test_predictions.txt

The O
rich O
media O
included O
tryptone O
soy O
agar O
1 O
% O
NaCl O
( O
TSA O
- O
1 O
) O
and O
marine O
agar O
( O
MA O
) O
suitable O
for O
eutrophic O
bacteria O
, O
and O
the O
low O
organic O
formulations O
included O
MA O
diluted O
1 O
/ O
100 O
with O
seawater O
( O
salinity O
35 O
g O
/ O
L O
) O
and O
filtered O
autoclaved O
seawater O
medium O
( O
FAS O
) O
supplemented O
with O
0 O
. O
5 O
g O
/ O
L O
of O
each O
of O
the O
following O
polymers O
: O
agarose O
, O
chitin O
, O
and O
starch O
( O
FAS O
- O
POL O
) O
. O

Genomic O
DNA O
was O
PCR O
amplified O
with O
primers O
515F O
modified O
and O
926R65 O
targeting O
the O
V4 O
- O
V5 O
regions O
of O
microbial O
16S O
rRNA O
genes O
using O
a O
two O
- O
stage O
targeted O
amplicon O
sequencing O
( O
TAS O
) O
protocol66 O
. O

Depending O
on O
the O
substrate O
composition O
, O
average O
residence O
times O
over O
both O
reactors O
compartments O
vary O
between O
110 O
and O
125days O
. O

No O
specific O
comorbidities O
in O
the O
autistic B
cohort O
were O
present O
with O
the O
single O
exception O
of O
a O
coexisting O
celiac O
disease O
in O
two O
patients O
( O
5 O
% O
) O
. O

Since O
this O
patient O
population O
is O
a O
major O
reservoir O
of O
MDRO O
, O
investigating O
their O
fecal O
resistomes O
to O
characterize O
and O
quantify O
fecal O
antimicrobial O
- O
resistance O
( O
AR O
) O
genes O
is O
needed O
( O
van O
Schaik O
, O
2015 O
) O
. O

The O
median O
age O
of O
participants B
was O
32 O
. O
5 O
( O
IQR O
2636 O
) O
, O
and O
all O
were O
homozygous O
for O
the O
F508del O
mutation O
except O
for O
one O
who O
was O
a O
compound O
heterozygote O
, O
F508del O
/ O
621 O
+ O
1G O
- O
T O
( O
Table O
1 O
) O
. O

The O
Nextera O
DNA O
sample O
Preparation O
kit O
including O
sequencing O
adapters O
and O
sample O
specific O
barcodes O
was O
used O
to O
prepare O
a O
DNA O
library O
and O
sequenced O
at O
MR O
DNA O
on O
an O
Illumina O
MiSeq O
instrument O
. O

The O
sponge O
carriers O
were O
soaked O
with O
the O
master O
slurry O
sample O
manually O
and O
placed O
into O
the O
glass O
column O
in O
a O
cold O
room O
maintained O
at O
4C O
. O

Notably O
, O
unFirm O
_ O
1 O
- O
like O
populations O
were O
found O
in O
other O
high O
- O
ammonia O
biogas O
installations O
, O
conjecturing O
a O
broader O
importance O
for O
this O
novel O
clade O
of O
SAOB O
in O
anaerobic O
fermentations O
. O

Biogas O
production O
was O
monitored O
by O
a O
gas O
flow O
measurement O
device O
( O
flow O
, O
Bioprocess O
Control O
, O
Lund O
, O
Sweden O
) O
and O
recorded O
daily O
. O

Switchgrass O
used O
to O
generate O
conversion O
residue O
was O
treated O
by O
ammonia O
fiber O
expansion O
and O
enzymatically O
treated O
with O
Cellic O
CTec3 O
and O
Cellic O
HTec3 O
( O
Novozymes O
) O
to O
digest O
cellulose O
and O
hemicellulose O
( O
to O
produce O
glucose O
and O
xylose O
, O
primarily O
) O
( O
38 O
) O
. O

Determination O
of O
Alkylbenzene O
Utilization O
in O
hNRB O
Enrichments O
To O
the O
first O
set O
of O
microcosms O
a O
known O
volume O
of O
mesitylene O
( O
1 O
, O
3 O
, O
5 O
- O
trimethylbenzene O
) O
was O
added O
to O
the O
oil O
layer O
at O
the O
end O
of O
incubation O
period O
. O

Two O
Plexiglas O
double O
- O
chamber O
MECs O
were O
operated O
as O
batch O
reactors O
, O
with O
a O
total O
volume O
of O
750 O
ml O
for O
each O
chamber O
( O
34 O
by O
6 O
by O
3 O
. O
5 O
cm O
) O
. O

DOC O
was O
concentrated O
from O
20 O
L O
of O
Animas O
River O
water O
from O
the O
32nd O
St O
. O
Bridge O
location O
using O
Agilent O
Bond O
Elute O
PPL O
columns O
( O
Agilent O
Technologies O
, O
Santa O
Clara O
, O
CA O
, O
USA O
) O
, O
methanol O
as O
the O
column O
eluent O
, O
and O
sterile O
deionized O
water O
as O
the O
final O
solvent O
. O

Before O
processing O
them O
, O
we O
used O
PEAR64 O
to O
merge O
all O
the O
Illumina O
pair O
- O
end O
reads O
retrieved O
. O

In O
recent O
decades O
, O
Populus B
canadensis I
Moench I
, O
Pinus O
sylvestris O
var O
. O

Metazoan O
18S O
rRNA O
gene O
sequences O
were O
downloaded O
from O
GenBank O
( O
TableS3 O
) O
and O
aligned O
using O
a O
MAFFT O
7 O
E O
- O
INS O
- O
i O
strategy59 O
. O

Molecular O
Techniques O
DNA O
Extraction O
Environmental O
DNA O
was O
extracted O
from O
the O
basalt O
panel O
surfaces O
using O
a O
large O
- O
volume O
CTAB O
( O
hexadecyltrimethylammonium O
bromide O
) O
extraction O
. O

Sample O
processing O
DNA O
extraction O
DNA O
was O
extracted O
using O
Qiagen O
' O
s O
DNeasy O
Plant O
Kit O
( O
Germantown O
, O
Maryland O
, O
USA O
) O
with O
some O
modifications O
to O
manufacturer O
' O
s O
instructions O
. O

Blood O
( O
serum O
lipid O
) O
analysis O
For O
triglycerides O
, O
cholesterol O
, O
LDL O
, O
and O
HDL O
levels O
, O
blood O
samples O
were O
taken O
prior O
to O
the O
start O
of O
the O
synbiotic O
supplementation O
and O
at O
one O
- O
month O
post O
- O
supplementation O
and O
submitted O
for O
serum O
lipid O
profile O
analysis O
. O

Water O
samples O
were O
taken O
in O
August O
and O
December O
2012 O
using O
a O
Ruttner O
sampler O
. O

Two O
types O
of O
sequencing O
strategies O
, O
paired O
- O
end O
( O
PE O
) O
and O
single O
- O
end O
( O
SE O
) O
, O
were O
followed O
using O
the O
BGISEQ O
- O
500 O
platform O
with O
read O
length O
of O
50 O
bp O
and O
100 O
bp O
, O
respectively O
( O
insert O
size O
250bp O
) O
. O

Non O
- O
purgeable O
Organic O
Carbon O
, O
Nitrogen O
, O
Sulfur O
, O
and O
Chloride O
Analysis O
Non O
- O
purgeable O
organic O
carbon O
( O
NPOC O
) O
was O
measured O
in O
the O
Marcellus O
- O
4 O
samples O
by O
a O
TOC O
/ O
TN O
analyzer O
equipped O
with O
autosampler O
( O
TOC O
- O
V O
CSN O
/ O
TNM O
- O
1 O
/ O
ASI O
- O
V O
, O
Shimadzu O
, O
Kyoto O
, O
Japan O
) O
. O

If O
two O
samples O
were O
collected O
within O
the O
luteal O
phase O
, O
they O
were O
numbered O
sequentially O
as O
luteal O
- O
I O
and O
luteal O
- O
II O
. O

DNA O
extraction O
, O
PCR O
, O
sequencing O
and O
data O
analysis O
Biomass O
for O
DNA O
extraction O
was O
collected O
three O
times O
per O
week O
, O
both O
from O
the O
withdrawn O
reactor O
samples O
( O
granular O
phase O
) O
and O
from O
the O
effluent O
( O
suspended O
phase O
) O
, O
at O
the O
end O
of O
the O
aerated O
phase O
. O

GJK O
is O
a O
Chinese O
experimental O
herb O
formula O
[ O
23 O
] O
, O
and O
ZQFTN O
is O
a O
monomer O
drug O
derived O
from O
the O
Chinese O
traditional O
herb O
- O
Caulis O
Sinomenii O
[ O
24 O
] O
. O

Sequencing O
was O
performed O
on O
an O
Illumina O
HiSeqPE250 O
platform O
( O
Illumina O
) O
. O

Table1Total O
liquid O
volume O
, O
L2 O
. O
5pH8 O
. O
500 O
. O
05Salinity O
, O
Na O
+ O
M1Temperature O
, O
C35 O
. O
00 O
. O
1H2S O
loading O
, O
mM O
S O
day O
- O
158 O
. O
2ORP O
set O
- O
point O
, O
mV O
- O
390 O
Biomass O
sources O
Biomass O
samples O
for O
inoculation O
were O
collected O
from O
four O
different O
full O
- O
scale O
systems O
for O
gas O
biodesulfurization O
, O
which O
have O
been O
in O
operation O
for O
more O
than O
ten O
years O
. O

The O
anions O
elements O
such O
as O
SO42 O
were O
measured O
with O
an O
Ion O
Chromatography O
( O
ICS O
- O
1000 O
, O
Dionex O
, O
Sunnyvale O
, O
CA O
, O
USA O
) O
. O

All O
animals B
were O
healthy O
and O
did O
not O
receive O
any O
antibiotic O
treatment O
in O
the O
two O
months O
prior O
to O
slaughter O
. O

Post O
weaning O
, O
the O
offspring O
were O
switched O
to O
an O
isocaloric O
control O
diet O
consisting O
of O
14 O
% O
fat O
( O
from O
soybean O
oil O
, O
Fiber O
- O
Balanced O
Monkey O
Diet O
5052 O
, O
Lab O
Diet O
, O
St O
. O
Louis O
, O
MO O
) O
. O
Fig O
. O

PCR O
amplification O
of O
the O
nifH O
gene O
used O
degenerate O
universal O
nifH O
primers O
YANNI O
/ O
450 O
and O
up O
/ O
down O
in O
a O
nested O
reaction O
( O
34 O
) O
, O
with O
the O
second O
round O
primers O
( O
up O
/ O
down O
) O
modified O
to O
contain O
common O
sequence O
linkers O
( O
35 O
) O
. O

DNA O
extraction O
DNA O
was O
extracted O
using O
the O
MO O
BIO O
Laboratories O
PowerSoil O
DNA O
Isolation O
Kit O
( O
Carlsbad O
, O
CA O
) O
. O

As O
expected O
, O
a O
large O
proportion O
of O
BGISEQ O
- O
500 O
generated O
sequences O
; O
95 O
. O
93 O
% O
98 O
. O
80 O
% O
and O
96 O
. O
47 O
% O
98 O
. O
61 O
% O
for O
SE100 O
and O
PE50 O
reads O
, O
respectively O
, O
remained O
as O
high O
- O
quality O
reads O
. O

The O
concentration O
of O
total O
dissolved O
phosphorus O
was O
determined O
spectrophotometrically O
using O
the O
molybdate O
method O
after O
digestion O
with O
sulfuric O
acid O
and O
hydrogen O
peroxide O
. O

Each O
content O
of O
archaeal O
and O
bacterial O
16S O
rRNA O
genes O
was O
measured O
by O
using O
a O
real O
- O
time O
quantitative O
PCR O
( O
qPCR O
) O
with O
the O
archaeal O
specific O
primer O
( O
F O
- O
arc O
, O
5 O
- O
CAGCMGCCGCGGTAA O
- O
3 O
; O
R O
- O
arc O
, O
5 O
- O
CCCGCCAATTCCTTTAAGTT O
- O
3 O
) O
12 O
and O
bacterial O
specific O
primer O
sets O
( O
F O
- O
bac O
, O
5 O
- O
ACTCCTACGGGAGGCAGC O
- O
3 O
) O
, O
R O
- O
bac O
( O
reverse O
, O
5 O
- O
ATTACCGCGGCTGCTGG O

