scholarly journals Molecular methods for exploring the intestinal ecosystem

2002 ◽  
Vol 87 (S2) ◽  
pp. S199-S201 ◽  
Author(s):  
G. W. Tannock
Keyword(s):  
Intestinal Microflora ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Molecular Methods ◽  
Bacterial Populations ◽  
Disease States ◽  
Large Numbers ◽  
Gradient Gel Electrophoresis ◽  
Health And Disease ◽  
Polymerase Chain

Molecular methods have provided renewed impetus for the analysis of the composition of the intestinal microflora in health and disease. The polymerase chain reaction coupled with denaturing gradient gel electrophoresis provides a method whereby the bacterial communities in large numbers of samples can be compared efficiently and effectively. Altered bacterial populations associated with disease states can then be targeted for further investigation. In the long-term, an ‘abnormal microflora’ might be rectified by the use of probiotics or prebiotics.

The comparison of the diversity of activated sludge plants

1998 ◽  
Vol 37 (4-5) ◽  
pp. 71-78 ◽  
Author(s):  
Thomas P. Curtis ◽  
Noel G. Craine
Keyword(s):  
Cluster Analysis ◽  
Activated Sludge ◽  
Treatment Process ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Optimal Sampling ◽  
Bacterial Populations ◽  
Large Numbers ◽  
Probable Presence ◽  
Gradient Gel Electrophoresis ◽  
Sampling Regime

The explicit engineering of bacterial populations requires that we know which organisms perform which tasks. The comparison of the bacterial diversity of activated sludge plants may give important information about the functions of different bacteria. This difficult task may be made easier by the use of technologies based on 16S rRNA based techniques. In this study we have used denaturing gradient gel electrophoresis (DGGE) to determine the optimal sampling regime for comparative studies and used cluster analysis to show how plants may be quantitatively compared. We sought evidence of spatial, diurnal and intrasample variation in a number of sites. No evidence for variation was found in the plants studied and we concluded that a single sample of an activated sludge plant was sufficient for a plant to plant comparison. The cluster analysis was able to distinguish between plants, though further work is required to find the most appropriate basis for such comparisons. We found organisms from raw sewage in the mixed liquor samples, these organisms may have no functional significance in the treatment process and thus complicate plant to plant comparisons as will the probable presence of heteroduplex rDNA products. Nevertheless we believe that these drawbacks do not outweigh the advantages of being able to take and compare relatively large numbers of samples.

Are some putative glycogen accumulating organisms (GAO) in anaerobic : aerobic activated sludge systems members of the α-Proteobacteria?

Microbiology ◽  
2004 ◽  
Vol 150 (7) ◽  
pp. 2267-2275 ◽  
Author(s):  
Michael Beer ◽  
Yun H. Kong ◽  
Robert J. Seviour
Keyword(s):  
Activated Sludge ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Batch Reactors ◽  
Sequencing Batch Reactors ◽  
Bacterial Populations ◽  
Removal Capacity ◽  
Large Numbers ◽  
Gradient Gel Electrophoresis ◽  
Polyphosphate Accumulating Organisms

Activated sludge plants designed to remove phosphorus microbiologically often perform unreliably. One suggestion is that the polyphosphate-accumulating organisms (PAO) are out-competed for substrates by another group of bacteria, the glycogen-accumulating organisms (GAO) in the anaerobic zones of these processes. This study used fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE) to analyse the communities from laboratory-scale anaerobic : aerobic sequencing batch reactors. Members of the genus Sphingomonas in the α-Proteobacteria were present in large numbers in communities with poor phosphorus removal capacity where the biomass had a high glycogen content. Their ability to store poly-β-hydroxyalkanoates anaerobically, but not aerobically, and not accumulate polyphosphate aerobically is consistent with these organisms behaving as GAO there. No evidence was found to support an important role for the γ-Proteobacteria as possible GAO in these communities, although these bacterial populations have been considered in other studies to act as possible competitors for the PAO.

