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. 2011 May;49(5):1799–1809. doi: 10.1128/JCM.02350-10

Table 1.

Identification of clinical bacterial isolates using 16SpathDB

Strain no. Identification by polyphasic approach Reference Identification results reported by 16SpathDB
 Best match in 16SpathDB Nucleotide identity (%) Second-best match in 16SpathDB Nucleotide identity (%) Third-best match in 16SpathDB Nucleotide identity (%)
Bacterial species Nucleotide identity (%)
1 Abiotrophia defectiva 21 Abiotrophia defectiva 99.54 Abiotrophia defectiva 99.54 Granulicatella adiacens 92.77 Granulicatella elegans 92.67
2 Actinobaculum schaalii Actinobaculum schaalii 99.35 Actinobaculum schaalii 99.35 Actinobaculum massiliense 95.69 Actinobaculum suis 94.52
3 Actinobaculum urinale Actinobaculum urinale 100.00 Actinobaculum urinale 100.00 Actinobaculum massiliense 91.57 Actinobaculum schaalii 91.01
4 Actinomyces meyeri Actinomyces meyeri 100.00 Actinomyces meyeri 100.00 Actinomyces odontolyticus 97.59 Actinomyces georgiae 97.16
5 Actinomyces odontolyticus 22 Actinomyces odontolyticus 98.92 Actinomyces odontolyticus 98.92 Actinomyces meyeri 97.78 Actinomyces turicensis 96.07
6 Actinomyces urogenitalis Actinomyces urogenitalis 100.00 Actinomyces urogenitalis 100.00 Actinomyces slackii 97.37 Actinomyces radicidentis 97.24
7 Actionmyces turicensis Actinomyces turicensis 99.44 Actinomyces turicensis 99.44 Actinomyces odontolyticus 97.04 Actinomyces meyeri 96.65
8 Aggregatibacter actinomycetemcomitans Aggregatibacter actinomycetemcomitans 98.62 Aggregatibacter actinomycetemcomitans 98.62 Aggregatibacter aphrophilus 94.12 Haemophilus aegyptius 93.73
9 Aggregatibacter aphrophilus 10 Aggregatibacter aphrophilus 99.59 Aggregatibacter aphrophilus 99.59 Aggregatibacter segnis 97.29 Haemophilus parahaemolyticus 95.31
10 Aggregatibacter segnis 10 Aggregatibacter segnis 99.59 Aggregatibacter segnis 99.59 Aggregatibacter aphrophilus 97.54 Haemophilus influenzae 95.73
11 Agrobacterium tumefaciens Agrobacterium tumefaciens 98.86 Agrobacterium tumefaciens 98.86 Ochrobactrum anthropi 94.25 Brucella melitensis 93.95
12 Arcanobacterium haemolyticum Arcanobacterium haemolyticum 99.80 Arcanobacterium haemolyticum 99.80 Arcanobacterium phocae 97.27 Arcanobacterium pluranimalium 94.39
13 Arcobacter butzleri Arcobacter butzleri 99.64 Arcobacter butzleri 99.64 Arcobacter cryaerophilus 96.76 Arcobacter skirrowii 96.61
14 Arcobacter cryaerophilus 7 Arcobacter cryaerophilus 100.00 Arcobacter cryaerophilus 100.00 Arcobacter skirrowii 98.42 Arcobacter butzleri 97.18
15 Averyella dalhousiensis Averyella dalhousiensis 99.18 Averyella dalhousiensis 99.18 Enterobacter cancerogenus 99.02 Enterobacter aerogenes 99.02
Enterobacter cancerogenus 99.02
Enterobacter aerogenes 99.02
16 Bifidobacterium breve Bifidobacterium breve 99.68 Bifidobacterium breve 99.68 Bifidobacterium longum 97.77 Bifidobacterium bifidum 95.96
