Nod2 Influences Microbial Resilience and Susceptibility to Colitis Following
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www.nature.com/mi ARTICLE Nod2 influences microbial resilience and susceptibility to colitis following antibiotic exposure A. Goethel1,2, W. Turpin2,3, S. Rouquier3, G. Zanello3, S. J. Robertson1, C. J. Streutker4, D. J. Philpott1 and K. Croitoru1,2,3,5 Inflammatory bowel disease (IBD) etiology involves genetic susceptibility, environmental triggers, and the gut microbiome. Antibiotic exposure is associated with IBD, both in early life and adulthood. Here, we investigated whether Nod2-deficiency influenced response of the gut microbiota to antibiotics and subsequent colitis susceptibility. Wild-type and Nod2−/− littermate mice were treated with amoxicillin as adults or neonates, and fecal samples were collected for 16S rRNA sequencing. Five weeks after antibiotic exposure, dextran sulfate sodium (DSS) colitis was induced. Antibiotic treatment altered the microbiota of adult WT and Nod2−/− mice, but recovery was delayed in Nod2−/− mice. Neonatal antibiotic treatment significantly changed the microbiota at weaning in WT and Nod2−/− littermates; however, Nod2−/− mice maintained reduced microbial diversity 14 days after cessation of antibiotics. Although treatment of adult mice did not influence susceptibility to colitis, neonatally treated Nod2−/− mice developed a more severe colitis. Moreover, the colitis phenotype was transferable through fecal transplantation into germ-free Nod2−/− recipients, and was associated with changes in intestinal T cells and the cytokine milieu following inflammation. These data demonstrate that neonatal antibiotic exposure has long-lasting influence on the microbiota and mucosal immunity, and may explain how NOD2 contributes to the risk of intestinal inflammation. Mucosal Immunology (2019) 12:720–732; https://doi.org/10.1038/s41385-018-0128-y INTRODUCTION sustained alterations of the gut microbiota following neonatal The mammalian gut typically harbors multiple types of microbes, antibiotic exposure combined with the absence of Nod2 signaling including ~4 × 1013 bacteria,1 in a dynamic community whose during mucosal barrier breach results in exacerbated mucosal structure depends on environmental and host genetic influ- damage. ences.2–6 Maintaining this symbiotic relationship is key to the balance between health and disease. Colonization of the gut microbiota during neonatal life influences the development of the RESULTS mucosal immune system.7 Environmental perturbations during Nod2 genotype influences microbiota resilience after antibiotic this critical window can alter the ‘normal’ development of the gut exposure in adult mice microbiota and the mucosal immune system, possibly increasing We first investigated how a single course of the broad-spectrum susceptibility to disease. Indeed, mouse and human studies antibiotic, amoxicillin, altered the adult murine microbiota, and suggest that neonatal antibiotic exposure is associated with an whether Nod2 genotype influenced this perturbation. Adult WT increased risk of inflammatory diseases, including asthma,8 and Nod2−/− littermate mice were given amoxicillin- obesity9, and inflammatory bowel disease (IBD).10–12 This is supplemented water for 7 days and stool samples were collected supported by observations that early life and repeated antibiotic at day 0 (pre-treatment) and on day 7 (Fig. 1a). In order to further exposure significantly increases the risk for developing IBD.11,13 assess whether Nod2 influenced the resilience or recovery of the Given that Nod2 mutations are one of the most important microbiota following antibiotic exposure, stool was collected on genetic risks for the development of Crohn’s disease, we day 21, i.e., 14 days after stopping antibiotic-supplemented water. investigated whether Nod2-deficiency altered the impact of Each mouse was compared to its pre-treatment composition antibiotic exposure on microbiota composition and susceptibility (day 0) and water-treated littermate controls. Using 16S rDNA to colitis. We found that Nod2 influenced microbial resilience sequencing, microbial diversity was evaluated for species richness following adult and neonatal antibiotic treatment. Although the (as measured by the Chao1 rarefaction index) and beta diversity adult treatment did not alter colitis susceptibility, neonatal (as measured by Bray–Curtis dissimilarity, which factors in antibiotic treatment resulted in increased colitis severity in presence/absence and relative abundance of operational taxo- Nod2−/− mice. Moreover, transfer of the neonatal antibiotic- nomic units). microbiota increased colitis severity in germ-free recipients. This As previously described,14 Nod2 genotype was not associated phenotype was associated with