c-section_meconium_shaimaa.Rmd
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] 2242 48
names(dat)## [1] "Study" "Study design"
## [3] "PMID" "DOI"
## [5] "URL" "Authors list"
## [7] "Title" "Journal"
## [9] "Year" "Experiment"
## [11] "Location of subjects" "Host species"
## [13] "Body site" "UBERON ID"
## [15] "Condition" "EFO ID"
## [17] "Group 0 name" "Group 1 name"
## [19] "Group 1 definition" "Group 0 sample size"
## [21] "Group 1 sample size" "Antibiotics exclusion"
## [23] "Sequencing type" "16S variable region"
## [25] "Sequencing platform" "Statistical test"
## [27] "Significance threshold" "MHT correction"
## [29] "LDA Score above" "Matched on"
## [31] "Confounders controlled for" "Pielou"
## [33] "Shannon" "Chao1"
## [35] "Simpson" "Inverse Simpson"
## [37] "Richness" "Signature page name"
## [39] "Source" "Curated date"
## [41] "Curator" "Revision editor"
## [43] "Description" "Abundance in Group 1"
## [45] "MetaPhlAn taxon names" "NCBI Taxonomy IDs"
## [47] "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$`Group 0 name`)## [1] "vaginal delivery"
## [2] "vaginal delivery after 7 days of delivery"
## [3] "vaginal delivery after 3 months of delivery"
## [4] "vaginal delivery after 6 months of delivery"
## [5] ">/=33 weeks"
## [6] "vaginal delivery at day 3"
## [7] "vaginal delivery at day 5"
## [8] "vaginal delivery at day 28"
## [9] "vaginal delivery at day 150"
## [10] "vaginal delivery at day 365"
## [11] "full-term delivery >39 weeks at day 3"
## [12] "vaginal delivery in transitional stools"
## [13] "mecomium in vaginal delivery"
## [14] "mecomium in C-section delivery"
## [15] "no"
## [16] "without prenatal antibiotics usages"
## [17] "without peripartum antibiotics usages"
included.group0 <- "vaginal delivery"
unique(subset.dat$`Group 1 name`)## [1] "C-section"
## [2] "C-section delivery"
## [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] "infants delivered to mothers with"
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:
select(subset.final, all_of(c("PMID", "Source", "Group 0 name", "Group 1 name", "Abundance in Group 1")))## PMID Source Group 0 name Group 1 name
