Journal articles on the topic 'Bacteria – Analysis'
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Kim, Su Yeong, and Dae Yong Yi. "Analysis of the human breast milk microbiome and bacterial extracellular vesicles in healthy mothers." Experimental & Molecular Medicine 52, no. 8 (August 2020): 1288–97. http://dx.doi.org/10.1038/s12276-020-0470-5.
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Abstract The microbiota of human breast milk (HBM) contribute to infant gut colonization; however, whether bacterial extracellular vesicles (EVs) are present in HBM or might contribute to this process remains unknown. In this study, we characterized the HBM microbiota of healthy Korean mothers and measured the key bacteria likely affecting infant gut colonization by analyzing both the microbiota and bacterial EVs. A total of 22 HBM samples were collected from lactating mothers. The DNA of bacteria and bacteria-derived EVs was extracted from each sample. In alpha-diversity analyses, bacterial samples showed higher richness and evenness than bacterial EV samples, and beta-diversity analyses showed significant differences between bacteria and bacterial EVs within identical individual samples. Firmicutes accounted for the largest proportion among the phyla, followed by Proteobacteria, Bacteroidetes, and Actinobacteria, in both bacteria and bacterial EV samples. At the genus level, Streptococcus (25.1%) and Staphylococcus (10.7%) were predominant in bacterial samples, whereas Bacteroides (9.1%), Acinetobacter (6.9%), and Lactobacillaceae(f) (5.5%) were prevalent in bacterial EV samples. Several genera, including Bifidobacterium, were significantly positively correlated between the two samples. This study revealed the diverse bacterial communities in the HBM of healthy lactating mothers, and found that gut-associated genera accounted for a high proportion in bacterial EV samples. Our findings suggest the existence of key bacteria with metabolic activity that are independent of the major bacterial populations that inhabit HBM, and the possibility that EVs derived from these bacteria are involved in the vertical transfer of gut microbiota.
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Kulakov, Leonid A., Morven B. McAlister, Kimberly L. Ogden, Michael J. Larkin, and John F. O'Hanlon. "Analysis of Bacteria Contaminating Ultrapure Water in Industrial Systems." Applied and Environmental Microbiology 68, no. 4 (April 2002): 1548–55. http://dx.doi.org/10.1128/aem.68.4.1548-1555.2002.
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ABSTRACT Bacterial populations inhabiting ultrapure water (UPW) systems were investigated. The analyzed UPW systems included pilot scale, bench scale, and full size UPW plants employed in the semiconductor and other industries. Bacteria present in the polishing loop of the UPW systems were enumerated by both plate counts and epifluorescence microscopy. Assessment of bacterial presence in UPW by epifluorescence microscopy (cyanotolyl tetrazolium chloride [CTC] and DAPI [4′,6′-diamidino-2-phenylindole] staining) showed significantly higher numbers (10 to 100 times more bacterial cells were detected) than that determined by plate counts. A considerable proportion of the bacteria present in UPW (50 to 90%) were cells that did not give a positive signal with CTC stain. Bacteria isolated from the UPW systems were mostly gram negative, and several groups seem to be indigenous for all of the UPW production systems studied. These included Ralstonia pickettii, Bradyrhizobium sp., Pseudomonas saccharophilia, and Stenotrophomonas strains. These bacteria constituted a significant part of the total number of isolated strains (≥20%). Two sets of primers specific to R. pickettii and Bradyrhizobium sp. were designed and successfully used for the detection of the corresponding bacteria in the concentrated UPW samples. Unexpectedly, nifH gene sequences were found in Bradyrhizobium sp. and some P. saccharophilia strains isolated from UPW. The widespread use of nitrogen gas in UPW plants may be associated with the presence of nitrogen-fixing genes in these bacteria.
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Djokic, Lidija, M. Savic, Tanja Narancic, and Branka Vasiljevic. "Metagenomic analysis of soil microbial communities." Archives of Biological Sciences 62, no. 3 (2010): 559–64. http://dx.doi.org/10.2298/abs1003559d.
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Ramonda serbica and Ramonda nathaliae, rare resurrection plants growing in the Balkan Peninsula, produce a high amount of phenolic compounds as a response to stress. The composition and size of bacterial communities in two rhizosphere soil samples of these plants were analyzed using a metagenomic approach. Fluorescent in situ hybridization (FISH) experiments together with DAPI staining showed that the metabolically active bacteria represent only a small fraction, approximately 5%, of total soil bacteria. Using universal bacteria - specific primers 16S rDNA genes were amplified directly from metagenomic DNAs and two libraries were constructed. The Restriction Fragment Length Polymorphism (RLFP) method was used in library screening. Amongst 192 clones, 35 unique operational taxonomic units (OTUs) were determined from the rhizosphere of R. nathaliae, and 13 OTUs out of 80 clones in total from the library of R. serbica. Representative clones from each OTU were sequenced. The majority of sequences from metagenomes showed very little similarity to any cultured bacteria. In conclusion, the bacterial communities in the studied soil samples showed quite poor diversity. .
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Perumal, Balaji, John Andrew Carlson, and Dale Robert Meyer. "A Pathological Analysis of Canaliculitis Concretions: More Than JustActinomyces." Scientifica 2016 (2016): 1–4. http://dx.doi.org/10.1155/2016/6313070.
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Purpose.Canaliculitis is classically associated withActinomycesspecies, which are filamentous bacteria; the purpose of this study was to evaluate the extent to which nonfilamentous bacteria colonize canalicular concretions by using graded histopathological analysis.Methods.This is a series of 16 cases. The percentage of Gram-positive/Gomori’s methenamine silver-positive filamentous bacteria (Actinomyces) versus the total bacteria identified was graded, and the types of bacteria seen were recorded. Nonfilamentous bacteria were categorized based upon Gram stain (positive or negative) and morphology (cocci or rods).Results. There were 11 females and 5 males. Nonfilamentous bacteria were identified in 16 of 16 (100%) specimens and filamentous bacteria were identified in 15 of 16 (94%) specimens. The mean percentage of filamentous bacteria relative to total bacteria was 57%. Regarding the nonfilamentous bacteria present, 69% of specimens had Gram-positive cocci only, 25% had Gram-positive and Gram-negative cocci, and 6% had Gram-positive cocci and Gram-positive rods.Conclusion. In the current study, there was a mix of filamentous and nonfilamentous bacteria in almost all canalicular concretions analyzed. Nonfilamentous bacteria may contribute to the pathogenesis of canaliculitis. In addition, the success of bacterial culture can be variable; therefore, pathological analysis can assist in determining the etiology.
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Tsibakhashvili, N. Ya, L. Mosulishvili, E. Kirkesali, T. Kalabegishvili, S. Kerkenjia, M. V. Frontasyeva, Gh Duca, and I. Zinicovscaia. "Epithermal Neutron Activation Analysis for Bacterial Transformations of Chromium." Chemistry Journal of Moldova 4, no. 2 (December 2009): 8–13. http://dx.doi.org/10.19261/cjm.2009.04(2).18.
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Most powerful primary analytical technique, neutron activation analysis, was applied to study indigenous bacteria, namely, Arthrobacter genera which can be successfully used in detoxification and immobilization of toxic substances. In the present study the effect of Cr(VI) on the elemental content of these bacteria has been examined. The concentrations from 12 to 19 elements such as Na, Al, Cl, K, Fe, Co, Zn, As, Br, Rb, Sr, Sb, Ba, Tb, Th, U were determined in the bacterial cells. The high rate of Cr accumulation in the tested bacterial cells was shown. In bacteria treated with chromate some similarity in the behaviour of the following essential elements − potassium, sodium, chlorine − was observed. Such non-essential elements as Ag, As, Br and U were determined in all bacteria and have to be considered by cells as toxins.
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Vinay, Oraon, Prasad Bhupendra, and Singh Kiran. "16S rDNA-RFLP analysis of phylogenetic tree of Rhizobium bacteria." Indian Journal of Applied Research 3, no. 12 (October 1, 2011): 474–76. http://dx.doi.org/10.15373/2249555x/dec2013/145.
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Bhattacharyya, Neil. "Bacterial Infection in Chronic Rhinosinusitis: A Controlled Paired Analysis." American Journal of Rhinology 19, no. 6 (November 2005): 544–48. http://dx.doi.org/10.1177/194589240501900602.
