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The promising next-generation probiotic Faecalibacterium prausnitzii is one of the most abundant acetate-consuming, butyrate-producing bacteria in the healthy human gut. Yet, little is known about how acetate availability affects this bacterium’s gene expression strategies. Here, we show that, in the early stationary phase, F. duncaniae strain A2-165 (previously known as F. prausnitzii) can strongly regulate the expression of metabolic and stress-response genes based on acetate availability. Using RNA-seq, we compared gene expression patterns between two growth phases (late exponential vs. early stationary) and two acetate levels (low: 3 mM vs. high: 23 mM). Remarkably, transcription levels were high for the gene encoding the MAM protein, a pattern that was unaffected by acetate levels. At low-acetate levels, a general stress response was activated, and protein synthesis expression was down-regulated. At high- acetate levels, there was greater expression of genes related to butyrate synthesis and to the importation of B vitamins and iron. Specifically, expression was strongly activated in the case of the feoAABC operon, which encodes a FeoB ferrous iron transporter, but not in the case of the feoABgene, which encodes a second FeoB transporter. RT-PCR revealed that excess ferrous iron repressed feoB gene expression. Finally, we detected FeoB peptides from strain A2-165 in a healthy human fecal metaproteome. In conclusion, we characterized two early stationary lifestyles for F. duncaniae A2-165 that relate to acetate consumption. Through multiomics and targeted approaches, this work highlights the crucial role that the feoAABCoperon might play in iron homeostasis in acetate-rich environments.

The gut microbiota are increasingly considered as a main partner of human health. Metaproteomics enables us to move from the functional potential revealed by metagenomics to the functions actually operating in the microbiome. However, metaproteome deciphering remains challenging. In particular, confident interpretation of a myriad of MS/MS spectra can only be pursued with smart database searches. Here, we compare the interpretation of MS/MS data sets from 48 individual human gut microbiomes using three interrogation strategies of the dedicated Integrated nonredundant Gene Catalog (IGC 9.9 million genes from 1267 individual fecal samples) together with the Homo sapiens database: the classical single-step interrogation strategy and two iterative strategies (in either two or three steps) aimed at preselecting a reduced-sized, more targeted search space for the final peptide spectrum matching. Both iterative searches outperformed the single-step classical search in terms of the number of peptides and protein clusters identified and the depth of taxonomic and functional knowledge, and this was the most convincing with the three-step approach. However, iterative searches do not help in reducing variability of repeated analyses, which is inherent to the traditional data-dependent acquisition mode, but this variability did not affect the hierarchical relationship between replicates and all other samples.

One of the difficulties encountered in the statistical analysis of metaproteomics data is the high proportion of missing values, which are usually treated by imputation. Nevertheless, imputation methods are based on restrictive assumptions regarding missingness mechanisms, namely “at random” or “not at random”. To circumvent these limitations in the context of feature selection in a multi-class comparison, we propose a univariate selection method that combines a test of association between missingness and classes, and a test for difference of observed intensities between classes. This approach implicitly handles both missingness mechanisms. We performed a quantitative and qualitative comparison of our procedure with imputation-based feature selection methods on two experimental data sets, as well as simulated data with various scenarios regarding the missingness mechanisms and the nature of the difference of expression (differential intensity or differential missingness). Whereas we observed similar performances in terms of prediction on the experimental data set, the feature ranking and selection from various imputation-based methods were strongly divergent. We showed that the combined test reaches a compromise by correlating reasonably with other methods, and remains efficient in all simulated scenarios unlike imputation-based feature selection methods.

Every day, up to 1 g of cholesterol, composed of the unabsorbed dietary cholesterol, the biliary cholesterol secretion, and cholesterol of cells sloughed from the intestinal epithelium, enters the colon. All cholesterol arriving in the large intestine can be metabolized by the colonic bacteria. Cholesterol is mainly converted into coprostanol, a non-absorbable sterol that is excreted in the feces. Interestingly, cholesterol-to-coprostanol conversion in human populations is variable, with a majority of high converters and a minority of low or inefficient converters. Two major pathways have been proposed, one involving the direct stereospecific reduction of the Δ5 double bond direct while the indirect pathway involves the intermediate formation of 4-cholelesten-3-one and coprostanone. Despite the fact that intestinal cholesterol conversion was discovered more than a century ago, only a few cholesterol-to-coprostanol-converting bacterial strains have been isolated and characterized. Moreover, the responsible genes were mainly unknown until recently. Interestingly, cholesterol-to-coprostanol conversion is highly regulated by the diet. Finally, this gut bacterial metabolism has been linked to health and disease, and recent evidence suggests it could contribute to lower blood cholesterol and cardiovascular risks.

Intestinal IgA is a key player in host-commensal symbiosis. Sterlin et al. report that human IgAs are microbiota cross-reactive at the clonal level. IgA1 and IgA2 mostly converge toward common gut microbiota targets but possess distinct carbohydrate repertoires., In humans, several grams of IgA are secreted every day in the intestinal lumen. While only one IgA isotype exists in mice, humans secrete IgA1 and IgA2, whose respective relations with the microbiota remain elusive. We compared the binding patterns of both polyclonal IgA subclasses to commensals and glycan arrays and determined the reactivity profile of native human monoclonal IgA antibodies. While most commensals are dually targeted by IgA1 and IgA2 in the small intestine, IgA1+IgA2+ and IgA1−IgA2+ bacteria coexist in the colon lumen, where Bacteroidetes is preferentially targeted by IgA2. We also observed that galactose-α terminated glycans are almost exclusively recognized by IgA2. Although bearing signs of affinity maturation, gut-derived IgA monoclonal antibodies are cross-reactive in the sense that they bind to multiple bacterial targets. Private anticarbohydrate-binding patterns, observed at clonal level as well, could explain these apparently opposing features of IgA, being at the same time cross-reactive and selective in its interactions with the microbiota.

