| 1 |
a |
Experiment schematic. |
n/a |
| 1 |
b |
Lifespan. |
lifespan.Rmd |
| 1 |
c |
Schematic of data generation. |
n/a |
| 1 |
d |
PCoA of all samples, genera. |
kraken.Rmd |
| 2 |
a |
Volcano plot of age coefficients. |
kraken.Rmd |
| 2 |
b |
Bifido versus age. |
kraken.Rmd |
| 2 |
c |
Uniqueness versus age. |
kraken.Rmd |
| 2 |
d |
Age prediction, AL, genera. |
prediction.Rmd |
| 2 |
e |
Most important genera for age prediction. |
prediction.Rmd |
| 3 |
a |
Schematic comparing DO AL mice, B6 mice, and human datasets. |
n/a |
| 3 |
b |
Percent genera associated with age in DO AL, B6, and human datasets. |
compare_DO_to_B6_to_humans.Rmd |
| 3 |
c |
Correlation of age coefficients across DO AL, B6, and human datasets. |
compare_DO_to_B6_to_humans.Rmd |
| 3 |
d |
Uniqueness across DO AL, B6, and human datasets. |
compare_DO_to_B6_to_humans.Rmd |
| 3 |
e |
Schematic of cohousing experiment. |
n/a |
| 3 |
f |
Cohousing PCoA. |
cohousing.Rmd |
| 3 |
g |
Distance to uncohoused control. |
cohousing.Rmd |
| 3 |
h |
Age prediction, cohousing experiment. |
cohousing.Rmd |
| 3 |
i |
Uniqueness in cohousing experiment. |
cohousing.Rmd |
| 4 |
a |
Heritability volcano plot. |
kraken.Rmd |
| 4 |
b |
Percent heritable taxa across studies. |
perc_heritable_taxa_by_study.Rmd |
| 4 |
c |
PVE for all experimental variables. |
kraken.Rmd |
| 4 |
d |
Genome-wide QTL mapping. |
QTL.Rmd |
| 5 |
a |
Barplots of DR coefficients. |
kraken.Rmd |
| 5 |
b |
UMGS1815 increased by diets. |
kraken.Rmd |
| 5 |
c |
Ligilactobacillus increased by diets. |
kraken.Rmd |
| 5 |
d |
Magnitude of DR coefficients. |
kraken.Rmd |
| 5 |
e |
Similarity of coefficients across diets. |
kraken.Rmd |
| 5 |
f |
Genera affected by CR or fasting exclusively. |
kraken.Rmd |
| 5 |
g |
Emergencia versus diet. |
kraken.Rmd |
| 5 |
h |
Roseburia versus diet. |
kraken.Rmd |
| 5 |
i |
Predicting binary DR status. |
prediction.Rmd |
| 5 |
j |
Predicting dietary group. |
prediction.Rmd |
| 5 |
k |
Predicting dietary group, stratified by diet. |
prediction.Rmd |
| 5 |
l |
Predicting age, trained on AL. |
prediction.Rmd |
| 5 |
m |
UBA11957 versus age. |
kraken.Rmd |
| 5 |
n |
Ligilactobacillus versus age. |
kraken.Rmd |
| 6 |
a |
Schematic of association and mediation analysis. |
n/a |
| 6 |
b |
Microbiome-phenotype associations by domain. |
pheno_assoc_and_mediation.Rmd |
| 6 |
c |
Examples of genera associated with body weight. |
pheno_assoc_and_mediation.Rmd |
| 6 |
d |
Paramuribaculum v. percent fat. |
pheno_assoc_and_mediation.Rmd |
| 6 |
e |
Overlap of microbiome-phenotype association and mediation hits. |
pheno_assoc_and_mediation.Rmd |
| 6 |
f |
Heatmap of microbiome-phenotype associations. |
pheno_assoc_and_mediation.Rmd |
| 6 |
g |
Akkermansia v. EE. |
pheno_assoc_and_mediation.Rmd |
| 6 |
h |
Pathway associated with CO2 production. |
pheno_assoc_and_mediation.Rmd |
| 6 |
i |
Microbiome-phenotype associations by domain, cross-sectional analysis. |
pheno_assoc_and_mediation.Rmd |
| ED1 |
a |
Number of read-pairs per sample, stratified by sample type. |
qc.Rmd |
| ED1 |
b |
PCoA including control samples. |
kraken_unaggregated.Rmd |
| ED1 |
c |
Stacked barplots of positive controls. |
metaphlan_poscons.Rmd |
| ED1 |
d |
PCoA without control samples (before aggregating by stool_ID). |
kraken_unaggregated.Rmd |
| ED1 |
e |
Same as d, but highlighting samples sequenced from the same DNA, different libraries. |
kraken_unaggregated.Rmd |
| ED1 |
f |
Same as d, but highlighting samples sequenced from the same library. |
kraken_unaggregated.Rmd |
| ED2 |
n/a |
Sample mix-ups: code not included (requires a file with 3M data points). |
n/a |
| ED3 |
a |
Histogram of pairwise sample distances, highlighting 13 outliers. |
qc.Rmd |
| ED3 |
b |
Kraken v. MPA, % unclassified. |
kraken_v_metaphlan.Rmd |
| ED3 |
c |
Kraken v. MPA, mean relab per genus. |
kraken_v_metaphlan.Rmd |
| ED3 |
d |
Example of community-wide and specialized pathways. |
humann.Rmd |
| ED3 |
e |
PCA of all samples, pathways. |
humann.Rmd |
| ED4 |
a |
Day of experiment versus age, colored by cohort. |
create_cross_sectional_slices.Rmd |
| ED4 |
b |
Number of age-associated features with time as a random effect, fixed effect, or omitted. |
effect_of_chronological_time.Rmd |
