Harnessing rhizosphere microbiomes for drought-resilient ...
Dysbiosis in the Oral Microbiomes of anti-CCP Positive ...This is a repository copy of Dysbiosis in...
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This is a repository copy of Dysbiosis in the Oral Microbiomes of anti-CCP Positive Individuals at Risk of Developing Rheumatoid Arthritis. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/164826/ Version: Supplemental Material Article: Cheng, Z, Do, TD orcid.org/0000-0002-5668-2181, Mankia, K et al. (7 more authors) (2020) Dysbiosis in the Oral Microbiomes of anti-CCP Positive Individuals at Risk of Developing Rheumatoid Arthritis. Annals of the Rheumatic Diseases. ISSN 0003-4967 https://doi.org/10.1136/annrheumdis-2020-216972 © Author(s) (or their employer(s)) 2020. This manuscript version is made available under the CC BY-NC 4.0 license https://creativecommons.org/licenses/by-nc/4.0/ [email protected] https://eprints.whiterose.ac.uk/ Reuse This article is distributed under the terms of the Creative Commons Attribution-NonCommercial (CC BY-NC) licence. This licence allows you to remix, tweak, and build upon this work non-commercially, and any new works must also acknowledge the authors and be non-commercial. You don’t have to license any derivative works on the same terms. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request.
Transcript of Dysbiosis in the Oral Microbiomes of anti-CCP Positive ...This is a repository copy of Dysbiosis in...
This is a repository copy of Dysbiosis in the Oral Microbiomes of anti-CCP Positive Individuals at Risk of Developing Rheumatoid Arthritis.
White Rose Research Online URL for this paper:http://eprints.whiterose.ac.uk/164826/
Version: Supplemental Material
Article:
Cheng, Z, Do, TD orcid.org/0000-0002-5668-2181, Mankia, K et al. (7 more authors) (2020) Dysbiosis in the Oral Microbiomes of anti-CCP Positive Individuals at Risk of Developing Rheumatoid Arthritis. Annals of the Rheumatic Diseases. ISSN 0003-4967
https://doi.org/10.1136/annrheumdis-2020-216972
© Author(s) (or their employer(s)) 2020. This manuscript version is made available under the CC BY-NC 4.0 license https://creativecommons.org/licenses/by-nc/4.0/
[email protected]://eprints.whiterose.ac.uk/
Reuse
This article is distributed under the terms of the Creative Commons Attribution-NonCommercial (CC BY-NC) licence. This licence allows you to remix, tweak, and build upon this work non-commercially, and any new works must also acknowledge the authors and be non-commercial. You don’t have to license any derivative works on the same terms. More information and the full terms of the licence here: https://creativecommons.org/licenses/
Takedown
If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request.
Figure 1
0.0
0.2
0.4
0.6
0.8
HC NORA
Top 20 predomiant genera
Actinomyces
Bacteroides
Bifidobacterium
Bradyrhizobium
Campylobacter
Capnocytophaga
Cardiobacterium
Clostridium
Corynebacterium
Fusobacterium
Neisseria
Porphyromonas
Prevotella
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Selenomonas
Streptococcus
Treponema
unclassified
Veillonella0.0
0.2
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Me
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Top 20 predomiant genera
Actinomyces
Bacteroides
Bifidobacterium
Bradyrhizobium
Campylobacter
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Fusobacterium
Neisseria
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Selenomonas
Streptococcus
Streptomyces
Treponema
unclassified
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*
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b
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HC CCP+ at Risk Early RA HC CCP+ at Risk Early RA
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i i
Ni tr o
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ea
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s
Xy l a
n i mon
a s c e l lu l o
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a
C l o s t r i d i u m b a r tl e t t i i
Ba
ci l lu
s l i c
he
ni f o
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My
co
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sm
a m
ob
ile
Pa
st e
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lla
mu
l to
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a
B i f i d o b a c t e r iu m c a t e n u l a t u m
A e r o m o n a s b e s t i a r u m
Pe c t o b
a c te r i u m w
a s a b ia e
Ak
ke
rma
ns
ia m
uc
inip
hila
Sh
ew
an
el l
a p
ut r
ef a
ci e
ns
My
co
ba
cte
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m p
ara
sc
ro
f ula
ce
um
A c h r o mo b a c te
r x yl o s o x ida n s
Pec t o
Or
i en
t i a t s
ut s
ug
am
us
hi
Y e rs i n i a i n t e r m e d i a
S t a c k e b r a n d t i a n a s s a u e n s i s
S a g i t t u la s t e l l a t a
D e s u lf i t o b a c t e r iu m h a f n i en se
M e t h y l o b a c t e r t u n d r i p a l u d u m
E s c h e r i c h i a a lb e r t ii
J a n i b a c t e r s p . H T CC 2 6 49
D o r e a f o r m i c i g e n e r a n s
Aq
uife
x a
eo
li cu
s
L a c t o b a c i l lu s c u r v a t u s
P e p t o s tr e p t o c o c c u s a n a e r o b i u s
Wig
gle
sw
orth
ia g
los
sin
idia
D ic t y o g lo m u s t h e r m o p h i l u m
M a r i p r o f u n d u s f e r r o o x y d a n s
A c i d a m i n o c o c c u s s p . D 2 1
B a c t e r o i d e s i n t e s t i n a l i s
g a mm
a pr o te o b a c te r iu
m Hd N
1
K o c u r i a r h i zo p h i l a
Ac
i ne
tob
ac
ter r a
dio
re
sis
t en
s
Ro s eo
b a c ter s
p. C
CS
2
B u r k h o l d e r ia s p . 3 8 3
P r e v o t e l l a o r i s
S t r e p t o c o c c u s v e s t i b u l a r i s
L i s t e r i a i n n o c u a
S t a p h y l o c o c c u s ho m
i n is
Ag
r ob
a cte
rium
rh
i z og
e ne
s
Ch
l or o
he
rpe
t on
th
al a
ss
i um
B a c il lu s c o a h u i le n s is
Ve
rmin
ep
hro
ba
cte
r eis
en
i ae
En
ter o
co
cc
us
fa
ec
i um
A n a e r o f u s t i s s t e r c o r i h o m in i s
Ac
ido
vo
rax
av
en
ae
Er w
i ni a
am
yl o
vo
r a
H e l io b a c t e r iu m m o d e s t i c a ld u m
Gr a
nul i b
a ct e r b
e th es d
ens i s
My
co
pla
sm
a p
ne
um
on
i ae
C o r y n e b a c t e r i u m d ip h t h e r ia e
La
ct o
ba
ci l
l us
pl a
nt a
r um
P s e u d o v ib r i o s p . J E 0 6 2
al p
ha
pr o
teo
ba
ct e
r i um
HIM
B11
4
S i n o r h iz o b i u m m e li l o t i
Sp
hin
go
mo
na
s s
p.
SK
A5
8
Rh
od
ot h
erm
us
ma r
i nu
s
Ge
ob
ac
ill us
sp
. WC
H7
0
S t r e p t o c o c c u s s p . 2 1 3 6 F A A
R u e ge r ia sp . T M
10 4 0
Vi b
r io
sp
. 0
90
22
No ca r d i a f a r c in
ic a
Eu
ba c
ter i u
m s a
bu
r reu
m
Tr e p o
n e ma d
en t ic
o la
R u b r o b a c t e r x y l a n o p h i l u s
Ric k e
t t s ia c ana d e n
s i s
T o lu m o n a s a u e n s i s
Fu
so
ba
cte
r iu
m s
p.
D1
1
C o p r o b a c i l lu s s p . D 7
S hig e
l la sp . D
9
Th
erm
oa n
ae
r o ba
ct e
r sp
. X5
14
A g r o b a c t e r i u m t u m e f a c ie n s
S e l e n o m o n a s f l u e g g e i
Pr o
v ide n
ci a r e
t tg er i
Pe d
i oc o
cc
us
da
mn
os
us
B r u c e l l a sp . B O 1
Gra
nu
li ca
t el la
el e
ga
ns
C a ldi c e ll u lo s ir u p t o r h
y d r o t h e r m a l is
B a c t e r o i d e s s p . 2 0 3
De
ha
loc
oc
co
ide
s s
p. G
T
S e r r a t i a e n t o m o p h il a
B o r r e l i a r e c u r r e n t i s
Am
i no
mo
na
s p
a uc
i vo
ran s
E g g e r t h e l l a le n t a
Rh
odo m
i c r o biu
m v
a n nie
l ii
N i t r o b a c t e r s p . N b - 3 1 1 A
Clo
str
idiu
m b
otu
lin
um
C a m i n i b a c t e r m e d i a t l a n t i c u s
La
c t ob
ac i l
lus
he
l ve t i
cu
s
B u r k h o l d e r i a v ie t n a m ie n s i s
Ac
tin
om
yc
es
sp
. o
ra
l ta
xo
n 8
48
Sh
ewa n
e l la d
e n i tri f
ican s
Th
a l as s
i ob
i um
sp
. R2
A6
2
Ca
ndi d
atu
s So
l iba c t e r u
si ta
tus
R o s e o v a r ius s
p . 2 1 7
I nt r
as
po
r an
gi u
m c
al v u
m
N e is s e r i a s i c c a
La
ct o
ba
ci l lu
s a
my
l ol y
t i cu
s
M o r a x e l l a c a t a r r h a l i s
Geo b a c te
r b e mi d j i e n s is
En
t er
oc
oc
cu
s g
all
ina
rum
C h l o r o b i u m f e r r o o x i d a n s
R ic k e t t s i a f e li s
C l o s t r i d iu m c a r b o x i d i v o r a n s
B e u t e n b e r g i a c a v e r n a e
B a c t e r o i d e s s p . D 2
L e a d b e t t e r e l l a b y s s o p h i la
S y n t r o p h o b a c t e r f u m a r o x i d a n s
C h l a m y d o p h i l a c a v ia e
Can d
ida tu
s P
hy to
pl a
s ma m
a l i
T h a u e r a s p . M Z 1 T
F e r r i m o n a s b a le a r i c a
J o n e s ia d e n it r if i c a n s
B a r t o n e l l a g r a h a m i i
Leg i o n e
l la d
r an c o u r t i i
Nitr o
so
sp
ira
mu
ltif orm
is
Ca
rbo
x yd
ot h
e r mu
s hy
dro
ge
no
f or m
an
s
C o r y n e b a c t e r i u m l i p o p h i lo f la v u m
Pr
ev
ot e
l la
sp
. o
r al
t ax
on
47
2
R o s e o m o n a s c e r v i c a l i s
S p hin g o b ac t e r iu m
s p ir i ti v o r u m
B a c t e r o i d e s ca c c a e
P la n c t o m y c e s b r a s il i e n s i s
My
xo
co
cc
us
xa
nt
hu
s
Clo
st r i d
ium
ph
yt o
f er
me
nta
ns
P e lo b a c t e r c a r b in o li c u s
T h e r m o a n a e r o b a c t e r p s e u d e t h a n o l i c u s
P r e v o t e l la t i m o n e n s is
F u s o b a c t e r iu m g o n i d i a fo r m
a n s
Ge
mm
atim
on
as
au
ran
tiac
a
Al k
a l ip
hi l
us
or e
ml a
nd
i i
Be
ije
rin
ck
ia i
nd
ica
u n c u l t u r e d e u b a c t e r iu m p I E 1 1 1 5
Pa
en
iba
cil
lus
la
r va
e
No
vo
sp
hi n
go
bi u
m a
rom
at i c
i vo
ran
s
c an
di d
at e
di v
i si o
n T
M7
si n
gl e
- ce
l l i
so
l at e
TM
7b
S y m b i o b a c t e r i u m t h e r m o p h il u m
A l l o c h r o m a t i u m v in o s u m
N e o r i c k e t t s i a s e n n e t s u
C lo s t r i d i u m s p ir o f o r m e
Ne
pt u
ni i b
ac
t er c
ae
sa
r i en
sis
Sp
hin
go
bi u
m j a
po n
i cu
m
P h o t o r h a b d u s lu m in e s c e n s
E d w a r d s i e l la i c t a l u r i
P s e u d o m o n a s f l u o r e s c e n s
St r
ep
toc
oc
cu
s g
or d
on
i i
L e p t ot r ic
hia
h o fst a d
i i
Di a
l is
t er i
nv
i su
s
H a lo m o n a s e lo n g a t a
My
co
ba
ct e
ri u
m s
me
gm
at i s
Tr ic
ho
de
sm
i um
er y
t hr a
eu
m
A c i d o b a c t e r i u m c a p s u la t u m
B a r t o n e l l a h e n s e l a e
L a c t o b a c i l l u s v a g i n a l is
L a c t o b a c i l lu s u l t u n e n s i s
N itr o s o m
o nas sp
. AL 2 1 2
Fu
so b
ac
ter i u
m n
uc
lea t u
m
Cl o
st r i d
i um
c el l u
l ol y t i c u
m
Clo
st r
idiu
m p
ap
yr o
so
lve
ns
M y c o b a c t e r i u m s p . S p y r 1
V i b r io s p le n d i d u s
B a c i ll u s a m y l o li q u e f a c i e n s
Ba
cte
r oid
et e
s o
ra
l t ax
on
27
4
F l a v o b a c t e r i a b a c t e r i u m B B F L 7
Ma
cro
co
cc
us
ca
se
oly
tic
us
B a c t e r o i d e s p l e b e i u s
Ro
se
ov
ar i
us
sp
. T
M1
03
5
S he w
a ne l la s
p . MR
-4
Ac
i ne
t ob
ac
ter s p
. AD
P1
An
ae roc o
c cu s
lac to ly
t ic us
Pe
pt o
nip
hil
us
ha
r ei
P s e u d o mo n a s s
p . ND6
Ca l d i c el lulo
s i r u p t o r k r o n o t s k y e n s i s
L e e u w e n h o e k i e l la b la n d e n s i s
Ne i s
s er i a
l ac
t am
i ca
E s c h e r i c h i a sp . S f l u 5
B o r r e l i a a f z e l ii
Ca
nd
i da tu
s Pro
toc
h l amy
dia
am
oe b
op
hi l a
M y c o b a c t e r i u m t u b e r c u l o s i s
Ba c
ter o id
es s
p . D 2
2
L ac t o b a c i l l u s ca s e i
P s e u d o m o n a s sp . C A 1 0
C e l lu l o m o n a s f l a v ig e n a
T h e r m o s ip h o a f r i c a n u s
B d e l l o v i b r i o b a c t e r i o v o r u s
Be
gg
i at o
a s
p.
