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Microbiota
Kinds of Microbiota Terms modified by Microbiota Selected AbstractsEffects of the Prebiotics GroBiotic® -A and Inulin on the Intestinal Microbiota of Red Drum, Sciaenops ocellatusJOURNAL OF THE WORLD AQUACULTURE SOCIETY, Issue 4 2009Gary Burr Two separate feeding trials examined the effects of dietary supplementation of the prebiotics GroBiotic® -A and inulin on growth performance and gastrointestinal tract microbiota of the red drum, Sciaenops ocellatus. In the first feeding trial, fish meal-based diets without prebiotics or supplemented with either GroBiotic® -A or inulin at 1% of dry weight were fed to triplicate groups of juvenile red drum (initial weight of 2.6 g) in 110-L aquaria operated as a brackish water (7 ppt) recirculating system for 8 wk. In the second feeding trial, soybean meal/fish meal-based diets supplemented with either GroBiotic® -A or inulin at 1% of dry weight were fed to triplicate groups of red drum (initial weight of 15.8 g) in 110-L aquaria operated as either a common recirculating water system or closed system with individual biofilters (independent aquaria) for 6 wk. Supplementation of the prebiotics in either feeding trial did not alter weight gain, feed efficiency ratio, or protein efficiency ratio of red drum fed the various diets. In the second feeding trial, the culture system significantly affected weight gain, feed efficiency ratio, and protein efficiency ratio although there were no effects of dietary treatments on fish performance or whole-body protein, lipid, moisture, or ash. Denaturing gradient gel electrophoresis (DGGE) analysis of the gastrointestinal tract microbial community showed no effect of the dietary prebiotics as the microbial community appeared to be dominated by a single organism with very low diversity when compared with other livestock and fish species. DGGE of the microbial community in the biofilters of the independent aquariums showed a diverse microbial community that was not affected by the dietary prebiotics. [source] Dietary Modification of the Intestinal MicrobiotaNUTRITION REVIEWS, Issue 6 2004M.P.H., Volker Mai Ph.D. Humans harbor a consortium of commensal bacteria in their gut that are thought to be crucial for normal health. However, the extent of microbial diversity in the gut and the physiologic functions of the microflora have not yet been fully characterized. Molecular tools are now available to characterize the associations between diet, microflora composition, and health in greater depth. New molecular studies have confirmed earlier culture-based observations that diet has a role in the regulation of microflora composition. In the near future, new insight into these associations should allow for the design of specific diets aimed at improving health by modulating microflora. [source] ORIGINAL ARTICLE: Prenatal Priming of Cord Blood T Lymphocytes by Microbiota in the Maternal VaginaAMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY, Issue 3 2009Krystyna Stencel-Gabriel Problem, In the vagina of women at the reproductive age, more than 170 strains of bacteria and yeasts are found. The effect of vaginal flora on neonatal T cells is yet to be investigated. Method of study, We analyzed CD45RA and CD45RO expression on neonatal CD4+ T cells and cytokine production in CBMC cultures (interferon-, (IFN-, ), interleukin-4 (IL-4) and IL-12) related to vaginal bacteria isolated from a maternal vagina. We collected vaginal swabs from 36 women at the first stage of the delivery and cord blood from their newborns. IFN-,, IL-4, and IL-12 in stimulated CBMC were measured and the expression of CD45RA/CD45RO on CD4+ T cells was assessed. Results, We noted the difference in CD45RO CD4+ expression and IL-12 levels between the newborns whose mothers were or were not colonized with Lactobacillus in the vagina (newborns whose mothers were colonized with Lactobacillus: CD45RO-10%±3; IL-12-0.2 pg/mL ± 0.05; newborns whose mothers were not colonized with Lactobacillus: CD45RO-6%±3; IL-12-2.0 pg/mL ± 0.7). Conclusion, Our results may indicate that lactobacilli in maternal vagina influence the development of neonatal immune system. Yet, more research is needed using specified bacterial antigens. [source] Response by Anu Huurre, on behalf of the NAMI (Nutrition, Allergy, Mucosal Immunology and Intestinal Microbiota) research groupCLINICAL & EXPERIMENTAL ALLERGY, Issue 10 2008Anu Huurre No abstract is available for this article. [source] Bacteria divert resources from growth for magellanic penguin chicksECOLOGY LETTERS, Issue 6 2002Jaime Potti Abstract The influence of bacteria on the growth of their wild avian hosts is unknown. We tested experimentally whether administration of a wide-spectrum antibiotic (cephalosporine) during early development of magellanic penguin (Spheniscus magellanicus) chicks had any effect on their growth rates in the wild. Chicks that were injected in two occasions with cephalosporine grew faster than control untreated chicks. The positive effect of medication on nestling growth disappeared after the treatment ceased, did not alter haematological indices indicative of health status, had no influence on chick survival until near independence and was related to a changed bacterial composition of the faecal microbiota of treated chicks when compared with that from control chicks. These results were similar to those obtained for poultry with antimicrobials promoting growth and chick nutrient assimilation rates. Gram-positive bacilli in the diphtheroid genus Corynebacterium are likely candidates to cause decreased growth rates in magellanic penguin chicks. [source] Salient virulence factors in anaerobic bacteria, with emphasis on their importance in endodontic infectionsENDODONTIC TOPICS, Issue 1 2004Ingar Olsen Endodontic infections by microbial invasion of the necrotic pulp