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We have analysed whether pulmonary arterial hypertension (PAH) alters the rat faecal microbiota. Wistar rats were injected with the VEGF receptor antagonist SU5416 (20 mg/kg s.c.) and followed for 2 weeks kept in hypoxia (10% O2, PAH) or injected with vehicle and kept in normoxia (controls). Faecal samples were obtained and microbiome composition was determined by 16S rRNA gene sequencing and bioinformatic analysis. No effect of PAH on the global microbiome was found (α- or β-diversity). However, PAH-exposed rats showed gut dysbiosis as indicated by a taxonomy-based analysis. Specifically, PAH rats had a three-fold increase in Firmicutes-to-Bacteroidetes ratio. Within the Firmicutes phylum, there were no large changes in the relative abundance of the bacterial families in PAH. Among Bacteroidetes, all families were less abundant in PAH. A clear separation was observed between the control and PAH clusters based on short chain fatty acid producing bacterial genera. Moreover, acetate was reduced in the serum of PAH rats. In conclusion, faecal microbiota composition is altered as a result of PAH. This misbalanced bacterial ecosystem might in turn play a pathophysiological role in PAH by altering the immunologic, hormonal and metabolic homeostasis. ; This study is supported by grants from Mineco (SAF2014-55399-R, SAF2014-55523-R, SAF2016-77222 and SAF2017-84494-C2-1R), Instituto de Salud Carlos III (PI15/01100), with funds from the European Union (Fondo Europeo de Desarrollo Regional FEDER). M.C., G.M-P. and S.E-R. are funded by Universidad Complutense, Fondo de Garantía Juvenil (Comunidad de Madrid) and Ciberes grant with funds from Fundación Contra la Hipertensión Pulmonar, a FPU grant from Ministerio de Educación, respectively. J.L.I.G is a CNIC IPP COFUND Fellow and has received funding from the People Programme (Marie Curie Actions) of the FP7/2007-2013 under REA grant agreement n° 600396. The CNIC is supported by MEIC-AEI and the Pro CNIC Foundation, and is a Severo Ochoa Center of Excellence (MEIC award SEV-2015-0505).

We have analysed whether pulmonary arterial hypertension (PAH) alters the rat faecal microbiota. Wistar rats were injected with the VEGF receptor antagonist SU5416 (20 mg/kg s.c.) and followed for 2 weeks kept in hypoxia (10\% O-2, PAH) or injected with vehicle and kept in normoxia (controls). Faecal samples were obtained and microbiome composition was determined by 165 rRNA gene sequencing and bioinformatic analysis. No effect of PAH on the global microbiome was found (alpha- or beta-diversity). However, PAH-exposed rats showed gut dysbiosis as indicated by a taxonomy-based analysis. Specifically, PAH rats had a three-fold increase in Firmicutes-to-Bacteroidetes ratio. Within the Firmicutes phylum, there were no large changes in the relative abundance of the bacterial families in PAH. Among Bacteroidetes, all families were less abundant in PAH. A clear separation was observed between the control and PAH clusters based on short chain fatty acid producing bacterial genera. Moreover, acetate was reduced in the serum of PAH rats. In conclusion, faecal microbiota composition is altered as a result of PAH. This misbalanced bacterial ecosystem might in turn play a pathophysiological role in PAH by altering the immunologic, hormonal and metabolic homeostasis. ; We thank Dr. Ricardo Ramos from Parque Cientifico de Madrid for helpful advices and for revising and editing the methods section. This study is supported by grants from Mineco (SAF2014-55399-R, SAF2014-55523-R, SAF2016-77222 and SAF2017-84494-C2-1R), Instituto de Salud Carlos III (PI15/01100), with funds from the European Union (Fondo Europeo de Desarrollo Regional FEDER). M.C., G.M-P. and S.E-R. are funded by Universidad Complutense, Fondo de Garantia Juvenil (Comunidad de Madrid) and Ciberes grant with funds from Fundacion Contra la Hipertension Pulmonar, a FPU grant from Ministerio de Educacion, respectively. J.L.I.G is a CNIC IPP COFUND Fellow and has received funding from the People Programme (Marie Curie Actions) of the FP7/2007-2013 under REA grant agreement no 600396. The CNIC is supported by MEIC-AEI and the Pro CNIC Foundation, and is a Severo Ochoa Center of Excellence (MEIC award SEV-2015-0505). ; Sí

