Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes

Earl, Joshua P.; Adappa, Nithin D.; Krol, Jaroslaw; Bhat, Archana S.; Balashov, Sergey; Ehrlich, Rachel L.; Palmer, James N.; Workman, Alan D.; Blasetti, Mariel; Sen, Bhaswati; Hammond, Jocelyn; Cohen, Noam A.; Ehrlich, Garth D.; Mell, Joshua Chang

doi:10.1186/s40168-018-0569-2

Table 3 Taxonomic classification of BEI

From: Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes

Centroids full-length			Centroids v3-v5			Clustered from V3-V5 truncated reads (Top 19)			Mothur/Silva full-length (Top 19)
Species	Genus conf	Species conf	Species	Genus conf	Species conf	Species	Genus conf	Species conf	Genus	Genus conf
Acinetobacter_baumannii	0.98	0.94	Acinetobacter_baumannii	0.88	0.42	Acinetobacter_baumannii	0.8784	0.42	Acinetobacter	100
Actinomyces_odontolyticus	0.99	0.94	Actinomyces_odontolyticus	0.97	0.62	Actinomyces_odontolyticus	0.9728	0.62	Actinomyces	100
Bacillus_anthracis	0.99	0.49	Bacillus_cereus	0.96	0.42	Bacillus_cereus	0.963	0.31	Bacillus	100
Bacteroides_vulgatus	0.99	0.94	Bacteroides_vulgatus	0.98	0.90	Bacteroides_vulgatus	0.9847	0.90	Bacteroides	100
Clostridium_beijerinckii	0.99	0.72	Clostridium_roseum	0.97	0.42	Clostridium_roseum	0.965	0.31	Clostridium_sensu_stricto	100
Deinococcus_radiodurans	0.99	0.94	Deinococcus_radiodurans	1.00	0.90	Deinococcus_radiodurans	0.9994	0.90	Deinococcus	100
Enterococcus_faecalis	0.99	0.94	Enterococcus_faecalis	0.88	0.83	Enterococcus_faecalis	0.8784	0.83	Enterococcus	100
Shigella_flexneri	0.69	0.49	Shigella_flexneri	0.67	0.42	Shigella_flexneri	0.6072	0.31	Escherichia_Shigella	100
Helicobacter_pylori	0.99	0.93	Helicobacter_pylori	0.98	0.90	Helicobacter_pylori	0.9787	0.90	Helicobacter	100
Lactobacillus_gasseri	0.99	0.72	Lactobacillus_gasseri	0.97	0.42	Lactobacillus_gasseri	0.9728	0.42	Lactobacillus	100
Listeria_monocytogenes	0.99	0.72	Listeria_ivanovii	0.96	0.42	Listeria_ivanovii	0.961	0.31	Listeria	100
Neisseria_meningitidis	0.97	0.93	Neisseria_meningitidis	0.95	0.62	Neisseria_meningitidis	0.9533	0.62	Neisseria	100
Propionibacterium_acnes	0.97	0.96	Propionibacterium_acnes	0.97	0.91	Propionibacterium_acnes	0.965	0.91	Propionibacterium	100
Pseudomonas_aeruginosa	0.97	0.93	Pseudomonas_aeruginosa	0.93	0.62	Pseudomonas_aeruginosa	0.9329	0.62	Pseudomonas	100
Rhodobacter_sphaeroides	0.97	0.60	Rhodobacter_sphaeroides	0.92	0.42	Rhodobacter_sphaeroides	0.9228	0.31	Rhodobacter	100
Staphylococcus_epidermidis	0.99	0.72	Staphylococcus_epidermidis	0.67	0.42	Staphylococcus_epidermidis	0.6661	0.31	Staphylococcus	100
Streptococcus_agalactiae	0.99	0.95	Streptococcus_agalactiae	0.97	0.90	Streptococcus_agalactiae	0.9728	0.90	Streptococcus	100
Streptococcus_mutans	0.99	0.95	Streptococcus_mutans	0.98	0.90	Streptococcus_mutans	0.9768	0.90	Streptococcus	100
Streptococcus_pneumoniae	0.99	0.49	Streptococcus_pneumoniae	0.98	0.42	Streptococcus_pneumoniae	0.9768	0.42	Streptococcus	100

Classification results from the BEI mock community. The performance of MCSMRT FL16S centroid OTU assignments (column 1), centroids truncated to V3-V5 (column 2), top 19 centroids found when clustering V3-V5 truncation reads (column 3), and the top 19 OTUs identified using Mothur/Silva with FL16S reads (column 4)

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ISSN: 2049-2618

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