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Background The aim of this study was to determine if pathogenic bacteria are involved in the pathogenesis of chronic rhinosinusitis (CRS). Methods A consecutive series of adult patients with unilateral sinus disease determined by unilateral radiographic involvement or unilateral purulent secretions was microbiologically studied. Aerobic and anaerobic bacterial and fungal cultures were obtained during endoscopic sinus surgery from purulent secretions or tissue culture. Positive culture rates were compared between the diseased sinus and the contralateral nondiseased (control) sinus to determine if pathogenic bacteria were more commonly recovered from the diseased sinuses. Results Forty-nine adult patients completed the study with appropriate microbiological data. Coagulase-negative staphylococci were the most commonly recovered bacteria followed by Staphylococcus aureus from the diseased side of the sinuses with similar findings for the control sinus. Bacterial species were recovered from 87.8% of the diseased side of the sinuses versus 85.7% from the control sinuses (p = 0.50). Reanalysis with coagulase-negative staphylococci considered as non-pathogen showed a 46.9 and 49.0% positive bacterial culture rate in diseased and control groups, respectively (p = 0.50). No significant difference in positive anaerobic culture rates were identified between groups (59.1% diseased versus 55.1% control, respectively, p = 0.61). Antibiotic resistance rates were no different between bacteria cultured from diseased sinuses versus control (p = 0.115). Conclusion Both aerobic and anaerobic bacterial species may be recovered from both diseased and nondiseased sinuses in patients with CRS. These findings cast some doubt on the exact etiologic role of bacteria in CRS, suggesting other factors or other agents also may be responsible in CRS pathogenesis.
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Kahlisch, L., K. Henne, L. Groebe, J. Draheim, M. G. Höfle, and I. Brettar. "Molecular analysis of the bacterial drinking water community with respect to live/dead status." Water Science and Technology 61, no. 1 (January 1, 2010): 9–14. http://dx.doi.org/10.2166/wst.2010.773.
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The assessment of the physiological state of the bacteria in drinking water is a critical issue, especially with respect to the presence of pathogenic bacteria. Though molecular methods can provide insight into the taxonomic composition of the drinking water microflora, the question if a bacterial species is alive or dead still needs to be addressed. To distinguish live and dead bacteria at the taxonomic level, we combined three methods: i) a staining procedure indicating membrane-injured cells (using SYTO9 and Propidium Iodide) that is considered to distinguish between live and dead cells, ii) Fluorescence Activated Cell Sorting (FACS) of the membrane injured and intact bacteria, and iii) molecular analyses of the RNA extracted from the bacteria before and after sorting to analyse the bacterial community at the species level. By staining and FACS analysis the drinking water bacteria could be separated according to their different membrane integrities, and RNA could be extracted from the live and dead sorted bacterial fractions. 16S rRNA based fingerprints revealed a diverse bacterial community in the drinking water samples with the majority being represented by 31 identified phylotypes. Most of the phylotypes referenced belonged to the phyla Proteobacteria (Alpha-, Beta-, Gamma-), Cyanobacteria and Bacteroidetes, and were mostly related to freshwater bacteria. 90% of the total phylotypes could be recovered after FAC-Sorting; 32% of the phylotypes occurred only in the “live” sorted fraction, 21% only in the “dead” sorted fraction, and 46% occurred in both fractions.
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Carels, Nicolas, Marcial Gumiel, Fabio Faria da Mota, Carlos José de Carvalho Moreira, and Patricia Azambuja. "A Metagenomic Analysis of Bacterial Microbiota in the Digestive Tract of Triatomines." Bioinformatics and Biology Insights 11 (January 1, 2017): 117793221773342. http://dx.doi.org/10.1177/1177932217733422.
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The digestive tract of triatomines (DTT) is an ecological niche favored by microbiota whose enzymatic profile is adapted to the specific substrate availability in this medium. This report describes the molecular enzymatic properties that promote bacterial prominence in the DTT. The microbiota composition was assessed previously based on 16S ribosomal DNA, and whole sequenced genomes of bacteria from the same genera were used to calculate the GC level of rare and prominent bacterial species in the DTT. The enzymatic reactions encoded by coding sequences of both rare and common bacterial species were then compared and revealed key functions explaining why some genera outcompete others in the DTT. Representativeness of DTT microbiota was investigated by shotgun sequencing of DNA extracted from bacteria grown in liquid Luria-Bertani broth (LB) medium. Results showed that GC-rich bacteria outcompete GC-poor bacteria and are the dominant components of the DTT microbiota. In addition, oxidoreductases are the main enzymatic components of these bacteria. In particular, nitrate reductases (anaerobic respiration), oxygenases (catabolism of complex substrates), acetate-CoA ligase (tricarboxylic acid cycle and energy metabolism), and kinase (signaling pathway) were the major enzymatic determinants present together with a large group of minor enzymes including hydrogenases involved in energy and amino acid metabolism. In conclusion, despite their slower growth in liquid LB medium, bacteria from GC-rich genera outcompete the GC-poor bacteria because their specific enzymatic abilities impart a selective advantage in the DTT.
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Crump, Byron C., E. Virginia Armbrust, and John A. Baross. "Phylogenetic Analysis of Particle-Attached and Free-Living Bacterial Communities in the Columbia River, Its Estuary, and the Adjacent Coastal Ocean." Applied and Environmental Microbiology 65, no. 7 (July 1, 1999): 3192–204. http://dx.doi.org/10.1128/aem.65.7.3192-3204.1999.
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ABSTRACT The Columbia River estuary is a dynamic system in which estuarine turbidity maxima trap and extend the residence time of particles and particle-attached bacteria over those of the water and free-living bacteria. Particle-attached bacteria dominate bacterial activity in the estuary and are an important part of the estuarine food web. PCR-amplified 16S rRNA genes from particle-attached and free-living bacteria in the Columbia River, its estuary, and the adjacent coastal ocean were cloned, and 239 partial sequences were determined. A wide diversity was observed at the species level within at least six different bacterial phyla, including most subphyla of the classProteobacteria. In the estuary, most particle-attached bacterial clones (75%) were related to members of the genusCytophaga or of the α, γ, or δ subclass of the classProteobacteria. These same clones, however, were rare in or absent from either the particle-attached or the free-living bacterial communities of the river and the coastal ocean. In contrast, about half (48%) of the free-living estuarine bacterial clones were similar to clones from the river or the coastal ocean. These free-living bacteria were related to groups of cosmopolitan freshwater bacteria (β-proteobacteria, gram-positive bacteria, andVerrucomicrobium spp.) and groups of marine organisms (gram-positive bacteria and α-proteobacteria [SAR11 andRhodobacter spp.]). These results suggest that rapidly growing particle-attached bacteria develop into a uniquely adapted estuarine community and that free-living estuarine bacteria are similar to members of the river and the coastal ocean microbial communities. The high degree of diversity in the estuary is the result of the mixing of bacterial communities from the river, estuary, and coastal ocean.
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Boaden, Elizabeth, Lois Thomas, Susan Caroline, and Higham Watkins. "Microbiological analysis of water and thickeners used for people with dysphagia." British Journal of Community Nursing 25, Sup8 (August 1, 2020): S16—S24. http://dx.doi.org/10.12968/bjcn.2020.25.sup8.s16.
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Thickened fluids are a recognised intervention strategy in use for people with dysphagia. However, their bacterial profile has not previously been examined. Aims: To identify bacteria and changes in bacterial profiles in a range of water sources and thickener preparations over a 5-day period. Methods: Nine experiments were performed using a range of preparations (sterile, drinking, non-drinking tap water) and a thickening agent (sterile sachet and a used tin). Findings: No bacteria were grown on serial subcultures of sterile water, both with and without thickener. Drinking, tap and thickened water left at room temperature for 24 hours may become contaminated with environmental organisms. Conclusions: The growth of bacteria in preparations of thickening agent appears to be dependent upon water quality, while the proliferation of bacteria is dependent upon the length of time the preparation is allowed to stand at room temperature.
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Murakami, Gen, Yuichi Sugai, and Kyuro Sasaki. "Preliminary Study on In Situ Realtime Quantitation of Target Bacteria on the Principle of Flow Cytometry." Solid State Phenomena 262 (August 2017): 224–27. http://dx.doi.org/10.4028/www.scientific.net/ssp.262.224.
