Oligonucleotide probes that detect quantitatively significant groups of butyrate-producing bacteria in human feces

The abundance of fecal Faecalibacterium prausnitzii in relation to obesity and gender in Chinese adults

The influence of gender and obesity on the abundance of human colonic Feacalibacterium prausnitzii is currently unclear. We collected fecal samples from 54 obese and 54 sex- and age-matched normal-weight Chinese adults and quantified the fecal F. prausnitzii as percentage of 16S rRNA gene copies of F. prausnitzii accounting to that of total gut bacteria with quantitative PCR. The fecal F. prausnitzii amount was not significantly different between obese and lean subjects. Men possessed significantly lower level of fecal F. prausnitzii than women, and the significant and positive correlation of fecal F. prausnitzii quantity with fasting glucose level was observed in men, not in women. Our results suggest that the gender effect, in addition to other factors including the geographic location, ethnicity, diet and gut transit times of study subjects, has to be considered when studying the relationship between gut F. prausnitzii and diseases.

Association of dietary type with fecal microbiota in vegetarians and omnivores in Slovenia

PURPOSE

The purpose of this study was to discover differences in the human fecal microbiota composition driven by long-term omnivore versus vegan/lacto-vegetarian dietary pattern. In addition, the possible association of demographic characteristics and dietary habits such as consumption of particular foods with the fecal microbiota was examined.

METHODS

This study was conducted on a Slovenian population comprising 31 vegetarian participants (11 lacto-vegetarians and 20 vegans) and 29 omnivore participants. Bacterial DNA was extracted from the frozen fecal samples by Maxwell 16 Tissue DNA Purification Kit (Promega). Relative quantification of selected bacterial groups was performed by real-time PCR. Differences in fecal microbiota composition were evaluated by PCR-DGGE fingerprinting of the V3 16S rRNA region. Participants' demographic characteristics, dietary habits and health status information were collected through a questionnaire.

RESULTS

Vegetarian diet was associated with higher ratio (% of group-specific DNA in relation to all bacterial DNA) of Bacteroides-Prevotella, Bacteroides thetaiotaomicron, Clostridium clostridioforme and Faecalibacterium prausnitzii, but with lower ratio (%) of Clostridium cluster XIVa. Real-time PCR also showed a higher concentration and ratio of Enterobacteriaceae (16S rDNA copies/g and %) in female participants (p < 0.05 and p < 0.01) and decrease in Bifidobacterium with age (p < 0.01). DGGE analysis of the 16S rRNA V3 region showed that relative quantity of DGGE bands from certain bacterial groups was lower (Bifidobacterium, Streptococus, Collinsella and Lachnospiraceae) or higher (Subdoligranulum) among vegetarians, indicating the association of dietary type with bacterial community composition. Sequencing of selected DGGE bands revealed the presence of common representatives of fecal microbiota: Bacteroides, Eubacterium, Faecalibacterium, Ruminococcaceae, Bifidobacterium and Lachnospiraceae. Up to 4 % of variance in microbial community analyzed by DGGE could be explained by the vegetarian type of diet.

CONCLUSIONS

Long-term vegetarian diet contributed to quantity and associated bacterial community shifts in fecal microbiota composition. Consumption of foods of animal origin (eggs, red meat, white meat, milk, yoghurt, other dairy products, fish and seafood) and vegetarian type of diet explained the largest share of variance in microbial community structure. Fecal microbiota composition was also associated with participants' age, gender and body mass.

Butyric acid in functional constipation

Butyric acid, a short-chain fatty acid, is a major energy source for colonocytes. It occurs in small quantities in some foods, and in the human body, it is produced in the large intestine by intestinalkacteria. This production can be reduced in some cases, for which butyric acid supplementation may be useful. So far, the use of butyric acid in the treatment of gastrointestinal disorders has been limited because of its specific characteristics such as its rancid smell and rapid absorption in the upper gastrointestinal tract. In the Polish market, sodium butyrate has been recently made available, produced by the modern technology of microencapsulation, which allows the active substance to reach the small and large intestines, where butyrate easily dissociates into butyric acid. This article presents the potential beneficial mechanisms of action of butyric acid in defecation disorders, which are primarily associated with reductions in pain during defecation and inflammation in the gut, among others.

Emerging aspects of food and nutrition on gut microbiota

The human gastrointestinal tract contains a highly complex ecosystem that harbors various microorganisms, which together create a unique environment within each individual. There is growing awareness that dietary habits are one of the essential factors contributing to the microbial diversity and community configuration that ultimately affects human health. From an evolutionary perspective, human dietary history can be viewed as a central factor in the selection of the gut microbial community and stabilization of the mutualistic host-microbial interaction, that together drive host phenotype. Herein, current knowledge concerning the influence of major dietary macrostructure and individual food ingredients is presented. This knowledge will provide perspectives for personalized gut microbiota management and, ultimately, movement toward an era of personalized nutrition and medicine.

Starch structure modulates metabolic activity and gut microbiota profile

Normal maize starch and high amylose maize starch (HAS) either in native or thermally treated forms were used to investigate the effect of starch structure on the production of metabolites and gut microbiota profile using an anaerobic in vitro system. The changes in starch structure during fermentation were investigated using scanning electron microscopy (SEM), high-performance liquid chromatography (HPLC) and Fourier transform infra-red spectroscopy (FTIR). The native normal starch showed a porous structure during fermentation, indicating it was quickly metabolized by gut bacteria, whereas the HAS showed a smooth structure, suggesting it was utilized gradually. HPLC chromatography showed that amylose fraction with low molecular weight (MW) had a higher resistance to be fermented by gut bacteria than other starch molecular fractions. Thermal treatment enhanced starch fermentation kinetics, especially for amylopectin and high MW amylose fractions. FTIR analysis suggests that the structure of the normal starch, either in native or thermally treated, was less organized compared to HAS, and this structural character led to the normal starch to be utilized more quickly by gut bacteria with a faster increase in the IR ratio 1047/1022 cm(-1) (P < 0.01) during fermentation. The measurement of metabolic activity indicates that the normal starch with a less organized structure was utilized faster and generated more acetate and lactate during fermentation; HAS with a highly organized structure was more likely to produce butyrate, corresponding the significant increase (P < 0.001) in the populations of butyrate-producing strains (Faecalibacterium prausnitzii and Eubacterium hallii) in the cultures. This study reveals that fermentation kinetics of starch substrate is one of important characteristics for manipulating gut microbiota fermentation behaviours.

Short-chain fructo-oligosaccharides modulate intestinal microbiota and metabolic parameters of humanized gnotobiotic diet induced obesity mice

Prebiotic fibres like short-chain fructo-oligosaccharides (scFOS) are known to selectively modulate the composition of the intestinal microbiota and especially to stimulate Bifidobacteria. In parallel, the involvement of intestinal microbiota in host metabolic regulation has been recently highlighted. The objective of the study was to evaluate the effect of scFOS on the composition of the faecal microbiota and on metabolic parameters in an animal model of diet-induced obesity harbouring a human-type microbiota. Forty eight axenic C57BL/6J mice were inoculated with a sample of faecal human microbiota and randomly assigned to one of 3 diets for 7 weeks: a control diet, a high fat diet (HF, 60% of energy derived from fat)) or an isocaloric HF diet containing 10% of scFOS (HF-scFOS). Mice fed with the two HF gained at least 21% more weight than mice from the control group. Addition of scFOS partially abolished the deposition of fat mass but significantly increased the weight of the caecum. The analysis of the taxonomic composition of the faecal microbiota by FISH technique revealed that the addition of scFOS induced a significant increase of faecal Bifidobacteria and the Clostridium coccoides group whereas it decreased the Clostridium leptum group. In addition to modifying the composition of the faecal microbiota, scFOS most prominently affected the faecal metabolome (e.g. bile acids derivatives, hydroxyl monoenoic fatty acids) as well as urine, plasma hydrophilic and plasma lipid metabolomes. The increase in C. coccoides and the decrease in C. leptum, were highly correlated to these metabolic changes, including insulinaemia, as well as to the weight of the caecum (empty and full) but not the increase in Bifidobacteria. In conclusion scFOS induce profound metabolic changes by modulating the composition and the activity of the intestinal microbiota, that may partly explain their effect on the reduction of insulinaemia.