- O
3 O
) O
69 O
. O

For O
intraperitoneal O
infection O
, O
mice B
were O
injected O
with O
~ O
20 O
L O
via O
insulin O
syringe O
( O
29 O
G O
needle O
) O
with O
undiluted O
virus O
into O
the O
peritoneal O
cavity O
. O

Arcobacter O
strains O
UTICA O
- O
S4D1 O
and O
MARC O
- O
MIP3H16 O
were O
isolated O
from O
produced O
fluids O
collected O
at O
159 O
days O
( O
from O
the O
Utica O
- O
Point O
Pleasant O
formation O
, O
Utica O
- O
8 O
) O
and O
93 O
days O
( O
from O
Marcellus O
Shale O
, O
Marcellus O
- O
4 O
) O
after O
hydraulic O
fracturing O
began O
, O
respectively O
( O
Figure O
1 O
, O
Panescu O
et O
al O
. O
, O
2018 O
) O
. O

One O
EC O
user O
( O
EC7 O
) O
reported O
occasionally O
smoking O
one O
tobacco O
cigarette O
per O
week O
and O
no O
other O
EC O
users O
reported O
use O
of O
tobacco O
cigarettes O
. O

DNA O
was O
extracted O
from O
the O
planktonic O
or O
solid O
phase O
of O
the O
wood O
chip O
reactors O
and O
from O
the O
drainage O
water O
( O
inoculum O
) O
. O

Following O
the O
inoculation O
of O
the O
reactors O
, O
seed O
sludge O
was O
acclimatised O
to O
the O
reactor O
environment O
at O
30C O
with O
1 O
. O
8g O
volatile O
solids O
( O
VS O
) O
L1day1 O
organic O
loading O
rate O
( O
OLR O
) O
and O
a O
hydraulic O
retention O
time O
( O
HRT O
) O
of O
20days O
for O
190days O
. O

The O
biological O
methane O
potential O
( O
BMP O
: O
mL O
CH4mL O
enzyme O
mixture1 O
) O
of O
the O
enzyme O
mixture O
was O
measured O
as O
described O
previously O
( O
Azman O
et O
al O
. O
2015b O
) O
. O

Samples O
were O
irradiated O
with O
a O
dose O
of O
10 O
kGy O
. O

The O
inflammatory O
cells O
may O
extend O
into O
submucosa O
, O
smooth O
muscle O
and O
serosal O
layer O
. O

Group O
II O
This O
group O
of O
four O
lakes O
follows O
the O
current O
of O
the O
main O
chain O
of O
lakes O
and O
includes O
the O
largest O
and O
deepest O
lake O
of O
the O
Osterseen O
Lake O
District O
, O
Lake O
Grosser O
Ostersee O
, O
which O
is O
2 O
. O
15 O
km O
long O
and O
0 O
. O
83 O
km O
wide O
with O
a O
maximum O
depth O
of O
29 O
m O
. O
The O
lakes O
in O
this O
group O
are O
less O
influenced O
by O
groundwater O
sources O
. O

At O
each O
sampling O
event O
, O
a O
volume O
of O
fresh O
synthetic O
feed O
was O
also O
added O
to O
the O
batch O
reactors O
to O
replace O
the O
sampled O
volume O
and O
to O
maintain O
0 O
. O
23kg O
COD O
/ O
( O
m3day O
) O
organic O
loading O
. O

Total O
Kjeldahl O
nitrogen O
( O
TKN O
) O
and O
ammonium O
- O
nitrogen O
( O
NH4 O
- O
N O
) O
were O
analysed O
according O
to O
the O
International O
Standardization O
Operation O
( O
ISO O
) O
methods O
( O
ISO O
10 O
, O
694 O
, O
1995andISO O
13 O
, O
878 O
, O
1998 O
) O
. O

Trophic O
state O
oligo O
- O
mesotrophic O
meso O
- O
eutrophic O
n O
. O
a O
. O

Ten O
PCR O
amplicons O
per O
sample O
were O
combined O
to O
allow O
for O
sufficient O
recovery O
after O
a O
gel O
extraction O
clean O
up O
. O

Material O
and O
Reagents O
Animal O
model O
and O
treatment O
Forty O
- O
two O
specific O
pathogen O
- O
free O
Wistar O
rats B
( O
100120g O
) O
were O
provided O
by O
the O
animal O
house O
of O
Biochemistry O
Department O
, O
King O
Abdulaziz O
University O
, O
Jeddah O
, O
Saudi O
Arabia O
. O

All O
high O
- O
throughput O
sequencing O
data O
were O
deposited O
in O
the O
short O
Read O
Archive O
( O
SRA O
) O
of O
the O
European O
Nucleotide O
Archive O
( O
ENA O
) O
under O
study O
accession O
number O
PRJEB17854 O
. O

Accumulibacter O
phosphatis O
, O
we O
performed O
a O
metagenomic O
assessment O
of O
the O
microbial O
community O
in O
the O
reactor O
. O

Furthermore O
, O
at O
this O
experimental O
stage O
, O
batch O
systems O
were O
utilized O
to O
avoid O
potential O
heterogeneity O
of O
granular O
sludge O
resulting O
from O
plug O
- O
flow O
hydraulic O
regimes O
associated O
with O
the O
operation O
of O
sludge O
bed O
up O
- O
flow O
reactors O
( O
Wu O
and O
Hickey O
, O
1997 O
) O
. O

Additional O
liquid O
samples O
( O
4mL O
) O
for O
metagenomic O
analyses O
were O
collected O
in O
three O
replicates O
and O
in O
three O
time O
points O
( O
days O
41 O
, O
52 O
, O
and O
61 O
) O
at O
steady O
- O
state O
condition O
from O
R1 O
and O
R3 O
. O

Basic O
metadata O
( O
sampling O
date O
, O
latitude O
, O
longitude O
, O
depth O
, O
bioproject O
identifiers O
, O
SRA O
accessions O
) O
, O
sequence O
statistics O
( O
number O
of O
reads O
, O
read O
length O
, O
dataset O
size O
) O
and O
% O
of O
Chloroflexi O
assigned O
16S O
rRNA O
reads O
identified O
in O
all O
metagenomes O
used O
for O
assembly O
are O
provided O
in O
Supplementary O
TableS1 O
. O

Materials O
and O
methods O
Reactors O
operation O
and O
sampling O
Anaerobic O
sludge O
was O
obtained O
from O
a O
well O
- O
performing O
anaerobic O
lab O
- O
scale O
CSTR O
reactor O
that O
had O
not O
been O
exposed O
to O
any O
antibiotics O
. O

The O
chimneys O
are O
porous O
structures O
, O
mainly O
composed O
of O
brucite O
[ O
Mg O
( O
OH O
) O
2 O
] O
, O
aragonite O
and O
calcite O
( O
CaCO3 O
) O
and O
magnesium O
carbonates O
( O
MgCO3 O
) O
( O
Pisapia O
et O
al O
. O
, O
2017 O
) O
. O

In O
order O
to O
sequence O
the O
MCP O
gene O
on O
Illumina O
Miseq O
platform O
, O
Illumina O
adapter O
, O
primer O
pad O
, O
linker O
, O
and O
barcodes O
were O
added O
to O
the O
5 O
ends O
of O
primer O
pairs O
according O
to O
a O
previous O
publication O
( O
Caporaso O
et O
al O
. O
, O
2012 O
) O
. O

Barcoded O
universal O
primers O
adapted O
from O
[ O
27 O
] O
were O
used O
to O
amplify O
the O
variable O
3 O
region O
of O
the O
16S O
rRNA O
gene O
. O

Following O
a O
centrifugation O
step O
( O
30 O
, O
000 O
gav O
) O
, O
supernatants O
were O
acidified O
with O
6 O
M O
HCl O
( O
pH O
< O
2 O
) O
and O
extracted O
and O
analyzed O
for O
putative O
hydrocarbon O
metabolites O
as O
silylated O
compounds O
by O
gas O
chromatography O
- O
mass O
spectrometry O
( O
GC O
- O
MS O
) O
following O
the O
procedure O
outlined O
by O
Berdugo O
- O
Clavijo O
and O
Gieg O
( O
2014 O
) O
. O

Maltose O
, O
glucose O
, O
fructose O
, O
lactic O
acid O
, O
acetic O
acid O
, O
and O
ethanol O
were O
determined O
in O
the O
water O
- O
soluble O
extract O
of O
sourdoughs O
by O
High O
Performance O
Liquid O
Chromatography O
( O
HPLC O
) O
( O
Zeppa O
et O
al O
. O
, O
2001 O
) O
, O
using O
an O
KTA O
Purifier O
system O
( O
GE O
Healthcare O
Bio O
- O
Sciences O
, O
Uppsala O
, O
Sweden O
) O
equipped O
with O
a O
300 O
mm O
7 O
. O
8 O
mm O
i O
. O
d O
. O

The O
13C O
and O
C O
and O
N O
concentrations O
of O
leaf O
material O
were O
measured O
using O
elemental O
analyzer O
/ O
continuous O
flow O
isotope O
ratio O
mass O
spectrometry O
( O
ANCA O
/ O
SL O
elemental O
analyzer O
coupled O
with O
a O
Finnigan O
MAT O
Delta O
PlusXL O
IRMS O
) O
. O

To O
quantify O
copy O
numbers O
of O
bacterial O
and O
archaeal O
16S O
rRNA O
genes O
, O
standard O
curves O
( O
ranging O
from O
2 O
104 O
to O
2 O
108 O
) O
for O
bacteria O
( O
slope O
= O
- O
3 O
. O
7 O
, O
r2 O
= O
0 O
. O
996 O
, O
efficiency O
= O
86 O
% O
) O
and O
archaea O
( O
slope O
= O
- O
3 O
. O
8 O
, O
r2 O
= O
0 O
. O
994 O
, O
efficiency O
= O
83 O
% O
) O
were O
constructed O
for O
each O
qPCR O
run O
by O
using O
dilution O
series O
of O
known O
concentrations O
of O
purified O
bacteria O
and O
archaea O
amplicons O
amplified O
from O
genomic O
DNA O
from O
Geobacter O
sulfurreducens O
and O

Methanosarcina O
barkeri O
, O
respectively O
. O

Biogas O
production O
rate O
, O
biogas O
composition O
( O
CH4 O
, O
CO2 O
, O
O2 O
, O
H2 O
, O
and O
H2S O
) O
, O
VFA O
concentrations O
, O
total O
solids O
content O
( O
TS O
) O
, O
volatile O
solids O
content O
( O
VS O
) O
, O
and O
pH O
were O
determined O
as O
described O
previously O
( O
Mulat O
et O
al O
. O
, O
2016 O
) O
. O

Twelve O
samples O
collected O
in O
the O
bioreactor O
from O
the O
start O
- O
up O
, O
steady O
- O
state O
, O
overloading O
and O
recovery O
periods O
of O
the O
AnMBR O
process O
were O
analyzed O
. O

Subsurface O
sediments O
of O
all O
zones O
( O
> O
2m O
below O
sea O
floor O
) O
were O
obtained O
by O
gravity O
corer O
. O

In O
order O
to O
quantify O
neustonic O
plastic O
debris O
, O
a O
manta O
trawl O
( O
91 O
) O
provided O
by O
the O
Algalita O
Marine O
Research O
Foundation O
with O
a O
rectangular O
opening O
of O
0 O
. O
9 O
by O
0 O
. O
15m O
, O
a O
3 O
. O
5 O
- O
m O
- O
long O
, O
333 O
- O
m O
mesh O
net O
, O
and O
a O
flowmeter O
was O
towed O
off O
the O
stern O
for O
~ O
90min O
at O
a O
speed O
of O
1 O
to O
2knots O
. O

Briefly O
, O
PCR O
was O
conducted O
with O
the O
primer O
set O
: O
PCR1 O
forward O
( O
5 O
TCGTCGGCAG O
CGTCAGATGT O
GTATAAGAGA O
CAGCCTACGG O
GNGGCWGCAG O
3 O
) O
and O
PCR1 O
reverse O
( O
5 O
GTCTCGTGGG O
CTCGGAGATG O
TGTATAAGAG O
ACAGGACTAC O
HVGGGTATCT O
AATCC O
3 O
) O
with O
KAPA O
HiFi O
Hotstart O
Readymix O
( O
Kapa O
Biosystems O
, O
Wilmington O
, O
MA O
, O
USA O

) O
and O
the O
following O
thermocycling O
parameters O
: O
( O
1 O
) O
95C O
for O
3 O
min O
, O
( O
2 O
) O
25 O
cycles O
of O
95C O
for O
30 O
s O
, O
55C O
for O
30 O
s O
, O
72C O
for O
30 O
s O
, O
72C O
for O
5 O
min O
, O
and O
( O
3 O
) O
holding O
the O
samples O
at O
4C O
. O

