The gastric microbiota in patients with Crohn’s disease; a preliminary study

AbstractThe gastric microbiota in Crohn’s disease (CD) has not been studied. The purpose of the study was to evaluate differences of stomach microbiota between CD patients and controls. DNA was extracted from gastric mucosal and fluid samples, from 24 CD patients and 19 controls. 16S rRNA gene sequencing identified 1511 operational taxonomic units (OTUs), of which 239 passed the low abundance and low variance filters. All but one CD patients were HP negative. Fifteen bacterial phyla were identified in at least one mucosal or fluid site. Of these, Bacteroidota and Firmicutes accounted for 70% of all phyla. Proteobacteria, Actinobacteriota, and Fusobacteriota combined accounted for 27%. There was significant difference in the relative abundance of Bacteroidota, Proteobacteria, Fusobacteriota, and Campilobacterota between CD patients and controls only in gastric corpus samples. In gastric liquid, there was a significant difference only in Actinobacteriota. Pairwise comparison identified 67 differentially abundant OTUs in at least one site. Of these, 13 were present in more than one comparison, and four differentiating OTUs (Neisseriaceae, Neisseria, Absconditabacteriales, and Microbacteriaceae) were identified at all tested sites. The results reveal significant changes in gastric microbial profiles (beta diversity, phylum, and individual taxa levels) between H. pylori-negative CD patients and controls.

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P683 Patients with newly diagnosed fistulizing perianal Crohn’s disease have a distinct microbial signature

Journal of Crohn s and Colitis ◽

10.1093/ecco-jcc/jjab076.803 ◽

2021 ◽

Vol 15 (Supplement_1) ◽

pp. S602-S602

Author(s):

I Goren ◽

W Ian ◽

L Reshef ◽

T Sharar Fischler ◽

M Pauker ◽

...

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

16S Rrna Gene Sequencing ◽

Fecal Calprotectin ◽

Fecal Microbiota ◽

Rrna Gene ◽

Newly Diagnosed ◽

Linear Discriminant ◽

Microbial Dysbiosis ◽

Log Ratio

Abstract Background Alterations in gut bacterial microbiota are strongly associated with the pathogenesis of Crohn’s disease (CD). Up to 1/3 of patients with CD have perianal involvement (P-CD), either fistulizing (f-P-CD) or non-fistulizing (nf-P-CD). We hypothesized that alterations in fecal microbiota might drive perianal CD phenotypes. Methods Patients with newly diagnosed treatment naive CD were consecutively recruited. Patients were stratified into f-P-CD and nf-P-CD, and compared with CD without perianal involvement (non-P-CD). Bacterial 16S rRNA gene sequencing was performed. Microbial dysbiosis index (MDI), Shannon diversity score (H) and log ratio between anaerobic and aerobic bacteria (anaerobic index, AI) were calculated. Linear discriminant analysis effect size (LEfSe) was used to identify specific taxa discriminating between different patient groups. Fecal calprotectin (FC) was measured. Results We included 97 CD patients (50 males, median age 28 [IQR 22–41] years). Other than perianal involvement patients in both groups had comparable distribution of CD location and phenotype. The microbial indices MDI, H and AI as well as FC levels, did not differ between the P-CD (n=25) and non-P-CD (n=72) groups. When compared to non-P-CD, the P-CD exhibited significantly lower relative abundance in the Streptococci genera (p=0.01) and in the Ruminiclostridium_5 genera (p=0.02). Within the P-CD group, patients with f-P-CD (n=12) had significantly lower H than those with nf-P-CD (means: 2.0 vs 2.45, p=0.045), while FC levels were comparable between f-P-CD and nf-P-CD. Moreover, proportions of Coprococcus_3 and Lacnoclostridium were reduced in patients with f-P-CD vs nf-P-CD (p= 0.008, p=0.05, respectively), while Streptococcus was elevated (p=0.03). Conclusion Perianal CD is a spectrum with distinct microbial alterations in different phenotypes. Microbial alterations correspond to the severity of perianal involvement. This finding may suggest that the microbiome has a mechanistic role in complicated perianal CD.

