STORMS Checklis o "Suga - ich oods exace ba e an ibio ic-induced mic obiome dis up ion" by Dai e al.
Ve sion: 1.03
Numbe I em Recommenda ion I em Sou ce Addi ional Guidance Yes/No/NA Commen s o loca ion in manusc ip
Abs ac
1.0
S uc u ed o Uns uc u ed Abs ac
Abs ac should include
in o ma ion on backg ound,
me hods, esul s, and
conclusions in s uc u ed o
uns uc u ed o ma .
STORMS Yes Uns uc u ed abs ac
1.1 S udy Design S a e s udy design in abs ac . STORMS
See 3.0 o addi ional
in o ma ion on s udy
design.
Yes Coho s udy
1.2 Sequencing me hods
S a e he s a egy used o
me agenomic classi ica ion.
STORMS
Fo example, a ge ed
16S by qPCR o
sequencing, sho gun
me agenomics,
me a ansc ip omics,
e c.
Yes a ge ed 16S amplicon sequencing
1.3 Specimens Desc ibe body si e(s) s udied. STORMS Yes ecal mic obiome
In oduc ion
2.0
Backg ound and Ra ionale
Summa ize he unde lying
backg ound, scien i ic
e idence, o heo y d i ing he
cu en hypo hesis as well as
he s udy objec i es.
STORMS Yes
2.1 Hypo heses
S a e he p e-speci ied
hypo hesis. I he s udy is
explo a o y, s a e any p e-
speci ied s udy objec i es.
STORMS Yes
Me hods
3.0 S udy Design Desc ibe he s udy design. STORMS
Obse a ional (Case-
Con ol, Coho ,
C oss-sec ional
su ey, e c.) o
Expe imen al
(Randomized
con olled ial, Non-
andomized con olled
ial, e c.). Fo a b ie
desc ip ion o common
s udy designs see:
DOI: 10.11613/BM.
2014.022
I applicable, desc ibe
any blinding (e.g.
single o double-
blinding) used in he
cou se o he s udy.
Yes Coho S udy
3.1 Pa icipan s
S a e wha he popula ion o
in e es is, and he me hod by
which pa icipan s a e sampled
om ha popula ion. Include
ele an in o ma ion on
physiological s a e o he
subjec s o s age in he li e
his o y o disease unde s udy
when pa icipan s we e
sampled.
STORMS
Examples o he
popula ion o in e es
could be: adul s wi h
no ch onic heal h
condi ions, adul s wi h
ype II diabe es,
newbo ns, e c. This is
he o al popula ion o
whom he s udy is
hoped o be
gene alizable o. The
sampling me hod
desc ibes how
po en ial pa icipan s
we e selec ed om
ha popula ion.
I he pa icipan s a e
om a subs udy o a
la ge s udy, p o ide a
b ie desc ip ion o ha
s udy and ci e ha
s udy.
Clea ly s a e how
cases and con ols a e
de ined.
An example o
ele an physiological
s a e migh be p e/pos
menopausal o a
aginal mic obiome
s udy; examples o
s age in he li e his o y
o disease could be
whe he specimens
we e collec ed du ing
ac i e o do man
disease, o be o e o
a e ea men .
Yes Me hods, "Pa ien s" subsec ion
3.2 Geog aphic loca ion
S a e he geog aphic egion(s)
whe e pa icipan s we e
sampled om.
MIxS: geog aphic
loca ion (coun y
and/o sea, egion)
Geog aphic
coo dina es can be
epo ed o p e en
po en ial ambigui ies i
necessa y.
Yes Me hods, "Pa ien s" subsec ion
3.3 Rele an Da es
S a e he s a and end da es
o ec ui men , ollow-up, and
da a collec ion.
STORMS
Rec ui men is he
pe iod in which
pa icipan s a e
ec ui ed o he s udy.
In longi udinal s udies,
ollow-up is he da e
ange in which
pa icipan s a e asked
o comple e a speci ic
assessmen . Finally,
da a collec ion is he
o al pe iod in which
da a is being collec ed
om pa icipan s
including du ing ini ial
ec ui men h ough all
ollow-ups.
Yes Me hods, "Pa ien s" subsec ion
3.4 Eligibili y c i e ia
Lis any c i e ia o inclusion
and exclusion o ec ui ed
pa icipan s.