17 Burkholderia pseudomallei 35 Burkholderia pseudomallei 100.00 Burkholderia pseudomallei 100.00 Burkholderia mallei 99.93 Burkholderia thailandensis 98.99
Burkholderia mallei 99.93
18 Campylobacter coli 7 Campylobacter coli 99.80 Campylobacter coli 99.80 Campylobacter jejuni 99.79 Campylobacter lari 98.33
Campylobacter jejuni 99.79
19 Campylobacter fetus 7 Campylobacter fetus 99.85 Campylobacter fetus 99.85 Campylobacter hyointestinalis 97.98 Campylobacter mucosalis 96.40
20 Campylobacter hyointestinalis Campylobacter hyointestinalis Campylobacter fetus 100.00 Campylobacter hyointestinalis 100.00 Campylobacter fetus 99.01 Campylobacter mucosalis 96.06
99.01
21 Campylobacter rectus Campylobacter rectus 99.34 Campylobacter rectus 99.34 Campylobacter showae 97.94 Campylobacter concisus 96.11
22 Capnocytophaga sputigena Capnocytophaga sputigena 99.24 Capnocytophaga sputigena 99.24 Capnocytophaga ochracea 95.67 Capnocytophaga cynodegmi 92.24
23 Citrobacter koseri Citrobacter koseri 99.92 Citrobacter koseri 99.92 Citrobacter farmeri 98.74 Salmonella enterica 98.74
Citrobacter farmeri 98.74
Salmonella enterica 98.74
24 Clostridium barati 24 Clostridium baratii 99.83 Clostridium baratii 99.83 Eubacterium budayi 99.41 Eubacterium nitritogenes 99.16
Eubacterium budayi 99.41
Eubacterium nitritogenes 99.16
25 Clostridium difficile 24 Clostridium difficile 99.51 Clostridium difficile 99.51 Clostridium sordellii 95.90 Eubacterium tenue 95.80
26 Clostridium disporicum 24 Clostridium disporicum 98.99 Clostridium disporicum 98.99 Clostridium celatum 97.57 Clostridium carnis 96.91
27 Clostridium hathewayi 28 Clostridium hathewayi 98.28 Clostridium hathewayi 98.28 Clostridium indolis 94.17 Clostridium sphenoides 93.86
28 Clostridium Innocuum 24 Clostridium innocuum 99.19 Clostridium innocuum 99.19 Holdemania filiformis 85.33 Erysipelothrix inopinata 84.82
29 Clostridium orbiscindens 24 Clostridium orbiscindens 100.00 Clostridium orbiscindens 100.00 Bacteroides capillosus 97.44 Clostridium sporosphaeroides 86.62
30 Clostridium paraputrificum 24 Clostridium paraputrificum 99.42 Clostridium paraputrificum 99.42 Clostridium carnis 96.81 Clostridium disporicum 96.53
31 Clostridium perfringens Clostridium perfringens 99.92 Clostridium perfringens 99.92 Clostridium baratii 94.60 Eubacterium budayi 94.19
32 Clostridium ramosum 24 Clostridium ramosum 99.92 Clostridium ramosum 99.92 Clostridium spiroforme 95.25 Lactobacillus vitulinus 86.78
33 Clostridium sordellii Clostridium sordellii 99.33 Clostridium sordellii 99.33 Eubacterium tenue 98.44 Clostridium ghonii 98.15
Eubacterium tenue 98.44
34 Clostridium symbiosum Clostridium symbiosum 99.49 Clostridium symbiosum 99.49 Clostridium bolteae 94.05 Clostridium clostridioforme 93.37
35 Clostridium tertium 24 Clostridium tertium 100.00 Clostridium tertium 100.00 Clostridium carnis 98.89 Clostridium chauvoei 97.90
