|The human gut harbors a complex ecosystem of microbial communities, consisting
of commensal inhabitants, which play crucial roles in maintaining gut homeostasis,
regulating host metabolism, and modulating immune responses. When a pathogenic
bacterium colonizes the gut, it is exposed to various environmental stressors, including
the presence of commensal bacteria but also exposure to toxic substances such as bile
acids. Investigation of the responses of gut pathogens to the natural inhabitants is
essential for the understanding of the mechanisms of microbial colonization and the
host’s health. Furthermore, the comprehension of the reaction of these microorganisms
to the challenging environment of the gut is relevant to examine microbial adaptions to
harsh conditions, such as bile acid stress.
This thesis investigates the proteomic adaptions of Campylobacter jejuni and two Enterococci
species with a particular focus on their coexistence and their response to bile acid
stress. The thesis covers four different research topics:
Project I: Bacterial communication is a relevant mechanism for interplay among various
microbial species, especially when a pathogen enters the human gastrointestinal tract.
To examine the proteomic response of C. jejuni to the presence of Enterococcus faecalis,
Enterococcus faecium and Staphylococcus aureus, co-incubation experiments of C. jejuni
with these bacteria were performed. The impact of S. aureus on the proteome of C. jejuni
was most significant, resulting in the up-expression of 215 proteins and the downexpression
of 230 proteins. These counts nevertheless remained notably lower compared
to the 526 up-expressed and 516 down-expressed proteins observed during exposure
to deoxycholic acid (DCA). Within the co-incubation, in all three microbial species, a
subgroup of 54 distinct proteins exhibited significant differential expression, indicating
a shared co-incubation response by C. jejuni. Although this shared proteomic response
partially overlapped with the DCA response, distinct proteins were exclusive in the
co-incubation response. Co-incubation unveiled three membrane-interactive proteins
among the top 20 up-expressed proteins, suggesting that the presence of other bacteria
might enhance environmental virulence. Furthermore, the exposure to both stressors,
co-incubation and DCA revealed a reciprocal influence, resulting in a unique synergistic
proteomic reaction that differed from the individual responses induced by each stimulus.
Project II: The proteomic response towards high concentrations of cholic acid (CA),
chenodeoxycholic acid (CDCA) and DCA of the gut inhabitants E. faecalis and E. faecium after long-term incubation was analyzed and compared, to simulate bile acid concentrations
these bacteria are exposed to during biliary tract infections. Both species show
similarities in the proteomic response, however, species-specific differences were also
found. In E. faecalis, DCA and CDCA strongly down-expressed proteins involved in translation,
transcription, and replication, whereas the effect was less significant in E. faecium.
E. faecium seems to be slightly more resistant towards CDCA and DCA, nevertheless, a
general bile acid response in both species consisting of the up-expression of V-type ATPase
subunits, different ABC-transporters, multi-drug transporters and proteins related to cell
wall biogenesis were detected in E. faecalis as well as in E. faecium.
Additionally, adaptions of E. faecalis in aerobic as well as microaerophilic environments
were analyzed. Interestingly, bile acid adaption in E. faecalis seems to be independent
from the oxygen level.
Project III: Genes encoding for proteins that are known to play a role in bile acid resistance
in C. jejuni were knocked out and a proteomic analyses of these knockout mutants was
performed in comparison to the parental C. jejuni strain in the presence and absence of bile
acids. The targets chosen for deletion were CmeB, which is a subunit of the Campylobacter
multidrug efflux CmeABC, CmeR which regulates the CmeABC transporter, and CbrR a
Campylobacter bile acid resistance regulator. The results indicate that the lack of CmeB
results in a notable shift in the proteome, while the impact of CmeR and CbrR lead to
less proteomic alterations. Besides, deletion of the respective genes unveils potential
alternative involvements in metabolic pathways.
Project IV: Co-incubation of C. jejuni in the presence of DCA with various Gram positive
bacteria such as E. faecalis, E. faecium and S. aureus generates an environment that leads
to increased bile acid resistance of the Gram positive bacteria. Therefore, a proteomic
analysis was conducted to identify C. jejuni proteins that are specifically induced under
these conditions. This study provides potential target proteins that might be involved
in inter-bacterial communication processes leading to the observed increased bile acid
resistance of these Gram positive bacteria.
Overall, this work contributes to the understanding of microbial adaptions to the challenging
gut environment consisting of stressors such as varying concentrations of bile
acids and the presence of commensal or pathogenic bacteria.