1
|
Arakawa T, Niikura T, Kita Y, Akuta T. Sodium Dodecyl Sulfate Analogs as a Potential Molecular Biology Reagent. Curr Issues Mol Biol 2024; 46:621-633. [PMID: 38248342 PMCID: PMC10814491 DOI: 10.3390/cimb46010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
In this study, we review the properties of three anionic detergents, sodium dodecyl sulfate (SDS), Sarkosyl, and sodium lauroylglutamate (SLG), as they play a critical role in molecular biology research. SDS is widely used in electrophoresis and cell lysis for proteomics. Sarkosyl and, more frequently, SDS are used for the characterization of neuropathological protein fibrils and the solubilization of proteins. Many amyloid fibrils are resistant to SDS or Sarkosyl to different degrees and, thus, can be readily isolated from detergent-sensitive proteins. SLG is milder than the above two detergents and has been used in the solubilization and refolding of proteins isolated from inclusion bodies. Here, we show that both Sarkosyl and SLG have been used for protein refolding, that the effects of SLG on the native protein structure are weaker for SLG, and that SLG readily dissociates from the native proteins. We propose that SLG may be effective in cell lysis for functional proteomics due to no or weaker binding of SLG to the native proteins.
Collapse
Affiliation(s)
- Tsutomu Arakawa
- Alliance Protein Labs, 13380 Pantera Rd., San Diego, CA 92130, USA;
| | - Takako Niikura
- Department of Information and Communication Sciences, Faculty of Science and Technology, Sophia University, Tokyo 102-8554, Japan;
| | - Yoshiko Kita
- Alliance Protein Labs, 13380 Pantera Rd., San Diego, CA 92130, USA;
| | - Teruo Akuta
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna, Takahagi-shi 318-0004, Japan;
| |
Collapse
|
2
|
Taylor M, Janasky L, Vega N. Convergent structure with divergent adaptations in combinatorial microbiome communities. FEMS Microbiol Ecol 2022; 98:6726631. [PMID: 36170949 DOI: 10.1093/femsec/fiac115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/13/2022] [Accepted: 09/26/2022] [Indexed: 01/21/2023] Open
Abstract
Adaptation of replicate microbial communities frequently produces shared trajectories of community composition and structure. However, divergent adaptation of individual community members can occur and is associated with community-level divergence. The extent to which community-based adaptation of microbes should be convergent when community members are similar but not identical is, therefore, not well-understood. In these experiments, adaptation of combinatorial minimal communities of bacteria with the model host Caenorhabditis elegans produces structurally similar communities over time, but with divergent adaptation of member taxa and differences in community-level resistance to invasion. These results indicate that community-based adaptation from taxonomically similar starting points can produce compositionally similar communities that differ in traits of member taxa and in ecological properties.
Collapse
Affiliation(s)
- Megan Taylor
- Biology Department, Emory University, Atlanta, GA, 30322, United States
| | - Lili Janasky
- Biology Department, Emory University, Atlanta, GA, 30322, United States
| | - Nic Vega
- Biology Department, Emory University, Atlanta, GA, 30322, United States.,Physics Department, Emory University, Atlanta, GA, 30322, United States
| |
Collapse
|
3
|
Ratnikova MS, Titok MA. Molecular Genetic Markers for Identification of Rhodococcus erythropolis and Rhodococcus qingshengii. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720040116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
4
|
Bodhaguru M, Prakash S, Ramasubburayan R, Ahila NK, Mariselvam L, Immanuel G, Palavesam A, Kannapiran E. Screening, partial purification of antivibriosis metabolite sterol-glycosides from Rhodococcus sp. against aquaculture associated pathogens. Microb Pathog 2019; 134:103597. [DOI: 10.1016/j.micpath.2019.103597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 10/26/2022]
|
5
|
Charniauskaya MI, Bukliarevich AA, Delegan YA, Akhremchuk AE, Filonov AE, Titok MA. Biodiversity of Hydrocarbon-Oxidizing Soil Bacteria from Various Climatic Zones. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718050065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
6
|