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In-situ realtime method that can monitor the target bacteria should be used to determine the real situation of the bacteria in deep parts of heaps in heap bioleaching plants. This study suggest to apply flow cytometry technology to in-situ realtime monitoring of target bacteria. Flow cytometry is a method that can rapidly quantify the bacterial cells in bacterial suspension based on the detection of lights that are emitted from bacterial cells. In this study, we estimated the possibility of the application of flow cytometry to the selective detection of target bacteria. The bacterial culture solution that had been diluted by water including other bacteria was provided for fluorescence spectral analysis and scattered light analysis that were functions of flow cytometry. Our target bacteria could be selectively detected by those analyses in this study, therefore, it was shown that the flow cytometry could be useful for detecting target bacteria selectively. Because the measurement principle of flow cytometry is quite simple, it can be expected to be installed into deep heaps through the monitoring wells and determine the dominance of target bacteria in-situ and realtime in the future.
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Cheng, Dandan, Zhongsai Tian, Liang Feng, Lin Xu, and Hongmei Wang. "Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range." PeerJ 6 (January 7, 2019): e6162. http://dx.doi.org/10.7717/peerj.6162.
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Increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, and thus it is hypothesized that interactions between bacteria and alien plants might play an important role in plant invasions. However, the diversity of the bacterial communities associated with invasive plants is poorly understood. We therefore investigated the diversity of rhizospheric and endophytic bacteria associated with the invasive annual plant Senecio vulgaris L. (Asteraceae) based on 16S rRNA gene data obtained from 57 samples of four Senecio vulgaris populations in a subtropical mountainous area in central China. Significant differences in diversity were observed between plant compartments. Specifically, the rhizosphere harbored many more bacterial operational taxonomic units and showed higher alpha diversity than the leaf and root endospheres. The relative abundance profiles of the bacterial community composition differed substantially between the compartments and populations, especially at the phylum and family levels. However, the top five phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Acidobacteria) accounted for more than 90% of all the bacterial communities. Moreover, similar endophytic communities with a shared core set of bacteria were observed from different Senecio vulgaris populations. Heavy-metal-resistant, phosphate-solubilizing bacteria (Brevundimonas diminuta), nitrogen-fixing bacteria (Rhizobium leguminosarum), and cold-resistant bacteria (Exiguobacterium sibiricum) were present in the endosphere at relatively high abundance. This study, which reveals the structure of bacterial communities and their putative function in invasive Senecio vulgaris plants, is the first step in investigating the role of plant–bacteria interactions in the invasion of this species in China.
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Boaden, Elizabeth, Lois Thomas, Susan Higham, and Caroline Watkins. "Microbiological analysis of water and thickeners used for people with dysphagia." British Journal of Neuroscience Nursing 16, Sup2 (April 1, 2020): S21—S28. http://dx.doi.org/10.12968/bjnn.2020.16.sup2.s21.
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Background: Thickened fluids are a recognised intervention strategy in use for people with dysphagia. However, their bacterial profile has not previously been examined. Aims: To identify bacteria and changes in bacterial profiles in a range of water sources and thickener preparations over a 5-day period. Methods: Nine experiments were performed using a range of preparations of water (sterile, drinking, non-drinking tap water) and a thickening agent (sterile sachet and a used tin). Findings: No bacteria were grown on serial subcultures of sterile water, both with and without thickener. Drinking, tap and thickened water left at room temperature for 24 hours may become contaminated with environmental organisms. Conclusions: The growth of bacteria in preparations of thickening agent appears to be dependent upon water quality, while the proliferation of bacteria is dependent upon the length of time the preparation is allowed to stand at room temperature.
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Boaden, Elizabeth, Lois Thomas, Susan Higham, and Caroline Watkins. "Microbiological analysis of water and thickeners used for people with dysphagia." Nursing and Residential Care 23, no. 1 (January 2, 2021): 1–10. http://dx.doi.org/10.12968/nrec.2021.23.1.6.
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Background: Thickened fluids are a recognised intervention strategy in use for people with dysphagia. However, their bacterial profile has not previously been examined. Aims: To identify bacteria and changes in bacterial profiles in a range of water sources and thickener preparations over a 5-day period. Methods: Nine experiments were performed using a range of preparations of water (sterile, drinking, non-drinking tap water) and a thickening agent (sterile sachet and a used tin). Findings: No bacteria were grown on serial subcultures of sterile water, both with and without thickener. Drinking, tap and thickened water left at room temperature for 24 hours may become contaminated with environmental organisms. Conclusions: The growth of bacteria in preparations of thickening agent appears to be dependent upon water quality, while the proliferation of bacteria is dependent upon the length of time the preparation is allowed to stand at room temperature.
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T, Ahmed. "Microbiological Analysis of Pharmaceutical Non Injectable Drugs Produced in Dhaka, Bangladesh." Open Access Journal of Microbiology & Biotechnology 5, no. 2 (2020): 1–9. http://dx.doi.org/10.23880/oajmb-16000160.
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Pharmaceutical drugs are applied and consumed by the patients with weak immune system and for this reason these products must be of good quality and within the required microbiological limit. Present study attempted to determine the microbiological quality of pharmaceutical non injectable oral and topical drugs as well as their antibacterial activity. A total of sixty samples were studied from different categories of medicine including syrup, tablet & capsule and ointments. Microbiological analysis was done after serial dilution. Antibacterial activity of the samples was also determined by Kirby-Bauer method. The total viable bacterial count of 9 syrups, 7 tablet & capsules and 13 ointments samples exceeded the microbial limit ˂102cfu/ml or cfu/gm recommended by USP (United States Pharmacopeia) and BP (British Pharmacopeia). Regarding to the presence of specific bacteria, about six, six and three samples from syrup, tablet & capsule and ointment samples were of good quality respectively out of twenty samples each. Some drug prevailed good activity towards few bacteria and no activity at all to some others. As the drugs possess antibacterial activity, the contaminants might represent some other species of the same genera of bacteria having some mechanisms to prohibit such activities towards them. More than 50% of the drugs contain higher bacterial and fungal load rendering the quality at risk and not recommended to use by the patients to whom these products will impart most harm as these patients are already immune compromised.
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Jung, Ryan, Minzae Kim, Bhoomi Bhatt, Jong Choi, and Jung Roh. "Identification of Pathogenic Bacteria from Public Libraries via Proteomics Analysis." International Journal of Environmental Research and Public Health 16, no. 6 (March 14, 2019): 912. http://dx.doi.org/10.3390/ijerph16060912.
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Hazardous organisms may thrive on surfaces that are often exposed to human contact, including children’s library books. In this study, swab samples were taken from 42 children’s books collected from four public libraries in Texas and California. Samples were then cultivated in brain–heart infusion (BHI) medium and then in Luria broth (LB) medium containing either ampicillin or kanamycin. All 42 samples (100%) were positive for bacterial growth in normal BHI medium. Furthermore, 35 samples (83.3%) and 20 samples (47.6%) in total were positive in LB medium containing ampicillin or kanamycin, respectively. Bacterial populations were then identified in samples using an Orbitrap Fusion™ Tribrid ™ mass spectrometer, a state-of-the-art proteomic analysis tool. Identified bacterial species grown in ampicillin included Bacillus, Acinetobacter, Pseudomonas, Staphylococcus, Enterobacter, Klebsiella, Serratia, Streptococcus, Escherichia, Salmonella, and Enterococcus. In contrast, identified bacteria grown in kanamycin included Staphylococcus, Streptococcus, Enterococcus, and Bacillus. The presences of pathogenic bacteria species were also confirmed. The results of this study warrant follow up studies to assess the potential health risks of identified pathogens. This study demonstrates the utility of proteomics in identifying environmental pathogenic bacteria for specific public health risk evaluations.
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Afianti, Nur Fitriah, and Yeti Darmayati. "PENDEKATAN CULTURE INDEPENDENT UNTUK ANALISIS KOMUNITAS BAKTERI." OSEANA 42, no. 1 (April 30, 2019): 9–17. http://dx.doi.org/10.14203/oseana.2017.vol.42no.1.34.
