Publications

luminal contents from the gut of colicky infants induce visceral hypersensitivity in mice.	the pathophysiology of infantile colic is poorly understood, though various studies report gut microbiota dysbiosis in colicky infants. we aimed to test the hypothesis that colic-related dysbiosis is associated with visceral hypersensitivity triggered by an altered luminal milieu.	2017	27910234
imbalance of bacteriome profiles within the finnish diabetes prediction and prevention study: parallel use of 16s profiling and virome sequencing in stool samples from children with islet autoimmunity and matched controls.	we set out to explore associations between the stool bacteriome profiles and early-onset islet autoimmunity, taking into account the interactions with the virus component of the microbiome.	2016	27860030
functional characterization of a gene locus from an uncultured gut bacteroides conferring xylo-oligosaccharides utilization to escherichia coli.	in prominent gut bacteroides strains, sophisticated strategies have been evolved to achieve the complete degradation of dietary polysaccharides such as xylan, which is one of the major components of the plant cell wall. polysaccharide utilization loci (puls) consist of gene clusters encoding different proteins with a vast arsenal of functions, including carbohydrate binding, transport and hydrolysis. transport is often attributed to tonb-dependent transporters, although major facilitator superfa ...	2016	27573446
identification of vaginal fluid, saliva, and feces using microbial signatures in a han chinese population.	in recent years, forensic scientists have focused on the discrimination of body fluids using microbial signatures. in this study, we performed pcr-based detection of microbial signatures of vaginal fluid, saliva, and feces in a han chinese population. we investigated the 16s rrna genes of lactobacillus crispatus, lactobacillus gasseri, lactobacillus jensenii, lactobacillus iners, and atopobium vaginae in vaginal fluid, the 16s rrna and the glucosyltransferase enzyme genes of streptococcus saliva ...	2016	27570236
structural and mechanistic insights into a bacteroides vulgatus retaining n-acetyl-β-galactosaminidase that uses neighbouring group participation.	bacteroides vulgatus is a member of the human microbiota whose abundance is increased in patients with crohn's disease. we show that a b. vulgatus glycoside hydrolase from the carbohydrate active enzyme family gh123, bvgh123, is an n-acetyl-β-galactosaminidase that acts with retention of stereochemistry, and, through a 3-d structure in complex with gal-thiazoline, provide evidence in support of a neighbouring group participation mechanism.	2016	27546776
symbiotic gut commensal bacteria act as host cathepsin s activity regulators.	cathepsin s (ctss) is a lysosomal protease whose activity regulation is important for mhc-ii signaling and subsequent activation of cd4(+) t cell mediated immune responses. dysregulation of its enzymatic activity or enhanced secretion into extracellular environments is associated with the induction or progression of several autoimmune diseases. here we demonstrate that commensal intestinal bacteria influence secretion rates and intracellular activity of host ctss and that symbiotic bacteria, i.e ...	2016	27484364
human gut microbes impact host serum metabolome and insulin sensitivity.	insulin resistance is a forerunner state of ischaemic cardiovascular disease and type 2 diabetes. here we show how the human gut microbiome impacts the serum metabolome and associates with insulin resistance in 277 non-diabetic danish individuals. the serum metabolome of insulin-resistant individuals is characterized by increased levels of branched-chain amino acids (bcaas), which correlate with a gut microbiome that has an enriched biosynthetic potential for bcaas and is deprived of genes encod ...	2016	27409811
microbial community of healthy thai vegetarians and non-vegetarians, their core gut microbiota, and pathogen risk.	pyrosequencing analysis of intestinal microflora from healthy thai vegetarians and non-vegetarians exhibited 893 otus covering 189 species. the strong species indicators of vegetarians and non-vegetarians were prevotella copri and bacteroides vulgatus as well as bacteria close to escherichia hermanii with % relative abundance of 16.9 and 4.5-4.7, respectively. core gut microbiota of the vegetarian and non-vegetarian groups consisted of 11 and 20 different bacterial species, respectively, belongi ...	2016	27381339
the evolution of cooperation within the gut microbiota.	cooperative phenotypes are considered central to the functioning of microbial communities in many contexts, including communication via quorum sensing, biofilm formation, antibiotic resistance, and pathogenesis. the human intestine houses a dense and diverse microbial community critical to health, yet we know little about cooperation within this important ecosystem. here we test experimentally for evolved cooperation within the bacteroidales, the dominant gram-negative bacteria of the human inte ...	2016	27111508
extensive mobilome-driven genome diversification in mouse gut-associated bacteroides vulgatus mpk.	like many other bacteroides species, bacteroides vulgatus strain mpk, a mouse fecal isolate which was shown to promote intestinal homeostasis, utilizes a variety of mobile elements for genome evolution. based on sequences collected by pacific biosciences smrt sequencing technology, we discuss the challenges of assembling and studying a bacterial genome of high plasticity. additionally, we conducted comparative genomics comparing this commensal strain with the b. vulgatus type strain atcc 8482 as ...	2016	27071651
expression of arsenic resistance genes in the obligate anaerobe bacteroides vulgatus atcc 8482, a gut microbiome bacterium.	the response of the obligate anaerobe bacteroides vulgatus atcc 8482, a common human gut microbiota, to arsenic was determined. b. vulgatus atcc 8482 is highly resistant to pentavalent as(v) and methylarsenate (mas(v)). it is somewhat more sensitive to trivalent inorganic as(iii) but 100-fold more sensitive to methylarsenite (mas(iii)) than to as(iii). b. vulgatus atcc 8482 has eight continuous genes in its genome that we demonstrate form an arsenical-inducible transcriptional unit. the first ge ...	2016	27040269
distinctly altered gut microbiota in the progression of liver disease.	recent studies underscore important roles of intestinal microbiota and the bacterial lipopolysaccharides (lps) production in the pathogenesis of liver disease. however, how gut microbiota alters in response to the development of steatosis and subsequent progression to nonalcoholic steatohepatitis (nash) and hepatocellular carcinoma (hcc) remains unclear. we aimed to study the gut microbial changes over liver disease progression using a streptozotocin-high fat diet (stz-hfd) induced nash-hcc c57b ...	2016	27036035
correlation between body mass index and faecal microbiota from children.	childhood obesity is an increasing problem at the global level and considered as a risk factor for obesity development and the associated co-morbidities in adult life. in this study, the occurrence of bacteroides fragilis group, clostridium spp., bifidobacterium spp. and escherichia coli in 84 faecal samples from 30 obese, 24 overweight and 30 lean children was verified by culture technique and quantitative determination by quantitative pcr. in addition, lactobacillus spp. and methanobrevibacter ...	2016	26551842
