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Psoralen (P) and isopsoralen (IP) are the main active ingredients in the dried fruit of Psoralen corylifolia L. (PC), with a wide range of pharmacology activities. The intestinal bacteria biotransformation plays a central role in the metabolism of the complex ingredients in traditional Chinese medicine (TCM). Our study aimed to investigated the metabolic profile of P and IP in the intestinal condition, co-cultured with human fecal bacteria anaerobically. Four bio-transforming products were obtained, including 6,7-furano-hydrocoumaric acid (P-1) and 6,7-furano-hydro- coumaric acid methyl ester (P-2), which transformed from P, and 5,6-furano-hydrocoumaric acid (IP-1) and 5,6-furano-hydrocoumaric acid methyl ester (IP-2), which were transformed from IP. It is worth mentioning that IP-2 is a new compound that has not been published. Their structures were analyzed based on their spectroscopic data. Moreover, a highly sensitive ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) method was used to characterize the metabolic pathways of P, IP, and their bio-transforming products in the reaction samples. In addition, the dampening effects against the oxidative stress of P, IP, and their bio-transforming products by human intestinal flora were estimated in vitro via the human colorectal cells (HCT116) and heterogeneous human epithelial colorectal adenocarcinoma cells (Caco-2) cell lines. The results showed that the metabolites have stronger activity than P and IP, which possibly provides a basis for elucidating the treating mechanisms of PC extract against inflammatory bowel disease.

Tongmai formula (TMF) is a well-known Chinese medicinal preparation that contains isoflavones as its major bioactive constituents. As traditional Chinese medicines (TCMs) are usually used by oral administration, their fate inside the intestinal lumen, including their biotransformation by human intestinal flora (HIF) and intestinal absorption deserves study. In this work TMF extract was incubated with human intestinal bacteria under anaerobic conditions and the changes in the twelve main constituents of TMF were then investigated. Their intestinal permeabilities, i.e., the transport capability across the intestinal brush border were investigated with a human colon carcinoma cell line (Caco-2) cell monolayer model to predict the absorption mechanism. Meanwhile, rapid HPLC-DAD methods were established for the assay. According to the biotransformation curves of the twelve constituents and the permeability coefficients, the intestinal absorption capacity of the typical compounds was elevated from the levels of 10(-7) cm/s to 10(-5) cm/s from those of the original compounds in TMF. Among them the main isoflavone glycosides puerarin (4), mirificin (6) and daidzin (7) were transformed into the same aglycone, daidzein (10). Therefore it was predicted that the aglycone compounds might be the real active ingredients in TMF. The models used can represent a novel path for the TCM studies.

The microbial flora is a micro-organism complex containing for example bacteria, archaea, lower eukaryotes and viruses, which play an important role in ecosystem equilibrium. This flora remains poorly defined as in 2012, only ~30% of the intestinal flora micro-organisms have been characterized, and less than 50% of traditional cheese floras were characterized at the functional level. Since 2006, the second generation of DNA sequencers have allowed the direct analysis of the genetic content from a microbial flora sample without isolation or culture limitation. However, the DNA reads generated are not structured with respect to genomes and also are highly fragmented, slowing down dramatically the exploitation and analysis of these data.In this work, a new methodology based on quantitative metagenomic are described., This allows the clustering of short DNA sequences with the same abundance in multiple metagenomic samples, which should originate from the same microbial species. A 3.9 million gene catalog has been built from the human intestinal tract microbiota and divided into 741 units or clusters corresponding to bacteria, archaea and eukaryote genomes. These have been defined as metagenomic species (MGS) and 6640 units of them corresponds mainly to viral genomes, plasmids and genetic islands like CRISPR, with the sub-name of metagenomic units (MGU). This methodology was then used to facilitate the association analysis of the intestinal flora composition with human diseases such as Crohn’s disease, obesity or type 2 diabetes. Within, the alimentary flora, our methods have also been used to constitute a 134 genomic catalog of cheese bacteria and characterize them from the surface of traditional cheeses. This allowed the detection of new alimentary bacteria, that will enriched the list of bacteria with potential interest for the commercial exploitation of fermented products.; La flore microbienne est un ensemble de micro-organismes comme les bactéries, archées, eucaryotes inférieurs et virus, jouant un rôle important dans l’équilibre d’un écosystème. Cette flore reste encore mal définie car en 2012, seules ~30% des micro-organismes de la flore intestinale humaine étaient caractérisés, et moins de 50% des micro-organismes de la flore fromagère traditionnelle étaient caractérisés au niveau fonctionnel. Depuis 2006, les séquenceurs à ADN de seconde génération permettent d’analyser directement le contenu génique d’un prélèvement de flore sans contrainte d’isolement ou de culture. Toutefois, les séquences d’ADN générées ne sont pas structurées en génome et sont hautement fragmentées, freinant considérablement l’analyse et l’exploitation de ces données. Dans ce travail, nous avons développé de nouvelles méthodes dites de métagénomiques quantitatives, car elles permettent de regrouper les courtes séquences d’ADN ayant la même abondance au sein de plusieurs échantillons métagénomiques, pouvant provenir d’une même espèce microbienne.Au niveau du microbiote intestinal humain, nous avons structuré un catalogue de 3,9 millions de gènes de la flore intestinale humaine en 741 unités ou « clusters » correspondant à des génomes de bactéries, d’archées et d’eucaryotes, que nous appelons espèces métagénomiques (MGS) et 6640 unités correspondant principalement à des génomes de virus, plasmides et divers ilots génomiques comme des CRISPR, que nous appelons unités métagénomiques (MGU). Cette méthode de structuration a ensuite été utilisée pour faciliter des analyses d’associations de la composition de la flore intestinale avec des maladies humaines comme la maladie de Crohn, l’obésité ou le diabète de type 2. Enfin, au niveau des flores alimentaires, nos méthodes ont été utilisées pour constituer un catalogue de 134 génomes d’espèces bactériennes fromagères et caractériser la flore de surface de fromages traditionnels. Ceci nous a permis de détecter la présence de nouvelles bactéries alimentaires, pouvant enrichir la liste des bactéries à possible intérêt technologique dans les produits laitiers fermentés.

