Search

Your search keyword '"Rodrigues, Joao Frederico Matias' showing total 18 results
Start Over Author "Rodrigues, Joao Frederico Matias
18 results on '"Rodrigues, Joao Frederico Matias'

2. A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer

Author

Swiss National Science Foundation, Shanghai Municipal Natural Science Foundation, Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), European Commission, Dmitrijeva, Marija [0000-0002-8561-6490], Tackmann, Janko [0000-0003-1467-2863], Matias Rodrigues, João Frederico [0000-0001-8413-9920], Huerta-Cepas, Jaime [0000-0003-4195-5025], Coelho, Luis Pedro [0000-0002-9280-7885], von Mering, Christian [0000-0001-7734-9102], Dmitrijeva, Marija, Tackmann, Janko, Matias Rodrigues, João Frederico, Huerta-Cepas, Jaime, Coelho, Luis Pedro, von Mering, Christian, Swiss National Science Foundation, Shanghai Municipal Natural Science Foundation, Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), European Commission, Dmitrijeva, Marija [0000-0002-8561-6490], Tackmann, Janko [0000-0003-1467-2863], Matias Rodrigues, João Frederico [0000-0001-8413-9920], Huerta-Cepas, Jaime [0000-0003-4195-5025], Coelho, Luis Pedro [0000-0002-9280-7885], von Mering, Christian [0000-0001-7734-9102], Dmitrijeva, Marija, Tackmann, Janko, Matias Rodrigues, João Frederico, Huerta-Cepas, Jaime, Coelho, Luis Pedro, and von Mering, Christian

Abstract

Horizontal gene transfer, the exchange of genetic material through means other than reproduction, is a fundamental force in prokaryotic genome evolution. Genomic persistence of horizontally transferred genes has been shown to be influenced by both ecological and evolutionary factors. However, there is limited availability of ecological information about species other than the habitats from which they were isolated, which has prevented a deeper exploration of ecological contributions to horizontal gene transfer. Here we focus on transfers detected through comparison of individual gene trees to the species tree, assessing the distribution of gene-exchanging prokaryotes across over a million environmental sequencing samples. By analysing detected horizontal gene transfer events, we show distinct functional profiles for recent versus old events. Although most genes transferred are part of the accessory genome, genes transferred earlier in evolution tend to be more ubiquitous within present-day species. We find that co-occurring, interacting and high-abundance species tend to exchange more genes. Finally, we show that host-associated specialist species are most likely to exchange genes with other host-associated specialist species, whereas species found across different habitats have similar gene exchange rates irrespective of their preferred habitat. Our study covers an unprecedented scale of integrated horizontal gene transfer and environmental information, highlighting broad eco-evolutionary trends.

