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Jin YH, Mah JH. Culture-dependent and -independent analyses of bacterial compositions and its contributions to formation of γ-aminobutyric acid and poly-γ-glutamic acid in Cheonggukjang. Food Res Int 2024; 179:114026. [PMID: 38342543 DOI: 10.1016/j.foodres.2024.114026] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 02/13/2024]
Abstract
This study was performed to unveil bacterial compositions and their contributions to the formation of γ-aminobutyric acid (GABA) and poly-γ-glutamic acid (γ-PGA) in Cheonggukjang. To predict possible key factors contributing to the content of the bioactive compounds in Cheonggukjang, commercial products were analyzed for various parameters. The content of GABA and γ-PGA showed a negative (R2 = 0.61 - 0.73) and positive correlation (R2 = 0.53 - 0.96) with antioxidative activity. Consistently, GABA content showed a moderate negative correlation with γ-PGA content (R2 = 0.58). Among the physicochemical and microbial parameters, only salinity showed a moderate negative correlation with γ-PGA content (R2 = 0.75), which might be due to the inhibition of bacterial growth. It was also suggested that multiple factors (including bacterial species) were involved in the formation of GABA and γ-PGA in Cheonggukjang. To reveal dominant bacterial species and further presume their contributions to the bioactive compound formation in Cheonggukjang, both culture-independent (metagenomic) and -dependent (culturomic) methods were used. Culture-independent method showed that Bacillus piscis was dominant (23.37 - 94.89 %), followed by B. hisashii (0.00 - 62.45 %) and B. coagulans (0.00 - 13.82 %). Considering the quantitative speciation data on the bioactive compound content in Cheonggukjang (and bacterial production capability) together, it was further elucidated that B. piscis contributed primarily to the bioactive compound formation. Unlike this, culture-dependent analysis revealed that B. licheniformis and B. subtilis were dominant (30.0 - 47.6 and 17.5 - 39.5 %, respectively). Based on the quantitative speciation data on the bacterial production capability of GABA and γ-PGA, B. subtilis was the primarily contributing bacterial species to the bioactive compound formation. Consequently, it was observed that the bacterial compositions and their contributions to the bioactive compound formation determined by the two methods differed considerably, i.e., B. piscis and B. subtilis were identified to be prominent bacterial contributors, respectively, depending on the method used.
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Affiliation(s)
- Young Hun Jin
- Department of Food and Biotechnology, Korea University, Sejong 30019, Republic of Korea
| | - Jae-Hyung Mah
- Department of Food and Biotechnology, Korea University, Sejong 30019, Republic of Korea.
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2
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Miyamoto H, Shigeta K, Suda W, Ichihashi Y, Nihei N, Matsuura M, Tsuboi A, Tominaga N, Aono M, Sato M, Taguchi S, Nakaguma T, Tsuji N, Ishii C, Matsushita T, Shindo C, Ito T, Kato T, Kurotani A, Shima H, Moriya S, Wada S, Horiuchi S, Satoh T, Mori K, Nishiuchi T, Miyamoto H, Kodama H, Hattori M, Ohno H, Kikuchi J, Hirai MY. An agroecological structure model of compost-soil-plant interactions for sustainable organic farming. ISME Commun 2023; 3:28. [PMID: 37002405 PMCID: PMC10066230 DOI: 10.1038/s43705-023-00233-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023]
Abstract
Compost is used worldwide as a soil conditioner for crops, but its functions have still been explored. Here, the omics profiles of carrots were investigated, as a root vegetable plant model, in a field amended with compost fermented with thermophilic Bacillaceae for growth and quality indices. Exposure to compost significantly increased the productivity, antioxidant activity, color, and taste of the carrot root and altered the soil bacterial composition with the levels of characteristic metabolites of the leaf, root, and soil. Based on the data, structural equation modeling (SEM) estimated that amino acids, antioxidant activity, flavonoids and/or carotenoids in plants were optimally linked by exposure to compost. The SEM of the soil estimated that the genus Paenibacillus and nitrogen compounds were optimally involved during exposure. These estimates did not show a contradiction between the whole genomic analysis of compost-derived Paenibacillus isolates and the bioactivity data, inferring the presence of a complex cascade of plant growth-promoting effects and modulation of the nitrogen cycle by the compost itself. These observations have provided information on the qualitative indicators of compost in complex soil-plant interactions and offer a new perspective for chemically independent sustainable agriculture through the efficient use of natural nitrogen.
