Cited by 894Gut microbiota and healthInflammatory Bowel DiseaseMicroscopic Colitis

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Spatial Organization and Composition of the Mucosal Flora in Patients with Inflammatory Bowel Disease

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Swidsinski, Alexander, Weber, Jutta, Loening-Baucke, Vera, Hale, Laura P., Lochs, Herbert·2005·Journal of Clinical Microbiology

DOI 10.1128/jcm.43.7.3380-3389.2005PMC PMC1169142

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Abstract

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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Bacterial Biofilms: A Common Cause of Persistent Infections
Costerton, J. W., Stewart, P. S., & Greenberg, E. P. (1999) · Science · doi:10.1126/science.284.5418.1318 · Cited by 12,167
Phylogenetic identification and in situ detection of individual microbial cells without cultivation
Amann, R., Ludwig, W., & SCHLEIFER, K. H. (1995) · Microbiological Reviews · doi:10.1128/mr.59.1.143-169.1995 · Cited by 9,218
Inflammatory Bowel Disease
Podolsky, D. K. (2002) · New England Journal of Medicine · doi:10.1056/nejmra020831 · Cited by 3,183
Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology
Amann, R., Krumholz, L. R., & Stahl, D. A. (1990) · Journal of Bacteriology · doi:10.1128/jb.172.2.762-770.1990 · Cited by 2,207
Inflammatory bowel disease: Etiology and pathogenesis
Fiocchi, C. (1998) · Gastroenterology · doi:10.1016/s0016-5085(98)70381-6 · Cited by 2,059
Phylogenetic Oligodeoxynucleotide Probes for the Major Subclasses of Proteobacteria: Problems and Solutions
Manz, W., Amann, R., Ludwig, W., Wagner, M., & SCHLEIFER, K. H. (1992) · Systematic and Applied Microbiology · doi:10.1016/s0723-2020(11)80121-9 · Cited by 2,044
Mucosal flora in inflammatory bowel disease
Swidsinski, A. V., Ladhoff, A., Pernthaler, A., Swidsinski, S., Loening-Baucke, V. A., Ortner, M., Weber, J., Hoffmann, U., Schreiber, S., Dietel, M., et al. (2002) · Gastroenterology · doi:10.1053/gast.2002.30294 · Cited by 1,344
Self-citation
Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment
Manz, W., Amann, R., Ludwig, W., Vancanneyt, M., & SCHLEIFER, K. H. (1996) · Microbiology · doi:10.1099/13500872-142-5-1097 · Cited by 1,176
Variations of Bacterial Populations in Human Feces Measured by Fluorescent In Situ Hybridization with Group-Specific 16S rRNA-Targeted Oligonucleotide Probes
Franks, A. H., Harmsen, H. J. M., Raangs, G. C., Jansen, G. J., Schut, F., & Welling, G. W. (1998) · Applied and Environmental Microbiology · doi:10.1128/aem.64.9.3336-3345.1998 · Cited by 1,056
Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and its application in fecal samples
Langendijk-Genevaux, P. S., Schut, F., Jansen, G. J., Raangs, G. C., Kamphuis, G. R., Wilkinson, M. H. F., & Welling, G. W. (1995) · Applied and Environmental Microbiology · doi:10.1128/aem.61.8.3069-3075.1995 · Cited by 974

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“2 Clostridiales Ruminococcaceae Ruminococcus 2 bromii @[67] 0.”
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Atherly, T. A., Mosher, C., Wang, C., Hostetter, J. M., Proctor, A., Brand, M. W., Phillips, G. J., Wannemuehler, M. J., & Jergens, A. E. (2016) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000000944 · Cited by 20
Bacterial driver–passenger model in biofilms: a new mechanism in the development of colorectal cancer
Xing, J., Fang, Y., Zhang, W., Zhang, H., Tang, D., & Wang, D. (2022) · Clinical & Translational Oncology · doi:10.1007/s12094-021-02738-y · Cited by 17
“fragilis biofilm is widely considered to be a core feature of IBD, as more than 60% of biofilms obtained from IBD patients’ samples contain such bacteria [43].”