Fluctuations in butyrate-producing bacteria in ulcerative colitis patients of North India

AIM: To study the interplay between butyrate concentration and butyrate-producing bacteria in fecal samples of ulcerative colitis (UC) patients vs control individuals.

METHODS: Fecal samples were collected from 14 control individuals (hemorrhoid patients only) and 26 UC patients (severe: n = 12, moderate: n = 6, remission: n = 8), recruited by the gastroenterologist at the Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India. Disease activity in UC patients was determined by clinical colitis activity index. We employed fluorescent in situ hybridization in combination with flow cytometry to enumerate the clostridium cluster population targeted by 16S rRNA gene probe. Major butyrate-producing species within this cluster were quantified to see if any change existed in control vs UC patients with different disease activity. This observed change was further validated by quantitative polymerase chain reaction. In addition to this, we carried out gas chromatography to evaluate the changes in concentration of major short chain fatty acids (SCFAs), namely acetate, n-butyrate, iso-butyrate, in the above samples. Student t test and Graph pad prism-6 were used to compare the data statistically.

RESULTS: There was a significant decrease of Clostridium coccoides (control, 25.69% ± 1.62% vs severe, 9.8% ± 2.4%, P = 0.0001) and Clostridium leptum clusters (control, 13.74% ± 1.05% vs severe, 6.2% ± 1.8%, P = 0.0001) in fecal samples of UC patients. Furthermore, we demonstrated that some butyrate-producing members of the clostridial cluster, like Fecalibacterium prausnitzii (control, 11.66% ± 1.55% vs severe, 6.01% ± 1.6%, P = 0.0001) and Roseburia intestinalis (control, 14.48% ± 1.52% vs severe, 9% ± 1.83%, P = 0.02) were differentially present in patients with different disease activity. In addition, we also demonstrated decreased concentrations of fecal SCFAs, especially of n-butyrate (control, 24.32 ± 1.86 mmol/μL vs severe, 12.74 ± 2.75 mmol/μL, P = 0.003), iso-butyrate (control, 1.70 ± 0.41 mmol/μL vs severe, 0.68 ± 0.24 mmol/μL, P = 0.0441) and acetate (control, 39.51 ± 1.76 mmol/μL vs severe, 32.12 ± 2.95 mmol/μL, P = 0.047), in the fecal samples of UC patients. The observed decrease of predominant butyrate producers of clostridial clusters correlated with the reduced SCFA levels in active UC patients. This was further confirmed by the restoration in the population of some butyrate producers with simultaneous increase in the level of SCFA in remission samples.

CONCLUSION: Our observations indicate that decreases in members of the clostridial cluster resulting in reduced butyrate levels contribute to the etiology of UC.

Analysis of fermentation selectivity of purified galacto-oligosaccharides by in vitro human faecal fermentation

The in vitro fermentation of several purified galacto-oligosaccharides (GOS), specifically the trisaccharides 4'-galactosyl-lactose and 6'-galactosyl-lactose and a mixture of the disaccharides 6-galactobiose and allolactose, was carried out. The bifidogenic effect of GOS at 1% (w/v) was studied in a pH-controlled batch culture fermentation system inoculated with healthy adult human faeces. Results were compared with those obtained with a commercial GOS mixture (Bimuno-GOS). Changes in bacterial populations measured through fluorescence in situ hybridization and short-chain fatty acid (SCFA) production were determined. Bifidobacteria increased after 10-h fermentation for all the GOS substrates, but the changes were only statistically significant (P<0.05) for the mixture of disaccharides and Bimuno-GOS. Acetic acid, whose formation is consistent with bifidobacteria metabolism, was the major SCFA synthesized. The acetate concentration at 10 h was similar with all the substrates (45-50 mM) and significantly higher than the observed for formic, propionic and butyric acids. All the purified GOS could be considered bifidogenic under the assayed conditions, displaying a selectivity index in the range 2.1-3.0, which was slightly lower than the determined for the commercial mixture Bimuno-GOS.

Habitual dietary intake is associated with stool microbiota composition in monozygotic twins

The impact of diet on the gut microbiota has usually been assessed by subjecting people to the same controlled diet and thereafter following the shifts in the microbiota. In the present study, we used habitual dietary intake, clinical data, quantitative polymerase chain reaction, and denaturing gradient gel electrophoresis (DGGE) to characterize the stool microbiota of Finnish monozygotic twins. The effect of diet on the numbers of bacteria was described through a hierarchical linear mixed model that included the twin individuals, stratified by body mass index, and their families as random effects. The abundance and diversity of the bacterial groups studied did not differ between normal-weight, overweight, and obese individuals with the techniques used. Intakes of energy, monounsaturated fatty acids, n3 polyunsaturated fatty acids (PUFAs), n6 PUFAs, and soluble fiber had significant associations with the stool bacterial numbers (e.g., increased energy intake was associated with reduced numbers of Bacteroides spp.). In addition, co-twins with identical energy intake had more similar numbers and DGGE-profile diversities of Bacteroides spp. than did the co-twins with different intake. Moreover, the co-twins who ingested the same amounts of saturated fatty acids had very similar DGGE profiles of Bacteroides spp., whereas the co-twins with similar consumption of fiber had a very low bifidobacterial DGGE-profile similarity. In conclusion, our findings confirm that the diet plays an important role in the modulation of the stool microbiota, in particular Bacteroides spp. and bifidobacteria.

Microbiota and healthy ageing: observational and nutritional intervention studies

Hundred years ago Metchnikoff associated human health and particularly healthy ageing with a specific type of gut microbiota. Classical culture methods associated a decrease in bifidobacteria and an increase in enterobacteria with ageing. Modern molecular methods blurred this simple picture and documented a substantial inter-individual variability for the gut microbiome even when stratifying the elderly subjects according to health status. Nutritional interventions with resistant starch showed consistent gut microbiota changes across studies from different geographical areas and prebiotic supplementation induced a 10-fold increase in gut bifidobacteria. However, in the ELDERMET study, microbiota changes do not precede, but follow the changes in health status of elderly subjects possibly as a consequence of diet changes.

A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community

BACKGROUND

Butyrate, which is produced by the human microbiome, is essential for a well-functioning colon. Bacteria that produce butyrate are phylogenetically diverse, which hinders their accurate detection based on conventional phylogenetic markers. As a result, reliable information on this important bacterial group is often lacking in microbiome research.

RESULTS

In this study we describe a gene-targeted approach for 454 pyrotag sequencing and quantitative polymerase chain reaction for the final genes in the two primary bacterial butyrate synthesis pathways, butyryl-CoA:acetate CoA-transferase (but) and butyrate kinase (buk). We monitored the establishment and early succession of butyrate-producing communities in four patients with ulcerative colitis who underwent a colectomy with ileal pouch anal anastomosis and compared it with three control samples from healthy colons. All patients established an abundant butyrate-producing community (approximately 5% to 26% of the total community) in the pouch within the 2-month study, but patterns were distinctive among individuals. Only one patient harbored a community profile similar to the healthy controls, in which there was a predominance of but genes that are similar to reference genes from Acidaminococcus sp., Eubacterium sp., Faecalibacterium prausnitzii and Roseburia sp., and an almost complete absence of buk genes. Two patients were greatly enriched in buk genes similar to those of Clostridium butyricum and C. perfringens, whereas a fourth patient displayed abundant communities containing both genes. Most butyrate producers identified in previous studies were detected and the general patterns of taxa found were supported by 16S rRNA gene pyrotag analysis, but the gene-targeted approach provided more detail about the potential butyrate-producing members of the community.

