Fusobacterium nucleatum Extracellular Vesicles Modulate Gut Epithelial Cell Innate Immunity via FomA and TLR2.

peer reviewedExtracellular vesicles (EVs) derived from the gut microbiota are largely uncharacterized and their impacts on host intestinal physiology remain unresolved. Here, we isolated EVs from F. nucleatum for detailed characterization. Our analyses highlight the presence of the outer membrane protein porin FomA on EVs. Besides, we evaluated the impact of EVs on human intestinal epithelial cells (IECs) in a non-inflammatory context. Our results show no detrimental impact on the epithelial barrier. No internalization of EVs was observed. Moreover, we demonstrate that F. nucleatum EVs trigger innate immunity of IECs by promoting NF-κB activation via the dynamin-mediated endocytosis. The NF-κB activation was found to be TLR2-dependent yet, TLR4 was dispensable. Using competitive binding assays, we establish that FomA is involved in the NF-κB response. Taken together, our data indicate that EVs induce effects similar to those observed with whole F. nucleatum bacteria on IECs. In particular, our study highlights the role of TLR2 and FomA as major modulators of the gut epithelium immune responses to F. nucleatum

Butyrate Produced by Commensal Bacteria Down-Regulates Indolamine 2,3-Dioxygenase 1 (IDO-1) Expression via a Dual Mechanism in Human Intestinal Epithelial Cells

Commensal bacteria are crucial for the development and maintenance of a healthy immune system therefore contributing to the global well-being of their host. A wide variety of metabolites produced by commensal bacteria are influencing host health but the characterization of the multiple molecular mechanisms involved in host-microbiota interactions is still only partially unraveled. The intestinal epithelial cells (IECs) take a central part in the host-microbiota dialogue by inducing the first microbial-derived immune signals. Amongst the numerous effector molecules modulating the immune responses produced by IECs, indoleamine 2,3-dioxygenase-1 (IDO-1) is essential for gut homeostasis. IDO-1 expression is dependent on the microbiota and despites its central role, how the commensal bacteria impacts its expression is still unclear. Therefore, we investigated the impact of individual cultivable commensal bacteria on IDO-1 transcriptional expression and found that the short chain fatty acid (SCFA) butyrate was the main metabolite controlling IDO-1 expression in human primary IECs and IEC cell-lines. This butyrate-driven effect was independent of the G-protein coupled receptors GPR41, GPR43, and GPR109a and of the transcription factors SP1, AP1, and PPARγ for which binding sites were reported in the IDO-1 promoter. We demonstrated for the first time that butyrate represses IDO-1 expression by two distinct mechanisms. Firstly, butyrate decreases STAT1 expression leading to the inhibition of the IFNγ-dependent and phosphoSTAT1-driven transcription of IDO-1. In addition, we described a second mechanism by which butyrate impairs IDO-1 transcription in a STAT1-independent manner that could be attributed to its histone deacetylase (HDAC) inhibitor property. In conclusion, our results showed that IDO-1 expression is down-regulated by butyrate via a dual mechanism: the reduction of STAT1 level and the HDAC inhibitor property of SCFAs

The gut microbiome molecular complex in human health and disease

The human gut microbiome produces a functional complex of biomolecules, including nucleic acids, (poly) peptides, structural molecules, and metabolites. This impacts human physiology in multiple ways, especially by triggering inflammatory pathways in disease. At present, much remains to be learned about the identity of key effectors and their causal roles