specific members of the predominant gut microbiota predict pouchitis following colectomy and ipaa in uc.	pouchitis is the most common complication after colectomy with ileal pouch-anal anastomosis (ipaa) for uc and the risk is the highest within the 1st year after surgery. the pathogenesis is not completely understood but clinical response to antibiotics suggests a role for gut microbiota. we hypothesised that the risk for pouchitis can be predicted based on the faecal microbial composition before colectomy.	2017	26423113
sialic acid catabolism drives intestinal inflammation and microbial dysbiosis in mice.	rapid shifts in microbial composition frequently occur during intestinal inflammation, but the mechanisms underlying such changes remain elusive. here we demonstrate that an increased caecal sialidase activity is critical in conferring a growth advantage for some bacteria including escherichia coli (e. coli) during intestinal inflammation in mice. this sialidase activity originates among others from bacteroides vulgatus, whose intestinal levels expand after dextran sulphate sodium administration ...	2015	26303108
functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a gpcr g2a/132 agonist.	the trillions of bacteria that make up the human microbiome are believed to encode functions that are important to human health; however, little is known about the specific effectors that commensal bacteria use to interact with the human host. functional metagenomics provides a systematic means of surveying commensal dna for genes that encode effector functions. here, we examine 3,000 mb of metagenomic dna cloned from three phenotypically distinct patients for effectors that activate nf-κb, a tr ...	2015	26283367
crohn associated microbial communities associated to colonic mucosal biopsies in patients of the western mediterranean.	next generation sequencing approaches allow the retrieval of several orders of magnitude larger numbers of amplified single sequences in 16s rrna diversity surveys than classical methods. however, the sequences are only partial and thus lack sufficient resolution for a reliable identification. the opu approach used here, based on a tandem combination of high quality 454 sequences (mean >500 nuc) applying strict otu thresholds, and phylogenetic inference based on parsimony additions to preexistin ...	2015	26275394
[bacteria isolated from surgical infections and its susceptibilities to antimicrobial agents - special references to bacteria isolated between april 2011 and march 2012].	bacteria isolated from surgical infections during the period from april 2011 to march 2012 were investigated in a multicenter study in japan, and the following results were obtained. in this series, 785 strains including 31 strains of candida spp. were isolated from 204 (78.8%) of 259 patients with surgical infections. five hundred and twenty three strains were isolated from primary infections, and 231 strains were isolated from surgical site infection. from primary infections, anaerobic gram-ne ...	2014	25796741
structure and sequence analyses of bacteroides proteins bvu_4064 and bf1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions.	n-terminal domains of bvu_4064 and bf1687 proteins from bacteroides vulgatus and bacteroides fragilis respectively are members of the pfam family pf12985 (duf3869). proteins containing a domain from this family can be found in most bacteroides species and, in large numbers, in all human gut microbiome samples. both bvu_4064 and bf1687 proteins have a consensus lipobox motif implying they are anchored to the membrane, but their functions are otherwise unknown. the c-terminal half of bvu_4064 is a ...	2015	25592227
bacteroides dorei dominates gut microbiome prior to autoimmunity in finnish children at high risk for type 1 diabetes.	the incidence of the autoimmune disease, type 1 diabetes (t1d), has increased dramatically over the last half century in many developed countries and is particularly high in finland and other nordic countries. along with genetic predisposition, environmental factors are thought to play a critical role in this increase. as with other autoimmune diseases, the gut microbiome is thought to play a potential role in controlling progression to t1d in children with high genetic risk, but we know little ...	2014	25540641
production of corticotropin-releasing factor and urocortin from human monocyte-derived dendritic cells is stimulated by commensal bacteria in intestine.	to examine whether commensal bacteria are a contributing cause of stress-related mucosal inflammation.	2014	25339828
antibacterial epipolythiodioxopiperazine and unprecedented sesquiterpene from pseudallescheria boydii, a beetle (coleoptera)-associated fungus.	pseudallescheria boydii residing in the gut of coleopteran (holotrichia parallela) larva produces four new epipolythiodioxopiperazine (etp) boydines a-d (3-6) and two novel sesquiterpene boydenes a (7) and b (10), in addition to bisdethiobis(methylthio)-deacetylaranotin (1), bisdethiodi(methylthio)-deacetylapoaranotin (2), am6898 a (8) and ovalicin (9). the structure elucidation was accomplished by a combination of spectral methods with quantum chemical calculations of optical rotations and elec ...	2014	25319640
model-based hypothesis of gut microbe populations and gut/brain barrier permeabilities in the development of regressive autism.	regressive autism is a devastating disorder affecting children between the ages of 15-30 months. the disorder is characterized by the loss of social interaction and communication ability following otherwise healthy development. in spite of rising autism prevalence, current detection methods and treatment options for this disease are lacking. therefore, this study introduces a systems-level model, which suggests that gut microbes and intestinal inflammation influence the onset of regressive autis ...	2014	25288537
hla-b27 and human β2-microglobulin affect the gut microbiota of transgenic rats.	the hla-b27 gene is a major risk factor for clinical diseases including ankylosing spondylitis, acute anterior uveitis, reactive arthritis, and psoriatic arthritis, but its mechanism of risk enhancement is not completely understood. the gut microbiome has recently been shown to influence several hla-linked diseases. however, the role of hla-b27 in shaping the gut microbiome has not been previously investigated. in this study, we characterize the differences in the gut microbiota mediated by the ...	2014	25140823
bacterial sensor nod2 prevents inflammation of the small intestine by restricting the expansion of the commensal bacteroides vulgatus.	nod2 has been extensively characterized as a bacterial sensor that induces an antimicrobial and inflammatory gene expression program. therefore, it is unclear why nod2 mutations that disrupt bacterial recognition are paradoxically among the highest risk factors for crohn's disease, which involves an exaggerated immune response directed at intestinal bacteria. here, we identified several abnormalities in the small-intestinal epithelium of nod2(-/-) mice including inflammatory gene expression and ...	2014	25088769