Environmental O
DNA O
from O
Trap O
and O
native O
Basalt O
samples O
was O
extracted O
with O
using O
the O
Ultraclean O
Soil O
DNA O
extraction O
kit O
( O
MoBio O
Laboratories O
) O
. O

The O
MALASPINA O
datasets O
are O
from O
the O
0 O
. O
2 O
to O
0 O
. O
8m O
fraction O
and O
were O
sequenced O
using O
HiSeq2000 O
( O
paired O
end O
reads O
of O
length O
150bp O
) O
. O

Microbiome O
Sampling O
and O
DNA O
Extraction O
The O
mouse B
fecal O
microbiome O
was O
sampled O
by O
collecting O
fresh O
fecal O
pellets O
upon O
defecation O
using O
sterile O
, O
RNA O
- O
/ O
DNA O
- O
/ O
RNAse O
- O
/ O
DNAse O
- O
free O
microcentrifuge O
tubes O
. O

Inoculation O
using O
solids O
to O
medium O
ratio O
of O
25 O
% O
( O
w O
/ O
v O
) O
resulted O
in O
the O
highest O
methane O
production O
rates O
( O
0 O
. O
27 O
mL O
mL1 O
cm2 O
, O
gas O
volume O
normalized O
by O
liquid O
volume O
and O
cathode O
projected O
area O
) O
and O
highest O
peak O
current O
densities O
( O
0 O
. O
5 O
mA O
cm2 O
) O
for O
the O
bog O
sample O
. O

DNA O
was O
extracted O
from O
the O
frozen O
cell O
pellets O
, O
using O
the O
FastDNA O
SPIN O
kit O
for O
soil O
( O
MP O
Biomedicals O
, O
Illkirch O
, O
France O
) O
. O

The O
16S O
rRNA O
libraries O
for O
sequencing O
were O
prepared O
according O
to O
the O
16S O
rRNA O
metagenomics O
protocol O
for O
MiSeq O
System O
( O
Illumina O
, O
San O
Diego O
, O
CA O
, O
USA O
) O
[ O
35 O
] O
, O
with O
minor O
modifications O
. O

Briefly O
, O
the O
luminal O
contents O
were O
separately O
gathered O
from O
the O
middle O
section O
of O
the O
colon O
and O
the O
ileum O
. O

This O
is O
especially O
relevant O
in O
the O
context O
of O
climate O
change O
, O
considering O
the O
Western O
Antarctic O
Peninsula O
( O
WAP O
) O
is O
one O
of O
the O
areas O
that O
is O
experiencing O
one O
of O
the O
fastest O
rates O
of O
warming O
on O
Earth O
( O
Cook O
et O
al O
. O
, O
2016 O
; O
Meredith O
& O
King O
, O
2005 O
) O
. O

In O
general O
, O
sample O
collection O
followed O
methods O
used O
previously O
for O
animals O
and O
sediments O
in O
nearby O
Lowes O
Cove O
, O
Maine O
( O
King O
, O
1986 O
; O

Comparison O
of O
taxonomic O
and O
bacterial O
functional O
gene O
abundances O
in O
plastic O
- O
associated O
communities O
and O
surrounding O
picoplankton O
communities O
. O

Finally O
, O
differentially O
abundant O
AR O
genes O
between O
subjects B
that O
acquired O
MDRO O
or O
not O
were O
investigated O
using O
LEfSe O
with O
default O
parameters O
( O
Segata O
et O
al O
. O
, O
2011 O
) O
. O

Italian O
adults O
, O
living O
in O
and O
around O
Bologna O
, O
recruited O
as O
a O
Western O
cohort O
in O
Schnorr O
et O
al O
. O
2 O
, O
were O
recalled O
to O
provide O
fecal O
specimens O
; O
as O
many O
as O
12 O
subjects B
( O
age O
: O
2340 O
years O
; O
mean O
, O
33 O
) O
provided O
the O
samples O
. O

In O
this O
study O
, O
the O
recalcitrance O
of O
birch O
was O
reduced O
by O
applying O
steam O
- O
explosion O
( O
SE O
) O
pretreatment O
( O
210C O
and O
10min O
) O
. O

In O
addition O
, O
trace O
elements O
( O
DIN O
ISO O
11885 O
) O
, O
nutrients O
( O
DIN O
ISO O
11885 O
) O
, O
fatty O
acids O
( O
DIN O
38409 O
H21 O
) O
, O
dry O
substance O
( O
DIN O
EN O
12880 O
) O
, O
organic O
dry O
substance O
( O
DIN O
EN O
12879 O
) O
, O
total O
nitrogen O
( O
DIN O
ISO O
11261 O
) O
, O
and O
ammonia O
nitrogen O
( O
DIN O
38406 O
- O
E O
5 O
) O
were O
determined O
by O
an O
external O
service O
laboratory O
( O
Schmack O
Biogas O
GmbH O
, O
Schwandorf O
, O
Germany O
) O
. O

Total O
DNA O
and O
RNA O
were O
extracted O
at O
the O
same O
time O
from O
the O
same O
filter O
using O
the O
NucleoSpin O
RNA O
L O
kit O
( O
Macherey O
- O
Nagel O
, O
Dren O
, O
Germany O
) O
. O

Specifically O
, O
after O
fragmentation O
, O
paired O
end O
fragment O
library O
in O
length O
of170bp O
was O
constructed O
. O

The O
V4 O
region O
of O
the O
16S O
rRNA O
gene O
from O
each O
sample O
was O
amplified O
and O
sequenced O
using O
the O
Illumina O
Sequencing O
platform O
within O
the O
Vanderbilt O
Technologies O
for O
Advanced O
Genomics O
Laboratory O
. O

The O
temperature O
of O
the O
bottom O
water O
, O
measured O
by O
thermometer O
, O
was O
around O
10C O
at O
both O
sampling O
times O
and O
the O
salinity O
was O
30 O
, O
determined O
by O
a O
handheld O
refractometer O
. O

The O
amplicons O
in O
the O
triplicate O
samples O
were O
pooled O
and O
purified O
using O
an O
AMPureXP O
PCR O
Purification O
Kit O
( O
Agencourt O
, O
Brea O
, O
CA O
, O
USA O
) O
and O
quantified O
using O
a O
Qubit O
dsDNA O
HS O
Assay O
Kit O
on O
a O
Qubit O
2 O
. O
0 O
Fluorometer O
( O
Invitrogen O
, O
Carlsbad O
, O
CA O
, O
USA O
) O
. O

The O
2000 O
m O
sample O
was O
characterized O
by O
an O
almost O
undetectable O
Chl O
- O
a O
concentration O
( O
0 O
. O
01 O
mg O
/ O
m3 O
) O
, O
lower O
TOC O
( O
0 O
. O
94 O
mg O
C O
/ O
L O
) O
, O
higher O
total O
N O
and O
p O
- O
values O
( O
8 O
. O
62 O
and O
0 O
. O
5 O
M O
, O
respectively O
) O
, O
and O
lower O
heterotrophic O
bacteria O
counts O
( O
4 O
. O
5 O
104 O
) O
[ O
55 O
, O
56 O
] O
. O

Accumulibacter O
phosphatis O
UW O
- O
LDO O
- O
ICs O
genes O
nirS O
, O
narG O
, O
norZ O
, O
and O
nosZ O
; O
the O
ccoN O
subunit O
of O
cbb3 O
; O
and O
the O
ctaD O
subunit O
of O
aa3 O
cytochrome O
oxidases O
were O
designed O
to O
quantify O
expression O
of O
these O
genes O
in O
cDNA O
samples O
from O
the O
reactor O
. O

Four O
transects O
were O
defined O
in O
north O
- O
east O
( O
S77 O
39 O
. O
489 O
, O
E163 O
07 O
. O
501 O
) O
, O
south O
- O
east O
( O
S77 O
39 O
. O
513 O
, O
E163 O
07 O
. O
626 O
) O
, O
south O
( O
S77 O
39 O
. O
589 O
, O
E163 O
07 O
. O
006 O
) O
, O
and O
north O
- O
west O
( O
S77 O
39 O
. O
470 O
, O
E163 O
06 O
. O
336 O
) O
facing O
hyporheic O
moisture O
gradients O
. O

Furthermore O
, O
bacterial O
DNA O
extraction O
from O
cecal O
samples O
was O
performed O
using O
PowerViral O
Environmental O
RNA O
/ O
DNA O
Isolation O
Kit O
Sample O
( O
Qiagen O
) O
following O
the O
protocols O
instruction O
. O

The O
primers O
515F O
( O
5 O
GTG O
CCA O
GCM O
GCC O
GCG O
GTA O
A O
) O
and O
806R O
( O
5GGA O
CTA O
CHV O
GGG O
TWT O
CTA O
AT O
) O
were O
used O
to O
amplify O
the O
V4 O
hypervariable O
region O
of O
bacterial O
16S O
rRNA O
( O
Caporaso O
et O
al O
. O
, O
2011 O
) O
. O

Each O
reverse O
primer O
( O
ITS4 O
) O
also O
contained O
a O
unique O
12 O
base O
pair O
Golay O
barcode O
[ O
57 O
] O
. O

16S O
rRNA O
Gene O
Amplicon O
Sequencing O
DNA O
was O
extracted O
from O
the O
initial O
activated O
sludge O
as O
well O
as O
from O
enrichment O
cultures O
at O
the O
final O
incubation O
time O
point O
using O
FastDNA O
Extraction O
Kit O
for O
Soil O
( O
MP O
Biomedicals O
, O
Santa O
Ana O
, O
CA O
, O
United O
States O
) O
according O
to O
the O
instruction O
manual O
. O

Material O
and O
Methods O
Sites O
description O
Research O
was O
conducted O
at O
Fujia O
forest O
farm O
, O
Changtu O
County O
, O
northwest O
of O
Liaoning O
province O
( O
12332E12355E4253N4321N O
) O
. O

The O
microbial O
communities O
dynamics O
were O
followed O
by O
16S O
rRNA O
gene O
PCR O
- O
DGGE O
fingerprinting O
, O
and O
microbial O
composition O
was O
obtained O
by O
cloning O
and O
sequencing O
of O
16S O
rRNA O
genes O
. O

Virome O
capture O
sequencing O
does O
not O
identify O
active O
viral O
infection O
in O
unicentric O
and O
idiopathic O
multicentric O
Castleman O
disease O
Castleman O
disease O
( O
CD O
) O
describes O
a O
spectrum O
of O
heterogeneous O
disorders O
defined O
by O
characteristic O
lymph O
node O
histopathology O
. O

Infants B
reported O
to O
have O
never O
been O
introduced O
to O
formula O
and O
to O
be O
breastfed O
were O
considered O
to O
be O
exclusively O
breastfed O
, O
while O
those O
who O
were O
ever O
breastfed O
and O
ever O
formula O
- O
fed O
were O
considered O
to O
be O
fed O
with O
a O
combination O
of O
breast O
milk O
and O
formula O
regardless O
of O
whether O
or O
not O
the O
infant B
was O
still O
breastfed O
at O
the O
time O
of O
stool O
collection O
. O

Most O
animals B
consumed O
the O
entire O
daily O
volume O
of O
DSSwater O
for O
the O
treatment O
duration O
, O
however O
, O
some O
animals B
failed O
to O
ingest O
the O
prescribed O
dose O
and O
some O
animals B
consumed O
each O
dose O
more O
rapidly O
than O
others O
, O
which O
may O
be O
reflected O
in O
some O
of O
the O
animal O
- O
to O
- O
animal O
variability O
seen O
in O
our O
measures O
of O
colitis O
. O

Methods O
Animals O
and O
Sample O
Collection O
We O
obtained O
female O
individuals O
of O
Peromyscus B
species O
( O
P B
. I
polionotus I
, O
P B
. I
maniculatus I
, O
P B
. I
leucopus I
, O
P B
. I
eremicus I
, O
P B
. I
californicus I
, O
5 O
individuals O
per O
species O
, O
except O
for O
P B
. I
maniculatus I
, O
where O
n O
= O
3 O
) O
from O
the O
Peromyscus B
Genetic O
Stock O
Center O
at O
the O
University O
of O
South O
Carolina O
. O

In O
this O
cohort O
study O
, O
data O
and O
rectal O
samples O
were O
collected O
at O
baseline O
and O
every O
3 O
months O
for O
up O
to O
12 O
months O
or O
until O
subject B
death O
, O
and O
included O
demographics O
, O
cause O
of O
dementia O
, O
comorbidities O
, O
functional O
status O
, O
and O
antimicrobial O
exposures O
. O

were O
between O
5 O
and O
8 O
months O
old O
, O
and O
were O
co O
- O
housed O
( O
within O
species O
) O
prior O
to O
our O
experiment O
. O

