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Koutsoumanis KP, Misiou OD, Kakagianni MN. Climate change threatens the microbiological stability of non-refrigerated foods. Food Res Int 2022; 162:111990. [DOI: 10.1016/j.foodres.2022.111990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 11/04/2022]
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2
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Shukla I, Hill JE. cpn60 barcode sequences accurately identify newly defined genera within the Lactobacillaceae. Can J Microbiol 2022; 68:457-464. [PMID: 35230911 DOI: 10.1139/cjm-2021-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The cpn60 barcode sequence is established as an informative target for microbial species identification. Applications of cpn60 barcode sequencing are supported by the availability of "universal" PCR primers for its amplification and a curated reference database of cpn60 sequences, cpnDB. A recent reclassification of lactobacilli involving the definition of 23 new genera provided an opportunity to update cpnDB and to determine if the cpn60 barcode could be used for accurate identification of species consistent with the new framework. Analysis of 275 cpn60 sequences representing 258/269 of the validly named species in Lactobacillus, Paralactobacillus and the 23 newer genera showed that cpn60-based sequence relationships were generally consistent with the whole-genome-based phylogeny. Aligning or mapping full length barcode sequences or a 150 bp subsequence resulted in accurate and unambiguous species identification in almost all cases. Taken together, our results show that the combination of available reference sequence data, "universal" barcode amplification primers, and the inherent sequence diversity within the cpn60 barcode make it a useful target for the detection and identification of lactobacilli as defined by the latest taxonomic framework.
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Affiliation(s)
- Ishika Shukla
- University of Saskatchewan, 7235, Veterinary Microbiology, Saskatoon, Saskatchewan, Canada;
| | - Janet E Hill
- University of Saskatchewan, 7235, Veterinary Microbiology, Saskatoon, Saskatchewan, Canada;
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Bacterial diversity in fumarole environments of the Paricutín volcano, Michoacán (Mexico). Extremophiles 2017; 21:499-511. [DOI: 10.1007/s00792-017-0920-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 02/13/2017] [Indexed: 10/20/2022]
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Durand L, Planchon S, Guinebretiere MH, André S, Carlin F, Remize F. Contamination pathways of spore-forming bacteria in a vegetable cannery. Int J Food Microbiol 2015; 202:10-9. [PMID: 25755080 DOI: 10.1016/j.ijfoodmicro.2015.02.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 12/19/2014] [Accepted: 02/17/2015] [Indexed: 11/29/2022]
Abstract
Spoilage of low-acid canned food during prolonged storage at high temperatures is caused by heat resistant thermophilic spores of strict or facultative bacteria. Here, we performed a bacterial survey over two consecutive years on the processing line of a French company manufacturing canned mixed green peas and carrots. In total, 341 samples were collected, including raw vegetables, green peas and carrots at different steps of processing, cover brine, and process environment samples. Thermophilic and highly-heat-resistant thermophilic spores growing anaerobically were counted. During vegetable preparation, anaerobic spore counts were significantly decreased, and tended to remain unchanged further downstream in the process. Large variation of spore levels in products immediately before the sterilization process could be explained by occasionally high spore levels on surfaces and in debris of vegetable combined with long residence times in conditions suitable for growth and sporulation. Vegetable processing was also associated with an increase in the prevalence of highly-heat-resistant species, probably due to cross-contamination of peas via blanching water. Geobacillus stearothermophilus M13-PCR genotypic profiling on 112 isolates determined 23 profile-types and confirmed process-driven cross-contamination. Taken together, these findings clarify the scheme of contamination pathway by thermophilic spore-forming bacteria in a vegetable cannery.
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Affiliation(s)
- Loïc Durand
- CTCPA, Unité d'Expertise dans la Maitrise du Risque Industriel en Thermorésistants Sporulés, F-84911 Avignon, France
| | - Stella Planchon
- CTCPA, Unité d'Expertise dans la Maitrise du Risque Industriel en Thermorésistants Sporulés, F-84911 Avignon, France
| | - Marie-Hélène Guinebretiere
- INRA, UMR408, Sécurité et Qualité des Produits d'Origine Végétale, F-84000 Avignon, France; Avignon Université, UMR408, Sécurité et Qualité des Produits d'Origine Végétale, F-84000 Avignon, France
| | - Stéphane André
- CTCPA, Unité d'Expertise dans la Maitrise du Risque Industriel en Thermorésistants Sporulés, F-84911 Avignon, France
| | - Frédéric Carlin
- INRA, UMR408, Sécurité et Qualité des Produits d'Origine Végétale, F-84000 Avignon, France; Avignon Université, UMR408, Sécurité et Qualité des Produits d'Origine Végétale, F-84000 Avignon, France
| | - Fabienne Remize
- CTCPA, Unité d'Expertise dans la Maitrise du Risque Industriel en Thermorésistants Sporulés, F-84911 Avignon, France.
