric excess observed in both strains.
    No preview · Article · Sep 2014 · Journal of oleo science
  • Shun Sato · Dai Kitamoto · Hiroshi Habe
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    ABSTRACT: We demonstrate that 0.78 mm glyceric acid activated the proliferation of human dermal fibroblasts by about 45%, whereas 34 mm α-glucosylglyceric acid (GGA) increased collagen synthesis by the fibroblasts by 1.4-fold compared to that in the absence of GGA. The two substances also exerted protective effects on both DNA scission by the hydroxyl radical and protein aggregation by heat in vitro.
    No preview · Article · Jul 2014 · Bioscience Biotechnology and Biochemistry
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    ABSTRACT: Carbazole 1,9a-dioxygenase (CARDO), a Rieske non-heme iron oxygenase (RO), is a three-component system composed of terminal oxygenase (Oxy), ferredoxin, and ferredoxin reductase. Oxy has angular dioxygenation activity against carbazole. Previously, site-directed mutagenesis of the Oxy gene from Janthinobacterium sp. strain J3 generated the Oxy derivatives I262V, F275W, Q282N and Q282Y, which showed different oxygenation capabilities than the wild-type enzyme. To understand the structural features resulting in the different oxidation reactions, we determined the crystal structures of the derivatives, both free and complexed with substrates. I262V, F275W, and Q282Y catalyze the lateral dioxygenation of carbazole with higher yields than the wild type. A previous study determined the crystal structure of Oxy complexed with carbazole and revealed that the carbonyl oxygen of Gly178 hydrogen bonds with the imino nitrogen of carbazole. In these derivatives, the carbazole was rotated approximately 15°, 25°, and 25°, respectively, compared to the wild type, creating space for a water molecule, which hydrogen bonds with the carbonyl oxygen of Gly178 and imino nitrogen of carbazole. In the crystal structure of F275W complexed with fluorene, C9 of fluorene, which corresponds to the imino nitrogen of carbazole, was oriented close to the mutated residue Trp275, which is on the opposite side of the binding pocket from the carbonyl oxygen of Gly178. Our structural analyses demonstrate that the fine-tuning of hydrophobic residues on the surface of the substrate-binding pocket in ROs causes a slight shift in the substrate binding position that in turn favors specific oxygenation reactions toward various substrates.
    Preview · Article · Feb 2014 · Applied and Environmental Microbiology
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    ABSTRACT: Pseudozyma antarctica is a non-pathogenic phyllosphere yeast known as an excellent producer of mannosylerythritol lipids (MELs), multi-functional extracellular glycolipids, from vegetable oils. To clarify the genetic characteristics of P. antarctica, we analyzed the 18 Mb genome of P. antarctica T-34. On the basis of KOG analysis, the number of genes (219 genes) categorized into lipid transport and metabolism classification in P. antarctica was one and a half times larger than that of yeast Saccharomyces cerevisiae (140 genes). The gene encoding an ATP/citrate lyase (ACL) related to acetyl-CoA synthesis conserved in oleaginous strains was found in P. antarctica genome: the single ACL gene possesses the four domains identical to that of the human gene, whereas the other oleaginous ascomycetous species have the two genes covering the four domains. P. antarctica genome exhibited a remarkable degree of synteny to U. maydis genome, however, the comparison of the gene expression profiles under the culture on the two carbon sources, glucose and soybean oil, by the DNA microarray method revealed that transcriptomes between the two species were significantly different. In P. antarctica, expression of the gene sets relating fatty acid metabolism were markedly up-regulated under the oily conditions compared with glucose. Additionally, MEL biosynthesis cluster of P. antarctica was highly expressed regardless of the carbon source as compared to U. maydis. These results strongly indicate that P. antarctica has an oleaginous nature which is relevant to its non-pathogenic and MEL-overproducing characteristics. The analysis and dataset contribute to stimulate the development of improved strains with customized properties for high yield production of functional bio-based materials.
