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Journal articles on the topic 'Microbial samples'

Author: Grafiati
Published: 28 June 2021
Last updated: 7 February 2022

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1

Fierer, Noah, and Craig Cary. "Don't let microbial samples perish." Nature 512, no. 7514 (August 2014): 253. http://dx.doi.org/10.1038/512253b.

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2

Haas, Charles N. "Microbial Sampling: Is It Better to Sample Many Times or Use Large Samples?" Water Science and Technology 27, no. 3-4 (February 1, 1993): 19–25. http://dx.doi.org/10.2166/wst.1993.0314.

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Repeated sampling of a water (raw, Ssished, recreational) is often used to assess microbial quality. Microbial distributions have often been found to be negative binomial distributed in such repeated samples. Under these conditions, it is shown that it is better to use a large number of small volume samples than vice versa, providing that the negative binomial dispersion parameter remains unaffected by volume. Further research is needed to determine if the latter assumption, which influences the conclusion proposed, is valid for various classes of microorganisms in various types of waters.
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3

Sharifullina, D. M., R. M. Vasil’eva, T. I. Yakovleva, E. G. Nikolaeva, O. K. Pozdeev, A. P. Lozhkin, and R. N. Khayrullin. "Microbial landscape of atherosclerotic plaques biopsy samples." Kazan medical journal 96, no. 6 (December 15, 2015): 979–82. http://dx.doi.org/10.17750/kmj2015-979.

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Aim. To study the microflora composition of different localization atherosclerotic plaques in patients with atherosclerosis. Methods. 88 samples of atherosclerotic plaques were analyzed, including brachycephalic arteries - 71, the coronary arteries - 13, the aorta - 2, vessels of lower extremities - 2. The specimens were obtained from 71 men and 17 women aged 30-79 years (mean age 50.8 years). The presence of aerobic and anaerobic microflora was determined by bacteriological method. Detection of the cytomegalovirus nucleic acid, herpes simplex virus types 1 and 2, Epstein-Barr virus was performed by real time polymerase chain reaction. Results. The most diverse microflora was represented in the plaques of the neck vessels (carotid arteries). Thereat we found bacteria in 77.5% of the samples, including Propionibacterium acnes - 40.8%, the Staphylococcus genus - 50.7%. 83.3% Staphylococcus isolates were identified as S. epidermidis. In 14.1% of the samples from the brachycephalic artery plaques microorganisms associations (P. acnes and S. epidermidis) were found. The coronary arteries and aorta plaques microflora was represented entirely by P. acnes - 15.4 and 50% respectively. Herpes simplex virus type 1 and 2, and Epstein-Barr virus nucleic acids were detected in 6.7% of samples of carotid artery atherosclerotic plaques. Bacteria associations were presented exclusively in atherosclerotic plaques from brachycephalic arteries - 11.4% of the samples, including 9 bacteria (P. acnes and S. epidermidis) associations, and one association consisted of 3 microorganisms: 2 bacteria (P. acnes and S. epidermidis) and the virus (Epstein-Barr virus). Conclusion. Observed high frequency of microorganisms detection in studied atherosclerotic plaques samples allows to suggest their possible pathogenetic role in the blood vessels endothelium atherosclerotic lesions formation.
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4

Ciafardini, G., and B. A. Zullo. "Assay of microbial enzymes in opaque samples." Journal of Microbiological Methods 34, no. 1 (September 1998): 73–79. http://dx.doi.org/10.1016/s0167-7012(98)00071-2.

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5

Hyvärinen, A., H. Rintala, S. Kokkonen, L. Larsson, and A. Nevalainen. "Microbial Exposure Assessment With House Dust Samples." Epidemiology 17, Suppl (November 2006): S227. http://dx.doi.org/10.1097/00001648-200611001-00582.

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6

Jufri, Rhezqy Furwati. "Microbial Isolation." Journal La Lifesci 1, no. 1 (January 30, 2020): 18–23. http://dx.doi.org/10.37899/journallalifesci.v1i1.33.

