Transformation of bile acids by mixed microbial cultures from human feces and bile acid transforming activities of isolated bacterial strains

Ex vivo metabolism kinetics of primary to secondary bile acids via a physiologically relevant human faecal microbiota model

Bile acids (BA) are synthesized in the human liver and undergo metabolism by host gut bacteria. In diseased states, gut microbial dysbiosis may lead to high primary unconjugated BA concentrations and significant perturbations to secondary BA. Hence, it is important to understand the microbial-mediated formation kinetics of secondary bile acids using physiologically relevant ex vivo human faecal microbiota models. Here, we optimized an ex vivo human faecal microbiota model to recapitulate the metabolic kinetics of primary unconjugated BA and applied it to investigate the formation kinetics of novel secondary BA metabolites and their sequential pathways. We demonstrated (1) first-order depletion of primary BA, cholic acid (CA) and chenodeoxycholic acid (CDCA), under non-saturable conditions and (2) saturable Michaelis-Menten kinetics for secondary BA metabolite formation with increasing substrate concentration. Notably, relatively lower Michaelis constants (Km) were associated with the formation of deoxycholic acid (DCA, 14.3 μM) and lithocholic acid (LCA, 140 μM) versus 3-oxo CA (>1000 μM), 7-keto DCA (443 μM) and 7-keto LCA (>1000 μM), thereby recapitulating clinically observed saturation of 7α-dehydroxylation relative to oxidation of primary BA. Congruently, metagenomics revealed higher relative abundance of functional genes related to the oxidation pathway as compared to the 7α-dehydroxylation pathway. In addition, we demonstrated gut microbial-mediated hyocholic acid (HCA) and hyodeoxycholic acid (HDCA) formation from CDCA. In conclusion, we optimized a physiologically relevant ex vivo human faecal microbiota model to investigate gut microbial-mediated metabolism of primary BA and present a novel gut microbial-catalysed two-step pathway from CDCA to HCA and, subsequently, HDCA.

The Hylemon-Björkhem pathway of bile acid 7-dehydroxylation: history, biochemistry, and microbiology

Bile acids are detergents derived from cholesterol that function to solubilize dietary lipids, remove cholesterol from the body, and act as nutrient signaling molecules in numerous tissues with functions in the liver and gut being the best understood. Studies in the early 20th century established the structures of bile acids, and by mid-century, the application of gnotobiology to bile acids allowed differentiation of host-derived "primary" bile acids from "secondary" bile acids generated by host-associated microbiota. In 1960, radiolabeling studies in rodent models led to determination of the stereochemistry of the bile acid 7-dehydration reaction. A two-step mechanism was proposed, which we have termed the Samuelsson-Bergström model, to explain the formation of deoxycholic acid. Subsequent studies with humans, rodents, and cell extracts of Clostridium scindens VPI 12708 led to the realization that bile acid 7-dehydroxylation is a result of a multi-step, bifurcating pathway that we have named the Hylemon-Björkhem pathway. Due to the importance of hydrophobic secondary bile acids and the increasing measurement of microbial bai genes encoding the enzymes that produce them in stool metagenome studies, it is important to understand their origin.

In vitro and in vivo characterization of Clostridium scindens bile acid transformations

The human gut hosts trillions of microorganisms that exert a profound influence on human biology. Gut bacteria communicate with their host by secreting small molecules that can signal to distant organs in the body. Bile acids are one class of these signaling molecules, synthesized by the host and chemically transformed by the gut microbiota. Among bile acid metabolizers, bile acid 7-dehydroxylating bacteria are commensals of particular importance as they carry out the 7-dehydroxylation of liver-derived primary bile acids to 7-dehydroxylated bile acids. The latter represents a major fraction of the secondary bile acid pool. The microbiology of this group of gut microorganisms is understudied and warrants more attention. Here, we detail the bile acid transformations carried out by the 7-dehydroxylating bacterium Clostridium scindens in vitro and in vivo. In vitro, C. scindens exhibits not only 7α-dehydroxylating capabilities but also, the ability to oxidize other hydroxyl groups and reduce ketone groups in primary and secondary bile acids. This study revealed 12-oxolithocholic acid as a major transient product in the 7α-dehydroxylation of cholic acid. Furthermore, the in vivo study included complementing a gnotobiotic mouse line (devoid of the ability to 7-dehydroxylate bile acids) with C. scindens and investigating its colonization dynamics and bile acid transformations. Using NanoSIMS (Nanoscale Secondary Ion Mass Spectrometry), we demonstrate that the large intestine constitutes a niche for C. scindens, where it efficiently 7-dehydroxylates cholic acid to deoxycholic acid. Overall, this work reveals a novel transient species during 7-dehydroxylation as well as provides direct evidence for the colonization and growth of 7-dehydroxylating bacteria in the large intestine.

