diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..b4ec107 --- /dev/null +++ b/.gitignore @@ -0,0 +1,5 @@ +.project +.settings +.RData +omixerRpm_*.tar.gz +*.Rout diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..68a473c --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,6 @@ +# General guidelines: + +1. Add and document a test case (in test/runitModules.R) +2. Implement the function until the test suite has no errors or failures. Please use `make test` to run the test suite +3. Document the function +4. Commit the changes diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..6393b18 --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,9 @@ +Package: omixerRpm +Type: Package +Title: Metabolic module profiling of microbiome samples +Version: 0.2.1 +Date: 2018-11-07 +Author: Youssef Darzi +Maintainer: Youssef Darzi +Description: An R interface to the omixer-rpm for metabolic module profiling of microbiome samples +License: GNU General Public License v3.0. The bundled omixer-rpm.jar is licensed under an Academic Non-commercial Software License Agreement, https://github.com/raeslab/omixer-rpm/blob/master/LICENSE diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..831a471 --- /dev/null +++ b/Makefile @@ -0,0 +1,18 @@ +OMIXER_RPM_JAR=https://github.com/raeslab/omixer-rpm/releases/download/1.0/omixer-rpm-1.0.jar + +build: clean + R CMD build . + +devbuild: clean + wget -O inst/java/omixer-rpm.jar $(OMIXER_RPM_JAR) + R CMD build . + +clean: + rm -f omixerRpm_*.tar.gz TestMain.Rout + +install: build + sudo R CMD INSTALL --byte-compile omixerRpm_*.tar.gz + +testSuite: + R CMD BATCH test/TestMain.R + grep "^Number of" TestMain.Rout diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000..d75f824 --- /dev/null +++ b/NAMESPACE @@ -0,0 +1 @@ +exportPattern("^[[:alpha:]]+") diff --git a/R/ModuleDB.R b/R/ModuleDB.R new file mode 100644 index 0000000..3798caf --- /dev/null +++ b/R/ModuleDB.R @@ -0,0 +1,81 @@ +ModuleDB <- setClass( + # Set the name for the class + "ModuleDB", + + # Define the slots + slots = c( + directory = "character", + modules = "character", + hierarchy = "data.frame", + module.names = "data.frame", + hierarchy.file = "character", + module.names.file = "character" + ), + + # Set the default values for the slots. (optional) + prototype = list( + directory = ".", + modules = "module.list", + hierarchy.file = "hierarchy.tsv", + module.names.file = "module.names" + ), + + # Make a function that can test to see if the data is consistent. + # This is not called if you have an initialize function defined! + validity = function(object) { + # Could validate by checking files exist + return(TRUE) + } +) + +# create a method to get the name fo a given module +setGeneric(name="getNames", + def=function(theObject, x){ + standardGeneric("getNames") + } +) + +setMethod(f = "getNames", + signature = "ModuleDB", + definition = function(theObject, x) { + if(nrow(theObject@module.names) == 0) { + theObject@module.names <- read.table( + file.path(theObject@directory, theObject@module.names.file), + row.names=1, + sep="\t", + header=F, + as.is=T) + } + idx <- which(rownames(theObject@module.names) == x) + if(length(idx) > 0 ){ + return(theObject@module.names[idx,1]) + } + return(NA) + } +) + + +setGeneric(name="getHierarchy", + def=function(theObject, x, level){ + standardGeneric("getHierarchy") + } +) + +setMethod(f="getHierarchy", + signature="ModuleDB", + definition=function(theObject, x, level){ + if(nrow(theObject@hierarchy) == 0) { + theObject@hierarchy <- read.table( + file.path(theObject@directory, theObject@hierarchy.file), + row.names=1, + sep="\t", + header=F, + as.is=T) + } + idx <- which(rownames(theObject@hierarchy) == x) + if(length(idx) > 0 ){ + return(theObject@hierarchy[idx, level]) + } + return(NA) + } +) \ No newline at end of file diff --git a/R/Modules.R b/R/Modules.R new file mode 100644 index 0000000..e763097 --- /dev/null +++ b/R/Modules.R @@ -0,0 +1,29 @@ +Modules <- setClass( + # Set the name for the class + "Modules", + + # Define the slots + slots = c( + coverage = "data.frame", + abundance = "data.frame", + annotation = "data.frame" + ), + + # Set the default values for the slots. (optional) + prototype = list( + coverage = NULL, + abundance = NULL, + annotation = NULL + ), + + # Make a function that can test to see if the data is consistent. + # This is not called if you have an initialize function defined! + validity = function(object) { + if(!is.null(object@coverage) && !is.null(object@abundance)) { + if(!all(dim(object@coverage) == dim(object@abundance))){ + return("Abundance and Coverage matrices are not of equal length") + } + } + return(TRUE) + } +) \ No newline at end of file diff --git a/R/loadDefaultDB.R b/R/loadDefaultDB.R new file mode 100644 index 0000000..6cee38a --- /dev/null +++ b/R/loadDefaultDB.R @@ -0,0 +1,6 @@ +loadDefaultDB <- function() { + gmms.db.path <- system.file("extdata", package = "omixerRpm") + gmms.db <- ModuleDB(directory = gmms.db.path, modules = "GMMs.v1.07.txt") + print("Loaded GMMs.v1.07.txt") + gmms.db +} \ No newline at end of file diff --git a/R/rpm.R b/R/rpm.R new file mode 100644 index 0000000..de02663 --- /dev/null +++ b/R/rpm.R @@ -0,0 +1,65 @@ +# x is a dataframe or a valid file path +# Add the Description of modules as a data object +rpm <- function(x, minimum.coverage=-1, score.estimator="median", annotation = 1, module.db = NULL, threads = 1) { + # link to the GMMs executable and DB + rpm.exec <- system.file("java", "omixer-rpm.jar", package = "omixerRpm") + if(is.null(module.db)) { + module.db.path <- system.file("extdata", package = "omixerRpm") + module.db <- ModuleDB(directory = module.db.path, modules = "GMMs.v1.07.txt") + } + + # Prepare output directories + out.dir <- tempfile() + dir.create(out.dir) + + # Is x a file or a data.frame + if(!is.character(x)) { + # write samples for processing with the GMMs + in.dir <- tempfile() + dir.create(in.dir) + input <- file.path(in.dir, "input.tsv") + write.table(x, input, col.names=T, row.names=F, quote=F, sep="\t") + } else { + input <- x + } + + # Run the module mapping + command <- paste("java -jar", rpm.exec, + "-c" , minimum.coverage, + "-s", score.estimator, + "-d", file.path(module.db@directory, module.db@modules), + "-i", input, + "-o", out.dir, + "-a", annotation, + "-t", threads, + "-e", 2) + #cat(command) + # try-catch + system(command) + abundance <- read.table(file.path(out.dir, "modules.tsv"), sep="\t", header=TRUE) + coverage <- read.table(file.path(out.dir, "modules-coverage.tsv"), sep="\t", header=TRUE) + + annotation.df <- NULL + + if (annotation == 1){ + # ortohology only + abundance.colnames <- colnames(abundance) + annotation.df <- as.data.frame(abundance[, 1]) + abundance <- as.data.frame(abundance[, -c(1)]) + coverage <- as.data.frame(coverage[, -c(1)]) + colnames(annotation.df) <- abundance.colnames[1] + colnames(abundance) <- abundance.colnames[2:length(abundance.colnames)] + colnames(coverage) <- abundance.colnames[2:length(abundance.colnames)] + } else if (annotation == 2) { + # orthology and taxonomy + abundance.colnames <- colnames(abundance) + annotation.df <- as.data.frame(abundance[, c(1, 2)]) + abundance <- as.data.frame(abundance[, -c(1, 2)]) + coverage <- as.data.frame(coverage[, -c(1, 2)]) + colnames(annotation.df) <- abundance.colnames[1:2] + colnames(abundance) <- abundance.colnames[3:length(abundance.colnames)] + colnames(coverage) <- abundance.colnames[3:length(abundance.colnames)] + } + + Modules(abundance=abundance, coverage=coverage, annotation=annotation.df) +} \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 0000000..c1b524b --- /dev/null +++ b/README.md @@ -0,0 +1,14 @@ +# omixer-rpmR +An R interface to [omixer-rpm](https://github.com/raeslab/omixer-rpm), the tool for metabolic module profiling of microbiome samples + +#### Dependencies +R and Java8 + +#### Installation +Download the latest release from [the release page](https://github.com/omixer/omixer-rpmR/releases), then install as follows after replacing x.y.z by the correct version + +R CMD INSTALL omixeRpm_x.y.z.tar.gz + +#### License +GNU General Public License v3.0. +The bundled omixer-rpm.jar is licensed under an [Academic Non-commercial Software License Agreement](https://github.com/raeslab/omixer-rpm/blob/master/LICENSE) diff --git a/inst/extdata/GMMs.v1.07.txt b/inst/extdata/GMMs.v1.07.txt new file mode 100644 index 0000000..ce3fcd1 --- /dev/null +++ b/inst/extdata/GMMs.v1.07.txt @@ -0,0 +1,476 @@ +MF0001 arabinoxylan degradation +K01209 K15921 K01181 K01198 K15531 K18205 +/// +MF0002 fructan degradation +K03332 K01193 +/// +MF0003 pectin degradation I +K01051 +K01184,K01213 K18650 +/// +MF0004 pectine degradation II +K01051 +K18650 +K01728 K19551 K01731 +K01730 +K01815 +K00874 +K01625 K17463 +/// +MF0005 starch degradation +K01176 K07405 K05343 +K01200 K01208 +K00688 K16153 K00705 K01187 K15922 K01178 K01182 +/// +MF0006 lactose degradation +K12111 K01190 K12308 +/// +MF0007 lactose and galactose degradation +K02786,K02787,K02788 +K01220 +K01819 +K00917 +K08302 K01635 +/// +MF0008 maltose degradation +K00691 +K01838 +/// +MF0009 melibiose degradation +K07406 K07407 +/// +MF0010 sucrose degradation I +K01193 +K00847 +/// +MF0011 sucrose degradation II +K00690 +K00847 +K01792 +K01835 K15778,K15779 +/// +MF0012 trehalose degradation +K03731 K01226 K01194 K05342 +/// +MF0013 allose degradation +K00881 +K01807,K01808 +/// +MF0014 arabinose degradation +K01804 +K00853 +/// +MF0015 fructose degradation +K00882 +/// +MF0016 fucose degradation +K02431 +K01818 +K00879 +K01628 +K01803 +/// +MF0017 galactose degradation +K01785 +K00849 +K00965 +K01784 K17716 +K01838 +/// +MF0018 mannose degradation +K01809 K15916 K16011 +/// +MF0019 rhamnose degradation +K03534 +K01813 K01820 +K00848 +K01629 +K01803 +/// +MF0020 ribose degradation +K06726 +K00852 +/// +MF0021 xylose degradation +K01805 +K00854 +/// +MF0022 galacturonate degradation I +K01812 +K00041 +K01685 K16849,K16850 +K00874 +K17463 K01625 K11395 +/// +MF0023 galacturonate degradation II +K18981 +K01707 +K13877 K19588 +/// +MF0024 phenylalanine degradation +K00832 K00812 K00813 K11358 K00817 +K04103 +K00146 K00129 +/// +MF0025 tryptophan degradation +K01667 +/// +MF0026 tyrosine degradation I +K00832 K00812 K00813 K11358 K00817 +K00129 K00055 +/// +MF0027 tyrosine degradation II +K01668 +/// +MF0028 aspartate degradation I +K00812 K00813 K11358 +/// +MF0029 aspartate degradation II +K01744 +/// +MF0030 glutamate degradation I +K00260 K15371 K00261 +K00109 +K01039,K01040 +K01615 +/// +MF0031 glutamate degradation II +K01580 +/// +MF0032 glutamate degradation III +K01846,K19268 +K04835 +/// +MF0033 alanine degradation I +K01775 +K00285 +/// +MF0034 alanine degradation II +K00814 K00259 K19244 +/// +MF0035 glycine degradation +K00281 K00282,K00283 +K00605 +K00382 +/// +MF0036 isoleucine degradation +K00826 +K00166,K00167,K09699,K00382 K11381,K09699,K00382 +K00248 K00249 K09478 K11410 +K01692 K01782 K01825 +K01782 K01825 K07547,K07548 K12405 K15016 +K00626 K00632 K07508 +/// +MF0037 leucine degradation +K00826 +K00166,K00167,K09699,K00382 K11381,K09699,K00382 +K00249 K00253 +K01968,K01969 +K13766 +K01640 +/// +MF0038 methionine degradation I +K00789 +K00558 K19398 K17399 +K01251 +/// +MF0039 methionine degradation II +K01761 +/// +MF0040 proline degradation +K00318,K00294 K13821 +/// +MF0041 valine degradation I +K00826 +K00166,K00167,K09699,K00382 K11381,K09699,K00382 +K00249 K00248 K09478 K11410 +K01692 K01715 K01782 K01825 K13767 K15016 +K05605 +K00020 K01782 K01825 K07547,K07548 K12405 K15016 +K00140,K00822 K00140,K13524 K00140,K07250 +/// +MF0042 asparagine degradation +K05597 +/// +MF0043 cysteine biosynthesis/homocysteine degradation +K01697 K10150 +K01758 +/// +MF0044 cysteine degradation I +K01758 K01760 K14155 +/// +MF0045 cysteine degradation II +K00812 K00813 K11358 +K01011 +/// +MF0046 glutamine degradation I +K01425 +/// +MF0047 glutamine degradation II +K00265,K00266 +/// +MF0048 serine degradation +K01752 K01753 +/// +MF0049 threonine degradation I +K01754 K17989 +K00656 +/// +MF0050 threonine degradation II +K00060,K00639 K01620,K00132 K01620,K04072 K01620,K04073 K01620,K18366 +/// +MF0051 arginine degradation I +K01583 K01584 K01585 K02626 K01476,K01581 +K10536,K12251 K01480 K01476,K01581 +/// +MF0052 arginine degradation II +K00673 +K01484 +K00840 +K06447 +K05526 +/// +MF0053 arginine degradation III +K12252 +K12253 +K12254 +K12255 +/// +MF0054 arginine degradation IV +K01476 +K00819,K00294 K00819,K13821 K00819,K00286 K01750 +/// +MF0055 arginine degradation V +K01478 +K00611 +K00926 +/// +MF0056 histidine degradation +K01745 +K01712 +K01468 +K01479 K05603,K01458 +/// +MF0057 lysine degradation I +K01843 +K01844,K18011 +K18012 +K00248 +K18014 +K01036 K01034,K01035 +/// +MF0058 lysine degradation II +K01582 +/// +MF0059 anaerobic fatty acid beta-oxidation +K06076 +K12507 +K06445 +K01782 +/// +MF0060 glycerol degradation I +K00005 +K00863 +K01803 +/// +MF0061 glycerol degradation II +K00864 +K00111,K00112,K00113 +K01803 +/// +MF0062 glycerol degradation III +K06120,K06121,K06122 +K00086 +/// +MF0063 glyoxylate bypass +K01647 +K01681 K01682 +K01637 +K01638 +K00024 +/// +MF0064 triacylglycerol degradation +K01046 +K01054 +/// +MF0065 Bifidobacterium shunt +K01621 K01632 +K00616 K13810 +K00615 +K01807 K01808 +K01783 +K01621 +/// +MF0066 Entner-Doudoroff pathway +K00036 +K01057 K07404 +K01690 +K01625 +/// +MF0067 glycolysis (preparatory phase) +K00844 K00845 +K01810 K06859 K13810 K15916 +K00850 K16370 +K01622 K01623 K01624 K11645 K16305 K16306 +K01803 +/// +MF0068 glycolysis (pay-off phase) +K00134 K00150 +K00927 +K01834 +K01689 +K00873 +/// +MF0069 NADH:ferredoxin oxidoreductase +K00529 K15758 K15765 K18088 K18090 K18227 K18254 K18293 +/// +MF0070 pentose phosphate pathway (oxidative phase) +K00036 K19243 +K01057 K07404 +K00033 +/// +MF0071 pentose phosphate pathway (non-oxidative branch) +K01807 K01808 +K01783 +K00615 +K00616 K13810 +/// +MF0072 pyruvate dehydrogenase complex +K00161,K00162,K00163 +K00382 +K00627 +/// +MF0073 pyruvate:ferredoxin oxidoreductase +K00169,K00170,K00171,K00172 K03737 +/// +MF0074 pyruvate:formate lyase +K00656 +/// +MF0075 acetate to acetyl-CoA +K01895 K01905 +/// +MF0076 4-aminobutyrate degradation +K00823 K07250 K13524 K14268 +K00043,K14534 K08318,K14534 K18120,K14534 K00135 K08324 +/// +MF0077 formate conversion +K00122 K00123,K00125,K00126 +/// +MF0078 lactaldehyde degradation +K00048 +/// +MF0079 lactate consumption I +K00101 K00102 +/// +MF0080 lactate consumption II +K01026 +K00249 +/// +MF0081 methanol conversion +K04480 +K14080,K14081 +/// +MF0082 putrescine degradation +K09251 K12256 K03343 +K00137 +/// +MF0083 succinate consumption +K18118 +K15017 K15038 K18119 +K00043 K08318 K18120 +K18122 +K14534 +/// +MF0084 succinate conversion to propionate +K11264 +/// +MF0085 urea degradation +K01941,K01457 K01428,K01429,K01430,K14048 K01427 +/// +MF0086 acetyl-CoA to acetate +K00625,K00925 K13788,K00925 K15024,K00925 K01905 K01067 K18118 +/// +MF0087 acetyl-CoA to crotonyl-CoA +K00626 +K00023 K01782 K01825 K07516 K07547,K07548 K12405 K15016 +K01715 K01692 K01782 K01825 K13767 K15016 +/// +MF0088 butyrate production I +K00248 +K00634 +K00929 +/// +MF0089 butyrate production II +K00248 +K01034,K01035 K19709 +/// +MF0090 ethanol production I +K00656 +K00132 K04072 K04073 K18366 +K00001 K00121 K04072 K11440 K13953 K13954 +/// +MF0091 ethanol production II +K01568 +K00001 K00121 K04072 K11440 K13953 K13954 +/// +MF0092 lactate production +K00016 K03777 K03778 +/// +MF0093 propionate production I +K13923 +K00932 +/// +MF0094 propionate production II +K01026 +/// +MF0095 propionate production III +K01847 K01849,K01848 K11942 +K05606 +K03416,K17489,K17490 +/// +MF0096 succinate production +K01596,K01595 +K00024 +K01676 K01677,K01678 K01679 +K00239,K00240,K00241,K00242 +/// +MF0097 homoacetogenesis +K05299,K15022 +K01938 +K01491 +K00297 +K15023 +K00198 +K14138,K00197,K00194 +/// +MF0098 hydrogen metabolism +K00532 K00533,K00534,K06441 K18016,K18017,K18023 K00436,K18005,K18006,K18007 +/// +MF0099 methanogenesis - methyl-coM +K00399,K00401,K00402 +/// +MF0100 methanogenesis from carbon dioxide +K00200,K00201,K00202,K00203,K11261 +K00204 K00205 K11260 +K00672 +K01499 +K00319 K13942 +K00320 +K00577,K00578,K00579,K00580,K00581,K00582,K00583,K00584 +/// +MF0101 nitrate reduction (dissimilatory) +K03385 +/// +MF0102 sulfate reduction (dissimilatory) +K13811 K00958 K00955 K00957,K00956 +K00394,K00395 +K11180,K11181 +/// +MF0103 mucin degradation +K01186 +K05970 +K01132 K01135 K01137 K01205 +K01207 K12373 K14459 +K01205 K01207 K12373 K01227 K13714 +K01206 +/// diff --git a/inst/extdata/module.names b/inst/extdata/module.names new file mode 100644 index 0000000..16a9ee7 --- /dev/null +++ b/inst/extdata/module.names @@ -0,0 +1,103 @@ +MF0001 arabinoxylan degradation +MF0002 fructan degradation +MF0003 pectin degradation I +MF0004 pectine degradation II +MF0005 starch degradation +MF0006 lactose degradation +MF0007 lactose and galactose degradation +MF0008 maltose degradation +MF0009 melibiose degradation +MF0010 sucrose degradation I +MF0011 sucrose degradation II +MF0012 trehalose degradation +MF0013 allose degradation +MF0014 arabinose degradation +MF0015 fructose degradation +MF0016 fucose degradation +MF0017 galactose degradation +MF0018 mannose degradation +MF0019 rhamnose degradation +MF0020 ribose degradation +MF0021 xylose degradation +MF0022 galacturonate degradation I +MF0023 galacturonate degradation II +MF0024 phenylalanine degradation +MF0025 tryptophan degradation +MF0026 tyrosine degradation I +MF0027 tyrosine degradation II +MF0028 aspartate degradation I +MF0029 aspartate degradation II +MF0030 glutamate degradation I +MF0031 glutamate degradation II +MF0032 glutamate degradation III +MF0033 alanine degradation I +MF0034 alanine degradation II +MF0035 glycine degradation +MF0036 isoleucine degradation +MF0037 leucine degradation +MF0038 methionine degradation I +MF0039 methionine degradation II +MF0040 proline degradation +MF0041 valine degradation I +MF0042 asparagine degradation +MF0043 cysteine biosynthesis/homocysteine degradation +MF0044 cysteine degradation I +MF0045 cysteine degradation II +MF0046 glutamine degradation I +MF0047 glutamine degradation II +MF0048 serine degradation +MF0049 threonine degradation I +MF0050 threonine degradation II +MF0051 arginine degradation I +MF0052 arginine degradation II +MF0053 arginine degradation III +MF0054 arginine degradation IV +MF0055 arginine degradation V +MF0056 histidine degradation +MF0057 lysine degradation I +MF0058 lysine degradation II +MF0059 anaerobic fatty acid beta-oxidation +MF0060 glycerol degradation I +MF0061 glycerol degradation II +MF0062 glycerol degradation III +MF0063 glyoxylate bypass +MF0064 triacylglycerol degradation +MF0065 Bifidobacterium shunt +MF0066 Entner-Doudoroff pathway +MF0067 glycolysis (preparatory phase) +MF0068 glycolysis (pay-off phase) +MF0069 NADH:ferredoxin oxidoreductase +MF0070 pentose phosphate pathway (oxidative phase) +MF0071 pentose phosphate pathway (non-oxidative branch) +MF0072 pyruvate dehydrogenase complex +MF0073 pyruvate:ferredoxin oxidoreductase +MF0074 pyruvate:formate lyase +MF0075 acetate to acetyl-CoA +MF0076 4-aminobutyrate degradation +MF0077 formate conversion +MF0078 lactaldehyde degradation +MF0079 lactate consumption I +MF0080 lactate consumption II +MF0081 methanol conversion +MF0082 putrescine degradation +MF0083 succinate consumption +MF0084 succinate conversion to propionate +MF0085 urea degradation +MF0086 acetyl-CoA to acetate +MF0087 acetyl-CoA to crotonyl-CoA +MF0088 butyrate production I +MF0089 butyrate production II +MF0090 ethanol production I +MF0091 ethanol production II +MF0092 lactate production +MF0093 propionate production I +MF0094 propionate production II +MF0095 propionate production III +MF0096 succinate production +MF0097 homoacetogenesis +MF0098 hydrogen metabolism +MF0099 methanogenesis - methyl-coM +MF0100 methanogenesis from carbon dioxide +MF0101 nitrate reduction (dissimilatory) +MF0102 sulfate reduction (dissimilatory) +MF0103 mucin degradation diff --git a/inst/java/.gitignore b/inst/java/.gitignore new file mode 100644 index 0000000..bcd3a5f --- /dev/null +++ b/inst/java/.gitignore @@ -0,0 +1 @@ +/omixer-rpm.jar diff --git a/man/ModuleDB.Rd b/man/ModuleDB.Rd new file mode 100644 index 0000000..c42b87f --- /dev/null +++ b/man/ModuleDB.Rd @@ -0,0 +1,70 @@ +\name{ModuleDB} +\alias{ModuleDB} +%- Also NEED an '\alias' for EACH other topic documented here. +\title{ +%% ~~function to do ... ~~ +Module database locator. +} +\description{ +%% ~~ A concise (1-5 lines) description of what the function does. ~~ +A simple object to locate the files of a module database. +} +\usage{ +ModuleDB(directory, modules, hierarchy.file, module.names.file) +} +%- maybe also 'usage' for other objects documented here. +\arguments{ + \item{directory}{ +The path to the directory containing all the module database files +} + \item{modules}{ +The name of the module definition file in the database. Defaults to modules.list. +The file should follow the KEGG format for module definition +} + \item{hierarchy.file}{ +The name of the module hierarchy definition file in the database. Defaults to hierarchy.tsv +} + \item{module.names.file}{ +The name of the module names file in the database. Defaults to modules.names +} +} +\details{ +%% ~~ If necessary, more details than the description above ~~ +} +\value{ +%% ~Describe the value returned +%% If it is a LIST, use +%% \item{comp1 }{Description of 'comp1'} +%% \item{comp2 }{Description of 'comp2'} +%% ... +} +\references{ +%% ~put references to the literature/web site here ~ +} +\author{ +%% ~~who you are~~ +Youssef Darzi +} +\note{ +%% ~~further notes~~ +} + +%% ~Make other sections like Warning with \section{Warning }{....} ~ + +\seealso{ +%% ~~objects to See Also as \code{\link{help}}, ~~~ +} +\examples{ +##---- Should be DIRECTLY executable !! ---- +##-- ==> Define data, use random, +##-- or do help(data=index) for the standard data sets. + +## The function is currently defined as +function (x, minimum.coverage = -1) +{ + } +} +% Add one or more standard keywords, see file 'KEYWORDS' in the +% R documentation directory. +\keyword{ ~kwd1 }% use one of RShowDoc("KEYWORDS") +\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line diff --git a/man/omixeRpm.Rd b/man/omixeRpm.Rd new file mode 100644 index 0000000..1338c25 --- /dev/null +++ b/man/omixeRpm.Rd @@ -0,0 +1,43 @@ +\name{omixerRpm-package} +\alias{omixerRpm-package} +\alias{omixerRpm} +\docType{package} +\title{ +\packageTitle{omixerRpm} +} +\description{ +\packageDescription{omixerRpm} +} +\details{ + +The DESCRIPTION file: +\packageDESCRIPTION{omixerRpm} +\packageIndices{omixerRpm} +~~ An overview of how to use the package, including the most important ~~ +~~ functions ~~ + +} +\author{ +\packageAuthor{omixerRpm} + +Maintainer: \packageMaintainer{omixerRpm} +} +\references{ +~~ Literature or other references for background information ~~ +omixerRpm was developed as part of GOmixer. If you use omixerRpm in your work please cite: + +Darzi, et al. Towards biome-specific analysis of meta-omics data, The ISME journal, 2015. http://www.nature.com/articles/ismej2015188 + +In case you use the bundled GMMs database, please also cite Vieira-Silva, et al. Species-function relationships shape ecological properties +of the human gut microbiome, Nature Microbiology, 2016 .http://www.nature.com/articles/nmicrobiol201688 + +} +\keyword{ package , microbiome, gut, metagenomics, metabolic pathways } +\seealso{ +~~ Optional links to other man pages, e.g. ~~ +~~ \code{\link[:-package]{}} ~~ +} +\examples{ +~~ simple examples of the most important functions ~~ +rpm() +} diff --git a/man/rpm.Rd b/man/rpm.Rd new file mode 100644 index 0000000..df01e12 --- /dev/null +++ b/man/rpm.Rd @@ -0,0 +1,81 @@ +\name{rpm} +\alias{rpm} +%- Also NEED an '\alias' for EACH other topic documented here. +\title{ +%% ~~function to do ... ~~ +Metabolic module profiling for gut microbiome samples +} +\description{ +%% ~~ A concise (1-5 lines) description of what the function does. ~~ +Generates metabolic module profiles from metagenomic samples. +} +\usage{ +rpm(x, minimum.coverage = -1, score.estimator = "median", + annotation = 1, module.db = NULL, threads = 1) +} +%- maybe also 'usage' for other objects documented here. +\arguments{ + \item{x}{ +A data.frame or a file path containing functional profiles with KEGG KO annotation. Taxonomic annotation could be included as well. +See annotation for more info on the formating +} + \item{minimum.coverage}{ +The minimum pathway coverage to consider a module present. +If set to -1 the threshold is guessed from the data. Otherwise the value should be between 0 and 1 [0, 1]. +By default it is set to -1. +} + \item{score.estimator}{ +One of median or mean to estimate the abundance of the module. Default is median. +} + \item{annotation}{ +Data annotation. Use 1 for taxonomic followed by KO annotation or 2 for KO annotation only +} + \item{module.db}{ +A ModuleDB object to locate the database files. If omitted the GMMS database from Vieira-Silva, et al 2016 Nat Microbiol (doi:10.1038/nmicrobiol.2016.88) +will be used by default. +} + \item{threads}{ +The number of threads to use when mapping KOs onto modules. If > 1, each different thread will handle one sample at a time, therefore the number +of threads should never be larger than the number of samples. +} +} +\details{ +%% ~~ If necessary, more details than the description above ~~ +} +\value{ +%% ~Describe the value returned +%% If it is a LIST, use +%% \item{comp1 }{Description of 'comp1'} +%% \item{comp2 }{Description of 'comp2'} +%% ... +} +\references{ +%% ~put references to the literature/web site here ~ +} +\author{ +%% ~~who you are~~ +Youssef Darzi +} +\note{ +%% ~~further notes~~ +} + +%% ~Make other sections like Warning with \section{Warning }{....