Enterobacteriaceae in the Human Gut: Dynamics and Ecological Roles in Health and Disease

The human gut microbiota plays a crucial role in maintaining host health. Our review explores the prevalence and dynamics of Enterobacteriaceae, a bacterial family within the Proteobacteria phylum, in the human gut which represents a small fraction of the gut microbiota in healthy conditions. Even though their roles are not yet fully understood, Enterobacteriaceae and especially Escherichia coli (E. coli) play a part in creating an anaerobic environment, producing vitamins and protecting against pathogenic infections. The composition and residency of E. coli strains in the gut fluctuate among individuals and is influenced by many factors such as geography, diet and health. Dysbiosis, characterized by alterations in the microbial composition of the gut microbiota, is associated with various diseases, including obesity, inflammatory bowel diseases and metabolic disorders. A consistent pattern in dysbiosis is the expansion of Proteobacteria, particularly Enterobacteriaceae, which has been proposed as a potential marker for intestinal and extra-intestinal inflammatory diseases. Here we develop the potential mechanisms contributing to Enterobacteriaceae proliferation during dysbiosis, including changes in oxygen levels, alterations in mucosal substrates and dietary factors. Better knowledge of these mechanisms is important for developing strategies to restore a balanced gut microbiota and reduce the negative consequences of the Enterobacteriaceae bloom.

Design and validation of a dual-fluorescence reporter system to monitor bacterial gene expression in the gut environment

Fluorescence-based reporter systems are valuable tools for studying gene expression dynamics in living cells. However, available strategies to follow gene expression in bacteria within their natural ecosystem that can be typically rich and complex are scarce. In this work, we designed a plasmid-based tool ensuring both the identification of a strain of interest in complex environments and the monitoring of gene expression through the combination of two distinct fluorescent proteins as reporter genes. The tool was validated in Escherichia coli to monitor the expression of eut genes involved in the catabolism of ethanolamine. We demonstrated that the constructed reporter strain gradually responds with a bimodal output to increasing ethanolamine concentrations during in vitro cultures. The reporter strain was next inoculated to mice, and flow cytometry was used to detect the reporter strain among the dense microbiota of intestinal samples and to analyze specifically the expression of eut genes. This novel dual-fluorescent reporter system would be helpful to evaluate transcriptional processes in bacteria within complex environments. KEY POINTS: • A reporter tool was developed to monitor bacterial gene expression in complex environments. • Ethanolamine utilization (eut) genes are expressed by commensal E. coli in the mouse gut. • Expression of eut genes follows a bimodal distribution.

Diversity of ethanolamine utilization by human commensal Escherichiacoli

Ethanolamine (EA) is a substrate naturally present in the human gut and its catabolism by bacteria relies on the presence of eut genes encoding specific metabolic enzymes and accessory proteins. To date, EA utilization has been mostly investigated in gut bacterial pathogens. The aim of this study was to evaluate the ability of human gut commensal Escherichia coli isolates to utilize EA as a nitrogen and/or carbon sources. Although the capacity to consume EA is heterogeneous between the 40 strains of our collection, we determined that most of them could degrade EA to generate ammonia, a useful nitrogen resource for growth. Three isolates were also able to exploit EA as a carbon source. We also revealed that the inability of some strains to catabolize EA is explained either by mutations in the eut locus or by a defect in gene transcription. Finally, we demonstrated the importance of EA utilization for an optimal fitness of commensal E. coli in vivo. Our study provides new insights on the diversity of commensal E. coli strains to utilize EA as a nutrient in the gut and opens the way for new research in the field of interactions between host, gut microbiota and pathogens.

