Introduction

Microscopic colitis (MC) refers to two pathologies – Collagenous colitis (CC) and Lymphocytic colitis (LC) that cause chronic watery diarrhoea, urgency, incontinence leading to significantly decreased quality of life¹. It is thought that MC develops due to a pathological immune response to intestinal luminal antigens in genetically predisposed individuals, with microbiota playing an important role^{2, 3}. However, the pathogenesis of MC is still unclear.

Aims & Methods

The aim of this study was to identify and characterize changes in bacterial composition of MC patients in terminal ileum and different colonic segments and determine its relation to the clinical course of disease. Biopsies from terminal ileum and six segments of the colon were collected during diagnostic colonoscopies. DNA extraction was performed using AllPrep DNA/RNA Micro Kit (Qiagen) following the manufacturer’s instructions. To determine bacterial composition, sequencing of the 16S rRNA variable region V3-V4 was conducted using the 27F and 338R polymerase chain reaction primers and sequenced on a MiSeq (2×250 bp; Illumina, Hayward, CA). Bioinformatic analysis was performed using DADA2, and taxonomic classification was carried out with the RDP classifier.

Results

Biopsy samples from 20 active CC patients, 20 active LC patients, and 50 controls demonstrated distinct microbial profiles across different intestinal segments, as revealed by beta-diversity and differential compositional analyses. Compared with controls, CC patients had consistent alterations in three bacterial families throughout the entire colon, with Erysipelatoclostridiaceae and Coriobacteriaceae decreased and Pasteurellaceae increased. Additionally, 35 families had segment-specific changes, and 25 families displayed altered abundance in the terminal ileum.
LC patients exhibited a consistent increase in Erisypelotrichaceae across the entire colon, with 38 other families showing segmental changes, and 12 families displaying altered abundance in the terminal ileum. Comparing LC and CC revealed a significantly different bacterial profile. LC showed lower abundance across many families, particularly in the right colon and terminal ileum. After sample collection, 15 CC patients and 12 LC patients received budesonide, with 3 CC and 2 LC patients having incomplete response. Beta diversity analysis revealed significant differences in the ascending colon and left side of the colon of CC patients based on response to budesonide. Patients with incomplete response to budesonide had an increased abundance of the genus Paucibacter. Similar tendencies were not observed in LC.
1 CC patient exhibited a quiescent disease course, 6 reached a sustained remission after treatment, 7 had a relapsing and 6 had a chronic active disease. Significant differences in beta diversity were observed in transverse, descending colon and rectum. Beta diversity of the descending colon had a medium correlation with disease behaviour. In the LC group 6 patients had a quiescent disease, 8 had a sustained remission after treatment, 3 exhibited a relapsing and 4 had a chronic active disease. No significant correlation between microbiota and disease behaviour was observed in LC.

Conclusion

This study showed significant differences in bacterial composition between CC, LC and controls in the terminal ileum and colon. In both CC and LC, bacterial alterations were not consistent throughout the entire colon but varied between different colonic segments. Microbiome differences based on response to budesonide and disease behaviour were observed in CC, but not LC.

References

1. Verhaegh BPM, Münch A, Guagnozzi D, et al. Course of Disease in Patients with Microscopic Colitis: A European Prospective Incident Cohort Study. J Crohns Colitis. 2021;15(7):1174-1183.
2. Miehlke S, Guagnozzi D, Zabana Y, et al. European guidelines on microscopic colitis: United European Gastroenterology (UEG) and European Microscopic Colitis Group (EMCG) statements and recommendations. United European Gastroenterol J. Published online 2020.
3. Burke KE, D’Amato M, Ng SC, Pardi DS, Ludvigsson JF, Khalili H. Microscopic colitis. Nat Rev Dis Primers. 2021;7(1).

Introduction

The human gut microbiome consists of a diverse range of microorganisms, including not only bacteria but also viruses, archaea and fungi. Among these, bacteria have been shown to have a significant impact on the health or disease status of the host. However, despite increasing evidence for the role of fungi in liver disease, inflammatory bowel disease and cancer, little is known about the interactions between bacteria and fungi.