} ~ + +\seealso{ +%% ~~objects to See Also as \code{\link{help}}, ~~~ +} +\examples{ +##---- Should be DIRECTLY executable !! ---- +##-- ==> Define data, use random, +##-- or do help(data=index) for the standard data sets. + +## The function is currently defined as +function (x, minimum.coverage = -1) +{ + } +} +% Add one or more standard keywords, see file 'KEYWORDS' in the +% R documentation directory. +\keyword{ ~kwd1 }% use one of RShowDoc("KEYWORDS") +\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line diff --git a/test/TestMain.R b/test/TestMain.R new file mode 100644 index 0000000..9100273 --- /dev/null +++ b/test/TestMain.R @@ -0,0 +1,3 @@ +library(RUnit) + +runTestFile("test/runitModules.R") diff --git a/test/matrix.tsv b/test/matrix.tsv new file mode 100644 index 0000000..bfadf7f --- /dev/null +++ b/test/matrix.tsv @@ -0,0 +1,4434 @@ +entry S1 S2 +K00001 47.1621546 329.9536215 +K00002 335.8490566 0 +K00003 277.0562771 0 +K00004 9.492025322 18.15543054 +K00005 265.6565657 10.06828354 +K00006 238.3966245 6.329113924 +K00007 88.36175207 76.37876657 +K00008 235.8309318 7.684918348 +K00009 250.3987241 7.974481659 +K00010 275.0316857 5.069708492 +K00011 219.343696 3.454231434 +K00012 249.2211838 4.672897196 +K00013 16.18413257 247.3674777 +K00014 266.2260517 11.81125068 +K00015 263.5253054 13.96160558 +K00016 313.6427567 5.625879044 +K00018 278.8550323 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37.92956106 +K18120 9.803921569 18.89788503 +K18122 24.10661234 258.3612072 +K18130 520.418356 87.19666255 +K18131 589.766584 218.4920304 +K18136 308.702328 38.35256697 +K18138 22.41106316 175.1412592 +K18139 58.91157538 61.77846835 +K18140 55.07246377 89.85507246 +K18141 355.4604943 131.9022638 +K18142 2.252252252 27.83693443 +K18143 857.7494692 336.455992 +K18144 224.9242024 290.3048826 +K18146 113.6468842 75.17831902 +K18148 38.28186688 75.42590033 +K18149 518.4817148 82.10350473 +K18153 661.6809529 110.1720839 +K18155 548.5461703 79.26947181 +K18158 153.0385854 89.58393607 +K18168 3.750011734 28.67662435 +K18170 0 2.544529262 +K18171 415.0110375 65.87519518 +K18172 24.37503888 45.04476817 +K18173 382.8096786 4.333694475 +K18176 357.8947368 10.52631579 +K18178 23.80952381 71.39775623 +K18179 277.0917108 73.71764757 +K18181 8.18119079 134.1011042 +K18182 36.58622301 60.67187151 +K18183 8.015649037 15.27973111 +K18184 0 7.653457654 +K18185 531.3473149 86.88823998 +K18187 15.71540988 108.276274 +K18188 45.667299 15.26508276 +K18191 12.95005982 25.83979328 +K18192 19.59016197 33.30453087 +K18203 81.37849751 85.93880052 +K18204 1138.465037 273.3795427 +K18205 546.1309524 386.9047619 +K18206 5.221932115 58.86695478 +K18209 90.49861795 80.93318555 +K18210 314.147025 147.5143001 +K18214 427.7870654 430.6555266 +K18216 0 90.8113392 +K18217 875.3301855 270.8763904 +K18218 263.3318891 183.1257631 +K18220 106.5661199 41.89801729 +K18221 1501.4862 222.0022098 +K18230 78.00529801 315.9526701 +K18231 33.88172527 663.1128313 +K18232 367.5276996 331.2565532 +K18234 351.4496593 243.2815496 +K18235 555.9983981 246.7483979 +K18236 359.3158776 299.1825247 +K18238 8.385744235 97.44446634 +K18240 40.35549103 322.735308 +K18277 737.2167445 274.6869949 \ No newline at end of file diff --git a/test/runitModules.R b/test/runitModules.R new file mode 100644 index 0000000..7b1a17b --- /dev/null +++ b/test/runitModules.R @@ -0,0 +1,27 @@ +library(omixerRpm) + +# Ensures correct number of modules and samples is returned +test.moduleMapping <- function (){ + # Test for data.frame, KO only annotation + dat <- read.table("test/matrix.tsv", header=T, sep="\t") + mods <- rpm(dat, minimum.coverage=0.3, annotation = 1) + checkEquals(nrow(mods@coverage), 96) + checkEquals(nrow(mods@abundance), 96) + checkEquals(ncol(mods@abundance), 2) + db <- loadDefaultDB() + # Test annotation is properly set + checkEquals(getNames(db, mods@annotation[1,]), "glyoxylate bypass") + + # Test for an input file with KO, taxonomic annotation + taxon.mods <- rpm("test/species_matrix.tsv", annotation = 2, minimum.coverage=0.3) + checkEquals(nrow(taxon.mods@coverage), 284) + checkEquals(ncol(taxon.mods@coverage), 2) +} + +# See code comments +test.moduleDbAnnotation <- function() { + # Setup the module database. This is an alternative to loadDefaultDB() + db <- ModuleDB(directory = "./inst/extdata", modules = "GMMs.v1.07.txt") + # check getNames returns the correct annotation + checkEquals(getNames(db, "MF0010"), "sucrose degradation I") +} \ No newline at end of file diff --git a/test/species_matrix.tsv b/test/species_matrix.tsv new file mode 100644 index 0000000..2876801 --- /dev/null +++ b/test/species_matrix.tsv @@ -0,0 +1,1677 @@ +species KO s06a s06b +Aeromonas hydrophila K04077 2.95 0.0 +Aeromonas hydrophila K03695 10.1 6.15 +Akkermansia muciniphila K02112 8.5 5.1499999999999995 +Akkermansia muciniphila K03737 0.0 3.1 +Akkermansia muciniphila K03695 9.0 7.199999999999999 +Akkermansia muciniphila K03046 8.95 1.0 +Akkermansia muciniphila K02358 4.550000000000001 4.1 +Akkermansia muciniphila K04077 3.2 1.05 +Akkermansia muciniphila 24.2 27.2 +Akkermansia muciniphila K00262 3.3 6.65 +Alistipes putredinis K02355 5.6 4.6 +Alistipes putredinis K01006 0.0 3.1 +Alistipes putredinis 0.0 0.0 +Alistipes putredinis K00239 5.050000000000001 6.15 +Alistipes putredinis K00262 14.1 11.850000000000001 +Alistipes putredinis K03046 13.4 2.05 +Alistipes putredinis K03043 10.0 3.1 +Alistipes putredinis K02358 14.55 6.6499999999999995 +Alistipes putredinis K00134 3.35 2.05 +Alistipes putredinis K00088 2.25 3.1 +Alistipes putredinis K01610 9.5 14.899999999999999 +Alistipes putredinis K03695 9.55 7.199999999999999 +Alistipes putredinis K04077 0.0 4.65 +Anaerofustis stercorihominis K02355 9.55 7.1499999999999995 +Anaerofustis stercorihominis K00262 8.5 19.0 +Anaerofustis stercorihominis 76.4 82.7 +Anaerofustis stercorihominis K01803 2.25 4.6 +Anaerofustis stercorihominis K00927 5.550000000000001 7.699999999999999 +Anaerofustis stercorihominis K00134 8.5 30.799999999999997 +Anaerofustis stercorihominis K00248 2.25 4.6 +Anaerofustis stercorihominis K00626 7.25 10.8 +Anaerofustis stercorihominis K03737 5.0 3.1 +Anaerofustis stercorihominis K03046 6.15 7.1499999999999995 +Anaerofustis stercorihominis K03695 14.6 10.25 +Anaerofustis stercorihominis K02358 2.1 1.55 +Anaerofustis stercorihominis K02112 8.4 6.15 +Bacteroides caccae 147.4 99.14999999999998 +Bacteroides caccae K01610 8.95 15.399999999999999 +Bacteroides caccae K02358 24.0 10.25 +Bacteroides caccae K02867 8.4 6.6499999999999995 +Bacteroides caccae K02863 0.0 2.55 +Bacteroides caccae K02864 10.1 7.7 +Bacteroides caccae K02935 13.350000000000001 5.65 +Bacteroides caccae K03043 31.35 5.1 +Bacteroides caccae K03046 31.950000000000003 3.1 +Bacteroides caccae K02992 1.2 0.0 +Bacteroides caccae K02355 15.15 6.1499999999999995 +Bacteroides caccae K02982 8.2 1.55 +Bacteroides caccae K03040 4.0 2.6 +Bacteroides caccae K00962 7.15 2.55 +Bacteroides caccae K01812 5.0 4.6 +Bacteroides caccae K02110 7.6 9.25 +Bacteroides caccae K02112 19.4 12.850000000000001 +Bacteroides caccae K01006 5.050000000000001 5.15 +Bacteroides caccae K00346 5.6 1.55 +Bacteroides caccae K00239 38.849999999999994 23.1 +Bacteroides caccae K00240 12.8 12.3 +Bacteroides caccae K00046 4.15 2.6 +Bacteroides caccae K01803 2.25 5.1 +Bacteroides caccae K00134 43.45 25.15 +Bacteroides caccae K02945 8.85 0.0 +Bacteroides caccae K01689 18.45 2.05 +Bacteroides caccae K03695 13.45 8.7 +Bacteroides caccae K04043 15.0 2.6 +Bacteroides caccae K01804 1.6 5.1 +Bacteroides caccae K03737 20.6 10.25 +Bacteroides caccae K01624 8.35 4.6 +Bacteroides caccae K01603 13.5 5.15 +Bacteroides caccae K01966 13.5 5.15 +Bacteroides caccae K00088 8.95 13.350000000000001 +Bacteroides caccae K00026 3.2 2.55 +Bacteroides caccae K03070 6.199999999999999 1.0 +Bacteroides caccae K00262 39.05 30.8 +Bacteroides caccae K04077 30.65 6.1499999999999995 +Bacteroides caccae K04078 5.65 2.05 +Bacteroides dorei K00088 11.05 11.850000000000001 +Bacteroides dorei K01955 5.6 4.1 +Bacteroides dorei 523.5000000000001 453.2500000000001 +Bacteroides dorei K04078 6.15 2.05 +Bacteroides dorei K04077 30.450000000000003 9.75 +Bacteroides dorei K00026 3.3 7.199999999999999 +Bacteroides dorei K00262 44.849999999999994 45.2 +Bacteroides dorei K03340 0.0 3.5999999999999996 +Bacteroides dorei K01624 8.4 3.1 +Bacteroides dorei K02355 13.85 9.25 +Bacteroides dorei K12373 5.15 1.0 +Bacteroides dorei K02564 7.25 1.05 +Bacteroides dorei K03287 0.0 0.0 +Bacteroides dorei K03286 23.5 24.15 +Bacteroides dorei K01209 1.2 7.699999999999999 +Bacteroides dorei K03615 1.6 2.6 +Bacteroides dorei K01190 9.850000000000001 6.6499999999999995 +Bacteroides dorei K03695 14.45 10.25 +Bacteroides dorei K00259 5.0 7.699999999999999 +Bacteroides dorei K03737 24.4 18.0 +Bacteroides dorei K00134 52.3 58.05 +Bacteroides dorei K01610 9.600000000000001 16.95 +Bacteroides dorei K00174 10.4 8.75 +Bacteroides dorei K00046 4.15 4.1 +Bacteroides dorei K00239 44.3 25.7 +Bacteroides dorei K00240 12.65 8.75 +Bacteroides dorei K01818 6.25 6.6499999999999995 +Bacteroides dorei K00962 3.8499999999999996 2.05 +Bacteroides dorei K00688 9.899999999999999 5.6 +Bacteroides dorei K00948 1.6 0.0 +Bacteroides dorei K01915 4.4 5.1 +Bacteroides dorei K01006 7.2 5.6499999999999995 +Bacteroides dorei K00058 2.8 1.0 +Bacteroides dorei K00351 2.65 2.05 +Bacteroides dorei K00346 8.35 5.1 +Bacteroides dorei K01812 3.8499999999999996 6.15 +Bacteroides dorei K01625 1.05 3.5999999999999996 +Bacteroides dorei K07386 6.65 1.0 +Bacteroides dorei K00895 2.25 4.6 +Bacteroides dorei K01804 4.4 4.1 +Bacteroides dorei K04043 15.6 3.5999999999999996 +Bacteroides dorei K01603 18.0 9.25 +Bacteroides dorei K01966 18.0 9.25 +Bacteroides dorei K03070 6.75 1.0 +Bacteroides dorei K02945 8.85 1.0 +Bacteroides dorei K01623 1.6 8.2 +Bacteroides dorei K01858 3.8499999999999996 3.0999999999999996 +Bacteroides dorei K01689 25.799999999999997 5.1499999999999995 +Bacteroides dorei K02959 0.0 0.0 +Bacteroides dorei K02112 22.25 14.85 +Bacteroides dorei K02110 5.45 0.0 +Bacteroides dorei K00283 6.15 9.25 +Bacteroides dorei K03040 4.45 2.6 +Bacteroides dorei K02986 2.25 1.05 +Bacteroides dorei K02982 8.2 2.6 +Bacteroides dorei K02926 1.6 2.05 +Bacteroides dorei K02992 0.0 0.0 +Bacteroides dorei K03046 31.35 4.1 +Bacteroides dorei K03043 26.8 7.2 +Bacteroides dorei K02935 12.75 5.65 +Bacteroides dorei K02864 11.8 12.850000000000001 +Bacteroides dorei K02863 0.0 3.5999999999999996 +Bacteroides dorei K02867 10.7 9.25 +Bacteroides dorei K02358 25.75 12.799999999999999 +Bacteroides fragilis K00046 3.55 0.0 +Bacteroides fragilis 71.6 91.94999999999999 +Bacteroides fragilis K00134 1.2 3.05 +Bacteroides fragilis K02945 8.85 0.0 +Bacteroides fragilis K03070 6.199999999999999 1.0 +Bacteroides fragilis K01689 20.3 3.05 +Bacteroides fragilis K03695 12.35 8.7 +Bacteroides fragilis K04043 16.65 3.0999999999999996 +Bacteroides fragilis K02112 20.049999999999997 14.35 +Bacteroides fragilis K02110 7.05 9.25 +Bacteroides fragilis K01812 3.85 6.1499999999999995 +Bacteroides fragilis K01006 5.050000000000001 5.15 +Bacteroides fragilis K02217 8.55 9.25 +Bacteroides fragilis K01603 8.55 4.1 +Bacteroides fragilis K01966 8.55 4.1 +Bacteroides fragilis K01624 6.65 2.6 +Bacteroides fragilis K03737 25.15 10.25 +Bacteroides fragilis K04077 22.1 4.1 +Bacteroides fragilis K04078 5.050000000000001 2.05 +Bacteroides fragilis K00262 41.349999999999994 30.3 +Bacteroides fragilis K01803 2.25 6.15 +Bacteroides fragilis K00026 2.8 0.0 +Bacteroides fragilis K00024 2.8 0.0 +Bacteroides fragilis K00088 6.75 6.65 +Bacteroides fragilis K03040 4.550000000000001 2.6 +Bacteroides fragilis K02982 8.2 1.55 +Bacteroides fragilis K02355 15.15 6.1499999999999995 +Bacteroides fragilis K02992 1.2 0.0 +Bacteroides fragilis K03046 28.55 2.05 +Bacteroides fragilis K03043 27.950000000000003 5.1 +Bacteroides fragilis K02935 12.65 5.65 +Bacteroides fragilis K02864 10.1 7.7 +Bacteroides fragilis K02863 0.0 2.55 +Bacteroides fragilis K02867 9.5 8.2 +Bacteroides fragilis K02358 21.2 9.25 +Bacteroides fragilis K00962 4.4 0.0 +Bacteroides fragilis K01610 5.0 16.9 +Bacteroides fragilis K00239 19.7 10.75 +Bacteroides fragilis K00240 9.399999999999999 4.65 +Bacteroides ovatus K00262 36.3 35.400000000000006 +Bacteroides ovatus K01580 9.100000000000001 3.1 +Bacteroides ovatus K00046 5.15 2.6 +Bacteroides ovatus 244.50000000000009 157.60000000000002 +Bacteroides ovatus K00088 9.45 13.350000000000001 +Bacteroides ovatus K03040 4.0 2.6 +Bacteroides ovatus K02982 8.2 1.55 +Bacteroides ovatus K02355 15.75 6.1499999999999995 +Bacteroides ovatus K03046 30.799999999999997 2.05 +Bacteroides ovatus K03043 31.35 5.1 +Bacteroides ovatus K02935 13.350000000000001 5.65 +Bacteroides ovatus K02864 11.8 8.75 +Bacteroides ovatus K02863 0.0 2.55 +Bacteroides ovatus K02867 9.5 8.2 +Bacteroides ovatus K02358 20.7 13.299999999999999 +Bacteroides ovatus K00026 3.2 2.55 +Bacteroides ovatus K01803 2.25 5.65 +Bacteroides ovatus K00962 8.35 3.1 +Bacteroides ovatus K01804 1.6 5.6 +Bacteroides ovatus K01610 8.35 19.5 +Bacteroides ovatus K01006 5.050000000000001 5.15 +Bacteroides ovatus K02112 18.95 12.850000000000001 +Bacteroides ovatus K02110 7.6 9.25 +Bacteroides ovatus K01805 7.3500000000000005 4.6 +Bacteroides ovatus K00239 38.3 23.6 +Bacteroides ovatus K00240 12.8 12.3 +Bacteroides ovatus K00346 7.35 3.5999999999999996 +Bacteroides ovatus K00351 7.15 4.6 +Bacteroides ovatus K01603 16.35 7.699999999999999 +Bacteroides ovatus K01966 16.35 7.699999999999999 +Bacteroides ovatus K01624 10.0 4.6 +Bacteroides ovatus K01952 2.8 2.55 +Bacteroides ovatus K03737 27.700000000000003 10.8 +Bacteroides ovatus K04077 34.55 6.6499999999999995 +Bacteroides ovatus K04078 5.65 2.05 +Bacteroides ovatus K00134 50.650000000000006 31.85 +Bacteroides ovatus K02945 8.85 0.0 +Bacteroides ovatus K03070 6.800000000000001 1.0 +Bacteroides ovatus K01689 23.0 3.05 +Bacteroides ovatus K03695 13.45 8.7 +Bacteroides ovatus K04043 17.8 3.5999999999999996 +Bacteroides pectinophilus K02888 0.0 6.1499999999999995 +Bacteroides pectinophilus K01681 1.75 7.2 +Bacteroides pectinophilus K01624 3.95 5.6 +Bacteroides pectinophilus 76.2 76.05 +Bacteroides pectinophilus K01876 1.05 5.6 +Bacteroides pectinophilus K04043 14.55 11.3 +Bacteroides pectinophilus K04077 17.95 24.2 +Bacteroides pectinophilus K04078 6.199999999999999 5.65 +Bacteroides pectinophilus K00962 5.050000000000001 3.5999999999999996 +Bacteroides pectinophilus K03737 7.25 7.1499999999999995 +Bacteroides pectinophilus K00046 3.55 2.55 +Bacteroides pectinophilus K00134 29.9 46.75 +Bacteroides pectinophilus K00927 7.15 8.7 +Bacteroides pectinophilus K01571 3.35 0.0 +Bacteroides pectinophilus K02867 9.0 7.699999999999999 +Bacteroides pectinophilus K02863 1.2 3.5999999999999996 +Bacteroides pectinophilus K02935 1.75 3.1 +Bacteroides pectinophilus K03043 16.9 15.9 +Bacteroides pectinophilus K03046 21.9 11.8 +Bacteroides pectinophilus K02992 3.35 1.0 +Bacteroides pectinophilus K02355 10.6 8.2 +Bacteroides pectinophilus K02358 18.05 17.95 +Bacteroides pectinophilus K01610 26.549999999999997 26.7 +Bacteroides pectinophilus K00088 5.050000000000001 7.699999999999999 +Bacteroides pectinophilus K03695 11.35 8.75 +Bacteroides pectinophilus K04759 0.0 0.0 +Bacteroides pectinophilus K10112 7.35 6.15 +Bacteroides pectinophilus K01689 1.6 0.0 +Bacteroides pectinophilus K02112 26.2 21.05 +Bacteroides pectinophilus K00262 3.3 8.7 +Bacteroides pectinophilus K00616 6.75 11.8 +Bacteroides pectinophilus K03040 6.15 5.65 +Bacteroides pectinophilus K02986 2.25 4.6 +Bacteroides pectinophilus K02948 3.35 1.05 +Bacteroides pectinophilus K02952 2.35 2.05 +Bacteroides pectinophilus K02988 2.35 4.1 +Bacteroides pectinophilus K02982 4.45 4.1 +Bacteroides pectinophilus K02965 6.050000000000001 4.1 +Bacteroides pectinophilus K00656 5.0 13.350000000000001 +Bacteroides sp. K00962 23.65 9.75 +Bacteroides sp. K01580 9.100000000000001 3.1 +Bacteroides sp. K01603 80.05 41.1 +Bacteroides sp. K01966 62.05 31.85 +Bacteroides sp. K01624 36.9 13.95 +Bacteroides sp. K01952 5.6 5.6 +Bacteroides sp. K03737 121.65 74.55 +Bacteroides sp. K04077 148.0 40.0 +Bacteroides sp. K04078 29.15 10.25 +Bacteroides sp. 1668.6999999999996 1691.449999999999 +Bacteroides sp. K04043 78.45 16.5 +Bacteroides sp. K03695 69.15 48.15 +Bacteroides sp. K01689 106.10000000000001 19.5 +Bacteroides sp. K00239 191.5 111.95 +Bacteroides sp. K00240 60.15 43.2 +Bacteroides sp. K00134 208.75 209.05 +Bacteroides sp. K02945 44.25 3.0 +Bacteroides sp. K03070 33.25 5.0 +Bacteroides sp. K00351 15.100000000000001 10.75 +Bacteroides sp. K00346 33.9 21.0 +Bacteroides sp. K00046 21.15 14.899999999999999 +Bacteroides sp. K00262 210.45 201.25 +Bacteroides sp. K01006 30.05 26.75 +Bacteroides sp. K00088 49.349999999999994 55.550000000000004 +Bacteroides sp. K00026 12.600000000000001 16.95 +Bacteroides sp. K01803 4.5 11.8 +Bacteroides sp. K03040 21.9 13.0 +Bacteroides sp. K02982 41.0 10.9 +Bacteroides sp. K02355 72.45 40.05 +Bacteroides sp. K03046 153.4 16.4 +Bacteroides sp. K03043 138.55 31.799999999999997 +Bacteroides sp. K02935 64.25 28.25 +Bacteroides sp. K02864 58.45 56.00000000000001 +Bacteroides sp. K02863 3.5999999999999996 15.899999999999999 +Bacteroides sp. K02867 51.099999999999994 44.15 +Bacteroides sp. K02358 118.60000000000001 61.49999999999999 +Bacteroides sp. K01610 34.85000000000001 70.85000000000001 +Bacteroides sp. K01805 7.3500000000000005 4.6 +Bacteroides sp. K02110 30.45 18.5 +Bacteroides sp. K00281 6.15 9.25 +Bacteroides sp. K02112 86.8 58.9 +Bacteroides sp. K02217 3.3 10.25 +Bacteroides sp. K02959 0.0 0.0 +Bacteroides sp. K01858 12.1 12.9 +Bacteroides sp. K01804 13.200000000000001 12.799999999999999 +Bacteroides sp. K00895 6.75 13.799999999999999 +Bacteroides sp. K07386 19.450000000000003 5.6 +Bacteroides sp. K03615 4.800000000000001 7.800000000000001 +Bacteroides sp. K01209 5.2 25.15 +Bacteroides sp. K03286 74.05 83.25 +Bacteroides sp. K02564 29.55 3.1500000000000004 +Bacteroides sp. K12373 22.200000000000003 7.65 +Bacteroides sp. K00174 31.200000000000003 26.25 +Bacteroides sp. K02992 1.2 0.0 +Bacteroides sp. K02926 4.800000000000001 6.1499999999999995 +Bacteroides sp. K02986 6.75 3.1500000000000004 +Bacteroides sp. K01190 28.35 19.95 +Bacteroides sp. K00688 29.699999999999996 16.799999999999997 +Bacteroides sp. K00948 4.800000000000001 0.0 +Bacteroides sp. K01915 13.200000000000001 16.799999999999997 +Bacteroides sp. K00058 8.399999999999999 3.0 +Bacteroides sp. K01955 15.700000000000001 12.299999999999999 +Bacteroides sp. K00024 3.3 7.199999999999999 +Bacteroides sp. K01818 16.35 16.9 +Bacteroides sp. K00259 16.05 29.3 +Bacteroides sp. K01625 3.1500000000000004 10.799999999999999 +Bacteroides sp. K01812 15.399999999999999 24.6 +Bacteroides sp. K03340 0.0 10.799999999999999 +Bacteroides sp. K01802 5.550000000000001 1.55 +Bacteroides sp. K11934 0.0 3.0999999999999996 +Bacteroides sp. K12308 0.0 0.0 +Bacteroides sp. K04773 0.0 4.1 +Bacteroides sp. K01623 1.6 8.2 +Bacteroides sp. K00283 12.3 19.5 +Bacteroides sp. K01212 0.0 0.0 +Bacteroides sp. K02967 0.0 3.05 +Bacteroides sp. D4 K01812 3.8499999999999996 6.15 +Bacteroides sp. D4 K01625 1.05 3.5999999999999996 +Bacteroides sp. D4 K00283 6.15 9.25 +Bacteroides sp. D4 K02110 5.45 0.0 +Bacteroides sp. D4 K02112 22.25 14.85 +Bacteroides sp. D4 349.4000000000001 377.8 +Bacteroides sp. D4 K02959 0.0 0.0 +Bacteroides sp. D4 K01689 25.799999999999997 5.1499999999999995 +Bacteroides sp. D4 K01858 3.8499999999999996 3.0999999999999996 +Bacteroides sp. D4 K02945 8.85 1.0 +Bacteroides sp. D4 K03070 6.75 1.0 +Bacteroides sp. D4 K01603 18.0 9.25 +Bacteroides sp. D4 K01966 18.0 9.25 +Bacteroides sp. D4 K04043 15.6 3.5999999999999996 +Bacteroides sp. D4 K01804 4.4 4.1 +Bacteroides sp. D4 K00895 2.25 4.6 +Bacteroides sp. D4 K03615 1.6 2.6 +Bacteroides sp. D4 K01209 1.2 7.699999999999999 +Bacteroides sp. D4 K03286 23.5 24.15 +Bacteroides sp. D4 K02564 10.05 1.05 +Bacteroides sp. D4 K12373 5.15 1.0 +Bacteroides sp. D4 K02355 13.85 9.25 +Bacteroides sp. D4 K01190 8.7 6.6499999999999995 +Bacteroides sp. D4 K03040 4.45 2.6 +Bacteroides sp. D4 K02986 2.25 1.05 +Bacteroides sp. D4 K02982 8.2 1.55 +Bacteroides sp. D4 K02926 1.6 2.05 +Bacteroides sp. D4 K02992 0.0 0.0 +Bacteroides sp. D4 K03046 31.35 4.1 +Bacteroides sp. D4 K03043 26.8 7.2 +Bacteroides sp. D4 K02935 12.75 5.65 +Bacteroides sp. D4 K02864 11.8 12.850000000000001 +Bacteroides sp. D4 K02863 1.2 3.5999999999999996 +Bacteroides sp. D4 K02867 10.7 9.25 +Bacteroides sp. D4 K02358 25.75 12.799999999999999 +Bacteroides sp. D4 K01610 9.600000000000001 16.95 +Bacteroides sp. D4 K00174 10.4 8.75 +Bacteroides sp. D4 K00046 4.15 4.1 +Bacteroides sp. D4 K00346 8.85 5.1 +Bacteroides sp. D4 K00351 2.65 2.05 +Bacteroides sp. D4 K00058 2.8 1.0 +Bacteroides sp. D4 K01006 7.2 5.6499999999999995 +Bacteroides sp. D4 K01915 4.4 5.6 +Bacteroides sp. D4 K00948 1.6 0.0 +Bacteroides sp. D4 K00688 9.899999999999999 5.6 +Bacteroides sp. D4 K00262 45.45 45.2 +Bacteroides sp. D4 K00026 3.3 7.199999999999999 +Bacteroides sp. D4 K04077 30.450000000000003 9.75 +Bacteroides sp. D4 K04078 6.15 2.05 +Bacteroides sp. D4 K01955 5.6 4.1 +Bacteroides sp. D4 K00088 11.05 11.850000000000001 +Bacteroides sp. D4 K00962 3.8499999999999996 2.05 +Bacteroides sp. D4 K01818 6.25 6.6499999999999995 +Bacteroides sp. D4 K00134 52.3 58.05 +Bacteroides sp. D4 K03737 24.4 18.0 +Bacteroides sp. D4 K00259 5.0 8.25 +Bacteroides sp. D4 K03695 14.45 10.25 +Bacteroides sp. D4 K00239 39.900000000000006 22.6 +Bacteroides sp. D4 K00240 12.65 8.75 +Bacteroides sp. D4 K07386 6.65 1.0 +Bacteroides sp. D4 K03340 0.0 3.5999999999999996 +Bacteroides sp. D4 K01624 8.4 3.1 +Bacteroides thetaiotaomicron 81.49999999999999 105.65 +Bacteroides thetaiotaomicron K01804 3.3 5.65 +Bacteroides thetaiotaomicron K01006 6.75 5.6499999999999995 +Bacteroides thetaiotaomicron K02112 18.4 12.850000000000001 +Bacteroides thetaiotaomicron K02110 7.6 9.25 +Bacteroides thetaiotaomicron K01805 6.65 3.5999999999999996 +Bacteroides thetaiotaomicron K01812 5.0 4.6 +Bacteroides thetaiotaomicron K01623 1.6 8.2 +Bacteroides thetaiotaomicron K02217 16.85 18.450000000000003 +Bacteroides thetaiotaomicron K01603 14.6 6.6499999999999995 +Bacteroides thetaiotaomicron K01966 14.6 6.6499999999999995 +Bacteroides thetaiotaomicron K01624 9.5 4.6 +Bacteroides thetaiotaomicron K03737 30.55 10.3 +Bacteroides thetaiotaomicron K04077 32.35 6.1499999999999995 +Bacteroides thetaiotaomicron K04078 5.65 2.05 +Bacteroides thetaiotaomicron K00262 37.35 33.3 +Bacteroides thetaiotaomicron K00962 6.0 2.05 +Bacteroides thetaiotaomicron K03040 4.0 2.6 +Bacteroides thetaiotaomicron K02982 8.2 1.55 +Bacteroides thetaiotaomicron K02926 2.1 9.25 +Bacteroides thetaiotaomicron K02355 15.15 6.1499999999999995 +Bacteroides thetaiotaomicron K03046 29.25 3.1 +Bacteroides thetaiotaomicron K03043 31.85 5.1 +Bacteroides thetaiotaomicron K02935 12.65 5.65 +Bacteroides thetaiotaomicron K02864 11.2 8.75 +Bacteroides thetaiotaomicron K02863 0.0 2.55 +Bacteroides thetaiotaomicron K02867 8.4 6.6499999999999995 +Bacteroides thetaiotaomicron K02358 24.0 10.25 +Bacteroides thetaiotaomicron K01610 10.1 18.5 +Bacteroides thetaiotaomicron K00239 38.3 23.6 +Bacteroides thetaiotaomicron K00240 12.8 12.3 +Bacteroides thetaiotaomicron K00046 4.15 3.5999999999999996 +Bacteroides thetaiotaomicron K00088 6.050000000000001 7.1499999999999995 +Bacteroides thetaiotaomicron K00026 4.25 5.15 +Bacteroides thetaiotaomicron K00024 4.25 5.15 +Bacteroides thetaiotaomicron K01803 2.25 5.1 +Bacteroides thetaiotaomicron K00134 44.6 25.65 +Bacteroides thetaiotaomicron K02945 8.85 0.0 +Bacteroides thetaiotaomicron K03070 6.800000000000001 1.0 +Bacteroides thetaiotaomicron K01689 18.45 2.05 +Bacteroides thetaiotaomicron K03695 12.35 8.7 +Bacteroides thetaiotaomicron K04043 13.25 1.55 +Bacteroides uniformis 317.74999999999994 60.550000000000004 +Bacteroides uniformis K00962 2.1 0.0 +Bacteroides uniformis K01812 4.4 4.6 +Bacteroides uniformis K03040 5.65 2.6 +Bacteroides uniformis K02982 7.65 1.55 +Bacteroides uniformis K02355 16.75 6.1499999999999995 +Bacteroides uniformis K03046 33.1 3.1 +Bacteroides uniformis K03043 32.4 5.1 +Bacteroides uniformis K02935 12.65 5.65 +Bacteroides uniformis K02864 12.35 8.75 +Bacteroides uniformis K02863 0.0 2.55 +Bacteroides uniformis K02867 8.95 7.1499999999999995 +Bacteroides uniformis K02358 26.35 6.6499999999999995 +Bacteroides uniformis K01623 1.6 8.2 +Bacteroides uniformis K04078 5.65 2.05 +Bacteroides uniformis K04077 32.25 6.65 +Bacteroides uniformis K03737 32.85 11.8 +Bacteroides uniformis K00615 7.15 1.05 +Bacteroides uniformis K01603 18.55 7.699999999999999 +Bacteroides uniformis K01966 18.55 7.699999999999999 +Bacteroides uniformis K01624 9.0 2.05 +Bacteroides uniformis K01689 45.95 3.5999999999999996 +Bacteroides uniformis K00262 48.550000000000004 33.35 +Bacteroides uniformis K01625 0.0 3.5999999999999996 +Bacteroides uniformis K03286 29.3 1.55 +Bacteroides uniformis K00346 8.8 0.0 +Bacteroides uniformis K00351 7.6 4.1 +Bacteroides uniformis K01006 5.050000000000001 5.15 +Bacteroides uniformis K02112 18.85 13.35 +Bacteroides uniformis K00088 11.2 11.850000000000001 +Bacteroides uniformis K01955 2.8 1.0 +Bacteroides uniformis K00026 4.4 2.55 +Bacteroides uniformis K01803 3.3 6.65 +Bacteroides uniformis K00134 53.0 24.65 +Bacteroides uniformis K01610 9.55 12.3 +Bacteroides uniformis K00239 35.9 19.0 +Bacteroides uniformis K00240 11.05 4.65 +Bacteroides uniformis K00046 4.15 2.6 +Bacteroides uniformis K04043 13.4 2.05 +Bacteroides uniformis K03695 13.45 8.7 +Bacteroides uniformis K03070 6.800000000000001 1.0 +Bacteroides uniformis K02945 8.85 0.0 +Bacteroides vulgatus K02355 13.85 9.25 +Bacteroides vulgatus 350.4500000000001 455.9000000000002 +Bacteroides vulgatus K01952 2.8 3.05 +Bacteroides vulgatus K00262 44.849999999999994 46.2 +Bacteroides vulgatus K00026 3.3 7.199999999999999 +Bacteroides vulgatus K00024 3.3 7.199999999999999 +Bacteroides vulgatus K04077 30.450000000000003 9.75 +Bacteroides vulgatus K04078 6.15 2.05 +Bacteroides vulgatus K01955 5.6 4.1 +Bacteroides vulgatus K00088 10.5 11.850000000000001 +Bacteroides vulgatus K01190 9.25 6.6499999999999995 +Bacteroides vulgatus K03040 4.45 2.6 +Bacteroides vulgatus K02986 2.25 1.05 +Bacteroides vulgatus K02982 8.2 2.6 +Bacteroides vulgatus K02926 1.6 2.05 +Bacteroides vulgatus K02992 0.0 0.0 +Bacteroides vulgatus K03046 31.35 4.1 +Bacteroides vulgatus K03043 26.8 7.2 +Bacteroides vulgatus K02935 12.75 5.65 +Bacteroides vulgatus K02864 12.95 13.850000000000001 +Bacteroides vulgatus K02863 1.2 3.5999999999999996 +Bacteroides vulgatus K02867 10.7 9.25 +Bacteroides vulgatus K02358 24.7 13.35 +Bacteroides vulgatus K01610 19.200000000000003 33.9 +Bacteroides vulgatus K00174 20.8 17.5 +Bacteroides vulgatus K00046 4.15 3.0999999999999996 +Bacteroides vulgatus K00239 44.3 25.7 +Bacteroides vulgatus K00240 12.65 8.75 +Bacteroides vulgatus K01818 6.25 6.6499999999999995 +Bacteroides vulgatus K01802 5.550000000000001 1.55 +Bacteroides vulgatus K00962 4.95 2.55 +Bacteroides vulgatus K04773 0.0 4.1 +Bacteroides vulgatus K02967 0.0 3.05 +Bacteroides vulgatus K03340 0.0 3.5999999999999996 +Bacteroides vulgatus K01212 0.0 0.0 +Bacteroides vulgatus K01624 7.8500000000000005 3.1 +Bacteroides vulgatus K07386 6.15 3.5999999999999996 +Bacteroides vulgatus K00895 2.25 4.6 +Bacteroides vulgatus K01804 3.8499999999999996 4.1 +Bacteroides vulgatus K04043 15.6 3.5999999999999996 +Bacteroides vulgatus K01603 18.0 9.25 +Bacteroides vulgatus K01966 18.0 9.25 +Bacteroides vulgatus K03070 6.75 1.0 +Bacteroides vulgatus K02945 8.85 1.0 +Bacteroides vulgatus K01858 4.4 6.7 +Bacteroides vulgatus K01689 14.55 3.0999999999999996 +Bacteroides vulgatus K02959 0.0 0.0 +Bacteroides vulgatus K02217 5.4 16.9 +Bacteroides vulgatus K02112 22.25 14.85 +Bacteroides vulgatus K02110 5.45 0.0 +Bacteroides vulgatus K00281 6.15 10.25 +Bacteroides vulgatus K00283 6.15 10.25 +Bacteroides vulgatus K01625 1.05 3.5999999999999996 +Bacteroides vulgatus K01812 3.8499999999999996 6.15 +Bacteroides vulgatus K11934 0.0 3.0999999999999996 +Bacteroides vulgatus K00346 9.399999999999999 7.199999999999999 +Bacteroides vulgatus K00351 2.65 2.05 +Bacteroides vulgatus K00058 2.8 1.0 +Bacteroides vulgatus K01006 5.550000000000001 5.15 +Bacteroides vulgatus K01623 1.6 8.2 +Bacteroides vulgatus K01915 4.4 5.6 +Bacteroides vulgatus K00948 1.6 0.0 +Bacteroides vulgatus K00688 9.899999999999999 5.6 +Bacteroides vulgatus K00134 52.3 58.05 +Bacteroides vulgatus K03737 24.4 18.0 +Bacteroides vulgatus K00259 6.050000000000001 12.8 +Bacteroides vulgatus K03695 14.45 10.25 +Bacteroides 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46.2 +Blautia hansenii K02967 8.55 10.25 +Blautia hansenii K00262 10.1 16.95 +Blautia hansenii K00962 3.35 6.15 +Blautia hansenii K02112 10.6 13.350000000000001 +Blautia hansenii K01610 18.65 22.6 +Blautia hansenii K01571 12.25 12.85 +Blautia hansenii K11174 5.6 9.75 +Blautia hansenii K02899 1.05 2.6 +Blautia hansenii K02888 5.15 7.6499999999999995 +Blautia hansenii K00133 2.8 5.15 +Blautia hansenii K01803 2.35 4.1 +Blautia hansenii K00927 9.399999999999999 12.3 +Blautia hansenii K00134 17.4 29.299999999999997 +Blautia hansenii K04079 3.8499999999999996 6.6499999999999995 +Blautia hansenii K03737 36.1 28.25 +Blautia hansenii K01938 8.85 7.2 +Blautia hydrogenotrophica K01006 31.950000000000003 42.15 +Blautia hydrogenotrophica K02884 1.75 1.55 +Blautia hydrogenotrophica K02888 0.0 5.65 +Blautia hydrogenotrophica K02945 12.85 11.3 +Blautia hydrogenotrophica K01571 11.2 12.85 +Blautia hydrogenotrophica K03737 35.6 29.799999999999997 +Blautia hydrogenotrophica K00962 5.6 7.699999999999999 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K02946 4.4 5.6 +Blautia hydrogenotrophica K02926 2.1 3.6 +Blautia hydrogenotrophica K02892 3.95 2.6 +Blautia hydrogenotrophica K02965 7.15 3.5999999999999996 +Blautia hydrogenotrophica K02982 6.65 4.65 +Blautia hydrogenotrophica K02961 2.65 2.6 +Blautia hydrogenotrophica K02931 16.3 12.3 +Blautia hydrogenotrophica K02933 6.800000000000001 6.15 +Blautia hydrogenotrophica K02988 5.6 5.1 +Blautia hydrogenotrophica K02952 4.45 2.55 +Blautia hydrogenotrophica K02948 6.050000000000001 1.05 +Blautia hydrogenotrophica K02986 5.6 3.6 +Blautia hydrogenotrophica K03040 5.0 4.1 +Blautia hydrogenotrophica K02879 5.6 4.1 +Blautia hydrogenotrophica K04043 29.6 18.5 +Blautia hydrogenotrophica K04077 16.8 25.2 +Blautia hydrogenotrophica K00088 4.550000000000001 4.1 +Blautia hydrogenotrophica K01939 5.65 5.15 +Blautia hydrogenotrophica K00616 7.35 8.7 +Blautia hydrogenotrophica K00262 7.35 6.1499999999999995 +Blautia hydrogenotrophica K00134 23.1 36.45 +Blautia hydrogenotrophica K04079 4.95 5.1 +Blautia hydrogenotrophica K01938 14.850000000000001 9.75 +Catenibacterium mitsuokai K02967 1.75 3.5999999999999996 +Catenibacterium mitsuokai 37.6 49.8 +Catenibacterium mitsuokai K00262 2.8 6.15 +Catenibacterium mitsuokai K01006 6.050000000000001 7.2 +Catenibacterium mitsuokai K00134 12.5 19.549999999999997 +Catenibacterium mitsuokai K04072 7.1 2.05 +Catenibacterium mitsuokai K02358 10.0 14.4 +Catenibacterium mitsuokai K02355 10.1 6.6499999999999995 +Catenibacterium mitsuokai K02992 2.8 2.55 +Catenibacterium mitsuokai K03043 5.65 4.6 +Catenibacterium mitsuokai K02112 8.4 8.7 +Catenibacterium mitsuokai K00656 6.15 12.3 +Citrobacter koseri K00134 6.300000000000001 25.650000000000002 +Citrobacter koseri 13.1 7.7 +Citrobacter koseri K04072 0.0 0.0 +Citrobacter koseri K06078 0.0 0.0 +Citrobacter koseri K00262 6.800000000000001 8.7 +Citrobacter koseri K00656 0.0 0.0 +Citrobacter koseri K04047 0.0 0.0 +Citrobacter koseri K03386 0.0 0.0 +Citrobacter koseri K03046 2.25 3.5999999999999996 +Citrobacter koseri K02867 1.2 4.6 +Citrobacter koseri K02358 14.700000000000001 24.7 +Citrobacter koseri K04077 2.95 0.0 +Citrobacter koseri K03695 11.2 8.2 +Citrobacter koseri K01689 0.0 0.0 +Citrobacter koseri K01624 0.0 0.0 +Citrobacter koseri K00927 0.0 0.0 +Clostridium bartlettii K02867 5.550000000000001 5.15 +Clostridium bartlettii K03043 6.800000000000001 6.15 +Clostridium bartlettii K03046 11.2 9.25 +Clostridium bartlettii K02992 2.8 1.55 +Clostridium bartlettii K02355 8.4 4.1 +Clostridium bartlettii K02358 12.399999999999999 10.8 +Clostridium bartlettii 27.65 41.1 +Clostridium bartlettii K00262 24.849999999999998 43.7 +Clostridium bartlettii K04077 9.600000000000001 4.1 +Clostridium bartlettii K00260 0.0 0.0 +Clostridium bartlettii K01624 5.0 4.1 +Clostridium bartlettii K03695 7.3500000000000005 5.1 +Clostridium bartlettii K10112 13.55 8.2 +Clostridium bartlettii K00616 5.050000000000001 1.55 +Clostridium bartlettii K02112 6.75 4.1 +Clostridium bartlettii K01006 0.0 3.6 +Clostridium bolteae K01610 22.7 26.15 +Clostridium bolteae K02647 3.85 5.6 +Clostridium bolteae K10112 9.75 10.25 +Clostridium bolteae K01810 2.8 1.0 +Clostridium bolteae K10540 1.75 5.6 +Clostridium bolteae K03527 7.35 8.25 +Clostridium bolteae K00616 7.25 12.3 +Clostridium bolteae K03695 11.899999999999999 8.2 +Clostridium bolteae K10670 2.8 1.55 +Clostridium bolteae K03737 47.8 28.25 +Clostridium bolteae K01812 0.0 0.0 +Clostridium bolteae K04043 19.6 14.4 +Clostridium bolteae 99.44999999999999 92.89999999999999 +Clostridium bolteae K02358 28.7 25.65 +Clostridium bolteae K02355 16.35 12.350000000000001 +Clostridium bolteae K02992 10.3 5.6499999999999995 +Clostridium bolteae K02950 4.4 4.6 +Clostridium bolteae K03046 21.950000000000003 16.4 +Clostridium bolteae K03043 13.45 20.55 +Clostridium bolteae K01915 1.75 2.05 +Clostridium bolteae K01624 9.600000000000001 10.8 +Clostridium bolteae K00133 2.8 4.6 +Clostridium bolteae K00046 5.75 1.05 +Clostridium bolteae K02112 1.2 4.6 +Clostridium bolteae K02888 0.0 6.6499999999999995 +Clostridium bolteae K02967 8.55 11.8 +Clostridium bolteae K00134 30.45 39.55 +Clostridium bolteae K00927 2.65 6.15 +Clostridium bolteae K01803 6.25 7.699999999999999 +Clostridium bolteae K00053 1.2 4.65 +Clostridium bolteae K03040 12.75 6.6499999999999995 +Clostridium bolteae K02986 3.85 5.6 +Clostridium bolteae K02948 3.95 0.0 +Clostridium bolteae K02988 1.2 0.0 +Clostridium bolteae K02931 12.2 10.25 +Clostridium bolteae K02874 2.8 4.1 +Clostridium bolteae K02982 4.95 9.8 +Clostridium bolteae K02965 4.4 2.05 +Clostridium bolteae K02886 6.199999999999999 1.05 +Clostridium bolteae K01006 10.5 9.25 +Clostridium bolteae K01804 0.0 1.05 +Clostridium bolteae K00262 2.8 1.05 +Clostridium bolteae K04072 9.5 7.2 +Clostridium bolteae K00088 3.4000000000000004 4.1 +Clostridium bolteae K04077 22.950000000000003 32.85 +Clostridium bolteae K04078 0.0 0.0 +Clostridium bolteae K02935 7.6 4.1 +Clostridium bolteae