Background
Inflammatory bowel disease-associated adherent-invasive Escherichia coli have elevated host-defense peptide resistance
Cho, Y. H., Renouf, M. J. D., Omotoso, O., & McPhee, J. B. (2022) · FEMS Microbiology Letters · doi:10.1093/femsle/fnac098 · Cited by 19
Focus on irritable bowel syndrome.
Scalera, A., & Loguercio, C. (2012) · PubMed · Cited by 19
Intestinal dysbiosis in irritable bowel syndrome: etiological factor or epiphenomenon?
Cremon, C., Carini, G., GIORGIO, R. D., Stanghellini, V., Corinaldesi, R., & Barbara, G. (2010) · Expert Review of Molecular Diagnostics · doi:10.1586/erm.10.33 · Cited by 19
Rewiring of the cellular and inter-cellular landscape of the human colon during ulcerative colitisPreprint
Smillie, C. S., Biton, M., Ordovás-Montañés, J., Sullivan, K. M., Burgin, G., Graham, D. B., Herbst, R. H., Rogel, N., Slyper, M., Waldman, J., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/455451 · Cited by 18
“Within the colon, pH and sour taste sensing may help detect members of the gut microbiota, for example, the Lactobacillales, which have established long-term symbioses with humans and inhabit colonic crypts [82].”
Background
Disturbance in the mucosa-associated commensal bacteria is associated with the exacerbation of chronic colitis by repeated psychological stress; is that the new target of probiotics
Arase, S., Watanabe, Y., Setoyama, H., Nagaoka, N., Kawai, M., & Matsumoto, S. (2016) · PLoS ONE · doi:10.1371/journal.pone.0160736 · Cited by 18
“Exacerbation of gut inflammation by chronic psychological stress It was reported that Tcra mice spontaneously develop human UC-like colitis, which may be due to a deregulated mucosal immune system evoked by the GI microbiota [14, 38].”
Background
Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohnʼs disease
Willing, B., Halfvarson, J., Dicksved, J., Rosenquist, M., Järnerot, G., Engstrand, L., Tysk, C., & Jansson, J. K. (2009) · Inflammatory Bowel Diseases · doi:10.1002/ibd.20783 · Cited by 455
“Reports of increased bacterial numbers associated with biopsies from CD patients as compared to healthy controls have been inconsistent.(47,50,51) We did not observe any differences in bacterial numbers associated with disease phenotype, however, this may be due to the nature of the control patients, as”
Background
Mucosa-associated bacteria and metabolites in inflammatory bowel disease: from inside to insight
Wang, X., He, L., Dong, Y., Qin, X., Zhang, H., Wang, B., Wang, S., & Cao, H. (2026) · npj Biofilms and Microbiomes · doi:10.1038/s41522-025-00887-4 · Cited by 21
RETRACTED ARTICLE: Gut microbiota and related diseases: clinical features
Stanghellini, V., Barbara, G., Cremon, C., Cogliandro, R. F., Antonucci, A., Gabusi, V., Frisoni, C., GIORGIO, R. D., Grasso, V., Serra, M., et al. (2010) · Internal and Emergency Medicine · doi:10.1007/s11739-010-0451-0 · Cited by 18
“the mucosal layer were higher in IBS (65%) compared with controls (35%) [ 30 ].”
