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Meng C, Wu J, Guo F, Dong B, Xu L. CWLy-pred: A novel cell wall lytic enzyme identifier based on an improved MRMD feature selection method. Genomics 2020; 112:4715-4721. [DOI: 10.1016/j.ygeno.2020.08.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/04/2020] [Accepted: 08/13/2020] [Indexed: 10/25/2022]
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Meng C, Guo F, Zou Q. CWLy-SVM: A support vector machine-based tool for identifying cell wall lytic enzymes. Comput Biol Chem 2020; 87:107304. [PMID: 32580129 DOI: 10.1016/j.compbiolchem.2020.107304] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 06/07/2020] [Accepted: 06/08/2020] [Indexed: 12/21/2022]
Abstract
Cell wall lytic enzymes, as an important biotechnical tool in drug development, agriculture and the food industry, have attracted more research attention. In this research, the accurate identification of cell wall lytic enzymes is one of the key and fundamental tasks. In this study, in order to eliminate the inefficiency of in vitro experiments, a support vector machine-based cell wall lytic enzyme identification model was constructed using bioinformatics. This machine learning process includes feature extraction, feature selection, model training and optimization. According to the jackknife cross validation test, this model obtained a sensitivity of 0.853, a specificity of 0.977, an MCC of 0.845 and an AUC of 0.915. These benchmark results demonstrate that the proposed model outperforms the state-of-the-art method and that it has powerful cell wall lytic enzyme identification ability. Furthermore, we comprehensively analyzed the selected optimal features and used the proposed model to construct a user friendly web server called the CWLy-SVM to identify cell wall lytic enzymes, which is available at http://server.malab.cn/CWLy-SVM/index.jsp.
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Affiliation(s)
- Chaolu Meng
- College of Intelligence and Computing, Tianjin University, Tianjin, China; College of Computer and Information Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Fei Guo
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China; Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
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3
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Detection of microbial genes in a single leukocyte by polymerase chain reaction following laser capture microdissection. J Microbiol Methods 2018; 155:42-48. [PMID: 30423364 DOI: 10.1016/j.mimet.2018.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/09/2018] [Accepted: 11/10/2018] [Indexed: 11/23/2022]
Abstract
Although isolation and identification of bacteria in a clinical specimen constitute essential steps for the diagnosis of bacterial infection, positive results of the bacterial culture are not always attained, despite observing the bacteria by Gram staining. As bacteria phagocytosed by the leukocytes are considered as the causative agents of infectious diseases, this study aims to introduce a new approach for the collection of only bacteria phagocytosed by the neutrophils in an animal model using laser capture microdissection (LCM) followed by the DNA identification using polymerase chain reaction (PCR). We inoculated representative bacteria (Escherichia coli and Staphylococcus aureus) into the abdominal cavities of specific pathogen-free C57BL/6 J mice. After 6 h inoculation, we collected the fluid samples from the peritoneal cavities of mice and demonstrated peritonitis by the increase of neutrophils. Then, we smeared the neutrophils on the membrane slides and collected single-cell phagocytosing bacteria by LCM. The supernatant of the cell lysate was supplied for the PCR reaction to amplify the 16S rRNA gene, and we validated the DNA sequences specific for the inoculated bacteria. In addition, PCR using specific primers for E. coli and S. aureus identified each species of bacteria. Hence, this study suggests that the combination of LCM and PCR could be a novel approach to determine bacteria in infectious diseases. Nevertheless, further investigation is warranted to test various additional bacterial taxa to demonstrate the general applicability of this method to clinical samples.