Modi ied STROBE
Among po en ial
ec ui ed pa icipan s,
how we e some
chosen and o he s
no ? This could
include c i e ia such as
sex, die , age, heal h
s a us, o BMI.
I he e is a p ima y
and alida ion sample,
desc ibe
inclusion/exclusion
c i e ia o each.
Yes Me hods, "Pa ien s" subsec ion
3.5 An ibio ics Usage
Lis wha is known abou
an ibio ics usage be o e o
du ing sample collec ion.
STORMS
I pa icipan s we e
excluded due o
cu en o ecen
an ibio ics usage, s a e
his he e.
O he ac o s (e.g.
p o on pump inhibi o s,
p obio ics, e c.) ha
may in luence he
mic obiome should
also be desc ibed as
well.
Yes Fig S5 and zenodo da a supplemen
3.6 Analy ic sample size
Explain how he inal analy ic
sample size was calcula ed,
including he numbe o cases
and con ols i ele an , and
easons o d opou a each
s age o he s udy. This should
include he numbe o
indi iduals in whom mic obiome
sequencing was a emp ed and
he numbe in whom
mic obiome sequencing was
success ul.
STORMS
Conside use o a low
diag am (see empla e
a h ps:
//s o msmic obiome.
o g/ igu es). Also s a e
sample size in
abs ac .
I powe analysis was
used o calcula e
sample size, desc ibe
hose calcula ions.
Yes Fig. S1
3.7 Longi udinal S udies
Fo longi udinal s udies, s a e
how many ollow-ups we e
conduc ed, desc ibe sample
size a ollow-up by g oup o
condi ion, and discuss any loss
o ollow-up.
STORMS
I he e is loss o
ollow-up, discuss he
likelihood ha d op-ou
is associa ed wi h
exposu es, ea men s,
o ou comes o
in e es .
Me hods, "Pa ien s" subsec ion
3.8 Ma ching
Fo ma ched s udies, gi e
ma ching c i e ia.
Modi ied STROBE
"Ma ched" e e s o
ma ching be ween
compa able s udy
pa icipan s as cases
and con ols o
exposed / unexposed.
Indica e whe he
pa icipan s we e
indi idual o equency
ma ched and in wha
a io we e hey
ma ched (e.g. 1 case
o 1 con ol).
NA
3.9 E hics
S a e he name o he
ins i u ional e iew boa d ha
app o ed he s udy and
p o ocols, p o ocol numbe and
da e o app o al, and
p ocedu es o ob aining
in o med consen om
pa icipan s.
STORMS Yes Me hods, "Pa ien s" subsec ion
4.0 Labo a o y me hods
S a e he labo a o y/cen e
whe e labo a o y wo k was
done.
STORMS
P o ide a e e ence o
comple e lab p o ocols
i p e iously published
elsewhe e such as on
p o ocols.io. No e any
modi ica ions o lab
p o ocols and he
eason o p o ocol
modi ica ions.
Yes Me hds, "Human ecal mic obiome analysis" subsec ion
4.1 Specimen collec ion S a e he body si e(s) sampled
om and how specimens we e
collec ed.
MIxS: sample
collec ion de ice o
me hod; hos body
si e
Use e ms om he
Ube -ana omy
On ology (h ps://www.
ebi.ac.
uk/ols/on ologies/ube
on) o desc ibe body
si es in a s anda dized
o ma .
Yes S ool samples we e collec ed om he eces (UBERON:
0001988) o pa ien s. Feces a e he exc e ed was e
p oduc s o he diges i e sys em (UBERON:0001007),
o med in he la ge in es ine (UBERON:0000059) and
s o ed in he ec um (UBERON:0001052) p io o
de eca ion
4.2 Shipping
Desc ibe how samples we e
s o ed and shipped o he
labo a o y.
STORMS
Include leng h o ime
om collec ion o
eceip by he lab and
i empe a u e con ol
was used du ing
shipping.
Yes Me hds, "Human ecal mic obiome analysis" subsec ion
4.3 S o age
Desc ibe how he labo a o y
s o ed samples, including ime
be ween collec ion and s o age
and any p ese a ion bu e s o
e ige a ion used.
STORMS
S a e whe e each
p ocedu e o lo o
samples was done i
no all in he same
place.
