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Herrera G, Arboleda JC, Pérez-Jaramillo JE, Patarroyo MA, Ramírez JD, Muñoz M. Microbial Interdomain Interactions Delineate the Disruptive Intestinal Homeostasis in Clostridioides difficile Infection. Microbiol Spectr 2022; 10:e0050222. [PMID: 36154277 PMCID: PMC9602525 DOI: 10.1128/spectrum.00502-22] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 09/06/2022] [Indexed: 11/20/2022] Open
Abstract
Clostridioides difficile infection (CDI) creates an imbalance in the intestinal microbiota due to the interaction of the components making up this ecosystem, but little is known about the impact of this disease on other microbial members. This work has thus been aimed at evaluating the taxonomic composition, potential gene-associated functions, virulence factors, and antimicrobial resistance profiles of gut microbiomes. A total of 48 DNA samples obtained from patients with health care facility-acquired (HCFO) and community-onset (CO) diarrhea were distributed in the following four groups according to CDI status: HCFO/+ (n = 13), HCFO/- (n = 8), CO/+ (n = 13), and CO/- (n = 14). These samples were subjected to shotgun metagenomics sequencing. Although the CDI groups' microbiota had microbiome alterations, the greatest imbalance was observed in the in the HCFO+/- groups, with an increase in common pathogens and phage populations, as well as a decrease in beneficial microorganisms that leads to a negative impact on some intestinal homeostasis-related metabolic processes. A reduction in the relative abundance of butyrate metabolism-associated genes was also detected in the HCFO groups (P < 0.01), with an increase in some virulence factors and antibiotic-resistance markers. A set of 51 differentially abundant species in the groups with potential association to CDI enabled its characterization, leading to their spatial separation by onset. Strong correlations between phages and some archaeal and bacterial phyla were identified. This highlighted the need to study the microbiota's various components since their imbalance is multifactorial, with some pathogens contributing to a greater or lesser extent because of their interaction with the ecosystem they inhabit. IMPORTANCE Clostridioides difficile infection represents a serious public health problem in different countries due to its high morbi-mortality and the high costs it represents for health care systems. Studies have shown the impact of this infection on intestinal microbiome homeostasis, mainly on bacterial populations. Our research provides evidence of the impact of CDI at both the compositional (bacteria, archaea, and viruses), and functional levels, allowing us to understand that the alterations of the microbiota occur systemically and are caused by multiple perturbations generated by different members of the microbiota as well as by some pathogens that take advantage of the imbalance to proliferate. Likewise, the 51 differentially abundant species in the study groups with potential association to CDI found in this study could help us envisage future treatments against this and other inflammatory diseases, improving future therapeutic options for patients.
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Affiliation(s)
- Giovanny Herrera
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan Camilo Arboleda
- Unidad de Bioprospección and Estudio de Microbiomas, Programa de Estudio y Control de Enfermedades Tropicales (PECET), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
- Semillero de Investigación en Bioinformática-GenomeSeq, Seccional Oriente, Universidad de Antioquia, Medellín, Colombia
- Grupo de Fundamentos y Enseñanza de la Física y los Sistemas Dinámicos, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Juan E. Pérez-Jaramillo
- Semillero de Investigación en Bioinformática-GenomeSeq, Seccional Oriente, Universidad de Antioquia, Medellín, Colombia
- Grupo de Fundamentos y Enseñanza de la Física y los Sistemas Dinámicos, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
- Health Sciences Division, Universidad Santo Tomás, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
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Grisales-Vargas CD, Ramírez-Cuartas CA, Pérez-Jaramillo JE. The First Complete Genome Resource of a Ralstonia solanacearum Phage UAM5 from Colombia. Mol Plant Microbe Interact 2022; 35:496-499. [PMID: 35395909 DOI: 10.1094/mpmi-01-22-0033-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Cristian D Grisales-Vargas
- Unidad de Bioprospección y Estudio de Microbiomas, Programa de Estudio y Control de Enfermedades Tropicales-PECET, Facultad de Medicina, Universidad de Antioquia, Medellín, 1226, Colombia
- Instituto de Biología, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Camilo A Ramírez-Cuartas
- Instituto de Biología, Universidad de Antioquia, Medellín, 050010, Colombia
- Grupo de Bacteriología Agrícola y Ambiental-BA&A, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Juan E Pérez-Jaramillo
- Unidad de Bioprospección y Estudio de Microbiomas, Programa de Estudio y Control de Enfermedades Tropicales-PECET, Facultad de Medicina, Universidad de Antioquia, Medellín, 1226, Colombia
- Instituto de Biología, Universidad de Antioquia, Medellín, 050010, Colombia
