c-section_meconium_shaimaa.RmdNot evaluated in vignette:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(c("devtools", "tidyverse", "kableExtra"))
BiocManager::install(c("waldronlab/bugSigSimple", "waldronlab/BugSigDBStats", "waldronlab/bugsigdbr"))
suppressPackageStartupMessages({
library(bugSigSimple)
library(BugSigDBStats)
library(bugsigdbr)
library(tidyverse)
library(stringr)
library(kableExtra)
library(dplyr)
})
# use version="devel" and cache = FALSE to take the latest version from bugsigdb.org
dat <- bugsigdbr::importBugSigDB(version = "devel", cache = FALSE)
dim(dat)## [1] 7115 50
names(dat)## [1] "BSDB ID" "Study"
## [3] "Study design" "PMID"
## [5] "DOI" "URL"
## [7] "Authors list" "Title"
## [9] "Journal" "Year"
## [11] "Keywords" "Experiment"
## [13] "Location of subjects" "Host species"
## [15] "Body site" "UBERON ID"
## [17] "Condition" "EFO ID"
## [19] "Group 0 name" "Group 1 name"
## [21] "Group 1 definition" "Group 0 sample size"
## [23] "Group 1 sample size" "Antibiotics exclusion"
## [25] "Sequencing type" "16S variable region"
## [27] "Sequencing platform" "Statistical test"
## [29] "Significance threshold" "MHT correction"
## [31] "LDA Score above" "Matched on"
## [33] "Confounders controlled for" "Pielou"
## [35] "Shannon" "Chao1"
## [37] "Simpson" "Inverse Simpson"
## [39] "Richness" "Signature page name"
## [41] "Source" "Curated date"
## [43] "Curator" "Revision editor"
## [45] "Description" "Abundance in Group 1"
## [47] "MetaPhlAn taxon names" "NCBI Taxonomy IDs"
## [49] "State" "Reviewer"
included.pmid <-
c(
28018325,
24614698,
29207565,
29459704,
29538354,
32012716,
20566857,
28512451,
28112736,
27362264
)
subset.dat <-
filter(dat, PMID %in% included.pmid)
unique(subset.dat$`Group 0 name`)## [1] "vaginal delivery after 7 days of delivery"
## [2] "vaginal delivery after 3 months of delivery"
## [3] "vaginal delivery after 6 months of delivery"
## [4] "vaginal delivery"
## [5] ">/=33 weeks"
## [6] "vaginal delivery at day 3"
## [7] "vaginal delivery at day 5"
## [8] "vaginal delivery at day 28"
## [9] "vaginal delivery at day 150"
## [10] "vaginal delivery at day 365"
## [11] "full-term delivery >39 weeks at day 3"
## [12] "mecomium in vaginal delivery"
## [13] "mecomium in C-section delivery"
## [14] "Antimicrobials use during delivery (no)"
## [15] "Maternal consumption of probiotics (NO)"
## [16] "Furry pets at home (NO)"
## [17] "Maternal samples taken at delivery."
## [18] "Maternal samples taken at 6 weeks postpartum"
## [19] "vaginal delivery (Va)"
included.group0 <- "vaginal delivery"
unique(subset.dat$`Group 1 name`)## [1] "C-section delivery"
## [2] "C-section"
## [3] "infants <33 weeks gestational age"
## [4] "c-section"
## [5] "late preterm 34-36 weeks"
## [6] "overall time point infants samples of c-section"
## [7] "transitional stool"
## [8] "Antimicrobials use during delivery (yes)"
## [9] "Maternal consumption of probiotics (YES)"
## [10] "Furry pets at home (YES)"
## [11] "Neonatal samples taken at delivery"
## [12] "Infant samples taken at 6 weeks postpartum"
## [13] "C-section (Cesarean section)"
included.group1 <- "C-section"
subset.final <-
filter(subset.dat, `Group 0 name` %in% included.group0 & `Group 1 name` %in% included.group1) %>%
filter(`Body site` == "Meconium") %>%
arrange(PMID)Show key characteristics of the included signatures:
detach("package:dplyr", unload = TRUE)## Warning: 'dplyr' namespace cannot be unloaded:
## namespace 'dplyr' is imported by 'BiocFileCache', 'bugSigSimple', 'tidyr', 'dbplyr' so cannot be unloaded##
## Attaching package: 'dplyr'## The following object is masked from 'package:kableExtra':
##
## group_rows## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
select(subset.final, "PMID", "Source", "Group 0 name", "Group 1 name", "Abundance in Group 1")## PMID Source Group 0 name Group 1 name