Microbiological Findings in Tracheal Wash From Mule Foals With and Without Clinical Evidence of Respiratory Disease. J Equine Vet Sci 2017. [DOI: 10.1016/j.jevs.2017.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
7
|
Rapheeha OKL, Roux-van der Merwe MP, Badenhorst J, Chhiba V, Bode ML, Mathiba K, Brady D. Hydrolysis of nitriles by soil bacteria: variation with soil origin. J Appl Microbiol 2016; 122:686-697. [PMID: 27930842 DOI: 10.1111/jam.13367] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/09/2016] [Accepted: 11/28/2016] [Indexed: 12/01/2022]
Abstract
AIMS The aim of this study was to explore bacterial soil diversity for nitrile biocatalysts, in particular, those for hydrolysis of β-substituted nitriles, to the corresponding carboxamides and acids that may be incorporated into peptidomimetics. To achieve this, we needed to compare the efficiency of isolation methods and determine the influence of land use and geographical origin of the soil sample. METHODS AND RESULTS Nitrile-utilizing bacteria were isolated from various soil environments across a 1000 km long transect of South Africa, including agricultural soil, a gold mine tailing dam and uncultivated soil. The substrate profile of these isolates was determined through element-limited growth studies on seven different aliphatic or aromatic nitriles. A subset of these organisms expressing broad substrate ranges was evaluated for their ability to hydrolyse β-substituted nitriles (3-amino-3-phenylpropionitrile and 3-hydroxy-4-phenoxybutyronitrile) and the active organisms were found to be Rhodococcus erythropolis from uncultivated soil and Rhodococcus rhodochrous from agricultural soils. CONCLUSIONS The capacity for hydrolysis of β-substituted nitriles appears to reside almost exclusively in Rhodococci. Land use has a much greater effect on the biocatalysis substrate profile than geographical location. SIGNIFICANCE AND IMPACT OF THE STUDY Enzymes are typically substrate specific in their catalytic reactions, and this means that a wide diversity of enzymes is required to provide a comprehensive biocatalysis toolbox. This paper shows that the microbial diversity of nitrile hydrolysis activity can be targeted according to land utilization. Nitrile biocatalysis is a green chemical method for the enzymatic production of amides and carboxylic acids that has industrial applications, such as in the synthesis of acrylamide and nicotinamide. The biocatalysts discovered in this study may be applied to the synthesis of peptidomimetics which are an important class of therapeutic compounds.
Collapse
Affiliation(s)
- O K L Rapheeha
- Department of Biotechnology and Food Technology, Tshwane University of Technology, Pretoria, South Africa
| | - M P Roux-van der Merwe
- Department of Biotechnology and Food Technology, Tshwane University of Technology, Pretoria, South Africa
| | - J Badenhorst
- Department of Biotechnology and Food Technology, Tshwane University of Technology, Pretoria, South Africa
| | - V Chhiba
- CSIR Biosciences, Pretoria, South Africa.,Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, South Africa
| | - M L Bode
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, South Africa
| | - K Mathiba
- CSIR Biosciences, Pretoria, South Africa
| | - D Brady
- Department of Biotechnology and Food Technology, Tshwane University of Technology, Pretoria, South Africa.,CSIR Biosciences, Pretoria, South Africa.,Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
8
|
Pathak A, Chauhan A, Blom J, Indest KJ, Jung CM, Stothard P, Bera G, Green SJ, Ogram A. Comparative Genomics and Metabolic Analysis Reveals Peculiar Characteristics of Rhodococcus opacus Strain M213 Particularly for Naphthalene Degradation. PLoS One 2016; 11:e0161032. [PMID: 27532207 PMCID: PMC4988695 DOI: 10.1371/journal.pone.0161032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 07/27/2016] [Indexed: 12/12/2022] Open
Abstract