Published
2024

3. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

Author

European Molecular Biology Laboratory, Swiss National Science Foundation, German Research Foundation, European Commission, Agencia Estatal de Investigación (España), Ministerio de Universidades (España), Fullam, Anthony [0000-0002-0884-8124], Letunic, Ivica [0000-0003-3560-4288], Schmidt, Thomas Sebastian [B0000-0001-8587-4177], Ducarmon, Quinten R. [0000-0001-7077-2127], Karcher, Nicolai [0000-0001-7894-8182], Khedkar, Supriya [0000-0001-6606-2202], Kuhn, Michael [0000-0002-2841-872X], Larralde, Martin [0000-0002-3947-4444], Maistrenko, Oleksandr M. [0000-0003-1961-7548], Malfertheiner, Lukas [0000-0002-5697-2007], Milanese, Alessio [0000-0002-7050-2239], Rodrigues, Joao Frederico Matias [0000-0001-8413-9920], Sanchis-López, Claudia [0000-0002-8206-1565], Schudoma, Christian [0000-0003-1157-1354], Szklarczyk, Damian [0000-0002-4052-5069], Sunagawa, Shinichi [0000-0003-3065-0314], Zeller, Georg [0000-0003-1429-7485], Huerta-Cepas, Jaime [0000-0003-4195-5025], von Mering, Christian [0000-0001-7734-9102], Bork, Peer [0000-0002-2627-833X], Mende, Daniel R. [0000-0001-6831-4557], Fullam, Anthony, Letunic, Ivica, Schmidt, Thomas Sebastian, Ducarmon, Quinten R., Karcher, Nicolai, Khedkar, Supriya, Kuhn, Michael, Larralde, Martin, Maistrenko, Oleksandr M., Malfertheiner, Lukas, Milanese, Alessio, Rodrigues, Joao Frederico Matias, Sanchis-López, Claudia, Schudoma, Christian, Szklarczyk, Damian, Sunagawa, Shinichi, Zeller, Georg, Huerta-Cepas, Jaime, von Mering, Christian, Bork, Peer, Mende, Daniel R., European Molecular Biology Laboratory, Swiss National Science Foundation, German Research Foundation, European Commission, Agencia Estatal de Investigación (España), Ministerio de Universidades (España), Fullam, Anthony [0000-0002-0884-8124], Letunic, Ivica [0000-0003-3560-4288], Schmidt, Thomas Sebastian [B0000-0001-8587-4177], Ducarmon, Quinten R. [0000-0001-7077-2127], Karcher, Nicolai [0000-0001-7894-8182], Khedkar, Supriya [0000-0001-6606-2202], Kuhn, Michael [0000-0002-2841-872X], Larralde, Martin [0000-0002-3947-4444], Maistrenko, Oleksandr M. [0000-0003-1961-7548], Malfertheiner, Lukas [0000-0002-5697-2007], Milanese, Alessio [0000-0002-7050-2239], Rodrigues, Joao Frederico Matias [0000-0001-8413-9920], Sanchis-López, Claudia [0000-0002-8206-1565], Schudoma, Christian [0000-0003-1157-1354], Szklarczyk, Damian [0000-0002-4052-5069], Sunagawa, Shinichi [0000-0003-3065-0314], Zeller, Georg [0000-0003-1429-7485], Huerta-Cepas, Jaime [0000-0003-4195-5025], von Mering, Christian [0000-0001-7734-9102], Bork, Peer [0000-0002-2627-833X], Mende, Daniel R. [0000-0001-6831-4557], Fullam, Anthony, Letunic, Ivica, Schmidt, Thomas Sebastian, Ducarmon, Quinten R., Karcher, Nicolai, Khedkar, Supriya, Kuhn, Michael, Larralde, Martin, Maistrenko, Oleksandr M., Malfertheiner, Lukas, Milanese, Alessio, Rodrigues, Joao Frederico Matias, Sanchis-López, Claudia, Schudoma, Christian, Szklarczyk, Damian, Sunagawa, Shinichi, Zeller, Georg, Huerta-Cepas, Jaime, von Mering, Christian, Bork, Peer, and Mende, Daniel R.

Abstract

The interpretation of genomic, transcriptomic and other microbial 'omics data is highly dependent on the availability of well-annotated genomes. As the number of publicly available microbial genomes continues to increase exponentially, the need for quality control and consistent annotation is becoming critical. We present proGenomes3, a database of 907 388 high-quality genomes containing 4 billion genes that passed stringent criteria and have been consistently annotated using multiple functional and taxonomic databases including mobile genetic elements and biosynthetic gene clusters. proGenomes3 encompasses 41 171 species-level clusters, defined based on universal single copy marker genes, for which pan-genomes and contextual habitat annotations are provided. The database is available at http://progenomes.embl.de/.

Published
2023

4. Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites

Author

Janko Tackmann, Natasha Arora, Thomas Sebastian Benedikt Schmidt, João Frederico Matias Rodrigues, and Christian von Mering

Subjects
Human microbiome, Biomarkers, Mixture, Random Forest, Generalized Local Learning, Microbial ecology, QR100-130
Abstract

Abstract Background The identification of body site-specific microbial biomarkers and their use for classification tasks have promising applications in medicine, microbial ecology, and forensics. Previous studies have characterized site-specific microbiota and shown that sample origin can be accurately predicted by microbial content. However, these studies were usually restricted to single datasets with consistent experimental methods and conditions, as well as comparatively small sample numbers. The effects of study-specific biases and statistical power on classification performance and biomarker identification thus remain poorly understood. Furthermore, reliable detection in mixtures of different body sites or with noise from environmental contamination has rarely been investigated thus far. Finally, the impact of ecological associations between microbes on biomarker discovery was usually not considered in previous work. Results Here we present the analysis of one of the largest cross-study sequencing datasets of microbial communities from human body sites (15,082 samples from 57 publicly available studies). We show that training a Random Forest Classifier on this aggregated dataset increases prediction performance for body sites by 35% compared to a single-study classifier. Using simulated datasets, we further demonstrate that the source of different microbial contributions in mixtures of different body sites or with soil can be detected starting at 1% of the total microbial community. We apply a biomarker selection method that excludes indirect environmental associations driven by microbe-microbe associations, yielding a parsimonious set of highly predictive taxa including novel biomarkers and excluding many previously reported taxa. We find a considerable fraction of unclassified biomarkers (“microbial dark matter”) and observe that negatively associated taxa have a surprisingly high impact on classification performance. We further detect a significant enrichment of rod-shaped, motile, and sporulating taxa for feces biomarkers, consistent with a highly competitive environment. Conclusions Our machine learning model shows strong body site classification performance, both in single-source samples and mixtures, making it promising for tasks requiring high accuracy, such as forensic applications. We report a core set of ecologically informed biomarkers, inferred across a wide range of experimental protocols and conditions, providing the most concise, general, and least biased overview of body site-associated microbes to date.

