Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985;82(20):6955–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vos M, Quince C, Pijl AS, de Hollander M, Kowalchuk GA. A comparison of rpoB and 16S rRNA as markers in pyrosequencing studies of bacterial diversity. PLoS One. 2012;7(2):e30600.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bukin YS, Galachyants YP, Morozov IV, Bukin SV, Zakharenko AS, Zemskaya TI. The effect of 16S rRNA region choice on bacterial community metabarcoding results. Sci Data. 2019;6(1):190007.
Article
CAS
PubMed
PubMed Central
Google Scholar
Flores R, Shi J, Yu G, Ma B, Ravel J, Goedert JJ, et al. Collection media and delayed freezing effects on microbial composition of human stool. Microbiome. 2015;3:33.
Article
PubMed
PubMed Central
Google Scholar
Choo JM, Leong LE, Rogers GB. Sample storage conditions significantly influence faecal microbiome profiles. Sci Rep. 2015;5:16350.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ma J, Sheng L, Hong Y, Xi C, Gu Y, Zheng N, et al. Variations of gut microbiome profile under different storage conditions and preservation periods: a multi-dimensional evaluation. Front Microbiol. 2020;11:972.
Penington JS, Penno MAS, Ngui KM, Ajami NJ, Roth-Schulze AJ, Wilcox SA, et al. Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis. Sci Rep. 2018;8(1):4386.
Article
PubMed
PubMed Central
CAS
Google Scholar
Abellan-Schneyder I, Matchado MS, Reitmeier S, Sommer A, Sewald Z, Baumbach J, et al. Primer, pipelines, parameters: issues in 16S rRNA gene sequencing. mSphere. 2021;6(1):e01202–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fouhy F, Clooney AG, Stanton C, Claesson MJ, Cotter PD. 16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform. BMC Microbiol. 2016;16(1):123.
Article
PubMed
PubMed Central
CAS
Google Scholar
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2012;41(1):e1.
Article
PubMed
PubMed Central
CAS
Google Scholar
Thijs S, Op De Beeck M, Beckers B, Truyens S, Stevens V, Van Hamme JD, et al. Comparative evaluation of four bacteria-specific primer pairs for 16S rRNA gene surveys. Front Microbiol. 2017;8:494.
Article
PubMed
PubMed Central
Google Scholar
Tremblay J, Singh K, Fern A, Kirton ES, He S, Woyke T, et al. Primer and platform effects on 16S rRNA tag sequencing. Front Microbiol. 2015;6:771.
PubMed
PubMed Central
Google Scholar
Almeida A, Mitchell AL, Tarkowska A, Finn RD. Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments. GigaScience. 2018;7(5):giy054.
De Filippis F, Parente E, Zotta T, Ercolini D. A comparison of bioinformatic approaches for 16S rRNA gene profiling of food bacterial microbiota. Int J Food Microbiol. 2018;265:9–17.
Article
PubMed
CAS
Google Scholar
Marizzoni M, Gurry T, Provasi S, Greub G, Lopizzo N, Ribaldi F, et al. Comparison of bioinformatics pipelines and operating Systems for the Analyses of 16S rRNA gene amplicon sequences in human fecal samples. Front Microbiol. 2020;11:1262.
Park S-C, Won S. Evaluation of 16S rRNA databases for taxonomic assignments using mock community. Genomics Inform. 2018;16(4):e24.
Article
PubMed
PubMed Central
Google Scholar
Sierra MA, Li Q, Pushalkar S, Paul B, Sandoval TA, Kamer AR, et al. The influences of bioinformatics tools and reference databases in analyzing the human oral microbial community. Genes (Basel). 2020;11(8):878.
Article
CAS
PubMed Central
Google Scholar
Nearing JT, Douglas GM, Comeau AM, Langille MGI. Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches. PeerJ. 2018;6:e5364.
Article
PubMed
PubMed Central
CAS
Google Scholar
Fiedorová K, Radvanský M, Němcová E, Grombiříková H, Bosák J, Černochová M, et al. The impact of DNA extraction methods on stool bacterial and fungal microbiota community recovery. Front Microbiol. 2019;10:821.
Wesolowska-Andersen A, Bahl MI, Carvalho V, Kristiansen K, Sicheritz-Pontén T, Gupta R, et al. Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis. Microbiome. 2014;2(1):19.