SS
S t r e p t o m y c e s c l a v u li g e r u s
M a r ic a u l is m a r i s
La
cto
ba
ci llu
s p
ara
ca
se
i
Ch
ry
se
ob
ac
ter iu
m g
l eu
m
A c h r o m o b a c t e r p ie c h a u d i i
L a ct o c
oc c us g
a r vie ae
A na e r o s
t ip es c a c c ae
Es
ch
er i
ch
i a s
p.
3 2
53
FA
A
Ac in
e t ob a
c ter jo
h ns o
n i i
B o r r e l i a s p ie l m a n i i
A nae r o m
y x o ba c te
r sp . F w
109 -5
Eu
b ac
t er i
um
el ig
en
s
Sy
ne c h
oc
y s t i s s
p. P
CC 6
80
3
T h e r mo m
i c r ob i u m
r o s e u m
Rh
od
ob
ac
ter s
ph
ae
roid
es
Pa
r ab
ac
t er
oid
es
sp
. D
13
Ge
ob
ac
il l us
sp
. Y4
. 1M
C1
Ca
ul o
ba
ct e
r sp
. K
31
Sp
i ro
ch
ae ta
th
er m
op
hi la
My c o
p l asm
a ho m
in is
A lc a n iv o r a x b o r k u me n s is
Sim
on
sie
l la
mu
el l
er
i
D e r m a c o c c u s s p . El l i n 1 8 5
T h e r ma n a e r o v ib r io a ci d a m
in o v o r a n s
Ba
cte
roi d
es
sp
. 2 1 1
6
Br
ev
un
dim
on
as
su
bv
ibri
oid
es
E t h a n o l i g e n e n s h a r b i n e n s e
Ar c
ob
ac
t er n
itro
figi lis
O c e a n i c o l a g r a n u lo s u s
Sh
ige
l la s
on
ne
i
K i ng el la
or a l is
Ps
eu
do
mo
na
s a
lca
lig
en
es
Ra
ph
i di o
ps
i s b
r oo
ki i
Ca
l dic
ell
ulo
si r
up
t or
ow
en
se
ns
is
Clo
str
idiu
m a
sp
ar
ag
i fo
rme
S e le n o m o n a s s p u t i g e n a
P o r p h y r o m o n a s g i n g iv a l i s
Ps
eu
do
mo
na
s s
t ut z
er i
Sh
ew
an
el l
a b
en
t hi c
a
S y n e c h o c o c c u s s p . W H 5 7 0 1E u b a c t e r i u m y u r i i
J o n q u e t e l l a a n t h r o p i
L e p t o s p i r a b i f l e x a
F i l if a c t o r a l o c is
C a n d id a t u s D e s u lf o r u d is a u d a x v iat o r
D e s u lf o m i c r o b i u m b a c u l a t u m
R o s e b u r i a i n t e s t in a l i s
M a g n e t o s p i r i l lu m m a g n e t o t a c t i c u m
Ps
eu
do
al t e
ro
mo
na
s h
alo
pla
nk
t is
C l o s t r id ium
le n toc e ll u m
B u r k h o l d e r i a s p . C C GE 1 0 0 2
Co
ryn e
b ac te
r ium
ps e
ud o
gen i t
a l iu m
N e i s s e r ia s u b f l a v a
Th
er m
oa
na
ero
ba c
t er w
i eg
el i i
A n a e r o b a c u lu m h y d r o g e n i f o r m a n s
B r u c e l l a o v is
S y n e c h o c o c c u s s p . R S 9 9 1 6
B a c i l lu s m e g a t e r i u m
S t r e p t o c o c c u s g a l lo ly t i c u s
B a c t e r o id e s s p . 2 1 2 2
Th i o
mo n
as s
p. 3
A s
Ra
lst o
ni a
so
l an
ac
ea
r um
V e i l lo n e l la
sp . 3 1 44
Sh u t t le w
o r t h i a s a t e l le s
C a n d i d a t u s A m o e b o p h i lu s a s i a t i c u s
D e s u lf o v i b r i o s a l e x i g e n s
Ri c ke t t s i a c
o n o r i i
C o r y n e b a c t e r i u m g e n i t a l i u m
H i s t o p h i lu s s o m n i
Ac
i ne
t ob
ac
ter
lwo
ffii
P ho t o
b a c t e r iu m s p
. S KA
3 4
Hy
dro
ge
no
ba
cu
lum
sp
. Y
04
AA
S1
Sa
lin
i sp
or a
ar
en
i co
l a
A z o s p ir i l lu m s p . B 5 1 0
A c i dam
in o co c c u s f e r me n t a n
s
Or ib
a cte
r ium
sin
u s
R ho d o p s eu
d o mo n
a s p a l u s t r is
Er
yth
r ob
ac
ter
lit ora
lis
C a n d i d a t u s P h y t o p la s m a a u s t r a l ie n s e
Pre
vo
tell a
or a
lis
C u p r i a v i d u s p i n a t u b o n e n s i s
W a d d l i a c h o n d r o p h i la
C a n d i d a t u s P e l a g ib a c t e r u b i q u e
C a n d id a t u s L i b e r i b a c t e r s o l a n a c e a r u m
Vi b
rio s
p. R
C3
41
D o k d o n ia d o n g h a e n s i s
Pa
nt o
ea
va
ga
ns
P a e n ib a c i l lu s c u r d la n o l y t ic u s
T h e r m o a n a e r o b a c t e r m a t h r a n i i
T h e r mo s y n e c h o c o c c u s e lo n g a t u s
Ru eg
e r ia l a
c us
c ae r u
l en s
is
E u b a c ter iu m
s a p h e n u m
R u e g e r ia s p . P R 1 b
L e p t o s p i r a b o r g p e te r s e n i i
Pse u
d om
ona s
sp
. CT 1
4
m a r i n e a c t in o b a c t e r i u m PH S C 2 0 C 1
N o s toc p
u n c t i f o r me
M y c o b a c t e r iu m k a n s a s i i
S t r e p t o c o c c u s u b er i s
m a r i n e g a m m a p r o t e o b a c t e r i u m H T C C 2 1 4 8
Sh
ew
an
el l
a w
oo
dy
i
P s e u d o mo n a s p u t id a
C o lwe ll i a p
s y c h r e r y t h r a e a
De
s ul f o
vi b
r i o d
e su
l fur i c a
ns
P s e u d o m o n a s s a v a s t a n o i
P o r p h y r o m o n a s e n d o d o n t a l i s
T h e r m u s s p . 4 C
B u r k h o ld e r i a d o l o s a
Gr i m
on
t i a h
ol l i s
ae
Ac
et o
ha l o
bi u
m a
r ab
at i
cu
m
Ac
i do
vo
rax
sp
. J
S4
2
B o r r e l i a g a r in ii
R ic ke tt s ia ty p
h i
C l o s t r i d i u m s p . 7 2 4 3 F A A
Ca ly p
t o ge na
o k uta n
i i t hi o au
t otr o
p hic g
i l l s y mb io
n t
Clo
str
idi u
m a
ce
tob
uty
l ic
um
Cam
p y lob a c te r c o n c is u
s
Cu
pr
iav
i du
s m
et a
l lid
ur a
ns
Ba c il lu s c o a g
u l an s
C lo s t r id iu m pr o t e o c l a s t i c u m
Ps
eu
do
mo
na
s s
yr i
ng
ae
gr o
up
ge
no
mo
sp
. 3
P a s t e u r e l l a da g m a t is
C a n d id a tu s H a m i lt o n e ll a d e f e n s a
Ye r s
i nia
mo
l la re
t i i
Ch
t ho
ni o
ba
ct e
r f lav
us
Kle b s i e l l a o x y to c a
A l c a n i v o r a x s p . D G 8 8 1
V i b r io s p . M E D 2 2 2
P o r p h y r o m o n a s a s a c c h a r o l y t i c a
S ta p h y l o c o c c u s h a e mo l y t ic u s
R u m ino c o c c u s a l b u s
M e t h y l o v o r u s s p . M P 6 8 8
Bo r d e t el la
pe t r i i
S h e w a n e l la b a l t ic a
V e r r u c o mi c r o b i u m s p i n o s u m
N a u t i l i a p r o f u n d i c o l a
P e lob a
c t e r p ro
pi o n
i cus
My c o
p l asm
a c
apr ic
o lum
Pa
r a co
c cu
s am
ino
ph
i l us
A c e t o b a c t e r p a s t e u r i a n u s
Le
uc
on
os
toc
ga
sic
om
it atu
m
B o r r e l ia h e r ms i i
N e i s s e r i a m u c o s a
He
l ic
ob
ac
t er
ci n
ae
di
No
dula r i a
s pu m
i gen
a
A l g o r i p h a g u s s p . P R 1
C a n d i d a t u s K o r i b a c t e r ve r s a t il is
En
ter
ob
ac
t er
ae
ro
ge
ne
s
V ib r i o o r i e n t a li s
B a c t e r o i d e s sp . 3 1
2 3
T h i o a l k a l i v i b r io s p . H L - E b G R 7
Ple
si o
c y st i s pa
c i fic a
Kr ib b el la fl av i d a
P r e v o t e ll a b u c c a l is
ga
mm
a p
r ot e
ob
ac
t er i
um
NO
R5
1- B
Ro
s eov a r iu
s nu b
i nh i b
e ns
A c in e t o b a c te r v e n e t ia n u s
Ps
eu
do
al t
ero
mo
na
s a
tla
nti
ca
Bi b e r s te
i n ia t r e h a lo
s i
O c e a n o b a c i l lu s i h e y e n s i s
Ca
mp
yl o
ba
ct e
r u
ps
al i e
ns
i s
Le
uc
on
os
t oc
ki m
ch
i i
Le g
i o ne
l l a l on
gb
e ac
h ae
A u r a n t i m o n a s m a n g a n o x y d a n s
He
rm