Here O
we O
show O
that O
with O
16 O
weeks O
of O
KD O
, O
mice B
had O
significant O
increases O
in O
CBF O
and O
P O
- O
glycoprotein O
transports O
on O
BBB O
to O
facilitate O
clearance O
of O
amyloid O
- O
beta O
, O
a O
hallmark O
of O
Alzheimers O
disease O
( O
AD O
) O
. O

mongolica O
( O
PS O
) O
, O
and O
Pinus B
tabuliformis I
( O
PT O
) O
. O

TransITS O
amplicons O
were O
fragmented O
using O
the O
Nextera O
kit O
( O
Illumina O
, O
San O
Diego O
, O
CA O
) O
, O
and O
both O
libraries O
were O
barcoded O
and O
sequenced O
with O
MiSeq O
V3 O
( O
300bp O
2 O
) O
( O
Illumina O
, O
San O
Diego O
, O
CA O
) O
. O

Mat O
samples O
and O
chimney O
and O
sediment O
sub O
- O
samples O
, O
respectively O
, O
were O
snap O
- O
frozen O
in O
liquid O
N2 O
, O
and O
stored O
at O
80C O
. O

Illumina O
MiSeq O
V3 O
- O
V4 O
16S O
rRNA O
metagenomics O
library O
preparation O
and O
sequencing O
The O
hypervariable O
V3 O
- O
V4 O
16S O
rRNA O
region O
of O
the O
bacterial O
gene O
was O
targeted O
by O
universal O
bacterial O
primer O
319F O
( O
5 O
- O
CCTACGGGNGGCWGCAG O
- O
3 O
) O
and O
806R O
( O
5 O
- O
GACTACHVGGGTATCTAATCC O
- O
3 O
) O
as O
previously O
described O
[ O
34 O
] O
. O

The O
selected O
pigs B
were O
slaughtered O
at O
141142 O
days O
of O
age O
, O
after O
overnight O
fasting O
. O

For O
third O
- O
generation O
sequencing O
, O
purified O
fecal O
DNA O
was O
amplified O
using O
bacterial O
16S O
rRNA O
full O
- O
length O
primers O
and O
sequenced O
using O
Pacbio O
RSII O
system O
( O
Pacific O
Biosciences O
, O
USA O
) O
. O

The O
microbiome O
in O
pediatric O
cystic O
fibrosis O
patients O
: O
the O
role O
of O
shared O
environment O
suggests O
a O
window O
of O
intervention O
Background O
Cystic O
fibrosis O
( O
CF O
) O
is O
caused O
by O
mutations O
in O
the O
CFTR O
gene O
that O
predispose O
the O
airway O
to O
infection O
. O

A O
multi O
- O
phylum O
assessment O
of O
marine O
animal O
diversity O
that O
includes O
water O
column O
and O
sediments O
, O
oxic O
and O
anoxic O
environments O
, O
and O
both O
DNA O
and O
RNA O
templates O
, O
revealed O
a O
high O
percentage O
of O
novel O
18S O
rRNA O
sequences O
in O
most O
phyla O
, O
suggesting O
that O
marine O
environments O
have O
not O
yet O
been O
fully O
sampled O
at O
a O
molecular O
level O
. O

On O
day O
62 O
( O
time O
point O
A O
) O
and O
day O
177 O
( O
time O
point O
B O
) O
, O
all O
reactors O
were O
opened O
and O
the O
carbon O
substrate O
from O
the O
center O
of O
the O
reactors O
and O
the O
planktonic O
phase O
from O
between O
the O
wood O
chips O
were O
sampled O
. O

One O
sample O
( O
E215m O
- O
2014 O
_ O
f O
, O
obtained O
during O
2014 O
from O
215m O
depth O
in O
borehole O
08E140C01 O
) O
was O
collected O
by O
passage O
of O
the O
0 O
. O
22m O
filtrate O
through O
a O
10000 O
nominal O
molecular O
weight O
limit O
filter O
( O
type O
PLGC O
; O
Merck O
Millipore O
) O
. O

We O
show O
that O
Bacteroides O
LPS O
is O
structurally O
distinct O
from O
E O
. O
coli O
LPS O
and O
inhibits O
innate O
immune O
signaling O
and O
endotoxin O
tolerance O
; O
furthermore O
, O
unlike O
LPS O
from O
E O
. O
coli O
, O
B O
. O
dorei O
LPS O
does O
not O
decrease O
incidence O
of O
autoimmune O
diabetes O
in O
non O
- O
obese O
diabetic O
mice B
. O

Sequencing O
Total O
RNA O
from O
each O
sample O
was O
converted O
to O
Illumina O
sequencing O
libraries O
using O
Illuminas O
TruSeq O
RNA O
Sample O
Prep O
Kit O
v2 O
according O
to O
manufacturers O
instructions O
. O

Fecal O
samples O
were O
collected O
at O
the O
hospital O
between O
24 O
and O
48 O
h O
of O
life O
and O
at O
10 O
, O
30 O
, O
and O
90 O
days O
of O
age O
, O
immediately O
frozen O
at O
20 O
C O
and O
processed O
as O
described O
by O
Arboleya O
and O
co O
- O
workers O
[ O
22 O
] O
. O

ABX O
- O
treated O
water O
was O
sterile O
filtered O
prior O
to O
placement O
in O
mouse B
cages O
and O
provided O
to O
mice B
ad O
libitum O
. O

All O
fecal O
samples O
were O
collected O
from O
individual O
mice B
into O
2 O
mL O
screw O
cap O
tubes O
( O
Axygen O
, O
CA O
, O
USA O
) O
. O

Upon O
eclosion O
, O
10 O
adults O
carrying O
either O
mun O
+ O
or O
mun O
- O
strains O
were O
dissected O
and O
their O
guts O
were O
plated O
onto O
non O
- O
selective O
MRS O
agar O
( O
S4 O
Fig O
) O
. O

All O
mice B
were O
fed O
ad O
libitum O
for O
16 O
weeks O
, O
and O
body O
weight O
was O
measured O
once O
a O
week O
. O

The O
contents O
of O
soil O
total O
C O
and O
total O
N O
were O
determined O
using O
an O
elemental O
analyzer O
( O
Elementar O
, O
Hesse O
, O
Germany O
) O
( O
Schrumpf O
et O
al O
. O
, O
2011 O
) O
. O

Seven O
of O
the O
soils O
studied O
were O
from O
sites O
that O
represent O
polar O
deserts O
in O
the O
Kongsfjorden O
region O
( O
SE O
, O
GS2 O
, O
OS O
, O
BR1 O
, O
NL2 O
, O
SL2 O
, O
and O
BZ2 O
) O
. O

Table2LocationIndustrySour O
gas O
compositionSour O
gas O
loading O
, O
m3 O
h O
- O
1ORP O
set O
- O
point O
, O
mVNa O
+ O
, O
MK O
+ O
, O
mMEerbeek O
( O
NL O
) O
aPaper O
millbiogas O
, O
0 O
. O
7 O
% O
H2S418 O
- O
3350 O
. O
80 O
. O
7Zuelpich O
( O
DE O
) O
bPaper O
millbiogas O
, O
0 O
. O
5 O
% O
H2S700 O
- O
3700 O
. O
91 O
. O
5Amersfoort O
( O
NL O
) O
Landfill O
wastelandfill O
gas O
, O
0 O
. O
3 O
% O
H2SNANA1 O
. O
31 O
. O

6Southern O
Illinois O
( O
USA O
) O
cOil O
and O
gasassociated O
gas O
, O
1 O
- O
5 O
% O
H2S O
, O
50 O
- O
200ppm O
VOSC800 O
- O
1100NA0 O
. O
93 O
. O
7a O
- O
( O
Janssen O
etal O
. O
, O
2009 O
) O
. O
b O
- O
( O
Driessen O
etal O
. O
, O
2011 O
) O
. O
c O
- O
( O
Roman O
etal O
. O
, O
2016 O
) O
. O

Physicochemical O
properties O
of O
oil O
samples O
used O
in O
this O
study O
. O

Between O
March O
2007 O
and O
October O
2007 O
, O
samples O
were O
taken O
from O
Lake O
Fuschlsee O
every O
3 O
weeks O
( O
ten O
samples O
in O
total O
, O
starting O
in O
week O
13 O
at O
the O
end O
of O
March O
) O
. O

Medium O
composition O
Both O
chemostat O
cultures O
were O
continuously O
supplied O
with O
identically O
prepared O
anoxic O
, O
sterile O
liquid O
medium O
containing O
a O
defined O
mixture O
of O
glucose O
, O
aminoacids O
, O
acetate O
, O
nitrite O
, O
and O
nitrate O
. O

Materials O
& O
Methods O
Study O
site O
and O
experimental O
design O
The O
study O
was O
carried O
out O
near O
Aranjuez O
, O
in O
central O
Spain O
( O
4002N332W O
, O
495 O
m O
altitude O
) O
. O

Samples O
that O
had O
1 O
. O
800 O
. O
15 O
260 O
/ O
280 O
values O
were O
considered O
as O
good O
- O
quality O
DNAs O
, O
and O
amplicon O
sequencing O
was O
performed O
with O
those O
samples O
. O

For O
K O
/ O
BxN O
colonization O
experiments O
, O
three O
- O
week O
- O
old O
SPF O
K O
/ O
BxN O
mice B
were O
treated O
with O
ampicillin O
( O
1g O
/ O
L O
) O
, O
neomycin O
( O
1g O
/ O
L O
) O
, O
and O
metronidazole O
( O
1g O
/ O
L O
) O
for O
10 O
days O
. O

Temporal O
sedimentwater O
samples O
were O
recovered O
biweekly O
from O
each O
microcosm O
during O
a O
28 O
day O
period O
in O
aliquots O
of O
3 O
mL O
using O
a O
3 O
mL O
syringe O
fitted O
with O
an O
21G O
needle O
. O

Flare O
is O
defined O
as O
presence O
of O
at O
least O
two O
minor O
criteria O
( O
including O
one O
abnormal O
laboratory O
test O
) O
in O
iMCD O
diagnostic O
criteria O
and O
/ O
or O
CRP O
> O
10 O
mg O
/ O
dL O
. O
All O
laboratory O
values O
, O
treatments O
, O
and O
sample O
collection O
dates O
were O
obtained O
from O
the O
patients O
medical O
records O
. O

Thus O
, O
to O
ensure O
feasibility O
of O
recruitment O
for O
this O
study O
we O
limited O
our O
population O
to O
women B
. O

Nucleic O
acids O
were O
extracted O
from O
the O
recovered O
cell O
pellets O
using O
the O
Fast O
DNA O
SPIN O
Kit O
for O
soil O
( O
MP O
Biomedicals O
, O
USA O
) O
according O
to O
manufacturers O
instructions O
. O

Hydrogen O
sulfide O
and O
nitrogen O
gas O
were O
continuously O
supplied O
, O
whereas O
the O
oxygen O
and O
carbon O
dioxide O
dosing O
rates O
were O
pulse O
- O
wise O
controlled O
with O
a O
multiparameter O
transmitter O
( O
Liquiline O
CM442 O
- O
1102 O
/ O
0 O
, O
Endress O
+ O
Hauser O
, O
Germany O
) O
based O
on O
the O
signals O
from O
a O
redox O
sensor O
, O
equipped O
with O
an O
internal O
Ag O
/ O
AgCl O
reference O
electrode O
( O
Orbisint O
12D O
- O
7PA41 O
; O
Endress O
+ O
Hauser O
, O
Germany O
) O
and O
a O
pH O
sensor O
( O
Orbisint O
11D O
- O
7AA41 O
; O
Endress O
+ O
Hauser O
, O
Germany O

To O
monitor O
reactor O
performance O
, O
mixed O
liquor O
and O
effluent O
samples O
were O
collected O
, O
filtered O
through O
a O
membrane O
filter O
( O
Whatman O
, O
Maidstone O
, O
United O
Kingdom O
) O
( O
0 O
. O
45 O
- O
m O
pore O
size O
) O
, O
and O
analyzed O
for O
acetate O
, O
PO43 O
- O
- O
P O
, O
NH3 O
plus O
NH4 O
+ O
- O
N O
, O
NO3 O
- O
- O
N O
, O
and O
NO2 O
- O
- O
N O
. O