coexpression and secretion of endoglucanase and phytase genes in lactobacillus reuteri.	a multifunctional transgenic lactobacillus with probiotic characteristics and an ability to degrade β-glucan and phytic acid (phytate) was engineered to improve nutrient utilization, increase production performance and decrease digestive diseases in broiler chickens. the bacillus subtilis wl001 endoglucanase gene (celw) and aspergillus fumigatus wl002 phytase gene (phyw) mature peptide (phywm) were cloned into an expression vector with the lactate dehydrogenase promoter of lactobacillus casei an ...	2014	25050780
l-galactose metabolism in bacteroides vulgatus from the human gut microbiota.	a previously unknown metabolic pathway for the utilization of l-galactose was discovered in a prevalent gut bacterium, bacteroides vulgatus. the new pathway consists of three previously uncharacterized enzymes that were found to be responsible for the conversion of l-galactose to d-tagaturonate. bvu0219 (l-galactose dehydrogenase) was determined to oxidize l-galactose to l-galactono-1,5-lactone with kcat and kcat/km values of 21 s(-1) and 2.0 × 10(5) m(-1) s(-1), respectively. the kinetic produc ...	2014	24963813
individually addressable arrays of replica microbial cultures enabled by splitting slipchips.	isolating microbes carrying genes of interest from environmental samples is important for applications in biology and medicine. however, this involves the use of genetic assays that often require lysis of microbial cells, which is not compatible with the goal of obtaining live cells for isolation and culture. this paper describes the design, fabrication, biological validation, and underlying physics of a microfluidic slipchip device that addresses this challenge. the device is composed of two co ...	2014	24953827
senior thai fecal microbiota comparison between vegetarians and non-vegetarians using pcr-dgge and real-time pcr.	the fecal microbiotas were investigated in 13 healthy thai subjects using polymerase chain reaction denaturing gradient gel electrophoresis (pcr-dgge). among the 186 dna bands detected on the polyacrylamide gel, 37 bands were identified as representing 11 species: bacteroides thetaiotaomicron, bacteroides ovatus, bacteroides uniformis, bacteroides vulgatus, clostridium colicanis, eubacterium eligenes, e. rectale, faecalibacterium prausnitzii, megamonas funiformis, prevotella copri, and roseburia ...	2014	24743571
disrupted intestinal microbiota and intestinal inflammation in children with cystic fibrosis and its restoration with lactobacillus gg: a randomised clinical trial.	intestinal inflammation is a hallmark of cystic fibrosis (cf). administration of probiotics can reduce intestinal inflammation and the incidence of pulmonary exacerbations. we investigated the composition of intestinal microbiota in children with cf and analyzed its relationship with intestinal inflammation. we also investigated the microflora structure before and after lactobacillus gg (lgg) administration in children with cf with and without antibiotic treatment.	2014	24586292
isolation of bacteroides from fish and human fecal samples for identification of unique molecular markers.	bacteroides molecular markers have been used to identify human fecal contamination in natural waters, but recent work in our laboratory confirmed cross-amplification of several human-specific bacteroides spp. assays with fecal dna from fish. for identification of unique molecular markers, bacteroides from human (n = 4) and fish (n = 7) fecal samples were cultured and their identities were further confirmed using rapid id 32a api strips. the 16s rdna from multiple isolates from each sample was pc ...	2013	24313449
production of ai-2 is mediated by the s-ribosylhomocystein lyase gene luxs in bacteroides fragilis and bacteroides vulgatus.	quorum sensing is a cell-cell signaling mechanism based on cell density and that involves the production of hormone-like molecules called autoinducers (ai). one of the most studied ais has been termed ai-2, and its biosynthesis requires the enzyme encoded by luxs. we have previously described for the first time that bacteroides species can produce molecules with ai-2 activity. in this study, we focus on the detection of luxs and its activity as the ai-2 synthase in bacteroides species. the strai ...	2014	24026770
utilization of major fucosylated and sialylated human milk oligosaccharides by isolated human gut microbes.	human milk oligosaccharides (hmos) are not digested in the proximal intestine. in distal intestine, hmos collectively modify the microbiota, but the response of individual bacteria to individual components of the hmos is not well defined. here, each of 25 major isolates of the human intestinal microbiota was fed individual major fucosylated and sialylated hmos in anaerobic culture. this allowed for an assessment of the influence of specific hmos on the growth and metabolic products of individual ...	2013	24013960
species differentiation of bacteroides dorei from bacteroides vulgatus and bacteroides ovatus from bacteroides xylanisolvens - back to basics.	we present the results from 16s sequencing and phenotypic tests for differentiation of bacteroides dorei from bacteroides vulgatus and bacteroides ovatus from bacteroides xylanisolvens, which was not possible with maldi-tof ms. testing with β-glucosidase could differentiate b. dorei from b. vulgatus and a negative catalase reaction could identify b. xylanisolvens.	2013	23994205
discovery of β-1,4-d-mannosyl-n-acetyl-d-glucosamine phosphorylase involved in the metabolism of n-glycans.	a gene cluster involved in n-glycan metabolism was identified in the genome of bacteroides thetaiotaomicron vpi-5482. this gene cluster encodes a major facilitator superfamily transporter, a starch utilization system-like transporter consisting of a tonb-dependent oligosaccharide transporter and an outer membrane lipoprotein, four glycoside hydrolases (α-mannosidase, β-n-acetylhexosaminidase, exo-α-sialidase, and endo-β-n-acetylglucosaminidase), and a phosphorylase (bt1033) with unknown function ...	2013	23943617
identification of household bacterial community and analysis of species shared with human microbiome.	microbial populations in indoor environments, where we live and eat, are important for public health. various bacterial species reside in the kitchen, and refrigerators, the major means of food storage within kitchens, can be a direct source of food borne illness. therefore, the monitoring of microbiota in the refrigerator is important for food safety. we investigated and compared bacterial communities that reside in the vegetable compartment of the refrigerator and on the seat of the toilet, wh ...	2013	23743600
pitfalls in mouse norovirus (mnv) detection in fecal samples using rt-pcr, and construction of new mnv-specific primers.	the murine norovirus (mnv), which belongs to the caliciviridae family, is prevalent in laboratory mice. since this virus affects macrophages and dendritic cells, infected mice are not suitable for immunological investigations, making it important to detect mnv infections accurately. when we tested rna extracts derived from mouse feces for mnv detection using nested rt-pcr with a set of mnv-specific primers reported by goto et al. (exp. anim. 58: 135-140, 2009), we found that these primers amplif ...	2013	23615307