In humans, several grams of IgA are secreted every day in the intestinal lumen. While only one IgA isotype exists in mice, humans secrete IgA1 and IgA2, whose respective relations with the microbiota remain elusive. We compared the binding patterns of both polyclonal IgA subclasses to commensals and glycan arrays and determined the reactivity profile of native human monoclonal IgA antibodies. While most commensals are dually targeted by IgA1 and IgA2 in the small intestine, IgA1+IgA2+ and IgA1-IgA2+ bacteria coexist in the colon lumen, where Bacteroidetes is preferentially targeted by IgA2. We also observed that galactose-α terminated glycans are almost exclusively recognized by IgA2. Although bearing signs of affinity maturation, gut-derived IgA monoclonal antibodies are cross-reactive in the sense that they bind to multiple bacterial targets. Private anticarbohydrate-binding patterns, observed at clonal level as well, could explain these apparently opposing features of IgA, being at the same time cross-reactive and selective in its interactions with the microbiota.

ObjectiveBased on animal models and human studies, there is now strong suspicion that host/microbiota mutualism in the context of gut microbial dysbiosis could influence immunity and multiple sclerosis (MS) evolution. Our goal was to seek evidence of deregulated microbiota-induced systemic immune responses in patients with MS.MethodsWe investigated gut and systemic commensal-specific antibody responses in healthy controls (n = 32), patients with relapsing-remitting MS (n = 30), and individuals with clinically isolated syndromes (CISs) (n = 15). Gut microbiota composition and diversity were compared between controls and patients by analysis of 16S ribosomal ribonucleic acid (rRNA) sequencing. Autologous microbiota and cultivable bacterial strains were used in bacterial flow cytometry assays to quantify autologous serum IgG and secretory IgA responses to microbiota. IgG-bound bacteria were sorted by flow cytometry and identified using 16S rRNA sequencing.ResultsWe show that commensal-specific gut IgA responses are drastically reduced in patients with severe MS, disease severity being correlated with the IgA-coated fecal microbiota fraction (r = −0.647, p < 0.0001). At the same time, IgA-unbound bacteria elicit qualitatively broad and quantitatively increased serum IgG responses in patients with MS and CIS compared with controls (4.1% and 2.5% vs 1.9%, respectively, p < 0.001).ConclusionsGut and systemic microbiota/immune homeostasis are perturbed in MS. Our results argue that defective IgA responses in MS are linked to a breakdown of systemic tolerance to gut microbiota leading to an enhanced triggering of systemic IgG immunity against gut commensals occurring early in MS.

Owing to the growing recognition of the gut microbiota as a main partner of human health, we are expecting that the number of indications for fecal microbiota transplantation (FMT) will increase. Thus, there is an urgent need for standardization of the entire process of fecal transplant production. This study provides a complete standardized procedure to prepare and store live and ready-to-use transplants that meet the standard requirements of good practices to applied use in pharmaceutical industry. We show that, if time before transformation to transplants would exceed 24hours, fresh samples should not be exposed to temperatures above 20°C, and refrigeration at 4°C can be a safe solution. Oxygen-free atmosphere was not necessary and simply removing air above collected samples was sufcient to preserve viability. Transplants prepared in maltodextrin-trehalose solutions, stored in a -80°C standard freezer and then rapidly thawed at 37°C, retained the best revivifcation potential as proven by 16S rRNA profles, metabolomic fngerprints, and fow cytometry assays over a 3-month observation period. Maltodextrin-trehalose containing cryoprotectants were also efcient in preserving viability of lyophilized transplants, either in their crude or purifed form, an option that can be attractive for fecal transplant biobanking and oral formulation. Te human intestinal microbiota ensures several essential functions that support maintenance of health and well-being. One of them is the prevention of colonization with allochtonous microbes including pathogens, also known as barrier efect or competitive exclusion. Tis is dependent on the maintenance of ecological homeostasis of the gut ecosystem1 . Another well-established function of the intestinal microbiota is its contribution to immune maturation and maintenance of a balanced immune tolerance and reactivity. It is mediated by a constant and intimate crosstalk between intestinal microbiota and the gut associated lymphoid tissues2 . Here again, a balanced microbiota-host crosstalk is dependent on the maintenance of ecological homeostasis of the gut ecosystem. In healthy adults, microbiota composition is individual specifc and for a given person, it remains fairly stable over time3 . Upon mild stress such as exposure to specifc nutrients or diverse conditions of modern daily life or clinical practices, including antibiotics, the intestinal microbiota can be temporarily altered but will eventually return to its original composition; it is resilient4 . Nonetheless, marked alterations of dietary habits, environmental exposures, drug therapy or surgical interventions will induce alterations of the intestinal microbiota that may exceed the resilience capacity5,6 and lead to onset of dysbiosis, i.e. distorted intestinal microbiota composition. Dysbiosis is now acknowledged as a common feature of numerous non-infectious diseases of modern societies, which have had a constant increase in incidence since the middle of the past century. Obesity is one of these

