Running Title: Microbial Ecology Network in Diverticulitis
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1 Running Title: Microbial Ecology Network in Diverticulitis The Microbial Ecosystem Distinguishes Chronically Diseased Tissue from Adjacent Tissue in the Sigmoid Colon of Chronic, Recurrent Diverticulitis Patients Kathleen M. Schieffer 1,#, Kate Sabey 2,#, Justin R. Wright 2,3, David R. Toole 2, Rebecca Drucker 2, Vasily Tokarev 2, Leonard R. Harris 1, Sue Deiling 1, Melanie A. Eshelman 1,4, John P. Hegarty 1, Gregory S. Yochum 1,4, Walter A. Koltun 1, Regina Lamendella 2,3, David B. Stewart Sr. 1*
2 Supplemental Table S1. PERMANOVA power analysis using the weighted UniFrac distances from our 16S rrna OTU data table Subjects/group Alpha Average effect size (omega2) Power
3 Supplemental Figure S1. Microbial alpha and beta diversity analysis. (A) Alpha diversity rarefaction plots of observed taxa within diverticulitis (red) tissue and adjacent (blue) tissue were generated within QIIME Differences in alpha diversity were not found to be statistically significant. (B) Principle coordinate analysis plot calculated from weighted UniFrac distances comparing bacterial community structures between diverticulitis (red) tissue and adjacent (blue) tissue. (C) Principle coordinate analysis plot calculated from weighted UniFrac distances comparing bacterial community structures between individual patients. Each color is indicative of an individual patient, with large points representing diverticular tissue, and small points representing adjacent tissue. Clustering was not found to be statistically significant based on tissue type nor patient.
4 Supplemental Table S2. Differentially expressed bacterial taxa unique between diverticulitis tissue (DT) and adjacent tissue (AT). Only taxonomically assigned OTUs at the kingdom are listed. DT Core (80%) Bacteria Phylum Class Order Family Genus Species Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Firmicutes Clostridia Clostridiales Peptococcaceae Desulfosporosinus meridiei Firmicutes Clostridia Clostridiales Syntrophomonadaceae Syntrophomonas Proteobacteria Gammaproteobacteria Alteromonadales Shewanellaceae Shewanella Proteobacteria Alphaproteobacteria Rhizobiales Bradyrhizobiaceae Proteobacteria Betaproteobacteria Burkholderiales Oxalobacteraceae Proteobacteria Betaproteobacteria Burkholderiales Oxalobacteraceae Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas veronii Synergistetes Synergistia Synergistales Synergistaceae vadinca02 Proteobacteria Gammaproteobacteria Methylococcales Methylococcaceae Actinobacteria Actinobacteria Actinomycetales Microbacteriaceae Proteobacteria Deltaproteobacteria Desulfobacterales Desulfobulbaceae Proteobacteria Alphaproteobacteria Caulobacterales Caulobacteraceae Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Proteobacteria Alphaproteobacteria Caulobacterales Caulobacteraceae Firmicutes Bacilli Bacillales Bacillaceae Bacillus foraminis AT Core (80%) Bacteria Phylum Class Order Family Genus Species Bacteroidetes Cytophagia Cytophagales Cytophagaceae Hymenobacter GN04 Proteobacteria Epsilonproteobacteria Campylobacterales Campylobacteraceae Arcobacter Bacteroidetes Sphingobacteriia Sphingobacteriales Proteobacteria Epsilonproteobacteria Campylobacterales Helicobacteraceae Bacteroidetes Bacteroidia Bacteroidales Proteobacteria Betaproteobacteria Methylophilales Methylophilaceae Methylotenera mobilis Cyanobacteria Chloroplast Stramenopiles Proteobacteria Deltaproteobacteria Desulfuromonadales Geobacteraceae Geobacter Chloroflexi Anaerolineae H39 Bacteroidetes Flavobacteriia Flavobacteriales Cryomorphaceae Fluviicola Bacteroidetes Flavobacteriia Flavobacteriales Cryomorphaceae Fluviicola Acidobacteria [Chloracidobacteria] Ellin7246 Rhodoferax