CONCLUSIONS

The presented approach provides quantitative and genotypic insights into butyrate-producing communities and facilitates a more specific functional characterization of the intestinal microbiome. Furthermore, our analysis refines but and buk reference annotations found in central databases.

Influence of fermented milk products, prebiotics and probiotics on microbiota composition and health

The gut microbiota is a highly diverse and relative stabile ecosystem increasingly recognized for its impact on human health. The homeostasis of microbes and the host is also referred to as eubiosis. In contrast, deviation from the normal composition, defined as dysbiosis, is often associated with localized diseases such as inflammatory bowel disease or colonic cancer, but also with systemic diseases like metabolic syndrome and allergic diseases. Modulating a gut microbiota dysbiosis with nutritional concepts may contribute to improving health status, reducing diseases or disease symptoms or supporting already established treatments. The gut microbiota can be modulated by different nutritional concepts, varying from specific food ingredients to complex diets or by the ingestion of particular live microorganisms. To underpin the importance of bacteria in the gut, we describe molecular mechanisms involved in the crosstalk between gut bacteria and the human host, and review the impact of different nutritional concepts such as pre-, pro- and synbiotics on the gastrointestinal ecosystem and their potential health benefits. The aim of this review is to provide examples of potential nutritional concepts that target the gut microbiota to support human physiology and potentially health outcomes.

In vitro fermentation of commercial α-gluco-oligosaccharide by faecal microbiota from lean and obese human subjects

The fermentation selectivity of a commercial source of a-gluco-oligosaccharides (BioEcolians; Solabia) was investigated in vitro. Fermentation by faecal bacteria from four lean and four obese healthy adults was determined in anaerobic, pH-controlled faecal batch cultures. Inulin was used as a positive prebiotic control. Samples were obtained at 0, 10, 24 and 36 h for bacterial enumeration by fluorescent in situ hybridisation and SCFA analyses. Gas production during fermentation was investigated in non-pH-controlled batch cultures. a-Gluco-oligosaccharides significantly increased the Bifidobacterium sp. population compared with the control. Other bacterial groups enumerated were unaffected with the exception of an increase in the Bacteroides–Prevotella group and a decrease in Faecalibacterium prausnitzii on both a-gluco-oligosaccharides and inulin compared with baseline. An increase in acetate and propionate was seen on both substrates. The fermentation of a-gluco-oligosaccharides produced less total gas at a more gradual rate of production than inulin. Generally, substrates fermented with the obese microbiota produced similar results to the lean fermentation regarding bacteriology and metabolic activity. No significant difference at baseline (0 h) was detected between the lean and obese individuals in any of the faecal bacterial groups studied.

Anaerostipes hadrus comb. nov., a dominant species within the human colonic microbiota; reclassification of Eubacterium hadrum Moore et al. 1976

Recent molecular analyses suggest that bacteria related to strains SS2/1 and SSC/2, previously reported to be distantly related to Anaerostipes caccae NCIMB 13811(T), represent one of the ten most abundant phylotypes detected in adult human faecal samples. These two strains were isolated as d-lactate-utilizing bacteria from faecal samples of a healthy individual. We show here that they share >99.9% similarity in 16S rRNA gene sequence with a new butyrate-producing isolate recovered from a colonic biopsy of a Crohn's disease patient, and also with the sequence reported recently for Eubacterium hadrum ATCC 29173(T). Biochemical profiling using API Rapid ID 32A and API ZYM test systems confirmed a close phenotypic similarity to E. hadrum ATCC 29173(T), but also indicated that the description of this species should be expanded to include the ability to produce butyrate from d-lactate and acetate. Phylogenetic analysis confirmed an affinity between E. hadrum and members of the genus Anaerostipes (92.3-94.2% sequence similarity) belonging to the family Lachnospiraceae (formerly Clostridium cluster XIVa). Based on phylogenetic, phenotypic and chemotaxonomic evidence it is proposed that E. hadrum be transferred to the genus Anaerostipes with the name Anaerostipes hadrus comb. nov. The type strain of A. hadrus comb. nov. is =ATCC 29173(T) (=DSM 3319(T) = VP 82-52(T)).

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

Background

To understand the relationship between our bacterial microbiome and health, it is essential to define the microbiome in the absence of disease. The digestive tract includes diverse habitats and hosts the human body's greatest bacterial density. We describe the bacterial community composition of ten digestive tract sites from more than 200 normal adults enrolled in the Human Microbiome Project, and metagenomically determined metabolic potentials of four representative sites.

Results

The microbiota of these diverse habitats formed four groups based on similar community compositions: buccal mucosa, keratinized gingiva, hard palate; saliva, tongue, tonsils, throat; sub- and supra-gingival plaques; and stool. Phyla initially identified from environmental samples were detected throughout this population, primarily TM7, SR1, and Synergistetes. Genera with pathogenic members were well-represented among this disease-free cohort. Tooth-associated communities were distinct, but not entirely dissimilar, from other oral surfaces. The Porphyromonadaceae, Veillonellaceae and Lachnospiraceae families were common to all sites, but the distributions of their genera varied significantly. Most metabolic processes were distributed widely throughout the digestive tract microbiota, with variations in metagenomic abundance between body habitats. These included shifts in sugar transporter types between the supragingival plaque, other oral surfaces, and stool; hydrogen and hydrogen sulfide production were also differentially distributed.

Conclusions

The microbiomes of ten digestive tract sites separated into four types based on composition. A core set of metabolic pathways was present across these diverse digestive tract habitats. These data provide a critical baseline for future studies investigating local and systemic diseases affecting human health.

Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome

BACKGROUND

The intestinal microbiota has been implicated in the pathophysiology of irritable bowel syndrome (IBS). Due to the variable resolutions of techniques used to characterize the intestinal microbiota, and the heterogeneity of IBS, the defined alterations of the IBS intestinal microbiota are inconsistent. We analyzed the composition of the intestinal microbiota in a defined subgroup of IBS patients (diarrhea-predominant IBS, D-IBS) using a technique that provides the deepest characterization available for complex microbial communities.

METHODS

Fecal DNA was isolated from 23 D-IBS patients and 23 healthy controls (HC). Variable regions V1-V3 and V6 of the 16S rRNA gene were amplified from all samples. PCR products were sequenced using 454 high throughput sequencing. The composition, diversity and richness of microbial communities were determined and compared between D-IBS and HC using the quantitative insights into microbial ecology pipeline.

KEY RESULTS

The contribution of bacterial groups to the composition of the intestinal microbiota differed between D-IBS and HC. D-IBS patients had significantly higher levels of Enterobacteriaceae (P = 0.03), and lower levels of Fecalibacterium genera (P = 0.04) compared to HC. β-Diversity values demonstrated significantly lower levels of UniFrac distances in HC compared to D-IBS patients. The richness of 16S rRNA sequences was significantly decreased in D-IBS patients (P < 0.04).

CONCLUSIONS & INFERENCES

Our 16S rRNA sequence data demonstrates a community-level dysbiosis in D-IBS. The altered composition of the intestinal microbiota in D-IBS is associated with significant increases in detrimental and decreases in beneficial bacterial groups, and a reduction in microbial richness.