International audience; BACKGROUND: Commensals induce local IgA responses essential to the induction of tolerance to gut microbiota, but it remains unclear whether antimicrobiota responses remain confined to the gut.OBJECTIVE: The aim of this study was to investigate systemic and intestinal responses against the whole microbiota under homeostatic conditions and in the absence of IgA.METHODS: We analyzed blood and feces from healthy donors, patients with selective IgA deficiency (SIgAd), and patients with common variable immunodeficiency (CVID). Immunoglobulin-coated bacterial repertoires were analyzed by using combined bacterial fluorescence-activated cell sorting and 16S rRNA sequencing. Bacterial lysates were probed by using Western blot analysis with healthy donor sera.RESULTS: Although absent from the healthy gut, serum antimicrobiota IgG are present in healthy subjects and increased in patients with SIgAd. IgG converges with nonoverlapping secretory IgA specificities to target the same bacteria. Each individual subject targets a diverse microbiota repertoire with a proportion that correlates inversely with systemic inflammation. Finally, intravenous immunoglobulin preparations target CVID gut microbiota much less efficiently than healthy microbiota.CONCLUSION: Secretory IgA and systemic IgG converge to target gut microbiota at the cellular level. SIgAd-associated inflammation is inversely correlated with systemic anticommensal IgG responses, which might serve as a second line of defense. We speculate that patients with SIgAd could benefit from oral IgA supplementation. Our data also suggest that intravenous immunoglobulin preparations can be supplemented with IgG from IgA-deficient patient pools to offer better protection against gut bacterial translocations in patients with CVID.

International audience; Paradoxically, loss of immunoglobulin A (IgA), one of the most abundant antibodies, does not irrevocably lead to severe infections in humans but rather is associated with relatively mild respiratory infections, atopy, and autoimmunity. IgA might therefore also play covert roles, not uniquely associated with control of pathogens. We show that human IgA deficiency is not associated with massive quantitative perturbations of gut microbial ecology. Metagenomic analysis highlights an expected pathobiont expansion but a less expected depletion in some typically beneficial symbionts. Gut colonization by species usually present in the oropharynx is also reminiscent of spatial microbiota disorganization. IgM only partially rescues IgA deficiency because not all typical IgA targets are efficiently bound by IgM in the intestinal lumen. Together, IgA appears to play a nonredundant role at the forefront of the immune/microbial interface, away from the intestinal barrier, ranging from pathobiont control and regulation of systemic inflammation to preservation of commensal diversity and community networks.

SummarySegmented filamentous bacterium (SFB) is a symbiont that drives postnatal maturation of gut adaptive immune responses. In contrast to nonpathogenic E. coli, SFB stimulated vigorous development of Peyer’s patches germinal centers but paradoxically induced only a low frequency of specific immunoglobulin A (IgA)-secreting cells with delayed accumulation of somatic mutations. Moreover, blocking Peyer’s patch development abolished IgA responses to E. coli, but not to SFB. Indeed, SFB stimulated the postnatal development of isolated lymphoid follicles and tertiary lymphoid tissue, which substituted for Peyer’s patches as inductive sites for intestinal IgA and SFB-specific T helper 17 (Th17) cell responses. Strikingly, in mice depleted of gut organized lymphoid tissue, SFB still induced a substantial but nonspecific intestinal Th17 cell response. These results demonstrate that SFB has the remarkable capacity to induce and stimulate multiple types of intestinal lymphoid tissues that cooperate to generate potent IgA and Th17 cell responses displaying only limited target specificity.

Resume Le microbiote intestinal humain, dont la densite atteint son maximum dans le colon distal avec 1011 bacteries par gramme de contenu, est compose de centaines d’especes. Les etudes moleculaires du microbiote fecal dominant ont conduit a la description d’une diversite d’especes qui apparait essentiellement specifique de l’individu sain. Cependant, l’analyse de sa composition en taxa (genres bacteriens et/ou grands groupes phylogenetiques) fait ressortir l’existence de composantes recurrentes, retrouvees chez tous les individus. Les groupes phylogenetiques dominants de la microflore fecale de l’adulte sont Firmicutes, Bacteroidetes et Actinobacteria. Apres une phase de colonisation lors des premiers mois de vie du nouveau-ne, l’ecosysteme microbien intestinal d’un adulte sain possede la capacite a resister aux perturbations exterieures, sans que les mecanismes sous-jacents a cette homeostasie soient encore identifies.

The objective of the present study was to evaluate the impact of a regular consumption of yogurt on the composition and metabolism of the human intestinal microbiota. Adult subjects were selected on the basis of daily food records and divided into two groups: yogurt consumers (at least 200 g yogurt consumed per d,n30); non-consumers (no yogurt,n21). Their faecal microbiota was analysed using molecular methods (in situhybridisation and PCR amplification combined with separation by denaturing gel electrophoresis) and its metabolic characteristics were assessed by measuring glycosidase, β-glucuronidase and reductase activities and profiling SCFA, neutral sterols and bile acids. The yogurt starterLactobacillus delbrueckiissp.bulgaricus(identity confirmed by 16S rRNA sequencing) was detected in 73 % of faecal samples from fermented milk consumersv. 28 % from non-consumers (P = 0·003). In yogurt consumers, the level of Enterobacteriaceae was significantly lower (P = 0·006) and β-galactosidase activity was significantly increased (P = 0·048). In addition, within this group, β-galactosidase activity and theBifidobacteriumpopulation were both positively correlated with the amount of fermented milk ingested (r0·66,P r0·43,P = 0·018, respectively). Apart from these effects, which can be considered beneficial to the host, no other major differences could be detected regarding the composition and metabolic activity of intestinal microbiota.