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The importance of isolating a microbe from the environment, such as food (solid substrate), drinks (liquid substrate), and yourself because of the many microbes that are difficult to observe or distinguish directly using the five senses. A sample can contain bacteria or fungi. By isolating, the shape of the colonies and the contents in a sample can be observed. Bacteria from the air and normal flora form colonies with lobate-shaped edges, whereas bacteria found in well water samples form colonies with irregular edges and there are also fungi found in the well water samples.
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7

Berthod, Alain, Mike A. Rodriguez, Marco Girod, and Daniel W. Armstrong. "Use of microbubbles in capillary electrophoresis for sample segregation when focusing microbial samples." Journal of Separation Science 25, no. 15-17 (November 1, 2002): 988–95. http://dx.doi.org/10.1002/1615-9314(20021101)25:15/17<988::aid-jssc988>3.0.co;2-i.

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8

Clarke, Erik L., Abigail P. Lauder, Casey E. Hofstaedter, Young Hwang, Ayannah S. Fitzgerald, Ize Imai, Wojciech Biernat, et al. "Microbial Lineages in Sarcoidosis. A Metagenomic Analysis Tailored for Low–Microbial Content Samples." American Journal of Respiratory and Critical Care Medicine 197, no. 2 (January 15, 2018): 225–34. http://dx.doi.org/10.1164/rccm.201705-0891oc.

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9

Poretsky, Rachel S., Nasreen Bano, Alison Buchan, Gary LeCleir, Jutta Kleikemper, Maria Pickering, Whitney M. Pate, Mary Ann Moran, and James T. Hollibaugh. "Analysis of Microbial Gene Transcripts in Environmental Samples†." Applied and Environmental Microbiology 71, no. 7 (July 2005): 4121–26. http://dx.doi.org/10.1128/aem.71.7.4121-4126.2005.

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ABSTRACT We analyzed gene expression in marine and freshwater bacterioplankton communities by the direct retrieval and analysis of microbial transcripts. Environmental mRNA, obtained from total RNA by subtractive hybridization of rRNA, was reverse transcribed, amplified with random primers, and cloned. Approximately 400 clones were analyzed, of which ∼80% were unambiguously mRNA derived. mRNAs appeared to be from diverse taxonomic groups, including both Bacteria (mainly α- and γ-Proteobacteria) and Archaea (mainly Euryarchaeota). Many transcripts could be linked to environmentally important processes such as sulfur oxidation (soxA), assimilation of C1 compounds (fdh1B), and acquisition of nitrogen via polyamine degradation (aphA). Environmental transcriptomics is a means of exploring functional gene expression within natural microbial communities without bias toward known sequences, and provides a new approach for obtaining community-specific variants of key functional genes.
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10

Webster, JoAnn J., Ginger J. Hampton, John T. Wilson, William C. Ghiorse, and Franklin R. Leach. "Determination of Microbial Cell Numbers in Subsurface Samples." Ground Water 23, no. 1 (January 1985): 17–25. http://dx.doi.org/10.1111/j.1745-6584.1985.tb02775.x.

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11

Valeur, J., E. Norin, T. Midtvedt, and A. Berstad. "Assessment of microbial fermentation products in fecal samples." Neurogastroenterology & Motility 22, no. 10 (September 2, 2010): 1147. http://dx.doi.org/10.1111/j.1365-2982.2010.01534.x.

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12

Kudryashova, E. B., E. Yu Chernousova, N. E. Suzina, E. V. Ariskina, and D. A. Gilichinsky. "Microbial diversity of Late Pleistocene Siberian permafrost samples." Microbiology 82, no. 3 (May 2013): 341–51. http://dx.doi.org/10.1134/s0026261713020082.

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13

Socransky, S. S., A. D. Haffajee, J. L. Dzink, and J. D. Hillman. "Associations between microbial species in subgingival plaque samples." Oral Microbiology and Immunology 3, no. 1 (March 1988): 1–7. http://dx.doi.org/10.1111/j.1399-302x.1988.tb00596.x.

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14

Fox, Bethany, Robin Thorn, Alexandre Anesio, Timothy Cox, John Attridge, and Darren Reynolds. "Microbial Processing and Production of Aquatic Fluorescent Organic Matter in a Model Freshwater System." Water 11, no. 1 (December 21, 2018): 10. http://dx.doi.org/10.3390/w11010010.