Effects of Long-Term Elevated CO2 on Rhizosphere and Bulk Soil Bacterial Community Structure in Pinus sylvestriformis Seedlings Fields

2011 ◽  
Vol 343-344 ◽  
pp. 351-356
Author(s):  
Xia Jia ◽  
Chun Juan Zhou
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pinus Sylvestriformis ◽  
Soil Bacterial Community Structure ◽  
Gradient Gel Electrophoresis ◽  
Polymerase Chain

The effect of long-term elevated CO2(as open top chambers) on rhizosphere and bulk bacterial community structure in Pinus sylvestriformis seedlings field was investigated in July, August, and September. The bacterial communities were processed by Denaturing Gradient Gel Electrophoresis (DGGE) analysis of bacterial 16S rDNA fragments amplified by PCR (Polymerase Chain Reaction) from DNA extracted directly from soil. DGGE profiles from rhizosphere samples showed large changes in rhizosphere bacterial community under elevated CO2compared to ambient except for that in September. For bulk samples, bacterial community structure changed when exposed to elevated CO2in three months. With the exception of bulk samples in August, a similitude of bacterial communities structures existed between different elevated CO2concentrations by analyzing UPGMA dendrogram based on Jaccard’s coefficient.

Screening and Identification of Glufosinate-Degrading Bacteria from Glufosinate-Treated Soils

Weed Science ◽  
2007 ◽  
Vol 55 (6) ◽  
pp. 631-637 ◽  
Author(s):  
Chau-Ling Hsiao ◽  
Chiu-Chung Young ◽  
Ching-Yuh Wang
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Strains ◽  
High Concentration ◽  
Degrading Bacteria ◽  
Gradient Gel Electrophoresis ◽  
Screening And Identification ◽  
Polymerase Chain ◽  
Competition Pressure ◽  
Rdna Analysis

In order to select efficient and competitive glufosinate-degrading bacteria, two soils which had been treated with glufosinate annually for more than 5 yr were screened. Three strains tolerant to this herbicide were identified by 16S rDNA analysis asBurkholderia sacchari,Serratia marcescens, andPseudomonas psychrotolerans. In addition, a moderately tolerant strain,P. citronellolis, was isolated from a soil which had received glufosinate treatment for only 6 mo. In culture medium containing high concentration of glufosinate, the former three strains showed significant ability to degrade this glutamine synthetase inhibitor, suggesting that glufosinate-degrading bacteria would be readily found in soils after a long-term induction or selection. A subsequent biodegradation experiment showed that 30 and 50% of glufosinate was degraded 7 and 21 d after treatment (DAT), respectively, in sterilized soils inoculated with the above-mentioned three tolerant strains. While more than 30% of the glufosinate in nonsterilized soils was degraded 7 DAT by the indigenous edaphic microbes, inoculation with the three selected strains enhanced glufosinate degradation to nearly 50%. A study on the competition from edaphic microorganisms in soils by polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) analysis revealed that within 21 d after inoculation (DAI), the propagation ofB. sacchariandP. psychrotoleranswas not affected, whereas that of the less tolerantP. citronelloliswas inhibited. This observation suggests that a long-term herbicide exposure is a promotive factor in generating bacterial strains having high degradation efficiency and showing vigorous propagation under the competition pressure arising from indigenous microbes.

Allelopathic and Medicinal plant. 26. Millettia speciosa

2020 ◽  
Vol 51 (2) ◽  
pp. 125-146
Author(s):  
Nasiruddin Nasiruddin ◽  
Yu Zhangxin ◽  
Ting Zhao Chen Guangying ◽  
Minghui Ji
Keyword(s):  
Community Structure ◽  
Medicinal Plant ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Wiener Index ◽  
Pseudomonas Spp ◽  
Evenness Index ◽  
Gradient Gel Electrophoresis ◽  
Rhizosphere Pseudomonas