in vitro growth of four individual human gut bacteria on oligosaccharides produced by chemoenzymatic synthesis.	the present study aimed at examining oligosaccharides (os) for potential stimulation of probiotic bacteria. nineteen structurally well-defined candidate os covering groups of β-glucosides, α-glucosides and α-galactosides with degree of polymerization 2-4 were prepared in >100 mg amounts by chemoenzymatic synthesis (i.e. reverse phosphorolysis or transglycosylation). fourteen of the os are not naturally occurring and five (β-d-glucosyl-fructose, β-d-glucosyl-xylitol, α-glucosyl-(1,4)-d-mannose, α ...	2013	23580006
ethnic diversity of gut microbiota: species characterization of bacteroides fragilis group and genus bifidobacterium in healthy belgian adults, and comparison with data from japanese subjects.	the composition of the human gut microbiota is related to host health, and it is thought that dietary habits may play a role in shaping this composition. here, we examined the population size and prevalence of six predominant bacterial genera and the species compositions of genus bifidobacterium (g-bifid) and bacteroides fragilis group (g-bfra) in 42 healthy belgian adults by quantitative pcr (qpcr) over a period of one month. the population sizes and prevalence of these bacteria were basically ...	2013	23522670
intake of whole-grain and fiber-rich rye bread versus refined wheat bread does not differentiate intestinal microbiota composition in finnish adults with metabolic syndrome.	whole-grain (wg) foods rich in indigestible carbohydrates are thought to modulate the composition of the intestinal microbiota. we investigated in a randomized, parallel, 2-arm 12-wk intervention whether consumption of wg and fiber-rich rye breads compared with refined wheat breads affected the microbiota composition in finnish individuals aged 60 ± 6 y with metabolic syndrome. fecal samples from 51 participants (25 males, 26 females) before and after the intervention were processed for the micr ...	2013	23514765
effects of antibiotics on bacterial species composition and metabolic activities in chemostats containing defined populations of human gut microorganisms.	the composition and metabolic activities of the human colonic microbiota are modulated by a number of external factors, including diet and antibiotic therapy. changes in the structure and metabolism of the gut microbiota may have long-term consequences for host health. the large intestine harbors a complex microbial ecosystem comprising several hundreds of different bacterial species, which complicates investigations on intestinal physiology and ecology. to facilitate such studies, a highly simp ...	2013	23403424
discrimination based on gly and arg/ser at position 673 between dipeptidyl-peptidase (dpp) 7 and dpp11, widely distributed dpps in pathogenic and environmental gram-negative bacteria.	porphyromonas gingivalis, an asaccharolytic gram-negative rod-shaped bacterium, expresses the novel asp/glu-specific dipeptidyl-peptidase (dpp) 11 (ohara-nemoto, y. et al. (2011) j. biol. chem. 286, 38115-38127), which has been categorized as a member of the s46/dpp7 family that is preferential for hydrophobic residues at the p1 position. from that finding, 129 gene products constituting five clusters from the phylum bacteroidetes have been newly annotated to either dpp7 or dpp11, whereas the re ...	2013	23246913
[role of infectious agents in the emergence of malignant tumors].	according to the data of the international agency for research on cancer (iarc), at least 6 virus species (hpv, ebv, hhv-8/kshv, htlv-1, hbv, hcv), 4 helminthes species (schistosoma haematobium and japonicum, opisthorchis viverrini, clonorchis sinensis) and i bacterium species (helicobacter pylori) have been proved to be capable of causing the development of cancer. the analysis of the data available shows that merkel cell polyomavirus (mcv), herpes simplex virus (hsv), john cunningham polyomavi ...	2012	23163048
solution nmr structure of the helicase associated domain bvu_0683(627-691) from bacteroides vulgatus provides first structural coverage for protein domain family pf03457 and indicates domain binding to dna.	a high-quality nmr structure of the helicase associated (ha) domain comprising residues 627-691 of the 753-residue protein bvu_0683 from bacteroides vulgatus exhibits an all α-helical fold. the structure presented here is the first representative for the large protein domain family pf03457 (currently 742 members) of ha domains. comparison with structurally similar proteins supports the hypothesis that ha domains bind to dna and that binding specificity varies greatly within the family of ha doma ...	2013	23160728
insight into the prebiotic concept: lessons from an exploratory, double blind intervention study with inulin-type fructans in obese women.	to highlight the contribution of the gut microbiota to the modulation of host metabolism by dietary inulin-type fructans (itf prebiotics) in obese women.	2013	23135760
identification of feces by detection of bacteroides genes.	in forensic science, the identification of feces is very important in a variety of crime investigations. however, no sensitive and simple fecal identification method using molecular biological techniques has been reported. here, we focused on the fecal bacteria, bacteroides uniformis, bacteroides vulgatus and bacteroides thetaiotaomicron, and developed a novel fecal identification method by detection of the gene sequences specific to these bacteria in various body (feces, blood, saliva, semen, u ...	2013	23068949
the antimicrobial action of chitosan, low molar mass chitosan, and chitooligosaccharides on human colonic bacteria.	antibacterial effect of chitooligosaccharides (cos) and low molar mass chitosans (lmwc) is considered as one of the most important characteristics of chitosan (cs) hydrolysates. here, we show the in vitro effect of different cos, lmwc, and cs on representative anaerobic bacteria isolated from human colon as a possibility of targeting modification of colonic microflora composition by supplementation of dietary cs products by humans. specific growth rate of seven selected nonpathogenic anaerobic b ...	2012	22528310
microbial composition and in vitro fermentation patterns of human milk oligosaccharides and prebiotics differ between formula-fed and sow-reared piglets.	the microbial composition and in vitro fermentation characteristics of human milk oligosaccharides (hmo), lacto-n-neotetraose (lnnt), a 2:1 mixture of polydextrose (pdx) and galactooligosaccharides (gos), and short-chain fructooligosaccharides (scfos) by pooled ascending colonic microbiota from 9- and 17-d-old formula-fed (ff) and sow-reared (sr) piglets were assessed. ph change and gas, scfa, and lactate production were determined after 0, 2, 4, 8, and 12 h of incubation. in most donor groups, ...	2012	22399522
olfactomedin-4 is a glycoprotein secreted into mucus in active ibd.	olfactomedin-4 (olfm4) is a glycoprotein characteristic of intestinal stem cells and apparently involved in mucosal defense of the stomach and colon. here we studied its expression, regulation and function in ibd.	2012	22398066