i nii
mo
na
s a
r se
ni c
ox
yd
an
s
F u s o b a c t e r i u m s p . 4 1 1 3
Ni t r a
t ir up
t or s
p. S
B1
55
- 2
Xe
no
rha
bd
us
bo
vi e
ni i
G l u c o n a c e t o b a c t e r d ia z o t r o p h i c u s
T h e r m o b a c u l u m t e r r e n u m
L a c t o b a c i ll u s a n t r i
Str e p t o m
y c es l i v ida n
s
Sp
hi n
go
bi u
m c
hlo
r op
he
no
l ic
um
St i g
ma
t el l a
au
r an
t iac
a
Ful v im
a r i n a p e
la gi
La
bre
nz
ia a
gg
re
ga
ta
M i c r o mo n o s p o r a a u r a n t ia c a
D e h a lo c o c c o i d e s e t h e n o g e n e s
B u r k h o l d e r i a o k la h o m e n s i s
R o s e b u r i a i n u l in i v o r a n s
V e r r u c o m ic r o b ia e b a c t e r i u m D G 1 2 3 5
Ge
ob
ac
illu
s k
au
sto
ph
i lu
s
Ge o
b ac i l lu s s p . G
11 MC
1 6
S y n e c h o c oc cu
s s p. R S 9 91 7
Nitr o
ba
cte
r ha
mb
urg
en
si s
Ph
en
ylo
ba
ct e
r iu
m z
uc
i ne
um
B a c i l lu s p s e u d o m y c o i d e s
Me
thy
lob
ac
teri
um
sp
. 4
-46
M a n n h e i m i a h a e m o l y t i c a
Myc o
p la sma
a l l i ga t o
r i s
H o e f l e a p h o t o t r o p h ic a
Bl a
st o
pi r
el l u
l a m
ar i
na
Ba
ct e
roi d
es
sp
. 9 1
42
FA
A
Ph o t o b a c t e r iu
m d
a ms e l a e
Me
s orh
i z o bi u
m o
p p or tu n
i stu
m
Ne
i ss
er i a
f l av
e sc
en
s
C lo s t r i d iu m s p . M 6 2 /1
Pi r
ell
ula
sta
l ey
i
Ro
s e i biu m
s p. T r ic h
SK D
4
Eu b
a c t e r i um r e c t a le
C u p r ia v i d u s n e c a t o r
Rh
o do
c oc
c us o
pa c
u s
Ca
nd
i da
tus A
cc u
mu
l i ba c
te r ph
os p
ha
t i s
C u p r i a v id u s t a i w a n e n s is
M o o r e l l a t h e r m o a c e t i c a
Cl o
st r
i di u
m n
ex
i le
Z u n o n g w a n g ia p r o f u n d a
Eh
rl i ch
i a c
ha f f e
en
s i s
R u e g e r ia p o m
e r o y i
Co
r y ne
ba c
te ri um
k rop
pen
ste
dt i i
Er y
thro
ba c
te r sp
. NA
P1
Sy
ntr
op
ho
mo
na
s w
olf
ei
Clo
s t rid
ium
the r m
oc e l lu
m
H a e mo p h i l u s d u c r e y i
P o r p h y r o mo n a s u e n o n is
S u l f u r o s p i r il l u m d e le y ia n u m
Co
ry
ne
ba
cte
riu
m a
my
co
latu
m
Rh
od
ob
ac
t era
ce
ae
ba
ct e
r i um
HT
CC
20
83
Ye
rsi n
ia f
red
er i k
s en
i i
B i f id o b a c t e r iu m a d o l e s c e n t is
F r a n c i s e ll a p h il o m i r a g ia
Cya n o b iu m
s p . P CC 70
0 1
C h l o r o f l e x u s s p . Y- 4 0 0 - f l
C o l li m o n a s f u n g iv o r a n s
P s e u d o m o n a s s y r i n g a e
C o r y n e b a c t e r iu m s p . L 2 - 7 9 - 0 5
Mu
c i lag
ini b
a c t er pa
lud i s
St re
pto
co c
cu
s an
gi n
os u
s
Th
er m
os
inu
s c
ar b
ox
yd
i vo
r an
s
S l a c k ia h e l i o t r i n i r e d u c e n s
Vi b r i o v u l n i f i c u s
Cl o
s tri d
ium
s ci n
d en
s
S p i r o p la s m a c i t r i
A r c ano b a ct e r iu
m h
ae mo ly
t icu m
Pe
di o
co
cc
us
pe n
tos
ac
eu
s
Stre
pto
co
cc
us
dy
sg
ala
ctia
e
Es
ch
er
i ch
ia s
p. 4
1 4
0B
P s e u d o m o n a s c o r o n a f a c ie n s
Xa
nt h
om
on
as
al b
i li ne
an
s
Clo
s trid
i um
hi ra
n on is
De
l f t ia a
ci d
ov
or
an
sPa
ra
ba
ct e
r oi d
es
me
r da
e
V ib r i o m e t s c h n i k o v ii
Di c
t yo
gl o
mu
s t
urg
idu
m
A t o p o b i u m p a r v u l u m
M e t h y lo p h i la l e s b a c t e r i u m H T C C 2 1 8 1
V i b r io c h o l e r a e
De
su
l furis
pir illu
m in
dic
um
M e t h y lo t e n e r a m o b i li s
Op
i tuta
c ea
e b
ac te
r i um
TA
V2
Kle
bs
iella p
ne
um
on
iae
N o s t o c s p . P C C 7 1 2 0
L a c t o b a c i l l u s o r is
M e t h y l o b a c t e r i u m c h l o r o m e t h a n ic u m
T r u e p e r a r a d i o v i c t r ix
Ne
iss
er
ia m
en
ing
itid
is
Ph
oto
rha
bd
us
as
y mb
i ot i c
a
Bo r d
e tel l
a pa r a
p er tu
s s i s
Sa
ng
uib
ac
ter
ke d
die
ii
Ye
r si n
i a r u
ck
eri
D e s u lf o n a t r o n o s p i r a t h io d i s m u t a n s
B r a c h y s p i r a mu r d o c h i i
P a r a b a c ter o id e s d is
t a s o n i s
Co l l in
s e l l a s ter c o r is
Ric
ke
tts
ia p
r ow
az
ek
ii
Ra
lsto
nia
pic
ke
ttii
V i b r i o s p . A N D 4
Pa
en
i ba
ci l
l us
po
l ym
yx a
Ex
ig uob
a ct e
r i um
s ib i r ic um
P s y c h r o b a c t e r a r c ti c u s
St r
ep
tom
yc e
s p
ris
t in
ae s p
i ra
l is
Bra
dy
rhi z
ob
i um
sp
. B
TA
i 1
La
ct o
ba
ci ll u
s a
ci d
op
hi lu
s
Ri e
me
rel l a
an a
t ip
es t i
fer
F u s o b a c ter i u m
sp . 3
1 3 3
C lo s t r i d i u m p e r f r i n g e n s
A c i n e to b a c te r g e n o mo s p . 3
C i t r o b a c t e r k o s e r i
M e t h y l o b a c t e r iu m e x t o r q u e n s
B l a tt a ba c te
r ium
sp
. - P e r ipla
n e ta a m
e r ica n a
B a c il lus p u m
i lus
Ca
mp
ylo
ba
ct e
r l ar i
Ba c
ter o
i de
s x
yl a
ni s
ol v
en
s
A c a r y o c h l o r i s m a r i n a
Kle b s i e l l a s p . 1 1 5 5
B a c t e r o id e s s p . 1 1 1 4
Ep
ulo
pi s
ci u
m s
p.
N. t
. m
or p
ho
t yp
e B
L a c t o b a c i l lu s s a k e i
Lis
t er i
a g
r ay
i
B if i d o b a c t e r i u m a n i m a l is
B u r k h o l d e r i a g r a min i s
T h e r m o d e s u lf o v i b r i o y e l lo w s t o n ii
B a c t e r o id e s s p . 2 1 3 3 B
Su
l f uri m
on
as
de
ni t ri f i c
an
s
Po l yn u c le
o b a c ter n ec e s s a r iu
s
Me
i ot h
erm
us
ru
be
r
A g r o b a c t e r i u m v it i s
H y d r o g e n o b a c t e r t h e r m o p h i l u s
S yn e
c ho c
o cc u
s sp . C
C9 3
1 1
Ac in e to b a
c te r c a lc o a ce t ic u s
A r t h r o b a c t e r a r i lai t e n s is
G e o b a c t e r s p . F RC - 3 2
S h e w a n e l la s p . M R - 7
Su
l fu
ri h
yd
rog
en
i bi u
m s
p.
YO
3A
OP
1
Ol ig
o t r o p h a c a r b o x i d o v o r a n s
Ex
igu
ob
ac
teriu
m a
rab
atu
m
P a r a s c a r d o v ia d e n t ic o le n s
Es
ch
er
i ch
i a f
er g
us
on
i i
X e n o r h a b d u s n e m a t o p h i la
Str
ep
to
my
ce
s s
p.
AA
4
Lim
no
ba
cte
r s
p.
ME
D1
05
H e r b a s p i r i ll u m s e r o p e d i c a e
B a c i ll u s c l a u s i i
C a l d ic e l l u l o s i r u p t o r l a c t o a c e t ic u s
A l ic y c l ip h i lu s den i tr i fi c an s
En
tero
co
c cu s
ca s
s el i f l a v
us
mar in e g a m
ma p
r ot e o bac t e r i u m
HT C
C20 8 0
Il yo
ba
ct e
r p
oly
t ro
pu
s
Ca
nd
i da
tus
Ri e
sia
pe
dic
ul ic
ola
Ac
t in
om
yc
es
co
l eo
ca
nis
W e i s s e ll a c i b a r i a
Ac in
e t o ba c t e r j u
n i i
B o r r e lia b a v a r ie n s is
Ba
ci ll u
s s
p. N
RR
L B
-14
91
1
G e o b a c t e r l o v l e y i
C h l o r o b a c u l u m p a r v u m
La
cto
ba
cill u
s i n
ers
M y c o p la s m a a g a l a c t ia e
No
ca
rdio
ide
s s
p.
