CCMP Report


Input File

Data Source: Ileal Chron's disease post-resection (Group 1) and Healthy control (Group 2) from Halfvarson et al.

Group 1

Sample Fastq
Sample 1 Sample107.fastq
Sample 2 Sample13.fastq
Sample 3 Sample3.fastq
Sample 4 Sample5.fastq
Sample 5 Sample121.fastq
Sample 6 Sample108.fastq
Sample 7 Sample53.fastq
Sample 8 Sample48.fastq
Sample 9 Sample21.fastq
Sample 10 Sample62.fastq
Sample 11 Sample89.fastq
Sample 12 Sample37.fastq
Sample 13 Sample24.fastq
Sample 14 Sample28.fastq
Sample 15 Sample98.fastq
Sample 16 Sample95.fastq
Sample 17 Sample109.fastq
Sample 18 Sample82.fastq
Sample 19 Sample23.fastq
Sample 20 Sample58.fastq
Sample 21 Sample51.fastq
Sample 22 Sample88.fastq
Sample 23 Sample56.fastq
Sample 24 Sample112.fastq
Sample 25 Sample55.fastq
Sample 26 Sample34.fastq
Sample 27 Sample123.fastq
Sample 28 Sample32.fastq
Sample 29 Sample18.fastq
Sample 30 Sample79.fastq
Sample 31 Sample19.fastq
Sample 32 Sample41.fastq
Sample 33 Sample26.fastq
Sample 34 Sample42.fastq
Sample 35 Sample74.fastq
Sample 36 Sample9.fastq
Sample 37 Sample115.fastq
Sample 38 Sample72.fastq
Sample 39 Sample86.fastq
Sample 40 Sample59.fastq
Sample 41 Sample117.fastq
Sample 42 Sample69.fastq
Sample 43 Sample16.fastq
Sample 44 Sample76.fastq
Sample 45 Sample73.fastq
Sample 46 Sample14.fastq
Sample 47 Sample110.fastq
Sample 48 Sample45.fastq
Sample 49 Sample64.fastq
Sample 50 Sample50.fastq
Sample 51 Sample102.fastq
Sample 52 Sample106.fastq
Sample 53 Sample71.fastq
Sample 54 Sample96.fastq
Sample 55 Sample84.fastq
Sample 56 Sample68.fastq
Sample 57 Sample100.fastq
Sample 58 Sample91.fastq
Sample 59 Sample83.fastq
Sample 60 Sample31.fastq
Sample 61 Sample78.fastq
Sample 62 Sample125.fastq
Sample 63 Sample118.fastq
Sample 64 Sample52.fastq
Sample 65 Sample101.fastq
Sample 66 Sample122.fastq
Sample 67 Sample17.fastq
Sample 68 Sample7.fastq
Sample 69 Sample43.fastq
Sample 70 Sample103.fastq
Sample 71 Sample66.fastq
Sample 72 Sample4.fastq
Sample 73 Sample6.fastq
Sample 74 Sample47.fastq
Sample 75 Sample46.fastq
Sample 76 Sample81.fastq
Sample 77 Sample85.fastq
Sample 78 Sample120.fastq
Sample 79 Sample57.fastq
Sample 80 Sample33.fastq
Sample 81 Sample93.fastq
Sample 82 Sample63.fastq
Sample 83 Sample77.fastq
Sample 84 Sample12.fastq
Sample 85 Sample8.fastq
Sample 86 Sample97.fastq
Sample 87 Sample2.fastq
Sample 88 Sample15.fastq
Sample 89 Sample67.fastq
Sample 90 Sample114.fastq
Sample 91 Sample44.fastq
Sample 92 Sample22.fastq
Sample 93 Sample119.fastq
Sample 94 Sample111.fastq
Sample 95 Sample49.fastq
Sample 96 Sample60.fastq
Sample 97 Sample27.fastq
Sample 98 Sample90.fastq
Sample 99 Sample80.fastq
Sample 100 Sample61.fastq
Sample 101 Sample36.fastq
Sample 102 Sample10.fastq
Sample 103 Sample99.fastq
Sample 104 Sample116.fastq
Sample 105 Sample65.fastq
Sample 106 Sample104.fastq
Sample 107 Sample40.fastq
Sample 108 Sample92.fastq
Sample 109 Sample29.fastq
Sample 110 Sample124.fastq
Sample 111 Sample87.fastq
Sample 112 Sample39.fastq
Sample 113 Sample105.fastq
Sample 114 Sample11.fastq
Sample 115 Sample113.fastq
Sample 116 Sample54.fastq
Sample 117 Sample1.fastq
Sample 118 Sample25.fastq
Sample 119 Sample35.fastq
Sample 120 Sample94.fastq
Sample 121 Sample38.fastq
Sample 122 Sample75.fastq
Sample 123 Sample20.fastq
Sample 124 Sample70.fastq
Sample 125 Sample30.fastq