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Kudryakova IV, Gabdulkhakov AG, Tishchenko SV, Lysanskaya VY, Suzina NE, Tsfasman IM, Afoshin AS, Vasilyeva NV. Structural and functional properties of antimicrobial protein L5 of Lysоbacter sp. XL1. Appl Microbiol Biotechnol 2018; 102:10043-10053. [PMID: 30229324 DOI: 10.1007/s00253-018-9364-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/30/2018] [Accepted: 08/26/2018] [Indexed: 11/30/2022]
Abstract
The Gram-negative bacterium Lysobacter sp. XL1 secretes into the extracellular space five bacteriolytic enzymes that lyse the cell walls of competing microorganisms. Of special interest are homologous lytic proteases L1 and L5. This work found protein L5 to possess Gly-Gly endopeptidase and N-acetylmuramoyl-L-Ala amidase activities with respect to staphylococcal peptidoglycan. Protein L5 was found to be capable of aggregating into amyloid-like fibril structures. The crystal structure of protein L5 was determined at a 1.60-Å resolution. Protein L5 was shown to have a rather high structural identity with bacteriolytic protease L1 of Lysobacter sp. XL1 and α-lytic protease of Lysobacter enzymogenes at a rather low identity of their amino acid sequences. Still, the structure of protein L5 was revealed to have regions that differed from their equivalents in the homologs. The revealed structural distinctions in L5 are suggested to be of importance in exhibiting its unique properties.
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Affiliation(s)
- I V Kudryakova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Pr. Nauki, Pushchino, Moscow Region, Russia, 142290
| | - A G Gabdulkhakov
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya Str., Pushchino, Moscow Region, Russia, 142290
| | - S V Tishchenko
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya Str., Pushchino, Moscow Region, Russia, 142290
| | - V Ya Lysanskaya
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Pr. Nauki, Pushchino, Moscow Region, Russia, 142290
| | - N E Suzina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Pr. Nauki, Pushchino, Moscow Region, Russia, 142290
| | - I M Tsfasman
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Pr. Nauki, Pushchino, Moscow Region, Russia, 142290
| | - A S Afoshin
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Pr. Nauki, Pushchino, Moscow Region, Russia, 142290
| | - N V Vasilyeva
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Pr. Nauki, Pushchino, Moscow Region, Russia, 142290.
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Burke RM, McKenna JP, Cox C, Coyle PV, Shields MD, Fairley DJ. A comparison of different pre-lysis methods and extraction kits for recovery of Streptococcus agalacticae (Lancefield group B Streptococcus) DNA from whole blood. J Microbiol Methods 2016; 129:103-108. [DOI: 10.1016/j.mimet.2016.08.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 08/15/2016] [Accepted: 08/18/2016] [Indexed: 10/21/2022]
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6
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Comparison of point-of-care-compatible lysis methods for bacteria and viruses. J Microbiol Methods 2016; 128:80-87. [DOI: 10.1016/j.mimet.2016.07.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 07/12/2016] [Accepted: 07/12/2016] [Indexed: 11/18/2022]
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7
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Sohrabi M, Nair RG, Samaranayake LP, Zhang L, Zulfiker AHM, Ahmetagic A, Good D, Wei MQ. The yield and quality of cellular and bacterial DNA extracts from human oral rinse samples are variably affected by the cell lysis methodology. J Microbiol Methods 2016; 122:64-72. [PMID: 26812577 DOI: 10.1016/j.mimet.2016.01.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/20/2016] [Accepted: 01/22/2016] [Indexed: 01/19/2023]
Abstract
Recent culture-independent studies have enabled detailed mapping of human microbiome that has not been hitherto achievable by culture-based methods. DNA extraction is a key element of bacterial culture-independent studies that critically impacts on the outcome of the detected microbial profile. Despite the variations in DNA extraction methods described in the literature, no standardized technique is available for the purpose of microbiome profiling. Hence, standardization of DNA extraction methods is urgently needed to yield comparable data from different studies. We examined the effect of eight different cell lysis protocols on the yield and quality of the extracted DNA from oral rinse samples. These samples were exposed to cell lysis techniques based on enzymatic, mechanical, and a combination of enzymatic-mechanical methods. The outcome measures evaluated were total bacterial population, Firmicutes levels and human DNA contamination (in terms of surrogate GAPDH levels). We noted that all three parameters were significantly affected by the method of cell lysis employed. Although the highest yield of gDNA was obtained using lysozyme-achromopeptidase method, the lysozyme-zirconium beads method yielded the peak quantity of total bacterial DNA and Firmicutes with a lower degree of GAPDH contamination compared with the other methods. Taken together our data clearly points to an urgent need for a consensus, standardized DNA extraction technique to evaluate the oral microbiome using oral rinse samples. Further, if Firmicutes levels are the focus of investigation in oral rinse microbiome analyses then the lysozyme-zirconium bead method would be the method of choice in preference to others.