JS
61
4
He
l ic
ob
ac
t er
bi l
i s
Sy
ne
ch
oc
oc
cu
s s
p. J
A- 3
- 3A
b
L e p t o tr ic h i a g o o d f e l l o w i i
A e r o c o c c u s vi r id
a n s
R o t h i a d e n t o c a r i o s a
Lis
teri a
se
elig
eri
Pa
ra
co
cc
us
de
nit
r if i
ca
ns
Bu
ty ri vi b
ri o c
ro ss o
t u s
S e l e n o m o n a s s p . o r a l t a x o n 1 3 7
Ga
llio
ne
lla
ca
ps
ife
rri f
orm
an
s
S t r e p t o m y c e s s p . S P B 7 4
B r u c e l l a s p . B O 2
En t e
rob
ac te r s
p. 6
3 8
C o r y n e b a c t e r iu m p s e u d o t u b e r c u l o s i s
De
su
l f ur o
mo
na
s a
ce
t ox
i da
ns
Rh
od o
ba c
ter ac
e ae b a
c t er iu m
HT
CC
21 5
0
Fr a
nk
i a s
p. E
uI 1
c
Op
i t ut u
s te rr a
e
My
co
ba
ct e
r i um
ma
ri nu
m
Ali c
yc
l ob
ac
i ll us
ac
i do
ca
l da
r i us
C a m p y lo b a c t e r j e ju n i
Ba
rt on
e l la b ac
i l l i form
i s
S t r e p t o m y c e s s p . e 1 4
A s t i c c a c a u l is e x c e n t r ic u s
J a n t h i n o b a c t e r i u m s p . M a r s e i l le
B a c i l lu s t h u r i n g i e n s is
As
te r ye l lo
ws
wi tc h
e s- b
ro om
p hy
top la
s ma
P l a n c t o m y c e s l im n o p h i lu s
Po la
r ibac
t er s p
. ME D
152
S a c c h a r o p h a g u s d e g r a d a n s
S h e w a n e ll a p i e z o t o l e r a n s
Vi b
ri o m
imi c
us
An
ap
l as
ma
ma
r gi n
al e
S p o r o s a r c in a u r e a e
De
su
l fo
vi b
r io
fr u
ct o
so
vo
r an
s
Cl o
st rid
i al e
s g
en
om
os
p. B
VA
B3
Co
pr
oth
erm
ob
ac
ter
pro
teo
lyti
cu
s
Ba c
t er o
i de
s c
op
roc
ol a
D e s u lf o v ib r i o v u l g a r i s
B a r t o n e ll a t r ib o c o r u m
L e u c o n o s t o c c i t r e u m
A z o t o b a c t e r v in e l a n d ii
P r e v o t e l la s p . o r a l t a xo n 2 9 9
A l b i d if e r a x f e r r i r e d u c e n s
Pre
vo
tell
a a
mn
ii
Ba
cte
roi d
e s d
ore
i
T hio b a c i l lu s d e n i t r i f i ca n s
La
ct o
ba
ci l l u
s g
as
se
r i
Si n
or
hiz
ob
i um
me
di c
ae
C l o s t r i d i u m c e l l u lo v o r a n s
O r n i t h o b a c t e r i u m r h i n o t r a c h e a l e
Mit
su
ok
ell
a m
ult
ac
ida B
ac
illus s
p. B
14
90
5
R ic k e t t s i a p e a c o c k ii
Ve
illo
ne
lla
dis
pa
r
En
hy
dro
ba
ct e
r a
er o
sa
cc
us
Me
t hyl
ot e
ne
r a s
p. 3
01
Ve il l o n e l la p a r v u l a
R i c k e t t s ia b e ll i i
R o s e o b a c t e r s p . S K 2 0 9 - 2 - 6
g a m ma p r o t e o b a c t e r i u m H T C C 2 2 0 7
Ca
rno
ba
ct e
riu
m s
p. A
T7
P a r a c o c c u s me t h y l u t e n s
Pre
vo
tella
ru
min
ico
la
Ja
nn
as
ch
i a s
p. C
CS
1
B r u c e ll a s p . 8 3 /1 3
Se
gn
il ipa
ru
s r
otu
nd
us
K le b s i e l l a v a r i i c o la
B r a d y r h i z o b iu m ja p o n i c u m
Ru
min
oc
oc
cu
s g
na
vu
s
Bla
uti
a h
yd
r og
en
otr
op
hi c
a
Th
er m
ae
r ob
ac
t er
su
bt e
r ra
ne
us
A l k a l i p h i lu s m e t a ll i r e d ig e n s
c a nd id
at e di v is
ion T M
7 ge n
o mo sp . G
TL 1
a lph a p
r o t e o b a c t e r ium
B A L 1 9 9
Th
er m
ot o
ga
l et t i n
ga
e
M e t h y l o b a c t e r i u m r a d io t o le r a n s
He
l ic ob ac te r a c i n
ony c h
i s
Fu
so
ba
ct e
r i um
sp
. 2 1
31
Am
i no
ba
ct e
r i um
co
l om
bi e
ns
e
B a c t e r o i d e s s p . 22 4
R ic k e t t s i a e n d o s y m b i o n t o f I x o d e s s c a p u l a r i s
Pe
l ot o
ma
cu
l um
th
erm
op
ro
pi o
ni c
um
3 - 1 3
A r o m a t o l e u m a r o m a t ic u m
Br e
vi b
ac
t er iu
m m
cb
r el l n
er i
Bl a t ta b
a c t e r iu m sp . -B la
t te l l a g er man i ca
St r
ep
t oc
oc c
us
or a
li s
A c i n e t o b a c t e r g e n o m o s p . 1 3 T U
Cy
an
oth
ec
e s
p.
PC
C 7
42
5
Ps
eu d
om
on
as s p
. AD
P
C l os t r i d i u m
di f f ic
i le
be
ta p
rote
ob
ac
ter
ium
KB
13
P r o p io n i b a c t e r i u m a c n e s
R ic k e t t s ia r ic k e t t s i i
Pe
do
ba
ct e
r he
pa
r i nu
s
Geo
d erm
a t oph
i lus ob
s cur u s
B urk
h ol d e ri a m
a l
Alt
er
om
on
a da
l es
ba
ct e
r iu
m T
W- 7
T u r i c ib a c t e r s a n g u i n i s
Tre
po
ne
ma
vin
ce
nti
i
O x a l o b a c t e r f o r m ig e n e s
A c i n e t o b a c t e r s p . E B 1 0 4
D e s u l f o t o m a c u l u m a c e t o x i d a n s
Bu r k
h old e
ri a s p
. Ch
1 - 1
Pro
st h
ec
oc
hl o
r is
ae
st u
ar i i
Str
ep
tom
yc
es
hy
gr
os
co
pi c
us
Ci t ro
ba
c ter y
ou
ng
a e
P s e u d o a l t e r o m o n a s s p . SM 9 9 1 3
Ca t o
n e l la m
orb
i
F u s o b a c ter i u m
s p . 3 1 3
6 A 2
B u r k h o ld e r i a a mb
i fa r i a
Ge
ob a
ci l l
us
th e
rmo
g l uc
os i d
as
i us
Po
l aro
mo
na
s s
p. J
S6
66
Br u
ce
l l a m
icr o
t i
C h e la t iv o r a n s s p . B N C 1
B u r k h o l d e r i a m u lt i v o r a n s
C a m p y l o b a c t e r a l e s b a c t e r iu m G D 1
A c id o b a c t e r iu m s p . M P 5 A C T X 9
C a t eni b a c te
r ium
mit s u o k a i
M y c o p l a s m a l e a c h i i
Ar t h r o b
a c t e r sp . A K
- 1
Ni tr o
s om
on a
s e ur o p
ae a
Sa
cc
ha
r op
ol y
sp
or a
er y
t hr a
ea
Sp
hi n
go
mo
na
s w
i tt i
ch
i i
Ph
ae
ob
ac
ter g
al la
ec
i en
si s
De s u lf o v ib r i o m
a g n e ti c u s
L a c tob a c il lu
s jen s e n i i
N i t r o c o c c u s m o b i li s
F r a n k i a a ln i
T h e r m u s t h e r m o p h il u s
M y c o b a c t e r i u m a b s c e s s u s
Pe
dio
co
cc
us
ac
idilac
tici
S u lf i t o b a c t e r s p . E E - 3 6
Co
ma
mo
na
s te
sto
ste
ro
ni
Pr e
v o t e l la b u
c c ae
Ca
mp
y lo
ba
cte
r c
ur
vu
s
La
cto
co
cc
us
l ac t i s
T e r e d i n i b a c t e r t u r n e r a e
C l o s t r i d iu m r a m o s u m
T h e r m o b is p o r a b is p o r a
Th
erm
ot o g
a ne a
po
l i tan
a
De in
oc o
cc u
s r
ad
i od
ura
ns
H i r s c h i a b a l t i c a
E lu s i m i c r o b iu m m in u t u m
C a n d id a t u s R e g i e l l a in s e c t ic o l a
C y a n o t h e c e s p . P C C 8 8 0 2
S h e w a n e l la v io la c e a
Bu
ch
ne
r a a
ph
i dic
ol a
Pr
ev
ote
lla m
ela
ni n
og
en
ica
Ko
r di a
al g
i cid
a
My c o b a c t e r iu
m v
a n b a a len i i
Mo
bilu
nc
us
mu
lier
is
A r c a n o b a c te r i u m p y o g e n e s
B i f i d o b a c t e r i u m g a l li c u m
d e lt a p r o t e o b a c t e r i u m M L M S - 1
Le
i f so
ni a
xy
l i
Sh
ew
an
el la
am
az
on
en
si s
Ni t
r os
om
on
as e
ut r
op
ha
M o b i lu n c u s c u r t i s ii
C y a n o t h e c e s p . P C C 8 8 0 1
H a lo t h i o b a c i ll u s n e a p o l it a n u s
Am
yc
ola
top
sis
me
dite
rran
ei
C l a v ib a c t e r m i c h i g a n e n s is
L ok ta n
e l l a ve s tf o
lde n
s i s
M y c o b a c t e r iu m a v i u m
D e s u l f a r c u lu s b a a r s i i
P r o v i d e n c i a a lc a l if a c i e n s
M i c r o c y s t is a e r u g i n o s a
P s e u d o m o n a s s p . U K 4
Eu b a c t e r iu
m c e l lu
l o s olv
e n s
D e h a l o c o c c o id e s s p . C B D B 1
S t r e p t o c o c c u s p y o g e n e s
Y e r s i n i a r o h d e i
A l is t i p e s p u t r e d i n is
Le
pt o
tric
hia
bu
cc
al i
s
Fu s o b a c t e r i u m m o r t i f e r u m
Tr e
po
ne
ma p
al l i d
um
Rh
od
ob
ac
ter
ca
ps
ula
tus
M y c o p l a s m a f e r m e n t a n s
Ha
h el la
c he j u
en s
is
b a c t e r i u m E l li n 5 1 4
Ne i ss e r ia
elo
n gat a
C o r y n e b a c t e r i u m t u b e r c u lo s t e a r i c u m
P s e u d o a lt e r o m o n a s t u n i c a t a
C r o n o b a c ter t u r i c e n s i s
E n t e r o c o c c u s fa e c a l is
G e o b a c t e r m e t a ll ir e d u c e n s
u n id e n t if i e d e u b a c t e r iu m S C B 4 9
O c e a n i t h e r mu s p r o f u n d u s
My
co
ba
ct e
r i um
sp
. MC
S
W o l b a c h i a e n d o s y m b i o n t o f C u le x q u in q u e f a s c i a t u s
R i c k e t t s i a m a s s il i a e
Bi f i d
ob
ac
t eri u
m l o
ng
um
T h e r m o t o g a m a r i t i m a
G e o b a c t e r s p . M 2 1
E ub
a cte
riu
m v
en
t rio s u
m
My
co
ba
ct e
r ium
l ep
r ae
O ls e n e l l a u l i
P s e u d o r a m i b a c t e r a l a c t o ly t i c u s
C o r y n e b a c t e r iu m e ff i c ie n s
Ali
ivib
rio
fis
ch
er
i
De
su
l f ur i v
i br i o
al k
al i p
hil u
s
P o l a r o m o n a s n a p h t h a l e n i v o r a n s
M y c o p l a s m a c r o c o d y l i
La
cto
ba
ci llu
s ru
mi n
i s
Ch
r om
ob
ac
t er
i um
vi o
l ac
eu
m
Ha
em
op
hi l
us
in
f lu
en
z ae
Ps
eu
do
mo
na
s a
eru
gi n
os
a
Sh
ige
l la b
oy
dii
F lav o b a c t e r i u m p s y c h r o p h i lu m
A na er o m
y x ob a c t e r s p . K
Rh
od
oc
oc
cu
s j
os
tii
E r y th r o b a c te r s p . SD - 21
Sy
ntr
oph
us
ac
idit
ro
ph
icu
s
S h e w a n e l l a h a l i f a x e n s i s
Po l a
r i ba
ct e
r i r
ge n
si i
U r e a p la s m a ur e a ly
t i c u m
P a r v u l a r c u la b e r m u d e n s is
Co
ryn
eb
ac t e
r i um
ma
t ruc
ho
t i i
F la v o b a c t e r iu m j o h n s o n i a e
S y n e c h o c o c c u s s p . W H 8 1 0 9
An a e r o t r u n c u s c o l ih o m
in is
St r e
pt o
