Integrity of the human faecal microbiota following long-term sample storage

PLoS ONE

Volumn 11, Issue 10, 2016, Pages

  Kia, Elahe ^a   MacKenzie, Brett Wagner ^b   Middleton, Danielle ^a   Lau, Anna ^a   Waite, David W ^a   Lewis, Gillian ^a   Chan, Yih Kai ^a,b   Silvestre, Marta ^a,b   Cooper, Garth J S ^a   Poppitt, Sally D ^a,b   Taylor, Michael W ^a  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

^b UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; RNA 16S;

16S RRNA GENE; AGAR GEL ELECTROPHORESIS; AMPLICON; ARTICLE; CONTROLLED STUDY; DNA EXTRACTION; FECES MICROFLORA; FREEZE DRYING; HUMAN; MOLECULAR WEIGHT; NON INSULIN DEPENDENT DIABETES MELLITUS; NONHUMAN; SPECTROPHOTOMETRY; STORAGE; STORAGE TEMPERATURE; BIODIVERSITY; FECES; METAGENOME; METAGENOMICS; MICROBIAL VIABILITY; MICROBIOLOGY; MICROFLORA; PRESERVATION; TIME FACTOR;

BIODIVERSITY; DNA, BACTERIAL; FECES; HUMANS; METAGENOME; METAGENOMICS; MICROBIAL VIABILITY; MICROBIOTA; PRESERVATION, BIOLOGICAL; RNA, RIBOSOMAL, 16S; TIME FACTORS;

EID: 84991233196     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0163666     Document Type: Article

References (16)

1. Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D, et al. Experimental and analytical tools for studying the human microbiome. Nat Rev Genet. 2012; 13: 47-58. doi: 10.1038/nrg3129 PMID: 22179717
2. Bahl MI, Bergstrom A, Licht TR. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis. FEMS Microbiol Lett. 2012; 329: 193-197. doi: 10.1111/j.1574-6968.2012.02523.x PMID: 22325006
3. 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: e130. doi: 10.3389/fmicb.2015.00130 PMID: 25741335
4. Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vazquez-Baeza Y, et al. Metaanalyses of studies of the human microbiota. Genome Res. 2013; 23: 1704-1714. doi: 10.1101/gr. 151803.112 PMID: 23861384
5. Werner JJ, Zhou D, Caporaso JG, Knight R, Angenent LT. Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys. ISME J. 2012; 6: 1273-1276. doi: 10.1038/ismej.2011.186 PMID: 22170427
6. Song SJ, Amir A, Metcalf JL, Amato KR. Preservation methods differ in fecal microbiome stability, affecting suitability for field studies. mSystems. 2016; 1: e00021-16. doi: 10.1128/mSystems.00021-16
7. Cooper GJS, Chan YK, Dissanayake AM, Leahy FE, Keogh GF, Frampton CM, et al. Demonstration of a hyperglycemia-driven pathogenic abnormality of copper homeostasis in diabetes and its reversibility by selective chelation: Quantitative comparisons between the biology of copper and eight other nutritionally essential elements in normal and diabetic individuals. Diabetes. 2005; 54: 1468-1476. doi: 10.2337/diabetes.54.5.1468 PMID: 15855335
8. 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. 2013; 41: e1. doi: 10.1093/nar/gks808 PMID: 22933715
9. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010; 26: 2460-2461. doi: 10.1093/bioinformatics/btq461 PMID: 20709691
10. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data Intensity normalization improves color calling in SOLiD sequencing. Nat Methods. 2010; 7: 335-336. doi: 10.1038/nmeth.f.303 PMID: 20383131
11. Clarke K, Gorley R. PRIMER v7: user manual/tutorial. Plymouth: PRIMER-E; 2015. 296 p.
12. Willerslev E, Cooper A. Ancient DNA. Proc R Soc London B. 2005; 272: 3-16.
13. Sambrook J, Russell DW. Molecular Cloning: a laboratory manual, vol. 3. 3rd ed. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press; 2001.
14. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature. 2012; 489: 220-230. doi: 10.1038/nature11550 PMID: 22972295
15. Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, et al. Population-level analysis of gut microbiome variation. Science. 2016; 352: 560-564. doi: 10.1126/science.aad3503 PMID: 27126039
16. Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, et al. Human genetics shape the gut microbiome. Cell. 2014; 159: 789-99. doi: 10.1016/j.cell.2014.09.053 PMID: 25417156