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Rossmann M, Pérez-Jaramillo JE, Kavamura VN, Chiaramonte JB, Dumack K, Fiore-Donno AM, Mendes LW, Ferreira MMC, Bonkowski M, Raaijmakers JM, Mauchline TH, Mendes R. Multitrophic interactions in the rhizosphere microbiome of wheat: from bacteria and fungi to protists. FEMS Microbiol Ecol 2020; 96:5775476. [PMID: 32124916 DOI: 10.1093/femsec/fiaa032] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/28/2020] [Indexed: 11/14/2022] Open
Abstract
Plants modulate the soil microbiota by root exudation assembling a complex rhizosphere microbiome with organisms spanning different trophic levels. Here, we assessed the diversity of bacterial, fungal and cercozoan communities in landraces and modern varieties of wheat. The dominant taxa within each group were the bacterial phyla Proteobacteria, Actinobacteria and Acidobacteria; the fungi phyla Ascomycota, Chytridiomycota and Basidiomycota; and the Cercozoa classes Sarcomonadea, Thecofilosea and Imbricatea. We showed that microbial networks of the wheat landraces formed a more intricate network topology than that of modern wheat cultivars, suggesting that breeding selection resulted in a reduced ability to recruit specific microbes in the rhizosphere. The high connectedness of certain cercozoan taxa to bacteria and fungi indicated trophic network hierarchies where certain predators gain predominance over others. Positive correlations between protists and bacteria in landraces were preserved as a subset in cultivars as was the case for the Sarcomonadea class with Actinobacteria. The correlations between the microbiome structure and plant genotype observed in our results suggest the importance of top-down control by organisms of higher trophic levels as a key factor for understanding the drivers of microbiome community assembly in the rhizosphere.
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Affiliation(s)
- Maike Rossmann
- Laboratory of Environmental Microbiology, Embrapa Environment, Rodovia SP 340 km 125.5, 13918-110, Jaguariúna SP, Brazil
| | - Juan E Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW); Institute of Biology, Leiden University, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Vanessa N Kavamura
- Sustainable Agriculture Sciences, West Common, AL5 2JQ, Harpenden, Rothamsted Research, UK
| | - Josiane B Chiaramonte
- Laboratory of Environmental Microbiology, Embrapa Environment, Rodovia SP 340 km 125.5, 13918-110, Jaguariúna SP, Brazil
| | - Kenneth Dumack
- Institute of Zoology & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Anna Maria Fiore-Donno
- Institute of Zoology & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Lucas W Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo, Av. Centenário, 303, 13416-000, Piracicaba SP, Brazil
| | - Márcia M C Ferreira
- Laboratory of Theoretical and Applied Chemometrics, Department of Chemistry, State University of Campinas (UNICAMP), Rua Josué de Castro, s/n, 13083-970, Campinas SP, Brazil
| | - Michael Bonkowski
- Institute of Zoology & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW); Institute of Biology, Leiden University, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Tim H Mauchline
- Sustainable Agriculture Sciences, West Common, AL5 2JQ, Harpenden, Rothamsted Research, UK
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Rodovia SP 340 km 125.5, 13918-110, Jaguariúna SP, Brazil
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Hannula SE, Ma HK, Pérez-Jaramillo JE, Pineda A, Bezemer TM. Structure and ecological function of the soil microbiome affecting plant-soil feedbacks in the presence of a soil-borne pathogen. Environ Microbiol 2019; 22:660-676. [PMID: 31788934 PMCID: PMC7027455 DOI: 10.1111/1462-2920.14882] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/22/2019] [Accepted: 11/28/2019] [Indexed: 11/30/2022]
Abstract
Interactions between plants and soil microbes are important for plant growth and resistance. Through plant–soil‐feedbacks, growth of a plant is influenced by the previous plant that was growing in the same soil. We performed a plant–soil feedback study with 37 grass, forb and legume species, to condition the soil and then tested the effects of plant‐induced changes in soil microbiomes on the growth of the commercially important cut‐flower Chrysanthemum in presence and absence of a pathogen. We analysed the fungal and bacterial communities in these soils using next‐generation sequencing and examined their relationship with plant growth in inoculated soils with or without the root pathogen, Pythium ultimum. We show that a large part of the soil microbiome is plant species‐specific while a smaller part is conserved at the plant family level. We further identified clusters of plant species creating plant growth promoting microbiomes that suppress concomitantly plant pathogens. Especially soil inocula with higher relative abundances of arbuscular mycorrhizal fungi caused positive effects on the Chrysanthemum growth when exposed to the pathogen. We conclude that plants differ greatly in how they influence the soil microbiome and that plant growth and protection against pathogens is associated with a complex soil microbial community.
