Molecular comparison of dominant microbiota associated with injured versus healthy mucosa in ulcerative colitis.
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Colitis, Ulcerative↗
Biomedical subjects
J Doré
Publications and source records attributed to J Doré.
Reducing weight increases postural stability in obese and morbid obese men.
OBJECTIVE: To investigate the effect of weight loss on balance control in obese and morbid obese men. METHODS: In a longitudinal and clinical intervention study, postural stability was measured with a force platform before and after weight loss in men. Weight loss was obtained in obese men (mean body mass index (BMI)=33.0 kg/m(2)) by hypocaloric diet until resistance and in morbid obese men (mean BMI=50.5 kg/m(2)) by bariatric surgery. Morbid obese men were tested before surgery, and 3 and 12 months after surgery when they had lost 20 and nearly 50% of initial body weight, respectively. Normal weight individuals (mean BMI=22.7 kg/m(2)) were tested twice within a 6- to 12-month period to serve as control. Body fatness and fat distribution measures, and posturographic parameters of the center of foot pressure (CP) along the antero-posterior and medio-lateral axes for conditions with and without vision were performed in all subjects. RESULTS: Weight loss averaged 12.3 kg after dieting and 71.3 kg after surgery. Body weight remained unchanged in the control group. After weight loss, nearly all measures of postural stability were improved with and without vision (i.e., CP speed and range in antero-posterior and medio-lateral axes). A strong linear relationship was observed between weight loss and improvement in balance control measured from CP speed (adjusted R (2)=0.65, P<0.001). CONCLUSION: Weight loss improves balance control in obese men and the extent of the improvement is directly related to the amount of weight loss. This should decrease the habitual greater risk of falling observed in obese individuals.
Adult↗
Review article: the role of bacteria in onset and perpetuation of inflammatory bowel disease.
We review the evidence that strongly suggests a role of the intestinal microbiota in the onset and perpetuation of inflammatory bowel disease (IBD). Experimental studies consisted of suppressing micro-organisms from the microbiota (using germ-free or gnotoxenic animals or antibiotics), introducing new micro-organisms or microbial components (e.g. probiotics, CpG-DNA) or selectively increasing some endogenous bacteria (e.g. using prebiotics). Intervention studies were performed in patients or animal models of spontaneous or chemically-induced colitis. Information was also obtained from observational studies that described the composition of the faecal and mucosal microbiota at various stages of the disease process and in controls. Many have used culture-independent techniques that identify bacteria based on the nucleic acid sequence of ribosomal RNA molecules. Microbiota in patients with IBD seem to be characterized by high concentrations of bacteria in contact with the mucosa, instability, the presence of high numbers of unusual bacteria and sometimes a reduction in the biodiversity. Studies searching for a generalized or localized dysbiosis in IBD are discussed, as well as those trying to identify bacterial molecules and receptors, which may be implicated in triggering the inflammatory process.
Bacterial Infections↗
Temperature gradient gel electrophoresis of fecal 16S rRNA reveals active Escherichia coli in the microbiota of patients with ulcerative colitis.
Previous studies of the endogenous microbiota in patients with ulcerative colitis (UC) have not taken bacterial activity into account, yet bacteria with high transcriptional activity might have a more important pathophysiological role than inactive bacteria. We therefore analyzed the biodiversity of active bacteria in the fecal microbiota of UC patients, in comparison with that of healthy subjects. Feces were collected from nine patients with active UC and from nine healthy controls. Total DNA and RNA were extracted, and 16S ribosomal DNA and RNA were amplified by PCR and reverse transcription-PCR, respectively. Amplification products were compared by means of temporal temperature gradient gel electrophoresis (TTGE). Bands of interest were excised, sequenced, and identified by comparison with the GenBank database (NCBI). The dominant-species diversity based on RNA-derived TTGE profiles was significantly lower for UC patients than for healthy controls (P = 0.01). The mean similarity index between the "present" and "active" microbiota was 74% +/- 18% for UC patients. Comparison of the individual "active" microbiota identified a band that was present for eight UC patients and only two controls (89% versus 22%; P = 0.008). The band was sequenced for 6 patients and always corresponded to Escherichia coli. The biodiversity of active bacteria in the dominant fecal microbiota of patients with UC is lower than that of healthy subjects. E. coli is more represented in the active microbiota of UC patients. The possible pathophysiological role of this difference remains to be determined.
Adult↗
Resilience of the dominant human fecal microbiota upon short-course antibiotic challenge.
