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Van Syoc E, Nixon MP, Silverman JD, Luo Y, Gonzalez FJ, Elbere I, Klovins J, Patterson AD, Rogers CJ, Ganda E. Changes in the type 2 diabetes gut mycobiome associate with metformin treatment across populations. mBio 2024; 15:e0016924. [PMID: 38767350 PMCID: PMC11237675 DOI: 10.1128/mbio.00169-24] [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: 01/18/2024] [Accepted: 04/08/2024] [Indexed: 05/22/2024] Open
Abstract
The human gut teems with a diverse ecosystem of microbes, yet non-bacterial portions of that community are overlooked in studies of metabolic diseases firmly linked to gut bacteria. Type 2 diabetes mellitus (T2D) is associated with compositional shifts in the gut bacterial microbiome and the mycobiome, the fungal portion of the microbiome. However, whether T2D and/or metformin treatment underpins fungal community changes is unresolved. To differentiate these effects, we curated a gut mycobiome cohort spanning 1,000 human samples across five countries and validated our findings in a murine experimental model. We use Bayesian multinomial logistic normal models to show that T2D and metformin both associate with shifts in the relative abundance of distinct gut fungi. T2D is associated with shifts in the Saccharomycetes and Sordariomycetes fungal classes, while the genera Fusarium and Tetrapisipora most consistently associate with metformin treatment. We confirmed the impact of metformin on individual gut fungi by administering metformin to healthy mice. Thus, metformin and T2D account for subtle, but significant and distinct variation in the gut mycobiome across human populations. This work highlights for the first time that metformin can confound associations of gut fungi with T2D and warrants the need to consider pharmaceutical interventions in investigations of linkages between metabolic diseases and gut microbial inhabitants. IMPORTANCE This is the largest to-date multi-country cohort characterizing the human gut mycobiome, and the first to investigate potential perturbations in gut fungi from oral pharmaceutical treatment. We demonstrate the reproducible effects of metformin treatment on the human and murine gut mycobiome and highlight a need to consider metformin as a confounding factor in investigations between type 2 diabetes mellitus and the gut microbial ecosystem.
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Affiliation(s)
- Emily Van Syoc
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Animal Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Michelle Pistner Nixon
- College of Information Sciences and Technology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Justin D. Silverman
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
- College of Information Sciences and Technology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Statistics, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Medicine, The Pennsylvania State University, Hershey, Pennsylvania, USA
| | - Yuhong Luo
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Frank J. Gonzalez
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ilze Elbere
- Latvian Biomedical Research and Study Center, Riga, Latvia
| | - Janis Klovins
- Latvian Biomedical Research and Study Center, Riga, Latvia
| | - Andrew D. Patterson
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Connie J. Rogers
- Department of Nutritional Sciences, University of Georgia, Athens, Georgia, USA
| | - Erika Ganda
- Department of Animal Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
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Ohtsuka H, Kawai S, Otsubo Y, Shimasaki T, Yamashita A, Aiba H. Metarhizium robertsii COH1 functionally complements Schizosaccharomyces pombe Ecl family proteins. J GEN APPL MICROBIOL 2024; 69:335-338. [PMID: 37813640 DOI: 10.2323/jgam.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
The fission yeast Schizosaccharomyces pombe ecl family genes respond to various starvation signals and induce appropriate intracellular responses, including the extension of chronological lifespan and induction of sexual differentiation. Herein, we propose that the colonization of hemocoel 1 (COH1) protein of Metarhizium robertsii, an insect-pathogenic fungus, is a functional homolog of S. pombe Ecl1 family proteins.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Sawa Kawai
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Yoko Otsubo
- Interdisciplinary Research Unit, National Institute for Basic Biology
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University
| | - Akira Yamashita
- Interdisciplinary Research Unit, National Institute for Basic Biology
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University
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Ohtsuka H, Shimasaki T, Aiba H. Low-Molecular Weight Compounds that Extend the Chronological Lifespan of Yeasts, Saccharomyces cerevisiae, and Schizosaccharomyces pombe. Adv Biol (Weinh) 2024; 8:e2400138. [PMID: 38616173 DOI: 10.1002/adbi.202400138] [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: 03/11/2024] [Revised: 04/04/2024] [Indexed: 04/16/2024]
Abstract
Yeast is an excellent model organism for research for regulating aging and lifespan, and the studies have made many contributions to date, including identifying various factors and signaling pathways related to aging and lifespan. More than 20 years have passed since molecular biological perspectives are adopted in this research field, and intracellular factors and signal pathways that control aging and lifespan have evolutionarily conserved from yeast to mammals. Furthermore, these findings have been applied to control the aging and lifespan of various model organisms by adjustment of the nutritional environment, genetic manipulation, and drug treatment using low-molecular weight compounds. Among these, drug treatment is easier than the other methods, and research into drugs that regulate aging and lifespan is consequently expected to become more active. Chronological lifespan, a definition of yeast lifespan, refers to the survival period of a cell population under nondividing conditions. Herein, low-molecular weight compounds are summarized that extend the chronological lifespan of Saccharomyces cerevisiae and Schizosaccharomyces pombe, along with their intracellular functions. The low-molecular weight compounds are also discussed that extend the lifespan of other model organisms. Compounds that have so far only been studied in yeast may soon extend lifespan in other organisms.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, Japan