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Organic matter (OM) has an essential biogeochemical influence along the hydrological continuum and within aquatic ecosystems. Organic matter derived via microbial processes was investigated within a range of model freshwater samples over a 10-day period. For this, excitation-emission matrix (EEM) fluorescence spectroscopy in combination with parallel factor (PARAFAC) analysis was employed. This research shows the origin and processing of both protein-like and humic-like fluorescence within environmental and synthetic samples over the sampling period. The microbial origin of Peak T fluorescence is demonstrated within both synthetic samples and in environmental samples. Using a range of incubation temperatures provides evidence for the microbial metabolic origin of Peak T fluorescence. From temporally resolved experiments, evidence is provided that Peak T fluorescence is an indication of metabolic activity at the microbial community level and not a proxy for bacterial enumeration. This data also reveals that humic-like fluorescence can be microbially derived in situ and is not solely of terrestrial origin, likely to result from the upregulation of cellular processes prior to cell multiplication. This work provides evidence that freshwater microbes can engineer fluorescent OM, demonstrating that microbial communities not only process, but also transform, fluorescent organic matter.
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15

Fujikawa, Hiroshi, and Hiroe Tsubaki. "Characteristics of Microbial Colony Counts on Agar Plates for Food and Microbial Culture Samples." Food Hygiene and Safety Science (Shokuhin Eiseigaku Zasshi) 60, no. 4 (August 25, 2019): 88–95. http://dx.doi.org/10.3358/shokueishi.60.88.

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16

Ishoey, Thomas, Tanja Woyke, Ramunas Stepanauskas, Mark Novotny, and Roger S. Lasken. "Genomic sequencing of single microbial cells from environmental samples." Current Opinion in Microbiology 11, no. 3 (June 2008): 198–204. http://dx.doi.org/10.1016/j.mib.2008.05.006.

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17

Kaarakainen, Pasi, Helena Rintala, Asko Vepsäläinen, Anne Hyvärinen, Aino Nevalainen, and Teija Meklin. "Microbial content of house dust samples determined with qPCR." Science of The Total Environment 407, no. 16 (August 2009): 4673–80. http://dx.doi.org/10.1016/j.scitotenv.2009.04.046.

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18

Olson, J. B., C. C. Lord, and P. J. McCarthy. "Improved Recoverability of Microbial Colonies from Marine Sponge Samples." Microbial Ecology 40, no. 2 (August 2000): 139–47. http://dx.doi.org/10.1007/s002480000058.

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19

Lipoglavšek, L., and G. Avguštin. "Obstacles to flow cytometric analysis of rumen microbial samples." Folia Microbiologica 49, no. 2 (March 2004): 183–86. http://dx.doi.org/10.1007/bf02931398.

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20

Kucnerowicz, Felix, and Willy Verstraete. "Direct measurement of microbial ATP in activated sludge samples." Journal of Chemical Technology and Biotechnology 29, no. 11 (April 24, 2007): 707–12. http://dx.doi.org/10.1002/jctb.503291107.

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21

Taylor, Craig D., Kenneth W. Doherty, Stephen J. Molyneaux, Archie T. Morrison, John D. Billings, Ivory B. Engstrom, Don W. Pfitsch, and Susumu Honjo. "Autonomous Microbial Sampler (AMS), a device for the uncontaminated collection of multiple microbial samples from submarine hydrothermal vents and other aquatic environments." Deep Sea Research Part I: Oceanographic Research Papers 53, no. 5 (May 2006): 894–916. http://dx.doi.org/10.1016/j.dsr.2006.01.009.

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22

Tandlich, Roman. "Citizen science based monitoring of microbial water quality at a single household level in a South African local municipality during the COVID19 lockdown." Nova Biotechnologica et chimica 19, no. 1 (June 30, 2020): 116–23. http://dx.doi.org/10.36547/nbc.v19i1.586.

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Personal hygiene and access to potable water, which is safe for human consumption, are critical to containing the COVID19 pandemic. Here monitoring results are reported for microbial quality of water samples from the municipal supply in Makana Local Municipality in the Eastern Cape Province, South Africa. Access of the human population to sufficient volumes of potable water of required (microbial) quality has been a problem in this local municipality. Samples were taken just before and during 30 days of the strictest phase of the nation-wide lockdown, related to COVID19 in South Africa. Aim of this short communication was to perform the water quality testing with limited to no access to laboratory facilities and using the principles of citizen science. The H2S test kit was used as the basis for the microbial testing, while a cell phone app was used for the temperature monitoring. Five H2S test kit were used per sampling at the author’s house and the kits was developed for the microbial water quality assessment in isolated settings such as those for the lockdown. During the study, the ambient temperature ranged from 17 to 29 °C, with decreases below 18 °C occurring on three out of 12 sampling occasions. Thus the results of the H2S test kit might have been slightly influenced by the fluctuations of the ambient temperature. On 8 sampling occasions between 1 and 4 H2S test kits were positive for faecal contamination. Three samples or 25 % were free of faecal contamination. One sample had all five H2S test kits were positive for faecal contamination. Results of statistical testing indicated that potable water in Makana Local Municipality was probably microbially contaminated at the author’s household on an intermittent basis. Ongoing monitoring of microbial drinking water quality is necessary and continuing at the sampled location.
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23

