Colonization resistance and microbial ecophysiology: using gnotobiotic mouse models and single-cell technology to explore the intestinal jungle

Abstract

The highly diverse intestinal microbiota forms a structured community engaged in constant communication with itself and its host and is characterized by extensive ecological interactions. A key benefit that the microbiota affords its host is its ability to protect against infections in a process termed colonization resistance (CR), which remains insufficiently understood. In this review, we connect basic concepts of CR with new insights from recent years and highlight key technological advances in the field of microbial ecology. We present a selection of statistical and bioinformatics tools used to generate hypotheses about synergistic and antagonistic interactions in microbial ecosystems from metagenomic datasets. We emphasize the importance of experimentally testing these hypotheses and discuss the value of gnotobiotic mouse models for investigating specific aspects related to microbiota-host-pathogen interactions in a well-defined experimental system. We further introduce new developments in the area of single-cell analysis using fluorescence in situ hybridization in combination with metabolic stable isotope labeling technologies for studying the in vivo activities of complex community members. These approaches promise to yield novel insights into the mechanisms of CR and intestinal ecophysiology in general, and give researchers the means to experimentally test hypotheses in vivo at varying levels of biological and ecological complexity.

Tracking heavy water (D 2 O) incorporation for identifying and sorting active microbial cells

“…The gut microbiota is important to human and animal health and nutrition (60,61). Competition for nutrients is thought to shape the overall composition of the gut microbiota as well as the colonization success of enteropathogens (62,63). For example, the availability of mucosally derived sugars has been shown to be a key factor in the colonization of E. coli, Salmonella typhimurium, and Clostridium difficile (64,65).…”

Strengths and Limitations of Model Systems for the Study of Urinary Tract Infections and Related Pathologies

“…Commensal E. coli strains are commonly found in association with the gastrointestinal tract of warm-blooded vertebrates, where the bacteria can establish mutually beneficial relationships with their hosts, providing necessary vitamins (e.g., vitamin K and B-complex vitamins), promoting gastrointestinal homeostasis, and protecting the gut from pathogens (20)(21)(22)(23). Pathogenic E. coli variants can cause a wide range of diseases both within and outside the gastrointestinal tract.…”

“…For instance, the natural microbial communities (the microbiota) that persist as commensals within the gastrointestinal tract and vagina can competitively interfere with UPEC survival by limiting space and nutrient availability and by altering host immunity (21,37,38). It is probable that phages and toxic products such as colicins produced by commensal organisms also restrict the growth and dissemination of UPEC.…”

Experimental approaches to phenotypic diversity in infection

“…Nano-SIMS can image the isotopic composition of a biological sample on nanoscale lateral resolution and thereby detect the spatial distribution of the labeled atoms of interest [117] (Figure 4b). Simultaneous imaging of up to seven ion masses can probe the metabolic interaction of individual bacterial cells within a community/host [118][119][120]. Alternatively, fluorescence reporters hold much promise for time-resolved, single cell analysis of one particular metabolite of interest (Figure 4c).…”