    Preview · Article · Feb 2014 · PLoS ONE
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    ABSTRACT: Bioethanol is an important renewable resource that facilitates the sustainable development of society. In Miyako Island, Okinawa Prefecture, bioethanol is produced from sugarcane molasses, but molasses-based distillery wastewater is a highly polluted and dark brown-colored effluent that can cause serious problems in wastewater treatment. In a trial of seven adsorbents to investigate the separation of the colorants from wastewater, Diaion HP20 was selected as the most suitable adsorbent. Adsorbing and desorbing operations using column chromatography with HP20 recovered 74.5% of the colorants from wastewater (33.7 and 40.8% for 20 and 50% ethanol-eluted fractions, respectively). The isolated colorants as well as the wastewater itself exhibited scavenging activity against 1,1-diphenyl-2-picrylhydrazyl (DPPH), and contained polyphenols. The distillery wastewater contained 11.3 g-tocopherol equivalent/L of DPPH radical-scavenging constituents and 7.66 g-catechin equivalent/L of polyphenol constituents.
    No preview · Article · Jan 2014 · Journal of Water and Environment Technology
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    ABSTRACT: To promote the effective use of raw glycerol, 13 yeast strains with the ability to produce mannitol from glycerol were isolated from environmental samples. Of the 13 strains, strain 7-12G was selected as an efficient mannitol producer from 25% (w/v) glycerol and was identified as Candida azyma by morphological, physicochemical, and phylogenetic analyses. When the ability to produce mannitol from raw glycerol in flask culture was compared among strains 7-12G, NBRC10406 (the type strain of C. azyma), and related strains, strain NBRC10406 exhibited the highest production level (31.8 g/l). Culture in jar fermentors was next investigated, and mannitol production reached 50.8 g/l over 7 days, corresponding to 0.30 g/g-glycerol. To the best of our knowledge, this is the highest reported level of mannitol produced by a microbe from glycerol under batch-type culture conditions.
    No preview · Article · Dec 2013 · Journal of Bioscience and Bioengineering
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    ABSTRACT: To promote the effective use of raw glycerol (a by-product of biodiesel production), 110 yeast strains that produce D-arabitol from glycerol were isolated from environmental samples. Among them, strain 17-2A was an effective D-arabitol producer in the presence of 250 g/l glycerol and was identified as Candida quercitrusa based on morphological, physicochemical, and phylogenetic analyses. C. quercitrusa type strain NBRC1022 produced the greatest quantity of D-arabitol (41.7 g/l) when the ability to produce D-arabitol from raw glycerol was compared among C. quercitrusa 17-2A and its phylogenetically related strains in flask culture. Under optimized culture conditions, strain NBRC1022 produced D-arabitol at a concentration of 58.2 g/l after a 7-day cultivation in 250 g/l glycerol, 6 g/l yeast extract, and 2 g/l CaCl2. The culture conditions were further investigated with raw glycerol using a jar fermenter; the concentration of D-arabitol reached 67.1 g/l after 7 days and 85.1 g/l after 10 days, respectively, which corresponded to 0.40 g/g of glycerol. To our knowledge, the present D-arabitol yield from glycerol is higher than reported previously using microbial production.
    No preview · Article · Dec 2013 · Applied Microbiology and Biotechnology
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    ABSTRACT: Bioethanol has recently become an important resource for chemical industries. The chemical compositions of 17 different types of bioethanol were investigated with a focus on impurities that could affect catalytic performances in the downstream chemical processes. Lignocellulosic ethanol contained higher concentrations and a greater variety of organic impurities compared to sugar- or starch-derived bioethanol. Twenty-nine impurities were identified in lignocellulosic ethanol, whereas 16 impurities were in sugar- or starch-derived bioethanol. Lignocellulosic ethanol contained high concentrations of acetic acid, acetaldehyde, methanol, and furan-related compounds such as furfural. In contrast, with the exception of molasses-derived bioethanol obtained by crude distillation, the concentrations of these components were lower in sugar- or starch-derived bioethanol samples. Lignocellulosic ethanol contained dimethyl disulfide and thiazole, whereas the only organosulfur compounds found in sugar- or starch-derived bioethanol were dimethyl sulfide and dimethyl sulfoxide. These sulfur-containing impurities can cause catalyst deactivation in the bioethanol transformation processes. In lignocellulosic ethanol, more than 0.1 μg/mL of Si was detected.
