1
nature research | reporting summary
April 2018
Corresponding author(s):
Sarkis Mazmanian, Ashlee Earl, Gregory
Donaldson
Reporting Summary
Nature Research wishes to improve the reproducibility of the work that we publish. This form provides structure for consistency
and transparency
in reporting. For further information on Nature Research policies, see
Authors & Referees
and the
Editorial Policy Checklist
.
Statistical parameters
When statistical analyses are reported, confirm that the following items are present in the relevant location (e.g. figure lege
nd, table legend, main
text, or Methods section).
n/a
Confirmed
The exact sample size (
n
) for each experimental group/condition, given as a discrete number and unit of measurement
An indication of whether measurements were taken from distinct samples or whether the same sample was measured repeatedly
The statistical test(s) used AND whether they are one- or two-sided
Only common tests should be described solely by name; describe
more complex techniques in the Methods section.
A description of all covariates tested
A description of any assumptions or corrections, such as tests of normality and adjustment for multiple comparisons
A full description of the statistics including central tendency (e.g. means) or other basic estimates (e.g. regression coeffici
ent) AND
variation (e.g. standard deviation) or associated estimates of uncertainty (e.g. confidence intervals)
For null hypothesis testing, the test statistic (e.g.
F
,
t
,
r
) with confidence intervals, effect sizes, degrees of freedom and
P
value noted
Give P values as exact values whenever suitable.
For Bayesian analysis, information on the choice of priors and Markov chain Monte Carlo settings
For hierarchical and complex designs, identification of the appropriate level for tests and full reporting of outcomes
Estimates of effect sizes (e.g. Cohen's
d
, Pearson's
r
), indicating how they were calculated
Clearly defined error bars
State explicitly what error bars represent (e.g. SD, SE, CI)
Our web collection on
statistics for biologists
may be useful.
Software and code
Policy information about
availability of computer code
Data collection
RNAseq data was collected on an Illumina HiSeq2500
Flow cytometry data was collected on a Miltenyi MACSQuant
Data analysis
Reads were trimmed using FASTX toolkit v.0.0.13
Bacterial read mapping was performed with Bowtie2 2.2.9
Read counts per gene were quantified using bedtools 2.25.0
Differential expression analyses were performed with edgeR 3.12.1
Genomic comparisons were made using the MEME suite 4.12.0 (GLAM2 and GLAM2Scan)
Structural modeling was done with Phyre 2.0
Graphing and statistical analysis was performed with GraphPad Prism 7
Flow Cytometry data were collected using MACSQuantify 2.0
Flow Cytometry data were analyzed with FlowJo 10.0.8
For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published lit
erature, software must be made available to editors/reviewers
upon request. We strongly encourage code deposition in a community repository (e.g. GitHub). See the Nature Research
guidelines for submitting code & software
for further information.
2
nature research | reporting summary
April 2018
Data
Policy information about
availability of data
All manuscripts must include a
data availability statement
. This statement should provide the following information, where applicable:
- Accession codes, unique identifiers, or web links for publicly available datasets
- A list of figures that have associated raw data
- A description of any restrictions on data availability
RNA-Seq and hsRNA-Seq data have been deposited in the NCBI Short Read Archive under a project accession number, PRJNA438372. Th
e B. fragilis NCTC9343
genome used for mapping is available at Genbank GCA_000025985.1. Analysis code is avilable on Github: https://github.com/wenchi
chou/bugInHost. All other
source data are provided with the paper.
Field-specific reporting
Please select the best fit for your research. If you are not sure, read the appropriate sections before making your selection.
Life sciences
Behavioural & social sciences
Ecological, evolutionary & environmental sciences
For a reference copy of the document with all sections, see
nature.com/authors/policies/ReportingSummary-flat.pdf
Life sciences study design
All studies must disclose on these points even when the disclosure is negative.
Sample size
Sample sizes were based on previous published reports or empirically chosen based on pilot studies because expected effect size
s were
unknown.
Data exclusions
Data were not excluded.
Replication
In vivo experiments were separately performed on at least two cohorts of mice (born months apart). Replication was successful i
n each case.