The genome of Rhodococcus opacus strain M213, isolated from a fuel-oil contaminated soil, was sequenced and annotated which revealed a genome size of 9,194,165 bp encoding 8680 putative genes and a G+C content of 66.72%. Among the protein coding genes, 71.77% were annotated as clusters of orthologous groups of proteins (COGs); 55% of the COGs were present as paralog clusters. Pulsed field gel electrophoresis (PFGE) analysis of M213 revealed the presence of three different sized replicons- a circular chromosome and two megaplasmids (pNUO1 and pNUO2) estimated to be of 750Kb 350Kb in size, respectively. Conversely, using an alternative approach of optical mapping, the plasmid replicons appeared as a circular ~1.2 Mb megaplasmid and a linear, ~0.7 Mb megaplasmid. Genome-wide comparative analysis of M213 with a cohort of sequenced Rhodococcus species revealed low syntenic affiliation with other R. opacus species including strains B4 and PD630. Conversely, a closer affiliation of M213, at the functional (COG) level, was observed with the catabolically versatile R. jostii strain RHA1 and other Rhodococcii such as R. wratislaviensis strain IFP 2016, R. imtechensis strain RKJ300, Rhodococcus sp. strain JVH1, and Rhodococcus sp. strain DK17, respectively. An in-depth, genome-wide comparison between these functional relatives revealed 971 unique genes in M213 representing 11% of its total genome; many associating with catabolic functions. Of major interest was the identification of as many as 154 genomic islands (GEIs), many with duplicated catabolic genes, in particular for PAHs; a trait that was confirmed by PCR-based identification of naphthalene dioxygenase (NDO) as a representative gene, across PFGE-resolved replicons of strain M213. Interestingly, several plasmid/GEI-encoded genes, that likely participate in degrading naphthalene (NAP) via a peculiar pathway, were also identified in strain M213 using a combination of bioinformatics, metabolic analysis and gene expression measurements of selected catabolic genes by RT-PCR. Taken together, this study provides a comprehensive understanding of the genome plasticity and ecological competitiveness of strain M213 likely facilitated by horizontal gene transfer (HGT), bacteriophage attacks and genomic reshuffling- aspects that continue to be understudied and thus poorly understood, in particular for the soil-borne Rhodococcii.
Collapse
Affiliation(s)
- Ashish Pathak
- School of the Environment, Florida A&M University, Tallahassee, Florida, United States of America
| | - Ashvini Chauhan
- School of the Environment, Florida A&M University, Tallahassee, Florida, United States of America
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Karl J. Indest
- Environmental Processes Branch, United States Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America
| | - Carina M. Jung
- Environmental Processes Branch, United States Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Gopal Bera
- Geochemical and Environmental Research Group, Texas A&M University, College Station, Texas, United States of America
| | - Stefan J. Green
- DNA Services Facility, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Andrew Ogram
- Soil and Water Science Department, University of Florida, Gainesville, Florida, United States of America
| |
Collapse
|
9
|
Yao L, Naeth MA, Jobson A. Soil microbial response to waste potassium silicate drilling fluid. J Environ Sci (China) 2015; 29:189-198. [PMID: 25766028 DOI: 10.1016/j.jes.2014.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 10/09/2014] [Accepted: 10/16/2014] [Indexed: 06/04/2023]
Abstract
Potassium silicate drilling fluids (PSDF) are a waste product of the oil and gas industry with potential for use in land reclamation. Few studies have examined the influence of PSDF on abundance and composition of soil bacteria and fungi. Soils from three representative locations for PSDF application in Alberta, Canada, with clay loam, loam and sand textures were studied with applications of unused, used once and used twice PSDF. For all three soils, applying ≥40 m3/ha of used PSDF significantly affected the existing soil microbial flora. No microbiota was detected in unused PSDF without soil. Adding used PSDF to soil significantly increased total fungal and aerobic bacterial colony forming units in dilution plate counts, and anaerobic denitrifying bacteria numbers in serial growth experiments. Used PSDF altered bacterial and fungal colony forming unit ratios of all three soils.
Collapse
Affiliation(s)
- Linjun Yao
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta T6G 2H1, Canada; School of Land Science and Technology, China University of Geosciences (Beijing), Beijing 100083, China.
