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For: Iturbe-Espinoza P, Brandt BW, Braster M, Bonte M, Brown DM, van Spanning RJM. Effects of DNA preservation solution and DNA extraction methods on microbial community profiling of soil. Folia Microbiol (Praha) 2021;66:597-606. [PMID: 33834428 PMCID: PMC8298342 DOI: 10.1007/s12223-021-00866-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/25/2021] [Indexed: 11/28/2022]
Number Cited by Other Article(s)
1
Smenderovac E, Rheault K, Moisan MA, Emilson C, Brazeau É, Morency MJ, Gagné P, Maire V, Emilson E, Venier L, Martineau C. Desiccation as a suitable alternative to cold-storage of phyllosphere samples for DNA-based microbial community analyses. Sci Rep 2025;15:4243. [PMID: 39905028 PMCID: PMC11794883 DOI: 10.1038/s41598-024-82367-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 12/04/2024] [Indexed: 02/06/2025]  Open
2
Purushothaman S, Meola M, Roloff T, Rooney AM, Egli A. Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection. Sci Rep 2024;14:29531. [PMID: 39604411 PMCID: PMC11603047 DOI: 10.1038/s41598-024-80660-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 11/21/2024] [Indexed: 11/29/2024]  Open
3
Child HT, Wierzbicki L, Joslin GR, Tennant RK. Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing. Access Microbiol 2024;6:000868.v3. [PMID: 39346682 PMCID: PMC11432601 DOI: 10.1099/acmi.0.000868.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 09/12/2024] [Indexed: 10/01/2024]  Open
4
Reynolds MC, Cadillo-Quiroz H. Microbial DNA sample preservation and possible artifacts for field-based research in remote tropical peatlands. J Microbiol Methods 2024;224:106997. [PMID: 39009285 DOI: 10.1016/j.mimet.2024.106997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 07/07/2024] [Accepted: 07/12/2024] [Indexed: 07/17/2024]
5
Mejait A, Fildier A, Giroud B, Daniele G, Wiest L, Raviglione D, Kotarba J, Toulza E, Ramirez T, Lanseman A, Clerissi C, Vulliet E, Calvayrac C, Salvia MV. Validation of the Chemical and Biological Steps Required Implementing an Advanced Multi-Omics Approach for Assessing the Fate and Impact of Contaminants in Lagoon Sediments. Metabolites 2024;14:454. [PMID: 39195550 DOI: 10.3390/metabo14080454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/26/2024] [Accepted: 08/02/2024] [Indexed: 08/29/2024]  Open
6
Jensen TBN, Dall SM, Knutsson S, Karst SM, Albertsen M. High-throughput DNA extraction and cost-effective miniaturized metagenome and amplicon library preparation of soil samples for DNA sequencing. PLoS One 2024;19:e0301446. [PMID: 38573983 PMCID: PMC10994328 DOI: 10.1371/journal.pone.0301446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024]  Open
7
Smenderovac E, Emilson C, Rheault K, Brazeau É, Morency MJ, Gagné P, Venier L, Martineau C. Drying as an effective method to store soil samples for DNA-based microbial community analyses: a comparative study. Sci Rep 2024;14:1725. [PMID: 38242898 PMCID: PMC10798986 DOI: 10.1038/s41598-023-50541-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/21/2023] [Indexed: 01/21/2024]  Open
8
Bomberg M, Miettinen H. Anionic nanocellulose as competing agent in microbial DNA extraction from mine process samples. J Microbiol Methods 2023;215:106850. [PMID: 37907119 DOI: 10.1016/j.mimet.2023.106850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/04/2023] [Accepted: 10/25/2023] [Indexed: 11/02/2023]
9
Iturbe-Espinoza P, Bonte M, Weedon JT, Braster M, Brandt BW, van Spanning RJ. Correlating the succession of microbial communities from Nigerian soils to petroleum biodegradation. World J Microbiol Biotechnol 2023;39:239. [PMID: 37392206 PMCID: PMC10314880 DOI: 10.1007/s11274-023-03656-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 05/19/2023] [Indexed: 07/03/2023]
10
Cesar T, Salgaço MK, Mesa V, Sartoratto A, Sivieri K. Exploring the Association between Citrus Nutraceutical Eriocitrin and Metformin for Improving Pre-Diabetes in a Dynamic Microbiome Model. Pharmaceuticals (Basel) 2023;16:650. [PMID: 37242433 PMCID: PMC10221435 DOI: 10.3390/ph16050650] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023]  Open
11
De Oliveira FL, Salgaço MK, de Oliveira MT, Mesa V, Sartoratto A, Peregrino AM, Ramos WS, Sivieri K. Exploring the Potential of Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 as Promising Psychobiotics Using SHIME. Nutrients 2023;15:nu15061521. [PMID: 36986251 PMCID: PMC10056475 DOI: 10.3390/nu15061521] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/12/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]  Open
12
Methanotrophy by a Mycobacterium species that dominates a cave microbial ecosystem. Nat Microbiol 2022;7:2089-2100. [PMID: 36329197 DOI: 10.1038/s41564-022-01252-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/14/2022] [Indexed: 11/06/2022]
13
Vita MM, Iturbe-Espinoza P, Bonte M, Brandt BW, Braster M, Brown DM, van Spanning RJM. Oil Absorbent Polypropylene Particles Stimulate Biodegradation of Crude Oil by Microbial Consortia. Front Microbiol 2022;13:853285. [PMID: 35677906 PMCID: PMC9169047 DOI: 10.3389/fmicb.2022.853285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022]  Open
14
Iturbe-Espinoza P, Bonte M, Gundlach E, Brandt BW, Braster M, van Spanning RJM. Adaptive changes of sediment microbial communities associated with cleanup of oil spills in Nigerian mangrove forests. MARINE POLLUTION BULLETIN 2022;176:113406. [PMID: 35180540 DOI: 10.1016/j.marpolbul.2022.113406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
15
Kawai Y, Ozawa N, Fukuda T, Suzuki N, Mikata K. Development of an efficient antimicrobial susceptibility testing method with species identification by Nanopore sequencing of 16S rRNA amplicons. PLoS One 2022;17:e0262912. [PMID: 35113894 PMCID: PMC8812843 DOI: 10.1371/journal.pone.0262912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 01/08/2022] [Indexed: 01/13/2023]  Open
16
Dully V, Rech G, Wilding TA, Lanzén A, MacKichan K, Berrill I, Stoeck T. Comparing sediment preservation methods for genomic biomonitoring of coastal marine ecosystems. MARINE POLLUTION BULLETIN 2021;173:113129. [PMID: 34784523 DOI: 10.1016/j.marpolbul.2021.113129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
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