The type and quantity of dietary fat and carbohydrate alter faecal microbiome and short-chain fatty acid excretion in a metabolic syndrome 'at-risk' population

INTRODUCTION AND OBJECTIVES

An obese-type human microbiota with an increased Firmicutes:Bacteroidetes ratio has been described that may link the gut microbiome with obesity and metabolic syndrome (MetS) development. Dietary fat and carbohydrate are modifiable risk factors that may impact on MetS by altering the human microbiome composition. We determined the effect of the amount and type of dietary fat and carbohydrate on faecal bacteria and short chain fatty acid (SCFA) concentrations in people 'at risk' of MetS.

DESIGN

A total of 88 subjects at increased MetS risk were fed a high saturated fat diet (HS) for 4 weeks (baseline), then randomised onto one of the five experimental diets for 24 weeks: HS; high monounsaturated fat (MUFA)/high glycemic index (GI) (HM/HGI); high MUFA/low GI (HM/LGI); high carbohydrate (CHO)/high GI (HC/HGI); and high CHO/low GI (HC/LGI). Dietary intakes, MetS biomarkers, faecal bacteriology and SCFA concentrations were monitored.

RESULTS

High MUFA diets did not affect individual bacterial population numbers but reduced total bacteria and plasma total and LDL-cholesterol. The low fat, HC diets increased faecal Bifidobacterium (P=0.005, for HC/HGI; P=0.052, for HC/LGI) and reduced fasting glucose and cholesterol compared to baseline. HC/HGI also increased faecal Bacteroides (P=0.038), whereas HC/LGI and HS increased Faecalibacterium prausnitzii (P=0.022 for HC/HGI and P=0.018, for HS). Importantly, changes in faecal Bacteroides numbers correlated inversely with body weight (r=-0.64). A total bacteria reduction was observed for high fat diets HM/HGI and HM/LGI (P=0.023 and P=0.005, respectively) and HS increased faecal SCFA concentrations (P<0.01).

CONCLUSION

This study provides new evidence from a large-scale dietary intervention study that HC diets, irrespective of GI, can modulate human faecal saccharolytic bacteria, including bacteroides and bifidobacteria. Conversely, high fat diets reduced bacterial numbers, and in the HS diet, increased excretion of SCFA, which may suggest a compensatory mechanism to eliminate excess dietary energy.

Characterization of the gastrointestinal microbiota in health and inflammatory bowel disease

The enteric bacterial flora play a key role in maintaining health. Inflammatory bowel disease is associated with quantitative and qualitative alterations in the microbiota. Early characterization of the microbiota involved culture-dependent techniques. The advent of metagenomic techniques, however, allows for structural and functional characterization using culture-independent methods. Changes in diversity, together with quantitative alterations in specific bacterial species, have been identified. The functional significance of these changes, and their pathogenic role, remain to be elucidated.

Changes in dominant groups of the gut microbiota do not explain cereal-fiber induced improvement of whole-body insulin sensitivity

BACKGROUND

Diets high in cereal-fiber (HCF) have been shown to improve whole-body insulin sensitivity. In search for potential mechanisms we hypothesized that a supplemented HCF-diet influences the composition of the human gut microbiota and/or biomarkers of colonic carbohydrate fermentation.

METHODS

We performed a randomized controlled 18-week intervention in group-matched overweight participants. Fecal samples of 69 participants receiving isoenergetic HCF (cereal-fiber 43 g/day), or control (cereal-fiber 14 g/day), or high-protein (HP, 28% of energy-intake, cereal-fiber 14 g/day), or moderately high cereal fiber/protein diets (MIX; protein 23% of energy-intake, cereal-fiber 26 g/day) with comparable fat contents were investigated for diet-induced changes of dominant groups of the gut microbiota, and of fecal short-chain fatty-acids (SCFA) including several of their proposed targets, after 0, 6, and 18-weeks of dietary intervention. In vitro fermentation of the cereal fiber extracts as used in the HCF and MIX diets was analyzed using gas chromatography. Diet-induced effects on whole-body insulin-sensitivity were measured using euglycaemic-hyperinsulinemic clamps and re-calculated in the here investigated subset of n = 69 participants that provided sufficient fecal samples on all study days.

RESULTS

Gut microbiota groups and biomarkers of colonic fermentation were comparable between groups at baseline (week 0). No diet-induced differences were detected between groups during this isoenergetic intervention, neither in the full model nor in uncorrected subgroup-analyses. The cereal-fiber extract as used for preparation of the supplements in the HCF and MIX groups did not support in vitro fermentation. Fecal acetate, propionate, and butyrate concentrations remained unchanged, as well as potential targets of increased SCFA, whereas valerate increased after 6-weeks in the HP-group only (p = 0.037). Insulin-sensitivity significantly increased in the HCF-group from week-6 (baseline M-value 3.8 ± 0.4 vs 4.3 ± 0.4 mg·kg-1·min-1, p = 0.015; full model 0-18-weeks, treatment-x-time interaction, p = 0.046).

CONCLUSIONS

Changes in the composition of the gut microbiota and/or markers of colonic carbohydrate fermentation did not contribute explaining the observed early onset and significant improvement of whole-body insulin sensitivity with the here investigated HCF-diet.

TRIAL REGISTRATION

This trial was registered at http://www.clinicaltrials.gov as NCT00579657.

Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth

Faecalibacterium prausnitzii is one of the most abundant commensal bacteria in the healthy human large intestine, but information on genetic diversity and substrate utilization is limited. Here, we examine the phylogeny, phenotypic characteristics, and influence of gut environmental factors on growth of F. prausnitzii strains isolated from healthy subjects. Phylogenetic analysis based on the 16S rRNA sequences indicated that the cultured strains were representative of F. prausnitzii sequences detected by direct analysis of fecal DNA and separated the available isolates into two phylogroups. Most F. prausnitzii strains tested grew well under anaerobic conditions on apple pectin. Furthermore, F. prausnitzii strains competed successfully in coculture with two other abundant pectin-utilizing species, Bacteroides thetaiotaomicron and Eubacterium eligens, with apple pectin as substrate, suggesting that this species makes a contribution to pectin fermentation in the colon. Many F. prausnitzii isolates were able to utilize uronic acids for growth, an ability previously thought to be confined to Bacteroides spp. among human colonic anaerobes. Most strains grew on N-acetylglucosamine, demonstrating an ability to utilize host-derived substrates. All strains tested were bile sensitive, showing at least 80% growth inhibition in the presence of 0.5 μg/ml bile salts, while inhibition at mildly acidic pH was strain dependent. These attributes help to explain the abundance of F. prausnitzii in the colonic community but also suggest factors in the gut environment that may limit its distribution.

High-level dietary fibre up-regulates colonic fermentation and relative abundance of saccharolytic bacteria within the human faecal microbiota in vitro

BACKGROUND

Health authorities around the world advise citizens to increase their intake of foods rich in dietary fibre because of its inverse association with chronic disease. However, a few studies have measured the impact of increasing mixed dietary fibres directly on the composition of the human gut microbiota.

AIMS OF THE STUDY

We studied the impact of high-level mixed dietary fibre intake on the human faecal microbiota using an in vitro three-stage colonic model.

METHODS

The colonic model was maintained on three levels of fibre, a basal level of dietary fibre, typical of a Western-style diet, a threefold increased level and back to normal level. Bacterial profiles and short chain fatty acids concentrations were measured.

