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The Dynamics of Interacting Bacterial and Fungal Communities of the Mouse Colon Following Antibiotics

Microbial Ecology volume 80, pages 573–592 (2020)Cite this article

Abstract

We tested two hypotheses concerning the dynamics of intestinal microbial communities of young mice following antibiotic-induced disturbance. The first is that disturbance of the bacterial community causes disturbance of the fungal community. Our results were consistent with that hypothesis. Antibiotics significantly altered bacterial community structure. Antibiotics also altered fungal community structure, significantly increasing the relative abundance of Candida lusitaniae, a known pathogen, while simultaneously significantly decreasing the relative abundances of several other common fungal species. The result was a temporary decrease in fungal diversity. Moreover, bacterial load was negatively correlated with the relative abundances of Candida lusitaniae and Candida parapsilosis, while it was positively correlated with the relative abundances of many other fungal species. Our second hypothesis is that control mice serve as a source of probiotics capable of invading intestines of mice with disturbed microbial communities and restoring pre-antibiotic bacterial and fungal communities. However, we found that control mice did not restore disturbed microbial communities. Instead, mice with disturbed microbial communities induced disturbance in control mice, consistent with the hypothesis that antibiotic-induced disturbance represents an alternate stable state that is easier to achieve than to correct. Our results indicate the occurrence of significant interactions among intestinal bacteria and fungi and suggest that the stimulation of certain bacterial groups may potentially be useful in countering the dominance of fungal pathogens such as Candida spp. However, the stability of disturbed microbial communities could complicate recovery.

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Data Availability

Illumina sequence data are deposited in the NCBI Sequence Read Archive (Bioproject Accession PRJNA633842).

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Acknowledgments

We are grateful for the helpful suggestions of two anonymous reviewers.

Funding

Financial support was given to RTK provided by the Brigham Young University and by the Sustainable Bioenergy Research Program of the US Department of Agriculture, National Institute of Food and Agriculture (no. 2011-67009-20072).

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Affiliations

  1. Department of Biology, Brigham Young University, Provo, UT, 84602, USA

    Rachel Nettles, Kevin D. Ricks & Roger T. Koide

  2. Currently: Kintai Therapeutics, 26 Landsdowne Street, Boston, MA, 02139, USA

    Rachel Nettles

  3. Currently: Program in Ecology, Evolution and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Kevin D. Ricks

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Contributions

Conceptualization: Rachel Nettles and Roger T. Koide; methodology: Rachel Nettles, Kevin D. Ricks, and Roger T. Koide; formal analysis and investigation: Rachel Nettles, Kevin D. Ricks, and Roger T. Koide; writing—original draft preparation: Roger T. Koide; writing—review and editing: Rachel Nettles, Kevin D. Ricks, and Roger T. Koide; funding acquisition: Roger T. Koide; resources: Roger T. Koide; supervision: Roger T. Koide

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Correspondence to Roger T. Koide.

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Nettles, R., Ricks, K.D. & Koide, R.T. The Dynamics of Interacting Bacterial and Fungal Communities of the Mouse Colon Following Antibiotics. Microb Ecol 80, 573–592 (2020). https://doi.org/10.1007/s00248-020-01525-6

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Keywords

  • Intestine
  • Fungal community
  • Bacterial community
  • Bacterial–fungal interaction
  • Disturbance
  • Antibiotics