1
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Auer L, Buée M, Fauchery L, Lombard V, Barry KW, Clum A, Copeland A, Daum C, Foster B, LaButti K, Singan V, Yoshinaga Y, Martineau C, Alfaro M, Castillo FJ, Imbert JB, Ramírez L, Castanera R, Pisabarro AG, Finlay R, Lindahl B, Olson A, Séguin A, Kohler A, Henrissat B, Grigoriev IV, Martin FM. Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems. New Phytol 2024; 242:1676-1690. [PMID: 38148573 DOI: 10.1111/nph.19471] [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] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/23/2023] [Indexed: 12/28/2023]
Abstract
Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. We showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.
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Affiliation(s)
- Lucas Auer
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Marc Buée
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Laure Fauchery
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, Marseille, 13288, France
- INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, 13009, France
| | - Kerry W Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alex Copeland
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Brian Foster
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuko Yoshinaga
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christine Martineau
- Laurentian Forestry Centre, Natural Resources Canada, Canadian Forest Service, Quebec, G1V4C7, QC, Canada
| | - Manuel Alfaro
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Federico J Castillo
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - J Bosco Imbert
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Lucia Ramírez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Raúl Castanera
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Antonio G Pisabarro
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Roger Finlay
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Björn Lindahl
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Ake Olson
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Armand Séguin
- Laurentian Forestry Centre, Natural Resources Canada, Canadian Forest Service, Quebec, G1V4C7, QC, Canada
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Bernard Henrissat
- DTU Bioengineering, Denmarks Tekniske Universitet, Copenhagen, 2800, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
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2
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Hibberd MC, Webber DM, Rodionov DA, Henrissat S, Chen RY, Zhou C, Lynn HM, Wang Y, Chang HW, Lee EM, Lelwala-Guruge J, Kazanov MD, Arzamasov AA, Leyn SA, Lombard V, Terrapon N, Henrissat B, Castillo JJ, Couture G, Bacalzo NP, Chen Y, Lebrilla CB, Mostafa I, Das S, Mahfuz M, Barratt MJ, Osterman AL, Ahmed T, Gordon JI. Bioactive glycans in a microbiome-directed food for children with malnutrition. Nature 2024; 625:157-165. [PMID: 38093016 PMCID: PMC10764277 DOI: 10.1038/s41586-023-06838-3] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/06/2023] [Indexed: 12/26/2023]
Abstract
Evidence is accumulating that perturbed postnatal development of the gut microbiome contributes to childhood malnutrition1-4. Here we analyse biospecimens from a randomized, controlled trial of a microbiome-directed complementary food (MDCF-2) that produced superior rates of weight gain compared with a calorically more dense conventional ready-to-use supplementary food in 12-18-month-old Bangladeshi children with moderate acute malnutrition4. We reconstructed 1,000 bacterial genomes (metagenome-assembled genomes (MAGs)) from the faecal microbiomes of trial participants, identified 75 MAGs of which the abundances were positively associated with ponderal growth (change in weight-for-length Z score (WLZ)), characterized changes in MAG gene expression as a function of treatment type and WLZ response, and quantified carbohydrate structures in MDCF-2 and faeces. The results reveal that two Prevotella copri MAGs that are positively associated with WLZ are the principal contributors to MDCF-2-induced expression of metabolic pathways involved in utilizing the component glycans of MDCF-2. The predicted specificities of carbohydrate-active enzymes expressed by their polysaccharide-utilization loci are correlated with (1) the in vitro growth of Bangladeshi P. copri strains, possessing varying degrees of polysaccharide-utilization loci and genomic conservation with these MAGs, in defined medium containing different purified glycans representative of those in MDCF-2, and (2) the levels of faecal carbohydrate structures in the trial participants. These associations suggest that identifying bioactive glycan structures in MDCFs metabolized by growth-associated bacterial taxa will help to guide recommendations about their use in children with acute malnutrition and enable the development of additional formulations.
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Affiliation(s)
- Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel M Webber
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Robert Y Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Hannah M Lynn
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Yi Wang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Evan M Lee
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Janaki Lelwala-Guruge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Marat D Kazanov
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Aleksandr A Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Semen A Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Juan J Castillo
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Nikita P Bacalzo
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Ye Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
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3
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Million M, Alou MT, Khelaifia S, Bachar D, Lagier JC, Dione N, Brah S, Hugon P, Lombard V, Armougom F, Fromonot J, Robert C, Michelle C, Diallo A, Fabre A, Guieu R, Sokhna C, Henrissat B, Parola P, Raoult D. Retraction Note: Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition. Sci Rep 2023; 13:18589. [PMID: 37903811 PMCID: PMC10616166 DOI: 10.1038/s41598-023-44597-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023] Open
Affiliation(s)
- Matthieu Million
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Maryam Tidjani Alou
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Saber Khelaifia
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Dipankar Bachar
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Jean-Christophe Lagier
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Niokhor Dione
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | | | - Perrine Hugon
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Vincent Lombard
- Centre National de la Recherche Scientifique, UMR 7257, 13288, Marseille, France
- Aix-Marseille Université, Architecture et Fonctions des Macromolécules Biologiques, 163, avenue de Luminy, 13288, Marseille cedex 9, France
| | - Fabrice Armougom
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Julien Fromonot
- Laboratoire de Biochimie, hôpital de la Timone, UMR MD2, IRBA, Marseille, France
| | - Catherine Robert
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Caroline Michelle
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Aldiouma Diallo
- Institut de Recherche pour le Développement (IRD), URMITE, Dakar, Sénégal
| | - Alexandre Fabre
- Service de Pédiatrie Multidisciplinaire, hôpital de la Timone Enfant, APHM, Marseille, France
- UMR_S 910, Aix-Marseille Université, Marseille, France
| | - Régis Guieu
- Laboratoire de Biochimie, hôpital de la Timone, UMR MD2, IRBA, Marseille, France
| | - Cheikh Sokhna
- Institut de Recherche pour le Développement (IRD), URMITE, Dakar, Sénégal
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique, UMR 7257, 13288, Marseille, France
- Aix-Marseille Université, Architecture et Fonctions des Macromolécules Biologiques, 163, avenue de Luminy, 13288, Marseille cedex 9, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Philippe Parola
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France.
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
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4
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Zeng Q, Lebreton A, Auer L, Man X, Jia L, Wang G, Gong S, Lombard V, Buée M, Wu G, Dai Y, Yang Z, Martin FM. Stable functional structure despite high taxonomic variability across fungal communities in soils of old-growth montane forests. Microbiome 2023; 11:217. [PMID: 37779194 PMCID: PMC10544587 DOI: 10.1186/s40168-023-01650-7] [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] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/11/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND Major advances over the past decade in molecular ecology are providing access to soil fungal diversity in forest ecosystems worldwide, but the diverse functions and metabolic capabilities of this microbial community remain largely elusive. We conducted a field survey in montane old-growth broadleaved and conifer forests, to investigate the relationship between soil fungal diversity and functional genetic traits. To assess the extent to which variation in community composition was associated with dominant tree species (oak, spruce, and fir) and environmental variations in the old-growth forests in the Jade Dragon Snow Mountain in Yunnan Province, we applied rDNA metabarcoding. We also assessed fungal gene expression in soil using mRNA sequencing and specifically assessed the expression of genes related to organic matter decomposition and nutrient acquisition in ectomycorrhizal and saprotrophic fungi. RESULTS Our taxonomic profiling revealed striking shifts in the composition of the saprotrophic and ectomycorrhizal guilds among the oak-, fir-, and spruce-dominated forests. The core fungal microbiome comprised only ~ 20% of the total OTUs across all soil samples, although the overlap between conifer-associated communities was substantial. In contrast, seasonality and soil layer explained only a small proportion of the variation in community structure. However, despite their highly variable taxonomic composition, fungal guilds exhibited remarkably similar functional traits for growth-related and core metabolic pathways across forest associations, suggesting ecological redundancy. However, we found that the expression profiles of genes related to polysaccharide and protein degradation and nutrient transport notably varied between and within the fungal guilds, suggesting niche adaptation. CONCLUSIONS Overall, our metatranscriptomic analyses revealed the functional potential of soil fungal communities in montane old-growth forests, including a suite of specialized genes and taxa involved in organic matter decomposition. By linking genes to ecological traits, this study provides insights into fungal adaptation strategies to biotic and environmental factors, and sheds light on the importance of understanding functional gene expression patterns in predicting ecosystem functioning. Video Abstract.
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Affiliation(s)
- Qingchao Zeng
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, Beijing, 100083, China
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Annie Lebreton
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France
- INRAE, Aix-Marseille Université, Biodiversité et Biotechnologie Fongiques, 13009, Marseille, France
| | - Lucas Auer
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France
| | - Xiaowu Man
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Liukun Jia
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Gengshen Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, 650201, Yunnan, China
| | - Sai Gong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Vincent Lombard
- Architecture Et Fonction Des Macromolécules Biologiques, CNRS, Aix-Marseille Université, UMR 7257, 13288, Marseille, France
| | - Marc Buée
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France
| | - Gang Wu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, 650201, Yunnan, China
| | - Yucheng Dai
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, Beijing, 100083, China.
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China.
| | - Zhuliang Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, 650201, Yunnan, China.
| | - Francis M Martin
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, Beijing, 100083, China.
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France.
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5
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Hibberd MC, Webber DM, Rodionov DA, Henrissat S, Chen RY, Zhou C, Lynn HM, Wang Y, Chang HW, Lee EM, Lelwala-Guruge J, Kazanov MD, Arzamasov AA, Leyn SA, Lombard V, Terrapon N, Henrissat B, Castillo JJ, Couture G, Bacalzo NP, Chen Y, Lebrilla CB, Mostafa I, Das S, Mahfuz M, Barratt MJ, Osterman AL, Ahmed T, Gordon JI. Bioactive glycans in a microbiome-directed food for malnourished children. medRxiv 2023:2023.08.14.23293998. [PMID: 37645824 PMCID: PMC10462212 DOI: 10.1101/2023.08.14.23293998] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Evidence is accumulating that perturbed postnatal development of the gut microbiome contributes to childhood malnutrition1-4. Designing effective microbiome-directed therapeutic foods to repair these perturbations requires knowledge about how food components interact with the microbiome to alter its expressed functions. Here we use biospecimens from a randomized, controlled trial of a microbiome-directed complementary food prototype (MDCF-2) that produced superior rates of weight gain compared to a conventional ready-to-use supplementary food (RUSF) in 12-18-month-old Bangladeshi children with moderate acute malnutrition (MAM)4. We reconstructed 1000 bacterial genomes (metagenome-assembled genomes, MAGs) present in their fecal microbiomes, identified 75 whose abundances were positively associated with weight gain (change in weight-for-length Z score, WLZ), characterized gene expression changes in these MAGs as a function of treatment type and WLZ response, and used mass spectrometry to quantify carbohydrate structures in MDCF-2 and feces. The results reveal treatment-induced changes in expression of carbohydrate metabolic pathways in WLZ-associated MAGs. Comparing participants consuming MDCF-2 versus RUSF, and MDCF-2-treated children in the upper versus lower quartiles of WLZ responses revealed that two Prevotella copri MAGs positively associated with WLZ were principal contributors to MDCF-2-induced expression of metabolic pathways involved in utilization of its component glycans. Moreover, the predicted specificities of carbohydrate active enzymes expressed by polysaccharide utilization loci (PULs) in these two MAGs correlate with the (i) in vitro growth of Bangladeshi P. copri strains, possessing differing degrees of PUL and overall genomic content similarity to these MAGs, cultured in defined medium containing different purified glycans representative of those in MDCF-2, and (ii) levels of carbohydrate structures identified in feces from clinical trial participants. In the accompanying paper5, we use a gnotobiotic mouse model colonized with age- and WLZ-associated bacterial taxa cultured from this study population, and fed diets resembling those consumed by study participants, to directly test the relationship between P. copri, MDCF-2 glycan metabolism, host ponderal growth responses, and intestinal gene expression and metabolism. The ability to identify bioactive glycan structures in MDCFs that are metabolized by growth-associated bacterial taxa will help guide recommendations about use of this MDCF for children with acute malnutrition representing different geographic locales and ages, as well as enable development of bioequivalent, or more efficacious, formulations composed of culturally acceptable and affordable ingredients.
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Affiliation(s)
- Matthew C. Hibberd
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University
School of Medicine, St. Louis, MO 63110 USA
| | - Daniel M. Webber
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University
School of Medicine, St. Louis, MO 63110 USA
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham
Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Architecture et Fonction des Macromolécules Biologiques,
CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Robert Y. Chen
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Cyrus Zhou
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Hannah M. Lynn
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Yi Wang
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Hao-Wei Chang
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Evan M. Lee
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Janaki Lelwala-Guruge
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
| | - Marat D. Kazanov
- Faculty of Engineering and Natural Sciences, Sabanci University,
Istanbul, Turkey, 34956
| | - Aleksandr A. Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham
Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Semen A. Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham
Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques,
CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques,
CNRS, Aix-Marseille University, F-13288, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering),
Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University,
Jeddah, Saudi Arabia
| | - Juan J. Castillo
- Department of Chemistry, University of California, Davis, CA
95616, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA
95616, USA
| | - Nikita P. Bacalzo
- Department of Chemistry, University of California, Davis, CA
95616, USA
| | - Ye Chen
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Department of Chemistry, University of California, Davis, CA
95616, USA
| | | | - Ishita Mostafa
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Subhasish Das
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Mustafa Mahfuz
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Michael J. Barratt
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University
School of Medicine, St. Louis, MO 63110 USA
| | - Andrei L. Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham
Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research,
Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Jeffrey I. Gordon
- Edison Family Center for Genome Sciences and Systems Biology,
Washington University School of Medicine, St. Louis, MO 63110 USA
- Center for Gut Microbiome and Nutrition Research, Washington
University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Washington University
School of Medicine, St. Louis, MO 63110 USA
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6
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Dorrell RG, Kuo A, Füssy Z, Richardson EH, Salamov A, Zarevski N, Freyria NJ, Ibarbalz FM, Jenkins J, Pierella Karlusich JJ, Stecca Steindorff A, Edgar RE, Handley L, Lail K, Lipzen A, Lombard V, McFarlane J, Nef C, Novák Vanclová AM, Peng Y, Plott C, Potvin M, Vieira FRJ, Barry K, de Vargas C, Henrissat B, Pelletier E, Schmutz J, Wincker P, Dacks JB, Bowler C, Grigoriev IV, Lovejoy C. Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae. Life Sci Alliance 2023; 6:6/3/e202201833. [PMID: 36522135 PMCID: PMC9756366 DOI: 10.26508/lsa.202201833] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison with Tara Oceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.
