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Samioti V, Kriti E, Spanou A, Tsironi T, Panagou EZ. Inactivation Kinetics of Pathogenic and Nonpathogenic Bacteria Upon In Vitro Treatment With Cold Atmospheric Pressure Plasma (CAPP). INTERNATIONAL JOURNAL OF FOOD SCIENCE 2024; 2024:7464133. [PMID: 39077375 PMCID: PMC11286313 DOI: 10.1155/2024/7464133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 06/06/2024] [Accepted: 06/20/2024] [Indexed: 07/31/2024]
Abstract
In the present study, selected pathogenic (Salmonella Typhimurium, Escherichia coli, Pseudomonas aeruginosa, Listeria monocytogenes, Bacillus cereus, and Staphylococcus aureus) and nonpathogenic (Pseudomonas fragi, Pseudomonas fluorescens, Brochothrix thermosphacta, Bacillus subtilis, Lactiplantibacillus plantarum, and Leuconostoc mesenteroides) bacteria were subjected in vitro in cold atmospheric pressure plasma (CAPP) treatment for up to 15 min and the changes in the surviving microbial population were determined. Plasma treatments were carried out by a plasma jet device, operating with argon (Ar) as carrier gas under constant flow (4.0 L/min) at a frequency of 1 MHz and an electrical voltage of 2-6 kV. Microbial inactivation data were modelled using linear and nonlinear (Geeraerd, Weibull) models, through which the corresponding kinetic parameters were calculated. After 15 min of exposure to plasma radiation, the total reduction in the bacterial populations was 2.12 log10 CFU mL-1 for P. fragi, 1.77 log10 CFU mL-1 for P. fluorescens, 2.30 log10 CFU mL-1 for B. thermosphacta, 1.58 log10 CFU mL-1 for B. subtilis, 1.31 log10 CFU mL-1 for L. plantarum, 3.80 log10 CFU mL-1 for L. mesenteroides (highest reduction observed), 1.12 log10 CFU mL-1 for S. Typhimurium, 1.18 log10 CFU mL-1 for E. coli, 1.43 log10 CFU mL-1 for L. monocytogenes, 1.32 log10 CFU mL-1 for B. cereus, 0.88 log10 CFU mL-1 for S. aureus, and 0.73 log10 CFU mL-1 for P. aeruginosa. The results showed a higher reduction in the population of nonpathogenic microorganisms compared to pathogens. The relatively small decrease in the inactivation of bacteria indicates that parameter optimization is necessary to be considered to improve the efficacy of the treatment.
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Affiliation(s)
- Venetia Samioti
- Laboratory of Microbiology and Biotechnology of FoodsDepartment of Food Science and Human NutritionSchool of Food and Nutritional SciencesAgricultural University of Athens, Iera Odos 75, Athens GR-11855, Greece
| | - Evangelia Kriti
- Laboratory of Microbiology and Biotechnology of FoodsDepartment of Food Science and Human NutritionSchool of Food and Nutritional SciencesAgricultural University of Athens, Iera Odos 75, Athens GR-11855, Greece
| | - Aikaterini Spanou
- Laboratory of Food Process EngineeringDepartment of Food Science and Human NutritionSchool of Food and Nutritional SciencesAgricultural University of Athens, Iera Odos 75, Athens GR-11855, Greece
| | - Theofania Tsironi
- Laboratory of Food Process EngineeringDepartment of Food Science and Human NutritionSchool of Food and Nutritional SciencesAgricultural University of Athens, Iera Odos 75, Athens GR-11855, Greece
| | - Efstathios Z. Panagou
- Laboratory of Microbiology and Biotechnology of FoodsDepartment of Food Science and Human NutritionSchool of Food and Nutritional SciencesAgricultural University of Athens, Iera Odos 75, Athens GR-11855, Greece
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Warren Norris MAH, Plaskon DM, Tamayo R. Phase Variation of Flagella and Toxins in Clostridioides difficile is Mediated by Selective Rho-dependent Termination. J Mol Biol 2024; 436:168456. [PMID: 38278436 PMCID: PMC10942720 DOI: 10.1016/j.jmb.2024.168456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 01/28/2024]
Abstract
Clostridioides difficile is an intestinal pathogen that exhibits phase variation of flagella and toxins through inversion of the flagellar (flg) switch controlling flagellar and toxin gene expression. The transcription termination factor Rho preferentially inhibits swimming motility of bacteria with the 'flg-OFF' switch sequence. How C. difficile Rho mediates this selectivity was unknown. C. difficile Rho contains an N-terminal insertion domain (NID) which is found in a subset of Rho orthologues and confers diverse functions. Here we determined how Rho distinguishes between flg-ON and -OFF mRNAs and the roles of the NID and other domains of C. difficile Rho. Using in vitro ATPase assays, we determined that Rho specifically binds a region containing the left inverted repeat of the flg switch, but only of flg-OFF mRNA, indicating that differential termination is mediated by selective Rho binding. Using a suite of in vivo and in vitro assays in C. difficile, we determined that the NID is essential for Rho termination of flg-OFF mRNA, likely by influencing the ability to form stable hexamers, and the RNA binding domain is critical for flg-OFF specific termination. This work gives insight into the novel mechanism by which Rho interacts with flg mRNA to mediate phase variation of flagella and toxins in C. difficile and broadens our understanding of Rho-mediated termination in an organism with an AT-rich genome.
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Affiliation(s)
- Mercedes A H Warren Norris
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Dylan M Plaskon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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3
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Silva-Pereira TT, Soler-Camargo NC, Guimarães AMS. Diversification of gene content in the Mycobacterium tuberculosis complex is determined by phylogenetic and ecological signatures. Microbiol Spectr 2024; 12:e0228923. [PMID: 38230932 PMCID: PMC10871547 DOI: 10.1128/spectrum.02289-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024] Open
Abstract
We analyzed the pan-genome and gene content modulation of the most diverse genome data set of the Mycobacterium tuberculosis complex (MTBC) gathered to date. The closed pan-genome of the MTBC was characterized by reduced accessory and strain-specific genomes, compatible with its clonal nature. However, significantly fewer gene families were shared between MTBC genomes as their phylogenetic distance increased. This effect was only observed in inter-species comparisons, not within-species, which suggests that species-specific ecological characteristics are associated with changes in gene content. Gene loss, resulting from genomic deletions and pseudogenization, was found to drive the variation in gene content. This gene erosion differed among MTBC species and lineages, even within M. tuberculosis, where L2 showed more gene loss than L4. We also show that phylogenetic proximity is not always a good proxy for gene content relatedness in the MTBC, as the gene repertoire of Mycobacterium africanum L6 deviated from its expected phylogenetic niche conservatism. Gene disruptions of virulence factors, represented by pseudogene annotations, are mostly not conserved, being poor predictors of MTBC ecotypes. Each MTBC ecotype carries its own accessory genome, likely influenced by distinct selective pressures such as host and geography. It is important to investigate how gene loss confer new adaptive traits to MTBC strains; the detected heterogeneous gene loss poses a significant challenge in elucidating genetic factors responsible for the diverse phenotypes observed in the MTBC. By detailing specific gene losses, our study serves as a resource for researchers studying the MTBC phenotypes and their immune evasion strategies.IMPORTANCEIn this study, we analyzed the gene content of different ecotypes of the Mycobacterium tuberculosis complex (MTBC), the pathogens of tuberculosis. We found that changes in their gene content are associated with their ecological features, such as host preference. Gene loss was identified as the primary driver of these changes, which can vary even among different strains of the same ecotype. Our study also revealed that the gene content relatedness of these bacteria does not always mirror their evolutionary relationships. In addition, some genes of virulence can be variably lost among strains of the same MTBC ecotype, likely helping them to evade the immune system. Overall, our study highlights the importance of understanding how gene loss can lead to new adaptations in these bacteria and how different selective pressures may influence their genetic makeup.