We grew cucumber in pots in greenhouse for 9-successive cropping cycles and analyzed the rhizosphere Pseudomonas spp. community structure and abundance by PCR-denaturing gradient gel electrophoresis and quantitative PCR. Results showed that continuous monocropping changed the cucumber rhizosphere Pseudomonas spp. community. The number of DGGE bands, Shannon-Wiener index and Evenness index decreased during the 3rd cropping and thereafter, increased up to the 7th cropping, however, however, afterwards they decreased again. The abundance of Pseudomonas spp. increased up to the 5th successive cropping and then decreased gradually. These findings indicated that the structure and abundance of Pseudomonas spp. community changed with long-term cucumber monocropping, which might be linked to soil sickness caused by its continuous monocropping.

scholarly journals Investigations on the Effects of Dietary Essential Oils and Different Husbandry Conditions on the Gut Ecology in Piglets after Weaning

2009 ◽  
Vol 2009 ◽  
pp. 1-9 ◽  
Author(s):  
P. Janczyk ◽  
R. Pieper ◽  
V. Urubschurov ◽  
K. R. Wendler ◽  
W. B. Souffrant
Keyword(s):  
Essential Oils ◽  
Dry Matter ◽  
Distal Part ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Control Diet ◽  
Short Chain Fatty Acids ◽  
Growth Promoters ◽  
Gradient Gel Electrophoresis ◽  
Antibiotic Growth Promoters ◽  
Polymerase Chain

Essential oils (EO) are being considered as possible alternatives to in-feed antibiotic growth promoters in pig nutrition. The effects of an EO mixture consisting of limonene, eugenol and pinene (10.0, 2.0, and 4.8 mg/kg diet, resp.) on gut physiology and ecology were studied in piglets. The experiment was conducted at low (commercial farm) and high hygienic conditions (experimental farm), to elucidate interactions between EO supplementation and husbandry methods. Piglets were weaned at 28 days of age, when they were offered either a control diet (C) or C with EO. Four piglets were sacrificed in each group on day 29, 30, 33 and 39. Digesta from the third distal part of the small intestine and from the colon were sampled and analysed for pH, dry matter, lactic acid, short chain fatty acids and ammonia concentrations. Enterobacteria, enterococci, lactobacilli and yeast counts were obtained by plating. Genomic DNA was extracted from digesta and polymerase chain reaction—denaturing gradient gel electrophoresis was performed. Individual microbial communities were identified at each farm. Age affected the intestinal parameters. No effects of the EO with exception for a significant reduction in colon bacterial diversity at 39 days of age could be recorded at experimental farm.

The assessment of the coke wastewater treatment efficacy in rotating biological contractor

2015 ◽  
Vol 73 (5) ◽  
pp. 1202-1210 ◽  
Author(s):  
G. Cema ◽  
S. Żabczyński ◽  
A. Ziembińska-Buczyńska
Keyword(s):  
Biological Treatment ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rotating Biological Contactor ◽  
Coke Wastewater ◽  
Promising Tool ◽  
Start Up ◽  
Gradient Gel Electrophoresis ◽  
Real Wastewater ◽  
Polymerase Chain ◽  
Anammox Process

Coke wastewater is known to be relatively difficult for biological treatment. Nonetheless, biofilm-based systems seem to be promising tool for such treatment. That is why a rotating biological contactor (RBC) system focused on the Anammox process was used in this study. The experiment was divided into two parts with synthetic and then real wastewater. It was proven that it is possible to treat coke wastewater with RBC but such a procedure requires a very long start-up period for the nitritation (190 days), as well as for the Anammox process, where stable nitrogen removal over 70% was achieved after 400 days of experiment. Interestingly, it was possible at a relatively low (20.2 ± 2.2 °C) temperature. The polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE) based monitoring of the bacterial community showed that its biodiversity decreased when the real wastewater was treated and it was composed mainly of GC-rich genotypes, probably because of the modeling influence of this wastewater and the genotypes specialization.

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