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Affiliation(s)
- Richard G Dorrell
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zoltan Füssy
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
| | - Elisabeth H Richardson
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikola Zarevski
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Nastasia J Freyria
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Federico M Ibarbalz
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Jerry Jenkins
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Juan Jose Pierella Karlusich
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Andrei Stecca Steindorff
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robyn E Edgar
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Lori Handley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kathleen Lail
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vincent Lombard
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - John McFarlane
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Charlotte Nef
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Anna Mg Novák Vanclová
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Yi Peng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Plott
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Marianne Potvin
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Fabio Rocha Jimenez Vieira
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Colomban de Vargas
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, Roscoff, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Eric Pelletier
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Patrick Wincker
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Chris Bowler
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Connie Lovejoy
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
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7
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Martins MP, Morais MAB, Persinoti GF, Galinari RH, Yu L, Yoshimi Y, Passos Nunes FB, Lima TB, Barbieri SF, Silveira JLM, Lombard V, Terrapon N, Dupree P, Henrissat B, Murakami MT. Glycoside hydrolase subfamily GH5_57 features a highly redesigned catalytic interface to process complex hetero-β-mannans. Acta Cryst Sect D Struct Biol 2022; 78:1358-1372. [DOI: 10.1107/s2059798322009561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022]
Abstract
Glycoside hydrolase family 5 (GH5) harbors diverse substrate specificities and modes of action, exhibiting notable molecular adaptations to cope with the stereochemical complexity imposed by glycosides and carbohydrates such as cellulose, xyloglucan, mixed-linkage β-glucan, laminarin, (hetero)xylan, (hetero)mannan, galactan, chitosan, N-glycan, rutin and hesperidin. GH5 has been divided into subfamilies, many with higher functional specificity, several of which have not been characterized to date and some that have yet to be discovered with the exploration of sequence/taxonomic diversity. In this work, the current GH5 subfamily inventory is expanded with the discovery of the GH5_57 subfamily by describing an endo-β-mannanase (CapGH5_57) from an uncultured Bacteroidales bacterium recovered from the capybara gut microbiota. Biochemical characterization showed that CapGH5_57 is active on glucomannan, releasing oligosaccharides with a degree of polymerization from 2 to 6, indicating it to be an endo-β-mannanase. The crystal structure, which was solved using single-wavelength anomalous diffraction, revealed a massively redesigned catalytic interface compared with GH5 mannanases. The typical aromatic platforms and the characteristic α-helix-containing β6–α6 loop in the positive-subsite region of GH5_7 mannanases are absent in CapGH5_57, generating a large and open catalytic interface that might favor the binding of branched substrates. Supporting this, CapGH5_57 contains a tryptophan residue adjacent and perpendicular to the cleavage site, indicative of an anchoring site for a substrate with a substitution at the −1 glycosyl moiety. Taken together, these results suggest that despite presenting endo activity on glucomannan, CapGH5_57 may have a new type of substituted heteromannan as its natural substrate. This work demonstrates the still great potential for discoveries regarding the mechanistic and functional diversity of this large and polyspecific GH family by unveiling a novel catalytic interface sculpted to recognize complex heteromannans, which led to the establishment of the GH5_57 subfamily.
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8
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Kamikawa R, Mochizuki T, Sakamoto M, Tanizawa Y, Nakayama T, Onuma R, Cenci U, Moog D, Speak S, Sarkozi K, Toseland A, van Oosterhout C, Oyama K, Kato M, Kume K, Kayama M, Azuma T, Ishii KI, Miyashita H, Henrissat B, Lombard V, Win J, Kamoun S, Kashiyama Y, Mayama S, Miyagishima SY, Tanifuji G, Mock T, Nakamura Y. Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida. Sci Adv 2022; 8:eabi5075. [PMID: 35486731 PMCID: PMC9054022 DOI: 10.1126/sciadv.abi5075] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Secondary loss of photosynthesis is observed across almost all plastid-bearing branches of the eukaryotic tree of life. However, genome-based insights into the transition from a phototroph into a secondary heterotroph have so far only been revealed for parasitic species. Free-living organisms can yield unique insights into the evolutionary consequence of the loss of photosynthesis, as the parasitic lifestyle requires specific adaptations to host environments. Here, we report on the diploid genome of the free-living diatom Nitzschia putrida (35 Mbp), a nonphotosynthetic osmotroph whose photosynthetic relatives contribute ca. 40% of net oceanic primary production. Comparative analyses with photosynthetic diatoms and heterotrophic algae with parasitic lifestyle revealed that a combination of gene loss, the accumulation of genes involved in organic carbon degradation, a unique secretome, and the rapid divergence of conserved gene families involved in cell wall and extracellular metabolism appear to have facilitated the lifestyle of a free-living secondary heterotroph.
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Affiliation(s)
- Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takako Mochizuki
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Mika Sakamoto
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Takuro Nakayama
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Ryo Onuma
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Ugo Cenci
- Université de Lille, CNRS, UMR 8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Daniel Moog
- Laboratory for Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8
- SYNMIKRO Research Center, Hans-Meerwein-Str. 6, 35032, Marburg, Germany
| | - Samuel Speak
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Krisztina Sarkozi
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew Toseland
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Kaori Oyama
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Misako Kato
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Keitaro Kume
- Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Motoki Kayama
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Tomonori Azuma
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Ken-ichiro Ishii
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Hideaki Miyashita
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yuichiro Kashiyama
- Graduate School of Engineering, Fukui University of Technology, Fukui, Japan
| | - Shigeki Mayama
- Advanced Support Center for Science Teachers, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Shin-ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Goro Tanifuji
- Department of Zoology, National Museum of Nature and Science, Tsukuba 305-0005, Japan
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
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9
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Ostrowski MP, La Rosa SL, Kunath BJ, Robertson A, Pereira G, Hagen LH, Varghese NJ, Qiu L, Yao T, Flint G, Li J, McDonald SP, Buttner D, Pudlo NA, Schnizlein MK, Young VB, Brumer H, Schmidt TM, Terrapon N, Lombard V, Henrissat B, Hamaker B, Eloe-Fadrosh EA, Tripathi A, Pope PB, Martens EC. Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota. Nat Microbiol 2022; 7:556-569. [PMID: 35365790 DOI: 10.1038/s41564-022-01093-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/24/2022] [Indexed: 12/13/2022]
Abstract
Processed foods often include food additives such as xanthan gum, a complex polysaccharide with unique rheological properties, that has established widespread use as a stabilizer and thickening agent. Xanthan gum's chemical structure is distinct from those of host and dietary polysaccharides that are more commonly expected to transit the gastrointestinal tract, and little is known about its direct interaction with the gut microbiota, which plays a central role in digestion of other dietary fibre polysaccharides. Here we show that the ability to digest xanthan gum is common in human gut microbiomes from industrialized countries and appears contingent on a single uncultured bacterium in the family Ruminococcaceae. Our data reveal that this primary degrader cleaves the xanthan gum backbone before processing the released oligosaccharides using additional enzymes. Some individuals harbour Bacteroides intestinalis that is incapable of consuming polymeric xanthan gum but grows on oligosaccharide products generated by the Ruminococcaceae. Feeding xanthan gum to germfree mice colonized with a human microbiota containing the uncultured Ruminococcaceae supports the idea that the additive xanthan gum can drive expansion of the primary degrader Ruminococcaceae, along with exogenously introduced B. intestinalis. Our work demonstrates the existence of a potential xanthan gum food chain involving at least two members of different phyla of gut bacteria and provides an initial framework for understanding how widespread consumption of a recently introduced food additive influences human microbiomes.
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Affiliation(s)
- Matthew P Ostrowski
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Benoit J Kunath
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Andrew Robertson
- Life Sciences Institute: Natural Products Discovery Core, University of Michigan, Ann Arbor, MI, USA
| | - Gabriel Pereira
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Ling Qiu
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Tianming Yao
- Department of Food Science and Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
| | - Gabrielle Flint
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - James Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean P McDonald
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Duna Buttner
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Matthew K Schnizlein
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.,Department of Internal Medicine, Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Nicolas Terrapon
- Centre National de la Recherche Scientifique, Aix-Marseille Univ, Marseille, France.,Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Marseille, France
| | - Vincent Lombard
- Centre National de la Recherche Scientifique, Aix-Marseille Univ, Marseille, France.,Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Marseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Technical University of Denmark, DTU Bioengineering, Lyngby, Denmark
| | - Bruce Hamaker
- Department of Food Science and Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
| | | | - Ashootosh Tripathi
- Life Sciences Institute: Natural Products Discovery Core, University of Michigan, Ann Arbor, MI, USA
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway. .,Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
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10
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Cabral L, Persinoti GF, Paixão DAA, Martins MP, Morais MAB, Chinaglia M, Domingues MN, Sforca ML, Pirolla RAS, Generoso WC, Santos CA, Maciel LF, Terrapon N, Lombard V, Henrissat B, Murakami MT. Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides. Nat Commun 2022; 13:629. [PMID: 35110564 PMCID: PMC8810776 DOI: 10.1038/s41467-022-28310-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 09/13/2021] [Accepted: 01/14/2022] [Indexed: 12/12/2022] Open
Abstract
The largest living rodent, capybara, can efficiently depolymerize and utilize lignocellulosic biomass through microbial symbiotic mechanisms yet elusive. Herein, we elucidate the microbial community composition, enzymatic systems and metabolic pathways involved in the conversion of dietary fibers into short-chain fatty acids, a main energy source for the host. In this microbiota, the unconventional enzymatic machinery from Fibrobacteres seems to drive cellulose degradation, whereas a diverse set of carbohydrate-active enzymes from Bacteroidetes, organized in polysaccharide utilization loci, are accounted to tackle complex hemicelluloses typically found in gramineous and aquatic plants. Exploring the genetic potential of this community, we discover a glycoside hydrolase family of β-galactosidases (named as GH173), and a carbohydrate-binding module family (named as CBM89) involved in xylan binding that establishes an unprecedented three-dimensional fold among associated modules to carbohydrate-active enzymes. Together, these results demonstrate how the capybara gut microbiota orchestrates the depolymerization and utilization of plant fibers, representing an untapped reservoir of enzymatic mechanisms to overcome the lignocellulose recalcitrance, a central challenge toward a sustainable and bio-based economy. Here, Cabral et al., perform a multi-omics analysis of the gut microbiome of capybara, the largest living rodent, unveiling enzymatic mechanisms for the breakdown of lignocellulosic biomass, and report two undescribed families of carbohydrate-active enzymes.
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Affiliation(s)
- Lucelia Cabral
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Gabriela F Persinoti
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.
| | - Douglas A A Paixão
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Marcele P Martins
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.,Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Mariana A B Morais
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Mariana Chinaglia
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.,Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Mariane N Domingues
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Mauricio L Sforca
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Renan A S Pirolla
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Wesley C Generoso
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Clelton A Santos
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Lucas F Maciel
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Nicolas Terrapon
- The Institut National de la Recherche Agronomique, USC 1408 AFMB, 13288, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Vincent Lombard
- The Institut National de la Recherche Agronomique, USC 1408 AFMB, 13288, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mario T Murakami
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.
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11
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Drula E, Garron ML, Dogan S, Lombard V, Henrissat B, Terrapon N. The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Res 2021; 50:D571-D577. [PMID: 34850161 PMCID: PMC8728194 DOI: 10.1093/nar/gkab1045] [Citation(s) in RCA: 614] [Impact Index Per Article: 204.7] [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: 09/14/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 02/01/2023] Open
Abstract
Thirty years have elapsed since the emergence of the classification of carbohydrate-active enzymes in sequence-based families that became the CAZy database over 20 years ago, freely available for browsing and download at www.cazy.org. In the era of large scale sequencing and high-throughput Biology, it is important to examine the position of this specialist database that is deeply rooted in human curation. The three primary tasks of the CAZy curators are (i) to maintain and update the family classification of this class of enzymes, (ii) to classify sequences newly released by GenBank and the Protein Data Bank and (iii) to capture and present functional information for each family. The CAZy website is updated once a month. Here we briefly summarize the increase in novel families and the annotations conducted during the last 8 years. We present several important changes that facilitate taxonomic navigation, and allow to download the entirety of the annotations. Most importantly we highlight the considerable amount of work that accompanies the analysis and report of biochemical data from the literature.
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Affiliation(s)
- Elodie Drula
- Aix Marseille Univ, CNRS, UMR7257 AFMB, Marseille, France.,INRAE, USC1408 AFMB, Marseille, France
| | - Marie-Line Garron
- Aix Marseille Univ, CNRS, UMR7257 AFMB, Marseille, France.,INRAE, USC1408 AFMB, Marseille, France
| | - Suzan Dogan
- Aix Marseille Univ, CNRS, UMR7257 AFMB, Marseille, France.,INRAE, USC1408 AFMB, Marseille, France
| | - Vincent Lombard
- Aix Marseille Univ, CNRS, UMR7257 AFMB, Marseille, France.,INRAE, USC1408 AFMB, Marseille, France
| | - Bernard Henrissat
- Aix Marseille Univ, CNRS, UMR7257 AFMB, Marseille, France.,INRAE, USC1408 AFMB, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Technical University of Denmark, DTU Bioengineering, Kgs Lyngby, Denmark
| | - Nicolas Terrapon
- Aix Marseille Univ, CNRS, UMR7257 AFMB, Marseille, France.,INRAE, USC1408 AFMB, Marseille, France
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12
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Tamburrini KC, Terrapon N, Lombard V, Bissaro B, Longhi S, Berrin JG. Bioinformatic Analysis of Lytic Polysaccharide Monooxygenases Reveals the Pan-Families Occurrence of Intrinsically Disordered C-Terminal Extensions. Biomolecules 2021; 11:1632. [PMID: 34827630 PMCID: PMC8615602 DOI: 10.3390/biom11111632] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/26/2021] [Accepted: 10/30/2021] [Indexed: 01/17/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are monocopper enzymes secreted by many organisms and viruses. LPMOs catalyze the oxidative cleavage of different types of polysaccharides and are today divided into eight families (AA9-11, AA13-17) within the Auxiliary Activity enzyme class of the CAZy database. LPMOs minimal architecture encompasses a catalytic domain, to which can be appended a carbohydrate-binding module. Intriguingly, we observed that some LPMO sequences also display a C-terminal extension of varying length not associated with any known function or fold. Here, we analyzed 27,060 sequences from different LPMO families and show that 60% have a C-terminal extension predicted to be intrinsically disordered. Our analysis shows that these disordered C-terminal regions (dCTRs) are widespread in all LPMO families (except AA13) and differ in terms of sequence length and amino-acid composition. Noteworthily, these dCTRs have so far only been observed in LPMOs. LPMO-dCTRs share a common polyampholytic nature and an enrichment in serine and threonine residues, suggesting that they undergo post-translational modifications. Interestingly, dCTRs from AA11 and AA15 are enriched in redox-sensitive, conditionally disordered regions. The widespread occurrence of dCTRs in LPMOs from evolutionarily very divergent organisms, hints at a possible functional role and opens new prospects in the field of LPMOs.
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Affiliation(s)
- Ketty C. Tamburrini
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université (AMU), UMR 7257, 13288 Marseille, France; (K.C.T.); (N.T.); (V.L.)
- Biodiversité et Biotechnologie Fongiques (BBF), French National Institute for Agriculture, Food, and Environment (INRAE), Aix-Marseille Université (AMU), UMR 1163, 13288 Marseille, France;
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université (AMU), UMR 7257, 13288 Marseille, France; (K.C.T.); (N.T.); (V.L.)
- Architecture et Fonction des Macromolécules Biologiques (AFMB), French National Institute for Agriculture, Food, and Environment (INRAE), USC 1408, 13288 Marseille, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université (AMU), UMR 7257, 13288 Marseille, France; (K.C.T.); (N.T.); (V.L.)