Group 2

Sample Fastq
Sample 1 Sample13.fastq
Sample 2 Sample3.fastq
Sample 3 Sample5.fastq
Sample 4 Sample53.fastq
Sample 5 Sample48.fastq
Sample 6 Sample21.fastq
Sample 7 Sample62.fastq
Sample 8 Sample37.fastq
Sample 9 Sample24.fastq
Sample 10 Sample28.fastq
Sample 11 Sample23.fastq
Sample 12 Sample58.fastq
Sample 13 Sample51.fastq
Sample 14 Sample56.fastq
Sample 15 Sample55.fastq
Sample 16 Sample34.fastq
Sample 17 Sample32.fastq
Sample 18 Sample18.fastq
Sample 19 Sample19.fastq
Sample 20 Sample41.fastq
Sample 21 Sample26.fastq
Sample 22 Sample42.fastq
Sample 23 Sample9.fastq
Sample 24 Sample59.fastq
Sample 25 Sample16.fastq
Sample 26 Sample14.fastq
Sample 27 Sample45.fastq
Sample 28 Sample50.fastq
Sample 29 Sample31.fastq
Sample 30 Sample52.fastq
Sample 31 Sample17.fastq
Sample 32 Sample7.fastq
Sample 33 Sample43.fastq
Sample 34 Sample4.fastq
Sample 35 Sample6.fastq
Sample 36 Sample47.fastq
Sample 37 Sample46.fastq
Sample 38 Sample57.fastq
Sample 39 Sample33.fastq
Sample 40 Sample12.fastq
Sample 41 Sample8.fastq
Sample 42 Sample2.fastq
Sample 43 Sample15.fastq
Sample 44 Sample44.fastq
Sample 45 Sample22.fastq
Sample 46 Sample49.fastq
Sample 47 Sample60.fastq
Sample 48 Sample27.fastq
Sample 49 Sample61.fastq
Sample 50 Sample36.fastq
Sample 51 Sample10.fastq
Sample 52 Sample40.fastq
Sample 53 Sample29.fastq
Sample 54 Sample39.fastq
Sample 55 Sample11.fastq
Sample 56 Sample54.fastq
Sample 57 Sample1.fastq
Sample 58 Sample25.fastq
Sample 59 Sample35.fastq
Sample 60 Sample38.fastq
Sample 61 Sample20.fastq
Sample 62 Sample30.fastq