## 1 20566857 <NA> vaginal delivery C-section
## 2 24614698 Table S6 in File S1 vaginal delivery C-section
## 3 27362264 Figure 1 vaginal delivery C-section
## 4 28018325 Table 2 & Figure 2 vaginal delivery C-section
## 5 28112736 <NA> vaginal delivery C-section
## 6 28512451 <NA> vaginal delivery C-section
## 7 29207565 <NA> vaginal delivery C-section
## 8 29459704 Figure 1 vaginal delivery C-section
## 9 29459704 Figure 1 vaginal delivery C-section
## 10 29538354 Table 3 vaginal delivery C-section
## 11 32012716 Figure 4 & text vaginal delivery C-section
## 12 32012716 Figure 4 & text vaginal delivery C-section
## Abundance in Group 1
## 1 <NA>
## 2 increased
## 3 decreased
## 4 decreased
## 5 <NA>
## 6 <NA>
## 7 <NA>
## 8 increased
## 9 decreased
## 10 decreased
## 11 increased
## 12 decreasedAre any studies missing?
## numeric(0)## numeric(0)## numeric(0)These are the studies included in the review:
bugSigSimple::createStudyTable(subset.final)## # A tibble: 10 × 5
## Study Condition Cases Controls `Study Design`
## <chr> <chr> <dbl> <dbl> <chr>
## 1 Ardissone 2014 cesarean section 33 19 cross-sectional observational…
## 2 Bello 2010 cesarean section NA NA cross-sectional observational…
## 3 Chu 2017 cesarean section 52 105 prospective cohort
## 4 Martin 2016 cesarean section 28 80 cross-sectional observational…
## 5 Mueller 2017 cesarean section 46 13 cross-sectional observational…
## 6 Nagpal 2016 cesarean section 17 134 cross-sectional observational…
## 7 Shi 2018 cesarean section 10 8 cross-sectional observational…
## 8 Tapiainen 2018 cesarean section 40 172 cross-sectional observational…
## 9 Wampach 2017 cesarean section 6 4 time series / longitudinal ob…
## 10 Wong 2020 cesarean section 43 62 cross-sectional observational…This 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 | Firmicutes | Bacilli | Bacillales | Staphylococcaceae | Staphylococcus | NA | 3 | k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus |
| Corynebacterium | genus | 2 | 1 | 1 | 1.0 | Bacteria | Actinobacteria | Actinomycetia | Corynebacteriales | Corynebacteriaceae | Corynebacterium | NA | 2 | k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium |
| Propionibacterium | genus | 2 | 1 | 1 | 1.0 | Bacteria | Actinobacteria | Actinomycetia | Propionibacteriales | Propionibacteriaceae | Propionibacterium | NA | 2 | k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium |
| Phocaeicola vulgatus | species | 2 | 1 | 1 | 1.0 | Bacteria | Bacteroidetes | Bacteroidia | Bacteroidales | Phocaeicola | Phocaeicola vulgatus | NA | 2 | k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|g__Phocaeicola|s__Phocaeicola vulgatus |
| Enterococcus | genus | 2 | 0 | 2 | 0.5 | Bacteria | Firmicutes | Bacilli | Lactobacillales | Enterococcaceae | Enterococcus | NA | 2 | k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus |
| Lactobacillus | genus | 2 | 1 | 1 | 1.0 | Bacteria | Firmicutes | Bacilli | Lactobacillales | Lactobacillaceae | Lactobacillus | NA | 2 | k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus |
| Streptococcus | genus | 2 | 1 | 1 | 1.0 | Bacteria | Firmicutes | Bacilli | Lactobacillales | Streptococcaceae | Streptococcus | NA | 2 | k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus |
| Comamonas | genus | 2 | 1 | 1 | 1.0 | Bacteria | Proteobacteria | Betaproteobacteria | Burkholderiales | Comamonadaceae | Comamonas | NA | 2 | k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas |
| Citrobacter | genus | 2 | 1 | 1 | 1.0 | Bacteria | Proteobacteria | Gammaproteobacteria | Enterobacterales | Enterobacteriaceae | Citrobacter | NA | 2 | k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter |
| Stenotrophomonas | genus | 2 | 2 | 0 | 0.5 | Bacteria | Proteobacteria | Gammaproteobacteria | Xanthomonadales | Xanthomonadaceae | Stenotrophomonas | NA | 2 | k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas |
| Actinobacteria | phylum | 1 | 0 | 1 | 1.0 | Bacteria | Actinobacteria | NA | NA | NA | NA | NA | 4 | k__Bacteria|p__Actinobacteria |
| Actinomycetia | class | 1 | 0 | 1 | 1.0 | Bacteria | Actinobacteria | Actinomycetia | NA | NA | NA | NA | 4 | k__Bacteria|p__Actinobacteria|c__Actinomycetia |
| Actinomycetales | order | 1 | 0 | 1 | 1.0 | Bacteria | Actinobacteria | Actinomycetia | Actinomycetales | NA | NA | NA | 1 | k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales |
| Bifidobacterium | genus | 1 | 0 | 1 | 1.0 | Bacteria | Actinobacteria | Actinomycetia | Bifidobacteriales | Bifidobacteriaceae | Bifidobacterium | NA | 2 | k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium |
| Bifidobacterium catenulatum | species | 1 | 0 | 1 | 1.0 | Bacteria | Actinobacteria | Actinomycetia | Bifidobacteriales | Bifidobacteriaceae | Bifidobacterium | Bifidobacterium catenulatum | 1 | k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum |
| Bifidobacterium longum subsp. longum | species | 1 | 0 | 1 | 1.0 | Bacteria | Actinobacteria | Actinomycetia | Bifidobacteriales | Bifidobacteriaceae | Bifidobacterium | Bifidobacterium longum | 1 | k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum |
| Pseudoscardovia | genus | 1 | 1 | 0 | 1.0 | Bacteria | Actinobacteria | Actinomycetia | Bifidobacteriales | Bifidobacteriaceae | Pseudoscardovia | NA | 1 | k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Pseudoscardovia |
| Propionibacteriaceae | family | 1 | 0 | 1 | 1.0 | Bacteria | Actinobacteria | Actinomycetia | Propionibacteriales | Propionibacteriaceae | NA | NA | 2 | k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae |