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Metabonomics and the Gut Microbiome Associated With Primary Response to Anti-TNF Therapy in Crohn’s Disease

Journal of Crohn s and Colitis ◽

10.1093/ecco-jcc/jjaa039 ◽

2020 ◽

Vol 14 (8) ◽

pp. 1090-1102 ◽

Cited By ~ 3

Author(s):

N S Ding ◽

J A K McDonald ◽

A Perdones-Montero ◽

Douglas N Rees ◽

S O Adegbola ◽

...

Keyword(s):

Crohn’S Disease ◽

Bile Acid ◽

Crohn's Disease ◽

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Primary Response ◽

Rrna Gene ◽

Rrna Gene Sequencing

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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OP30 The interplay of microbiome dysbiosis and immune system deregulation in patients with Crohn’s disease

Journal of Crohn s and Colitis ◽

10.1093/ecco-jcc/jjz203.029 ◽

2020 ◽

Vol 14 (Supplement_1) ◽

pp. S028-S030

Author(s):

N S Seyed Tabib ◽

C Caenepeel ◽

K Machiels ◽

S Verstockt ◽

B Verstockt ◽

...

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

Regression Model ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Serum Samples ◽

Faecal Calprotectin ◽

Key Factor ◽

Inflammatory State ◽

Inflammatory Proteins

Abstract Background The perturbation of composition, function, and structure of the gut microbiota known as dysbiosis is a key factor in inflammatory bowel disease (IBD) pathogenesis. There is a crosstalk between the microbiota and the gut immunological niche. To better understand this interaction, we characterised the degree of dysbiosis and dysregulation of the immune proteome in Crohn’s disease (CD) patients to see whether subtypes of patients could be identified. Methods We collected faecal and serum samples of 146 CD patients and 63 healthy controls (HC) (Figure 1), and studied microbiota phylogenetic (16S rRNA gene sequencing) and serum proteomic (91 inflammatory proteins OLINK). Microbial dysbiotic index (MDI), defined as the logarithm of the sum of [abundance in organisms increased in CD] over the [abundance of organisms decreased in CD] was calculated and patients were ranked from Q1 (the least dysbiotic state) to Q4 (the most dysbiotic state). For the proteomic score, 32 proteins that correlated (adj. p ≤ 0.01) with faecal calprotectin (FC) were selected. A penalised logistic regression model was trained on these proteins, to distinguish HC from super active (defined as FC ≥ 1800 μg/g). We next developed an inflammatory proteomic score (IPS) defined as the weighted sum of the serum level of inflammatory proteins, using the coefficient value of the regression model as the protein’s weight. Using the IPS score, patients were clustered from Q1 (the least inflammatory state) to Q4 (the most inflammatory state). Statistical analyses were performed in R 3.5.2. Results The MDI did not correlate with standard phenotypic subgroups based on the Montreal classification but did positively correlate with C-reactive protein (CRP) and FC level (p ≤ 0.001). The regression model identified 14 proteins [including CCL20, CXCL1, IL-7, IL-17A, FGF-19] distinguishing super active CD patients from HC with accuracy, sensitivity, and specificity of 95.6%, 92.3%, 100%, respectively. IPS positively correlated with CRP and FC level (p ≤ 0.001). Likewise, MDI and IPS-based clusters were significantly different in CRP and FC levels. Different components of the microbiome correlated with the proteome in a subset of samples. For example, fibroblast growth factor 19 (FGF-19) positively correlated with Faecalibacterium and negatively with Fusicatenibacterium. Of note, we observed a significant positive correlation between MDI and IPS (r = 0.33, p ≤ 0.001) (Figure 2). Conclusion We were able to define clusters of patients based on molecular characterisation of different players in IBD pathogenesis such as microbiota and proteome. This molecular clustering in a given patient could be considered as a novel therapeutic and personalised approach to IBD. Further validation in larger cohorts is required.

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Differentially Abundant Bacterial Taxa Associated with Prognostic Variables of Crohn’s Disease: Results from the IMPACT Study

Journal of Clinical Medicine ◽

10.3390/jcm9061748 ◽

2020 ◽

Vol 9 (6) ◽

pp. 1748

Author(s):

Soo-kyung Park ◽

Han-Na Kim ◽

Chang Hwan Choi ◽

Jong Pil Im ◽

Jae Myung Cha ◽

...

