Introduction

The pathogenesis of inflammatory bowel disease (IBD) involves a complex interplay among a genetically susceptible host, environmental factors, dysregulated immune response, and intestinal microbiota. Multiple studies have documented differences in the composition of gut microbiota between patients with IBD and healthy individuals, particularly regarding microbial diversity and relative abundance of specific bacteria. However, studies generally include patients treated with immunosuppressive therapy, which may modify the microbiota and can make a result harder to interpret.

Aims & Methods

Our aim was to elucidate the microbiota in newly diagnosed IBD patients compared to healthy controls (HC), and the differences between patients with Crohn’s disease (CD) and ulcerative colitis (UC). Stool samples were collected from IBD patients before having started any treatment for the disease and HC from a biobank. Shotgun metagenomic sequencing was performed in each sample, and subsequent bioinformatic analyses were done with Cutadapt, Kraken2 and Bracken programs. IBD activity was classified by the Simple Endoscopic Score in the case of CD (SES-CD) and by the endoscopic subscore of the Mayo index in the case of UC.

Results

We included 104 patients with CD, 145 with UC and 49 HC. Patients with CD had a statistically significant decrease in the α-diversity, calculated with Shannon Index on species-level taxa, compared with UC and HC groups; in addition, an inverse relationship was observed between the severity of activity and microbial α-diversity. However, in patients with UC the microbial α-diversity was similar to HC cohort. We also calculated the β-diversity between pair-wise combinations using Bray-Curtis dissimilarity, showing that this index was lower in UC vs. HC compared to CD vs. HC. Regarding to the severity of disease in CD patients, β-diversity index increased directly with severity. On the other hand, we found no differences between severity activity groups in UC patients. Considering the taxonomic abundance at the microbial species taxonomic level, the greatest differences in patients with CD globally and those with severe activity, were found in Lactobacillus paragasseri and Gemella haemolysans, compared to HC. However, patients with mild CD had the greatest differences in several species of Shigella genus, and those with moderate CD in Granulicatella elegans. Patients with UC globally, and particularly with mild, moderate and severe activity, showed the greatest differences in Toxoplasma gondii and Aspergillus oryzae, compared with HC.

Conclusion

Our data suggest that patients with CD, from the moment of diagnosis, showed relevant differences in the composition of the microbiota compared with UC patients and HC individuals; however, UC microbiome is relatively closer to HC. Moreover, the severity of IBD is associated with the distribution of species in fecal microbiota.

Clinical Case Summary

A 54-year-old male presented by jaundice for two weeks. The condition associated with right hypochondrial colicky pain, dark urine, clay stool and itching. He denied any significant past medical or surgical history. The physical examination revealed deep jaundice and scratch skin marks.

References

Figure 1: Intrahepatic and extrahepatic biliary anomalies

Clinical Case Summary

A 53 year-old woman complained of chronic diarrhea, lack of appetitis and weight loss, that started two years before her admission. She described watery stools without bleeding or pus, as well as a 14 kg weight loss, but she had no fever, pruritus or night sweating. She had received a previous treatment for Graves’ disease during her pregnancy. Her physical examination was unremarkable, but she had a calprotectin fecal of 1028. Her last colonoscopy (performed 1 month before her admission) revealed an unspecific ileocolitis saving the sigmoid colon and the rectum, showing a friable and diffuse enanthematous mucous with some raised areas simulating a polypoid aspect. First she was empirically treated for parasitosis, and images were obtained, in addition to a wide range of laboratory tests. She presented a mild anemia associated with a thickened biliary tree and a pancreatic volume prominence with loss of its lobulations, as well as parietal enhancement of the ascending colon and enlarged mesenteric lymph nodes with hypodense centers suggesting necrosis.Upper GI biopsies were negative for H pylori infection, but biopsies of the colons showed a diffuse atypical lymphoplasmacytic infiltrate in the lamina propria. Medications and infectios were ruled out, and a PET-CT scan showed diffuse thickened wall of the colons (particularly cecum and transverse colon), as well as a mild thickened biliary tree, an enlarged thyroid and both mesenteric and pericolic lymphadenopathies - all of these areas showed a glycolytic activity slightly increased. IgG4 disease was also excluded after a normal IgG4/IgG relation from biopsy samples. Finally, a immunophenotyping study of the colons' samples was conducted, confirming a MALT lymphoma. The patient received rituximab for 9 months and a tumor restaging was conducted afterwards. A post-treatment PET-CT showed complete remission of the disease, with no areas of abnormal glycolytic metabolism, in addition to a fecal calprotectin of 11mcg/g.