Zhu, Xiang Y., John Lubeck, and John J. Kilbane. "Characterization of Microbial Communities in Gas Industry Pipelines." Applied and Environmental Microbiology 69, no. 9 (September 2003): 5354–63. http://dx.doi.org/10.1128/aem.69.9.5354-5363.2003.

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ABSTRACT Culture-independent techniques, denaturing gradient gel electrophoresis (DGGE) analysis, and random cloning of 16S rRNA gene sequences amplified from community DNA were used to determine the diversity of microbial communities in gas industry pipelines. Samples obtained from natural gas pipelines were used directly for DNA extraction, inoculated into sulfate-reducing bacterium medium, or used to inoculate a reactor that simulated a natural gas pipeline environment. The variable V2-V3 (average size, 384 bp) and V3-V6 (average size, 648 bp) regions of bacterial and archaeal 16S rRNA genes, respectively, were amplified from genomic DNA isolated from nine natural gas pipeline samples and analyzed. A total of 106 bacterial 16S rDNA sequences were derived from DGGE bands, and these formed three major clusters: beta and gamma subdivisions of Proteobacteria and gram-positive bacteria. The most frequently encountered bacterial species was Comamonas denitrificans, which was not previously reported to be associated with microbial communities found in gas pipelines or with microbially influenced corrosion. The 31 archaeal 16S rDNA sequences obtained in this study were all related to those of methanogens and phylogenetically fall into three clusters: order I, Methanobacteriales; order III, Methanomicrobiales; and order IV, Methanosarcinales. Further microbial ecology studies are needed to better understand the relationship among bacterial and archaeal groups and the involvement of these groups in the process of microbially influenced corrosion in order to develop improved ways of monitoring and controlling microbially influenced corrosion.
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24

Ameri, Abdolghani, Maryam Ekhtelat, and Sara Shamsaei. "Microbial indices of industrial and traditional medicinal herbs in Ahvaz, Iran." Foods and Raw Materials 8, no. 1 (February 26, 2020): 134–40. http://dx.doi.org/10.21603/2308-4057-2020-1-134-139.

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Introduction. Medicinal herbs are susceptible to microbial contamination which can have profound effects on the consumer’s health. Our study aimed to evaluate microbial contamination of common medicinal herbs in Ahvaz. Study objects and methods. We collected 80 samples of traditional and industrial medicinal plants from the supply market, namely valeriana, fennel, licorice, and shirazi thyme. The reference method was used to determine microbial indices such as the total count of microorganisms, yeast and mold, Bacillus cereus, coliforms, and Escherichia coli. Results and discussion. We found that the total microbial count, yeast and mold, B. cereus, and coliform contamination accounted for 45, 77, 55, and 55% of the total samples, respectively, exceeding the allowed limits. There was a significant difference between the industrial and traditional samples in fungal and coliform contamination, with the traditional samples being more highly contaminated. However, no significant difference was observed between them in total count and B. cereus contamination. E. coli contamination was detected in 31.2% of the samples, mostly in traditional. Total microbial count and yeast and mold contamination were highest among valeriana plants. Fennel showed the highest B. cereus and coliform contamination. The lowest contamination was observed in licorice. Conclusion. The results showed that a considerable percentage of the medicinal herbs under study were contaminated at levels exceeding the standard limits. Plants could be contaminated during harvesting, processing or storage. Finally, different species of plants have different antimicrobial activities that affect their microbial contamination.
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25

Coleman, Max L., Magali Ader, Swades Chaudhuri, and John D. Coates. "Microbial Isotopic Fractionation of Perchlorate Chlorine." Applied and Environmental Microbiology 69, no. 8 (August 2003): 4997–5000. http://dx.doi.org/10.1128/aem.69.8.4997-5000.2003.