co
cc
us
t he
r mo
ph
il us
Ge
mm
at a
ob
sc
ur i g
l ob
us
A ch r o mo b a c t e r d
e n it r i f ica n s
H e l ic o b a c t e r c a n a d e n s i s
B a c i l lu s s u b t i li s
An
a b ae na a z o
l l ae
C r y p t o b a c t e r iu m c u r t u m
C o r y n e b a c t e r i u m a m m o n i a g e n e s
B a c i l lu s m e t h a n o l i c u s
C h l a my d o p h il a f e l is
H e r p e t o s i p h o n a u r a n t ia c u s
C a n d i d a t u s B lo c h m a n n i a p e n n s y l v a n i c u s
D e n i t r o v i b r i o a c e t i p h i l u s
L y s i n i b a c i ll u s s p h a e r i c u s
F e r v i d o b a c t e r i u m n o d o s u m
A l ii v ib r i o s a lmo n i c id a
Group
HC
CCP+ at-risk
Early RA
Staphylococcus warneri
Serratia odor ifera
En
te rob
act e
r cl oaca
e
Pectobac terium
atrosepticum
Gord
onia
westf a
l ica
Paenibacillus vortex
Ca
ndid
atu
s S
ulc
ia m
uelle
ri
Eubacterium saphenum
Bacillus atrophaeus
Mycobacte
rium va
nbaalen ii
Ar t
hro
sp
ira m
axi m
a
Sulfurihydrogen ibium
azorense
Cyanothece sp. PCC 8802
Blattabacterium sp. -Blattella germanica
Synechococcus sp. WH 8109
Neisseria
elongata
Aerococcus virid
ans
Francisella philomiragia
Lactobacillus h ilga rd ii
Corynebacteriu m ammoniagenes
K ineoc
occu
s ra
d ioto
lera
ns
Lutiella nitroferrum
Bacteroides sp. D20
Shewanella balt ica
Lac tococcus garv ieae
Vib
ri o s
p. E
x25
Meth
yl opha
g a th
iooxyd
ans
Calyptogena okutani i thioa
List
eria
iva
no
v ii
Rickettsia massiliae
Xan thomonas fuscans
Acinetob
Th iobacillus denitrificans
Veillonella
sp . 3 1 44
Selen
om
onas sp
. oral ta
xon 14
9
Ve
i ll on
el la
at y
pic
a
Streptococcus galloly ticus
Shewanella sediminis
Yersinia rohdei
Corynebacter ium pseudotuberculosis
A liivibrio salmonic ida
Xanthom
ona s campestris
Acti n
obacil lu
s por cito
nsil la
rum
En te
rococcus ita
lic us
Selenomonas flueggei
Mega
sph
aer a
gen
om
osp
. t y
pe
1
Mycoplasma bovis
Anaerofustis stercorihominis
Bur
kho
lder
ia g
lum
ae
Flavobacterium johnsoniae
cand
idate
divisi
on TM
7 sin
gle-
cell i
solat
e TM
7a
Acido
vora
x de
lafie
ldi i
Desulfovibrio sp . 3 1 syn3
Wolbach
ia sp
. wRi
Burkh olderia
malle
i
Pre
vote
lla s
p. ora
l taxo
n 31
7
Nitro
ba
c ter w
inog
rads
ky i
Lep
t ospira
inte
rro
gans
Listeria monocytogenes
Bac illus clausii
Strep toco
ccus in fantis
Streptococcus mitis
Lactobacillus antri
Wo lbachia endosym
biont of B rugia malayi
Baci
llus s
ele
niti
red
ucen
s
Acinetobacter sp. DR1
Bacillus coahuilensis
Yers
inia
ald
ova
e
Staphylococcus hominis
Bacteroides intest inalis
Geobac ter sulfurreducens
Planctomyces limnophilus
Sphaerobacter thermophilus
Borrelia afzelii
Burkh
older
i a rhiz ox
inica
Co
ryneb
acte
riu
m u
realy
t icu
m
Bar
tone
lla q
uin t
ana
Veillonella parvula
Acineto bacter haem
olyt icus
Cupriavidus necator
Ochrobact rum
intermedium
Mannheimia haemolytica
Bacillus amyloliquefaciens
Str
epto
myce
s g
rise
oflavu
s
Leeuwenhoekiella b landens is
Syn
echoc
occu
s sp
. CC
9902
Beu tenbergia cavernae
Bibersteinia tr
ehalosi
Aggregatibacte r actinomycetemcom
itans
Borrel ia valaisiana
nniel ii
Magnetospirillum magnetotact icum
Bac illus methanolicus
Fus o
ba
cte
rium
sp. 7
1
Rick
ettsia a
fricae
Alcanivorax bo rkumensis
Oceanobacillus iheyensis
Rho
do
c occ u
s e
r yth
rop
oli s
Mar in
omonas sp. M
WYL1
Sca
rdovi
a in
opin
ata
Therm
us aqua ticus
Sta
ph
y loc o
ccus a
ureu
s
Klebsie lla oxyt oca
Pa r
vim
ona
s m
icra
Cand
idatu
s Blo
ch
mannia
florid
anus
Vibrio vulnificus
Borre lia bavariensis
Cronobacter sakazakii
marine gamm
a proteobacterium HTCC
2080
Campylobacter concisus
Burkholderia multivorans
Bacteroides sp. 1 1 14
Geobacillus stearothermophilus
Bacillus h
alodurans
Bacte
roides f in
ego
ldii
Pa
enib
acill
us
sp.
Y41
2MC
10
Lactobacillus sakei
Cam
pylobac
ter f
etu
s
Oribacte
r ium
s inus
Nakamurel la multipar tit
a
A lterom
onas macleodii
Cl o
s tr idi u
m s
p. L
2- 5
0
Psy
chr
ofle
xus
torq
uis
Sphin gobac terium spirit ivorum
Stre
pto
my
c es
av e
rmi ti
l is
Nitrobacter sp. Nb-311A
Fusobacterium sp. 4 1 13
Moraxella catarrhalis
Pseudoalteromonas tunicata
Pseudoramibacter alactolyticus
Pelobact
er pro
pionic
us
Bacillus sp. m3-13
Bartonella tribocorum
cand idate division TM
7 genomosp. G
TL1
Therm obispora bispora
Ery
sip
eloth
rix
rhus
i op
athi
ae
Clostridium bart lettii
Ch lamydia trachomatis
Pelagibaca bermudensis
Methylovorus sp. MP688
Desu lfovibrio magneticus
Me
i oth
er m
us si lva
nu
s
Meth
y loc
ell a
silv
es
tris
Ca
pno
cyt op
ha
ga
spu
t i ge
na
Capnocytophaga ochracea
Stre
pt ob
acillus mon
ilif orm
is
Hoeflea phototrophica
marine gamma proteobacterium HTCC2148
Pro
teus
vu l
garis
Chlorobium ferrooxidans
Ana
eroc
occu
s pr
evo
tii
Thermotogales bacterium mesG1.Ag.4.2
Shewanella sp. MR-7
Burkholderia dolosa
Cam
pylo
bacte
r rec
tus
Leptosp ira borgpetersen ii
Bacteroides plebeius
Tolumonas auens is
Elusimicrob ium minutum
Psy
chro
ba
ct er cry
oh
alo
l en
ti s
Roseburia intestinalis
Synechococcus sp. RS9916
Stre
ptococc u
s ps eu
doporcin
us
Brucella suis
Ruegeria sp. TM1040
Clostridium leptum
Ac idobacterium sp. MP5ACTX9
Thermoanaerobacter brock ii
Marivi rga tractuosa
Pre
v otella
bryantii
Ca
ndid
at u
s Ho
dgkin
ia cic
adic
ola
He
licob
ac t
er m
uste
lae
Synechococcus sp. WH 5701
Helicobacter felis
Leptotric
hia hofstadii
Ge
mel la
hae
moly s
ans
Geobacillus sp. C56-T3
Chl
orob
i um
lim
icol
a
St reptococcus sp. o ral taxon 071
Thioalkalivibrio sp. HL-EbGR7
Prevo
tella
copri
Pseudomonas sp. ND6
Flavobacteria bacterium BBFL7
Methylobacterium chloromethanicum
Bacteroides sp. 2 1 22
Labrenzia alexandrii
Burk
hol
deria
phy
t of ir
mans
Sh
ew
an
el la
sp. W
3-1
8- 1
Thermobaculum terrenum
Brucell a neotom
ae
Clostridium sp. 7 2 43FAA
Lactobacillus curvatus
Streptoco
ccus pa rasa
nguinis
Prochlorococcus marinus
Rhi zo
biu
m le
gum
inos
aru
m
Ca
mpylo
bac t
er g
r ac i
lis
Cor
ynebac
teriu
m je
ikeium
Klebsiella variicola
Anabaena variabilis
Ru
mi n
oc o
ccu
s sp
. 5
1 3
9B
FAA
Stre
pto
myce
s s
p. A
CT
E
Acetobacter pasteurianus
Streptococcus uberis
Porphyromonas gingivalis
Halothiobacillus neapolitanus
Bac illus mycoides
Streptococcus pyogenes
He
li cobac te
r py lo
ri
Bifidobacterium animalis
marine gamma proteobacterium HTCC2143
Allochromatium vinosum
Methylobacterium extorquens
Str
epto
my c
es
s p. C
Geobacter metallire
ducens
Pelobacter carbinolicus
Citrobacter sp. 30 2
Parv
ibaculu
m la
vam
en
tiv o
r an
s
Campylobacterales bacterium GD 1
Spiroplasma c itri
Eh
r li c
hi a
can
is
Ma
r inoba c
ter hyd ro
ca rbono
clastic
us
Geobacter uraniireducens
Meth
y lovo
rus s p
. SIP
3-4
Dein
ococcus deserti
Petro
toga
mobi
lis
Saccharophagus degradans
Am
monife
x d
egensii
H irschia baltica
Clostridium ramosum
Pseudomonas putida
Leptosp
ir illum
fe rroox id
ans
Ent
ero
bac t
er c
ance
rogen
us
Anaerotruncus colihomin is
Psychrobacter arcticus
Chelativorans sp. BNC1
Brucella cet i
Agrobacterium v it is
Clostridium carboxidivorans
Bacteroides fragilis
Steno tro
phomona s m
altophilia
Ruminococcus albus
The rmosynechococcus elongatus
Bordete lla pertussis
Deha lococcoides ethenogenes
Pectobacte rium
wasabiae
Rhizobium etli
Ru
eger ia sp
. R11
Rhodop seudomonas palustris
Mycop
lasma m
ycoid e
s
Blattabacteriu
m sp. -P
eripla
neta amer ic
ana
Bradyrhizob ium japonicum
Bacillus thuringiensis
Halomonas elongata
Dech loromonas aromatica
Sta
phy
loco
c cus
sap
r ophyt
icu
s
Pr e
v ote
ll a v
er o
rali s
Roseobacter sp. SK209-2-6
Gra
mell a
fors
etii
Mo ra
xella
bov
i s
Fusobacter ium sp. 3 1 5R
Stre
pto c
occ
u s p
neu
mon
iae
Cryptobacterium curtum
Candidatus C loacamonas acidam inovorans
Al k
ali l im
ni co
l a e
hr li ch
i i
Chlamydophila caviae
Bacillus pumilus
Eubacterium re
ctale
Oscil loch loris trichoides
Ery
sipelo
trichaceae
ba
cte
rium
3 1
53
Acinetobac ter baum
annii
Naut ilia profundicola
Fusobacterium mortiferum
Acinetobacter genomosp. 13TU
Maritimibacter alkaliphilus
Bartonella grahamii
Acidaminococcus sp. D21
Helicobac ter ac i
Desulfo
talea psychro
phi la
Clos tridium cellulovorans
Ve illo n
ella sp. 6 1 2
7
Eubacterium limosum
del ta
pro
t eo
bact e
ri um N
aph
S2
cya
no
bact
er iu
m U
CY
N- A
Des
u lfo
bact
e riu
m a
utotrop
hic
um
Therm
oan
ae
roba
cte
riu
m th
erm
osa
c cha
roly
t icu
m
Achromobac te
r denitri
fica ns
Oceanicola granulosus
Shu ttlew
orthia sa telles
Bacte
roid
es s
terco
ris
Cald
anae
robacte
r su
bt e
rran
eus
Cr o
ceib
acter a
tlantic
us
Borrelia garinii
Bor relia recurrentis
Rhodo
coccu
s e
qu
i
Oxalobacter formigenes
Aci
dithio
baci
llus fe
rroo
x idans
Streptomyces coelico lor
Actinobacil lu
s succin
ogenes
Sulfurimonas autotroph ica
Osc
illat
or ia
sp.