Family Profiles



Statistical Tests of Family Abundance

Linear Model DESeq2 Permutation Test
Family log2(fold change)     padj         p    log2(fold change)     padj         p    log2(fold change)     padj         p   
Mollicutes_RF9_fa 3.77 <0.001 <0.001 3.87 <0.001 <0.001 3.77 <0.001 <0.001
Christensenellaceae 3.05 <0.001 <0.001 3.41 <0.001 <0.001 3.05 <0.001 <0.001
Enterobacteriaceae -3.03 <0.001 <0.001 -7.84 <0.001 <0.001 -3.03 <0.001 <0.001
Prevotellaceae 2.41 <0.001 <0.001 0.89 0.071 0.057 2.41 <0.001 <0.001
Ruminococcaceae 2.25 <0.001 <0.001 1.8 <0.001 <0.001 2.25 <0.001 <0.001
Bacteroidaceae -1.24 <0.001 <0.001 -4.74 <0.001 <0.001 -1.24 <0.001 <0.001
Gastranaerophilales_fa 3.21 <0.001 <0.001 1.11 0.143 0.13 3.21 <0.001 <0.001
Rikenellaceae 0.89 0.007 0.002 -0.6 0.134 0.117 0.89 <0.001 <0.001
Bacteroidales_S24-7_group 7.46 0.011 0.003 6.58 <0.001 <0.001 7.46 <0.001 <0.001
Fusobacteriaceae -10.71 0.014 0.005 -14.25 <0.001 <0.001 -10.71 <0.001 <0.001
Lactobacillaceae -4.86 0.026 0.01 -8.44 <0.001 <0.001 -4.86 <0.001 <0.001
Veillonellaceae -1.33 0.029 0.012 -3.68 <0.001 <0.001 -1.33 0.003 0.001
Clostridiaceae_1 2.39 0.037 0.017 -0.22 0.637 0.637 2.39 0.005 0.002
Bifidobacteriaceae -1.18 0.081 0.039 -3.72 <0.001 <0.001 -1.18 0.024 0.013
Alcaligenaceae -4.45 0.155 0.083 -4.35 <0.001 <0.001 -4.45 0.018 0.009
Enterococcaceae -9.24 0.155 0.086 -11.12 <0.001 <0.001 -9.24 <0.001 <0.001
Acidaminococcaceae -1.49 0.236 0.141 -1.27 0.009 0.006 -1.49 0.092 0.056
Porphyromonadaceae -0.55 0.236 0.147 -3.21 <0.001 <0.001 -0.55 0.088 0.05
Streptococcaceae -0.97 0.287 0.188 -3.73 <0.001 <0.001 -0.97 0.135 0.09
Erysipelotrichaceae 0.39 0.385 0.291 -1.58 <0.001 <0.001 0.39 0.142 0.1
Lachnospiraceae -0.2 0.385 0.292 -2.76 <0.001 <0.001 -0.2 0.16 0.123
Verrucomicrobiaceae 0.68 0.42 0.333 0.39 0.477 0.461 0.68 0.157 0.115
Peptostreptococcaceae -0.44 0.563 0.466 -1.91 <0.001 <0.001 -0.44 0.29 0.232
Campylobacteraceae -5.61 0.579 0.499 -1.83 0.048 0.036 -5.61 0.457 0.426
Desulfovibrionaceae -0.22 0.735 0.672 -2.1 <0.001 <0.001 -0.22 0.392 0.34
Victivallaceae -1.15 0.735 0.709 1.33 0.059 0.046 -1.15 0.673 0.673
Coriobacteriaceae -0.12 0.735 0.71 -2.29 <0.001 <0.001 -0.12 0.394 0.355
Pasteurellaceae 0.2 0.901 0.901 0.8 0.134 0.114 0.2 0.392 0.332


