Targeted Metagenomic Databases Provide Improved Analysis of Microbiota Samples
Abstract
:1. Introduction
2. Materials and Methods
2.1. Programing Environment
2.2. Building Prerequisite Files
2.3. Artificial Samples
2.4. Phylogenetic Tree
2.5. Diversity Calculations
2.6. Benchmark Comparisons
3. Results
3.1. A Project-Specific Database
3.2. Running the Moonbase Pipeline
3.3. The Customized Database Improves Detection and Quantification
3.4. Assessment of Correct Genome Assignment
3.5. Whole-Genome Metagenomic Diversity with Phylogeny
3.6. Inclusion of Phylogenetic Diversity Increases Statistical Power
4. Discussion
4.1. An Improvement over a Large General Database for Metagenomics
4.2. Perspectives and Improvements
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A. The InSPIRe Consortium
Microbiology: | |
Claire Poyart: U 1016 Institut Cochin Bacteria and Perinatality, FHU Prema, Université Paris Cité, APHP Centre, NRC des Streptocoques Cochin | |
Asmaa Tazi: U 1016 Institut Cochin Cochin Bacteria and Perinatality, FHU Prema Université Paris Cité, APHP Centre, NRC des Streptocoques Cochin | |
Céline Plainvert: NRC des Streptocoques, APHP Cochin | |
Luce Landraud: Inserm 1137 IAME Université Paris Cité, APHP Louis Mourier | |
Microbiology | |
Clermont Olivier: Inserm 1137 IAME Université Paris Cité | |
Nathalie Grall: APHP Bichat Microbiology | |
Methodology: | |
Pierre-Yves Ancel: APHP URC-CIC Cochin-Necker Mère-Enfant U1153 EPOPé, FHU Prema | |
Laurence Lecomte: APHP DRCI, FHU Prema | |
Hendy Abdoul: APHP URC-CIC Cochin-Necker Mère-Enfant, FHU Prema | |
Jessica Rousseau: Data Manager, APHP URC-CIC Cochin-Necker Mère-Enfant | |
Obstetrics: | |
Laurent Mandelbrot: APHP Louis Mourier Obstetrics/Gynecology, FHU Prema, Inserm 1137 IAME Université Paris Cité | |
François Goffinet: APHP Cochin Port-Royal Obstetrics/Gynecology, FHU Prema, U1153 EPOPé, Université Paris Cité | |
Dominique Luton: APHP Bichat Obstetrics/Gynecology, Université Paris Cité | |
Neonatalogy: | |
Pierre-Henri Jarreau: APHP Cochin Port-Royal, Neonatalogy, FHU Prema, Université Paris Cité | |
Luc Desfrère: APHP Louis Mourier Neonatalogy, FHU Prema | |
Lahçene Allal: APHP Bichat Neonatalogy, FHU Prema | |
Metagenomics: | |
Sean P Kennedy: Institut Pasteur, Université Paris Cité, Département de biologie computationnelle, F-75015 Paris, France | |
Agnes Baud: Institut Past, Institut Pasteur, Université Paris Cité, Département de biologie computationnelle, F-75015 Paris, France | |
Kenzo-Hugo Hillion: Institut Past, Institut Pasteur, Université Paris Cité, Département de biologie computationnelle, F-75015 Paris, France | |
Genomics: | |
Céline Méhats: Institut Cochin Inserm U 1016, UMR CNRS 8104, Université Paris Cité, « Des gamètes à la naissance », Génomique, épigénétique et physiopathologie de la reproduction, FHU Prema | |
Frédéric Batteux: Institut Cochin Inserm U 1016, UMR CNRS 8104, Université Paris Cité, «Des gamètes à la naissance», Stress oxydant, prolifération cellulaire et inflammation, FHU Prema | |
Program manager: | |
Véronique Tessier: APHP DRCI | |
Data monitoring and management: | |
Sinthiya Sivanesan: APHP URC/CIC Necker Cochin, FHU Prema | |
Hélène Jabbarian: APHP Louis Mourier, URC Paris-Nord, FHU Prema | |
Industrial partner: | |
Christophe Pannetier: BforCure | |
Laura Lesimple: Université Paris Cité, Institut Cochin, Inserm U1016, CNRS UMR8104, Bacteria and Perinatality team, BforCure |
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Baud, A.; Kennedy, S.P. Targeted Metagenomic Databases Provide Improved Analysis of Microbiota Samples. Microorganisms 2024, 12, 135. https://doi.org/10.3390/microorganisms12010135
Baud A, Kennedy SP. Targeted Metagenomic Databases Provide Improved Analysis of Microbiota Samples. Microorganisms. 2024; 12(1):135. https://doi.org/10.3390/microorganisms12010135
Chicago/Turabian StyleBaud, Agnes, and Sean P. Kennedy. 2024. "Targeted Metagenomic Databases Provide Improved Analysis of Microbiota Samples" Microorganisms 12, no. 1: 135. https://doi.org/10.3390/microorganisms12010135
APA StyleBaud, A., & Kennedy, S. P. (2024). Targeted Metagenomic Databases Provide Improved Analysis of Microbiota Samples. Microorganisms, 12(1), 135. https://doi.org/10.3390/microorganisms12010135