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Affiliation(s)
- Mohsen Sohrabi
- School of Medical Science, Menzies Health Institute Queensland, Griffith University, Gold Coast 4215, Australia
| | - Raj G Nair
- School of Dentistry and Oral Health, Menzies Health Institute Queensland, Griffith University, Gold Coast 4215, Australia.
| | | | - Li Zhang
- Centre for Health Practice Innovation, Menzies Health Institute Queensland, Griffith University, Nathan 4111, Australia
| | - Abu Hasanat Md Zulfiker
- School of Medical Science, Menzies Health Institute Queensland, Griffith University, Gold Coast 4215, Australia
| | - Adnan Ahmetagic
- School of Medical Science, Menzies Health Institute Queensland, Griffith University, Gold Coast 4215, Australia
| | - David Good
- School of Medical Science, Menzies Health Institute Queensland, Griffith University, Gold Coast 4215, Australia; School of Physiotherapy, Australian Catholic University, Banyo 4014, Australia
| | - Ming Q Wei
- School of Medical Science, Menzies Health Institute Queensland, Griffith University, Gold Coast 4215, Australia.
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Portable lysis apparatus for rapid single-step DNA extraction of Bacillus subtilis. J Appl Microbiol 2016; 120:379-87. [DOI: 10.1111/jam.13011] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/01/2015] [Accepted: 11/11/2015] [Indexed: 12/01/2022]
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9
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Comparison between a chimeric lysin ClyH and other enzymes for extracting DNA to detect methicillin resistant Staphylococcus aureus by quantitative PCR. World J Microbiol Biotechnol 2015; 32:1. [PMID: 26596268 DOI: 10.1007/s11274-015-1971-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 10/14/2015] [Indexed: 02/01/2023]
Abstract
Extracting DNA from Staphylococcus aureus cells is important for detecting MRSA by PCR. However, S. aureus cells are known to be difficult to disrupt due to their compact cell walls. Here, we systematically studied the efficiency of a highly active lysin ClyH for extracting DNA of S. aureus in comparison with commonly used enzymes, such as lysostaphin and achromopeptidase (ACP), and its compatibility in quantitative PCR (qPCR) detection of MRSA. qPCR analysis of S. aureus specific gene femB showed that ClyH was much faster than lysostaphin, ACP and lysozyme for releasing DNA. Five minutes disruption with ClyH at room temperature was enough to release all the DNA from S. aureus. Analysis of the spiked nasal swabs by a dual qPCR assay of the β-lactam resistance mecA gene and the staphylococcal cassette chromosome (SCCmec)-open reading frame X (orfX) junction (SCCmec-orfX) after ClyH lysis showed 100% sensitivity and specificity to the commercial BD GeneOhm™ MRSA test with ACP lysis, but the lysis time was reduced from 20 min by ACP to 5 min by ClyH. Our research shows that ClyH could be a better option than the currently used enzymes for DNA extraction from S. aureus, which can provide simpler and faster PCR detection of MRSA.
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Gabardo CM, Kwong AM, Soleymani L. Rapidly prototyped multi-scale electrodes to minimize the voltage requirements for bacterial cell lysis. Analyst 2015; 140:1599-608. [PMID: 25597363 DOI: 10.1039/c4an02150a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Lab-on-a-chip systems used for nucleic acid based detection of bacteria rely on bacterial lysis for the release of cellular material. Although electrical lysis devices can be miniaturized for on-chip integration and reagent-free lysis, they often suffer from high voltage requirements, and rely on the use of off-chip voltage supplies. To overcome this barrier, we developed a rapid prototyping method for creating multi-scale electrodes that are structurally tuned for lowering the voltage needed for electrical bacterial lysis. These three-dimensional multi-scale electrodes – with micron scale reaction areas and nanoscale features – are fabricated using benchtop methods including craft cutting, polymer-induced wrinkling, and electrodeposition, which enable a lysis device to be designed, fabricated, and optimized in a matter of hours. These tunable electrodes show superior behaviour compared to lithographically-prepared electrodes in terms of lysis efficiency and voltage requirement. Successful extraction of nucleic acids from bacterial samples processed by these electrodes demonstrates the potential for these rapidly prototyped devices to be integrated within practical lab-on-a-chip systems.