lead to apical periodontitis of both acute and chronic forms. Acute lesions often develop from multiplication of bacteria in primary infections. Such lesions may also occur as exacerbations of chronic forms provoked for example in conjunction with endodontic treatment measures. The clinical course appears related to the character of the microflora. While primary infections are predominated by a mixed flora of anaerobic bacteria and resembles that of aggressive marginal periodontitis, chronic forms of apical periodontitis emerge following regression of the acute infection, whereupon prevailing bacteria have assumed low activity. The significance of virulence factors is easy to understand as far as acute inflammatory conditions are concerned. The role of virulence factors for sustaining chronic inflammation is more unclear and complex. This review is about salient virulence factors in some selected bacterial genera such as Peptostreptococcus, Porphyromonas, Prevotella and Fusobacterium, which often predominate the root canal microbiota in the acute phase of endodontic infections. [source] Halophilic archaea in the human intestinal mucosaENVIRONMENTAL MICROBIOLOGY, Issue 9 2010Andrew P. A. Oxley Summary The human gastrointestinal tract microbiota, despite its key roles in health and disease, remains a diverse, variable and poorly understood entity. Current surveys reveal a multitude of undefined bacterial taxa and a low diversity of methanogenic archaea. In an analysis of the microbiota in colonic mucosal biopsies from patients with inflammatory bowel disease we found 16S rDNA sequences representing a phylogenetically rich diversity of halophilic archaea from the Halobacteriaceae (haloarchaea), including novel phylotypes. As the human colon is not considered a salty environment and haloarchaea are described as extreme halophiles, we evaluated and further discarded the possibility that these sequences originated from pre-colonoscopy saline lavage solutions. Furthermore, aerobic enrichment cultures prepared from a patient biopsy at low salinity (2.5% NaCl) yielded haloarchaeal sequence types. Microscopic observation after fluorescence in situ hybridization provided evidence of the presence of viable archaeal cells in these cultures. These results prove the survival of haloarchaea in the digestive system and suggest that they may be members of the mucosal microbiota, even if present in low numbers in comparison with methanogenic archaea. Investigation of a potential physiological basis of this association may lead to new insights into gastrointestinal health and disease. [source] The hologenome theory of evolution contains Lamarckian aspects within a Darwinian frameworkENVIRONMENTAL MICROBIOLOGY, Issue 12 2009Eugene Rosenberg Summary The hologenome theory of evolution emphasizes the role of microorganisms in the evolution of animals and plants. The theory posits that the holobiont (host plus all of its symbiont microbiota) is a unit of selection in evolution. Genetic variation in the holobiont that can occur either in the host and/or in the microbial symbiont genomes (together termed hologenome) can then be transmitted to offspring. In addition to the known modes of variation, i.e. sexual recombination, chromosomal rearrangement and mutation, variation in the holobiont can occur also via two mechanisms that are specific to the hologenome theory: amplification of existing microorganisms and acquisition of novel strains from the environment. These mechanisms are Lamarckian in that (i) they are regulated by ,use and disuse' (of microbes) and (ii) the variations in the hologenome are transmitted to offspring, thus satisfying also the Lamarckian principle of ,inheritance of acquired characteristics'. Accordingly, the hologenome theory incorporates Lamarckian aspects within a Darwinian framework, accentuating both cooperation and competition within the holobiont and with other holobionts. [source] Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adultsENVIRONMENTAL MICROBIOLOGY, Issue 7 2009-Stojanovi, Mirjana Rajili Summary In this paper we present the in silico assessment of the diversity of variable regions of the small subunit ribosomal RNA (SSU rRNA) gene based on an ecosystem-specific curated database, describe a probe design procedure based on two hypervariable regions with minimal redundancy and test the potential of such probe design strategy for the design of a flexible microarray platform. This resulted in the development and application of a phylogenetic microarray for studying the human gastrointestinal microbiota , referred as the human intestinal tract chip (HITChip). Over 4800 dedicated tiling oligonucleotide probes were designed based on two hypervariable regions of the SSU rRNA gene of 1140 unique microbial phylotypes (< 98% identity) following analysis of over 16 000 human intestinal SSU rRNA sequences. These HITChip probes were hybridized to a diverse set of human intestinal samples and SSU rRNA clones to validate its fingerprinting and quantification potential. Excellent reproducibility (median Pearson's correlation of 0.99) was obtained following hybridization with T7 polymerase transcripts generated in vitro from SSU rRNA gene amplicons. A linear dose,response was observed with artificial mixtures of 40 different representative amplicons with relative abundances as low as 0.1% of total microbiota. Analysis of three consecutively collected faecal samples from ten individuals (five young and five elderly adults) revealed temporal dynamics and confirmed that the adult intestinal microbiota is an individual-specific and relatively stable ecosystem. Further analysis of the stable part allowed for the identification of a universal microbiota core at the approximate genus level (90% sequence similarity). This core consists of members of Actinobacteria, Bacteroidetes and Firmicutes. Used as a