In Vitro Modeling of Bile Acid Processing by the Human Fecal Microbiota

Bile acids, the products of concerted host and gut bacterial metabolism, have important signaling functions within the mammalian metabolic system and a key role in digestion. Given the complexity of the mega-variate bacterial community residing in the gastrointestinal tract, studying associations between individual bacterial genera and bile acid processing remains a challenge. Here, we present a novel in vitro approach to determine the bacterial genera associated with the metabolism of different primary bile acids and their potential to contribute to inter-individual variation in this processing. Anaerobic, pH-controlled batch cultures were inoculated with human fecal microbiota and treated with individual conjugated primary bile acids (500 μg/ml) to serve as the sole substrate for 24 h. Samples were collected throughout the experiment (0, 5, 10, and 24 h) and the bacterial composition was determined by 16S rRNA gene sequencing and the bile acid signatures were characterized using a targeted ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) approach. Data fusion techniques were used to identify statistical bacterial-metabolic linkages. An increase in gut bacteria associated bile acids was observed over 24 h with variation in the rate of bile acid metabolism across the volunteers (n = 7). Correlation analysis identified a significant association between the Gemmiger genus and the deconjugation of glycine conjugated bile acids while the deconjugation of taurocholic acid was associated with bacteria from the Eubacterium and Ruminococcus genera. A positive correlation between Dorea and deoxycholic acid production suggest a potential role for this genus in cholic acid dehydroxylation. A slower deconjugation of taurocholic acid was observed in individuals with a greater abundance of Parasutterella and Akkermansia. This work demonstrates the utility of integrating compositional (metataxonomics) and functional (metabonomics) systems biology approaches, coupled to in vitro model systems, to study the biochemical capabilities of bacteria within complex ecosystems. Characterizing the dynamic interactions between the gut microbiota and the bile acid pool enables a greater understanding of how variation in the gut microbiota influences host bile acid signatures, their associated functions and their implications for health.

Metabolic and Microbial Modulation of the Large Intestine Ecosystem by Non-Absorbed Diet Phenolic Compounds: A Review

Phenolic compounds represent a diverse group of phytochemicals whose intake is associated with a wide spectrum of health benefits. As consequence of their low bioavailability, most of them reach the large intestine where, mediated by the action of local microbiota, a series of related microbial metabolites are accumulated. In the present review, gut microbial transformations of non-absorbed phenolic compounds are summarized. Several studies have reached a general consensus that unbalanced diets are associated with undesirable changes in gut metabolism that could be detrimental to intestinal health. In terms of explaining the possible effects of non-absorbed phenolic compounds, we have also gathered information regarded their influence on the local metabolism. For this purpose, a number of issues are discussed. Firstly, we consider the possible implications of phenolic compounds in the metabolism of colonic products, such as short chain fatty acids (SCFA), sterols (cholesterol and bile acids), and microbial products of non-absorbed proteins. Due to their being recognized as affective antioxidant and anti-inflammatory agents, the ability of phenolic compounds to counteract or suppress pro-oxidant and/or pro-inflammatory responses, triggered by bowel diseases, is also presented. The modulation of gut microbiota through dietetic maneuvers including phenolic compounds is also commented on. Although the available data seems to assume positive effects in terms of gut health protection, it is still insufficient for solid conclusions to be extracted, basically due to the lack of human trials to confirm the results obtained by the in vitro and animal studies. We consider that more emphasis should be focused on the study of phenolic compounds, particularly in their microbial metabolites, and their power to influence different aspects of gut health.