36 Clostridium sporosphaeroides 24 Clostridium sporosphaeroides 98.80 Clostridium sporosphaeroides 98.80 Clostridium orbiscindens 87.17 Bacteroides capillosus 85.97
37 Desulfovibrio desulfuricans Desulfovibrio desulfuricans 99.07 Desulfovibrio desulfuricans 99.07 Desulfovibrio fairfieldensis 95.58 Desulfovibrio piger 95.07
38 Desulfovibrio fairfieldensis Desulfovibrio fairfieldensis 99.92 Desulfovibrio fairfieldensis 99.92 Desulfovibrio desulfuricans 96.75 Desulfovibrio piger 95.83
39 Dolosigranulum pigrum Dolosigranulum pigrum 98.97 Dolosigranulum pigrum 98.97 Alloiococcus otitis 91.40 Aerococcus sanguinicola 88.79
40 Eggerthella hongkongensis 11 Eggerthella hongkongensis 100.00 Eggerthella hongkongensis 100.00 Eggerthella lenta 93.08 Slackia exigua 90.09
41 Eggerthella lenta 9 Eggerthella lenta 99.74 Eggerthella lenta 99.74 Slackia exigua 89.48 Slackia heliotrinireducens 89.10
42 Enterobacter hormaechei Enterobacter hormaechei 98.60 Enterobacter hormaechei 98.60 Enterobacter asburiae 98.45 Enterobacter ludwigii 98.22
Enterobacter asburiae 98.45
Enterobacter ludwigii 98.22
43 Enterococcus cecorum 29 Enterococcus cecorum 98.72 Enterococcus cecorum 98.72 Enterococcus columbae 96.50 Enterococcus casseliflavus 96.06
44 Enterococcus raffinosus Enterococcus raffinosus 99.93 Enterococcus raffinosus 99.93 Enterococcus gilvus 99.39 Enterococcus malodoratus 99.25
Enterococcus gilvus 99.39
Enterococcus malodoratus 99.25
45 Facklamia hominis Facklamia hominis 99.38 Facklamia hominis 99.38 Facklamia languida 96.82 Facklamia ignava 93.16
46 Fusobacterium necrophorum Fusobacterium necrophorum 99.78 Fusobacterium necrophorum 99.78 Fusobacterium gonidiaformans 97.65 Fusobacterium russii 93.95
47 Gemella haemolysans 7 Gemella haemolysans 99.62 Gemella haemolysans 99.62 Gemella sanguinis 97.67 Gemella morbillorum 97.15
48 Gemella morbillorum Gemella morbillorum 99.68 Gemella morbillorum 99.68 Gemella haemolysans 98.30 Gemella sanguinis 97.50
49 Gordonia terrae Gordonia terrae 100.00 Gordonia terrae 100.00 Gordonia polyisoprenivorans 98.31 Gordonia bronchialis 98.30
50 Gordonibacter pamelaeae 30 No match - Eggerthella sinensis 94.00 Eggerthella hongkongensis 93.53 Eggerthella lenta 91.74
51 Granulicatella adiacens 21 Granulicatella adiacens 99.77 Granulicatella adiacens 99.77 Granulicatella elegans 97.40 Enterococcus villorum 94.58
52 Haemophilus parainfluenzae 10 Haemophilus parainfluenzae 99.53 Haemophilus parainfluenzae 99.53 Haemophilus pittmaniae 96.51 Haemophilus haemolyticus 95.33
53 Helcococcus kunzii 34 Helcococcus kunzii 99.59 Helcococcus kunzii 99.59 Parvimonas micra 84.57 Anaerococcus hydrogenalis 83.62
54 Kytococcus sedentarius Kytococcus sedentarius 98.12 Kytococcus sedentarius 98.12 Dermacoccus nishinomiyaensis 94.48 Janibacter sanguinis 93.24
55 Lactobacillus casei 7 Lactobacillus casei 100.00 Lactobacillus casei 100.00 Lactobacillus rhamnosus 99.51 Pediococcus pentosaceus 92.94
