TABLE 1.

Species and phylotypes for each clinical group, arranged in order of decreasing frequencya

Overall rankSpecies/phylotype(s)% of total clonesbMean % of total clones ± SD for individuals with the following clinical status:
StableBetterWorse
1 Veillonella sp. oral clone X0429.5210.3 ± 4.08.1 ± 7.59.8 ± 8.1
2 Campylobacter gracilis 3.654.5 ± 4.34.2 ± 4.71.9 ± 2.6
3 Streptococcus mitis 3.483.4 ± 3.23.4 ± 3.23.5 ± 2.2
4 Streptococcus gordonii 3.214.5 ± 5.73.1 ± 1.81.5 ± 1.7
5 Streptococcus oralis 2.752.7 ± 2.33.4 ± 2.92.1 ± 1.9
6 Streptococcus sanguinis 2.423.2 ± 3.91.9 ± 2.41.9 ± 2.0
7 Streptococcus sp. oral strain 12F2.422.7 ± 2.03.5 ± 3.91.0 ± 1.7
8 Peptostreptococcus sp. oral clone FG0142.172.1 ± 2.12.3 ± 2.62.1 ± 5.1
9 Selenomonas infelix 2.132.0 ± 1.91.8 ± 1.42.7 ± 2.4
10 Campylobacter showae 1.921.9 ± 2.12.0 ± 2.91.9 ± 2.8
11 Peptostreptococcus sp. oral clone AJ0621.900.9 ± 2.30.5 ± 1.44.8 ± 17.0
12 Streptococcus genomospecies C81.882.3 ± 4.01.7 ± 2.81.5 ± 4.0
13 Streptococcus intermedius 1.811.9 ± 1.71.6 ± 2.31.9 ± 3.2
14 Gemella morbillorum 1.731.5 ± 1.72.4 ± 3.51.4 ± 1.7
15 Gemella haemolysans 1.631.9 ± 1.61.5 ± 1.71.4 ± 1.8
16 Streptococcus pneumoniae 1.631.8 ± 2.11.4 ± 2.21.6 ± 1.8
17 Filifactor alocis 1.480.2 ± 0.41.4 ± 2.93.4 ± 3.8
18 Granulicatella elegans 1.461.6 ± 1.61.6 ± 1.41.2 ± 1.4
19 Peptostreptococcus sp. oral clone BS0441.461.3 ± 1.81.7 ± 1.91.4 ± 1.6
20 Veillonella atypica 1.421.6 ± 2.11.2 ± 2.21.4 ± 1.9
21 Streptococcus sp. oral clone 2056B1.231.0 ± 1.41.6 ± 2.31.3 ± 2.0
22 Peptostreptococcus micros 1.191.9 ± 2.80.7 ± 1.70.7 ± 1.5
23 Neisseria elongata 1.171.4 ± 3.71.3 ± 1.90.6 ± 2.8
24 Streptococcus sp. oral strain 7A1.080.9 ± 1.51.4 ± 1.71.4 ± 1.8
25 Selenomonas sputigena 0.980.8 ± 1.41.1 ± 2.21.1 ± 1.9
26 Streptococcus sp. oral clone FN0510.960.7 ± 1.51.7 ± 2.20.7 ± 1.5
27 Capnocytophaga gingivalis 0.940.7 ± 0.90.9 ± 1.21.3 ± 1.5
28 Campylobacter concisus 0.901.3 ± 2.00.6 ± 1.00.6 ± 1.2
29 Selenomonas sp. oral clone EW051a0.881.0 ± 1.40.1 ± 0.51.5 ± 2.2
30 Streptococcus anginosus 0.810.5 ± 0.90.6 ± 1.01.4 ± 1.3
31 Megasphaera sp. oral clone BB1660.790.8 ± 1.20.9 ± 1.50.6 ± 1.0
32 Eikenella corrodens 0.730.8 ± 1.00.9 ± 1.00.6 ± 1.2
33 Dialister sp. oral clone E2_200.710.5 ± 1.01.1 ± 1.60.7 ± 1.1