PC
C 6
506
Alicycliphilus denitrificans
Afipia sp. 1NLS2
Methylobacter tundripaludum
Corynebacterium str ia tum
gamma proteobac terium
HdN1
Shewanella oneidensis
Eremococcus coleocola
Vib
r io a lg
ino lyticu
s
Pe l
od
icty
on l
ute
o lum
Dokdon ia donghaens is
Clo
stridium
k luyve
ri
Thermoanaerobacter sp. X513
Mycoplasma agalactiae
Rh
odo
ba
cter sp. S
W2
Paracoccus methylutens
Ruegeria sp. PR1b
Mobiluncus curtisii
Glu
c on
ace
tob
ac te
r ha
ns e
ni i
Coprococcus com es
Prevotella oris
Yersinia pestis
Anaerom
yxobacter s
p. Fw109-5
Ae
rom
onas
sa
lmo
ni c
i da
Chl
orob
ium
chl
oroc
hrom
atii
Teredinibacter turnerae
Sy
nech
oc o
ccu
s s
p. C
C9
605
ga
mm
a p
r ote
oba
c ter iu
m N
OR
5- 3
K lebsiella sp. 1 1 55
marine actinobacterium PHSC20C1
Bacteroides caccae
Zym
om
on
as m
obili
s
Catone
l la m
orbi
Eggerthella lenta
Yersin ia bercovieri
Aromatoleum aromat icum
Mesorh izob ium loti
Neorickettsia ristic ii
Ahre
nsia
sp. R
2A
13
0
Roseova rius sp . 2
17
Card
iobac
ter iu
m h
omin
is
Corynebacterium sp. L2-79-05
Fra
nk i
a s
p.
EU
N1f
Ps y
ch
rom
ona
s sp
. C
NP
T3
Stackebrand tia nassauensis
Bacteroides s p. 2 2 4
Desulfovibrio piger
Thermotoga maritima
Terriglobus sa
anensis
Prevo tella bivia
Holdemania filiformis
Jonquetella anthropi
Bacillus subt ilis
Hydrog enobacter thermophilus
Turic ibacter sanguinis
Mo ritella
sp. PE36
Cam inibacter med iatlanticus
Le
pto
t hrix
cho
l od
ni i
Lact
obac
illus
col
eoho
min
is
Geod
Flavobacterium psychrophilum
Fu
s obacte
ri u
m s
p.
D12
Lyngb
ya
sp. P
CC
81
06
Roseobacte
r sp. M
ED193
Rum
inococcus torques
Pseudovibrio sp. JE062
Staphylococcus haemo lyticus
Lysin
ibac ill u
s f us
ifor m
is
St reptomyces c lavuligerus
Pseudom onas syringae
Victiva
l lis v
adensi
s
Tsuka
mur e
lla p
au
r om
et a
bol a
Lacto
baci
l lus am
y lovo
rus
Porphyromonas endodonta lis
Citrobacter koseri
Acholeplasm
a la idlawii
gam
ma
pr o
teo
ba c
terium
HT
CC
501 5
Porphy romonas asaccharolyt ica
Vario
vorax p
arado
xus
Flavo
bac
teria
ceae
bac
teriu
m 3
519-1
0
Pe
dob
ac
t er s
al ta
ns
Histophilus somni
Cl o
stri
diu
m h
ath
ew
ayi
L isteria
mar
thii
Xanth
om
on
as
axo
no
po
di s
Dial ister m
ic rae rophilus
Erwin
ia p
yri fo
liae
Comam
onas sp. C
NB-1
Fla
vo
bacte
r ia b
acte
rium
MS
02
4-3 C
Vibrio orientalis
Collimonas fungivorans
Clostridium sp. SS2/1
Se lenomonas sp. oral taxo n 137
Candidatus Phytoplasma australienseEubacterium siraeum
Syn trophotherm
us lipocalidus
Thermus thermophilus
Ch
lam
y dop
h ila pne
umonia
e
Agrobacterium tumefac iens
Acinetobacter venet ianus
Alis tipes putredinis
Arthro bacte r sp. FB24
Nitr
oso
cocc
us w
atso
n i
Muc ilagin
ibacte
r palu
dis
Ge
obacte
r sp
. M1
8
Roseo
bact er l ito ralis
Bordetel la bronchiseptica
Waddlia cho ndrophila
Therm
osipho m
ela
nesiens is
Candidatus Regiella insecticola
Calditerrivibrio n itroreducens
Th
er m
om
onosp
ora
curv a
ta
Ente rococcus f aecalis
Pa
ludib
act er p
ropio
nicigenes
Bac
illus
cer
eus
Burkholderia pseudomallei
Fibrobacter succinogenes
Cand ida tus N
itrosp ira defluvii
Caldicellulosiruptor lactoaceticus
Candidatus Poribacteria sp. WGA-A3
Sta
rkey
a no
vella
Ferrimonas balearica
Pseudoalteromonas sp. SM9913
Neorickettsia sennetsu
Seba
ldel la
termitid
is
Pae
n iba
c illu
s sp
. or a
l tax
on 7
86
Burk
hold
eria
phy
ma
tum
Ve
i llon
e lla
sp
. or
al t
axo
n 1
58
Sy n
ech
oco
ccus
sp.
BL
1 07
Burk
hol d
er ia
les b
ac te
ri um
1 1
47
Weissella cibaria
Ha
lor h
odo
s pir a
ha
lophil a
Sta
ph
ylo
c occus p
aste
uri
Bo
r relia
sp. S
V1
Mannheim
ia succ
iniciprodu ce
ns
Escherichia sp. Sflu5
Bra
dyr h
izobiu
m s p
. OR
S278
Olsenella uli
Serratia marcescens
Bifidobacterium dentium
Myc
opl
asm
a p
enetran
s
Aeromonas bestiarum
Bacillus megaterium
Mag
neto
coccu
s sp. M
C-1
Colwellia psychrerythraea
Pse
ud
om
onas s
p. S
LT2001
Helicobacte
r hepatic
us
Parabacteroides distasonis
Staphylococcus epiderm idis
Streptococcus sp . 2 1 36FAA
Brucella sp. BO1
Ch lamydophila fe lis
Cor
yneb
acteriu
m aurim
ucosu
m
Parvularcula bermudensis
Candida tus Liberibac ter a
siat icus
Burkholderia cenocepacia
Para
coccus p
a nto
tr oph
usA
ctino
synne
ma m
ir um
Bac
t er o
ide
s sp
. 2
1 7
Desulfomicrobium baculatum
Oc t
ad
ec
aba
cte
r an
tarc
t icus
Burkholderia vietnamiensis
Hyphomicrobium denitrif icans
La
ct obac
i llus c ris
pa
tus
Roseobacte r denitr ificans
Bacteroides pec tinophilus
Synechococcus sp. WH 8102
Dictyoglomus thermophilum
Lactobacillu
s case
i
L ac
tob
acil l us
delb
rueck ii
Borrelia spielmanii
Aeromicrobium m arinum
Frankia alni
mocellu
m
Clostridium sp. M62 /1
Sh igel la flexneri
Geobacter sp. M21
Geobaci llus sp. G11MC16
Sul
furih
yd r
oge
nib
ium
yel lo
ws t
onen
s e
Can
did
atu s
Ba
uma
nni
a c
ica
dell i
nic
ola
Filifactor alocis
Kocuria rhizophila
Oceanithermus profundus
Neisseria g
onorrhoeae
Pseudomonas savastanoi
Clostridium proteoclast icum
Vibrio sp. AND4
Fin
egol di a magn
a
Cand idatus B lochmannia pennsylvanicus
Pre
vote
lla m
arshii
Chlamydoph ila abortus
Legionella pneumophila
Sh
ew
anella
l oih
i ca
Corynebacterium lipophiloflavum
Chlorob ium
p haeobacteroides
Streptococ cus equinus
Halothermothrix orenii
Rose
obac ter sp. G
AI101
Streptococcus sanguinis
Anaero c
occ u
s v a
gin
al i s
Sh
i ge
ll a d
yse
nt e
r iae
Len
tisph
aera
ara
ne
osa
Bruce
l la canis
Dorea formicigenerans
N itrococcus mobilis
Syn
ech
oc o
ccu
s el
ong
atus
Ethanoligenens harbinense
Therm
oan
aero
bac ter i
tal ic
us
delta proteobacterium MLMS-1
Burkholde ria sp. CCGE1001
Erysipe lotrichaceae bacte
rium 5 2 54FA
A
H erbasp irillum seropedicae
Corynebacterium g lucuronolyticum
Vi brio
par
ahaem
olyt
icus
Azospirillum sp. B510
Pe
lodic
t yon
ph
ae
ocl a
thra
ti form
e
Achromobacter x
ylosoxidans
Shewane lla piezotolerans
Thauera sp. MZ1T
Thio
alkaliv
ibr io sp. K
90m
ix
Sp
hin
go
bi u
m x
en
op
hag
um
Sorang
ium cel
lulo
sum
Slackia heliotrin
ireducens
Slackia exigua
Di c
ke
ya z
eae
Streptomyces sp. ACT-1
Cupriavidus ta
iwanensis
Thermoanaerobacter pseudethanolicus
Roseif lexus castenholzii
Mar in
oba
cte
r a
lgi c
ola
Thiom onas inte
rmedia
Mic
roco
ccus
sp.