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CULTURE INDEPENDENT APPROACH FOR BACTERIAL COMMUNITY ANALYSIS. Analysis of bacterial community can be through two approaches, through cultivation (culture dependent) and without cultivation (culture independent). Culture dependent approach is conventional method which only covered few bacteria because not all bacteria could be cultured. Culture independent approach with molecular techniques based on DNA communities can provide more information about the structure and diversity of bacteria in nature, both culturable bacteria and unculturable bacteria. 16S rRNA gene is commonly target gene used in bacterial communities analysis. Other specific target genes also being developed for specific groups of bacteria. Several methods are developed for the analysis of molecular markers 16S rRNA or other specific genes, including Denaturing Gradient Gel Electrophoresis (DGGE), Terminal Restriction Fragment Length Polymorphism (TRFLP), and Single Strand Conformation Polymorphism (SSCP).
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Larcia II, L. L., R. Estacio, and L. M. Dalmacio. "Bacterial diversity in Philippine fermented mustard (burong mustasa) as revealed by 16S rRNA gene analysis." Beneficial Microbes 2, no. 4 (December 1, 2011): 263–71. http://dx.doi.org/10.3920/bm2011.0019.
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Previous studies on the bacterial profile of burong mustasa, a traditional Philippine fermented food, had been conducted using culture-dependent techniques. Since these methods may underestimate the total microbiota of a sample, a culture-independent study was done to determine the bacterial diversity in burong mustasa through molecular biology techniques. Bacterial DNA was isolated from fermented mustard samples at different stages of fermentation. The isolated genomic DNA was amplified by PCR using specific primers for the 16S ribosomal RNA gene (16S rDNA). The 1.5 kb amplicons obtained were subjected to nested PCR using primers for the internal variable region of the 16S rDNA. The 585 bp nested PCR amplicons were then subjected to denaturing gradient gel electrophoresis (DGGE) to separate the different bacteria present in each sample. Distinct and unique bands in the DGGE profile were excised, reamplified, purified and sequenced for bacterial identification. Molecular cloning of the 1.5 kb 16S rDNA was also performed using the pGEM-T Easy Vector System. The cloned gene was sequenced for bacterial identification. The identified microbiota in burong mustasa at different stages of fermentation include lactic acid bacteria and several uncultured bacteria (initial up to the final stages); acetic acid bacteria (middle stage); and Streptobacillus and Fusobacterium species (initial stage). The potential probiotic bacteria found in burong mustasa are Weissella and Lactobacillus.
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Kay, Emily, Victor I. Lesk, Alireza Tamaddoni-Nezhad, Paul G. Hitchen, Anne Dell, Michael J. Sternberg, Stephen Muggleton, and Brendan W. Wren. "Systems analysis of bacterial glycomes." Biochemical Society Transactions 38, no. 5 (September 24, 2010): 1290–93. http://dx.doi.org/10.1042/bst0381290.
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Bacteria produce an array of glycan-based structures including capsules, lipo-oligosaccharide and glycosylated proteins, which are invariably cell-surface-located. For pathogenic bacteria, such structures are involved in diverse roles in the life cycle of the bacterium, including adhesion, colonization, avoidance of predation and interactions with the immune system. Compared with eukaryotes, bacteria produce huge combinatorial variations of glycan structures, which, coupled to the lack of genetic data, has previously hampered studies on bacterial glycans and their role in survival and pathogenesis. The advent of genomics in tandem with rapid technological improvements in MS analysis has opened a new era in bacterial glycomics. This has resulted in a rich source of novel glycan structures and new possibilities for glycoprospecting and glycoengineering. However, assigning genetic information in predicted glycan biosynthetic pathways to the overall structural information is complex. Bioinformatic analysis is required, linked to systematic mutagenesis and functional analysis of individual genes, often from diverse biosynthetic pathways. This must then be related back to structural analysis from MS or NMR spectroscopy. To aid in this process, systems level analysis of the multiple datasets can be used to make predictions of gene function that can then be confirmed experimentally. The present paper exemplifies these advances with reference to the major gastrointestinal pathogen Campylobacter jejuni.
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Gladka, G. V., V. A. Romanovskaya, H. O. Tashyreva, and O. B. Tashyrev. "Phylogenetic Analysis and Autecology of Spore-Forming Bacteria from Hypersaline Environments." Mikrobiolohichnyi Zhurnal 77, no. 6 (November 30, 2015): 31–38. http://dx.doi.org/10.15407/microbiolj77.06.031.
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Shihora, Nidhi A. "Isolation and characterizations of halotolerant bacteria and identification by FAME analysis." Indian Journal of Applied Research 3, no. 9 (October 1, 2011): 51–53. http://dx.doi.org/10.15373/2249555x/sept2013/16.
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Seo, Youngwook, Bosoon Park, Seung-Chul Yoon, Kurt C. Lawrence, and Gary R. Gamble. "Morphological Image Analysis for Foodborne Bacteria Classification." Transactions of the ASABE 61, no. 1 (2018): 5–13. http://dx.doi.org/10.13031/trans.11800.
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Abstract. The hyperspectral imaging methods used previously for analyzing food quality and safety focused on spectral data analysis to elucidate the spectral characteristics relevant to the quality and safety of food and agricultural commodities. However, the use of spatial information, including physical size, geometric characteristics, orientation, shape, color, and texture, in hyperspectral imaging analysis of food safety and quality has been limited. In this study, image processing techniques were employed for extracting information related to the morphological features of fifteen different foodborne bacterial species and serotypes, including eight Gram-negatives and seven Gram-positives, for classification. The values of nine morphological features (maximum axial length, minimum axial length, orientation, equivalent diameter, solidity, extent, perimeter, eccentricity, and equivalent circular diameter) of bacterial cells were calculated from their spectral images at 570 nm, which were selected from hyperspectral images at 89 wavelengths based on peak scattering intensity. First, two classes (Gram-negative and Gram-positive) were classified using a support vector machine (SVM) algorithm, resulted in a classification accuracy of 82.9% and kappa coefficient (kc) of 0.65. Thereafter, a classification model was developed with two features (cell orientation and perimeter) selected by principal component analysis. In addition, a decision tree (DT) algorithm was used for classification with all nine morphological features. With respect to differentiation into two classes (Gram-positive and Gram-negative), the classification accuracy for five selected bacteria species (, , Typhimurium, , and ) decreased to 80.0% (0.74 of kc) with the DT algorithm and to only 72.5% (0.64 of kc) with the SVM algorithm. Thus, the hyperspectral microscopy image analysis with morphological features is limited for classifying foodborne pathogens, so additional spectral features would be helpful for classification of foodborne bacteria. Keywords: Bacteria, Classification, E. coli, Food safety, Foodborne pathogen, Hyperspectral microscopy, Morphology, Salmonella.
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Syamsussabri, Muhamad, Riza Nurhermi Ningtyas, Amalia Ainun Najah, M. Saiful Fahmi, and Endang Suarsini. "Analysis of Coliform Bacteria Contamination in Drinking Water Sources in Malang City." El-Hayah 7, no. 1 (May 3, 2019): 28–35. http://dx.doi.org/10.18860/elha.v7i1.7244.
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This study aims to determine the contamination of coliform bacteria in drinking water sources of residents in Malang City. Type of this research is explorative descriptive research. The study population was all drinking water sources of residents throughout Malang City, while the research sample was 15 residents wells in five subdistricts of Malang City with each sample taken three sample points. The samples were tested using 3M petrifilm E. coli/coliform count plate. The results showed that all the samples studied were contaminated with coliform bacteria with the highest percentage of 23.01% for E. coli bacteria contamination and 15.41% for total coliform bacterial contamination with an average of bacterial colonies 200 colonies.
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Nie, J. Y., N. W. Zhu, K. Zhao, L. Wu, and Y. H. Hu. "Analysis of the bacterial community changes in soil for septic tank effluent treatment in response to bio-clogging." Water Science and Technology 63, no. 7 (April 1, 2011): 1412–17. http://dx.doi.org/10.2166/wst.2011.319.
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Soil columns were set up to survey the bacterial community in the soil for septic tank effluent treatment. When bio-clogging occurred in the soil columns, the effluent from the columns was in poorer quality. To evaluate changes of the soil bacterial community in response to bio-clogging, the bacterial community was characterized by DNA gene sequences from soil samples after polymerase chain reaction coupled with denaturing gradient gel electrophoresis process. Correspondence analysis showed that Proteobacteria related bacteria were the main bacteria within the soil when treating septic tank effluent. However, Betaproteobacteria related bacteria were the dominant microorganisms in the normal soil, whereas Alphaproteobacteria related bacteria were more abundant in the clogged soil. This study provided insight into changes of the soil bacterial community in response to bio-clogging. The results can supply some useful information for the design and management of soil infiltration systems.