phylogenetic fingerprinting tool with the possibility for relative quantification, the HITChip has the potential to bridge the gaps in our knowledge in the quantitative and qualitative description of the human gastrointestinal microbiota composition. [source] Quantitative, longitudinal profiling of the primate fecal microbiota reveals idiosyncratic, dynamic communitiesENVIRONMENTAL MICROBIOLOGY, Issue 3 2006Joy Wireman Summary We used slot blot hybridization, quantitative polymerase chain reaction (qPCR), and flow cytometry microarrays to quantify specific 16S rDNAs in weekly fecal specimens from four monkeys housed in a research vivarium for periods ranging from five to 8 months. Even in these uniformly housed and fed animals the gut microbiota is idiosyncratic, very dynamic on short timescales, and shows significant positive and negative correlations among some bacteria as well as responses to heavy metal exposure. The relative quantification (fmol targets per total fmol bacterial 16S rDNA) afforded by flow cytometry microarrays agreed well with the absolute quantification (nanogram of target DNA per nanogram of fecal DNA) afforded by slot blots and qPCR. We also noted strengths and weaknesses in inter-method comparisons for DNA-based quantification of these complex bacterial communities. [source] Niche heterogeneity determines bacterial community structure in the termite gut (Reticulitermes santonensis)ENVIRONMENTAL MICROBIOLOGY, Issue 7 2005Hong Yang Summary Differences in microenvironment and interactions of microorganisms within and across habitat boundaries should influence structure and diversity of the microbial communities within an ecosystem. We tested this hypothesis using the well characterized gut tract of the European subterranean termite Reticulitermes santonensis as a model. By cloning and sequencing analysis and molecular fingerprinting (terminal restriction fragment length polymorphism), we characterized the bacterial microbiota in the major intestinal habitats , the midgut, the wall of the hindgut paunch, the hindgut fluid and the intestinal protozoa. The bacterial community was very diverse (> 200 ribotypes) and comprised representatives of several phyla, including Firmicutes (mainly clostridia, streptococci and Mycoplasmatales -related clones), Bacteroidetes, Spirochaetes and a number of Proteobacteria, all of which were unevenly distributed among the four habitats. The largest group of clones fell into the so-called Termite group 1 (TG-1) phylum, which has no cultivated representatives. The majority of the TG-1 clones were associated with the protozoa and formed two phylogenetically distinct clusters, which consisted exclusively of clones previously retrieved from the gut of this and other Reticulitermes species. Also the other clones represented lineages of microorganisms that were exclusively recovered from the intestinal tract of termites. The termite specificity of these lineages was underscored by the finding that the closest relatives of the bacterial clones obtained from R. santonensis were usually derived also from the most closely related termites. Overall, differences in diversity between the different gut habitats and the uneven distribution of individual phylotypes support conclusively that niche heterogeneity is a strong determinant of the structure and spatial organization of the microbial community in the termite gut. [source] Changes in faecal bacteria associated with concentrate and forage-only diets fed to horses in trainingEQUINE VETERINARY JOURNAL, Issue 9 2009B. WILLING Summary Reasons for performing study: Diets rich in readily fermentable carbohydrates, fed traditionally to meet the increased energy requirements of the performance horse, are associated with a number of gastrointestinal disorders that involve disturbances in the intestinal microbiota, however, these changes are poorly understood. Objectives: With the long-term objective of improving intestinal health and to increase understanding of the relationship between diet and microbiota, the effect of feeding Standardbred horses a high-energy forage-only (F) diet was studied compared to a more traditional forage-concentrate (C) diet on faecal microbiota. Methods: Diets were fed in a cross-over design to 6 mature geldings on a scheduled training regime, both periods consisting of 29 days. DNA was extracted from faecal samples collected at 4 time points from each period, bacterial 16S rRNA genes were amplified and community composition assessed by terminal-restriction fragment length polymorphism, cloning and sequencing. Faecal pH and cultivable lactic acid bacteria (LAB) and enterobacteria were also assessed on the final collection day of each period. Results: Diet F resulted in a microbial composition that was more stable between sampling periods and had lower counts (P<0.05) of cultivable LAB and specifically members of the Streptococcus bovis/equinus complex. Motile and swarming Lactobacillus ruminis was present in all horses on diet C and not in horses on diet F. Diet C also resulted in the increase (P<0.05) in members of Clostridiaceae cluster III and a concomitant reduction (P<0.05) in an unknown group of Bacteroidales. Conclusions and potential relevance: The greater microbial stability and reduction in LAB and members of the Streptococcus bovis/equinus complex on diet F indicate an opportunity to develop feeding strategies that support equine health and welfare. Novel changes identified in the faecal microbiota that resulted from carbohydrate inclusion merit further investigation. [source] The role of colonic metabolism in lactose intoleranceEUROPEAN JOURNAL OF CLINICAL INVESTIGATION, Issue 8 2008T. He ABSTRACT Lactose maldigestion and intolerance affect a large part of the world population. The underlying factors of lactose intolerance are not fully understood. In this review, the role of colonic