1
|
Rasmussen TS, Koefoed AK, Deng L, Muhammed MK, Rousseau GM, Kot W, Sprotte S, Neve H, Franz CMAP, Hansen AK, Vogensen FK, Moineau S, Nielsen DS. CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice. THE ISME JOURNAL 2023; 17:432-442. [PMID: 36631688 PMCID: PMC9938214 DOI: 10.1038/s41396-023-01358-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 12/22/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023]
Abstract
Many bacteria and archaea harbor the adaptive CRISPR-Cas system, which stores small nucleotide fragments from previous invasions of nucleic acids via viruses or plasmids. This molecular archive blocks further invaders carrying identical or similar nucleotide sequences. However, few of these systems have been confirmed experimentally to be active in gut bacteria. Here, we demonstrate experimentally that the type I-C CRISPR-Cas system of the prevalent gut bacterium Eggerthella lenta can specifically target and cleave foreign DNA in vitro by using a plasmid transformation assay. We also show that the CRISPR-Cas system acquires new immunities (spacers) from the genome of a virulent E. lenta phage using traditional phage assays in vitro but also in vivo using gnotobiotic (GB) mice. Both high phage titer and an increased number of spacer acquisition events were observed when E. lenta was exposed to a low multiplicity of infection in vitro, and three phage genes were found to contain protospacer hotspots. Fewer new spacer acquisitions were detected in vivo than in vitro. Longitudinal analysis of phage-bacteria interactions showed sustained coexistence in the gut of GB mice, with phage abundance being approximately one log higher than the bacteria. Our findings show that while the type I-C CRISPR-Cas system is active in vitro and in vivo, a highly virulent phage in vitro was still able to co-exist with its bacterial host in vivo. Taken altogether, our results suggest that the CRISPR-Cas defense system of E. lenta provides only partial immunity in the gut.
Collapse
Affiliation(s)
- Torben Sølbeck Rasmussen
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg, Denmark.
| | - Anna Kirstine Koefoed
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Ling Deng
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Musemma K Muhammed
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Geneviève M Rousseau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de 1enie, Université Laval, Québec, QC, G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Witold Kot
- Section of Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark
| | - Sabrina Sprotte
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103, Kiel, Germany
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103, Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103, Kiel, Germany
| | - Axel Kornerup Hansen
- Section of Experimental Animal Models, Department of Veterinary and Animal Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark
| | - Finn Kvist Vogensen
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de 1enie, Université Laval, Québec, QC, G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC, G1V 0A6, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Dennis Sandris Nielsen
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg, Denmark.
| |
Collapse
|
2
|
Bartula K, Begley M, Latour N, Callanan M. Growth of food-borne pathogens Listeria and Salmonella and spore-forming Paenibacillus and Bacillus in commercial plant-based milk alternatives. Food Microbiol 2023; 109:104143. [DOI: 10.1016/j.fm.2022.104143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/09/2022] [Accepted: 09/10/2022] [Indexed: 11/25/2022]
|
3
|
Draft Genome Sequence of Paenibacillus odorifer V, Isolated from the Fecal Material of a Rabbit. Microbiol Resour Announc 2022; 11:e0040522. [PMID: 35727020 PMCID: PMC9302113 DOI: 10.1128/mra.00405-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the draft genome sequence of Paenibacillus odorifer strain V, which was isolated from the fecal material of a rabbit living in the wild. The genome size is 6,863,583 bp, with 44.35 mol% G+C content.
Collapse
|
4
|
Rush CE, Johnson J, Burroughs S, Riesgaard B, Torres A, Meunier-Goddik L, Waite-Cusic J. Evaluating Paenibacillus odorifer for its potential to reduce shelf life in reworked high-temperature, short-time fluid milk products. JDS COMMUNICATIONS 2022; 3:91-96. [PMID: 36339734 PMCID: PMC9623621 DOI: 10.3168/jdsc.2021-0168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/21/2021] [Indexed: 06/16/2023]
Abstract
Rework is a common practice used in the dairy industry as a strategy to help minimize waste from processing steps or errors that might otherwise render the product unsaleable. Dairy processors may rework their high-temperature, short-time (HTST) fluid milk products up to code date (21 d) at a typical dilution rate of ≤20% rework into ≥80% fresh raw milk. Bacterial spores present in raw milk that can survive pasteurization and grow at refrigeration temperatures are often responsible for milk spoilage. However, the potential impact of growth and thermal resistance of organisms in reworked product has not been investigated. Our objective was to characterize growth, sporulation, and thermal resistance of Paenibacillus odorifer under conditions representative of extreme storage conditions (time and temperature) of reduced fat (2%) and chocolate milk to evaluate whether product containing rework would have a reduced shelf life. Commercial UHT-pasteurized 2% milk and chocolate milk were independently inoculated with 4 strains of P. odorifer at 1 to 2 log cfu/mL and stored at 4°C and 7°C for 30 d. Changes in P. odorifer cell densities were determined by standard serial dilution with spread plating on tryptic soy agar with yeast extract and incubation at 25°C for 48 h. Spore counts were determined following thermal treatment at 80°C for 12 min. Thermal resistance of a cocktail of P. odorifer in milk was determined after treatments at 63°C for 30 min and 72°C for 15 s. Strains of P. odorifer grew rapidly at 7°C and reached a maximum cell density of ~8 log cfu/g in both 2% and chocolate milk within 12 d. All strains grew more slowly at 4°C and had not reached maximum cell density by 21 d. With extreme temperature abuse (25°C, 24 h), P. odorifer will sporulate in milk; however, thermally resistant subpopulations, including spores, did not develop in milk at 4°C until after stationary phase was achieved (>24 d). Vegetative cells of P. odorifer were verified to be sensitive to pasteurization (>7 log reduction); therefore, P. odorifer would not be expected to contribute to reduced shelf life of fluid milk products containing rework, even with extended storage before rework.