- Architecture et Fonction des Macromolécules Biologiques (AFMB), French National Institute for Agriculture, Food, and Environment (INRAE), USC 1408, 13288 Marseille, France
| | - Bastien Bissaro
- Biodiversité et Biotechnologie Fongiques (BBF), French National Institute for Agriculture, Food, and Environment (INRAE), Aix-Marseille Université (AMU), UMR 1163, 13288 Marseille, France;
| | - Sonia Longhi
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université (AMU), UMR 7257, 13288 Marseille, France; (K.C.T.); (N.T.); (V.L.)
| | - Jean-Guy Berrin
- Biodiversité et Biotechnologie Fongiques (BBF), French National Institute for Agriculture, Food, and Environment (INRAE), Aix-Marseille Université (AMU), UMR 1163, 13288 Marseille, France;
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13
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Delannoy-Bruno O, Desai C, Raman AS, Chen RY, Hibberd MC, Cheng J, Han N, Castillo JJ, Couture G, Lebrilla CB, Barve RA, Lombard V, Henrissat B, Leyn SA, Rodionov DA, Osterman AL, Hayashi DK, Meynier A, Vinoy S, Kirbach K, Wilmot T, Heath AC, Klein S, Barratt MJ, Gordon JI. Evaluating microbiome-directed fibre snacks in gnotobiotic mice and humans. Nature 2021; 595:91-95. [PMID: 34163075 PMCID: PMC8324079 DOI: 10.1038/s41586-021-03671-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [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: 07/01/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023]
Abstract
Changing food preferences brought about by westernization that have deleterious health effects1,2-combined with myriad forces that are contributing to increased food insecurity-are catalysing efforts to identify more nutritious and affordable foods3. Consumption of dietary fibre can help to prevent cardiovascular disease, type 2 diabetes and obesity4-6. A substantial number of reports have explored the effects of dietary fibre on the gut microbial community7-9. However, the microbiome is complex, dynamic and exhibits considerable intra- and interpersonal variation in its composition and functions. The large number of potential interactions between the components of the microbiome makes it challenging to define the mechanisms by which food ingredients affect community properties. Here we address the question of how foods containing different fibre preparations can be designed to alter functions associated with specific components of the microbiome. Because a marked increase in snack consumption is associated with westernization, we formulated snack prototypes using plant fibres from different sustainable sources that targeted distinct features of the gut microbiomes of individuals with obesity when transplanted into gnotobiotic mice. We used these snacks to supplement controlled diets that were consumed by adult individuals with obesity or who were overweight. Fibre-specific changes in their microbiomes were linked to changes in their plasma proteomes indicative of an altered physiological state.
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Affiliation(s)
- Omar Delannoy-Bruno
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Chandani Desai
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Arjun S Raman
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Robert Y Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Jiye Cheng
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Nathan Han
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Juan J Castillo
- Department of Chemistry, University of California, Davis, CA, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA, USA
| | | | - Ruteja A Barve
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille Université, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille Université, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Semen A Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | | | | | - Kyleigh Kirbach
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Tara Wilmot
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Andrew C Heath
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Samuel Klein
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
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14
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Patnode ML, Guruge JL, Castillo JJ, Couture GA, Lombard V, Terrapon N, Henrissat B, Lebrilla CB, Gordon JI. Strain-level functional variation in the human gut microbiota based on bacterial binding to artificial food particles. Cell Host Microbe 2021; 29:664-673.e5. [PMID: 33571448 DOI: 10.1016/j.chom.2021.01.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 09/08/2020] [Revised: 12/07/2020] [Accepted: 01/18/2021] [Indexed: 01/26/2023]
Abstract
Greater understanding of the spatial relationships between members of the human gut microbiota and available nutrients is needed to gain deeper insights about community dynamics and expressed functions. Therefore, we generated a panel of artificial food particles with each type composed of microscopic paramagnetic beads coated with a fluorescent barcode and one of 60 different dietary or host glycan preparations. Analysis of 160 Bacteroides and Parabacteroides strains disclosed diverse strain-specific and glycan-specific binding phenotypes. We identified carbohydrate structures that correlated with binding by specific bacterial strains in vitro and noted strain-specific differences in the catabolism of glycans that mediate adhesion. Mixed in vitro cultures revealed that these adhesion phenotypes are maintained in more complex communities. Additionally, orally administering glycan beads to gnotobiotic mice confirmed specificity in glycan binding. This approach should facilitate analyses of how strains occupying the same physical niche interact, and it should advance the development of synbiotics, more nutritious foods, and microbiota-based diagnostics.
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Affiliation(s)
- Michael L Patnode
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Janaki L Guruge
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Juan J Castillo
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Garret A Couture
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, UMR7257 Centre National de la Recherche Scientifique and Aix-Marseille Université, USC1408 Institut National de la Recherche Agronomique, 13288 Marseille cedex 9, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, UMR7257 Centre National de la Recherche Scientifique and Aix-Marseille Université, USC1408 Institut National de la Recherche Agronomique, 13288 Marseille cedex 9, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR7257 Centre National de la Recherche Scientifique and Aix-Marseille Université, USC1408 Institut National de la Recherche Agronomique, 13288 Marseille cedex 9, France; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Jeffrey I Gordon
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA.
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15
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Aymé L, Hébert A, Henrissat B, Lombard V, Franche N, Perret S, Jourdier E, Heiss-Blanquet S. Characterization of three bacterial glycoside hydrolase family 9 endoglucanases with different modular architectures isolated from a compost metagenome. Biochim Biophys Acta Gen Subj 2021; 1865:129848. [PMID: 33460770 DOI: 10.1016/j.bbagen.2021.129848] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND Environmental bacteria express a wide diversity of glycoside hydrolases (GH). Screening and characterization of GH from metagenomic sources provides an insight into biomass degradation strategies of non-cultivated prokaryotes. METHODS In the present report, we screened a compost metagenome for lignocellulolytic activities and identified six genes encoding enzymes belonging to family GH9 (GH9a-f). Three of these enzymes (GH9b, GH9d and GH9e) were successfully expressed and characterized. RESULTS A phylogenetic analysis of the catalytic domain of pro- and eukaryotic GH9 enzymes suggested the existence of two major subgroups. Bacterial GH9s displayed a wide variety of modular architectures and those harboring an N-terminal Ig-like domain, such as GH9b and GH9d, segregated from the remainder. We purified and characterized GH9 endoglucanases from both subgroups and examined their stabilities, substrate specificities and product profiles. GH9e exhibited an original hydrolysis pattern, liberating an elevated proportion of oligosaccharides longer than cellobiose. All of the enzymes exhibited processive behavior and a synergistic action on crystalline cellulose. Synergy was also evidenced between GH9d and a GH48 enzyme identified from the same metagenome. CONCLUSIONS The characterized GH9 enzymes displayed different modular architectures and distinct substrate and product profiles. The presence of a cellulose binding domain was shown to be necessary for binding and digestion of insoluble cellulosic substrates, but not for processivity. GENERAL SIGNIFICANCE The identification of six GH9 enzymes from a compost metagenome and the functional variety of three characterized members highlight the importance of this enzyme family in bacterial biomass deconstruction.
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Affiliation(s)
- Laure Aymé
- IFP Energies Nouvelles, 1 - 4 avenue du Bois-Préau, 92852 Rueil-Malmaison, France
| | - Agnès Hébert
- IFP Energies Nouvelles, 1 - 4 avenue du Bois-Préau, 92852 Rueil-Malmaison, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, 163 avenue de Luminy, 13288 Aix Marseille Université, Marseille, France; INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), 163 avenue de Luminy, 13288 Marseille, France; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, 163 avenue de Luminy, 13288 Aix Marseille Université, Marseille, France; INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), 163 avenue de Luminy, 13288 Marseille, France
| | - Nathalie Franche
- Aix Marseille Université, CNRS, LCB, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Stéphanie Perret
- Aix Marseille Université, CNRS, LCB, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Etienne Jourdier
- IFP Energies Nouvelles, 1 - 4 avenue du Bois-Préau, 92852 Rueil-Malmaison, France
| | - Senta Heiss-Blanquet
- IFP Energies Nouvelles, 1 - 4 avenue du Bois-Préau, 92852 Rueil-Malmaison, France.
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16
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Lafond M, Tauzin AS, Bruel L, Laville E, Lombard V, Esque J, André I, Vidal N, Pompeo F, Quinson N, Perrier J, Fons M, Potocki-Veronese G, Giardina T. α-Galactosidase and Sucrose-Kinase Relationships in a Bi-functional AgaSK Enzyme Produced by the Human Gut Symbiont Ruminococcus gnavus E1. Front Microbiol 2020; 11:579521. [PMID: 33281771 PMCID: PMC7688924 DOI: 10.3389/fmicb.2020.579521] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/19/2020] [Indexed: 12/31/2022] Open
Abstract
Plant α-galactosides belonging to the raffinose family oligosaccharides (RFOs) and considered as prebiotics, are commonly degraded by α-galactosidases produced by the human gut microbiome. In this environment, the Ruminococcus gnavus E1 symbiont-well-known for various benefit-is able to produce an original RgAgaSK bifunctional enzyme. This enzyme contains an hydrolytic α-galactosidase domain linked to an ATP dependent extra-domain, specifically involved in the α-galactoside hydrolysis and the phosphorylation of the glucose, respectively. However, the multi-modular relationships between both catalytic domains remained hitherto unexplored and has been, consequently, herein investigated. Biochemical characterization of heterologously expressed enzymes either in full-form or in separated domains revealed similar kinetic parameters. These results were supported by molecular modeling studies performed on the whole enzyme in complex with different RFOs. Further enzymatic analysis associated with kinetic degradation of various substrates followed by high pressure anionic exchange chromatography revealed that catalytic efficiency decreased as the number of D-galactosyl moieties branched onto the oligosaccharide increased, suggesting a preference of RgAgaSK for RFO's short chains. A wide prevalence and abundance study on a human metagenomic library showed a high prevalence of the RgAgaSK encoding gene whatever the health status of the individuals. Finally, phylogeny and synteny studies suggested a limited spread by horizontal transfer of the clusters' containing RgAgaSK to only few species of Firmicutes, highlighting the importance of these undispersed tandem activities in the human gut microbiome.
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Affiliation(s)
- Mickael Lafond
- Aix-Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | | | - Laetitia Bruel
- Aix-Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | | | | | - Jérémy Esque
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Isabelle André
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Nicolas Vidal
- Yelen Analytics, Aix-Marseille Université, ICR, Marseille, France
| | | | - Nathalie Quinson
- Aix-Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Josette Perrier
- Aix-Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Michel Fons
- Aix-Marseille Université, CNRS, IMM, BIP, Marseille, France
| | | | - Thierry Giardina
- Aix-Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
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17
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Tauzin AS, Pereira MR, Van Vliet LD, Colin PY, Laville E, Esque J, Laguerre S, Henrissat B, Terrapon N, Lombard V, Leclerc M, Doré J, Hollfelder F, Potocki-Veronese G. Investigating host-microbiome interactions by droplet based microfluidics. Microbiome 2020; 8:141. [PMID: 33004077 PMCID: PMC7531118 DOI: 10.1186/s40168-020-00911-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [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: 03/27/2020] [Accepted: 08/23/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Despite the importance of the mucosal interface between microbiota and the host in gut homeostasis, little is known about the mechanisms of bacterial gut colonization, involving foraging for glycans produced by epithelial cells. The slow pace of progress toward understanding the underlying molecular mechanisms is largely due to the lack of efficient discovery tools, especially those targeting the uncultured fraction of the microbiota. RESULTS Here, we introduce an ultra-high-throughput metagenomic approach based on droplet microfluidics, to screen fosmid libraries. Thousands of bacterial genomes can be covered in 1 h of work, with less than ten micrograms of substrate. Applied to the screening of the mucosal microbiota for β-N-acetylgalactosaminidase activity, this approach allowed the identification of pathways involved in the degradation of human gangliosides and milk oligosaccharides, the structural homologs of intestinal mucin glycans. These pathways, whose prevalence is associated with inflammatory bowel diseases, could be the result of horizontal gene transfers with Bacteroides species. Such pathways represent novel targets to study the microbiota-host interactions in the context of inflammatory bowel diseases, in which the integrity of the mucosal barrier is impaired. CONCLUSION By compartmentalizing experiments inside microfluidic droplets, this method speeds up and miniaturizes by several orders of magnitude the screening process compared to conventional approaches, to capture entire metabolic pathways from metagenomic libraries. The method is compatible with all types of (meta)genomic libraries, and employs a commercially available flow cytometer instead of a custom-made sorting system to detect intracellular or extracellular enzyme activities. This versatile and generic workflow will accelerate experimental exploration campaigns in functional metagenomics and holobiomics studies, to further decipher host-microbiota relationships. Video Abstract.
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Affiliation(s)
- Alexandra S Tauzin
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Mariana Rangel Pereira
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- CAPES Foundation, Ministry of Education of Brazil, BrasÍlia, DF, 70040-020, Brazil
| | - Liisa D Van Vliet
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Drop-Tech, Canterbury Court, Cambridge, CB4 3QU, UK
| | - Pierre-Yves Colin
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Elisabeth Laville
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Jeremy Esque
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Sandrine Laguerre
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Bernard Henrissat
- CNRS, UMR 7257, Aix-Marseille Université, F-13288, Marseille, France
- USC 1408 AFMB, INRAE, F-13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nicolas Terrapon
- CNRS, UMR 7257, Aix-Marseille Université, F-13288, Marseille, France
- USC 1408 AFMB, INRAE, F-13288, Marseille, France
| | - Vincent Lombard
- CNRS, UMR 7257, Aix-Marseille Université, F-13288, Marseille, France
- USC 1408 AFMB, INRAE, F-13288, Marseille, France
| | - Marion Leclerc
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, F-78350, Jouy-en-Josas, France
| | - Joël Doré
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, F-78350, Jouy-en-Josas, France
- Metagenopolis, INRAE, F-78350, Jouy-en-Josas, France
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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18
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Li A, Laville E, Tarquis L, Lombard V, Ropartz D, Terrapon N, Henrissat B, Guieysse D, Esque J, Durand J, Morgavi DP, Potocki-Veronese G. Analysis of the diversity of the glycoside hydrolase family 130 in mammal gut microbiomes reveals a novel mannoside-phosphorylase function. Microb Genom 2020; 6:mgen000404. [PMID: 32667876 PMCID: PMC7660257 DOI: 10.1099/mgen.0.000404] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/20/2020] [Indexed: 12/04/2022] Open
Abstract
Mannoside phosphorylases are involved in the intracellular metabolization of mannooligosaccharides, and are also useful enzymes for the in vitro synthesis of oligosaccharides. They are found in glycoside hydrolase family GH130. Here we report on an analysis of 6308 GH130 sequences, including 4714 from the human, bovine, porcine and murine microbiomes. Using sequence similarity networks, we divided the diversity of sequences into 15 mostly isofunctional meta-nodes; of these, 9 contained no experimentally characterized member. By examining the multiple sequence alignments in each meta-node, we predicted the determinants of the phosphorolytic mechanism and linkage specificity. We thus hypothesized that eight uncharacterized meta-nodes would be phosphorylases. These sequences are characterized by the absence of signal peptides and of the catalytic base. Those sequences with the conserved E/K, E/R and Y/R pairs of residues involved in substrate binding would target β-1,2-, β-1,3- and β-1,4-linked mannosyl residues, respectively. These predictions were tested by characterizing members of three of the uncharacterized meta-nodes from gut bacteria. We discovered the first known β-1,4-mannosyl-glucuronic acid phosphorylase, which targets a motif of the Shigella lipopolysaccharide O-antigen. This work uncovers a reliable strategy for the discovery of novel mannoside-phosphorylases, reveals possible interactions between gut bacteria, and identifies a biotechnological tool for the synthesis of antigenic oligosaccharides.