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ABSTRACT Perchlorate contamination can be microbially respired to innocuous chloride and thus can be treated effectively. However, monitoring a bioremediative strategy is often difficult due to the complexities of environmental samples. Here we demonstrate that microbial respiration of perchlorate results in a significant fractionation (∼−15‰) of the chlorine stable isotope composition of perchlorate. This can be used to quantify the extent of biotic degradation and to separate biotic from abiotic attenuation of this contaminant.
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26

Navarro, David, A. González, and A. Saiz O y Odriozola. "Sample collection/stabilization and DNA/RNA extraction from swab samples for microbiome or metagenome analyses." BioTechniques 71, no. 3 (September 2021): 499–500. http://dx.doi.org/10.2144/btn-2021-1000ap.

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Good preservation and storage are essential to preserving microorganisms’ genetic material in microbial communities from wide array of sample inputs and accurately represent the bacterial composition for further analysis and applications. The objective is to develop a proper preservation and storage medium to preserve DNA and RNA from those microorganisms. DANAGEN-BIOTED has developed a new product to deal with this problem. Click on the To read the full Application forum, click on the View Article button above and download the PDF.
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27

Listgarten, Max A., Chern-Hsiung Lai, and Virginia Young. "Microbial Composition and Pattern of Antibiotic Resistance in Subgingival Microbial Samples From Patients With Refractory Periodontitis." Journal of Periodontology 64, no. 3 (March 1993): 155–61. http://dx.doi.org/10.1902/jop.1993.64.3.155.

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28

Chang, Beom-Seok. "Microbial Composition and Pattern of Antibiotic Resistance in Subgingival Microbial Samples From Patients With Refractory Periodontitis." Journal of the Korean Academy of Periodontology 30, no. 4 (2000): 725. http://dx.doi.org/10.5051/jkape.2000.30.4.725.

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29

Chen, Yu-Wei, and Jacques Buffle. "Physicochemical and microbial preservation of colloid characteristics of natural water samples. II: Physicochemical and microbial evolution." Water Research 30, no. 9 (September 1996): 2185–92. http://dx.doi.org/10.1016/0043-1354(96)00096-6.

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30

KENNEDY, J. E., and J. L. OBLINGER. "Application of Bioluminescence to Rapid Determination of Microbial Levels in Ground Beef." Journal of Food Protection 48, no. 4 (April 1, 1985): 334–40. http://dx.doi.org/10.4315/0362-028x-48.4.334.

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The relationship between microbial ATP measurements and aerobic plate counts (APC's at 35, 20 and 7°C) was investigated for 75 ground beef samples. Samples (n = 27) were obtained from several local retail markets in one experiment, and ground beef samples obtained from a single, processing facility were sampled throughout 15 d of storage at 1°C for a total of 48 samples in another experiment. Bioluminescent assay time for a given sample was less than 1 h. The correlation coefficient (r) between log10 microbial ATP and log10 APC (20°C) per g was 0.86 and 0.99 for retail and single source samples, respectively. Differences between actual log10 APC (20°C)/g and corresponding values predicted by linear regression equations were ≤log10 0.5 for 25 of 27 retail samples and 48 of 48 single source samples. Variation was noted in values of ATP per bacterial cell and relative bioluminescent quenching (ATP per relative light unit, RLU) for most retail samples and for single source samples having low APC (20°C) levels (≤log10 7.0).
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31

White, David C., and David B. Ringelberg. "Monitoring deep subsurface microbiota for assessment of safe long-term nuclear waste disposal." Canadian Journal of Microbiology 42, no. 4 (April 1, 1996): 375–81. http://dx.doi.org/10.1139/m96-053.

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Microbes with their resistance to heat and radioactivity, if present and metabolically active, could have major effects on the safety of nuclear waste disposal by posing potential problems in long-term containment. This paper reviews the applicability of the signature lipid biomarker (SLB) analysis in the quantitative assessment of the viable biomass, community composition, and nutritional/physiological status of the subsurface microbiota as it exists in situ in subsurface samples. The samples described in this review are not unlike those expected to be recovered from proposed deep subsurface disposal sites. Assessment of the microbial community ecology using SLB analysis can be utilized to predict potential problems engendered by microbial metabolic activities of these communities in breaching containment by microbially facilitated corrosion and in the potential for subsequent facilitated transport of nuclides into the environment. SLB analysis of the in situ microbial ecology can be utilized to monitor the feasibility of containment options in modeling tests at the specific disposal sites.Key words: nuclear waste, deep subsurface, microbiota, microbial corrosion, safe long-term storage, signature lipid biomarkers.
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32

Kowalenko, C. G., L. J. P. van Vliet, G. Derksen, and S. Yu. "Limitations of methods for preserving ammonium in agricultural runoff samples." Canadian Journal of Soil Science 82, no. 4 (November 1, 2002): 439–44. http://dx.doi.org/10.4141/s01-056.