Family Abundance Heatmap



Family Volcano Plots



Statistical Tests of Genus Abundance

Linear Model DESeq2 Permutation Test
Genus log2(fold change)     padj         p     log2(fold change)     padj         p     log2(fold change)     padj         p    
Catenibacterium 5.74 <0.001 <0.001 5.64 <0.001 <0.001 5.74 <0.001 <0.001
Ruminococcaceae_UCG-010 4.71 <0.001 <0.001 4.45 <0.001 <0.001 4.71 <0.001 <0.001
Ruminococcaceae_UCG-002 3.78 <0.001 <0.001 3.35 <0.001 <0.001 3.78 <0.001 <0.001
Mollicutes_RF9_ge 3.77 <0.001 <0.001 3.05 <0.001 <0.001 3.77 <0.001 <0.001
Ruminococcaceae_UCG-005 3.59 <0.001 <0.001 2.5 <0.001 <0.001 3.59 <0.001 <0.001
Gastranaerophilales_ge 3.21 <0.001 <0.001 0.33 0.67 0.641 3.21 <0.001 <0.001
Ruminococcus_1 3.09 <0.001 <0.001 2.4 <0.001 <0.001 3.09 <0.001 <0.001
Christensenellaceae_R-7_group 3.06 <0.001 <0.001 3.05 <0.001 <0.001 3.06 <0.001 <0.001
Anaerotruncus 2.72 <0.001 <0.001 1.28 <0.001 <0.001 2.72 <0.001 <0.001
Ruminococcaceae_UCG-014 2.64 <0.001 <0.001 2.65 <0.001 <0.001 2.64 <0.001 <0.001
Coprococcus_2 2.56 <0.001 <0.001 2.57 <0.001 <0.001 2.56 <0.001 <0.001
Odoribacter 2.48 <0.001 <0.001 0.3 0.487 0.457 2.48 <0.001 <0.001
Prevotella_9 2.47 <0.001 <0.001 1.45 0.008 0.006 2.47 <0.001 <0.001
Subdoligranulum 2.07 <0.001 <0.001 1.1 0.004 0.003 2.07 <0.001 <0.001
Faecalibacterium 1.97 <0.001 <0.001 1.03 0.005 0.004 1.97 <0.001 <0.001
Bacteroides -1.24 <0.001 <0.001 -6.62 <0.001 <0.001 -1.24 <0.001 <0.001
Alloprevotella 7.43 0.001 <0.001 5.54 <0.001 <0.001 7.43 <0.001 <0.001
Butyrivibrio 8.16 0.002 <0.001 2.22 0.023 0.018 8.16 <0.001 <0.001
Ruminococcaceae_ge 1.72 0.003 <0.001 0.51 0.227 0.202 1.72 <0.001 <0.001
Alistipes 0.91 0.006 0.002 -2.29 <0.001 <0.001 0.91 <0.001 <0.001
Roseburia 1 0.011 0.003 -1.16 <0.001 <0.001 1.0 <0.001 <0.001
Phascolarctobacterium 2.13 0.011 0.003 0.18 0.781 0.771 2.13 <0.001 <0.001
Bacteroidales_S24-7_group_ge 7.46 0.011 0.003 5.51 <0.001 <0.001 7.46 <0.001 <0.001
Blautia -1.5 0.015 0.005 -5.95 <0.001 <0.001 -1.5 <0.001 <0.001
Coprococcus_3 1.32 0.015 0.005 -0.53 0.267 0.24 1.32 0.001 <0.001
Tyzzerella_4 -7.43 0.016 0.005 -16.99 <0.001 <0.001 -7.43 <0.001 <0.001
Prevotellaceae_UCG-001 6.56 0.022 0.008 3.09 0.032 0.026 6.56 <0.001 <0.001
Lactobacillus -4.98 0.028 0.01 -10.36 <0.001 <0.001 -4.98 <0.001 <0.001
Erysipelatoclostridium -3.2 0.033 0.013 -9.17 <0.001 <0.001 -3.2 <0.001 <0.001
Morganella -9.47 0.033 0.013 -17.33 <0.001 <0.001 -9.47 <0.001 <0.001
Clostridium_sensu_stricto_1 2.93 0.033 0.013 -0.41 0.462 0.422 2.93 0.002 <0.001
Veillonella -4.06 0.033 0.014 -8.16 <0.001 <0.001 -4.06 <0.001 <0.001
Ruminiclostridium_6 1.97 0.038 0.016 2.2 <0.001 <0.001 1.97 <0.001 <0.001
Desulfovibrio 5.19 0.039 0.017 -0.55 0.692 0.675 5.19 0.002 0.001
Ruminococcaceae_NK4A214_group 3.98 0.045 0.02 2.27 <0.001 <0.001 3.98 <0.001 <0.001
Bilophila -1.98 0.048 0.022 -5.75 <0.001 <0.001 -1.98 0.003 0.002
Holdemanella 1.72 0.055 0.027 3.39 <0.001 <0.001 1.72 <0.001 <0.001
Parabacteroides -1.13 0.059 0.029 -5.52 <0.001 <0.001 -1.13 0.003 0.002
