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Lick S, Wibberg D, Busche T, Blom J, Grimmler C, Goesmann A, Kalinowski J. Pseudomonas kulmbachensis sp. nov. and Pseudomonas paraveronii sp. nov., originating from chilled beef and chicken breast. Int J Syst Evol Microbiol 2024; 74. [PMID: 38587505 DOI: 10.1099/ijsem.0.006293] [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] [Indexed: 04/09/2024] Open
Abstract
By investigating wet and dry age-related ripening of beef, Pseudomonas strains V3/3/4/13T and V3/K/3/5T were isolated. Strain V3/3/4/13T exhibited more than 99 % 16S rRNA gene-based similarity to Pseudomonas fragi and other members of this group, while isolate V3/K/3/5T was very close to Pseudomonas veronii and a number of relatives within the Pseudomonas fluorescens group. Additional comparisons of complete rpoB sequences and draft genomes allowed us to place isolate V3/3/4/13T close to Pseudomonas deceptionensis DSM 26521T. In the case of V3/K/3/5T the closest relative was P. veronii DSM 11331T. Average nucleotide identity (ANIb) and digital DNA-DNA hybridization (dDDH) values calculated from the draft genomes of V3/3/4/13T and P. deceptionensis DSM 26521T were 88.5 and 39.8 %, respectively. For V3/K/3/5T and its closest relative P. veronii DSM 11331T, the ANIb value was 95.1 % and the dDDH value was 60.7 %. The DNA G+C contents of V3/3/4/13T and V3/K/3/5T were 57.4 and 60.8 mol%, respectively. Predominant fatty acids were C16 : 0, C18 : 1 ω7c, C17 : 0 cyclo and summed feature C16 : 1 ω7ct/C15 : 0 iso 2OH. The main respiratory quinones were Q9, with minor proportions of Q8 and, in the case of V3/K/3/5T, additional Q10. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and, in the case of V3/K/3/5T, additional phosphatidylcholine. Based on the combined data, isolates V3/3/4/13T and V3/K/3/5T should be considered as representatives of two novel Pseudomonas species. The type strain of the newly proposed Pseudomonas kulmbachensis sp. nov. is V3/3/4/13T (=DSM 113654T=LMG 32520T), a second strain belonging to the same species is FLM 004-28 (=DSM 113604=LMG 32521); the type strain for the newly proposed Pseudomonas paraveronii sp. nov. is V3/K/3/5T (=DSM 113573T=LMG 32518T) with a second isolate FLM 11 (=DSM 113572=LMG 32519).
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Affiliation(s)
- Sonja Lick
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Safety and Quality of Meat, E.-C.-Baumann Straße 20, D-95326 Kulmbach, Germany
| | - Daniel Wibberg
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
- ELIXIR DE Administration Office, Institute of Bio- and Geosciences IBG-5, Forschungszentrum Jülich GmbH - Branch office Bielefeld, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
- Medical School East Westphalia-Lippe, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Ludwigsstraße 23, D-35392 Gießen, Germany
| | - Christina Grimmler
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Safety and Quality of Meat, E.-C.-Baumann Straße 20, D-95326 Kulmbach, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Ludwigsstraße 23, D-35392 Gießen, Germany
| | - Jörn Kalinowski
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
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Okolo EA, de Alencar ER, Machado SG, Faroni LRD, Silva MVDA, Costa NADS, Falqueto A. Ozonation for Pseudomonas paracarnis control: biofilm removal and preservation of chicken meat during refrigerated storage. Braz J Microbiol 2023; 54:3051-3060. [PMID: 37910305 PMCID: PMC10689663 DOI: 10.1007/s42770-023-01157-1] [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: 02/16/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023] Open
Abstract
Ozone has been studied to control microorganisms in food, as well as to control biofilm. In this context, the goals of this work were to determine the effect of ozonated water in the removal of Pseudomonas paracarnis biofilm and the effect of ozone gas and ozonated water on inactivating P. paracarnis in deboned chicken breast meat and its effect on product color. AISI 304 coupons were used as a surface for biofilm formation. The coupons were immerged into minimal medium for Pseudomonas inoculated with the P. paracarnis overnight culture (1% w/v) followed by incubation at 25 °C for 7 days. To obtain ozonized water, two different systems were used: system with microbubble generator (MB) and system with porous stone diffuser (PSD). The inlet ozone concentration was 19 mg/L and flow rate of 1 L/min. The coupons were subjected to ozonized water for 10 and 20 min. The chicken breast meat was exposed to gaseous ozone and ozonized water for 40 min. After the ozonation process, chicken meat samples were stored at 8 °C, for 5 days. More expressive removals of biofilm were obtained when using ozonized water obtained in the system with microbubble generator (MB for 20 min-reduction of 2.3 log cycles) and system with porous stone diffuser (PSD for 10 min-reduction of 2.7 log cycles; PSD for 20 min-reduction of 2.6 log cycles). The treatment of chicken meat with ozone gas resulted in lower counting of Pseudomonas, when compared with the control treatments and with ozonized water, both immediately after ozonation (day 1) and after 5 days of storage. The luminosity in the chicken meat samples treated with ozonized water was higher than that verified in the control treatments and with ozone gas, immediately after ozonation (day 1). A similar trend was observed in hue angle and color difference, in which the highest values were obtained for treatment with ozonized water. Based on the results obtained in this study, it was concluded that ozonated water can be used to remove P. paracarnis biofilm from stainless steel under static conditions and gaseous ozone is more efficient in the inactivation of P. paracarnis from chicken breast meat, when compared to ozonated water.