28
Mycobacterium kansasii
Faecalibacterium p
rausnitzi i
Anaerococcus tet radius
Arcanobacteriu
m haemolytic
um
Cupriavidus pina tubonensis
Campylobact
er homin
is
Bac
ill u
s cy
toto
xicus
Coprococcus eutactus
Paenibacillus curdlanolyticus
Acaryochloris marina
Bifidobacterium catenu latum
Clostrid
ium stickla
ndii
Ruegeria pomeroyi
Sagittula stellata
Prevote lla buccalis
Wo
lbach
i a e
ndos
ymbi o
nt
of D
r os
op
hila
mel a
noga
ste
r
The
rmin
cola
pote
ns
Brucella ovis
Mycoplasm
a hominis
Gluco
nacet
obacter
xyl in
us
Sphingobium
yano ikuyae
Marinomonas sp. MED121
Arth robac ter chlo rophenolicus
Parascardovia denticolens
Geobac il lus sp. Y41
Ureap lasma urealyticum
uncultured eubacterium pIE1115
bac terium Ellin514
candi
date
divisi
on TM
7 sin
g le-c
ell is
olate
TM
7c
Clostridium spiroforme
Syn
ech
oco
cc us sp
. WH
780
5A
top
ob iu
m rim
ae
Stre
ptomy ces
sp. SPB
78
Sili
cib
acte
r sp
. Tr i
chC
H4B
Selenomonas noxia
Pro
v ide
ncia
stu
art ii
Vibrio sp. MED222
Pseudomonas fluorescens
Burkholderia sp. 383
Maricaulis mar is
Ricketts
ia conorii
Aci
dim
i cro
bium
ferr
oo
xid
ans
Ba
ci ll
us
an
thra
cis
Beggia to
a sp. P
S
Cal dicel lu
losiruptor saccha
rolyt icus
Ricketts ia felis
Glac ie
cola
sp.
HTC
C29
99
Corynebacterium e fficiens
Streptococcus downei
Ricke ttsia peacockii
Bacteroides sp . 2 1 33B
Sulfurospirillum deley ianum
Mycoplasma conjunctivae
Collinse lla aerofaciens
Dorea longicate
na
Geobacter lov leyi
Staphy lococcus chromogenes
Providencia rus tigianii
E ubacteriu
m do lichum
Nitrosomonas sp. A
L212
Ricketts iella gryll i
Glu
cono
ba
ct er o
xyd
ans
Citreicel
la s
p. SE45
Bruce lla sp. BO2
Synechococcus sp. JA-2-3Ba-2-13
Photobacterium profundum
Clo
str id
ium
be
ijerinc
kii
Lactobacillus oris
Geobacillus th
ermoden it ri
ficans
Atopobium vaginae
Janibacter sp . HTCC2649Candida tus Koribacter versa tilis
Methylosinus trichosporium
Bac
tero
ides
sp.
4 3
47FA
A
Bacte ro ides sp . 3 1 23
C lostridium d if fic
ile
Chlo
robiu
m p
hae
ovib
ri oi d
es
Flavobacter ia bacte riu
m MS024-2
A
Onio
n ye
llow
s p
hy
t op
las m
a
Cyanothece sp. PC
C 7424
Des
ulfo
vibr
io a
esp
oeen
sis
Bartonella henselae
Vib
r io c
ora
l lii lyt ic
us
Cyanothece sp. PCC 8801
Heliobacterium modesticaldum
Dehalococcoides sp. C BDB1
Bacillus pseudofirmus
Shew
anella
peale
ana
Sy
necho c
occu
s sp
. PC
C 7
33
5
Pro teus m irabilis
Robiginitale a bifo
rmata
Pseudomonas coronafac iens
Di n
oro
seob
acte
r shib
ae
Lact
obac
illus
john
sonii
Cam
pyl obac ter col i
Bacte
roid
es th
eta
iota
om
icro
n
Anaerostipes caccae
Bac
tero
ides
egg
erth
ii
Sin
orh
izo
biu
m fre
dii
C lostridiales bacterium 1 7 47FAA
Ac i
di p
hili
um
cry
pt u
m
Roseomonas cervicalis
Stre
pto
myc
es s
p. M
g1
Acinetoba cter calcoaceticus
Neisseria sicca
Arcanobacterium pyogenes
Br u
cella
me
liten
sis
Clos
tridium
sp
. HG
F2
Prevote lla berg
ensis
Synechococcus sp. WH 7803
Prevotella sp. o ral taxon 299
Hyd
roge
n ivirg
a s
p . 1
28-5
-R1-
1
Truepe ra rad iovictrix
Rhodococcus rhodochrous
Aggre
ga
tibact
er segnis
Marib
acte
r sp
. H
TC
C2
17
0
Myco
bacter iu
m u
lcera
ns
Mycoplasma pulmonis
Ori b
acte
ri um
s p. o
ra l tax o
n 0
78
Desulfovibrio vulgaris
S
Fusobacte rium
sp . 3 1 33
Str
ep
toco
c cus
agala
ctia
e
Arthro
bacter a
uresce
ns
Ac inetobacter sp. EB104
Glo
eoba
c ter
vio
lace
us
Act
inom
yce
s sp
. ora
l ta
xon
1 80
Photobacteriu
m damse lae
Bor
dete
lla a
vium
Zunongwangia profunda
Candidatus Amoebophilus asiaticus
Spirosom
a linguale
Rhodococcus s
p. NS1
Streptococcus suis
Bra
ch
yspir
a h
yodyse
nte
r iae
Acid
ovorax e
b reus
L actobacillus vaginalis
Be
r ma
ne
lla m
aris r
ub
ri
Brachyspira murdoch ii
P lanctomyces brasiliensis
Pe
dobac
ter s
p. B
AL39
He lico
bac ter p
ullo rum
Chlorobaculum parvum
Spirochaeta smaragdinae
Wo
lba
ch
ia e
nd
osym
bio
nt
of D
r os
op
hi la
si m
ula
ns
St reptom
yces vi r idochrom
ogenes
Thermom
icrob ium roseum
Caldicellulosiru
p tor hydrothe rm
alis
Pseudom onas sp. UK4
Borrelia hermsii
Bur
kho ld
e ria u
bonens
is
Ca ldice
llulosir u
pto r kr ist jansso
nii
Microscilla mar ina
Pre
votella tannerae
Staphylococcus capitis
Porphyromonas uenonis
Roseburia inulinivorans
Coryn
ebact er iu
m a
ccole
ns
Acine tobacter genomosp . 3
Fusobacterium
sp. 3 1 27
Haem
ophilus parasuis
Abiot roph ia defectiv
a
Cellulomonas f lavigena
Vib
rio sp.
RC
586
Kte
dono
bact
er r
acem
ifer
Desulfonatronospira thiodismutans
De
thio
ba c
ter a
l kal ip
hi lus
Haliangium ochraceum
Str
ept
osp
ora
ngiu
m r
oseum
Pecto
bacterium ca
rotovoru
m
Pa
nt oea
sp
. aB
St rep
tom
yces
gh
anae
nsis
Ureaplasma parvum
Fervidobacterium nodosum
Thermus sp. 4C
Natranaerobi us
thermophi lus
Bacillus
tusc
iae
Alcanivorax sp. DG881
Strepto myces roche i
Sphin
go
pyx
is a
las ke
nsis
Kytococcus seden tarius
Ac
i do
vora
x c
itr ul li
Anoxy
bacillu
s fla
vitherm
us
Burkholder ia oklahomensi s
Corynebacterium tuberculostearicum
Ye
r sini a
ente
r oco
l it ica
Lysinibacillus sphaericus
Dic
keya
dad
ant ii
Cyanob ium sp. PCC 7001
Col li
nse
l la in
t es
tina
lis
F lavobacteriales bacter ium ALC-1
Vibrio splendidus
Erythro bacter sp. SD-21
Leuconostoc mesentero ides
Anaeromyxobacter sp. K
Roseobacte
r sp. C
CS2
Bacteroides sp. 20 3
Ch rom
ohalob
acte
r sa
lexi
gens
Bre
vu
n dim
ona
s s p
. BA
L3
Mesop lasma florum
Dethiosul
fovibrio
peptid
ovorans
Gord
onia
bro
nc h
ial is
Bacteroides sp. D2
Brucella sp. 83/13
Cronobacter turic
ensis
Tro
phery
ma w
hipplei
Clostridium lentocellu
m
Ne isseria cinerea
Candid
atu
s Carso
nell a
ruddii
En
do
riftia p
ers
eph
one
Lactobacillus je
nsenii
Vibrio cholerae
Albidiferax ferrireducens
Bul
leid
i a e
xtru
cta
Staph
y lococcus sp. 693
-2
R ickettsia bellii
Cald icellulosiru
ptor kro
notskyensis
Desulfotomaculum acetoxidans
Thermoanaerobacter mathranii
Bi fi d
ob a
cte
ri um
ang
ul a
t um
Mycobacterium tuberculosis
Pseudomonas entomophila
Lactobac illus u ltunensis
Th
erm
ocr i
nis
alb
us
Prevot
e lla d
isien
s
Escherichia coli
Mi c
roc
ole
us c
ht h
on
op l
as
t es
Propionibacterium acnes
Shewanella violacea
Actinobacillus m inor
Ne
isse
ri a s
p. o
r al t a
x on 0
14
Bactero ides coprophilus
Pasteurella dagmatis
Desulfatibacillum a lkenivorans
Vibr io ca
r ibbenth
icus
Helicobacter canad ensis
Ps
ych
rom
on
as
ingra
ham
ii
Strepto
coccus
sp. M143
Syn
ec
hoco
ccu
s s
p. P
CC
7002
Serratia entomophila
Oce
anic
ola
batse
nsis
Bacillus coagulans
Pepto
nip
hilu
s lac
rima
lis
Bact
ero
ides
sp.
