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Faure E, Ayata SD, Bittner L. Towards omics-based predictions of planktonic functional composition from environmental data. Nat Commun 2021; 12:4361. [PMID: 34272373 PMCID: PMC8285379 DOI: 10.1038/s41467-021-24547-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
Marine microbes play a crucial role in climate regulation, biogeochemical cycles, and trophic networks. Unprecedented amounts of data on planktonic communities were recently collected, sparking a need for innovative data-driven methodologies to quantify and predict their ecosystemic functions. We reanalyze 885 marine metagenome-assembled genomes through a network-based approach and detect 233,756 protein functional clusters, from which 15% are functionally unannotated. We investigate all clusters' distributions across the global ocean through machine learning, identifying biogeographical provinces as the best predictors of protein functional clusters' abundance. The abundances of 14,585 clusters are predictable from the environmental context, including 1347 functionally unannotated clusters. We analyze the biogeography of these 14,585 clusters, identifying the Mediterranean Sea as an outlier in terms of protein functional clusters composition. Applicable to any set of sequences, our approach constitutes a step towards quantitative predictions of functional composition from the environmental context.
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Affiliation(s)
- Emile Faure
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.
| | - Sakina-Dorothée Ayata
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Lucie Bittner
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
- Institut Universitaire de France, Paris, France
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2
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The gut microbiome regulates the increases in depressive-type behaviors and in inflammatory processes in the ventral hippocampus of stress vulnerable rats. Mol Psychiatry 2020; 25:1068-1079. [PMID: 30833676 DOI: 10.1038/s41380-019-0380-x] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 01/24/2019] [Accepted: 02/11/2019] [Indexed: 12/11/2022]
Abstract
Chronic exposure to stress is associated with increased incidence of depression, generalized anxiety, and PTSD. However, stress induces vulnerability to such disorders only in a sub-population of individuals, as others remain resilient. Inflammation has emerged as a putative mechanism for promoting stress vulnerability. Using a rodent model of social defeat, we have previously shown that rats with short-defeat latencies (SL/vulnerable rats) show increased anxiety- and depression-like behaviors, and these behaviors are mediated by inflammation in the ventral hippocampus. The other half of socially defeated rats show long-latencies to defeat (LL/resilient) and are similar to controls. Because gut microbiota are important activators of inflammatory substances, we assessed the role of the gut microbiome in mediating vulnerability to repeated social defeat stress. We analyzed the fecal microbiome of control, SL/vulnerable, and LL/resilient rats using shotgun metagenome sequencing and observed increased expression of immune-modulating microbiota, such as Clostridia, in SL/vulnerable rats. We then tested the importance of gut microbiota to the SL/vulnerable phenotype. In otherwise naive rats treated with microbiota from SL/vulnerable rats, there was higher microglial density and IL-1β expression in the vHPC, and higher depression-like behaviors relative to rats that received microbiota from LL/resilient rats, non-stressed control rats, or vehicle-treated rats. However, anxiety-like behavior during social interaction was not altered by transplant of the microbiome of SL/vulnerable rats into non-stressed rats. Taken together, the results suggest the gut microbiome contributes to the depression-like behavior and inflammatory processes in the vHPC of stress vulnerable individuals.
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3
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Gross F, Kranke N, Meunier R. Pluralization through epistemic competition: scientific change in times of data-intensive biology. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2019; 41:1. [PMID: 30603778 DOI: 10.1007/s40656-018-0239-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
Abstract
We present two case studies from contemporary biology in which we observe conflicts between established and emerging approaches. The first case study discusses the relation between molecular biology and systems biology regarding the explanation of cellular processes, while the second deals with phylogenetic systematics and the challenge posed by recent network approaches to established ideas of evolutionary processes. We show that the emergence of new fields is in both cases driven by the development of high-throughput data generation technologies and the transfer of modeling techniques from other fields. New and emerging views are characterized by different philosophies of nature, i.e. by different ontological and methodological assumptions and epistemic values and virtues. This results in a kind of conflict we call "epistemic competition" that manifests in two ways: On the one hand, opponents engage in mutual critique and defense of their fundamental assumptions. On the other hand, they compete for the acceptance and integration of the knowledge they provide by a broader scientific community. Despite an initial rhetoric of replacement, the views as well as the respective audiences come to be seen as more clearly distinct during the course of the debate. Hence, we observe-contrary to many other accounts of scientific change-that conflict results in the formation of new niches of research, leading to co-existence and perceived complementarity of approaches. Our model thus contributes to the understanding of the pluralization of the scientific landscape.
