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Matchado MS, Lauber M, Reitmeier S, Kacprowski T, Baumbach J, Haller D, List M. Network analysis methods for studying microbial communities: A mini review. Comput Struct Biotechnol J 2021; 19:2687-2698. [PMID: 34093985 PMCID: PMC8131268 DOI: 10.1016/j.csbj.2021.05.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [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: 02/01/2021] [Revised: 05/01/2021] [Accepted: 05/01/2021] [Indexed: 12/20/2022] Open
Abstract
Microorganisms including bacteria, fungi, viruses, protists and archaea live as communities in complex and contiguous environments. They engage in numerous inter- and intra- kingdom interactions which can be inferred from microbiome profiling data. In particular, network-based approaches have proven helpful in deciphering complex microbial interaction patterns. Here we give an overview of state-of-the-art methods to infer intra-kingdom interactions ranging from simple correlation- to complex conditional dependence-based methods. We highlight common biases encountered in microbial profiles and discuss mitigation strategies employed by different tools and their trade-off with increased computational complexity. Finally, we discuss current limitations that motivate further method development to infer inter-kingdom interactions and to robustly and comprehensively characterize microbial environments in the future.
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Affiliation(s)
- Monica Steffi Matchado
- Chair of Experimental Bioinformatics, Technical University of Munich, 85354 Freising, Germany
| | - Michael Lauber
- Chair of Experimental Bioinformatics, Technical University of Munich, 85354 Freising, Germany
| | - Sandra Reitmeier
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
- Chair of Nutrition and Immunology, Technical University of Munich, 85354 Freising, Germany
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics, TU Braunschweig and Hannover Medical School, 38106 Brunswick, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), 38106 Brunswick, Germany
| | - Jan Baumbach
- Institute of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark
- Chair of Computational Systems Biology, University of Hamburg, 22607 Hamburg, Germany
| | - Dirk Haller
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
- Chair of Nutrition and Immunology, Technical University of Munich, 85354 Freising, Germany
| | - Markus List
- Chair of Experimental Bioinformatics, Technical University of Munich, 85354 Freising, Germany
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Dupont S, Lokmer A, Corre E, Auguet JC, Petton B, Toulza E, Montagnani C, Tanguy G, Pecqueur D, Salmeron C, Guillou L, Desnues C, La Scola B, Bou Khalil J, de Lorgeril J, Mitta G, Gueguen Y, Escoubas JM. Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and viruses. Anim Microbiome 2020; 2:12. [PMID: 33499958 PMCID: PMC7807429 DOI: 10.1186/s42523-020-00032-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 11/20/2019] [Accepted: 04/14/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The impact of the microbiota on host fitness has so far mainly been demonstrated for the bacterial microbiome. We know much less about host-associated protist and viral communities, largely due to technical issues. However, all microorganisms within a microbiome potentially interact with each other as well as with the host and the environment, therefore likely affecting the host health. RESULTS We set out to explore how environmental and host factors shape the composition and diversity of bacterial, protist and viral microbial communities in the Pacific oyster hemolymph, both in health and disease. To do so, five oyster families differing in susceptibility to the Pacific oyster mortality syndrome were reared in hatchery and transplanted into a natural environment either before or during a disease outbreak. Using metabarcoding and shotgun metagenomics, we demonstrate that hemolymph can be considered as an ecological niche hosting bacterial, protist and viral communities, each of them shaped by different factors and distinct from the corresponding communities in the surrounding seawater. Overall, we found that hemolymph microbiota is more strongly shaped by the environment than by host genetic background. Co-occurrence network analyses suggest a disruption of the microbial network after transplantation into natural environment during both non-infectious and infectious periods. Whereas we could not identify a common microbial community signature for healthy animals, OsHV-1 μVar virus dominated the hemolymph virome during the disease outbreak, without significant modifications of other microbiota components. CONCLUSION Our study shows that oyster hemolymph is a complex ecosystem containing diverse bacteria, protists and viruses, whose composition and dynamics are primarily determined by the environment. However, all of these are also shaped by oyster genetic backgrounds, indicating they indeed interact with the oyster host and are therefore not only of transient character. Although it seems that the three microbiome components respond independently to environmental conditions, better characterization of hemolymph-associated viruses could change this picture.
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Affiliation(s)
- S Dupont
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan Via Domitia, 34095, Montpellier, France
| | - A Lokmer
- Coastal Ecology, Wadden Sea Station Sylt, Alfred Wegener Institute - Helmholtz Centre for Polar and Marine Research, List auf Sylt, Germany.,Current affiliation UMR 7206 Eco-anthropologie et Ethnologie, CNRS - MNHN Univ. Paris Diderot Sorbonne Paris Cité, Paris, France
| | - E Corre
- Sorbonne Université, CNRS, FR2424 ABiMS (Analysis and Bioanalysis for Marine Sciences), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - J-C Auguet
- MARBEC, Université Montpellier, CNRS, IFREMER, IRD, CC093, place Eugène Bataillon, 34095, Montpellier, France
| | - B Petton
- Ifremer, LEMAR UMR 6539, 11 presqu'île du Vivier, 29840, Argenton-en-Landunvez, France
| | - E Toulza
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan Via Domitia, 34095, Montpellier, France
| | - C Montagnani
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan Via Domitia, 34095, Montpellier, France
| | - G Tanguy
- Sorbonne Université, CNRS, FR2424, Genomer, Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - D Pecqueur
- Observatoire Océanologique de Banyuls sur Mer, FR 3724, BioPIC, CNRS/SU, Avenue Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | - C Salmeron
- Observatoire Océanologique de Banyuls sur Mer, FR 3724, BioPIC, CNRS/SU, Avenue Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | - L Guillou
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - C Desnues
- Aix-Marseille Université, IRD 257, Assistance-Publique des Hôpitaux de Marseille, UMR Microbes, Evolution, Phylogeny and Infections (MEPHI), IHU Méditerranée Infection, 13005, Marseille, France.,Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography, UM 110, 13288, Marseille, France
| | - B La Scola
- Microbes, Evolution, Phylogeny and Infection (MEΦI), Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique - Hôpitaux de Marseille (AP-HM), Marseille, France.,Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - J Bou Khalil
- Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - J de Lorgeril
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan Via Domitia, 34095, Montpellier, France
| | - G Mitta
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan Via Domitia, 34095, Montpellier, France
| | - Y Gueguen
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan Via Domitia, 34095, Montpellier, France
| | - J-M Escoubas
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan Via Domitia, 34095, Montpellier, France.
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