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Affiliation(s)
- Ao Li
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31077 Toulouse, France
| | - Elisabeth Laville
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31077 Toulouse, France
| | - Laurence Tarquis
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31077 Toulouse, France
| | - Vincent Lombard
- AFMB, UMR 7257 CNRS, Aix-Marseille Université, F-13288 Marseille, France
- INRAE, USC 1408 AFMB, F-13288 Marseille, France
| | - David Ropartz
- INRAE, UR BIA, F-44316 Nantes, France
- INRAE, BIBS facility, F-44316 Nantes, France
| | - Nicolas Terrapon
- AFMB, UMR 7257 CNRS, Aix-Marseille Université, F-13288 Marseille, France
- INRAE, USC 1408 AFMB, F-13288 Marseille, France
| | - Bernard Henrissat
- AFMB, UMR 7257 CNRS, Aix-Marseille Université, F-13288 Marseille, France
- INRAE, USC 1408 AFMB, F-13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - David Guieysse
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31077 Toulouse, France
| | - Jeremy Esque
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31077 Toulouse, France
| | - Julien Durand
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31077 Toulouse, France
| | - Diego P. Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
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19
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Hagen LH, Brooke CG, Shaw CA, Norbeck AD, Piao H, Arntzen MØ, Olson HM, Copeland A, Isern N, Shukla A, Roux S, Lombard V, Henrissat B, O'Malley MA, Grigoriev IV, Tringe SG, Mackie RI, Pasa-Tolic L, Pope PB, Hess M. Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber. ISME J 2020; 15:421-434. [PMID: 32929206 PMCID: PMC8026616 DOI: 10.1038/s41396-020-00769-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 08/21/2020] [Accepted: 09/02/2020] [Indexed: 12/17/2022]
Abstract
The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa, and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 h in nylon bags within the rumen of cannulated dairy cows. Across a gene catalog covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of hemicelluloses, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8, and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggest that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.
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Affiliation(s)
- Live H Hagen
- Faculty of Biotechnology, Chemistry and Food Science, Norwegian University of Life Sciences, Aas, Norway.
| | | | | | | | - Hailan Piao
- Washington State University, Richland, WA, USA
| | - Magnus Ø Arntzen
- Faculty of Biotechnology, Chemistry and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Heather M Olson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, CA, USA
| | - Alex Copeland
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nancy Isern
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, CA, USA
| | - Anil Shukla
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Simon Roux
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vincent Lombard
- CNRS, UMR 7257, Université Aix-Marseille, 13288, Marseille, France.,Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, 13288, Marseille, France
| | - Bernard Henrissat
- CNRS, UMR 7257, Université Aix-Marseille, 13288, Marseille, France.,Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, 13288, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Susannah G Tringe
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Roderick I Mackie
- Department of Animal Science, University of Illinois, Urbana-Champaign, IL, USA
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, CA, USA
| | - Phillip B Pope
- Faculty of Biotechnology, Chemistry and Food Science, Norwegian University of Life Sciences, Aas, Norway.,Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
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20
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Li J, Zhong H, Ramayo-Caldas Y, Terrapon N, Lombard V, Potocki-Veronese G, Estellé J, Popova M, Yang Z, Zhang H, Li F, Tang S, Yang F, Chen W, Chen B, Li J, Guo J, Martin C, Maguin E, Xu X, Yang H, Wang J, Madsen L, Kristiansen K, Henrissat B, Ehrlich SD, Morgavi DP. A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment. Gigascience 2020; 9:5849033. [PMID: 32473013 PMCID: PMC7260996 DOI: 10.1093/gigascience/giaa057] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 11/07/2019] [Accepted: 05/06/2020] [Indexed: 01/10/2023] Open
Abstract
Background The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen. Results Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig, and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only <0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e., 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes, which explains the great adaptability of cattle to rapidly adjust to dietary changes. Conclusions These data bring new insights into functions, carbohydrate-degrading enzymes, and microbes of the rumen to complement the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data are made available.
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Affiliation(s)
- Junhua Li
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Huanzi Zhong
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Yuliaxis Ramayo-Caldas
- INRAE, Génétique Animale et Biologie Intégrative, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.,Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes de Montbui 08140, Spain
| | - Nicolas Terrapon
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRAE, USC 1408 AFMB, 13288 Marseille, France
| | - Vincent Lombard
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRAE, USC 1408 AFMB, 13288 Marseille, France
| | | | - Jordi Estellé
- INRAE, Génétique Animale et Biologie Intégrative, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Milka Popova
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès Champanelle, France
| | - Ziyi Yang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Hui Zhang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Fang Li
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Shanmei Tang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Fangming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing 101408, China
| | | | - Bing Chen
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Jiyang Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jing Guo
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Cécile Martin
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès Champanelle, France
| | - Emmanuelle Maguin
- INRAE, Micalis Institute, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Lise Madsen
- BGI-Shenzhen, Shenzhen 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark.,Institute of Marine Research (IMR), Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRAE, USC 1408 AFMB, 13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Stanislav D Ehrlich
- BGI-Shenzhen, Shenzhen 518083, China.,MGP MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy en Josas, France.,Centre for Host Microbiome Interactions, Dental Institute, King's College London, London, UK
| | - Diego P Morgavi
- BGI-Shenzhen, Shenzhen 518083, China.,Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès Champanelle, France
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21
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Strazzulli A, Cobucci-Ponzano B, Iacono R, Giglio R, Maurelli L, Curci N, Schiano-di-Cola C, Santangelo A, Contursi P, Lombard V, Henrissat B, Lauro FM, Fontes CMGA, Moracci M. Discovery of hyperstable carbohydrate-active enzymes through metagenomics of extreme environments. FEBS J 2019; 287:1116-1137. [PMID: 31595646 DOI: 10.1111/febs.15080] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 05/24/2019] [Revised: 07/23/2019] [Accepted: 10/01/2019] [Indexed: 12/11/2022]
Abstract
The enzymes from hyperthermophilic microorganisms populating volcanic sites represent interesting cases of protein adaptation and biotransformations under conditions where conventional enzymes quickly denature. The difficulties in cultivating extremophiles severely limit access to this class of biocatalysts. To circumvent this problem, we embarked on the exploration of the biodiversity of the solfatara Pisciarelli, Agnano (Naples, Italy), to discover hyperthermophilic carbohydrate-active enzymes (CAZymes) and to characterize the entire set of such enzymes in this environment (CAZome). Here, we report the results of the metagenomic analysis of two mud/water pools that greatly differ in both temperature and pH (T = 85 °C and pH 5.5; T = 92 °C and pH 1.5, for Pool1 and Pool2, respectively). DNA deep sequencing and following in silico analysis led to 14 934 and 17 652 complete ORFs in Pool1 and Pool2, respectively. They exclusively belonged to archaeal cells and viruses with great genera variance within the phylum Crenarchaeota, which reflected the difference in temperature and pH of the two Pools. Surprisingly, 30% and 62% of all of the reads obtained from Pool1 and 2, respectively, had no match in nucleotide databanks. Genes associated with carbohydrate metabolism were 15% and 16% of the total in the two Pools, with 278 and 308 putative CAZymes in Pool1 and 2, corresponding to ~ 2.0% of all ORFs. Biochemical characterization of two CAZymes of a previously unknown archaeon revealed a novel subfamily GH5_19 β-mannanase/β-1,3-glucanase whose hemicellulose specificity correlates with the vegetation surrounding the sampling site, and a novel NAD+ -dependent GH109 with a previously unreported β-N-acetylglucosaminide/β-glucoside specificity. DATABASES: The sequencing reads are available in the NCBI Sequence Read Archive (SRA) database under the accession numbers SRR7545549 (Pool1) and SRR7545550 (Pool2). The sequences of GH5_Pool2 and GH109_Pool2 are available in GenBank database under the accession numbers MK869723 and MK86972, respectively. The environmental data relative to Pool1 and Pool2 (NCBI BioProject PRJNA481947) are available in the Biosamples database under the accession numbers SAMN09692669 (Pool1) and SAMN09692670 (Pool2).
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Affiliation(s)
- Andrea Strazzulli
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Italy
| | | | - Roberta Iacono
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy.,Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Rosa Giglio
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Luisa Maurelli
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Nicola Curci
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy.,Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Corinna Schiano-di-Cola
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Annalisa Santangelo
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Patrizia Contursi
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Italy
| | - Vincent Lombard
- Centre National de la Recherche Scientifique, INRA, AFMB, USC 1408, Aix Marseille Univ, France
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique, INRA, AFMB, USC 1408, Aix Marseille Univ, France.,Department Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Federico M Lauro
- Asian School of the Environment, Nanyang Technological University, Singapore City, Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore City, Singapore
| | - Carlos M G A Fontes
- NZYTech LDA, Estrada Do Paco Do Lumiar, Lisbon, Portugal.,CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Portugal
| | - Marco Moracci
- Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Italy.,Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
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22
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Viborg AH, Terrapon N, Lombard V, Michel G, Czjzek M, Henrissat B, Brumer H. A subfamily roadmap of the evolutionarily diverse glycoside hydrolase family 16 (GH16). J Biol Chem 2019; 294:15973-15986. [PMID: 31501245 PMCID: PMC6827312 DOI: 10.1074/jbc.ra119.010619] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/05/2019] [Indexed: 12/12/2022] Open
Abstract
Glycoside hydrolase family (GH) 16 comprises a large and taxonomically diverse family of glycosidases and transglycosidases that adopt a common β-jelly-roll fold and are active on a range of terrestrial and marine polysaccharides. Presently, broadly insightful sequence–function correlations in GH16 are hindered by a lack of a systematic subfamily structure. To fill this gap, we have used a highly scalable protein sequence similarity network analysis to delineate nearly 23,000 GH16 sequences into 23 robust subfamilies, which are strongly supported by hidden Markov model and maximum likelihood molecular phylogenetic analyses. Subsequent evaluation of over 40 experimental three-dimensional structures has highlighted key tertiary structural differences, predominantly manifested in active-site loops, that dictate substrate specificity across the GH16 evolutionary landscape. As for other large GH families (i.e. GH5, GH13, and GH43), this new subfamily classification provides a roadmap for functional glycogenomics that will guide future bioinformatics and experimental structure–function analyses. The GH16 subfamily classification is publicly available in the CAZy database. The sequence similarity network workflow used here, SSNpipe, is freely available from GitHub.
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Affiliation(s)
- Alexander Holm Viborg
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France.,USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France.,USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France
| | - Gurvan Michel
- Sorbonne Universités, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Mirjam Czjzek
- Sorbonne Universités, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France .,USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada .,Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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23
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Terrapon N, Lombard V, Drula É, Lapébie P, Al-Masaudi S, Gilbert HJ, Henrissat B. PULDB: the expanded database of Polysaccharide Utilization Loci. Nucleic Acids Res 2019; 46:D677-D683. [PMID: 29088389 PMCID: PMC5753385 DOI: 10.1093/nar/gkx1022] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [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: 09/17/2017] [Accepted: 10/25/2017] [Indexed: 12/12/2022] Open
Abstract
The Polysaccharide Utilization Loci (PUL) database was launched in 2015 to present PUL predictions in ∼70 Bacteroidetes species isolated from the human gastrointestinal tract, as well as PULs derived from the experimental data reported in the literature. In 2018 PULDB offers access to 820 genomes, sampled from various environments and covering a much wider taxonomical range. A Krona dynamic chart was set up to facilitate browsing through taxonomy. Literature surveys now allows the presentation of the most recent (i) PUL repertoires deduced from RNAseq large-scale experiments, (ii) PULs that have been subjected to in-depth biochemical analysis and (iii) new Carbohydrate-Active enzyme (CAZyme) families that contributed to the refinement of PUL predictions. To improve PUL visualization and genome browsing, the previous annotation of genes encoding CAZymes, regulators, integrases and SusCD has now been expanded to include functionally relevant protein families whose genes are significantly found in the vicinity of PULs: sulfatases, proteases, ROK repressors, epimerases and ATP-Binding Cassette and Major Facilitator Superfamily transporters. To cope with cases where susCD may be absent due to incomplete assemblies/split PULs, we present ‘CAZyme cluster’ predictions. Finally, a PUL alignment tool, operating on the tagged families instead of amino-acid sequences, was integrated to retrieve PULs similar to a query of interest. The updated PULDB website is accessible at www.cazy.org/PULDB_new/
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Affiliation(s)
- Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France.,USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France.,USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France
| | - Élodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France.,USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France
| | - Pascal Lapébie
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France.,USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France
| | - Saad Al-Masaudi
- Department of Biological Sciences, King Abdulaziz University, 23218 Jeddah, Saudi Arabia
| | - Harry J Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France.,USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, 23218 Jeddah, Saudi Arabia
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Lapébie P, Lombard V, Drula E, Terrapon N, Henrissat B. Bacteroidetes use thousands of enzyme combinations to break down glycans. Nat Commun 2019; 10:2043. [PMID: 31053724 PMCID: PMC6499787 DOI: 10.1038/s41467-019-10068-5] [Citation(s) in RCA: 199] [Impact Index Per Article: 39.8] [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: 10/09/2018] [Accepted: 04/18/2019] [Indexed: 01/21/2023] Open
Abstract
Unlike proteins, glycan chains are not directly encoded by DNA, but by the specificity of the enzymes that assemble them. Theoretical calculations have proposed an astronomical number of possible isomers (> 1012 hexasaccharides) but the actual diversity of glycan structures in nature is not known. Bacteria of the Bacteroidetes phylum are considered primary degraders of polysaccharides and they are found in all ecosystems investigated. In Bacteroidetes genomes, carbohydrate-degrading enzymes (CAZymes) are arranged in gene clusters termed polysaccharide utilization loci (PULs). The depolymerization of a given complex glycan by Bacteroidetes PULs requires bespoke enzymes; conversely, the enzyme composition in PULs can provide information on the structure of the targeted glycans. Here we group the 13,537 PULs encoded by 964 Bacteroidetes genomes according to their CAZyme composition. We find that collectively Bacteroidetes have elaborated a few thousand enzyme combinations for glycan breakdown, suggesting a global estimate of diversity of glycan structures much smaller than the theoretical one. Bacteroidetes genomes contain polysaccharide utilization loci (PULs), each of which encodes enzymes for the breakdown of one particular glycan. By analyzing the enzyme composition of 13,537 PULs, the authors suggest that the natural glycan diversity is orders of magnitude lower than previously proposed.
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Affiliation(s)
- Pascal Lapébie
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS, UMR7257), Institut National Agronomique (INRA, USC 1408) and Aix-Marseille Université (AMU), 13288 Marseille cedex 9, Marseille, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS, UMR7257), Institut National Agronomique (INRA, USC 1408) and Aix-Marseille Université (AMU), 13288 Marseille cedex 9, Marseille, France
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS, UMR7257), Institut National Agronomique (INRA, USC 1408) and Aix-Marseille Université (AMU), 13288 Marseille cedex 9, Marseille, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS, UMR7257), Institut National Agronomique (INRA, USC 1408) and Aix-Marseille Université (AMU), 13288 Marseille cedex 9, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS, UMR7257), Institut National Agronomique (INRA, USC 1408) and Aix-Marseille Université (AMU), 13288 Marseille cedex 9, Marseille, France. .,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
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25
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Al-Masaudi S, El Kaoutari A, Drula E, Redwan EM, Lombard V, Henrissat B. A metagenomics investigation of carbohydrate-active enzymes along the goat and camel intestinal tract. Int Microbiol 2019; 22:429-435. [PMID: 30875036 DOI: 10.1007/s10123-019-00068-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 10/24/2018] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 12/14/2022]
Abstract
Studies of the digestive microbiota of ruminant animals most often focus on the bacterial diversity in the rumen or the feces of the animals, but little is known about the diversity and functions of their distal intestine. Here, the bacterial microbiota of the distal intestinal tract of two goats and two camels was investigated by metagenomics techniques. The bacterial taxonomic diversity and carbohydrate-active enzyme profile were estimated for samples taken from the small intestine, the large intestine, and the rectum of each animal. The bacterial diversity and abundance in the small intestine were lower than in the rectal and large intestinal samples. Analysis of the carbohydrate-active enzyme profiles at each site revealed a comparatively low abundance of enzymes targeting xylan and cellulose in all animals examined, similar to what has been reported earlier for sheep and therefore suggesting that plant cell wall digestion probably takes place elsewhere, such as in the rumen.