MORE SMOKE THAN FIRE NO SPEEDING UP OF PARKINSON‘S DISEASE AFTER COVID-10 LOCKDOWN

peer reviewedBackground and objectives As the influence of stress syndromes on the evolution of Parkinson’s disease (PD) remains largely unexplored, the COVID-19 pandemic offers the opportunity to evaluate the stress impact of the COVID-19 pandemic on PD trajectories. Methods This longitudinal observational case-control study used data from the Luxembourg Parkinson’s Study (1). A pandemic PD group with exposure to the restrictions imposed by the COVID-19 pandemic but without COVID-19 infection (n=79) was compared to a prepandemic PD control group (n= 117) that has never been exposed to any pandemic restrictions. All patients underwent three annual visits. The last analyzed in-person visit of the pandemic group occurred during the early pandemic phase, between September 2020 and March 2021. Motor and cognitive status were established through standardized in-person exams. Patients of the PD pandemic group selfrated their resilience and risk for posttraumatic stress disorder (PTSD) and, at visit 2 and 3, underwent the Olink panel of 92 serological inflammation markers. The primary outcome was motor PD progression as rated by the MDS-UPDRS part III score. The secondary outcomes were other progression scores (MDS-UPDRS I and II), cognitive performance (Montreal Cognitive Assessment), symptoms of depression (Beck Depression Inventory), risk for PTSD (revised Impact of Event Scale) and resilience (Brief Resilience Scale). Measures tested for statistical associations with these outcomes include demographic, lifestyle data and serological inflammation markers. To assess variable associations and correct effects from confounding factors, we used a multiple linear regression approach. Results The deterioration of the motor and cognitive scores from visit 1 to visit 3 was not different in the pandemic group compared to the prepandemic group. 74.7 % of the pandemic PD patients had normal or high resilience scores, whereas 20.3% were at risk of developing PTSD. Resilience was neither correlated with motor scores nor with cognitive scores but was negatively associated with depressive symptomatology and posttraumatic stress. Except for Axin-1, there was no increase in the inflammation markers at visit 3 compared to visit 2. Discussion This case-control study shows that there was no influence by the pandemic-induced stress on the natural progression of PD motor and cognitive trajectories.R-AGR-0592 - FNR - NCER-PD Phase II Coordination (01/06/2015 - 30/11/2023) - KRÜGER Rejko3. Good health and well-bein

Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses

Background: Alterations to the gut microbiome have been linked to multiple chronic diseases. However, the drivers of such changes remain largely unknown. The oral cavity acts as a major route of exposure to exogenous factors including pathogens, and processes therein may affect the communities in the subsequent compartments of the gastrointestinal tract. Here, we perform strain‑resolved, integrated meta‑genomic, transcriptomic, and proteomic analyses of paired saliva and stool samples collected from 35 individuals from eight families with multiple cases of type 1 diabetes mellitus (T1DM). Results: We identified distinct oral microbiota mostly reflecting competition between streptococcal species. More specifically, we found a decreased abundance of the commensal Streptococcus salivarius in the oral cavity of T1DM individuals, which is linked to its apparent competition with the pathobiont Streptococcus mutans. The decrease in S. salivarius in the oral cavity was also associated with its decrease in the gut as well as higher abundances in facultative anaerobes including Enterobacteria. In addition, we found evidence of gut inflammation in T1DM as reflected in the expression profiles of the Enterobacteria as well as in the human gut proteome. Finally, we were able to follow transmitted strain‑variants from the oral cavity to the gut at the individual omic levels, highlighting not only the transfer, but also the activity of the transmitted taxa along the gastrointestinal tract. Conclusions: Alterations of the oral microbiome in the context of T1DM impact the microbial communities in the lower gut, in particular through the reduction of “mouth‑to‑gut” transfer of Streptococcus salivarius. Our results indicate that the observed oral‑cavity‑driven gut microbiome changes may contribute towards the inflammatory processes involved in T1DM. Through the integration of multi‑omic analyses, we resolve strain‑variant “mouth‑to‑gut” transfer in a disease context

Altered infective competence of the human gut microbiome in COVID-19

BACKGROUND: Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group. RESULTS: We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls. CONCLUSIONS: Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract

The gut microbial metabolite formate exacerbates colorectal cancer progression

The gut microbiome is a key player in the immunomodulatory and protumorigenic microenvironment during colorectal cancer (CRC), as different gut-derived bacteria can induce tumour growth. However, the crosstalk between the gut microbiome and the host in relation to tumour cell metabolism remains largely unexplored. Here we show that formate, a metabolite produced by the CRC-associated bacterium Fusobacterium nucleatum, promotes CRC development. We describe molecular signatures linking CRC phenotypes with Fusobacterium abundance. Cocultures of F. nucleatum with patient-derived CRC cells display protumorigenic effects, along with a metabolic shift towards increased formate secretion and cancer glutamine metabolism. We further show that microbiome-derived formate drives CRC tumour invasion by triggering AhR signalling, while increasing cancer stemness. Finally, F. nucleatum or formate treatment in mice leads to increased tumour incidence or size, and Th17 cell expansion, which can favour proinflammatory profiles. Moving beyond observational studies, we identify formate as a gut-derived oncometabolite that is relevant for CRC progression