Ursodeoxycholic acid-producing bacteria are of clinical and industrial interest due to the multiple beneficial effects of this bile acid on human health. This work reports the first isolation of 7-epimerizing bacteria from feces of a healthy volunteer, on the basis of their capacity to epimerize the primary bile acid, chenodeoxycholic acid, to ursodeoxycholic acid. Five isolates were found to be active starting from unconjugated chenodeoxycholic acid and its tauro-conjugated homologue, but none of these strains could epimerize the glyco-conjugated form. Biochemical testing and 16S ribosomal DNA sequencing converged to show that all five isolates were closely related to Clostridium baratii (99% sequence similarity), suggesting that this bacterial species could be responsible at least partially, for this bioconversion in the human gut.

International audience; OBJECTIVE: No Crohn's disease (CD) molecular maker has advanced to clinical use, and independent lines of evidence support a central role of the gut microbial community in CD. Here we explore the feasibility of extracting bacterial protein signals relevant to CD, by interrogating myriads of intestinal bacterial proteomes from a small number of patients and healthy controls. DESIGN: We first developed and validated a workflow-including extraction of microbial communities, two-dimensional difference gel electrophoresis (2D-DIGE), and LC-MS/MS-to discover protein signals from CD-associated gut microbial communities. Then we used selected reaction monitoring (SRM) to confirm a set of candidates. In parallel, we used 16S rRNA gene sequencing for an integrated analysis of gut ecosystem structure and functions. RESULTS: Our 2D-DIGE-based discovery approach revealed an imbalance of intestinal bacterial functions in CD. Many proteins, largely derived from Bacteroides species, were over-represented, while under-represented proteins were mostly from Firmicutes and some Prevotella members. Most overabundant proteins could be confirmed using SRM. They correspond to functions allowing opportunistic pathogens to colonise the mucus layers, breach the host barriers and invade the mucosae, which could still be aggravated by decreased host-derived pancreatic zymogen granule membrane protein GP2 in CD patients. Moreover, although the abundance of most protein groups reflected that of related bacterial populations, we found a specific independent regulation of bacteria-derived cell envelope proteins. CONCLUSIONS: This study provides the first evidence that quantifiable bacterial protein signals are associated with CD, which can have a profound impact on future molecular diagnosis.

We explored the possibility that the biliary protein fraction may support part of the variation in the nucleating activity previously measured in gallbladder biles of pigs. Eighteen gallbladder aspirates freshly obtained from three dietary groups (0, 5, or 10% beta-cyclodextrin) of six pigs were chromatographed to purify their total protein fraction. Proteins were quantified, and analysed through electrophoresis and immunoblotting or enzyme-linked immunosorbent assay for albumin, and five putative effectors of cholesterol crystallisation, mucins, immunoglobulin A, 130 kDa, apolipoprotein A-I, and anionic polypeptide fraction. Each total protein fraction was also assayed for its ability to influence cholesterol precipitation, when added to supersaturated model bile. The current data provided evidence that the cholesterol crystallisation-promoting activity of biliary proteins in model biles increased with the beta-cyclodextrin dietary content. This occurred without any significant change in the total biliary protein content, but was associated with a significant decrease in the concentration of albumin and apolipoprotein A-I, resulting in changes in the overall balance of proteins in bile. Comparison of these results with the crystallisation figures previously obtained from the corresponding native biles led us to conclude that biliary proteins might influence the outcome of the crystallisation process, namely the final crystal concentration at equilibrium, but would not systematically represent a major driving force for determining the velocity of crystal formation in native bile of pigs.

In this study, pigs fed for 3 weeks a well-balanced semi-purified diet enriched with 0.3% cholesterol and 0, 5 or 10% beta-cyclodextrin were proposed as new animal donors of gallbladder bile exhibiting different rates of cholesterol crystallization, in order to gain insight into the early mechanisms underlying cholesterol precipitation in vivo. The appearance and growth of cholesterol crystals were monitored in the incubated freshly collected gallbladder biles through light microscopy and concomitant time-sequential determination of crystallized cholesterol concentration, and interpreted in terms of the composition of the bile.Although the concentration of total lipids and proteins and the relative proportions of bile acids, phospholipids, and cholesterol remained unchanged under beta-cyclodextrin, the cholesterol crystallization increased in the following order: 0105% beta-cyclodextrin. Concomitantly, the proportion of chenodeoxycholic acid in bile, and the hydrophobicity index of the biliary bile acid mixture increased in the following order: 0510% beta-cyclodextrin (the same as reported elsewhere for the decrease in the antinucleating ApoA1), while sn-2 arachidonoyl biliary lecithins were specifically increased with 5% beta-cyclodextrin in the diet.We hypothesized that lecithin molecular species may be the determinant factor in modulating high cholesterol crystallization rates in biles otherwise enriched with hydrophobic bile acids.