Published
2018
Full Text
View/download PDF

5. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

Author

Fullam, Anthony; https://orcid.org/0000-0002-0884-8124, Letunic, Ivica; https://orcid.org/0000-0003-3560-4288, Schmidt, Thomas S B; https://orcid.org/0000-0001-8587-4177, Ducarmon, Quinten R; https://orcid.org/0000-0001-7077-2127, Karcher, Nicolai; https://orcid.org/0000-0001-7894-8182, Khedkar, Supriya; https://orcid.org/0000-0001-6606-2202, Kuhn, Michael; https://orcid.org/0000-0002-2841-872X, Larralde, Martin; https://orcid.org/0000-0002-3947-4444, Maistrenko, Oleksandr M; https://orcid.org/0000-0003-1961-7548, Malfertheiner, Lukas; https://orcid.org/0000-0002-5697-2007, Milanese, Alessio; https://orcid.org/0000-0002-7050-2239, Rodrigues, Joao Frederico Matias; https://orcid.org/0000-0001-8413-9920, Sanchis-López, Claudia; https://orcid.org/0000-0002-8206-1565, Schudoma, Christian; https://orcid.org/0000-0003-1157-1354, Szklarczyk, Damian; https://orcid.org/0000-0002-4052-5069, Sunagawa, Shinichi; https://orcid.org/0000-0003-3065-0314, Zeller, Georg; https://orcid.org/0000-0003-1429-7485, Huerta-Cepas, Jaime; https://orcid.org/0000-0003-4195-5025, von Mering, Christian; https://orcid.org/0000-0001-7734-9102, Bork, Peer; https://orcid.org/0000-0002-2627-833X, Mende, Daniel R; https://orcid.org/0000-0001-6831-4557, Fullam, Anthony; https://orcid.org/0000-0002-0884-8124, Letunic, Ivica; https://orcid.org/0000-0003-3560-4288, Schmidt, Thomas S B; https://orcid.org/0000-0001-8587-4177, Ducarmon, Quinten R; https://orcid.org/0000-0001-7077-2127, Karcher, Nicolai; https://orcid.org/0000-0001-7894-8182, Khedkar, Supriya; https://orcid.org/0000-0001-6606-2202, Kuhn, Michael; https://orcid.org/0000-0002-2841-872X, Larralde, Martin; https://orcid.org/0000-0002-3947-4444, Maistrenko, Oleksandr M; https://orcid.org/0000-0003-1961-7548, Malfertheiner, Lukas; https://orcid.org/0000-0002-5697-2007, Milanese, Alessio; https://orcid.org/0000-0002-7050-2239, Rodrigues, Joao Frederico Matias; https://orcid.org/0000-0001-8413-9920, Sanchis-López, Claudia; https://orcid.org/0000-0002-8206-1565, Schudoma, Christian; https://orcid.org/0000-0003-1157-1354, Szklarczyk, Damian; https://orcid.org/0000-0002-4052-5069, Sunagawa, Shinichi; https://orcid.org/0000-0003-3065-0314, Zeller, Georg; https://orcid.org/0000-0003-1429-7485, Huerta-Cepas, Jaime; https://orcid.org/0000-0003-4195-5025, von Mering, Christian; https://orcid.org/0000-0001-7734-9102, Bork, Peer; https://orcid.org/0000-0002-2627-833X, and Mende, Daniel R; https://orcid.org/0000-0001-6831-4557

Abstract

The interpretation of genomic, transcriptomic and other microbial 'omics data is highly dependent on the availability of well-annotated genomes. As the number of publicly available microbial genomes continues to increase exponentially, the need for quality control and consistent annotation is becoming critical. We present proGenomes3, a database of 907 388 high-quality genomes containing 4 billion genes that passed stringent criteria and have been consistently annotated using multiple functional and taxonomic databases including mobile genetic elements and biosynthetic gene clusters. proGenomes3 encompasses 41 171 species-level clusters, defined based on universal single copy marker genes, for which pan-genomes and contextual habitat annotations are provided. The database is available at http://progenomes.embl.de/.