Result
Retracted
Characterizing the Pathogenic Potential of Crohn’s Disease-Associated Adherent-Invasive Escherichia coli
Zangara, M. T., Darwish, L., & Coombes, B. K. (2023) · EcoSal Plus · doi:10.1128/ecosalplus.esp-0018-2022 · Cited by 19
Single-cell analysis and spatial resolution of the gut microbiome
Madhu, B., Miller, B. M., & Levy, M. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1271092 · Cited by 18
Control of host inflammatory responsiveness by indigenous microbiota reveals an adaptive component of the innate immune system
Fagundes, C. T., Souza, D. G., Nicoli, J. R., & Teixeira, M. M. (2011) · Microbes and Infection · doi:10.1016/j.micinf.2011.07.012 · Cited by 18
Diversity of caecal bacteria is altered in interleukin-10 gene-deficient mice before and after colitis onset and when fed polyunsaturated fatty acids
Knoch, B., Nones, K., Barnett, M. P. G., McNabb, W. C., & Roy, N. C. (2010) · Microbiology · doi:10.1099/mic.0.041723-0 · Cited by 18
MyD88 Mediates the Protective Effects of Probiotics Against the Arteriolar Thrombosis and Leukocyte Recruitment Associated with Experimental Colitis
Souza, D. G., Senchenkova, E. Y., Russell, J., & Granger, D. N. (2015) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000000331 · Cited by 18
“These changes include reduced bacterial diversity, decreased levels of resident Firmicutes and/or Bacteroidetes, an overgrowth of Proteobacteria, and abnormal adherence of bacteria to the gut mucosa.(50,51) To avoid the microbiota disturbance in this study, we recolonized GF mice with feces derived from Souza et al In…”
Method
Antibiofilm and antibacterial activities of repurposing auranofin against Bacteroides fragilis
Jang, H.-I., & Eom, Y. (2019) · Archives of Microbiology · doi:10.1007/s00203-019-01764-3 · Cited by 18
Increased Antibody Response to Fucosylated Oligosaccharides and Fucose-Carrying Bacteroides Species in Crohn’s Disease
Kappler, K., Lasanajak, Y., Smith, D. F., Opitz, L., & Hennet, T. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01553 · Cited by 17
“Bacteroides Fucosylation and Recognition by IgG in CD Patients Bacteroidetes is a major phylum of the human intestinal microbiota and several Bacteroides species have been found to be enriched in IBD (Swidsinski et al., 2005; Gevers et al., 2014).”
Background
Impact of the ileal microbiota on colon cancer
Roberti, M. P., Rauber, C., Kroemer, G., & Zitvogel, L. (2021) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2021.09.016 · Cited by 18
Friendly pathogens: prevent or provoke autoimmunity
Sathyabama, S., Khan, N., & Agrewala, J. N. (2013) · Critical Reviews in Microbiology · doi:10.3109/1040841x.2013.787043 · Cited by 18
“However, the human intestine is dominated by bacteroidetes and firmicutes, which represents more than two-thirds of the total gut microbiota (Frank et al., 2007; Swidsinski et al., 2005).”
Background
A short-oligonucleotide microarray that allows improved detection of gastrointestinal tract microbial communities
Harrington, C. R., Lucchini, S., Ridgway, K. P., Wegmann, U., Eaton, T. J., Hinton, J. C. D., Gasson, M. J., & Narbad, A. (2008) · BMC Microbiology · doi:10.1186/1471-2180-8-195 · Cited by 18
“It is estimated that more than one million Americans have UC or Crohn's disease (CD), the two most common forms of Inflammatory Bowel Disease (IBD) [45].”
Abnormal CX3CR1+ Lamina Propria Myeloid Cells From Intestinal Transplant Recipients with NOD2 Mutations
Lough, D., Abdo, J., Guerra-Castro, J. F., Matsumoto, C., Kaufman, S. S., Shetty, K., Kwon, Y., ZASLOFF, M. A., & Fishbein, T. (2012) · American Journal of Transplantation · doi:10.1111/j.1600-6143.2011.03897.x · Cited by 18
“(20,21) using the “universal” bacterial nucleic acid probe EUB338, which targets the 16S rRNA of bacteria.”
Method
Enterocloster clostridioformis protects against Salmonella pathogenesis and modulates epithelial and mucosal immune function
Beresford-Jones, B. S., Suyama, S., Clare, S., Soderholm, A. T., Xia, W., Sardar, P., Lee, J., Harcourt, K., Lawley, T. D., & Pedicord, V. A. (2025) · Microbiome · doi:10.1186/s40168-025-02050-9 · Cited by 17
A pilot study characterizing longitudinal changes in fecal microbiota of patients with Hirschsprung-associated enterocolitis
Parker, K. D., Mueller, J. L., Westfal, M. L., Goldstein, A. M., & Ward, N. L. (2022) · Pediatric Surgery International · doi:10.1007/s00383-022-05191-2 · Cited by 18
Flagellin is essential for initial attachment to mucosal surfaces by Clostridioides difficile
Sidner, B. S., Lerma, A. I., Biswas, B., Do, T. V. T., Yu, Y., Ronish, L. A., McCullough, H. C., Auchtung, J. M., & Piepenbrink, K. H. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.02120-23 · Cited by 16
“However, tissue fixation with Carnoy’s fixative or paraformaldehyde has allowed for better preservation of mucous structure (15, 16) and microscopic observation of bacterial species localized to this region of the mucosa.”