For O
16S O
rRNA O
- O
based O
tag O
sequencing O
and O
metagenomic O
analyses O
, O
biomass O
samples O
from O
the O
reactors O
were O
collected O
weekly O
and O
stored O
at O
80C O
until O
DNA O
extraction O
was O
performed O
. O

For O
inflammation O
scores O
, O
0 O
corresponded O
to O
no O
detectable O
inflammation O
; O
1 O
to O
mild O
peribronchiolar O
/ O
perivascular O
cuffing O
with O
inflammatory O
cells O
; O
2 O
to O
significant O
peribronchiolar O
/ O
perivascular O
clustering O
; O
and O
3 O
to O
significant O
clustering O
and O
airway O
remodeling O
( O
e O
. O
g O
. O
smooth O
muscle O
hypertrophy O
and O
hyperplasia O
) O
. O

Alpha O
diversity O
measures O
of O
the O
samples O
were O
averaged O
across O
the O
100 O
bootstrapped O
datasets O
at O
1 O
, O
000 O
reads O
per O
sample O
, O
and O
compared O
among O
the O
four O
menstrual O
phases O
( O
menstrual O
, O
follicular O
, O
periovulatory O
, O
and O
luteal O
) O
by O
using O
a O
linear O
nested O
mixed O
- O
effects O
model O
for O
Shannon O
diversity O
and O
a O
Poisson O
nested O
mixed O
- O
effects O
model O
for O
Chao1 O
nested O
within O
subject B
. O

Approximately O
one O
- O
third O
of O
the O
women B
( O
32 O
. O
2 O
% O
) O
were O
currently O
cigarette O
smokers O
. O

Microbial O
Community O
Analysis O
DNA O
was O
extracted O
using O
a O
soil O
total O
DNA O
kit O
( O
MP O
Biomedicals O
, O
Solon O
, O
OH O
, O
USA O
) O
in O
accordance O
with O
the O
manufacturers O
instructions O
. O

coluzzii O
adults O
, O
mating O
couples O
were O
collected O
in O
natural O
swarms O
in O
three O
villages O
near O
Bobo O
- O
Dioulasso O
, O
Burkina O
Faso O
: O
Valle O
du O
Kou O
5 O
( O
VK5 O
) O
and O
Valle O
du O
Kou O
7 O
( O
VK7 O
) O
, O
highly O
populated O
by O
An O
. O

Second O
, O
we O
analyzed O
each O
CVL O
sample O
using O
its O
paired O
plasma O
sample O
as O
an O
internal O
control O
. O

Sequences O
of O
the O
primers O
used O
for O
16S O
rRNA O
gene O
amplicon O
sequencing O
of O
the O
bacterial O
and O
archaeal O
domain O
Primer O
name O
Sequence O
of O
the O
primers O
Archaea O
Fwd O
Ar0787 O
AATGATACGGCGACCACCGAGATCTACACACACTCTTTCCCTACACGACGCTCTTCCGATCT O
ATTAGATACCCSBGTAGTCC O
Rev O
Ar1059 O

CAAGCAGAAGACGGCATACGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT O
GCCATGCACCWCCTCT O
Bacteria O
Fwd O
Ba0027 O
AATGATACGGCGACCACCGAGATCTACACTATGGTAATTGT O
AGAGTTTGATCCTGGCTCAG O
Rev O
Ba0338 O
CAAGCAGAAGACGGCATACGAGATAGTCAGTCAGCC O
TGCTGCCTCCCGTAGGAGT O

Primer O
sequence O
consisted O
of O
an O
initial O
standardized O
Illumina O
adapter O
( O
regular O
) O
, O
followed O
by O
an O
eight O
nucleotide O
barcode O
( O
X O
' O
s O
) O
and O
a O
primer O
sequence O
( O
bold O
) O
. O

Genomic O
DNA O
extraction O
from O
the O
nine O
sampling O
points O
( O
P0 O
to O
P8 O
) O
was O
performed O
using O
Fast O
DNA O
SPIN O
kit O
for O
soil O
( O
MP O
Biomedicals O
, O
Solon O
, O
OH O
) O
following O
the O
manufacturers O
protocol O
with O
additional O
washing O
steps O
before O
starting O
to O
the O
extraction O
. O

16S O
rRNA O
gene O
microbial O
community O
analysis O
PCR O
and O
amplicon O
sequencing O
Primers O
applied O
for O
the O
amplification O
of O
the O
amplification O
of O
the O
bacterial O
and O
archaeal O
16SrRNA O
gene O
fragments O
are O
listed O
in O
Table2 O
and O
were O
previously O
tested O
for O
applicability O
to O
monitor O
the O
microbial O
community O
in O
biogas O
environments O
( O
Fischer O
etal O
. O
, O
2016 O
) O
. O

Aliquots O
of O
caecal O
contents O
were O
collected O
and O
frozen O
at O
- O
20C O
within O
10 O
min O
after O
collection O
for O
microbiota O
characterisation O
. O

Within O
24h O
after O
admission O
, O
a O
nasopharyngeal O
aspirate O
( O
NPA O
) O
was O
collected O
and O
parents O
from O
hospitalized O
children B
were O
asked O
for O
permission O
to O
collect O
a O
second O
NPA O
sample O
46weeks O
after O
admission O
( O
recovery O
) O
. O

To O
get O
an O
overview O
of O
the O
distribution O
of O
16S O
rRNA O
reads O
assigned O
to O
Chloroflexi O
across O
the O
global O
ocean O
, O
in O
addition O
to O
the O
Mediterranean O
( O
DCM O
and O
Deep O
) O
, O
Caspian O
[ O
32 O
] O
and O
MALASPINA O
[ O
36 O
] O
datasets O
, O
we O
also O
used O
surface O
, O
DCM O
and O
mesopelagic O
datasets O
generated O
by O
the O
TARA O
expedition O
[ O
37 O
] O
. O

Subsequently O
, O
rats B
were O
randomized O
in O
two O
groups O
( O
n O
= O
10 O
each O
) O
and O
were O
either O
fed O
with O
a O
standard O
diet O
supplemented O
with O
COLOSTRONONI O
( O
Product O
Number O
934744602 O
, O
Lot O
# O
A04268 O
, O
Guna O
S O
. O
p O
. O
a O
. O
, O
Milan O
, O
Italy O
) O
dissolved O
in O
sucrose O
solution O
( O
2 O
% O
) O
( O
CN O
group O
) O
[ O
0 O
. O
500 O
gr O
/ O
kg O
( O
w O
/ O
w O
) O
] O
, O
or O
maintained O
with O
a O
standard O
diet O
supplemented O
with O
sucrose O
solution O
( O
2 O
% O
) O
( O
CTRL O
group O
) O
for O
the O
following O
12 O
days O
. O

16S O
rRNA O
gene O
V4 O
sequencing O
Microbiota O
profiling O
was O
performed O
targeting O
the O
V4 O
region O
of O
the O
16S O
rRNA O
gene O
. O

The O
packer O
leak O
was O
repaired O
and O
pumping O
continued O
but O
microbiological O
samples O
were O
not O
collected O
in O
July O
and O
sampling O
resumed O
in O
August O
. O

Collection O
of O
sample O
Samples O
were O
collected O
from O
two O
hot O
springs O
( O
65C O
and O
54C O
) O
of O
Bakreshwar O
. O

A O
major O
feature O
of O
all O
deserts O
is O
the O
microbial O
communities O
that O
develop O
in O
soil O
as O
biological O
soil O
crusts O
( O
BSC O
) O
or O
as O
cryptoendoliths B
within O
porous O
rocks O
such O
as O
sandstone O
( O
Pointing O
and O
Belnap O
, O
2012 O
; O
Makhalanyane O
et O
al O
. O
, O
2015 O
) O
. O

Overall O
, O
field O
evidence O
suggests O
that O
hyperalkaline O
seepages O
are O
numerous O
and O
are O
active O
late O
in O
the O
baseflow O
period O
of O
perennial O
streams O
( O
December O
to O
April O
) O
. O

Metaproteomics O
Samples O
used O
for O
metaproteomics O
experiments O
were O
collected O
from O
in O
situ O
nylon O
bags O
containing O
5g O
of O
air O
- O
dried O
switch O
grass O
or O
corn O
stover O
that O
were O
placed O
in O
the O
rumen O
of O
two O
cannulated O
cows B
( O
designated O
Y O
and O
Z O
) O
. O

For O
inclusion O
as O
a O
Case O
a O
dog B
had O
to O
show O
typical O
areas O
of O
diffuse O
hyperintensity O
on O
T2 O
- O
weighted O
MRI O
scans O
( O
Fig O
1 O
) O
and O
increased O
cell O
counts O
( O
> O
5 O
white O
cells O
per O
L O
) O
on O
CSF O
analysis O
. O

To O
search O
for O
MAME O
1 O
like O
sequences O
in O
other O
metabarcoding O
studies O
we O
downloaded O
487 O
marine O
pelagic O
environmental O
18S O
amplicon O
datasets O
from O
NCBIs O
SRA O
( O
March O
2016 O
) O
using O
fastq O
- O
dump O
from O
SRA O
- O
toolkit O
with O
- O
R O
option O
( O
List O
of O
amplicons O
available O
in O
the O
online O
supplementary O
material O
: O
https O
: O
/ O
/ O
figshare O
. O
com O
/ O
articles O
/ O
Supplementary O
_ O
Data O
_ O
Lopez O
- O
Escardo O
_ O
et O
_ O
al O
_ O
2016 O
/ O
3475007 O
) O
, O
which O
selects O
the O
high O
quality O
reads63 O
. O

MATERIALS O
AND O
METHODS O
Bioelectrochemical O
cell O
. O

( O
B O
and O
C O
) O
Linear O
strips O
of O
gastric O
tissue O
, O
extending O
from O
the O
squamocolumnar O
junction O
to O
the O
proximal O
duodenum O
, O
were O
fixed O
in O
10 O
% O
neutral O
buffered O
formalin O
, O
embedded O
in O
paraffin O
, O
and O
stained O
with O
hematoxylin O
and O
eosin O
. O

The O
Association O
of O
Specific O
Constituents O
of O
the O
Fecal O
Microbiota O
with O
Immune O
- O
Mediated O
Brain O
Disease O
in O
Dogs B
Meningoencephalomyelitis O
of O
unknown O
origin O
( O
MUO O
) O
is O
a O
common O
, O
naturally O
- O
occurring O
, O
clinical O
disease O
of O
pet O
dogs B
. O

None O
of O
the O
extracted O
DNA O
samples O
produced O
16S O
amplicons O
, O
suggesting O
that O
the O
DNA O
isolated O
was O
predominately O
viral O
. O

Immunohistochemistry O
and O
quantitative O
image O
analysis O
Tissue O
samples O
were O
collected O
at O
necropsy O
and O
immediately O
placed O
in O
cold O
media O
( O
for O
cell O
isolation O
and O
fluorescence O
- O
activated O
cell O
sorting O
analysis O
) O
or O
fixed O
in O
freshly O
prepared O
neutral O
buffered O
4 O
% O
paraformaldehyde O
for O
24h O
at O
room O
temperature O
. O

DNA O
extraction O
, O
PCR O
amplification O
, O
and O
sequencing O
Total O
bacterial O
DNA O
from O
the O
luminal O
samples O
was O
extracted O
using O
a O
Soil O
GenomeTM O
DNA O
Isolation O
kit O
( O
Qiagen O
, O
Germany O
) O
, O
according O
to O
the O
manufacturer O
instructions O
. O

For O
RT O
- O
PCR O
, O
total O
RNA O
from O
the O
remaining O
spinal O
cord O
sample O
was O
extracted O
using O
a O
Qiagen O
RNeasy O
Plus O
Micro O
Kit O
with O
RNA O
carrier O
( O
Hilden O
, O
GER O
) O
to O
facilitate O
RNA O
pull O
- O
down O
from O
this O
small O
tissue O
. O

The O
CSTRs O
were O
inoculated O
from O
a O
lab O
- O
scale O
digester O
operated O
at O
a O
dilution O
rate O
of O
0 O
. O
125 O
days O
- O
1 O
with O
the O
same O
synthetic O
substrate O
for O
7 O
months O
. O

When O
three O
or O
more O
of O
the O
MRI O
criteria O
for O
inflammation O
were O
present O
, O
the O
segment O
was O
judged O
severely O
inflamed O
( O
grade O
3 O
) O
. O

All O
the O
experiments O
were O
conducted O
in O
triplicate O
inside O
a O
shaker O
( O
Multitron O
Standard O
, O
Infors O
HT O
, O
Switzerland O
) O
under O
thermophilic O
conditions O
( O
62C O
, O
120rpm O
) O
. O

