Microbiota | EPFL Graph Search

Microbiota are the range of microorganisms that may be commensal, mutualistic, or pathogenic found in and on all multicellular organisms, including plants. Microbiota include bacteria, archaea, protists, fungi, and viruses, and have been found to be crucial for immunologic, hormonal, and metabolic homeostasis of their host. The term microbiome describes either the collective genomes of the microbes that reside in an ecological niche or within the microbes themselves. The microbiome and host emerged during evolution as a synergistic unit from epigenetics and genetic characteristics, sometimes collectively referred to as a holobiont. The presence of microbiota in human and other metazoan guts has been critical for understanding the co-evolution between metazoans and bacteria. Microbiota play key roles in the intestinal immune and metabolic responses via their fermentation product (short-chain fatty acid), acetate. Introduction All plants and animals, from simple life for

Multidisciplinary Investigation of the Gut-Brain Ecosystem in a Model of Alzheimer's Disease

Arielle Louise Planchette

The search for an understanding of the causal elements that lead to neurodegenerative diseases has motivated researchers for decades. Today, Alzheimer's disease is the most prevalent form of dementia and affects approximately fifty million people worldwide, with only 5% of patients carrying causal genetic mutations. In recent years, studies of animal models as well as observations in humans have brought the gut microbiome to the forefront of AD research, as a significant contributor to the development of Alzheimer's disease. In fact, the gut microbiome is now understood to be a modulator of health and disease in numerous areas of physiology, including energy metabolism, immunity, endocrinology, and most relevant to this thesis, brain health and cognition. The gut microbiome is a complex environment composed of symbiotic bacteria, fungi and viruses (the microbiota) that produce a wide range of signalling molecules that are interpreted both by members of the microbiota and by the host (the microbiome). The host-gut interface is an ecosystem that consists of bi-directional signals and pressures applied by both constituents in order to maintain symbiotic homeostasis. Significant deleterious effects on health occur when homeostasis is lost, which may take place due to a variety of factors. These include host genetic factors and environmental factors, such as diet. Modulation of the gut microbiome has become a potentially viable therapeutic avenue for Alzheimer's disease, though it currently remains at the early stage of discovery. In this thesis, I characterize the evolution of Alzheimer's disease in the 5xFAD mouse model, with a focus on the gut microbiome and on cognitive decline and brain biochemistry. Gut microbiota modulaiton was implemented using germ-free and low-complexity bacterial cocktails, in which I outline the effects microbiota modulation on hallmarks of AD and provide insights into the metabolite profile of the brain altered by the microbiota and AD. The work in this thesis was equally motivated by the development of diagnostic tools using microscopy techniques. Biochemical assessments of disease status and progression provide information pertaining to "what" is interacting and "how much" this affects disease. With microscopy, we may gain the additional knowledge of "where" physiological constituents are and how they interact with the surrounding environment. I describe a novel multi-modal microscopy pipeline that enables the observation of signals of interest in large volumes and at high resolution with a capacity to cross-reference regions of interest in both modalities. The pipeline, known as gutOPT, consists of a sample preparation workflow compatible with mesoscale optical projection tomography (OPT) of fluorescently-labelled targets and subsequent imaging of pre-selected regions of interest in high-resolution modalities, such as confocal microscopy.

EPFL2022

Biogeography and biochemistry of bile acid 7-dehydroxylation in the mammalian gut

