The Bacterial Gut Microbiota of Adult Patients Infected, Colonized or Noncolonized by Clostridioides difficile
by
Monique J. T. Crobach 1,†, Quinten R. Ducarmon 1,2,†, Elisabeth M. Terveer 1,2,3, Celine Harmanus 1, Ingrid M. J. G. Sanders 1, Kees M. Verduin 4, Ed J. Kuijper 1,2,3 and Romy D. Zwittink 1,2,*
Monique J. T. Crobach 1,†, Quinten R. Ducarmon 1,2,†, Elisabeth M. Terveer 1,2,3, Celine Harmanus 1, Ingrid M. J. G. Sanders 1, Kees M. Verduin 4, Ed J. Kuijper 1,2,3 and Romy D. Zwittink 1,2,*
1
Experimental Bacteriology, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
2
Center for Microbiome Analyses and Therapeutics, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
3
Netherlands Donor Feces Bank, 2333ZA Leiden, The Netherlands
4
Department of Microbiology and Infection Prevention, Amphia Hospital, 4818CK Breda, The Netherlands
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Microorganisms 2020, 8(5), 677; https://doi.org/10.3390/microorganisms8050677
Received: 21 April 2020 / Revised: 1 May 2020 / Accepted: 4 May 2020 / Published: 6 May 2020
(This article belongs to the Special Issue Clostridium difficile)
Gut microbiota composition in patients with Clostridioides difficile colonization is not well investigated. We aimed to identify bacterial signatures associated with resistance and susceptibility to C. difficile colonization (CDC) and infection (CDI). Therefore, gut microbiota composition from patients with CDC (n = 41), with CDI (n = 41), and without CDC (controls, n = 43) was determined through 16S rRNA gene amplicon sequencing. Bacterial diversity was decreased in CDC and CDI patients (p < 0.01). Overall microbiota composition was significantly different between control, CDC, and CDI patients (p = 0.001). Relative abundance of Clostridioides (most likely C. difficile) increased stepwise from controls to CDC and CDI patients. In addition, differential abundance analysis revealed that CDI patients’ gut microbiota was characterized by significantly higher relative abundance of Bacteroides and Veillonella than CDC patients and controls. Control patients had significantly higher Eubacterium hallii and Fusicatenibacter abundance than colonized patients. Network analysis indicated that Fusicatenibacter was negatively associated with Clostridioides in CDI patients, while Veillonella was positively associated with Clostridioides in CDC patients. Bacterial microbiota diversity decreased in both CDC and CDI patients, but harbored a distinct microbiota. Eubacterium hallii and Fusicatenibacter may indicate resistance against C. difficile colonization and subsequent infection, while Veillonella may indicate susceptibility to colonization and infection by C. difficile.
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Keywords:
Clostridioides difficile; Clostridium difficile; gut microbiota; colonization; 16S rRNA gene amplicon sequencing
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MDPI and ACS Style
Crobach, M.J.T.; Ducarmon, Q.R.; Terveer, E.M.; Harmanus, C.; Sanders, I.M.J.G.; Verduin, K.M.; Kuijper, E.J.; Zwittink, R.D. The Bacterial Gut Microbiota of Adult Patients Infected, Colonized or Noncolonized by Clostridioides difficile. Microorganisms 2020, 8, 677.
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