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Microbial Composition (microbial + composition)
Selected AbstractsMicrobial composition and structure of a multispecies biofilm from a trickle-bed reactor used for the removal of volatile aromatic hydrocarbons from a waste gasJOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 1 2004Dariusch Hekmat Abstract The microbial composition and structure of a multispecies biofilm of a laboratory-scale trickle-bed bioreactor for the treatment of waste gas was examined. The model pollutant was a volatile organic compound-mixture of polyalkylated benzenes called Solvesso 100®. Fluorescent in-situ hybridization (FISH) and confocal laser scanning microscopy (CLSM) were applied. Two new Solvesso 100® -degrading Pseudomonas sp strains were isolated from the multispecies biofilm. Corresponding isolate-specific oligonucleotide probes were designed and applied successfully. A major finding was that the fraction of Solvesso 100® -degrading bacteria in the biofilm was low (about 3,6% during long-term operation). The majority of the active cells were saprophytes which utilized intermediates and cell lysis products. The measured fraction of extracellular polymeric substances of the mature biofilm was 89,93% of the total biomass. The CLSM examinations of a 3-days-old approx 10 µm thick biofilm revealed highly heterogeneous structures with distinguished three-dimensional matrix-enclosed microcolony bodies spread across the substratum surface. The 28-days-old 80,960 µm thick biofilm exhibited voids, cell-free channels, and pores of variable sizes. In both cases, an even distribution of active cells and pollutant-degrading bacteria throughout the biofilm cross-section as well as through the biofilm depth was observed. Copyright © 2003 Society of Chemical Industry [source] Microbial composition of supra- and subgingival plaque in subjects with adult periodontitisJOURNAL OF CLINICAL PERIODONTOLOGY, Issue 10 2000Laurie Ann Ximénez-Fyvie Abstract Background, aims: The purpose of the present study was to compare and relate the microbial composition of supra and subgingival plaque in 23 adult periodontitis subjects (mean age 51±14 years). Methods: A total of 1,170 samples of supra and subgingival plaque were collected from the mesial aspect of every tooth (up to 28 supra and 28 subgingival samples) from each subject and evaluated for the presence and levels of 40 bacterial taxa using whole genomic DNA probes and checkerboard DNA-DNA hybridization. Clinical assessments including dichotomous measures of gingival redness, bleeding on probing, plaque accumulation and suppuration, as well as duplicate measures of pocket depth and attachment level, were made at 6 sites per tooth. The counts (levels), % DNA probe count (proportion) and % of sites colonized (prevalence) of each species in supra and separately in subgingival plaque were computed for each subject. Significance of differences between supra and subgingival plaque for each species was sought using the Wilcoxon signed ranks test and adjusted for multiple comparisons. Results: All 40 taxa were detected in both supra and subgingival plaque. Actinomyces species were the most prevalent taxa in both habitats. 75 to 100% of supra and 62 to 100% of subgingival sites were colonized by at least one of the 5 Actinomyces species. Supragingival samples exhibited significantly higher counts of Actinomyces naeslundii genospecies 1, Actinomyces israelii, Actinomyces odontolyticus, Neisseria mucosa, Streptococcus gordonii, Capnocytophaga ochracea and Capnocytophaga sputigena when compared with mean counts in subgingival samples taken from the same tooth surfaces. Subgingival plaque samples presented significantly higher counts of Prevotella nigrescens, Prevotella intermedia, Bacteroides forsythus and Porphyromonas gingivalis. Subgingival samples exhibited a significantly higher proportion of "red" and "orange complex" species, while supragingival plaque exhibited higher proportions of "green" and "purple" complex species as well as Actinomyces species. Suspected periodontal pathogens could be detected in supragingival plaque from sites where subgingival samples were negative for the same species. Conclusions: The data indicate that supragingival plaque can harbor putative periodontal pathogens, suggesting a possible rôle of this environment as a reservoir of such species for the spread or reinfection of subgingival sites. [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] Yeast species composition differs between artisan bakery and spontaneous laboratory sourdoughsFEMS YEAST RESEARCH, Issue 4 2010Gino Vrancken Abstract Sourdough fermentations are characterized by the combined activity of lactic acid bacteria and yeasts. An investigation of the microbial composition of 21 artisan sourdoughs from 11 different Belgian bakeries yielded 127 yeast isolates. Also, 12 spontaneous 10-day laboratory sourdough fermentations with daily backslopping were performed with rye, wheat, and spelt flour, resulting in the isolation of 217 yeast colonies. The isolates were grouped according