The fate of tetrathionate during the development of a biofilm in biogenic sulfuric acid attack on different cementitious materials

The biodeterioration of cement-based materials in sewer environments occurs because of the production of sulfuric acid from the biochemical oxidation of H₂S by sulfur-oxidizing bacteria (SOB). In the perspective of determining the possible reaction pathways for the sulfur cycle in such conditions, hydrated cementitious binders were exposed to an accelerated laboratory test (BAC test) to reproduce a biochemical attack similar to the one occurring in the sewer networks. Tetrathionate was used as a reduced sulfur source to naturally develop sulfur-oxidizing activities on the surfaces of materials. The transformation of tetrathionate was investigated on materials made from different binders: Portland cement, calcium aluminate cement, calcium sulfoaluminate cement and alkali-activated slag. The pH and the concentration of the different sulfur species were monitored in the leached solutions during 3 months of exposure. The results showed that the formation of different polythionates was independent of the nature of the material. The main parameter controlling the phenomena was the evolution of the pH of the leached solutions. Moreover, tetrathionate disproportionation was detected with the formation of more reduced forms of sulfur compounds (pentathionate, hexathionate and elemental sulfur) along with thiosulfate and sulfate. The experimental findings allowed numerical models to be developed to estimate the amount of sulfur compounds as a function of the pH evolution. In addition, biomass samples were collected from the exposed surface and from the deteriorated layers to identify the microbial populations. No clear influence of the cementitious materials on the selected populations was detected, confirming the previous results concerning the impact of the materials on the selected reaction pathways for tetrathionate transformation.

In Vivo Competitions between Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminoccus albus in a Gnotobiotic Sheep Model Revealed by Multi-Omic Analyses

Fibrobacter succinogenes, Ruminococcus albus, and Ruminococcus flavefaciens are the three predominant cellulolytic bacterial species found in the rumen. In vitro studies have shown that these species compete for adherence to, and growth upon, cellulosic biomass. Yet their molecular interactions in vivo have not heretofore been examined. Gnotobiotically raised lambs harboring a 17-h-old immature microbiota devoid of culturable cellulolytic bacteria and methanogens were inoculated first with F. succinogenes S85 and Methanobrevibacter sp. strain 87.7, and 5 months later, the lambs were inoculated with R. albus 8 and R. flavefaciens FD-1. Longitudinal samples were collected and profiled for population dynamics, gene expression, fibrolytic enzyme activity, in sacco fibrolysis, and metabolite profiling. Quantitative PCR, metagenome and metatranscriptome data show that F. succinogenes establishes at high levels initially but is gradually outcompeted following the introduction of the ruminococci. This shift resulted in an increase in carboxymethyl cellulase (CMCase) and xylanase activities but not in greater fibrolysis, suggesting that F. succinogenes and ruminococci deploy different but equally effective means to degrade plant cell walls. Expression profiles showed that F. succinogenes relied upon outer membrane vesicles and a diverse repertoire of CAZymes, while R. albus and R. flavefaciens preferred type IV pili and either CBM37-harboring or cellulosomal carbohydrate-active enzymes (CAZymes), respectively. The changes in cellulolytics also affected the rumen metabolome, including an increase in acetate and butyrate at the expense of propionate. In conclusion, this study provides the first demonstration of in vivo competition between the three predominant cellulolytic bacteria and provides insight on the influence of these ecological interactions on rumen fibrolytic function and metabolomic response.IMPORTANCE Ruminant animals, including cattle and sheep, depend on their rumen microbiota to digest plant biomass and convert it into absorbable energy. Considering that the extent of meat and milk production depends on the efficiency of the microbiota to deconstruct plant cell walls, the functionality of predominant rumen cellulolytic bacteria, Fibrobacter succinogenes, Ruminococcus albus, and Ruminococcus flavefaciens, has been extensively studied in vitro to obtain a better knowledge of how they operate to hydrolyze polysaccharides and ultimately find ways to enhance animal production. This study provides the first evidence of in vivo competitions between F. succinogenes and the two Ruminococcus species. It shows that a simple disequilibrium within the cellulolytic community has repercussions on the rumen metabolome and fermentation end products. This finding will have to be considered in the future when determining strategies aiming at directing rumen fermentations for animal production.