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

Intestinal Resection ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Microbiota Composition ◽

Prognostic Variables ◽

E Coli ◽

Α Diversity ◽

The Impact

Limited studies have examined the intestinal microbiota composition in relation to Crohn’s disease (CD) prognosis. We analyzed the differences in microbial communities and relevant metabolic pathways associated with prognostic variables in patients with CD. We applied 16S rRNA gene sequencing to analyze a cohort of 1110 CD and healthy control (HC) fecal samples. We categorized patients with CD into good (CD-G), intermediate (CD-I) and poor (CD-P) prognosis groups, according to the history of using biologics and intestinal resection. Microbiota α-diversity decreased more in CD-P than CD-G and CD-I. Microbiota ß-diversity in CD-P differed from that in CD-G and CD-I. Thirteen genera and 10 species showed differential abundance between CD-G and CD-P groups. Escherichia coli (p = 0.001) and species Producta (p = 0.01) and genera Lactobacillus (p = 0.003) and Coprococcus (p = 0.01) consistently showed differences between CD-G and CD-P groups after adjusting for confounding variables. Functional profiling suggested that the microbial catabolic pathways and pathways related to enterobacterial common antigen and lipopolysaccharide biosynthesis were better represented in the CD-P group than in the CD-G group, and E. coli were the top contributors to these pathways. CD prognosis is associated with altered microbiota composition and decreased diversity, and E. coli might be causally involved in CD progression, and may have adapted to live in inflammatory environments.

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Influence of Enteral Nutrition on Gut Microbiota Composition in Patients with Crohn’s Disease: A Systematic Review

Nutrients ◽

10.3390/nu12092551 ◽

2020 ◽

Vol 12 (9) ◽

pp. 2551 ◽

Cited By ~ 1

Author(s):

Paulina Horwat ◽

Stanisław Kopeć ◽

Aleksandra Garczyk ◽

Iwona Kaliciak ◽

Zuzanna Staręga ◽

...

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

Enteral Nutrition ◽

Gut Microbiota ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Exclusive Enteral Nutrition ◽

Faecal Samples ◽

Hs Crp ◽

Rrna Gene Sequencing

The aim of the study was to systematically and comprehensively evaluate whether exclusive enteral nutrition (EEN) has impact on gut microbiota in patients with Crohn’s disease (CD). The databases PUBMED (MEDLINE), SCOPUS and WEB OF SCIENCE were searched. Out of 232 studies, 9 met inclusion criteria. The combined analyzed population consists of 118 patients with CD and treated with EEN with a time of intervention of 2–12 weeks. Studies were conducted in children, with the exception of one study. All applied feeding formulas had similar energy value and composition. The microbiome analysis was based on 16S rRNA gene sequencing of faecal samples. In all studies, EEN treatment decreases inflammatory markers (i.e., hs-CRP and FCP). A change in abundance of numerous bacterial families (Clostridiaceae, Eubacteriaceae, Bacteroidaceae) was noticed, especially in Bacteroidaceae. An increase in families connected to the more severe clinical course (Fusobacteria, Prevotella, Lachnospiraceae) was observed in only 2.5% of CD patients. Our analyses suggest EEN has a beneficial influence on gut microbiome in patients with CD, which is interrelated with clinical patient’s improvement and time of disease remission.

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Assessment of the Microbiota in Microdissected Tissues of Crohn's Disease Patients

International Journal of Inflammation ◽

10.1155/2012/505674 ◽

2012 ◽

Vol 2012 ◽

pp. 1-11 ◽

Cited By ~ 7

Author(s):

Gert De Hertogh ◽

Bart Lemmens ◽

Peter Verhasselt ◽

Ronald de Hoogt ◽

Xavier Sagaert ◽

...