Sequencing O
was O
conducted O
with O
an O
Illumina O
MiSeq O
system O
( O
Illumina O
) O
with O
the O
500 O
cycle O
V2chemistry O
at O
Auckland O
University O
of O
Technology O
, O
New O
Zealand O
. O

For O
comparison O
, O
we O
also O
collected O
one O
barite O
- O
rich O
silica O
chimney O
( O
SiCh O
) O
from O
the O
extinct O
vent O
area O
( O
Figure O
1G O
) O
at O
7333 O
. O
99N O
and O
0809 O
. O
58E O
at O
a O
water O
depth O
of O
2367 O
m O
. O
An O
overview O
of O
examined O
mat O
- O
samples O
and O
chimney O
sub O
- O
samples O
, O
respectively O
, O
are O
given O
in O
Table O
1 O
. O

A O
total O
of O
12l O
of O
blood O
sample O
were O
used O
to O
measure O
blood O
glucose O
level O
using O
a O
blood O
glucose O
meter O
and O
a O
test O
strip O
( O
Clarity O
Plus O
, O
Boca O
Raton O
, O
FL O
, O
USA O
) O
. O

To O
investigate O
potential O
sources O
of O
the O
microorganisms O
in O
the O
cryoconite O
holes O
we O
also O
collected O
a O
total O
of O
eleven O
samples O
from O
different O
surface O
habitats O
nearby O
for O
DNA O
sequencing O
. O

Three O
biopsies O
were O
obtained O
from O
the O
greater O
curvature O
sides O
of O
the O
mid O
- O
antrum O
and O
mid O
- O
body O
, O
in O
addition O
to O
the O
descending O
duodenum O
. O

DNA O
extraction O
and O
real O
- O
time O
quantitative O
PCR O
gDNAs O
were O
extracted O
from O
the O
freeze O
dried O
sediments O
( O
each O
0 O
. O
25g O
dry O
weight O
) O
using O
the O
MOBIOs O
PowerSoil O
DNA O
extraction O
kit O
and O
PowerClean O
Pro O
DNA O
Clean O
- O
Up O
Kit O
( O
MOBIO O
, O
Carlsbad O
, O
CA O
) O
according O
to O
the O
manufacturers O
specifications O
. O

For O
16S O
rRNA O
gene O
amplification O
for O
denaturing O
gradient O
gel O
electrophoresis O
( O
DGGE O
) O
, O
primers O
set O
1401r O
/ O
968GCf O
was O
used O
for O
bacteria O
and O
515GCr O
/ O
A109 O
( O
T O
) O
f O
for O
archaea O
( O
Sousa O
etal O
. O
, O
2007 O
) O
. O

Domain O
- O
specific O
primers O
, O
958F O
and O
1048R O
for O
Archaea O
and O
967F O
and O
1064R O
for O
Bacteria O
, O
targeted O
the O
V6 O
hypervariable O
region O
of O
the O
16S O
rRNA O
gene O
( O
Sogin O
et O
al O
. O
, O
2006 O
) O
. O

Seven O
individuals B
collected O
in O
2016 O
were O
treated O
similarly O
, O
with O
the O
exception O
that O
whole O
, O
sediment O
- O
free O
animals B
were O
transferred O
to O
centrifuge O
tubes O
with O
Lifeguard O
. O

MATERIALS O
AND O
METHODS O
Sampling O
and O
physiochemical O
measurements O
Benthic O
mat O
samples O
were O
collected O
on O
26 O
June O
2012 O
at O
16 O
: O
00 O
PDT O
( O
photon O
flux O
490 O
mol O
photons O
PAR O
m2 O
s1 O
; O
due O
to O
partial O
cloudiness O
) O
and O
27 O
June O
2012 O
at O
01 O
: O
00 O
PDT O
( O
photon O
flux O
0 O
mol O
photons O
PAR O
m2 O
s1 O
) O
and O
at O
16 O
: O
00 O
PDT O
( O
photon O
flux O
1225 O
mol O
photon O
PAR O
m2 O
s1 O
) O
from O
a O
water O
depth O
of O
3540cm O
located O
in O
northeastern O
Washington O
state O
( O
USA O
) O
( O
48 O

. O
97347119 O
. O
476322 O
) O
. O

To O
test O
viral O
extractions O
for O
putative O
bacterial O
contamination O
, O
each O
DNA O
sample O
was O
assessed O
using O
the O
16S O
63F O
/ O
1087R O
primer O
pair O
following O
standard O
PCR O
protocols O
[ O
6 O
] O
. O

Sequences O
analyzed O
in O
a O
previous O
study O
of O
the O
microbial O
diversity O
of O
Mono O
Lake O
by O
Humayoun O
et O
al O
. O
( O
2003 O
) O
, O
who O
sampled O
different O
depths O
from O
the O
same O
redox O
zones O
at O
Station O
6 O
( O
2 O
m O
, O
aerobic O
; O
17 O
. O
5 O
m O
, O
microaerophilic O
, O
23 O
m O
, O
anoxic O
; O
and O
35 O
m O
, O
sulfidic O
, O
see O
Humayoun O
et O
al O
. O
, O
2003 O
) O
, O
were O
downloaded O
from O
NCBI O
GenBank O
( O
n O
= O
274 O
) O
. O

Preparation O
of O
Libraries O
, O
Shotgun O
Metagenomic O
Sequencing O
, O
and O
Data O
Preprocessing O
All O
materials O
and O
apparatus O
were O
from O
Thermo O
Fisher O
Scientific O
( O
Wilmington O
, O
DE O
, O
United O
States O
) O
, O
unless O
stated O
otherwise O
. O

An O
aliquot O
of O
300l O
was O
analyzed O
for O
cholesterol O
, O
triglyceride O
, O
high O
- O
and O
low O
- O
density O
lipoproteins O
. O

Paired O
- O
end O
sequencing O
with O
a O
100 O
cycle O
Illumina O
HiSeq O
run O
generated O
partial O
~ O
30 O
bp O
overlaps O
, O
and O
six O
libraries O
were O
multiplexed O
per O
lane O
. O

To O
sequence O
the O
library O
preparation O
, O
Illumina O
adapters O
were O
attached O
to O
the O
amplicons O
by O
using O
an O
Illumina O
TruSeq O
DNA O
sample O
preparation O
kit O
, O
v2 O
. O

Major O
capsid O
protein O
fragments O
were O
sequenced O
with O
three O
strategies O
, O
i O
. O
e O
. O
, O
clone O
- O
library O
Sanger O
sequencing O
( O
about O
100 O
reads O
) O
, O
shallow O
Illumina O
sequencing O
( O
1 O
, O
0002 O
, O
000 O
reads O
) O
, O
and O
deep O
Illumina O
sequencing O
( O
more O
than O
100 O
, O
000 O
reads O
) O
. O

Gnotobiotic O
mouse B
experiments O
All O
experiments O
involving O
mice B
were O
performed O
using O
protocols O
approved O
by O
the O
Animal O
Studies O
Committee O
of O
the O
Washington O
University O
School O
of O
Medicine O
. O

All O
mothers B
attending O
the O
clinics O
during O
the O
recruitment O
periods O
at O
each O
location O
were O
invited O
to O
participate O
in O
the O
study O
and O
written O
consent O
was O
obtained O
from O
all O
who O
agreed O
to O
participate O
. O

Animal O
models O
such O
as O
adjuvant O
- O
induced O
arthritis O
( O
AIA O
) O
, O
one O
of O
the O
most O
widely O
accepted O
animal O
models O
[ O
1316 O
] O
, O
may O
provide O
new O
knowledge O
on O
the O
relationship O
between O
the O
microbiota O
and O
RA O
and O
possibly O
contribute O
to O
the O
development O
of O
novel O
microbial O
- O
based O
drugs O
. O

Nucleotide O
sequence O
accession O
and O
contextual O
data O
availability O
16S O
rRNA O
amplicon O
and O
shotgun O
metagenomic O
data O
are O
publicly O
available O
under O
SRA O
Bioproject O
PRJNA248084 O
( O
https O
: O
/ O
/ O
www O
. O
ncbi O
. O
nlm O
. O
nih O
. O
gov O
/ O
bioproject O
/ O
PRJNA248084 O
/ O
) O
. O

Symptoms O
with O
respect O
to O
Cough O
, O
Sputum O
Production O
, O
Shortness O
of O
Breath O
, O
Wheezing O
, O
Nasal O
Irritation O
, O
Throat O
Irritation O
, O
Fatigue O
, O
and O
Appetite O
were O
independently O
scored O
relative O
to O
an O
individual B
' O
s O
norm O
/ O
baseline O
( O
= O
0 O
) O
with O
increased O
symtomatology O
scored O
as O
1 O
= O
mild O
, O
2 O
= O
moderate O
, O
or O
3 O
= O
severe O
deterioration O
. O

A O
B O
C O
D O
E O
Sampling O
site O
Underwater O
depth O
[ O
m O
] O
( O
Depth O
) O
548 O
24 O
54 O
48 O
110 O
Bottom O
temperature O
[ O
C O
] O
( O
Temp O
) O
6 O
11 O
3 O
6 O
2 O
Bottom O
salinity O
( O
Sal O
) O
35 O
21 O
8 O
7 O
4 O
Oxygen O
bottom O
water O
[ O
mL O
/ O
L O
] O
6 O
. O
1 O
4 O
. O
8 O
3 O
. O
6 O
5 O
. O
6 O
7 O
. O
5 O
SO42 O
- O
[ O
mM O
] O
calculated1 O
28 O
. O
2 O
16 O
. O
9 O
6 O
. O
4 O
5 O
. O
6 O
3 O
. O
2 O
Sediment O
characteristics O
Median O
grain O
size O
[ O
Q50 O
] O
5 O
11 O
12 O
3377 O
10 O
Sediment O
type O
Fine O

silt O
Middle O
silt O
Middle O
silt O
Silty O
- O
sandy O
Middle O
silt O
Water O
content O
[ O
% O
] O
76 O
78 O
54 O
33 O
87 O
Total O
nitrogen O
[ O
% O
] O
( O
TN O
) O
0 O
. O
3 O
0 O
. O
0 O
0 O
. O
5 O
0 O
. O
0 O
0 O
. O
3 O
0 O
. O
3 O
0 O
. O
04 O
0 O
. O
0 O
0 O
. O
4 O
0 O
. O
0 O
Total O
organic O
carbon O

ALOHA O
( O
A O
Long O
- O
term O
Oligotrophic O
Habitat O
Assessment O
; O
22 O
. O
45N O
, O
158W O
) O
, O
an O
open O
- O
ocean O
field O
site O
~ O
100 O
km O
north O
of O
Oahu O
( O
Table O
1 O
) O
. O

Patients O
in O
the O
cohort O
had O
scheduled O
visits O
every O
three O
months O
from O
their O
inclusion O
and O
unscheduled O
visits O
when O
exacerbations O
symptoms O
appeared O
, O
as O
described O
elsewhere O
[ O
15 O
] O
. O

Foods O
and O
portions O
from O
24 O
- O
hour O
dietary O
recalls O
were O
entered O
into O
the O
USDA O
SuperTracker O
system O
( O
Britten O
, O
2013 O
) O
. O

Findings O
Background O
Cystic O
fibrosis O
( O
CF O
) O
is O
an O
inherited O
disease O
that O
affects O
over O
70 O
, O
000 O
people B
worldwide O
. O

For O
shotgun O
pyrosequenced O
data O
, O
sequences O
were O
first O
analysed O
with O
the O
MOTHUR O
software O
package O
1 O
. O
27 O
to O
remove O
sequences O
shorter O
than O
100 O
bp O
. O

Establishment O
of O
light O
and O
heavy O
oil O
- O
degrading O
produced O
water O
cultures O
Oil O
- O
free O
produced O
water O
from O
all O
five O
PW O
samples O
was O
combined O
in O
equal O
ratios O
and O
500 O
mL O
aliquots O
were O
dispensed O
into O
five O
sterile O
, O
custom O
- O
made O
glass O
vessels O
. O

Methods O
Materials O
and O
methods O
Fecal O
samples O
were O
collected O
from O
dogs B
( O
Cases O
) O
diagnosed O
with O
MUO O
at O
the O
veterinary O
hospitals O
of O
Iowa O
State O
University O
( O
ISU O
) O
and O
Texas O
A O
& O
M O
University O
( O
TAMU O
) O
and O
stored O
in O
a O
- O
80C O
freezer O
for O
analysis O
at O
completion O
of O
case O
recruitment O
. O