An archaeal compound as a driver of Parkinson’s disease pathogenesis

Patients with Parkinson’s disease (PD) exhibit differences in their gut microbiomes compared to healthy individuals. Although differences have most commonly been described in the abundances of bacterial taxa, changes to viral and archaeal populations have also been observed. Mechanistic links between gut microbes and PD pathogenesis remain elusive but could involve molecules that promote α-synuclein aggregation. Here, we show that 2-hydroxypyridine (2-HP) represents a key molecule for the pathogenesis of PD. We observe significantly elevated 2-HP levels in faecal samples from patients with PD or its prodrome, idiopathic REM sleep behaviour disorder (iRBD), compared to healthy controls. 2-HP is correlated with the archaeal species Methanobrevibacter smithii and with genes involved in methane metabolism, and it is detectable in isolate cultures of M. smithii. We demonstrate that 2-HP is selectively toxic to transgenic α-synuclein overexpressing yeast and increases α-synuclein aggregation in a yeast model as well as in human induced pluripotent stem cell derived enteric neurons. It also exacerbates PD-related motor symptoms, α-synuclein aggregation, and striatal degeneration when injected intrastriatally in transgenic mice overexpressing human α-synuclein. Our results highlight the effect of an archaeal molecule in relation to the gut-brain axis, which is critical for the diagnosis, prognosis, and treatment of PD.

Impact du microbiote sur les fonctions immuno-régulatrices des cellules épithéliales intestinales humaines

Exchange with the gut microbiota are key for immune system development and host intestinal homeostasis. Bacterial molecules sensed by epithelial cells in the intestine are challenging permanently the host immune system. In response, epithelial cells secrete numerous immuno-regulator factors favouring gut tolerance. However, the molecular mechanisms involved in these processes, remain poorly understand. We studied bacterial-dependent regulation of TGFB1 and IDO1 genes as well as the TLR independent activation of the NFκB pathway, in epithelial cells. We screened the activities of a hundred of gut bacterial species on human epithelial cell lines. We showed that short chain fatty acids, and specially butyrate secreted by Clostridiales and Fusobacterium, were potent modulators of TGFb1 and IDO1 via their histone deacetylase inhibition properties. Butyrate upregulated TGFB1 by a mechanism dependent of the SP1 transcription factor. Moreover, butyrate inhibited IDO1 by two distinct mechanisms, by down-regulating the STAT1/IFNγ pathway and by preventing IDO1 expression independently of IFNγ. Eventually, we described that specific group of gut bacteria activated NFκB in a short-chain fatty acids, TLR and MYD88 independent manner. Interestingly, some Gram+ bacteria stimulated NFκB via the NOD1 pathway. Furthermore, we identified for the first time in a non-pathogenic context, commensal bacteria promoting NFκB by the newly discovered ALPK1-TIFA-TRAF6 axis. Overall, our work support the specific functions of the intestinal epithelial cells in the regulation of the host-microbiote symbiosis.Les échanges avec le microbiote intestinal sont indispensables au développement du système immunitaire et à l’homéostasie intestinale. Les bactéries produisent des molécules perçues par les cellules épithéliales de l’intestin qui mettent à l’épreuve en permanence notre immunité. En réponse, ces cellules sécrètent des facteurs immuno-régulateurs qui contribuent à la tolérance intestinale mais dont les mécanismes sont encore peu compris. Nous nous sommes intéressés à la régulation par les bactéries des gènes TGFb1 et IDO1 et à l’activation du facteur de transcription NFκB, indépendamment des TLR. Pour mieux caractériser ses échanges, nous avons étudié les activités de bactéries commensales sur des lignées de cellules épithéliales intestinales humaines. Nous avons démontré que les acides à chaînes courtes, en particulier le butyrate présent dans les surnageants bactériens des Clostridiales et des Fusobacterium, est un puissant modulateur de TGFb1 et d’IDO1 par ses propriétés inhibitrices d’histone déacétylase. Le butyrate active la transcription de TGFb1 par un mécanisme dépendant du facteur de transcription SP1. En outre, le butyrate inhibe la transcription d’IDO1 par deux mécanismes distincts, l’un ciblant la voie STAT1/IFNγ et le second agissant indépendamment de l’IFNγ. Enfin, certaines bactéries intestinales activent NFκB, indépendamment des acides gras à chaînes courtes, des TLR et de MYD88. Une partie de ces bactéries stimulent la voie NOD1 tandis que d’autres utilisent la voie ALPK1-TIFA-TRAF6, jusqu'à présent activée uniquement par des pathogènes. Ce travail met en valeur le rôle des cellules épithéliales dans la régulation de la symbiose hôte-microbiote

