OP020 16S rRNA gene pyrosequencing indicate that siblings of Crohn's disease patients exhibit a biologically relevant dysbiosis in the mucosal microbiota communities

Abstract Background and Aims Anti-tumour necrosis factor [anti-TNF] therapy is indicated for treatment of moderate to severe inflammatory bowel disease [IBD], but has a primary non-response rate of around 30%. We aim to use metabonomic and metataxonomic profiling to identify predictive biomarkers of anti-TNF response in Crohn’s disease. Methods Patients with luminal Crohn’s disease, commencing anti-TNF therapy, were recruited with urine, faeces, and serum samples being collected at baseline and 3-monthly. Primary response was defined according to a combination of clinical and objective markers of inflammation. Samples were measured using three UPLC-MS assays: lipid, bile acid, and Hydrophillic Interaction Liquid Chromatography [HILIC] profiling with 16S rRNA gene sequencing of faeces. Results Samples were collected from 76 Crohn’s disease patients who were anti-TNF naïve and from 13 healthy controls. There were 11 responders, 37 non-responders, and 28 partial responders in anti-TNF-treated Crohn’s patients. Histidine and cysteine were identified as biomarkers of response from polar metabolite profiling [HILIC] of serum and urine. Lipid profiling of serum and faeces found phosphocholines, ceramides, sphingomyelins, and triglycerides, and bile acid profiling identified primary bile acids to be associated with non-response to anti-TNF therapy, with higher levels of phase 2 conjugates in non-responders. Receiver operating curves for treatment response demonstrated 0.94 +/ -0.10 [faecal lipid], 0.81 +/- 0.17 [faecal bile acid], and 0.74 +/- 0.15 [serum bile acid] predictive ability for anti-TNF response in Crohn’s disease. Conclusions This prospective, longitudinal cohort study of metabonomic and 16S rRNA gene sequencing analysis demonstrates that a range of metabolic biomarkers involving lipid, bile acid, and amino acid pathways may contribute to prediction of response to anti-TNF therapy in Crohn’s disease. Podcast This article has an associated podcast which can be accessed at https://academic.oup.com/ecco-jcc/pages/podcast

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The bacteriology of biopsies differs between newly diagnosed, untreated, Crohn's disease and ulcerative colitis patients

Journal of Medical Microbiology ◽

10.1099/jmm.0.46498-0 ◽

2006 ◽

Vol 55 (8) ◽

pp. 1141-1149 ◽

Cited By ~ 156

Author(s):

Rodrigo Bibiloni ◽

Marco Mangold ◽

Karen L. Madsen ◽

Richard N. Fedorak ◽

Gerald W. Tannock

Keyword(s):

Ulcerative Colitis ◽

Crohn’S Disease ◽

Crohn's Disease ◽

16S Rrna ◽

16S Rrna Gene ◽

Denaturing Gradient Gel Electrophoresis ◽

Rrna Gene ◽

Newly Diagnosed ◽

Real Time Quantitative Pcr ◽

Gene Libraries

The bacterial community (microbiota) that inhabits the gut of humans appears to be an important source of antigens that drive the chronic immunological processes characteristic of Crohn's disease (CD) and ulcerative colitis (UC). Most of the members of the microbiota have not yet been cultured, but nucleic-acid-based methods of detection and enumeration can provide information about the community. This investigation used these methods to obtain information about the bacteria associated with mucosal surfaces in the gut of 20 CD and 15 UC patients. Biopsies were collected from inflamed and non-inflamed sites in the intestines of newly diagnosed, untreated patients. Biopsies were also collected from several intestinal sites of 14 healthy subjects. The bacterial collections associated with the biopsies were analysed by generating PCR/denaturing gradient gel electrophoresis (DGGE) profiles, the preparation of 16S rRNA gene clone libraries, and qualitative PCR to detect specific groups of bacteria. The total numbers of bacteria associated with the biopsies were determined by real-time quantitative PCR. DGGE profiles generated from the terminal ileum and various colonic regions were characteristic of each individual but differed between subjects. DGGE profiles and 16S rRNA gene libraries showed that the bacteria associated with inflamed and non-inflamed tissues did not differ. UC patients had more bacteria associated with biopsies than did CD patients (P<0.01). Statistical analysis of the composition of 16S rRNA gene libraries showed that the bacterial collections in UC and CD patients differed (P<0.05). Unclassified members of the phylum Bacteroidetes were more prevalent in CD than in UC patients. Therefore, the types and numbers of bacteria associated with biopsy samples were distinctly different for UC and CD patients. The observations made in this study should permit targeting of specific bacteriological abnormalities in investigations of the pathogenesis of inflammatory bowel diseases and provide targets for medical interventions.

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Presence of eubacteria in biopsies from Crohn's disease inflammatory lesions as determined by 16S rRNA gene-based PCR.