Published
2023

6. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

Author

Anthony Fullam, Ivica Letunic, Thomas S B Schmidt, Quinten R Ducarmon, Nicolai Karcher, Supriya Khedkar, Michael Kuhn, Martin Larralde, Oleksandr M Maistrenko, Lukas Malfertheiner, Alessio Milanese, Joao Frederico Matias Rodrigues, Claudia Sanchis-López, Christian Schudoma, Damian Szklarczyk, Shinichi Sunagawa, Georg Zeller, Jaime Huerta-Cepas, Christian von Mering, Peer Bork, Daniel R Mende, Medical Microbiology and Infection Prevention, AII - Infectious diseases, University of Zurich, European Molecular Biology Laboratory, Swiss National Science Foundation, German Research Foundation, European Commission, Agencia Estatal de Investigación (España), Ministerio de Universidades (España), Fullam, Anthony, Letunic, Ivica, Schmidt, Thomas Sebastian, Ducarmon, Quinten R., Karcher, Nicolai, Khedkar, Supriya, Kuhn, Michael, Larralde, Martin, Maistrenko, Oleksandr M., Malfertheiner, Lukas, Milanese, Alessio, Rodrigues, Joao Frederico Matias, Sanchis-López, Claudia, Schudoma, Christian, Szklarczyk, Damian, Sunagawa, Shinichi, Zeller, Georg, Huerta-Cepas, Jaime, von Mering, Christian, Bork, Peer, and Mende, Daniel R.

Subjects
UFSP13-7 Evolution in Action: From Genomes to Ecosystems, Cardiovascular and Metabolic Diseases, Genetics, 570 Life sciences, biology, 10124 Institute of Molecular Life Sciences
Abstract

7 Pág., The interpretation of genomic, transcriptomic and other microbial 'omics data is highly dependent on the availability of well-annotated genomes. As the number of publicly available microbial genomes continues to increase exponentially, the need for quality control and consistent annotation is becoming critical. We present proGenomes3, a database of 907 388 high-quality genomes containing 4 billion genes that passed stringent criteria and have been consistently annotated using multiple functional and taxonomic databases including mobile genetic elements and biosynthetic gene clusters. proGenomes3 encompasses 41 171 species-level clusters, defined based on universal single copy marker genes, for which pan-genomes and contextual habitat annotations are provided. The database is available at http://progenomes.embl.de/., Amsterdam UMC; European Molecular Biology Laboratory (EMBL); Swiss National Science Foundation (SNSF) [205321_184955 to S.S.]; NCCR Microbiomes [51NF40_180575 to S.S. and C.v.M.]; German Federal Ministry of Education and Research (BMBF); de.NBI network [031A537B to P.B., 031L0181A to G.Z.]; German Research Foundation (DFG) [395357507 – SFB 1371 to G.Z., ‘NFDI4Microbiota’ to P.B.]; European Grant with code [PGC2018-098073-A-I00MCIU/AEI/FEDER to J.H.-C.]; Spanish Ministry of Universities [FPU-19/06635 to C.S.-L.]. Funding for open access charge: EMBL.

Published
2022

7. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

Author

Fullam, Anthony, primary, Letunic, Ivica, additional, Schmidt, Thomas S B, additional, Ducarmon, Quinten R, additional, Karcher, Nicolai, additional, Khedkar, Supriya, additional, Kuhn, Michael, additional, Larralde, Martin, additional, Maistrenko, Oleksandr M, additional, Malfertheiner, Lukas, additional, Milanese, Alessio, additional, Rodrigues, Joao Frederico Matias, additional, Sanchis-López, Claudia, additional, Schudoma, Christian, additional, Szklarczyk, Damian, additional, Sunagawa, Shinichi, additional, Zeller, Georg, additional, Huerta-Cepas, Jaime, additional, von Mering, Christian, additional, Bork, Peer, additional, and Mende, Daniel R, additional