The Staphylococcus hyicus lip gene was cloned in Lactococcus lactis . Pancreatic insufficiency was induced by ligation of the pancreatic duct in pigs. In pigs who had undergone pancreatic ligation, the coefficient of fat absorption was higher after consumption of lipase-expressing L. lactis (91.9% ± 3.7%) than that after consumption of the inactive control strain (78.4% ± 2.4%).

Ursodeoxycholic acid (UDCA)-producing bacteria are of clinical and industrial interest due to the multiple beneficial effects of this bile acid on human health. UDCA is the 7β-OH epimer of the primary (i.e. synthesized by the liver) bile acid chenodeoxycholic acid (CDCA). Epimerization proceeds in two subsequent and reversible steps, catalysed by a 7α- and a 7β-hydroxysteroid dehydrogenase (7α- and 7β- HSDH), with 7oxo-lithocholic acid (7oxo-LCA) as the intermediate product. The aim of this study was to test the 7α- and 7β-HSDH activities of anaerobic whole cell cultures of a number of lactic acid bacteria and human intestinal isolates, using CDCA, UDCA and 7oxo- LCA as the substrates. Among 140 strains tested, 21 exhibited at least one of both 7-HSDH activities. 7α-HSDH activity was detected in six strains, 7β-HSDH in nine strains, and both activities in six other strains. All active strains were isolated from normal human and infant faeces. They belonged to the genera Clostridium , Eubacterium and Ruminococcus, whereas no strain of Lactobacillus, Bifidobacterium or Streptococcus was found to be active under our study conditions. The present study therefore revealed, for the first time, a number of normal human intestinal isolates supporting the epimerization of CDCA to UDCA, and further extended our knowledge of those intestinal bacteria which are responsible for 7α- or 7β-HSDH activity.Key words: screening, bile acids, epimerization, intestinal microflora, lactic acid bacteria, probiotics.

Background Peptide spectrum matching (PSM) is the standard method in shotgun proteomics data analysis. It relies on the availability of an accurate and complete sample proteome that is used to make interpretation of the spectra feasible. Although this procedure has proven to be effective in many proteomics studies, the approach has limitations when applied on complex samples of microbial communities, such as those found in the human intestinal tract. Metagenome studies have indicated that the human intestinal microbiome contains over 100 times more genes than the human genome and it has been estimated that this ecosystem contains over 5000 bacterial species. The genomes of the vast majority of these species have not yet been sequenced and hence their proteomes remain unknown. To enable data analysis of shotgun proteomics data using PSM, and circumvent the lack of a defined matched metaproteome, an iterative workflow was developed that is based on a synthetic metaproteome and the developing metagenomic databases that are both representative for but not necessarily originating from the sample of interest. Results Two human fecal samples for which metagenomic data had been collected, were analyzed for their metaproteome using liquid chromatography-mass spectrometry and used to benchmark the developed iterative workflow to other methods. The results show that the developed method is able to detect over 3,000 peptides per fecal sample from the spectral data by circumventing the lack of a defined proteome without naive translation of matched metagenomes and cross-species peptide identification. Conclusions The developed iterative workflow achieved an approximate two-fold increase in the amount of identified spectra at a false discovery rate of 1% and can be applied in metaproteomic studies of the human intestinal tract or other complex ecosystems.

International audience; Fecal water is a complex mixture of various metabolites with a wide range of physicochemical properties and boiling points. The analytical method developed here provides a qualitative and quantitative gas chromatography/mass spectrometry (GC/MS) analysis, with high sensitivity and efficiency, coupled with derivatization of ethyl chloroformate in aqueous medium. The water/ethanol/pyridine ratio was optimized to 12: 6: 1, and a two-step derivatization with an initial pH regulation of 0.1 M sodium bicarbonate was developed. The deionized water exhibited better extraction efficiency for fecal water compounds than did acidified and alkalized water. Furthermore, more amino acids were extracted from frozen fecal samples than from fresh samples based on multivariate statistical analysis and univariate statistical validation on GC/MS data. Method validation by 34 reference standards and fecal water samples showed a correlation coefficient higher than 0.99 for each of the standards, and the limit of detection (LOD) was from 10 to 500 pg on-column for most of the standards. The analytical equipment exhibited excellent repeatability, with the relative standard deviation (RSD) lower than 4% for standards and lower than 7% for fecal water. The derivatization method also demonstrated good repeatability, with the RSD lower than 6.4% for standards (except 3,4-dihydroxyphenylacetic acid) and lower than 10% for fecal water (except dicarboxylic acids). The qualitative means by searching the electron impact (EI) mass spectral database, chemical ionization (CI) mass spectra validation, and reference standards comparison totally identified and structurally confirmed 73 compounds, and the fecal water compounds of healthy humans were also quantified. This protocol shows a promising application in metabolome analysis based on human fecal water samples.