to PCR-fingerprints obtained with the primer M13. Representative isolates of each M13 fingerprint group were identified using the D1/D2 region of the large subunit rRNA gene, internal transcribed spacer sequences, and partial actin gene sequences, leading to the detection of six species. The dominant species in the bakery sourdoughs were Saccharomyces cerevisiae and Wickerhamomyces anomalus (formerly Pichia anomala), while the dominant species in the laboratory sourdough fermentations were W. anomalus and Candida glabrata. The presence of S. cerevisiae in the bakery sourdoughs might be due to contamination of the bakery environment with commercial bakers yeast, while the yeasts in the laboratory sourdoughs, which were carried out under aseptic conditions with flour as the only nonsterile component, could only have come from the flour used. [source] Chemical composition and microbial evaluation of Argentinean Corrientes cheeseINTERNATIONAL JOURNAL OF DAIRY TECHNOLOGY, Issue 3 2008OLGA M VASEK The chemical and microbial composition of an artisanal cheese made from raw cow's milk produced and consumed in the province of Corrientes (north-eastern Argentina) was evaluated using standard methods. Corrientes cheese has high moisture content (50,60%), normal protein and fat contents (21,27 and 22,26% respectively), and is low in salt (0.5,2.0% w/w). Microbial counts also varied significantly between samples (colony-forming units per gram ranges covering logs of 5,11), probably due to environmental contamination in the raw material. These results will help produce higher quality Corrientes cheeses with well-defined characteristics. [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] Pro-inflammatory biomarkers during experimental gingivitis in patients with type 1 diabetes mellitus: a proof-of-concept studyJOURNAL OF CLINICAL PERIODONTOLOGY, Issue 1 2010Giovanni E. Salvi Abstract Aim: To compare gingival crevicular fluid (GCF) biomarker levels and microbial distribution in plaque biofilm (SP) samples for subjects with type 1 diabetes (T1DM) versus healthy subjects without diabetes during experimental gingivitis (EG). Materials and Methods: A total of nine T1DM patients and nine healthy controls of age and gender similar to the T1DM patients were monitored for 35 days during EG. Hygiene practices were stopped for 3 weeks, and GCF, SP, plaque index (PI) and gingival index were determined. IL-1,, IL-8, MMP-8 and MMP-9 were quantified by enzyme-linked immunosorbent assay, and SP samples were assessed by DNA,DNA hybridization for a panel of 40 subgingival microbial species. Results: IL-1, levels in T1DM patients were elevated compared with healthy individuals, and showed differences between groups at 7,21 days while healthy patients showed IL-1, increases from baseline to 14,21 days (p<0.05). Differences were observed in MMP-9 levels between patients with and without T1DM at 7,14 days (p<0.05). Orange complex species and PI measurements displayed a superior correlation with biomarker levels when compared with other complexes or clinical measurements during EG. Conclusions: The mean GCF biomarker levels for IL-1, and MMP-8 were most significantly elevated in T1DM subjects compared with healthy individuals during EG, not resulting from differences in the mean PI or microbial composition. [source] Microbial composition of supra- and subgingival plaque in subjects with adult periodontitisJOURNAL OF CLINICAL PERIODONTOLOGY, Issue 10 2000Laurie Ann Ximénez-Fyvie Abstract Background, aims: The purpose of the present study was to compare and relate the microbial composition of supra and subgingival plaque in 23 adult periodontitis subjects (mean age 51±14 years). Methods: A total of 1,170 samples of supra and subgingival plaque were collected from the mesial aspect of every tooth (up to 28 supra and 28 subgingival samples) from each subject and evaluated for the presence and levels of 40 bacterial taxa using whole genomic DNA probes and checkerboard DNA-DNA hybridization. Clinical assessments including dichotomous measures of gingival redness, bleeding on probing, plaque accumulation and suppuration, as well as duplicate measures of pocket depth and attachment level, were made at 6 sites per tooth. The counts (levels), % DNA probe count (proportion) and % of sites colonized (prevalence) of each species in supra and separately in subgingival plaque were computed for each subject. Significance of differences between supra and subgingival plaque for each species was sought using the Wilcoxon signed ranks test and adjusted for multiple comparisons. Results: All 40 taxa were detected in both supra and subgingival plaque. Actinomyces species were the most prevalent taxa in both habitats. 