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Affiliation(s)
- Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan.
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan.
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan.
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan.
| | | | - Wataru Suda
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | | | - Naoto Nihei
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, Fukushima, 960-1296, Japan
| | - Makiko Matsuura
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Arisa Tsuboi
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | | | | | - Muneo Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Shunya Taguchi
- Center for Frontier Medical Engineering, Chiba University, Chiba, Chiba, 263-8522, Japan
| | - Teruno Nakaguma
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | - Naoko Tsuji
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Chitose Ishii
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Teruo Matsushita
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | - Chie Shindo
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Toshiaki Ito
- Keiyo Gas Energy Solution Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
| | - Tamotsu Kato
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Atsushi Kurotani
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-0856, Japan
| | - Hideaki Shima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Shigeharu Moriya
- RIKEN, Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Satoshi Wada
- RIKEN, Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Sankichi Horiuchi
- Division of Gastroenterology and Hepatology, The Jikei University School of Medicine, Kashiwa Hospital, Kashiwa, Chiba, 277-8567, Japan
| | - Takashi Satoh
- Division of Hematology, Kitasato University School of Allied Health Sciences, Sagamihara, Kanagawa, 252-0373, Japan
| | - Kenichi Mori
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba, 260-0034, Japan
| | - Takumi Nishiuchi
- Division of Integrated Omics research, Bioscience Core Facility, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan
| | - Hisashi Miyamoto
- Sermas Co., Ltd., Ichikawa, Chiba, 272-0033, Japan
- Miroku Co., Ltd., Kitsuki, Oita, 873-0021, Japan
| | - Hiroaki Kodama
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
| | - Masahira Hattori
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
- School of Advanced Science and Engineering, Waseda University, Tokyo, 169-8555, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
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Munson E, Lawhon SD, Burbick CR, Zapp A, Villaflor M, Thelen E. An Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Domestic Animals Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0028122. [PMID: 36533907 DOI: 10.1128/jcm.00281-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Novel bacterial taxonomy and nomenclature revisions can have significant impacts on clinical practice, disease epidemiology, and veterinary microbiology laboratory operations. Expansion of research on the microbiota of humans, animals, and insects has significant potential impacts on the taxonomy of organisms of clinical interest. Implications of taxonomic changes may be especially important when considering zoonotic diseases. Here, we address novel taxonomy and nomenclature revisions of veterinary significance. Noteworthy discussion centers around descriptions of novel mastitis pathogens in Streptococcaceae, Staphylococcaceae, and Actinomycetaceae; bovine reproductive tract pathogens in Corynebacteriaceae; novel members of Mannheimia spp., Leptospira spp., and Mycobacterium spp.; the transfer of Ochrobactrum spp. to Brucella spp.; and revisions to the genus Mycoplasma.