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Affiliation(s)
- Taiana Tainá Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Naila Cristina Soler-Camargo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana Marcia Sá Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Shen Z, Lin L, Zhai Z, Liang J, Chen L, Hao Y, Zhao L. bglG Regulates the Heterogeneity Driven by the Acid Tolerance Response in Lacticaseibacillus paracasei L9. Foods 2023; 12:3971. [PMID: 37959089 PMCID: PMC10650579 DOI: 10.3390/foods12213971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/24/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023] Open
Abstract
The acid tolerance of lactic acid bacteria is crucial for their fermentation and probiotic functions. Acid adaption significantly enhances the acid tolerance of strains, and the phenotypic heterogeneity driven by the acid tolerance response (ATR) contributes to this process by providing a selective advantage in harsh environments. The mechanism of heterogeneity under the ATR is not yet clear, but individual gene expression differences are recognized as the cause. In this study, we observed four heterogeneous subpopulations (viable, injured, dead, and unstained) of Lacticaseibacillus paracasei L9 (L9) induced by acid adaption (pH 5.0, 40 min) using flow cytometry. The viable subpopulation represented a significantly superior acid tolerance to the injured subpopulation or total population. Different subpopulations were sorted and transcriptomic analysis was performed. Five genes were found to be upregulated in the viable subpopulation and downregulated in the injured subpopulation, and bglG (LPL9_RS14735) was identified as having a key role in this process. Using salicin (glucoside)-inducing gene expression and gene insertion mutagenesis, we verified that bglG regulated the heterogeneity of the acid stress response and that the relevant mechanisms might be related to activating hsp20. This study provides new evidence for the mechanism of the ATR and may contribute to the theoretical basis of improving the acid tolerance of Lacticaseibacillus paracasei L9.
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Affiliation(s)
- Zhichao Shen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Z.S.); (L.L.); (Z.Z.); (J.L.); (L.C.)
- Key Laboratory of Functional Dairy, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China;
| | - Li Lin
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Z.S.); (L.L.); (Z.Z.); (J.L.); (L.C.)
| | - Zhengyuan Zhai
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Z.S.); (L.L.); (Z.Z.); (J.L.); (L.C.)
| | - Jingjing Liang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Z.S.); (L.L.); (Z.Z.); (J.L.); (L.C.)
| | - Long Chen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Z.S.); (L.L.); (Z.Z.); (J.L.); (L.C.)
| | - Yanling Hao
- Key Laboratory of Functional Dairy, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China;
| | - Liang Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Z.S.); (L.L.); (Z.Z.); (J.L.); (L.C.)
- Key Laboratory of Functional Dairy, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China;
- Research Center for Probiotics, China Agricultural University, Sanhe 065200, China
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Nikolaev YA, Demkina EV, Ilicheva EA, Kanapatskiy TA, Borzenkov IA, Ivanova AE, Tikhonova EN, Sokolova DS, Ruzhitsky AO, El-Registan GI. Ways of Long-Term Survival of Hydrocarbon-Oxidizing Bacteria in a New Biocomposite Material-Silanol-Humate Gel. Microorganisms 2023; 11:1133. [PMID: 37317107 DOI: 10.3390/microorganisms11051133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/19/2023] [Accepted: 04/22/2023] [Indexed: 06/16/2023] Open
Abstract
Immobilized bacterial cells are presently widely used in the development of bacterial preparations for the bioremediation of contaminated environmental objects. Oil hydrocarbons are among the most abundant pollutants. We have previously described a new biocomposite material containing hydrocarbon-oxidizing bacteria (HOB) embedded in silanol-humate gels (SHG) based on humates and aminopropyltriethoxysilane (APTES); high viable cell titer was maintained in this material for at least 12 months. The goal of the work was to describe the ways of long-term HOB survival in SHG and the relevant morphotypes using the techniques of microbiology, instrumental analytical chemistry and biochemistry, and electron microscopy. Bacteria surviving in SHG were characterized by: (1) capacity for rapid reactivation (growth and hydrocarbon oxidation) in fresh medium; (2) ability to synthesize surface-active compounds, which was not observed in the cultures stored without SHG); (3) elevated stress resistance (ability to grow at high Cu2+ and NaCl concentrations); (4) physiological heterogeneity of the populations, which contained the stationary hypometabolic cells, cystlike anabiotic dormant forms (DF), and ultrasmall cells; (5) occurrence of piles in many cells, which were probably used to exchange genetic material; (6) modification of the phase variants spectrum in the population growing after long-term storage in SHG; and (7) oxidation of ethanol and acetate by HOB populations stored in SHG. The combination of the physiological and cytomorphological properties of the cells surviving in SHG for long periods may indicate a new type of long-term bacterial survival, i.e., in a hypometabolic state.
