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Table 4 Vaginal microbiome species profiling

From: Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification

 

Singleton-free unique OTU and no. of species

MiSeq V1V2

129 OTUs = 70 species

Subsampled to 27596

PacBio in silico V1V2

154 OTUs = 63 species

Minscore = 80 Minsim = 80

(39 species (58%) shared with MiSeq V1V2)

PacBio in silico V1V2

131 OTUs = 48 species

Minscore = 90 Minsim = 90

(26 species (37%) shared with MiSeq V1V2)

PacBio V1V9

261 OTUs = 52 species

Minscore = 80 minsim = 80

(28 species (40%) shared with MiSeq V1V2)

(32 species (62%) shared with PacBio in silico V1V2, minscore = 80, minsim = 80)

PacBio V1V9

148 OTUs = 48 species

Minscore = 90 minsim = 90

(26 species (37%) shared with MiSeq V1V2)

(48 species (100%) shared with PacBio in silico V1V2, minscore = 90, minsim = 90)

  1. Abbreviations: minscore minimum alignment score during post alignment screening, minsim minimum similarity score during post alignment screening, OTU operational taxonomic units, MiSeq Illumina MiSeq sequencing, V1V2 bacterial 16S rRNA V1V2 gene region, V1V9 full-length bacterial 16S rRNA gene
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BMC Microbiology

ISSN: 1471-2180

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