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Umar, ZD, A. Bilkisu, and A. Bashir. "Bacteriological analysis of date palm fruits sold in Katsina metropolis." International Journal of Environment 3, no. 2 (May 30, 2014): 83–86. http://dx.doi.org/10.3126/ije.v3i2.10517.
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Date palm is widely cultivated, distributed and consumed by various individuals. Most of the date palm fruits sold in Nigeria are either damaged or has insufficient quality for human consumption. This study was carried out to determine the bacterial load of date fruits in Katsina metropolis. Enumeration of bacteria was determined using pour plate technique. Serial dilution was carried out, where 10g of date fruits was homogenized in 90ml of diluents and used as stock solution. The bacterial counts were determined using colony forming unit per gram of the date fruit samples (cfu/g). The results obtained revealed high bacterial load in all the samples analyzed, which indicates the fruits contamination with bacteria. This may be due to unhygienic handling of the fruits from the local sellers and the nutritional contents of the fruit that may serve as good source of nutrients to bacteria. Date fruits should be packed and processed in a very hygienic condition for public health importance DOI: http://dx.doi.org/10.3126/ije.v3i2.10517 International Journal of the Environment Vol.3(2) 2014: 83-86
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Matsunaga, T. "Genetic analysis of magnetic bacteria." Materials Science and Engineering: C 4, no. 4 (April 1997): 287–89. http://dx.doi.org/10.1016/s0928-4931(97)00012-x.
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Römling, Ute, Dietmar Grothues, Thomas Heuer, and Burkhard Tümmler. "Physical genome analysis of bacteria." Electrophoresis 13, no. 1 (1992): 626–31. http://dx.doi.org/10.1002/elps.11501301128.
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Tunick, M. H., D. O. Bayles, and J. S. Novak. "DSC Analysis of foodborne bacteria." Journal of Thermal Analysis and Calorimetry 83, no. 1 (January 2006): 23–26. http://dx.doi.org/10.1007/s10973-005-7042-8.
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Apajalahti, J. H. A. "Microbial community analysis and its application in gastrointestinal health." Proceedings of the British Society of Animal Science 2003 (2003): 228. http://dx.doi.org/10.1017/s1752756200013855.
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The intestinal microflora are an integral part of the digestive system of all animals. Bacteria in the gastrointestinal tract derive most of their energy for reproduction and growth from dietary compounds, which are either resistant to attack by digestive fluids or absorbed so slowly that bacteria can successfully compete for them. Since bacterial species differ from each other in relation to their substrate preferences and growth requirements, the chemical composition and structure of the digesta largely determines the species distribution of the microbial community in the gastrointestinal tract. As a consequence, bacterial community structure is very much dependent upon the diet as the ultimate source of substrates for metabolism.
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Halbritter, András, and T. Mogyoróssy. "Phospholipid Fatty Acid (PLFA) Analysis of Rhizosphere Bacterial Communities in a Peat Soil." Agrokémia és Talajtan 51, no. 1-2 (March 1, 2002): 123–28. http://dx.doi.org/10.1556/agrokem.51.2002.1-2.15.
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To analyze the rhizosphere bacterial communities in wetlands, the total lipid content was extracted from a peat soil and 4 abundant wetland plant roots ( Typha angustifolia L., Salix cinerea L., Carex pseudocyperus L., Thelypteris palustris Salisb.). The separated phospholipid fraction was further fractionated and derivatized prior to gas chromatography-mass spectrometry (GC-MS) measurement. In the evaluation only the bacteria-specific fatty acids were used in order to neglect fatty acid information derived from plant root cells. Based on these analyses, a high level bacterial concentration was demonstrated in the rhizosphere, and the relative occurrence of aerobe and anaerobe, Gram positive and negative bacteria, methanotrophs, sulphate reducers and Actinobacteria was determined. Through the PLFA analysis the study of bacteria regardless of culturability was possible.
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WIRASWATI, SRI MARTINA, ARIS TRI WAHYUDI, IMAN RUSMANA, and ABDJAD ASIH NAWANGSIH. "TRFLP analysis for revealing the diversity of rice phyllosphere bacteria." Biodiversitas Journal of Biological Diversity 19, no. 5 (September 21, 2018): 1743–49. http://dx.doi.org/10.13057/biodiv/d190521.
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Wiraswati SM, Wahyudi AT, Rusmana I, Nawangsih AA. 2018. TRFLP analysis for revealing the diversity of rice phyllospherebacteria. Biodiversitas 19: 1743-1749. Phyllosphere environment of rice plant is usually inhabited by diverse bacteria which mostlycontribute beneficial effects to the plant fitness. TRFLP method is a rapid and straightforward method to determine the bacterialdiversity of many environments, including rice phyllosphere environment. This study aimed to analyze rice phyllosphere bacterialdiversity of healthy rice plant cultivar Ciherang obtained from Sukabumi, Jasinga, and Situgede. The bacterial genomes were amplifiedand digested with two restriction enzymes, i.e., MspI and BstUI. The bacterial diversity (H’ index) and evenness (E index) werecalculated from the peak value. From TRFs analysis, Betaproteobacteria and Pseudomonadales were dominantly found in nearly allsamples with different relative abundance. In addition, Alphaproteobacteria and Gammaproteobacteria were also dominant in the severalsamples. The unique bacteria groups were inhabited in the sample from specific regions with certain growth phase. This finding informsus that the geographical factors might be more influent than the growth phase factor. Furthermore, the bacterial diversity and evennessof the metagenomic approach are higher than cultivation-dependent approach.
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Wu, Shao-Chun, Cheng-Shyuan Rau, Hang-Tsung Liu, Pao-Jen Kuo, Peng-Chen Chien, Ting-Min Hsieh, Ching-Hua Tsai, et al. "Metagenome Analysis as a Tool to Study Bacterial Infection Associated with Acute Surgical Abdomen." Journal of Clinical Medicine 7, no. 10 (October 12, 2018): 346. http://dx.doi.org/10.3390/jcm7100346.
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Background: The purpose of this study was to profile the bacterium in the ascites and blood of patients with acute surgical abdomen by metagenome analysis. Methods: A total of 97 patients with acute surgical abdomen were included in this study. Accompanied with the standard culture procedures, ascites and blood samples were collected for metagenome analysis to measure the relative abundance of bacteria among groups of patients and between blood and ascites. Results: Metagenomic analysis identified 107 bacterial taxa from the ascites of patients. A principal component analysis (PCA) could separate the bacteria of ascites into roughly three groups: peptic ulcer, perforated or non-perforated appendicitis, and a group which included cholecystitis, small bowel lesion, and colon perforation. Significant correlation between the bacteria of blood and ascites was found in nine bacterial taxa both in blood and ascites with more than 500 sequence reads. However, the PCA failed to separate the variation in the bacteria of blood into different groups of patients, and the bacteria of metagenomic analysis is only partly in accordance with those isolated from a conventional culture method. Conclusion: This study indicated that the metagenome analysis can provide limited information regarding the bacteria in the ascites and blood of patients with acute surgical abdomen.
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Yusuf, Biçer. "Analysis of the kefir and koumiss microbiota with the focus on certain functional properties of selected lactic acid bacteria." Mljekarstvo 71, no. 2 (March 16, 2021): 112–23. http://dx.doi.org/10.15567/mljekarstvo.2021.0204.
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The aim of this research was to determine the microbiota of commercial kefir, koumiss and homemade kefir samples using metagenomic analysis and compare some probiotic properties of lactic acid bacteria isolated from these beverages and Lactobacillus casei, used in yakult production. One koumiss, 5 commercially available kefir beverages with different brands, and 1 homemade kefir were used as samples. Microbial diversity of kefir and koumiss samples were determined by metagenomic analysis, targeting V1-V2 region of 16S rRNA gene. Streptococcus thermophilus and Lactococcus lactis were detected as dominant in direct DNA isolation from commercially available kefir beverages. Lc. lactis and Leuconostoc mesenteroides were dominant in MRS agars, and Lc. lactis were dominant in M17 agars. In kefir beverages produced by kefir grains, Lb. kefiranofaciens was determined as the dominant bacteria. Lb. kefiri and Enterococcus durans were found dominant in MRS and M17 agars respectively. Lb. kefiranofaciens, Lb. kefiri, and Str. thermophilus were the dominant bacterias of koumiss beverages. Microorganisms isolated from kefir and koumiss beverages were found to exhibit basic probiotic properties, similar to the lactic acid bacteria isolated from yakult. This research presented bacterial microflora and probiotic properties of lactic acid bacteria isolated from kefir and koumiss beverages consumed in Turkey.