Background
Immunomodulation of periodontitis with SPMs
Sahni, V., & Dyke, T. E. V. (2023) · Frontiers in Oral Health · doi:10.3389/froh.2023.1288722 · Cited by 20
The Host and the Flora
Nuding, S., Antoni, L., & Stange, E. F. (2013) · Digestive Diseases · doi:10.1159/000354680 · Cited by 20
Emergent Behavior of IBD-AssociatedEscherichia coliDuring Disease
Renouf, M. J. D., Cho, Y. H., & McPhee, J. B. (2018) · Inflammatory Bowel Diseases · doi:10.1093/ibd/izy312 · Cited by 16
Gastrointestinal Microbiota Dysbiosis Associated with SARS-CoV-2 Infection in Colorectal Cancer: The Implication of Probiotics
Odun-Ayo, F., & Reddy, L. (2022) · Gastroenterology Insights · doi:10.3390/gastroent13010006 · Cited by 18
Examination of a Culturable Microbial Population from the Gastrointestinal Tract of the Wood-Eating Loricariid Catfish Panaque nigrolineatus
Watts, J. E. M., McDonald, R. C., Daniel, R., & Schreier, H. J. (2013) · Diversity · doi:10.3390/d5030641 · Cited by 17
“Attempts to visualize a mucus-associated community in 4% paraformaldehyde-fixed tissues were unsuccessful, which may be explained by the inability of formaldehyde-based fixatives to preserve mucus [49].”
Background
A Bacteroides fragilis protease activates host PAR2 to induce intestinal pain and inflammation
Lakemeyer, M., Latorre, R., Blažková, K., Wood, H. M., Jensen, D. D., Shakil, N., Thomas, S. C., Saxena, D. B., Mulpuri, Y., Poolman, D., et al. (2025) · Cell Host & Microbe · doi:10.1016/j.chom.2025.09.010 · Cited by 26
Linking bacterial enterotoxins and alpha defensin 5 expansion in the Crohn’s colitis: A new insight into the etiopathogenetic and differentiation triggers driving colonic inflammatory bowel disease
Rana, T., Korolkova, O. Y., Rachakonda, G., Williams, A. D., Hawkins, A. T., James, S. D., Sakwe, A. M., Nian, H., Wang, L., Yu, C. S., et al. (2021) · PLoS ONE · doi:10.1371/journal.pone.0246393 · Cited by 16
The role of gut microbiota in the treatment of irritable bowel syndrome
Leylabadlo, H. E., Heravi, F. S., Soltani, E., Abbasi, A., Kafil, H. S., Parsaei, M., Sanaie, S., Ahmadian, Z., & Ghotaslou, R. (2021) · Reviews in Medical Microbiology · doi:10.1097/mrm.0000000000000284 · Cited by 16
“Higher and lower [133,140] Flavobacteria Lower [141] Prevotella Lower [142] Proteobacteria Escherichia Higher [87] Desulfovibrio spp.”
Background
Denosumab Regulates Gut Microbiota Composition and Cytokines in Dinitrobenzene Sulfonic Acid (DNBS)-Experimental Colitis
Khafipour, A., Eissa, N., Munyaka, P. M., Rabbi, M. F., Kapoor, K., Kermarrec, L., Khafipour, E., Bernstein, C. N., & Ghia, J. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01405 · Cited by 19
Lactobacillus paracasei CNCM I 1572: A Promising Candidate for Management of Colonic Diverticular Disease
Bretto, E., D’Amico, F., Fiore, W., Tursi, A., & Danese, S. (2022) · Journal of Clinical Medicine · doi:10.3390/jcm11071916 · Cited by 19
“016) known for its role in the etiopathogenesis of IBS [73,84,85].”