Published
2022
Full Text
View/download PDF

9. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

Author

European Commission, EMBO, Maistrenko, Oleksandr M. [0000-0003-1961-7548], Mende, Daniel R. [0000-0001-6831-4557], Hildebrand, Falk [0000-0002-0078-8948], Schmidt, Thomas Sebastian [0000-0001-8587-4177], Li, Simone S. [0000-0002-0073-3656], Rodrigues, Joao Frederico Matias [0000-0001-8413-9920], von Mering, Christian [0000-0001-7734-9102], Coelho, Luis Pedro [0000-0002-9280-7885], Huerta-Cepas, Jaime [0000-0003-4195-5025], Sunagawa, Shinichi [0000-0003-3065-0314], Bork, Peer [0000-0002-2627-833X], Maistrenko, Oleksandr M., Mende, Daniel R., Luetge, Mechthild, Hildebrand, Falk, Schmidt, Thomas Sebastian, Li, Simone S., Rodrigues, Joao Frederico Matias, von Mering, Christian, Coelho, Luis Pedro, Huerta-Cepas, Jaime, Sunagawa, Shinichi, Bork, Peer, European Commission, EMBO, Maistrenko, Oleksandr M. [0000-0003-1961-7548], Mende, Daniel R. [0000-0001-6831-4557], Hildebrand, Falk [0000-0002-0078-8948], Schmidt, Thomas Sebastian [0000-0001-8587-4177], Li, Simone S. [0000-0002-0073-3656], Rodrigues, Joao Frederico Matias [0000-0001-8413-9920], von Mering, Christian [0000-0001-7734-9102], Coelho, Luis Pedro [0000-0002-9280-7885], Huerta-Cepas, Jaime [0000-0003-4195-5025], Sunagawa, Shinichi [0000-0003-3065-0314], Bork, Peer [0000-0002-2627-833X], Maistrenko, Oleksandr M., Mende, Daniel R., Luetge, Mechthild, Hildebrand, Falk, Schmidt, Thomas Sebastian, Li, Simone S., Rodrigues, Joao Frederico Matias, von Mering, Christian, Coelho, Luis Pedro, Huerta-Cepas, Jaime, Sunagawa, Shinichi, and Bork, Peer

Abstract

Microbial organisms inhabit virtually all environments and encompass a vast biological diversity. The pangenome concept aims to facilitate an understanding of diversity within defined phylogenetic groups. Hence, pangenomes are increasingly used to characterize the strain diversity of prokaryotic species. To understand the interdependence of pangenome features (such as the number of core and accessory genes) and to study the impact of environmental and phylogenetic constraints on the evolution of conspecific strains, we computed pangenomes for 155 phylogenetically diverse species (from ten phyla) using 7,000 high-quality genomes to each of which the respective habitats were assigned. Species habitat ubiquity was associated with several pangenome features. In particular, core-genome size was more important for ubiquity than accessory genome size. In general, environmental preferences had a stronger impact on pangenome evolution than phylogenetic inertia. Environmental preferences explained up to 49% of the variance for pangenome features, compared with 18% by phylogenetic inertia. This observation was robust when the dataset was extended to 10,100 species (59 phyla). The importance of environmental preferences was further accentuated by convergent evolution of pangenome features in a given habitat type across different phylogenetic clades. For example, the soil environment promotes expansion of pangenome size, while host-associated habitats lead to its reduction. Taken together, we explored the global principles of pangenome evolution, quantified the influence of habitat, and phylogenetic inertia on the evolution of pangenomes and identified criteria governing species ubiquity and habitat specificity.

Published
2020

10. proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.

Author

Fullam, Anthony, Letunic, Ivica, Schmidt, Thomas S B, Ducarmon, Quinten R, Karcher, Nicolai, Khedkar, Supriya, Kuhn, Michael, Larralde, Martin, Maistrenko, Oleksandr M, Malfertheiner, Lukas, Milanese, Alessio, Rodrigues, Joao Frederico Matias, Sanchis-López, Claudia, Schudoma, Christian, Szklarczyk, Damian, Sunagawa, Shinichi, Zeller, Georg, Huerta-Cepas, Jaime, von Mering, Christian, and Bork, Peer

Published
2023
Full Text
View/download PDF

12. A family of interaction-adjusted indices of community similarity

Author

Schmidt, Thomas Sebastian Benedikt, Matias Rodrigues, Joao Frederico, von Mering, Christian, University of Zurich, and Schmidt, Thomas Sebastian Benedikt