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Affiliation(s)
- Yury A Nikolaev
- The Federal State Institution "Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences" (Research Center of Biotechnology RAS), Leninsky Prospect 14, 119991 Moscow, Russia
| | - Elena V Demkina
- The Federal State Institution "Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences" (Research Center of Biotechnology RAS), Leninsky Prospect 14, 119991 Moscow, Russia
| | - Ekaterina A Ilicheva
- The Federal State Institution "Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences" (Research Center of Biotechnology RAS), Leninsky Prospect 14, 119991 Moscow, Russia
| | - Timur A Kanapatskiy
- The Federal State Institution "Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences" (Research Center of Biotechnology RAS), Leninsky Prospect 14, 119991 Moscow, Russia
| | - Igor A Borzenkov
- The Federal State Institution "Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences" (Research Center of Biotechnology RAS), Leninsky Prospect 14, 119991 Moscow, Russia
| | - Anna E Ivanova
- The Federal State Institution "Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences" (Research Center of Biotechnology RAS), Leninsky Prospect 14, 119991 Moscow, Russia
| | - Ekaterina N Tikhonova
- The Federal State Institution "Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences" (Research Center of Biotechnology RAS), Leninsky Prospect 14, 119991 Moscow, Russia
| | - Diyana S Sokolova
- The Federal State Institution "Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences" (Research Center of Biotechnology RAS), Leninsky Prospect 14, 119991 Moscow, Russia
| | - Alexander O Ruzhitsky
- The Federal State Institution "Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences" (Research Center of Biotechnology RAS), Leninsky Prospect 14, 119991 Moscow, Russia
| | - Galina I El-Registan
- The Federal State Institution "Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences" (Research Center of Biotechnology RAS), Leninsky Prospect 14, 119991 Moscow, Russia
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6
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Lowrey LC, Kent LA, Rios BM, Ocasio AB, Cotter PA. An IS-mediated, RecA-dependent, bet-hedging strategy in Burkholderia thailandensis. eLife 2023; 12:e84327. [PMID: 36715687 PMCID: PMC9946442 DOI: 10.7554/elife.84327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Adaptation to fluctuating environmental conditions is difficult to achieve. Phase variation mechanisms can overcome this difficulty by altering genomic architecture in a subset of individuals, creating a phenotypically heterogeneous population with subpopulations optimized to persist when conditions change, or are encountered, suddenly. We have identified a phase variation system in Burkholderia thailandensis that generates a genotypically and phenotypically heterogeneous population. Genetic analyses revealed that RecA-mediated homologous recombination between a pair of insertion sequence (IS) 2-like elements duplicates a 208.6 kb region of DNA that contains 157 coding sequences. RecA-mediated homologous recombination also resolves merodiploids, and hence copy number of the region is varied and dynamic within populations. We showed that the presence of two or more copies of the region is advantageous for growth in a biofilm, and a single copy is advantageous during planktonic growth. While IS elements are well known to contribute to evolution through gene inactivation, polar effects on downstream genes, and altering genomic architecture, we believe that this system represents a rare example of IS element-mediated evolution in which the IS elements provide homologous sequences for amplification of a chromosomal region that provides a selective advantage under specific growth conditions, thereby expanding the lifestyle repertoire of the species.
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Affiliation(s)
- Lillian C Lowrey
- Department of Microbiology and Immunology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Leslie A Kent
- Department of Microbiology and Immunology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Bridgett M Rios
- Department of Microbiology and Immunology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Angelica B Ocasio
- Department of Microbiology and Immunology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Peggy A Cotter
- Department of Microbiology and Immunology, University of North Carolina at Chapel HillChapel HillUnited States
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Yeap CSY, Nguyen NHA, Spanek R, Too CC, Benes V, Provaznik J, Cernik M, Sevcu A. Dissolved iron released from nanoscale zero-valent iron (nZVI) activates the defense system in bacterium Pseudomonas putida, leading to high tolerance to oxidative stress. JOURNAL OF HAZARDOUS MATERIALS 2022; 439:129627. [PMID: 35872458 DOI: 10.1016/j.jhazmat.2022.129627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/03/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Nanoscale zero-valent iron (nZVI) has increasingly been applied to remediate aquifers polluted by organochlorines or heavy metals. As a result, bacteria in the vicinity of remediate action can be stressed by surplus iron released from nZVI. However, the understanding of the iron stress defense pathways during this process is currently incomplete. Therefore, we aimed to elucidate the physiological and transcriptomic response of the bacterium, Pseudomonas putida NCTC 10936, to 100 mg/L of nZVI and 44.5 µg/L of dissolved iron obtained from nZVI suspension. Cell viability was neither affected by nZVI nor dissolved iron, although the dissolved iron caused stress that altered the cell physiology and caused the generation of smaller cells, whereas cells were elongated in the presence of nZVI. Transcriptomic analysis confirmed the observed stronger physiological effect caused by dissolved iron (in total 3839 differentially expressed genes [DEGs]) than by nZVI (945 DEGs). Dissolved iron (but not nZVI) activated genes involved in oxidative stress-related pathways, antioxidant activity, carbohydrate and energy metabolism, but downregulated genes associated with flagellar assembly proteins and two-component systems involved in sensing external stimuli. As a result, bacteria very effectively faced oxidative insults and cell viability was not affected.
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Affiliation(s)
- Cheryl S Y Yeap
- Institute for Nanomaterials Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 1409/7, 46117 Liberec 1, Czechia; Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, Studentská 2, 461 17 Liberec 1, Czechia
| | - Nhung H A Nguyen
- Institute for Nanomaterials Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 1409/7, 46117 Liberec 1, Czechia
| | - Roman Spanek
- Institute for Nanomaterials Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 1409/7, 46117 Liberec 1, Czechia; Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, Studentská 2, 461 17 Liberec 1, Czechia
| | - Chin Chin Too
- Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, Campus Ledeganck, 9000 Ghent, Belgium
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory of Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Jan Provaznik
- Genomics Core Facility, European Molecular Biology Laboratory of Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Miroslav Cernik
- Institute for Nanomaterials Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 1409/7, 46117 Liberec 1, Czechia
| | - Alena Sevcu
- Institute for Nanomaterials Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 1409/7, 46117 Liberec 1, Czechia; Faculty of Science, Humanities and Education, Technical University of Liberec, Studentská 2, 461 17 Liberec 1, Czechia.
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Bystritskaya E, Chernysheva N, Stenkova A, Guzev K, Rakin A, Isaeva M. Differential Expression of Yersinia pseudotuberculosis General Porin Genes during Short- and Long-Term Antibiotic Stresses. Molecules 2021; 26:3956. [PMID: 34203552 PMCID: PMC8272246 DOI: 10.3390/molecules26133956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 11/25/2022] Open
Abstract
Here, we investigated general porin regulation in Yersinia pseudotuberculosis 488, the causative agent of Far Eastern scarlet-like fever, in response to sublethal concentrations of antibiotics. We chose four antibiotics of different classes and measured gene expression using qRT-PCR and GFP reporter systems. Our data showed temporal regulation of the general porin genes ompF and ompC caused by antibiotic stress. The porin transcription initially decreased, providing early defensive response of the bacterium, while it returned to that of the untreated cells on prolonged antibiotic exposure. Unlike the major porin genes, the transcription of the alternative porin genes ompX and lamB was increased. Moreover, a short-term ompR- and marA-mediated porin regulation was observed. The main finding was a phenotypic heterogeneity of Y. pseudotuberculosis population manifested in variable porin gene expression under carbenicillin exposure. This may offer adaptive fitness advantages for a particular bacterial subpopulation.
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Affiliation(s)
- Evgeniya Bystritskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 Let Vladivostoku, 690022 Vladivostok, Russia; (E.B.); (N.C.); (K.G.)
| | - Nadezhda Chernysheva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 Let Vladivostoku, 690022 Vladivostok, Russia; (E.B.); (N.C.); (K.G.)
| | - Anna Stenkova
- School of Biomedicine, Far Eastern Federal University, 8 Sukhanova St., 690090 Vladivostok, Russia;
| | - Konstantin Guzev
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 Let Vladivostoku, 690022 Vladivostok, Russia; (E.B.); (N.C.); (K.G.)
| | - Alexander Rakin
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute for Bacterial Infections and Zoonoses, Naumburger Str. 96a, D-07743 Jena, Germany;
| | - Marina Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 Let Vladivostoku, 690022 Vladivostok, Russia; (E.B.); (N.C.); (K.G.)