34 Streptococcus genomospecies C70.670.6 ± 1.21.3 ± 2.30.2 ± 0.6
35 Neisseria sp. oral clone AP0600.670.9 ± 1.70.9 ± 1.50.2 ± 0.8
36 Streptococcus salivarius 0.630.8 ± 1.80.3 ± 0.60.7 ± 1.4
37 Selenomonas sp. oral clone AA0240.631.1 ± 2.50.3 ± 0.70.2 ± 0.8
38 Selenomonas sp. oral clone AJ0360.630.6 ± 0.80.6 ± 1.00.6 ± 1.2
39 Streptococcus infantis 0.580.6 ± 1.00.5 ± 1.30.6 ± 1.0
40 Dialister sp. oral clone BS0950.580.7 ± 1.00.4 ± 0.90.7 ± 0.8
41 Selenomonas noxia 0.560.7 ± 1.20.7 ± 0.90.3 ± 0.6
42 Gemella sanguinis 0.500.6 ± 1.90.6 ± 1.30.2 ± 0.4
43 Dialister pneumosintes 0.500.4 ± 0.80.4 ± 0.80.8 ± 1.1
44 Dialister invisus 0.500.7 ± 1.30.5 ± 0.90.2 ± 0.4
45 Selenomonas sp. oral clone DY0270.480.5 ± 1.00.4 ± 0.90.5 ± 1.1
46 Selenomonas sp. oral clone DS0510.480.4 ± 0.71.0 ± 1.70.1 ± 0.4
47 Selenomonas sp. oral clone IK0040.460.3 ± 0.70.6 ± 1.70.5 ± 1.3
48 Veillonella sp. oral clone BU0830.460.4 ± 0.90.2 ± 0.40.9 ± 1.9
49 Capnocytophaga granulosa 0.440.9 ± 1.40.1 ± 0.50.1 ± 0.3
50 Streptococcus sp. oral clone EK0480.440.3 ± 0.80.6 ± 1.40.5 ± 0.8
51 Abiotrophia para-adiacens 0.420.6 ± 1.10.4 ± 0.80.2 ± 0.6
52 Abiotrophia sp. oral clone P4PA_1550.420.5 ± 0.90.4 ± 0.80.5 ± 0.9
53 Streptococcus parasanguinis 0.420.4 ± 1.20.7 ± 1.90.2 ± 0.6
54 Selenomonas sp. oral clone DS0710.420.1 ± 0.20.6 ± 1.20.8 ± 1.3
55 Selenomonas sp. oral clone EQ0540.420.5 ± 1.20.4 ± 0.80.3 ± 0.6
56 Neisseria meningitidis 0.420.5 ± 0.80.2 ± 0.60.5 ± 0.8
57 Campylobacter rectus 0.420.1 ± 0.50.6 ± 1.00.7 ± 1.1
58 Rothia dentocariosa 0.400.6 ± 1.10.4 ± 0.90.1 ± 0.3
59 Streptococcus cristatus 0.400.3 ± 0.60.5 ± 0.90.4 ± 0.9
60 Selenomonas dianae 0.400.6 ± 0.90.1 ± 0.30.4 ± 0.8
61 Capnocytophaga sp. oral clone AH0150.380.3 ± 0.40.6 ± 1.30.4 ± 0.8
62 Streptococcus sinensis 0.380.3 ± 0.60.3 ± 0.50.6 ± 0.8
63 Kingella oralis 0.380.3 ± 0.70.9 ± 1.20.0 ± 0.0
64 Neisseria denitrificans 0.380.4 ± 0.70.7 ± 1.30.1 ± 0.3
65 Enterococcus faecalis 0.350.6 ± 0.90.2 ± 0.60.1 ± 0.4
66 Eubacterium brachy 0.350.3 ± 0.70.6 ± 1.00.2 ± 0.6
67 Capnocytophaga sputigena 0.330.3 ± 0.70.5 ± 0.80.2 ± 0.6
68 Eubacterium sp. oral clone EW0530.330.3 ± 1.00.4 ± 0.80.2 ± 0.6
69 Selenomonas sp. oral clone EW0840.330.5 ± 0.10.2 ± 0.60.2 ± 0.6