The microbial community in the human colon contains bacteria that reduce cholesterol to coprostanol, but the species responsible for this conversion are still unknown. We describe here the first isolation and characterization of a cholesterol-reducing bacterium of human intestinal origin. Strain D8 was isolated from a 10 −8 dilution of a fresh stool sample provided by a senior male volunteer with a high capacity to reduce luminal cholesterol to coprostanol. Cholesterol-to-coprostanol conversion by strain D8 started on the third day, while cells were in stationary phase, and was almost complete after 7 days. Intermediate products (4-cholesten-3-one and coprostanone) were occasionally observed, suggesting an indirect pathway for cholesterol-to-coprostanol conversion. Resting-cell assays showed that strain D8 could reduce 1.5 μmol of cholesterol/mg bacterial protein/h. Strain D8 was a gram-negative, non-spore-forming, rod-shaped organism identified as a member of the genus Bacteroides closely related to Bacteroides vulgatus , based on its morphological and biochemical characteristics. The 16S rRNA gene sequence of strain D8 was most similar (>99.5%) to those of two isolates of the recently described species Bacteroides dorei . Phylogenetic tree construction confirmed that Bacteroides sp. strain D8 clustered within an independent clade together with these B. dorei strains. Nevertheless, no cholesterol-reducing activity could be detected in cultures of the B. dorei type strain. Based on Bacteroides group-specific PCR-temporal temperature gradient gel electrophoresis, there was no correlation between the presence of a band comigrating with the band of Bacteroides sp. strain D8 and cholesterol conversion in 11 human fecal samples, indicating that this strain is unlikely to be mainly responsible for cholesterol conversion in the human population.

The interactions between dietary fatty acids (FA) and the intestinal microbiota were reviewed, with their possible relationships to colon and breast cancers. Free and esterified FA in the colon are from dietary, endogenous and microbial origin. Their quantity and quality vary according to dietary FA. Some FA but not all are powerful antimicrobial agents, and different bacteria exhibit distinct sensitivity to FA. These data converge to suggest that dietary FA could influence the biodiversity of the intestinal microbiota and its functions. Conversely, bacteria can modify lipid substrates due to their enormous metabolic potential, and several studies demonstrated that dietary FA did influence the nature of the metabolites produced. Some of these, like hydroxylated FA or sn-1,2-diglycerides, have recognized biological activities on the intestinal mucosa, either as surfactants or intracellular messengers. The intestinal microbiota also represents a substantial source of usual and unusual FA whose biological activities remain to be explored. Dietary FA can influence the secretion of bile and bile acids into the duodenum, the bile acid flux and/or concentration into the feces and that of cholesterol and its bacterial products. This is expected to modify the cytotoxicity of the colonic contents which remains to be evaluated under different lipid diets. Lastly, the intestinal microbiota is very efficient in hydrolyzing conjugated endobiotics and xenobiotics, and this favours the reactivation and the enterohepatic circulation of compounds which have been eliminated through the bile. Hormones are especially concerned, and the intestinal microbiota could thus be implicated in breast cancer. Some dietary FA are known to increase bacterial beta-glucuronidases whereas their effect on other bacterial hydrolases or other enzymes capable of modifying the steroid nucleus remains unknown. In conclusion, numerous data suggest that a strong relationship could exist between dietary FA, the intestinal microbiota and the risk of colon and breast cancer. In the same time, data are still fragmentary so that the effects of dietary FA on the overall biodiversity and numerous functions of the intestinal microbiota cannot be hitherto predicted. Future investigations in this field are discussed.

Intensity of the cholesterol-to-coprostanol conversion in the intestine, as assessed by the coprostanol-to-cholesterol ratio in faeces, was found highly variable among 15 human volunteers, ranging from absent to almost complete cholesterol conversion. The number of coprostanoligenic bacteria in the same faecal samples, as estimated by the most probable number method, was found to be less than 10(6) cellsg-1 of fresh stools in the low-to-inefficient converters and at least 10(8) cellsg-1 of fresh stools in the highest converters, indicating that the population level of cultivable faecal coprostanoligenic bacteria correlated with the intensity of cholesterol-to-coprostanol conversion in the human gut. Microbial communities of the samples were profiled by temporal temperature gradient gel electrophoresis (TTGE) of bacterial 16S rRNA gene amplicons. Dendrogram analysis of the TTGE profiles using the Pearson product moment correlation coefficient and a unweighted pair group method with arithmetic averages (UPGMA) algorithm clearly separated banding patterns from low-to-inefficient and high converters in two different clusters suggesting a relationship between TTGE profiles and coprostanoligenic activity. Principal components analysis further demonstrated that a large subset of bands rather than some individual bands contributed to this clustering.

Ursodeoxycholic acid (UDCA)-producing bacteria are of clinical and industrial interest due to the multiple beneficial effects of this bile acid on human health. UDCA is the 7 b -OH epimer of the primary (i.e. synthesized by the liver) bile acid chenodeoxycholic acid (CDCA). Epimerization proceeds in two subsequent and reversible steps, catalysed by a 7 a - and a 7 b -hydroxysteroid dehydrogenase (7 a - and 7 b - HSDH), with 7oxo-lithocholic acid (7oxo-LCA) as the intermediate product. The aim of this study was to test the 7 a - and 7 b -HSDH activities of anaerobic whole cell cultures of a number of lactic acid bacteria and human intestinal isolates, using CDCA, UDCA and 7oxo- LCA as the substrates. Among 140 strains tested, 21 exhibited at least one of both 7-HSDH activities. 7 a -HSDH activity was detected in six strains, 7 b -HSDH in nine strains, and both activities in six other strains. All active strains were isolated from normal human and infant faeces. They belonged to the genera Clostridium , Eubacterium and Ruminococcus , whereas no strain of Lactobacillus , Bifidobacterium or Streptococcus was found to be active under our study conditions. The present study therefore revealed, for the first time, a number of normal human intestinal isolates supporting the epimerization of CDCA to UDCA, and further extended our knowledge of those intestinal bacteria which are responsible for 7 a -or7 b -HSDH activity. Key words: screening, bile acids, epimerization, intestinal microflora, lactic acid bacteria, probiotics.