Sequencing O
of O
16S O
rRNA O
genes O
by O
Illumina O
MiSeq O
was O
performed O
to O
check O
the O
purity O
of O
the O
culture O
. O

The O
cohort O
included O
COPD O
patients O
with O
a O
FEV1 O
below O
50 O
% O
from O
the O
reference O
[ O
16 O
] O
, O
who O
reported O
three O
or O
more O
exacerbations O
in O
the O
previous O
year O
and O
who O
had O
attended O
the O
Day O
Care O
Unit O
of O
Sabadell O
University O
Hospital O
since O
2005 O
. O

Briefly O
, O
vertical O
profiles O
of O
relevant O
environmental O
variables O
: O
photosynthetically O
active O
radiation O
( O
PAR O
, O
LiCor O
2 O
quantum O
sensor O
, O
400700 O
nm O
, O
E O
m2 O
s2 O
) O
, O
fluorescence O
( O
WetLabs O
fluorometer O
, O
relative O
fluorescence O
units O
) O
, O
dissolved O
oxygen O
( O
SBE O
43 O
, O
mg O
L1 O
) O
and O
attenuation O
coefficient O
( O
WetLabs O
transmissometer O
, O
600 O
nm O
wavelength O
light O
source O
, O
10 O
cm O
path O
length O
, O
m1 O
) O
were O
obtained O
using O
sensors O
mounted O
on O
the O
frame O
holding O
a O
SeaBird O
SBE O
19 O
CTD O
( O
conductivity O
, O
temperature O
, O
depth O
) O

recorder O
, O
modified O
and O
calibrated O
for O
use O
in O
Mono O
Lake O
. O

Enrichments O
were O
set O
up O
in O
triplicates O
with O
lactate O
( O
40 O
mM O
) O
as O
the O
electron O
donor O
and O
manganese O
oxide O
( O
21 O
. O
5 O
mM O
) O
as O
the O
electron O
acceptor O
. O

All O
batch O
reactors O
were O
then O
incubated O
at O
37C O
to O
simulate O
the O
typical O
temperature O
in O
Saudi O
Arabia O
, O
and O
continuously O
mixed O
at O
100rpm O
for O
sludge O
acclimation O
. O

Metabolic O
Potential O
of O
As O
- O
yet O
- O
uncultured O
Archaeal O
Lineages O
of O
Candidatus O
Hydrothermarchaeota O
Thriving O
in O
Deep O
- O
sea O
Metal O
Sulfide O
Deposits O
Candidatus O
Hydrothermarchaeota O
, O
formally O
called O
Marine O
Benthic O
Group O
E O
, O
has O
often O
been O
detected O
in O
iron O
- O
and O
sulfur O
- O
rich O
marine O
environments O
, O
such O
as O
hydrothermal O
vents O
and O
cold O
seeps O
. O

The O
overlapping O
paired O
- O
end O
reads O
were O
stitched O
together O
( O
approximately O
97bp O
overlap O
) O
, O
and O
size O
selected O
to O
reduce O
non O
- O
specific O
amplification O
products O
from O
host O
DNA O
( O
225275bp O
) O
. O

Adaptor O
- O
appended O
fragments O
were O
sequenced O
on O
Illumina O
MiSeq O
desktop O
sequencer O
( O
2300bp O
paired O
- O
end O
run O
, O
San O
Diego O
, O
CA O
) O
according O
to O
standard O
protocols O
. O

The O
PCRs O
included O
about O
5ng O
of O
DNA O
extract O
, O
15pmol O
of O
each O
forward O
primer O
U341F O
5 O
- O
NNNNNNNNNNCCTAYGGGRBGCASCAG O
and O
reverse O
primer O
U806R O
5 O
- O
NNNNNNNNNNGGACTACNNGGGTATCTAAT O
in O
a O
20L O
volume O
of O
MyTaq O
buffer O
containing O
1 O
. O
5 O
units O
MyTaq O
DNA O
polymerase O
( O
Bioline O
) O
and O
2L O
of O
BioStabII O
PCR O
Enhancer O
( O
Sigma O
) O
. O

Further O
bioinformatic O
analysis O
of O
the O
16S O
rRNA O
gene O
amplicon O
sequencing O
( O
primer O
cutting O
, O
quality O
and O
length O
trimming O
, O
merging O
, O
OTU O
clustering O
, O
and O
phylogenetic O
analysis O
) O
was O
conducted O
using O
the O
CLC O
Genomic O
Workbench O
software O
10 O
. O
0 O
. O
1 O
with O
the O
additional O
microbial O
genomic O
module O
2 O
. O
0 O
. O

Bacterial O
and O
archaeal O
16S O
rRNA O
gene O
fragments O
were O
amplified O
as O
described O
before O
( O
Gonzalez O
- O
Gil O
et O
al O
. O
, O
2015 O
) O
. O

The O
16S O
and O
18S O
rRNA O
amplicons O
were O
prepared O
according O
to O
the O
Illumina O
16S O
Metagenomic O
Sequencing O
Library O
Preparation O
guide O
[ O
19 O
] O
and O
as O
described O
previously O
[ O
20 O
] O
. O

Definition O
of O
carriage O
by O
lytA O
Pcr O
The O
presence O
of O
S O
. O
pneumoniae O
was O
assessed O
using O
a O
lytA O
qPCR O
as O
described O
( O
WHO O
and O
CDC O
, O
2011 O
) O
using O
primers O
F373 O
: O
5 O
- O
ACGCAATCTAGCAGATGAAGCA O
- O
3 O
and O
R424 O
: O
5 O
TCGTGCGTTTTAATTCCAGCT O
- O
3 O
. O

All O
samples O
were O
de O
- O
identified O
, O
and O
by O
using O
information O
from O
participants B
assigned O
to O
a O
menstrual O
phase O
by O
using O
a O
calendar O
- O
based O
method O
: O
menstrual O
, O
day O
1 O
( O
onset O
of O
menstruation O
) O
to O
cessation O
of O
bleeding O
( O
day O
4 O
to O
7 O
) O
; O
follicular O
, O
cessation O
of O
bleeding O
to O
day O
12 O
; O
periovulatory O
, O
day O
13 O
to O
day O
16 O
; O
luteal O
, O
day O
17 O
to O
days O
26 O
to O
32 O
( O
commencement O
of O
bleeding O
) O
. O

Donors B
stated O
that O
their O
last O
menstrual O
period O
had O
ended O
at O
least O
3days O
prior O
to O
donating O
and O
that O
they O
had O
not O
used O
vaginal O
products O
or O
participated O
in O
intercourse O
within O
24h O
prior O
to O
donating O
. O

Genomic O
DNA O
libraries O
were O
generated O
using O
TruSeq O
Nano O
DNA O
Sample O
Prep O
Kit O
( O
Illumina O
, O
San O
Diego O
, O
CA O
, O
USA O
) O
according O
to O
the O
manufacturers O
instructions O
. O

Flour O
( O
120 O
g O
) O
and O
sterile O
tap O
water O
( O
60 O
g O
) O
were O
kneaded O
with O
a O
continuous O
high O
- O
speed O
mixer O
( O
60 O
g O
, O
dough O
mixing O
time O
5 O
min O
) O
( O
Chopin O
& O
Co O
. O
, O
Boulogne O
, O
Seine O
, O
France O
) O
. O

The O
pH O
of O
the O
water O
was O
measured O
varying O
from O
7 O
. O
8 O
to O
8 O
. O
0 O
. O

The O
sandstone O
and O
lignite O
samples O
were O
preserved O
in O
sterile O
glass O
bottles O
under O
anaerobic O
conditions O
with O
filtered O
N2 O
gas O
, O
and O
stored O
at O
4C O
in O
the O
dark O
prior O
to O
use O
in O
the O
shore O
- O
based O
laboratory O
. O

Dissolved O
oxygen O
and O
temperature O
( O
Oxymeter O
YSI O
550A O
) O
, O
conductivity O
( O
Digimed O
DM O
- O
3P O
) O
, O
turbidity O
( O
Motte O
202VE O
) O
, O
and O
water O
transparency O
( O
Secchi O
disk O
) O
were O
measured O
in O
the O
field O
. O

16S O
rDNA O
sequencing O
of O
selected O
samples O
DNA O
samples O
( O
from O
two O
independent O
replicates O
) O
collected O
on O
days O
30 O
, O
37 O
and O
50 O
( O
phase O
2 O
) O
, O
and O
days O
178 O
, O
192 O
and O
206 O
( O
phase O
4 O
) O
from O
the O
fermenter O
and O
post O
- O
digester O
were O
selected O
for O
high O
throughput O
sequencing O
of O
the O
amplified O
16S O
rDNA O
fragments O
as O
described O
by O
Sundberg O
et O
al O
. O
( O
2013 O
) O
. O

The O
samples O
( O
27 O
pooled O
and O
4 O
individual O
replicates O
) O
were O
next O
individually O
barcoded O
and O
sequenced O
using O
the O
Illumina O
MiSeq O
platform O
via O
the O
MiSeq O
Reagent O
Kit O
v2 O
( O
500 O
cycle O
) O
, O
producing O
paired O
- O
end O
reads O
each O
250 O
nucleotides O
in O
length O
. O

Spring O
samples O
were O
collected O
according O
to O
following O
criteria O
: O
evidence O
of O
continuous O
water O
flow O
from O
the O
rock O
, O
close O
to O
bubbling O
zones O
, O
and O
near O
the O
most O
reductive O
point O
. O

Introduction O
Anaerobic O
digestion O
( O
AD O
) O
involves O
the O
conversion O
of O
organics O
to O
valuable O
methane O
, O
which O
is O
facilitated O
by O
the O
tightly O
coupled O
synergistic O
activities O
of O
complex O
microbial O
communities O
. O

Duplicate O
filters O
were O
collected O
in O
August O
2008 O
and O
2009 O
, O
1 O
h O
before O
both O
day O
and O
night O
high O
tide O
on O
consecutive O
days O
( O
11 O
) O
. O

Study O
on O
a O
Fermented O
Whole O
Wheat O
: O
Phenolic O
Content O
, O
Activity O
on O
PTP1B O
Enzyme O
and O
In O
Vitro O
Prebiotic O
Properties O
Fermented O
cereals O
, O
staple O
foods O
in O
Asia O
and O
Africa O
, O
are O
recently O
receiving O
a O
growing O
interest O
in O
Western O
countries O
. O

The O
V3 O
- O
V4 O
region O
of O
16S O
rRNA O
genes O
( O
representing O
bacteria O
) O
and O
the O
internal O
transcribed O
spacer O
region O
2 O
( O
ITS2 O
) O
( O
representing O
fungi O
) O
( O
19 O
) O
were O
amplified O
with O
the O
primers O
( O
for O
16S O
rRNA O
genes O
, O
primers O
F341 O
and O
R806 O
[ O
PCR O
product O
, O
425bp O
] O
; O
for O
ITS2 O
, O
primers O
ITS3 O
and O
ITS4 O
[ O
PCR O
product O
, O
320bp O
] O
) O
. O

SamplingReadsEnvironmental O
parametersSiteCoordinatesDateDepth O
( O
m O
) O
rDNArRNATemperature O
( O
C O
) O
SalinityChl O
a O
( O
g O
L1 O
) O
Blanes4140N O
, O
0248E09 O
/ O
02 O
/ O
2010Subsurface O
( O
1 O
) O
440329412 O
. O
537 O
. O
60 O
. O
7Sediment O
( O
20 O
) O
126255412 O
. O
637 O
. O
8Gijn4340N O
, O
535W14 O
/ O
09 O
/ O
2010Subsurface O
( O
1 O
) O
764520 O

. O
235 O
. O
70 O
. O
6Naples4048N O
, O
1415E13 O
/ O
10 O
/ O
2009Subsurface O
( O
1 O
) O
89852966722 O
. O
837 O
. O
71 O
. O
7DCM O
( O
26 O
) O
73001838819 O
. O
237 O
. O
91 O
. O
5Sediment O
( O
78 O
) O
5484552414 O
. O
637 O
. O
914 O
/ O
05 O
/ O
2010Subsurface O
( O
1 O
) O
2769119 O
. O
237 O
. O
21 O
. O
1DCM O
( O
34 O
) O
30532615 O
. O
537 O
. O
71Sediment O
( O
78 O
) O