BackgroundInfluential
Beneficial Effects of Linseed Supplementation on Gut Mucosa-Associated Microbiota in a Physically Active Mouse Model of Crohn’s Disease
Plissonneau, C., Sivignon, A., Chassaing, B., Capel, F., Martin, V., Etienne, M., Wawrzyniak, I., Chaussé, P., Dutheil, F., Mairesse, G., et al. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23115891 · Cited by 21
Microbial networking in cancer: when two toxins collide
Tomkovich, S., & Jobin, C. (2018) · British Journal of Cancer · doi:10.1038/s41416-018-0101-2 · Cited by 16
Biofilms: A cause for the development of cancer: A review
Gupta, A., Bhattacharya, D., Elayaperumal, S., Sivamani, Y., Lahiri, D., & Nag, M. (2025) · The Microbe · doi:10.1016/j.microb.2025.100236 · Cited by 15
Fecal microbiota transplantation refurbishes the crypt-associated microbiota in ulcerative colitis
Markandey, M., Bajaj, A., Verma, M., Virmani, S., Singh, M. K., Gaur, P., Das, P., Srikanth, C. V., Makharia, G. K., Kedia, S., et al. (2023) · iScience · doi:10.1016/j.isci.2023.106738 · Cited by 15
“Initial reports provided fluorescence images that proved bacterial colonization of the crypt region and also went on to analyze quantitative variation in crypt colonization between healthy and inflamedmucosal tissue.(3,4) The composition of the crypt-resident community, however, was still unexplored.”
Background
The Role of the Gut Microbiome in Inflammatory Bowel Disease: The Middle East Perspective
El-Sayed, A., Kapila, D., Taha, R. S. I., El-Sayed, S., Mahen, M. R. A., Taha, R., & Alrubaiy, L. (2024) · Journal of Personalized Medicine · doi:10.3390/jpm14060652 · Cited by 17
“Colonic epithelium in CD has been shown to harbour biofilms dominated by Bacteriodes fragilis , Enterobacteriaceae , Helicobacter pylori , Pseudomonas aeruginosa , and E. coli [55].”
Background
Polymicrobial consortia in the pathogenesis of biofilm vaginosis visualized by FISH. Historic review outlining the basic principles of the polymicrobial infection theory
Swidsinski, A. V., Amann, R., Guschin, A. E., Swidsinski, S., Loening-Baucke, V. A., Mendling, W., Sobel, J. D., Lamont, R., Vaneechoutte, M., Vieira‐Baptista, P., et al. (2024) · Microbes and Infection · doi:10.1016/j.micinf.2024.105403 · Cited by 15
Self-citation
Differential Susceptibility of the Gut Microbiota to DSS Treatment Interferes in the Conserved Microbiome Association in Mouse Models of Colitis and Is Related to the Initial Gut Microbiota Difference
KHAN, I. A., Bai, Y., Ullah, N., Liu, G., Rajoka, M. S. R., & Zhang, C. (2022) · Advanced Gut & Microbiome Research · doi:10.1155/2022/7813278 · Cited by 17
“Furthermore, the key evidence that determines the gut microbiota involvement in IBD development comes from antibiotic use in IBD patients and animal colitis models [18, 19], colitis development in wild-type mice with microbiota transfer from colitis-bearing mice [20], and colitis development in germ-free mice with ino…”
Background
Reduced hydrophobicity of the colonic mucosal surface in ulcerative colitis as a hint at a physicochemical barrier defect
Braun, A., Schönfeld, U., Welsch, T., Kadmon, M., Funke, B., Gotthardt, D. N., Zahn, A., Autschbach, F., Kienle, P., Zharnikov, M., et al. (2011) · International Journal of Colorectal Disease · doi:10.1007/s00384-011-1190-z · Cited by 15

Authors: Swidsinski, A., Weber, J., Loening-Baucke, V., Hale, L. P., & Lochs, H.
Affiliations: Humboldt-Universität zu Berlin (DE)
Duke Medical Center (US)
ORCID: Swidsinski, Alexander
Hale, Laura P.
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
DOI: 10.1128/jcm.43.7.3380-3389.2005
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
Licence: journals.asm.org/non-commercial-tdm-license (tdm)
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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Spatial Organization and Composition of the Mucosal Flora in Patients with Inflammatory Bowel Disease

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