Aims & Methods

In this study, we aimed to investigate in depth the interkingdom relationship between fungal and bacterial communities in the gut of healthy monozygotic and dizygotic twins using a novel merging analysis method. Faecal samples from 106 twin pairs were analysed using 16S rRNA gene sequencing for bacteria and ITS sequencing for fungi. To enable a comprehensive analysis of the interactions between these two microbial communities, we adapted a novel merging normalisation method and linked it to systematic dietary and environmental characteristics.

Results

The implementation of the merging normalisation method allowed for an in-depth comparison of the fungal and bacterial communities independent of the low read counts. In direct comparison, bacteria were significantly more abundant and diverse than fungi, with Bacteroides and Prevotella being the most dominant bacterial genera. Within the fungal community, Candida was the most abundant genus in the cohort, followed by Geotrichum, while Saccharomyces was less abundant. Other fungal genera were detected sporadically between individuals. Most bacterial taxa showed a negative correlation with both Candida and Geotrichum at some level of abundance. For example, Bacteroides showed no antagonism towards Candida when its relative abundance was below 5%, whereas genera such as Prevotella (rho=-0.16, p=0.02), Alistipes (rho=-0.16, p=0.02) and Faecalibacterium (rho=-0.17, p=0.01) showed antagonistic interactions with Candida at relative abundances as low as 0.1%. These correlations were calculated across different abundances of the interacting fungi and bacteria, showing that negative associations increased with higher abundance (up to rho=-0.6 for Alistipes). An interkingdom network analysis further revealed a complex dynamic involving the three most abundant genera - Bacteroides, Prevotella and Candida - which showed mutually antagonistic relationships.

Conclusion

The implementation of the novel, easy-to-use merging analysis provided an in-depth view of the interactions between bacterial and fungal communities in the human gut, which are predominantly antagonistic in nature. The bacterial community appears to use several mechanisms to protect the gut environment from fungal colonisation.

Disclosure

Nothing to disclose

Introduction

Colorectal cancer (CRC) is currently on of the most common cancer types worldwide and is the second leading cause of cancer-related mortality (Bray et al., 2018). Regardless of increasing access to CRC screening programs in many EU countries, more precise methods for early non-invasive disease discovery are highly needed (Kalager et al., 200; Benard et al., 2018). Currently CRC screening programs are based on fecal occult blood tests and/or colonoscopy, but this approach lacks of specificity and a large number or premalignant and malignant alterations in the colon are being overlooked (Click et al., 2019). Furthermore, current CRC programs result in high rate of expensive and unnecessary colonoscopy procedures, that pose significant risk for absolute healthy individuals (Ladabaum et al., 2019).
It is known that microbiome takes part in cancer genesis, its development, progression and even to its response to different treatment methods. Recent publication proves that gut microbiota (GM) can be used as novel biomarker tool in some disease (Russo et al., 2022, Roda et al., 2020). However, in order to, know whether microbiota is altered, studies identifying its profile in CRC patients are highly needed.

Aims & Methods

The aim of this study was to identify microbiome profile of CRC patients using gut mucosa biopsy and blood plasma samples.
In total, 313 individuals were included in this study, 104 of them were patients with CRC, 101 patients with adenomatous polyps (AP), and 108 were control individuals. Biopsies were taken from damaged mucosa during colonoscopy. Extracted DNA from all the samples was used to V1–V2 region of bacterial 16S rRNA gene amplification and sequencing on an Illumina MiSeq platform. To construct sample-similarity matrices abundances of taxonomic ranks in each sample type were used by applying Bray-Curtis algorithm. For significant differences between groups Permutational multivariate analysis of variance (PERMANOVA) and Mann-Whitney test followed by false-discovery rate test were used.

Results

Comparison between the global tissues bacterial assemblages revealed that the global structures at all taxonomic ranks were significantly different between control, CRC, and AP groups. Analysis revealed list of bacteria at the different taxonomic levels, the number of which was statistically significantly different between the groups. Moreover, analysis revealed bacteria that were associated with such clinical data as TNM classification, stage, and grade.

