Feb 12, 2024
Bioinformatic procedure for shotgun metagenomic analysis of human saliva microbiota
- Victoria Meslier1,
- Florence Thirion 1,
- Florian Plaza-Onate 1,
- Emmanuelle Le Chatelier 1,
- Mathieu Almeida2
- 1Université Paris Saclay, INRAE MetaGenoPolis, 78350 Jouy-en-Josas, France;
- 2INRAE MetaGenoPolis
Protocol Citation: Victoria Meslier, Florence Thirion , Florian Plaza-Onate , Emmanuelle Le Chatelier , Mathieu Almeida 2024. Bioinformatic procedure for shotgun metagenomic analysis of human saliva microbiota. protocols.io https://dx.doi.org/10.17504/protocols.io.bp2l6x5q1lqe/v1
Manuscript citation:
Meslier, V.; Menozzi, E.; David, A.; Morabito, C.; Lucas Del Pozo, S.; Famechon, A.;
North, J.; Quinquis, B.; Koletsi, S.; Macnaughtan, J.; et al. Evaluation of an
Adapted Semi-Automated DNA Extraction for Human Salivary Shotgun Metagenomics.
Biomolecules 2023, 13, 1505. https://doi.org/10.3390/biom13101505
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: February 09, 2024
Last Modified: May 31, 2024
Protocol Integer ID: 94972
Keywords: ASAPCRN, bioinformatics, human saliva samples, shotgun metagenomics
Funders Acknowledgements:
Agence Nationale de la Recherche
Grant ID: ANR-11-DPBS-0001
Aligning Science Across Parkinson's
Grant ID: ASAP-000420
Disclaimer
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Abstract
This protocol describes the bioinformatical procedure for the study of human saliva microbiota.
Attachments
Guidelines
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Materials
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Safety warnings
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Ethics statement
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Before start
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General description
General description
Read Quality check
Mapping and microbial gene count procedure
Metagenomic Pangenome Species MSP profiles
Protocol references
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2. Langmead, B.; Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 2012, 9, 357–359.
3. Le Chatelier, E.; Almeida, M.; Oñate, F.P.; Pons, N.; Gauthier, F.; Ghozlane, A.; Ehrlich, S.D.; Witherden, E.;
Gomez-Cabrero, D. A catalog of genes and species of the human oral microbiota. Data INRAE Recherche Data Gouv. 2021 .https://doi.org/10.15454/WQ4UTV
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5. Le Chatelier E, Prifti E. Mining Metaomics Data In R. Retrived from https://forgemia.inra.fr/metagenopolis/momr
6. Nielsen, H.B.; Almeida, M.; Juncker, A.S.; Rasmussen, S.; Li, J.; Sunagawa, S.; Plichta, D.R.; Gautier, L.; Pedersen,
A.G.; Le Chatelier, E.; et al. Identification and assembly of genomes andgenetic elements in complex metagenomic samples without using reference genomes. Nat. Biotechnol. 2014, 32, 822–828
7. Plaza-Oñate, F; Le Chatelier, E.; Almeida, M.; Cervino, A.C.L.; Gauthier, F.; Magoulès, F.; Ehrlich, S.D.; Pichaud, M.
MSPminer: Abundance-based reconstitution of microbial pan-genomes from shotgun
metagenomic data. Bioinformatics 2019, 35, 1544–1552
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consistent, rank normalized and complete genome-based taxonomy." Nucleic Acids Research, https://doi.org/10.1093/nar/gkab776
9. Sayers EW, Agarwala R, Bolton EE, Brister JR, Canese K, Clark K, et al. (2019): Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 47: D23–D28
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