Top

Published in:

Open Access 01-12-2018 | Research

Microbiota profile in new-onset pediatric Crohn’s disease: data from a non-Western population

Authors: Mohammad I. El Mouzan, Harland S. Winter, Assad A. Assiri, Kirill S. Korolev, Ahmad A. Al Sarkhy, Scot E. Dowd, Mohammad A. Al Mofarreh, Rajita Menon

Published in: Gut Pathogens | Issue 1/2018

Abstract

Background

The role of microbiota in Crohn’s disease (CD) is increasingly recognized. However, most of the reports are from Western populations. Considering the possible variation from other populations, the aim of this study was to describe the microbiota profile in children with CD in Saudi Arabia, a non-Western developing country population.

Results

Significantly more abundant genera in children with CD included Fusobacterium, Peptostreptococcus, Psychrobacter, and Acinetobacter; whereas the most significantly-depleted genera included Roseburia, Clostridium, Ruminococcus, Ruminoclostridium, Intestinibacter, Mitsuokella, Megasphaera, Streptococcus, Lactobacillus, Turicibacter, and Paludibacter. Alpha diversity was significantly reduced in stool (p = 0.03) but not in mucosa (p = 0.31). Beta diversity showed significant difference in community composition between control and CD samples (p = 0.03).

Conclusion

In this developing country, we found a pattern of microbiota in children with CD similar to Western literature, suggesting a role of recent dietary lifestyle changes in this population on microbiota structure.

Kappelman MD, Moore KR, Allen JK, Cook SF. Recent trends in the prevalence of Crohn’s disease and ulcerative colitis in a commercially insured US population. Dig Dis Sci. 2009;58:519–25.CrossRef

Molodecky NA, Soon IS, Rabi DM, Ghali WA, Ferris M, Chernoff G, et al. Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review. Gastroenterology. 2012;142:46–54.CrossRef

Benchimol EI, Fortinsky KJ, Gozdyra P, den Heuvel M, Limbergen JV, Griffiths AM. Epidemiology of pediatric inflammatory bowel disease: a systematic review of international trends. Inflamm Bowel Dis. 2011;17:423–39.CrossRef

Green C, Elliott L, Beaudoin C, Bernstein CN. A population-based ecologic study of inflammatory bowel disease: searching for etiologic clues. Am J Epidemiol. 2006;164:615–23.CrossRef

Hou JK, Abraham B, El-Serag H. Dietary intake and risk of developing inflammatory bowel disease: a systematic review of the literature. Am J Gastroenterol. 2011;106:563–73.CrossRef

Ananthakrishnan AN, Khalili H, Konijeti GG, Higuchi LM, de Silva P, Korzenik JR, et al. A prospective study of long-term intake of dietary fiber and risk of Crohn’s disease and ulcerative colitis. Gastroenterology. 2013;145:970–7.CrossRef

Li F, Liu X, Wang W, Zhang D. Consumption of vegetables and fruit and the risk of inflammatory bowel disease: a meta-analysis. Eur J Gastroenterol Hepatol. 2015;27:623–30.CrossRef

Ananthakrishnan AN, Khalili H, Konijeti GG, Higuchi LM, de Silva P, Fuchs CS, et al. Long-term intake of dietary fat and risk of ulcerative colitis and Crohn’s disease. Gut. 2014;63:776–84.CrossRef

Chan SSM, Luben R, Olsen A, Tjonneland A, Kaaks R, Lindgren S, et al. Association between high dietary intake of the n3 polyunsaturated fatty acid docosahexaenoic acid and reduced risk of Crohn’s disease. Aliment Pharmacol Ther. 2014;39:834–42.CrossRef

10.

Lewis JD, Abreu MT. Diet as a trigger or therapy for inflammatory bowel diseases. Gastroenterology. 2017;152:398–414.CrossRef

11.

Shaw KA, Bertha M, Hofmekler T, Chopra P, Vatanen T, Srivatsa A, et al. Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease. Genome Med. 2016;8:75.CrossRef

12.

Maukonen J, Kolho KL, Paasela M, Honkanen J, Klemetti P, Vaarala O, et al. Altered fecal microbiota in paediatric inflammatory bowel disease. J Crohns Colitis. 2015;9:1088–95.CrossRef

13.

Kolho KL, Korpela K, Jaakkola T, Pichai MV, Zoetendal EG, Salonen A, et al. Fecal microbiota in pediatric inflammatory bowel disease and its relation to inflammation. Am J Gastroenterol. 2015;110:921–30.CrossRef

14.

Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe. 2014;15:382–92.CrossRef

15.

El Mouzan MI, Saadah O, Al-Saleem K, Al Edreesi M, Hasosah M, Alanazi A, et al. Incidence of pediatric inflammatory bowel disease in Saudi Arabia: a multicenter national study. Inflamm Bowel Dis. 2014;20:1085–90.PubMed

16.