Dynamic changes of the luminal and mucosa-associated gut microbiota during and after antibiotic therapy with paromomycin

Gut microbiota play a key role in the host's health system. Broad antibiotic therapy is known to disrupt the microbial balance affecting pathogenic as well as host-associated microbes. The aim of the present study was to investigate the influence of antibiotic paromomycin on the luminal and mucosa-associated microbiota at the DNA (abundance) and RNA (potential activity) level as well as to identify possible differences. The influence of antibiotic treatment on intestinal microbiota was investigated in 5 healthy individuals (age range: 20-22 years). All participants received the antibiotic paromomycin for 3 d. Fecal samples as well as sigmoidal biopsies were collected before and immediately after cessation of antibiotic treatment as well as after a recovery phase of 42 d. Compartment- and treatment status-specific indicator operational taxonomic units (OTUs) as well as abundance- and activity-specific patterns were identified by 16S rRNA and 16S rRNA gene amplicon libraries and high-throughput pyrosequencing. Microbial composition of lumen and mucosa were significantly different at the DNA compared to the RNA level. Antibiotic treatment resulted in changes of the microbiota, affecting the luminal and mucosal bacteria in a similar way. Several OTUs were identified as compartment- and/or treatment status-specific. Abundance and activity patterns of some indicator OTUs differed considerably. The study shows fundamental changes in composition of gut microbiota under antibiotic therapy at both the potential activity and the abundance level at different treatment status. It may help to understand the complex processes of gut microbiota changes involved in resilience mechanisms and on development of antibiotic-associated clinical diseases.

Enzymatic routes for the synthesis of ursodeoxycholic acid

Ursodeoxycholic acid, a secondary bile acid, is used as a drug for the treatment of various liver diseases, the optimal dose comprises the range of 8-10mg/kg/day. For industrial syntheses, the structural complexity of this bile acid requires the use of an appropriate starting material as well as the application of regio- and enantio-selective enzymes for its derivatization. Most strategies for the synthesis start from cholic acid or chenodeoxycholic acid. The latter requires the conversion of the hydroxyl group at C-7 from α- into β-position in order to obtain ursodeoxycholic acid. Cholic acid on the other hand does not only require the same epimerization reaction at C-7 but the removal of the hydroxyl group at C-12 as well. There are several bacterial regio- and enantio-selective hydroxysteroid dehydrogenases (HSDHs) to carry out the desired reactions, for example 7α-HSDHs from strains of Clostridium, Bacteroides or Xanthomonas, 7β-HSDHs from Clostridium, Collinsella, or Ruminococcus, or 12α-HSDH from Clostridium or from Eggerthella. However, all these bioconversion reactions need additional steps for the regeneration of the coenzymes. Selected multi-step reaction systems for the synthesis of ursodeoxycholic acid are presented in this review.

Strategies for regeneration of nicotinamide coenzymes emphasizing self-sufficient closed-loop recycling systems

Biocatalytic reduction reactions depending on nicotinamide coenzymes require an additional reaction to regenerate the consumed cofactor. For preparative application the preferred method is the simultaneous coupling of an in situ regeneration reaction. There are different strategically advantageous routes to achieve this goal. The standard method uses a second enzyme and a second co-substrate, for example formate and formate dehydrogenase or glucose and glucose dehydrogenase. Alternatively, a second substrate is employed which is converted by the same enzyme used for the primary reaction. For example, alcohol dehydrogenase catalyzed reactions are often coupled with excess 2-propanol which is oxidized to acetone during the regeneration of NAD(P)H. A third method utilizes a reaction-internal sequence by the direct coupling of an oxidizing and a reducing enzyme reaction. Neither an additional substrate nor a further regenerating enzyme are required for the recycling reaction. This kind of "closed-loop" or "self-sufficient" redox process for cofactor regeneration has been used rarely so far. Its most intriguing advantage is that even redox reactions with unstable precursors can be realized provided that this compound is produced in situ by an opposite redox reaction. This elegant method is applicable in special cases only but increasing numbers of examples have been published during the last years.

Xanthomonas maltophilia CBS 897.97 as a source of new 7beta- and 7alpha-hydroxysteroid dehydrogenases and cholylglycine hydrolase: improved biotransformations of bile acids

The paper reports the partial purification and characterization of the 7beta- and 7alpha-hydroxysteroid dehydrogenases (HSDH) and cholylglycine hydrolase (CGH), isolated from Xanthomonas maltophilia CBS 897.97. The activity of 7beta-HSDH and 7alpha-HSDH in the reduction of the 7-keto bile acids is determined. The affinity of 7beta-HSDH for bile acids is confirmed by the reduction, on analytical scale, to the corresponding 7beta-OH derivatives. A crude mixture of 7alpha- and 7beta-HSDH, in soluble or immobilized form, is employed in the synthesis, on preparative scale, of ursocholic and ursodeoxycholic acids starting from the corresponding 7alpha-derivatives. On the other hand, a partially purified 7beta-HSDH in a double enzyme system, where the couple formate/formate dehydrogenase allows the cofactor recycle, affords 6alpha-fluoro-3alpha, 7beta-dihydroxy-5beta-cholan-24-oic acid (6-FUDCA) by reduction of the corresponding 7-keto derivative. This compound is not obtainable by microbiological route. The efficient and mild hydrolysis of glycinates and taurinates of bile acids with CGH is also reported. Very promising results are also obtained with bile acid containing raw materials.

