DOI: 10.5281/zenodo.4492210
title: The tpm metabarcoding DNA sequence database for taxonomic allocations using RDP classifier implemented in DADA2.

description: <strong>The </strong><em>tpm</em><strong> metabarcoding DNA sequence database for taxonomic allocations using the Mothur and DADA2 bio-informatic tools</strong> A.C.M. Pozzi<sup>1</sup>, R. Bouchali<sup>1</sup>, L. Marjolet<sup>1</sup>, B. Cournoyer<sup>1</sup> <sup>1 </sup><em>University of Lyon, UMR Ecologie Microbienne Lyon (LEM), CNRS 5557, INRAE 1418, Université Claude Bernard Lyon 1, VetAgro Sup, Research Team “Bacterial Opportunistic Pathogens and Environment” (BPOE), 69280 Marcy L’Etoile, France.</em> <strong>Corresponding authors: </strong> A.C.M. Pozzi, UMR Microbial Ecology, CNRS 5557, CNRS 1418, VetAgro Sup, Main building, aisle 3, 1st floor, 69280 Marcy-L’Etoile, France. Tel. (+33) 478 87 39 47. Fax. (+33) 472 43 12 23. Email: adrien.meynier_pozzi@vetagro-sup.fr B. Cournoyer, UMR Microbial Ecology, CNRS 5557, CNRS 1418, VetAgro Sup, Main building, aisle 3, 1st floor, 69280 Marcy-L’Etoile, France. Tel. (+33) 478 87 56 47. Fax. (+33) 472 43 12 23. Email: and benoit.cournoyer@vetagro-sup.fr <strong>Keywords:</strong> BACtpm, Bacteria, <em>tpm</em>, thiopurine-<em>S</em>-methyltransferase EC:2.1.1.67, Nucleotide sequences, PCR products, Next-Generation-Sequencing, OTHU <strong>Description:</strong> The <em>tpm</em> gene codes for the thiopurine-<em>S</em>-methyltransferase (TPMT), an enzyme that can detoxify metalloid-containing oxyanions and xenobiotics (Cournoyer et al., 1998). Bacterial TPMTs radiated apart from human and animal TPMTs, and showed a vertical evolution in line with the 16S rRNA gene molecular phylogeny (Favre‐Bonté et al., 2005). The <em>tpm</em> database, named BACtpm, was designed to apply the <em>tpm</em>-metabarcoding analytical scheme published in Aigle et al. (2021). It includes the full <em>tpm</em> identifiers, GenBank accession numbers, complete taxonomic records (domain down to strain code) of about 215 nucleotide-long <em>tpm</em> sequences of 840 unique taxa belonging to 139 genera. Nucleotide sequences of <em>tpm</em> (range: 190-233 nucleotides) were either retrieved from public repositories (GenBank) or made available by B. Cournoyer’s research group. Colin et al. (2020) described the PCR and high throughput Illumina Miseq DNA sequencing procedures used to produce <em>tpm</em> sequences. BACtpm v.2.0.1 (June 2021 release) is made available under the Creative Commons Attribution 4.0 International Licence. It can be used for the taxonomic allocations of <em>tpm </em>sequences down to the species and strain levels. Data is stored in the csv format enabling future user to reformat it to fit their specific needs. <strong>Acknowledgments:</strong> We thank the worldwide community of microbiologists who made contributions to public databases in the past decades, and made possible the elaboration of the BACtpm database. We also thank the Field Observatory in Urban Hydrology (OTHU, www.graie.org/othu/), Labex IMU (Intelligence des Mondes Urbains), the Greater Lyon Urban Community, the School of Integrated Watershed Sciences H2O'LYON, and the Lyon Urban School for their support in the development of this database. This work was funded by the French national research program for environmental and occupational health of ANSES under the terms of project “Iouqmer” EST 2016/1/120, l'Agence Nationale de la Recherche through ANR-16-CE32-0006, ANR-17-CE04-0010, ANR-17-EURE-0018 and ANR-17-CONV-0004, by the MITI CNRS project named Urbamic, and the French water agency for the Rhône, Mediterranean and Corsica areas through the Desir and DOmic projects. We thank former BPOE lab members who contributed to start and expand the BACtpm database: Céline COLINON, Romain MARTI, Emilie BOURGEOIS, Sébastien RIBUN and Yannick COLIN. <strong>References:</strong> Aigle, A., Colin, Y., Bouchali, R., Bourgeois, E., Marti, R., Ribun, S., Marjolet, L., Pozzi, A.C.M., Misery, B., Colinon, C., Bernardin-Souibgui, C., Wiest, L., Blaha, D., Galia, W., Cournoyer, B., 2021. Spatio-temporal variations in chemical pollutants found among urban deposits match changes in thiopurine S-methyltransferase-harboring bacteria tracked by the tpm metabarcoding approach. Sci. Total Environ. 767, 145425. https://doi.org/10.1016/j.scitotenv.2021.145425 Colin, Y., Bouchali, R., Marjolet, L., Marti, R., Vautrin, F., Voisin, J., Bourgeois, E., Rodriguez-Nava, V., Blaha, D., Winiarski, T., Mermillod-Blondin, F., Cournoyer, B., 2020. Coalescence of bacterial groups originating from urban runoffs and artificial infiltration systems among aquifer microbiomes. Hydrol. Earth Syst. Sci. 24, 4257–4273. https://doi.org/10.5194/hess-24-4257-2020 Cournoyer, B., Watanabe, S., Vivian, A., 1998. A tellurite-resistance genetic determinant from phytopathogenic pseudomonads encodes a thiopurine methyltransferase: evidence of a widely-conserved family of methyltransferases1The International Collaboration (IC) accession number of the DNA sequence is L49178.1. Biochim. Biophys. Acta BBA - Gene Struct. Expr. 1397, 161–168. https://doi.org/10.1016/S0167-4781(98)00020-7 Favre‐Bonté, S., Ranjard, L., Colinon, C., Prigent‐Combaret, C., Nazaret, S., Cournoyer, B., 2005. Freshwater selenium-methylating bacterial thiopurine methyltransferases: diversity and molecular phylogeny. Environ. Microbiol. 7, 153–164. https://doi.org/10.1111/j.1462-2920.2004.00670.x
description: Change Log; [2.0.1] - 2021-06-23: tpm nucleotide sequences now provided in two separated columns, either aligned with gaps for repeatable use in Mothur or not aligned and without gaps for use with DADA2. [2.1.1] - 2023-10-10: tpm nucleotide sequences added for 20 taxa (Actinoplanes sp. N902-109, Ancylobacter polymorphus DSM2457, Aromatoleum toluclasticum ATCC700605, Aromatoleum bremense PbN1, Aromatoleum diolicum, Candidatus_Macondimonas diazotrophica, Collimonas sp. PAH2, Collimonas humicolas, Emcibacter nanhaiensis CGMCC112471, Leptospira yasudae, Lysobacter sp. TY298, Lysobacter spongiae KACC19276, Lysobacter sp. CF310, Nitrospira sp. ND1, Pseudanabaena biceps PCC7429, Pseudomonas eucalypticola NP1, Pseudomonas alcaligenes MB-090714 , Pseudomonas peli DSM17833, Pseudomonas sp. 9AZ, and Pseudomonas sp. NFACC02), Proteobacteria updated to Pseudomonadota, database formatted uniquely for use with RDP/dada2.