Lactobacillus rhamnosus 99.51
56 Lactobacillus fermentum 25 Lactobacillus fermentum 99.77 Lactobacillus fermentum 99.77 Pediococcus acidilactici 93.6 Pediococcus pentosaceus 93.5
57 Lactobacillus gasseri Lactobacillus gasseri 99.92 Lactobacillus gasseri 99.92 Lactobacillus acidophilus 93.94 Lactobacillus plantarum 90.32
58 Lactobacillus rhamnosus 7 Lactobacillus rhamnosus 99.83 Lactobacillus rhamnosus 99.83 Lactobacillus casei 99.66 Pediococcus pentosaceus 93.31
Lactobacillus casei 99.66
59 Lactococcus garvieae Lactococcus garvieae 99.92 Lactococcus garvieae 99.92 Lactococcus lactis 92.07 Streptococcus iniae 89.32
60 Lactococcus lactis Lactococcus lactis 99.52 Lactococcus lactis 99.52 Lactococcus garvieae 92.75 Streptococcus agalactiae 89.34
61 Laribacter hongkongensis 27 Laribacter hongkongensis 99.93 Laribacter hongkongensis 99.93 Chromobacterium violaceum 92.39 Eikenella corrodens 89.82
62 Leptotrichia buccalis Leptotrichia buccalis 99.56 Leptotrichia buccalis 99.56 Streptobacillus moniliformis 86.68 Sneathia sanguinegens 83.96
63 Microbacterium paraoxydans Microbacterium paraoxydans 99.49 Microbacterium paraoxydans 99.49 Microbacterium oxydans 98.87 Microbacterium resistens 98.25
Microbacterium oxydans 98.87
64 Micrococcus luteus 7 Micrococcus luteus 98.11 Micrococcus luteus 98.11 Micrococcus lylae 97.78 Micrococcus antarcticus 97.32
Micrococcus lylae 97.78
Micrococcus antarcticus 97.32
65 Moraxella osloensis Moraxella osloensis 99.53 Moraxella osloensis 99.53 Moraxella lincolnii 92.49 Moraxella lacunata 92.41
66 Mycobacterium chelonae 7 Mycobacterium chelonae 99.79 Mycobacterium chelonae 99.79 Mycobacterium abscessus 99.79 Mycobacterium immunogenum 98.97
Mycobacterium abscessus 99.79
Mycobacterium immunogenum 98.97
67 Mycobacterium marinum Mycobacterium marinum 100.00 Mycobacterium marinum 100.00 Mycobacterium ulcerans 100.00 Mycobacterium asiaticum 98.71
Mycobacterium ulcerans 100.00
68 Mycobacterium nonchromogenicum 7 Mycobacterium nonchromogenicum 98.13 Mycobacterium nonchromogenicum 98.13 Mycobacterium terrae 96.69 Mycobacterium cookii 95.56
69 Mycoplasma hominis 7 Mycoplasma hominis 100.00 Mycoplasma hominis 100.00 Brevibacillus parabrevis 76.75 Clostridium ramosum 76.07
70 Nocardia cyriacigeorgica Nocardia cyriacigeorgica 100.00 Nocardia cyriacigeorgica 100.00 Nocardia abscessus 98.73 Nocardia paucivorans 98.33
71 Olsenella uli 7 Olsenella uli 100.00 Olsenella uli 100.00 Atopobium vaginae 92.15 Atopobium parvulum 91.97
72 Pantoea dispersa Pantoea dispersa 99.92 Pantoea dispersa 99.92 Enterobacter cancerogenus 97.49 Kluyvera cryocrescens 97.49
73 Propionibacterium acnes 7 Propionibacterium acnes 99.80 Propionibacterium acnes 99.80 Propionibacterium propionicum 93.46 Propionibacterium avidum 93.27
74 Propionibacterium avidum Propionibacterium avidum 99.45 Propionibacterium avidum 99.45 Propionibacterium propionicum 99.30 Propionibacterium acnes 96.10