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Affiliation(s)
- S Emilia Hannula
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Hai-Kun Ma
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.,Institute of Biology, Section Plant Ecology and Phytochemistry, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Juan E Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Ana Pineda
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - T Martijn Bezemer
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.,Institute of Biology, Section Plant Ecology and Phytochemistry, Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
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Pérez-Jaramillo JE, de Hollander M, Ramírez CA, Mendes R, Raaijmakers JM, Carrión VJ. Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia. Microbiome 2019; 7:114. [PMID: 31412927 PMCID: PMC6694607 DOI: 10.1186/s40168-019-0727-1] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/30/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood. RESULTS Here, we investigated if the transition from a native to an agricultural soil affected rhizobacterial community assembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterial diversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agricultural soil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 were shared by all eight bean accessions grown in native and agricultural soils, this core microbiome represented a large fraction (25.9%) of all sequence reads. More OTUs were exclusively found in the rhizosphere of common bean in the agricultural soil as compared to the native soil and in the rhizosphere of modern bean accessions as compared to wild accessions. Co-occurrence analyses further showed a reduction in complexity of the interactions in the bean rhizosphere microbiome in the agricultural soil as compared to the native soil. CONCLUSIONS Collectively, these results suggest that habitat expansion of common bean from its native soil environment to an agricultural context had an unexpected overall positive effect on rhizobacterial diversity and led to a stronger bean genotype-dependent effect on rhizosphere microbiome assembly.
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Affiliation(s)
- Juan E. Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
- Institute of Biology, University of Antioquia, Calle 67 #53-108, Medellín, Colombia
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
| | - Camilo A. Ramírez
- Institute of Biology, University of Antioquia, Calle 67 #53-108, Medellín, Colombia
| | - Rodrigo Mendes
- Embrapa Meio Ambiente, Rodovia SP 340 - km 127.5, Jaguariúna, 13820-000 Brazil
| | - Jos M. Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
| | - Víctor J. Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
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Pérez-Jaramillo JE, Carrión VJ, de Hollander M, Raaijmakers JM. The wild side of plant microbiomes. Microbiome 2018; 6:143. [PMID: 30115122 PMCID: PMC6097318 DOI: 10.1186/s40168-018-0519-z] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/17/2018] [Indexed: 05/18/2023]
Affiliation(s)
- Juan E Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands.
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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Pérez-Jaramillo JE, Mendes R, Raaijmakers JM. Impact of plant domestication on rhizosphere microbiome assembly and functions. Plant Mol Biol 2016; 90:635-44. [PMID: 26085172 PMCID: PMC4819786 DOI: 10.1007/s11103-015-0337-7] [Citation(s) in RCA: 283] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/04/2015] [Indexed: 05/18/2023]
Abstract
The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. Plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. Domestication of plant species has substantially contributed to human civilization, but also caused a strong decrease in the genetic diversity of modern crop cultivars that may have affected the ability of plants to establish beneficial associations with rhizosphere microbes. Here, we review how plants shape the rhizosphere microbiome and how domestication may have impacted rhizosphere microbiome assembly and functions via habitat expansion and via changes in crop management practices, root exudation, root architecture, and plant litter quality. We also propose a "back to the roots" framework that comprises the exploration of the microbiome of indigenous plants and their native habitats for the identification of plant and microbial traits with the ultimate goal to reinstate beneficial associations that may have been undermined during plant domestication.
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Affiliation(s)
- Juan E Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands
- Sylvius Laboratories, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, Embrapa Environment, Rodovia SP 340 - km 127.5, Jaguariúna, 13820-000, Brazil
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands.
- Sylvius Laboratories, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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