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Affiliation(s)
- Christine M Gabardo
- School of Biomedical Engineering, McMaster University, 1280 Main St. West, Hamilton, Canada
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Irwin P, Nguyen L, He Y, Paoli G, Gehring A, Chen CY. The near-quantitative sampling of genomic DNA from various food-borne Eubacteria. BMC Microbiol 2014; 14:326. [PMID: 25551371 PMCID: PMC4302497 DOI: 10.1186/s12866-014-0326-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 12/16/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The disruption of the bacterial cell wall plays an important part in achieving quantitative extraction of DNA from Eubacteria essential for accurate analyses of genetic material recovered from environmental samples. RESULTS In this work we have tested a dozen commercial bacterial genomic DNA extraction methodologies on an average of 7.70 × 10(6) (±9.05%), 4.77 × 10(8) (±31.0%), and 5.93 × 10(8) (±4.69%) colony forming units (CFU) associated with 3 cultures (n = 3) each of Brochothrix thermosphacta (Bt; Gram-positive), Shigella sonnei (Ss; Gram-negative), and Escherichia coli O79 (Ec; Gram-negative). We have utilized real-time PCR (qPCR) quantification with two specific sets of primers associated with the 16S rRNA "gene" to determine the number of copies CFU(-1) by comparing the unknown target DNA qPCR results with standards for each primer set. Based upon statistical analyses of our results, we determined that the Agencourt Genfind v2, High Pure PCR Template Prep Kit, and Omnilyse methods consistently provided the best yield of genomic DNA ranging from 141 to 934, 8 to 21, and 16 to 27 16S rDNA copies CFU(-1) for Bt, Ss, and Ec. If one assumes 6-7 copies of the 16S rRNA gene per genome, between 1 and 3 genomes per actively dividing cell and ≥ 100 cells CFU(-1) for Bt (found to be a reasonable assumption using an optical method expounded upon herein) or between 1 and 2 cells CFU(-1) for either Ss or Ec, then the Omnilyse procedure provided nearly quantitative extraction of genomic DNA from these isolates (934 ± 19.9 copies CFU(-1) for Bt; 20.8 ± 2.68 copies CFU(-1) for Ss; 26.9 ± 3.39 copies CFU(-1) for Ec). The Agencourt, High Pure, and Omnilyse technologies were subsequently assessed using 5 additional Gram-positive and 10 Gram-negative foodborne isolates (n = 3) using a set of "universal" 16S rDNA primers. CONCLUSION Overall, the most notable DNA extraction method was found to be the Omnilyse procedure which is a "bead blender" technology involving high frequency agitation in the presence of zirconium silicate beads.
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Affiliation(s)
- Peter Irwin
- Agricultural Research Service, U. S. Department of Agriculture, Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA.
| | - Ly Nguyen
- Agricultural Research Service, U. S. Department of Agriculture, Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA.
| | - Yiping He
- Agricultural Research Service, U. S. Department of Agriculture, Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA.
| | - George Paoli
- Agricultural Research Service, U. S. Department of Agriculture, Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA.
| | - Andrew Gehring
- Agricultural Research Service, U. S. Department of Agriculture, Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA.
| | - Chin-Yi Chen
- Agricultural Research Service, U. S. Department of Agriculture, Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA.
