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Microbial biofilms in the human gastrointestinal tract
Abstract
The human gastrointestinal tract contains rich and diverse microbiotas along its length. However, while extensive studies have been made on lumenal bacterial communities in the gut, less work has been carried out on organisms growing in biofilms, where individual groups of bacteria exist in a multiplicity of different microhabitats and metabolic niches associated with the mucosa, the mucus layer and particulate surfaces in the gut lumen. Bacteria and yeasts also occur in biofilms attached to artificial surfaces and devices implanted in the host, such as in patients being fed via enteral tubes. Although we are just beginning to investigate the composition and metabolic activities of these structures, increasing evidence suggests that they are important to the host in both health and disease. There is mounting interest in mucosal biofilms in the colon, especially with respect to their role in inflammatory bowel disease. Because bacteria growing in biofilms are more resistant to antibiotics than unattached organisms, it is often difficult to modify the structure and composition of these communities, or to eradicate them from the body. However, recent work has shown that there is considerable potential to alter the species composition of mucosal biofilms in a beneficial way using synbiotics.
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“The size and quality of the intestinal mucus layer is believed to be mediated by sympathetic innervation where mucosal immune system modulation (Elenkov et al., 2000) and microbial composition and behavior alterations (commensal and pathogenic) were seen (Macfarlane and Dillon, 2007;Rhee et al., 2009)”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Macfarlane and Dillon, 2007
In the citing paper
“The ANS-mediated modulation of mucus secretion is likely to have important effects on the size and quality of the intestinal mucus layer, an important habitat for the biofilm, where the majority of the enteric microbiota reside.19”
From Principles and clinical implications of the brain-gut-enteric microbiota axis (2009) · cites this paper as [19]
In the citing paper
“In general, bacteria located in the biofilm seem to be less affected by environmental alterations, such as changes in intestinal transit rate and luminal contents, than luminal populations are, but seem to have increased involvement in bidirectional signaling with the host.19”
From Principles and clinical implications of the brain-gut-enteric microbiota axis (2009) · cites this paper as [19]
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Wey, A. S. V., Cookson, A. L., Roy, N. C., McNabb, W. C., Soboleva, T. K., & Shorten, P. R. (2014) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2014.09.006 · Cited by 23
Boonzaier, J., der Merwe, E. L. V., Bennett, N. C., & Kotzé, S. H. (2013) · Acta Histochemica · doi:10.1016/j.acthis.2012.12.003 · Cited by 23
Microbial functionality in the human intestinal tract
Salonen, A. (2009) · Frontiers in bioscience · doi:10.2741/3436 · Cited by 23
“Current knowledge on the structure and function of microbial biofilms on different surfaces through the whole GI track has recently been reviewed (22).”
BackgroundPossible Roles of Cyclic Meditation in Regulation of the Gut-Brain Axis
Ningthoujam, D. S., Singh, N., & Mukherjee, S. (2021) · Frontiers in Psychology · doi:10.3389/fpsyg.2021.768031 · Cited by 25
“Moreover, the brain modulates myriad gut functions that includes mucosal immune response; secretion of acids, bicarbonates, and mucus; and gastric motility (Macfarlane and Dillon, 2007).”
BackgroundRecent progress in experimental and human disease-associated multi-species biofilms
Bai, F., Cai, Z., & Yang, L. (2019) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2019.09.010 · Cited by 25
“fecal population, mucosal population and lumen population [69,77,78].”
Antibiotic resistance in Helicobacter pylori: a genetic and physiological perspective
Elbaiomy, R. G., Luo, X., Guo, R., Deng, S., Du, M., El‐Sappah, A. H., Bakeer, M. S., Azzam, M. M., Elolimy, A. A., Madkour, M., et al. (2025) · Gut Pathogens · doi:10.1186/s13099-025-00704-5 · Cited by 21
“The scientific community has long denied bacterial biofilms, leading to our current predicament [93, 94].”
Cruz-Córdova, A., Espinosa-Mazariego, K., Ochoa, S. A., Saldaña, Z., Rodea, G. E., Cázares-Domínguez, V., Rodríguez-Ramírez, V., Eslava-Campos, C., Navarro-Ocaña, A., Arrellano-Galindo, J., et al. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00709 · Cited by 22
“Biofilms are matrix-enclosed communities of bacteria that show increased antibiotic resistance and the ability to evade the immune system (MacFarlane and Dillon, 2007).”