Include
eagen /lo /ca alogue
#s o s o age bu e s.
Yes Me hods "Fecal mic obiome analysis" subsec ion
4.4 DNA ex ac ion
P o ide DNA ex ac ion
me hod, including ki and
e sion i ele an .
MIxS: nucleic acid
ex ac ion
I any DNA
quan i ica ion me hods
we e used p io o
DNA ampli ica ion o
a he pooling s ep o
lib a y p epa a ion,
s a e so he e.
Yes in he "Fecal mic obiome analysis" sec ion
4.5
Human DNA sequence
deple ion o mic obial
DNA en ichmen
Desc ibe whe he human DNA
sequence deple ion o
en ichmen o mic obial o i al
DNA was pe o med.
STORMS Yes No deple ion no en ichmen
4.6 P ime selec ion
P o ide p ime selec ion and
DNA ampli ica ion me hods as
well as a iable egion
sequenced (i applicable).
MIxS: pc p ime s Yes Me hods "Fecal mic obiome analysis" subsec ion
4.7 Posi i e Con ols
Desc ibe any posi i e con ols
(mock communi ies) i used.
STORMS
I used, should be
deposi ed unde
guidance p o ided in
he 8.X i ems.
NA Me hods "Fecal mic obiome analysis" subsec ion
4.8 Nega i e Con ols
Desc ibe any nega i e con ols
i used.
STORMS
I used, should be
deposi ed unde
guidance p o ided in
he 8.X i ems.
NA Me hods "Fecal mic obiome analysis" subsec ion
4.9
Con aminan mi iga ion
and iden i ica ion
P o ide any labo a o y o
compu a ional me hods used o
con ol o o iden i y
mic obiome con amina ion om
he en i onmen , eagen s, o
labo a o y.
STORMS
Includes il e ing o
eagen s and o he
s eps o minimize
con amina ion. I is
ele an o s a e
whe he he
specimens o in e es
ha e low mic obial
load, which makes
con amina ion
especially ele an .
Yes Me hods "Fecal mic obiome analysis" subsec ion
4.10 Replica ion
Desc ibe any biological o
echnical eplica es included in
he sequencing, including which
s eps we e eplica ed be ween
hem.
STORMS
Replica ion may be
biological ( edundan
biological specimens)
o echnical (aliquo s
aken a di e en
s ages o analysis)
and used in ex ac ion,
sequencing,
p ep ocessing, and/o
da a analysis.
Yes Me hods "Fecal mic obiome analysis" subsec ion ci es
PMID 37295406
4.11 Sequencing s a egy Majo di isions o s a egy,
such as sho gun o amplicon
sequencing.
MIxS: sequencing
me hod
Fo amplicon
sequencing ( o
example, 16S a iable
egion), s a e he
egion selec ed. S a e
he model o
sequence used.
Yes Me hods "Fecal mic obiome analysis" subsec ion ci es
PMID 37295406
4.12 Sequencing me hods
S a e whe he expe imen al
quan i ica ion was used
(QMP/cell coun based, spike-in
based) o whe he ela i e
abundance me hods we e
applied.
STORMS
These include ead
leng h, sequencing
dep h pe sample
(a e age and
minimum), whe he
eads a e pai ed, and
o he pa ame e s.
Yes Me hods "Fecal mic obiome analysis" subsec ion
4.13 Ba ch e ec s
De ail any blocking o
andomiza ion used in s udy
design o a oid con ounding o
ba ches wi h exposu es o
ou comes. Discuss any likely
sou ces o ba ch e ec s, i
known.
STORMS
Sou ces o ba ch
e ec s include sample
collec ion, s o age,
lib a y p epa a ion,
and sequencing and
a e commonly
una oidable in all bu
he smalles o s udies.
No
4.14 Me a ansc ip omics
De ail whe he any mRNA
en ichmen was pe o med and
whe he /how e o ansc ip ion
was pe o med p io o
sequencing. P o ide size ange
o isola ed ansc ip s. Desc ibe
whe he he sequencing lib a y
was s anded o no . P o ide
de ails on sequencing me hods
and pla o ms.
STORMS
P o ide de ails on any
in e nal s anda ds
which may ha e been
used as well as
pa ame e s and
e sions o any
so wa e o da abases
used.