Article
PubMed
PubMed Central
Google Scholar
Hart ML, Meyer A, Johnson PJ, Ericsson AC. Comparative evaluation of DNA extraction methods from feces of multiple host species for downstream next-generation sequencing. PLoS One. 2015;10(11):e0143334.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lim MY, Song E-J, Kim SH, Lee J, Nam Y-D. Comparison of DNA extraction methods for human gut microbial community profiling. Syst Appl Microbiol. 2018;41(2):151–7.
Article
CAS
PubMed
Google Scholar
Wagner Mackenzie B, Waite DW, Taylor MW. Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences. Front Microbiol. 2015;6:130.
Santiago A, Panda S, Mengels G, Martinez X, Azpiroz F, Dore J, et al. Processing faecal samples: a step forward for standards in microbial community analysis. BMC Microbiol. 2014;14(1):112.
Article
PubMed
PubMed Central
Google Scholar
Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, et al. Towards standards for human fecal sample processing in metagenomic studies. Nat Biotechnol. 2017;35(11):1069–76.
Article
CAS
PubMed
Google Scholar
McOrist AL, Jackson M, Bird AR. A comparison of five methods for extraction of bacterial DNA from human faecal samples. J Microbiol Methods. 2002;50(2):131–9.
Article
CAS
PubMed
Google Scholar
Multinu F, Harrington SC, Chen J, Jeraldo PR, Johnson S, Chia N, et al. Systematic Bias introduced by genomic DNA template dilution in 16S rRNA gene-targeted microbiota profiling in human stool homogenates. mSphere. 2018;3(2):e00560–17.
Article
PubMed
PubMed Central
Google Scholar
Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014;12(1):87.
Article
PubMed
PubMed Central
CAS
Google Scholar
Glassing A, Dowd SE, Galandiuk S, Davis B, Chiodini RJ. Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples. Gut Pathogens. 2016;8(1):24.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dahlberg J, Sun L, Persson Waller K, Östensson K, McGuire M, Agenäs S, et al. Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination. PLoS One. 2019;14(6):e0218257.
Article
CAS
PubMed
PubMed Central
Google Scholar
Claassen-Weitz S, Gardner-Lubbe S, Mwaikono KS, du Toit E, Zar HJ, Nicol MP. Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens. BMC Microbiol. 2020;20(1):113.
Article
CAS
PubMed
PubMed Central
Google Scholar
Saladié M, Caparrós-Martín JA, Agudelo-Romero P, Wark PAB, Stick SM, O’Gara F. Microbiomic analysis on low abundant respiratory biomass samples; improved recovery of microbial DNA from bronchoalveolar lavage fluid. Front Microbiol. 2020;11:2477.
Stinson LF, Keelan JA, Payne MS. Identification and removal of contaminating microbial DNA from PCR reagents: impact on low-biomass microbiome analyses. Lett Appl Microbiol. 2019;68(1):2–8.
Article
CAS
PubMed
Google Scholar
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(6):285–9.
Article
CAS
PubMed
Google Scholar
Douglas CA, Ivey KL, Papanicolas LE, Best KP, Muhlhausler BS, Rogers GB. DNA extraction approaches substantially influence the assessment of the human breast milk microbiome. Sci Rep. 2020;10(1):123.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brandt J, Albertsen M. Investigation of detection limits and the influence of DNA extraction and primer choice on the observed microbial communities in drinking water samples using 16S rRNA gene amplicon sequencing. Front Microbiol. 2018;9:2140.
Article
PubMed
PubMed Central
Google Scholar
Velásquez-Mejía EP, de la Cuesta-Zuluaga J, Escobar JS. Impact of DNA extraction, sample dilution, and reagent contamination on 16S rRNA gene sequencing of human feces. Appl Microbiol Biotechnol. 2018;102(1):403–11.
Article
PubMed
CAS
Google Scholar
Reitmeier S, Kiessling S, Neuhaus K, Haller D. Comparing circadian rhythmicity in the human gut microbiome. STAR Protoc. 2020;1(3):100148.
Dreo T, Pirc M, Ramsak Z, Pavsic J, Milavec M, Zel J, et al. Optimising droplet digital PCR analysis approaches for detection and quantification of bacteria: a case study of fire blight and potato brown rot. Anal Bioanal Chem. 2014;406(26):6513–28.
Article
CAS
PubMed
Google Scholar
Hindson BJ, Ness KD, Masquelier DA, Belgrader P, Heredia NJ, Makarewicz AJ, et al. High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal Chem. 2011;83(22):8604–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Demeke T, Dobnik D. Critical assessment of digital PCR for the detection and quantification of genetically modified organisms. Anal Bioanal Chem. 2018;410(17):4039–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gobert G, Cotillard A, Fourmestraux C, Pruvost L, Miguet J, Boyer M. Droplet digital PCR improves absolute quantification of viable lactic acid bacteria in faecal samples. J Microbiol Methods. 2018;148:64–73.