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

Bacterial Pathogen ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Mucosal Healing ◽

Rrna Gene ◽

Excellent Method ◽

Rrna Gene Sequencing ◽

Laser Capture

The microbiota of the gastrointestinal tract is frequently mentioned as one of the key players in the etiopathogenesis of Crohn's disease (CD). Four hypotheses have been suggested: the single, still unknown bacterial pathogen, an abnormal overall composition of the bowel microbiota (“dysbiosis”), an abnormal immunological reaction to an essentially normally composed microbiota, and increased bacterial translocation. We propose that laser capture microdissection of selected microscopic structures, followed by broad-range 16S rRNA gene sequencing, is an excellent method to assess spatiotemporal alterations in the composition of the bowel microbiota in CD. Using this approach, we demonstrated significant changes of the composition, abundance, and location of the gut microbiome in this disease. Some of these abnormal findings persisted even after macroscopic mucosal healing. Further investigations along these lines may lead to a better understanding of the possible involvement of the bowel bacteria in the development of clinical Crohn's disease.

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Alterations of Gut Microbiota in Patients With Intestinal Tuberculosis That Different From Crohn’s Disease

Frontiers in Bioengineering and Biotechnology ◽

10.3389/fbioe.2021.673691 ◽

2021 ◽

Vol 9 ◽

Author(s):

Cong He ◽

Huan Wang ◽

Chen Yu ◽

Chao Peng ◽

Xu Shu ◽

...

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

Gut Microbiota ◽

Intestinal Tuberculosis ◽

Alpha Diversity ◽

16S Rrna Gene Sequencing ◽

Short Chain Fatty Acids ◽

Bacterial Invasion ◽

Rrna Gene ◽

Microbial Structure

Intestinal tuberculosis (ITB) and Crohn’s disease (CD) are chronic inflammatory bowel disorders that are associated with dysregulated mucosal immunity. The gut microbiota plays an important role in the regulation of host immunity and inflammatory response. Although mounting evidence has linked CD with the dysbiosis of gut microbiota, the characteristic profiles of mucosal bacteria in ITB remain unclear. The aim of this study was to assess the alterations of the gut microbiota in ITB and compare the microbial structure of ITB with CD. A total of 71 mucosal samples were collected from patients with ITB, CD, and healthy controls (HC), and then, 16S rRNA gene sequencing was performed. The overall composition of gut microbiota in ITB was strikingly different from HC, with the dominance of Proteobacteria and reduction of Firmicutes. Of note, the short-chain fatty acids (SCFAs)-producing bacteria such as Faecalibacterium, Roseburia, and Ruminococcus were decreased in ITB relative to HC, while Klebsiella and Pseudomonas were enriched. Multiple predictive functional modules were altered in ITB, including the over-representation of lipopolysaccharide biosynthesis, bacterial invasion of epithelial cells, and pathogenic Escherichia coli infection that can promote inflammation. Additionally, the microbial structure in CD was distinctly different from ITB, characterized by lower alpha diversity and increased abundance of Bacteroides, Faecalibacterium, Collinsella, and Klebsiella. These four bacterial markers distinguished ITB from CD with an area under the curve of 97.6%. This study established the compositional and functional perturbation of the gut microbiome in ITB and suggested the potential for using gut microbiota as biomarkers to differentiate ITB from CD.

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Diversity, Composition and Functional Inference of Gut Microbiota in Indian Cabbage white Pieris canidia (Lepidoptera: Pieridae)

Life ◽

10.3390/life10110254 ◽

2020 ◽

Vol 10 (11) ◽

pp. 254

Author(s):

Ying Wang ◽

Jianqing Zhu ◽

Jie Fang ◽

Li Shen ◽

Shuojia Ma ◽

...

Keyword(s):

Gut Microbiota ◽

16S Rrna Gene Sequencing ◽

Adult Survival ◽

Rrna Gene ◽

Life Stages ◽

Microbial Composition ◽

Significant Difference ◽

Functional Inference ◽

Rrna Gene Sequencing ◽

Insect Fitness

We characterized the gut microbial composition and relative abundance of gut bacteria in the larvae and adults of Pieris canidia by 16S rRNA gene sequencing. The gut microbiota structure was similar across the life stages and sexes. The comparative functional analysis on P. canidia bacterial communities with PICRUSt showed the enrichment of several pathways including those for energy metabolism, immune system, digestive system, xenobiotics biodegradation, transport, cell growth and death. The parameters often used as a proxy of insect fitness (development time, pupation rate, emergence rate, adult survival rate and weight of 5th instars larvae) showed a significant difference between treatment group and untreated group and point to potential fitness advantages with the gut microbiomes in P. canidia. These data provide an overall view of the bacterial community across the life stages and sexes in P. canidia.