NA
4.15 Me ap o eomics
De ail which p o ease was used
o diges ion. P o ide de ails on
p o eomic me hods and
pla o ms (e.g. LC-MS/MS,
ins umen ype, column ype,
mass ange, esolu ion, scan
speed, maximum injec ion ime,
isola ion window, no malised
collision ene gy, and
esolu ion).
STORMS
P o ide de ails on any
in e nal s anda ds
which may ha e been
used as well as
pa ame e s and
e sions o any
so wa e o da abases
used.
NA
4.16 Me abolomics
Speci y he analy ic me hod
used (such as nuclea magne ic
esonance spec oscopy o
mass spec ome y). Fo mass
spec ome y, de ail which
ac ions we e ob ained (pola
and/o non pola ) and how
hese we e analyzed. P o ide
de ails on me abolomics
me hods and pla o ms (e.g.
de i a iza ion, ins umen ype,
injec ion ype, column ype and
ins umen se ings).
STORMS
P o ide de ails on any
in e nal s anda ds
which may ha e been
used as well as
pa ame e s and
e sions o any
so wa e o da abases
used.
NA
5.0
Da a sou ces/
measu emen
Fo each non-mic obiome
a iable, including he heal h
condi ion, in e en ion, o o he
a iable o in e es , s a e how i
was de ined, how i was
measu ed o collec ed, and any
ans o ma ions applied o he
a iable p io o analysis.
MIxS: hos disease
s a us
S a e any sou ces o
po en ial bias in
measu emen s, o
example mul iple
in e iewe s o
measu emen
ins umen s, and
whe he hese
po en ial biases we e
assessed o
accoun ed o in s udy
design.
Use e ms om a
s anda dized on ology
such as he
Expe imen al Fac o
On ology (h ps://www.
ebi.ac.uk/e o/) o
desc ibe a iables o
in e es in a
s anda dized o ma .
Yes Me hods
6.0
Resea ch design o
causal in e ence
Discuss any po en ial o
con ounding by a iables ha
may in luence bo h he
ou come and exposu e o
in e es . S a e any a iables
con olled o and he a ionale
o con olling o hem.
STORMS
Fo causal in e ence,
his i em e e s o
desc ibing he
assump ions ha
would be equi ed o
d aw causal
in e ences om
obse a ional da a.
See Vujko ic-C ijin, I.,
Skla , J., Jiang, L. e
al. Hos a iables
con ound gu
mic obio a s udies o
human disease.
Na u e 587, 448–454
(2020). h ps://doi.
o g/10.1038/s41586-
020-2881-9 o mo e
de ails on con ounding
in obse a ional
mic obiome s udies.
Fo example,
hypo hesized
con ounde s may be
con olled o by
mul i a iable
adjus men . Conside
using a di ec ed
acyclic g aph (DAG) o
desc ibe you causal
model and jus i y any
a iables con olled
o . DAGs can be
made using www.
dagi y.ne .
Yes Me hods, "Bayesian mul ile el model" subsec ion
6.1 Selec ion bias
Discuss po en ial o selec ion
o su i al bias.
STORMS
Selec ion bias can
occu when some
membe s o he a ge
s udy popula ion a e
mo e likely o be
included in he
s udy/ inal analy ic
sample han o he s.
Some examples
include su i al bias
(whe e pa o he
a ge s udy popula ion
is mo e likely o die
be o e hey can be
s udied), con enience
sampling (whe e
membe s o he a ge
s udy popula ion a e
no selec ed a
andom), and loss o
ollow-up (when
p obabili y o d opping
ou is ela ed o one o
he hings being
s udied).
Yes Discussion, hi d pa ag aph
7.0
Bioin o ma ic and
S a is ical Me hods
Desc ibe any ans o ma ions o
quan i a i e a iables used in
analyses (e.g. use o
pe cen ages ins ead o coun s,
no maliza ion, a e ac ion,
ca ego iza ion).
STORMS
I a a iable is
analyzed using
di e en
ans o ma ions, s a e
a ionale o he
ans o ma ion and o
each analyses which
e sion o he a iable
is used.
In case o any
complex o mul is ep
ans o ma ions, gi e
enume a ed
ins uc ions o
ep oducing hose
ans o ma ions.