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Banerjee I, Pangule RC, Kane RS. Antifouling coatings: recent developments in the design of surfaces that prevent fouling by proteins, bacteria, and marine organisms. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2011; 23:690-718. [PMID: 20886559 DOI: 10.1002/adma.201001215] [Citation(s) in RCA: 1554] [Impact Index Per Article: 119.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Revised: 06/06/2010] [Indexed: 05/21/2023]
Abstract
The major strategies for designing surfaces that prevent fouling due to proteins, bacteria, and marine organisms are reviewed. Biofouling is of great concern in numerous applications ranging from biosensors to biomedical implants and devices, and from food packaging to industrial and marine equipment. The two major approaches to combat surface fouling are based on either preventing biofoulants from attaching or degrading them. One of the key strategies for imparting adhesion resistance involves the functionalization of surfaces with poly(ethylene glycol) (PEG) or oligo(ethylene glycol). Several alternatives to PEG-based coatings have also been designed over the past decade. While protein-resistant coatings may also resist bacterial attachment and subsequent biofilm formation, in order to overcome the fouling-mediated risk of bacterial infection it is highly desirable to design coatings that are bactericidal. Traditional techniques involve the design of coatings that release biocidal agents, including antibiotics, quaternary ammonium salts (QAS), and silver, into the surrounding aqueous environment. However, the emergence of antibiotic- and silver-resistant pathogenic strains has necessitated the development of alternative strategies. Therefore, other techniques based on the use of polycations, enzymes, nanomaterials, and photoactive agents are being investigated. With regard to marine antifouling coatings, restrictions on the use of biocide-releasing coatings have made the generation of nontoxic antifouling surfaces more important. While considerable progress has been made in the design of antifouling coatings, ongoing research in this area should result in the development of even better antifouling materials in the future.
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Affiliation(s)
- Indrani Banerjee
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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De S, Kaur G, Roy A, Dogra G, Kaushik R, Yadav P, Singh R, Datta TK, Goswami SL. A Simple Method for the Efficient Isolation of Genomic DNA from Lactobacilli Isolated from Traditional Indian Fermented Milk (dahi). Indian J Microbiol 2011; 50:412-8. [PMID: 22282608 DOI: 10.1007/s12088-011-0079-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Accepted: 11/11/2009] [Indexed: 11/25/2022] Open
Abstract
A simple, inexpensive and effective genomic DNA isolation procedure for Lactobacillus isolates from traditional Indian fermented milk (dahi) is described. A total of 269 Lactobacillus isolates from fermented milk collected from four places in North and west India were tested for lysis by an initial weakening of the Gram positive cell wall with Ampicillin followed by Lysozyme treatment. The average genomic DNA yield was ~50 μg/ml log phase culture. Quality and repeatability of the method was found to be adequate for subsequent molecular applications. The quality of the genomic DNA isolated by this method was verified by restriction digestion and polymerase chain reaction (PCR). No inhibition was observed in subsequent PCR amplification and restriction digestion. The presented method is rapid, cheap and useful for routine DNA isolation from gram positive bacteria such as Lactobacillus.
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Bacterial community analysis of activated sludge: an evaluation of four commonly used DNA extraction methods. Appl Microbiol Biotechnol 2010; 88:299-307. [PMID: 20652692 DOI: 10.1007/s00253-010-2770-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 07/05/2010] [Accepted: 07/05/2010] [Indexed: 10/19/2022]
Abstract
The effectiveness of three commercially available direct DNA isolation kits (Mobio, Fast, Qiagen) and one published direct DNA extraction protocol (Bead) for extracting bacterial DNA from different types of activated sludge was investigated and mutually compared. The DNA quantity and purity were determined using real-time PCR targeting the bacterial 16S rDNA gene. Microbial community fingerprints were assessed by automated ribosomal intergenic spacer analysis. The resulting community profiles were analyzed with canonical correspondence analysis. Our results clearly demonstrate that direct DNA extraction methods can significantly influence the DNA quantity, purity, and observed community patterns of microbiota in activated sludge. Fast and Mobio generated high amounts of good quality DNA compared to Bead and Qiagen. Mobio also resulted in the detection of the highest number of species while Fast scored the best in discriminating between the community patterns of different activated sludge types. With respect to the characterization of community profiles, our analyses demonstrated a strong sludge type dependent variability among methods. Taking into account our results, we recommend Fast as the most suitable DNA extraction method for activated sludge samples used for bacterial community studies.