Collapse
|
5
|
Gaballa A, Cheng RA, Trmcic A, Kovac J, Kent DJ, Martin NH, Wiedmann M. Development of a database and standardized approach for rpoB sequence-based subtyping and identification of aerobic spore-forming Bacillales. J Microbiol Methods 2021; 191:106350. [PMID: 34710512 DOI: 10.1016/j.mimet.2021.106350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 10/20/2022]
Abstract
Aerobic spore-forming Bacillales are a highly diverse and ubiquitous group that includes organisms that cause foodborne illnesses and food spoilage. Classical microbiological and biochemical identification of members of the order Bacillales represents a challenge due to the diversity of organisms in this group as well as the fact that the phenotypic-based taxonomic assignment of some named species in this group is not consistent with their phylogenomic characteristics. DNA-sequencing-based tools, on the other hand, can be fast and cost-effective, and can provide for a more reliable identification and characterization of Bacillales isolates. In comparison to 16S rDNA, rpoB was shown to better discriminate between Bacillales isolates and to allow for improved taxonomic assignment to the species level. However, the lack of a publicly accessible rpoB database, as well as the lack of standardized protocols for rpoB-based typing and strain identification, is a major challenge. Here, we report (i) the curation of a DNA sequence database for rpoB-based subtype classification of Bacillales isolates; (ii) the development of standardized protocols for generating rpoB sequence data, and a scheme for rpoB-based initial taxonomic identification of Bacillales isolates at the species level; and (iii) the integration of the database in a publicly accessible online platform that allows for the analysis of rpoB sequence data from uncharacterized Bacillales isolates. Specifically, we curated a database of DNA sequences for a 632-nt internal variable region within the rpoB gene from representative Bacillales reference type strains and a large number of isolates that we have previously isolated and characterized through multiple projects. As of May 21, 2021, the rpoB database contained more than 8350 rpoB sequences representing 1902 distinct rpoB allelic types that can be classified into 160 different genera. The database also includes 1129 rpoB sequences for representative Bacillales reference type strains as available on May 21, 2021 in the NCBI database. The rpoB database is integrated into the online Food Microbe Tracker platform (www.foodmicrobetracker.com) and can be queried using the integrated BLAST tool to initially subtype and taxonomically identify aerobic and facultative anaerobic spore-formers. While whole-genome sequencing is increasingly used in bacterial taxonomy, the rpoB sequence-based identification scheme described here provides a valuable tool as it allows for rapid and cost-effective initial isolate characterization, which can help to identify and characterize foodborne pathogens and food spoilage bacteria. In addition, the database and primers described here can also be adopted for metagenomics approaches that include rpoB as a target, improving discriminatory power and identification over what can be achieved using 16S rDNA as a target.
Collapse
Affiliation(s)
- Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA.
| | - Rachel A Cheng
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Aljosa Trmcic
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Jasna Kovac
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA; Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - David J Kent
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Nicole H Martin
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
6
|
Hwang J, Shin SC, Han JW, Hong SP, Min WK, Chung D, Kim HJ. Complete genome sequence of Paenibacillus xylanexedens PAMC 22703, a xylan-degrading bacterium. Mar Genomics 2020; 55:100788. [PMID: 32563695 DOI: 10.1016/j.margen.2020.100788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 12/30/2022]
Abstract
Paenibacillus is widely distributed in various environments and has the potential for use as a biotechnological agent in industrial processes. Here, we report the complete genome sequence of the marine bacterium, Paenibacillus xylanexedens PAMC 22703, which utilizes xylan. The P. xylanexedens PAMC 22703 strain was isolated from marine sediments. P. xylanexedens PAMC 22703 utilizes xylan as a carbon source to grow. The genome sequence clarified that this strain possesses genes for utilizing xylan. The complete genome sequence contained one chromosome (7,053,622 bp with 46.0% GC content) and one plasmid (44,617 bp with 44.1% C + G content). The genome harbored genes that fully deploy the xylan assimilation pathway. The complete genome sequence of P. xylanexedens PAMC 22703 would prove useful in acquiring information for its application with xylan in various industries.
Collapse
Affiliation(s)
- Junsang Hwang
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 1447, Republic of Korea
| | - Seung Chul Shin
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jae Won Han
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 1447, Republic of Korea
| | - Sang Pil Hong
- Research Group of Traditional Food, Research Division of Strategic Food Technology, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea
| | - Won-Ki Min
- Department of Food Science and Development, Kyungil University, Gyeongsan 38428, Republic of Korea
| | - Donghwa Chung
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 1447, Republic of Korea; Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Republic of Korea; Center for Food Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyo Jin Kim
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 1447, Republic of Korea; Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Republic of Korea.
| |
Collapse
|