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Affiliation(s)
- Saad Al-Masaudi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdessamad El Kaoutari
- Marseille Cancer Research Center, Institut Paoli-Calmettes, INSERM, CNRS, Aix-Marseille University, Marseille, France
| | - Elodie Drula
- CNRS UMR 7257, Aix-Marseille University, 13288, Marseille, France
- INRA, USC 1408 AFMB, 13288, Marseille, France
| | - Elrashdy M Redwan
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vincent Lombard
- CNRS UMR 7257, Aix-Marseille University, 13288, Marseille, France
- INRA, USC 1408 AFMB, 13288, Marseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
- CNRS UMR 7257, Aix-Marseille University, 13288, Marseille, France.
- INRA, USC 1408 AFMB, 13288, Marseille, France.
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26
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Liang X, Whitham JM, Holwerda EK, Shao X, Tian L, Wu YW, Lombard V, Henrissat B, Klingeman DM, Yang ZK, Podar M, Richard TL, Elkins JG, Brown SD, Lynd LR. Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times. Biotechnol Biofuels 2018; 11:243. [PMID: 30202438 PMCID: PMC6126044 DOI: 10.1186/s13068-018-1238-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Anaerobic fermentation of lignocellulose occurs in both natural and managed environments, and is an essential part of the carbon cycle as well as a promising route to sustainable production of fuels and chemicals. Lignocellulose solubilization by mixed microbiomes is important in these contexts. RESULTS Here, we report the development of stable switchgrass-fermenting enrichment cultures maintained at various residence times and moderately high (55 °C) temperatures. Anaerobic microbiomes derived from a digester inoculum were incubated at 55 °C and fed semi-continuously with medium containing 30 g/L mid-season harvested switchgrass to achieve residence times (RT) of 20, 10, 5, and 3.3 days. Stable, time-invariant cellulolytic methanogenic cultures with minimal accumulation of organic acids were achieved for all RTs. Fractional carbohydrate solubilization was 0.711, 0.654, 0.581 and 0.538 at RT = 20, 10, 5 and 3.3 days, respectively, and glucan solubilization was proportional to xylan solubilization at all RTs. The rate of solubilization was described well by the equation r = k(C - C0fr), where C represents the concentration of unutilized carbohydrate, C0 is the concentration of carbohydrate (cellulose and hemicellulose) entering the bioreactor and fr is the extrapolated fraction of entering carbohydrate that is recalcitrant at infinite residence time. The 3.3 day RT is among the shortest RT reported for stable thermophilic, methanogenic digestion of a lignocellulosic feedstock. 16S rDNA phylotyping and metagenomic analyses were conducted to characterize the effect of RT on community dynamics and to infer functional roles in the switchgrass to biogas conversion to the various microbial taxa. Firmicutes were the dominant phylum, increasing in relative abundance from 54 to 96% as RT decreased. A Clostridium clariflavum strain with genetic markers for xylose metabolism was the most abundant lignocellulose-solubilizing bacterium. A Thermotogae (Defluviitoga tunisiensis) was the most abundant bacterium in switchgrass digesters at RT = 20 days but decreased in abundance at lower RTs as did multiple Chloroflexi. Synergistetes and Euryarchaeota were present at roughly constant levels over the range of RTs examined. CONCLUSIONS A system was developed in which stable methanogenic steady-states were readily obtained with a particulate biomass feedstock, mid-season switchgrass, at laboratory (1 L) scale. Characterization of the extent and rate of carbohydrate solubilization in combination with 16S rDNA and metagenomic sequencing provides a multi-dimensional view of performance, species composition, glycoside hydrolases, and metabolic function with varying residence time. These results provide a point of reference and guidance for future studies and organism development efforts involving defined cultures.
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Affiliation(s)
- Xiaoyu Liang
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- BioEnergy Sciences Center, Oak Ridge, TN 37830 USA
| | - Jason M. Whitham
- BioEnergy Sciences Center, Oak Ridge, TN 37830 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Evert K. Holwerda
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- BioEnergy Sciences Center, Oak Ridge, TN 37830 USA
| | - Xiongjun Shao
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- BioEnergy Sciences Center, Oak Ridge, TN 37830 USA
| | - Liang Tian
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- BioEnergy Sciences Center, Oak Ridge, TN 37830 USA
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, 106 Taiwan
| | - Vincent Lombard
- CNRS, UMR 7257, Aix-Marseille University, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Bernard Henrissat
- CNRS, UMR 7257, Aix-Marseille University, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Dawn M. Klingeman
- BioEnergy Sciences Center, Oak Ridge, TN 37830 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Zamin K. Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Tom L. Richard
- Department of Agricultural and Biological Engineering, The Pennsylvania State University, University Park, State College, PA 16802 USA
| | - James G. Elkins
- BioEnergy Sciences Center, Oak Ridge, TN 37830 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Steven D. Brown
- BioEnergy Sciences Center, Oak Ridge, TN 37830 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- Present Address: LanzaTech, Inc., Skokie, IL 60077 USA
| | - Lee R. Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
- BioEnergy Sciences Center, Oak Ridge, TN 37830 USA
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Schoville SD, Chen YH, Andersson MN, Benoit JB, Bhandari A, Bowsher JH, Brevik K, Cappelle K, Chen MJM, Childers AK, Childers C, Christiaens O, Clements J, Didion EM, Elpidina EN, Engsontia P, Friedrich M, García-Robles I, Gibbs RA, Goswami C, Grapputo A, Gruden K, Grynberg M, Henrissat B, Jennings EC, Jones JW, Kalsi M, Khan SA, Kumar A, Li F, Lombard V, Ma X, Martynov A, Miller NJ, Mitchell RF, Munoz-Torres M, Muszewska A, Oppert B, Palli SR, Panfilio KA, Pauchet Y, Perkin LC, Petek M, Poelchau MF, Record É, Rinehart JP, Robertson HM, Rosendale AJ, Ruiz-Arroyo VM, Smagghe G, Szendrei Z, Thomas GWC, Torson AS, Vargas Jentzsch IM, Weirauch MT, Yates AD, Yocum GD, Yoon JS, Richards S. A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). Sci Rep 2018; 8:1931. [PMID: 29386578 PMCID: PMC5792627 DOI: 10.1038/s41598-018-20154-1] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/13/2018] [Indexed: 01/04/2023] Open
Abstract
The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.
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Affiliation(s)
- Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, USA.
| | - Yolanda H Chen
- Department of Plant and Soil Sciences, University of Vermont, Burlington, USA
| | | | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, USA
| | - Anita Bhandari
- Department of Molecular Physiology, Christian-Albrechts-University at Kiel, Kiel, Germany
| | - Julia H Bowsher
- Department of Biological Sciences, North Dakota State University, Fargo, USA
| | - Kristian Brevik
- Department of Plant and Soil Sciences, University of Vermont, Burlington, USA
| | - Kaat Cappelle
- Department of Crop Protection, Ghent University, Ghent, Belgium
| | - Mei-Ju M Chen
- USDA-ARS National Agricultural Library, Beltsville, MD, USA
| | - Anna K Childers
- USDA-ARS Bee Research Lab, Beltsville, MD, USA
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA
| | | | | | - Justin Clements
- Department of Entomology, University of Wisconsin-Madison, Madison, USA
| | - Elise M Didion
- Department of Biological Sciences, University of Cincinnati, Cincinnati, USA
| | - Elena N Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moskva, Russia
| | - Patamarerk Engsontia
- Department of Biology, Faculty of Science, Prince of Songkla University, Amphoe Hat Yai, Thailand
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, USA
| | | | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Chandan Goswami
- National Institute of Science Education and Research, Bhubaneswar, India
| | | | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Marcin Grynberg
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288, Marseille, France
- INRA, USC 1408 AFMB, F-13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, King Abdulaziz, Saudi Arabia
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, USA
| | - Megha Kalsi
- Department of Entomology, University of Kentucky, Lexington, USA
| | - Sher A Khan
- Department of Entomology, Texas A&M University, College Station, USA
| | - Abhishek Kumar
- Department of Genetics & Molecular Biology in Botany, Christian-Albrechts-University at Kiel, Kiel, Germany
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Fei Li
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288, Marseille, France
- INRA, USC 1408 AFMB, F-13288, Marseille, France
| | - Xingzhou Ma
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Alexander Martynov
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Nicholas J Miller
- Department of Biology, Illinois Institute of Technology, Chicago, USA
| | - Robert F Mitchell
- Department of Biology, University of Wisconsin-Oshkosh, Oshkosh, USA
| | - Monica Munoz-Torres
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Brenda Oppert
- USDA-ARS Center for Grain and Animal Health Research, New York, USA
| | | | - Kristen A Panfilio
- Institute for Developmental Biology, University of Cologne, Köln, Germany
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, England, UK
| | - Yannick Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Lindsey C Perkin
- USDA-ARS Center for Grain and Animal Health Research, New York, USA
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - Éric Record
- INRA, Aix-Marseille Université, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Joseph P Rinehart
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, USA
| | | | - Guy Smagghe
- Department of Crop Protection, Ghent University, Ghent, Belgium
| | - Zsofia Szendrei
- Department of Entomology, Michigan State University, East Lansing, USA
| | - Gregg W C Thomas
- Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, USA
| | - Alex S Torson
- Department of Biological Sciences, North Dakota State University, Fargo, USA
| | | | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, USA
| | - Ashley D Yates
- Department of Entomology, The Ohio State University, Columbus, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, USA
| | - George D Yocum
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA
| | - June-Sun Yoon
- Department of Entomology, University of Kentucky, Lexington, USA
| | - Stephen Richards
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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Wong MT, Wang W, Couturier M, Razeq FM, Lombard V, Lapebie P, Edwards EA, Terrapon N, Henrissat B, Master ER. Comparative Metagenomics of Cellulose- and Poplar Hydrolysate-Degrading Microcosms from Gut Microflora of the Canadian Beaver ( Castor canadensis) and North American Moose ( Alces americanus) after Long-Term Enrichment. Front Microbiol 2017; 8:2504. [PMID: 29326667 PMCID: PMC5742341 DOI: 10.3389/fmicb.2017.02504] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/01/2017] [Indexed: 11/13/2022] Open
Abstract
To identify carbohydrate-active enzymes (CAZymes) that might be particularly relevant for wood fiber processing, we performed a comparative metagenomic analysis of digestive systems from Canadian beaver (Castor canadensis) and North American moose (Alces americanus) following 3 years of enrichment on either microcrystalline cellulose or poplar hydrolysate. In total, 9,386 genes encoding CAZymes and carbohydrate-binding modules (CBMs) were identified, with up to half predicted to originate from Firmicutes, Bacteroidetes, Chloroflexi, and Proteobacteria phyla, and up to 17% from unknown phyla. Both PCA and hierarchical cluster analysis distinguished the annotated glycoside hydrolase (GH) distributions identified herein, from those previously reported for grass-feeding mammals and herbivorous foragers. The CAZyme profile of moose rumen enrichments also differed from a recently reported moose rumen metagenome, most notably by the absence of GH13-appended dockerins. Consistent with substrate-driven convergence, CAZyme profiles from both poplar hydrolysate-fed cultures differed from cellulose-fed cultures, most notably by increased numbers of unique sequences belonging to families GH3, GH5, GH43, GH53, and CE1. Moreover, pairwise comparisons of moose rumen enrichments further revealed higher counts of GH127 and CE15 families in cultures fed with poplar hydrolysate. To expand our scope to lesser known carbohydrate-active proteins, we identified and compared multi-domain proteins comprising both a CBM and domain of unknown function (DUF) as well as proteins with unknown function within the 416 predicted polysaccharide utilization loci (PULs). Interestingly, DUF362, identified in iron-sulfur proteins, was consistently appended to CBM9; on the other hand, proteins with unknown function from PULs shared little identity unless from identical PULs. Overall, this study sheds new light on the lignocellulose degrading capabilities of microbes originating from digestive systems of mammals known for fiber-rich diets, and highlights the value of enrichment to select new CAZymes from metagenome sequences for future biochemical characterization.
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Affiliation(s)
- Mabel T Wong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Weijun Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Marie Couturier
- Centre de Recherches sur les Macromolécules Végétales - Université Grenoble Alpes, Grenoble, France.,Centre National de la Recherche Scientifique, Centre de Recherches sur les Macromolécules Végétales, Grenoble, France
| | - Fakhria M Razeq
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Marseille, France.,UMR 7257, Centre National de la Recherche Scientifique, Marseille, France
| | - Pascal Lapebie
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Marseille, France
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Marseille, France
| | - Bernard Henrissat
- UMR 7257, Centre National de la Recherche Scientifique, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada.,Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
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29
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Žifčáková L, Větrovský T, Lombard V, Henrissat B, Howe A, Baldrian P. Feed in summer, rest in winter: microbial carbon utilization in forest topsoil. Microbiome 2017; 5:122. [PMID: 28923122 PMCID: PMC5604414 DOI: 10.1186/s40168-017-0340-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [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: 08/16/2017] [Accepted: 09/12/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Evergreen coniferous forests contain high stocks of organic matter. Significant carbon transformations occur in litter and soil of these ecosystems, making them important for the global carbon cycle. Due to seasonal allocation of photosynthates to roots, carbon availability changes seasonally in the topsoil. The aim of this paper was to describe the seasonal differences in C source utilization and the involvement of various members of soil microbiome in this process. RESULTS Here, we show that microorganisms in topsoil encode a diverse set of carbohydrate-active enzymes, including glycoside hydrolases and auxiliary enzymes. While the transcription of genes encoding enzymes degrading reserve compounds, such as starch or trehalose, was high in soil in winter, summer was characterized by high transcription of ligninolytic and cellulolytic enzymes produced mainly by fungi. Fungi strongly dominated the transcription in litter and an equal contribution of bacteria and fungi was found in soil. The turnover of fungal biomass appeared to be faster in summer than in winter, due to high activity of enzymes targeting its degradation, indicating fast growth in both litter and soil. In each enzyme family, hundreds to thousands of genes were typically transcribed simultaneously. CONCLUSIONS Seasonal differences in the transcription of glycoside hydrolases and auxiliary enzyme genes are more pronounced in soil than in litter. Our results suggest that mainly fungi are involved in decomposition of recalcitrant biopolymers in summer, while bacteria replace them in this role in winter. Transcripts of genes encoding enzymes targeting plant biomass biopolymers, reserve compounds and fungal cell walls were especially abundant in the coniferous forest topsoil.