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Levashov PA, Sedov SA, Shipovskov S, Belogurova NG, Levashov AV. Quantitative turbidimetric assay of enzymatic gram-negative bacteria lysis. Anal Chem 2010; 82:2161-3. [PMID: 20136093 DOI: 10.1021/ac902978u] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this Technical Note, the quantitative turbidimetric assay for determination of the bacteriolytic activity of enzymes with gram-negative bacteria is proposed. The reactivity of hen white-egg lysozyme toward gram-negative E. coli intact cells was studied. It was found that the highest lysis rate occurred at pH 8.9 in the system containing 0.03 M NaCl. The mechanism of the reaction is discussed and applied for the quantitative evaluation of the reaction rate. The proposed method enables fast, reliable, and reproducible analysis of bacteriolytic activity of lysozyme with gram-negative bacteria.
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Affiliation(s)
- Pavel A Levashov
- Department of Chemical Enzymology, Chemical Faculty, Moscow State University, 119992 Moscow, Russia.
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16
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Elwan AE, Zarouk WA. Diagnosis of Neonatal Bacterial Sepsis by Polymerase Chain Reaction. ACTA ACUST UNITED AC 2009. [DOI: 10.3923/jbs.2009.533.540] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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17
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Transfer of the chromosomally encoded tetracycline resistance gene tet(M) from marine bacteria to Escherichia coli and Enterococcus faecalis. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0004-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Oana K, Kawakami Y, Hayashi T, Ohnishi M. Simple broad-spectrum protocol using labiase for bacterial cell lysis to prepare genomic DNA for pulsed-field gel electrophoresis analysis. Microbiol Immunol 2009; 53:45-8. [PMID: 19161557 DOI: 10.1111/j.1348-0421.2008.00084.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have developed a simple broad-spectrum protocol using labiase for bacterial cell lysis in pulsed-field gel electrophoresis analysis. The protocol reported here is widely applicable to the preparations of genomic DNA from Gram-negative and -positive pathogens, including enterococcal strains resistant to any conventional lysis protocols.
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Affiliation(s)
- Kozue Oana
- Department of Biomedical Laboratory Sciences, School of Health Sciences, Shinshu University, 3-1-1 Asahi, Matsumoto, Japan
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Lactobacillus senmaizukei sp. nov., isolated from Japanese pickle. Int J Syst Evol Microbiol 2008; 58:1625-9. [DOI: 10.1099/ijs.0.65677-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Abstract
Enzymatic methods provide a convenient alternative for overcoming technical disadvantages of mechanical disruption. Protocols for protein extraction from bacteria and Saccharomyces cerevisiae using lytic enzymes are presented in this chapter. Adaptation of the yeast protocol to a microtiter plate format makes this protocol amenable for proteomic applications and high-throughput screening of libraries expressing genetic variants in yeast. This methodology can also be applied to bacteria.