In vivo characterization of the immune response towards the pathogenic Escherichia coli antigen SslE and modulation of the intestinal microbiota

Pathogenic E. coli, both intestinal (InPEC) and extraintestinal (ExPEC), account for a wide range of diseases, which can be fatal across developing and developed countries. They can acquire a vast array of virulence factors which may dramatically increase the severity of the infection. Emergence of resistant strains often renders antibiotics inefficient; in the case of Shiga toxin-producing E. coli, antibiotics therapy can even be detrimental. Hence, an E. coli vaccine with broad coverage could be a promising alternative to prevent the spread of such diseases, while offering the potential for protection against several InPEC and ExPEC at once.

Using the «reverse vaccinology» approach on ExPEC strains, nine antigens were identified as protective against a murine sepsis model. With 82% protective efficacy, SslE (Secreted and Surface-associated Lipoprotein of E. coli) was the most potent candidate. Additional models showed SslE to also be cross-protective against other ExPEC strains. Functional assays have demonstrated in vitro and ex vivo that SslE is a mucinase which plays an important role in colonization and virulence of E. coli.

To better understand the mechanism behind such protection, we are investigating the intestinal and systemic immune responses obtained after immunization with SslE using different routes of administration. In-depth analysis of each regimen will allow us to determine the most efficient method of immunization for SslE to be protective. Further, using this selected model of immunization, we will evaluate the potential perturbation caused by SslE immunization on the murine intestinal microbiome. These findings will be important to help us optimize the development of a potential broad spectrum E. coli vaccine.

An antimicrobial peptide-resistant minor subpopulation of Photorhabdus luminescens is responsible for virulence

Some of the bacterial cells in isogenic populations behave differently from others. We describe here how a new type of phenotypic heterogeneity relating to resistance to cationic antimicrobial peptides (CAMPs) is determinant for the pathogenic infection process of the entomopathogenic bacterium Photorhabdus luminescens. We demonstrate that the resistant subpopulation, which accounts for only 0.5% of the wild-type population, causes septicemia in insects. Bacterial heterogeneity is driven by the PhoPQ two-component regulatory system and expression of pbgPE, an operon encoding proteins involved in lipopolysaccharide (LPS) modifications. We also report the characterization of a core regulon controlled by the DNA-binding PhoP protein, which governs virulence in P. luminescens. Comparative RNAseq analysis revealed an upregulation of marker genes for resistance, virulence and bacterial antagonism in the pre-existing resistant subpopulation, suggesting a greater ability to infect insect prey and to survive in cadavers. Finally, we suggest that the infection process of P. luminescens is based on a bet-hedging strategy to cope with the diverse environmental conditions experienced during the lifecycle.

Xylan degradation by the human gut Bacteroides xylanisolvens XB1A(T) involves two distinct gene clusters that are linked at the transcriptional level

Background

Plant cell wall (PCW) polysaccharides and especially xylans constitute an important part of human diet. Xylans are not degraded by human digestive enzymes in the upper digestive tract and therefore reach the colon where they are subjected to extensive degradation by some members of the symbiotic microbiota. Xylanolytic bacteria are the first degraders of these complex polysaccharides and they release breakdown products that can have beneficial effects on human health. In order to understand better how these bacteria metabolize xylans in the colon, this study was undertaken to investigate xylan breakdown by the prominent human gut symbiont Bacteroides xylanisolvens XB1A^T.

Results

Transcriptomic analyses of B. xylanisolvens XB1A^T grown on insoluble oat-spelt xylan (OSX) at mid- and late-log phases highlighted genes in a polysaccharide utilization locus (PUL), hereafter called PUL 43, and genes in a fragmentary remnant of another PUL, hereafter referred to as rPUL 70, which were highly overexpressed on OSX relative to glucose. Proteomic analyses supported the up-regulation of several genes belonging to PUL 43 and showed the important over-production of a CBM4-containing GH10 endo-xylanase. We also show that PUL 43 is organized in two operons and that the knockout of the PUL 43 sensor/regulator HTCS gene blocked the growth of the mutant on insoluble OSX and soluble wheat arabinoxylan (WAX). The mutation not only repressed gene expression in the PUL 43 operons but also repressed gene expression in rPUL 70.