- School of Biomedicine, Far Eastern Federal University, 8 Sukhanova St., 690090 Vladivostok, Russia;
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Both Pseudomonas aeruginosa and Candida albicans Accumulate Greater Biomass in Dual-Species Biofilms under Flow. mSphere 2021; 6:e0041621. [PMID: 34160236 PMCID: PMC8265656 DOI: 10.1128/msphere.00416-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Microbe-microbe interactions can strongly influence growth and biofilm formation kinetics. For Pseudomonas aeruginosa and Candida albicans, which are found together in diverse clinical sites, including urinary and intravenous catheters and the lungs of individuals with cystic fibrosis (CF), we compared the kinetics of biofilm formation by each species in dual-species and single-species biofilms. We engineered fluorescent protein constructs for P. aeruginosa (producing mKO-κ) and C. albicans (producing mKate2) that did not alter growth and enabled single-cell resolution imaging by live-sample microscopy. Using these strains in an optically clear derivative of synthetic CF sputum medium, we found that both P. aeruginosa and C. albicans displayed increased biovolume accumulation—by three- and sixfold, respectively—in dual-species biofilms relative to single-species biofilms. This result was specific to the biofilm environment, as enhanced growth was not observed in planktonic cocultures. Stimulation of C. albicans biofilm formation occurred regardless of whether P. aeruginosa was added at the time of fungal inoculation or 24 h after the initiation of biofilm development. P. aeruginosa biofilm increases in cocultures did not require the Pel extracellular polysaccharide, phenazines, and siderophores known to influence C. albicans. P. aeruginosa mutants lacking Anr, LasR, and BapA were not significantly stimulated by C. albicans, but they still promoted a significant enhancement of biofilm development of the fungus, suggesting a fungal response to the presence of bacteria. Last, we showed that a set of P. aeruginosa clinical isolates also prompted an increase of biovolume by C. albicans in coculture. IMPORTANCE There is an abundance of work on both P. aeruginosa and C. albicans in isolation, and quite some work as well on the way these two microbes interact. These studies do not, however, consider biofilm environments under flow, and our results here show that the expected outcome of interaction between these two pathogens can actually be reversed under flow, from pure antagonism to an increase in biomass on the part of both. Our work also highlights the importance of cellular-scale spatial structure in biofilms for understanding multispecies population dynamics.
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Dawan J, Ahn J. Assessment of cooperative antibiotic resistance of Salmonella Typhimurium within heterogeneous population. Microb Pathog 2021; 157:104973. [PMID: 34029657 DOI: 10.1016/j.micpath.2021.104973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 11/29/2022]
Abstract
This study was designed to investigate the cooperative resistance in the mixed culture of antibiotic-sensitive and antibiotic-resistant Salmonella Typhimurium. Strains of S. Typhimurium ATCC 19585 (STS) and clinically isolated antibiotic-resistant S. Typhimurium CCARM 8009 (STR) grown in single and mixture with 1 × MIC ceftriaxone (CEF) were used to determine the viability, β-lactamase activity, and gene expression. The MIC50 values of STR to CEF was increased by more than 5-fold with increasing inoculum densities from 102 to 107 CFU/mL. STS was resistant to 1 × MIC CEF in the mixed culture of STS and STR, showing the more than 108 CFU/mL after 20 h of incubation at 37 °C. The highest β-lactamase activity was 18 μmol/min/mL in the mixed culture, corresponding to the highest relative expression of β-lactamase-related genes (blaTEM). These results shed new light on the cooperative resistance of antibiotic-sensitive bacteria within a heterogeneous population including β-lactamase-producing bacteria.
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Affiliation(s)
- Jirapat Dawan
- Department of Biomedical Science and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Juhee Ahn
- Department of Biomedical Science and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea.
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Garrett EM, Mehra A, Sekulovic O, Tamayo R. Multiple Regulatory Mechanisms Control the Production of CmrRST, an Atypical Signal Transduction System in Clostridioides difficile. mBio 2021; 13:e0296921. [PMID: 35164558 PMCID: PMC8844915 DOI: 10.1128/mbio.02969-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/20/2022] [Indexed: 12/16/2022] Open
Abstract
Clostridioides difficile, an intestinal pathogen and leading cause of nosocomial infection, exhibits extensive phenotypic heterogeneity through phase variation. The signal transduction system CmrRST, which encodes two response regulators (CmrR and CmrT) and a sensor kinase (CmrS), impacts C. difficile cell and colony morphology, surface and swimming motility, biofilm formation, and virulence in an animal model. CmrRST is subject to phase variation through site-specific recombination and reversible inversion of the "cmr switch," and expression of cmrRST is also regulated by cyclic diguanylate (c-di-GMP) through a riboswitch. The goal of this study was to determine how the cmr switch and c-di-GMP work together to regulate cmrRST expression. We generated "phase-locked" strains by mutating key residues in the right inverted repeat flanking the cmr switch. Phenotypic characterization of these phase-locked cmr-ON and -OFF strains demonstrates that they cannot switch between rough and smooth colony morphologies, respectively, or other CmrRST-associated phenotypes. Manipulation of c-di-GMP levels in these mutants showed that c-di-GMP promotes cmrRST expression and associated phenotypes independently of cmr switch orientation. We identified multiple promoters controlling cmrRST transcription, including one within the ON orientation of the cmr switch and another that is positively autoregulated by CmrR. Overall, this work reveals a complex regulatory network that governs cmrRST expression and a unique intersection of phase variation and c-di-GMP signaling. These findings suggest that multiple environmental signals impact the production of this signaling transduction system. IMPORTANCE Clostridioides difficile is a leading cause of hospital-acquired intestinal infections in the United States. The CmrRST signal transduction system controls numerous physiological traits and processes in C. difficile, including cell and colony morphology, motility, biofilm formation, and virulence. Here, we define the complex, multilevel regulation of cmrRST expression, including stochastic control through phase variation, modulation by the second messenger c-di-GMP, and positive autoregulation by CmrR. The results of this study suggest that multiple, distinct environmental stimuli and selective pressures must be integrated to appropriately control cmrRST expression.