Yes Me hods, "Bayesian mul ile el model" subsec ion
7.1 Quali y Con ol
Desc ibe any me hods o
iden i y o il e low quali y
eads o samples.
MIxS: sequence
quali y check
I samples we e
excluded based on
quali y o ead dep h,
lis he c i e ia used,
he numbe o samples
excluded, and he inal
sample size a e
quali y con ol.
Me hods "Fecal mic obiome analysis" subsec ion ci es
PMID 37295406
7.2 Sequence analysis
Desc ibe any axonomic,
unc ional p o iling, o o he
sequence analysis pe o med.
MIxS: ea u e
p edic ion;
simila i y sea ch
me hod
Yes in he "Fecal mic obiome analysis" sec ion
7.3 S a is ical me hods Desc ibe all s a is ical me hods. Modi ied STROBE
Desc ibe any
s a is ical es s used,
explo a o y da a
analysis pe o med,
dimension educ ion
me hods/unsupe ised
analysis, alpha/be a
me ics, and/o
me hods o adjus ing
o measu emen bias.
I mul iple s a is ical
me hods a e possible,
discuss why he
me hods used we e
selec ed.
I a mul iple hypo hesis
es ing co ec ion
me hod was used,
desc ibe he ype o
co ec ion used.
S a e which axonomic
le els a e analyzed.
Yes Me hods, "Bayesian mul ile el model" subsec ion
7.4 Longi udinal analysis
I he s udy is longi udinal,
include a sec ion ha explici ly
s a es wha analysis me hods
we e used (i any) o accoun
o g ouping o measu emen s
by indi idual o pa e ns o e
ime.
STORMS NA
7.5 Subg oup analysis
Desc ibe any me hods used o
examine subg oups and
in e ac ions.
STROBE Yes Figu e S10 (p e- ansplan subg oup analysis)
7.6 Missing da a
Explain how missing da a we e
add essed.
STROBE
"Missing da a" e e s
o pa icipan
measu emen s such
as co a ia es,
exposu es, ou comes,
o ime poin s ha
should ha e been
collec ed bu we e no ,
no o ze os in
axonomic abundance
ables o da a poin s
no applicable o ha
obse a ion.
Yes
Me hods, "Nu i ion da a collec ion and anno a ion"
subsec ion
7.7 Sensi i i y analyses
Desc ibe any sensi i i y
analyses.
STROBE Yes Figu e S8, S9
7.8 Findings
S a e c i e ia used o selec
indings o epo ing.
STORMS
Fo example, alse
disco e y a e wi h
o al numbe o es s,
e ec size h eshold,
signi icance h eshold,
mic obes o in e es .
Yes Me hods, "Bayesian mul ile el model" subsec ion
7.9 So wa e
Ci e all so wa e (including ead
mapping so wa e) and
da abases (including any used
o axonomic e e ence o
anno a ing amplicons, i
applicable) used. Include
e sion numbe s.
Modi ied STREGA
Ins alled packages,
add-ons o lib a ies
should be s a ed and
ci ed in addi ion o he
so wa e used.
All pa ame e s
employed ha di e
om he de aul o ha
so wa e/ e sion
should be p o ided.
This is in addi ion o,
no a eplacemen o ,
publishing o code as
ou lined in he sec ion
Rep oducible
Resea ch.
Yes Me hods
8.0 Rep oducible esea ch
Make a s a emen abou
whe he and how o he s can
ep oduce he epo ed
analysis.
STORMS
Any p o ec ed
in o ma ion ha has
been excluded o
p o ided unde
con olled access
should be lis ed along
wi h any ele an da a
access p ocedu es.
"On eques om
au ho s" is no
su icien ly de ailed;
o mal da a access
p ocedu es and
condi ions should be
de ined.
I da a a e una ailable,
s a e so clea ly.
Conside using a
specialized ub ic o
ep oducible esea ch
(such as: h ps://mbio.
asm.
o g/con en /9/3/e0052
5-18.sho ).
Conside
p e egis e ing he
s udy p o ocol (such
as on os .io o h ps:
//plos.o g/open-
science/p e egis a ion
/).
Yes Da a a ailabili y s a emen jus be o e e e ences
8.1 Raw da a access
S a e whe e aw da a may be
accessed including
demul iplexing in o ma ion.