Rapid and improved method for the determination of bile acids in human feces using MS

A simple method for the determination of bile acids in adult human fecal samples using GC-MS is described. Bile acids are directly extracted from feces by ethanol (95%) containing 0.1 N NaOH. Extracts are purified by passage through a reversed-phase C18 silica cartridge and then analyzed by GC-MS. The present study has shown that lyophilized human feces contain mainly free bile acids, with lithocholic acid (LCA) and deoxycholic acid (DCA) as the major bile acids; however, isomers of LCA and DCA, keto-bile acids, and cholic acid are also present. Any traces of conjugated bile acids are hydrolyzed before the C18 extraction by deconjugating enzymes, which are present in feces and are activated by the addition of water during the homogenization step. Thus, the analysis of fecal bile acids can be performed without the hydrolysis step in less than 4 h in comparison to traditional techniques, which usually require at least 48 h.

Biotransformations on steroid nucleus of bile acids

The bile acids in mammals are all derivatives of 5 beta-cholan-26-oic acid. They represent the major quantitative pathway by which cholesterol is metabolized in the body. This article covers the microbial and enzymatic transformations of free, saturated bile acids, that kept unaltered the C-24 cyclopentane-perhydrophenantrene nucleus. The bile acids that have been considered include the primary cholic and chenodeoxycholic acids, the secondary deoxycholic and lithocholic acids as well as the relevant dehydrocholic, ursocholic and ursodeoxycholic acids. Among the bile acid biotransformations, attention is paid to reactions that lead to pharmaceutically significant compounds. This is the case of 7 alpha-hydroxy epimerization of chenodeoxycholic acid to ursodeoxycholic acid, currently used for cholesterol galistone dissolution therapy and in the treatment of cholestatic liver diseases. Emphasis has placed on reporting reactions that may be of general interest and on the practical aspects of work in the field of biotransformations.

Taurocholic acid adsorption during non-starch polysaccharide fermentation: an in vitro study

The association of radiolabelled taurocholic acid with the solid fraction of a faecal fermentation mixture was measured. A human faecal inoculum was incubated with [24-14C]taurocholic acid and several non-starch polysaccharide sources (pectin, wheat bran, ispaghula (Plantago ovata) husk and seed), glucose or a substrate-free control. Portions of fermentation mixture were taken at 0, 3, 6, 21 and 24 h and centrifuged to acquire a supernatant fraction and a pellet containing the fermentation residue. 14C was measured in supernatant fractions and pellets at all time points. Volatile fatty acids (VFA) were measured at 0 and 24 h to confirm bacterial growth. Radioactivity in the pellet increased over time for all substrates. Glucose resulted in the greatest incorporation of taurocholic acid into the pellet, followed by pectin. At 24 h the proportion of the total radioactivity found in the pellet was 92% for glucose, 79% for pectin, 60% for wheat bran, 59% for ispaghula seed, 53% for ispaghula husk and 26% for the control (mean of duplicates). Glucose and pectin produced the greatest quantity of VFA at 24 h. VFA production was highly correlated with radioactivity in the pellet (r0.976, P < 0.005). These results suggest that the bile acid binding capacity of a faecal culture mixture may be strongly influenced by the fermentability of the available substrate and hence related to bacterial metabolic activity.

Plantago ovata seeds as dietary fibre supplement: physiological and metabolic effects in rats

In rats, the effects of a 4-week supplementation of a fibre-free elemental diet with 100 or 200 g Plantago ovata seeds/kg was compared with that of the husks and wheat bran. The seeds increased faecal fresh weight up to 100%, faecal dry weight up to 50% and faecal water content up to 50%. The husks, at the high concentration only, were more effective and wheat bran less effective. Length and weight of the small intestine were not greatly affected by the seeds, but both variables increased significantly in the large intestine. The husks had more pronounced effects, especially in the small intestine, and wheat bran almost no effect. Faecal bacterial mass as estimated from the 2,6-diaminopimelic acid output was increased to the greatest extent by the seed-containing diet and by the high concentration of husks, but to a lesser extent by wheat bran. Faecal and caecal protein content was enhanced by the seeds and wheat bran, but to a lesser extent by the husks. Total acetate in caecal contents or faeces was highest on the seeds and husks diet and not elevated by wheat bran. Total faecal bile acid excretion was stimulated and beta-glucuronidase (EC 3.2.1.31) activity reduced by both Plantago ovata preparations, but not by wheat bran. Mucosal digestive enzyme activities were inhibited to different degrees by all dietary fibres in the jejunum, and sometimes activated in the ileum. These results suggest that Plantago ovata seeds are a partly-fermentable dietary fibre supplement which increases stool bulk; metabolic and mucosa-protective effects are also probable.