The objective of the present study was to evaluate the consequence of Camembert consumption on the composition and metabolism of human intestinal microbiota. Camembert cheese was compared with milk fermented by yoghurt starters andLactobacillus caseias a probiotic reference. The experimental model was the human microbiota-associated (HM) rat. HM rats were fed a basal diet (HMB group), a diet containing Camembert made from pasteurised milk (HMCp group) or a diet containing fermented milk (HMfm group). The level of micro-organisms from dairy products was measured in faeces using cultures on a specific medium and PCR–temporal temperature gradient gel electrophoresis. The metabolic characteristics of the caecal microbiota were also studied: SCFA, NH3, glycosidase and reductase activities, and bile acid degradations. The results showed that micro-organisms from cheese comprised 105–108bacteria/g faecal sample in the HMCp group.Lactobacillusspecies from fermented milk were detected in HMfm rats. Consumption of cheese and fermented milk led to similar changes in bacterial metabolism: a decrease in azoreductase activity and NH3concentration and an increase in mucolytic activities. However, specific changes were observed: in HMCp rats, the proportion of ursodeoxycholic resulting from chenodeoxycholic epimerisation was higher; in HMfm rats, α and β-galactosidases were higher than in other groups and both azoreductases and nitrate reductases were lower. The results show that, as for fermented milk, Camembert consumption did not greatly modify the microbiota profile or its major metabolic activities. Ingested micro-organisms were able to survive in part during intestinal transit. These dairy products exert a potentially beneficial influence on intestinal metabolism.

The efficiency of microbial reduction of cholesterol to coprostanol in human gut is highly variable among population and mechanisms remain unexplored. In the present study, we investigated whether microbial communities and their cholesterol metabolism characteristics can be transferred to germ-free rats. Two groups of six, initially germ-free rats were associated with two different human microbiota, exhibiting high and low cholesterol-reducing activities. Four months after inoculation, enumeration of coprostanoligenic bacteria, fecal coprostanol levels and composition of the fecal microbial communities were studied in gnotobiotic rats and compared with those of the human donors. Combination of culture (most probable number enumeration of active bacteria) and biochemical approaches (extraction followed by gas chromatography of sterols) showed that gnotobiotic rats harbored a coprostanoligenic bacterial population level and exhibited coprostanoligenic activities similar to those of the corresponding human donor. On the other hand, molecular approaches (whole-cell hybridization with fluorescently labeled 16S rRNA-targeted oligonucleotide probes, and temporal temperature gradient gel electrophoresis of bacterial 16S rRNA gene amplicons) demonstrated that gnotobiotic rats reproduced a stable microbial community, close to the human donor microbiota at the group or genus levels but different at the dominant species level. These results suggest that the gnotobiotic rat model can be used to explore the still unknown human intestinal microbiota involved in luminal cholesterol metabolism, including regulation of expression of its activity and impact on health.

This study was performed to determine whether erythrocyte and digestive lumenal polyamine concentrations are affected by a soy protein diet when compared to a casein diet. We also determined the effects of these diets on colonic cell proliferation. Sixteen pigs received either a 16% soy protein or casein diet for 25 days. The erythrocyte putrescine was higher in pigs fed the soy protein diet. Significant levels of polyamines were observed in the digestive lumen on both diets. Lumenal putrescine and cadaverine were higher in the proximal colon in the casein group. Lumenal spermidine was higher in the caecum and colon in the soy protein group. No significant differences in the ornithine decarboxylase activity nor in the proliferative cell nuclear antigen labelling index were observed in the colonic mucosa regardless of the regimen. These results indicate that the dietary source of protein induces significant changes in lumenal polyamines in the colon. The physiological effects of these changes need to be further investigated.

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Time-sequential enzymatic determination of cholesterol (CH) crystals harvested by ultrafiltration, and concomitant polarizing light microscopy observations corroborated the striking importance of the bile salts (BS) species in determining CH crystals formation rate from supersaturated model biles incubated in vitro. The more hydrophilic tauroursodeoxycholate, taurohyocholate, glycohyocholate, taurohyodeoxycholate, glycohyodeoxycholate and glyco-3α, hydroxy-6 oxo-5s-cholanate inhibited CH precipitation through the formation of a stabilized liquid-crystalline phase. In contrast, in all hydrophobic systems (taurine (T) and glycine (G) conjugates of cholate (C), deoxycholate (DC) and chenodeoxycholate (CDC)), CH crystals precipitated with time. When crystallized CH concentrations were plotted vs. time, the figures showed a sigmoidal pattern, consistent with the transition from metastable systems to stable equilibrium states. Over the equilibration period, the nucleation kinetics (as inferred from enzymatic measurements) and all crystallization events (as microscopically observed) were both shifted in time, depending on the BS species: they were earliest in CDC systems, then in DC systems, and finally in C systems. In the latter, the delay was clearly due to the formation of a transient labile liquid-crystalline phase. G-conjugation also induced a significant delay in CH precipitation, compared to T-conjugation. At last, maximum crystallized CH concentrations at equilibrium were in the decreasing order: C > CDC > DC and T-conjugates > G-homologues. All data are discussed in connection with BS hydrophobicities, with predictions from the phase equilibria of aqueous biliary lipid systems and with new insights into CH crystal habits.