altered cytokines and increased with any difference in the microbiota in terms of species richness, colonic Gata3+Foxp3+ regulatory T cells. This suggests that the beta diversity, or composition at day 0 (Fig. 1b–d), indicating that 1Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada; 2Zane Cohen Centre for Digestive Diseases, The Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5T 3L9, Canada; 3Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; 4St. Michael’s Hospital, Toronto, ON M5B 1W8, Canada and 5Division of Gastroenterology, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada Correspondence: K Croitoru ([email protected]) Received: 9 September 2018 Revised: 5 December 2018 Accepted: 16 December 2018 Published online: 16 January 2019 © Society for Mucosal Immunology 2019 Nod2 influences microbial resilience and susceptibility to colitis. A Goethel et al. 721 ab WT Water Water 300 WT Water Nod2–/– Water Water ** * Nod2–/– Water WT Abx Water 200 WT + Abx Day 0 –/– Abx Water *** *** WT + Abx Day 7 Nod2 WT + Abx Day 21 Chao1 index 100 Nod2–/– + Abx Day 0 Day 0 7 Nod2–/– + Abx Day 7 21 –/– Age (w) Nod2 + Abx Day 21 8 9 11 0 1000 2000 3000 4000 5000 6000 7000 8000 9000 10,000 Sequences per sample c Day 0 Day 7 Day 21 0.3 0.4 0.3 0.2 0.3 0.2 0.2 0.1 0.1 0.1 0.0 0.0 0.0 –0.1 –0.1 –0.1 –0.2 WT –0.2 Nod2–/– –0.2 –0.3 –0.3 WT + Abx Nod2–/– + Abx –0.4 –0.4 –0.3 –0.20 –0.15 –0.10 –0.05 0.00 0.05 –0.4 –0.2 0.0 0.2 0.4 0.6 0.8 –0.20 –0.15 –0.10 –0.05 0.00 0.05 0.10 0.15 0.20 0.25 PC2 11.8% PC1 28.1% d f –2 –1 0 1 2 Row Z-Score Lactobacillus 1234567890();,: Undefined_clostridiales 10000100 Allobaculum Oscillospira Family Undefined_rikenellaceae Ruminococcus_lachnospiraceae Other Undefined_ruminococcaceae Verrucomicrobiaceae Aldercreutzia Bifidobacterium Enterobacteriaceae Turicibacter Desulfovibrionaceae Ruminococcus_ruminococcaceae Coprococcus Erysipelotrichaceae Undefined_lachnospiraceae Ruminococcaceae Undefined_clostridiaceae Lachnospiraceae Odoribacter Desulfovibrio Clostridiales_unspecified Undefined_F16 Lactobacillaceae Sutterella [Paraprevotellaceae] Dorea Undefined_erysipelotrichaceae S24-7 Undefined_christensenellaceae Rikenellaceae Undefined_RF32 Prevotellaceae Undefined_mogibacteriaceae Clostridium Relative Abundance (%) Bacteroidaceae Undefined_helicobacteraceae Bacteroidales_unspecified Undefined_enterobacteriaceae Coriobacteriaceae Dehalobacterium Parabacteroides Bifidobacteriaceae Undefined_enterobacteriaceae Undefined_lachnospiraceae 0 Akkermansia Bacteroides –/– –/– –/– Undefined_S24-7 WT WT WT Nod2 Nod2 Nod2 –/– Day 0721 WT Nod2 + Abx: d7 + Abx: d0 + Abx: d21 e –/– WT Nod2 –/– –/– –/– WT + Abx: d7 WT + Abx: d0 22 Bilophila Bacteroides WT + Abx: d21 Nod2 Bacteroidaceae Nod2 21 Bacteroides * Enterobacteriales Nod2 20 Bacteroidaceae * Enterobacteriaceae Bilophila 19 Allobaculum * Clostridium 18 Erysipelotrichi * Desulfovibrionaceae_unspecified 17 * Enterobacteriaceae_unspecified Erysipelotrichales * Gammaproteobacteria 16 Erysipelotrichaceae Allobaculum 15 Rikenellaceae Erysipelotrichaceae 14 Rikenellaceae_unspecified Erysipelotrichi 13 Erysipelotrichales Candidatus Arthomitus Rikenellaceae 12 Odoribacter Rikenellaceae_unspecified 11 Odoribacteraceae Odoribacteraceae 10 Odoribacter RF32 Desulfovibrio 9 F16 F16_unspecified 8 F16_unspecified TM7 7 TM7_3 TM7_3 F16 6 Alphaproteobacteria Mogibacteriaceae * 5 CW040 Mogibacteriaceae_unspecified * Alphaproteobacteria 4 RF32_unspecified Candidatus Arthomitus 3 TM7 RF32_unspecified 2 Desulfovibrio RF32 1 CW040 46 –6 –4 –2 0 2 4 6 –6 –4 –2 0 2 LDA score (log 10) LDA score (log 10) Nod2-deficiency alone was not sufficient to alter microbial (Fig. 1b, c). This was characterized by reduced species richness colonization. Antibiotic treatment shifted the microbial commu- (Fig. 1b), and loss of taxa including Erysipelotrichaceae, Clos- nity away from pre-treatment composition in both WT (R = 0.6778, tridiales, and Lactobacillaceae, with corresponding increases in p = 0.001) and Nod2−/− (R = 0.7922, p = 0.001) littermates at day 7 Enterobacteriaceae and Bacteroidaceae (Fig. 1d). Thus, the Mucosal Immunology (2019) 12:720 – 732 Nod2 influences microbial resilience and susceptibility to colitis. A Goethel et al. 722 Fig. 1 Nod2 genotype influences microbiota resilience after antibiotic exposure in adult mice. a Experimental strategy. Starting at 8 weeks of age, littermate WT and Nod2−/− mice received either water or antibiotic (Abx) treatment for 7 days followed by 2 weeks of water to allow for microbial recovery. Arrows indicate time points of stool collection for sequencing. b Species richness at day 0, 7, and 21 as measured by the Chao1 rarefaction index. c Principal coordinates plot of Bray–Curtis dissimilarity for each time point. Each dot represents one mouse. (ANOSIM, WT+Abx d0 vs. 7: R = 0.6778,