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Affiliation(s)
- Ejima Akogwu Okolo
- Department of Agricultural Engineering, Universidade Federal de Viçosa, Viçosa, MG, 36570900, Brazil
- Agricultural and Bio-Environmental Engineering Department, Federal Polytechnic Nekede, Imo State, P.M.B. 1036, Owerri, Nigeria
| | | | - Solimar Goncalves Machado
- Department of Food Technology, INOVALEITE, Universidade Federal de Viçosa, Viçosa, MG, 36570900, Brazil
| | | | | | | | - Andressa Falqueto
- Department of Food Technology, INOVALEITE, Universidade Federal de Viçosa, Viçosa, MG, 36570900, Brazil
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Rodrigues RDS, Machado SG, de Carvalho AF, Nero LA. Pseudomonas carnis isolated from blue discolored fresh cheese and insights into the phylogeny. World J Microbiol Biotechnol 2023; 40:3. [PMID: 37923846 DOI: 10.1007/s11274-023-03817-8] [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: 04/27/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023]
Abstract
Most Pseudomonas spp. are responsible for spoilage in refrigerated foods such as alteration in flavor, texture and appearance. Samples of Minas Frescal cheese with blue discoloration were analysed and contained a high Pseudomonas concentration (7.72 ± 0.36 log CFU/g). Out of the 26 Pseudomonas isolates that were analyzed in our study, 19 demonstrated the capability of producing a diffusible dark pigment. Thus, a pigment-producing isolate (C020) was selected by rep-PCR fingerprinting and subsequently subjected to whole-genome sequencing. The draft genome assembled comprises 42 contigs totaling 6,366,75 bp with an average G + C content of 59.97%, and the species prediction performed by TYGS server, based on the draft genome sequence, identified the C020 as Pseudomonas carnis. In order to investigate the phylogenetic relationships of this isolate with strains already identified of this species, we performed an analysis based on whole-genomic sequences. First, an analysis of all P. carnis genomes deposited in GenBank to date shows that 11% (4/37) are misidentified, and belong to the Pseudomonas paracarnis species. A comparative analysis based on phylogenomic analysis has showed that there is no evolutionary relationship between P. carnis strains carrying second copies of trp genes related to blue discoloration (trpABCDF). This finding reinforces the assertion that these genes are contained in a mobile genetic element. However, it is worth noting that all strains carrying these secondary gene copies have exclusively been isolated from food sources. This observation provides valuable insights into the potential origins and dispersion dynamics of this genetic trait within the species.
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Affiliation(s)
| | | | | | - Luís Augusto Nero
- InsPOA, Department of Veterinary Medicine, Federal University of Viçosa, Viçosa, MG, Brazil.
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Neumann GB, Korkuć P, Reißmann M, Wolf MJ, May K, König S, Brockmann GA. Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in german black Pied cattle. Vet Res 2023; 54:95. [PMID: 37853447 PMCID: PMC10585868 DOI: 10.1186/s13567-023-01227-0] [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: 03/02/2023] [Accepted: 09/27/2023] [Indexed: 10/20/2023] Open
Abstract
When resequencing animal genomes, some short reads cannot be mapped to the reference genome and are usually discarded. In this study, unmapped reads from 302 German Black Pied cattle were analyzed to identify potential pathogenic DNA. These unmapped reads were assembled and blasted against NCBI's database to identify bacterial and viral sequences. The results provided evidence for the presence of pathogens. We found sequences of Bovine parvovirus 3 and Mycoplasma species. These findings emphasize the information content of unmapped reads for gaining insight into bacterial and viral infections, which is important for veterinarians and epidemiologists.
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Affiliation(s)
- Guilherme B Neumann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Paula Korkuć
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Monika Reißmann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Manuel J Wolf
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Katharina May
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Gudrun A Brockmann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany.
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