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Vaskevicius L, Malunavicius V, Jankunec M, Lastauskiene E, Talaikis M, Mikoliunaite L, Maneikis A, Gudiukaite R. Insights in MICP dynamics in urease-positive Staphylococcus sp. H6 and Sporosarcina pasteurii bacterium. Environ Res 2023; 234:116588. [PMID: 37423368 DOI: 10.1016/j.envres.2023.116588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/22/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Microbially induced calcite precipitation (MICP) is an efficient and eco-friendly technique that has attracted significant interest for resolving various problems in the soil (erosion, improving structural integrity and water retention, etc.), remediation of heavy metals, production of self-healing concrete or restoration of different concrete structures. The success of most common MICP methods depends on microorganisms degrading urea which leads to the formation of CaCO3 crystals. While Sporosarcina pasteurii is a well-known microorganism for MICP, other soil abundant microorganisms, such as Staphylococcus bacteria have not been thoroughly studied for its efficiency in bioconsolidation though MICP is a very important proccess which can ensure soil quality and health. This study aimed to analyze MICP process at the surface level in Sporosarcina pasteurii and a newly screened Staphylococcus sp. H6 bacterium as well as show the possibility of this new microorganism to perform MICP. It was observed that Staphylococcus sp. H6 culture precipitated 157.35 ± 3.3 mM of Ca2+ ions from 200 mM, compared to 176 ± 4.8 mM precipitated by S. pasteurii. The bioconsolidation of sand particles was confirmed by Raman spectroscopy and XRD analysis, which indicated the formation of CaCO3 crystals for both Staphylococcus sp. H6 and S. pasteurii cells. The water-flow test suggested a significant reduction in water permeability in bioconsolidated sand samples for both Staphylococcus sp. H6 and S. pasteurii. Notably, this study provides the first evidence that CaCO3 precipitation occurs on the surface of Staphylococcus and S. pasteurii cells within the initial 15-30 min after exposure to the biocementation solution. Furthermore, Atomic force microscopy (AFM) indicated rapid changes in cell roughness, with bacterial cells becoming completely coated with CaCO3 crystals after 90 min incubation with a biocementation solution. To our knowledge, this is the first time where atomic force microscopy was used to visualize the dynamic of MICP on cell surface.
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Affiliation(s)
- Laurynas Vaskevicius
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257, Vilnius, Lithuania
| | - Vilius Malunavicius
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257, Vilnius, Lithuania
| | - Marija Jankunec
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257, Vilnius, Lithuania
| | - Egle Lastauskiene
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257, Vilnius, Lithuania
| | - Martynas Talaikis
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257, Vilnius, Lithuania
| | - Lina Mikoliunaite
- Department of Physical Chemistry, Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko St. 24, LT-03225, Vilnius, Lithuania; Laboratory of Spectroelectrochemistry, Department of Organic Chemistry, Center for Physical Sciences and Technology, Sauletekis Av. 3, LT-10257, Vilnius, Lithuania
| | - Andrius Maneikis
- Vilnius Gediminas Technical University, Sauletekis Av. 11, LT-10223, Vilnius, Lithuania
| | - Renata Gudiukaite
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257, Vilnius, Lithuania.
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Bharti M, Khurana H, Sharma M, Choksket S, Nagar S, Yadav S, Modeel S, Korpole S, Negi RK. Taxonomic and genomic characterization of Sporosarcina cyprini sp. nov., moderately tolerant of Cr+6 and Cd+2 isolated from the gut of invasive fish Cyprinus carpio var. communis (Linn., 1758). Antonie Van Leeuwenhoek 2023; 116:193-206. [PMID: 36400900 DOI: 10.1007/s10482-022-01794-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2022]
Abstract
A Gram-stain-positive, motile, and rod-shaped bacterium, designated as strain MB25T, was isolated from the gut of Cyprinus carpio from the highly polluted river Yamuna, India. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain MB25T belonged to the genus Sporosarcina, sharing the highest sequence similarity with S. luteola Y1T (98.98%) and S. koreensis S-K12T (98.91%). Digital DNA-DNA hybridization and average nucleotide identity values of strain MB25T with strain Y1T and S-K12T were 18.9, 77.69, and 18.2, 76.80 respectively. Genome analysis of strain MB25T revealed its biotechnological properties such as tolerance to potent heavy metals, genes for the production of carbohydrate-active enzymes, antimicrobial compounds, and also degradation of aromatic compounds. The G + C content of strain MB25T genome was 45%. Growth observed at 10-40 °C (optimum, 28-30 °C), pH 6.0-8.5 (optimum pH 7.5-8.0); NaCl concentrations up to 6.0% (w/v). The dominant respiratory quinone was MK-7, cell wall peptidoglycan is of the A-4 type containing amino acids Lys-Glu and the major fatty acids are anteiso-C11:0 and iso-C15: 0. The major polar lipids of strain MB25T are diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. On the basis of phenotypic, chemotaxonomic, phylogenetic, and phylogenomic data, strain MB25T represents a novel species of the genus Sporosarcina, for which the name Sporosarcina cyprini sp. nov. is proposed. The type strain is MB25T (= MCC 4366 T = JCM 34521 T = CCM 9113 T).