75 to 100% of supra and 62 to 100% of subgingival sites were colonized by at least one of the 5 Actinomyces species. Supragingival samples exhibited significantly higher counts of Actinomyces naeslundii genospecies 1, Actinomyces israelii, Actinomyces odontolyticus, Neisseria mucosa, Streptococcus gordonii, Capnocytophaga ochracea and Capnocytophaga sputigena when compared with mean counts in subgingival samples taken from the same tooth surfaces. Subgingival plaque samples presented significantly higher counts of Prevotella nigrescens, Prevotella intermedia, Bacteroides forsythus and Porphyromonas gingivalis. Subgingival samples exhibited a significantly higher proportion of "red" and "orange complex" species, while supragingival plaque exhibited higher proportions of "green" and "purple" complex species as well as Actinomyces species. Suspected periodontal pathogens could be detected in supragingival plaque from sites where subgingival samples were negative for the same species. Conclusions: The data indicate that supragingival plaque can harbor putative periodontal pathogens, suggesting a possible rôle of this environment as a reservoir of such species for the spread or reinfection of subgingival sites. [source] Factors affecting human supragingival biofilm composition.JOURNAL OF PERIODONTAL RESEARCH, Issue 4 2009Background and Objective:, Little is known about the factors that affect the microbial composition of supragingival biofilms. This study was designed to examine the relationship between total DNA probe counts of supragingival biofilm samples, clinical parameters and supragingival biofilm composition. Material and Methods:, Supragingival plaque samples were taken from 187 systemically healthy adult subjects (n = 4745 samples). All samples were individually analyzed for their content of 40 bacterial species using checkerboard DNA,DNA hybridization. The relationship between total DNA probe counts and microbial composition was examined by subsetting the data into 10 groups based on 10 percentile increments of the total DNA probe counts. Differences among groups in terms of species counts and proportions were sought, as well as relationships of total plaque DNA probe count and clinical parameters. Results:, There was a wide distribution in mean total DNA probe counts among the 187 subjects. With increasing total plaque levels there was a change in the proportions of individual species and microbial complexes. ,Small plaques' were characterized by high proportions of species in the yellow, orange, purple and ,other' complexes; plaques of moderate mass were characterized by high proportions of Actinomyces and purple complex species, while ,large plaques' exhibited increased proportions of green and orange complex species. Measures of gingival inflammation, pocket depth and recession were significantly positively associated with total DNA probe counts. Increased plaque numbers were related to increased pocket depth irrespective of presence or absence of gingival inflammation. Conclusion:, The proportions of individual species and microbial complexes in supragingival biofilms are influenced by the total numbers of organisms in the biofilm. [source] Factors affecting human supragingival biofilm composition.JOURNAL OF PERIODONTAL RESEARCH, Issue 4 2009Background and Objective:, Little is known regarding the factors that affect the microbial composition of supragingival biofilms. This study was designed to test the hypothesis that tooth location affects the microbial composition of supragingival plaque beyond the effect due to plaque mass as reflected by total DNA probe count. Material and Methods:, Supragingival plaque samples were taken from the mesiobuccal aspect of each tooth in 187 subjects (n = 4745 samples). All samples were individually analyzed for their content of 40 bacterial species using checkerboard DNA,DNA hybridization. Significance of differences in mean species counts and proportions were determined among tooth surfaces and six tooth type categories: molars, bicuspids, incisors/canines in the mandible and maxilla separately using the Kruskal,Wallis test. Stepwise multiple linear regression was employed to examine the relationship between species proportions and total DNA probe count, tooth location, periodontal and smoking status, age and sex. Results:, All species differed significantly among tooth types and among the six tooth categories. Higher plaque levels were seen on molars and lower incisors. Some differences observed between tooth types could be partly explained by the level of plaque. Teeth with high plaque mass exhibited high levels of Capnocytophaga gingivalis, Actinomyces naeslundii genospecies 2, Campylobacter rectus and Campylobacter showae. However, certain species, such as Veillonella parvula and Streptococcus sanguinis, differed significantly at different tooth locations despite similarities in plaque mass. Twenty of the test species exhibited a significant association with tooth location after adjusting for total DNA probe count and subject level factors. Conclusion:, While plaque mass was associated with differences in proportions of many species in supragingival biofilms, tooth location also was strongly associated with species proportions in both univariate and multivariate analyses. [source] A microbial world within usMOLECULAR MICROBIOLOGY, Issue 6 2006Erwin G. Zoetendal Summary The microbial world within us includes a vast array of gastrointestinal (GI) tract