first national survey of antibiotic susceptibility of the bacteroides fragilis group: emerging resistance to carbapenems in argentina.	the antibiotic susceptibility rates of 363 clinical bacteroides fragilis group isolates collected from 17 centers in argentina during the period from 2006 to 2009 were as follows: piperacillin-tazobactam, 99%; ampicillin-sulbactam, 92%; cefoxitin, 72%; tigecycline, 100%; moxifloxacin, 91%; and clindamycin, 52%. no metronidazole resistance was detected in these isolates during this time period. resistance to imipenem, doripenem, and ertapenem was observed in 1.1%, 1.6%, and 2.3% of b. fragilis gr ...	2012	22232282
solution nmr structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family pf10771.	high-quality nmr structures of the homo-dimeric proteins bvu3908 (69-residues in monomeric unit) from bacteroides vulgatus and bt2368 (74-residues) from bacteroides thetaiotaomicron reveal the presence of winged helix-turn-helix (whth) motifs mediating tight complex formation. such homo-dimer formation by winged hth motifs is otherwise found only in two dna-binding proteins with known structure: the c-terminal whth domain of transcriptional activator fadr from e. coli and protein tubr from b. th ...	2012	22223187
corticotropin-releasing factor secretion from dendritic cells stimulated by commensal bacteria.	to study the production and secretion of corticotropin-releasing factor (crf) by dendritic cells and the influence of commensal bacteria.	2011	22046091
A Molecular Enrichment Strategy Based on cpn60 for Detection of Epsilon-Proteobacteria in the Dog Fecal Microbiome.	Members of the rare microbiome can be important components of complex microbial communities. For example, pet dog ownership is a known risk factor for human campylobacteriosis, and Campylobacter is commonly detected in dog feces by targeted assays. However, these organisms have not been detected by metagenomic methods. The goal of this study was to characterize fecal microbiota from healthy and diarrheic pet dogs using two different levels of molecular detection. PCR amplification and pyrosequen ...	2011	21881944
Structural characterization of BVU_3255, a methyltransferase from human intestine antibiotic resistant pathogen Bacteroides vulgatus.	Methylation is important for various cellular activities. To date, there is no report of any methyltransferase structure from the human intestine antibiotic resistant pathogen Bacteroides vulgatus. The protein BVU_3255 from B. vulgatus ATCC 8482 belongs to a SAM-dependent methyltransferase. Here, we report the crystal structure of apo BVU_3255, and its complexes with SAM and SAH, which revealed a typical class I Rossmann Fold Methyltransferase. Isothermal titration calorimetric studies showed th ...	2011	21872662
structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers.	despite a long-suspected role in the development of human colorectal cancer (crc), the composition of gut microbiota in crc patients has not been adequately described. in this study, fecal bacterial diversity in crc patients (n=46) and healthy volunteers (n=56) were profiled by 454 pyrosequencing of the v3 region of the 16s ribosomal rna gene. both principal component analysis and unifrac analysis showed structural segregation between the two populations. forty-eight operational taxonomic units ...	2011	21850056
identification and characterization of potential performance-related gut microbiotas in broiler chickens across various feeding trials.	three broiler feeding trials were investigated in order to identify gut bacteria consistently linked with improvements in bird performance as measured by feed efficiency. trials were done in various geographic locations and varied in diet composition, broiler breed, and bird age. gut microbial communities were investigated using microbial profiling. eight common performance-linked operational taxonomic units (otus) were identified within both the ilea (180, 492, and 564-566) and ceca (140-142, 2 ...	2011	21742925
molecular characterization of fecal microbiota in patients with viral diarrhea.	the study provides molecular analyses of fecal microbiota of diarrhea patients infected with four different types of viruses. fecal specimens from 52 patients with viral diarrhea (13 each of adenovirus, norovirus, rotavirus, and astrovirus) and six healthy individuals were collected and etiological viral agent was confirmed by enzyme immunoassay and specific pcr. to assess the changes in microbial diversity in patients with viral diarrhea, dna from stool were extracted and characterized by pcr-d ...	2011	21739252
the draft genome sequence of bacteroides vulgatus pc510, a strain isolated from human faeces.	although bacteroides vulgatus is one of the most prevalent microorganisms in the human gastrointestinal tract little is known about the genetic potential of this species. here we describe the annotated draft genome sequence of b. vulgatus pc510 isolated from human faeces.	2011	21622758
design of species-specific oligonucleotide probes for the detection of bacteroides and parabacteroides by fluorescence in situ hybridization and their application to the analysis of mouse caecal bacteroides-parabacteroides microbiota.	aims: to develop species-specific monitoring techniques for rapid detection of bacteroides and parabacteroides inhabiting the mouse intestine by fluorescence in situ hybridization. methods and results: the specificity of oligonucleotide probes was evaluated by fluorescence whole-cell hybridization. oligonucleotide probes specific for each species hybridized only with the target bacteria. using these probes, caecal bacteroides-parabacteroides microbiota of conventional mice and specific pathoge ...	2011	21535330
application of quantitative real-time pcr for rapid identification of bacteroides fragilis group and related organisms in human wound samples.	our goal was to establish a quantitative real-time pcr (qrt-pcr) method to detect bacteroides fragilis group and related organisms from clinical specimens. compared to conventional anaerobic culture, qrt-pcr can provide accurate and more rapid detection and identification of b.-áfragilis group and similar species. b.-áfragilis group and related organisms are the most frequently isolated anaerobic pathogens from clinical samples. however, culture and phenotypic identification is quite time-consum ...	2011	21439390
ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of the gut microbiota.	previous studies suggest a link between gut microbiota and the development of ulcerative colitis (uc) and irritable bowel syndrome (ibs). our aim was to investigate any quantitative differences in faecal bacterial compositions in uc and ibs patients compared to healthy controls, and to identify individual bacterial species that contribute to these differences.	2010	21073731
intestinal bacteroides species associated with coeliac disease.	to characterise the predominant species of bacterial populations associated with duodenal biopsies of paediatric patients with active and treated coeliac disease.	2010	20972239