Randomization
Age-matched mice (within 1 week) were randomly sorted into experimental groups.
Blinding
Blinding was used for histological scoring (Fig. 5d). All other experiments were unblinded because the microbiological data col
lection methods
are objective (ie CFU plating).
Reporting for specific materials, systems and methods
Materials & experimental systems
n/a
Involved in the study
Unique biological materials
Antibodies
Eukaryotic cell lines
Palaeontology
Animals and other organisms
Human research participants
Methods
n/a
Involved in the study
ChIP-seq
Flow cytometry
MRI-based neuroimaging
Antibodies
Antibodies used
rat anti-mouse CD4 (clone RM4-5) PE-Cy7 (eBioscience ThermoFisher #25-0042-81) (1:200 dilution)
rat anti-mouse IFNgamma (clone XMG1.2) FITC (eBioscience ThermoFisher #11-7311-41) (1:200 dilution)
rat anti-mouse IL-10 (clone JES5-16E3) PE (eBioscience ThermoFisher #12-7101-81) (1:200 dilution)
rat anti-mouse IL-17A (clone eBio17B7) PerCP-Cy5.5 (eBioscience ThermoFisher #45-7177-82) (1:200 dilution)
rat anti-mouse FOXP3 (clone FJK-16s) APC (eBioscience ThermoFisher #17-5773-82) (1:200 dilution)
We did not keep record of the lot numbers
Validation
All were validated for flow cytometry using mouse samples by the manufacturer. Further validation details:
CD4: relative expression verification by manufacturer and 80 citations available on website
IFNgamma: cell treatment verification by manufacturer and 140 citations available on website
3
nature research | reporting summary
April 2018
IL-10: 43 citations available on website
IL-17A: 54 citations available on website
FOXP3: relative expression verification by manufacturer and 270 citations available on website
Eukaryotic cell lines
Policy information about
cell lines
Cell line source(s)
NA
Authentication
Describe
the
authentication
procedures
for
each
cell
line
used
OR
declare
that
none
of
the
cell
lines
used
were
authenticated.
Mycoplasma contamination
Confirm
that
all
cell
lines
tested
negative
for
mycoplasma
contamination
OR
describe
the
results
of
the
testing
for
mycoplasma contamination OR declare that the cell lines were no
t tested for mycoplasma contamination.
Commonly misidentified lines
(See
ICLAC
register)
Name
any
commonly
misidentified
cell
lines
used
in
the
study
and
provide
a
rationale
for
their
use.
Animals and other organisms
Policy information about
studies involving animals
;
ARRIVE guidelines
recommended for reporting animal research
Laboratory animals
Swiss Webster and C57BL/6 mice (Mus musculus) were purchased from Taconic Farms and bred at Caltech. For all experiments
female 7-8 week-old germfree mice were used with the following exceptions: Fig. 3d-f (half male, half female), DNBS
experiments (3 week-old, just-weaned mice were colonized to allow the induction of colitis at 7 weeks of age). For Fig. 4 mice
with full microbiome, 7 week-old excluded flora Swiss Webster mice were purchased from Taconic.
Wild animals
No wild animals
Field-collected samples
No field-collected samples
Flow Cytometry
Plots
Confirm that:
The axis labels state the marker and fluorochrome used (e.g. CD4-FITC).
The axis scales are clearly visible. Include numbers along axes only for bottom left plot of group (a 'group' is an analysis of
identical markers).
All plots are contour plots with outliers or pseudocolor plots.
A numerical value for number of cells or percentage (with statistics) is provided.
Methodology
Sample preparation
Mesenteric lymph nodes from gnotobiotic C57BL/6 mice were isolated and processed by dissociating tissues through a 70
μ
m
cell strainer (BD Falcon) to generate single cell suspensions.
Instrument
Miltenyi MACSQuant 10
Software
The MIltenyi software for the MACSQuant was used for acquisition of data. Flowjo 10.0.8 was used to analyze the data.
Cell population abundance
No sorting in this study
Gating strategy
A live/dead stain over SSC gate was used to identify live cells followed by a CD4+ gate to identify T cells.
Tick this box to confirm that a figure exemplifying the gating strategy is provided in the Supplementary Information.