communities that play an important role in health and disease. Significant progress has been made in recent years in describing the intestinal microbial composition based on the application of 16S ribosomal RNA (rRNA)-based approaches. These were not only instrumental in providing a phylogenetic framework of the more than 1000 different intestinal species but also illustrated the temporal and spatial diversity of the microbial GI tract composition that is host-specific and affected by the genotype. However, our knowledge of the molecular and cellular bases of host,microbe interactions in the GI tract is still very limited. Here an overview is presented of the most recent developments and applications of novel culture-independent approaches that promise to unravel the mechanisms of GI tract functionality and subsequent possibilities to exploit specifically these mechanisms in order to improve gut health. [source] Bifidobacterium carbohydrases-their role in breakdown and synthesis of (potential) prebioticsMOLECULAR NUTRITION & FOOD RESEARCH (FORMERLY NAHRUNG/FOOD), Issue 1 2008Lambertus A. M. van den Broek Abstract There is an increasing interest to positively influence the human intestinal microbiota through the diet by the use of prebiotics and/or probiotics. It is anticipated that this will balance the microbial composition in the gastrointestinal tract in favor of health promoting genera such as Bifidobacterium and Lactobacillus. Carbohydrates like non-digestible oligosaccharides are potential prebiotics. To understand how these bacteria can grow on these carbon sources, knowledge of the carbohydrate-modifying enzymes is needed. Little is known about the carbohydrate-modifying enzymes of bifidobacteria. The genome sequence of Bifidobacterium adolescentis and Bifidobacterium longum biotype longum has been completed and it was observed that for B. longum biotype longum more than 8% of the annotated genes were involved in carbohydrate metabolism. In addition more sequence data of individual carbohydrases from other Bifidobacterium spp. became available. Besides the degradation of (potential) prebiotics by bifidobacterial glycoside hydrolases, we will focus in this review on the possibilities to produce new classes of non-digestible oligosaccharides by showing the presence and (transglycosylation) activity of the most important carbohydrate modifying enzymes in bifidobacteria. Approaches to use and improve carbohydrate-modifying enzymes in prebiotic design will be discussed. [source] Effect of Thymus vulgaris essential oil on intestinal bacterial microbiota of rainbow trout, Oncorhynchus mykiss (Walbaum) and bacterial isolatesAQUACULTURE RESEARCH, Issue 10 2010Paola Navarrete Abstract The application of natural and innocuous compounds has potential in aquaculture as an alternative to antibiotics. We evaluated the effect of diet supplementation with Thymus vulgaris essential oil (TVEO) on the allochthonous microbial composition of rainbow trout. DNA was extracted directly from the intestinal contents, and the V3-V4 regions of the 16S rRNA genes were amplified by PCR. The bacterial composition was analysed using temporal temperature gradient electrophoresis (TTGE). No significant changes (P>0.05) were detected in the TTGE profiles of TVEO-treated trout compared with the controls. The Dice similarity index revealed a high stability (Cs >70%) of the intestinal microbiota in both groups during the 5-week period. Sequence analyses of the TTGE bands revealed the same bacterial composition in both groups, with most bacteria belonging to the Proteobacteria and Firmicutes phyla. The in vitro antibacterial activity of TVEO was assessed using a range of normal intestinal isolates and fish pathogens. The inhibitory concentrations for all the tested bacteria were higher than the TVEO levels used in trout, which may explain the in vivo results. [source] Bacterial diversity in various coastal mariculture ponds in Southeast China and in diseased eels as revealed by culture and culture-independent molecular techniquesAQUACULTURE RESEARCH, Issue 9 2010Yonghui Zeng Abstract Mariculture ponds are widely distributed in Chinese coasts and have become a threat to the health of coastal ecosystems. In order to improve our understanding on the microbial composition in mariculture environments, we sampled a variety of ponds farming different animals or plants around the Dongshan Island and Xiamen Island in Southeast China and isolated cultures from the tissues of diseased eels. Analysis by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE), clone library and direct culturing methods revealed highly diverse bacterial communities in these samples. Bacterial communities in the Dongshan samples were dominated by Alphaproteobacteria, Gammaproteobacteria and Bacteroidetes. The Gracilaria verrucosa pond harbours the most abundant species (20 DGGE bands), followed by Epinephelus diacanthus pond (18 bands), Haliotis diversicolor supertexta pond I (18 bands) and Penaeus vannamei pond (11 bands). In comparison with surface waters, Penacus orientalis pond sediment