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Ammonium concentrations in simulated and actual field runoff samples were not stable within 1 d under refrigeration due to microbial activity as shown by evolution of CO2. Changes in frozen samples after freezing and thawing appeared to be due to non-biological processes and this type of preservation should be avoided. A few drops of toluene added to 10 mL of simulated runoff sample stabilized ammonium concentrations at room temperature for 4 d and reduced CO2 evolution during that time substantially. Chemical preservation by adding sufficient HCl, LiCl and CuSO4 to have molarities of these chemicals up to 0.1 M strength was not acceptable because of limited reduction in microbial activity and chemical changes to the sample. Preservation effects of prestorage filtration were not consistent and this would not be a suitable procedure if total N measurements are to be included because a portion of the sample would be removed. It is apparent that microbial activity in runoff or similar types of water samples that contain organic C must be controlled immediately after collection if measurements of specific N ion species are to be made. Although refrigeration slows microbial activity, it may not be an adequate method of preservation for more than 1 d of storage. Even 1 d of refrigeration will be difficult to do under field conditions. Addition of a small amount of toluene to the runoff sample was the most promising preservation method examined. Key words: Runoff samples, sample preservation, ammonium
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33

Cook, Freeman J., and Francis M. Kelliher. "Determining Vertical Root and Microbial Biomass Distributions from Soil Samples." Soil Science Society of America Journal 70, no. 3 (May 2006): 728–35. http://dx.doi.org/10.2136/sssaj2005.0173.

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34

Chua, Lee Suan, and Nurul Izzati Mohd Ismail. "Anti-Inflammatory and Anti-Microbial Activities of Selected Honey Samples." Asian Journal of Agricultural Research 9, no. 6 (October 15, 2015): 293–304. http://dx.doi.org/10.3923/ajar.2015.293.304.

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35

Al Johny, Bassam Oudh. "Comparative Microbial Assessment of Local and Commercial Spirulina platessis Samples." Bioscience Biotechnology Research Communications 12, no. 4 (December 28, 2019): 921–26. http://dx.doi.org/10.21786/bbrc/12.4/12.

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36

K, Manikandan. "Evaluation of Microbial & Allergen Content (Gluten) In Wheat Samples." International Journal for Research in Applied Science and Engineering Technology V, no. IX (September 30, 2017): 211–16. http://dx.doi.org/10.22214/ijraset.2017.9031.

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37

Pieterse, Bart, Renger H. Jellema, and Mariët J. van der Werf. "Quenching of microbial samples for increased reliability of microarray data." Journal of Microbiological Methods 64, no. 2 (February 2006): 207–16. http://dx.doi.org/10.1016/j.mimet.2005.04.035.

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38

Zhu, Lin, Yifan Xu, Joseph J. Ferretti, and Jens Kreth. "Probing Oral Microbial Functionality – Expression of spxB in Plaque Samples." PLoS ONE 9, no. 1 (January 29, 2014): e86685. http://dx.doi.org/10.1371/journal.pone.0086685.

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39

Sagripanti, Jose-Luis, Birgit Hülseweh, Gudrun Grote, Luzie Voß, Katrin Böhling, and Hans-Jürgen Marschall. "Microbial Inactivation for Safe and Rapid Diagnostics of Infectious Samples." Applied and Environmental Microbiology 77, no. 20 (August 19, 2011): 7289–95. http://dx.doi.org/10.1128/aem.05553-11.

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ABSTRACTThe high risk associated with biological threat agents dictates that any suspicious sample be handled under strict surety and safety controls and processed under high-level containment in specialized laboratories. This study attempted to find a rapid, reliable, and simple method for the complete inactivation of a wide range of pathogens, including spores, vegetative bacteria, and viruses, while preserving microbial nucleic acid fragments suitable for PCRs and proteinaceous epitopes for detection by immunoassays. Formaldehyde, hydrogen peroxide, and guanidium thiocyanate did not completely inactivate high titers of bacterial spores or viruses after 30 min at 21°C. Glutaraldehyde and sodium hypochlorite showed high microbicidal activity but obliterated the PCR or enzyme-linked immunosorbent assay (ELISA) detection of bacterial spores or viruses. High-level inactivation (more than 6 log10) of bacterial spores (Bacillus atrophaeus), vegetative bacteria (Pseudomonas aeruginosa), an RNA virus (the alphavirus Pixuna virus), or a DNA virus (the orthopoxvirus vaccinia virus) was attained within 30 min at 21°C by treatment with either peracetic acid or cupric ascorbate with minimal hindrance of subsequent PCR tests and immunoassays. The data described here should provide the basis for quickly rendering field samples noninfectious for further analysis under lower-level containment and considerably lower cost.
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40