RESULTS

High-level dietary fibre treatment significantly stimulated the growth of Bifidobacterium, Lactobacillus-Enterococcus group, and Ruminococcus group (p < 0.05) and significantly increased clostridial cluster XIVa and Faecalibacterium prausnitzii in vessel 1 mimicking the proximal colon (p < 0.05). Total short chain fatty acids concentrations increased significantly upon increased fibre fermentation, with acetate and butyrate increasing significantly in vessel 1 only (p < 0.05). Bacterial species richness changed upon increased fibre supplementation. The microbial community and fermentation output returned to initial levels once supplementation with high fibre ceased.

CONCLUSIONS

This study shows that high-level mixed dietary fibre intake can up-regulate both colonic fermentation and the relative abundance of saccharolytic bacteria within the human colonic microbiota. Considering the important role of short chain fatty acids in regulating human energy metabolism, this study has implications for the health-promoting potential of foods rich in dietary fibres.

In vitro fermentation of linear and alpha-1,2-branched dextrans by the human fecal microbiota

The role of structure and molecular weight in fermentation selectivity in linear α-1,6 dextrans and dextrans with α-1,2 branching was investigated. Fermentation by gut bacteria was determined in anaerobic, pH-controlled fecal batch cultures after 36 h. Inulin (1%, wt/vol), which is a known prebiotic, was used as a control. Samples were obtained at 0, 10, 24, and 36 h of fermentation for bacterial enumeration by fluorescent in situ hybridization and short-chain fatty acid analyses. The gas production of the substrate fermentation was investigated in non-pH-controlled, fecal batch culture tubes after 36 h. Linear and branched 1-kDa dextrans produced significant increases in Bifidobacterium populations. The degree of α-1,2 branching did not influence the Bifidobacterium populations; however, α-1,2 branching increased the dietary fiber content, implying a decrease in digestibility. Other measured bacteria were unaffected by the test substrates except for the Bacteroides-Prevotella group, the growth levels of which were increased on inulin and 6- and 70-kDa dextrans, and the Faecalibacterium prausnitzii group, the growth levels of which were decreased on inulin and 1-kDa dextrans. A considerable increase in short-chain fatty acid concentration was measured following the fermentation of all dextrans and inulin. Gas production rates were similar among all dextrans tested but were significantly slower than that for inulin. The linear 1-kDa dextran produced lower total gas and shorter time to attain maximal gas production compared to those of the 70-kDa dextran (branched) and inulin. These findings indicate that dextrans induce a selective effect on the gut flora, short-chain fatty acids, and gas production depending on their length.

Cross-feeding between bifidobacteria and butyrate-producing colon bacteria explains bifdobacterial competitiveness, butyrate production, and gas production

Inulin-type fructans are not digested and reach the human colon intact, where they are selectively fermented by the colon microbiota, in particular bifidobacteria. As a result, they are converted, directly or indirectly, to short-chain fatty acids and other organic acids, as well as gases, and lead to both bifidogenic and butyrogenic health-promoting effects. Bifidobacteria display phenotypic variation on strain level as to their capacity to degrade inulin-type fructans. Also, different chain lengths of inulin-type fructans may stimulate different subgroups within the bifidobacterial population. The end-metabolites of inulin-type fructan degradation by bifidobacteria reflect their growth rates on these polymers. Other colon bacteria are also able to degrade inulin-type fructans, as is the case for lactobacilli, Bacteroides, certain enterobacteria, and butyrate producers. Bacterial cross-feeding mechanisms in the colon lay at the basis of overall butyrate production, a functional characteristic of several colon bacteria that is always accompanied by gas production. Finally, specificity of polysaccharide use by the colon microbiota may determine diet-induced alterations in the microbiota and consequent metabolic effects.

Adherence and cytokine induction in Caco-2 cells by bacterial populations from a three-stage continuous-culture model of the large intestine

Adherence of bacteria to epithelial cells is an important step in colonization and immune modulation in the large bowel. The aims of this study were to use a three-stage continuous-culture system (CCS) to investigate how environmental factors affect bacterial attachment to Caco-2 cells and modulation of cytokine expression by gut microorganisms, including a probiotic Bifidobacterium longum strain, DD2004. The CCS simulated environmental conditions in the proximal large intestine (vessel 1 [V1]) and distal colon (V2 and V3) at two different system retention times (R) within the range of normal colonic transits (20 and 60 h). The model was inoculated with human fecal material, and fluorescence in situ hybridization (FISH) was used to characterize microbial populations and to assess bacterial attachment to Caco-2 cells. Real-time quantitative PCR (qPCR) was employed to measure cytokine gene expression following challenge with bacteria from different components of the CCS in the presence and absence of B. longum. At an R of 60 h, bacterial adherence increased from V1 to V3, but this trend was reversed at an R of 20 h. Atopobia were the predominant adherent organisms detected at both system retention times in each culture vessel. Modulation of transforming growth factor β1 (TGF-β1), interleukin 6 (IL-6), and IL-18 gene expression by CCS bacteria was marked at an R of 60 h, while at an R of 20 h, IL-4, IL-10, TGF-β2, IL-1α, and tumor necrosis factor alpha (TNF-α) were significantly affected. The addition of B. longum affected cytokine expression significantly at both retention times. This study demonstrates that environmental determinants regulate the adherence properties of intestinal bacteria and their abilities to regulate cytokine synthesis.

Microbiota in pediatric inflammatory bowel disease

OBJECTIVE

To test the hypothesis that compared with controls, children with inflammatory bowel disease (IBD) exhibit differences in the relationships between gut microbiota and disease activity.

STUDY DESIGN

Children and adolescents (n = 69; median age, 14 years) with IBD and 25 healthy controls (median age, 14 years) were recruited for the study. The disease activity was determined according to the Pediatric Ulcerative Colitis Activity Index or the Pediatric Crohn Disease Activity Index. Cell counts of 9 bacterial groups and species in the fecal microbiota were monitored by real-time polymerase chain reaction analysis.

RESULTS

Although no major changes were observed in patients with ulcerative colitis, except for a decrease in bifidobacteria in the active state of IBD, children with active and inactive Crohn's disease (CD) had lower numbers of Faecalibacterium prausnitzii and bifidobacteria (P <.05), and patients with active CD had higher numbers of Escherichia coli (P <.05).

CONCLUSIONS

The microbiota in children with CD is characterized by decreased numbers of F praunsitzii and increased numbers of E coli.

Growth performance and carcass characteristics of broiler chickens fed diets supplemented with graded levels of charcoal from maize cob or seed of Canarium schweinfurthii Engl

Growth performances and carcass characteristics of broiler chickens fed diets supplemented with graded levels of Canarium schweinfurthii Engl seed (charcoal A) or maize cob (charcoal B) were studied using a total of 110 3-week-old male chicks. 11 experimental diets including a control and other containing either 0.2, 0.4, 0.6, 0.8 or 1% charcoal from C. schweinfurthii Engl seed (A(0.2), A(0.4), A(0.6), A(0.8), and A(1%), respectively) or from maize cob (B(0.2), B(0.4), B(0.6), B(0.8), and B(1%), respectively) supplements were used. Each of the diets was fed to ten individually birds caged in a completely randomized design. Results indicated that birds fed 0.2, 0.4, and 0.6% of either charcoal A or B had significantly (P < 0.05) higher final body weights as compared to control birds, while, above 0.6% slightly depressed average final body weights and weight gain. The best growth performance was achieved with 0.2% inclusion of charcoals. There was no significant (P > 0.05) influence of charcoal B on the overall feed intake. Only the B(0.6) feed significantly (P < 0.05) improved feed conversion ratio as compared with the control. Dressing percentage, liver weight and abdominal fat were not significantly (P > 0.05) affected by charcoal. However, there was a significant (P < 0.05) reduction in gizzard weight with charcoal B. Charcoal had no significant (P > 0.05) influence on intestine length and weight. More than 0.6% of charcoal A significantly (P < 0.05) depressed intestine density. It was concluded that under the conditions of this study, charcoal from maize cob or Canarium seeds could be used to improve growth performances and some carcass traits in broiler chickens.