    No preview · Article · Nov 2013 · Journal of the Japan Petroleum Institute
  • Shun Sato · Naoki Morita · Dai Kitamoto · Hiroshi Habe
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    ABSTRACT: Some acetic acid bacteria have been shown to produce large amounts of glyceric acid (GA) from glycerol, which is a by-product of biodiesel fuel (BDF) production. Previously, a Gluconobacter strain was found that produced decreased amounts of GA from glycerol in the presence of methanol, a major ingredient of raw glycerol derived from the BDF industry. Thus, a comparative transcriptome analysis of Gluconobacter frateurii NBRC103465 was performed to investigate changes in gene expression during GA production from glycerol in the presence of methanol. Cells grown with methanol showed upregulated expression of a class III alcohol dehydrogenase homolog (adhCGf) and decreased GA production. adhCGf was cloned and expressed heterologously in Escherichia coli, and the presence of an additional protein with an approximate molecular mass of 39 kDa in the cytosol of the recombinant E. coli cells was identified by SDS-PAGE. Activity measurements of the cytosol revealed that the translational product of adhCGf exhibited formaldehyde dehydrogenase activity in the presence of nicotinamide adenine dinucleotide and glutathione. Gluconobacter frateurii cells grown in 1% methanol-containing glycerol were found to have fivefold higher formaldehyde dehydrogenase activity than cells grown without methanol, suggesting that adhCGf in G. frateurii cells functions in the dissimilation of methanol-derived formaldehyde.
    No preview · Article · Oct 2013 · Journal of oleo science
  • Shun Sato · Dai Kitamoto · Hiroshi Habe
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    ABSTRACT: To produce glyceric acid (GA) from methanol-containing glycerol, resistance to methanol of Gluconobacter frateurii NBRC103465 was improved by chemical mutagenesis using N-methyl-N'-nitro-N-nitrosoguanidine. The obtained mutant Gf398 produced 6.3 g/L GA in 5% (v/v) methanol-containing 17% (w/v) glycerol medium, in which the wild-type strain neither grew nor produced GA.
    No preview · Article · Aug 2013 · Journal of Bioscience and Bioengineering
  • Naohiro Fukuda · Hiroshi Habe · Masataka Ito
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    ABSTRACT: The objective of this research was the modification of our biodiesel fuel (BDF) production process to make higher quality BDF. The existing process which does not include a water washing process for raw BDF, has the advantage of no wash water discharge, but occasionally the resultant BDF is of lower grade due to residual ingredients. First, we attempted to integrate water washing into the existing process. After being neutralized and washed with H2SO4, the raw BDF was then washed with water equal to 20% of the raw BDF volume. A good separation of BDF and wash water was achieved, and the resultant wash water contained less than 2% methanol. Second, we evaluated biodegradation of the resultant wash water constituents, and 70% of the strains isolated from environmental samples removed 80 to 90% of total organic carbon. Among these, strain No. 20-68 removed both glycerol and methanol in the wash water within 7 days and was identified as Fusarium falciforme, a ubiquitous environmental microorganisms. These results suggest that if the wash water is released to the environments, the effects on environmental microorganisms will be minimal.
    No preview · Article · Jul 2013 · Journal of oleo science
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    Shun Sato · Maiko Umemura · Hideaki Koike · Hiroshi Habe
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    ABSTRACT: Gluconobacter frateurii strain NBRC 103465 can efficiently produce glyceric acid (GA) from raw glycerol feedstock derived from biodiesel fuel production processes. Here, we report the 3.4-Mb draft genome sequence of G. frateurii NBRC 103465. The draft genome sequence can be applied to examine the enzymes and electron transport system involved in GA production.
    Preview · Article · Jun 2013 · Genome Announcements

Publication Stats

3k Citations
248.29 Total Impact Points


  • 2007-2015
    • National Institute of Advanced Industrial Science and Technology
      • Research Institute for Innovation in Sustainable Chemistry
      Tsukuba, Ibaraki, Japan
  • 1996-2014
    • The University of Tokyo
      • Center for Biotechnology Research
      白山, Tōkyō, Japan
  • 2006
    • Shibaura Institute of Technology
      Tōkyō, Japan
    • Tohoku University
      • Department of Environmental Life Sciences
      Sendai, Kagoshima, Japan
  • 2002
    • Gadjah Mada University
      • Department of Soil Science
      Jogjakarta, Daerah Istimewa Yogyakarta, Indonesia