16S sequencing and functional analysis of the fecal microbiome during treatment of newly diagnosed pediatric inflammatory bowel disease

James J. Ashton, Catherine M. Colquhoun, David W . Cleary, Tracy Coelho, Rachel Haggarty, Imke Mulder, Akshay Batra, Nadeem A. Afzal, R. Mark Beattie, Karen P. Scott, Sarah Ennis

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Abstract

The human microbiome is of considerable interest to pediatric inflammatory bowel disease (PIBD) researchers with 1 potential mechanism for disease development being aberrant immune handling of the intestinal bacteria. This study analyses the fecal microbiome through treatment in newly diagnosed PIBD patients and compares to cohabiting siblings where possible. Patients were recruited on clinical suspicion of PIBD before diagnosis. Treatment-naïve fecal samples were collected, with further samples at 2 and 6 weeks into treatment. Samples underwent 16S ribosomal ribonucleic acid (RNA) gene sequencing and short-chain fatty acids (SCFAs) analysis, results were analyzed using quantitative-insights-into-microbial-ecology. Six PIBD patients were included in the cohort: 4 Crohn disease (CD), 1 ulcerative colitis (UC), 1 inflammatory bowel disease (IBD) unclassified, and median age 12.6 (range 10–15.1 years); 3 patients had an unaffected healthy sibling recruited. Microbial diversity (observed species/Chao1/Shannon diversity) was reduced in treatment-naïve patients compared to siblings and patients in remission. Principal coordinate analysis using Bray–Curtis dissimilarity and UniFrac revealed microbial shifts in CD over the treatment course. In treatment-naïve PIBD, there was reduction in functional ability for amino acid metabolism and carbohydrate handling compared to controls (P = .038) and patients in remission (P = .027). Metabolic function returned to normal after remission was achieved. SCFA revealed consistent detection of lactate in treatment-naïve samples. This study adds in-depth 16S rRNA sequencing analysis on a small longitudinal cohort to the literature and includes sibling controls and patients with UC/IBD unclassified. It highlights the initial dysbiosis, reduced diversity, altered functional potential, and subsequent shifts in bacteria from diagnosis over time to remission.
Original languageEnglish
Article numbere7347
Pages (from-to)1-10
Number of pages10
JournalMedicine
Volume96
Issue number26
DOIs
Publication statusPublished - Jun 2017

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Microbiota
Inflammatory Bowel Diseases
Pediatrics
Siblings
Crohn Disease
Volatile Fatty Acids
Therapeutics
Ulcerative Colitis
Dysbiosis
Bacteria
Aptitude
Carbohydrate Metabolism
Ecology
Lactic Acid
Research Personnel
RNA
Amino Acids
Genes

Keywords

  • 16S
  • Crohn’s disease
  • inflammatory bowel disease
  • pediatrics
  • microbiome

Cite this

Ashton, J. J., Colquhoun, C. M., Cleary, D. W. ., Coelho, T., Haggarty, R., Mulder, I., ... Ennis, S. (2017). 16S sequencing and functional analysis of the fecal microbiome during treatment of newly diagnosed pediatric inflammatory bowel disease. Medicine, 96(26), 1-10. [e7347]. https://doi.org/10.1097/MD.0000000000007347

16S sequencing and functional analysis of the fecal microbiome during treatment of newly diagnosed pediatric inflammatory bowel disease. / Ashton, James J.; Colquhoun, Catherine M.; Cleary, David W .; Coelho, Tracy ; Haggarty, Rachel; Mulder, Imke; Batra, Akshay; Afzal, Nadeem A.; Beattie, R. Mark; Scott, Karen P.; Ennis, Sarah .

In: Medicine, Vol. 96, No. 26, e7347, 06.2017, p. 1-10.

Research output: Contribution to journalArticle

Ashton, JJ, Colquhoun, CM, Cleary, DW, Coelho, T, Haggarty, R, Mulder, I, Batra, A, Afzal, NA, Beattie, RM, Scott, KP & Ennis, S 2017, '16S sequencing and functional analysis of the fecal microbiome during treatment of newly diagnosed pediatric inflammatory bowel disease', Medicine, vol. 96, no. 26, e7347, pp. 1-10. https://doi.org/10.1097/MD.0000000000007347
Ashton, James J. ; Colquhoun, Catherine M. ; Cleary, David W . ; Coelho, Tracy ; Haggarty, Rachel ; Mulder, Imke ; Batra, Akshay ; Afzal, Nadeem A. ; Beattie, R. Mark ; Scott, Karen P. ; Ennis, Sarah . / 16S sequencing and functional analysis of the fecal microbiome during treatment of newly diagnosed pediatric inflammatory bowel disease. In: Medicine. 2017 ; Vol. 96, No. 26. pp. 1-10.
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