Saadah OI, El Mouzan M, Al Mofarreh M, Al Mehaidib A, Al Edreesi M, Hasosah M, Al-Hussaini A, et al. Characteristics of pediatric Crohn’s disease in Saudi children: a multicenter national study. Gastroenterol Res Pract. 2016;2016:7403129.CrossRef

17.

Al-Hussaini A, El Mouzan M, Hasosah M, Al-Mehaidib A, ALSaleem K, Saadah OI, et al. Clinical pattern of early-onset inflammatory bowel disease in Saudi Arabia: a multicenter national study. Inflamm Bowel Dis. 2016;22:1961–70.CrossRef

18.

El Mouzan M, Al Mofarreh M, Al Sarkhy A, Assiri A, Hamed Y. Pre-Illness diet as risk factor in pediatric inflammatory bowel disease in Saudi Arabia. Saudi J Gastroenterol. 2017;23:287–90.CrossRef

19.

Grimm KA, Kim SA, Yaroch AL, Scanlon KS. Fruit and vegetable intake during infancy and early childhood. Pediatrics. 2014;134(Suppl 1):S63–9.CrossRef

20.

Savige GS, Ball K, Worsley A, Crawford D. Food intake patterns among Australian adolescents. Asia Pac J Clin Nutr. 2007;16:738–47.PubMed

21.

Laitinen K, Collado MC, Isolauri E. Early nutritional environment: focus on health effects of microbiota and probiotics. Benef Microbes. 2010;1:383–90.CrossRef

22.

Kau AL, Ahern PP, Griffin NW, Goodman AL, Gordon JI. Human nutrition, the gut microbiome and the immune system. Nature. 2011;474:327–36.CrossRef

23.

Clemente JC, Ursell LK, Parfrey LW, Knight R. The impact of the gut microbiota on human health: an integrative view. Cell. 2012;148:1258–70.CrossRef

24.

Rapozo D, Bernardazzi C, Pereira de Souza H. Diet and microbiota in inflammatory bowel disease: the gut in disharmony. World J Gastroenterol. 2017;23:2124–40.CrossRef

25.

Bibiloni R, Mangold M, Madsen KL, Fedorak RN, Tannock GW. The bacteriology of biopsies differs between newly diagnosed, untreated, Crohn’s disease and ulcerative colitis patients. J Med Microbiol. 2006;55:1141–9.CrossRef

26.

Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 2012;13:R79.CrossRef

27.

Papa E, Docktor M, Smillie C, Weber S, Preheim SP, Gevers D, et al. Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. PLoS ONE. 2012;7:e39242.CrossRef

28.

Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermúdez-Humarán LG, Gratadoux JJ, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. PNAS. 2008;105:16731–6.CrossRef

29.

Hansen R, Russell RK, Reiff C, Louis P, McIntosh F, Berry SH, et al. Microbiota of de-novo pediatric IBD: increased Faecalibacterium prausnitzii and reduced bacterial diversity in Crohn’s but not in ulcerative colitis. Am J Gastroenterol. 2012;107:1913–22.CrossRef

30.

Assa A, Butcher J, Li J, Sherman PM, Muise AM, Stintzi A, et al. Mucosa-associated ileal microbiota in new onset pediatric Crohn’s disease. Inflamm Bowel Dis. 2016;22:1533–9.CrossRef

31.

Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, et al. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut. 2006;55:205–511.CrossRef

32.

Seksik P, Lepage P, de la Cochetière MF, Bourreille A, Sutren M, Galmiche JP, et al. Search for localized dysbiosis in Crohn’s disease ulcerations by temporal temperature gradient gel electrophoresis of 16S rRNA. J Clin Microbiol. 2005;43:4654–8.CrossRef

33.

Vasquez N, Mangin I, Lepage P, Seksik P, Duong JP, Blum S, et al. Patchy distribution of mucosal lesions in ileal Crohn’s disease is not linked to differences in the dominant mucosa-associated bacteria: a study using fluorescence in situ hybridization and temporal temperature gradient gel electrophoresis. Inflamm Bowel Dis. 2007;13:684–92.CrossRef

34.

Sepehri S, Kotlowski R, Bernstein CN, Krause DO. Microbial diversity of inflamed and noninflamed gut biopsy tissues in inflammatory bowel disease. Inflamm Bowel Dis. 2007;13:675–83.CrossRef

35.

Walker AW, Sanderson JD, Churcher C, Parkes GC, Hudspith BN, Rayment N, et al. High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and noninflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol. 2011;11:7.CrossRef

36.

Levine A, Koletzko S, Turner D, Escher JC, Cucchiara S, de Ridder L, et al. European society of pediatric gastroenterology, hepatology, and nutrition. ESPGHAN revised Porto criteria for the diagnosis of inflammatory bowel disease in children and adolescents. J Pediatr Gastroenterol Nutr. 2014;58:795–806.PubMed

37.