Subjects
0301 basic medicine, Oceans and Seas, Ecology (disciplines), media_common.quotation_subject, Context (language use), Biology, Models, Biological, Microbiology, UFSP13-7 Evolution in Action: From Genomes to Ecosystems, 03 medical and health sciences, Similarity (network science), Humans, Ecosystem, Phylogeny, Soil Microbiology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, media_common, 0303 health sciences, Bacteria, Phylogenetic tree, Community, 030306 microbiology, Ecology, 2404 Microbiology, Computational Biology, Biota, 10124 Institute of Molecular Life Sciences, 1105 Ecology, Evolution, Behavior and Systematics, 030104 developmental biology, Taxon, Habitat, Evolutionary biology, 570 Life sciences, biology, Original Article, Water Microbiology, Diversity (politics)
Abstract

Interactions between taxa are essential drivers of ecological community structure and dynamics, but they are not taken into account by traditional indices of diversity. In this study, we propose a novel family of indices that quantify community similarity in the context of taxa interaction networks. Using publicly available datasets, we assess the performance of two specific indices which are Taxa INteraction-Adjusted (TINA, based on taxa co-occurrence networks), and Phylogenetic INteraction-Adjusted (PINA, based on phylogenetic similarities). TINA and PINA outperformed traditional indices when partitioning human-associated microbial communities according to habitat, even for extremely downsampled datasets, and when organising ocean micro-eukaryotic plankton diversity according to geographical and physicochemical gradients. We argue that interaction-adjusted indices capture novel aspects of diversity outside the scope of traditional approaches, highlighting the biological significance of ecological association networks in the interpretation of community similarity.

Published
2016
Full Text
View/download PDF

15. Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites

Author

Tackmann, Janko, Arora, Natasha, Schmidt, Thomas Sebastian Beedikt, Rodrigues, João Frederico Matias, von Mering, Christian; https://orcid.org/0000-0001-7734-9102, Tackmann, Janko, Arora, Natasha, Schmidt, Thomas Sebastian Beedikt, Rodrigues, João Frederico Matias, and von Mering, Christian; https://orcid.org/0000-0001-7734-9102

Abstract

BACKGROUND: The identification of body site-specific microbial biomarkers and their use for classification tasks have promising applications in medicine, microbial ecology, and forensics. Previous studies have characterized site-specific microbiota and shown that sample origin can be accurately predicted by microbial content. However, these studies were usually restricted to single datasets with consistent experimental methods and conditions, as well as comparatively small sample numbers. The effects of study-specific biases and statistical power on classification performance and biomarker identification thus remain poorly understood. Furthermore, reliable detection in mixtures of different body sites or with noise from environmental contamination has rarely been investigated thus far. Finally, the impact of ecological associations between microbes on biomarker discovery was usually not considered in previous work. RESULTS: Here we present the analysis of one of the largest cross-study sequencing datasets of microbial communities from human body sites (15,082 samples from 57 publicly available studies). We show that training a Random Forest Classifier on this aggregated dataset increases prediction performance for body sites by 35% compared to a single-study classifier. Using simulated datasets, we further demonstrate that the source of different microbial contributions in mixtures of different body sites or with soil can be detected starting at 1% of the total microbial community. We apply a biomarker selection method that excludes indirect environmental associations driven by microbe-microbe associations, yielding a parsimonious set of highly predictive taxa including novel biomarkers and excluding many previously reported taxa. We find a considerable fraction of unclassified biomarkers ("microbial dark matter") and observe that negatively associated taxa have a surprisingly high impact on classification performance. We further detect a significant enrichment of r

Published
2018

18. A family of interaction-adjusted indices of community similarity.

Author

Schmidt, Thomas Sebastian Benedikt, Matias Rodrigues, João Frederico, and von Mering, Christian

Abstract

Interactions between taxa are essential drivers of ecological community structure and dynamics, but they are not taken into account by traditional indices of β diversity. In this study, we propose a novel family of indices that quantify community similarity in the context of taxa interaction networks. Using publicly available datasets, we assessed the performance of two specific indices that are Taxa INteraction-Adjusted (TINA, based on taxa co-occurrence networks), and Phylogenetic INteraction-Adjusted (PINA, based on phylogenetic similarities). TINA and PINA outperformed traditional indices when partitioning human-associated microbial communities according to habitat, even for extremely downsampled datasets, and when organising ocean micro-eukaryotic plankton diversity according to geographical and physicochemical gradients. We argue that interaction-adjusted indices capture novel aspects of diversity outside the scope of traditional approaches, highlighting the biological significance of ecological association networks in the interpretation of community similarity. [ABSTRACT FROM AUTHOR]

Published
2017
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results