Propionibacterium propionicum 99.30
75 Providencia stuartii Providencia stuartii 99.77 Providencia stuartii 99.77 Providencia rettgeri 98.75 Providencia rustigianii 98.13
76 Pseudomonas oryzihabitans Pseudomonas oryzihabitans 99.79 Pseudomonas oryzihabitans 99.79 Pseudomonas pseudoalcaligenes 96.84 Pseudomonas aeruginosa 96.21
77 Salmonella enterica 23 Salmonella enterica 99.93 Salmonella enterica 99.93 Citrobacter farmeri 98.47 Enterobacter cloacae 98.46
78 Shewanella algae Shewanella algae 99.92 Shewanella algae 99.92 Shewanella putrefaciens 95.02 Aeromonas hydrophila 90.90
79 Solobacterium moorei 8 Solobacterium moorei 98.33 Solobacterium moorei 98.33 Bulleidia extructa 93.20 Holdemania filiformis 88.86
80 Staphylococcus aureus 7 Staphylococcus aureus 99.63 Staphylococcus aureus 99.63 Staphylococcus epidermidis 97.66 Staphylococcus caprae 97.64
81 Staphylococcus epidermidis 7 Staphylococcus epidermidis 100.00 Staphylococcus epidermidis 100.00 Staphylococcus caprae 99.21 Staphylococcus capitis 99.02
Staphylococcus caprae 99.21
Staphylococcus capitis 99.02
82 Staphylococcus lugdunensis 18 Staphylococcus lugdunensis 99.93 Staphylococcus lugdunensis 99.93 Staphylococcus haemolyticus 99.05 Staphylococcus hominis 98.84
Staphylococcus haemolyticus 99.05
83 Streptococcus anginosus 33 Streptococcus anginosus 99.77 Streptococcus anginosus 99.77 Streptococcus intermedius 97.37 Streptococcus constellatus 96.62
84 Streptococcus dysgalactiae 31 Streptococcus dysgalactiae 99.62 Streptococcus dysgalactiae 99.62 Streptococcus iniae 97.47 Streptococcus agalactiae 97.33
85 Streptococcus iniae 7 Streptococcus iniae 99.62 Streptococcus iniae 99.62 Streptococcus porcinus 95.21 Streptococcus dysgalactiae 95.11
86 Streptococcus porcinus Streptococcus porcinus 99.76 Streptococcus porcinus 99.76 Streptococcus agalactiae 96.79 Streptococcus iniae 96.79
87 Streptococcus pyogenes 12 Streptococcus pyogenes 100.00 Streptococcus pyogenes 100.00 Streptococcus canis 98.24 Streptococcus agalactiae 96.93
88 Tsukamurella pulmonis 20 Tsukamurella pulmonis 99.13 Tsukamurella pulmonis 99.13 Tsukamurella tyrosinosolvens 99.05 Tsukamurella strandjordii 98.90
Tsukamurella tyrosinosolvens 99.05
Tsukamurella strandjordii 98.90
Tsukamurella inchonensis 98.74
Tsukamurella paurometabola 98.66
89 Tsukamurella tyrosinosolvens 20 Tsukamurella tyrosinosolvens 100.00 Tsukamurella tyrosinosolvens 100.00 Tsukamurella pulmonis 99.69 Tsukamurella strandjordii 99.69
Tsukamurella pulmonis 99.69
Tsukamurella strandjordii 99.69
Tsukamurella inchonensis 99.39
Tsukamurella paurometabola 99.24
90 Veillonella atypica Veillonella atypica 98.95 Veillonella atypica 98.95 Veillonella dispar 98.42 Veillonella parvula 97.71
Veillonella dispar 98.42
91 Vibrio furnissii Vibrio furnissii 99.62 Vibrio furnissii 99.62 Vibrio fluvialis 98.85 Vibrio vulnificus 97.02
Vibrio fluvialis 98.85