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Affiliation(s)
- Elizabeth M. Garrett
- Department of Microbiology and Immunology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, USA
| | - Anchal Mehra
- Department of Microbiology and Immunology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ognjen Sekulovic
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, USA
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Somova LM, Timchenko NF, Lyapun IN, Drobot EI, Matosova EV, Bynina MP. Ultrastructural Changes of Bacteria in Static Cultures of Yersinia pseudotuberculosis under Long Storage under Conditions of Low Temperature. Bull Exp Biol Med 2020; 170:223-225. [PMID: 33263854 DOI: 10.1007/s10517-020-05038-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Indexed: 11/25/2022]
Abstract
Electron microscopy study revealed changes in the ultrastructure of bacteria of Yersinia pseudotuberculosis strains characterized by significantly reduced reproductive ability and virulence potential after long-term storage at low temperature of 4-8°C. Most bacterial cells contained dark cytosol with reduced cellular material or empty cytosol, while the cell wall was preserved. The revealed ultrastructural changes in the bacterial cells of the static culture of Y. pseudotuberculosis suggest that storage of strains under low positive temperatures could induce the transition of the majority of bacterial cell population to a dormant, non-cultivated state with a decrease in their virulence. This fact is of great scientific and applied importance in studies of causative agents of saprozoonoses, including pseudotuberculosis, which has the etiopathogenetic background of persistent infection.
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Affiliation(s)
- L M Somova
- G. P. Somov Research Institute of Epidemiology and Microbiology, Vladivostok, Russia.
| | - N F Timchenko
- G. P. Somov Research Institute of Epidemiology and Microbiology, Vladivostok, Russia
| | - I N Lyapun
- G. P. Somov Research Institute of Epidemiology and Microbiology, Vladivostok, Russia
| | - E I Drobot
- G. P. Somov Research Institute of Epidemiology and Microbiology, Vladivostok, Russia
| | - E V Matosova
- G. P. Somov Research Institute of Epidemiology and Microbiology, Vladivostok, Russia
| | - M P Bynina
- G. P. Somov Research Institute of Epidemiology and Microbiology, Vladivostok, Russia
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13
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Genomic plasticity of pathogenic Escherichia coli mediates d-serine tolerance via multiple adaptive mechanisms. Proc Natl Acad Sci U S A 2020; 117:22484-22493. [PMID: 32848072 PMCID: PMC7486766 DOI: 10.1073/pnas.2004977117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Pathogens ensure infection of favored sites in the body by responding to chemical signals. One chemical abundant in urine, the amino acid d-Ser, is toxic to EHEC and reduces expression of the machinery used for host cell attachment, making the bladder an unfavorable environment. We observed that under d-Ser stress, EHEC acquires genetic changes that lead to blocking d-Ser uptake into the cell or activating a silent enzyme for degrading d-Ser. This prevents growth inhibition and, critically, inhibits the repression of attachment machinery normally caused by d-Ser. These findings highlight the importance of pathogen evolution in determining how host molecules regulate colonization. These interactions underpin a process known as niche restriction that is important for pathogen success within the host. The molecular environment of the host can have profound effects on the behavior of resident bacterial species. We recently established how the sensing and response of enterohemorrhagic Escherichia coli (EHEC) to d-serine (d-Ser) resulted in down-regulation of type 3 secretion system-dependent colonization, thereby avoiding unfavorable environments abundant in this toxic metabolite. However, this model ignores a key determinant of the success of bacterial pathogens, adaptive evolution. In this study, we have explored the adaptation of EHEC to d-Ser and its consequences for pathogenesis. We rapidly isolated multiple, independent, EHEC mutants whose growth was no longer compromised in the presence of d-Ser. Through a combination of whole-genome sequencing and transcriptomics, we showed that tolerance could be attributed to disruption of one of two d-Ser transporters and/or activation of a previously nonfunctional d-Ser deaminase. While the implication of cytoplasmic transport in d-Ser toxicity was unsurprising, disruption of a single transporter, CycA, was sufficient to completely overcome the repression of type 3 secretion system activity normally associated with exposure to d-Ser. Despite the fact that this reveals a mechanism by which evolution could drive a pathogen to colonize new niches, interrogation of sequenced E. coli O157:H7 genomes showed a high level of CycA conservation, highlighting a strong selective pressure for functionality. Collectively, these data show that CycA is a critically important conduit for d-Ser uptake that is central to the niche restriction of EHEC.
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Nikolaev YA, Loiko NG, Demkina EV, Atroshchik EA, Konstantinov AI, Perminova IV, El’-Registan GI. Functional Activity of Humic Substances in Survival Prolongation of Populations of Hydrocarbon-Oxidizing Bacteria Acinetobacter junii. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720010105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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15
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Paranjape SS, Shashidhar R. Inhibition of protein synthesis eradicates persister cells of V. cholerae. 3 Biotech 2019; 9:380. [PMID: 31588404 PMCID: PMC6776735 DOI: 10.1007/s13205-019-1916-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/24/2019] [Indexed: 12/19/2022] Open
Abstract
In the present work, we studied the antibiotic-induced persister formation in Vibrio cholerae. Persisters vary with the bacterial growth phase with minimum persisters in log phase and maximum in stationary phase. Only 10% of the stationary phase cells of V. cholerae were tolerant of ampicillin and ciprofloxacin. In comparison, more than 90% of the stationary phase cells of E. coli were tolerant of ampicillin and ciprofloxacin. Frequency of ciprofloxacin-induced persisters of V. cholerae would vary with the bacteriological media used for the growth of the cells. In tryptone soy broth (TSB) and in buffered peptone water (BPW), V. cholerae could form more than 10% persisters, whereas in Luria-Bertani broth (LB) and alkaline peptone water (APW) persister fraction was less than 1%. When exposed to protein synthesis inhibitors (kanamycin, chloramphenicol, tetracycline, erythromycin and gentamicin), V. cholerae did not form persisters. Persister recovery assay, LIVE/DEAD analysis and QRDR sequence analysis showed that persister population neither included resistant mutants nor VBNC population. Starvation, anaerobic conditions and inhibition of ATP synthesis also induced persisters, but not when protein synthesis is inhibited. These observations suggest that the protein synthesis is critical for persister formation, persister maintenance, and also for dormancy maintenance in V. cholerae. Contrary to these observations, E. coli can form persisters when protein synthesis is inhibited, suggesting fundamental mechanistic differences between the two species.
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Affiliation(s)
- Shridhar S. Paranjape
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
- Department of Life Sciences, Homi Bhabha National Institute (Deemed to be University), Mumbai, 400094 India
| | - Ravindranath Shashidhar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
- Department of Life Sciences, Homi Bhabha National Institute (Deemed to be University), Mumbai, 400094 India
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Artyukhova S, Kozlova O, Tolstoguzova T. Developing freeze-dried bioproducts for the Russian military in the Arctic. FOODS AND RAW MATERIALS 2019. [DOI: 10.21603/2308-4057-2019-1-202-209] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The Arctic is currently a strategic region of Russia and it requires military protection. Good nutrition is a prerequisite for successful performance of the servicemen in such extreme conditions. The Russian armed forces do not have a special ration for the Arctic region. The existing rations lack products enriched with biologically ac- tive substances, probiotics, prebiotics, or vitamin and mineral complexes. Subcaloric nutrition, even with short-term physical exertion, in combination with low temperatures deprives the human body of vitamins and minerals. There- fore, the development of freeze-dried bioproducts with functional properties is highly relevant. This article presents the results of a study aimed to develop new freeze-dried milk-based bioproducts for the Russian military in the Arc- tic. For this, we created a microbial consortium of lactic acid bacteria with a wide spectrum of antimicrobial activity. We also used a range of functional ingredients, namely pectin, pine nut meal, a ‘Lactobel’ prebiotic protein-and-car- bohydrate product, rowan puree, and rosehip syrup in the amounts established during the study. The new freeze- dried milk-based bioproducts named ‘Pobeda’, enriched with combiotics and metabiotics, will provide the Russian military with better nutrition in the extreme conditions of the Arctic.