Conclusion

This study shows that xylan degradation by B. xylanisolvens XB1A^T is orchestrated by one PUL and one PUL remnant that are linked at the transcriptional level. Coupled to studies on other xylanolytic Bacteroides species, our data emphasize the importance of one peculiar CBM4-containing GH10 endo-xylanase in xylan breakdown and that this modular enzyme may be used as a functional marker of xylan degradation in the human gut. Our results also suggest that B. xylanisolvens XB1A^T has specialized in the degradation of xylans of low complexity. This functional feature may provide a niche to all xylanolytic bacteria harboring similar PULs. Further functional and ecological studies on fibrolytic Bacteroides species are needed to better understand their role in dietary fiber degradation and their impact on intestinal health.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2680-8) contains supplementary material, which is available to authorized users.

In vivo characterization of the immune response towards the pathogenic Escherichia coli antigen SslE and modulation of the intestinal microbiota

Pathogenic E. coli, both intestinal (InPEC) and extraintestinal (ExPEC), account for a wide range of diseases, which can be fatal, across developing and developed countries. The vast array of virulence factors they can acquire may dramatically increase the severity of the infection. Emergence of resistant strains often renders antibiotics inefficient; in the case of Shiga toxin-producing E. coli, antibiotics can even be detrimental. Hence, a broad spectrum E. coli vaccine could be a promising alternative to prevent the spread of such diseases, while offering the potential for covering against several InPEC and ExPEC at once.

Using the «reverse vaccinology» approach on an ExPEC strain, nine antigens were identified as protective against a mouse sepsis model. With 82% protective efficacy, SslE (Secreted and Surface-associated Lipoprotein of E. coli) was the most potent candidate; additional models demonstrated that SslE was also cross-protective against other ExPEC strains. Functional assays have demonstrated in vitro and in vivo that SslE is a mucinase which plays an important role for colonization and virulence of E. coli.

To better understand the mechanism behind such protection, particularly at the mucosa, we are investigating the intestinal immune response obtained after immunizations with SslE using different routes of injection. In-depth analysis of each regimen will allow us to determine the most efficient method of immunization and adjuvant choice for SslE to be protective. Further, using this model of immunization, we will evaluate the potential perturbation caused by SslE on a human intestinal microbiota. These findings will be important to help us optimize the development of a potential broad spectrum vaccine.

CpxR/OmpR interplay regulates curli gene expression in response to osmolarity in Escherichia coli

Curli fibers could be described as a virulence factor able to confer adherence properties to both abiotic and eukaryotic surfaces. The ability to adapt rapidly to changing environmental conditions through signal transduction pathways is crucial for the growth and pathogenicity of bacteria. OmpR was shown to activate csgD expression, resulting in curli production. The CpxR regulator was shown to negatively affect curli gene expression when binding to its recognition site that overlaps the csgD OmpR-binding site. This study was undertaken to clarify how the interplay between the two regulatory proteins, OmpR and CpxR, can affect the transcription of the curli gene in response to variation of the medium osmolarity. Band-shift assays with purified CpxR proteins indicate that CpxR binds to the csgD promoter region at multiple sites that are ideally positioned to explain the csg repression activity of CpxR. To understand the physiological meaning of this in vitro molecular phenomenon, we analyzed the effects of an osmolarity shift on the two-component pathway CpxA/CpxR. We establish here that the Cpx pathway is activated at both transcriptional and posttranscriptional levels in response to a high osmolarity medium and that CpxR represses csgD expression in high-salt-content medium, resulting in low curli production. However, csgD repression in response to high sucrose content is not mediated by CpxR but by the global regulatory protein H-NS. Therefore, multiple systems (EnvZ/OmpR, Cpx, Rcs, and H-NS) appear to be involved in sensing environmental osmolarity, leading to sophisticated regulation of the curli genes.