K02864 1.2 0.0 +Clostridium bolteae K02863 3.85 3.05 +Clostridium bolteae K02867 6.050000000000001 5.6499999999999995 +Clostridium leptum K04043 6.15 4.1 +Clostridium leptum K03695 15.2 9.25 +Clostridium leptum K01006 6.800000000000001 11.8 +Clostridium leptum K01571 0.0 6.7 +Clostridium leptum K00262 11.8 19.0 +Clostridium leptum K02965 3.8499999999999996 2.55 +Clostridium leptum K02946 0.0 3.5999999999999996 +Clostridium leptum 44.95 42.1 +Clostridium leptum K10112 4.4 3.55 +Clostridium leptum K04077 9.55 18.5 +Clostridium leptum K02967 0.0 4.1 +Clostridium leptum K03737 3.95 7.699999999999999 +Clostridium leptum K02867 4.4 4.6 +Clostridium leptum K03043 6.199999999999999 8.25 +Clostridium leptum K03046 15.7 18.0 +Clostridium leptum K02358 12.95 26.7 +Clostridium nexile K00262 15.7 25.700000000000003 +Clostridium nexile K04043 32.65 22.6 +Clostridium nexile K02967 5.6 9.25 +Clostridium nexile K00088 6.800000000000001 5.65 +Clostridium nexile K04077 20.15 18.5 +Clostridium nexile K03043 18.55 23.1 +Clostridium nexile K03046 25.3 16.45 +Clostridium nexile K02992 9.7 7.1499999999999995 +Clostridium nexile K02355 22.3 18.5 +Clostridium nexile K02358 35.35 28.2 +Clostridium nexile K02946 8.0 7.199999999999999 +Clostridium nexile K02886 7.35 3.1 +Clostridium nexile K02965 6.050000000000001 4.1 +Clostridium nexile K02890 2.8 1.05 +Clostridium nexile K02982 7.2 13.35 +Clostridium nexile K02874 4.4 6.65 +Clostridium nexile K02931 10.55 7.699999999999999 +Clostridium nexile K02988 7.3500000000000005 4.1 +Clostridium nexile 86.05000000000001 83.7 +Clostridium nexile K02986 5.550000000000001 6.6499999999999995 +Clostridium nexile K10540 6.199999999999999 3.1 +Clostridium nexile K02996 5.050000000000001 4.6 +Clostridium nexile K00053 15.299999999999999 14.899999999999999 +Clostridium nexile K02899 1.05 2.6 +Clostridium nexile K02888 2.95 6.6499999999999995 +Clostridium nexile K02935 6.65 5.15 +Clostridium nexile K02863 3.4000000000000004 4.1 +Clostridium nexile K02867 6.15 5.15 +Clostridium nexile K04759 0.0 0.0 +Clostridium nexile K02112 16.65 8.2 +Clostridium nexile K02111 7.8 2.55 +Clostridium nexile K01681 3.35 6.7 +Clostridium nexile K02945 14.45 13.850000000000001 +Clostridium nexile K01571 13.5 15.399999999999999 +Clostridium nexile K01803 6.25 7.699999999999999 +Clostridium nexile K00927 11.600000000000001 13.850000000000001 +Clostridium nexile K00134 29.25 39.55 +Clostridium nexile K00133 1.6 5.1 +Clostridium nexile K01610 19.15 17.950000000000003 +Clostridium nexile K00616 15.3 8.7 +Clostridium nexile K00975 4.95 8.2 +Clostridium nexile K10112 12.35 9.25 +Clostridium nexile K01006 25.15 40.1 +Clostridium nexile K03737 12.35 19.55 +Clostridium nexile K03695 9.75 9.75 +Clostridium nexile K04072 5.65 5.1 +Clostridium sp. K01006 31.950000000000003 43.699999999999996 +Clostridium sp. 147.24999999999997 143.20000000000002 +Clostridium sp. K00656 5.0 7.1499999999999995 +Clostridium sp. K01624 21.35 27.7 +Clostridium sp. K00088 7.25 15.4 +Clostridium sp. K04077 35.300000000000004 30.25 +Clostridium sp. K03522 4.25 15.899999999999999 +Clostridium sp. K03521 22.95 22.1 +Clostridium sp. K00248 20.25 50.35 +Clostridium sp. K00626 16.25 21.05 +Clostridium sp. K03695 24.9 19.0 +Clostridium sp. K00053 15.799999999999999 7.1499999999999995 +Clostridium sp. K03527 3.2 13.350000000000001 +Clostridium sp. K00133 2.8 5.1 +Clostridium sp. K01681 4.45 6.7 +Clostridium sp. K00262 57.45 85.80000000000001 +Clostridium sp. K01689 0.0 0.0 +Clostridium sp. K02996 5.1 7.199999999999999 +Clostridium sp. K02986 6.65 10.75 +Clostridium sp. K02948 8.350000000000001 1.05 +Clostridium sp. K02952 3.95 2.55 +Clostridium sp. K02994 7.8500000000000005 4.6 +Clostridium sp. K02931 26.65 19.5 +Clostridium sp. K02874 2.4 6.6499999999999995 +Clostridium sp. K02982 10.0 11.299999999999999 +Clostridium sp. K02965 9.3 4.1 +Clostridium sp. K02886 5.65 1.55 +Clostridium sp. K03737 44.0 39.050000000000004 +Clostridium sp. K00134 43.349999999999994 69.9 +Clostridium sp. K00927 22.8 27.750000000000004 +Clostridium sp. K01803 12.5 15.899999999999999 +Clostridium sp. K04043 38.35 32.4 +Clostridium sp. K01810 1.2 14.9 +Clostridium sp. K02867 12.75 12.299999999999999 +Clostridium sp. K02863 6.250000000000001 18.450000000000003 +Clostridium sp. K02935 9.399999999999999 7.75 +Clostridium sp. K03043 25.349999999999998 36.5 +Clostridium sp. K03046 41.050000000000004 27.200000000000003 +Clostridium sp. K02950 9.9 9.2 +Clostridium sp. K02992 11.25 4.6 +Clostridium sp. K02355 29.900000000000002 24.150000000000002 +Clostridium sp. K02358 61.95 63.599999999999994 +Clostridium sp. K02112 11.75 12.8 +Clostridium sp. K03530 2.35 17.5 +Clostridium sp. K00616 9.100000000000001 14.35 +Clostridium sp. K02945 5.050000000000001 8.25 +Clostridium sp. K02967 5.75 10.75 +Clostridium sp. K04078 7.35 3.0999999999999996 +Clostridium sp. K04079 5.050000000000001 5.6 +Clostridium sp. K02888 2.95 6.6499999999999995 +Clostridium sp. K02879 6.65 6.1499999999999995 +Clostridium sp. K03040 12.2 7.1499999999999995 +Clostridium sp. K02933 3.95 1.05 +Collinsella aerofaciens K02887 0.0 0.0 +Collinsella aerofaciens 54.4 93.05 +Collinsella aerofaciens K00046 5.15 0.0 +Collinsella aerofaciens K02358 9.55 7.2 +Collinsella aerofaciens K02935 0.0 3.5999999999999996 +Collinsella aerofaciens K03737 10.55 6.15 +Collinsella aerofaciens K03695 6.800000000000001 6.6499999999999995 +Collinsella aerofaciens K02986 1.05 0.0 +Collinsella aerofaciens K02990 0.0 3.5999999999999996 +Collinsella aerofaciens K10112 5.65 3.1 +Collinsella aerofaciens K00134 5.6 21.1 +Collinsella intestinalis 42.60000000000001 63.150000000000006 +Collinsella intestinalis K03695 6.800000000000001 6.6499999999999995 +Collinsella intestinalis K00134 5.050000000000001 18.5 +Collinsella intestinalis K00262 8.5 14.350000000000001 +Collinsella intestinalis K02986 1.05 0.0 +Collinsella intestinalis K02358 9.55 2.05 +Collinsella intestinalis K03737 11.05 6.6499999999999995 +Coprococcus comes K01803 7.35 5.15 +Coprococcus comes K00927 5.0 10.75 +Coprococcus comes K00134 24.75 42.15 +Coprococcus comes K01810 12.8 19.0 +Coprococcus comes K02867 5.0 4.6 +Coprococcus comes K02863 10.15 4.6 +Coprococcus comes K02864 1.2 0.0 +Coprococcus comes K02935 12.75 16.4 +Coprococcus comes K03043 15.75 17.45 +Coprococcus comes 79.65 101.15 +Coprococcus comes K03046 24.7 16.45 +Coprococcus comes K02992 9.100000000000001 4.65 +Coprococcus comes K02355 23.55 18.5 +Coprococcus comes K02358 32.05 27.2 +Coprococcus comes K02996 5.050000000000001 7.6499999999999995 +Coprococcus comes K02946 2.35 7.1499999999999995 +Coprococcus comes K02965 7.15 4.1 +Coprococcus comes K02982 7.8 10.3 +Coprococcus comes K02874 1.2 4.6 +Coprococcus comes K02931 9.5 7.699999999999999 +Coprococcus comes K02988 7.3500000000000005 5.6 +Coprococcus comes K02952 5.050000000000001 2.55 +Coprococcus comes K03040 10.0 4.65 +Coprococcus comes K01571 13.5 13.85 +Coprococcus comes K00053 5.6 18.95 +Coprococcus comes K00975 5.0 6.6499999999999995 +Coprococcus comes K03521 6.15 4.1 +Coprococcus comes K00248 19.6 13.350000000000001 +Coprococcus comes K00074 11.8 26.7 +Coprococcus comes K00626 12.35 18.5 +Coprococcus comes K00656 5.050000000000001 12.3 +Coprococcus comes K01006 36.95 57.05 +Coprococcus comes K03737 14.0 23.1 +Coprococcus comes K02111 7.8 4.6 +Coprococcus comes K02112 11.649999999999999 7.199999999999999 +Coprococcus comes K04043 31.5 22.049999999999997 +Coprococcus comes K00262 11.2 23.1 +Coprococcus comes K04077 27.549999999999997 29.25 +Coprococcus comes K00088 6.199999999999999 7.1499999999999995 +Coprococcus comes K02945 14.45 15.4 +Coprococcus comes K02967 6.800000000000001 12.850000000000001 +Coprococcus comes K10670 13.5 8.2 +Coprococcus comes K02899 1.05 2.6 +Coprococcus comes K02888 2.95 6.6499999999999995 +Coprococcus comes K02884 5.15 4.65 +Coprococcus comes K03695 9.15 6.65 +Coprococcus comes K01610 22.0 23.6 +Coprococcus comes K01624 12.85 17.5 +Coprococcus comes K01840 5.6 6.6499999999999995 +Coprococcus comes K10112 11.8 10.25 +Coprococcus comes K00616 6.75 9.25 +Coprococcus comes K01681 3.35 6.7 +Dialister invisus K02967 3.95 7.2 +Dialister invisus K03530 1.2 0.0 +Dialister invisus K04077 18.45 13.350000000000001 +Dialister invisus K02358 33.5 14.299999999999999 +Dialister invisus K01847 3.8499999999999996 17.45 +Dialister invisus K01966 11.600000000000001 8.2 +Dialister invisus K01849 21.65 9.75 +Dialister invisus K01848 27.700000000000003 19.5 +Dialister invisus K01067 16.2 11.3 +Dialister invisus K03043 6.800000000000001 7.699999999999999 +Dialister invisus K03046 5.550000000000001 4.1 +Dialister invisus K02867 1.2 4.6 +Dialister invisus K03737 25.35 13.350000000000001 +Dorea formicigenerans K03043 20.8 25.65 +Dorea formicigenerans K03046 23.55 16.45 +Dorea formicigenerans K00053 5.0 20.0 +Dorea formicigenerans 61.75 70.4 +Dorea formicigenerans K10670 13.45 4.6 +Dorea formicigenerans K01756 6.199999999999999 4.1 +Dorea formicigenerans K00262 11.8 24.65 +Dorea formicigenerans K04043 29.15 19.0 +Dorea formicigenerans K00088 3.35 9.25 +Dorea formicigenerans K04077 18.45 30.8 +Dorea formicigenerans K02992 3.35 4.6 +Dorea formicigenerans K02355 33.0 30.299999999999997 +Dorea formicigenerans K02358 33.15 26.200000000000003 +Dorea formicigenerans K01624 5.050000000000001 7.1499999999999995 +Dorea formicigenerans K02867 5.550000000000001 5.15 +Dorea formicigenerans K02863 8.95 4.1 +Dorea formicigenerans K02864 1.75 0.0 +Dorea formicigenerans K02935 19.1 21.55 +Dorea formicigenerans K04072 7.25 7.699999999999999 +Dorea formicigenerans K02879 1.05 1.0 +Dorea formicigenerans K03040 10.0 4.65 +Dorea formicigenerans K02986 5.0 7.1499999999999995 +Dorea formicigenerans K02952 4.45 6.15 +Dorea formicigenerans K02988 4.6 4.6 +Dorea formicigenerans K02931 6.65 4.6 +Dorea formicigenerans K02874 3.35 4.1 +Dorea formicigenerans K02982 5.0 8.75 +Dorea formicigenerans K02890 2.8 1.05 +Dorea formicigenerans K02965 7.15 4.1 +Dorea formicigenerans K02886 6.800000000000001 4.6 +Dorea formicigenerans K02926 2.1 3.6 +Dorea formicigenerans K02946 4.6 3.55 +Dorea formicigenerans K00134 23.65 38.05 +Dorea formicigenerans K00927 9.45 9.75 +Dorea formicigenerans K01803 6.199999999999999 8.2 +Dorea formicigenerans K00656 10.1 16.4 +Dorea formicigenerans K02899 1.05 2.6 +Dorea formicigenerans K02888 2.95 6.6499999999999995 +Dorea formicigenerans K02945 6.75 7.199999999999999 +Dorea formicigenerans K01571 10.7 11.8 +Dorea formicigenerans K00133 2.8 4.6 +Dorea formicigenerans K01938 3.95 10.8 +Dorea formicigenerans K01610 20.45 19.5 +Dorea formicigenerans K10540 6.800000000000001 2.6 +Dorea formicigenerans K10542 0.0 6.7 +Dorea formicigenerans K03695 16.4 10.75 +Dorea formicigenerans K01006 18.25 23.1 +Dorea formicigenerans K03737 10.1 15.4 +Dorea formicigenerans K10112 13.5 8.75 +Dorea formicigenerans K02647 3.85 5.6 +Dorea formicigenerans K01681 3.35 6.7 +Dorea formicigenerans K02112 10.7 9.75 +Dorea formicigenerans K00975 3.3 7.2 +Dorea formicigenerans K00616 12.55 8.2 +Dorea formicigenerans K02967 9.100000000000001 11.3 +Dorea formicigenerans K02996 4.4 4.6 +Enterococcus faecalis K03695 10.7 7.699999999999999 +Enterococcus faecalis K02967 0.0 4.6 +Enterococcus faecalis K10112 8.95 3.1 +Enterococcus faecalis K00134 5.050000000000001 20.549999999999997 +Enterococcus faecalis K03046 5.0 4.6 +Enterococcus faecalis K02867 4.4 4.6 +Enterococcus faecalis K00046 4.15 0.0 +Enterococcus faecalis K00088 1.2 6.1499999999999995 +Enterococcus faecalis K02355 7.3500000000000005 5.65 +Enterococcus faecalis K02358 11.3 12.799999999999999 +Escherichia coli str. K-12 substr. MG1655 K03386 0.0 0.0 +Escherichia coli str. K-12 substr. MG1655 K04047 0.0 0.0 +Escherichia coli str. K-12 substr. MG1655 K00656 0.0 0.0 +Escherichia coli str. K-12 substr. MG1655 K04072 0.0 0.0 +Escherichia coli str. K-12 substr. MG1655 K06078 0.0 0.0 +Escherichia coli str. K-12 substr. MG1655 K00262 5.75 5.65 +Escherichia coli str. K-12 substr. MG1655 K00134 2.25 2.05 +Escherichia coli str. K-12 substr. MG1655 K01689 0.0 0.0 +Escherichia coli str. K-12 substr. MG1655 K01624 0.0 0.0 +Escherichia coli str. K-12 substr. MG1655 K00927 0.0 0.0 +Escherichia coli