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Garrett EM, Sekulovic O, Wetzel D, Jones JB, Edwards AN, Vargas-Cuebas G, McBride SM, Tamayo R. Phase variation of a signal transduction system controls Clostridioides difficile colony morphology, motility, and virulence. PLoS Biol 2019; 17:e3000379. [PMID: 31658249 PMCID: PMC6837544 DOI: 10.1371/journal.pbio.3000379] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 11/07/2019] [Accepted: 10/15/2019] [Indexed: 12/20/2022] Open
Abstract
Recent work has revealed that Clostridioides difficile, a major cause of nosocomial diarrheal disease, exhibits phenotypic heterogeneity within a clonal population as a result of phase variation. Many C. difficile strains representing multiple ribotypes develop two colony morphotypes, termed rough and smooth, but the biological implications of this phenomenon have not been explored. Here, we examine the molecular basis and physiological relevance of the distinct colony morphotypes produced by this bacterium. We show that C. difficile reversibly differentiates into rough and smooth colony morphologies and that bacteria derived from the isolates display discrete motility behaviors. We identified an atypical phase-variable signal transduction system consisting of a histidine kinase and two response regulators, named herein colony morphology regulators RST (CmrRST), which mediates the switch in colony morphology and motility behaviors. The CmrRST-regulated surface motility is independent of flagella and type IV pili, suggesting a novel mechanism of cell migration in C. difficile. Microscopic analysis of cell and colony structure indicates that CmrRST promotes the formation of elongated bacteria arranged in bundled chains, which may contribute to bacterial migration on surfaces. In a hamster model of acute C. difficile disease, the CmrRST system is required for disease development. Furthermore, we provide evidence that CmrRST phase varies during infection, suggesting that the intestinal environment impacts the proportion of CmrRST-expressing C. difficile. Our findings indicate that C. difficile employs phase variation of the CmrRST signal transduction system to generate phenotypic heterogeneity during infection, with concomitant effects on bacterial physiology and pathogenesis.
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Affiliation(s)
- Elizabeth M. Garrett
- Department of Microbiology and Immunology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ognjen Sekulovic
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Daniela Wetzel
- Department of Microbiology and Immunology, Emory University, Rollins Research Center, Atlanta, Georgia, United States of America
| | - Joshua B. Jones
- Department of Microbiology and Immunology, Emory University, Rollins Research Center, Atlanta, Georgia, United States of America
| | - Adrianne N. Edwards
- Department of Microbiology and Immunology, Emory University, Rollins Research Center, Atlanta, Georgia, United States of America
| | - Germán Vargas-Cuebas
- Department of Microbiology and Immunology, Emory University, Rollins Research Center, Atlanta, Georgia, United States of America
| | - Shonna M. McBride
- Department of Microbiology and Immunology, Emory University, Rollins Research Center, Atlanta, Georgia, United States of America
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
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Orozco-Gómez DI, Sosa-Hernández JE, Gallardo-Navarro ÓA, Santana-Solano J, Santillán M. Bistable behaviour and medium-dependent post-translational regulation of the tryptophanase operon regulatory pathway in Echerichia coli. Sci Rep 2019; 9:5451. [PMID: 30931970 PMCID: PMC6443796 DOI: 10.1038/s41598-019-41856-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/15/2019] [Indexed: 11/28/2022] Open
Abstract
The present work is aimed at studying the dynamic behaviour of the tryptopnanase (tna) operon, which encodes the proteins necessary to uptake and metabolise tryptophan to use it as a carbon source in the absence of glucose. To this end, we designed a micro-bioreactor capable of driving a bacterial culture to a stationary state. This allowed us to explore (at the single cell level) the tna operon steady-state dynamics under multiple culture conditions. Our experimental results suggest that the tna operon is bistable for a specific range of environmental tryptophan and glucose concentrations, and evidence that both reagents play a role on the activation of the enzyme in charge of metabolising tryptophan: tryptophanase (TnaA). Based on our experimental data and the already known regulatory mechanisms, we developed a mathematical model for the tna operon regulatory pathway. Our modelling results reinforce the claim that the tna operon is bistable, and further suggest that the activity of enzyme TnaA is regulated by the environmental levels of glucose and tryptophan via a common signalling pathway. Possible biological implications of our findings are further discussed.
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Affiliation(s)
- David I Orozco-Gómez
- Centro de Investigación y de Estudios Avanzados del IPN, Unidad Monterrey, Vía del Conocimiento 201, Parque PIIT, 66600, Apodaca, NL, Mexico
| | - Juan Eduardo Sosa-Hernández
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, 64849, Monterrey, NL, Mexico
| | - Óscar Adrián Gallardo-Navarro
- Centro de Investigación y de Estudios Avanzados del IPN, Unidad Monterrey, Vía del Conocimiento 201, Parque PIIT, 66600, Apodaca, NL, Mexico
| | - Jesús Santana-Solano
- Centro de Investigación y de Estudios Avanzados del IPN, Unidad Monterrey, Vía del Conocimiento 201, Parque PIIT, 66600, Apodaca, NL, Mexico
| | - Moisés Santillán
- Centro de Investigación y de Estudios Avanzados del IPN, Unidad Monterrey, Vía del Conocimiento 201, Parque PIIT, 66600, Apodaca, NL, Mexico.
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Huang S, Huang X, Dai S, Wang X, Wang G. Single-cell Raman spectroscopy reveals microsporidia spore heterogeneity in various insect hosts. APPLIED OPTICS 2018; 57:9189-9194. [PMID: 30461909 DOI: 10.1364/ao.57.009189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/02/2018] [Indexed: 06/09/2023]
Abstract
Single-cell Raman spectroscopy was used to analyze the spore heterogeneity of 16 microsporidia strains from various insect hosts in order to better understand the basic biology of microsporidia. The Raman spectrum of a single spore revealed basic spore composition, and microsporidia spores in various hosts were found to be rich in trehalose. Principal component analysis and Raman intensity showed obvious heterogeneity in the trehalose, nucleic acid, and protein content of various spores; however, there was no correlation between various spore groups and host type. Trehalose content correlated with spore infectivity on Bombyx mori. Raman spectroscopy is an excellent tool for label-free investigation of intercellular molecular constituents, providing insight into the heterogeneity of microsporidia spores.