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Yuan, Zong-Sheng, Fang Liu, and Guo-Fang Zhang. "Isolation of culturable endophytic bacteria from Moso bamboo (Phyllostachys edulis) and 16S rDNA diversity analysis." Archives of Biological Sciences 67, no. 3 (2015): 1001–8. http://dx.doi.org/10.2298/abs141212063y.
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We analyzed culturable endophytic bacteria from Moso bamboo (Phyllostachys edulis) using traditional bacterial isolation and culture methods and then studied the colony characteristics and diversity with a 16S rDNA sequence analysis. We isolated 82 endophytic bacteria strains belonging to 47 species in 26 genera from the root, rhizome, stem and leaves of Moso bamboo species from populations on Wuyi Mountain, and in the Jiangle and Changting regions. There were significant differences in the composition of the culturable endophytic bacteria isolated from the different areas and from different tissues. The dominant bacteria strains from the Wuyi Mountain samples were Arthrobacter, Staphylococcus, Bacillus and Enterobacter, while the dominant bacteria from the Jiangle samples were Bacillus, Staphylococcus and Curtobacterium, and the dominant bacteria in the Changting samples were Alcaligenes, Pseudomonas, Staphylococcus and Bacillus. Our results demonstrate the abundant diversity of endophytic bacteria in Moso bamboo.
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Hamdan, Mahmoud, and Wafa Masoud. "Characterization of Bacterial Communities in Palestinian Lamb Meat by Phenotyping and 16S rRNA Gene Sequence Analysis." مجلة جامعة فلسطين التقنية خضوري للأبحاث 8, no. 2 (September 1, 2020): 12–22. http://dx.doi.org/10.53671/ptukrj.v8i2.89.
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The main purpose of the present study was to isolate, identify and quantify bacteria in Palestinian fresh lamb meat. Phenotyping and 16S rRNA gene sequence analysis was used to identify bacteria present in lamb meat samples. Thirty-four bacterial isolates were obtained from 20 samples of fresh lamb meat collected from 4 meat shops in Tulkarem city in Palestine. Bacterial counts were in a range of 3 x 103 - 1.5 x 105 cfu / g with Staphylococcus aureus being the highest in numbers among other bacteria. Enterobacteriaceae and Staphylococcaceae were the predominant bacterial families detected in fresh lamb meat samples. Two bacterial isolates, which were not identified by phenotyping, were identified by 16S rRNA gene sequence analysis. There was an agreement between phenotyping and 16S rRNA gene sequencing in identification of 19 bacterial isolates. On the other hand, a disagreement was observed between phenotyping and 16S rRNA gene sequencing in identification of the remaining bacterial isolates. Fresh lamb meat seems to be a good medium for growth of various bacterial species
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Hamdan, Mahmoud, and Wafa Masoud. "Characterization of Bacterial Communities in Palestinian Lamb Meat by Phenotyping and 16S rRNA Gene Sequence Analysis." مجلة جامعة فلسطين التقنية للأبحاث 8, no. 2 (September 1, 2020): 12–22. http://dx.doi.org/10.53671/pturj.v8i2.89.
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The main purpose of the present study was to isolate, identify and quantify bacteria in Palestinian fresh lamb meat. Phenotyping and 16S rRNA gene sequence analysis was used to identify bacteria present in lamb meat samples. Thirty-four bacterial isolates were obtained from 20 samples of fresh lamb meat collected from 4 meat shops in Tulkarem city in Palestine. Bacterial counts were in a range of 3 x 103 - 1.5 x 105 cfu / g with Staphylococcus aureus being the highest in numbers among other bacteria. Enterobacteriaceae and Staphylococcaceae were the predominant bacterial families detected in fresh lamb meat samples. Two bacterial isolates, which were not identified by phenotyping, were identified by 16S rRNA gene sequence analysis. There was an agreement between phenotyping and 16S rRNA gene sequencing in identification of 19 bacterial isolates. On the other hand, a disagreement was observed between phenotyping and 16S rRNA gene sequencing in identification of the remaining bacterial isolates. Fresh lamb meat seems to be a good medium for growth of various bacterial species
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Fischer, Kathrin, Dittmar Hahn, Otto Daniel, Josef Zeyer, and Rudolf I. Amann. "In situ analysis of the bacterial community in the gut of the earthwormLumbricus terrestrisL. by whole-cell hybridization." Canadian Journal of Microbiology 41, no. 8 (August 1, 1995): 666–73. http://dx.doi.org/10.1139/m95-092.
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The bacterial community in the gut of the earthworm Lumbricus terrestris was analyzed by whole-cell hybridization with 16S rRNA targeted oligonucleotide probes. Whole-cell hybridization protocols using fluorescence-, peroxidase-, or digoxigenin-labeled oligonucleotide probes facilitated detection of significant fractions of bacterial cells stained with 4′,6-diamidino-2-phenylindole (DAPI) in the fore-, mid-, and hind-gut and cast of the earthworm. The application of peroxidase- and digoxigenin-labeled probes, however, was hampered by several methodological drawbacks: the requirement of enzymatic permeabilization, the diffuse images of stained cells, and the incompatibility with DAPI staining used as control. Quantitative analysis of the bacterial community was also influenced by its considerable variability in different individual earthworms. Though the number of bacteria detected by DAPI staining as well as by whole-cell hybridization with the fluorescent eubacterial probe Eub338 generally showed a significant increase in the number of bacteria towards the end of the gut, a decrease in bacterial numbers could be found in some earthworms. In situ analysis of the bacterial community in the fore-, mid-, and hind-gut of one individual earthworm by whole-cell hybridization with the fluorescent eubacterial probe Eub338 recorded 15, 30, and 25% of DAPI-stained bacteria, respectively. In the cast 37% of the bacteria were detected. Similar to counts obtained by DAPI and by whole-cell hybridization with probe Eub338, the number of bacteria belonging to the α-, β-, and γ-subgroups of proteobacteria increased significantly towards the end of the gut and remained high in the cast. While the most significant difference in the counts of bacteria belonging to the α-subgroup was obtained between the hind-gut and cast, bacterial populations of the β- and γ- subgroups of proteobacteria increased most prominently between the fore- and hind-gut.Key words: digoxigenin, fluorescent probes, in situ detection, Lumbricus terrestris, rRNA, whole-cell hybridization.
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Seccareccia, Ivana, Christian Kost, and Markus Nett. "Quantitative Analysis of Lysobacter Predation." Applied and Environmental Microbiology 81, no. 20 (July 31, 2015): 7098–105. http://dx.doi.org/10.1128/aem.01781-15.
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ABSTRACTBacteria of the genusLysobacterare considered to be facultative predators that use a feeding strategy similar to that of myxobacteria. Experimental data supporting this assumption, however, are scarce. Therefore, the predatory activities of threeLysobacterspecies were tested in the prey spot plate assay and in the lawn predation assay, which are commonly used to analyze myxobacterial predation. Surprisingly, only one of the testedLysobacterspecies showed predatory behavior in the two assays. This result suggested that not allLysobacterstrains are predatory or, alternatively, that the assays were not appropriate for determining the predatory potential of this bacterial group. To differentiate between the two scenarios, predation was tested in a CFU-based bioassay. For this purpose, defined numbers ofLysobactercells were mixed together with potential prey bacteria featuring phenotypic markers, such as distinctive pigmentation or antibiotic resistance. After 24 h, cocultivated cells were streaked out on agar plates and sizes of bacterial populations were individually determined by counting the respective colonies. Using the CFU-based predation assay, we observed thatLysobacterspp. strongly antagonized other bacteria under nutrient-deficient conditions. Simultaneously, theLysobacterpopulation was increasing, which together with the killing of the cocultured bacteria indicated predation. Variation of the predator/prey ratio revealed that all threeLysobacterspecies tested needed to outnumber their prey for efficient predation, suggesting that they exclusively practiced group predation. In summary, the CFU-based predation assay not only enabled the quantification of prey killing and consumption byLysobacterspp. but also provided insights into their mode of predation.