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Miyamoto H, Kawachi N, Kurotani A, Moriya S, Suda W, Suzuki K, Matsuura M, Tsuji N, Nakaguma T, Ishii C, Tsuboi A, Shindo C, Kato T, Udagawa M, Satoh T, Wada S, Masuya H, Miyamoto H, Ohno H, Kikuchi J. Computational estimation of sediment symbiotic bacterial structures of seagrasses overgrowing downstream of onshore aquaculture. Environ Res 2023; 219:115130. [PMID: 36563976 DOI: 10.1016/j.envres.2022.115130] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 10/29/2022] [Revised: 12/14/2022] [Accepted: 12/18/2022] [Indexed: 05/02/2023]
Abstract
Coastal seagrass meadows are essential in blue carbon and aquatic ecosystem services. However, this ecosystem has suffered severe eutrophication and destruction due to the expansion of aquaculture. Therefore, methods for the flourishing of seagrass are still being explored. Here, data from 49 public coastal surveys on the distribution of seagrass and seaweed around the onshore aquaculture facilities are revalidated, and an exceptional area where the seagrass Zostera marina thrives was found near the shore downstream of the onshore aquaculture facility. To evaluate the characteristics of the sediment for growing seagrass, physicochemical properties and bacterial ecological evaluations of the sediment were conducted. Evaluation of chemical properties in seagrass sediments confirmed a significant increase in total carbon and a decrease in zinc content. Association analysis and linear discriminant analysis refined bacterial candidates specified in seagrass overgrown- and nonovergrown-sediment. Energy landscape analysis indicated that the symbiotic bacterial groups of seagrass sediment were strongly affected by the distance close to the seagrass-growing aquaculture facility despite their bacterial population appearing to fluctuate seasonally. The bacterial population there showed an apparent decrease in the pathogen candidates belonging to the order Flavobacteriales. Moreover, structure equation modeling and a linear non-Gaussian acyclic model based on the machine learning data estimated an optimal sediment symbiotic bacterial group candidate for seagrass growth as follows: the Lachnospiraceae and Ruminococcaceae families as gut-inhabitant bacteria, Rhodobacteraceae as photosynthetic bacteria, and Desulfobulbaceae as cable bacteria modulating oxygen or nitrate reduction and oxidation of sulfide. These observations confer a novel perspective on the sediment symbiotic bacterial structures critical for blue carbon and low-pathogenic marine ecosystems in aquaculture.
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Affiliation(s)
- Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University: Matsudo, Chiba, 271-8501, Japan; RIKEN Center for Integrated Medical Science, Yokohama, Kanagawa, 230-0045, Japan; Japan Eco-science (Nikkan Kagaku) Co. Ltd.: Chiba, Chiba, 263-8522, Japan; Sermas Co., Ltd.: Ichikawa, Chiba, 272-0033, Japan.
| | | | - Atsushi Kurotani
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-0856, Japan
| | - Shigeharu Moriya
- RIKEN, Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Wataru Suda
- RIKEN Center for Integrated Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Kenta Suzuki
- RIKEN, BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Makiko Matsuura
- Graduate School of Horticulture, Chiba University: Matsudo, Chiba, 271-8501, Japan; Sermas Co., Ltd.: Ichikawa, Chiba, 272-0033, Japan
| | - Naoko Tsuji
- Sermas Co., Ltd.: Ichikawa, Chiba, 272-0033, Japan
| | - Teruno Nakaguma
- Graduate School of Horticulture, Chiba University: Matsudo, Chiba, 271-8501, Japan; Japan Eco-science (Nikkan Kagaku) Co. Ltd.: Chiba, Chiba, 263-8522, Japan; Sermas Co., Ltd.: Ichikawa, Chiba, 272-0033, Japan
| | - Chitose Ishii
- RIKEN Center for Integrated Medical Science, Yokohama, Kanagawa, 230-0045, Japan; Sermas Co., Ltd.: Ichikawa, Chiba, 272-0033, Japan
| | - Arisa Tsuboi
- Japan Eco-science (Nikkan Kagaku) Co. Ltd.: Chiba, Chiba, 263-8522, Japan
| | - Chie Shindo
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-0856, Japan
| | - Tamotsu Kato
- RIKEN Center for Integrated Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Motoaki Udagawa
- Keiyo Gas Energy Solution Co. Ltd.: Ichikawa, Chiba, 272-0033, Japan
| | - Takashi Satoh
- Division of Hematology, Kitasato University School of Allied Health Sciences, Sagamihara, Kanagawa, 252-0329, Japan
| | - Satoshi Wada
- RIKEN, Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Hiroshi Masuya
- RIKEN, BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Hisashi Miyamoto
- Sermas Co., Ltd.: Ichikawa, Chiba, 272-0033, Japan; Miroku Co.Ltd.: Kitsuki, Oita, 873-0021, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrated Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