metabolism is discussed, i.e. fermentation of lactose by the colonic microbiota, colonic processing of the fermentation metabolites and how these processes would play a role in the pathophysiology of lactose intolerance. We suggest that the balance between the removal and production rate of osmotic,active components (lactose, and intermediate metabolites, e.g. lactate, succinate, etc.) in the colon is a key factor in the development of symptoms. The involvement of the colon may provide the basis for designing new targeted strategies for dietary and clinical management of lactose intolerance. [source] Periodontal microbiota and clinical periodontal status in a rural sample in southern ThailandEUROPEAN JOURNAL OF ORAL SCIENCES, Issue 5 2002P. N. Papapanou We sought to determine (i) the association of subgingival bacterial profiles to clinical periodontal status in a population with limited access to dental care in Thailand, and (ii) the external validity of our earlier findings from a similar study in rural China. We examined 356 subjects, 30,39 yr old and 50,59 yr old, with respect to clinical periodontal status and subgingival plaque at maximally 14 sites per subject. Checkerboard hybridizations were used to analyse a total of 4343 samples. The prevalence of the 27 species investigated ranged between 87.2% and 100%. Discriminant analysis based on microbial profiles classified correctly 67.5% of all deep (, 5 mm) and 64.2% of all shallow sites, and 67.4% of all subjects with and 69.3% of all subjects without , 3 deep pockets. High colonization by ,red complex' bacteria was four times as likely (95% Confidence Limits (CL) 2.5,6.6) in subjects with ,,10 sites with attachment loss of ,,5 mm, and 4.3 times as likely (95% CL 2.6,7.1) in subjects with , 30 such sites. The data confirmed (i) the ubiquitous prevalence of the bacteria investigated in subjects with no regular access to dental care; and (ii) the high odds for periodontal pathology conferred by increased levels of specific periodontal bacteria. [source] Bifidobacterium longum lysate, a new ingredient for reactive skinEXPERIMENTAL DERMATOLOGY, Issue 8 2010Audrey Guéniche Please cite this paper as: Bifidobacterium longum lysate, a new ingredient for reactive skin. Experimental Dermatology 2010; 19: e1,e8. Abstract:, Reactive skin is characterized by marked sensitivity to physical (heat, cold, wind) or chemical (topically applied products) stimuli and by the impairment of the skin barrier's ability to repair itself. Several lines of evidence suggest that beyond their capacity to positively influence the composition of intestinal microbiota, some probiotic bacteria can modulate the immune system both at local and systemic levels, thereby improving immune defense mechanisms and/or down-regulating immune disorders such as allergies and intestinal inflammation. Several recent human clinical trials clearly suggest that probiotic supplementation might be beneficial to the skin. Using a probiotic lysate, Bifidobacterium longum sp. extract (BL), we demonstrated first in vitro, and then in a clinical trial, that this non-replicating bacteria form applied to the skin was able to improve sensitive skin. The effect of BL were evaluated first on two different models. Using ex vivo human skin explant model we found a statistically significant improvement versus placebo in various parameters associated with inflammation such as a decrease in vasodilation, oedema, mast cell degranulation and TNF-alpha release. Moreover, using nerve cell cultures in vitro, we showed that after 6 h of incubation in culture medium (0.3,1%), the probiotic lysate significantly inhibited capsaicin-induced CGRP release by neurones. Then, a topical cream containing the active extract was tested in a randomized, double-blind, placebo-controlled trial. Sixty-six female volunteers with reactive skin were randomly given either the cream with the bacterial extract at 10% (n = 33) or the control cream (n = 33). The volunteers applied the cream to the face, arms and legs twice a day for two months. Skin sensitivity was assessed by stinging test (lactic acid) and skin barrier recovery was evaluated by measuring trans-epidermal water loss following barrier disruption induced by repeated tape-stripping at D1, D29 and D57. The results demonstrated that the volunteers who applied the cream with bacterial extract had a significant decrease in skin sensitivity at the end of the treatment. Moreover, the treatment led to increase skin resistance against physical and chemical aggression compared to the group of volunteers who applied the control cream. Notably, the number of strippings required to disrupt skin barrier function was significantly increased for volunteers treated with the active cream. Clinical and self-assessment scores revealed a significant decrease in skin dryness after 29 days for volunteers treated with the cream containing the 10% bacterial extract. Since in vitro studies demonstrated that, on one hand, isolate sensitive neurones release less CGRP under capsaicin stimulation in the presence of the bacterial extract and, on the other hand, increased skin resistance in volunteers applying the test cream, we speculate that this new ingredient may decrease skin sensitivity by reducing neurone reactivity and neurone accessibility. The results of this studies demonstrate that this specific bacterial extract has a beneficial effect on reactive skin. These findings suggest that new approaches, based on a bacteria lysate, could be developed for the treatment and/or prevention of symptoms related to reactive skin. [source] A review on the interactions between gut microbiota and innate immunity of fishFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 2 2008Geovanny D. Gómez Abstract Although fish immunology has progressed in the last few years, the contribution of the normal endogenous microbiota to the