title: Comparison of microbial diversity determined with the same variable tag sequence extracted from two different PCR amplicons.
abstract: BACKGROUND
  Deep sequencing of the variable region of 16S rRNA genes has become the predominant tool for studying microbial ecology. As sequencing datasets have accumulated, meta-analysis of sequences obtained with different variable 16S rRNA gene targets and by different sequencing methods has become an intriguing prospect that remains to be evaluated experimentally.
  
  
  RESULTS
  We amplified a group of fecal samples using both V4F-V6R and V6F-V6R primer sets, excised the same V6 fragment from the two sets of Illumina sequencing data, and compared the resulting data in terms of the α-diversity, β-diversity, and community structure. Principal component analysis (PCA) comparing the microbial community structures of different datasets, including those with simulated sequencing errors, was very reliable. Procrustes analysis showed a high degree of concordance between the different datasets for both abundance-weighted and binary Jaccard distances (P < 0.05), and a meta-analysis of individual datasets resulted in similar conclusions. The Shannon's diversity index was consistent as well, with comparable values obtained for the different datasets and for the meta-analysis of different datasets. In contrast, richness estimators (OTU and Chao) varied significantly, and the meta-analysis of richness estimators was also biased. The community structures of the two datasets were obviously different and led to significant changes in the biomarkers identified by the LEfSe statistical tool.
  
  
  CONCLUSIONS
  Our results suggest that beta-diversity analysis and Shannon's diversity are relatively reliable for meta-analysis, while community structures and biomarkers are less consistent. These results should be useful for future meta-analyses of microbiomes from different data sources.
authors.affiliation: Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China. biodegradation@gmail.com.
authors.forename: Yan
authors.initials: Y
authors.lastname: He
authors.forename: Ben-Jie
authors.initials: BJ
authors.lastname: Zhou
authors.forename: Guan-Hua
authors.initials: GH
authors.lastname: Deng
authors.forename: Xiao-Tao
authors.initials: XT
authors.lastname: Jiang
authors.forename: Hai
authors.initials: H
authors.lastname: Zhang
authors.forename: Hong-Wei
authors.initials: HW
authors.lastname: Zhou
mesh_terms: D000818:Animals; D058448:Biota; D017931:DNA Primers / Q000235:genetics*; D005243:Feces / Q000382:microbiology*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D056186:Metagenomics / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*
chemical_list: D017931:DNA Primers; D012336:RNA, Ribosomal, 16S
references.citation: PLoS Genet. 2008 Nov;4(11):e1000255
references.pmid: 19023400
references.citation: Nat Rev Genet. 2011 Dec 16;13(1):47-58
references.pmid: 22179717
references.citation: Environ Microbiol. 2010 Jan;12(1):118-23
references.pmid: 19725865
references.citation: PLoS One. 2013;8(1):e53649
references.pmid: 23341963
references.citation: Appl Environ Microbiol. 2009 Dec;75(23):7537-41
references.pmid: 19801464
references.citation: PLoS One. 2012;7(1):e30230
references.pmid: 22253923
references.citation: Environ Microbiol. 2010 Jul;12(7):1889-98
references.pmid: 20236171
references.citation: PLoS One. 2012;7(6):e34242
references.pmid: 22719824
references.citation: Appl Environ Microbiol. 2008 Aug;74(16):5231-6
references.pmid: 18567688
references.citation: PLoS One. 2012;7(6):e39315
references.pmid: 22720093
references.citation: Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12115-20
references.pmid: 16880384
references.citation: ISME J. 2011 Apr;5(4):741-9
references.pmid: 20962877
references.citation: Nature. 2007 Oct 18;449(7164):804-10
references.pmid: 17943116
references.citation: Genome Biol. 2011 Jun 24;12(6):R60
references.pmid: 21702898
references.citation: Science. 2009 Dec 18;326(5960):1694-7
references.pmid: 19892944
references.citation: Nat Methods. 2010 May;7(5):335-6
references.pmid: 20383131
references.citation: Bioinformatics. 2011 Aug 15;27(16):2194-200
references.pmid: 21700674
references.citation: Appl Environ Microbiol. 2012 Dec;78(23):8264-71
references.pmid: 23001654
references.citation: Clin Infect Dis. 2008 Dec 15;47(12):1562-70
references.pmid: 18991508
references.citation: Genome Res. 2011 Mar;21(3):494-504
references.pmid: 21212162
references.citation: Science. 2011 Feb 25;331(6020):1008-9
references.pmid: 21350145