Supplementary material

Proteobacteria: microbial signature of dysbiosis in gut microbiota

Na-Ri Shin*, Tae Woong Whon*, and Jin-Woo Bae

Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Korea

*These authors contributed equally to this work.

Corresponding author: Bae, J.W. ()

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Table S1.Blooms of particular Proteobacteria family or genus in theinflammatory milieu

Disease model / Model Organism / Treatment / Target Sample / Disease-associated Proteobacteria / Significant Finding / Technique / Ref
Acute Inflammation
Parasite infection / C57BL/6 mice / Toxoplasma gondii infection / SI luminal content / Enterobacteriaceae
Escherichia/Shigella / Infection-induced IFN-γ and TLR11-MyD88-dependent Paneth cell loss / pyrosequencing / [1]
Parasite infection / C57BL/6 mice / Toxoplasma gondii infection / SI mucosa and feces / Enterobacteriaceae / N-formyl peptide receptor (Fpr1) sensing Gammaproteobacteria establishes intraluminal casts to promote bacterial clearance and limit commensal outgrowth / pyrosequencing / [2]
Bacterial infection / C57BL/6 mice / Citrobacter rodentium infection / Colon biopsy / Enterobacteriaceae / Infection-induced inflammation alters colonic microbial community / clone library / [3]
Bacterial infection / C57BL/6 mice / Salmonella enterica infection / Cecal content / Proteobacteria
Escherichia coli / Microbiota-host immunity-pathogen interaction (colonization resistance) / clone library / [4]
Intestinal Cancer
CRC / Il10 KO mice / Azoxymethane / Colon biopsy / Enterobacteriaceae
Escherichia coli / Inflammation-microbial activity (E. coli pks gene)-cancer development interaction / Illumina Hiseq / [5]
Serrated SI tumor / K-rasG12Dintmice / High-fat diet / SI biopsy and feces / Escherichia/Shigella
Helicobacter / Diet-shaped microbiota synergizes with oncogenic K-ras during tumorigenesis in the intestine independently of obesity / pyrosequencing / [6]
CRC / Il10 KO mice / Azoxymethane / Colon biopsy and feces / Enterobacteriaceae / Colitis can promote tumorigenesis by altering microbial composition and inducing the expansion of microorganisms with genotoxic capabilities / Illumina Hiseq / [7]
Colon cancer / human patients / - / Colon biopsy / Escherichia coli / Colon cancer-associated E. coli strain 11G5 possesses carcinogenic property in multiple intestinal neoplasia mice / microarray / [8]
Colon cancer / human patients / - / Colon biopsy / Enterobacteriaceae
Enterobacter / Bacterial driver-passenger model for CRC / pyrosequencing / [9]
Colorectal cancer / human patients / - / Feces / Enterobacteriaceae
Escherichia/Shigella / Reduction of butyrate producers and increase of opportunistic pathogens in CRC patients / pyrosequencing / [10]
Colorectal cancer / human patients / - / Colonic mucosal biopsy / Proteobacteria
Helicobacter / Differences in the microbiota from normal rectal mucosa of adenoma cases and controls / pyrosequencing / [11]

Studies representing predominance of Proteobacteria in disease models (e.g., experimental acute inflammation and colitis-associated colorectal cancer) with detailed disease phenotypes were highlighted.

CRC, colitis-associated colorectal cancer; KO, knock-out; SI, small-intestine; IFN, interferon; MyD88, myeloid differentiation primary-response protein 88.

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Supplementary References

S1.Raetz, M., et al. (2013) Parasite-induced TH1 cells and intestinal dysbiosis cooperate in IFN-gamma-dependent elimination of Paneth cells. Nat. Immunol. 14, 136-142.

S2.Molloy, M.J., et al. (2013) Intraluminal containment of commensal outgrowth in the gut during infection-induced dysbiosis. Cell Host Microbe 14, 318-328.

S3.Lupp, C., et al. (2007) Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe 2, 119-129.

S4.Stecher, B., et al. (2007) Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol. 5, 2177-2189.

S5.Arthur, J.C., et al. (2014) Microbial genomic analysis reveals the essential role of inflammation in bacteria-induced colorectal cancer. Nat. Commun. 5, 4724.

S6.Schulz, M.D., et al. (2014) High-fat-diet-mediated dysbiosis promotes intestinal carcinogenesis independently of obesity. Nature 514, 508-512.

S7.Arthur, J.C., et al. (2012) Intestinal inflammation targets cancer-inducing activity of the microbiota. Science 338, 120-123.

S8.Bonnet, M., et al. (2014) Colonization of the human gut by E. coli and colorectal cancer risk. Clin. Cancer. Res. 20, 859-867.

S9.Geng, J., et al. (2014) Co-occurrence of driver and passenger bacteria in human colorectal cancer. Gut Pathog. 6, 26.

S10.Wang, T., et al. (2012) Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J. 6, 320-329.

S11.Sanapareddy, N., et al. (2012) Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans. ISME J. 6, 1858-1868.

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