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Berthelot H, Duhamel S, L'Helguen S, Maguer JF, Wang S, Cetinić I, Cassar N. NanoSIMS single cell analyses reveal the contrasting nitrogen sources for small phytoplankton. ISME JOURNAL 2018; 13:651-662. [PMID: 30323264 DOI: 10.1038/s41396-018-0285-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 07/09/2018] [Accepted: 09/08/2018] [Indexed: 12/16/2022]
Abstract
Nitrogen (N) is a limiting nutrient in vast regions of the world's oceans, yet the sources of N available to various phytoplankton groups remain poorly understood. In this study, we investigated inorganic carbon (C) fixation rates and nitrate (NO3-), ammonium (NH4+) and urea uptake rates at the single cell level in photosynthetic pico-eukaryotes (PPE) and the cyanobacteria Prochlorococcus and Synechococcus. To that end, we used dual 15N and 13C-labeled incubation assays coupled to flow cytometry cell sorting and nanoSIMS analysis on samples collected in the North Pacific Subtropical Gyre (NPSG) and in the California Current System (CCS). Based on these analyses, we found that photosynthetic growth rates (based on C fixation) of PPE were higher in the CCS than in the NSPG, while the opposite was observed for Prochlorococcus. Reduced forms of N (NH4+ and urea) accounted for the majority of N acquisition for all the groups studied. NO3- represented a reduced fraction of total N uptake in all groups but was higher in PPE (17.4 ± 11.2% on average) than in Prochlorococcus and Synechococcus (4.5 ± 6.5 and 2.9 ± 2.1% on average, respectively). This may in part explain the contrasting biogeography of these picoplankton groups. Moreover, single cell analyses reveal that cell-to-cell heterogeneity within picoplankton groups was significantly greater for NO3- uptake than for C fixation and NH4+ uptake. We hypothesize that cellular heterogeneity in NO3- uptake within groups facilitates adaptation to the fluctuating availability of NO3- in the environment.
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Affiliation(s)
- Hugo Berthelot
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR 6539 UBO/CNRS/IRD/IFREMER, Institut Universitaire Européen de la Mer (IUEM), Brest, France.
| | - Solange Duhamel
- Division of Biology and Paleo Environment, Lamont-Doherty Earth Observatory, PO Box 1000, 61 Route 9W, Palisades, NY, 10964, USA
| | - Stéphane L'Helguen
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR 6539 UBO/CNRS/IRD/IFREMER, Institut Universitaire Européen de la Mer (IUEM), Brest, France
| | - Jean-Francois Maguer
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR 6539 UBO/CNRS/IRD/IFREMER, Institut Universitaire Européen de la Mer (IUEM), Brest, France
| | - Seaver Wang
- Division of Earth and Ocean Sciences, Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
| | - Ivona Cetinić
- NASA Goddard Space Flight Center, Ocean Ecology Laboratory, Code 616, Greenbelt, MD, USA.,GESTAR/Universities Space Research Association, Columbia, MD, USA
| | - Nicolas Cassar
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR 6539 UBO/CNRS/IRD/IFREMER, Institut Universitaire Européen de la Mer (IUEM), Brest, France. .,Division of Earth and Ocean Sciences, Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA.
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21
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Kang CW, Lim HG, Yang J, Noh MH, Seo SW, Jung GY. Synthetic auxotrophs for stable and tunable maintenance of plasmid copy number. Metab Eng 2018; 48:121-128. [PMID: 29864582 DOI: 10.1016/j.ymben.2018.05.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 05/28/2018] [Accepted: 05/31/2018] [Indexed: 12/20/2022]
Abstract
Although plasmid-based expression systems have advantages in multi-copy expression of genes, heterogeneity of plasmid copy number (PCN) in individual cells is inevitable even with the addition of antibiotics. Here, we developed a synthetic auxotrophic system for stable and tunable maintenance of the PCN in Escherichia coli without addition of antibiotics. This auxotroph expresses infA, one of the essential genes encoding a translation initiation factor, on a plasmid instead of on the chromosome. With this system, the gene expression was stably maintained for 40 generations with minimized cell-to-cell variation under antibiotic-free conditions. Moreover, varying the expression level of infA enabled us to rationally tune the PCN by more than 5.6-fold. This antibiotic-free PCN control system significantly improved the production of itaconic acid and lycopene compared to the conventional system based on antibiotics (2-fold). Collectively, the developed strategy could be a platform for the production of value-added products in antibiotic-free cultivation.
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Affiliation(s)
- Chae Won Kang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jina Yang
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul 08826, Republic of Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1 Gwanak-Ro, Gwanak-Gu, Seoul 08826, Republic of Korea.
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea.
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22
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Denisova TP, Simonova EV, Kokorina LA, Maximova EN, Samatov OM, Safronov AP, Kurlyandskaya GV. Heterogeneity of population of microorganisms grown in presence of iron oxide maghemite nanoparticles. EPJ WEB OF CONFERENCES 2018. [DOI: 10.1051/epjconf/201818510002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work γ-Fe2O3 MNPs were obtained by laser target evaporation and water based suspensions were prepared. Maximum permissive dose of iron in water (MPD) is 0.3 mg/L. It was found that 100 MPD dose of iron induces formation of non-typical colonies after 72 or 96 hours exposition: against a background of small black colonies large white colonies appeared due to a disruption in tyrosine synthesis. Multiple re-cloning of the white colonies grown with MNPs showed that they retained their properties both under standard conditions (temperature of 24 °C) and at the temperatures up to 37o C. E.nigrum grown with MNPs demonstrated very scant extension of small colonies at the cultivation temperature of 24o C, their growth was completely blocked at 37°C. Significant changes in the structure of the population were noted. First of all, large cells with pronounced aggregation were observed among the black colonies. These aggregates consisted of large cells connected to each other by matrix. In the white colonies the appearance of very long threadlike cells connecting different groups of the cells establishing an intercellular communication was evident. Fe2O3 MNPs induce an increase in the heterogeneity of the population, expressed as a change in morpho-physiological states.
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Rubin IN, Doebeli M. Rethinking the evolution of specialization: A model for the evolution of phenotypic heterogeneity. J Theor Biol 2017; 435:248-264. [PMID: 28943404 DOI: 10.1016/j.jtbi.2017.09.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 09/11/2017] [Accepted: 09/19/2017] [Indexed: 10/18/2022]
Abstract
Phenotypic heterogeneity refers to genetically identical individuals that express different phenotypes, even when in the same environment. Traditionally, "bet-hedging" in fluctuating environments is offered as the explanation for the evolution of phenotypic heterogeneity. However, there are an increasing number of examples of microbial populations that display phenotypic heterogeneity in stable environments. Here we present an evolutionary model of phenotypic heterogeneity of microbial metabolism and a resultant theory for the evolution of phenotypic versus genetic specialization. We use two-dimensional adaptive dynamics to track the evolution of the population phenotype distribution of the expression of two metabolic processes with a concave trade-off. Rather than assume a Gaussian phenotype distribution, we use a Beta distribution that is capable of describing genotypes that manifest as individuals with two distinct phenotypes. Doing so, we find that environmental variation is not a necessary condition for the evolution of phenotypic heterogeneity, which can evolve as a form of specialization in a stable environment. There are two competing pressures driving the evolution of specialization: directional selection toward the evolution of phenotypic heterogeneity and disruptive selection toward genetically determined specialists. Because of the lack of a singular point in the two-dimensional adaptive dynamics and the fact that directional selection is a first order process, while disruptive selection is of second order, the evolution of phenotypic heterogeneity dominates and often precludes speciation. We find that branching, and therefore genetic specialization, occurs mainly under two conditions: the presence of a cost to maintaining a high phenotypic variance or when the effect of mutations is large. A cost to high phenotypic variance dampens the strength of selection toward phenotypic heterogeneity and, when sufficiently large, introduces a singular point into the evolutionary dynamics, effectively guaranteeing eventual branching. Large mutations allow the second order disruptive selection to dominate the first order selection toward phenotypic heterogeneity.