Letourneau, Alexander, Jack Kegel, Jehad Al-Ramahi, Emily Yachinich, Harris B. Krause, Cameron J. Stewart, and Megan N. McClean. "A Microfluidic Device for Imaging Samples from Microbial Suspension Cultures." MethodsX 7 (2020): 100891. http://dx.doi.org/10.1016/j.mex.2020.100891.

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41

Banerjee, Pratik, Irshad M. Sulaiman, György Schneider, Udayan Ray, and Bala Jagadeesan. "Novel Microbial Diagnostic Methods for Clinical, Environmental, and Food Samples." BioMed Research International 2017 (2017): 1–3. http://dx.doi.org/10.1155/2017/3942801.

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42

Labare, M. P., and M. Alexander. "Microbial cometabolism of sucralose, a chlorinated disaccharide, in environmental samples." Applied Microbiology and Biotechnology 42, no. 1 (November 1, 1994): 173–78. http://dx.doi.org/10.1007/s002530050234.

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43

Tillett, H. E., J. Sellwood, N. F. Lightfoot, P. Boyd, and S. Eaton. "Correlations between microbial parameters from water samples: expectations and reality." Water Science and Technology 43, no. 12 (June 1, 2001): 19–22. http://dx.doi.org/10.2166/wst.2001.0705.

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Data which are collected in order to estimate the correlation between parameters must be analysed with caution. Classical statistics of correlation are often inappropriate. The “r” statistic is very easily distorted by non-Normal data. Non-parametric statistics can be helpful. The interpretation and usefulness of the estimates of correlation will depend on the study plan. If water samples come from disparate sources (e.g. upstream or downstream from sewage outlets) then parameters A and B may occur in their highest and lowest numbers according to how close the samples were to contamination sources thus correlating closely. However, if all samples come from sources with similar pollution levels then plots of A and B will show considerable scatter and apparently little correlation. So what is the relationship between A and B? An example of “perfect” correlation, as demonstrated by replicate counts of a single parameter from split samples, gave an r value of only 0.63 (ρ = 0.62) due to random variation in numbers of organisms between the two halves of the sample. Thus large amounts of data are needed for studying true correlation because relationships between parameters are embedded in the natural variation. This also illustrated that Standards for a single parameter can be “passed” or “failed” by two halves of the same sample. Study design is clearly of fundamental importance. Consideration must be given to the appropriate way of asking questions about correlation between different parameters.
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Purswani, Jessica, Antonio Manuel Martín-Platero, Patricia Reboleiro-Rivas, Jesús González-López, and Clementina Pozo. "Comparative analysis of microbial DNA extraction protocols for groundwater samples." Analytical Biochemistry 416, no. 2 (September 2011): 240–42. http://dx.doi.org/10.1016/j.ab.2011.05.024.

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45

Labare, M. P., and M. Alexander. "Microbial cometabolism of sucralose, a chlorinated disaccharide, in environmental samples." Applied Microbiology and Biotechnology 42, no. 1 (October 1994): 173–78. http://dx.doi.org/10.1007/bf00170242.

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46

Labare, MP, and M. Alexander. "Microbial cometabolism of sucralose, a chlorinated disaccharide, in environmental samples." Applied Microbiology and Biotechnology 43, no. 1 (April 1995): 194. http://dx.doi.org/10.1007/bf00170643.

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47

Gao, P. K., G. Q. Li, H. M. Tian, Y. S. Wang, H. W. Sun, and T. Ma. "Differences in microbial community composition between injection and production water samples of water flooding petroleum reservoirs." Biogeosciences 12, no. 11 (June 5, 2015): 3403–14. http://dx.doi.org/10.5194/bg-12-3403-2015.