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Hemmatian and Kim. "Quantification Methods for Textile-Adhered Bacteria: Extraction, Colorimetric, and Microscopic Analysis." Polymers 11, no. 10 (October 12, 2019): 1666. http://dx.doi.org/10.3390/polym11101666.
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Quantification of bacteria adhered on porous, multi-layered fibers is a challenging task. The goal of this study is to compare different assessment procedures on counting textile-adhered bacteria, and to guide relevant analytical techniques. Three different methods were compared in measuring the amount of Escherichia coli (E. coli) adhered to polymeric film and fibrous nonwovens. In the extraction method, the adhered bacteria were released with the assistance of surfactant/enzyme, where the measurement was rather reproducible. For colorimetric method, stained bacteria enabled direct visualization without needing to detach cells from the surface, yet the linearity of color absorbency to cell counts was limited. The microscopic analysis provided direct observation of bacterial distribution over the surface, but accurate quantification was not possible for porous, fibrous surfaces. This study intends to help choosing a suitable test method to accurately quantify the textile-adhered bacteria, as well as broadly impact the research on anti-bioadhesive surfaces.
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Hill, K. E., C. E. Davies, M. J. Wilson, P. Stephens, K. G. Harding, and D. W. Thomas. "Molecular analysis of the microflora in chronic venous leg ulceration." Journal of Medical Microbiology 52, no. 4 (April 1, 2003): 365–69. http://dx.doi.org/10.1099/jmm.0.05030-0.
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There is growing evidence to suggest that the resident microflora of chronic venous leg ulcers impairs cellular wound-healing responses, thereby playing an important role in maintaining the non-healing phenotype of many of these wounds. The significance of individual species of bacteria will remain unclear until it is possible to characterize fully the microflora of such lesions. The limitations and biases of culture-based microbiology are being realized and the subsequent application of molecular methods is revealing greater diversity within mixed bacterial populations than that demonstrated by culture alone. To date, this approach has been limited to a small number of systems, including the oral microflora. Here, for the first time, the comprehensive characterization of the microflora present in the tissue of a chronic venous leg ulcer is described by the comparison of 16S rDNA sequences amplified directly from the wound tissue with sequences obtained from bacteria that were isolated by culture. The molecular approach demonstrated significantly greater bacterial diversity than that revealed by culture. Furthermore, sequences were retrieved that may possibly represent novel species of bacteria. It is only by the comprehensive analysis of the wound microflora by both molecular and cultural methods that it will be possible to further our understanding of the role of bacteria in this important condition.
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Wangka, Meivyarni, Stenly Wullur, Esther Angkouw, Jane Mamuaja, Reiny Tumbol, and Elvy Like Ginting. "Analysis of Bacteria Community in the sediment from Bangka Island, North Sulawesi." Jurnal Ilmiah PLATAX 8, no. 2 (August 14, 2020): 196. http://dx.doi.org/10.35800/jip.8.2.2020.29887.
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Marine sediments are nutrient-rich and is a suitable habitat of bacteria. This research is a preliminary study of molecular analysis to identify the bacteria in the sediments from the littoral area that covered by mangroves in Bangka Island, North Sulawesi. The purposes of this study are to obtain the uncultivated bacterial DNA genome which is used to identify the bacteria and bacterial community in the sediments. Isolation of DNA genome from uncultured bacterial was carried out by following the genomic DNA extraction procedure using the DNeasy® PowerSoil Extraction Kit. Before isolating the bacterial DNA, sample were went through freezing and thawing processes. The DNA isolation result was subsequently tested using electrophoresis and UV-Vis spectrophotometers. Subsequently the genomic DNA was amplified using Polymerase Chain Reaction and the bacteria were identified using Next Generation Sequencing (NGS) analysis. The results of this study showed that the DNA of uncultured bacteria from sediment have the purity of 1.05 and the DNA amplification band was detected at 1300-1600bp. The bacteria in Bangka Island, North Sulawesi sediments were consisted of Gemmatimonadetes, Acidobacteria, Chioroflexi, Firmicutes, Bacteroidetes, Actinobacteria, Cyanobacteria and Proteobacteria respectively. Phylum Proteobacteria was found has the highest relative abundance in the sediment.Keywords : Bacteria, Deoxyribo Nucleic Acid, Sediment, Uncultured. ABSTRAKSedimen laut merupakan suatu habitat yang kaya akan nutrient dan merupakan habitat dari bakteri. Penelitian ini merupakan tahapan awal dalam rangkaian analisis molekuler bakteri yang hidup di sedimen dari daerah litoral yang ditumbuhi oleh mangrove pada Pulau Bangka Sulawesi Utara. Tujuan penelitian ini adalah untuk mendapatkan DNA genom bakteri tanpa kultivasi yang digunakan dalam analisis jenis dan komunitas bakteri pada sedimen. Isolasi DNA genom bakteri tanpa kultivasi dilakukan dengan mengikuti prosedur Kit ekstraksi DNA DNeasy® PowerSoil. Sebelum tahap isolasi DNA bakteri, sampel diperlakukan proses freezing and thawing. Hasil isolasi DNA diuji menggunakan elektroforesis dan spektrofotometer UV-Vis. DNA genom diamplifikasi menggunakan Polymerase Chain Reaction dan ditentukan jenis bakteri dengan menggunakan Next Generation Sequencing analysis. Hasil penelitian menujukkan bahwa DNA bakteri tanpa kultivasi memiliki kemurnian 1,05. DNA amplifikasi terdeteksi pada posisi 1300-1600bp. Dan jenis bakteri yang hidup pada sedimen di Pulau Bangka Sulawesi Utara, terdiri dari filum Gemmatimonadetes, Acidobacteria, Chioroflexi, Firmicutes, Bacteroidetes, Actinobacteria, Cyanobacteria dan Proteobacteria. Kelimpahan tertinggi bakteri yang hidup pada sedimen tersebut adalah filum Proteobacteria.Kata kunci : Bakteri, Deoxyribo Nucleic Acid, Sedimen, Tanpa kultivasi.
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Hari Kusumawati, Anggun, Neni Sri Gunarti, Maya Arfania, Dedy Frianto, Dadan Ridwanuloh, and Ova Shofa Mudrofah. "MICROBIOLOGICAL QUALITY ANALYSIS OF FERMENTED AND UHT MILK SAMPLES COLLECTED FROM DIFFERENT LOCATIONS IN INDONESIA." Bacterial Empire 3, no. 4 (December 1, 2020): 84–87. http://dx.doi.org/10.36547/be.2020.3.4.84-87.
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Diarrhea can occur due to food and beverage poisoning, with the highest cause being caused by infection with various bacteria, viruses, or parasites. Bacteria that can cause this disease are Escherichia coli bacteria which are known as good bacteria in the digestive tract. But the reality is that in microbiology not all types of Escherichia coli are good bacteria. Aim to find out the content and number of Escherichia coli bacteria colonies in UHT milk brands A and B as well as brand x yogurt products. Identification of Escherichia coli bacteria by the IMVIC Test method (Indole, Methyl-Red (MR) test, Voges Proskauer (VP), and Citrate), TPC (Total Plate Count), bacterial staining and microscope observation. Negative and positive results were obtained in the indole test and the methyl-red test was characterized by the formation of a red ring at the top for positive results and a yellow ring at the top for negative results, as well as negative results obtained in the Voges Proskauer test and the citrate test. Then for the results of gram staining and microscope testing the bacterial morphology was not seen. For the calculation of colonies, 45 colonies of sample A, 60 colonies of sample B, and 38 colonies of sample X. Samples containing Escherichia coli are contained in sample A of UHT milk and sample X of yogurt products and microbial contamination in samples according to SNI 2009.
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Si-Ping, Zheng, Chen Bin, Guan Xiong, and Zheng Wei-Wen. "Diversity analysis of endophytic bacteria withinAzolla microphyllausing PCR-DGGE and electron microscopy." Chinese Journal of Agricultural Biotechnology 5, no. 3 (December 2008): 269–76. http://dx.doi.org/10.1017/s1479236208002441.