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Affiliation(s)
- Ilan N Rubin
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada.
| | - Michael Doebeli
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada; Department of Mathematics, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada.
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24
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Ryzhkova EP. Alternative enzymes as a special strategy for the adaptation of procaryotic organisms (Review). APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s0003683817050131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Loiko NG, Lobanov KV, Nikolaev YA, Kozlova AN, El’-Registan GI. Regulation of phase variation in type I pili formation in Escherichia coli: Role of alkylresorcinols, microbial autoregulators. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717050149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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Abda EM, Krysciak D, Krohn-Molt I, Mamat U, Schmeisser C, Förstner KU, Schaible UE, Kohl TA, Nieman S, Streit WR. Phenotypic Heterogeneity Affects Stenotrophomonas maltophilia K279a Colony Morphotypes and β-Lactamase Expression. Front Microbiol 2015; 6:1373. [PMID: 26696982 PMCID: PMC4667094 DOI: 10.3389/fmicb.2015.01373] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/18/2015] [Indexed: 12/22/2022] Open
Abstract
Phenotypic heterogeneity at the cellular level in response to various stresses, e.g., antibiotic treatment has been reported for a number of bacteria. In a clonal population, cell-to-cell variation may result in phenotypic heterogeneity that is a mechanism to survive changing environments including antibiotic therapy. Stenotrophomonas maltophilia has been frequently isolated from cystic fibrosis patients, can cause numerous infections in other organs and tissues, and is difficult to treat due to antibiotic resistances. S. maltophilia K279a produces the L1 and L2 β-lactamases in response to β-lactam treatment. Here we report that the patient isolate S. maltophilia K279a diverges into cellular subpopulations with distinct but reversible morphotypes of small and big colonies when challenged with ampicillin. This observation is consistent with the formation of elongated chains of bacteria during exponential growth phase and the occurrence of mainly rod-shaped cells in liquid media. RNA-seq analysis of small versus big colonies revealed differential regulation of at least seven genes among the colony morphotypes. Among those, bla L1 and bla L2 were transcriptionally the most strongly upregulated genes. Promoter fusions of bla L1 and bla L2 genes indicated that expression of both genes is also subject to high levels of phenotypic heterogeneous expression on a single cell level. Additionally, the comE homolog was found to be differentially expressed in homogenously versus heterogeneously bla L2 expressing cells as identified by RNA-seq analysis. Overexpression of comE in S. maltophilia K279a reduced the level of cells that were in a bla L2-ON mode to 1% or lower. Taken together, our data provide strong evidence that S. maltophilia K279a populations develop phenotypic heterogeneity in an ampicillin challenged model. This cellular variability is triggered by regulation networks including bla L1, bla L2, and comE.
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Affiliation(s)
- Ebrahim M Abda
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek - University of Hamburg Hamburg, Germany
| | - Dagmar Krysciak
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek - University of Hamburg Hamburg, Germany
| | - Ines Krohn-Molt
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek - University of Hamburg Hamburg, Germany
| | - Uwe Mamat
- Priority Program Asthma and Allergy, Leibniz-Center for Medicine and Biosciences - Research Center Borstel Borstel, Germany
| | - Christel Schmeisser
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek - University of Hamburg Hamburg, Germany
| | - Konrad U Förstner
- Core Unit Systems Medicine, University of Würzburg Würzburg, Germany
| | - Ulrich E Schaible
- Priority Program Infections, Leibniz-Center for Medicine and Biosciences - Research Center Borstel Borstel, Germany
| | - Thomas A Kohl
- Priority Program Infections, Leibniz-Center for Medicine and Biosciences - Research Center Borstel Borstel, Germany
| | - Stefan Nieman
- Priority Program Infections, Leibniz-Center for Medicine and Biosciences - Research Center Borstel Borstel, Germany ; German Center for Infection Research Borstel, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek - University of Hamburg Hamburg, Germany
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Kryazhevskikh NA, Loiko NG, Demkina EV, Mulyukin AL, Lebedev AT, Gaponov AM, Tutel’yan AV, Nikolaev YA, El’-Registan GI. Applicability of MALDI mass spectrometry for diagnostics of phase variants in bacterial populations. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715030121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Ivanov V, Rezaeinejad S, Stabnikova O. Physiological comparison of cells with high and low alcohol dehydrogenase activities in bacterial populations consuming ethanol. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-014-0945-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Milko ES, Milko DM. The process of bacterial population splitting into dissociants and long-term batch cultivation of bacteria. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683814040097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Loiko NG, Krasnova MA, Pichugina TV, Grinevich AI, Ganina VI, Kozlova AN, Nikolaev YA, Gal’chenko VF, El’-Registan GI. Changes in the phase variant spectra in the populations of lactic acid bacteria under antibiotic treatment. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714030114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Erickson M, Habteselassie M, Liao J, Webb C, Mantripragada V, Davey L, Doyle M. Examination of factors for use as potential predictors of human enteric pathogen survival in soil. J Appl Microbiol 2013; 116:335-49. [DOI: 10.1111/jam.12373] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 10/04/2013] [Accepted: 10/21/2013] [Indexed: 11/29/2022]
Affiliation(s)
- M.C. Erickson
- Department of Food Science and Technology; Center for Food Safety; Griffin GA USA
| | - M.Y. Habteselassie
- Department of Food Science and Technology; Center for Food Safety; Griffin GA USA
- Department of Crops and Soil Science; University of Georgia; Griffin GA USA
| | - J. Liao
- Department of Food Science and Technology; Center for Food Safety; Griffin GA USA
| | - C.C. Webb
- Department of Food Science and Technology; Center for Food Safety; Griffin GA USA
| | - V. Mantripragada
- Department of Crops and Soil Science; University of Georgia; Griffin GA USA
| | - L.E. Davey
- Department of Food Science and Technology; Center for Food Safety; Griffin GA USA
| | - M.P. Doyle
- Department of Food Science and Technology; Center for Food Safety; Griffin GA USA
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