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Affiliation(s)
- Lucia Žifčáková
- Institute of Microbiology of the CAS, Vídeňská 1083, 14220 Praha 4, Czech Republic
- Faculty of Science, Charles University, Albertov 6, 128 43 Praha 2, Czech Republic
| | - Tomáš Větrovský
- Institute of Microbiology of the CAS, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Petr Baldrian
- Institute of Microbiology of the CAS, Vídeňská 1083, 14220 Praha 4, Czech Republic
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30
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Lenfant N, Hainaut M, Terrapon N, Drula E, Lombard V, Henrissat B. A bioinformatics analysis of 3400 lytic polysaccharide oxidases from family AA9. Carbohydr Res 2017; 448:166-174. [DOI: 10.1016/j.carres.2017.04.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/12/2017] [Accepted: 04/12/2017] [Indexed: 12/20/2022]
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Svartström O, Alneberg J, Terrapon N, Lombard V, de Bruijn I, Malmsten J, Dalin AM, El Muller E, Shah P, Wilmes P, Henrissat B, Aspeborg H, Andersson AF. Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation. ISME J 2017; 11:2538-2551. [PMID: 28731473 DOI: 10.1038/ismej.2017.108] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 05/05/2017] [Accepted: 05/30/2017] [Indexed: 12/25/2022]
Abstract
The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes and were overall overrepresented in the moose microbiome compared with other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci, which has never been reported before. The almost 100 CAZyme-annotated genomes reconstructed in this study provide an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries.
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Affiliation(s)
- Olov Svartström
- School of Biotechnology, Division of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Johannes Alneberg
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Nicolas Terrapon
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Vincent Lombard
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Ino de Bruijn
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Jonas Malmsten
- Department of Pathology and Wildlife Diseases, National Veterinary Institute, Uppsala, Sweden.,Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ann-Marie Dalin
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Emilie El Muller
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Pranjul Shah
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Henrik Aspeborg
- School of Biotechnology, Division of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anders F Andersson
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
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Cartmell A, Lowe EC, Baslé A, Firbank SJ, Ndeh DA, Murray H, Terrapon N, Lombard V, Henrissat B, Turnbull JE, Czjzek M, Gilbert HJ, Bolam DN. How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans. Proc Natl Acad Sci U S A 2017; 114:7037-7042. [PMID: 28630303 PMCID: PMC5502631 DOI: 10.1073/pnas.1704367114] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [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] [Indexed: 12/13/2022] Open
Abstract
The human microbiota, which plays an important role in health and disease, uses complex carbohydrates as a major source of nutrients. Utilization hierarchy indicates that the host glycosaminoglycans heparin (Hep) and heparan sulfate (HS) are high-priority carbohydrates for Bacteroides thetaiotaomicron, a prominent member of the human microbiota. The sulfation patterns of these glycosaminoglycans are highly variable, which presents a significant enzymatic challenge to the polysaccharide lyases and sulfatases that mediate degradation. It is possible that the bacterium recruits lyases with highly plastic specificities and expresses a repertoire of enzymes that target substructures of the glycosaminoglycans with variable sulfation or that the glycans are desulfated before cleavage by the lyases. To distinguish between these mechanisms, the components of the B. thetaiotaomicron Hep/HS degrading apparatus were analyzed. The data showed that the bacterium expressed a single-surface endo-acting lyase that cleaved HS, reflecting its higher molecular weight compared with Hep. Both Hep and HS oligosaccharides imported into the periplasm were degraded by a repertoire of lyases, with each enzyme displaying specificity for substructures within these glycosaminoglycans that display a different degree of sulfation. Furthermore, the crystal structures of a key surface glycan binding protein, which is able to bind both Hep and HS, and periplasmic sulfatases reveal the major specificity determinants for these proteins. The locus described here is highly conserved within the human gut Bacteroides, indicating that the model developed is of generic relevance to this important microbial community.
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Affiliation(s)
- Alan Cartmell
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Elisabeth C Lowe
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Susan J Firbank
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Didier A Ndeh
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Heath Murray
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France
- Institut National de la Recherche Agronomique, USC1408 Architecture et Fonction des Macromolécules Biologiques, F-13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jeremy E Turnbull
- Centre for Glycobiology, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Mirjam Czjzek
- Sorbonne Universités, Université Pierre-et-Marie-Curie, Université Paris 06, F-29688 Roscoff cedex, Bretagne, France
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff cedex, Bretagne, France
| | - Harry J Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - David N Bolam
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom;
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Al-Masaudi S, El Kaoutari A, Drula E, Al-Mehdar H, Redwan EM, Lombard V, Henrissat B. A Metagenomics Investigation of Carbohydrate-Active Enzymes along the Gastrointestinal Tract of Saudi Sheep. Front Microbiol 2017; 8:666. [PMID: 28473812 PMCID: PMC5397404 DOI: 10.3389/fmicb.2017.00666] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/31/2017] [Indexed: 12/16/2022] Open
Abstract
The digestive microbiota of humans and of a wide range of animals has recently become amenable to in-depth studies due to the emergence of DNA-based metagenomic techniques that do not require cultivation of gut microbes. These techniques are now commonly used to explore the feces of humans and animals under the assumption that such samples are faithful proxies for the intestinal microbiota. Sheep (Ovis aries) are ruminant animals particularly adapted to life in arid regions and in particular Najdi, Noaimi (Awassi), and Harrei (Harri) breeds that are raised in Saudi Arabia for milk and/or meat production. Here we report a metagenomics investigation of the distal digestive tract of one animal from each breed that (i) examines the microbiota at three intestinal subsites (small intestine, mid-colon, and rectum), (ii) performs an in-depth analysis of the carbohydrate-active enzymes genes encoded by the microbiota at the three subsites, and (iii) compares the microbiota and carbohydrate-active enzyme profile at the three subsites across the different breeds. For all animals we found that the small intestine is characterized by a lower taxonomic diversity than that of the large intestine and of the rectal samples. Mirroring this observation, we also find that the spectrum of encoded carbohydrate-active enzymes of the mid-colon and rectal sites is much richer than that of the small intestine. However, the number of encoded cellulases and xylanases in the various intestinal subsites was found to be surprisingly low, indicating that the bulk of the fiber digestion is performed upstream in the rumen, and that the carbon source for the intestinal flora is probably constituted of the rumen fungi and bacteria that pass in the intestines. In consequence we argue that ruminant feces, which are often analyzed for the search of microbial genes involved in plant cell wall degradation, are probably a poor proxy for the lignocellulolytic potential of the host.
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Affiliation(s)
- Saad Al-Masaudi
- Department of Biological Sciences, King Abdulaziz UniversityJeddah, Saudi Arabia
| | - Abdessamad El Kaoutari
- Marseille Cancer Research Center, Institut Paoli-Calmettes, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Aix-Marseille UniversityMarseille, France
| | - Elodie Drula
- Centre National de la Recherche Scientifique UMR 7257, Aix-Marseille UniversityMarseille, France.,INRA, USC 1408 AFMBMarseille, France
| | - Hussein Al-Mehdar
- Department of Biological Sciences, King Abdulaziz UniversityJeddah, Saudi Arabia
| | - Elrashdy M Redwan
- Department of Biological Sciences, King Abdulaziz UniversityJeddah, Saudi Arabia
| | - Vincent Lombard
- Centre National de la Recherche Scientifique UMR 7257, Aix-Marseille UniversityMarseille, France.,INRA, USC 1408 AFMBMarseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz UniversityJeddah, Saudi Arabia.,Centre National de la Recherche Scientifique UMR 7257, Aix-Marseille UniversityMarseille, France.,INRA, USC 1408 AFMBMarseille, France
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Montella S, Ventorino V, Lombard V, Henrissat B, Pepe O, Faraco V. Discovery of genes coding for carbohydrate-active enzyme by metagenomic analysis of lignocellulosic biomasses. Sci Rep 2017; 7:42623. [PMID: 28198423 PMCID: PMC5309792 DOI: 10.1038/srep42623] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [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: 04/27/2016] [Accepted: 01/13/2017] [Indexed: 12/03/2022] Open
Abstract
In this study, a high-throughput sequencing approach was applied to discover novel biocatalysts for lignocellulose hydrolysis from three dedicated energy crops, Arundo donax, Eucalyptus camaldulensis and Populus nigra, after natural biodegradation. The microbiomes of the three lignocellulosic biomasses were dominated by bacterial species (approximately 90%) with the highest representation by the Streptomyces genus both in the total microbial community composition and in the microbial diversity related to GH families of predicted ORFs. Moreover, the functional clustering of the predicted ORFs showed a prevalence of poorly characterized genes, suggesting these lignocellulosic biomasses are potential sources of as yet unknown genes. 1.2%, 0.6% and 3.4% of the total ORFs detected in A. donax, E. camaldulensis and P. nigra, respectively, were putative Carbohydrate-Active Enzymes (CAZymes). Interestingly, the glycoside hydrolases abundance in P. nigra (1.8%) was higher than that detected in the other biomasses investigated in this study. Moreover, a high percentage of (hemi)cellulases with different activities and accessory enzymes (mannanases, polygalacturonases and feruloyl esterases) was detected, confirming that the three analyzed samples were a reservoir of diversified biocatalysts required for an effective lignocellulose saccharification.
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Affiliation(s)
- Salvatore Montella
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, via Cintia, 4 80126 Naples, Italy
| | - Valeria Ventorino
- Department of Agricultural Sciences, University of Naples "Federico II", Portici (Napoli), Italy
| | - Vincent Lombard
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Olimpia Pepe
- Department of Agricultural Sciences, University of Naples "Federico II", Portici (Napoli), Italy
| | - Vincenza Faraco
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, via Cintia, 4 80126 Naples, Italy
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35
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Bensoussan L, Moraïs S, Dassa B, Friedman N, Henrissat B, Lombard V, Bayer EA, Mizrahi I. Broad phylogeny and functionality of cellulosomal components in the bovine rumen microbiome. Environ Microbiol 2016; 19:185-197. [PMID: 27712009 PMCID: PMC6487960 DOI: 10.1111/1462-2920.13561] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [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: 06/23/2016] [Accepted: 09/29/2016] [Indexed: 11/30/2022]
Abstract
The cellulosome is an extracellular multi‐enzyme complex that is considered one of the most efficient plant cell wall‐degrading strategies devised by nature. Its unique modular architecture, achieved by high affinity and specific interaction between protein modules (cohesins and dockerins) enables formation of various enzyme combinations. Extensive research has been dedicated to the mechanistic nature of the cellulosome complex. Nevertheless, little is known regarding its distribution and abundance among microbes in natural plant fibre‐rich environments. Here, we explored these questions in bovine rumen microbial communities, specialized in efficient degradation of lignocellulosic plant material. We bioinformatically screened for cellulosomal modules in this complex environment using a previously published ultra‐deep fibre‐adherent rumen metagenome. Intriguingly, a large portion of the functions of the dockerin‐containing proteins were related to alternative biological processes, and not necessarily to the classic fibre degradation function. Our analysis was experimentally validated by characterizing specific interactions between selected cohesins and dockerins and revealed that cellulosome is a more generalized strategy used by diverse bacteria, some of which were not previously associated with cellulosome production. Remarkably, our results provide additional proof of similarity among rumen microbial communities worldwide. This study suggests a broader and widespread role for the cellulosomal machinery in nature.
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Affiliation(s)
- Lizi Bensoussan
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Moraïs
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Nir Friedman
- The Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, Aix-Marseille University, CNRS UMR7257, Marseille, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, Aix-Marseille University, CNRS UMR7257, Marseille, France
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Itzhak Mizrahi
- The Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Million M, Tidjani Alou M, Khelaifia S, Bachar D, Lagier JC, Dione N, Brah S, Hugon P, Lombard V, Armougom F, Fromonot J, Robert C, Michelle C, Diallo A, Fabre A, Guieu R, Sokhna C, Henrissat B, Parola P, Raoult D. Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition. Sci Rep 2016; 6:26051. [PMID: 27183876 PMCID: PMC4869025 DOI: 10.1038/srep26051] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 04/27/2016] [Indexed: 02/08/2023] Open
Abstract
Severe acute malnutrition (SAM) is associated with inadequate diet, low levels of plasma antioxidants and gut microbiota alterations. The link between gut redox and microbial alterations, however, remains unexplored. By sequencing the gut microbiomes of 79 children of varying nutritional status from three centers in Senegal and Niger, we found a dramatic depletion of obligate anaerobes in malnutrition. This was confirmed in an individual patient data meta-analysis including 107 cases and 77 controls from 5 different African and Asian countries. Specifically, several species of the Bacteroidaceae, Eubacteriaceae, Lachnospiraceae and Ruminococceae families were consistently depleted while Enterococcus faecalis, Escherichia coli and Staphylococcus aureus were consistently enriched. Further analyses on our samples revealed increased fecal redox potential, decreased total bacterial number and dramatic Methanobrevibacter smithii depletion. Indeed, M. smithii was detected in more than half of the controls but in none of the cases. No causality was demonstrated but, based on our results, we propose a unifying theory linking microbiota specificity, lacking anaerobes and archaea, to low antioxidant nutrients, and lower food conversion.
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Affiliation(s)
- Matthieu Million
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Maryam Tidjani Alou
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Saber Khelaifia
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Dipankar Bachar
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Jean-Christophe Lagier
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Niokhor Dione
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | | | - Perrine Hugon
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Vincent Lombard
- Centre National de la Recherche Scientifique, UMR 7257, 13288 Marseille, France
- Aix-Marseille Université, Architecture et Fonctions des Macromolécules Biologiques, 163, avenue de Luminy, 13288 Marseille cedex 9, France
| | - Fabrice Armougom
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Julien Fromonot
- Laboratoire de Biochimie, hôpital de la Timone, UMR MD2, IRBA, Marseille, France
| | - Catherine Robert
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Caroline Michelle
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Aldiouma Diallo
- Institut de Recherche pour le Développement (IRD), URMITE, Dakar, Sénégal
| | - Alexandre Fabre
- Service de pédiatrie multidisciplinaire, hôpital de la Timone Enfant, APHM, Marseille France
- UMR_S 910, Aix-Marseille Université, Marseille, France
| | - Régis Guieu
- Laboratoire de Biochimie, hôpital de la Timone, UMR MD2, IRBA, Marseille, France
| | - Cheikh Sokhna
- Institut de Recherche pour le Développement (IRD), URMITE, Dakar, Sénégal
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique, UMR 7257, 13288 Marseille, France
- Aix-Marseille Université, Architecture et Fonctions des Macromolécules Biologiques, 163, avenue de Luminy, 13288 Marseille cedex 9, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Philippe Parola
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Tap J, Furet J, Bensaada M, Philippe C, Roth H, Rabot S, Lakhdari O, Lombard V, Henrissat B, Corthier G, Fontaine E, Doré J, Leclerc M. Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults. Environ Microbiol 2015; 17:4954-64. [DOI: 10.1111/1462-2920.13006] [Citation(s) in RCA: 228] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 07/27/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Julien Tap
- INRA Micalis Institute UMR1319 Jouy‐en‐Josas 78350 France
| | | | | | | | - Hubert Roth
- CHU Grenoble Bioénergétique‐INSERM U1055 Université J. Fourier Grenoble 38000 France
- CRNH Rhône‐Alpes Pierre Benite 69310 France
| | - Sylvie Rabot
- INRA Micalis Institute UMR1319 Jouy‐en‐Josas 78350 France
| | - Omar Lakhdari
- INRA Micalis Institute UMR1319 Jouy‐en‐Josas 78350 France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques Aix‐Marseille Université CNRS UMR 7257, 163 Avenue de Luminy Marseille F‐13288 France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques Aix‐Marseille Université CNRS UMR 7257, 163 Avenue de Luminy Marseille F‐13288 France
| | | | - Eric Fontaine
- CHU Grenoble Bioénergétique‐INSERM U1055 Université J. Fourier Grenoble 38000 France
- CRNH Rhône‐Alpes Pierre Benite 69310 France
| | - Joël Doré
- INRA Micalis Institute UMR1319 Jouy‐en‐Josas 78350 France
| | - Marion Leclerc
- INRA Micalis Institute UMR1319 Jouy‐en‐Josas 78350 France
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Chatelard P, Reinke N, Ezzidi A, Lombard V, Barnak M, Lajtha G, Slaby J, Constantin M, Majumdar P. Synthesis of the ASTEC integral code activities in SARNET – Focus on ASTEC V2 plant applications. ANN NUCL ENERGY 2014. [DOI: 10.1016/j.anucene.2014.05.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Terrapon N, Lombard V, Gilbert HJ, Henrissat B. Automatic prediction of polysaccharide utilization loci in Bacteroidetes species. Bioinformatics 2014; 31:647-55. [DOI: 10.1093/bioinformatics/btu716] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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40
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Lipski A, Hervé M, Lombard V, Nurizzo D, Mengin-Lecreulx D, Bourne Y, Vincent F. Structural and biochemical characterization of the β-N-acetylglucosaminidase from Thermotoga maritima: toward rationalization of mechanistic knowledge in the GH73 family. Glycobiology 2014; 25:319-30. [PMID: 25344445 DOI: 10.1093/glycob/cwu113] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [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: 12/25/2022] Open
Abstract
Members of the GH73 glycosidase family cleave the β-1,4-glycosidic bond between the N-acetylglucosaminyl (GlcNAc) and N-acetylmuramyl (MurNAc) moieties in bacterial peptidoglycan. A catalytic mechanism has been proposed for members FlgJ, Auto, AcmA and Atl(WM) and the structural analysis of FlgJ and Auto revealed a conserved α/β fold reminiscent of the distantly related GH23 lysozyme. Comparison of the active site residues reveals variability in the nature of the catalytic general base suggesting two distinct catalytic mechanisms: an inverting mechanism involving two distant glutamate residues and a substrate-assisted mechanism involving anchimeric assistance by the C2-acetamido group of the GlcNAc moiety. Herein, we present the biochemical characterization and crystal structure of TM0633 from the hyperthermophilic bacterium Thermotoga maritima. TM0633 adopts the α/β fold of the family and displays β-N-acetylglucosaminidase activity on intact peptidoglycan sacculi. Site-directed mutagenesis identifies Glu34, Glu65 and Tyr118 as important residues for catalysis. A thorough bioinformatic analysis of the GH73 sequences identified five phylogenetic clusters. TM0633, FlgJ and Auto belong to a group of three clusters that conserve two carboxylate residues involved in a classical inverting acid-base mechanism. Members of the other two clusters lack a conserved catalytic general base supporting a substrate-assisted mechanism. Molecular modeling of representative members from each cluster suggests that variability in length of the β-hairpin region above the active site confers ligand-binding specificity and modulates the catalytic mechanisms within the GH73 family.