Recent studies have shown that the human fecal microbiota is composed of a consortium of species specific to the host and resistant to modifications over time. Antibiotics are known to affect the intestinal microflora, and ensuing changes may result in antibiotic-associated diarrhea. It is therefore important to characterize the nature and amplitude of these modifications and the ability of this ecosystem to return to its original profile-i.e., its resilience. Six healthy volunteers received oral amoxicillin (1.5 g/day) for 5 days. Fecal samples were collected at day 0 (D0) before antibiotic treatment and at set intervals until 60 days thereafter. Fecal DNA was isolated, and V6-to-V8 regions of the 16S rRNA genes were amplified by PCR with general primers and analyzed by temporal temperature gradient gel electrophoresis. Dominant species profiles were compared on the basis of similarity (Pearson correlation coefficient). Dominant species profiles at D0 were used as a reference. The fecal microbiota showed a major shift in dominant species upon antibiotic treatment, starting 24 h after treatment initiation and reaching an average similarity of only 74% after 4 days. Within 30 days following antibiotic treatment, the fecal microbiota tended to reach an average similarity of 88% to the D0 value; within 60 days, the average similarity to the D0 value was 89%. However, in one subject, important modifications persisted for at least 2 months, with similarity to the D0 value remaining below 70%. We demonstrated the resilience of the dominant human fecal microbiota upon short-course antibiotic challenge. Yet the persistence of long-term alterations in some subjects may explain susceptibilities to antibiotic-associated diarrhea. Furthermore, these findings suggest that strategies reinforcing the ability of the fecal microbiota to resist modifications would be of clinical relevance.
Administration, Oral↗
Review article: gut flora and inflammatory bowel disease.
The pathogenesis of inflammatory bowel disease involves interactions between the host susceptibility, mucosal immunity and intestinal microflora. There is therefore great interest in the changes in the endogenous flora in inflammatory bowel disease patients and in the establishment of potential genetic variations in host responses to endogenous bacteria. In this review, we summarize the modifications in the various regional ecosystems in the gastrointestinal tract during inflammatory bowel disease (luminal bacteria in faeces or inside the gastrointestinal tract, bacteria in mucus and bacteria directly attached to the mucosa). Results were obtained following a 'candidate microorganism strategy' and, as is occurring increasingly frequently, following a 'full description strategy', which has progressed largely due to the development of culture-independent techniques. The possibility of modifying the ecosystem using prebiotics or probiotics offers hope for new treatment developments, particularly in the prevention of relapse.
Bacteria↗
Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon.
BACKGROUND AND AIMS: The colonic microflora is involved in the pathogenesis of Crohn's disease (CD) but less than 30% of the microflora can be cultured. We investigated potential differences in the faecal microflora between patients with colonic CD in remission (n=9), patients with active colonic CD (n=8), and healthy volunteers (n=16) using culture independent techniques. METHODS: Quantitative dot blot hybridisation with six radiolabelled 16S ribosomal ribonucleic acid (rRNA) targeting oligonucleotide probes was used to measure the proportions of rRNA corresponding to each phylogenetic group. Temporal temperature gradient gel electrophoresis (TTGE) of 16S rDNA was used to evaluate dominant species diversity. RESULTS: Enterobacteria were significantly increased in active and quiescent CD. Probe additivity was significantly lower in patients (65 (11)% and 69 (6)% in active CD and quiescent CD) than in healthy controls (99 (7)%). TTGE profiles varied markedly between active and quiescent CD but were stable in healthy conditions. CONCLUSION: The biodiversity of the microflora remains high in patients with CD. Enterobacteria were observed significantly more frequently in CD than in health, and more than 30% of the dominant flora belonged to yet undefined phylogenetic groups.
Adolescent↗
Gastrointestinal tract and the elderly: functional foods, gut microflora and healthy ageing.
Advances in science and medicine as well as improved living standards have led to a steady increase in life expectancy. Yet ageing is associated with increased susceptibility to degenerative or infectious diseases, which may be exacerbated by a poor nutritional status. The intestinal microflora will mediate crucial events towards the protection or degradation of health. It is hence essential and timely that strategies of preventive nutrition aimed at maintaining or improving the quality of life of the ageing population be developed. "CROWNALIFE" is a newly funded EuropeanUnion project, so called because of its emphasis on the preservation of the period of independence of the elderly, recognised as the "crown of life". The project aims at assessing age-related alterations and exploring strategies to restore and maintain a balanced healthy intestinal environment. Current knowledge on the composition and function of the human intestinal microflora is still improving with the use of better methodologies and yet their evolution with ageing has not been investigated in detail. There have been a few reports that putatively protective lactic acid bacteria, in general, and bifidobacteria, in particular, seem less represented in the elderly faecal flora. We have also observed an increase in species diversity of the dominant faecal microflora with ageing. This certainly warrants confirmation and is being addressed by the investigation of age-related changes in the structure and function of the intestinal flora of the elderly in countries across Europe. Ensuing results will constitute a baseline for functional-food based strategies aimed at providing health benefits for the elderly.
