Dynamics of the human gut microbiome in inflammatory bowel disease
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1 In the format provided by the authors and unedited. SUPPLEMENTARY INFORMATION VOLUME: 2 ARTICLE NUMBER: 174 Dynamics of the human gut microbiome in inflammatory bowel disease Jonas Halfvarson, Colin J. Brislawn, Regina Lamendella, Yoshiki VázquezBaeza, William A. Walters, Lisa M. Bramer, Mauro D Amato, Ferdinando Bonfiglio, Daniel McDonald, Antonio Gonzalez, Erin E. McClure, Mitchell F. Dunklebarger, Rob Knight and Janet K. Jansson Supplementary Video 1. Dynamics of healthy controls and IBD subtypes within ordinated UniFrac space. This video illustrates the dynamics along a "healthy plane" for healthy controls. By contrast, the IBD subjects move in a 3rd dimension away from the healthy plane. The extent of this deviation from the healthy plane is quantified and significant for the different IBD subtypes (data shown in Figure 2). Legend for Supplementary Video 1. Supplementary Dataset 1. Clinical metadata for patients and samples. This QIIME compatible mapping file lists the genetic and clinical context of each sample used in this study. It is available on Qiita as study 1629 and is linked to the online version of the paper at NATURE MICROBIOLOGY DOI: 1.138/nmicrobiol Macmillan Publishers Limited, part of Springer Nature. All rights reserved.
2 Supplementary Table 1. Summary of the patient cohort Collected samples Samples used in downstream analysis Category Patients Samples Category Patients Samples Healthy Controls 9 62 Healthy Controls 7 32 Colonic Crohn's Disease Colonic Crohn's Disease Ileal Crohn's Disease, nonresected 6 32 Ileal Crohn's Disease, nonresected 4 16 Ileal Crohn's Disease, resected Ileal Crohn's Disease, resected 15 6 Ulcerative colitis Ulcerative colitis Collagenous colitis Collagenous colitis Lymphocytic colitis 4 1 Lymphocytic colitis Total Total Female Female Male Male Supplementary Table 2. Clinical features of the Random Forests model Model CCD HC ICD_nr ICD_r UC Mean Decrease Accuracy in Feature Distance to the Healthy Plane OTUs and clinical BMI metadata sex Accuracy: 66.6% fcalprotectin With Genetic Load Scores (GLS) Accuracy: 68% Distance to the Healthy Plane Genetic Load Scores sex fcalprotectin BMI Clinical and microbial features as predicted by the Random Forests model, with and without the addition of Genetic Load Scores.
3 Supplementary Table 3. Top features of the Random Forests model Model Mean Decrease CCD HC ICD_nr ICD_r UC Feature Name or Taxonomy in Accuracy Distance to the Healthy Plane Proteobacteria Gammaproteobacteria Alteromonadales [Chromatiaceae] [Unassigned] [Unassigned] OTUs and clinical metadata. Accuracy: 66.6% With Genetic Load Scores (GLS) Accuracy: 68% Firmicutes Clostridia Clostridiales Ruminococcaceae [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales Ruminococcaceae [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium [Unassigned] Firmicutes Clostridia Clostridiales Ruminococcaceae [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnospira [Unassigned] Firmicutes Clostridia Clostridiales Ruminococcaceae [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales [Unassigned] [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales Ruminococcaceae [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales Ruminococcaceae [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales Ruminococcaceae [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales Lachnospiraceae [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales Ruminococcaceae Oscillospira [Unassigned] Firmicutes Clostridia Clostridiales Ruminococcaceae [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales Lachnospiraceae [Unassigned] [Unassigned] Distance to the Healthy Plane Firmicutes Clostridia Clostridiales Ruminococcaceae [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales Ruminococcaceae [Unassigned] [Unassigned] Proteobacteria Gammaproteobacteria Alteromonadales [Chromatiaceae] [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium [Unassigned] Firmicutes Clostridia Clostridiales Ruminococcaceae [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales [Unassigned] [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales Ruminococcaceae [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnospira [Unassigned] Firmicutes Clostridia Clostridiales Ruminococcaceae Oscillospira [Unassigned] Firmicutes Clostridia Clostridiales Ruminococcaceae [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales Ruminococcaceae [Unassigned] [Unassigned] Genetic Load Score
![.7.5. 4.75 4.2 5.29 Firmicutes Clostridia Clostridiales Lachnospiraceae [Unassigned] [Unassigned].73.68 1.34 5.44 3.2 5.28 Firmicutes Clostridia Clostridiales Ruminococcaceae [Unassigned] [Unassigned] 1.](/docs-images/85/92855899/images/4-0.jpg "87.99 1.73 6.8.73 5.24 Firmicutes Clostridia Clostridiales Ruminococcaceae [Unassigned] [Unassigned].54 2.94 1.64 4.13 3.54 5.")
4 Firmicutes Clostridia Clostridiales Lachnospiraceae [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales Ruminococcaceae [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales Ruminococcaceae [Unassigned] [Unassigned] Firmicutes Clostridia Clostridiales Lachnospiraceae [Unassigned] [Unassigned] Clinical and microbial features are shown that were predicted by the Random Forests model to decrease cumulative accuracy by at least 5% if permuted. Supplementary Table 4. Power Analysis for differential abundance tests FoldChange in Means Proportion of OTUS with >8% Power Median Power The proportion of the 1 OTUs which had at least 8% power and the median power over the 1 OTUs for each fold change. Supplementary Figure 1. The gut microbiomes of different IBD subtypes differ in community composition
5 Alpha Diversity Measure UC ICD_r ICD_nr HC CCD UC ICD_r ICD_nr HC CCD UC ICD_r ICD_nr HC CCD Supplementary Figure 2. Alpha diversity of IBDsubtypes and healthy controls 4 Observed ACE Shannon IBD Subtype
6 Rarified Abundance of Common Taxa at the Family Level Supplementary Figure 3. Microbiome dynamics of all individuals used in downstream analysis 15 CCD 1 CCD 141 CCD 187 CCD 193 CCD 288 CCD 413 CCD 427 CCD 564 CCD 68 CCD 769 CCD 875 HC 882 HC 896 HC 898 HC 9 HC 91 HC 96 HC ICD nr 492 ICD nr 651 ICD nr 913 ICD nr 93 ICD r 129 ICD r 19 ICD r 191 ICD r 211 ICD r 245 ICD r 26 ICD r 315 ICD r 39 ICD r 416 ICD r 57 ICD r 525 ICD r 543 ICD r 553 ICD r ICD r 74 UC 122 UC 136 UC 138 UC 143 UC 152 UC 162 UC 19 UC 195 UC 26 UC 21 UC 235 UC 242 UC 264 UC 295 UC 34 UC 31 UC UC 336 UC 347 UC 385 UC 45 UC 456 UC 467 UC 471 UC 487 UC 521 UC 552 UC 566 UC 623 UC 634 UC 64 UC TIMEPOINT_NUMBER f f Bacteroidaceae f Bifidobacteriaceae f Enterobacteriaceae f Lachnospiraceae f Porphyromonadaceae f Prevotellaceae f Rikenellaceae f Ruminococcaceae f Veillonellaceae f Verrucomicrobiaceae
7 Supplementary Figure 4. Shifts in microbiome structure in IBD patients with unstable medications
Figure S1, SDC Additional measures of microbial diversity during perioperative period In addition to the Shannon diversity index of Figure 1,
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