Article
CAS
PubMed
Google Scholar
Wouters Y, Dalloyaux D, Christenhusz A, Roelofs HMJ, Wertheim HF, Bleeker-Rovers CP, et al. Droplet digital polymerase chain reaction for rapid broad-spectrum detection of bloodstream infections. Microb Biotechnol. 2020;13(3):657–68.
Article
CAS
PubMed
Google Scholar
Boers SA, Hays JP, Jansen R. Micelle PCR reduces chimera formation in 16S rRNA profiling of complex microbial DNA mixtures. Sci Rep. 2015;5:14181.
Article
CAS
PubMed
PubMed Central
Google Scholar
Valencia CA, Rhodenizer D, Bhide S, Chin E, Littlejohn MR, Keong LM, et al. Assessment of target enrichment platforms using massively parallel sequencing for the mutation detection for congenital muscular dystrophy. J Mol Diagn. 2012;14(3):233–46.
Article
CAS
PubMed
PubMed Central
Google Scholar
Komori HK, LaMere SA, Torkamani A, Hart GT, Kotsopoulos S, Warner J, et al. Application of microdroplet PCR for large-scale targeted bisulfite sequencing. Genome Res. 2011;21(10):1738–45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Philippe J, Derhourhi M, Durand E, Vaillant E, Dechaume A, Rabearivelo I, et al. What is the best NGS enrichment method for the molecular diagnosis of monogenic diabetes and obesity? PLoS One. 2015;10(11):e0143373.
Article
PubMed
PubMed Central
CAS
Google Scholar
Pruvost M, Grange T, Geigl E-M. Minimizing DNA contamination by using UNG-coupled quantitative real-time PCR on degraded DNA samples: application to ancient DNA studies. BioTech. 2005;38(4):569–75.
Article
CAS
Google Scholar
Kasalický V, Jezbera J, Hahn MW, Šimek K. The diversity of the Limnohabitans genus, an important group of freshwater bacterioplankton, by characterization of 35 isolated strains. PLoS One. 2013;8(3):e58209.
Article
PubMed
PubMed Central
CAS
Google Scholar
Nelson MC, Morrison HG, Benjamino J, Grim SL, Graf J. Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys. PLoS One. 2014;9(4):e94249.
Article
PubMed
PubMed Central
CAS
Google Scholar
Manzari C, Oranger A, Fosso B, Piancone E, Pesole G, D’Erchia AM. Accurate quantification of bacterial abundance in metagenomic DNAs accounting for variable DNA integrity levels. Microb Genomics. 2020;6(10). https://doi.org/10.1099/mgen.0.000417.
Pacocha N, Scheler O, Nowak MM, Derzsi L, Cichy J, Garstecki P. Direct droplet digital PCR (dddPCR) for species specific, accurate and precise quantification of bacteria in mixed samples. Anal Methods. 2019;11(44):5730–5.
Article
Google Scholar
Ziegler I, Lindström S, Källgren M, Strålin K, Mölling P. 16S rDNA droplet digital PCR for monitoring bacterial DNAemia in bloodstream infections. PLoS One. 2019;14(11):e0224656.
Article
CAS
PubMed
PubMed Central
Google Scholar
Godon JJ, Zumstein E, Dabert P, Habouzit F, Moletta R. Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl Environ Microbiol. 1997;63(7):2802–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Foote AD, Thomsen PF, Sveegaard S, Wahlberg M, Kielgast J, Kyhn LA, et al. Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PLoS One. 2012;7(8):e41781.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lagkouvardos I, Joseph D, Kapfhammer M, Giritli S, Horn M, Haller D, et al. IMNGS: a comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies. Sci Rep. 2016;6:33721.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10(10):996–8.
Article
CAS
PubMed
Google Scholar
Reitmeier S, Hitch TCA, Treichel N, et al. Handling of spurious sequences affects the outcome of highthroughput
16S rRNA gene amplicon profiling. ISME Commun. 2021;1(1):1–12.
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27(16):2194–200.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edgar RC. UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. BioRxiv. 2016:081257.
Lagkouvardos I, Fischer S, Kumar N, Clavel T. Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons. PeerJ. 2017;5:e2836.
Article
PubMed
PubMed Central
Google Scholar
Turner S, Pryer KM, Miao VP, Palmer JD. Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J Eukaryot Microbiol. 1999;46(4):327–38.
Article
CAS
PubMed
Google Scholar