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Affiliation(s)
- Meghali Bharti
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, New Delhi, 110007, India
| | - Himani Khurana
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, New Delhi, 110007, India
| | - Monika Sharma
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, New Delhi, 110007, India
| | - Stanzin Choksket
- CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Shekhar Nagar
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, New Delhi, 110007, India.,Deshbandhu College, University of Delhi, Delhi, 110019, India
| | - Sheetal Yadav
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, New Delhi, 110007, India
| | - Sonakshi Modeel
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, New Delhi, 110007, India
| | - Suresh Korpole
- CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, New Delhi, 110007, India.
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Zeng Y, Chen Z, Lyu Q, Cheng Y, Huan C, Jiang X, Yan Z, Tan Z. Microbiologically induced calcite precipitation for in situ stabilization of heavy metals contributes to land application of sewage sludge. J Hazard Mater 2023; 441:129866. [PMID: 36063711 DOI: 10.1016/j.jhazmat.2022.129866] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Microbiologically induced calcite precipitation (MICP) has shed new light on solving the problem of in situ stabilization of heavy metals (HMs) in sewage sludge before land disposal. In this study, we examined whether MICP treatment can be integrated into a sewage sludge anaerobic digestion-land application process. Our results showed that MICP treatment not only prevented the transfer of ionic-state Cd from the sludge to the supernatant (98.46 % immobilization efficiency) but also reduced the soluble exchangeable Pb and Cd fractions by up to 100 % and 48.54 % and increased the residual fractions by 22.54 % and 81.77 %, respectively. In addition, the analysis of the stability of HMs in MICP-treated sludge revealed maximum reductions of 100 % and 89.56 % for TCLP-extractable Pb and Cd, respectively. Three-dimensional fluorescence, scanning electron microscopy-energy-dispersive X-ray spectroscopy, X-ray diffraction, and Fourier-transform infrared spectroscopy analyses confirmed the excellent performance of the ureolytic bacteria Sporosarcina ureilytica ML-2 in the sludge system. High-throughput sequencing showed that the relative abundance of Sporosarcina sp. reached 53.18 % in MICP-treated sludge, and the urease metabolism functional genes unit increased by a maximum of 239.3 %. The MICP technology may be a feasible method for permanently stabilizing HMs in sewage sludge before land disposal.
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Affiliation(s)
- Yong Zeng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China.
| | - Zezhi Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China.
| | - Qingyang Lyu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Yapeng Cheng
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Chenchen Huan
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Xinru Jiang
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Zhiying Yan
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China.