The gut microbiota – the collection of micro-organisms in the gut – can best be viewed as a newly discovered organ, defined as a group of adjacent cells with a function. The gut microbiota, in fact, fulfils a number of important functions: it digests our food, synthesizes amino acids, trains our immune system, and helps resist gastrointestinal infections. The composition and functions of the gut microbiota can therefore have a large impact on our health. In this thesis the role of the gut microbiota in intestinal disorders is systematically analysed using DNA sequencing techniques. The intestinal disease we focus on most is inflammatory bowel disease (IBD), a recurrent remittent inflammatory disease of the gut that comprises Crohn's disease and ulcerative colitis. However, irritable bowel syndrome (IBS), traditionally characterized as a functional disorder consisting of a combination of gut complaints, and bacterial gastroenteritis, a bacterial infection often leading to diarrhoea, were also investigated. One of the most important discoveries of this thesis is the relationship between use of proton pump inhibitors (PPIs), one of most prescribed drugs in Europe and the United States, and the gut microbiota. PPIs work by reducing stomach acid, normally an important barrier to bacteria entering the intestinal tract, and we observed that bacteria normally found in the mouth were now present in the gut of PPI users. PPI users also have a more pro-inflammatory gut microbiota, showing a decrease in favourable butyrate-producing bacteria and an increase in the Enterobacteriaceae that can produce toxin. As a consequence, PPI users are more susceptible to both bacterial gastroenteritis, e.g. that caused by Salmonella spp, and to Clostridium difficile infections. After these results were published in 2016, government officials began to question whether PPIs should remain available as over-the-counter drugs in grocery stores, and this debate was still ongoing as of the writing of this thesis. This discovery received a lot of media attention in the written press: De Telegraaf, Reuters and Scientific American, on the radio: RTV Noord and BNR Nieuwsradio and on the television show Kassa. Another important discovery, the gut metagenomes of IBD and IBS are compared to those of population controls and are described in great detail using the metagenomic sequencing technique. With this technique, we were able to both determine the composition of the gut microbiome and infer its function, strain diversity, the level of virulence and the level of antibiotic resistance, leading to thousands of new results. We also present a computer algorithm that uses gut metagenomes to reliably distinguish IBD from IBS (AUC=0.93), performing much better than faecal calprotectin, which is currently used as a marker to distinguish between the two conditions. In the future, a gut microbiome-based test could reduce the number of painful and costly colonoscopies. This discovery was published in the renowned journal Science Translation Medicine and the Dutch television programme Editie NL on RTL4 discussed its importance for patients with irritable bowel syndrome. The results of this thesis allow us to better understand intestinal disesases and to work towards microbiota-based diagnostics and therapeutics.

Inadequate immunologic, metabolic and cardiovascular homeostasis has been related to either an alteration of the gut microbiota or to vitamin D deficiency. We analyzed whether vitamin D deficiency alters rat gut microbiota. Male Wistar rats were fed a standard or a vitamin D-free diet for seven weeks. The microbiome composition was determined in fecal samples by 16S rRNA gene sequencing. The vitamin D-free diet produced mild changes on alpha- diversity but no effect on -diversity in the global microbiome. Markers of gut dysbiosis like Firmicutes-to-Bacteroidetes ratio or the short chain fatty acid producing bacterial genera were not significantly affected by vitamin D deficiency. Notably, there was an increase in the relative abundance of the Enterobacteriaceae, with significant rises in its associated genera Escherichia, Candidatus blochmannia and Enterobacter in vitamin D deficient rats. Prevotella and Actinomyces were also increased and Odoribacteraceae and its genus Butyricimonas were decreased in rats with vitamin D-free diet. In conclusion, vitamin D deficit does not induce gut dysbiosis but produces some specific changes in bacterial taxa, which may play a pathophysiological role in the immunologic dysregulation associated with this hypovitaminosis. ; This study is supported by grants from Mineco (SAF2016-77222-R and SAF2017-8489-R), with funds from the European Union (Fondo Europeo de Desarrollo Regional FEDER) and Fundación Contra la Hipertensión Pulmonar (Empathy grant). I.R.V and M.C. are funded by Mineco (FPU grant) and Universidad Complutense de Madrid, respectively. FPV was funded by a Mobility grant from CIBERES

Background: In recent decades, dominant models of mental illness have become increasingly focused on the head, with mental disorders being figured as brain disorders. However, research into the active role that the microbiome-gut-brain axis plays in affecting mood and behaviour may lead to the conclusion that mental health is more than an internalised problem of individual brains. Objective: This article explores the implications of shifting understandings about mental health that have come about through research into links between the gut microbiome and mental health problems such as depression and anxiety. It aims to analyse the different ways that the lines between mind and body and mental and physical health are re-shaped by this research, which is starting to inform clinical and public understanding. Design: As mental health has become a pressing issue of political and public concern it has become increasingly constructed in socio-cultural and personal terms beyond clinical spaces, requiring a conceptual response that exceeds biomedical inquiry. This article argues that an interdisciplinary critical medical humanities approach is well positioned to analyse the impact of microbiome-gut-brain research on conceptions of mind. Results: The entanglement of mind and matter evinced by microbiome-gut-brain axis research potentially provides a different way to conceptualise the physical and social concomitants of mental distress. Conclusion: Mental health is not narrowly located in the head but is assimilated by the physical body and intermingled with the natural world, requiring different methods of research to unfold the meanings and implications of gut thinking for conceptions of human selfhood.