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Yang SH, Park MJ, Oh HM, Kwon KK. Description of Fervidibacillus gen. nov. with Two Species, Fervidibacillus albus sp. nov., and Fervidibacillus halotolerans sp. nov., Isolated from Tidal Flat Sediments and Emendation of Misclassificed Taxa in the Genus Caldibacillus. J Microbiol 2023; 61:175-87. [PMID: 36800167 DOI: 10.1007/s12275-023-00022-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 02/18/2023]
Abstract
Two Gram-stain-positive, motile, endospore-forming, facultatively anaerobic strains, designated MEBiC13591T and MEBiC13594T, were isolated from tidal flat sediment of the Incheon City on the west coast of Korea. Growth of both novel strains was observed at pH 5-9 (optimum, pH 7-7.5), and in 0-8% NaCl (optimum, 2% for MEBiC13591T and 3% for MEBiC13594T). Strains MEBiC13591T and MEBiC13594T grew optimally at 50 °C, (37.5-56.1 °C) and 44 °C (20.7-50.7 °C), respectively. The main cellular fatty acids of strain MEBiC13591T were iso-C15: 0, anteiso-C15: 0, iso-C16: 0, iso-C17: 0 and anteiso-C17: 0, while those for strain MEBiC13594T were C14: 0, iso-C14: 0, iso-C15: 0, anteiso-C15: 0 and C16: 0. In both taxa, the major isoprenoid was MK-7. The genomic DNA G + C contents were 34.1 and 37.0 mol% for MEBiC13591T and MEBiC13594T, respectively. A 16S rRNA gene sequence analysis revealed that the novel strains showed high similarity with members of the genera Aeribacillus (95.0%) and Caldibacillus (93.5-94.5%); however, showed lower than 90% with Caldibacillus debilis TfT. Phylogenetic and Phylogenomic analysis revealed that two novel strains comprised distinct phyletic line with members formerly assigned to Caldibacillus. Based on genomic indices, such as AAI and ANI, members formerly affiliated with Caldibacillus and Bacillus as well as the novel strains should be classified into five independent genera. Based on the phenotypic, genomic and biochemical data, strains MEBiC13591T and MEBiC13594T represent two novel species in the novel genus, for which the names Fervidibacillus albus gen. nov., sp. nov. (MEBiC13591T [= KCCM 43317T = KCTC 43181T = JCM 33662T = MCCC 1K04565T]), and Fervidibacillus halotolerans sp. nov. (MEBiC13594T [= KCTC 43182T = JCM 34001T]) are proposed. Three additional genera Caldifermentibacillus, Palidibacillus, and Perspicuibacillus are also proposed by reclassification of the several species with valid names that formerly affiliated with the genera Caldibacillus.
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Inabu Y, Taguchi Y, Miyamoto H, Etoh T, Shiotsuka Y, Fujino R, Okada T, Udagawa M, Tsuji N, Matsuura M, Tsuboi A, Kato T, Kodama H, Ohno H, Takahashi H. Development of a novel feeding method for Japanese black calves with thermophile probiotics at postweaning. J Appl Microbiol 2022; 132:3870-3882. [PMID: 35261112 DOI: 10.1111/jam.15519] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 10/24/2021] [Revised: 02/23/2022] [Accepted: 03/03/2022] [Indexed: 11/29/2022]
Abstract
AIMS Probiotic effects of compost containing thermophiles on productivity have been reported in domestic animals, although not cattle. We evaluated the effects of administering Caldibacillus hisashii, a thermophile contained in compost, on growth, blood components, faecal organic acid concentrations and microbiota population in Japanese black calves. METHODS AND RESULTS Calves were administered C. hisashii from 3 to 5 mo of age. Administering C. hisashii decreased feed intake without affecting body weight, indicating that feed efficiency is improved by administration. Administering C. hisashii decreased plasma insulin concentration without affecting glucose and nonesterified fatty acid concentrations. Chao1 was decreased by exposure at 5 mo of age. Similarly, weighted- and unweighted UniFrac distances were affected by treatment at 5 mo of age. Faecal abundance of the phylum Bacteroidetes tended to be increased by exposure. Faecal propionic acid concentration was correlated positively with faecal abundance of phylum Bacteroidetes but negatively with that of Firmicutes. Interestingly, the population of the genus Methanobrevibacter, representing the majority of methanogens, was lowered by exposure and was negatively correlated with faecal propionic acid concentration. CONCLUSION Administration of C. hisashii has the potential to improve growth performance of Japanese black calves and to contribute to reducing environmental load, which may be associated with altered endocrine kinetics and gut microbial populations. SIGNIFICANCE AND IMPACTS OF THE STUDY This study revealed that isolated thermophiles included in compost may exert probiotic effects on calves.