Swidsinski A, Ladhoff A, Pernthaler A, Swidsinski S, Loening-Baucke V, Ortner M, et al. Mucosal flora in inflammatory bowel disease. Gastroenterology. 2002;122:44–54.CrossRef

38.

Hu S, WangY Lichtenstein L, TaoY Musch MW, Jabri B, et al. Regional differences in colonic mucosa-associated microbiota determine the physiological expression of host heashock proteins. Am J Physiol Gastrointest Liver Physiol. 2010;299:G1266–75.CrossRef

39.

WangY Antonopoulos D, Zhu X, Harrell L, Hanan I, Alverdy J, et al. Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon. Appl Microbiol Biotechnol. 2010;88:1333–42.CrossRef

40.

WangY Devkota S, Musch MW, Jabri B, Nagler C, Antonopoulos DA, et al. Regional mucosa—associated microbiota determine physiological expression of TLR2 and TLR4 in murin colon. PLoS ONE. 2010;5:e13607.CrossRef

41.

Shobar RM, Velineni S, Keshavarzian A, Swanson G, DeMeo MT, Melson JE, et al. The effects of bowel preparation on microbiota-related metrics differ in health and in inflammatory bowel disease and for the mucosal and luminal microbiota compartments. Clin Transl Gastroenterol. 2016;7:e143.CrossRef

42.

Dowd SE, Callaway TR, Wolcott RD, Sun Y, McKeehan T, Hagevoort RG, et al. Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing [bTEFAP]. BMC Microbiol. 2008;8:125.CrossRef

43.

Dowd SE, Sun Y, Wolcott RD, Domingo A, Carroll JA. Bacterial tag encoded FLX amplicon pyrosequencing [bTEFAP] for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. Foodborne Pathog Dis. 2008;5:459–72.CrossRef

44.

Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.CrossRef

45.

Eren AM, Zozaya M, Taylor CM, Dowd SE, Martin DH, Ferris MJ. Exploring the diversity of Gardnerella virginals in the genitourinary tract microbiota of monogamous couples through subtle nucleotide variation. PLoS ONE. 2011;6:e26732.CrossRef

46.

Swanson KS, Dowd SE, Suchodolski JS, Middelbos IS, Vester BM, Barry KA, et al. Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice. ISME J. 2011;5:639–49.CrossRef

47.

Core R, Team R. A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2015.

48.

McMurdie PJ, Holmes S. An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8:e61217.CrossRef

49.

Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B. 1995;1995:289–300.

Title: Microbiota profile in new-onset pediatric Crohn’s disease: data from a non-Western population
Authors: Mohammad I. El Mouzan
Harland S. Winter
Assad A. Assiri
Kirill S. Korolev
Ahmad A. Al Sarkhy
Scot E. Dowd
Mohammad A. Al Mofarreh
Rajita Menon
Publication date: 01-12-2018
Publisher: BioMed Central
Published in: Gut Pathogens / Issue 1/2018
Electronic ISSN: 1757-4749
DOI: https://doi.org/10.1186/s13099-018-0276-3

ACC 2024 Congress Coverage

Heart Failure Video

Keynote webinar | Spotlight on sleep in brain health

Springer Medicine

Microbiota profile in new-onset pediatric Crohn’s disease: data from a non-Western population

Abstract

Background

Results

Conclusion

ACC 2024 Congress Coverage

Year in Review: Heart failure and cardiomyopathies

Semaglutide benefits people with type 2 diabetes and obesity-related heart failure

Incentivised to exercise

New intervention for STEMI-related cardiogenic shock

» View more highlights on the ACC 2024 congress hub page

Keynote webinar | Spotlight on sleep in brain health

Springer Medicine

Abstract

Background

Results

Conclusion

Please log in to get access to this content

Other articles of this Issue 1/2018

Genomic characterization of malonate positive Cronobacter sakazakii serotype O:2, sequence type 64 strains, isolated from clinical, food, and environment samples

The prevalence of Helicobacter pylori infection and other risk factors among Mongolian dyspeptic patients who have a high incidence and mortality rate of gastric cancer

Molecular detection of human enteric viruses circulating among children with acute gastroenteritis in Valencia, Venezuela, before rotavirus vaccine implementation

Identification of a new alanine racemase in Salmonella Enteritidis and its contribution to pathogenesis

Involvement of gut microbiome in human health and disease: brief overview, knowledge gaps and research opportunities

Genome sequence and comparative genomic analysis of a clinically important strain CD11-4 of Janibacter melonis isolated from celiac disease patient

ACC 2024 Congress Coverage

Year in Review: Heart failure and cardiomyopathies

Semaglutide benefits people with type 2 diabetes and obesity-related heart failure

Incentivised to exercise

New intervention for STEMI-related cardiogenic shock

» View more highlights on the ACC 2024 congress hub page