| ED4 |
c |
Correlation of age coefficients between longitudinal (time as fixef, time as ranef, no time) models and cross-sectional models. |
effect_of_chronological_time.Rmd |
| ED5 |
a |
Uniqueness versus age, for different numbers of mice per age. |
kraken.Rmd |
| ED5 |
b |
Alpha diversity versus age. |
kraken.Rmd |
| ED5 |
c |
Proportion age-associated features, genera versus species. |
kraken.Rmd |
| ED5 |
d |
Uniqueness versus age, species-level data. |
kraken.Rmd |
| ED5 |
e |
Kraken v. MPA, age coefficients. |
kraken_v_metaphlan.Rmd |
| ED5 |
f |
Volcano plot of age coefficients, pathways. |
humann.Rmd |
| ED5 |
g |
Example pathway that decreases with age. |
humann.Rmd |
| ED5 |
h |
Example of community-wide age-associated pathway. |
humann.Rmd |
| ED5 |
i |
Example of specialized age-associated pathway. |
humann.Rmd |
| ED5 |
j |
Example pathway that increases with age. |
humann.Rmd |
| ED5 |
k |
Functional uniqueness versus age. |
humann.Rmd |
| ED5 |
l |
Age prediction, all mice, genera. |
prediction.Rmd |
| ED5 |
m |
Age prediction, AL mice, species. |
prediction.Rmd |
| ED5 |
n |
Age prediction, AL mice, pathways. |
prediction.Rmd |
| ED5 |
o |
Most important pathways for age prediction. |
prediction.Rmd |
| ED6 |
a |
Percent pathways associated with age in DO AL, B6, and human datasets. |
compare_DO_to_B6_to_humans.Rmd |
| ED6 |
b |
Uniqueness across human studies. |
compare_DO_to_B6_to_humans.Rmd |
| ED6 |
c |
Blautia across human studies. |
compare_DO_to_B6_to_humans.Rmd |
| ED6 |
d |
ɑ-diversity across human studies. |
compare_DO_to_B6_to_humans.Rmd |
| ED6 |
e |
Correlation of pathway age coefficients across DO AL, B6, and human datasets. |
compare_DO_to_B6_to_humans.Rmd |
| ED6 |
f |
Flavin biosynthesis pathway across DO AL, B6, and human datasets. |
compare_DO_to_B6_to_humans.Rmd |
| ED6 |
g |
Correlations with genera for universal age-associated pathways. |
humann.Rmd |
| ED6 |
h |
Schematic of germ-free cohousing experiment. |
n/a |
| ED6 |
i |
PCoA of germ-free cohousing experiment. |
germfree_cohousing.Rmd |
| ED7 |
a |
Volcano plot of pathway heritability. |
humann.Rmd |
| ED7 |
b |
Correlations with genera for example heritable pathways. |
humann.Rmd |
| ED7 |
c |
Proportion heritable features, genera versus species. |
kraken.Rmd |
| ED7 |
d |
Kraken v. MPA, heritability. |
kraken_v_metaphlan.Rmd |
| ED7 |
e |
Heritability, ASReml versus lme4qtl. |
asreml_v_lme4qtl.Rmd |
| ED7 |
f |
Heritability, our study versus Schlamp 2021. |
compare_to_schlamp.Rmd |
| ED7 |
g |
Cross-sectional versus longitudinal heritability. |
asreml_longitudinal_v_cross_sectional_age.Rmd |
| ED7 |
h |
PVE for all experimental variables, pathways. |
humann.Rmd |
| ED7 |
i |
Allele effects for top 6 QTL. |
QTL.Rmd |
| ED8 |
a |
Barplots of DR coefficients, pathways. |
humann.Rmd |
| ED8 |
b |
L-lysine biosynthesis II increased by DR. |
humann.Rmd |
| ED8 |
c |
L-lysine biosynthesis II is a specialized pathway. |
humann.Rmd |
| ED8 |
d |
Urea cycle decreased by DR. |
humann.Rmd |
| ED8 |
e |
Urea cycle is a community-wide pathway. |
humann.Rmd |
| ED8 |
f |
Magnitude of DR coefficients, pathways. |
humann.Rmd |
| ED8 |
g |
Similarity of DR coefficiencts, pathways. |
humann.Rmd |
| ED8 |
h |
Pathways affected by CR or fasting exclusively. |
humann.Rmd |
| ED8 |
i |
Predicting DR status, pathways. |
prediction.Rmd |
| ED8 |
j |
Most important genera for binary DR prediction. |
prediction.Rmd |
| ED8 |
k |
Most important pathways for binary DR prediction. |
prediction.Rmd |
| ED8 |
l |
Predicting dietary group, pathways. |
prediction.Rmd |
| ED8 |
m |
Predicting dietary group, pathways, stratified by diet. |
prediction.Rmd |
| ED8 |
n |
Proportion DR-associated features, genera versus species. |
kraken.Rmd |
| ED8 |
o |
Kraken v. MPA, DR coefficients. |
kraken_v_metaphlan.Rmd |
| ED9 |
a |
Predicting age, trained on AL, pathways. |
prediction.Rmd |
| ED9 |
b |
Predicting age, trained on 40% CR. |
prediction.Rmd |
| ED9 |
c |
PCoA of just AL and 40% CR 10 and 28-month-old samples. |
kraken.Rmd |
| ED10 |
n/a |
Histogram of microbiome-phenotype assocation p-values. |
pheno_assoc_and_mediation.Rmd |
| ED10 |
n/a |
Histograms of microbiome-phenotype p-values. |
pheno_assoc_and_mediation.Rmd |