Longitudinal microbiome abundances from the PLEASE study
please_microbiome.RdA long-format data frame of genus-level relative abundances and
associated clinical covariates from the pediatric study of
Lewis et al. (2015). The analytic dataset was reconstructed from the
public chvlyl/PLEASE repository and processed following the
filtering and recoding conventions of the ZIBR package
(Chen and Li, 2016). Genus-level relative abundances were originally
quantified from shotgun metagenomic sequencing using MetaPhlAn 1.7.6
(Segata et al., 2012).
Format
A data frame with 3186 rows and 7 variables. Each row is one post-baseline observation of a genus in a subject, so the 18 genera contribute 177 rows each (3 visits \(\times\) 59 subjects).
- Genus
character. Genus name, e.g.
"g__Bacteroides".- Sample
character. Sample identifier.
- Subject
character. Subject identifier (e.g.
"S5001").- Time
numeric. Follow-up week:
1,4or8. The baseline (week 0) is stored inBaselineand does not appear here.- Treat
factor. Treatment arm with levels
"antiTNF"(reference) and"EEN"(exclusive enteral nutrition).- Baseline
numeric. Subject's relative abundance of the same genus at week 0, on its original proportion scale in \([0,1]\).
- Y
numeric. Relative abundance of the genus at the given post-baseline visit, in \([0,1]\). May contain zeros.
Source
PLEASE repository: https://github.com/chvlyl/PLEASE
Original study: Lewis, J. D., Chen, E. Z., Baldassano, R. N., et al. (2015). Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohn's disease. Cell Host & Microbe, 18(4), 489–500. doi:10.1016/j.chom.2015.09.008
Details
The dataset covers \(59\) subjects (\(47\) anti-TNF, \(12\) EEN) with observations at all four scheduled visits (baseline and weeks 1, 4 and 8) and \(18\) bacterial genera, for a total of \(236\) samples in the wide format used by Chen and Li (2016). The long format provided here contains the \(177\) post-baseline observations per genus, together with the baseline abundance replicated within subject and genus.
Processing followed the ZIBR workflow: samples with fewer than \(10{,}000\) non-human reads were removed; genera were retained if present in more than \(40\%\) of the remaining samples and if their \(90\)th percentile of relative abundance, computed including zeros, exceeded \(1\%\); and the abundances of the retained genera were renormalized to sum to one within each sample, so that each modeled abundance is relative to the retained genera rather than to the whole community. These steps preceded the restriction to the anti-TNF and EEN arms (the partial enteral nutrition arm was excluded) and the selection of subjects with observations at all four scheduled visits.
In the analysis reported in the companion paper, baseline abundance was used as a subject-level covariate on its original proportion scale, without centering or standardization, and both components of each two-part model included baseline abundance, week, and treatment. One genus, Bacteroides, had only three zeros among the post-baseline observations and was excluded from the Beta–Vasicek model comparison, leaving 17 genera; its observations are nonetheless retained here for completeness.
References
Chen, E. Z. and Li, H. (2016). A two-part mixed-effects model for analyzing longitudinal microbiome compositional data. Bioinformatics, 32(17), 2611–2617. doi:10.1093/bioinformatics/btw308
Segata, N., Waldron, L., Ballarini, A., et al. (2012). Metagenomic microbial community profiling using unique clade-specific marker genes. Nature Methods, 9(8), 811–814. doi:10.1038/nmeth.2066
Examples
data(please_microbiome)
head(please_microbiome)
#> Genus Sample Subject Time Treat Baseline Y
#> 5001-02 g__Bacteroides 5001-02 S5001 1 antiTNF 0.004514608 0.0023451675
#> 5001-03 g__Bacteroides 5001-03 S5001 4 antiTNF 0.004514608 0.0002086198
#> 5001-04 g__Bacteroides 5001-04 S5001 8 antiTNF 0.004514608 0.0000769457
#> 5002-02 g__Bacteroides 5002-02 S5002 1 antiTNF 0.732645555 0.5981502341
#> 5002-03 g__Bacteroides 5002-03 S5002 4 antiTNF 0.732645555 0.0698715533
#> 5002-04 g__Bacteroides 5002-04 S5002 8 antiTNF 0.732645555 0.0460852342
# Dimensions and structure
dim(please_microbiome) # 3186 x 7
#> [1] 3186 7
length(unique(please_microbiome$Genus)) # 18 genera
#> [1] 18
length(unique(please_microbiome$Subject)) # 59 subjects
#> [1] 59
table(please_microbiome$Treat) # 47 antiTNF, 12 EEN
#>
#> antiTNF EEN
#> 2538 648
# Balanced within genus: 177 rows each
table(please_microbiome$Genus)
#>
#> g__Alistipes g__Bacteroides g__Bifidobacterium g__Clostridium
#> 177 177 177 177
#> g__Collinsella g__Coprobacillus g__Dialister g__Dorea
#> 177 177 177 177
#> g__Escherichia g__Eubacterium g__Faecalibacterium g__Haemophilus
#> 177 177 177 177
#> g__Lactobacillus g__Parabacteroides g__Roseburia g__Ruminococcus
#> 177 177 177 177
#> g__Streptococcus g__Veillonella
#> 177 177