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Kurotani A, Miyamoto H, Kikuchi J. Validation of causal inference data using DirectLiNGAM in an environmental small-scale model and calculation settings. MethodsX 2024; 12:102528. [PMID: 38274701 PMCID: PMC10809110 DOI: 10.1016/j.mex.2023.102528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
The development of data science has been needed in environmental fields such as marine, weather, and soil data. In general, the datasets are large in some cases, but they are often small because they contain observation data that the analyses themselves are limited. In such a case, the data are statistically evaluated by increasing or decreasing the levels of factors using differential analysis, resulting in the essential factors are estimated. However, there is no consistent approach to the means of assessing strong associations as a group between factors. Causal inference method has the possibility to output effective results for small data, and the results are expected to provide important information for understanding the potential highly association between factors, not necessarily the inference with big data. Here, we describe essential checkpoints and settings for the calculation by a direct method for learning a linear non-Gaussian structural equation model (DirectLiNGAM) and validation methods for the calculation results by using DirectLiNGAM with small-scale model data as an additional discussion of DirectLiNGAM portion of the related research article. Thus, this study provides the statistical validation methods for the association networks, treatments, and interventions for structural inference as a group of essential factors.•Causal inference with DirectLiNGAM•Validation of correlation coefficient and feature importance•Validation using causal effect object and propensity scores.
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Affiliation(s)
- Atsushi Kurotani
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-0856, Japan
- Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-0012, Japan
| | - Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University: Matsudo, Chiba 271-8501, Japan
- 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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Nakashima Y, Sonobe T, Hanada M, Kitano G, Sonoyama Y, Iwai K, Kimura T, Kusube M. Microbial Detoxification of Sediments Underpins Persistence of Zostera marina Meadows. Int J Mol Sci 2024; 25:5442. [PMID: 38791480 PMCID: PMC11122150 DOI: 10.3390/ijms25105442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Eelgrass meadows have attracted much attention not only for their ability to maintain marine ecosystems as feeding grounds for marine organisms but also for their potential to store atmospheric and dissolved CO2 as blue carbon. This study comprehensively evaluated the bacterial and chemical data obtained from eelgrass sediments of different scales along the Japanese coast to investigate the effect on the acclimatization of eelgrass. Regardless of the eelgrass habitat, approximately 1% Anaerolineales, Babeliales, Cytophagales, and Phycisphaerales was present in the bottom sediment. Sulfate-reducing bacteria (SRB) were present at 3.69% in eelgrass sediment compared to 1.70% in bare sediment. Sulfur-oxidizing bacteria (SOB) were present at 2.81% and 1.10% in the eelgrass and bare sediment, respectively. Bacterial composition analysis and linear discriminant analysis revealed that SOB detoxified H2S in the eelgrass meadows and that the larger-scale eelgrass meadows had a higher diversity of SOB. Our result indicated that there were regional differences in the system that detoxifies H2S in eelgrass meadows, either microbial oxidation mediated by SOB or O2 permeation via the physical diffusion of benthos. However, since bacterial flora and phylogenetic analyses cannot show bias and/or causality due to PCR, future kinetic studies on microbial metabolism are expected.
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Affiliation(s)
- Yuki Nakashima
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Osaka, Japan;
- Advanced Engineering Faculty, National Institute of Technology, Wakayama College, Gobo 644-0023, Wakayama, Japan
| | - Takumi Sonobe
- Advanced Engineering Faculty, National Institute of Technology, Wakayama College, Gobo 644-0023, Wakayama, Japan
| | - Masashi Hanada
- Promotion of Technical Support, National Institute of Technology, Wakayama College, Gobo 644-0023, Wakayama, Japan
| | - Goushi Kitano
- Agri-Light Lab. Inc., Minamata 867-0068, Kumamoto, Japan
| | | | - Katsumi Iwai
- Study Team for Creation of Waterfront, Yokohama 220-0023, Kanagawa, Japan
| | - Takashi Kimura
- Study Team for Creation of Waterfront, Yokohama 220-0023, Kanagawa, Japan
| | - Masataka Kusube
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College, Gobo 644-0023, Wakayama, Japan
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Tamura Y, Takai Y, Miyamoto H, SeokHyun L, Liu Y, Qiu X, Kang LJ, Simasaki Y, Shindo C, Suda W, Ohno H, Oshima Y. Alteration of shoaling behavior and dysbiosis in the gut of medaka (Oryzias latipes) exposed to 2-μm polystyrene microplastics. CHEMOSPHERE 2024; 353:141643. [PMID: 38447901 DOI: 10.1016/j.chemosphere.2024.141643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/27/2024] [Accepted: 03/02/2024] [Indexed: 03/08/2024]
Abstract
There is global concern that microplastics may harm aquatic life. Here, we examined the effects of fine polystyrene microplastics (PS-MPs, 2-μm diameter, 0.1 mg/L, 2.5 × 107 particles/L) on the behavior and the microbiome (linked to brain-gut interaction) of a fish model using medaka, Oryzias latipes. We found that shoaling behavior was reduced in PS-MP-exposed medaka compared with control fish during the exposure period, but it recovered during a depuration period. There was no difference in swimming speed between the PS-MP-exposed and control groups during the exposure period. Analysis of the dominant bacterial population (those comprising ≥1% of the total bacterial population) in the gut of fish showed that exposure to PS-MPs tended to increase the relative abundance of the phylum Fusobacteria and the genus Vibrio. Furthermore, structural-equation modeling of gut bacteria on the basis of machine-learning data estimated strong relationship involved in the reduction of the functional bacterial species of minority (<1% of the total bacterial population) such as the genera Muribaculum (an undefined role), Aquaspirillum (a candidate for nitrate metabolism and magnetotactics), and Clostridium and Phascolarctobacterium (potential producers of short-chain fatty acids, influencing behavior by affecting levels of neurotransmitters) as a group of gut bacteria in association with PS-MP exposure. Our results suggest that fish exposure to fine microplastics may cause dysbiosis and ultimately cause social behavior disorders linked to brain-gut interactions. This effect could be connected to reduction of fish fitness in the ecosystem and reduced fish survival.