STORMS
Robus , long- e m
da abases such as
hose hos ed by NCBI
and EBI a e p e e ed.
I using a p i a e
eposi o y, p o ide
a ionale.
Yes
NCBI SRA and zenodo (h ps://zenodo.
o g/ eco ds/14538106), as de ailed in Da a a ailabili y
s a emen
8.2 P ocessed da a access
S a e whe e p ocessed da a
may be accessed.
STORMS
Un il e ed da a should
be p o ided.
Robus , long- e m
da abases such as
hose hos ed by NCBI
and EBI-EMBL a e
p e e ed. Reposi o ies
like zenodo (h ps:
//zenodo.o g/) o
publisso (h ps://www.
publisso.
de/en/wo king- o -
you/doi-se ice/)
can be used o p o ide
a DOI and long- e m
s o age o p ocessed
da ase s, e en hose
which canno be
published openly.
Yes
NCBI SRA and zenodo (h ps://zenodo.
o g/ eco ds/14538106), as de ailed in Da a a ailabili y
s a emen
8.3 Pa icipan da a access
S a e whe e indi idual
pa icipan da a such as
demog aphics and o he
co a ia es may be accessed,
and how hey can be ma ched
o he mic obiome da a.
STORMS
I e-ca ego ized,
ans o med, o
o he wise de i ed
a iables we e used in
he analysis, hese
a iables o code o
de i ing hem should
be p o ided.
Examples o how
pa icipan da a can be
ma ched o
mic obiome da a a e:
using he same se o
anonymized
iden i ie s, o using
di e en anonymized
iden i ie s bu
p o iding a map.
P o ided da a should
be su icien o
independen ly
eplica e he cu en
analysis.
Yes zenodo (h ps://zenodo.o g/ eco ds/14538106), as
de ailed in Da a a ailabili y s a emen
8.4 Sou ce code access
S a e whe e code may be
accessed.
STORMS
I a s anda d o
o malized wo k low
was employed,
e e ence i he e.
Yes
Gi hub eposi o y as linked o in he Da a a ailabili y
s a emen
8.5 Full esul s
P o ide ull esul s o all
analyses, in compu e - eadable
o ma , in supplemen a y
ma e ials.
STORMS
Fo example, any old-
changes, p- alues, o
FDR alues
calcula ed, p o ided
as a sp eadshee .
Use a machine-
eadable, plain- ex
o ma such as cs o
s .
No
Resul s
9.0 Desc ip i e da a
Gi e cha ac e is ics o s udy
pa icipan s (e.g. die a y,
demog aphic, clinical, social)
and in o ma ion on exposu es
and po en ial con ounde s.
STROBE
Typically epo ed in a
able included in he
pape o as a
supplemen a y able.
Indica e numbe o
pa icipan s wi h
missing da a o each
a iable o in e es .
This includes
en i onmen al and
li es yle ac o s ha
may a ec he
ela ionship be ween
he mic obiome and
he condi ion o
in e es . Pa icipan
die and medica ion
use should be
summa ized, i known.
A minimum, age and
sex o all pa icipan s
should be
summa ized.
Yes Table 1
10.0 Mic obiome da a
Repo desc ip i e indings o
mic obiome analyses wi h all
applicable ou comes and
co a ia es.
STORMS
This includes
measu es o di e si y
as well as ela i e
abundances. These
desc ip i e indings
should be epo ed
bo h o he sample
o e all and o
indi idual g oups.
Yes
10.1 Taxonomy
Iden i y axonomy using
s anda dized axon
classi ica ions ha a e su icien
o uniquely iden i y axa.
STORMS
I no using ull
axonomic hie a chy,
make su e i is clea
whe he names s a ed
a e species, gene a,
amily, e c.
I alicize genus/species
pai s. Consul jou nal
guidelines o
s anda dized
e e ences on
axonomic
nomencla u e. Fo
ins ance, h ps:
//wwwnc.cdc.
go /eid/page/scien i ic-
nomencla u e
Yes
10.2 Di e en ial abundance
Repo esul s o di e en ial
abundance analysis by he
a iable o in e es and (i
applicable) by ime, clea ly
indica ing he di ec ion o
change and o al numbe o
axa es ed.