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Affiliation(s)
- Yudai Inabu
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, Japan
| | - Yutaka Taguchi
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, Japan
| | - Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University, Chiba, Japan.,RIKEN IMS, Yokohama, Kanagawa, Japan.,Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Japan.,Sermas, Co., Ltd., Chiba, Japan
| | - Tetsuji Etoh
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, Japan
| | - Yuji Shiotsuka
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, Japan
| | - Ryoichi Fujino
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, Japan
| | - Toru Okada
- Asuka Animal Health Co., Ltd., Tokyo, Japan
| | | | | | - Makiko Matsuura
- Graduate School of Horticulture, Chiba University, Chiba, Japan.,Sermas, Co., Ltd., Chiba, Japan
| | - Arisa Tsuboi
- Graduate School of Horticulture, Chiba University, Chiba, Japan.,Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Japan.,Sermas, Co., Ltd., Chiba, Japan.,RIKEN CSRS, Yokohama, Kanagawa, Japan
| | | | - Hiroaki Kodama
- Graduate School of Horticulture, Chiba University, Chiba, Japan
| | | | - Hideyuki Takahashi
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, Japan
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Yue S, Mizoguchi T, Kohara T, Zhang M, Watanabe K, Miyamoto H, Tashiro Y, Sakai K. Meta-fermentation system with a mixed culture for the production of optically pure l-lactic acid can be reconstructed using the minimum isolates with a simplified pH control strategy. Biotechnol J 2021; 16:e2100277. [PMID: 34472222 DOI: 10.1002/biot.202100277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/27/2021] [Revised: 08/24/2021] [Accepted: 08/30/2021] [Indexed: 11/06/2022]
Abstract
Meta-l-lactic acid fermentation from non-treated kitchen refuse was reconstructed using a combination of isolated bacterial strains under several pH control strategies. The meta-fermentation system was successfully reconstructed using a combination of Weizmannia coagulans MN-07, Caldibacillus thermoamylovorans OM55-6, and Caldibacillus hisashii N-11 strains. Additionally, a simplified constant pH control strategy was employed, which decreased fermentation time and increased production. The optimum pH (6.5) for the reconstructed meta-fermentation was favorable for the respective pure cultures of the three selected strains. The l-lactic acid production performance of the reconstructed meta-fermentation system was as follows: concentration, 24.5 g L-1 ; optical purity, 100%; productivity, 0.341 g L-1 h-1 ; yield, 1.06 g g-1 . These results indicated that constant pH control was effective in the reconstructed meta-fermentation with the best performance of l-lactic acid production at pH optimal for the selected bacterial growth, while the switching from swing pH control would suppress the activities of unfavorable bacterial species in un-isolated meta-fermentation.