| | - M Anne Naeth
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta T6G 2H1, Canada
| | - Allen Jobson
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta T6G 2H1, Canada
| |
Collapse
|
10
|
Drotaverine Hydrochloride Degradation Using Cyst-like Dormant Cells of Rhodococcus ruber. Curr Microbiol 2014; 70:307-14. [DOI: 10.1007/s00284-014-0718-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/18/2014] [Indexed: 12/12/2022]
|
11
|
Kuyukina MS, Ivshina IB, Serebrennikova MK, Rubtsova EV, Krivoruchko AV. Simultaneous species-specific PCR detection and viability testing of poly(vinyl alcohol) cryogel-entrapped Rhodococcus spp. after their exposure to petroleum hydrocarbons. J Microbiol Methods 2013; 94:135-140. [DOI: 10.1016/j.mimet.2013.05.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/22/2013] [Accepted: 05/28/2013] [Indexed: 10/26/2022]
|
12
|
Comparative analysis of tertiary alcohol esterase activity in bacterial strains isolated from enrichment cultures and from screening strain libraries. Appl Microbiol Biotechnol 2011; 90:929-39. [DOI: 10.1007/s00253-011-3124-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 01/07/2011] [Accepted: 01/08/2011] [Indexed: 11/26/2022]
|
13
|
Kuyukina MS, Rubtsova EV, Ivshina IB, Ivanov RV, Lozinsky VI. Selective adsorption of hydrocarbon-oxidizing Rhodococcus cells in a column with hydrophobized poly(acrylamide) cryogel. J Microbiol Methods 2009; 79:76-81. [DOI: 10.1016/j.mimet.2009.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Revised: 08/03/2009] [Accepted: 08/04/2009] [Indexed: 10/20/2022]
|
14
|
Frascari D, Pinelli D, Nocentini M, Baleani E, Cappelletti M, Fedi S. A kinetic study of chlorinated solvent cometabolic biodegradation by propane-grown Rhodococcus sp. PB1. Biochem Eng J 2008. [DOI: 10.1016/j.bej.2008.06.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
15
|
Characterization of a second Rhodococcus erythropolis SQ1 3-ketosteroid 9alpha-hydroxylase activity comprising a terminal oxygenase homologue, KshA2, active with oxygenase-reductase component KshB. Appl Environ Microbiol 2008; 74:7197-203. [PMID: 18836008 DOI: 10.1128/aem.00888-08] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previously we have characterized 3-ketosteroid 9alpha-hydroxylase (KSH), a key enzyme in microbial steroid degradation in Rhodococcus erythropolis strain SQ1, as a two-component iron-sulfur monooxygenase, comprised of the terminal oxygenase component KshA1 and the oxygenase-reductase component KshB. Deletion of the kshA1 gene resulted in the loss of the ability of mutant strain RG2 to grow on the steroid substrate 4-androstene-3,17-dione (AD). Here we report characteristics of a close KshA1 homologue, KshA2 of strain SQ1, sharing 60% identity at the amino acid level. Expression of the kshA2 gene in mutant strain RG2 restored growth on AD and ADD, indicating that kshA2 also encodes KSH activity. The functional complementation was shown to be dependent on the presence of kshB. Transcriptional analysis showed that expression of kshA2 is induced in parent strain R. erythropolis SQ1 in the presence of AD. However, promoter activity studies, using beta-lactamase of Escherichia coli as a convenient transcription reporter protein for Rhodococcus, revealed that the kshA2 promoter in fact is highly induced in the presence of 9alpha-hydroxy-4-androstene-3,17-dione (9OHAD) or a metabolite thereof. Inactivation of kshA2 in parent strain SQ1 by unmarked gene deletion did not affect growth on 9OHAD, cholesterol, or cholic acid. We speculate that KshA2 plays a role in preventing accumulation of toxic intracellular concentrations of ADD during steroid catabolism. A third kshA homologue was additionally identified in a kshA1 kshA2 double gene deletion mutant strain of R. erythropolis SQ1. The developed degenerate PCR primers for kshA may be useful for isolation of kshA homologues from other (actino) bacteria.