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Affiliation(s)
- Fridolin Gross
- Institut für Philosophie, Universität Kassel, Henschelstr. 2, 34127, Kassel, Germany
| | - Nina Kranke
- Philosophisches Seminar, Westfälische Wilhelms-Universität Münster, Domplatz 23, 48143, Münster, Germany.
| | - Robert Meunier
- Institut für Philosophie, Universität Kassel, Henschelstr. 2, 34127, Kassel, Germany
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Watson AK, Lannes R, Pathmanathan JS, Méheust R, Karkar S, Colson P, Corel E, Lopez P, Bapteste E. The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution. Methods Mol Biol 2019; 1910:271-308. [PMID: 31278668 DOI: 10.1007/978-1-4939-9074-0_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In the post genomic era, large and complex molecular datasets from genome and metagenome sequencing projects expand the limits of what is possible for bioinformatic analyses. Network-based methods are increasingly used to complement phylogenetic analysis in studies in molecular evolution, including comparative genomics, classification, and ecological studies. Using network methods, the vertical and horizontal relationships between all genes or genomes, whether they are from cellular chromosomes or mobile genetic elements, can be explored in a single expandable graph. In recent years, development of new methods for the construction and analysis of networks has helped to broaden the availability of these approaches from programmers to a diversity of users. This chapter introduces the different kinds of networks based on sequence similarity that are already available to tackle a wide range of biological questions, including sequence similarity networks, gene-sharing networks and bipartite graphs, and a guide for their construction and analyses.
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Affiliation(s)
- Andrew K Watson
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
| | - Romain Lannes
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
| | - Jananan S Pathmanathan
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
| | - Raphaël Méheust
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
| | - Slim Karkar
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
- Department of Ecology, Evolution, and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of NJ, New Brunswick, NJ, USA
| | - Philippe Colson
- Fondation Institut Hospitalo-Universitaire Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Tione, Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM U1095, Aix-Marseille University, Marseille, France
| | - Eduardo Corel
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
| | - Philippe Lopez
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
| | - Eric Bapteste
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France.
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Bernard G, Pathmanathan JS, Lannes R, Lopez P, Bapteste E. Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery. Genome Biol Evol 2018; 10:707-715. [PMID: 29420719 PMCID: PMC5830969 DOI: 10.1093/gbe/evy031] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2018] [Indexed: 02/07/2023] Open
Abstract
Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics data sets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists. Based on former empirical findings of microbial studies, we sketch a logic of discovery with the potential to further highlight the microbial unknowns.
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Affiliation(s)
- Guillaume Bernard
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris-Seine (IBPS), France
| | - Jananan S Pathmanathan
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris-Seine (IBPS), France
| | - Romain Lannes
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris-Seine (IBPS), France
| | - Philippe Lopez
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris-Seine (IBPS), France
| | - Eric Bapteste
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris-Seine (IBPS), France
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6
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Meng A, Corre E, Probert I, Gutierrez-Rodriguez A, Siano R, Annamale A, Alberti A, Da Silva C, Wincker P, Le Crom S, Not F, Bittner L. Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network. Mol Ecol 2018; 27:2365-2380. [PMID: 29624751 DOI: 10.1111/mec.14579] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 02/23/2018] [Accepted: 03/21/2018] [Indexed: 02/06/2023]
Abstract
Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core-predicted proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated with functional traits. With respect to toxicity, sequences homologous to those of proteins found in species with toxicity potential (e.g., sxtA4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of, respectively, the toxic and symbiotic species represented in our analyses. Of these, 56% and 57%, respectively (i.e., 25,393 and 52,193 pCDs), completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization.