overall health status has been so far underestimated. In this context, the establishment of a normal or protective microbiota constitutes a key component to maintain good health, through competitive exclusion mechanisms, and has implications for the development and maturation of the immune system. The normal microbiota influences the innate immune system, which is of vital importance for the disease resistance of fish and is divided into physical barriers, humoral and cellular components. Innate humoral parameters include antimicrobial peptides, lysozyme, complement components, transferrin, pentraxins, lectins, antiproteases and natural antibodies, whereas nonspecific cytotoxic cells and phagocytes (monocytes/macrophages and neutrophils) constitute innate cellular immune effectors. Cytokines are an integral component of the adaptive and innate immune response, particularly IL-1,, interferon, tumor necrosis factor-,, transforming growth factor-, and several chemokines regulate innate immunity. This review covers the innate immune mechanisms of protection against pathogens, in relation with the installation and composition of the normal endogenous microbiota in fish and its role on health. Knowledge of such interaction may offer novel and useful means designing adequate therapeutic strategies for disease prevention and treatment. [source] Abundance, diversity, and activity of microbial assemblages associated with coral reef fish guts and fecesFEMS MICROBIOLOGY ECOLOGY, Issue 1 2010Steven Smriga Abstract Feces and distal gut contents were collected from three coral reef fish species. Bacteria cell abundances, as determined via epifluorescence microscopy, ranged two orders of magnitude among the fishes. Mass-specific and apparent cell-specific hydrolytic enzyme activities in feces from Chlorurus sordidus were very high, suggesting that endogenous fish enzymes were egested into feces. Denaturing gradient gel electrophoresis profiles of 16S rRNA genes were more similar among multiple individuals of the surgeonfish Acanthurus nigricans than among individuals of the parrotfish C. sordidus or the snapper Lutjanus bohar. Analyses of feces-derived 16S rRNA gene clones revealed that at least five bacterial phyla were present in A. nigricans and that Vibrionaceae comprised 10% of the clones. Meanwhile, C. sordidus contained at least five phyla and L. bohar three, but Vibrionaceae comprised 71% and 76% of the clones, respectively. Many sequences clustered phylogenetically to cultured Vibrio spp. and Photobacterium spp. including Vibrio ponticus and Photobacterium damselae. Other Vibrionaceae -like sequences comprised a distinct phylogenetic group that may represent the presence of ,feces-specific' bacteria. The observed differences among fishes may reflect native gut microbiota and/or bacterial assemblages associated with ingested prey. [source] PCR DGGE and RT-PCR DGGE show diversity and short-term temporal stability in the Clostridium coccoides,Eubacterium rectale group in the human intestinal microbiotaFEMS MICROBIOLOGY ECOLOGY, Issue 3 2006Johanna Maukonen Abstract As the Clostridium coccoides,Eubacterium rectale (Erec; clostridial phylogenetic cluster XIVa) group is one of the major groups of the human intestinal microbiota, DNA- and RNA-based population analysis techniques (denaturing gradient gel electrophoresis; DGGE) were developed and applied to assess the diversity and temporal stability (6 months,2 years) of this faecal clostridial microbiota in 12 healthy adults. The stability of the Erec group was compared with the stability of the predominant bacterial microbiota, which was also assessed with PCR-DGGE. In addition, the Erec group was quantified with a hybridization-based method. According to our results, the Erec group was diverse in each subject, but interindividual uniqueness was not as clear as that of the predominant bacteria. The Erec group was found to be temporally as stable as the predominant bacteria. Over 200 clones obtained from two samples proved the developed method to be specific. However, the amount of bacteria belonging to the Erec group was not related to the diversity of that same bacterial group. In conclusion, the newly developed DGGE method proved to be a valuable and specific tool for the direct assessment of the stability of the Erec group, demonstrating diversity in addition to short-term stability in most of the subjects studied. [source] Erratum to "Molecular analysis of bacterial microbiota in the gut of the termite Reticulitermes speratus (Isoptera; Rhinotermitidae)"FEMS MICROBIOLOGY ECOLOGY, Issue 3 2003[FEMS Microbiol. No abstract is available for this article. [source] Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle's feed efficiencyFEMS MICROBIOLOGY LETTERS, Issue 1 2008Le Luo Guan Abstract Linkage of rumen microbial structure to host phenotypical traits may enhance the understanding of host,microbial interactions in livestock species. This study used culture-independent PCR-denaturing gradient gel electrophoresis (PCR-DGGE) to investigate the microbial profiles in the rumen of cattle differing in feed efficiency. The analysis of detectable bacterial PCR-DGGE profiles showed that the profiles generated from efficient steers clustered together and were clearly separated from those obtained from inefficient steers, indicating that specific bacterial groups may only inhabit in efficient steers. In addition, the bacterial profiles were more likely clustered within a certain breed, suggesting that host genetics may play an important role in rumen microbial structure. The correlations between the concentrations of volatile fatty acids and feed efficiency traits were also observed. Significantly higher concentrations of butyrate (P<0.001) and valerate (P=0.006) were detected in the efficient steers. Our results revealed potential associations between the detectable rumen microbiota and its fermentation parameters with the feed efficiency of cattle. [source] Microbial biodiversity in groundwater ecosystemsFRESHWATER BIOLOGY, Issue 4 2009C. GRIEBLER Summary 1. Groundwater ecosystems offer vast and complex habitats for diverse microbial communities. Here we review the current status of groundwater microbial biodiversity research with a focus on Bacteria and Archaea and on the prospects of modern techniques for enhancing our understanding of microbial biodiversity patterns and their relation to environmental conditions. 