Collapse
|
16
|
Putnam ML, Miller ML. Rhodococcus fascians in Herbaceous Perennials. PLANT DISEASE 2007; 91:1064-1076. [PMID: 30780643 DOI: 10.1094/pdis-91-9-1064] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
|
17
|
Guo CL, Zhou HW, Wong YS, Tam NFY. Isolation of PAH-degrading bacteria from mangrove sediments and their biodegradation potential. MARINE POLLUTION BULLETIN 2005; 51:1054-61. [PMID: 16291206 DOI: 10.1016/j.marpolbul.2005.02.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Surface sediment samples were collected from seven mangrove swamps in Hong Kong SAR with different degrees of contamination. The total concentrations of 16 PAHs in these sediments ranged from 169.41 to 1058.37 ng g(-1) with the highest concentration found in Ma Wan and the lowest in Kei Ling Ha Lo Wai mangrove swamp. In each swamp, three bacterial consortia were enriched from sediments using phenanthrene (Phe) as the sole carbon and energy source, and individual bacterial colony showing Phe degradation was isolated and identified by 16S rDNA gene sequence. The consortia enriched from Sai Keng and Ho Chung sediments had highest ability to degrade mixed PAHs in liquid medium, with 90% Phe and Fla (fluoranthene) degraded in 7 days. On the other hand, Kei Ling Ha Lo Wai-enriched consortia degraded less than 40% Phe and Fla. Pyrene (Pyr) was hardly degraded by the consortia enriched from sediments. Bacterial isolates, namely Rhodococcus (HCCS), Sphingomonas (MWFG) and Paracoccus (SPNT) were capable to degrade mixed PAHs (Phe + Fla + Pyr). Their degradation percentages could be lower, comparable or even higher than their respective enriched consortia, depending on the consortium and the type of PAH compounds. These results suggest that PAH-degrading bacteria enriched from mangrove sediments, either as a mixed culture or as a single isolate could be used for PAHs bioremediation.
Collapse
Affiliation(s)
- C L Guo
- Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | | | | | | |
Collapse
|
18
|
Lemarchand K, Masson L, Brousseau R. Molecular biology and DNA microarray technology for microbial quality monitoring of water. Crit Rev Microbiol 2004; 30:145-72. [PMID: 15490968 DOI: 10.1080/10408410490435142] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Public concern over polluted water is a major environmental issue worldwide. Microbial contamination of water arguably represents the most significant risk to human health on a global scale. An important challenge in modern water microbial quality monitoring is the rapid, specific, and sensitive detection of microbial indicators and waterborne pathogens. Presently, microbial tests are based essentially on time-consuming culture methods. Rapid microbiological analyses and detection of rare events in water systems are important challenges in water safety assessment since culture methods present serious limitations from both quantitative and qualitative points of view. To circumvent lengthy culture methods, newer enzymatic, immunological, and genetic methods are being developed as an alternative. DNA microarray technology is a new and promising tool that allows the detection of several hundred or even thousands DNA sequences simultaneously. Recent advances in sample processing and DNA microarray technologies provide new perspectives to assess microbial water quality. The aims of this review are to (1) summarize what is currently known about microbial indicators, (2) describe the most important waterborne pathogens, (3) present molecular methods used to monitor the presence of pathogens in water, and (4) show the potential of DNA microarrays in water quality monitoring.
Collapse
Affiliation(s)
- Karine Lemarchand
- National Research Council of Canada, Biotechnology Research Institute, Montreal, Quebec, Canada
| | | | | |
Collapse
|
19
|
Kim SH, An H, Field KG, Wei CI, Velazquez JB, Ben-Gigirey B, Morrissey MT, Price RJ, Pitta TP. Detection of Morganella morganii, a prolific histamine former, by the polymerase chain reaction assay with 16S rDNA-targeted primers. J Food Prot 2003; 66:1385-92. [PMID: 12929824 DOI: 10.4315/0362-028x-66.8.1385] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A polymerase chain reaction (PCR) assay for the rapid and sensitive detection of the most prolific histamine former, Morganella morganii, was developed. 16S rDNA targeted PCR primers were designed, and the primer specificity and sensitivity of the PCR assay were evaluated. The 16S rDNA sequence (1,503 bp) for M. morganii showed 95% identity to those for enteric bacteria, i.e., Enterobacter spp., Klebsiella spp., Citrobacter spp., Hafnia alvei, Proteus spp., and Providencia spp. The unique primers for M. morganii were designed on the basis of the variable regions in the 16S rDNA sequence. The primers showed positive reactions with all M. morganii strains tested. However, PCR amplification was not detected when the primers were tested with other enteric or marine bacteria. When the sensitivity of the assay was evaluated, M. morganii was detected at levels ranging from 10(6) to 10(8) CFU/ml in albacore homogenate after the PCR amplification. The sensitivity of the assay was greatly improved with the enrichment of samples, and 9 CFU of M. morganii per ml of albacore homogenate was detected after 6 h of enrichment at 37 degrees C.