the structure of bvu2987 from bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function.	proteins that contain the duf2874 domain constitute a new pfam family pf11396. members of this family have predominantly been identified in microbes found in the human gut and oral cavity. the crystal structure of one member of this family, bvu2987 from bacteroides vulgatus, has been determined, revealing a β-lactamase inhibitor protein-like structure with a tandem repeat of domains. sequence analysis and structural comparisons reveal that bvu2987 and other duf2874 proteins are related to β-lact ...	2010	20944221
german multicentre survey of the antibiotic susceptibility of bacteroides fragilis group and prevotella species isolated from intra-abdominal infections: results from the prisma study.	to determine the susceptibility of gram-negative anaerobic bacteria of the family bacteroidaceae from hospitalized patients with intra-abdominal infections (iais) to moxifloxacin and other antimicrobial agents with known activity against anaerobes.	2010	20851813
pyrosequencing study of fecal microflora of autistic and control children.	there is evidence of genetic predisposition to autism, but the percent of autistic subjects with this background is unknown. it is clear that other factors, such as environmental influences, may play a role in this disease. in the present study, we have examined the fecal microbial flora of 33 subjects with various severities of autism with gastrointestinal symptoms, 7 siblings not showing autistic symptoms (sibling controls) and eight non-sibling control subjects, using the bacterial tag encode ...	2010	20603222
a distinctive 'microbial signature' in celiac pediatric patients.	celiac disease (cd) is an autoimmune disorder of the small intestine in which dietary gluten ingestion leads to a chronic enteropathy. recently, scientific evidence suggested a potential role of gut microbiota in cd. to have a snapshot of dominant duodenal microbiota we analyzed the mucosa-associated microbiota of 20 children with cd, before and after a gluten-free diet (gfd) regimen, and of 10 controls. total dna was extracted from duodenal biopsies and amplification products of 16s ribosomal d ...	2010	20565734
bacteroides chinchillae sp. nov. and bacteroides rodentium sp. nov., isolated from chinchilla (chinchilla lanigera) faeces.	gram-negative anaerobic rods were isolated from chinchilla (chinchilla lanigera) faeces and three strains, st170(t), st180 and st28(t), were investigated taxonomically. on the basis of phylogenetic analyses and specific phenotypic characteristics, the three strains belonged to the genus bacteroides. phylogenetic analysis of their 16s rrna gene sequences revealed that strains st170(t) and st180 formed a single cluster and a distinct line of descent. strain st170(t) exhibited 99.7 % 16s rrna gene ...	2011	20495039
ompa variants affecting the adherence of ulcerative colitis-derived bacteroides vulgatus.	to investigate the adhesion factor of bacteroides vulgatus derived from ulcerative colitis (uc), we isolated b. vulgatus strains from the large intestinal mucosa of uc patients and non-uc individuals, and examined their adherence to tissue-cultured cells. the adherence to tissue-cultured cells in uc-derived strains (36.5 +/- 7.9 %) was higher than that in non-uc-derived strains (13.2 +/- 7.7 %). pcr and sequencing analysis of outer membrane proteins revealed that the strains derived from five of ...	2010	20437766
safety of probiotic escherichia coli strain nissle 1917 depends on intestinal microbiota and adaptive immunity of the host.	probiotics are viable microorganisms that are increasingly used for treatment of a variety of diseases. occasionally, however, probiotics may have adverse clinical effects, including septicemia. here we examined the role of the intestinal microbiota and the adaptive immune system in preventing translocation of probiotics (e.g., escherichia coli nissle). we challenged c57bl/6j mice raised under germfree conditions (gf-raised c57bl/6j mice) and rag1(-/-) mice raised under germfree conditions (gf-r ...	2010	20421387
consumption of human milk oligosaccharides by gut-related microbes.	human milk contains large amounts of complex oligosaccharides that putatively modulate the intestinal microbiota of breast-fed infants by acting as decoy binding sites for pathogens and as prebiotics for enrichment of beneficial bacteria. several bifidobacterial species have been shown to grow well on human milk oligosaccharides. however, few data exist on other bacterial species. this work examined 16 bacterial strains belonging to 10 different genera for growth on human milk oligosaccharides. ...	2010	20394371
isolation of bacteria from mouse caecal samples and description of bacteroides sartorii sp. nov.	caecal samples from wild-type and tnf(deltaare) mice were cultured on selective media containing bile salts, amino acids or casein macro-peptides. twenty-two strains were isolated and identified by 16s rrna gene sequencing. twenty-one strains showed >98% similarity to known bacteria (blautia spp., clostridium innocuum, enterococcus spp., escherichia coli, lactobacillus murinus, parabacteroides goldsteinii and shigella dysenteriae). one additional isolate, strain a-c2-0, was a new bacterium. the ...	2010	20369227
bacteroides paurosaccharolyticus sp. nov., isolated from a methanogenic reactor treating waste from cattle farms.	a strictly anaerobic bacterial strain (wk042(t)) was isolated from rice-straw residue in a methanogenic reactor treating waste from cattle farms in japan. cells were gram-staining-negative, non-motile, non-spore-forming rods. growth was stimulated well by haemin, and was enhanced by cobalamin (vitamin b(12)). strain wk042(t) utilized arabinose, xylose, glucose, mannose and aesculin as preferred substrates. maltose, dextrin, glycogen, starch and pectin were also utilized, although growth on these ...	2011	20348319
identification of clinically important anaerobic bacteria by an oligonucleotide array.	anaerobic bacteria can cause a wide variety of infections, and some of these infections can be serious. conventional identification methods based on biochemical tests are often lengthy and can produce inconclusive results. an oligonucleotide array based on the 16s-23s rrna intergenic spacer (its) sequences was developed to identify 28 species of anaerobic bacteria and veillonella. the method consisted of pcr amplification of the its regions with universal primers, followed by hybridization of th ...	2010	20129959
molecular characterisation of the faecal microbiota in patients with type ii diabetes.	the investigation provides molecular analyses of the faecal microbiota in type 2 diabetic patients. in order to characterise the gut microbiota in diabetic patients and to assess whether there are changes in the diversity and similarity of gut microbiota in diabetic patients when compared with healthy individuals, bacterial dnas from 16 type 2 diabetic patients and 12 healthy individuals were extracted from faecal samples and characterised by pcr-denaturing gradient gel electrophoresis (dgge) wi ...	2010	20087741
lessons learned from the anaerobe survey: historical perspective and review of the most recent data (2005-2007).	the rationale and lessons learned through the evolution of the national survey for the susceptibility of bacteroides fragilis group from its initiation in 1981 through 2007 are reviewed here. the survey was conceived in 1980 to track emerging antimicrobial resistance in bacteroides species.	2010	20067390