| | - Zhouliang Tan
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
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Voulgari-Kokota A, Steffan-Dewenter I, Keller A. Susceptibility of Red Mason Bee Larvae to Bacterial Threats Due to Microbiome Exchange with Imported Pollen Provisions. Insects 2020; 11:E373. [PMID: 32549328 PMCID: PMC7348846 DOI: 10.3390/insects11060373] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/12/2020] [Accepted: 06/13/2020] [Indexed: 12/22/2022]
Abstract
Solitary bees are subject to a variety of pressures that cause severe population declines. Currently, habitat loss, temperature shifts, agrochemical exposure, and new parasites are identified as major threats. However, knowledge about detrimental bacteria is scarce, although they may disturb natural microbiomes, disturb nest environments, or harm the larvae directly. To address this gap, we investigated 12 Osmia bicornis nests with deceased larvae and 31 nests with healthy larvae from the same localities in a 16S ribosomal RNA (rRNA) gene metabarcoding study. We sampled larvae, pollen provisions, and nest material and then contrasted bacterial community composition and diversity in healthy and deceased nests. Microbiomes of pollen provisions and larvae showed similarities for healthy larvae, whilst this was not the case for deceased individuals. We identified three bacterial taxa assigned to Paenibacillus sp. (closely related to P. pabuli/amylolyticus/xylanexedens), Sporosarcina sp., and Bacillus sp. as indicative for bacterial communities of deceased larvae, as well as Lactobacillus for corresponding pollen provisions. Furthermore, we performed a provisioning experiment, where we fed larvae with untreated and sterilized pollens, as well as sterilized pollens inoculated with a Bacillus sp. isolate from a deceased larva. Untreated larval microbiomes were consistent with that of the pollen provided. Sterilized pollen alone did not lead to acute mortality, while no microbiome was recoverable from the larvae. In the inoculation treatment, we observed that larval microbiomes were dominated by the seeded bacterium, which resulted in enhanced mortality. These results support that larval microbiomes are strongly determined by the pollen provisions. Further, they underline the need for further investigation of the impact of detrimental bacterial acquired via pollens and potential buffering by a diverse pollen provision microbiome in solitary bees.
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Affiliation(s)
- Anna Voulgari-Kokota
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany;
- Center for Computational and Theoretical Biology, Biocenter, University of Würzburg, Hubland Nord, 97074 Würzburg, Germany
- Current Address: Faculty of Science and Engineering, Groningen Institute for Evolutionary Life Sciences, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Ingolf Steffan-Dewenter
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany;
| | - Alexander Keller
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany;
- Center for Computational and Theoretical Biology, Biocenter, University of Würzburg, Hubland Nord, 97074 Würzburg, Germany
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Oliver A, Kay M, Cooper KK. Comparative genomics of cocci-shaped Sporosarcina strains with diverse spatial isolation. BMC Genomics 2018; 19:310. [PMID: 29716534 PMCID: PMC5930826 DOI: 10.1186/s12864-018-4635-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 03/28/2018] [Indexed: 12/31/2022] Open
Abstract
Background Cocci-shaped Sporosarcina strains are currently one of the few known cocci-shaped spore-forming bacteria, yet we know very little about the genomics. The goal of this study is to utilize comparative genomics to investigate the diversity of cocci-shaped Sporosarcina strains that differ in their geographical isolation and show different nutritional requirements. Results For this study, we sequenced 28 genomes of cocci-shaped Sporosarcina strains isolated from 13 different locations around the world. We generated the first six complete genomes and methylomes utilizing PacBio sequencing, and an additional 22 draft genomes using Illumina sequencing. Genomic analysis revealed that cocci-shaped Sporosarcina strains contained an average genome of 3.3 Mb comprised of 3222 CDS, 54 tRNAs and 6 rRNAs, while only two strains contained plasmids. The cocci-shaped Sporosarcina genome on average contained 2.3 prophages and 15.6 IS elements, while methylome analysis supported the diversity of these strains as only one of 31 methylation motifs were shared under identical growth conditions. Analysis with a 90% identity cut-off revealed 221 core genes or ~ 7% of the genome, while a 30% identity cut-off generated a pan-genome of 8610 genes. The phylogenetic relationship of the cocci-shaped Sporosarcina strains based on either core genes, accessory genes or spore-related genes consistently resulted in the 29 strains being divided into eight clades. Conclusions This study begins to unravel the phylogenetic relationship of cocci-shaped Sporosarcina strains, and the comparative genomics of these strains supports identification of several new species. Electronic supplementary material The online version of this article (10.1186/s12864-018-4635-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew Oliver
- Department of Biology, California State University Northridge, Northridge, CA, USA.,Present Address: Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Matthew Kay
- Department of Biology, California State University Northridge, Northridge, CA, USA
| | - Kerry K Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA.
