Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life
Marie-Madlen Pust1,2, Burkhard Tümmler1,2
1Department of Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Germany
2Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Germany
Reference databases
The one-strain per species multi-FASTA file
# Download database
wget https://sync.academiccloud.de/index.php/s/h1it8NhwGSMaKGe/download
# Unzip the reference database
gunzip complete_bacterialRefSeqs_201910_3.fasta.gz
# Generate an index of the reference fasta depending on the alignment tool of your choice
samtools complete_bacterialRefSeqs_201910_3.fasta
bwa index complete_bacterialRefSeqs_201910_3.fastaThe pangenome multi-FASTA file
# Download database
wget https://sync.academiccloud.de/index.php/s/vOTDJ9qDR6tvn0w/download
# Unzip the reference database
gunzip 2020_09_reference.fa.gz
# Generate an index of the reference fasta depending on the alignment tool of your choice
samtools faidx 2020_09_reference.fa
bwa index 2020_09_reference.faThe adhesin protein sequence multi-FASTA file
# Download database
wget https://sync.academiccloud.de/index.php/s/YaL6NXMEavuZWkd/downloadR files with in-text comments
- step_1_bootstrapping_aggregations.R
- step_2_simulation_runs.R
- step_3_functional_analysis.R
R session, information
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
LC_COLLATE=German_Germany.1252
LC_CTYPE=German_Germany.1252
LC_MONETARY=German_Germany.1252
LC_NUMERIC=C
LC_TIME=German_Germany.1252
attached base packages:
grid, stats, graphics, grDevices, utils, datasets, methods, base
other attached packages:
[01] Boruta_7.0.0 ggVennDiagram_1.1.4 randomForest_4.6-14 RVAideMemoire_0.9-80 microbiome_1.14.0 phyloseq_1.36.0 data.table_1.14.0 graphkernels_1.6 CINNA_1.1.54
[10] NetSwan_0.1 igraph_1.2.6 expm_0.999-6 Matrix_1.3-4 tidygraph_1.2.0 sna_2.6 network_1.17.1 statnet.common_4.5.0 qgraph_1.6.9
[19] popgraph_1.5.2 cowplot_1.1.1 forcats_0.5.1 ggrepel_0.9.1 knitr_1.33 SimilarityMeasures_1.4 rcompanion_2.4.1 reshape2_1.4.4 scales_1.1.1
[28] magrittr_2.0.1 reshape_0.8.8 Hmisc_4.5-0 Formula_1.2-4 survival_3.2-11 gmodels_2.18.1 rstatix_0.7.0 viridis_0.6.1 viridisLite_0.4.0
[37] tidyr_1.1.3 ggdendro_0.1.22 RColorBrewer_1.1-2 pheatmap_1.0.12 stringr_1.4.0 factoextra_1.0.7 ggpubr_0.4.0 vegan_2.5-7 lattice_0.20-44
[46] permute_0.9-5 ggplot2_3.3.5 dplyr_1.0.7 purrr_0.3.4 plyr_1.8.6 readr_2.0.1
loaded via a namespace (and not attached):
[01] GGally_2.1.2 qdapTools_1.3.5 lavaan_0.6-9 coda_0.19-4 ragg_1.1.3 bit64_4.0.5 multcomp_1.4-17 rpart_4.1-15 RCurl_1.98-1.4
[10] generics_0.1.0 BiocGenerics_0.38.0 TH.data_1.0-10 proxy_0.4-26 chron_2.3-56 bit_4.0.4 tzdb_0.1.2 assertthat_0.2.1 xfun_0.25
[19] hms_1.1.0 fansi_0.5.0 dendextend_1.15.1 readxl_1.3.1 DBI_1.1.1 tmvnsim_1.0-2 htmlwidgets_1.5.3 stats4_4.1.1 ellipsis_0.3.2
[28] corrplot_0.90 backports_1.2.1 FactoMineR_2.4 pbivnorm_0.6.0 libcoin_1.0-8 vctrs_0.3.8 Biobase_2.52.0 abind_1.4-5 withr_2.4.2
[37] RVenn_1.1.0 checkmate_2.0.0 vroom_1.5.4 fdrtool_1.2.16 mnormt_2.0.2 cluster_2.1.2 ape_5.5 crayon_1.4.1 pkgconfig_2.0.3
[46] labeling_0.4.2 units_0.7-2 GenomeInfoDb_1.28.1 nlme_3.1-152 nnet_7.3-16 rlang_0.4.11 lifecycle_1.0.0 sandwich_3.0-1 cellranger_1.1.0
[55] matrixStats_0.60.0 lmtest_0.9-38 carData_3.0-4 Rhdf5lib_1.14.2 boot_1.3-28 zoo_1.8-9 base64enc_0.1-3 png_0.1-7 rootSolve_1.8.2.2
[64] bitops_1.0-7 KernSmooth_2.23-20 rhdf5filters_1.4.0 Biostrings_2.60.2 classInt_0.4-3 multcompView_0.1-8 coin_1.4-1 jpeg_0.1-9 S4Vectors_0.30.0
[73] ggsignif_0.6.2 leaps_3.1 lpSolve_5.6.15 gdata_2.18.0 zlibbioc_1.38.0 compiler_4.1.1 intergraph_2.0-2 cli_3.0.1 ade4_1.7-17
[82] XVector_0.32.0 pbapply_1.4-3 htmlTable_2.2.1 MASS_7.3-54 mgcv_1.8-36 tidyselect_1.1.1 stringi_1.7.3 textshaping_0.3.5 latticeExtra_0.6-29
[91] tools_4.1.1 lmom_2.8 parallel_4.1.1 rio_0.5.27 rstudioapi_0.13 foreach_1.5.1 foreign_0.8-81 gridExtra_2.3 gld_2.6.2
[100] scatterplot3d_0.3-41 farver_2.1.0 Rtsne_0.15 digest_0.6.27 nortest_1.0-4 Rcpp_1.0.7 car_3.0-11 broom_0.7.9 sf_1.0-2
[109] psych_2.1.6 colorspace_2.0-2 ranger_0.13.1 IRanges_2.26.0 splines_4.1.1 centiserve_1.0.0 sp_1.4-5 multtest_2.48.0 Exact_2.1
[118] systemfonts_1.0.2 jsonlite_1.7.2 corpcor_1.6.9 glasso_1.11 flashClust_1.01-2 modeltools_0.2-23 R6_2.5.1 pillar_1.6.2 htmltools_0.5.1.1
[127] glue_1.4.2 DT_0.18 class_7.3-19 codetools_0.2-18 mvtnorm_1.1-2 utf8_1.2.2 tibble_3.1.3 curl_4.3.2 DescTools_0.99.42
[136] gtools_3.9.2 zip_2.2.0 openxlsx_4.2.4 sampling_2.9 biomformat_1.20.0 munsell_0.5.0 e1071_1.7-8 rhdf5_2.36.0 GenomeInfoDbData_1.2.6
[145] iterators_1.0.13 haven_2.4.3 gtable_0.3.0