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Affiliation(s)
- Siyuan Yue
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Takaharu Mizoguchi
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Toshiya Kohara
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Min Zhang
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Kota Watanabe
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan.,Sermas Co., Ltd., Ichikawa, Chiba, Japan.,Japan Eco-science (Nikkan Kagaku) Co. Ltd., Chiba, Chiba, Japan.,RIKEN IMS, Yokohama, Kanagawa, Japan
| | - Yukihiro Tashiro
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan.,Laboratory of Microbial Environmental Protection, Tropical Microbiology Unit, Center for International Education and Research of Agriculture, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Kenji Sakai
- Laboratory of Soil and Environmental Microbiology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Bioresources and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan.,Laboratory of Microbial Environmental Protection, Tropical Microbiology Unit, Center for International Education and Research of Agriculture, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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8
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Hasanah U, Miki K, Nitoda T, Kanzaki H. Aerobic bioconversion of C-glycoside mangiferin into its aglycone norathyriol by an isolated mouse intestinal bacterium. Biosci Biotechnol Biochem 2021; 85:989-997. [PMID: 33710320 DOI: 10.1093/bbb/zbaa121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 10/23/2020] [Accepted: 12/22/2020] [Indexed: 12/23/2022]
Abstract
Norathyriol is an aglycone of a xanthonoid C-glycoside mangiferin that possesses different bioactive properties useful for humans compared to mangiferin. Mangiferin is more readily available in nature than norathyriol; thus, efficient mangiferin conversion into norathyriol is desirable. There are a few reports regarding mangiferin C-deglycosylation because of the C-C bond resistance toward acid, alkaline, and enzyme hydrolysis. In this study, we isolated a mangiferin-deglycosylating bacterium strain KM7-1 from the mouse intestine. 16S rDNA sequencing indicated that KM7-1 belongs to the Bacillus genus. Compared to the taxonomically similar bacteria, the growth characteristic of facultative anaerobic and thermophilic resembled, yet only Bacillus sp. KM7-1 was able to convert mangiferin into norathyriol. Resting cells of Bacillus sp. KM7-1 obtained from aerobic cultivation at 50 °C showed high norathyriol formation from 1 m m of mangiferin. Norathyriol formation can be conducted either under aerobic or anaerobic conditions, and the reaction depended on time and bacterial amount.
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Affiliation(s)
- Uswatun Hasanah
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Kasumi Miki
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Teruhiko Nitoda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Hiroshi Kanzaki
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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Gupta RS, Patel S, Saini N, Chen S. Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species. Int J Syst Evol Microbiol 2020; 70:5753-5798. [PMID: 33112222 DOI: 10.1099/ijsem.0.004475] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [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: 11/18/2022] Open
Abstract
To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium. The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer 'Bacillus kyonggiensis' to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis) or the Cereus clade (containing B. anthracis and B. cereus). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.
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Key Words
- classification of Bacillus species
- conserved signature indels
- emendation of genus Bacillus
- genus Bacillus and the family Bacillaceae
- novel Bacillaceae genera Alteribacter, Ectobacillus, Evansella, Ferdinandcohnia, Gottfriedia, Heyndrickxia, Lederbergia, Litchfieldia, Margalitia, Niallia, Priestia, Robertmurraya, Rossellomorea, Schinkia, Siminovitchia, Sutcliffiella and Weizmannia
- phylogenomic and comparative genomic analyses
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Sudip Patel
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Navneet Saini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Shu Chen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
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Rekadwad B, Gonzalez JM. Multidisciplinary involvement and potential of thermophiles. Folia Microbiol (Praha) 2019; 64:389-406. [PMID: 30386965 DOI: 10.1007/s12223-018-0662-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/25/2018] [Indexed: 12/15/2022]
Abstract
The full biotechnological exploitation of thermostable enzymes in industrial processes is necessary for their commercial interest and industrious value. The heat-tolerant and heat-resistant enzymes are a key for efficient and cost-effective translation of substrates into useful products for commercial applications. The thermophilic, hyperthermophilic, and microorganisms adapted to extreme temperatures (i.e., low-temperature lovers or psychrophiles) are a rich source of thermostable enzymes with broad-ranging thermal properties, which have structural and functional stability to underpin a variety of technologies. These enzymes are under scrutiny for their great biotechnological potential. Temperature is one of the most critical parameters that shape microorganisms and their biomolecules for stability under harsh environmental conditions. This review describes in detail the sources of thermophiles and thermostable enzymes from prokaryotes and eukaryotes (microbial cell factories). Furthermore, the review critically examines perspectives to improve modern biocatalysts, its production and performance aiming to increase their value for biotechnology through higher standards, specificity, resistance, lowing costs, etc. These thermostable and thermally adapted extremophilic enzymes have been used in a wide range of industries that span all six enzyme classes. Thus, in particular, target of this review paper is to show the possibility of both high-value-low-volume (e.g., fine-chemical synthesis) and low-value-high-volume by-products (e.g., fuels) by minimizing changes to current industrial processes.
