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For: Davis A, Kohler C, Alsallaq R, Hayden R, Maron G, Margolis E. Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass. Biotechniques 2019;66:285-9. [PMID: 31124702 DOI: 10.2144/btn-2019-0016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
Number Cited by Other Article(s)
1
Lee AWT, Ng ICF, Wong EYK, Wong ITF, Sze RPP, Chan KY, So TY, Zhang Z, Ka-Yee Fung S, Choi-Ying Wong S, Tam WY, Lao HY, Lee LK, Leung JSL, Chan CTM, Ng TTL, Zhang J, Chow FWN, Leung PHM, Siu GKH. Comprehensive identification of pathogenic microbes and antimicrobial resistance genes in food products using nanopore sequencing-based metagenomics. Food Microbiol 2024;121:104493. [PMID: 38637066 DOI: 10.1016/j.fm.2024.104493] [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: 01/08/2024] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 04/20/2024]
2
Tansirichaiya S, Songsomboon K, Chaianant N, Lertsivawinyu W, Al‐Haroni M. Impact of cell lysis treatment before saliva metagenomic DNA extraction on the oral microbiome and the associated resistome. Clin Exp Dent Res 2024;10:e905. [PMID: 38938117 PMCID: PMC11211641 DOI: 10.1002/cre2.905] [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: 12/09/2023] [Revised: 04/30/2024] [Accepted: 05/13/2024] [Indexed: 06/29/2024]  Open
3
Moinet M, Collis RM, Rogers L, Devane ML, Biggs PJ, Stott R, Marshall J, Muirhead R, Cookson AL. Development of a multiplex droplet digital PCR assay for simultaneous detection and quantification of Escherichia coli, E. marmotae, and E. ruysiae in water samples. J Microbiol Methods 2024;220:106909. [PMID: 38432551 DOI: 10.1016/j.mimet.2024.106909] [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: 12/03/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
4
Merker Breyer G, De Carli S, Rocha Jacques Da Silva ME, Dias ME, Muterle Varela AP, Bertoni Mann M, Frazzon J, Quoos Mayer F, Góes Neto A, Maboni Siqueira F. Alternative amplicon-PCR protocol for maximizing bacterial and fungal sequencing in low-biomass samples. Anal Biochem 2024;687:115449. [PMID: 38145697 DOI: 10.1016/j.ab.2023.115449] [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: 08/23/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 12/27/2023]
5
Neidhöfer C, Bagniceva M, Wetzig N, Sieber MA, Thiele R, Parčina M. Pragmatic Considerations When Extracting DNA for Metagenomics Analyses of Clinical Samples. Int J Mol Sci 2023;24:11262. [PMID: 37511022 PMCID: PMC10379426 DOI: 10.3390/ijms241411262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023]  Open
6
Shen J, McFarland AG, Blaustein RA, Rose LJ, Perry-Dow KA, Moghadam AA, Hayden MK, Young VB, Hartmann EM. An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics. MICROBIOME 2022;10:206. [PMID: 36457108 PMCID: PMC9716758 DOI: 10.1186/s40168-022-01412-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
7
Lima A, França A, Muzny CA, Taylor CM, Cerca N. DNA extraction leads to bias in bacterial quantification by qPCR. Appl Microbiol Biotechnol 2022;106:7993-8006. [PMID: 36374332 PMCID: PMC10493044 DOI: 10.1007/s00253-022-12276-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]
8
Vaher K, Bogaert D, Richardson H, Boardman JP. Microbiome-gut-brain axis in brain development, cognition and behavior during infancy and early childhood. DEVELOPMENTAL REVIEW 2022. [DOI: 10.1016/j.dr.2022.101038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
9
Springer A, Wagner L, Koehler S, Klinger S, Breves G, Brüggemann DA, Strube C. Modulation of the porcine intestinal microbiota in the course of Ascaris suum infection. Parasit Vectors 2022;15:433. [PMID: 36397169 PMCID: PMC9673396 DOI: 10.1186/s13071-022-05535-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/10/2022] [Indexed: 11/18/2022]  Open
10
Inferring Species Compositions of Complex Fungal Communities from Long- and Short-Read Sequence Data. mBio 2022;13:e0244421. [PMID: 35404122 PMCID: PMC9040722 DOI: 10.1128/mbio.02444-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
11
Abellan-Schneyder I, Schusser AJ, Neuhaus K. ddPCR allows 16S rRNA gene amplicon sequencing of very small DNA amounts from low-biomass samples. BMC Microbiol 2021;21:349. [PMID: 34922460 PMCID: PMC8684222 DOI: 10.1186/s12866-021-02391-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 11/15/2021] [Indexed: 12/15/2022]  Open
12
A Simple, Cost-Effective, and Automation-Friendly Direct PCR Approach for Bacterial Community Analysis. mSystems 2021;6:e0022421. [PMID: 34581599 PMCID: PMC8547444 DOI: 10.1128/msystems.00224-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
13
Nearing JT, Comeau AM, Langille MGI. Identifying biases and their potential solutions in human microbiome studies. MICROBIOME 2021;9:113. [PMID: 34006335 PMCID: PMC8132403 DOI: 10.1186/s40168-021-01059-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 03/24/2021] [Indexed: 05/13/2023]
14
Respiratory Bacteria Stabilize and Promote Airborne Transmission of Influenza A Virus. mSystems 2020;5:5/5/e00762-20. [PMID: 32873612 PMCID: PMC7470989 DOI: 10.1128/msystems.00762-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
15
Janes VA, van der Laan JS, Matamoros S, Mende DR, de Jong MD, Schultsz C. Thermus thermophilus DNA can be used as internal control for process monitoring of clinical metagenomic next-generation sequencing of urine samples. J Microbiol Methods 2020;176:106005. [PMID: 32687865 DOI: 10.1016/j.mimet.2020.106005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/14/2020] [Accepted: 07/14/2020] [Indexed: 12/20/2022]
16
Validating DNA Extraction Protocols for Bentonite Clay. mSphere 2019;4:4/5/e00334-19. [PMID: 31666313 PMCID: PMC6821930 DOI: 10.1128/msphere.00334-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]  Open
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