Solenne Anne Marie Marion

Bile acids (BAs) are small molecules synthesized by the host and chemically modified by the microorganisms inhabiting the intestinal tract. The microbial transformation of BAs in the gut is critical to BA-mediated signaling as it modifies their amount and affinity for specific BA receptors. Bile acid 7-dehydroxylating bacteria are intestinal commensals of particular importance as they catalyze the dehydroxylation of liver-derived (primary) bile acids at the C7 position (i.e., 7-dehydroxylation) and produce secondary bile acids. One of the major receptors for secondary BAs is Takeda G-protein receptor 5 (TGR5), and it is associated with regulation of energy expenditure and glucose management, protection from liver steatosis and inflammation. In addition, 7-dehydroxylated bile acids are also associated with protection from infection by specific intestinal pathogens (i.e., Clostridioides difficile). Thus, through their action on primary BAs, 7-dehydroxylating (7-DH-ing) bacteria play an important role in health promotion and in the functioning of major physiological processes in the body such as insulin secretion, thermogenesis and immune responses. Despite these potentially important roles in the mammalian host, bile acid 7-dehydroxylating bacteria are poorly studied and much remains to be deciphered regarding their metabolism, diversity, abundance in the gut, and colonization dynamics in the host. Here, we use Clostridium scindens, as model organism to study bile acid 7-dehydroxylation in vitro and in gnotobiotic mice. We found that C. scindens metabolize only human primary bile acids (CA and CDCA). We uncovered the formation of a novel intermediate during CA 7-dehydroxylation by C. scindens in vitro: 12-oxoLCA. In vivo, using NanoSIMS and metabolomic analysis, we demonstrated that the large intestine constitutes C. scindens primary ecological niche in gnotobiotic mice. Following up on the discovery of the 12oxoLCA, we hypothesized the existence of another 7-dehydroxylation pathway for cholic acid. We postulated that it may involve the B and C rings of the steroid structure and may entail the oxidation/reduction of the C12- hydroxyl group. Thus, it was dubbed the putative vertical pathway. Conducting in vitro enzymatic assays with purified enzymes, we confirmed the existence of this novel vertical biosynthetic 7-dehydroxylation pathway for cholic acid, the most abundant primary bile acid in humans, and identified the core of enzymes necessary and sufficient for CA 7-dehydroxylation. Furthermore, we used a coupled metabolomic and metaproteomic approach to probe in vivo activity of the gut microbial community in a gnotobiotic mouse model. Additionnally, we also considered the bile acid profile in mice with more complex microbiota or with no microbiota. By comparing the bile acid profile of the different mice models along with expression of key genes of bile acid synthesis, we emphasized the profound influence of the gut microbial community on BA pool homeostasis. Altogether, our data provides a significant contribution to our collective understanding of the microbiology of bile acid 7-dehydroxylating bacteria, a group of gut commensals highly relevant to host health but that remains poorly characterized. The discovery of a novel 7-dehydroxylation pathway is a major scientific achievement of this thesis.

EPFL2020

Biogeography of microbial bile acid transformations along the murine gut

Rizlan Bernier-Latmani, Lyne Desharnais, Solenne Anne Marie Marion, Laure Menin

Bile acids, which are synthesized from cholesterol by the liver, are chemically transformed along the intestinal tract by the gut microbiota, and the products of these transformations signal through host receptors, affecting overall host health. These transformations include bile acid deconjugation, oxidation, and 7 alpha-dehydroxylation. An understanding of the biogeography of bile acid transformations in the gut is critical because deconjugation is a prerequisite for 7 alpha-dehydroxylation and because most gut microorganisms harbor bile acid transformation capacity. Here, we used a coupled metabolomic and metaproteomic approach to probe in vivo activity of the gut microbial community in a gnotobiotic mouse model. Results revealed the involvement of Clostridium scindens in 7 alpha-dehydroxylation, of the genera Muribaculum and Bacteroides in deconjugation, and of six additional organisms in oxidation (the genera Clostridium, Muribaculum, Bacteroides, Bifidobacterium, Acutalibacter, and Akkermansia). Furthermore, the bile acid profile in mice with a more complex microbiota, a dysbiosed microbiota, or no microbiota was considered. For instance, conventional mice harbor a large diversity of bile acids, but treatment with an antibiotic such as clindamycin results in the complete inhibition of 7 alpha-dehydroxylation, underscoring the strong inhibition of organisms that are capable of carrying out this process by this compound. Finally, a comparison of the hepatic bile acid pool size as a function of microbiota revealed that a reduced microbiota affects host signaling but not necessarily bile acid synthesis. In this study, bile acid transformations were mapped to the associated active microorganisms, offering a systematic characterization of the relationship between microbiota and bile acid composition.

AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC2020