Association between Faecalibacterium prausnitzii and dietary fibre in colonic fermentation in healthy human subjects

The intestinal microbiota are a complex ecosystem influencing the immunoregulation of the human host, providing protection from colonising pathogens and producing SCFA as the main energy source of colonocytes. Our objective was to investigate the effect of dietary fibre exclusion and supplementation on the intestinal microbiota and SCFA concentrations. Faecal samples were obtained from healthy volunteers before and after two 14 d periods of consuming formulated diets devoid or supplemented with fibre (14 g/l). The faecal microbiota were analysed using fluorescent in situ hybridisation and SCFA were measured using GLC. There were large and statistically significant reductions in the numbers of the Faecalibacterium prausnitzii (P < or = 0.01) and Roseburia spp. (P < or = 0.01) groups during both the fibre-free and fibre-supplemented diets. Significant and strong positive correlations between the proportion of F. prausnitzii and the proportion of butyrate during both baseline normal diets were found (pre-fibre free r 0.881, P = 0.001; pre-fibre supplemented r 0.844, P = 0.002). A significant correlation was also found between the proportional reduction in F. prausnitzii and the proportional reduction in faecal butyrate during both the fibre-free (r 0.806; P = 0.005) and the fibre-supplemented diet (r 0.749; P = 0.013). These findings may contribute to the understanding of the association between fibre, microbiota and fermentation in health, during enteral nutrition and in disease states such as Crohn's disease.

Prebiotic effect of fruit and vegetable shots containing Jerusalem artichoke inulin: a human intervention study

The present study aimed to determine the prebiotic effect of fruit and vegetable shots containing inulin derived from Jerusalem artichoke (JA). A three-arm parallel, placebo-controlled, double-blind study was carried out with sixty-six healthy human volunteers (thirty-three men and thirty-three women, age range: 18-50 years). Subjects were randomised into three groups (n 22) assigned to consume either the test shots, pear-carrot-sea buckthorn (PCS) or plum-pear-beetroot (PPB), containing JA inulin (5 g/d) or the placebo. Fluorescent in situ hybridisation was used to monitor populations of total bacteria, bacteroides, bifidobacteria, Clostridium perfringens/histolyticum subgroup, Eubacterium rectale/Clostridium coccoides group, Lactobacillus/Enterococcus spp., Atopobium spp., Faecalibacterium prausnitzii and propionibacteria. Bifidobacteria levels were significantly higher on consumption of both the PCS and PPB shots (10.0 (sd 0.24) and 9.8 (sd 0.22) log10 cells/g faeces, respectively) compared with placebo (9.3 (sd 0.42) log10 cells/g faeces) (P < 0.0001). A small though significant increase in Lactobacillus/Enterococcus group was also observed for both the PCS and PPB shots (8.3 (sd 0.49) and 8.3 (sd 0.36) log10 cells/g faeces, respectively) compared with placebo (8.1 (sd 0.37) log10 cells/g faeces) (P = 0.042). Other bacterial groups and faecal SCFA concentrations remained unaffected. No extremities were seen in the adverse events, medication or bowel habits. A slight significant increase in flatulence was reported in the subjects consuming the PCS and PPB shots compared with placebo, but overall flatulence levels remained mild. A very high level of compliance (>90 %) to the product was observed. The present study confirms the prebiotic efficacy of fruit and vegetable shots containing JA inulin.

Lactate has the potential to promote hydrogen sulphide formation in the human colon

High concentrations of sulphide are toxic for the gut epithelium and may contribute to bowel disease. Lactate is a favoured cosubstrate for the sulphate-reducing colonic bacterium Desulfovibrio piger, as shown here by the stimulation of sulphide formation by D. piger DSM749 by lactate in the presence of sulphate. Sulphide formation by D. piger was also stimulated in cocultures with the lactate-producing bacterium Bifidobacterium adolescentis L2-32. Other lactate-utilizing bacteria such as the butyrate-producing species Eubacterium hallii and Anaerostipes caccae are, however, expected to be in competition with the sulphate-reducing bacteria (SRB) for the lactate formed in the human colon. Strains of E. hallii and A. caccae produced 65% and 96% less butyrate from lactate, respectively, in a coculture with D. piger DSM749 than in a pure culture. In triculture experiments involving B. adolescentis L2-32, up to 50% inhibition of butyrate formation by E. hallii and A. caccae was observed in the presence of D. piger DSM749. On the other hand, sulphide formation by D. piger was unaffected by E. hallii or A. caccae in these cocultures and tricultures. These experiments strongly suggest that lactate can stimulate sulphide formation by SRB present in the colon, with possible consequences for conditions such as colitis.

In vitro kinetics of prebiotic inulin-type fructan fermentation by butyrate-producing colon bacteria: implementation of online gas chromatography for quantitative analysis of carbon dioxide and hydrogen gas production

Kinetic analyses of bacterial growth, carbohydrate consumption, and metabolite production of five butyrate-producing clostridial cluster XIVa colon bacteria grown on acetate plus fructose, oligofructose, inulin, or lactate were performed. A gas chromatography method was set up to assess H2 and CO2 production online and to ensure complete coverage of all metabolites produced. Method accuracy was confirmed through the calculation of electron and carbon recoveries. Fermentations with Anaerostipes caccae DSM 14662(T), Roseburia faecis DSM 16840(T), Roseburia hominis DSM 16839(T), and Roseburia intestinalis DSM 14610(T) revealed similar patterns of metabolite production with butyrate, CO2, and H2 as the main metabolites. R. faecis DSM 16840(T) and R. intestinalis DSM 14610(T) were able to degrade oligofructose, displaying a nonpreferential breakdown mechanism. Lactate consumption was only observed with A. caccae DSM 14662(T). Roseburia inulinivorans DSM 16841(T) was the only strain included in the present study that was able to grow on fructose, oligofructose, and inulin. The metabolites produced were lactate, butyrate, and CO2, without H2 production, indicating an energy metabolism distinct from that of other Roseburia species. Oligofructose degradation was nonpreferential. In a coculture of R. inulinivorans DSM 16841(T) with the highly competitive strain Bifidobacterium longum subsp. longum LMG 11047 on inulin, hardly any production of butyrate and CO2 was detected, indicating a lack of competitiveness of the butyrate producer. Complete recovery of metabolites during fermentations of clostridial cluster XIVa butyrate-producing colon bacteria allowed stoichiometric balancing of the metabolic pathway for butyrate production, including H2 formation.

Effects of a gluten-free diet on gut microbiota and immune function in healthy adult human subjects

Diet influences the composition of the gut microbiota and host's health, particularly in patients suffering from food-related diseases. Coeliac disease (CD) is a permanent intolerance to cereal gluten proteins and the only therapy for the patients is to adhere to a life-long gluten-free diet (GFD). In the present preliminary study, the effects of a GFD on the composition and immune function of the gut microbiota were analysed in ten healthy subjects (mean age 30·3 years) over 1 month. Faecal microbiota was analysed by fluorescencein situhybridisation (FISH) and quantitative PCR (qPCR). The ability of faecal bacteria to stimulate cytokine production by peripheral blood mononuclear cells (PBMC) was determined by ELISA. No significant differences in dietary intake were found before and after the GFD except for reductions (P = 0·001) in polysaccharides.Bifidobacterium,Clostridium lituseburenseandFaecalibacterium prausnitziiproportions decreased (P = 0·007,P = 0·031 andP = 0·009, respectively) as a result of the GFD analysed by FISH.Bifidobacterium,LactobacillusandBifidobacterium longumcounts decreased (P = 0·020,P = 0·001 andP = 0·017, respectively), whileEnterobacteriaceaeandEscherichia colicounts increased (P = 0·005 andP = 0·003) after the GFD assessed by qPCR. TNF-α, interferon-γ, IL-10 and IL-8 production by PBMC stimulated with faecal samples was also reduced (P = 0·021,P = 0·037,P = 0·002 andP = 0·007, respectively) after the diet. Therefore, the GFD led to reductions in beneficial gut bacteria populations and the ability of faecal samples to stimulate the host's immunity. Thus, the GFD may constitute an environmental variable to be considered in treated CD patients for its possible effects on gut health.

Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine

Butyrate-producing bacteria play a key role in colonic health in humans. This review provides an overview of the current knowledge of the diversity, metabolism and microbial ecology of this functionally important group of bacteria. Human colonic butyrate producers are Gram-positive firmicutes, but are phylogenetically diverse, with the two most abundant groups related to Eubacterium rectale/Roseburia spp. and to Faecalibacterium prausnitzii. Five different arrangements have been identified for the genes of the central pathway involved in butyrate synthesis, while in most cases butyryl-CoA : acetate CoA-transferase, rather than butyrate kinase, appears to perform the final step in butyrate synthesis. Mechanisms have been proposed recently in non-gut Clostridium spp. whereby butyrate synthesis can result in energy generation via both substrate-level phosphorylation and proton gradients. Here we suggest that these mechanisms also apply to the majority of butyrate producers from the human colon. The roles of these bacteria in the gut community and their influence on health are now being uncovered, taking advantage of the availability of cultured isolates and molecular methodologies. Populations of F. prausnitzii are reported to be decreased in Crohn's disease, for example, while populations of Roseburia relatives appear to be particularly sensitive to the diet composition in human volunteer studies.

The commensal microbiology of the gastrointestinal tract

The gastrointestinal (GI) tract is a dynamic environment and therefore the stability of the commensal community, or microbiota, is under constant challenge. Microscopic observations have revealed that the majority of bacteria present in the GI tract are not detected using standard culturing techniques, however with the application of culture-independent techniques it has been estimated that between 500 to 1000 bacterial species inhabit the human GI tract. Numerically predominant organisms in the microbiota belong to two eubacterial divisions, the Cytophaga-Flavobacterium-Bacteroides (CFB) and the Firmicutes, and fall into three main groups; Clostridium rRNA subcluster XIVa, Clostridium rRNA subcluster IV and Bacteroides. The prevalence and diversity of bacteria in different areas of the GI tract is influenced by the different conditions at these sites and thus the microbiota of the stomach and jejunum varies with that of the large intestine. Additionally, host genotype, age and diet have all been shown to affect microbial diversity in the GI tract. The distal intestine harbours the highest bacterial cell densities for any known ecosystem. Characterizing the species composition of the healthy microbiota may be a key step in identifying bacterial or associated physiological conditions that are present or absent in an unhealthy microbiota.

In vitro kinetic analysis of fermentation of prebiotic inulin-type fructans by Bifidobacterium species reveals four different phenotypes

Kinetic analyses of bacterial growth, carbohydrate consumption, and metabolite production of 18 Bifidobacterium strains grown on fructose, oligofructose, or inulin were performed. A principal component analysis of the data sets, expanded with the results of a genetic screen concerning the presence of a beta-fructofuranosidase gene previously encountered in Bifidobacterium animalis subsp. lactis DSM 10140(T), revealed the existence of four clusters among the bifidobacteria tested. Strains belonging to a first cluster could not degrade oligofructose or inulin. Strains in a second cluster could degrade oligofructose, displaying a preferential breakdown mechanism, but did not grow on inulin. Fructose consumption was faster than oligofructose degradation. A third cluster was composed of strains that degraded all oligofructose fractions simultaneously and could partially break down inulin. Oligofructose degradation was substantially faster than fructose consumption. A fourth, smaller cluster consisted of strains that shared high fructose consumption and oligofructose degradation rates and were able to perform partial breakdown of inulin. For all strains, a metabolic shift toward more acetate, formate, and ethanol production, at the expense of lactate production, was observed during growth on less readily fermentable energy sources. No correlation between breakdown patterns and the presence of the beta-fructofuranosidase gene could be detected. These variations indicate niche-specific adaptation of bifidobacteria and could have in vivo implications on the strain specificity of the stimulatory effect of inulin-type fructans on bifidobacteria.

Bacterial, archaeal, and eukaryal diversity in the intestines of Korean people

The bacterial, archaeal, and eukaryal diversity in fecal samples from ten Koreans were analyzed and compared by using the PCR-fingerprinting method, denaturing gradient gel electrophoresis (DGGE). The bacteria all belonged to the Firmicutes and Bacteroidetes phyla, which were known to be the dominant bacterial species in the human intestine. Most of the archaeal sequences belonged to the methane-producing archaea but several halophilic archarea-related sequences were also detected unexpectedly. While a small number of eukaryal sequences were also detected upon DGGE analysis, these sequences were related to fungi and stramenopiles (Blastocystis hominis). With regard to the bacterial and archaeal DGGE analysis, all ten samples had one and two prominent bands, respectively, but many individual-specific bands were also observed. However, only five of the ten samples had small eukaryal DGGE bands and none of these bands was observed in all five samples. Unweighted pair group method and arithmetic averages clustering algorithm (UPGMA) clustering analysis revealed that the archaeal and bacterial communities in the ten samples had relatively higher relatedness (the average Dice coefficient values were 68.9 and 59.2% for archaea and bacteria, respectively) but the eukaryal community showed low relatedness (39.6%).

Assessment of metabolic diversity within the intestinal microbiota from healthy humans using combined molecular and cultural approaches

The human gut harbours a wide range of bacterial communities that play key roles in supplying nutrients and energy to the host through anaerobic fermentation of dietary components and host secretions. This fermentative process involves different functional groups of microorganisms linked in a trophic chain. Although the diversity of the intestinal microbiota has been studied extensively using molecular techniques, the functional aspects of this biodiversity remain mostly unexplored. The aim of the present work was to enumerate the principal metabolic groups of microorganisms involved in the fermentative process in the gut of healthy humans. These functional groups of microorganisms were quantified by a cultural approach, while the taxonomic composition of the microbiota was assessed by in situ hybridization on the same faecal samples. The functional groups of microorganisms that predominated in the gut were the polysaccharide-degrading populations involved in the breakdown of the most readily available exogenous and endogenous substrates and the predominant butyrate-producing species. Most of the functional groups of microorganisms studied appeared to be present at rather similar levels in all healthy volunteers, suggesting that optimal numbers of these various bacterial groups are crucial for efficient gut fermentation, as well as for host nutrition and health. Significant interindividual differences were, however, confirmed with respect to the numbers of methanogenic archaea, filter paper-degrading and acetogenic bacteria and the products formed by lactate-utilizing bacteria.

Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea

Although of limited metabolic diversity, methanogenic archaea or methanogens possess great phylogenetic and ecological diversity. Only three types of methanogenic pathways are known: CO(2)-reduction, methyl-group reduction, and the aceticlastic reaction. Cultured methanogens are grouped into five orders based upon their phylogeny and phenotypic properties. In addition, uncultured methanogens that may represent new orders are present in many environments. The ecology of methanogens highlights their complex interactions with other anaerobes and the physical and chemical factors controlling their function.