70 Eubacterium saphenum 0.310.3 ± 0.80.1 ± 0.30.6 ± 1.0
71 Porphyromonas gingivalis 0.290.0 ± 0.00.2 ± 0.60.8 ± 2.4
72 Streptococcus agalactiae 0.290.3 ± 1.10.3 ± 0.80.2 ± 0.6
73 Selenomonas sp. oral clone DO0420.290.2 ± 0.40.5 ± 0.90.3 ± 0.8
74 Streptococcus bovis 0.270.2 ± 0.40.5 ± 1.10.2 ± 0.4
75 Streptococcus suis 0.270.3 ± 0.50.1 ± 0.30.4 ± 0.8
76 Peptostreptococcus sp. oral clone CK0350.270.4 ± 0.90.1 ± 0.30.3 ± 0.8
77 Selenomonas-like sp. oral clone CS0150.270.1 ± 0.20.3 ± 0.70.5 ± 0.8
78 Selenomonas sp. oral clone CS0020.270.1 ± 0.20.6 ± 1.30.2 ± 0.6
79 Corynebacterium matruchotii 0.250.2 ± 0.40.4 ± 0.90.1 ± 0.5
80 Streptococcus sp. oral clone 4093B0.250.2 ± 0.70.3 ± 0.80.3 ± 0.5
81 Streptococcus sp. oral clone FX0030.250.3 ± 0.60.1 ± 0.50.4 ± 0.9
82 Eubacterium sp. oral clone E1-K170.250.3 ± 0.70.2 ± 0.40.2 ± 0.6
83 Treponema sp. strain Smibert-50.250.2 ± 0.40.2 ± 0.80.4 ± 0.9
84 Atopobium rimae 0.230.4 ± 0.90.0 ± 0.00.2 ± 0.6
85 Streptococcus pyogenes 0.230.3 ± 0.80.3 ± 0.60.1 ± 0.4
86 Desulfobulbus sp. oral clone CH0310.230.3 ± 0.80.0 ± 0.00.4 ± 1.2
87 Peptostreptococcus sp. oral clone MDA2346-20.230.0 ± 0.00.3 ± 0.60.5 ± 1.2
88 Selenomonas sp. oral clone CS0240.230.4 ± 0.80.3 ± 0.00.3 ± 0.6
89 Selenomonas sp. oral clone GT0100.230.5 ± 1.40.1 ± 0.00.1 ± 0.5
90 Selenomonas lacticifex 0.230.6 ± 1.60.0 ± 0.00.0 ± 0.0
91 Alysiella filiformis 0.230.0 ± 0.00.8 ± 1.90.0 ± 0.0
92 Lautropia sp. oral clone AP0090.230.1 ± 0.20.7 ± 1.30.0 ± 0.0
93 Granulicatella adiacens 0.210.3 ± 0.60.2 ± 0.60.1 ± 0.5
94 Gemella sp. strain 1754-940.210.1 ± 0.30.0 ± 0.00.6 ± 0.9
95 Streptococcus intestinalis 0.210.3 ± 0.80.2 ± 0.60.1 ± 0.3
96 Streptococcus mutans 0.210.2 ± 0.70.1 ± 0.40.3 ± 0.6
97 Streptococcus peroris 0.210.2 ± 0.40.1 ± 0.50.4 ± 0.7
98 Catonella sp. oral clone FL0370.210.3 ± 0.80.0 ± 0.00.4 ± 0.9
99 Catonella morbi 0.210.1 ± 0.30.4 ± 0.60.2 ± 0.6
100 Selenomonas noxia-like sp. oral clone CI0020.210.5 ± 1.10.0 ± 0.00.1 ± 0.3
101 Selenomonas sp. oral clone GI0640.210.0 ± 0.00.7 ± 0.20.0 ± 0.0
102 Neisseria flava 0.210.3 ± 0.80.1 ± 0.40.2 ± 0.8
103 Campylobacter hominis 0.210.2 ± 0.50.4 ± 0.90.0 ± 0.0
104 Corynebacterium sp. oral clone AK1530.190.2 ± 0.50.4 ± 0.90.0 ± 0.0
105 Streptococcus hyointestinalis 0.190.0 ± 0.00.2 ± 0.60.4 ± 0.9