transepithelial activation of human leukocytes by probiotics and commensal bacteria: role of enterobacteriaceae-type endotoxin.	the goal of the current study was to clarify whether commercially available probiotics induce greater trans-epithelial activation of human leukocytes than do commensal, food-derived and pathogenic bacteria and to identify the compounds responsible for this activation. eleven different bacterial strains, and some of their pathogen-associated molecular patterns, were incubated apically on a confluent layer of intestinal epithelial cells (caco-2), which were basolaterally co-cultured with human mon ...	2009	19714861
molecular inventory of faecal microflora in patients with crohn's disease.	intestinal microbial community is involved in the pathogenesis of crohn's disease, but knowledge of its potential abnormalities has been limited by the impossibility to grow many dominant intestinal bacteria. using sequence analysis of randomly cloned bacterial 16s ribosomal dna, the dominant faecal species from four crohn's disease patients and four controls were compared. whereas marked inter-individual differences were observed in the faecal microflora of patients, three remained distantly re ...	2004	19712374
modulation of the intestinal microbiota alters colitis-associated colorectal cancer susceptibility.	it is well established that the intestinal microbiota plays a key role in the pathogenesis of crohn's disease (cd) and ulcerative colitis (uc) collectively referred to as inflammatory bowel disease (ibd). epidemiological studies have provided strong evidence that ibd patients bear increased risk for the development of colorectal cancer (crc). however, the impact of the microbiota on the development of colitis-associated cancer (cac) remains largely unknown. in this study, we established a new mo ...	2009	19551144
pattern extraction of structural responses of gut microbiota to rotavirus infection via multivariate statistical analysis of clone library data.	this study developed a new statistical strategy for analyzing clone library data to observe whether there is a defined pattern in structural responses of gut microbiota to environmental perturbations. a large clone library of genus bacteroides was constructed with fecal samples for each subject in rotavirus-infected (group r) and healthy children (group h). in all, 665 clones of the 12 group h subjects and 284 clones of the nine group r subjects were sequenced and classified into 34 operational ...	2009	19453743
commensal bacteria can enter colonic epithelial cells and induce proinflammatory cytokine secretion: a possible pathogenic mechanism of ulcerative colitis.	interleukin 2 (il-2)- and il-10-knockout mice develop spontaneous colitis under conventional but not germ-free conditions, suggesting that commensal bacteria play an important role in the pathogenesis of colitis. however, interactions between commensal bacteria and colonic epithelial cells have not been fully investigated. we therefore assessed the ability of various commensal bacteria and probiotics to adhere to and invade colonic epithelial cells. effects of the bacteria on production of proin ...	2009	19369513
bioactivation of selenocysteine derivatives by beta-lyases present in common gastrointestinal bacterial species.	studies in cell cultures and animal models have demonstrated cancer chemopreventive effects of certain selenium compounds. here we describe the screening of cysteine s-conjugate beta-lyase activity in bacterial species that are implicated in the bio-activation of sulfur- and selenocysteine derivatives. we screened a range of bacterial species commonly found in the human intestine for beta-lyase activity on se-p-methoxybenzylselenocysteine and the natural occurring s-methylcysteine and se-methyls ...	2008	19326339
detection and persistence of fecal bacteroidales as water quality indicators in unchlorinated drinking water.	the results of this study support the use of fecal bacteroidales qpcr as a rapid method to complement traditional, culture-dependent, water quality indicators in systems where drinking water is supplied without chlorination or other forms of disinfection. a sybr-green based, quantitative pcr assay was developed to determine the concentration of fecal bacteroidales 16s rrna gene copies. the persistence of a bacteroides vulgatus pure culture and fecal bacteroidales from a wastewater inoculum was d ...	2009	19261420
detection of possible ai-2-mediated quorum sensing system in commensal intestinal bacteria.	the vibrio harveyi strain bb170-autoinducer bioassay was used to detect possible quorum sensing autoinducer-2 molecule (ai-2) in culture fluids of commensal intestinal bacteria. culture fluids of bacteroides vulgatus, clostridium proteoclasticum, escherichia coli, eubacterium rectale, lachnospira multipara, pseudobutyrivibrio ruminis, roseburia intestinalis, ruminococcus albus and ruminococcus flavefaciens contained ai-2-like molecules. the pcr bands from some of the tested strains could be also ...	2008	18661296
effects of rosa rugosa petals on intestinal bacteria.	the effects of pulverized petal of rosa rugosa on the growth of 10 species of intestinal and pathogenic bacteria were investigated. growth of bifidobacteria and lactobacilli was not affected by the addition of the petal in plate cultivation. however, the growth of bacteroides vulgatus, escherichia coli, staphylococcus aureus, and bacillus cereus was completely inhibited by the addition of 0.1, 0.5, 0.1, and 0.05% (w/v) of the petal respectively. in liquid cultivation, the addition of the petal ( ...	2008	18323655
gut microbes in crohn's disease: getting to know you better?	biomarkers in inflammatory bowel disease (ibd) are needed to help in disease diagnosis, prognosis, and assessment of disease activity. the best serologic markers to date measure antibody responses to normal commensal flora. these antibody responses can provide prognostic information as well as clues to disease pathogenesis. there remains room for additional biomarkers to clarify the diagnosis for certain patients with indeterminate colitis or small bowel crohn's disease (cd) with protean manifes ...	2008	18289202
dual-association of gnotobiotic il-10-/- mice with 2 nonpathogenic commensal bacteria induces aggressive pancolitis.	monoassociating gnotobiotic il-10-deficient (-/-) mice with either nonpathogenic enterococcus faecalis or a nonpathogenic escherichia coli strain induces t-cell-mediated colitis with different kinetics and anatomical location (e. faecalis: late onset, distal colonic; e. coli: early onset, cecal). hypothesis: e. faecalis and e. coli act in an additive manner to induce more aggressive colitis than disease induced by each bacterial species independently.	2007	17763473
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 ...	2007	17616613
evolution of symbiotic bacteria in the distal human intestine.	the adult human intestine contains trillions of bacteria, representing hundreds of species and thousands of subspecies. little is known about the selective pressures that have shaped and are shaping this community's component species, which are dominated by members of the bacteroidetes and firmicutes divisions. to examine how the intestinal environment affects microbial genome evolution, we have sequenced the genomes of two members of the normal distal human gut microbiota, bacteroides vulgatus ...	2007	17579514
