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Spatial Organization and Composition of the Mucosal Flora in Patients with Inflammatory Bowel Disease
Open accessAbstract
The composition and spatial organization of the mucosal flora in biopsy specimens from patients with inflammatory bowel disease (IBD; either Crohn's disease or ulcerative colitis), self-limiting colitis, irritable-bowel syndrome (IBS), and healthy controls were investigated by using a broad range of fluorescent bacterial group-specific rRNA-targeted oligonucleotide probes. Each group included 20 subjects. Ten patients who had IBD and who were being treated with antibiotics were also studied. Use of nonaqueous Carnoy fixative to preserve the mucus layer was crucial for detection of bacteria adherent to the mucosal surface (mucosal bacteria). No biofilm was detectable in formalin-fixed biopsy specimens. Mucosal bacteria were found at concentrations greater than 10 9 /ml in 90 to 95% of IBD patients, 95% of patients with self-limiting colitis, 65% of IBS patients, and 35% of healthy controls. The mean density of the mucosal biofilm was 2 powers higher in IBD patients than in patients with IBS or controls, and bacteria were mostly adherent. Bacteroides fragilis was responsible for >60% of the biofilm mass in patients with IBD but for only 30% of the biofilm mass in patients with self-limiting colitis and <15% of the biofilm mass in patients with IBS. In contrast, bacteria which positively hybridized with the probe specific for Eubacterium rectale - Clostridium coccoides accounted for >40% of the biofilm in IBS patients but for <15% of the biofilm in IBD patients. In patients treated with (5-ASA) or antibiotics, the biofilm could be detected with 4,6-diamidino-2-phenylindole but did not hybridize with fluorescence in situ hybridization probes. A Bacteroides fragilis biofilm is the main feature of IBD. This was not previously recognized due to a lack of appropriate tissue fixation. Both 5-ASA and antibiotics suppress but do not eliminate the adherent biofilm.
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“Spatial niche partitioning of microbial populations can also be a result of mucus from goblet cells 46 and differential oxygen tolerance47.”
From The gut Microbiome in adult and pediatric functional gastrointestinal disorders (2019) · cites this paper as [46]
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Therapeutic microbiome modulation: new frontiers in HIV treatment
Bulnes, R., & Utay, N. S. (2024) · Current Opinion in HIV and AIDS · doi:10.1097/coh.0000000000000864 · Cited by 7
Significance of Gut Microbiota on Graves’ Disease
Chen, H., Cao, J., Zhang, F., & Xiong, W. (2024) · International Journal of General Medicine · doi:10.2147/ijgm.s467888 · Cited by 6
“26 16S rRNA sequencing analyzed the fecal microbiota of 45 GD patients and 59 healthy controls, and found that the abundance of lactobacilli in TPOAb positive GD patients was significantly higher than that in TPOAb negative GD patients.”
ResultChallenges in IBD research: Assessing progress and rethinking the research agenda
Stenson, W. F., & Snapper, S. B. (2008) · Inflammatory Bowel Diseases · doi:10.1002/ibd.20371 · Cited by 6
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Diversity of the human gastrointestinal microbiota
Rajilić-Stojanović, M. D., & de Vos, W. M. (2007) · TechnoRep (University of Belgrade – Faculty of Technology and Metallurgy) · Cited by 6
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Bacterial immune interaction in experimental colitis
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Flore et syndrome de l’intestin irritable
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“We have successfully used this approach in case of colonic cancer [2], inflammatory bowel disease [3], gallstones [4], tonsillitis [5], appendicitis [6], bacterial vaginosis [7], candidiasis [8], and urethritis [9].”
MethodSelf-citationLong term management of ulcerative colitis with Faecal Microbiota Transplantation
Singh, A., Mahajan, R., Kao, D. H., Midha, V., & Sood, A. (2020) · Medicine in Microecology · doi:10.1016/j.medmic.2020.100026 · Cited by 6
The Gut Microbiome in Inflammatory Bowel Disease
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Cystic fibrosis and inflammatory bowel disease: parallels in gut physiology and microbiota
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“In UC cohorts, there is a similar decrease in Firmicutes members, including the Clostridium cluster XIVa (114).”
InfluentialPhenotypic characterization and complete genome of a tumorigenic pathobiont Escherichia coli LI60C3
Yu, L. C., Wei, S., Li, Y.-H., Huang, C., Pai, Y.-C., Hung, Y.-M., Lai, L., & Ni, Y. (2025) · Gut Pathogens · doi:10.1186/s13099-025-00732-1 · Cited by 5
“While symbiotic commensals inhabit the gut lumen in healthy humans, elevated levels of mucosal bacteria were detected in clinical specimens from patients [4–6].”
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Postoperative Ileus Murine Model
Tian, D., Liu, B., Huang, S., Shi, W., Tian, Y., Yang, Y., Zhang, D., Zhang, Z., & Bu, F. (2024) · Journal of Visualized Experiments · doi:10.3791/66465 · Cited by 5
Microbiota intestinal: estado da arte
Perez, H. J., Menezes, M. E., & d'Acâmpora, A. J. (2014) · DOAJ (DOAJ: Directory of Open Access Journals) · Cited by 5
Caracterización, influencia y manipulación de la microbiota gastrointestinal en salud y enfermedad
García-Mazcorro, J. F., Garza‐González, E., Marroquín-Cardona, A. G., & Tamayo, J. L. (2015) · Gastroenterología y Hepatología · doi:10.1016/j.gastrohep.2015.01.004 · Cited by 5
The profiles of dysbiotic microbial communities
Brun, P. (2019) · AIMS Microbiology · doi:10.3934/microbiol.2019.1.87 · Cited by 6
“Biofilms of Bacteroides fragilis, usually a commensal microbe in the gut microbiota, have been described in close proximity with inflamed mucosa in the biopsies of patients suffering from Crohn’s disease and ulcerative colitis [57].”
Background
Metadata
- Authors
- Swidsinski, A., Weber, J., Loening-Baucke, V., Hale, L. P., & Lochs, H.
- Affiliations
- Humboldt-Universität zu Berlin (DE)
- Duke Medical Center (US)
- Venue
- Journal of Clinical Microbiology
- Publisher
- American Society for Microbiology
- Published
- 2005-07
- Volume
- 43
- Issue
- 7
- Pages
- 3380-3389
- ISSN
- 0095-1137 (ISSN-L)
- 1098-660X
- PMC
- PMC1169142
- OpenAlex
- W2097177097
- Cited by
- 894
- References
- 36
- Citations by year
- 2026: 15 · 2025: 27 · 2024: 45 · 2023: 47 · 2022: 59 · 2021: 47 · 2020: 50 · 2019: 54 · 2018: 46 · 2017: 35 · 2016: 47 · 2015: 49 · 2014: 41 · 2013: 43 · 2012: 44
- FWCI
- 12.71
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Journal of Clinical Microbiology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Eli and Edythe Broad Foundation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Gastroenterology › Inflammatory Bowel Disease
- Health Sciences › Medicine › Gastroenterology › Microscopic Colitis
- Keywords
- inflammatory bowel disease, Crohn's disease, ulcerative colitis, Bacteroides fragilis, irritable bowel syndrome, 5-aminosalicylic acid, antibiotic therapy, bacterial adhesion, fluorescence in situ hybridization, rRNA-targeted oligonucleotide probes
- MeSH terms
- Adult, Bacteria, Bacteroides fragilis, Biopsy, Colitis, Ulcerative, Crohn Disease, Female, Humans, Intestinal Mucosa, Male, Middle Aged, Colon, Sigmoid, In Situ Hybridization, Fluorescence, Ecosystem, Biofilms
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