Skip to main content

Advertisement

Table 3 Stool sample analysis

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

  Capillary Sequencing PacBio PacBio PacBio PacBio PacBio PacBio
97% 98% unique 97% 98% unique
OTU OTU OTU OTU OTU OTU
90/90 90/90 90/90 80/80 80/80 80/80
  No of OTUs NA 33 36 81 129 545 1513
  No of species 40 32 33 33 39 46 48
  Shared with Capillary NA 27 28 28 31 31 32
  Shared in %   67.50% 70% 70% 77.50% 77.50% 80%
Phyla Genera Species  
Actinobacteria Bifidobacterium adolscent yes yes yes yes yes yes yes
Actinobacteria Bifidobacterium bifidum yes yes yes yes yes yes yes
Actinobacteria Bifidobacterium pseudoca yes yes yes yes yes yes yes
Actinobacteria Collinsella aerofaciens yes yes yes yes yes yes yes
Bacterium Bacterium R 2 yes yes yes yes yes yes yes
Bacteroidetes Bacteroides uniformis yes yes yes yes yes yes yes
Firmicutes Clostridium baratti yes yes yes yes yes yes yes
Firmicutes Clostridium bartlettii yes yes yes yes yes yes yes
Firmicutes Clostridium clostridiofo yes yes yes yes yes yes yes
Firmicutes Clostridium disporicum yes yes yes yes yes yes yes
Firmicutes Clostridium hathewayi yes yes yes yes yes yes yes
Firmicutes Clostridium leptum yes yes yes yes yes yes yes
Firmicutes Clostridium ramosum yes yes yes yes yes yes yes
Firmicutes Clostridium aff. innocuum CM970 yes yes yes yes yes yes yes
Firmicutes Coprococcus comes yes yes yes yes yes yes yes
Firmicutes Butyricicoccus pullicaecorum yes yes yes yes yes yes yes
Firmicutes Dorea formicigenerans yes yes yes yes yes yes yes
Firmicutes Eubacterium cylindroides yes yes yes yes yes yes yes
Firmicutes Eubacterium eligens yes yes yes yes yes yes yes
Firmicutes Flavonifractor plautii yes yes yes yes yes yes yes
Firmicutes Megasphaera elsdenii yes yes yes yes yes yes yes
Firmicutes Mitsuokella jalaludinii yes yes yes yes yes yes yes
Firmicutes Roseburia faecis yes yes yes yes yes yes yes
Firmicutes Ruminococcus gnavus yes yes yes yes yes yes yes
Bacteroidetes Parabacteroides distasoni yes yes yes yes yes yes yes
Firmicutes Clostridium symbiosum yes yes yes yes yes yes yes
Firmicutes Catenibacterium mitsuokai yes yes yes yes yes yes yes
Firmicutes Roseburia hominis yes   yes yes yes yes yes
Bacterium Bacterium ic1340 yes     yes yes yes
Bacterium Bacterium New Zealand 4 yes     yes yes yes
Bacteroidetes Alistipes onderdonkii yes     yes yes yes
Firmicutes Ruminococcus bromii yes       yes
Bacteroidetes Bacteroides coprocola yes       
Bacteroidetes Prevotella copri yes       
Firmicutes Clostridium lituseburense yes       
Firmicutes Clostridium xylanolyticus yes       
Firmicutes Coprococcus eutactus yes       
Firmicutes Ruminococcus albus yes       
Firmicutes Ruminococcus flavefacien yes       
Firmicutes Turicibacter sanguinis yes       
Bacteroidetes Alistipes indistinctus   yes yes yes yes yes yes
Firmicutes Clostridium stramisolven   yes yes yes yes yes yes
Firmicutes Eubacterium Tenue   yes yes yes yes yes yes
Firmicutes Faecalibacterium prausnitzi   yes yes yes yes yes yes
Bacteroidetes Bacteriodes vulgatus   yes yes yes yes yes  
Bacteroidetes Bacteroides plebeius      yes yes yes
Firmicutes Mitsuokella multacida      yes yes yes
Firmicutes Ruminococcus torques      yes yes yes
Firmicutes Christensenella minuta     yes   yes yes
Firmicutes Clostridium aminovalericum     yes   yes yes
Firmicutes Clostridium bolteae       yes yes
Firmicutes Clostridium disporicum       yes yes
Firmicutes Clostridium spiroforme       yes yes
Firmicutes Blautia coccoides       yes yes
Firmicutes Coprobacillus cateniformis       yes yes
Firmicutes Lactobacillus salivarius        yes
Firmicutes Catabacter hongkongensis        yes
  1. Abbreviations: 90/90 minimum alignment and similarity score of 90% during post alignment screening, 80/80 minimum alignment and similarity score of 80% during post alignment screening, No number, OTU operational taxonomic units