identification of commensal bacterial strains that modulate yersinia enterocolitica and dextran sodium sulfate-induced inflammatory responses: implications for the development of probiotics.	an increasing body of evidence suggests that probiotic bacteria are effective in the treatment of enteric infections, although the molecular basis of this activity remains elusive. to identify putative probiotics, we tested commensal bacteria in terms of their toxicity, invasiveness, inhibition of yersinia-induced inflammation in vitro and in vivo, and modulation of dextran sodium sulfate (dss)-induced colitis in mice. the commensal bacteria escherichia coli, bifidobacterium adolescentis, bacter ...	2007	17485456
reduced mucosal antimicrobial activity in crohn's disease of the colon.	in order to maintain the mucosal barrier against luminal microorganisms the intestinal epithelial cells synthesise various broad-spectrum antimicrobial peptides including defensins and cathelicidins. recent studies indicate that both may be deficient in crohn's disease. to elucidate the possible functional consequences of this deficiency antimicrobial activity in colonic mucosa from patients with inflammatory bowel disease and healthy controls was investigated.	2007	17456510
epithelial barrier disruption allows nondisease-causing bacteria to initiate and sustain ibd in the il-10 gene-deficient mouse.	in the il-10 gene-deficient mouse model, development of intestinal inflammation is associated with a defect in epithelial barrier integrity that is thought to allow sufficient passage of bacteria or bacterial antigens to initiate a mucosal immune response. microbial monoassociation experiments into axenic animals have shown that some, but not all, endogenous bacteria will initiate an intestinal inflammatory response. for instance, bacteroides vulgatus does not initiate intestinal inflammation in ...	2007	17427241
therapeutic effects of roxithromycin in interleukin-10-deficient colitis.	a limited number of therapeutic strategies are currently available to treat patients with inflammatory bowel disease (ibd). interleukin-10 (il-10)-deficient mice, well characterized as an experimental model of ibd, develop severe chronic colitis because of aberrant th1 responses. roxithromycin (rxm), a macrolide antibiotic, has received attention because it offers not only antibacterial but also immunosuppressive effects. we examined the immunosuppressive effect of rxm on the development of ibd.	2007	17245768
cd4(+) t lymphocytes mediate colitis in hla-b27 transgenic rats monoassociated with nonpathogenic bacteroides vulgatus.	hla-b27/beta2 microglobulin transgenic (tg) rats develop spontaneous colitis when raised under specific pathogen-free (spf) conditions or after mono-association with bacteroides vulgatus (b. vulgatus), whereas germ-free tg rats fail to develop intestinal inflammation. spf hla-b27 tg rnu/rnu rats, which are congenitally athymic, remain disease free. these results indicate that commensal intestinal bacteria and t cells are both pivotal for the development of colitis in tg rats. however, it is not ...	2007	17206701
deoxycholic acid formation in gnotobiotic mice associated with human intestinal bacteria.	in humans and animals, intestinal flora is indispensable for bile acid transformation. the goal of our study was to establish gnotobiotic mice with intestinal bacteria of human origin in order to examine the role of intestinal bacteria in the transformation of bile acids in vivo using the technique of gnotobiology. eight strains of bile acid-deconjugating bacteria were isolated from ex-germ-free mice inoculated with a human fecal dilution of 10(-6), and five strains of 7alpha-dehydroxylating bac ...	2006	17152920
bacteroides dorei sp. nov., isolated from human faeces.	two gram-negative, anaerobic, non-spore-forming rod-shaped organisms were isolated from human faeces. these isolates were tentatively identified as bacteroides based on morphological and biochemical criteria and appeared closely related to bacteroides vulgatus atcc 8482(t). the 16s rrna gene sequence analysis showed that the isolates were highly related to each other (99.5 %) and confirmed their placement in the genus bacteroides. 16s rrna gene sequence similarity values with close phylogenetic ...	2006	16825642
persistence and growth of fecal bacteroidales assessed by bromodeoxyuridine immunocapture.	extraintestinal growth of fecal bacteria can impair accurate assessment of watershed health. anaerobic fecal bacteria belonging to the order bacteroidales are attractive candidates for fecal source tracking because they have host-specific distributions and do not grow well in the presence of high oxygen concentrations. growth of general and human-specific fecal bacteroidales marker organisms in environmental samples (sewage) and persistence of the corresponding genetic markers were investigated ...	2006	16820440
colitogenic and non-colitogenic commensal bacteria differentially trigger dc maturation and th cell polarization: an important role for il-6.	we investigated whether commensal bacteria modulate activation and maturation of bone marrow-derived dc and their ability to prime cd4(+) t cells. we used escherichia coli mpk, which induces colitis in gnotobiotic il-2-deficient (il-2(-/-)) mice, and bacteroides vulgatus mpk, which prevents e. coli-induced colitis. stimulation of dc with e. coli induced tnf-alpha, il-12 and il-6 secretion and expression of activation markers. moreover, stimulation of dc with e. coli increased t cell activation a ...	2006	16708404
gut-associated bacterial microbiota in paediatric patients with inflammatory bowel disease.	clinical and experimental observations in animal models indicate that intestinal commensal bacteria are involved in the initiation and amplification of inflammatory bowel disease (ibd). no paediatric reports are available on intestinal endogenous microflora in ibd.	2006	16648155
bacterial-induced inflammation in germ-free rabbit appendix.	the intestinal ecosystem is defined by a series of interactions between the microbiota, the mucosal epithelium, and the gut-associated lymphoid tissue (galt). perturbations in the fine balance of the interactions between these components can result in gastrointestinal diseases such as inflammatory bowel disease (ibd). the pathophysiology of ibd is thought to develop as a result of dysregulated mucosal immune responses to normal luminal microflora. several animal models for ibd have been develope ...	2005	16239845
effects of difructose anhydride iii (dfa iii) administration on rat intestinal microbiota.	the effects of difructose anhydride iii (di-d-fructofuranose-1,2':2,3'-dianhydride; dfa iii) administration (3% dfa iii for 4 weeks) on rat intestinal microbiota were examined using denaturing gradient gel electrophoresis (dgge). according to dgge profiles, the number of bacteria related to bacteroides acidofaciens and uncultured bacteria within the clostridium lituseburense group decreased, while that of bacteria related to bacteroides vulgatus, bacteroides uniformis and ruminococcus productus ...	2005	16233782