showed a much more complex bacterial community, from which only sequences affiliated with Deltaproteobacteria, Firmicutes, Acidobacteria and candidate phylum TM6 were found. Bacterial cultures in diseased eels were closely related to two pathogenic genera, Aeromonas in Gammaproteobacteria and Bacillus, in Firmicutes. Clones affiliated with another two genera, Escherichia and Vibrio, that have pathogenic potentials were also identified. Phylogenetic analysis of a total of 131 sequences showed that 48.9% of the sequences were clustered into Gammaproteobacteria and formed the most abundant group, followed by Alphaproteobacteria (19.1%), Firmicutes (7.6%), Bacteroidetes (5.3%), Deltaproteobacteria (5.3%), Actinobacteria (4.6%), Chloroplast (3.8%), Acidobacteria (2.3%), Cyanobacteria (1.5%), Betaproteobacteria (0.7%) and TM6 (0.7%). 43.7% (28/64) of the phylogenetic clusters cannot be classified into any known genus and 44.3% (58/131) of the sequences show <95% similarity to public database records, suggesting that abundant novel species exist in mariculture ponds. Gathering bacterial diversity data in mariculture ponds and diseased fish is meaningful for the prevention and control of fish diseases and for the improvement of our understanding of microbial ecology in a pond environment. [source] Complex trait differentiation between host-populations of the pea aphid Acyrthosiphon pisum (Harris): implications for the evolution of ecological specialisationBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2009ADRIEN FRANTZ Variation in traits affecting preference for, and performance on, new habitats is a key factor in the initiation of ecological specialisation and adaptive speciation. However, habitat and resource use also involves other traits whose influence on ecological and genetic divergence remains poorly understood. In the present study, we investigated the extent of variation of life-history traits among sympatric populations of the pea aphid Acyrthosiphon pisum, which shows several host races that are specialised on various plants of the family Fabaceae plants and is an established model for ecological speciation. First, we assessed the community structure of microbial partners within host populations of the pea aphid. The effect of these microbes on host fitness is uncertain, although there is growing evidence that they may modulate various important adaptive traits of their host such as plant utilisation and resistance against natural enemies. Second, we performed a multivariate analysis on several ecologically relevant features of host populations recorded in the present and previous studies (including microbial composition, colour morph, reproductive mode, and male dispersal phenotype), enabling the identification of correlations between phenotypic traits. We discuss the ecological significance of these associations of traits in relation to the habitat characteristics of pea aphid populations, and their consequences for the evolution of ecological specialisation and sympatric speciation. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 718,727. [source] Early colonization of non-submerged dental implants in patients with a history of advanced aggressive periodontitisCLINICAL ORAL IMPLANTS RESEARCH, Issue 1 2006Annemarie L. De Boever Abstract: The aim of the study was to evaluate the early colonization of non-submerged implants over a 6-month period in partially edentulous patients treated for advanced aggressive periodontal disease. In 22 patients treated for advanced aggressive periodontitis and in a supportive maintenance program for a period between 12 and 240 months at implant surgery, a total of 68 non-submerged dental implants were installed. Patients had a plaque score below 20%, and less than 20% of the pockets around the teeth were bleeding on probing (BOP). Using DNA-probes (micro-IDent®), the presence and concentration of five periodontal pathogens (Actinobacillus actinomycetemcomitans (Aa), Porphyromonas gingivalis (Pg), Prevotella intermedia (Pi), Tannerella forsythensis (Tf) and Treponema denticola (Td)) were determined in the five deepest pockets of the rest dentition pre-operatively and after 6 months as well as five places around each implant 10 days, 1 month, 3 months and 6 months after surgery. In each patient, a test to determine the genotype interleukin-1 (IL-1) was performed (PST , micro-IDent®). After 6 months, no difference in microbial composition as compared with baseline was found around the teeth in five patients, in 12 minute differences and in five patients important differences were observed. Ten days after surgery, three patients had a complete similar bacterial composition between teeth and implants. In 14 patients, the composition was fairly similar, while large differences in composition and concentration occurred in five patients. This microbiota around the implants remained almost unchanged over a 6-month period and did not hamper the clinical and radiographic osseointegration and did not lead to peri-implantitis, mucositis or initiation of bone destruction. [source] | ||||||||||||||||