Collapse
Affiliation(s)
- Shin-Hee Kim
- Department of Nutrition and Food Science, 328 Spidle Hall, Auburn University, Auburn, Alabama 36849, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Miller SCM, LiPuma JJ, Parke JL. Culture-based and non-growth-dependent detection of the Burkholderia cepacia complex in soil environments. Appl Environ Microbiol 2002; 68:3750-8. [PMID: 12147469 PMCID: PMC124052 DOI: 10.1128/aem.68.8.3750-3758.2002] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Burkholderia cepacia complex (Bcc) bacteria reside in soil, plant rhizospheres, and water, but their prevalence and distribution in outdoor environments is not clear. We sampled a variety of soil and rhizosphere environments with which people may have contact: playgrounds, athletic fields, parks, hiking trails, residential yards, and gardens. A total of 91 sites was sampled in three large U.S. cities. In the first phase of the study, putative Bcc isolates were recovered on Burkholderia cepacia selective agar and trypan blue tetracycline medium and subsequently examined for biochemical reactivity and growth at 32 and 22 degrees C. Isolates were further examined by PCR assays targeting Bcc-specific ribosomal DNA and recA gene sequences. Among the 1,013 bacterial isolates examined, 68 were identified as Bcc; 14 (15%) of 91 sampled sites yielded Bcc isolates. In the second phase, DNA was extracted directly from soil samples and examined with PCR assays targeting Bcc 16S rRNA gene sequences. Either 82 or 93% of the soil samples were positive for at least one Bcc genomovar, depending on the PCR assay system used. Cloning and sequencing were performed to check the specificity of the PCR assays. Sequence analysis of the 463-bp 16S rRNA inserts from eight clones indicated that all were from members of the Bcc. The four soil samples from which these clones were generated did not yield isolates identified as Bcc. Based on PCR detection, Bcc appears to be prevalent in soil from urban and suburban environments. Culture-based recovery of Bcc may underestimate environmental populations.
Collapse
Affiliation(s)
- Suzanne C. M. Miller
- Department of Crop and Soil Science, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331-7306, Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan 48109-0646
| | - John J. LiPuma
- Department of Crop and Soil Science, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331-7306, Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan 48109-0646
| | - Jennifer L. Parke
- Department of Crop and Soil Science, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331-7306, Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan 48109-0646
- Corresponding author. Mailing address: Department of Crop and Soil Science, Oregon State University, ALS 3017, Corvallis, OR 97331-7106. Phone: (541) 737-8170. Fax: (541) 737-5725. E-mail:
| |
Collapse
|
21
|
Savill MG, Murray SR, Scholes P, Maas EW, McCormick RE, Moore EB, Gilpin BJ. Application of polymerase chain reaction (PCR) and TaqMan PCR techniques to the detection and identification of Rhodococcus coprophilus in faecal samples. J Microbiol Methods 2001; 47:355-68. [PMID: 11714526 DOI: 10.1016/s0167-7012(01)00343-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Rhodococcus coprophilus, a natural inhabitant of herbivore faeces, has been suggested as a good indicator of animal (as opposed to human) faecal contamination of aquatic environments. However, conventional detection methods limit its use for this as they require up to 21 days to obtain a result. In this paper an optimised method for extracting R. coprophilus DNA from faecal samples is described. PCR and 5'-nuclease (TaqMan) PCR methods were developed to allow the detection and enumeration of R. coprophilus in faecal samples within 2-3 days. Both PCR methods targeted the 16S rRNA gene, producing an amplicon of 443 bp which was specific for R. coprophilus. Sixty cells were required to produce an amplification product by conventional PCR, while as little as one cell was required for the TaqMan PCR method. The latter approach gave a linear quantitative response over at least four log units with both bacterial cells and DNA. Successful amplification by PCR was achieved using DNA extracted from cow, sheep, horse and deer faeces but was negative for samples from humans, pig, possum, duck and rabbit. These PCR methods enhance the feasibility of using R. coprophilus to distinguish faecal pollution of farmed herbivores from human pollution.
Collapse
Affiliation(s)
- M G Savill
- Christchurch Science Centre, Institute of Environmental Science and Research (ESR) Ltd., PO Box 29-181, Christchurch, New Zealand.
| | | | | | | | | | | | | |
Collapse
|