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Affiliation(s)
- Alexandra Lipski
- Laboratory for Biocrystallography and Structural Biology of Therapeutic Targets, Molecular and Structural Bases of Infectious Diseases, UMR 5086 CNRS and University of Lyon, 7 passage du Vercors, F-69367 Lyon Cedex 07, France CNRS, AFMB UMR7257, 163 avenue de luminy, 13288 Marseille cedex 09, France
| | - Mireille Hervé
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, UMR 8619 CNRS, Université de Paris-Sud, 91405 Orsay, France
| | - Vincent Lombard
- CNRS, AFMB UMR7257, 163 avenue de luminy, 13288 Marseille cedex 09, France Aix-Marseille University, AFMB UMR7257, 163 avenue de luminy, 13288 Marseille cedex 09, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, Polygone Scientifique Louis Néel, 6 rue Jules Horowitz, 38000 Grenoble, France
| | - Dominique Mengin-Lecreulx
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, UMR 8619 CNRS, Université de Paris-Sud, 91405 Orsay, France
| | - Yves Bourne
- CNRS, AFMB UMR7257, 163 avenue de luminy, 13288 Marseille cedex 09, France Aix-Marseille University, AFMB UMR7257, 163 avenue de luminy, 13288 Marseille cedex 09, France
| | - Florence Vincent
- CNRS, AFMB UMR7257, 163 avenue de luminy, 13288 Marseille cedex 09, France Aix-Marseille University, AFMB UMR7257, 163 avenue de luminy, 13288 Marseille cedex 09, France
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Riley R, Salamov AA, Brown DW, Nagy LG, Floudas D, Held BW, Levasseur A, Lombard V, Morin E, Otillar R, Lindquist EA, Sun H, LaButti KM, Schmutz J, Jabbour D, Luo H, Baker SE, Pisabarro AG, Walton JD, Blanchette RA, Henrissat B, Martin F, Cullen D, Hibbett DS, Grigoriev IV. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proc Natl Acad Sci U S A 2014; 111:9923-8. [PMID: 24958869 PMCID: PMC4103376 DOI: 10.1073/pnas.1400592111] [Citation(s) in RCA: 411] [Impact Index Per Article: 41.1] [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] [Indexed: 01/08/2023] Open
Abstract
Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood-decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white-rot/brown-rot classification paradigm, we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically informed principal-components analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white-rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown-rot fungi. Our results suggest a continuum rather than a dichotomy between the white-rot and brown-rot modes of wood decay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay.
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Affiliation(s)
- Robert Riley
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598
| | - Asaf A Salamov
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598
| | - Daren W Brown
- US Department of Agriculture (USDA), Peoria, IL 61604
| | - Laszlo G Nagy
- Department of Biology, Clark University, Worcester, MA 01610
| | | | | | - Anthony Levasseur
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1163, Aix-Marseille Université, 13288 Marseille, France
| | - Vincent Lombard
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7257, Aix-Marseille Université, 13288 Marseille, France
| | - Emmanuelle Morin
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136, Institut National de la Recherche Agronomique-Université de Lorraine, Interactions Arbres/Micro-organismes, 54280 Champenoux, France
| | - Robert Otillar
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598
| | - Erika A Lindquist
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598
| | - Hui Sun
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598
| | - Kurt M LaButti
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598
| | - Jeremy Schmutz
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598;HudsonAlpha Institute of Biotechnology, Huntsville, AL 35806
| | - Dina Jabbour
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824
| | - Hong Luo
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824
| | - Scott E Baker
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Antonio G Pisabarro
- Departamento de Producción Agraria, Universidad Pública de Navarra, 31006 Pamplona, Spain; and
| | - Jonathan D Walton
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824
| | | | - Bernard Henrissat
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7257, Aix-Marseille Université, 13288 Marseille, France
| | - Francis Martin
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136, Institut National de la Recherche Agronomique-Université de Lorraine, Interactions Arbres/Micro-organismes, 54280 Champenoux, France
| | - Dan Cullen
- USDA Forest Products Laboratory, Madison, WI 53726
| | - David S Hibbett
- Department of Biology, Clark University, Worcester, MA 01610;
| | - Igor V Grigoriev
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598;
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Levasseur A, Lomascolo A, Chabrol O, Ruiz-Dueñas FJ, Boukhris-Uzan E, Piumi F, Kües U, Ram AFJ, Murat C, Haon M, Benoit I, Arfi Y, Chevret D, Drula E, Kwon MJ, Gouret P, Lesage-Meessen L, Lombard V, Mariette J, Noirot C, Park J, Patyshakuliyeva A, Sigoillot JC, Wiebenga A, Wösten HAB, Martin F, Coutinho PM, de Vries RP, Martínez AT, Klopp C, Pontarotti P, Henrissat B, Record E. The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown. BMC Genomics 2014; 15:486. [PMID: 24942338 PMCID: PMC4101180 DOI: 10.1186/1471-2164-15-486] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [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: 01/17/2014] [Accepted: 05/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Saprophytic filamentous fungi are ubiquitous micro-organisms that play an essential role in photosynthetic carbon recycling. The wood-decayer Pycnoporus cinnabarinus is a model fungus for the study of plant cell wall decomposition and is used for a number of applications in green and white biotechnology. RESULTS The 33.6 megabase genome of P. cinnabarinus was sequenced and assembled, and the 10,442 predicted genes were functionally annotated using a phylogenomic procedure. In-depth analyses were carried out for the numerous enzyme families involved in lignocellulosic biomass breakdown, for protein secretion and glycosylation pathways, and for mating type. The P. cinnabarinus genome sequence revealed a consistent repertoire of genes shared with wood-decaying basidiomycetes. P. cinnabarinus is thus fully equipped with the classical families involved in cellulose and hemicellulose degradation, whereas its pectinolytic repertoire appears relatively limited. In addition, P. cinnabarinus possesses a complete versatile enzymatic arsenal for lignin breakdown. We identified several genes encoding members of the three ligninolytic peroxidase types, namely lignin peroxidase, manganese peroxidase and versatile peroxidase. Comparative genome analyses were performed in fungi displaying different nutritional strategies (white-rot and brown-rot modes of decay). P. cinnabarinus presents a typical distribution of all the specific families found in the white-rot life style. Growth profiling of P. cinnabarinus was performed on 35 carbon sources including simple and complex substrates to study substrate utilization and preferences. P. cinnabarinus grew faster on crude plant substrates than on pure, mono- or polysaccharide substrates. Finally, proteomic analyses were conducted from liquid and solid-state fermentation to analyze the composition of the secretomes corresponding to growth on different substrates. The distribution of lignocellulolytic enzymes in the secretomes was strongly dependent on growth conditions, especially for lytic polysaccharide mono-oxygenases. CONCLUSIONS With its available genome sequence, P. cinnabarinus is now an outstanding model system for the study of the enzyme machinery involved in the degradation or transformation of lignocellulosic biomass.
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Affiliation(s)
- Anthony Levasseur
- INRA, UMR1163 Biotechnologie des Champignons Filamenteux, Aix-Marseille Université, Polytech Marseille, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France.
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Abstract
The Carbohydrate-Active Enzymes database (CAZy; http://www.cazy.org) provides online and continuously updated access to a sequence-based family classification linking the sequence to the specificity and 3D structure of the enzymes that assemble, modify and breakdown oligo- and polysaccharides. Functional and 3D structural information is added and curated on a regular basis based on the available literature. In addition to the use of the database by enzymologists seeking curated information on CAZymes, the dissemination of a stable nomenclature for these enzymes is probably a major contribution of CAZy. The past few years have seen the expansion of the CAZy classification scheme to new families, the development of subfamilies in several families and the power of CAZy for the analysis of genomes and metagenomes. This article outlines the changes that have occurred in CAZy during the past 5 years and presents our novel effort to display the resolution and the carbohydrate ligands in crystallographic complexes of CAZymes.
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Affiliation(s)
- Vincent Lombard
- Centre National de la Recherche Scientifique, CNRS UMR 7257, 13288 Marseille, France and Aix-Marseille Université, AFMB, 163 Avenue de Luminy, 13288 Marseille, France
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Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, Muehlbauer MJ, Ilkayeva O, Semenkovich CF, Funai K, Hayashi DK, Lyle BJ, Martini MC, Ursell LK, Clemente JC, Van Treuren W, Walters WA, Knight R, Newgard CB, Heath AC, Gordon JI. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 2013; 341:1241214. [PMID: 24009397 DOI: 10.1126/science.1241214] [Citation(s) in RCA: 2473] [Impact Index Per Article: 224.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The role of specific gut microbes in shaping body composition remains unclear. We transplanted fecal microbiota from adult female twin pairs discordant for obesity into germ-free mice fed low-fat mouse chow, as well as diets representing different levels of saturated fat and fruit and vegetable consumption typical of the U.S. diet. Increased total body and fat mass, as well as obesity-associated metabolic phenotypes, were transmissible with uncultured fecal communities and with their corresponding fecal bacterial culture collections. Cohousing mice harboring an obese twin's microbiota (Ob) with mice containing the lean co-twin's microbiota (Ln) prevented the development of increased body mass and obesity-associated metabolic phenotypes in Ob cage mates. Rescue correlated with invasion of specific members of Bacteroidetes from the Ln microbiota into Ob microbiota and was diet-dependent. These findings reveal transmissible, rapid, and modifiable effects of diet-by-microbiota interactions.
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Affiliation(s)
- Vanessa K Ridaura
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
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Ladevèze S, Tarquis L, Cecchini DA, Bercovici J, André I, Topham CM, Morel S, Laville E, Monsan P, Lombard V, Henrissat B, Potocki-Véronèse G. Role of glycoside phosphorylases in mannose foraging by human gut bacteria. J Biol Chem 2013; 288:32370-32383. [PMID: 24043624 DOI: 10.1074/jbc.m113.483628] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [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: 01/29/2023] Open
Abstract
To metabolize both dietary fiber constituent carbohydrates and host glycans lining the intestinal epithelium, gut bacteria produce a wide range of carbohydrate-active enzymes, of which glycoside hydrolases are the main components. In this study, we describe the ability of phosphorylases to participate in the breakdown of human N-glycans, from an analysis of the substrate specificity of UhgbMP, a mannoside phosphorylase of the GH130 protein family discovered by functional metagenomics. UhgbMP is found to phosphorolyze β-D-Manp-1,4-β-D-GlcpNAc-1,4-D-GlcpNAc and is also a highly efficient enzyme to catalyze the synthesis of this precious N-glycan core oligosaccharide by reverse phosphorolysis. Analysis of sequence conservation within family GH130, mapped on a three-dimensional model of UhgbMP and supported by site-directed mutagenesis results, revealed two GH130 subfamilies and allowed the identification of key residues responsible for catalysis and substrate specificity. The analysis of the genomic context of 65 known GH130 sequences belonging to human gut bacteria indicates that the enzymes of the GH130_1 subfamily would be involved in mannan catabolism, whereas the enzymes belonging to the GH130_2 subfamily would rather work in synergy with glycoside hydrolases of the GH92 and GH18 families in the breakdown of N-glycans. The use of GH130 inhibitors as therapeutic agents or functional foods could thus be considered as an innovative strategy to inhibit N-glycan degradation, with the ultimate goal of protecting, or restoring, the epithelial barrier.