5 Supplemental Table S3. Enriched bacterial and archaeal taxa identified by LefSe analysis. Enriched Bacterial and Archaeal Taxonomy LDA Score LefSe P value Archaea.Crenarchaeota.Thaumarchaeota Archaea.Crenarchaeota.Thaumarchaeota.Cenarchaeales Archaea.Crenarchaeota.Thaumarchaeota.Cenarchaeales.Cenarchaeaceae Archaea.Euryarchaeota.Thermoplasmata Bacteria.Acidobacteria.Acidobacteria_ DT Bacteria.Actinobacteria.Acidimicrobiia.Acidimicrobiales Bacteria.Actinobacteria.Actinobacteria.Actinomycetales.Microbacteriaceae Bacteria.Proteobacteria.Alphaproteobacteria.Rhodeobacterales.Rhodobacteraceae.Pseudoruegeria Bacteria.Proteobacteria.Betaproteobacteria_SC_I_ Bacteria.Proteobacteria.Deltaproteobacteria.Desulfobacterales.Desulfobulbaceae Bacteria.Spirochaetes.Leptospirae.Leptospirales_Sediment_4_SJA_ Bacteria.Actinobacteria.Actinobacteria.Actinomycetales.Kineosporiaceae Bacteria.Actinobacteria.Thermoleophilia Bacteria.Actinobacteria.Thermoleophilia.Gaiellales.Gaiellaceae Bacteria.Armatimonadetes_0319_6E Bacteria.Chloroflexi.Anaerolineae_H Bacteria.Cyanobacteria_4C0d_2_MLE1_ AT Bacteria.Gemmatimonadetes_Gemm_ Bacteria.Planctomycetes_OM Bacteria.Planctomycetes.Phycisphaerae.Phycisphaerales Bacteria.Proteobacteria.Alphaproteobacteria.Rhizobiales.Hyphomicrobiaceae.Parvibaculum Bacteria.Proteobacteria.Alphaproteobacteria.Sphingomonadales Bacteria.Proteobacteria.Deltaproteobacteria.Desulfovibrionales.Desulfovibrionaceae Bacteria.Proteobacteria.Gammaproteobacteria.Alteromonadales.Alteromonadaceae.Marinobacter Bacteria.Proteobacteria.Gammaproteobacteria.Pseudomonadales.Pseudomonadaceae.Pseudomonas
6 Supplemental Table S4. Enriched predicted function from PICRUSt analysis. Enriched Function LDA Score LefSe P value C5 Branched dibasic acid metabolism DT Methane metabolism Valine, leucine, and isoleucine biosynthesis AT Carbohydrate metabolism Glycosyltransferases
7 Supplemental Figure S2. Fungal alpha and beta diversity analysis. (A) Alpha diversity rarefaction plots of observed taxa within diverticulitis (red) tissue and adjacent (blue) tissue were generated within QIIME Differences in alpha diversity were not found to be statistically significant. (B) Principle coordinate analysis plot calculated from weighted UniFrac distances comparing bacterial community structures between diverticulitis (red) tissue and adjacent (blue) tissue. (C) Principle coordinate analysis plot calculated from weighted UniFrac distances comparing bacterial community structures between individual patients. Each color is indicative of an individual patient, with large points representing diverticular tissue, and small points representing adjacent tissue. Clustering was not found to be statistically significant based on tissue type, but was found to be statistically significant based on patient ID (ANOSIM P=0.01).
8 Supplemental Table S5. Differentially expressed fungal taxa unique between diverticulitis tissue (DT) and adjacent tissue (AT). Only taxonomically assigned OTUs at the kingdom are listed. DT Core (80%) Fungi Phylum Class Order Family Genus Species Ascomycota Leotiomycetes AT Core (80%) Fungi Phylum Class Order Family Genus Species Ascomycota Saccharomycetes Saccharomycetales Incertae sedis Cyberlindnera jadinii Ascomycota Eurotiomycetes Eurotiales Trichocomaceae Aspergillus subversicolor
9 Supplemental Table S6. Enriched fungal taxonomy from LefSe analysis. Enriched function LDA score LefSe P value DT Fungi.Ascomycota.Chaetothyriomycetes.Chaetothyriales.Herpotrichiellaceae.Exophiala Fungi.Basidiomycota.Agaricomycetes. Agaricomycetidae.Agaricales AT Fungi.Basidiomycota.Agaricomycetes.Agaricomycetidae.Agaricales.Plutaceae Fungi.Basidiomycota.Agaricomycetes.Agaricomycetidae.Agaricales.Plutaceae.Pluteus
Observed # of species (normalized) Chao 1 (richness) Nonsmoker 21 Male 2418 (337) 67 (33)
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