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Affiliation(s)
- Yui Tamura
- Laboratory of Marine Environmental Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Yuki Takai
- Laboratory of Marine Environmental Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Hirokuni Miyamoto
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan; Graduate School of Horticulture, Chiba University, Matsudo, Chiba, 271-8501, Japan
| | - Lee SeokHyun
- Laboratory of Marine Environmental Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Yangqing Liu
- Laboratory of Marine Environmental Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Xuchun Qiu
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Lk Joon Kang
- School of Interdisciplinary Science and Innovation, Kyushu University, Fukuoka, 819-0395, Japan
| | - Yohei Simasaki
- Laboratory of Marine Environmental Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Chie Shindo
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Wataru Suda
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuji Oshima
- Laboratory of Marine Environmental Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan; Institute of Nature and Environmental Technology, Kanazawa University, Kanazawa, 920-1192, Japan.
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Okada S, Inabu Y, Miyamoto H, Suzuki K, Kato T, Kurotani A, Taguchi Y, Fujino R, Shiotsuka Y, Etoh T, Tsuji N, Matsuura M, Tsuboi A, Saito A, Masuya H, Kikuchi J, Nagasawa Y, Hirose A, Hayashi T, Ohno H, Takahashi H. Estimation of silent phenotypes of calf antibiotic dysbiosis. Sci Rep 2023; 13:6359. [PMID: 37076584 PMCID: PMC10115819 DOI: 10.1038/s41598-023-33444-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 04/12/2023] [Indexed: 04/21/2023] Open
Abstract
Reducing antibiotic usage among livestock animals to prevent antimicrobial resistance has become an urgent issue worldwide. This study evaluated the effects of administering chlortetracycline (CTC), a versatile antibacterial agent, on the performance, blood components, fecal microbiota, and organic acid concentrations of calves. Japanese Black calves were fed with milk replacers containing CTC at 10 g/kg (CON group) or 0 g/kg (EXP group). Growth performance was not affected by CTC administration. However, CTC administration altered the correlation between fecal organic acids and bacterial genera. Machine learning (ML) methods such as association analysis, linear discriminant analysis, and energy landscape analysis revealed that CTC administration affected populations of various types of fecal bacteria. Interestingly, the abundance of several methane-producing bacteria at 60 days of age was high in the CON group, and the abundance of Lachnospiraceae, a butyrate-producing bacterium, was high in the EXP group. Furthermore, statistical causal inference based on ML data estimated that CTC treatment affected the entire intestinal environment, potentially suppressing butyrate production, which may be attributed to methanogens in feces. Thus, these observations highlight the multiple harmful impacts of antibiotics on the intestinal health of calves and the potential production of greenhouse gases by calves.
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Affiliation(s)
- Shunnosuke Okada
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, 878-0201, Japan
| | - Yudai Inabu
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, 878-0201, Japan
| | - Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University, Matsudo, 271-8501, Japan.
- RIKEN Integrated Medical Science Center, Yokohama, Kanagawa, 230-0045, Japan.
- Japan Eco-Science (Nikkan Kagaku) Co., Ltd., Chiba, 260-0034, Japan.
- Sermas, Co., Ltd., Chiba, 271-8501, Japan.
| | - Kenta Suzuki
- RIKEN BioResource Research Center, Ibaraki, 305-0074, Tsukuba, Japan
| | - Tamotsu Kato
- RIKEN Integrated Medical Science Center, 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
| | - Yutaka Taguchi
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, 878-0201, Japan
| | - Ryoichi Fujino
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, 878-0201, Japan
| | - Yuji Shiotsuka
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, 878-0201, Japan
| | - Tetsuji Etoh
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, 878-0201, Japan
| | | | - Makiko Matsuura
- Graduate School of Horticulture, Chiba University, Matsudo, 271-8501, Japan
- Sermas, Co., Ltd., Chiba, 271-8501, Japan
| | - Arisa Tsuboi
- Japan Eco-Science (Nikkan Kagaku) Co., Ltd., Chiba, 260-0034, Japan
- Sermas, Co., Ltd., Chiba, 271-8501, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Akira Saito
- Feed-Livestock and Guidance Department, Dairy Technology Research Institute, The National Federation of Dairy Co-operative Associations (ZEN-RAKU-REN), Fukushima, 969-0223, Japan
| | - Hiroshi Masuya
- RIKEN BioResource Research Center, Ibaraki, 305-0074, Tsukuba, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuya Nagasawa
- Pathology and Production Disease Group, Division of Hygiene Management, Hokkaido Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, Hokkaido, 062-0045, Japan
| | - Aya Hirose
- Pathology and Production Disease Group, Division of Hygiene Management, Hokkaido Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, Hokkaido, 062-0045, Japan
| | - Tomohito Hayashi
- Pathology and Production Disease Group, Division of Hygiene Management, Hokkaido Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, Hokkaido, 062-0045, Japan
| | - Hiroshi Ohno
- RIKEN Integrated Medical Science Center, Yokohama, Kanagawa, 230-0045, Japan.
| | - Hideyuki Takahashi
- Kuju Agricultural Research Center, Graduate School of Agriculture, Kyushu University, Oita, 878-0201, Japan.
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