B cells possess a predominant role in adaptive immune responses via antibodydependent and -independent functions. The microbiome of the gastrointestinal tract is currently being intensively investigated due to its profound impact on various immune responses, including B cell maturation, activation, and IgA antibody responses. Recent findings have demonstrated the interplay between dietary components, gut microbiome, and autoantibody production. "Western" dietary patterns, such as high fat and high salt diets, can induce alterations in the gut microbiome that in turn affects IgA responses and the production of autoantibodies. This could contribute to multiple pathologies including autoimmune and inflammatory diseases. Here, we summarize current knowledge on the influence of various dietary components on B cell function and (auto)antibody production in relation to the gut microbiota, with a particular focus on the gut–brain axis in the pathogenesis of multiple sclerosis. ; MK was supported by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (640116), by a SALK-grant from the government of Flanders, Belgium, and by an Odysseus grant of the Research Foundation Flanders, Belgium (FWO). JF is a postdoctoral fellow of the FWO.

International audience ; Individuals who are minoritized as a result of race, sexual identity, gender, or socioeconomic status experience a higher prevalence of many diseases. Understanding the biological processes that cause and maintain these socially driven health inequities is essential for addressing them. The gut microbiome is strongly shaped by host environments and affects host metabolic, immune, and neuroendocrine functions, making it an important pathway by which differences in experiences caused by social, political, and economic forces could contribute to health inequities. Nevertheless, few studies have directly integrated the gut microbiome into investigations of health inequities. Here, we argue that accounting for host–gut microbe interactions will improve understanding and management of health inequities, and that health policy must begin to consider the microbiome as an important pathway linking environments to population health.

International audience ; Individuals who are minoritized as a result of race, sexual identity, gender, or socioeconomic status experience a higher prevalence of many diseases. Understanding the biological processes that cause and maintain these socially driven health inequities is essential for addressing them. The gut microbiome is strongly shaped by host environments and affects host metabolic, immune, and neuroendocrine functions, making it an important pathway by which differences in experiences caused by social, political, and economic forces could contribute to health inequities. Nevertheless, few studies have directly integrated the gut microbiome into investigations of health inequities. Here, we argue that accounting for host–gut microbe interactions will improve understanding and management of health inequities, and that health policy must begin to consider the microbiome as an important pathway linking environments to population health.

International audience ; Individuals who are minoritized as a result of race, sexual identity, gender, or socioeconomic status experience a higher prevalence of many diseases. Understanding the biological processes that cause and maintain these socially driven health inequities is essential for addressing them. The gut microbiome is strongly shaped by host environments and affects host metabolic, immune, and neuroendocrine functions, making it an important pathway by which differences in experiences caused by social, political, and economic forces could contribute to health inequities. Nevertheless, few studies have directly integrated the gut microbiome into investigations of health inequities. Here, we argue that accounting for host–gut microbe interactions will improve understanding and management of health inequities, and that health policy must begin to consider the microbiome as an important pathway linking environments to population health.

Individuals who are minoritized as a result of race, sexual identity, gender, or socioeconomic status experience a higher prevalence of many diseases. Understanding the biological processes that cause and maintain these socially driven health inequities is essential for addressing them. The gut microbiome is strongly shaped by host environments and affects host metabolic, immune, and neuroendocrine functions, making it an important pathway by which differences in experiences caused by social, political, and economic forces could contribute to health inequities. Nevertheless, few studies have directly integrated the gut microbiome into investigations of health inequities. Here, we argue that accounting for host-gut microbe interactions will improve understanding and management of health inequities, and that health policy must begin to consider the microbiome as an important pathway linking environments to population health.

Individuals who are minoritized as a result of race, sexual identity, gender, or socioeconomic status experience a higher prevalence of many diseases. Understanding the biological processes that cause and maintain these socially driven health inequities is essential for addressing them. The gut microbiome is strongly shaped by host environments and affects host metabolic, immune, and neuroendocrine functions, making it an important pathway by which differences in experiences caused by social, political, and economic forces could contribute to health inequities. Nevertheless, few studies have directly integrated the gut microbiome into investigations of health inequities. Here, we argue that accounting for host–gut microbe interactions will improve understanding and management of health inequities, and that health policy must begin to consider the microbiome as an important pathway linking environments to population health.