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Endoscopic and Histopathological Findings of the Esophagus, Stomach, and Duodenum in Patients with Crohn’s Disease from a Reference Center in Bahia, Brazil

Clinics and Practice ◽

10.3390/clinpract11020052 ◽

2021 ◽

Vol 11 (2) ◽

pp. 374-385

Author(s):

Andrea Maia Pimentel ◽

Luiz Antônio Rodrigues de Freitas ◽

Rita de Cássia Reis Cruz ◽

Isaac Neri de Novais Silva ◽

Laíla Damasceno Andrade ◽

...

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

Mononuclear Cells ◽

Erosive Esophagitis ◽

Gastric Body ◽

Polymorphonuclear Cells ◽

Cross Sectional ◽

Histopathological Findings ◽

Focally Enhanced Gastritis ◽

H Pylori

(1) The aim of the present study was to describe the endoscopic and histopathological findings in the esophagus, stomach, and duodenum in patients with Crohn’s disease. (2) Methods: This was a cross-sectional study that included patients receiving treatment from the inflammatory bowel disease outpatient clinic. Esophagogastroduodenoscopies with biopsies of the stomach and proximal duodenum were performed. Presence of Helicobacter pylori bacteria was assessed by Giemsa staining. (3) Results: We included 58 patients. Erosive esophagitis was identified in 25 patients (43.1%), gastritis was diagnosed in 32 patients (55.2%) and erosive duodenitis was found in eight (13.8%). The most frequent histopathological finding in the H. pylori-positive group was increased inflammatory activity in the gastric body and antrum, with a predominance of mononuclear and polymorphonuclear cells. In turn, the most frequent finding in the H. pylori-negative group was chronic inflammation with predominance of mononuclear cells. Focally enhanced gastritis was identified in four patients (6.9%), all of whom were negative for H. pylori. Granulomas were not observed. H. pylori infection was present in 19 patients (32.8%). (4) Conclusions: Nonspecific endoscopic and histological findings were frequent in patients with Crohn’s disease. Focally enhanced gastritis was uncommon and observed only in H. pylori-negative patients. The time from the diagnosis, patient age, and therapy in use may have influenced the nondetection of epithelioid granuloma.

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Novel strain-level resolution of Crohn’s disease mucosa-associated microbiota via an ex vivo combination of microbe culture and metagenomic sequencing

The ISME Journal ◽

10.1038/s41396-021-00991-1 ◽

2021 ◽

Author(s):

J. J. Teh ◽

E. M. Berendsen ◽

E. C. Hoedt ◽

S. Kang ◽

J. Zhang ◽

...

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

Ex Vivo ◽

Taxonomic Composition ◽

Strain Level ◽

Patient Specific ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Functional Characterisation ◽

Bacterial Lineages

AbstractThe mucosa-associated microbiota is widely recognized as a potential trigger for Crohn’s disease pathophysiology but remains largely uncharacterised beyond its taxonomic composition. Unlike stool microbiota, the functional characterisation of these communities using current DNA/RNA sequencing approaches remains constrained by the relatively small microbial density on tissue, and the overwhelming amount of human DNA recovered during sample preparation. Here, we have used a novel ex vivo approach that combines microbe culture from anaerobically preserved tissue with metagenome sequencing (MC-MGS) to reveal patient-specific and strain-level differences among these communities in post-operative Crohn’s disease patients. The 16 S rRNA gene amplicon profiles showed these cultures provide a representative and holistic representation of the mucosa-associated microbiota, and MC-MGS produced both high quality metagenome-assembled genomes of recovered novel bacterial lineages. The MC-MGS approach also produced a strain-level resolution of key Enterobacteriacea and their associated virulence factors and revealed that urease activity underpins a key and diverse metabolic guild in these communities, which was confirmed by culture-based studies with axenic cultures. Collectively, these findings using MC-MGS show that the Crohn’s disease mucosa-associated microbiota possesses taxonomic and functional attributes that are highly individualistic, borne at least in part by novel bacterial lineages not readily isolated or characterised from stool samples using current sequencing approaches.

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