Adolescent↗
Molecular biological methods for studying the gut microbiota: the EU human gut flora project.
Seven European laboratories co-operated in a joint project (FAIR CT97-3035) to develop, refine and apply molecular methods towards facilitating elucidation of the complex composition of the human intestinal microflora and to devise robust methodologies for monitoring the gut flora in response to diet. An extensive database of 16S rRNA sequences for tracking intestinal bacteria was generated by sequencing the 16S rRNA genes of new faecal isolates and of clones obtained by amplification with polymerase chain reaction (PCR) on faecal DNA from subjects belonging to different age groups. The analyses indicated that the number of different species (diversity) present in the human gut increased with age. The sequence information generated, provided the basis for design of 16S rRNA-directed oligonucleotide probes to specifically detect bacteria at various levels of phylogenetic hierarchy. The probes were tested for their specificity and used in whole-cell and dot-blot hybridisations. The applicability of the developed methods was demonstrated in several studies and the major outcomes are described.
Adult↗
Fusobacterium prausnitzii and related species represent a dominant group within the human fecal flora.
The human gut microflora plays a key role in nutrition and health. It has been extensively studied by conventional culture techniques. However these methods are difficult, time consuming and their results not always consistent. Furthermore microscopic counts indicate that only 20 to 40% of the total flora can be cultivated. Among the predominant species of the human gut, Fusobacterium prausnitzii was reported either as one of the most frequent and numerous species or was seldom retrieved. We designed and validated a specific rRNA-targeted oligonucleotide probe, called S-*-Fprau-0645-a-A-23, to accurately detect and quantify F. prausnitzii and relatives within the human fecal microflora. The target group accounted for 5.3 +/- 3% of total bacterial 16S rRNA using dot blot hybridization (10 human fecal samples) and 16.5 +/- 7% of cells stained with Dapi using in situ hybridization (10 other human fecal samples). A specific morphology seemed to be typical and dominant: two cells forming an asymmetrical double droplet. This work showed that F. prausnitzii and phylogenetically related species represent a dominant group within the human fecal flora.
Adult↗
Molecular phylogenetic profiling of prokaryotic communities in guts of termites with different feeding habits.
Termites are an important group of terrestrial insects that harbor an abundant gut microbiota, many of which contribute to digestion, termite nutrition and gas (CH(4), CO(2) and H(2)) emission. With 2200 described species, termites also provide a good model to study relationships between host diet and gut microbial community structure and function. We examined the relationship between diet and gut prokaryotic community profiles in 24 taxonomically and nutritionally diverse species of termites by using nucleic acid probes targeting 16S-like ribosomal RNAs. The relative abundance of domain-specific 16S-like rRNAs recovered from gut extracts varied considerably (ranges: Archaea (0-3%); Bacteria (15-118%)). Although Bacteria were always detectable and the most abundant, differences in domain-level profiles were correlated with termite diet, as evidenced by higher relative abundances of Archaea in guts of soil-feeding termites, compared to those of wood-feeding species in the same family. The oligonucleotide probes also readily distinguished gut communities of wood-feeding taxa in the family Termitidae (higher termites) from those of other wood-feeding termite families (lower termites). The relative abundances of 16S-like archaeal rRNA in guts were positively correlated with rates of methane emission by live termites, and were consistent with previous work linking high relative rates of methanogenesis with the soil (humus)-feeding habit. Probes for methanogenic Archaea detected members of only two families (Methanobacteriaceae and Methanosarcinaceae) in termite guts, and these typically accounted for 60% of the all archaeal probe signal. In four species of termites, Methanosarcinaceae were dominant, a novel observation for animal gut microbial communities, but no clear relationship was apparent between methanogen family profiles and termite diet or taxonomy.
Journal Article↗
Comparative study of bacterial groups within the human cecal and fecal microbiota.
The composition of the human cecal microbiota is poorly known because of sampling difficulties. Samples of cecal fluid from eight subjects were collected via an intestinal tube. Feces were also collected. Total anaerobes, facultative anaerobes, bifidobacteria, and Bacteroides were enumerated by culture methods, and the predominant phylogenetic groups were quantified by molecular hybridization using a set of six rRNA-targeted probes. The numbers of strict anaerobes, bifidobacteria, Bacteroides, and members of the Clostridium coccoides group and Clostridium leptum subgroup were lower in the cecum. Facultative anaerobes represented 25% of total bacteria in the cecum versus 1% in the feces.
Adult↗
Distance perception of vehicle rear lights in fog.