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Sun QL, Yu C, Luan ZD, Lian C, Hu YH, Sun L. Description of Bacillus kexueae sp. nov. and Bacillus manusensis sp. nov., isolated from hydrothermal sediments. Int J Syst Evol Microbiol 2018; 68:829-834. [PMID: 29458542 DOI: 10.1099/ijsem.0.002594] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 11/18/2022] Open
Abstract
Two Gram-staining-positive, strictly aerobic bacilli, designated as strains Ma50-5T and Ma50-6T, were isolated from the hydrothermal sediments of Manus Basin in the western Pacific Ocean. Based on 16S rRNA gene sequence, strains Ma50-5T and Ma50-6T were most closely related to Bacillus alveayuensis (97.0 and 97.2 % identity, respectively). The 16S rRNA gene sequence identity between strains Ma50-5T and Ma50-6T was 97.4 %. The identities between strains Ma50-5T and Ma50-6T and other closely related organisms were below 97.0 %. The G+C contents of the genomic DNA of strains Ma50-5T and Ma50-6T were 43.4 and 47.6 mol%, respectively. The major fatty acids (>10 %) of both strains were iso-C15 : 0 and iso-C17 : 0. The predominant isoprenoid quinone detected in both strains was menaquinone-7. Phylogenetic, physiological, biochemical and morphological analyses suggested that strains Ma50-5T and Ma50-6T represent two novel species of the genus Bacillus, for which the names Bacillus kexueae sp. nov. (type strain Ma50-5T=KCTC 33881T=CCTCC AB 2017020T) and Bacillus manusensis sp. nov. (type strain Ma50-6T=KCTC 33882T=CCTCC AB 2017019T), respectively, are proposed.
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Affiliation(s)
- Qing-Lei Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Chao Yu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Zhen-Dong Luan
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China
| | - Chao Lian
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China
| | - Yong-Hua Hu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Li Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
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Kajihara Y, Yoshikawa S, Cho Y, Ito T, Miyamoto H, Kodama H. Preferential isolation of Megasphaera elsdenii from pig feces. Anaerobe 2017; 48:160-4. [PMID: 28842275 DOI: 10.1016/j.anaerobe.2017.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/20/2017] [Accepted: 08/21/2017] [Indexed: 01/19/2023]
Abstract
Lactic acid produced by intestinal bacteria is fermented by lactate-utilizing bacteria. In this study, we developed a selective culture medium (KMI medium) for Megasphaera elsdenii, a lactate-utilizing bacterium that is abundant in pig intestines. Supplementation of the medium with lactate and beef extract powder was necessary for the preferential growth of M. elsdenii. In addition, we designed a species-specific primer set to detect M. elsdenii. When pig fecal samples were plated on KMI agar medium, approximately 60-100% of the resulting colonies tested positive using the M. elsdenii-specific PCR primers. In fact, nearly all of the large, yellow-white colonies that grew on the KMI agar medium tested positive by PCR with this primer set. The 16S rRNA gene sequences of three representative PCR-positive strains showed strong similarities to that of M. elsdenii ATCC 25940T (98.9-99.2% identity). These three strains were approximately 1.5 μm sized cocci that were primarily arranged in pairs, as was observed for M. elsdenii JCM 1772T. The selective KMI medium and species-specific primer set developed in this study are useful for the isolation and detection of M. elsdenii and will be useful in research aimed at increasing our understanding of intestinal short-chain fatty acid metabolism in pigs.
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