Procyanidin-Cell Wall Interactions within Apple Matrices Decrease the Metabolization of Procyanidins by the Human Gut Microbiota and the Anti-Inflammatory Effect of the Resulting Microbial Metabolome In Vitro

B-type oligomeric procyanidins in apples constitute an important source of polyphenols in the human diet. Their role in health is not known, although it is suggested that they generate beneficial bioactive compounds upon metabolization by the gut microbiota. During apple processing, procyanidins interact with cell-wall polysaccharides and form stable complexes. These interactions need to be taken into consideration in order to better assess the biological effects of fruit constituents. Our objectives were to evaluate the impact of these interactions on the microbial metabolization of cell walls and procyanidins, and to investigate the potential anti-inflammatory activity of the resulting metabolome, in addition to analyzing the taxonomical changes which the microbiota undergo. In vitro fermentation of three model apple matrices with microbiota from 4 healthy donors showed that the binding of procyanidins to cell-wall polysaccharides, whether covalently or non-covalently, substantially reduced procyanidin degradation. Although cell wall-unbound procyanidins negatively affected carbohydrate fermentation, they generated more hydroxyphenylvaleric acid than bound procyanidins, and increased the abundance of Adlercreutzia and Gordonibacter genera. The best results in terms of production of anti-inflammatory bioactive metabolites were observed from the apple matrix with no bonds between procyanidins and cell wall polysaccharides, although the matrix with non-covalent bonds was not far behind.

Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet

Ruminants have a unique ability to derive energy from the degradation of plant polysaccharides through the activity of the rumen microbiota. Although this process is well studied in vitro, knowledge gaps remain regarding the relative contribution of the microbiota members and enzymes in vivo. The present study used RNA-sequencing to reveal both the expression of genes encoding carbohydrate-active enzymes (CAZymes) by the rumen microbiota of a lactating dairy cow and the microorganisms forming the fiber-degrading community. Functional analysis identified 12,237 CAZymes, accounting for 1% of the transcripts. The CAZyme profile was dominated by families GH94 (cellobiose-phosphorylase), GH13 (amylase), GH43 and GH10 (hemicellulases), GH9 and GH48 (cellulases), PL11 (pectinase) as well as GH2 and GH3 (oligosaccharidases). Our data support the pivotal role of the most characterized fibrolytic bacteria (Prevotella, Ruminocccus and Fibrobacter), and highlight a substantial, although most probably underestimated, contribution of fungi and ciliate protozoa to polysaccharide degradation. Particularly these results may motivate further exploration of the role and the functions of protozoa in the rumen. Moreover, an important part of the fibrolytic bacterial community remains to be characterized since one third of the CAZyme transcripts originated from distantly related strains. These findings are used to highlight limitations of current metatranscriptomics approaches to understand the functional rumen microbial community and opportunities to circumvent them.

Xylan degradation by the human gut Bacteroides xylanisolvens XB1A(T) involves two distinct gene clusters that are linked at the transcriptional level

BACKGROUND

Plant cell wall (PCW) polysaccharides and especially xylans constitute an important part of human diet. Xylans are not degraded by human digestive enzymes in the upper digestive tract and therefore reach the colon where they are subjected to extensive degradation by some members of the symbiotic microbiota. Xylanolytic bacteria are the first degraders of these complex polysaccharides and they release breakdown products that can have beneficial effects on human health. In order to understand better how these bacteria metabolize xylans in the colon, this study was undertaken to investigate xylan breakdown by the prominent human gut symbiont Bacteroides xylanisolvens XB1A(T).

RESULTS

Transcriptomic analyses of B. xylanisolvens XB1A(T) grown on insoluble oat-spelt xylan (OSX) at mid- and late-log phases highlighted genes in a polysaccharide utilization locus (PUL), hereafter called PUL 43, and genes in a fragmentary remnant of another PUL, hereafter referred to as rPUL 70, which were highly overexpressed on OSX relative to glucose. Proteomic analyses supported the up-regulation of several genes belonging to PUL 43 and showed the important over-production of a CBM4-containing GH10 endo-xylanase. We also show that PUL 43 is organized in two operons and that the knockout of the PUL 43 sensor/regulator HTCS gene blocked the growth of the mutant on insoluble OSX and soluble wheat arabinoxylan (WAX). The mutation not only repressed gene expression in the PUL 43 operons but also repressed gene expression in rPUL 70.

CONCLUSION

This study shows that xylan degradation by B. xylanisolvens XB1A(T) is orchestrated by one PUL and one PUL remnant that are linked at the transcriptional level. Coupled to studies on other xylanolytic Bacteroides species, our data emphasize the importance of one peculiar CBM4-containing GH10 endo-xylanase in xylan breakdown and that this modular enzyme may be used as a functional marker of xylan degradation in the human gut. Our results also suggest that B. xylanisolvens XB1A(T) has specialized in the degradation of xylans of low complexity. This functional feature may provide a niche to all xylanolytic bacteria harboring similar PULs. Further functional and ecological studies on fibrolytic Bacteroides species are needed to better understand their role in dietary fiber degradation and their impact on intestinal health.

Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis

Background

Diet and particularly dietary fibres have an impact on the gut microbiome and play an important role in human health and disease. Pectin is a highly consumed dietary fibre found in fruits and vegetables and is also a widely used additive in the food industry. Yet there is no information on the effect of pectin on the human gut microbiome. Likewise, little is known on gut pectinolytic bacteria and their enzyme systems. This study was undertaken to investigate the mechanisms of pectin degradation by the prominent human gut symbiont Bacteroides xylanisolvens.

Results

Transcriptomic analyses of B. xylanisolvens XB1A grown on citrus and apple pectins at mid- and late-log phases highlighted six polysaccharide utilization loci (PUL) that were overexpressed on pectin relative to glucose. The PUL numbers used in this report are those given by Terrapon et al. (Bioinformatics 31(5):647-55, 2015) and found in the PUL database: http://www.cazy.org/PULDB/. Based on their CAZyme composition, we propose that PUL 49 and 50, the most overexpressed PULs on both pectins and at both growth phases, are involved in homogalacturonan (HG) and type I rhamnogalacturonan (RGI) degradation, respectively. PUL 13 and PUL 2 could be involved in the degradation of arabinose-containing side chains and of type II rhamnogalacturonan (RGII), respectively. Considering that HG is the most abundant moiety (>70 %) within pectin, the importance of PUL 49 was further investigated by insertion mutagenesis into the susC-like gene. The insertion blocked transcription of the susC-like and the two downstream genes (susD-like/FnIII). The mutant showed strong growth reduction, thus confirming that PUL 49 plays a major role in pectin degradation.

Conclusion

This study shows the existence of six PULs devoted to pectin degradation by B. xylanisolvens, one of them being particularly important in this function. Hence, this species deploys a very complex enzymatic machinery that probably reflects the structural complexity of pectin. Our findings also highlight the metabolic plasticity of B. xylanisolvens towards dietary fibres that contributes to its competitive fitness within the human gut ecosystem. Wider functional and ecological studies are needed to understand how dietary fibers and especially plant cell wall polysaccharides drive the composition and metabolism of the fibrolytic and non-fibrolytic community within the gut microbial ecosystem.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2472-1) contains supplementary material, which is available to authorized users.

Bacterial protein signals are associated with Crohn's disease

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.

Bacteroides sp. strain D8, the first cholesterol-reducing bacterium isolated from human feces

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 mumol 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.

Influence of Camembert consumption on the composition and metabolism of intestinal microbiota: a study in human microbiota-associated rats

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.

Increasing ursodeoxycholic acid in the enterohepatic circulation of pigs through the administration of living bacteria

We investigated the feasibility of increasing ursodeoxycholic acid (UDCA) in the enterohepatic circulation of pigs by administering living bacteria capable of epimerising endogenous amidated chenodeoxycholic acid (CDCA) to UDCA. We first demonstrated that combining Bifidobacterium animalis DN-173 010, as a bile salt-hydrolysing bacterium, and Clostridium absonum ATCC 27555, as a CDCA to UDCA epimerising bacterium, led to the efficient epimerisation of glyco- and tauro-CDCA in vitro, with respective UDCA yields of 55·8 (se 2·8) and 36·6 (se 1·5)%. This strain combination was then administered to hypercholesterolaemic pigs over a 3-week period, as two daily preprandial doses of either viable (six experimental pigs) or heat-inactivated bacteria (six controls). The main effects of treatment were on unconjugated bile acids (P=0·035) and UDCA (P<0·0001) absorbed into the portal vein, which increased 1·6–1·7- and 3·5–7·5-fold, respectively, under administration of living compared with inactivated bacteria. In bile, UDCA did not increase significantly, but the increase in biliary lithocholic acid with time in the controls was not observed in the experimental pigs (P=0·007), and the same trend was observed in faeces. All other variables (biliary lipid equilibrium, plasma lipid levels and partition of cholesterol between the different lipoprotein classes) remained unaffected by treatment throughout the duration of the experiment. In conclusion, it is feasible to increase the bioavailability of UDCA to the intestine and the liver by administering active bacteria. This may represent an interesting new probiotic activity, provided that in future it could be expressed by a safe food micro-organism.