BackgroundIsolation and Purification of Sulfate-Reducing Bacteria
Kushkevych, I. V. (2019) · IntechOpen eBooks · doi:10.5772/intechopen.86786 · Cited by 21
“microorganisms on the surface of the intestinal mucosa [2, 9, 28, 34].”
BackgroundDevelopment of an In Vitro Model of the Gut Microbiota Enriched in Mucus-Adhering Bacteria
Calvigioni, M., Panattoni, A., Biagini, F., Donati, L., Mazzantini, D., Massimino, M., Daddi, C., Celandroni, F., Vozzi, G., & Ghelardi, E. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.00336-23 · Cited by 22
“also constitute biofilms in vitro (23, 24).”
Chaperone DnaJ Influences the Formation of Biofilm by Escherichia coli
Grudniak, A., Włodkowska, J., & Wolska, K. I. (2015) · Polish Journal of Microbiology · doi:10.5604/01.3001.0009.2123 · Cited by 21
Focal Infection and Periodontitis: A Narrative Report and New Possible Approaches
Rocca, J., Fornaini, C., Wang, Z., Tan, L., & Merigo, E. (2020) · International Journal of Microbiology · doi:10.1155/2020/8875612 · Cited by 21
“+us, bacteria organized in biofilms might escape host immune systems [13] and are protected from ecological competition of other microorganisms, thus increasing their pathogenicity [14].”
BackgroundPiotrowski, M., Wultańska, D., & Pituch, H. M. (2022) · Future Microbiology · doi:10.2217/fmb-2021-0206 · Cited by 20
Activation of class 1 integron integrase is promoted in the intestinal environment
Baltazar, M., Bourgeois‐Nicolaos, N., Larroude, M., Couet, W. R., Uwajeneza, S., Doucet‐Populaire, F., Ploy, M.-C., & Re, S. D. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010177 · Cited by 21
“In the gut, bacteria form biofilms on the epithelial mucosa and on various particles present in the lumen [46,47].”
BackgroundCharacterization of Mixed-Species Biofilms Formed by Four Gut Microbiota
Tao, X., Xiao, Y., Wang, H., Zhu, J., Lee, Y. K., Zhao, J., Lu, W., & Zhang, H. (2022) · Microorganisms · doi:10.3390/microorganisms10122332 · Cited by 20
Zhang, D., Wu, M., Guo, Y., Xun, M., Wang, W., Wu, Z. F., & Pan, D. (2017) · Journal of the Science of Food and Agriculture · doi:10.1002/jsfa.8294 · Cited by 20
Restoring balance: biofilms and wound dressings
Percival, S. L. (2018) · Journal of Wound Care · doi:10.12968/jowc.2018.27.2.102 · Cited by 20
A toddler SHIME® model to study microbiota of young children
Bondue, P., Lebrun, S., Taminiau, B., Everaert, N., LaPointe, G., Crèvecoeur, S., Daube, G., & Delcenserie, V. (2020) · FEMS Microbiology Letters · doi:10.1093/femsle/fnaa135 · Cited by 20
Sequence analysis of the 16s rRNA gene of sulfate-reducing bacteria isolated from human intestine
Kushkevych, I. V., Barto, M., & Barto, L. (2014) · Cited by 19
Sulfate-reducing bacteria of the human intestine. II. The role in the diseases development
Kushkevych, I. V. (2012) · Studia Biologica · doi:10.30970/sbi.0602.207 · Cited by 19
Amund, D., Ouoba, L. I. I., Sutherland, J. P., & Ghoddusi, H. B. (2014) · Beneficial Microbes · doi:10.3920/bm2013.0099 · Cited by 20
“Biofilm formation may also aid interaction with the immune system (Macfarlane and Dillon, 2007).”
BackgroundSadiq, F. A., Lu, W., Heyndrickx, M., Flint, S., Wei, C., Jian-xin, Z., & Zhang, H. (2021) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiab096 · Cited by 19
dos Santos, R. B., Fonseca, L. E., Santana, A. T. D. A., Silva, C. A. C., & Guedes, J. C. (2011) · Arquivos de Gastroenterologia · doi:10.1590/s0004-28032011000400002 · Cited by 19
“In the study performed by Macfarlane et al.(7) just 1 of 6 cases showed crypts atrophy.”