The high-performance liquid chromatographic separation and quantitation of conjugated bile salts from pig bile is reported. Synthetic standards and bile samples were chromatographed on a C18 reversed phase column using acetonitrile/water/tetrabutyl ammonium phosphate as an isocratic mobile phase at a flow rate of 1 mL/min. Detection of the ion-pairs was at 214 nm. The method permits efficient separation of all conjugated pig biliary bile salts without prior modification or treatment of the samples. Analysis of 12 pig biles showed that 85% of the bile salts are conjugated to glycine. The three main conjugated bile salts were glyco-3 alpha,6 alpha,7 alpha-trihydroxy-5 beta-cholanoic acid (GHC), glyco-3 alpha,7 alpha-dihydroxy-5 beta-cholanoic acid (GCDC), and glyco-3 alpha,6 alpha-dihydroxy-5 beta-cholanoic acid (GHDC). Glyco-3 alpha-hydroxy-6-oxo-5 beta-cholanoic acid (G3 alpha 6oxo), tauro-3 alpha,7 alpha-dihydroxy-5 beta-cholanoic acid (TCDC), tauro-3 alpha,6 alpha,7 alpha-trihydroxy-5 beta-cholanoic acid (THC), and tauro-3 alpha,6 alpha-dihydroxy-5 beta-cholanoic acid (THDC) were found to contribute each for 4 to 5% to the total. An excellent correlation was found between the sum of conjugated bile salts quantitated by high-performance liquid chromatography (HPLC) and values obtained by conventional enzymatic assay. Simplicity, efficiency and relative rapidity of the method render it suitable for routine analyses.

A technique for permanent fistulation of the bile duct, associated with a permanent fistulation of the duodenum allowing continuous reintroduction of the collected bile, was used to investigate the level and daily kinetics of biliary excretion in the conscious pig. Seven Large-White pigs of 45 kg live weight were fistulated. Volumes and total excreted bile salts were measured in hourly samples. Results show that within 24 hrs.the volume of the collected bile was about 2100 ml and the total amount of bile salts about 37 g. The bile excretion (volume and bile salts) was minimum before the morning meal (9:00 a. m.) and the total amount of the excreted bile salts immediately increased after diet intake. Within 2 hrs. after the morning and afternoon meals, values were about 300 p. 100 higher than those determined at 9:00 a. m. This increase was essentially the result of the excretion of a highly concentrated bile (200 to 300 p. 100 more than the values at 9:00 a. m.). On the other hand, the bile volumes were only affected 2 to 3 hrs. after diet intake.

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The aim of this work was to investigate the effects on bile secretion of flow rate and site of reinfusion of the collected bile to the animal. Thirty-two pigs weighing 50 +/- 3 kg at the beginning of the experiment were fitted with a reentrant fistula in the lower common bile duct and in the upper duodenum. Bile collected from the bile duct was reinfused in four different ways (four groups of 8 animals each): into the duodenum or the lower common bile duct at a constant flow rate using a peristaltic pump, or into the duodenum or the lower common bile duct at a rate mimicking the flow rate of the secretion using an automatic apparatus. Reinfusing the bile into the lower common bile duct at a rate mimicking the secretion rate provided a daily bile acid production about 21% higher than the level recorded with the other three methods. This was mainly due to a higher bile acid concentration since the bile flow was only slightly affected by the treatment.

Bile flow, biliary lipids and bile acid pool have been studied in growing pigs adapted to a semipurified diet of 2, 10 or 20% lard. After a 5-day period of apparent digestibility measurement, bile secretion was studied in previously fistulated pigs. The apparent digestibility of lard was maintained at a very high level, whatever quantity of lard was ingested. Daily bile acid output was 49% higher with the 10% lard diet than with the 2% lard diet, whereas no further increase was observed with the 20% lard diet. There was a direct relationship between bile acid output and pool size. Biliary phospholipid output increased by 29.0% between 2 and 10% dietary lard and by 69.5% between 10 and 20% lard. The corresponding rise in biliary cholesterol output was +33% between 2 and 10 or 10 and 20% lard in the diet. A study of biliary kinetics showed that this adaptation of biliary lipid to dietary fat was observed whatever time of the light/dark cycle was considered. These results, together with a recent demonstration of the implication of endogenous phospholipids in fat digestion, suggested that, in the course of biliary lipid adaptation to dietary fat content, biliary phospholipid could act in synergy with bile salt, resulting in the maintenance of excellent dietary fat digestion.

A study of the relationship between bile secretion and nutrition in the pig requires a complete and continuous collection of the bile and its reinfusion to the animal. In most of the studies performed in different species, bile has been directly reinfused into the duodenum, leading to the exclusion of the sphincter of Oddi from the biliary pathway. It has been postulated that such an exclusion could inhibit gallbladder emptying. The aim of the present work was to study postprandial gallbladder emptying in the pig, depending on the site of bile reinfusion, i.e. the duodenum or the lower bile duct. The gallbladder bile was coloured with indocyanine green (ICG) and marker secretion was recorded after a test-meal. The results showed that after meal intake, the gallbladder emptied over a similar period of time and according to similar kinetics, whatever the site of bile reinfusion.