processes
Article
Metabolic Modeling of Clostridium difficile
Associated Dysbiosis of the Gut Microbiota
Poonam Phalak and Michael A. Henson *
Department of Chemical Engineering and Institute of Applied Life Science, University of Massachusetts,
Amherst, MA 01003, USA; pphalak@umass.edu
* Correspondence: mhenson@umass.edu; Tel.: +1-413-545-3481
Received: 16 December 2018; Accepted: 6 February 2019; Published: 15 February 2019
Abstract: Recent in vitro experiments have demonstrated the ability of the pathogen Clostridium
difficile and commensal gut bacteria to form biofilms on surfaces, and biofilm development in
vivo is likely. Various studies have reported that 3%–15% of healthy adults are asymptomatically
colonized with C. difficile, with commensal species providing resistance against C. difficile pathogenic
colonization. C. difficile infection (CDI) is observed at a higher rate in immunocompromised
patients previously treated with broad spectrum antibiotics that disrupt the commensal microbiota
and reduce competition for available nutrients, resulting in imbalance among commensal species
and dysbiosis conducive to C. difficile propagation. To investigate the metabolic interactions of
C. difficile with commensal species from the three dominant phyla in the human gut, we developed a
multispecies biofilm model by combining genome-scale metabolic reconstructions of C. difficile,
Bacteroides thetaiotaomicron from the phylum Bacteroidetes, Faecalibacterium prausnitzii from the
phylum Firmicutes, and Escherichia coli from the phylum Proteobacteria. The biofilm model was used
to identify gut nutrient conditions that resulted in C. difficile-associated dysbiosis characterized by
large increases in C. difficile and E. coli abundances and large decreases in F. prausnitzii abundance.
We tuned the model to produce species abundances and short-chain fatty acid levels consistent
with available data for healthy individuals. The model predicted that experimentally-observed
host-microbiota perturbations resulting in decreased carbohydrate/increased amino acid levels
and/or increased primary bile acid levels would induce large increases in C. difficile abundance
and decreases in F. prausnitzii abundance. By adding the experimentally-observed perturbation
of increased host nitrate secretion, the model also was able to predict increased E. coli abundance
associated with C. difficile dysbiosis. In addition to rationalizing known connections between nutrient
levels and disease progression, the model generated hypotheses for future testing and has the
capability to support the development of new treatment strategies for C. difficile gut infections.
Keywords: gut microbiota dysbiosis; Clostridium difficile infection; bacterial biofilms; metabolic modeling
1. Introduction
The gut microbiota comprise a complex ecological system that maintains a critical symbiotic
relationship with the human host [1,2]. The microbiota provide essential nutrients such as short-chain
fatty acids (SCFAs; acetate, butyrate, and propionate), support colonization resistance to pathogens,
participate in the degradation of toxic compounds, and regulate the immune responses [3–7].
Bacteroidetes and Firmicutes are the two dominant phyla in the healthy gut, comprising approximately
90% of the community. Other important but less abundant phyla are Proteobacteria, Actinobacteria,
Euryarchaeota and Verrucomicrobia, as well as Eukaryota such as fungi [8,9]. The gut microbiota
composition can be altered by numerous factors including diet, antibiotic treatment, stress, and
lifestyle [10,11]. Dietary components including carbohydrates, protein, fat, and host secretions
Processes 2019, 7, 97; doi:10.3390/pr7020097
www.mdpi.com/journal/processes
21
Article
Metabolic Modeling of Clostridium difficile
Associated Dysbiosis of the Gut Microbiota
Poonam Phalak and Michael A. Henson *
Department of Chemical Engineering and Institute of Applied Life Science, University of Massachusetts,
Amherst, MA 01003, USA; pphalak@umass.edu
* Correspondence: mhenson@umass.edu; Tel.: +1-413-545-3481
Received: 16 December 2018; Accepted: 6 February 2019; Published: 15 February 2019
Abstract: Recent in vitro experiments have demonstrated the ability of the pathogen Clostridium
difficile and commensal gut bacteria to form biofilms on surfaces, and biofilm development in
vivo is likely. Various studies have reported that 3%–15% of healthy adults are asymptomatically
colonized with C. difficile, with commensal species providing resistance against C. difficile pathogenic
colonization. C. difficile infection (CDI) is observed at a higher rate in immunocompromised
patients previously treated with broad spectrum antibiotics that disrupt the commensal microbiota
and reduce competition for available nutrients, resulting in imbalance among commensal species
and dysbiosis conducive to C. difficile propagation. To investigate the metabolic interactions of
C. difficile with commensal species from the three dominant phyla in the human gut, we developed a
multispecies biofilm model by combining genome-scale metabolic reconstructions of C. difficile,
Bacteroides thetaiotaomicron from the phylum Bacteroidetes, Faecalibacterium prausnitzii from the
phylum Firmicutes, and Escherichia coli from the phylum Proteobacteria. The biofilm model was used
to identify gut nutrient conditions that resulted in C. difficile-associated dysbiosis characterized by
large increases in C. difficile and E. coli abundances and large decreases in F. prausnitzii abundance.
We tuned the model to produce species abundances and short-chain fatty acid levels consistent
with available data for healthy individuals. The model predicted that experimentally-observed
host-microbiota perturbations resulting in decreased carbohydrate/increased amino acid levels
and/or increased primary bile acid levels would induce large increases in C. difficile abundance
and decreases in F. prausnitzii abundance. By adding the experimentally-observed perturbation
of increased host nitrate secretion, the model also was able to predict increased E. coli abundance
associated with C. difficile dysbiosis. In addition to rationalizing known connections between nutrient
levels and disease progression, the model generated hypotheses for future testing and has the
capability to support the development of new treatment strategies for C. difficile gut infections.
Keywords: gut microbiota dysbiosis; Clostridium difficile infection; bacterial biofilms; metabolic modeling
1. Introduction
The gut microbiota comprise a complex ecological system that maintains a critical symbiotic
relationship with the human host [1,2]. The microbiota provide essential nutrients such as short-chain
fatty acids (SCFAs; acetate, butyrate, and propionate), support colonization resistance to pathogens,
participate in the degradation of toxic compounds, and regulate the immune responses [3–7].
Bacteroidetes and Firmicutes are the two dominant phyla in the healthy gut, comprising approximately
90% of the community. Other important but less abundant phyla are Proteobacteria, Actinobacteria,
Euryarchaeota and Verrucomicrobia, as well as Eukaryota such as fungi [8,9]. The gut microbiota
composition can be altered by numerous factors including diet, antibiotic treatment, stress, and
lifestyle [10,11]. Dietary components including carbohydrates, protein, fat, and host secretions
Processes 2019, 7, 97; doi:10.3390/pr7020097
www.mdpi.com/journal/processes
21