Intestinal biofilms: pathophysiological relevance, host defense, and therapeutic opportunities

Abstract

SUMMARYThe human intestinal tract harbors a profound variety of microorganisms that live in symbiosis with the host and each other. It is a complex and highly dynamic environment whose homeostasis directly relates to human health. Dysbiosis of the gut microbiota and polymicrobial biofilms have been associated with gastrointestinal diseases, including irritable bowel syndrome, inflammatory bowel diseases, and colorectal cancers. This review covers the molecular composition and organization of intestinal biofilms, mechanistic aspects of biofilm signaling networks for bacterial communication and behavior, and synergistic effects in polymicrobial biofilms. It further describes the clinical relevance and diseases associated with gut biofilms, the role of biofilms in antimicrobial resistance, and the intestinal host defense system and therapeutic strategies counteracting biofilms. Taken together, this review summarizes the latest knowledge and research on intestinal biofilms and their role in gut disorders and provides directions toward the development of biofilm-specific treatments.

Keywords: antibiofilm drug development; antimicrobial peptides; gastrointestinal biofilms; inflammatory bowel diseases (IBD); irritable bowel syndrome (IBS).

Fig 1

Gut microbiota influencing factors and the biofilm life cycle. (A) Different factors that can influence the gut microbiota. Changes in the gut microbiota can lead to dysbiosis and biofilm formation. (B) The biofilm life cycle. The four key stages of the biofilm life cycle include (1) Attachment: bacteria attach to the mucosal surface using surface-expressed adhesion proteins, flagella, and pili; (2) Microcolony: mucus-attached bacteria form microcolonies and start biofilm matrix production; (3) Maturation: biofilm maturation leads to a complex extracellular polymeric substance (EPS) matrix architecture with a heterogeneous chemical and physical microenvironment supporting multi-species co-existence and efficient communication; in a mature biofilm, persister cells are present at the bottom of the biofilm, characterized by a strong tolerance against environmental stress and antimicrobial exposure; (4) Dispersal: biofilm dispersal starts with EPS matrix remodeling, resulting in the release of biofilm aggregates that subsequently can colonize new surfaces. Dispersed biofilm is a distinct phenotype that can cause the spread of biofilm-associated infections.

Fig 2

Microbiota distribution, biofilm prevalence in gastrointestinal disorders, key biofilm-forming pathogens, and the appearance of colonic biofilms. (A) Biofilm prevalence, key pathogenic biofilm bacteria, microbiota distribution, and the human digestive system. The human digestive system comprises the oral cavity, pharynx, esophagus, stomach, liver, gallbladder, small and large intestines, appendix, rectum, and anus. Key biofilm-forming and disease-associated pathogens are Clostridioides difficile, enterotoxigenic Bacteroides fragilis (64), adherent-invasive Escherichia coli, and Salmonella (65). (B) Biofilm appearance in a colon cross-section. Higher-ordered bacterial assemblies in the human gut are mucosal biofilms, luminal biofilms, and luminal floating biofilm clusters aggregated to food particles and mucins (27, 30, 61–63). CRC, colorectal cancer; UC, ulcerative colitis.

Fig 3

The intestinal host defense system. The GI mucosa consists of the mucus layer, the epithelium, the lamina propria, and the muscularis mucosa. The epithelium comprises inter alia Paneth cells (predominantly in the crypts) and goblet cells. Paneth cells secrete antimicrobial peptides into the lumen, which play a crucial role in the host’s defense against bacterial invasion. Goblet cells produce a thick layer of protective mucus. Multi-potent stem cells are located at the base of the GI crypts. The lamina propria comprises several immune cells, including macrophages, T cells, and dendritic cells.

Fig 4

Human α- and β-defensin sequences, their disulfide pattern, and representative structures. (A) Six human α-defensin amino acid sequences. (B) Four human β-defensin amino acid sequences. (C) Structure of human α-defensin 4 (HAD4). (D) Structure of human β-defensin 2 (HBD2). Cysteine residues are highlighted in red; red lines represent conserved disulfide linkages; disulfide bonds are presented in yellow.

Fig 5

Molecular targets and therapeutic strategies to combat gastrointestinal biofilms. Several targets for therapeutic interventions are outlined, including the biofilm matrix, regulatory networks, and molecular targets and mechanisms of biofilm cells.