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Kim HJ, Eom HJ, Park C, Jung J, Shin B, Kim W, Chung N, Choi IG, Park W. Calcium Carbonate Precipitation by Bacillus and Sporosarcina Strains Isolated from Concrete and Analysis of the Bacterial Community of Concrete. J Microbiol Biotechnol 2016; 26:540-8. [PMID: 26699752 DOI: 10.4014/jmb.1511.11008] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Microbially induced calcium carbonate precipitation (CCP) is a long-standing but re-emerging environmental engineering process for production of self-healing concrete, bioremediation, and long-term storage of CO2. CCP-capable bacteria, two Bacillus strains (JH3 and JH7) and one Sporosarcina strain (HYO08), were isolated from two samples of concrete and characterized phylogenetically. Calcium carbonate crystals precipitated by the three strains were morphologically distinct according to field emission scanning electron microscopy. Energy dispersive X-ray spectrometry mapping confirmed biomineralization via extracellular calcium carbonate production. The three strains differed in their physiological characteristics: growth at alkali pH and high NaCl concentrations, and urease activity. Sporosarcina sp. HYO08 and Bacillus sp. JH7 were more alkali- and halotolerant, respectively. Analysis of the community from the same concrete samples using barcoded pyrosequencing revealed that the relative abundance of Bacillus and Sporosarcina species was low, which indicated low culturability of other dominant bacteria. This study suggests that calcium carbonate crystals with different properties can be produced by various CCP-capable strains, and other novel isolates await discovery.
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Affiliation(s)
- Hyun Jung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Hyo Jung Eom
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Chulwoo Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Jaejoon Jung
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Bora Shin
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Wook Kim
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Namhyun Chung
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - In-Geol Choi
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
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Tsuda K, Nagano H, Ando A, Shima J, Ogawa J. Isolation and characterization of psychrotolerant endospore-forming Sporosarcina species associated with minced fish meat (surimi). Int J Food Microbiol 2015; 199:15-22. [PMID: 25621716 DOI: 10.1016/j.ijfoodmicro.2014.12.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 12/25/2014] [Accepted: 12/29/2014] [Indexed: 10/24/2022]
Abstract
We studied the changes of resident microbiota in surimi-minced fish meat-during heat-treatment and subsequent cold-storage via the sequencing of partial 16S rRNA gene. Raw surimi made from Alaska pollock, pike conger, and white croaker was contaminated with 10(4) to 10(6)CFU/g of various non-endospore-forming bacteria. Immediately after heat-treatment, the bacterial counts were significantly reduced to less than 1CFU/g, and only endospore-forming bacteria, identified as Bacillus species were retrieved. Subsequently, the bacterial counts increased up to 10 to 10(5)CFU/g in the heated surimi after refrigerated storage at 5 °C for 2 weeks or at 10 °C for 1 week. Most of the isolates from the refrigerated surimi were identified as Sporosarcina species. The Sporosarcina isolates have an increased ability to grow at 10 °C than the isolates related to the other endospore-forming bacteria, such as Bacillus, Lysinibacillus, and Paenibacillus species. Endospores of the Sporosarcina isolates were able to germinate and proliferate in a fish-paste product model system stored at 10 °C within 8 days. In order to study the cold-adaptation mechanism of Sporosarcina species, the fatty acid composition of the isolates was analyzed. At the growth temperature of 10 °C, the proportions of unsaturated to saturated fatty acids and anteiso to iso fatty acids were higher than those at 28 °C. The alteration of the fatty acid composition suggests that Sporosarcina species adapt to cold by maintaining the fluidity of the cell membrane because unsaturated and anteiso fatty acids have lower melting points than saturated and iso fatty acids, respectively. We concluded that the endospores of Sporosarcina species are widely distributed in surimi, and that they can survive heat-treatment and proliferate during cold-storage in fish-paste products. Controlling Sporosarcina species would contribute to improving the quality of surimi product.
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Affiliation(s)
- Kentaro Tsuda
- Food Development Laboratories, Nippon Shinyaku Co., Ltd., 14 Nishinosho-monguchicho, Kisshoin, Minami-ku, Kyoto 601-8550, Japan; Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Hideaki Nagano
- Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Akinori Ando
- Research Unit for Physiological Chemistry, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Jun Shima
- Research Division of Microbial Sciences, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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