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Van Syoc E, Nixon MP, Silverman JD, Luo Y, Gonzalez FJ, Elbere I, Klovins J, Patterson AD, Rogers CJ, Ganda E. Changes in the Type 2 diabetes gut mycobiome associate with metformin treatment across populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542255. [PMID: 37398234 PMCID: PMC10312434 DOI: 10.1101/2023.05.25.542255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The human gut teems with a diverse ecosystem of microbes, yet non-bacterial portions of that community are overlooked in studies of metabolic diseases firmly linked to gut bacteria. Type 2 diabetes mellitus (T2D) associates with compositional shifts in the gut bacterial microbiome and fungal mycobiome, but whether T2D and/or pharmaceutical treatments underpin the community change is unresolved. To differentiate these effects, we curated a gut mycobiome cohort to-date spanning 1,000 human samples across 5 countries and a murine experimental model. We use Bayesian multinomial logistic normal models to show that metformin and T2D both associate with shifts in the relative abundance of distinct gut fungi. T2D associates with shifts in the Saccharomycetes and Sordariomycetes fungal classes, while the genera Fusarium and Tetrapisipora most consistently associate with metformin treatment. We confirmed the impact of metformin on individual gut fungi by administering metformin to healthy mice. Thus, metformin and T2D account for subtle, but significant and distinct variation in the gut mycobiome across human populations. This work highlights for the first time that oral pharmaceuticals can confound associations of gut fungi with T2D and warrants the need to consider pharmaceutical interventions in investigations of linkages between metabolic diseases and gut microbial inhabitants.
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Affiliation(s)
- Emily Van Syoc
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA 16802, USA
| | - Michelle Pistner Nixon
- College of Information Sciences and Technology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Justin D. Silverman
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA 16802, USA
- College of Information Sciences and Technology, The Pennsylvania State University, University Park, PA 16802, USA
- Departments of Statistics and Medicine, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yuhong Luo
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frank J. Gonzalez
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ilze Elbere
- Latvian Biomedical Research and Study Center, Riga, Latvia
| | - Janis Klovins
- Latvian Biomedical Research and Study Center, Riga, Latvia
| | - Andrew D. Patterson
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Connie J. Rogers
- Department of Nutritional Sciences, University of Georgia, Athens, GA 30602, USA
| | - Erika Ganda
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA 16802, USA
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Soberanes-Gutiérrez CV, Pérez-Rueda E, Ruíz-Herrera J, Galán-Vásquez E. Identifying Genes Devoted to the Cell Death Process in the Gene Regulatory Network of Ustilago maydis. Front Microbiol 2021; 12:680290. [PMID: 34093501 PMCID: PMC8175908 DOI: 10.3389/fmicb.2021.680290] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/30/2021] [Indexed: 01/26/2023] Open
Abstract
Cell death is a process that can be divided into three morphological patterns: apoptosis, autophagy and necrosis. In fungi, cell death is induced in response to intracellular and extracellular perturbations, such as plant defense molecules, toxins and fungicides, among others. Ustilago maydis is a dimorphic fungus used as a model for pathogenic fungi of animals, including humans, and plants. Here, we reconstructed the transcriptional regulatory network of U. maydis, through homology inferences by using as templates the well-known gene regulatory networks (GRNs) of Saccharomyces cerevisiae, Aspergillus nidulans and Neurospora crassa. Based on this GRN, we identified transcription factors (TFs) as hubs and functional modules and calculated diverse topological metrics. In addition, we analyzed exhaustively the module related to cell death, with 60 TFs and 108 genes, where diverse cell proliferation, mating-type switching and meiosis, among other functions, were identified. To determine the role of some of these genes, we selected a set of 11 genes for expression analysis by qRT-PCR (sin3, rlm1, aif1, tdh3 [isoform A], tdh3 [isoform B], ald4, mca1, nuc1, tor1, ras1, and atg8) whose homologues in other fungi have been described as central in cell death. These genes were identified as downregulated at 72 h, in agreement with the beginning of the cell death process. Our results can serve as the basis for the study of transcriptional regulation, not only of the cell death process but also of all the cellular processes of U. maydis.
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Affiliation(s)
- Cinthia V. Soberanes-Gutiérrez
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
- Laboratorio de Ciencias Agrogenómicas, de la Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, León, Mexico
| | - Ernesto Pérez-Rueda
- Unidad Académica Yucatán, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Mérida, Mexico
| | - José Ruíz-Herrera
- Laboratorio de Ciencias Agrogenómicas, de la Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, León, Mexico
| | - Edgardo Galán-Vásquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigación en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México - Ciudad Universitaria, Mexico City, Mexico
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