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Wang CM, Shyu CL, Ho SP, Chiou SH. Species diversity and substrate utilization patterns of thermophilic bacterial communities in hot aerobic poultry and cattle manure composts. MICROBIAL ECOLOGY 2007; 54:1-9. [PMID: 17450396 DOI: 10.1007/s00248-006-9139-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2006] [Accepted: 07/06/2006] [Indexed: 05/15/2023]
Abstract
This study investigated the species diversity and substrate utilization patterns of culturable thermophilic bacterial communities in hot aerobic poultry and cattle manure composts by coupling 16S rDNA analysis with Biolog data. Based on the phylogenetic relationships of 16S rDNA sequences, 34 thermophilic (grown at 60 degrees C) bacteria isolated during aerobic composting of poultry manure and cattle manure were classified as Bacillus licheniformis, B. atrophaeus, Geobacillus stearothermophilus, G. thermodenitrificans, Brevibacillus thermoruber, Ureibacillus terrenus, U. thermosphaericus, and Paenibacillus cookii. In this study, B. atrophaeus, Br. thermoruber, and P. cookii were recorded for the first time in hot compost. Physiological profiles of these bacteria, obtained from the Biolog Gram-positive (GP) microplate system, were subjected to principal component analysis (PCA). All isolates were categorized into eight different PCA groups based on their substrate utilization patterns. The bacterial community from poultry manure compost comprised more divergent species (21 isolates, seven species) and utilized more diverse substrates (eight PCA groups) than that from cattle manure compost (13 isolates, five species, and four PCA groups). Many thermophilic bacteria isolated in this study could use a variety of carboxylic acids. Isolate B110 (from poultry manure compost), which is 97.6% similar to U. terrenus in its 16S rDNA sequence, possesses particularly high activity in utilizing a broad spectrum of substrates. This isolate may have potential applications in industry.
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Affiliation(s)
- Chao-Min Wang
- Graduate Institute of Veterinary Microbiology, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China
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Salazar O, Asenjo JA. Enzymatic lysis of microbial cells. Biotechnol Lett 2007; 29:985-94. [PMID: 17464453 DOI: 10.1007/s10529-007-9345-2] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Revised: 02/15/2007] [Accepted: 02/19/2007] [Indexed: 10/23/2022]
Abstract
Cell wall lytic enzymes are valuable tools for the biotechnologist, with many applications in medicine, the food industry, and agriculture, and for recovering of intracellular products from yeast or bacteria. The diversity of potential applications has conducted to the development of lytic enzyme systems with specific characteristics, suitable for satisfying the requirements of each particular application. Since the first time the lytic enzyme of excellence, lysozyme, was discovered, many investigations have contributed to the understanding of the action mechanisms and other basic aspects of these interesting enzymes. Today, recombinant production and protein engineering have improved and expanded the area of potential applications. In this review, some of the recent advances in specific enzyme systems for bacteria and yeast cells rupture and other applications are examined. Emphasis is focused in biotechnological aspects of these enzymes.
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Affiliation(s)
- Oriana Salazar
- Centre for Chemical Engineering and Biotechnology, Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 861, Santiago, Chile.
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Jordan JA, Durso MB, Butchko AR, Jones JG, Brozanski BS. Evaluating the near-term infant for early onset sepsis: progress and challenges to consider with 16S rDNA polymerase chain reaction testing. J Mol Diagn 2006; 8:357-63. [PMID: 16825509 PMCID: PMC1867603 DOI: 10.2353/jmoldx.2006.050138] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2006] [Indexed: 11/20/2022] Open
Abstract
Although the rate of early onset sepsis in the near-term neonate is low (one to eight of 1,000 cases), the rate of mortality and morbidity is high. As a result, infants receive multiple, broad-spectrum antibiotic therapy, many for up to 7 days despite blood cultures showing no growth. Maternal intrapartum antibiotic prophylaxis and small blood volume collections from infants are cited as reasons for the lack of confidence in negative culture results. Incorporating an additional, more rapid test could facilitate a more timely diagnosis in these infants. To this end, a 16S rDNA polymerase chain reaction (PCR) assay was compared to blood culturing for use as a tool in evaluating early onset sepsis. Of 1,751 neonatal intensive care unit admissions that were screened, 1,233 near-term infants met inclusion criteria. Compared to culture, PCR demonstrated excellent analytical specificity (1,186 of 1,216, 97.5%) and negative predictive value (1,186 of 1,196, 99.2%); however, PCR failed to detect a significant number of culture-proven cases. These findings underscore the cautionary stance that should be taken at this time when considering the use of a molecular amplification test for diagnosing neonatal sepsis. The experience gained from this study illustrates the need for changes in sample collection and preparation techniques so as to improve analytical sensitivity of the assay.
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Affiliation(s)
- Jeanne A Jordan
- Department of Pathology, Magee-Women's Research Institute, 204 Craft Ave., Pittsburgh, PA 15213, USA.
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