Perceptual difficulty is one of the main explanations given for the behavioral modifications and high accident rate associated with driving in fog. The present study investigates how fog and the characteristics of vehicle rear lights affect distance perception. Two experiments in a fog chamber (meteorological visibility range of 5-15 m) were run under conditions simulating nighttime fog. The participants gave verbal estimates of the distance (8-28 m) of vehicles simulated by rear-light arrangements. The results revealed an average increase of 60% in the perceived distance of vehicles in fog as compared with normal visibility conditions. Distance overestimation was particularly pronounced when the vehicle had only 1 fog light instead of 2 and when the lights were close together. No effect of light height was observed. These results suggest that the perception of vehicle distance in nighttime fog could be significantly improved by the presence of 2 lights with maximal spacing. Actual or potential applications of this research include vehicle rear light design.
Accidents, Traffic↗
[Molecular analysis of the colonic microflora].
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Bacteria↗
Ecological study of a bioaugmentation failure.
A nitrifying sequencing batch reactor was inoculated twice with the aerobic denitrifying bacterium Microvirgula aerodenitrificans and fed with acetate. No improvement was obtained on nitrogen removal. The second more massive inoculation was even followed by a nitrification breakdown, while at the same time, nitrification remained stable in a second reactor operated under the same conditions without bioaugmentation. Fluorescent in situ hybridization with rRNA-targeted probes revealed that the added bacteria almost disappeared from the reactor within 2 days, and that digestive vacuoles of protozoa gave strong hybridization signals with the M. aerodenitrificans-specific probe. An overgrowth of protozoa, coincident with the disappearance of free-living bacteria, was monitored by radioactive dot-blot hybridization only in the bioaugmented reactor. Population dynamics were analysed with a newly developed in situ quantification procedure of the probe-targeted bacteria. The nitrifying groups of bacteria decreased in a similar way in the bioaugmented and non-bioaugmented reactors. Other bacterial groups evolved differently. The involvement of different ecological parameters are discussed separately for each reactor. These results underline the importance of predator-prey interaction and illustrate the undesirable effects of massive bioaugmentation.
Animals↗
Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut.
The human intestinal tract harbors a complex microbial ecosystem which plays a key role in nutrition and health. Although this microbiota has been studied in great detail by culture techniques, microscopic counts on human feces suggest that 60 to 80% of the observable bacteria cannot be cultivated. Using comparative analysis of cloned 16S rRNA gene (rDNA) sequences, we have investigated the bacterial diversity (both cultivated and noncultivated bacteria) within an adult-male fecal sample. The 284 clones obtained from 10-cycle PCR were classified into 82 molecular species (at least 98% similarity). Three phylogenetic groups contained 95% of the clones: the Bacteroides group, the Clostridium coccoides group, and the Clostridium leptum subgroup. The remaining clones were distributed among a variety of phylogenetic clusters. Only 24% of the molecular species recovered corresponded to described organisms (those whose sequences were available in public databases), and all of these were established members of the dominant human fecal flora (e.g., Bacteroides thetaiotaomicron, Fusobacterium prausnitzii, and Eubacterium rectale). However, the majority of generated rDNA sequences (76%) did not correspond to known organisms and clearly derived from hitherto unknown species within this human gut microflora.
Bacteroides↗
[Is it possible to die a good death?].
Is there any sense in wondering if one can "die a good death" Indeed, the word "euthanasia" as such offers food for thought. Obviously, human beings must die. The only real question is: Can help and assistance be given (through others) to a person when facing this ineluctable issue; and, if so, in which way and how far? To make things clearer, two points may be taken into consideration. On the one hand, it is a fact that the roman-catholic tradition has been able to set up a practice of a "good death piety", or even a "good death pastoral". But, on the other hand, we must not forget that when we consider what "euthanasia" means for the end of life and bear in mind what "eugenism" means for the beginning of life as well as the way it has been used, then it can only put us on the alert for possible serious abuse.... Considering all this, the question may be put as follows: not: is it possible, under certain circumstances, to give someone his or her death; but: how must I help and assist a person to live his or her life to the very end, if possible up to death?
Attitude to Death↗
Recovery and phylogenetic analysis of archaeal rRNA sequences from continental shelf sediments.
Phylogenetic analyses of archaeal 16S rRNA genes (rDNA) from DNA extracted from continental shelf sediments revealed the presence of two major lineages, belonging to the kingdoms Crenarchaeota and Euryarchacota, respectively. Our analyses indicate that the benthic Archaea belong to a new group, divergent from the marine low-temperature planktonic Archaea. This is the first report showing the existence of Archaea, unrelated to methanogens, specifically associated with low-temperature anoxic marine sediments.
Archaea↗