Journal of Medical Microbiology ◽

10.1099/00222615-48-3-263 ◽

1999 ◽

Vol 48 (3) ◽

pp. 263-268 ◽

Cited By ~ 28

Author(s):

ANNIKA TIVEUUNG ◽

JOHAN D SÖDERHOLM ◽

GUNNAR OLAISON ◽

JON JONASSON ◽

HANS-JÜRG MONSTEIN

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

16S Rrna ◽

16S Rrna Gene ◽

Rrna Gene ◽

Inflammatory Lesions

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16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles

Microbiome ◽

10.1186/2049-2618-2-31 ◽

2014 ◽

Vol 2 (1) ◽

pp. 31 ◽

Cited By ~ 35

Author(s):

Jun Hang ◽

Valmik Desai ◽

Nela Zavaljevski ◽

Yu Yang ◽

Xiaoxu Lin ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Temperature Stability ◽

Clinical Samples ◽

Rrna Gene ◽

16S Rrna Gene Pyrosequencing

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Identification of microbiome with 16S rRNA gene pyrosequencing and antimicrobial effect of egg white in bovine mastitis

Korean Journal of Veterinary Research ◽

10.14405/kjvr.2017.57.2.117 ◽

2017 ◽

Vol 57 (2) ◽

pp. 117-126

Author(s):

Danil Kim ◽

Eun-Kyung Kim ◽

Won-Jin Seong ◽

Younghye Ro ◽

Dae-Sung Ko ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Bovine Mastitis ◽

Antimicrobial Effect ◽

Egg White ◽

Rrna Gene ◽

16S Rrna Gene Pyrosequencing

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Evolution of bacterial diversity during two-phase olive mill waste (“alperujo”) composting by 16S rRNA gene pyrosequencing

Bioresource Technology ◽

10.1016/j.biortech.2016.11.098 ◽

2017 ◽

Vol 224 ◽

pp. 101-111 ◽

Cited By ~ 35

Author(s):

Germán Tortosa ◽

Antonio Castellano-Hinojosa ◽

David Correa-Galeote ◽

Eulogio J. Bedmar

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Diversity ◽

Rrna Gene ◽

Two Phase ◽

Olive Mill Waste ◽

16S Rrna Gene Pyrosequencing ◽

Mill Waste ◽

Olive Mill

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Aberrant structures of fecal bacterial community in allergic infants profiled by 16S rRNA gene pyrosequencing

FEMS Immunology & Medical Microbiology ◽

10.1111/j.1574-695x.2011.00872.x ◽

2011 ◽

Vol 63 (3) ◽

pp. 397-406 ◽

Cited By ~ 47

Author(s):

Jiro Nakayama ◽

Takako Kobayashi ◽

Shigemitsu Tanaka ◽

Yuki Korenori ◽

Atsushi Tateyama ◽

...

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Rrna Gene ◽

16S Rrna Gene Pyrosequencing ◽

Fecal Bacterial Community

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Impact of a probiotic, inulin, or their combination on the piglets’ microbiota at different intestinal locations

Beneficial Microbes ◽

10.3920/bm2014.0030 ◽

2015 ◽

Vol 6 (4) ◽

pp. 473-483 ◽

Cited By ~ 10

Author(s):

V.A. Sattler ◽

K. Bayer ◽

G. Schatzmayr ◽

A.G. Haslberger ◽

V. Klose

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

16S Rrna Gene ◽

Real Time ◽

Relative Abundance ◽

Real Time Pcr ◽

Denaturing Gradient Gel Electrophoresis ◽

Feed Additives ◽

Rrna Gene ◽

16S Rrna Gene Pyrosequencing

Natural feed additives are used to maintain health and to promote performance of pigs without antibiotics. Effects of a probiotic, inulin, and their combination (synbiotic), on the microbial diversity and composition at different intestinal locations were analysed using denaturing gradient gel electrophoresis (DGGE), real-time PCR, and 16S rRNA gene pyrosequencing. Bacterial diversity assessed by DGGE and/or pyrosequencing was increased by inulin in all three gut locations and by the synbiotic in the caecum and colon. In contrast, the probiotic did only affect the microbiota diversity in the ileum. Shifts in the DGGE microbiota profiles of the caecum and colon were detected for the pro- and synbiotic fed animals, whereas inulin profiles were more similar to the ones of the control. 16S rRNA gene pyrosequencing revealed that all three additives could reduce Escherichia species in each gut location, indicating a potential beneficial effect on the gut microbiota. An increase of relative abundance of Clostridiaceae in the large intestine was found in the inulin group and of Enterococcaceae in the ileum of probiotic fed pigs. Furthermore, real-time PCR results showed that the probiotic and synbiotic increased bifidobacterial numbers in the ileum, which was supported by sequencing results. The probiotic and inulin, to different extents, changed the diversity, relative abundance of phylotypes, and community profiles of the porcine microbiota. However, alterations of the bacterial community were not uniformly between gut locations, demonstrating that functionality of feed additives is site specific. Therefore, gut sampling from various locations is crucial when investigations aim to identify the composition of a healthy gut microbiota after its manipulation through feed additives.

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