15878791437 O
. O
9Oslo5916N O
, O
1043E22 O
/ O
09 O
/ O
2009Subsurface O
( O
1 O
) O
7023804615 O
. O
525 O
. O
22 O
. O
5DCM O
( O
20 O
) O
2212617916 O
. O
129 O
. O
21 O
. O
1Sediment O
( O
103 O
) O
190410748 O
. O
235Sediment O
( O
24 O
) O
2057145116 O
. O
229 O
. O
722 O
/ O
06 O
/ O
2010Subsurface O
( O
1 O
) O
31058881521 O
. O
51 O
. O
1DCM O
( O
10 O
) O
5433405611 O
. O
929 O
. O

51 O
. O
9Sediment O
( O
103 O
) O
3596975635Roscoff4846N O
, O
357W20 O
/ O
04 O
/ O
2010Subsurface O
( O
1 O
) O
174638159 O
. O
934 O
. O
90 O
. O
2Sediment O
( O
60 O
) O
2647959 O
. O
934 O
. O
9Varna4310N O
, O
2850E27 O
/ O
05 O
/ O
2010Subsurface O
( O
3 O
) O
12923581816 O
. O
55 O
. O
2DCM O

In O
addition O
to O
synbiotic O
supplementation O
, O
juveniles O
were O
HFD O
challenged O
at O
23 O
to O
24months O
of O
age O
. O

Taxonomic O
Comparison O
of O
Phylotypes O
in O
Serpentinizing O
Environments O
The O
correctly O
formatted O
amplicons O
and O
clone O
libraries O
of O
five O
serpentinizing O
ecosystems O
were O
downloaded O
from O
public O
databases O
( O
SRA O
and O
Genbank O
) O
. O

The O
DGGE O
profiles O
of O
the O
individual O
clones O
were O
compared O
with O
each O
other O
and O
with O
the O
DGGE O
profile O
of O
the O
entire O
community O
[ O
17 O
] O
; O
the O
profiles O
were O
obtained O
through O
seminested O
PCR O
amplification O
with O
the O
primers O
Arc344f O
- O
mod O
- O
GC O
and O
524F O
- O
10 O
- O
ext O
- O
rv O
( O
5 O
- O
TTA O
CCG O
CGG O
CTG O
RCA O
- O
3 O
) O
[ O
16 O
] O
. O

A O
single O
pathologist O
( O
M O
. O
B O
. O
Piazuelo O
) O
, O
blind O
to O
treatment O
groups O
, O
assessed O
and O
scored O
indices O
of O
inflammation O
and O
injury O
6 O
weeks O
postchallenge O
. O

DNA O
extraction O
DNA O
was O
extracted O
from O
all O
samples O
using O
the O
MO O
BIO O
Laboratories O
UltraClean O
DNA O
Isolation O
Kit O
( O
Carlsbad O
, O
CA O
) O
. O

A O
conventional O
TSF O
maximum O
intensity O
threshold O
of O
10 O
, O
000 O
is O
often O
used O
as O
an O
indicator O
of O
migrated O
petroleum O
in O
prospective O
basins O
around O
the O
world O
[ O
41 O
] O
; O
however O
, O
this O
threshold O
was O
elevated O
five O
- O
fold O
( O
50 O
, O
000 O
intensity O
units O
) O
for O
interpreting O
the O
TSF O
values O
obtained O
in O
this O
study O
. O

For O
each O
DNA O
sample O
, O
we O
amplified O
respectively O
the O
bacterial O
16S O
rRNA O
genes O
using O
a O
primer O
set O
specific O
for O
V3V5 O
hypervariable O
regions O
( O
F357 O
: O
5 O
- O
TCCTACGGGAGGCAGCAG O
- O
3 O
and O
R937 O
: O
5 O
- O
TGTGCGGGCCCCCGTCAATT O
- O
3 O
) O
and O
the O
internal O
transcribed O
spacer O
( O
ITS O
) O
using O
a O
primer O
set O
specific O
for O
fungal O
ITS1 O
rDNA O
region O
( O
18SF O
: O
5 O
- O
GTAAAAGTCGTAACAAGGTTTC O
- O
3 O
and O
5 O

. O
8S1R O
: O
5 O
- O
GTTCAAAGAYTCGATGATTCAC O
- O
3 O
) O
[ O
62 O
] O
containing O
adaptors O
, O
key O
sequence O
, O
and O
barcode O
sequences O
as O
described O
by O
the O
454 O
Sequencing O
System O
Guidelines O
for O
Amplicon O
Experimental O
Design O
( O
Roche O
, O
Basel O
, O
Switzerland O
) O
. O

Ten O
to O
twenty O
- O
five O
nanograms O
genomic O
( O
g O
) O
DNA O
was O
used O
as O
template O
for O
the O
first O
PCR O
with O
a O
total O
volume O
of O
50l O
using O
the O
341F O
( O
5 O
- O
CCT O
ACG O
GGN O
GGC O
WGC O
AG O
- O
3 O
) O
and O
the O
785R O
( O
5 O
- O
GAC O
TAC O
HVG O
GGT O
ATC O
TAA O
TCC O
- O
3 O
) O
primers O
appended O
with O
Illumina O
adaptor O
sequences O
. O

Samples O
were O
centrifuged O
at O
200g O
for O
1min O
to O
collect O
the O
secretions O
. O

Additional O
sequencing O
was O
conducted O
at O
Los O
Alamos O
National O
Laboratory O
using O
Illumina O
GAIIx O
PE O
and O
HiSeq O
SE O
machines O
. O

The O
remaining O
cohort O
of O
chicks O
from O
the O
sampled O
breeder O
flock B
was O
placed O
in O
the O
lower O
story O
of O
a O
two O
- O
story O
commercial O
broiler O
house O
( O
hereafter O
called O
the O
monitored O
flock B
) O
. O

Incubation O
of O
pasteurized O
sediment O
slurries O
at O
50C O
Triplicate O
slurries O
were O
prepared O
from O
0 O
to O
20cm O
surface O
sediment O
from O
each O
of O
the O
111 O
locations O
in O
order O
to O
investigate O
thermospore O
germination O
and O
growth O
. O

SourceTracker O
( O
v O
. O
0 O
. O
9 O
. O
5 O
) O
[ O
26 O
] O
was O
used O
to O
predict O
the O
source O
of O
the O
bacterial O
and O
eukaryotic O
communities O
using O
the O
cryoconite O
hole O
samples O
as O
sinks O
and O
lake O
, O
soil O
, O
endolith O
and O
snow O
samples O
as O
potential O
sources O
of O
microbial O
inputs O
. O

When O
the O
AnMBR O
faced O
hydraulic O
overloading O
due O
to O
the O
technical O
failure O
, O
one O
sample O
( O
F10 O
) O
was O
collected O
on O
day O
210 O
( O
29 O
April O
2016 O
) O
, O
and O
after O
twenty O
days O
later O
on O
day O
230 O
( O
21 O
May O
2016 O
) O
, O
a O
second O
sample O
( O
J15 O
) O
was O
collected O
to O
further O
understand O
this O
phenomenon O
, O
as O
a O
new O
inoculum O
( O
Seed O
2 O
) O
was O
used O
on O
the O
day O
220 O
( O
10 O
May O
2016 O
) O
to O
prevent O
the O
AnMBR O
process O
from O
failing O
. O

The O
batch O
reactors O
were O
placed O
on O
a O
stir O
- O
bar O
hot O
plate O
( O
VWR O
, O
# O
97042 O
- O
642 O
) O
operated O
at O
321C O
and O
150rpm O
. O

DNA O
was O
extracted O
using O
an O
UltraClean O
soil O
DNA O
isolation O
kit O
( O
MoBIO O
Laboratories O
, O
Carlsbad O
, O
CA O
) O
. O

using O
an O
Illumina O
HiSeq2000 O
( O
San O
Diego O
, O
CA O
, O
USA O
) O
. O

T O
- O
RFLP O
Primers O
targeting O
the O
glycoside O
hydrolase O
families O
5 O
( O
cel5 O
_ O
392F O
5 O
- O
GAG O
CAT O
GGG O
CTG O
GAA O
YHT O
NGG O
NAA O
- O
3 O
and O
cel5 O
_ O
754R O
5 O
- O
CAT O
CAT O
AAT O
CTT O
TGA O
AGT O
GGT O
TTG O
CAA O
TYT O
GDK O
TCC O
A O
- O
3 O
) O
and O
48 O
( O
cel48 O
_ O
490F O
5 O
TNA O
TGG O
TTG O
AAG O
CTC O
CDG O
AYT O
AYG O
G O
- O
3 O
and O
cel48 O
_ O

920R O
5 O
- O
CCA O
AAN O
CCR O
TAC O
CAG O
TTR O
TCA O
ACR O
TC O
- O
3 O
) O
[ O
86 O
] O
were O
used O
to O
study O
the O
cellulose O
- O
degrading O
bacterial O
community O
structures O
in O
the O
different O
inoculum O
samples O
and O
at O
the O
end O
of O
the O
batch O
test O
by O
terminal O
restriction O
fragment O
length O
polymorphism O
( O
T O
- O
RFLP O
) O
analysis O
. O

RNA O
was O
extracted O
using O
the O
RNeasy O
MiniKit O
( O
Qiagen O
) O
according O
to O
manufacturer O
instructions O
, O
with O
additional O
steps O
for O
cell O
disruption O
through O
flash O
- O
freezing O
and O
bead O
- O
beating O
filters O
in O
mixtures O
of O
500 O
L O
RLT O
buffer O
, O
5 O
L O
- O
mercaptoethanol O
, O
and O
200 O
L O
of O
mixed O
0 O
. O
1 O
mm O
and O
0 O
. O
5 O
mm O
glass O
beads O
( O
Biospec O
products O
) O
. O

In O
brief O
, O
stool O
samples O
were O
collected O
, O
and O
approximately O
2ml O
of O
stool O
was O
homogenized O
by O
vortexing O
in O
5ml O
of O
MO O
BIO O
lysis O
buffer O
( O
PowerLyzer O
PowerSoil O
Bead O
solution O
, O
MO O
BIO O
Laboratories O
) O
. O

This O
study O
, O
therefore O
, O
investigated O
the O
degradation O
rate O
of O
cellulose O
and O
straw O
in O
batch O
cultivation O
test O
initiated O
with O
inoculums O
from O
four O
co O
- O
digestion O
biogas O
plants O
( O
CD O
) O
and O
six O
wastewater O
treatment O
plants O
( O
WWTP O
) O
. O

The O
properties O
of O
the O
primers O
that O
were O
tested O
in O
silico O
and O
in O
vitro O
are O
summarized O
in O
Table2 O
. O
Table2Description O
of O
designed O
species O
- O
specific O
primers O
descriptionPrimer O
IDPrimer O
sequenceE O
. O
coli O
positionTheoretical O
Tm O
( O
C O
) O
Length O
( O
bp O
) O
GC O
content O
( O
% O
) O
Thio O
- O
6FAGG O
GCT O
AGA O
GTT O
TGG O
TAG647521850Thio O
- O
8RAGA O
GGC O
ATA O
ATC O
CTC O
CCA834541850Alkali O
- O
4AFGTT O

AAT O
AGC O
CGT O
GGG O
TCT462541850Alkali O
- O
6BRTAC O
CAG O
ACT O
CTA O
GCC O
CGA646561856Tab O
- O
137 O
- O
G O
_ O
FCTT O
AGG O
TGG O
GGG O
ATA O
ACA O
CG137572055Tab O
- O
210RATC O
CTT O
TGG O
CGC O
GAG O
GTC O
CG210652065F O
, O
forward O
; O
R O
, O
reverse O
; O
Thio O
, O
Thioalkalivibrio O
spp O
. O

16S O
rDNA O
extraction O
Microbial O
community O
taxonomic O
composition O
was O
assessed O
via O
Illumina O
sequencing O
of O
16S O
rRNA O
gene O
fragments O
amplified O
from O
bacterioplankton O
DNA O
from O
stations O
2 O
and O
6 O
. O

In O
total O
, O
12 O
RMs B
were O
used O
across O
the O
various O
groups O
in O
our O
DSS O
studies O
( O
6 O
RMs B
for O
SIV O
- O
uninfected O
acute O
colitis O
model O
, O
2 O
RMs B
for O
SIV O
- O
uninfected O
chronic O
colitis O
model O
and O
MRI O
and O
4 O
RMs B
for O
SIV O
- O
uninfected O
untreated O
controls O
) O
. O

Materials O
and O
Methods O
Primer O
Design O
Multiple O
degenerate O
primer O
sets O
were O
designed O
using O
BioEdit O
v7 O
. O
0 O
. O
1 O
package1 O
to O
amplify O
the O
myocyanophage O
g23 O
MCP O
gene O
fragments O
by O
identifying O
conserved O
sequences O
after O
aligning O
20 O
gene O
sequences O
retrieved O
from O
GenBank O
. O