Community composition shapes microbial-specific phenotypes in a cystic fibrosis polymicrobial model system

  1. Fabrice Jean-Pierre  Is a corresponding author
  2. Thomas H Hampton
  3. Daniel Schultz
  4. Deborah A Hogan
  5. Marie-Christine Groleau
  6. Eric Déziel
  7. George A O'Toole  Is a corresponding author
  1. Geisel School of Medicine at Dartmouth, United States
  2. Dartmouth College, United States
  3. Institut National de la Recherche Scientifique, Canada

Abstract

Interspecies interactions can drive the emergence of unexpected microbial phenotypes that are not observed when studying monocultures. The cystic fibrosis (CF) lung consists of a complex environment where microbes, living as polymicrobial biofilm-like communities, are associated with negative clinical outcomes for persons with CF (pwCF). However, the current lack of in vitro models integrating the microbial diversity observed in the CF airway hampers our understanding of why polymicrobial communities are recalcitrant to therapy in this disease. Here, integrating computational approaches informed by clinical data, we built a mixed community of clinical relevance to the CF lung composed of Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sanguinis and Prevotella melaninogenica. We developed and validated this model biofilm community with multiple isolates of these four genera. When challenged with tobramycin, a front-line antimicrobial used to treat pwCF, the microorganisms in the polymicrobial community show altered sensitivity to this antibiotic compared to monospecies biofilms. We observed that wild-type P. aeruginosa is sensitized to tobramycin in a mixed community versus monoculture, and this observation holds across a range of community relative abundances. We also report that LasR loss-of-function, a variant frequently detected in the CF airway, drives tolerance of P. aeruginosa to tobramycin specifically in the mixed community. Our data suggest that the molecular basis of this community-specific recalcitrance to tobramycin for the P. aeruginosa LasR mutant is increased production of phenazines. Our work support the importance of studying a clinically-relevant model polymicrobial biofilms to understand community-specific traits relevant to infections.

Data availability

Figure 1 - figure supplement 3 & Source Data 1 contains the numerical data used to generate the figure.Figure 1 - figure supplement 4 & Source Data 2 contains numerical data used to generate the figure.Source Code 1 contains the script used to generate Figure 1, Figure 1 - figure supplement 1 and Figure 1 - figure supplement 4.Source Code 2 contains the script used to generate the modeling data presented Figure 1 - figure supplement 1.

The following previously published data sets were used

Article and author information

Author details

  1. Fabrice Jean-Pierre

    Geisel School of Medicine at Dartmouth, Hanover, United States
    For correspondence
    jeanpierre.fabrice@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3056-8356
  2. Thomas H Hampton

    Department of Microbiology and Immunology, Dartmouth College, Hanover, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Daniel Schultz

    Department of Microbiology and Immunology, Dartmouth College, Hanover, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Deborah A Hogan

    Department of Microbiology and Immunology, Dartmouth College, Hanover, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Marie-Christine Groleau

    Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Canada
    Competing interests
    The authors declare that no competing interests exist.
  6. Eric Déziel

    Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Canada
    Competing interests
    The authors declare that no competing interests exist.
  7. George A O'Toole

    Department of Microbiology and Immunology, Dartmouth College, Hanover, United States
    For correspondence
    georgeo@dartmouth.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2861-4392

Funding

Cystic Fibrosis Foundation (JEAN21F0)

  • Fabrice Jean-Pierre

National Institutes of Health (R01 AI155424)

  • George A O'Toole

Canadian Institutes of Health Research (MOP-142466)

  • Eric Déziel

National Institutes of Health (5 P20 GM130454)

  • Daniel Schultz

Cystic Fibrosis Foundation (HOGAN19G0)

  • Deborah A Hogan

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Vaughn S Cooper, University of Pittsburgh, United States

Publication history

  1. Received: July 4, 2022
  2. Accepted: January 19, 2023
  3. Accepted Manuscript published: January 20, 2023 (version 1)
  4. Accepted Manuscript updated: January 23, 2023 (version 2)

Copyright

© 2023, Jean-Pierre et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 524
    Page views
  • 128
    Downloads
  • 0
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Fabrice Jean-Pierre
  2. Thomas H Hampton
  3. Daniel Schultz
  4. Deborah A Hogan
  5. Marie-Christine Groleau
  6. Eric Déziel
  7. George A O'Toole
(2023)
Community composition shapes microbial-specific phenotypes in a cystic fibrosis polymicrobial model system
eLife 12:e81604.
https://doi.org/10.7554/eLife.81604

Further reading

    1. Microbiology and Infectious Disease
    Saba Naz, Kumar Paritosh ... Vinay Kumar Nandicoori
    Research Article Updated

    The emergence of drug resistance in Mycobacterium tuberculosis (Mtb) is alarming and demands in-depth knowledge for timely diagnosis. We performed genome-wide association analysis using 2237 clinical strains of Mtb to identify novel genetic factors that evoke drug resistance. In addition to the known direct targets, we identified for the first time, a strong association between mutations in DNA repair genes and the multidrug-resistant phenotype. To evaluate the impact of variants identified in the clinical samples in the evolution of drug resistance, we utilized knockouts and complemented strains in Mycobacterium smegmatis and Mtb. Results show that variant mutations compromised the functions of MutY and UvrB. MutY variant showed enhanced survival compared with wild-type (Rv) when the Mtb strains were subjected to multiple rounds of ex vivo antibiotic stress. In an in vivo guinea pig infection model, the MutY variant outcompeted the wild-type strain. We show that novel variant mutations in the DNA repair genes collectively compromise their functions and contribute to better survival under antibiotic/host stress conditions.

    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease
    Justin L Roncaioli, Janet Peace Babirye ... Russell E Vance
    Research Advance Updated

    Bacteria of the genus Shigella cause shigellosis, a severe gastrointestinal disease driven by bacterial colonization of colonic intestinal epithelial cells. Vertebrates have evolved programmed cell death pathways that sense invasive enteric pathogens and eliminate their intracellular niche. Previously we reported that genetic removal of one such pathway, the NAIP–NLRC4 inflammasome, is sufficient to convert mice from resistant to susceptible to oral Shigella flexneri challenge (Mitchell et al., 2020). Here, we investigate the protective role of additional cell death pathways during oral mouse Shigella infection. We find that the Caspase-11 inflammasome, which senses Shigella LPS, restricts Shigella colonization of the intestinal epithelium in the absence of NAIP–NLRC4. However, this protection is limited when Shigella expresses OspC3, an effector that antagonizes Caspase-11 activity. TNFα, a cytokine that activates Caspase-8-dependent apoptosis, also provides potent protection from Shigella colonization of the intestinal epithelium when mice lack both NAIP–NLRC4 and Caspase-11. The combined genetic removal of Caspases-1, -11, and -8 renders mice hyper-susceptible to oral Shigella infection. Our findings uncover a layered hierarchy of cell death pathways that limit the ability of an invasive gastrointestinal pathogen to cause disease.