Impact of the gut microbiota on the immuno-modulatory functions of the intestinal epithelial humans cells

Les échanges avec le microbiote intestinal sont indispensables au développement du système immunitaire et à l’homéostasie intestinale. Les bactéries produisent des molécules perçues par les cellules épithéliales de l’intestin qui mettent à l’épreuve en permanence notre immunité. En réponse, ces cellules sécrètent des facteurs immuno-régulateurs qui contribuent à la tolérance intestinale mais dont les mécanismes sont encore peu compris. Nous nous sommes intéressés à la régulation par les bactéries des gènes TGFb1 et IDO1 et à l’activation du facteur de transcription NFκB, indépendamment des TLR. Pour mieux caractériser ses échanges, nous avons étudié les activités de bactéries commensales sur des lignées de cellules épithéliales intestinales humaines. Nous avons démontré que les acides à chaînes courtes, en particulier le butyrate présent dans les surnageants bactériens des Clostridiales et des Fusobacterium, est un puissant modulateur de TGFb1 et d’IDO1 par ses propriétés inhibitrices d’histone déacétylase. Le butyrate active la transcription de TGFb1 par un mécanisme dépendant du facteur de transcription SP1. En outre, le butyrate inhibe la transcription d’IDO1 par deux mécanismes distincts, l’un ciblant la voie STAT1/IFNγ et le second agissant indépendamment de l’IFNγ. Enfin, certaines bactéries intestinales activent NFκB, indépendamment des acides gras à chaînes courtes, des TLR et de MYD88. Une partie de ces bactéries stimulent la voie NOD1 tandis que d’autres utilisent la voie ALPK1-TIFA-TRAF6, jusqu'à présent activée uniquement par des pathogènes. Ce travail met en valeur le rôle des cellules épithéliales dans la régulation de la symbiose hôte-microbiote.Exchange with the gut microbiota are key for immune system development and host intestinal homeostasis. Bacterial molecules sensed by epithelial cells in the intestine are challenging permanently the host immune system. In response, epithelial cells secrete numerous immuno-regulator factors favouring gut tolerance. However, the molecular mechanisms involved in these processes, remain poorly understand. We studied bacterial-dependent regulation of TGFB1 and IDO1 genes as well as the TLR independent activation of the NFκB pathway, in epithelial cells. We screened the activities of a hundred of gut bacterial species on human epithelial cell lines. We showed that short chain fatty acids, and specially butyrate secreted by Clostridiales and Fusobacterium, were potent modulators of TGFb1 and IDO1 via their histone deacetylase inhibition properties. Butyrate upregulated TGFB1 by a mechanism dependent of the SP1 transcription factor. Moreover, butyrate inhibited IDO1 by two distinct mechanisms, by down-regulating the STAT1/IFNγ pathway and by preventing IDO1 expression independently of IFNγ. Eventually, we described that specific group of gut bacteria activated NFκB in a short-chain fatty acids, TLR and MYD88 independent manner. Interestingly, some Gram+ bacteria stimulated NFκB via the NOD1 pathway. Furthermore, we identified for the first time in a non-pathogenic context, commensal bacteria promoting NFκB by the newly discovered ALPK1-TIFA-TRAF6 axis. Overall, our work support the specific functions of the intestinal epithelial cells in the regulation of the host-microbiote symbiosis