2. The enormous volume of the saturated terrestrial underground forms the largest habitat for microorganisms on earth. Up to 40% of prokaryotic biomass on earth is hidden within this terrestrial subsurface. Besides representing a globally important pool of carbon and nutrients in organisms, these communities harbour a degree of microbial diversity only marginally explored to date. 3. Although first observations of groundwater microbiota date back to Antonie van Leeuwenhoek in 1677, the systematic investigation of groundwater microbial biodiversity has gained momentum only within the last few decades. These investigations were initiated by an increasing awareness of the importance of aquifer microbiota for ecosystem services and functioning, including the provision of drinking water and the degradation of contaminants. 4. The development of sampling techniques suitable for microbiological investigations as well as the application of both cultivation-based and molecular methods has yielded substantial insights into microbial communities in contaminated aquifers, whereas knowledge of microbial biodiversity in pristine habitats is still poor at present. 5. Several novel phylogenetic lineages have been described from groundwater habitats, but to date no clearly ,endemic' subsurface microbial phyla have been identified. The future will show if the rather low diversity generally found in pristine oligotrophic aquifers is a fact or just a result of low abundances and insufficient resolution of today's methods. Refined approaches complemented by statistically rigorous applications of biodiversity estimates are urgently needed. 6. Factors identified to control microbial diversity in aquifers include spatial heterogeneity, temporal variability and disturbances such as pollution with chemical anthropogenic contaminants. Although first insights into the importance of individual biogeochemical processes may be obtained from surveys of microbial diversity within functional groups, direct links to groundwater ecosystem functioning have rarely been established so far. [source] Intestinal dendritic cells: Their role in bacterial recognition, lymphocyte homing, and intestinal inflammationINFLAMMATORY BOWEL DISEASES, Issue 10 2010S.C. Ng PhD Abstract Dendritic cells (DCs) play a key role in discriminating between commensal microorganisms and potentially harmful pathogens and in maintaining the balance between tolerance and active immunity. The regulatory role of DC is of particular importance in the gut where the immune system lies in intimate contact with the highly antigenic external environment. Intestinal DC constantly survey the luminal microenvironment. They act as sentinels, acquiring antigens in peripheral tissues before migrating to secondary lymphoid organs to activate naive T cells. They are also sensors, responding to a spectrum of environmental cues by extensive differentiation or maturation. Recent studies have begun to elucidate mechanisms for functional specializations of DC in the intestine that may include the involvement of retinoic acid and transforming growth factor-,. Specialized CD103+ intestinal DC can promote the differentiation of Foxp3+ regulatory T cells via a retinoic acid-dependent process. Different DC outcomes are, in part, influenced by their exposure to microbial stimuli. Evidence is also emerging of the close interaction between bacteria, epithelial cells, and DC in the maintenance of intestinal immune homeostasis. Here we review recent advances of functionally specialized intestinal DC and their mechanisms of antigen uptake and recognition. We also discuss the interaction of DC with intestinal microbiota and their ability to orchestrate protective immunity and immune tolerance in the host. Lastly, we describe how DC functions are altered in intestinal inflammation and their emerging potential as a therapeutic target in inflammatory bowel disease. (Inflamm Bowel Dis 2010) [source] Low counts of Faecalibacterium prausnitzii in colitis microbiotaINFLAMMATORY BOWEL DISEASES, Issue 8 2009H. Sokol MD Abstract Background: The intestinal microbiota is suspected to play a role in colitis and particularly in inflammatory bowel disease (IBD) pathogenesis. The aim was to compare the fecal microbiota composition of patients with colitis to that of healthy subjects (HS). Methods: fecal samples from 22 active Crohn's disease (A-CD) patients, 10 CD patients in remission (R-CD), 13 active ulcerative colitis (A-UC) patients, 4 UC patients in remission (R-UC), 8 infectious colitis (IC) patients, and 27 HS were analyzed by quantitative real-time polymerase chain reaction (PCR) targeting the 16S rRNA gene. Bacterial counts were transformed to logarithms (Log10 CFU) for statistical analysis. Results: Bacteria of the phylum Firmicutes (Clostridium leptum and Clostridium coccoides groups) were less represented in A-IBD patients (9.7; P = 0.004) and IC (9.4; P = 0.02), compared to HS (10.8). Faecalibacterium prausnitzii species (a major representative of the C. leptum group) had lower counts in A-IBD and IC patients compared to HS (8.8 and 8.3 versus 10.4; P = 0.0004 and P = 0.003). The Firmicutes/Bacteroidetes ratio was lower in A-IBD (1.3; P = 0.0001) and IC patients (0.4; P = 0.002). Compared to HS, Bifidobacteria were less represented in A-IBD and IC (7.9 and 7.7 