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Leonardo IC, Barreto Crespo MT, Gaspar FB. Unveiling the complete genome sequence of Alicyclobacillus acidoterrestris DSM 3922T, a taint-producing strain. G3 (BETHESDA, MD.) 2022; 12:jkac225. [PMID: 36240455 PMCID: PMC9713406 DOI: 10.1093/g3journal/jkac225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/26/2022] [Indexed: 09/10/2024]
Abstract
Several species from the Alicyclobacillus genus have received much attention from the food and beverages industries. Their presence has been co-related with spoilage events of acidic food matrices, namely fruit juices and other fruit-based products, the majority attributed to Alicyclobacillus acidoterrestris. In this work, a combination of short and long reads enabled the assembly of the complete genome of A. acidoterrestris DSM 3922T, perfecting the draft genome already available (AURB00000000), and revealing the presence of one chromosome (4,222,202 bp; GC content 52.3%) as well as one plasmid (124,737 bp; GC content 46.6%). From the 4,288 genes identified, 4,004 sequences were attributed to coding sequences with proteins, with more than 80% being functionally annotated. This allowed the identification of metabolic pathways and networks and the interpretation of high-level functions with significant reliability. Furthermore, the additional genes of interest related to spore germination, off-flavor production, namely the vdc cluster, and CRISPR arrays, were identified. More importantly, this is the first complete and closed genome sequence for a taint-producing Alicyclobacillus species and thus represents a valuable reference for further comparative and functional genomic studies.
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Affiliation(s)
- Inês Carvalho Leonardo
- Food & Health Division, iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Maria Teresa Barreto Crespo
- Food & Health Division, iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Frédéric Bustos Gaspar
- Food & Health Division, iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
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Dekowska A, Niezgoda J, Sokołowska B. Genetic Heterogeneity of Alicyclobacillus Strains Revealed by RFLP Analysis of vdc Region and rpoB Gene. BIOMED RESEARCH INTERNATIONAL 2018; 2018:9608756. [PMID: 30515419 PMCID: PMC6236696 DOI: 10.1155/2018/9608756] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/27/2018] [Indexed: 11/23/2022]
Abstract
PCR-RFLP targeting of the 16S rDNA and rpoB genes, as well as the vdc region, was applied to identify and differentiate between the spoilage and non-spoilage Alicyclobacillus species. Eight reference strains and 75 strains isolated from spoiled juices, juice concentrates, drinks, its intermediates, and fresh apples were subject to study. Hin6I restriction patterns of the 16S rDNA gene enabled distinguishing between all the species analyzed, while the rpoB gene and vdc gene cluster analysis also revealed that there were two major types among the A. acidoterrestris isolates, one similar to the reference strain A. acidoterrestris DSM 2498, and the other similar to the reference strain A. acidoterrestris ATCC 49025. Heterogeneity was also observed among the A. acidocaldarius isolates. RFLP analysis of the 16S rDNA and rpoB genes, as well as vdc region, can be used successfully in the identification and research of intraspecies heterogeneity of the Alicyclobacillus species.
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Affiliation(s)
- Agnieszka Dekowska
- Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology, 36 Rakowiecka Street, 02-532 Warsaw, Poland
| | - Jolanta Niezgoda
- Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology, 36 Rakowiecka Street, 02-532 Warsaw, Poland
| | - Barbara Sokołowska
- Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology, 36 Rakowiecka Street, 02-532 Warsaw, Poland
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Adey A, Kitzman JO, Burton JN, Daza R, Kumar A, Christiansen L, Ronaghi M, Amini S, Gunderson KL, Steemers FJ, Shendure J. In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Res 2014; 24:2041-9. [PMID: 25327137 PMCID: PMC4248320 DOI: 10.1101/gr.178319.114] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We describe a method that exploits contiguity preserving transposase sequencing (CPT-seq) to facilitate the scaffolding of de novo genome assemblies. CPT-seq is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to >1 megabase. These pools are “subhaploid,” in that the lengths of fragments contained in each pool sums to ∼5% to 10% of the full genome. The scaffolding approach described here, termed fragScaff, leverages coincidences between the content of different pools as a source of contiguity information. Specifically, CPT-seq data is mapped to a de novo genome assembly, followed by the identification of pairs of contigs or scaffolds whose ends disproportionately co-occur in the same indexed pools, consistent with true adjacency in the genome. Such candidate “joins” are used to construct a graph, which is then resolved by a minimum spanning tree. As a proof-of-concept, we apply CPT-seq and fragScaff to substantially boost the contiguity of de novo assemblies of the human, mouse, and fly genomes, increasing the scaffold N50 of de novo assemblies by eight- to 57-fold with high accuracy. We also demonstrate that fragScaff is complementary to Hi-C-based contact probability maps, providing midrange contiguity to support robust, accurate chromosome-scale de novo genome assemblies without the need for laborious in vivo cloning steps. Finally, we demonstrate CPT-seq as a means of anchoring unplaced novel human contigs to the reference genome as well as for detecting misassembled sequences.