The effect of diet on the mammalian gut flora and its metabolic activities

The review will encompass the following points: A brief introduction to the role of the gut flora in the toxicology of ingested food components, contaminants, and additives, including known pathways of activation and detoxication of foreign compounds and the implication of the flora in enterohepatic circulation of xenobiotics. The advantages and disadvantages of the various methods of studying the gut flora (classical bacteriological techniques, metabolic and enzymological methods) will be critically discussed with special reference to their relevance to dietary, toxicological, and biochemical studies. Sources of nutrients available to the gut flora will be described including host products (mucus, sloughed mucosal cells, hormones, proteins) and exogenous nutrients derived from diet. An account of the problems involved in studies of dietary modification with special reference to the use of stock laboratory animal diets, purified diets, and human dietary studies. The influence of dietary modification on the flora will be assessed on the basis of changes in numbers and types of bacteria and their metabolic activity, drawing on data from human and animal studies. The effects of manipulation of the quantity and quality of protein, fat, and indigestible residues (fiber) of the diet will be described together with their possible implications for toxicity of ingested compounds.

7 alpha-Dehydroxylation of bile acids by resting cells of a Eubacterium lentum-like intestinal anaerobe, strain c-25

7 alpha-Dehydroxylation of cholic acid and chenodeoxycholic acid by whole cells of strain c-25, a Eubacterium lentum-like intestinal anaerobe, was studied. 7 alpha-Dehydroxylase activity was observed only in whole cells grown in the presence of the primary bile acid (cholic acid or chenodeoxycholic acid). Chenodeoxycholic acid was twice as effective as cholic acid as an inducer. Although cells grown in the presence of chenodeoxycholic acid had no significant substrate specificity for the two primary bile acids, cells grown in the presence of cholic acid showed two times greater activity against cholic acid than chenodeoxycholic acid. Exposure of cell suspensions to atmospheric oxygen resulted in little loss of the 7 alpha-dehydroxylase activity. The induced enzyme had an optimal pH range of 7.3 to 7.7. Although adding flavin mononucleotide to the growth medium significantly increased the 7 alpha-dehydroxylation of bile acids without an increase in cell growth, inhibition of the enzyme activity was observed in the resting cell system when flavin mononucleotide was included in the reaction mixture.

7 alpha-Dehydroxylation of bile acids by resting cells of an unidentified, gram-positive, nonsporeforming anaerobic bacterium

Transformation of bile acids by washed whole cells of strain HD-17, an unidentified gram-positive anaerobic bacterium isolated from human feces, was studied. 7 alpha-Dehydroxylase was produced only during adaptive growth on medium containing 7 alpha-hydroxy bile acids. Both the extent of hydroxylation and the state of conjugation of the bile acids had marked effects on the induction of the enzyme, and the order of the enzyme induction was conjugated cholic acid much greater than cholic acid greater than taurochenodeoxycholic acid greater than or equal to chenodeoxycholic acid. The addition of excess glucose to the growth medium appreciably reduced the enzyme level. The induced enzyme required strict anaerobic conditions for activity and had an optimal pH range of 6.5 to 7.5. In contrast with the induction of the enzyme, the induced enzyme showed a low degree of substrate specificity between cholic acid and chenodeoxycholic acid, with some preference for the former. In addition, the organism contained 3 alpha-, 7 alpha-, and 12 alpha-hydroxysteroid dehydrogenases, and the addition of bile acids to the medium somewhat enhanced the production of the oxidoreductases. The dehydrogenations were obviously stimulated by oxygen as a terminal electron acceptor. The organism also contained bile salt hydrolase.

Transformation of bile acids by Eubacterium lentum

A group of fecal isolates identified as Eubacterium lentum elaborated 3 alpha-, 7 alpha-, and 12 alpha-dehydrogenases and also an epimerizing enzyme(s) for the 3 alpha-hydroxy group. The activities of the enzymes, however, were variably manifested according to the kind of bile acid substrate and the oxygen tension under which the reaction occurred.