str. K-12 substr. MG1655 K02358 14.700000000000001 24.7 +Escherichia coli str. K-12 substr. MG1655 K02867 1.2 4.6 +Escherichia coli str. K-12 substr. MG1655 K01744 0.0 0.0 +Escherichia coli str. K-12 substr. MG1655 K04077 2.95 0.0 +Eubacterium rectale K01681 3.35 10.8 +Eubacterium rectale K00611 0.0 8.7 +Eubacterium rectale K02111 4.95 6.6499999999999995 +Eubacterium rectale K02112 2.25 19.5 +Eubacterium rectale 66.3 209.35 +Eubacterium rectale K01810 4.45 52.9 +Eubacterium rectale K02867 10.15 4.6 +Eubacterium rectale K02863 3.85 9.75 +Eubacterium rectale K02864 1.2 8.7 +Eubacterium rectale K02935 19.1 22.1 +Eubacterium rectale K03043 15.799999999999999 38.0 +Eubacterium rectale K03046 13.95 19.55 +Eubacterium rectale K02950 4.4 4.1 +Eubacterium rectale K02992 5.2 12.3 +Eubacterium rectale K02355 19.7 51.35 +Eubacterium rectale K02358 32.7 65.2 +Eubacterium rectale K02946 5.65 6.7 +Eubacterium rectale K02926 0.0 14.9 +Eubacterium rectale K02886 6.75 6.15 +Eubacterium rectale K02965 6.050000000000001 4.1 +Eubacterium rectale K02890 0.0 5.65 +Eubacterium rectale K02982 6.6 14.4 +Eubacterium rectale K02874 2.35 6.6499999999999995 +Eubacterium rectale K02931 14.0 12.3 +Eubacterium rectale K02933 3.85 7.1499999999999995 +Eubacterium rectale K02988 2.35 18.0 +Eubacterium rectale K02876 0.0 8.2 +Eubacterium rectale K00939 1.6 9.75 +Eubacterium rectale K02952 5.0 6.15 +Eubacterium rectale K02948 3.35 5.15 +Eubacterium rectale K02986 6.25 15.399999999999999 +Eubacterium rectale K03040 12.2 9.25 +Eubacterium rectale K02879 5.0 6.1499999999999995 +Eubacterium rectale K00789 3.3 2.55 +Eubacterium rectale K00656 2.8 25.15 +Eubacterium rectale K10540 6.199999999999999 5.6 +Eubacterium rectale K10542 0.0 8.7 +Eubacterium rectale K07407 0.0 4.65 +Eubacterium rectale K03530 2.35 20.0 +Eubacterium rectale K10108 0.0 8.2 +Eubacterium rectale K06023 0.0 6.15 +Eubacterium rectale K01269 0.0 11.850000000000001 +Eubacterium rectale K01624 21.799999999999997 38.0 +Eubacterium rectale K01915 1.05 11.3 +Eubacterium rectale K00626 31.65 58.050000000000004 +Eubacterium rectale K00074 18.05 44.2 +Eubacterium rectale K00248 14.6 76.5 +Eubacterium rectale K03521 28.15 41.1 +Eubacterium rectale K03522 0.0 35.45 +Eubacterium rectale K01358 0.0 7.1499999999999995 +Eubacterium rectale K01715 0.0 10.8 +Eubacterium rectale K02026 0.0 5.6 +Eubacterium rectale K10188 0.0 0.0 +Eubacterium rectale K03737 63.6 84.19999999999999 +Eubacterium rectale K00925 0.0 7.6499999999999995 +Eubacterium rectale K02884 3.35 5.15 +Eubacterium rectale K01952 5.050000000000001 15.399999999999999 +Eubacterium rectale K00134 49.6 69.85 +Eubacterium rectale K00927 6.15 30.299999999999997 +Eubacterium rectale K01803 2.25 36.45 +Eubacterium rectale K00602 0.0 25.7 +Eubacterium rectale K01492 0.0 25.7 +Eubacterium rectale K04079 4.4 7.699999999999999 +Eubacterium rectale K01966 0.0 7.6499999999999995 +Eubacterium rectale K01571 9.5 20.0 +Eubacterium rectale K02945 1.05 11.8 +Eubacterium rectale K02888 5.15 9.25 +Eubacterium rectale K02357 0.0 14.4 +Eubacterium rectale K02967 8.5 14.9 +Eubacterium rectale K00705 0.0 15.4 +Eubacterium rectale K01006 28.5 78.05000000000001 +Eubacterium rectale K01880 3.8499999999999996 4.1 +Eubacterium rectale K00831 0.0 18.5 +Eubacterium rectale K04043 24.15 24.15 +Eubacterium rectale K00962 7.65 18.5 +Eubacterium rectale K02887 1.2 4.6 +Eubacterium rectale K00053 3.85 32.35 +Eubacterium rectale K01610 28.7 50.85 +Eubacterium rectale K00133 1.75 7.699999999999999 +Eubacterium rectale K04072 6.199999999999999 9.75 +Eubacterium rectale K04077 21.9 70.9 +Eubacterium rectale K04078 2.8 5.1 +Eubacterium rectale K10112 22.55 60.599999999999994 +Eubacterium rectale K00688 1.6 34.95 +Eubacterium rectale K00615 2.1 12.85 +Eubacterium rectale K00616 16.5 27.2 +Eubacterium rectale K01591 0.0 9.75 +Eubacterium rectale K10206 0.0 10.25 +Eubacterium rectale K00088 2.25 23.6 +Eubacterium rectale K03695 9.55 12.350000000000001 +Eubacterium rectale K01689 2.1 1.0 +Eubacterium rectale K02996 4.45 8.2 +Eubacterium rectale K02871 0.0 8.7 +Eubacterium rectale K00262 34.0 63.15 +Eubacterium rectale K02406 0.0 4.6 +Faecalibacterium prausnitzii K02804 10.2 0.0 +Faecalibacterium prausnitzii K03737 236.25 55.95 +Faecalibacterium prausnitzii K03527 20.200000000000003 0.0 +Faecalibacterium prausnitzii K02355 114.05 30.25 +Faecalibacterium prausnitzii K02996 19.1 6.199999999999999 +Faecalibacterium prausnitzii K01006 157.75 13.85 +Faecalibacterium prausnitzii K02112 78.10000000000001 33.400000000000006 +Faecalibacterium prausnitzii K02111 17.9 5.2 +Faecalibacterium prausnitzii K00703 20.95 11.8 +Faecalibacterium prausnitzii K00975 17.200000000000003 2.05 +Faecalibacterium prausnitzii K02358 65.0 35.95 +Faecalibacterium prausnitzii K02992 9.9 4.1 +Faecalibacterium prausnitzii K03046 50.35 14.35 +Faecalibacterium prausnitzii K03043 16.8 10.2 +Faecalibacterium prausnitzii K07335 8.3 6.2 +Faecalibacterium prausnitzii K01803 15.75 4.6 +Faecalibacterium prausnitzii K00927 56.849999999999994 17.95 +Faecalibacterium prausnitzii K00134 138.45 73.95 +Faecalibacterium prausnitzii K02935 8.4 1.05 +Faecalibacterium prausnitzii K02863 13.45 2.0 +Faecalibacterium prausnitzii K02867 20.0 13.299999999999999 +Faecalibacterium prausnitzii K01689 3.35 1.0 +Faecalibacterium prausnitzii K00040 39.199999999999996 2.0 +Faecalibacterium prausnitzii K01686 7.2 1.0 +Faecalibacterium prausnitzii K01625 38.7 39.6 +Faecalibacterium prausnitzii K00874 33.35 8.75 +Faecalibacterium prausnitzii K00046 17.75 3.05 +Faecalibacterium prausnitzii K00041 23.5 5.1499999999999995 +Faecalibacterium prausnitzii K00761 24.1 0.0 +Faecalibacterium prausnitzii K03798 3.3 0.0 +Faecalibacterium prausnitzii K10542 40.050000000000004 8.2 +Faecalibacterium prausnitzii K10540 16.35 0.0 +Faecalibacterium prausnitzii K00625 28.25 9.2 +Faecalibacterium prausnitzii 444.20000000000005 216.14999999999998 +Faecalibacterium prausnitzii K04077 118.4 11.3 +Faecalibacterium prausnitzii K01081 28.1 0.0 +Faecalibacterium prausnitzii K01966 10.6 0.0 +Faecalibacterium prausnitzii K01571 30.799999999999997 9.2 +Faecalibacterium prausnitzii K00626 172.6 53.95 +Faecalibacterium prausnitzii K01715 31.550000000000004 0.0 +Faecalibacterium prausnitzii K00074 73.1 60.05 +Faecalibacterium prausnitzii K00248 134.9 56.95 +Faecalibacterium prausnitzii K03521 36.949999999999996 11.25 +Faecalibacterium prausnitzii K03522 50.1 20.0 +Faecalibacterium prausnitzii K02967 16.450000000000003 9.8 +Faecalibacterium prausnitzii K02356 10.9 0.0 +Faecalibacterium prausnitzii K01810 12.8 1.05 +Faecalibacterium prausnitzii K00962 32.1 14.899999999999999 +Faecalibacterium prausnitzii K00048 41.85 1.55 +Faecalibacterium prausnitzii K01840 10.55 4.1 +Faecalibacterium prausnitzii K00262 31.65 22.6 +Faecalibacterium prausnitzii K02027 36.3 9.7 +Faecalibacterium prausnitzii K00925 32.7 14.849999999999998 +Faecalibacterium prausnitzii K04043 56.25 12.3 +Faecalibacterium prausnitzii K01610 56.800000000000004 44.65 +Faecalibacterium prausnitzii K03040 25.05 0.0 +Faecalibacterium prausnitzii K02986 15.899999999999999 0.0 +Faecalibacterium prausnitzii K02948 14.700000000000001 8.2 +Faecalibacterium prausnitzii K02952 12.200000000000001 2.0 +Faecalibacterium prausnitzii K02988 14.0 0.0 +Faecalibacterium prausnitzii K02933 6.15 4.65 +Faecalibacterium prausnitzii K02994 12.5 2.0 +Faecalibacterium prausnitzii K02931 9.9 0.0 +Faecalibacterium prausnitzii K02982 13.7 3.0999999999999996 +Faecalibacterium prausnitzii K02965 8.8 4.65 +Faecalibacterium prausnitzii K02926 10.0 4.1 +Faecalibacterium prausnitzii K10192 22.4 1.55 +Faecalibacterium prausnitzii K00656 5.949999999999999 19.0 +Faecalibacterium prausnitzii K03615 6.75 1.0 +Faecalibacterium prausnitzii K01624 42.1 23.1 +Faecalibacterium prausnitzii K10112 114.25 29.8 +Faecalibacterium prausnitzii K04567 26.55 0.0 +Faecalibacterium prausnitzii K03531 5.6 2.0 +Faecalibacterium prausnitzii K03695 19.6 3.55 +Faecalibacterium prausnitzii K01812 3.55 6.7 +Lactobacillus reuteri K03043 4.6 5.1 +Lactobacillus reuteri K02358 0.0 7.699999999999999 +Lactobacillus reuteri K00134 5.6 18.5 +Lactobacillus reuteri K02867 1.2 4.6 +Methanobrevibacter smithii 10.1 15.35 +Methanobrevibacter smithii K00262 8.4 15.4 +Mycobacterium tuberculosis 3.35 0.0 +Parascardovia denticolens K10243 7.8500000000000005 4.1 +Parascardovia denticolens K02355 6.199999999999999 6.15 +Parascardovia denticolens K02946 8.4 4.6 +Parascardovia denticolens K02886 3.85 3.05 +Parascardovia denticolens K02895 3.95 4.1 +Parascardovia denticolens K01915 2.65 1.05 +Parascardovia denticolens K01689 6.65 4.6 +Parascardovia denticolens K04043 3.4000000000000004 3.05 +Parascardovia denticolens K02963 1.2 0.0 +Parascardovia denticolens K04077 5.050000000000001 2.6 +Prevotella copri K00041 0.0 0.0 +Prevotella copri K00346 0.0 0.0 +Prevotella copri K00040 9.600000000000001 1.0 +Prevotella copri 21.9 24.65 +Prevotella copri K00134 5.65 4.1 +Prevotella copri K04077 2.65 5.1 +Prevotella copri K03287 0.0 0.0 +Prevotella copri K00088 1.2 0.0 +Prevotella copri K00239 8.5 4.6 +Prevotella copri K00240 0.0 0.0 +Prevotella copri K00656 6.15 13.350000000000001 +Prevotella copri K00262 4.550000000000001 9.25 +Prevotella copri K02967 0.0 1.05 +Prevotella copri K02355 6.199999999999999 1.0 +Prevotella copri K03043 8.35 0.0 +Prevotella copri K02935 0.0 0.0 +Prevotella copri K02864 0.0 0.0 +Prevotella copri K02867 3.35 3.5999999999999996 +Prevotella copri K02358 4.550000000000001 1.55 +Prevotella copri K02557 0.0 0.0 +Prevotella copri K01952 0.0 0.0 +Prevotella copri K05349 0.0 0.0 +Prevotella copri K01610 16.2 12.3 +Prevotella copri K00874 0.0 0.0 +Prevotella copri K00895 0.0 0.0 +Prevotella copri K01858 1.6 2.6 +Prevotella copri K01785 0.0 0.0 +Prevotella copri K02110 0.0 0.0 +Prevotella copri K01603 0.0 0.0 +Prevotella copri K01966 0.0 0.0 +Prevotella copri K03737 7.8 6.65 +Roseburia intestinalis K02888 6.800000000000001 7.699999999999999 +Roseburia intestinalis 350.19999999999993 162.75 +Roseburia intestinalis K03043 23.1 25.65 +Roseburia intestinalis K02950 4.95 4.1 +Roseburia intestinalis K02992 14.75 5.6499999999999995 +Roseburia intestinalis K02355 34.45 21.05 +Roseburia intestinalis K02358 44.0 14.9 +Roseburia intestinalis K02946 7.35 4.6 +Roseburia intestinalis K02965 7.15 4.1 +Roseburia intestinalis K02890 5.050000000000001 0.0 +Roseburia intestinalis K02982 9.5 9.75 +Roseburia intestinalis K02931 20.65 13.350000000000001 +Roseburia intestinalis K02994 10.2 3.5999999999999996 +Roseburia intestinalis K02988 12.399999999999999 5.1 +Roseburia intestinalis K02948 5.6 1.05 +Roseburia intestinalis K02986 8.4 8.2 +Roseburia intestinalis K03040 15.450000000000001 6.6499999999999995 +Roseburia intestinalis K00975 8.95 2.05 +Roseburia intestinalis K01681 7.8 5.65 +Roseburia intestinalis K00789 3.3 2.55 +Roseburia intestinalis K03530 2.35 17.5 +Roseburia intestinalis K02871 10.55 0.0 +Roseburia intestinalis K02996 10.0 2.05 +Roseburia intestinalis K03737 133.7 29.25 +Roseburia intestinalis K01952 6.15 9.25 +Roseburia intestinalis K00134 52.8 65.25 +Roseburia intestinalis K00927 23.6 15.9 +Roseburia intestinalis K01803 7.949999999999999 7.7 +Roseburia intestinalis K00616 25.05 24.65 +Roseburia intestinalis K01938 2.8 3.5999999999999996 +Roseburia intestinalis K03521 37.099999999999994 33.9 +Roseburia intestinalis K00248 38.15 31.299999999999997 +Roseburia intestinalis K00626 83.25 35.45 +Roseburia intestinalis K01915 6.65 1.0 +Roseburia intestinalis K01624 24.7 20.55 +Roseburia intestinalis K03695 16.3 8.7 +Roseburia intestinalis K02967 13.1 11.3 +Roseburia intestinalis K01689 2.8 1.0 +Roseburia intestinalis K00133 4.0 3.1 +Roseburia intestinalis K00053 27.1 7.699999999999999 +Roseburia intestinalis K01006 56.8 42.65 +Roseburia intestinalis K01939 9.0 5.65 +Roseburia intestinalis K01571 16.1 13.350000000000001 +Roseburia intestinalis K00962 8.35 4.1 +Roseburia intestinalis K01880 5.550000000000001 3.55 +Roseburia intestinalis K04043 33.55 15.4 +Roseburia intestinalis K02406 11.8 0.0 +Roseburia intestinalis K01810 16.75 25.65 +Roseburia intestinalis K01610 46.1 25.15 +Roseburia intestinalis K02112 21.9 