Conclusion

The global circulating and tissues microbiome profile of CRC and AP patients differs from that of the control group. Based on tissue and blood microbial profile it is possible to distinguish healthy state from CRC or AP. Mucosa tissue microbiome turns to be 20 times richer than blood microbiome. In CRC case bacterial richness and diversity decreases. Also there is distinct list of bacteria differed between CRC and control groups that could presumably be used as clinical biomarkers for CRC.

References

Bénard F, Barkun AN. Systematic review of colorectal cancer screening guidelines for average-risk adults: Summarizing the current global recommendations. World journal of gastroenterology. 2018; 24(1): 124. doi:
10.3748/wjg.v24.i1.124.
Bray F, Ferlay J, Soerjomataram I, et al. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2018;68(6):394–424. doi: 10.3322/caac.21492
Click B, Pinsky PF, Hickey T, et al. Association of Colonoscopy Adenoma Findings With Long-term Colorectal Cancer Incidence. JAMA, 2018; 319(19): 2021-31. doi: 10.1001/jama.2018.5809
Kalager M, Bretthauer M, et al. Improving cancer screening programs. Science. 2020; 367 (6474): 143-144; doi: 10.1126/science.aay3156
Ladabaum U, Mannalithara A, et al. Cost-Effectiveness and National Effects of Initiating Colorectal Cancer Screening for Average-Risk Persons at Age 45 Years Instead of 50 Years. Gastroenterology. 2019; 157(1):137-148. doi:
10.1053/j.gastro.2019.03.023
Senore C, Basu P, Anttila A, et al. Performance of Colorectal Cancer Screening in the European Union Member States: Data From the Second European Screening Report. Gut, 2019; 68(7):1232-44. doi: 10.1136/gutjnl-2018-317293
Roda G, Chien Ng S, et al. Crohn's disease. Nat Rev Dis Primers. 2020 Apr 2;6(1):22. doi: 10.1038/s41572-020-0156-2.
Russo E. The gut microbiota as a biomarker in epilepsy. Neurobiol Dis. 2022 Feb;163:105598. doi: 10.1016/j.nbd.2021.105598

Disclosure

The authors declare no conflict of interest.

Introduction

A wide range of relationships between the microbial community and various environmental or individual factors have been proposed. Monozygotic and dizygotic twins provide a unique model for assessing host-microbial interactions. The mycobiome has been increasingly implicated in the development of several diseases, but knowledge of the dynamics of the fungal community, particularly in twins, has not been addressed.

Aims & Methods

In this work, we investigated the fungal community in a twin cohort and explored its relationship with associated genetic and environmental factors through in-depth analysis.
The twin cohort consisted of 106 well-characterised and systematically studied monozygotic and dizygotic pairs (212 stool samples). DNA was extracted and PCR reactions were performed to sequence the lower gastrointestinal microbiome and the mycobiome community. The bacterial community was characterised using the V1-V2 region of the 16 rRNA gene and the fungal community was analysed using the ITS1-ITS2 region.

Results

The fungal community, represented by the sum of all fungal sequences, showed a significantly higher heterogeneity than the bacterial community. Several individual and genetic factors, such as the zygotic status of the twins (monozygotic vs. dizygotic), as well as sex, mode of birth, breast-feeding as newborns or living in the same household, were independent of the total number of fungal sequences. The bacterial community was significantly more abundant than the fungal community, the most common representatives of which were Candida and Geotrichum with sometimes very high abundances. Saccharomyces was also common in the cohort, but only in low abundance, other fungi with a wider distribution were Cladosporium or Penicillium. The environmental and individual factors mentioned above were also correlated with the individual fungal genera, but there were no significant correlations found here either. The next step was to correlate the bacterial and fungal communities with each other, and strong negative correlations were found with certain bacteria such as Prevotella.

Conclusion

Genetic factors in twins are not associated with dynamics in the faecal fungal community and were the subject of high inter-individual variability. However, there is a strong association between bacterial and mycobial interaction, which requires further in-depth understanding of microbial interactions.

Disclosure

No conflict of interest to declare