106 Streptococcus sp. oral clone CH0160.190.1 ± 0.20.5 ± 0.80.1 ± 0.3
107 Streptococcus sp. oral clone BM0350.190.4 ± 0.80.0 ± 0.00.1 ± 0.5
108 Eubacterium saburreum 0.190.4 ± 0.80.1 ± 0.30.0 ± 0.0
109 Megasphaera micronuciformis 0.190.1 ± 0.50.2 ± 0.60.3 ± 0.8
110 Selenomonas sp. oral clone EW0760.190.3 ± 0.60.1 ± 0.30.2 ± 0.4
111 Selenomonas sp. oral clone DD0200.190.3 ± 0.60.1 ± 0.50.1 ± 0.5
112 Veillonella parvula 0.190.1 ± 0.30.2 ± 0.60.3 ± 0.6
113 Neisseria genomospecies P1 clone P4PC_200.190.4 ± 1.10.0 ± 0.00.1 ± 0.4
114 Neisseria pharyngis 0.190.3 ± 0.60.0 ± 0.00.2 ± 0.4
115 Deferribacteres sp. oral clone BH0070.170.0 ± 0.00.4 ± 0.90.1 ± 0.4
116 Streptococcus didelphis 0.170.4 ± 0.90.1 ± 0.30.1 ± 0.3
117 Streptococcus oligofermentans 0.170.1 ± 0.20.4 ± 0.60.1 ± 0.4
118 Streptococcus sp. oral clone 3097C0.170.1 ± 0.20.1 ± 0.50.4 ± 0.6
119 Streptococcus sp. oral clone AY0200.170.3 ± 0.60.1 ± 0.40.1 ± 0.3
120 Streptococcus sp. oral clone BW0090.170.4 ± 0.80.0 ± 0.00.0 ± 0.0
121 Catonella sp. oral clone EZ0060.170.1 ± 0.20.2 ± 0.80.3 ± 0.8
122 Johnsonella ignava 0.170.2 ± 0.70.3 ± 0.80.0 ± 0.0
123 Selenomonas sp. oral clone EW0790.170.2 ± 0.50.1 ± 0.40.2 ± 0.6
124 Veillonella dispar 0.170.2 ± 0.40.1 ± 0.50.2 ± 0.4
125 Treponema sp. strain VI:G:G470.170.0 ± 0.00.1 ± 0.50.4 ± 0.9
126 Treponema sp. strain V:19:D360.170.0 ± 0.00.3 ± 0.70.3 ± 0.8
127 Deferribacteres sp. oral clone BA1210.150.2 ± 0.70.2 ± 1.00.0 ± 0.0
128 Gemella sp. oral strain C24KA0.150.1 ± 0.30.2 ± 0.60.1 ± 0.4
129 Streptococcus sp. oral clone 2061A0.150.1 ± 0.20.1 ± 0.30.4 ± 0.9
130 Streptococcus uberis 0.150.1 ± 0.20.3 ± 0.60.1 ± 0.4
131 Dialister sp. oral strain GBA270.150.2 ± 0.40.2 ± 0.40.1 ± 0.3
132 Eubacterium sp. oral clone EI0740.150.1 ± 0.30.3 ± 0.60.1 ± 0.5
133 Eubacterium sp. oral clone DO0080.150.1 ± 0.30.0 ± 0.00.4 ± 1.2
134 Eubacterium sp. oral clone IR0090.150.2 ± 0.70.1 ± 0.30.1 ± 0.5
135 Megasphaera sp. oral clone BU0570.150.2 ± 0.50.1 ± 0.50.1 ± 0.4
136 Selenomonas-like sp. oral strain FNA30.150.3 ± 0.70.0 ± 0.00.1 ± 0.3
  • a The 136 most common species are listed here. For a complete listing of all 260 species detected, see Table S1A in the supplemental material.

  • b Values are means of baseline and 24-month samples.