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AbstractUsing 16S rDNA-polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE), electron microscopy and a conventional plating method, the genetic diversity and phenotype polymorphism of the endophytic bacteria withinAzolla microphyllawere explored. The 16S rDNA-PCR-DGGE profile showed a complex and divergent bacterial community, withBacillus cereusas the dominant species, within theAzolla–cyanobacteria association. This result was supported by the fact that endobacterial cells exhibited distinct ultrastructural characteristicsin vivoand,in vitro, bacteria displayed various colonies with different sizes, shapes and colours. This study demonstrates that the genetic diversity of endophytic bacteria inAzollacan be investigated using the16S rDNA-PCR-DGGE technique.
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Lopez, Isabel, Fernanda Ruiz-Larrea, Luca Cocolin, Erica Orr, Trevor Phister, Megan Marshall, Jean VanderGheynst, and David A. Mills. "Design and Evaluation of PCR Primers for Analysis of Bacterial Populations in Wine by Denaturing Gradient Gel Electrophoresis." Applied and Environmental Microbiology 69, no. 11 (November 2003): 6801–7. http://dx.doi.org/10.1128/aem.69.11.6801-6807.2003.
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ABSTRACT Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified ribosomal DNA (rDNA) is routinely used to compare levels of diversity of microbial communities and to monitor population dynamics. While using PCR-DGGE to examine the bacteria in wine fermentations, we noted that several commonly used PCR primers for amplifying bacterial 16S rDNA also coamplified yeast, fungal, or plant DNA present in samples. Unfortunately, amplification of nonbacterial DNA can result in a masking of bacterial populations in DGGE profiles. To surmount this problem, we developed two new primer sets for specific amplification of bacterial 16S rDNA in wine fermentation samples without amplification of eukaryotic DNA. One primer set, termed WLAB1 and WLAB2, amplified lactic acid bacteria, while another, termed WBAC1 and WBAC2, amplified both lactic acid bacterial and acetic acid bacterial populations found in wine. Primer specificity and efficacy were examined with DNA isolated from numerous bacterial, yeast, and fungal species commonly found in wine and must samples. Importantly, both primer sets effectively distinguished bacterial species in wine containing mixtures of yeast and bacteria.
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Mahesh, Lanka, Varun Raj Kumar, Anshi Jain, Sagrika Shukla, Juan Manuel Aragoneses, José María Martínez González, Manuel Fernández-Domínguez, and José Luis Calvo-Guirado. "Bacterial Adherence Around Sutures of Different Material at Grafted Site: A Microbiological Analysis." Materials 12, no. 18 (September 4, 2019): 2848. http://dx.doi.org/10.3390/ma12182848.
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Closure of the surgical incision has been the primary function of sutures since their introduction. However, whatever the type, they are known to carry bacteria, which can be a source of infection. Five types of surgical sutures, Gut, Silk, Vicryl, PTFE, and Polyamide, were selected and tested on their ability to carry aerobic and anaerobic bacteria and were rated on the basis of forming colony-forming units (CFUs). Aerobic bacteria grown around gut sutures showed minimum CFUs (≈30 × 104/suture). Though very less anaerobic bacteria growth was seen among all tested suture materials, it was maximum around Vicryl and polyamide sutures. Every suture material is capable, albeit not equally, of holding bacterial biofilm formation, which can be a source of surgical site infection.
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Stenfors, Lars-Eric, and Simo Räisänen. "Quantitative analysis of the bacterial findings in otitis media." Journal of Laryngology & Otology 104, no. 10 (October 1990): 749–57. http://dx.doi.org/10.1017/s0022215100113842.
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AbstractQualitative and quantitative bacterial analysis of 200 samples of middle ear effusions collected from patients with current otitis media was performed. When middle ear pathogens (S. pneumoniae, H. influenzaeandB. catarrhalis) where found during current acute otitis media or otitis media with effusion infection, the quantity of these bacteria was of the magnitude 106–108/ml and 0–5 × 105/ml effusion material, respectively. Mucopurulent effusion material contained 6 × 105–108bacteria per ml whereas effusion from chronically discharging ears exceeded 109bacteria per ml. Serous effusions did not harbour middle ear pathogens. The appearance of the effusion material was dependent on the number of bacteria involved. Quantification of bacteria in various middle ear effusions offers opportunities to make the diagnosis of various otitis media infections more accurate and readily comparable.
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Ding, Ting, and Yong Li. "Quorum sensing inhibitory effects of vanillin on the biofilm formation of Pseudomonas fluorescens P07 by transcriptome analysis." SDRP Journal of Food Science & Technology 5, no. 7 (2021): 275–92. http://dx.doi.org/10.25177/jfst.5.7.ra.10686.
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Pseudomonas fluorescens is an important psychrotrophic food-spoilage bacterium. Quorum sensing (QS) enables bacteria to control various physiological processes. Hence, targeting bacterial QS would be a novel method to improve food quality. In this study, P. fluorescens P07 was treated with vanillin, which showed strong QS inhibitory activity, and its resultant effects on swarming motility, biofilm formation, and extracellular polymeric substance (EPS) secretion were measured. The mechanisms underlying the inhibitory effects were then explored by transcriptomic analysis. The results showed that vanillin had inhibitory effects on swarming motility, biofilm formation, N-acyl-L-homoserine Lactone (AHLs) and EPS secretion of P. fluorescens P07. The result of transcriptionomic tests indicated that the decrease in bacterial biofilm formation was probably due to the influence of vanillin on mobility, adhesion, chemotaxis, EPS secretion, and QS system of the bacteria. Keywords: Pseudomonas fluorescens, quorum sensing, biofilm formation, transcriptome analysis, swarming motility
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Aguirre, J. S., C. Pin, M. R. Rodr�guez, and G. D. Garc�a de Fernando. "Analysis of the Variability in the Number of Viable Bacteria after Mild Heat Treatment of Food." Applied and Environmental Microbiology 75, no. 22 (October 2, 2009): 6992–97. http://dx.doi.org/10.1128/aem.00452-09.
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ABSTRACT Variability in the numbers of bacteria remaining in saline solution and whole milk following mild heat treatment has been studied with Listeria innocua, Enterococcus faecalis, Salmonella enterica serovar Enteritidis, and Pseudomonas fluorescens. As expected, the most heat-resistant bacterium was E. faecalis, while P. fluorescens was the least heat resistant, and all bacteria showed greater thermal resistance in whole milk than in saline solution. Despite the differences in the inactivation kinetics of these bacteria in different media, the variability in the final number of bacteria was affected neither by the species nor by the heating substrate, but it did depend on the intensity of the heat treatment. The more severe the heat treatment was, the lower the average number of surviving bacteria but the greater the variability. Our results indicated that the inactivation times for the cells within a population are not identically distributed random variables and that, therefore, the population includes subpopulations of cells with different distributions for the heat resistance parameters. A linear relationship between the variability of the log of the final bacterial concentration and the logarithmic reduction in the size of the bacterial population was found.
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Priya A, Hari, Kannan A, and Krithika C L. "Metagenome Analysis of Buccal Mucosal Biofilms to Identify Bacterial Prevalence in Subjects with and without type II Diabetes." International Journal of Research in Pharmaceutical Sciences 11, no. 2 (April 19, 2020): 2018–29. http://dx.doi.org/10.26452/ijrps.v11i2.2132.
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To quantify the two most prevalent bacteria among Type II diabetic individuals and controls from the buccal mucosal biofilms using molecular methods. To compare the percent prevalence of Veillonella and Granulicetella bacteria in uncontrolled Type II diabetic individuals with a control group. Subjects selected randomly and categorized into two groups within the age range of 25 to 40 years diagnosed with and without Type II diabetes based on their HbA1c values. The samples of buccal mucosa biofilms are collected in sterile swabs and stored in bacterial lysis buffer, which was later subjected to quantification of DNA followed by 16S rRNA amplification and sequencing. The sequence obtained is then surveyed using BLAST Analysis to define the bacterial flora and two bacteria, namely Veillonella and Granulicatella are selected for further amplification and quantification by real-time PCR to express the bacteria in copy numbers. From the collected buccal mucosal biofilm samples (n=24), which was categorized into Type II diabetes (12) and non-diabetic (12). The sequence subjected to BLAST analysis gave a List of bacteria from which Veillonella sp. and Granulicatella sp. were selected and administered to real-time PCR for amplification and quantification, which revealed an increased bacterial prevalence in Type II diabetic subjects to non-diabetic subjects which was also proved statistically. Based on the results obtained, there is a significant prevalence of bacterial content in Type II diabetic subjects compared to non-diabetic subjects