versus 9.2; P = 0.001 and P = 0.01). Conclusions: The fecal microbiota of patients with IBD differs from that of HS. The phylum Firmicutes and particularly the species F. prausnitzii, are underrepresented in A-IBD patients as well as in IC patients. These bacteria could be crucial to gut homeostasis since lower counts of F. prausnitzii are consistently associated with a reduced protection of the gut mucosa. (Inflamm Bowel Dis 2009) [source] Isolation of flagellated bacteria implicated in Crohn's diseaseINFLAMMATORY BOWEL DISEASES, Issue 10 2007L. Wayne Duck BS Abstract Background: Serologic expression cloning has identified flagellins of the intestinal microbiota as immunodominant antigens in experimental colitis in mice and in individuals with Crohn's disease (CD). The present study was done to identify the microbial source of such flagellins. Methods: Using a variety of isolation and culture approaches, a number of previously unknown flagellated bacteria were isolated. Based on 16S ribosomal DNA sequences, these bacteria fall into the family Lachnospiraceae of the phylum Firmicutes. Results: Serum IgG from patients with CD and from mice with colitis reacted to the flagellins of these bacteria, and only their flagellins, whereas serum IgG from controls did not. The sequence of these flagellins demonstrate conserved amino- and carboxy-terminal domains that cluster phylogenetically and have a predicted 3D structure similar to Salmonella fliC, including an intact TLR5 binding site. The flagellin of 1 of these bacteria was likely O -glycosylated. Conclusions: The conserved immune response in both mouse and human to these previously unknown flagellins of the microbiota indicate that they play an important role in host,microbe interactions in the intestine. (Inflamm Bowel Dis 2007) [source] Segmented filamentous bacteria in a defined bacterial cocktail induce intestinal inflammation in SCID mice reconstituted with CD45RBhigh CD4+ T cellsINFLAMMATORY BOWEL DISEASES, Issue 10 2007Renata Stepankova PhD Abstract Background: The aim was to analyze the influence of intestinal microbiota on the development of intestinal inflammation. We used the model of chronic inflammation that develops spontaneously in the colon of conventional severe combined immunodeficiency (SCID) mice restored with the CD45 RBhigh subset of CD4+T cells isolated from the spleen of normal BALB/c mice. Methods: A CD4+CD45RBhigh subpopulation of T cells was purified from the spleen of conventional BALB/c mice by magnetic separation (MACS) and transferred into immunodeficient SCID mice. Germ-free (GF) SCID mice or SCID mice monoassociated with Enterococcus faecalis, SFB (segmented filamentous bacteria), Fusobacterium mortiferum, Bacteroides distasonis, and in combination Fusobacterium mortiferum + SFB or Bacteroides distasonis + SFB were used as recipients. SCID mice were colonized by a defined cocktail of specific pathogen-free (SPF) bacteria. Mice were evaluated 8,12 weeks after the cell transfer for clinical and morphological signs of inflammatory bowel disease (IBD). Results: After the transfer of the CD4+CD45RBhigh T-cell subpopulation to SCID mice severe colitis was present in conventional animals and in mice colonized with a cocktail of SPF microflora plus SFB. Altered intestinal barrier in the terminal ileum of mice with severe colitis was documented by immunohistology using antibodies to ZO-1 (zona occludens). Conclusions: Only SFB bacteria together with a defined SPF mixture were effective in triggering intestinal inflammation in the model of IBD in reconstituted SCID mice, while no colitis was detected in GF mice or in mice colonized either with SPF microflora or monoassociated only with SFB or colonized by Bacteroides distasonis + SFB or Fusobacterium mortiferum + SFB. (Inflamm Bowel Dis 2007) [source] Microbial diversity of inflamed and noninflamed gut biopsy tissues in inflammatory bowel diseaseINFLAMMATORY BOWEL DISEASES, Issue 6 2007Shadi Sepehri MD Abstract Background: Inflammatory bowel disease (IBD) is a chronic gastrointestinal condition without any known cause or cure. An imbalance in normal gut biota has been identified as an important factor in the inflammatory process. Methods: Fifty-eight biopsies from Crohn's disease (CD, n = 10), ulcerative colitis (UC, n = 15), and healthy controls (n = 16) were taken from a population-based case-control study. Automated ribosomal intergenic spacer analysis (ARISA) and terminal restriction fragment length polymorphisms (T-RFLP) were used as molecular tools to investigate the intestinal microbiota in these biopsies. Results: ARISA and T-RFLP data did not allow a high level of clustering based on disease designation. However, if clustering was done based on the inflammation criteria, the majority of biopsies grouped either into inflamed or noninflamed groups. We conducted statistical analyses using incidence-based species richness and diversity as well as the similarity measures. These indices suggested that the noninflamed tissues form an intermediate population between controls and inflamed tissue for both CD and UC. Of particular interest was that species richness increased from control to noninflamed tissue, and then declined in fully inflamed tissue. Conclusions: We hypothesize that there is a recruitment phase in which potentially pathogenic bacteria colonize tissue, and once the inflammation sets in, a decline in diversity occurs that may be a byproduct of the inflammatory process. Furthermore, we suspect that a better knowledge of the microbial species in the noninflamed tissue, thus before inflammation sets in, holds the clues to the microbial pathogenesis of IBD. (Inflamm Bowel Dis 2007) [source] Weaning pig performance and faecal microbiota with and without in-feed addition of rare earth elementsJOURNAL OF ANIMAL PHYSIOLOGY AND NUTRITION, Issue 9-10 2006M. Kraatz Summary Two 6-week