Effect of inulin on the human gut microbiota: stimulation ofBifidobacterium adolescentisandFaecalibacterium prausnitzii

Prebiotics are food ingredients that improve health by modulating the colonic microbiota. The bifidogenic effect of the prebiotic inulin is well established; however, it remains unclear which species ofBifidobacteriumare stimulatedin vivoand whether bacterial groups other than lactic acid bacteria are affected by inulin consumption. Changes in the faecal microbiota composition were examined by real-time PCR in twelve human volunteers after ingestion of inulin (10 g/d) for a 16-d period in comparison with a control period without any supplement intake. The prevalence of most bacterial groups examined did not change after inulin intake, although the low G+C % Gram-positive speciesFaecalibacterium prausnitziiexhibited a significant increase (10·3 % for control periodv.14·5 % during inulin intake,P = 0·019). The composition of the genusBifidobacteriumwas studied in four of the volunteers by clone library analysis. Between three and fiveBifidobacteriumspp. were found in each volunteer.Bifidobacterium adolescentisandBifidobacterium longumwere present in all volunteers, andBifidobacterium pseudocatenulatum,Bifidobacterium animalis,Bifidobacterium bifidumandBifidobacterium dentiumwere also detected. Real-time PCR was employed to quantify the four most prevalentBifidobacteriumspp.,B. adolescentis,B. longum,B. pseudocatenulatumandB. bifidum, in ten volunteers carrying detectable levels of bifidobacteria.B. adolescentisshowed the strongest response to inulin consumption, increasing from 0·89 to 3·9 % of the total microbiota (P = 0·001).B. bifidumwas increased from 0·22 to 0·63 % (P < 0·001) for the five volunteers for whom this species was present.

Phylotypes related to Ruminococcus bromii are abundant in the large bowel of humans and increase in response to a diet high in resistant starch

To further understand how diets containing high levels of fibre protect against colorectal cancer, we examined the effects of diets high in nonstarch polysaccharides (NSP) or high in NSP plus resistant starch (RS) on the composition of the faecal microbial community in 46 healthy adults in a randomized crossover intervention study. Changes in bacterial populations were examined using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Bacterial profiles demonstrated changes in response to the consumption of both RS and NSP diets [analysis of similarities (ANOSIM): R=0.341-0.507, P<0.01]. A number of different DGGE bands with increased intensity in response to dietary intervention were attributed to as-yet uncultivated bacteria closely related to Ruminococcus bromii. A real-time PCR assay specific to the R. bromii group was applied to faecal samples from the dietary study and this group was found to comprise a significant proportion of the total community when individuals consumed their normal diets (4.4+/-2.6% of total 16S rRNA gene abundance) and numbers increased significantly (+/-67%, P<0.05) with the RS, but not the NSP, dietary intervention. This study indicates that R. bromii-related bacteria are abundant in humans and may be significant in the fermentation of complex carbohydrates in the large bowel.

Isolation of lactate-utilizing butyrate-producing bacteria from human feces and in vivo administration of Anaerostipes caccae strain L2 and galacto-oligosaccharides in a rat model

Lactate-utilizing butyrate-producers were isolated from human feces and identified based on the sequences of 16S rRNA gene. Anaerostipes caccae strain L2, one of the seven human fecal isolates, was administered to rats with galacto-oligosaccharides (GOS) as bifidogenic carbohydrates for stimulating lactate formation in the hindgut. Ingestion of GOS alone increased concentrations of cecal lactate and butyrate compared with control rats (P<0.05). Additional administration of strain L2 on GOS tended to enhance the promoting effect of GOS on cecal butyrate formation (P=0.06) and lowered the mean value of cecal lactate concentration (P=0.32). Consequently, cecal and fecal butyrate concentrations in rats administered with both strain L2 and GOS were significantly higher than those in the control rats (P<0.01 and P<0.05, respectively). Significant changes were observed in the other fermentation acids, such as succinate, acetate, and propionate, depending on the ingestion of strain L2. Administered strain L2 was retrieved from the cecal content of a rat based on randomly amplified polymorphic DNA analysis. The results suggest that synbiotic ingestion of lactate-utilizing butyrate-producers and GOS alters the microbial fermentation and promotes the formation of beneficial fermentation acids, including butyrate, in the gut.

Imbalance in the composition of the duodenal microbiota of children with coeliac disease

Coeliac disease (CD) is the most common immune-mediated enteropathy characterized by chronic inflammation of the small intestinal mucosa. The ingestion of gluten is responsible for the symptoms of CD, but other environmental factors are also thought to play a role in this disorder. In this study, the composition of the duodenal microbiota of coeliac children with active disease, symptom-free CD patients on a gluten-free diet and control children was determined. Bacteriological analyses of duodenal biopsy specimens were carried out by fluorescent in situ hybridization coupled with flow cytometry. The proportions of total bacteria and Gram-negative bacteria were significantly higher in CD patients with active disease than in symptom-free CD patients and controls. Bacteroides and Escherichia coli groups were significantly more abundant in CD patients with active disease than in controls, whilst these bacterial deviations were normalized in symptom-free CD patients. The ratio of Lactobacillus--Bifidobacterium to Bacteroides--E. coli was significantly reduced in coeliac patients with either active or inactive disease compared with controls. The differences in Atopobium, Eubacterium rectale--Clostridium coccoides, Clostridium histolyticum, Clostridium lituseburense, sulphate-reducing bacteria and Faecalibacterium prausnitzii populations among the three groups of children were less relevant. Overall, the higher incidence of Gram-negative and potentially pro-inflammatory bacteria in the duodenal microbiota of coeliac children was linked to the symptomatic presentation of the disease and could favour the pathological process of the disorder.

Understanding the effects of diet on bacterial metabolism in the large intestine

Recent analyses of ribosomal RNA sequence diversity have demonstrated the extent of bacterial diversity in the human colon, and have provided new tools for monitoring changes in the composition of the gut microbial community. There is now an excellent opportunity to correlate ecological niches and metabolic activities with particular phylogenetic groups among the microbiota of the human gut. Bacteria that associate closely with particulate material and surfaces in the gut include specialized primary degraders of insoluble substrates, including resistant starch, plant structural polysaccharides and mucin. Butyrate-producing bacteria found in human faeces belong mainly to the clostridial clusters IV and XIVa. In vitro and in vivo evidence indicates that a group related to Roseburia and Eubacterium rectale plays a major role in mediating the butyrogenic effect of fermentable dietary carbohydrates. Additional cluster XIVa species can convert lactate to butyrate, while some members of the clostridial cluster IX convert lactate to propionate. The metabolic outputs of the gut microbial community depend not only on available substrate, but also on the gut environment, with pH playing a major role. Better understanding of the colonic microbial ecosystem will help to explain and predict the effects of dietary additives, including nondigestible carbohydrates, probiotics and prebiotics.

The Bacillus subtilis quorum-sensing molecule CSF contributes to intestinal homeostasis via OCTN2, a host cell membrane transporter

Bacteria use quorum-sensing molecules (QSMs) to communicate within as well as across species. However, the effects of QSMs on eukaryotic host cells have received limited attention. We report that the quorum-sensing pentapeptide, competence and sporulation factor (CSF), of the Gram-positive bacterium Bacillus subtilis activates key survival pathways, including p38 MAP kinase and protein kinase B (Akt), in intestinal epithelial cells. CSF also induces cytoprotective heat shock proteins (Hsps), which prevent oxidant-induced intestinal epithelial cell injury and loss of barrier function. These effects of CSF depend on its uptake by an apical membrane organic cation transporter-2 (OCTN2). Thus, OCTN2-mediated CSF transport serves as an example of a host-bacterial interaction that allows the host to monitor and respond to changes in the behavior or composition of colonic flora.