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Affiliation(s)
- Andrew Adey
- Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA
| | - Jacob O Kitzman
- Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA
| | - Joshua N Burton
- Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA
| | - Riza Daza
- Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA
| | - Akash Kumar
- Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA
| | - Lena Christiansen
- Illumina, Inc., Advanced Research Group, San Diego, California 92122, USA
| | - Mostafa Ronaghi
- Illumina, Inc., Advanced Research Group, San Diego, California 92122, USA
| | - Sasan Amini
- Illumina, Inc., Advanced Research Group, San Diego, California 92122, USA
| | - Kevin L Gunderson
- Illumina, Inc., Advanced Research Group, San Diego, California 92122, USA
| | - Frank J Steemers
- Illumina, Inc., Advanced Research Group, San Diego, California 92122, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA;
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Shemesh M, Pasvolsky R, Zakin V. External pH is a cue for the behavioral switch that determines surface motility and biofilm formation of Alicyclobacillus acidoterrestris. J Food Prot 2014; 77:1418-23. [PMID: 25198607 DOI: 10.4315/0362-028x.jfp-13-425] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacteria use different strategies to survive unfavorable environmental conditions. Alicyclobacillus acidoterrestris is a bacterium capable of surviving extremely harsh conditions, for instance, during industrial food processing. A. acidoterrestris is a spore-forming, thermoacidophilic, nonpathogenic bacterium that commonly contaminates commercial pasteurized fruit juices and is, therefore, considered a major microbiological contaminant in the juice industry. The purpose of this study was to elucidate whether A. acidoterrestris is capable of multicellular behavior by testing its ability of biofilm formation and surface motility. A. acidoterrestris was found to be proficient in migration over a surface that is apparently powered by flagella. It was further shown that lowering the external pH leads to inhibition in surface motility of these bacteria. Concomitantly, the reduction in the external pH triggered biofilm formation of A. acidoterrestris cells. Thus, although no significant biofilm was formed at pH 4.5, robust cell adhesion and confluent biofilm formation was seen below the pH 3.6. These findings indicate that the reduction of external pH is an environmental cue for the behavioral switch that inhibits surface motility and triggers biofilm formation of A. acidoterrestris. Gaining insight into the multicellular behavior that facilitates A. acidoterrestris survival in food contact surfaces may contribute to the development of novel antimicrobial means to prevent cross-contamination caused by this bacterium.
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Affiliation(s)
- Moshe Shemesh
- Department of Food Quality and Safety, Institute for Postharvest Technology and Food Sciences, Agricultural Research Organization (ARO), The Volcani Center, P.O. Box 6, Bet-Dagan 50250, Israel.
| | - Ronit Pasvolsky
- Department of Food Quality and Safety, Institute for Postharvest Technology and Food Sciences, Agricultural Research Organization (ARO), The Volcani Center, P.O. Box 6, Bet-Dagan 50250, Israel, Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Varda Zakin
- Department of Food Quality and Safety, Institute for Postharvest Technology and Food Sciences, Agricultural Research Organization (ARO), The Volcani Center, P.O. Box 6, Bet-Dagan 50250, Israel
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Draft genome sequences for oil-degrading bacterial strains from beach sands impacted by the deepwater horizon oil spill. GENOME ANNOUNCEMENTS 2013; 1:1/6/e01015-13. [PMID: 24356826 PMCID: PMC3868850 DOI: 10.1128/genomea.01015-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the draft genome sequences of 10 proteobacterial strains isolated from beach sands contaminated with crude oil discharged from the Deepwater Horizon spill, which were cultivated under aerobic and anaerobic conditions with crude oil as the sole carbon source. All strains contain multiple putative genes belonging to hydrocarbon degradation pathways.
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