La flore microbienne est un ensemble de micro-organismes comme les bactéries, archées, eucaryotes inférieurs et virus, jouant un rôle important dans l’équilibre d’un écosystème. Cette flore reste encore mal définie car en 2012, seules ~30% des micro-organismes de la flore intestinale humaine étaient caractérisés, et moins de 50% des micro-organismes de la flore fromagère traditionnelle étaient caractérisés au niveau fonctionnel. Depuis 2006, les séquenceurs à ADN de seconde génération permettent d’analyser directement le contenu génique d’un prélèvement de flore sans contrainte d’isolement ou de culture. Toutefois, les séquences d’ADN générées ne sont pas structurées en génome et sont hautement fragmentées, freinant considérablement l’analyse et l’exploitation de ces données. Dans ce travail, nous avons développé de nouvelles méthodes dites de métagénomiques quantitatives, car elles permettent de regrouper les courtes séquences d’ADN ayant la même abondance au sein de plusieurs échantillons métagénomiques, pouvant provenir d’une même espèce microbienne.Au niveau du microbiote intestinal humain, nous avons structuré un catalogue de 3,9 millions de gènes de la flore intestinale humaine en 741 unités ou « clusters » correspondant à des génomes de bactéries, d’archées et d’eucaryotes, que nous appelons espèces métagénomiques (MGS) et 6640 unités correspondant principalement à des génomes de virus, plasmides et divers ilots génomiques comme des CRISPR, que nous appelons unités métagénomiques (MGU). Cette méthode de structuration a ensuite été utilisée pour faciliter des analyses d’associations de la composition de la flore intestinale avec des maladies humaines comme la maladie de Crohn, l’obésité ou le diabète de type 2. Enfin, au niveau des flores alimentaires, nos méthodes ont été utilisées pour constituer un catalogue de 134 génomes d’espèces bactériennes fromagères et caractériser la flore de surface de fromages traditionnels. Ceci nous a permis de détecter la présence de nouvelles bactéries alimentaires, pouvant enrichir la liste des bactéries à possible intérêt technologique dans les produits laitiers fermentés., The microbial flora is a micro-organism complex containing for example bacteria, archaea, lower eukaryotes and viruses, which play an important role in ecosystem equilibrium. This flora remains poorly defined as in 2012, only ~30% of the intestinal flora micro-organisms have been characterized, and less than 50% of traditional cheese floras were characterized at the functional level. Since 2006, the second generation of DNA sequencers have allowed the direct analysis of the genetic content from a microbial flora sample without isolation or culture limitation. However, the DNA reads generated are not structured with respect to genomes and also are highly fragmented, slowing down dramatically the exploitation and analysis of these data.In this work, a new methodology based on quantitative metagenomic are described., This allows the clustering of short DNA sequences with the same abundance in multiple metagenomic samples, which should originate from the same microbial species. A 3.9 million gene catalog has been built from the human intestinal tract microbiota and divided into 741 units or clusters corresponding to bacteria, archaea and eukaryote genomes. These have been defined as metagenomic species (MGS) and 6640 units of them corresponds mainly to viral genomes, plasmids and genetic islands like CRISPR, with the sub-name of metagenomic units (MGU). This methodology was then used to facilitate the association analysis of the intestinal flora composition with human diseases such as Crohn’s disease, obesity or type 2 diabetes. Within, the alimentary flora, our methods have also been used to constitute a 134 genomic catalog of cheese bacteria and characterize them from the surface of traditional cheeses. This allowed the detection of new alimentary bacteria, that will enriched the list of bacteria with potential interest for the commercial exploitation of fermented products.

Analysis of 16S ribosomal RNA (rRNA)-encoding gene sequences from gut microbial ecosystems reveals bewildering genetic diversity. Some metabolic functions, such as glucose utilisation, are fairly widespread throughout the genetic spectrum. Others, however, are not. Despite so many phylotypes being present, single species or perhaps only two or three species often carry out key functions. Among ruminal bacteria, only three species can break down highly structured cellulose, despite the prevalence and importance of cellulose in ruminant diets, and one of those species, Fibrobacter succinogenes, is distantly related to the most abundant ruminal species. Fatty acid biohydrogenation in the rumen, particularly the final step of biohydrogenation of C18 fatty acids, stearate formation, is achieved only by a small sub-group of bacteria related to Butyrivibrio fibrisolvens. Individuals who lack Oxalobacter formigenes fail to metabolise oxalate and suffer kidney stones composed of calcium oxalate. Perhaps the most celebrated example of the difference a single species can make is the ‘mimosine story’ in ruminants. Mimosine is a toxic amino acid found in the leguminous plant, Leucaena leucocephala. Mimosine can cause thyroid problems by being converted to the goitrogen, 3-hydroxy-4(1H)-pyridone, in the rumen. Observations that mimosine-containing plants were toxic to ruminants in some countries but not others led to the discovery of Synergistes jonesii, which metabolises 3-hydroxy-4(1H)-pyridone and protects animals from toxicity. Thus, despite the complexities indicated by molecular microbial ecology and genomics, it should never be forgotten that gut communities contain important metabolic niches inhabited by species with highly specific metabolic capability.