## 1 24614698 Table S6 in File S1 vaginal delivery C-section
## 2 27362264 Figure 1 vaginal delivery C-section
## 3 28512451 <NA> vaginal delivery C-section
## 4 29459704 Figure 1 vaginal delivery C-section
## 5 29459704 Figure 1 vaginal delivery C-section
## 6 29538354 Table 3 vaginal delivery C-section
## 7 32012716 Figure 4 & text vaginal delivery C-section
## 8 32012716 Figure 4 & text vaginal delivery C-section
## Abundance in Group 1
## 1 increased
## 2 decreased
## 3 <NA>
## 4 increased
## 5 decreased
## 6 decreased
## 7 increased
## 8 decreasedAre any studies missing?
## numeric(0)## [1] 20566857 28018325 28112736 29207565## [1] 20566857 28018325 28112736 29207565These are the studies included in the review:
bugSigSimple::createStudyTable(subset.final)## # A tibble: 6 × 5
## Study Condition Cases Controls `Study Design`
## <chr> <chr> <dbl> <dbl> <chr>
## 1 Ardissone 2014 Cesarean section 33 19 cross-sectional observational,…
## 2 Martin 2016 Cesarean section 28 80 cross-sectional observational,…
## 3 Shi 2018 Cesarean section 10 8 cross-sectional observational,…
## 4 Tapiainen 2018 Cesarean section 40 172 cross-sectional observational,…
## 5 Wampach 2017 Cesarean section 6 4 time series / longitudinal obs…
## 6 Wong 2020 Cesarean section 43 62 prospective cohortThis table summarizes the results for the top n most
frequently identified taxa.
kable_styling(kbl(bugSigSimple::createTaxonTable(subset.final, n = 20)))## Warning: Expected 7 pieces. Additional pieces discarded in 1 rows [16].| Taxon Name | Taxonomic Level | total_signatures | increased_signatures | decreased_signatures | Binomial Test pval | kingdom | phylum | class | order | family | genus | species | n_signatures | metaphlan_name |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Staphylococcus | genus | 3 | 1 | 2 | 1.0 | Bacteria | Bacillota | Bacilli | Bacillales | Staphylococcaceae | Staphylococcus | NA | 3 | k__Bacteria|p__Bacillota|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus |
| Corynebacterium | genus | 2 | 1 | 1 | 1.0 | Bacteria | Actinomycetota | Actinomycetes | Mycobacteriales | Corynebacteriaceae | Corynebacterium | NA | 2 | k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Mycobacteriales|f__Corynebacteriaceae|g__Corynebacterium |
| Propionibacterium | genus | 2 | 1 | 1 | 1.0 | Bacteria | Actinomycetota | Actinomycetes | Propionibacteriales | Propionibacteriaceae | Propionibacterium | NA | 2 | k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium |
| Enterococcus | genus | 2 | 0 | 2 | 0.5 | Bacteria | Bacillota | Bacilli | Lactobacillales | Enterococcaceae | Enterococcus | NA | 2 | k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus |
| Streptococcus | genus | 2 | 1 | 1 | 1.0 | Bacteria | Bacillota | Bacilli | Lactobacillales | Streptococcaceae | Streptococcus | NA | 2 | k__Bacteria|p__Bacillota|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus |
| Phocaeicola vulgatus | species | 2 | 1 | 1 | 1.0 | Bacteria | Bacteroidota | Bacteroidia | Bacteroidales | Bacteroidaceae | Phocaeicola | Phocaeicola vulgatus | 2 | k__Bacteria|p__Bacteroidota|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Phocaeicola|s__Phocaeicola vulgatus |
| Comamonas | genus | 2 | 1 | 1 | 1.0 | Bacteria | Pseudomonadota | Betaproteobacteria | Burkholderiales | Comamonadaceae | Comamonas | NA | 2 | k__Bacteria|p__Pseudomonadota|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas |
| Citrobacter | genus | 2 | 1 | 1 | 1.0 | Bacteria | Pseudomonadota | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Citrobacter | NA | 2 | k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter |
| Stenotrophomonas | genus | 2 | 2 | 0 | 0.5 | Bacteria | Pseudomonadota | Gammaproteobacteria | Lysobacterales | Lysobacteraceae | Stenotrophomonas | NA | 2 | k__Bacteria|p__Pseudomonadota|c__Gammaproteobacteria|o__Lysobacterales|f__Lysobacteraceae|g__Stenotrophomonas |
| Actinomycetota | phylum | 1 | 0 | 1 | 1.0 | Bacteria | Actinomycetota | NA | NA | NA | NA | NA | 4 | k__Bacteria|p__Actinomycetota |
| Actinomycetes | class | 1 | 0 | 1 | 1.0 | Bacteria | Actinomycetota | Actinomycetes | NA | NA | NA | NA | 4 | k__Bacteria|p__Actinomycetota|c__Actinomycetes |
| Actinomycetales | order | 1 | 0 | 1 | 1.0 | Bacteria | Actinomycetota | Actinomycetes | Actinomycetales | NA | NA | NA | 1 | k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Actinomycetales |
| Bifidobacterium | genus | 1 | 0 | 1 | 1.0 | Bacteria | Actinomycetota | Actinomycetes | Bifidobacteriales | Bifidobacteriaceae | Bifidobacterium | NA | 2 | k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium |
| Bifidobacterium bifidum | species | 1 | 0 | 1 | 1.0 | Bacteria | Actinomycetota | Actinomycetes | Bifidobacteriales | Bifidobacteriaceae | Bifidobacterium | Bifidobacterium bifidum | 1 | k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium bifidum |
| Bifidobacterium catenulatum | species | 1 | 0 | 1 | 1.0 | Bacteria | Actinomycetota | Actinomycetes | Bifidobacteriales | Bifidobacteriaceae | Bifidobacterium | Bifidobacterium catenulatum | 1 | k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum |
| Bifidobacterium longum subsp. longum | species | 1 | 0 | 1 | 1.0 | Bacteria | Actinomycetota | Actinomycetes | Bifidobacteriales | Bifidobacteriaceae | Bifidobacterium | Bifidobacterium longum | 1 | k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum |
| Pseudoscardovia | genus | 1 | 1 | 0 | 1.0 | Bacteria | Actinomycetota | Actinomycetes | Bifidobacteriales | Bifidobacteriaceae | Pseudoscardovia | NA | 1 | k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Pseudoscardovia |
| Propionibacteriaceae | family | 1 | 0 | 1 | 1.0 | Bacteria | Actinomycetota | Actinomycetes | Propionibacteriales | Propionibacteriaceae | NA | NA | 2 | k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae |
| Cutibacterium acnes | species | 1 | 0 | 1 | 1.0 | Bacteria | Actinomycetota | Actinomycetes | Propionibacteriales | Propionibacteriaceae | Cutibacterium | Cutibacterium acnes | 1 | k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes |
| Pseudonocardiaceae | family | 1 | 0 | 1 | 1.0 | Bacteria | Actinomycetota | Actinomycetes | Pseudonocardiales | Pseudonocardiaceae | NA | NA | 1 | k__Bacteria|p__Actinomycetota|c__Actinomycetes|o__Pseudonocardiales|f__Pseudonocardiaceae |
These are not needed because of the taxon table above, but they list a larger number of taxa.
getMostFrequentTaxa(subset.final, n = 50)## 1279 1301 1350 1716 1743 283 40323 544 821 114248
## 3 2 2 2 2 2 2 2 2 1
## 117563 118964 1236 1239 1243 12916 1297 1298 1302778 135614
## 1 1 1 1 1 1 1 1 1 1
## 1357 1380 1385 1386 1390 1402 1485 1502 150247 1578
## 1 1 1 1 1 1 1 1 1 1
## 158851 1596 1598 1678 1679 1681 1686 1730 1747 1760
## 1 1 1 1 1 1 1 1 1 1
## 183710 186806 186817 188787 201174 2037 2070 216851 222 2737
## 1 1 1 1 1 1 1 1 1 1
getMostFrequentTaxa(subset.final, direction="UP")## 40323 114248 117563 118964 1239 1243 1279 12916 1297 1298
## 2 1 1 1 1 1 1 1 1 1
getMostFrequentTaxa(subset.final, direction="DOWN")## 1279 1350 1236 1301 1380 1485 1502 158851 1596 1598
## 2 2 1 1 1 1 1 1 1 1