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Tenea GN, Molina D. Bacterial community structure of Physalis peruviana L. fruit exocarp and the presence of pathogens with possible implications on food safety. FRONTIERS IN PLANT SCIENCE 2024; 15:1410314. [PMID: 39091311 PMCID: PMC11291218 DOI: 10.3389/fpls.2024.1410314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 07/04/2024] [Indexed: 08/04/2024]
Abstract
Introduction Cape gooseberry (Physalis peruviana L.) is a wellconsumed crop in Ecuador, whose fruits are abundant in bioactive molecules. Its rapid post-harvest deterioration and safety limit its market potential. Methodology To gather baseline data on the prevalence of bacterial taxa among groups, we employed 16S ribosomal RNA (16S rRNA) amplicon gene sequencing to detect changes in the bacterial community structure in cape gooseberry fruits harvested from an organic farm production system (# 270 samples x two ripeness stages), and fruits obtained from an open-air market (#270). Results This is the first report of bacterial taxa inhabiting cape gooseberry fruits. Shannon's diversity index revealed that the fruits purchased from the market and the unripe stage had the highest level of bacterial diversity (average Shannon indices of 3.3 and 3.1) followed by those collected from the field at the mature ripe stage (2.07). Alpha diversity analysis indicated that there were no significant differences in the number of taxa or evenness within the sample, whereas there was a significant difference in beta diversity between the groups. Rhizobiaceae was the most abundant family in fruits originating from the field regardless of the ripe stage, while Acetobacteraceae, Pseudomonadaceae, Fusobacteriaceae, Bacteroidaceae, and Erwiniaceae were the most abundant families in the market group. At the genus level, Liberibacter was the most abundant phytopathogen in fruits originating from the field, while Gluconobacter was the most abundant in samples collected from the market. The phytopathogen Candidatus_Liberibacter was the most abundant in samples collected from the field, while the fruits purchased from the market stands contained opportunistic enteric pathogens such as Escherichia vulneris, Klebsiella pneumoniae, and K. variicola, their relative abundance varied with the sample. In addition, potential pathogens of animal origin such as Fusobacterium necrophorum, Porphyromonas levii, Helcococcus ovis, and Trueperella pyogenes were found in almost all samples at varying relative abundance. Conclusion Our study provides basic information on the microbiome of cape gooseberries from agriculture fields to the table along with the detection of several pathogenic microorganisms with possible impact on food safety and public health therefore, strategies for reducing bacterial contamination in both farm and retail markets are compulsory.
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Affiliation(s)
- Gabriela N. Tenea
- Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Universidad Técnica del Norte, Ibarra, Ecuador
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Sombolestani AS, Bongaerts D, Depoorter E, Cleenwerck I, Wieme AD, Britton SJ, Weckx S, De Vuyst L, Vandamme P. Brytella acorum gen. nov., sp. nov., a novel acetic acid bacterium from sour beverages. Syst Appl Microbiol 2023; 46:126440. [PMID: 37429096 DOI: 10.1016/j.syapm.2023.126440] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/12/2023]
Abstract
Polyphasic taxonomic and comparative genomic analyses revealed that a series of lambic beer isolates including strain LMG 32668T and the kombucha isolate LMG 32879 represent a novel species among the acetic acid bacteria, with Acidomonas methanolica as the nearest phylogenomic neighbor with a valid name. Overall genomic relatedness indices and phylogenomic and physiological analyses revealed that this novel species was best classified in a novel genus for which we propose the name Brytella acorum gen. nov., sp. nov., with LMG 32668T (=CECT 30723T) as the type strain. The B. acorum genomes encode a complete but modified tricarboxylic acid cycle, and complete pentose phosphate, pyruvate oxidation and gluconeogenesis pathways. The absence of 6-phosphofructokinase which rendered the glycolysis pathway non-functional, and an energy metabolism that included both aerobic respiration and oxidative fermentation are typical metabolic characteristics of acetic acid bacteria. Neither genome encodes nitrogen fixation or nitrate reduction genes, but both genomes encode genes for the biosynthesis of a broad range of amino acids. Antibiotic resistance genes or virulence factors are absent.
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Affiliation(s)
- Atena Sadat Sombolestani
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Dries Bongaerts
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Eliza Depoorter
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Anneleen D Wieme
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Scott J Britton
- Department of Research & Development, Brewery Duvel Moortgat, 2870 Puurs-Sint-Amands, Belgium; International Centre for Brewing and Distilling, Institute of Biological Chemistry, Biophysics, and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Riccarton, Edinburgh EH14 4AS, United Kingdom
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium; BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium.
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Botero J, Sombolestani AS, Cnockaert M, Peeters C, Borremans W, De Vuyst L, Vereecken NJ, Michez D, Smagghe G, Bonilla-Rosso G, Engel P, Vandamme P. A phylogenomic and comparative genomic analysis of Commensalibacter, a versatile insect symbiont. Anim Microbiome 2023; 5:25. [PMID: 37120592 PMCID: PMC10149009 DOI: 10.1186/s42523-023-00248-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/21/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND To understand mechanisms of adaptation and plasticity of pollinators and other insects a better understanding of diversity and function of their key symbionts is required. Commensalibacter is a genus of acetic acid bacterial symbionts in the gut of honey bees and other insect species, yet little information is available on the diversity and function of Commensalibacter bacteria. In the present study, whole-genome sequences of 12 Commensalibacter isolates from bumble bees, butterflies, Asian hornets and rowan berries were determined, and publicly available genome assemblies of 14 Commensalibacter strains were used in a phylogenomic and comparative genomic analysis. RESULTS The phylogenomic analysis revealed that the 26 Commensalibacter isolates represented four species, i.e. Commensalibacter intestini and three novel species for which we propose the names Commensalibacter melissae sp. nov., Commensalibacter communis sp. nov. and Commensalibacter papalotli sp. nov. Comparative genomic analysis revealed that the four Commensalibacter species had similar genetic pathways for central metabolism characterized by a complete tricarboxylic acid cycle and pentose phosphate pathway, but their genomes differed in size, G + C content, amino acid metabolism and carbohydrate-utilizing enzymes. The reduced genome size, the large number of species-specific gene clusters, and the small number of gene clusters shared between C. melissae and other Commensalibacter species suggested a unique evolutionary process in C. melissae, the Western honey bee symbiont. CONCLUSION The genus Commensalibacter is a widely distributed insect symbiont that consists of multiple species, each contributing in a species specific manner to the physiology of the holobiont host.
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Affiliation(s)
- Juliana Botero
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Atena Sadat Sombolestani
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Wim Borremans
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Bioengineering Sciences, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Nicolas J Vereecken
- Agroecology Lab, Université libre de Bruxelles, Boulevard du Triomphe CP 264/02, 1050, Brussels, Belgium
| | - Denis Michez
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Place du parc 20, 7000, Mons, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - German Bonilla-Rosso
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000, Ghent, Belgium.
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