feeding trials were conducted on a total of 112 newly weaned piglets to examine the recently reported growth promoting effects of dietary rare earth elements (REE) in European pig production. Rare earth element-diets were supplemented with a REE-citrate premix of lanthanum and the light lanthanoides cerium, praseodymium and neodymium at 200 mg/kg for 6 weeks after weaning. Overall for both trials, growth performance of REE-citrate and control fed piglets did not differ significantly (p > 0.05). An early enhancive tendency for REE-citrate in trial 1 (feed conversion ratio, FCR ,3%, p = 0.15) proved irreproducible in trial 2. In the late period of trial 1, in-feed addition of REE-citrate significantly impaired piglet performance (FCR + 8%, p =0.01). A cultivation-independent molecular approach, polymerase chain reaction-denaturing gradient gel electrophoresis was further applied to assess REE induced alterations in the predominant faecal microbiota from weaning pigs. Calculation of various ecological characteristics does not indicate (p > 0.05) an often discussed selective effect on local microbial composition of dietary REE. [source] Bacteria,diet interactions affect longevity in the medfly ,Ceratitis capitataJOURNAL OF APPLIED ENTOMOLOGY, Issue 9-10 2008M. Ben-Yosef Abstract Mediterranean fruit flies (Ceratitis capitata Wiedemann, Dipt.: Tephritidae) harbour a diverse community of bacteria in their digestive system. This microbiota may have important functions impacting on the fly's fitness. Recently, we described the effect of eliminating intestinal bacteria on the reproductive success of C. capitata males and females. Here, we expand the view on the nature of fly,bacteria interactions by examining the effect of bacteria on male and female longevity. Antibiotics were used to suppress the gut bacterial community and mortality rates were compared between antibiotic-treated and non-treated flies when either nutritionally stressed (maintained on sugar) or provided with a full diet. These tests revealed that eliminating the gut bacterial population prolonged longevity, but only when flies were nutritionally stressed, indicating that the effect of bacteria on lifespan was diet dependent. Considering these results in light of other known effects of bacteria on fitness components of the fly demonstrates a cost-benefit relationship between C. capitata and its gut microbiota. [source] Comparison of alternatives to in-feed antimicrobials for the prevention of clinical necrotic enteritisJOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2010M.S. Geier Abstract Aims:, The capacity for Lactobacillus johnsonii and an organic acid (OA) blend to prevent Clostridium perfringens -induced clinical necrotic enteritis (NE) in chickens was studied. Methods and Results:, Cobb 500 birds were allocated into six groups (n = 25 birds/pen, eight pens/treatment); Unchallenged, Challenged, Antimicrobial (zinc bacitracin (ZnB)/monensin), OA, probiotic Lact. johnsonii and probiotic sham (Phosphate,buffered saline). All birds were challenged with Eimeria spp. and Cl. perfringens except for unchallenged controls. Birds fed antimicrobials were protected from NE development as indicated by maintenance of body weight, low mortality and clostridium levels, and decreased intestinal macroscopic lesion scores compared to challenged controls (P < 0·05). Lactobacillus johnsonii -fed birds had reduced lesion scores, whilst OA-fed birds had decreased Cl. perfringens levels. Both Lact. johnsonii and OA-fed birds had improved feed efficiency between days 0 and 28 compared to challenged controls; however, mortality and body weights were not improved by either treatment. Microbial profiling indicated that the challenge procedure significantly altered the jejunal microbiota. The microbiota of antimicrobial-fed birds was significantly different from all other groups. Conclusions:, Whilst Lact. johnsonii and OA altered specific intestinal parameters, significant protection against NE was not observed. Significance and Impact of the Study:,Lactobacillus johnsonii and OA did not prevent NE; however, some improvements were evident. Other related treatments, or combinations of these two treatments, may provide greater protection. [source] The effect of Pediococcus acidilactici on the gut microbiota and immune status of on-growing red tilapia (Oreochromis niloticus)JOURNAL OF APPLIED MICROBIOLOGY, Issue 3 2010R.M.W. Ferguson Abstract Aim:, To assess Pediococcus acidilactici as a dietary supplement for on-growing red tilapia (Oreochromis niloticus). Methods and Results:, Tilapia were fed either a control diet or control diet supplemented with Ped. acidilactici at 107 CFU g,1 for 32 days. Ped. acidilactici colonized the intestinal tract and significantly affected the intestinal microbial communities. PCR-DGGE revealed direct antagonism of gastric Ped. acidilactici with an endogenous uncultured bacterium during a period of reverting to nonsupplemented feeding. Light microscopy revealed that gut integrity and leucocyte levels were unaffected by Ped. acidilactici; however, blood leucocyte levels and serum lysozyme activity were elevated after 14-days' feeding. No significant improvements in growth performance were observed at the end of the trial (day 32), but survival was significantly higher in the probiotic group. Conclusions:, The study demonstrates that oral supplementation of Ped. acidilactici modulates intestinal bacterial communities in on-growing red tilapia and also stimulates some aspects of the nonspecific immune response. Significance and Impact of the study:, To our knowledge this is the first study assessing the effects of probiotics on the gut microbiota of tilapia using culture-independent methods. Such methods are crucial to understand the mechanisms which underpin and mediate host benefits. [source] | |||||||||||||||||||||||||||||||||||||||||||