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Affiliation(s)
- Arnaud Meng
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles Guyane, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), Paris, France
| | - Erwan Corre
- CNRS, UPMC, FR2424, ABiMS, Station Biologique, Roscoff, France
| | - Ian Probert
- UPMC-CNRS, FR2424, Roscoff Culture Collection, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | | | - Raffaele Siano
- Ifremer - Centre de Brest, DYNECO PELAGOS, Plouzané, France
| | - Anita Annamale
- CEA - Institut de Génomique, GENOSCOPE, Evry, France.,CNRS, UMR8030, Evry, France.,Université d'Evry Val d'Essonne, Evry, France
| | - Adriana Alberti
- CEA - Institut de Génomique, GENOSCOPE, Evry, France.,CNRS, UMR8030, Evry, France.,Université d'Evry Val d'Essonne, Evry, France
| | - Corinne Da Silva
- CEA - Institut de Génomique, GENOSCOPE, Evry, France.,CNRS, UMR8030, Evry, France.,Université d'Evry Val d'Essonne, Evry, France
| | - Patrick Wincker
- CEA - Institut de Génomique, GENOSCOPE, Evry, France.,CNRS, UMR8030, Evry, France.,Université d'Evry Val d'Essonne, Evry, France
| | - Stéphane Le Crom
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles Guyane, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), Paris, France
| | - Fabrice Not
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Lucie Bittner
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles Guyane, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), Paris, France
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List JM. Cultural Phylogenetics: Concepts and Applications in Archaeology. — Edited by Larissa Mendoza Straffon. Syst Biol 2016. [DOI: 10.1093/sysbio/syw085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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8
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List JM, Pathmanathan JS, Lopez P, Bapteste E. Unity and disunity in evolutionary sciences: process-based analogies open common research avenues for biology and linguistics. Biol Direct 2016; 11:39. [PMID: 27544206 PMCID: PMC4992195 DOI: 10.1186/s13062-016-0145-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/06/2016] [Indexed: 11/13/2022] Open
Abstract
Background For a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have persisted, and some even turned out to be fruitful, inspiring the transfer of methods and models between biology and linguistics up to today. Most proposed analogies were based on a comparison of the research objects rather than the processes that shaped their evolution. Focusing on process-based analogies, however, has the advantage of minimizing the risk of overstating similarities, while at the same time reflecting the common strategy to use processes to explain the evolution of complexity in both fields. Results We compared important evolutionary processes in biology and linguistics and identified processes specific to only one of the two disciplines as well as processes which seem to be analogous, potentially reflecting core evolutionary processes. These new process-based analogies support novel methodological transfer, expanding the application range of biological methods to the field of historical linguistics. We illustrate this by showing (i) how methods dealing with incomplete lineage sorting offer an introgression-free framework to analyze highly mosaic word distributions across languages; (ii) how sequence similarity networks can be used to identify composite and borrowed words across different languages; (iii) how research on partial homology can inspire new methods and models in both fields; and (iv) how constructive neutral evolution provides an original framework for analyzing convergent evolution in languages resulting from common descent (Sapir’s drift). Conclusions Apart from new analogies between evolutionary processes, we also identified processes which are specific to either biology or linguistics. This shows that general evolution cannot be studied from within one discipline alone. In order to get a full picture of evolution, biologists and linguists need to complement their studies, trying to identify cross-disciplinary and discipline-specific evolutionary processes. The fact that we found many process-based analogies favoring transfer from biology to linguistics further shows that certain biological methods and models have a broader scope than previously recognized. This opens fruitful paths for collaboration between the two disciplines. Reviewers This article was reviewed by W. Ford Doolittle and Eugene V. Koonin. Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0145-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johann-Mattis List
- CRLAO/EHESS, 2 rue de Lille, Paris, 75007, France. .,Equipe AIRE, UMR 7138, Laboratoire Evolution Paris-Seine, Université Pierre et Marie Curie, 7 quai St Bernard, Paris, 75005, France.
| | - Jananan Sylvestre Pathmanathan
- Equipe AIRE, UMR 7138, Laboratoire Evolution Paris-Seine, Université Pierre et Marie Curie, 7 quai St Bernard, Paris, 75005, France
| | - Philippe Lopez
- Equipe AIRE, UMR 7138, Laboratoire Evolution Paris-Seine, Université Pierre et Marie Curie, 7 quai St Bernard, Paris, 75005, France
| | - Eric Bapteste
- Equipe AIRE, UMR 7138, Laboratoire Evolution Paris-Seine, Université Pierre et Marie Curie, 7 quai St Bernard, Paris, 75005, France
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Shapiro JA. Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process. BIOLOGY 2016; 5:E27. [PMID: 27338490 PMCID: PMC4929541 DOI: 10.3390/biology5020027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/20/2016] [Accepted: 06/02/2016] [Indexed: 01/15/2023]
Abstract
The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess "Read-Write Genomes" they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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