6.6499999999999995 +Roseburia intestinalis K02867 6.800000000000001 2.55 +Roseburia intestinalis K02863 12.95 4.1 +Roseburia intestinalis K02864 6.800000000000001 0.0 +Roseburia intestinalis K02935 19.0 20.5 +Roseburia intestinalis K02884 3.35 5.15 +Roseburia intestinalis K04759 0.0 0.0 +Roseburia intestinalis K00262 41.95 54.95 +Roseburia intestinalis K00625 6.15 3.5999999999999996 +Ruminococcus gnavus K03695 15.350000000000001 10.25 +Ruminococcus gnavus K00262 16.3 27.200000000000003 +Ruminococcus gnavus K01571 12.35 12.85 +Ruminococcus gnavus K02945 13.850000000000001 11.3 +Ruminococcus gnavus K04043 37.55 23.65 +Ruminococcus gnavus 98.7 89.85 +Ruminococcus gnavus K01939 6.199999999999999 4.6 +Ruminococcus gnavus K02996 3.95 4.6 +Ruminococcus gnavus K10439 0.0 0.0 +Ruminococcus gnavus K01818 1.2 3.5999999999999996 +Ruminococcus gnavus K01610 24.3 27.700000000000003 +Ruminococcus gnavus K02867 5.0 5.1 +Ruminococcus gnavus K02863 9.100000000000001 5.1 +Ruminococcus gnavus K02935 6.65 5.65 +Ruminococcus gnavus K03043 15.299999999999999 19.0 +Ruminococcus gnavus K03046 12.85 9.25 +Ruminococcus gnavus K02992 9.100000000000001 5.15 +Ruminococcus gnavus K02355 17.200000000000003 16.450000000000003 +Ruminococcus gnavus K02358 39.45 34.4 +Ruminococcus gnavus K01624 9.55 12.8 +Ruminococcus gnavus K01756 6.199999999999999 4.1 +Ruminococcus gnavus K00134 18.55 30.8 +Ruminococcus gnavus K00927 8.35 9.75 +Ruminococcus gnavus K01803 6.800000000000001 5.15 +Ruminococcus gnavus K02899 1.05 2.6 +Ruminococcus gnavus K00053 8.95 20.05 +Ruminococcus gnavus K00656 8.4 20.55 +Ruminococcus gnavus K04078 3.35 3.5999999999999996 +Ruminococcus gnavus K04077 26.95 26.15 +Ruminococcus gnavus K00088 6.199999999999999 5.1 +Ruminococcus gnavus K02967 9.55 10.25 +Ruminococcus gnavus K04072 6.15 6.6499999999999995 +Ruminococcus gnavus K02879 0.0 0.0 +Ruminococcus gnavus K03040 10.55 5.65 +Ruminococcus gnavus K02986 3.85 6.1499999999999995 +Ruminococcus gnavus K02988 2.35 0.0 +Ruminococcus gnavus K02994 2.35 2.05 +Ruminococcus gnavus K02931 9.5 8.2 +Ruminococcus gnavus K02874 1.2 4.1 +Ruminococcus gnavus K02982 7.8 8.2 +Ruminococcus gnavus K02965 7.15 4.1 +Ruminococcus gnavus K02886 6.75 3.1 +Ruminococcus gnavus K02946 2.35 3.55 +Ruminococcus gnavus K10112 12.95 8.75 +Ruminococcus gnavus K00616 13.700000000000001 10.8 +Ruminococcus gnavus K01681 4.45 7.2 +Ruminococcus gnavus K00133 3.3 4.6 +Ruminococcus gnavus K01006 33.45 42.6 +Ruminococcus gnavus K03737 14.6 17.450000000000003 +Ruminococcus lactaris K01740 4.550000000000001 3.1 +Ruminococcus lactaris K01952 7.2 6.15 +Ruminococcus lactaris K01939 7.3500000000000005 4.6 +Ruminococcus lactaris K10112 20.2 15.95 +Ruminococcus lactaris K02996 4.45 3.05 +Ruminococcus lactaris K02888 4.550000000000001 6.6499999999999995 +Ruminococcus lactaris K02899 1.05 2.6 +Ruminococcus lactaris K00262 20.2 30.799999999999997 +Ruminococcus lactaris K01006 43.400000000000006 50.85 +Ruminococcus lactaris K00048 7.25 3.5999999999999996 +Ruminococcus lactaris K01610 23.1 24.15 +Ruminococcus lactaris K02355 26.799999999999997 20.5 +Ruminococcus lactaris 142.29999999999998 95.45 +Ruminococcus lactaris K00616 6.6 5.6 +Ruminococcus lactaris K01810 13.4 19.0 +Ruminococcus lactaris K03695 15.299999999999999 9.25 +Ruminococcus lactaris K01624 14.0 11.8 +Ruminococcus lactaris K03737 17.200000000000003 21.049999999999997 +Ruminococcus lactaris K01681 3.35 7.199999999999999 +Ruminococcus lactaris K00053 18.45 18.45 +Ruminococcus lactaris K00625 2.8 4.1 +Ruminococcus lactaris K00133 3.8499999999999996 4.1 +Ruminococcus lactaris K01689 1.2 1.0 +Ruminococcus lactaris K00134 41.7 46.75 +Ruminococcus lactaris K00927 13.95 14.9 +Ruminococcus lactaris K01803 6.199999999999999 7.6499999999999995 +Ruminococcus lactaris K01571 12.95 13.35 +Ruminococcus lactaris K02945 11.649999999999999 8.2 +Ruminococcus lactaris K04078 4.45 2.05 +Ruminococcus lactaris K04077 26.8 19.5 +Ruminococcus lactaris K00088 5.6 7.699999999999999 +Ruminococcus lactaris K02967 9.5 10.75 +Ruminococcus lactaris K02946 6.800000000000001 6.6499999999999995 +Ruminococcus lactaris K02965 7.15 4.1 +Ruminococcus lactaris K02982 7.25 9.8 +Ruminococcus lactaris K02874 1.75 4.1 +Ruminococcus lactaris K02931 7.25 6.7 +Ruminococcus lactaris K02994 12.45 6.7 +Ruminococcus lactaris K02988 10.1 3.5999999999999996 +Ruminococcus lactaris K02952 3.95 2.05 +Ruminococcus lactaris K02986 4.4 7.1499999999999995 +Ruminococcus lactaris K03040 10.6 5.15 +Ruminococcus lactaris K04072 25.2 21.05 +Ruminococcus lactaris K04043 39.35 23.65 +Ruminococcus lactaris K02358 27.049999999999997 20.0 +Ruminococcus lactaris K02992 9.15 4.65 +Ruminococcus lactaris K00975 5.0 5.65 +Ruminococcus lactaris K10540 17.65 5.65 +Ruminococcus lactaris K03046 16.8 12.350000000000001 +Ruminococcus lactaris K03043 15.75 21.05 +Ruminococcus lactaris K02935 6.6 4.1 +Ruminococcus lactaris K02864 4.45 8.75 +Ruminococcus lactaris K02863 10.7 4.6 +Ruminococcus lactaris K02867 5.550000000000001 5.15 +Ruminococcus lactaris K00850 5.6 1.0 +Ruminococcus lactaris K01840 7.25 6.7 +Ruminococcus lactaris K00656 14.6 13.9 +Ruminococcus obeum K02996 3.85 6.15 +Ruminococcus obeum K02871 6.15 4.6 +Ruminococcus obeum K10439 4.95 5.65 +Ruminococcus obeum K01818 7.2 7.2 +Ruminococcus obeum 175.7 125.35 +Ruminococcus obeum K01628 1.6 2.55 +Ruminococcus obeum K10112 17.299999999999997 13.35 +Ruminococcus obeum K07567 1.05 3.0999999999999996 +Ruminococcus obeum K02112 23.75 10.25 +Ruminococcus obeum K01689 2.1 1.0 +Ruminococcus obeum K04072 6.199999999999999 5.6499999999999995 +Ruminococcus obeum K01681 1.75 6.15 +Ruminococcus obeum K02967 8.0 6.7 +Ruminococcus obeum K01610 13.45 14.850000000000001 +Ruminococcus obeum K01803 2.8 4.1 +Ruminococcus obeum K00927 8.85 10.8 +Ruminococcus obeum K00134 51.05 49.35 +Ruminococcus obeum K01006 26.35 37.5 +Ruminococcus obeum K02355 9.45 9.25 +Ruminococcus obeum K01571 11.2 12.85 +Ruminococcus obeum K02945 14.45 12.850000000000001 +Ruminococcus obeum K04078 8.95 3.5999999999999996 +Ruminococcus obeum K04077 22.35 25.2 +Ruminococcus obeum K00088 3.95 4.6 +Ruminococcus obeum K00262 5.550000000000001 13.850000000000001 +Ruminococcus obeum K02888 5.15 7.6499999999999995 +Ruminococcus obeum K01810 13.4 19.5 +Ruminococcus obeum K00656 9.55 10.8 +Ruminococcus obeum K02864 4.45 8.75 +Ruminococcus obeum K02935 7.25 5.15 +Ruminococcus obeum K03043 10.55 13.350000000000001 +Ruminococcus obeum K03046 17.8 17.45 +Ruminococcus obeum K02950 4.4 4.1 +Ruminococcus obeum K02992 11.9 7.1499999999999995 +Ruminococcus obeum K02358 27.65 32.849999999999994 +Ruminococcus obeum K00133 2.8 5.65 +Ruminococcus obeum K03737 45.650000000000006 29.799999999999997 +Ruminococcus obeum K02948 6.050000000000001 1.05 +Ruminococcus obeum K02986 6.15 5.15 +Ruminococcus obeum K02879 1.05 1.55 +Ruminococcus obeum K01952 6.65 5.65 +Ruminococcus obeum K03530 9.100000000000001 16.450000000000003 +Ruminococcus obeum K01939 5.65 5.15 +Ruminococcus obeum K01938 33.349999999999994 25.15 +Ruminococcus obeum K04043 35.3 23.65 +Ruminococcus obeum K01624 8.4 6.15 +Ruminococcus obeum K03695 12.45 6.15 +Ruminococcus obeum K02946 2.35 1.55 +Ruminococcus obeum K02926 2.1 4.6 +Ruminococcus obeum K02892 2.95 3.1 +Ruminococcus obeum K02890 0.0 0.0 +Ruminococcus obeum K02982 10.0 10.25 +Ruminococcus obeum K02961 2.65 2.6 +Ruminococcus obeum K02874 4.45 6.15 +Ruminococcus obeum K02931 11.649999999999999 11.3 +Ruminococcus obeum K02994 14.45 12.350000000000001 +Ruminococcus obeum K02933 7.2 5.1 +Ruminococcus obeum K02881 3.8499999999999996 5.65 +Ruminococcus obeum K02988 6.75 6.7 +Ruminococcus obeum K01955 2.65 9.75 +Ruminococcus obeum K00962 3.85 7.699999999999999 +Ruminococcus obeum K04567 2.25 4.65 +Ruminococcus obeum K00053 13.5 11.850000000000001 +Ruminococcus obeum K02867 9.0 6.6499999999999995 +Ruminococcus obeum K02863 4.6 14.350000000000001 +Ruminococcus obeum K00616 11.649999999999999 4.1 +Ruminococcus obeum K00197 4.4 5.65 +Ruminococcus obeum K11174 13.4 18.0 +Ruminococcus obeum K00198 13.45 7.699999999999999 +Ruminococcus obeum K00625 4.4 4.1 +Ruminococcus sp. 157.85000000000002 145.8 +Ruminococcus sp. K00278 8.35 12.3 +Ruminococcus sp. K00239 8.35 12.3 +Ruminococcus sp. K04759 0.0 0.0 +Ruminococcus sp. K01689 2.1 1.0 +Ruminococcus sp. K07567 1.05 3.0999999999999996 +Ruminococcus sp. K00656 11.899999999999999 11.3 +Ruminococcus sp. K03737 49.05 30.35 +Ruminococcus sp. K01006 32.55 50.349999999999994 +Ruminococcus sp. K00262 11.149999999999999 19.0 +Ruminococcus sp. K02967 7.5 7.2 +Ruminococcus sp. K00197 5.6 6.1499999999999995 +Ruminococcus sp. K11174 9.5 16.45 +Ruminococcus sp. K00198 9.7 7.199999999999999 +Ruminococcus sp. K02884 2.25 2.05 +Ruminococcus sp. K01610 19.7 23.65 +Ruminococcus sp. K01803 6.199999999999999 8.75 +Ruminococcus sp. K00927 14.55 16.450000000000003 +Ruminococcus sp. K00134 48.3 33.9 +Ruminococcus sp. K02945 23.85 20.049999999999997 +Ruminococcus sp. K01571 11.05 11.3 +Ruminococcus sp. K01966 1.75 0.0 +Ruminococcus sp. K02355 33.55 27.2 +Ruminococcus sp. K02959 5.050000000000001 5.1499999999999995 +Ruminococcus sp. K00925 1.05 1.0 +Ruminococcus sp. K00625 3.85 4.1 +Ruminococcus sp. K00053 7.8 16.45 +Ruminococcus sp. K02112 21.5 10.25 +Ruminococcus sp. K01681 1.75 6.65 +Ruminococcus sp. K02358 32.15 32.9 +Ruminococcus sp. K02992 12.5 7.1499999999999995 +Ruminococcus sp. K02950 4.95 4.1 +Ruminococcus sp. K03046 24.55 18.0 +Ruminococcus sp. K03043 12.8 17.95 +Ruminococcus sp. K02935 10.1 12.3 +Ruminococcus sp. K02864 8.95 10.8 +Ruminococcus sp. K01810 5.0 9.25 +Ruminococcus sp. K02863 6.75 9.25 +Ruminococcus sp. K02867 10.6 9.25 +Ruminococcus sp. K10188 10.0 16.4 +Ruminococcus sp. K03704 5.0 5.6 +Ruminococcus sp. K10439 4.45 5.15 +Ruminococcus sp. K01818 12.8 11.3 +Ruminococcus sp. K01628 3.3 3.5999999999999996 +Ruminococcus sp. K00088 5.050000000000001 5.1 +Ruminococcus sp. K04077 43.05 38.55 +Ruminococcus sp. K04078 14.6 11.3 +Ruminococcus sp. K02996 6.75 7.699999999999999 +Ruminococcus sp. K02871 7.3500000000000005 4.65 +Ruminococcus sp. K10112 17.85 14.4 +Ruminococcus sp. K01955 2.65 8.75 +Ruminococcus sp. K04072 1.6 4.6 +Ruminococcus sp. K03615 3.95 2.6 +Ruminococcus sp. K03695 11.899999999999999 7.699999999999999 +Ruminococcus sp. K00615 4.4 4.65 +Ruminococcus sp. K00616 15.75 12.850000000000001 +Ruminococcus sp. K02946 7.3500000000000005 5.65 +Ruminococcus sp. K02926 3.2 7.1499999999999995 +Ruminococcus sp. K02892 5.6 4.6 +Ruminococcus sp. K02886 3.2 2.6 +Ruminococcus sp. K02965 9.850000000000001 4.6 +Ruminococcus sp. K02890 0.0 0.0 +Ruminococcus sp. K02982 7.75 11.8 +Ruminococcus sp. K02961 2.65 2.6 +Ruminococcus sp. K02874 4.95 2.6 +Ruminococcus sp. K02895 1.05 0.0 +Ruminococcus sp. K02931 14.55 14.899999999999999 +Ruminococcus sp. K02994 15.0 16.95 +Ruminococcus sp. K02933 7.9 7.699999999999999 +Ruminococcus sp. K02881 7.25 8.2 +Ruminococcus sp. K02988 11.3 7.2 +Ruminococcus sp. K02876 0.0 0.0 +Ruminococcus sp. K02952 3.8499999999999996 1.55 +Ruminococcus sp. K02948 6.050000000000001 1.05 +Ruminococcus sp. K02986 6.65 5.1499999999999995 +Ruminococcus sp. K03040 4.45 4.6 +Ruminococcus sp. K02879 7.8 3.5999999999999996 +Ruminococcus sp. K01952 6.15 7.1499999999999995 +Ruminococcus sp. K04043 34.0 21.549999999999997 +Ruminococcus sp. K00133 3.3 5.65 +Ruminococcus sp. K00962 3.85 7.199999999999999 +Ruminococcus sp. K01840 5.0 6.6499999999999995 +Ruminococcus sp. K03530 9.0 16.95 +Ruminococcus sp. K01624 11.3 10.75 +Ruminococcus sp. K01875 2.1 2.6 +Ruminococcus sp. K07469 5.0 7.1499999999999995 +Ruminococcus sp. K01938 23.3 14.35 +Ruminococcus sp. K01804 2.8 5.65 +Shigella sp. K00134 4.4 9.2 +Shigella sp. K00262 5.75 5.65 +Shigella sp. K06078 0.0 0.0 +Shigella sp. K04072 0.0 0.0 +Shigella sp. K03286 0.0 0.0 +Shigella sp. K09476 0.0 0.0 +Shigella sp. K00927 0.0 0.0 +Shigella sp. K01624 0.0 0.0 +Shigella sp. K01689 0.0 0.0 +Shigella sp. K03695 11.2 8.2 +Shigella sp. K01744 0.0 0.0 +Shigella sp. K04077 2.95 0.0 +Shigella sp. K04043 1.2 0.0 +Shigella sp. K03386 0.0 0.0 +Shigella sp. K00656 0.0 0.0 +Shigella sp. K11934 0.0 0.0 +Shigella sp. K04047 0.0 0.0 +Shigella sp. K03046 4.45 4.1 +Shigella sp. K02867 1.2 4.6 \ No newline at end of file