Composition and metabolism of the intestinal microbiota in consumers and non-consumers of yogurt

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, n 30); non-consumers (no yogurt, n 21). Their faecal microbiota was analysed using molecular methods (in situ hybridisation and PCR amplification combined with separation by denaturing gel electrophoresis) and its metabolic characteristics were assessed by measuring glycosidase, P-glucuronidase and reductase activities and profiling SCFA, neutral sterols and bile acids. The yogurt starter Lactobacillus delbrueckii ssp. bulgaricus (identity confirmed by 16S rRNA sequencing) was detected in 73% of faecal samples from fermented milk consumers v. 28% from non-consumers (P=0.003). In yogurt consumers, the level of Enterobacteriaceae was significantly lower (P=0.006) and 13-galactosidase activity was significantly increased (P=0.048). In addition, within this group, 3-galactosidase activity and the Bifidobacterium population were both positively correlated with the amount of fermented milk ingested (r 0.66, P<0.0001 and r 0.43, 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.

Correlation between faecal microbial community structure and cholesterol-to-coprostanol conversion in the human gut

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.

Bifidobacterium animalis strain DN-173 010 hydrolyses bile salts in the gastrointestinal tract of pigs

BACKGROUND

Bile salt hydrolase (BSH) activity is widespread among ingested bifidobacteria and lactobacilli. It is sometimes considered to be beneficial because of its putative lowering effect on cholesterol absorption and sometimes considered to be deleterious because it may compromise normal fat absorption and even promote the formation of secondary cytotoxic bile acids by the resident intestinal flora. However, the true hydrolysis of bile salts in vivo by ingested living bacteria remains unexplored. The aim of the study was to examine whether or not Bifidobacterium animalis DN-173 010 (used in fermented milks), which demonstrates a BSH activity in vitro, was also active in vivo during its transit in the intestine of pigs.

METHODS

Direct measurement of total and unconjugated bile acids reabsorbed into the portal vein was done, before and after the pigs had been treated for 2 weeks with two daily doses of approximately 3.5 x 10(11) colony-forming units of living (6 pigs) or inactivated B. animalis (6 pigs).

RESULTS

None of the treatments modified the portal serum concentration of total bile acids over a 6-h postprandial period. Unconjugated bile acids represented up to 44% and 53% of total bile acids after 1 and 2 weeks of treatment with living bacteria, respectively, compared with only 25% (P < 0.05) before treatment or after 1 or 2 weeks of treatment with inactivated bacteria.

CONCLUSIONS

Living B. animalis DN-173 010 exhibited a BSH activity in the gastrointestinal tract of pigs, most probably in the small bowel. There was no sign of increased formation of secondary bile acids beyond the hydrolysis reaction.

Epimerization of chenodeoxycholic acid to ursodeoxycholic acid by Clostridium baratii isolated from human feces

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.

Xylanase and beta-glucanase supplementation improve conjugated bile acid fraction in intestinal contents and increase villus size of small intestine wall in broiler chickens fed a rye-based diet

This study was performed with growing chickens (4 to 22 d of age) to evaluate the effects of feeding a rye-based diet supplemented with commercial enzyme preparation containing xylanase and beta-glucanase (Quatrazyme HP, Nutri-Tomen, France) on small intestine wall morphology, bile acid composition, nutrient digestibility, and bird performance compared with unsupplemented rye- or corn-based diets. The rye-based diet decreased (P < or = 0.05) weight gain, feed intake, and feed efficiency and increased water intake compared with the corn-based diet. Moreover, rye consumption reduced crude fat and protein digestibility as well as apparent metabolizable energy (P < or = 0.05). The small intestine wall showed that villus length, width, and surface were decreased in broiler chickens fed the rye-based diet compared with those fed the corn-based diet. However, crypt morphometry parameters were not affected by diet type. The concentration of conjugated bile acids in the small intestine contents of broiler chickens fed the rye-based diet was decreased (P < or = 0.05) compared with those fed the corn-based diet. These findings suggest that feeding a rye-based diet reduces villus capacity for nutrient absorption and bile acid capacity for fat solubilization and emulsification, resulting in decreased bird performance. The addition of xylanase and beta-glucanase to the rye-based diet improved (P < or = 0.05) weight gain, feed intake, and feed efficiency, and decreased water intake. The digestibility of nutrients and apparent metabolizable energy were also increased (P < or = 0.05). Addition of xylanase and beta-glucanase increased (P < or = 0.05) villus size and the villus height-to-crypt depth ratio, as well as the concentration of conjugated bile acids (P < or = 0.05) in the small intestine contents. Exogenous enzymes improved nutrient digestibility and broiler chicken performance, probably by improving the absorption capacity ofthe small intestine through increased villus surface and intestinal concentration of conjugated bile acids.