3 1
33F
AA
Sta
phyl o
coc
c us
lug
du
ne
nsis
Me
gasp
haera
micro
nuci form
is
Shew
anella
frigid
imar
ina
Kribbella flavida
Citrobacter rodentium
Vib
rio h
ar v
eyi
Bifidobacterium pseudoca tenulatum
Lactobacillus rh
amnosus
Streptomyces sp. e14
Sulf itobacter sp. NAS-14.1
Fluoribacter dumoffii
Thermodesulfovibrio yellowstonii
Clostridium butyricum
Thermanaerovibrio acidaminovorans
Neisseria mucosa
Cory
neb
acte
rium
re
sis
tens
Methylacid iphilum infernorum
un
cul tu
red
bac
teriu
m
Providencia alca lifac iens
Herpetosiphon aurantiacus
Symbiobacterium thermophilum
Dyado
bacter f
ermenta
ns
Geobacter bemidjie
nsis
Esche richia albe rt ii
Borrelia dutto
nii
Bru
cell a
sp.
NVSL
07-0
026
Peptostreptococcus anaerobius
Met
hylo
baci
llus fl
agel
latu
s
Mycoplasma hyopneumoniae
Alkaliphilus metalliredigens
Methylotenera mobilis
Ko
smo
tog
a ol
ea
r ia
Borde tella
pe trii
Se rratia p roteam
ac ulans
Myco
bacte
r ium
intr a
cellu
l ar e
Burkho lder ia sp. CCGE1002
Sulfuro
vum
sp. N
BC
37-1
Asticcacaulis excentricus
Corynebacterium diphtheriae
Meth
ylo
bacte
rium
nod
ula
ns
Fusobacterium gonidiaformans
gamma proteobacterium HTCC2207
Xenorhabdus nematophila
Candidatus Desu lforudis audaxviator
Cyt
oph
aga h
utc
hin
so
nii
Ca
ndid
atu
s R
uth
ia m
agni
fica
She
wa
ne
lla sp. A
NA
-3
Vibrio metschnikovii
Deha
lococco
ides
sp. B
AV
1
M icromonospora sp. L5
Peptostreptococcus stomatis
Rubro bacter xylanophilus
S taph
yloc
occu
s sc
iuri
Myc obacterium
gilvum
Burkholderia graminis
Rhodobacte rales b
acterium Y
4I
Mycoplasma fermentans
The
rmo to
ga pet ro
phila
Parachlamydia acanthamoebae
Verrucomicrobium spinosum
Roseibiums
Capnocyto
phaga gingivalis
Methy lophilales bacterium HTCC2181
Nocardia fa
rcinica
Clo
strid
ium l ju
ngdahl
ii
Cam
pyl
oba
c ter
show
ae
Mycoplasm a crocodyli
Lactobacil lus brevis
Orn ithobacterium rh
inotracheale
Denitrovibrio acetiphilus
Idiomarina loihiensis
Clo
strid
ium
nov
yi
De
inococ
c us ge
oth
erm
alis
Camp ylobacter jejuniBifi
dob
act e
rium
bre
ve
Ricket tsia typhi
Fra n
cisella tulare n
sis
unide ntified eubacterium SCB49
Bu
rk hold
er ia
thaila
ndensis
Bacillus pseudomycoides
Ren
ibacterium
salmoninaru
m
Defe
rr iba
ct er d
es
ul fu
ri cans
Lacto
baci
ll us
ferm
entu
m
Desulfovibrio salexigens
Shewane lla halifaxensis
St r
epto
myce
s s
vice
us
Nitr
osococc
us halo
philus
Myc
opla
sma
hyorh
inis
Corynebacterium genitalium
Gluconacetobacter diazotrophicus
Dermacoccus sp. Ellin
185
Photobacter ium sp. SKA34
Streptococcus infantarius
Azo
rhiz
ob i
um
ca
ul in
od
ans
Synechococcus sp. R
S9917
Jones ia denit rificans
Listeria innocua
Atopobium parvulum
Ricket tsia endosymbiont of Ixodes scapularis
Collinsella
stercor is
is
Cya
noth
ece
sp. C
CY0 11
0
Paenib
acil lus
sp. JD
R-2
Desulfoto
macu
lum re
ducens
Clostridium m
ethylpentosum
Rei
nekea
blande
nsis
Vib
rio
na l
es
bac
teriu
m S
WAT
-3
Neisseria subflava
Ac inetobacter sp. SUN
Sa
l inis p
or a tro
pic
a
B lautia hansenii
Ehr
lich
ia r
um
ina n
t ium
Wolbachia endosymbiont of Culex quinquefasciatus
Lister ia welshimer i
Shewanella sp. MR-4
Treponema d
entico la
Methy lobacterium radiotolerans
Mycobacterium sp. JLS
Strepto
myce
s albus
Bruce lla abortus
Th
erm
oto
ga
sp. R
Q2
Polynucleobacter n
ecessarius
Aurantimonas manganoxydans
Cand idatus Pe lag ibacter sp. H
TCC7211
Pseudomonas mendocina
Acid
obac
t erium
sp.
MP
5A
CTX
8
Photorhabdus luminescens
Pantoea sp. At-9b
Lac
tob
aci ll
us r
eu
t eri
Mycobacterium abscessus
Ca tenibacte
rium m
itsuoka
i
Mariprofundus ferrooxydans
Bacteroides sp. 3 1 19
Lari b
acte
r hon
gk
on
gen
sis
Bre
viba
cte
rium
lin
en
s
Nostoc punctiform
e
Mycobacterium av ium
Pyramidobacter piscolens
Corali om
a rgarita akaj imensis
Deh
aloc
oc c
oid
es s
p. V
S
Persephonella m
arina
Thermaerobacter m
arianensis
Haemophilus d ucre
yi
Mic
rom
onos
pora
sp.
AT
CC
391
49
An
apl a
sma c
ent ra
l e
Eubacter iu
m ce
lluloso
lvens
My
cop
lasm
a g
enita
lium
Eubacterium yurii
Pse
udoa
lteromona
s s p. 643A
Edwardsiella ictaluri
Ba
c tero
id es ca
pi llo
sus
Syntrophobacter fumaroxidans
Pl a
ncto
myc
es m
aris
Candidatus Liberibacter solanacearum
Prevotella timonensis
Clavibacter mich iganensis
Verrucomicrobiae bacterium DG1235
Geobacte r sp. FRC-32
Achromobacter piechaudii
Actinomyces viscosus
Anaerobaculum hydrogen iformans
Mycop lasma leachii
Bdellovibrio bacteriovorus
Can
di d
atu
s P
un
ic ei s
pirillu
m m
arin
um
Yersin
ia k ris tensenii
Stenotrophom
onas sp. S
KA14
Nostoc sp. PCC 7120
Parabactero ides johnsoni i
Bifidobacterium gallicum
Rho
dospiril
lum
rubr
um
Rothia dentocariosa
Pep
tonip
h ilus
duerdeni
i
Legionella dra
ncourti
i
Acidaminococcus fermen tans
Yersinia intermedia
B ifidobacterium adolesce ntis
Myc
obac
teriu
m b
ovi
s
Burkholderia cepacia
Thermotoga naphthophila
Arthro
bacter sp. A
K-1
Brucella pinnipedialis
Ralstonia sp. 5 7 47FAA
Cau
loba cte
r seg
nis
a capric
olum
Leadbetterella byssophila
Frankia sp. EAN1pec
Cl o
st r
idiu
mb
ol te
ae
Myc
opl a
sma
ar t
hri
tid
i s
Chloroflexus sp. Y-400-f l
Streptococcus mutans
Streptococcus vestibularis
Methylibium petroleiphilum
Wo lb
achia e
ndosy
mbi
ont o
f Dro
soph
ila w
i llisto
ni
Xanth
ob
act
er
au
totr
oph
icus
Chla
myd
ia m
urida
rum
Acetivibrio cellulolyticus
C lostridium sporogenes
Xantho
mona
s oryzae
A lgoriphagus sp. PR1
Clostridium perfringens
Mycobacterium sp. Spyr1
Erw
inia tasm
anie
ns is
Meth
ylococc
us
ca
psu
lat u
s
Bactero
ides s
p. D22
Ric
ket ts
i a s
ibiri
ca
Coprobacillus sp . D7
Rh o
do
bact
era
les
ba
cter
ium
HT
CC
22
55
Stre
pto
coccu
s eq
ui
Burkholderia
sp. H160
Str e
p tom
yces
sca
bie
i
Sporosarcina ureae
Sa
cch
aro
mon
ospo
ra v
ir idis
Mycoplasma gal lisepticum
Cau
l ob
ac t e
r vi b
rioi d
es
Moorella thermoacetica
Cox
iella
burn
e tii
Micromonospora aurant iaca
Desulfarculus baarsii
Cya n
ot he
ce sp. AT
CC
5114 2
Staphylococcus s imulans
Streptomyces sp. SPB74
S trepto
myces lividans
Caldicellulos iruptor besc ii
Thiomic rospira crunogena
Psychro
bacter s
p. P
Rwf-1
Noca
r dio
psi
s d
ass
on
ville
i
Bru
c el la
sp. N
F 2
653
Ricket tsia
akar i
Fusobacterium sp. 1 1 41FAA
Lept otrichia goodfellow ii
Polaromonas naphthalenivorans
Rickettsia ricketts ii
Actinobacillus p leuropneumoniae
Cald ic
ellu
l osi
rupt
or o
bsid
ians
is
Fusobacteriu
m sp. 3
1 36A2
Acidobacterium capsulatum
Oligotro
pha carboxido vorans
Des
ul fohalo
bium
retb
aense
Granulica tella adiacens
Cel
lvib
rio
japo
nicu
s
Arthrobac ter arilaitensis
Arthrospira p latensis
Sulf itobacter sp. EE-36
Candidatus Pelagibacter ub ique
Idio
mar
ina
bal
tica
Burkholderia ambifar ia
Bra
chyb
acte
rium
fa
eci
um
Eubac t
er i
um
biform
e
Candidatus Hamiltonella defensa
Rum inococcus lactaris
Rhod
ob
act e
r aceae b
act e
r ium
KLH
11
Sta
phylo
coc
cus c
apr a
e
Candidatus Zinderia insectico la
Leptospira bif lexa
Azotobacter v inelandii
Ps
eud
om
onas am
ygd
ali
Thermosipho africanus
Leuconostoc citreum
Pseudomonas sp. CA10
Borrelia burgdorferi
M icrocystis aeruginosa
alpha proteobacteriu
m BA
L199
Sinorh izobium meliloti
Hala
naer o
bi u
m s
p. sa
pola
ni c
us
Bifi
dob
act
er ium
bifi
d um
Kingella
oralis
Acinetobacter j
unii
Lawso
n ia in
trace
llula
ris
Clo
str idium
hylem
o nae
Cro
cosph
aer a
watso
nii
Bacteroides sp. 3 2 5
Desu lfov ibrio sp
. FW
1012B
Aer
omon
as h
ydro
phil a
Bacte roides uniform is
Weis
sel la
pa
r ame
sen
tero
ides
Roth
ia m
uc i
lagin
osa
Ma
gn
eto
spir i ll u
m m
ag
ne ti c
um
Sta
phyl o
co
ccu
s carn
os
us
Ac inetobacter sp. ATCC 27244
St re
ptomyce
s grise
us
Selenomonas sputigena
Yersinia pseudotuberculosis
Xy l
ell a
fast idio
sa
Fusob
acterium
var ium
Desu lfitobacterium hafn iense
Sphingomonas sp. A1
Jan thinobacterium sp. Mar seille
Fra
nci
s ella
no
v ici
da
Xanthom
onas e
uves icato
r ia
G
b
Figure 3
35
79
00
225 0
81
HC CCP+ at Risk
Early RA
6
190
20
49 9
42
HC CCP+ at Risk
Early RA
a b
Figure 4
a
b
Figure 5
Figure 6