STORMS
I he e a e mo e han
wo g oups, include
omnibus (mul ig oup)
es esul s i
applicable o he
esea ch ques ion.
I applicable, epo ed
e ec sizes should
include a measu e o
unce ain y such as
he con idence
in e al.
NA
10.3 O he da a ypes
Repo o he da a analyzed--e.
g. me abolic unc ion, unc ional
po en ial, MAG assembly, and
RNAseq.
STORMS Yes
10.4
O he s a is ical analysis
Repo any s a is ical da a
analysis no co e ed abo e.
STORMS
This could include
subg oup analysis,
sensi i i y analyses,
and clus e analysis.
Visualiza ions should
be easily in e p e able
and colo blind- iendly.
The cap ion and/o
main ex should
p o ide a de ailed
desc ip ion o
isualiza ions o
isually-impai ed
eade s.
Yes
Discussion
11.0 Key esul s
Summa ise key esul s wi h
e e ence o s udy objec i es
STROBE Yes
12.0 In e p e a ion
Gi e a cau ious o e all
in e p e a ion o esul s
conside ing objec i es,
limi a ions, mul iplici y o
analyses, esul s om simila
s udies, and o he ele an
e idence.
STROBE
De ine o cla i y any
subjec i e e ms such
as "dominan ,"
"dysbiosis," and
simila wo ds used in
in e p e a ion o
esul s.
When in e p e ing he
indings, conside how
he in e p e a ion o
he indings may be
summa ized o quo ed
o he gene al public
such as in p ess
eleases o news
a icles.
I causal language is
used in he
in e p e a ion (such as
"al e s," "a ec s,"
" esul s in," "causes,"
o "impac s"),
assump ions made o
causal in e ence
should be explici ly
s a ed as pa o 6.0
and 13.0.
Dis inguish be ween
unc ion po en ial (ie
in e ed om
me agenomics) and
obse ed ac i i y (ie
me a ansc ip omic,
me abolomic,
p o eomic) i
discussing mic obial
unc ion.
Yes
13.0 Limi a ions
Discuss limi a ions o he s udy,
aking in o accoun sou ces o
po en ial bias o imp ecision.
STROBE
Also conside
limi a ions esul ing
om he me hods
(especially no el
me hods), he s udy
design, and he
sample size.
Yes
13.1 Bias
Discuss any po en ial o bias o
in luence s udy indings.
STORMS
May include sampling
me hod,
ep esen a i eness o
s udy pa icipan s, o
po en ial con ounding.
Yes
13.2 Gene alizabili y
Discuss he gene alisabili y
(ex e nal alidi y) o he s udy
esul s
STROBE
To wha popula ions o
o he se ings do you
expec he conclusions
o gene alize?
Yes
14.0 Ongoing/ u u e wo k
Desc ibe po en ial u u e
esea ch o ongoing esea ch
based on he s udy's indings.
STORMS Yes
O he in o ma ion
15.0 Funding
Gi e he sou ce o unding and
he ole o he unde s o he
p esen s udy and, i applicable,
o he o iginal s udy on which
he p esen a icle is based
STROBE Yes
15.1 Acknowledgemen s
Include acknowledgemen s o
hose who con ibu ed o he
esea ch bu did no mee
c i e a o au ho ship.
STORMS
Fo gene al guidelines
on au ho ship, see
h p://www.icmje.o g
and h ps://www.
else ie .
com/au ho s/jou nal-
au ho s/policies-and-
e hics/c edi -au ho -
s a emen
Yes
15.2 Con lic s o In e es
Include a con lic s o in e es
s a emen .
STORMS Yes
16.0 Supplemen s
Indica e whe e supplemen s
may be accessed and wha
ma e ials hey con ain.
STORMS Yes
17.0 Supplemen a y da a
P o ide supplemen a y da a
iles o esul s wi h o all axa
and all ou come a iables
analyzed. Indica e he
axonomic le el o all axa.
STORMS
Depending on he
analysis pe o med,
examples o he
supplemen al esul s
included could be
mean ela i e
abundance, di e en ial
abundance, aw p-
alue, mul iple
hypo hesis es ing-
adjus ed p- alues, and
s anda d e o .
All discussed axa
should include he
axonomic le el (e.g.
class, o de , genus).
Yes