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Affiliation(s)
- Simon Ladevèze
- From the Institut National des Sciences Appliquées, Université Paul Sabatier, Institut National Polytechnique, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, 135 Avenue de Rangueil, F-31077 Toulouse,; the CNRS, UMR5504, F-31400 Toulouse,; the Institut National de Recherche Agronomique, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse
| | - Laurence Tarquis
- From the Institut National des Sciences Appliquées, Université Paul Sabatier, Institut National Polytechnique, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, 135 Avenue de Rangueil, F-31077 Toulouse,; the CNRS, UMR5504, F-31400 Toulouse,; the Institut National de Recherche Agronomique, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse
| | - Davide A Cecchini
- From the Institut National des Sciences Appliquées, Université Paul Sabatier, Institut National Polytechnique, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, 135 Avenue de Rangueil, F-31077 Toulouse,; the CNRS, UMR5504, F-31400 Toulouse,; the Institut National de Recherche Agronomique, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse
| | - Juliette Bercovici
- From the Institut National des Sciences Appliquées, Université Paul Sabatier, Institut National Polytechnique, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, 135 Avenue de Rangueil, F-31077 Toulouse,; the CNRS, UMR5504, F-31400 Toulouse,; the Institut National de Recherche Agronomique, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse
| | - Isabelle André
- From the Institut National des Sciences Appliquées, Université Paul Sabatier, Institut National Polytechnique, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, 135 Avenue de Rangueil, F-31077 Toulouse,; the CNRS, UMR5504, F-31400 Toulouse,; the Institut National de Recherche Agronomique, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse
| | - Christopher M Topham
- From the Institut National des Sciences Appliquées, Université Paul Sabatier, Institut National Polytechnique, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, 135 Avenue de Rangueil, F-31077 Toulouse,; the CNRS, UMR5504, F-31400 Toulouse,; the Institut National de Recherche Agronomique, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse
| | - Sandrine Morel
- From the Institut National des Sciences Appliquées, Université Paul Sabatier, Institut National Polytechnique, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, 135 Avenue de Rangueil, F-31077 Toulouse,; the CNRS, UMR5504, F-31400 Toulouse,; the Institut National de Recherche Agronomique, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse
| | - Elisabeth Laville
- From the Institut National des Sciences Appliquées, Université Paul Sabatier, Institut National Polytechnique, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, 135 Avenue de Rangueil, F-31077 Toulouse,; the CNRS, UMR5504, F-31400 Toulouse,; the Institut National de Recherche Agronomique, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse
| | - Pierre Monsan
- From the Institut National des Sciences Appliquées, Université Paul Sabatier, Institut National Polytechnique, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, 135 Avenue de Rangueil, F-31077 Toulouse,; the CNRS, UMR5504, F-31400 Toulouse,; the Institut National de Recherche Agronomique, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse
| | - Vincent Lombard
- the Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, CNRS UMR 7257, 163 Avenue de Luminy, F-13288 Marseille, France
| | - Bernard Henrissat
- the Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, CNRS UMR 7257, 163 Avenue de Luminy, F-13288 Marseille, France
| | - Gabrielle Potocki-Véronèse
- From the Institut National des Sciences Appliquées, Université Paul Sabatier, Institut National Polytechnique, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, 135 Avenue de Rangueil, F-31077 Toulouse,; the CNRS, UMR5504, F-31400 Toulouse,; the Institut National de Recherche Agronomique, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse.
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Gruet A, Dosnon M, Vassena A, Lombard V, Gerlier D, Bignon C, Longhi S. Dissecting partner recognition by an intrinsically disordered protein using descriptive random mutagenesis. J Mol Biol 2013; 425:3495-509. [PMID: 23811056 DOI: 10.1016/j.jmb.2013.06.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [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: 03/26/2013] [Revised: 06/14/2013] [Accepted: 06/18/2013] [Indexed: 02/06/2023]
Abstract
In view of getting insights into the molecular determinants of the binding efficiency of intrinsically disordered proteins (IDPs), we used random mutagenesis. As a proof of concept, we chose the interaction between the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (NTAIL) and the X domain (XD) of the viral phosphoprotein and assessed how amino acid substitutions introduced at random within NTAIL affect partner recognition. In contrast with directed evolution approaches, we did not apply any selection and used the gene library approach not for production purposes but for achieving a better understanding of the NTAIL/XD interaction. For that reason, and to differentiate our approach from similar approaches that make use of systematic (i.e., targeted) mutagenesis, we propose to call it "descriptive random mutagenesis" (DRM). NTAIL variants generated by error-prone PCR were picked at random in the absence of selection pressure and were characterized in terms of sequence and binding abilities toward XD. DRM not only identified determinants of NTAIL/XD interaction that were in good agreement with previous work but also provided new insights. In particular, we discovered that the primary interaction site is poorly evolvable in terms of binding abilities toward XD. We also identified a critical NTAIL residue whose role in stabilizing the NTAIL/XD complex had previously escaped detection, and we identified NTAIL regulatory sites that dampen the interaction while being located outside the primary interaction site. Results show that DRM is a valuable approach to study binding abilities of IDPs.
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Affiliation(s)
- Antoine Gruet
- CNRS and Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13288 Marseille, France
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Levasseur A, Drula E, Lombard V, Coutinho PM, Henrissat B. Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol Biofuels 2013; 6:41. [PMID: 23514094 PMCID: PMC3620520 DOI: 10.1186/1754-6834-6-41] [Citation(s) in RCA: 742] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 03/11/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Since its inception, the carbohydrate-active enzymes database (CAZy; http://www.cazy.org) has described the families of enzymes that cleave or build complex carbohydrates, namely the glycoside hydrolases (GH), the polysaccharide lyases (PL), the carbohydrate esterases (CE), the glycosyltransferases (GT) and their appended non-catalytic carbohydrate-binding modules (CBM). The recent discovery that members of families CBM33 and family GH61 are in fact lytic polysaccharide monooxygenases (LPMO), demands a reclassification of these families into a suitable category. RESULTS Because lignin is invariably found together with polysaccharides in the plant cell wall and because lignin fragments are likely to act in concert with (LPMO), we have decided to join the families of lignin degradation enzymes to the LPMO families and launch a new CAZy class that we name "Auxiliary Activities" in order to accommodate a range of enzyme mechanisms and substrates related to lignocellulose conversion. Comparative analyses of these auxiliary activities in 41 fungal genomes reveal a pertinent division of several fungal groups and subgroups combining their phylogenetic origin and their nutritional mode (white vs. brown rot). CONCLUSIONS The new class introduced in the CAZy database extends the traditional CAZy families, and provides a better coverage of the full extent of the lignocellulose breakdown machinery.
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Affiliation(s)
- Anthony Levasseur
- INRA, UMR1163 Biotechnologie des Champignons Filamenteux, Aix-Marseille Université, ESIL Polytech Marseille, 163 avenue de Luminy, CP 925, 13288, Marseille, Cedex 09, France
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Aix-Marseille Université, 163 Avenue de Luminy, Marseille, 13288, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Aix-Marseille Université, 163 Avenue de Luminy, Marseille, 13288, France
| | - Pedro M Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Aix-Marseille Université, 163 Avenue de Luminy, Marseille, 13288, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Aix-Marseille Université, 163 Avenue de Luminy, Marseille, 13288, France
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Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martínez AT, Otillar R, Spatafora JW, Yadav JS, Aerts A, Benoit I, Boyd A, Carlson A, Copeland A, Coutinho PM, de Vries RP, Ferreira P, Findley K, Foster B, Gaskell J, Glotzer D, Górecki P, Heitman J, Hesse C, Hori C, Igarashi K, Jurgens JA, Kallen N, Kersten P, Kohler A, Kües U, Kumar TKA, Kuo A, LaButti K, Larrondo LF, Lindquist E, Ling A, Lombard V, Lucas S, Lundell T, Martin R, McLaughlin DJ, Morgenstern I, Morin E, Murat C, Nagy LG, Nolan M, Ohm RA, Patyshakuliyeva A, Rokas A, Ruiz-Dueñas FJ, Sabat G, Salamov A, Samejima M, Schmutz J, Slot JC, St John F, Stenlid J, Sun H, Sun S, Syed K, Tsang A, Wiebenga A, Young D, Pisabarro A, Eastwood DC, Martin F, Cullen D, Grigoriev IV, Hibbett DS. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 2012; 336:1715-9. [PMID: 22745431 DOI: 10.1126/science.1221748] [Citation(s) in RCA: 993] [Impact Index Per Article: 82.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.
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Abstract
The various ecological habitats in the human body provide microbes a wide array of nutrient sources and survival challenges. Advances in technology such as DNA sequencing have allowed a deeper perspective into the molecular function of the human microbiota than has been achievable in the past. Here we aimed to examine the enzymes that cleave complex carbohydrates (CAZymes) in the human microbiome in order to determine (i) whether the CAZyme profiles of bacterial genomes are more similar within body sites or bacterial families and (ii) the sugar degradation and utilization capabilities of microbial communities inhabiting various human habitats. Upon examination of 493 bacterial references genomes from 12 human habitats, we found that sugar degradation capabilities of taxa are more similar to others in the same bacterial family than to those inhabiting the same habitat. Yet, the analysis of 520 metagenomic samples from five major body sites show that even when the community composition varies the CAZyme profiles are very similar within a body site, suggesting that the observed functional profile and microbial habitation have adapted to the local carbohydrate composition. When broad sugar utilization was compared within the five major body sites, the gastrointestinal track contained the highest potential for total sugar degradation, while dextran and peptidoglycan degradation were highest in oral and vaginal sites respectively. Our analysis suggests that the carbohydrate composition of each body site has a profound influence and probably constitutes one of the major driving forces that shapes the community composition and therefore the CAZyme profile of the local microbial communities, which in turn reflects the microbiome fitness to a body site.
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Affiliation(s)
- Brandi L Cantarel
- Institute for Genome Sciences, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America.
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50
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Olson Å, Aerts A, Asiegbu F, Belbahri L, Bouzid O, Broberg A, Canbäck B, Coutinho PM, Cullen D, Dalman K, Deflorio G, van Diepen LTA, Dunand C, Duplessis S, Durling M, Gonthier P, Grimwood J, Fossdal CG, Hansson D, Henrissat B, Hietala A, Himmelstrand K, Hoffmeister D, Högberg N, James TY, Karlsson M, Kohler A, Kües U, Lee YH, Lin YC, Lind M, Lindquist E, Lombard V, Lucas S, Lundén K, Morin E, Murat C, Park J, Raffaello T, Rouzé P, Salamov A, Schmutz J, Solheim H, Ståhlberg J, Vélëz H, de Vries RP, Wiebenga A, Woodward S, Yakovlev I, Garbelotto M, Martin F, Grigoriev IV, Stenlid J. Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen. New Phytol 2012; 194:1001-1013. [PMID: 22463738 DOI: 10.1111/j.1469-8137.2012.04128.x] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Parasitism and saprotrophic wood decay are two fungal strategies fundamental for succession and nutrient cycling in forest ecosystems. An opportunity to assess the trade-off between these strategies is provided by the forest pathogen and wood decayer Heterobasidion annosum sensu lato. We report the annotated genome sequence and transcript profiling, as well as the quantitative trait loci mapping, of one member of the species complex: H. irregulare. Quantitative trait loci critical for pathogenicity, and rich in transposable elements, orphan and secreted genes, were identified. A wide range of cellulose-degrading enzymes are expressed during wood decay. By contrast, pathogenic interaction between H. irregulare and pine engages fewer carbohydrate-active enzymes, but involves an increase in pectinolytic enzymes, transcription modules for oxidative stress and secondary metabolite production. Our results show a trade-off in terms of constrained carbohydrate decomposition and membrane transport capacity during interaction with living hosts. Our findings establish that saprotrophic wood decay and necrotrophic parasitism involve two distinct, yet overlapping, processes.
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Affiliation(s)
- Åke Olson
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | - Andrea Aerts
- US DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Fred Asiegbu
- Department of Forest Ecology, PO Box 27 Latokartanonkaari 7, 00014 University of Helsinki, Helsinki, Finland
| | - Lassaad Belbahri
- Laboratory of Soil Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Ourdia Bouzid
- Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Anders Broberg
- Department of Chemistry, Swedish University of Agricultural Sciences, Box 7015, 750 05 Uppsala, Sweden
| | - Björn Canbäck
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | - Pedro M Coutinho
- AFMB UMR 6098 CNRS/UI/UII, Case 932, 163 Avenue de Luminy 13288 Marseille cedex 9, France
| | - Dan Cullen
- Forest Products Laboratory, Madison, WI 53726, USA
| | - Kerstin Dalman
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | - Giuliana Deflorio
- Department of Plant and Soil Science, Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen, AB24 3UU, Scotland UK
| | - Linda T A van Diepen
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christophe Dunand
- Laboratory of Cell Surfaces and Plant Signalisation 24, University Paul Sabatier (Toulouse III), UMR5546- CNRS, Chemin de Borde-Rouge, BP 42617, Auzeville 31326 Castanet-Tolosan, France
| | - Sébastien Duplessis
- UMR INRA-UHP 'Interactions Arbres/Micro-Organismes' IFR 110 'Genomique, Ecophysiologie et Ecologie Fonctionnelles' INRA-Nancy 54280 Champenoux, France
| | - Mikael Durling
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | - Paolo Gonthier
- Department of Exploitation and Protection of Agricultural and Forest Resources (Di. Va. P. R. A.) - Plant Pathology, University of Torino, Via L. da Vinci 44, I-10095 Grugliasco, Italy
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Huntsville, AL 35806, USA
| | - Carl Gunnar Fossdal
- Norwegian Forest and Landscape Institute, Høgskoleveien 8, NO-1432 Ås, Norway
| | - David Hansson
- Department of Chemistry, Swedish University of Agricultural Sciences, Box 7015, 750 05 Uppsala, Sweden
| | - Bernard Henrissat
- AFMB UMR 6098 CNRS/UI/UII, Case 932, 163 Avenue de Luminy 13288 Marseille cedex 9, France
| | - Ari Hietala
- Norwegian Forest and Landscape Institute, Høgskoleveien 8, NO-1432 Ås, Norway
| | - Kajsa Himmelstrand
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | - Dirk Hoffmeister
- Pharmaceutical Biology, Friedrich-Schiller-Universität Jena, Winzerlaer Str. 2, 07745 Jena, Germany
| | - Nils Högberg
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Magnus Karlsson
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | - Annegret Kohler
- UMR INRA-UHP 'Interactions Arbres/Micro-Organismes' IFR 110 'Genomique, Ecophysiologie et Ecologie Fonctionnelles' INRA-Nancy 54280 Champenoux, France
| | - Ursula Kües
- Büsgen-Institute, Section Molecular Wood Biotechnology and Technical Mycology, University of Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
| | - Yao-Cheng Lin
- VIB Department of Plant Systems Biology, Ghent University, Bioinformatics and Evolutionary Genomics, Technologiepark 927, B-9052 Gent, Belgium
| | - Mårten Lind
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | | | - Vincent Lombard
- AFMB UMR 6098 CNRS/UI/UII, Case 932, 163 Avenue de Luminy 13288 Marseille cedex 9, France
| | - Susan Lucas
- US DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Karl Lundén
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | - Emmanuelle Morin
- UMR INRA-UHP 'Interactions Arbres/Micro-Organismes' IFR 110 'Genomique, Ecophysiologie et Ecologie Fonctionnelles' INRA-Nancy 54280 Champenoux, France
| | - Claude Murat
- UMR INRA-UHP 'Interactions Arbres/Micro-Organismes' IFR 110 'Genomique, Ecophysiologie et Ecologie Fonctionnelles' INRA-Nancy 54280 Champenoux, France
| | - Jongsun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
| | - Tommaso Raffaello
- Department of Forest Ecology, PO Box 27 Latokartanonkaari 7, 00014 University of Helsinki, Helsinki, Finland
| | - Pierre Rouzé
- VIB Department of Plant Systems Biology, Ghent University, Bioinformatics and Evolutionary Genomics, Technologiepark 927, B-9052 Gent, Belgium
| | - Asaf Salamov
- US DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Huntsville, AL 35806, USA
| | - Halvor Solheim
- Norwegian Forest and Landscape Institute, Høgskoleveien 8, NO-1432 Ås, Norway
| | - Jerry Ståhlberg
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, Husargatan 3, 751 24 Uppsala, Sweden
| | - Heriberto Vélëz
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
| | - Ronald P de Vries
- Microbiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Ad Wiebenga
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Steve Woodward
- Department of Plant and Soil Science, Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen, AB24 3UU, Scotland UK
| | - Igor Yakovlev
- Norwegian Forest and Landscape Institute, Høgskoleveien 8, NO-1432 Ås, Norway
| | | | - Francis Martin
- UMR INRA-UHP 'Interactions Arbres/Micro-Organismes' IFR 110 'Genomique, Ecophysiologie et Ecologie Fonctionnelles' INRA-Nancy 54280 Champenoux, France
| | | | - Jan Stenlid
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsväg 26, 750 05 Uppsala, Sweden
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