| Cutibacterium acnes | species | 1 | 0 | 1 | 1.0 | Bacteria | Actinobacteria | Actinomycetia | Propionibacteriales | Propionibacteriaceae | Cutibacterium | Cutibacterium acnes | 1 | k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes |
| Pseudonocardiaceae | family | 1 | 0 | 1 | 1.0 | Bacteria | Actinobacteria | Actinomycetia | Pseudonocardiales | Pseudonocardiaceae | NA | NA | 1 | k__Bacteria|p__Actinobacteria|c__Actinomycetia|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)##
## k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus
## 3
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium
## 2
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium
## 2
## k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|g__Phocaeicola|s__Phocaeicola vulgatus
## 2
## k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus
## 2
## k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus
## 2
## k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus
## 2
## k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Comamonadaceae|g__Comamonas
## 2
## k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Citrobacter
## 2
## k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas
## 2
## k__Bacteria|p__Actinobacteria
## 1
## k__Bacteria|p__Actinobacteria|c__Actinomycetia
## 1
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales
## 1
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium
## 1
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum
## 1
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum
## 1
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Pseudoscardovia
## 1
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae
## 1
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium acnes
## 1
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Pseudonocardiales|f__Pseudonocardiaceae
## 1
## k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Atopobium
## 1
## k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides
## 1
## k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides caccae
## 1
## k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides fragilis
## 1
## k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides ovatus
## 1
## k__Bacteria|p__Bacteroidetes|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium
## 1
## k__Bacteria|p__Deinococcus-Thermus
## 1
## k__Bacteria|p__Deinococcus-Thermus|c__Deinococci
## 1
## k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Deinococcales
## 1
## k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae
## 1
## k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus
## 1
## k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Thermales|f__Thermaceae|g__Meiothermus
## 1
## k__Bacteria|p__Firmicutes
## 1
## k__Bacteria|p__Firmicutes|c__Bacilli
## 1
## k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales
## 1
## k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae
## 1
## k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Anoxybacillus
## 1
## k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus
## 1
## k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus amyloliquefaciens
## 1
## k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus licheniformis
## 1
## k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella
## 1
## k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Vagococcus
## 1
## k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus|s__Lactobacillus gasseri
## 1
## k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Leuconostoc
## 1
## k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Lactococcus
## 1
## k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium
## 1
## k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium|s__Clostridium perfringens
## 1
## k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae
## 1
## k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriaceae|g__Eubacterium
## 1
## k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Butyrivibrio
## 1
getMostFrequentTaxa(subset.final, sig.type = "increased")##
## k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Xanthomonadales|f__Xanthomonadaceae|g__Stenotrophomonas
## 2
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Pseudoscardovia
## 1
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium
## 1
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium
## 1
## k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|g__Phocaeicola|s__Phocaeicola vulgatus
## 1
## k__Bacteria|p__Bacteroidetes|c__Chitinophagia|o__Chitinophagales|f__Chitinophagaceae|g__Sediminibacterium
## 1
## k__Bacteria|p__Deinococcus-Thermus
## 1
## k__Bacteria|p__Deinococcus-Thermus|c__Deinococci
## 1
## k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Deinococcales
## 1
## k__Bacteria|p__Deinococcus-Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae
## 1
getMostFrequentTaxa(subset.final, sig.type = "decreased")##
## k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus
## 2
## k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus
## 2
## k__Bacteria|p__Actinobacteria
## 1
## k__Bacteria|p__Actinobacteria|c__Actinomycetia
## 1
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Actinomycetales
## 1
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium
## 1
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium catenulatum
## 1
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium longum|s__Bifidobacterium longum subsp. longum
## 1
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium
## 1
## k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae
## 1