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Miyamoto H, Kikuchi J. An evaluation of homeostatic plasticity for ecosystems using an analytical data science approach. Comput Struct Biotechnol J 2023; 21:869-878. [PMID: 36698969 PMCID: PMC9860287 DOI: 10.1016/j.csbj.2023.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/05/2023] Open
Abstract
The natural world is constantly changing, and planetary boundaries are issuing severe warnings about biodiversity and cycles of carbon, nitrogen, and phosphorus. In other views, social problems such as global warming and food shortages are spreading to various fields. These seemingly unrelated issues are closely related, but it can be said that understanding them in an integrated manner is still a step away. However, progress in analytical technologies has been recognized in various fields and, from a microscopic perspective, with the development of instruments including next-generation sequencers (NGS), nuclear magnetic resonance (NMR), gas chromatography-mass spectrometry (GC/MS), and liquid chromatography-mass spectrometry (LC/MS), various forms of molecular information such as genome data, microflora structure, metabolome, proteome, and lipidome can be obtained. The development of new technology has made it possible to obtain molecular information in a variety of forms. From a macroscopic perspective, the development of environmental analytical instruments and environmental measurement facilities such as satellites, drones, observation ships, and semiconductor censors has increased the data availability for various environmental factors. Based on these background, the role of computational science is to provide a mechanism for integrating and understanding these seemingly disparate data sets. This review describes machine learning and the need for structural equations and statistical causal inference of these data to solve these problems. In addition to introducing actual examples of how these technologies can be utilized, we will discuss how to use these technologies to implement environmentally friendly technologies in society.
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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
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Jun Kikuchi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
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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] [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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Preferential isolation of Megasphaera elsdenii from pig feces. Anaerobe 2017; 48:160-164. [PMID: 28842275 DOI: 10.1016/j.anaerobe.2017.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [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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Tanaka R, Miyamoto H, Inoue SI, Shigeta K, Kondo M, Ito T, Kodama H, Miyamoto H, Matsushita T. Thermophile-fermented compost as a fish feed additive modulates lipid peroxidation and free amino acid contents in the muscle of the carp, Cyprinus carpio. J Biosci Bioeng 2016; 121:530-5. [DOI: 10.1016/j.jbiosc.2015.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/08/2015] [Accepted: 10/06/2015] [Indexed: 10/22/2022]
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Miyamoto H, Seta M, Horiuchi S, Iwasawa Y, Naito T, Nishida A, Miyamoto H, Matsushita T, Itoh K, Kodama H. Potential probiotic thermophiles isolated from mice after compost ingestion. J Appl Microbiol 2013; 114:1147-57. [DOI: 10.1111/jam.12131] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 12/11/2012] [Accepted: 12/13/2012] [Indexed: 12/20/2022]
Affiliation(s)
- H. Miyamoto
- Japan Eco-science (Nikkan Kagaku) Co. Ltd; Chuuou-ku Chiba Japan
- Faculty of Horticulture; Chiba University; Matsudo, Chiba Japan
- Department of Biochemistry and Integrative Medical Biology; Keio School of Medicine; Shinjuku-ku Tokyo Japan
- Miroku Co. Ltd; Kitsuki Oita Japan
| | - M. Seta
- Faculty of Horticulture; Chiba University; Matsudo, Chiba Japan
| | - S. Horiuchi
- Department of Molecular Virology; Tokyo Medical and Dental University; Bunkyo-ku Tokyo Japan
| | - Y. Iwasawa
- Faculty of Horticulture; Chiba University; Matsudo, Chiba Japan
| | - T. Naito
- Department of Biochemistry and Integrative Medical Biology; Keio School of Medicine; Shinjuku-ku Tokyo Japan
| | - A. Nishida
- Graduate School of Advanced Integration Science; Chiba University; Chiba Japan
| | | | - T. Matsushita
- Department of Food Science and Technology; National Fisheries University; Shimonoseki Yamaguchi Japan
| | - K. Itoh
- Veterinary Public Health; Graduate School of Agricultural and Life Sciences; The University of Tokyo; Bunkyo-ku Tokyo Japan
| | - H. Kodama
- Graduate School of Advanced Integration Science; Chiba University; Chiba Japan
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