Fusobacterium -9.74 0.065 0.033 -13.93 <0.001 <0.001 -9.74 <0.001 <0.001
Flavonifractor -3.58 0.067 0.035 -7.77 <0.001 <0.001 -3.58 <0.001 <0.001
Bifidobacterium -1.22 0.069 0.037 -5.71 <0.001 <0.001 -1.22 0.019 0.012
Acidaminococcus -4.36 0.081 0.045 -6.79 <0.001 <0.001 -4.36 0.01 0.006
Fusicatenibacter 0.73 0.081 0.045 -1.19 0.003 0.002 0.73 0.007 0.004
Lachnospiraceae_AC2044_group 1.95 0.088 0.05 3 <0.001 <0.001 1.95 <0.001 <0.001
Parasutterella -4.45 0.139 0.083 -5.58 <0.001 <0.001 -4.45 0.019 0.012
Enterococcus -9.23 0.139 0.083 -12.35 <0.001 <0.001 -9.23 <0.001 <0.001
Anaeroglobus -7.85 0.143 0.087 -14.81 <0.001 <0.001 -7.85 <0.001 <0.001
Olsenella 4.37 0.15 0.094 -0.46 0.474 0.439 4.37 0.002 <0.001
Dialister 0.74 0.152 0.097 -2.08 <0.001 <0.001 0.74 0.034 0.022
Collinsella -0.75 0.152 0.099 -4.64 <0.001 <0.001 -0.75 0.053 0.035
Streptococcus -0.99 0.279 0.185 -5.71 <0.001 <0.001 -0.99 0.123 0.085
Tyzzerella -4.3 0.363 0.245 -7.84 <0.001 <0.001 -4.3 0.001 <0.001
Proteus -5.1 0.416 0.291 -15.3 <0.001 <0.001 -5.1 0.004 0.003
Lachnospiraceae_ge 0.55 0.416 0.291 -2.33 <0.001 <0.001 0.55 0.144 0.102
Akkermansia 0.68 0.468 0.334 -1.71 0.002 0.001 0.68 0.156 0.112
Parvimonas -5.93 0.534 0.39 -3.46 <0.001 <0.001 -5.93 0.35 0.279
Prevotellaceae_NK3B31_group -5.64 0.534 0.395 -4.96 <0.001 <0.001 -5.64 0.333 0.258
Megamonas 1.16 0.587 0.442 2.11 0.019 0.014 1.16 0.228 0.166
Terrisporobacter -0.92 0.613 0.48 -4.22 <0.001 <0.001 -0.92 0.354 0.286
Peptostreptococcus -4.34 0.613 0.482 -4.04 <0.001 <0.001 -4.34 0.364 0.298
Campylobacter -5.61 0.613 0.485 -2.56 0.004 0.003 -5.61 0.459 0.429
Barnesiella 0.39 0.666 0.538 -1.67 <0.001 <0.001 0.39 0.327 0.247
Lachnospiraceae_UCG-004 -1.03 0.666 0.545 -1.85 <0.001 <0.001 -1.03 0.431 0.386
Ruminococcus_2 0.35 0.666 0.554 -0.77 0.096 0.082 0.35 0.31 0.23
Ruminococcaceae_UCG-004 0.47 0.704 0.594 -1.94 0.004 0.003 0.47 0.333 0.26
Victivallis -1.22 0.799 0.688 0.29 0.67 0.646 -1.22 0.67 0.67
Erysipelotrichaceae_UCG-003 -0.19 0.799 0.704 -3.9 <0.001 <0.001 -0.19 0.398 0.347
Coprobacter 0.36 0.799 0.706 -1.22 0.043 0.036 0.36 0.394 0.33
Succiniclasticum -1.02 0.81 0.726 -4.94 0.031 0.025 -1.02 0.664 0.656
Dorea 0.12 0.869 0.805 -3.64 <0.001 <0.001 0.12 0.406 0.359
Romboutsia 0.24 0.869 0.807 -1.01 0.024 0.019 0.24 0.398 0.343
Paraprevotella -0.13 0.869 0.813 -3.77 <0.001 <0.001 -0.13 0.441 0.407
Lachnospira 0.1 0.91 0.868 -2.67 <0.001 <0.001 0.1 0.441 0.405
Megasphaera -0.15 0.91 0.875 -1.91 0.022 0.017 -0.15 0.468 0.444
Anaerostipes -0.06 0.918 0.894 -3.96 <0.001 <0.001 -0.06 0.472 0.46
Butyricicoccus 0.03 0.95 0.938 -3.24 <0.001 <0.001 0.03 0.472 0.455
Haemophilus 0.06 0.973 0.973 0.09 0.882 0.882 0.06 0.394 0.333


Genus Abundance Heatmap



Genus Volcano Plots



Principal Coordinate Analyses



α Diversity

Group Shannon Entropy Simpson's Index
Group 1 3.36 ± (1.02) 0.78 ± (0.16)
Group 2 4.76 ± (1.22) 0.84 ± (0.15)


α Diversity Plots



β Diversity

Group β Diversity
Group 1 0.74 ± (0.09)
Group 2 0.65 ± (0.11)
Group 1 - Group 2 0.77 ± (0.09)


β Diversity Plot