MethodMining the human gut microbiome for novel stress resistance genes
Culligan, E. P., Marchesi, J. R., Hill, C., & Sleator, R. D. (2012) · Gut Microbes · doi:10.4161/gmic.20984 · Cited by 19
Innate Immune Response in Implant-Associated Infections: Neutrophils against Biofilms
Dapunt, U., Hänsch, G. M., & Arciola, C. R. (2016) · Materials · doi:10.3390/ma9050387 · Cited by 18
“Some biofilms are well tolerated by the immune system (such as mucosal biofilms, for example) [16], whereas in other settings, like in the case of artificial joint replacement in orthopaedics, bacterial biofilms are thought to be the main reason for persistent and highly destructive infections [17–20], whose etiologic…”
BackgroundEnterocyte-Associated Microbiome of the Hadza Hunter-Gatherers
Turroni, S., Rampelli, S., Centanni, M., Schnorr, S. L., Consolandi, C., Severgnini, M., Peano, C., Soverini, M., Falconi, M., Crittenden, A. N., et al. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00865 · Cited by 18
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
Could the Gut Microbiota Serve as a Therapeutic Target in Ischemic Stroke?
Zhang, J., Tang, Q., & Zhu, L. (2021) · Evidence-based Complementary and Alternative Medicine · doi:10.1155/2021/1391384 · Cited by 17
“Autonomic nervous system-mediated regulation of mucus secretion plays an important role in the thickness and quality of the intestinal mucus epithelium [144].”
BackgroundMeasuring gene expression in single bacterial cells: recent advances in methods and micro-devices
Shi, X., Gao, W., Wang, J., Chao, S.-H., Zhang, W., & Meldrum, D. R. (2014) · Critical Reviews in Biotechnology · doi:10.3109/07388551.2014.899556 · Cited by 17
Kosikowska, U., Malm, A., Pitucha, M., Rajtar, B., & Polz‐Dacewicz, M. (2013) · Medicinal Chemistry Research · doi:10.1007/s00044-013-0700-7 · Cited by 17
“interventional strategies infections (Donlan, 2001; Steward and Costeron, 2001; Gilbert et al., 2002; Stoodley et al., 2004; Lasa et al., 2005; Sanclement et al., 2005; Macfarlane and Dillon, 2007; Vlastarakos et al., 2007; Macedo and Abraham, 2009; Wolcott and Ehrlich, 2008; Coenye and Nelis, 2010; Drago et al., 2012…”
BackgroundWittung-Stafshede, P. E. (2021) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2021.07.009 · Cited by 16
Bioinspired in vitro intestinal mucus model for 3D-dynamic culture of bacteria
Sardelli, L., Vangosa, F. B., Merli, M., Ziccarelli, A., Visentin, S., Visai, L., & Petrini, P. (2022) · Biomaterials Advances · doi:10.1016/j.bioadv.2022.213022 · Cited by 16
“This dynamics influences the bacterial gene expression, adhesion to substrate and molecules production [12], resulting, at the macroscopic scale, in changes in growth rate, clearance [13] and intestinal biofilm formation [14].”
Metadata
- Authors
- Macfarlane, S., & Dillon, J. F.
- Affiliations
- University of Dundee (GB)
- Corresponding author
- Macfarlane, S.
- Venue
- Journal of Applied Microbiology
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-05
- Volume
- 102
- Issue
- 5
- Pages
- 1187-1196
- ISSN
- 1364-5072 (ISSN-L)
- 1365-2672
- OpenAlex
- W2041418306
- Cited by
- 379
- References
- 55
- Citations by year
- 2026: 11 · 2025: 10 · 2024: 20 · 2023: 26 · 2022: 24 · 2021: 25 · 2020: 28 · 2019: 31 · 2018: 22 · 2017: 26 · 2016: 14 · 2015: 17 · 2014: 32 · 2013: 16 · 2012: 20
- FWCI
- 0.98
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Applied Microbiology (publishedVersion)
- PubMed (publishedVersion)
- Discovery Research Portal (University of Dundee) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bacterial biofilms and quorum sensing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Keywords
- biofilm, gastrointestinal tract, gut microbiota, mucus layer, inflammatory bowel disease, antibiotic resistance, synbiotics
- MeSH terms
- Bacteria, Humans, Intestinal Mucosa, Biofilms, Probiotics, Gastrointestinal Tract
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