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Abstract. Microbial communities in injected water are expected to have significant influence on those of reservoir strata in long-term water flooding petroleum reservoirs. To investigate the similarities and differences in microbial communities in injected water and reservoir strata, high-throughput sequencing of microbial partial 16S rRNA of the water samples collected from the wellhead and downhole of injection wells, and from production wells in a homogeneous sandstone reservoir and a heterogeneous conglomerate reservoir were performed. The results indicate that a small number of microbial populations are shared between the water samples from the injection and production wells in the sandstone reservoir, whereas a large number of microbial populations are shared in the conglomerate reservoir. The bacterial and archaeal communities in the reservoir strata have high concentrations, which are similar to those in the injected water. However, microbial population abundance exhibited large differences between the water samples from the injection and production wells. The number of shared populations reflects the influence of microbial communities in injected water on those in reservoir strata to some extent, and show strong association with the unique variation of reservoir environments.
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Spring, Allison M., Kathryn M. Docherty, Kenneth D. Domingue, Thomas V. Kerber, Margaret M. Mooney, and Kristina M. Lemmer. "A Method for Collecting Atmospheric Microbial Samples From Set Altitudes for Use With Next-Generation Sequencing Techniques to Characterize Communities." Air, Soil and Water Research 11 (January 1, 2018): 117862211878887. http://dx.doi.org/10.1177/1178622118788871.

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Dispersal of airborne microorganisms is an important ecological process, resulting in the distribution of bacteria to all habitats on Earth. Investigation of this process is limited by the ability to collect uncontaminated high-altitude microbial samples for use with next-generation sequencing approaches. Here, we describe the design of a Remote Airborne Microbial Passive sampling system. Troubleshooting experiments demonstrate that the samplers collect adequate DNA for bacterial 16S rRNA (ribosomal RNA) amplicon–based Mi-Seq sequencing at 2 and 150 m from the ground. When samplers are closed, they retain only a low number of sequences, and may be used as a negative control. We also demonstrate that the optimal amount of collection dishes to include in the sampler is 8, and that freezing collection dishes at −80°C is an alternative to immediate DNA extraction. Samplers may be used to address a variety of ecological and human health–related questions.
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FRÖDER, HANS, CECÍLIA GERALDES MARTINS, KATIA LEANI OLIVEIRA de SOUZA, MARIZA LANDGRAF, BERNADETTE D. G. M. FRANCO, and MARIA TERESA DESTRO. "Minimally Processed Vegetable Salads: Microbial Quality Evaluation." Journal of Food Protection 70, no. 5 (May 1, 2007): 1277–80. http://dx.doi.org/10.4315/0362-028x-70.5.1277.

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The increasing demand for fresh fruits and vegetables and for convenience foods is causing an expansion of the market share for minimally processed vegetables. Among the more common pathogenic microorganisms that can be transmitted to humans by these products are Listeria monocytogenes, Escherichia coli O157:H7, and Salmonella. The aim of this study was to evaluate the microbial quality of a selection of minimally processed vegetables. A total of 181 samples of minimally processed leafy salads were collected from retailers in the city of Sao Paulo, Brazil. Counts of total coliforms, fecal coliforms, Enterobacteriaceae, psychrotrophic microorganisms, and Salmonella were conducted for 133 samples. L. monocytogenes was assessed in 181 samples using the BAX System and by plating the enrichment broth onto Palcam and Oxford agars. Suspected Listeria colonies were submitted to classical biochemical tests. Populations of psychrotrophic microorganisms &gt;106 CFU/g were found in 51% of the 133 samples, and Enterobacteriaceae populations between 105 and 106 CFU/g were found in 42% of the samples. Fecal coliform concentrations higher than 102 CFU/g (Brazilian standard) were found in 97 (73%) of the samples, and Salmonella was detected in 4 (3%) of the samples. Two of the Salmonella-positive samples had &lt;102 CFU/g concentrations of fecal coliforms. L. monocytogenes was detected in only 1 (0.6%) of the 181 samples examined. This positive sample was simultaneously detected by both methods. The other Listeria species identified by plating were L. welshimeri (one sample of curly lettuce) and L. innocua (2 samples of watercress). The results indicate that minimally processed vegetables had poor microbiological quality, and these products could be a vehicle for pathogens such as Salmonella and L. monocytogenes.
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Nelson, A., A. De Soyza, S. J. Bourke, J. D. Perry, and S. P. Cummings. "Assessment of sample handling practices on microbial activity in sputum samples from patients with cystic fibrosis." Letters in Applied Microbiology 51, no. 3 (August 16, 2010): 272–77. http://dx.doi.org/10.1111/j.1472-765x.2010.02891.x.

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