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Tomás AF, Karakashev D, Angelidaki I. Thermoanaerobacter pentosaceus sp. nov., an anaerobic, extremely thermophilic, high ethanol-yielding bacterium isolated from household waste. Int J Syst Evol Microbiol 2013. [DOI: 10.1099/ijs.0.045211-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An extremely thermophilic, xylanolytic, spore-forming and strictly anaerobic bacterium, strain DTU01T, was isolated from a continuously stirred tank reactor fed with xylose and household waste. Cells stained Gram-negative and were rod-shaped (0.5–2 µm in length). Spores were terminal with a diameter of approximately 0.5 µm. Optimal growth occurred at 70 °C and pH 7, with a maximum growth rate of 0.1 h−1. DNA G+C content was 34.2 mol%. Strain DTU01T could ferment arabinose, cellobiose, fructose, galactose, glucose, lactose, mannitol, mannose, melibiose, pectin, starch, sucrose, xylan, yeast extract and xylose, but not cellulose, Avicel, inositol, inulin, glycerol, rhamnose, acetate, lactate, ethanol, butanol or peptone. Ethanol was the major fermentation product and a maximum yield of 1.39 mol ethanol per mol xylose was achieved when sulfite was added to the cultivation medium. Thiosulfate, but not sulfate, nitrate or nitrite, could be used as electron acceptor. On the basis of 16S rRNA gene sequence similarity, strain DTU01T was shown to be closely related to
Thermoanaerobacter mathranii
A3T,
Thermoanaerobacter italicus
Ab9T and
Thermoanaerobacter thermocopriae
JT3-3T, with 98–99 % similarity. Despite this, the physiological and phylogenetic differences (DNA G+C content, substrate utilization, electron acceptors, phylogenetic distance and isolation site) allow for the proposal of strain DTU01T as a representative of a novel species within the genus
Thermoanaerobacter
, for which the name Thermoanaerobacter pentosaceus sp. nov. is proposed, with the type strain DTU01T ( = DSM 25963T = KCTC 4529T = VKM B-2752T = CECT 8142T).
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Affiliation(s)
- Ana Faria Tomás
- Department of Environmental Engineering, Technical University of Denmark, Miljoevej 113, 2800 Kongens Lyngby, Denmark
| | - Dimitar Karakashev
- Department of Environmental Engineering, Technical University of Denmark, Miljoevej 113, 2800 Kongens Lyngby, Denmark
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Miljoevej 113, 2800 Kongens Lyngby, Denmark
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André S, Zuber F, Remize F. Thermophilic spore-forming bacteria isolated from spoiled canned food and their heat resistance. Results of a French ten-year survey. Int J Food Microbiol 2013; 165:134-43. [DOI: 10.1016/j.ijfoodmicro.2013.04.019] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 04/19/2013] [Accepted: 04/22/2013] [Indexed: 11/25/2022]
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Natural competence in Thermoanaerobacter and Thermoanaerobacterium species. Appl Environ Microbiol 2010; 76:4713-9. [PMID: 20472726 DOI: 10.1128/aem.00402-10] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Low-G+C thermophilic obligate anaerobes in the class Clostridia are considered among the bacteria most resistant to genetic engineering due to the difficulty of introducing foreign DNA, thus limiting the ability to study and exploit their native hydrolytic and fermentative capabilities. Here, we report evidence of natural genetic competence in 13 Thermoanaerobacter and Thermoanaerobacterium strains previously believed to be difficult to transform or genetically recalcitrant. In Thermoanaerobacterium saccharolyticum JW/SL-YS485, natural competence-mediated DNA incorporation occurs during the exponential growth phase with both replicating plasmid and homologous recombination-based integration, and circular or linear DNA. In T. saccharolyticum, disruptions of genes similar to comEA, comEC, and a type IV pilus (T4P) gene operon result in strains unable to incorporate further DNA, suggesting that natural competence occurs via a conserved Gram-positive mechanism. The relative ease of employing natural competence for gene transfer should foster genetic engineering in these industrially relevant organisms, and understanding the mechanisms underlying natural competence may be useful in increasing the applicability of genetic tools to difficult-to-transform organisms.
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Iyer AV, Blinkova AL, Yang SY, Harrison M, Tepp WH, Jacobson MJ, Johnson EA, Bennett GN, Walker JR. Clostridium taeniosporum is a close relative of the Clostridium botulinum Group II. Anaerobe 2008; 14:318-24. [PMID: 19135540 PMCID: PMC5614447 DOI: 10.1016/j.anaerobe.2008.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Revised: 10/31/2008] [Accepted: 11/21/2008] [Indexed: 11/30/2022]
Abstract
Clostridium taeniosporum is a Gram-positive, anaerobic, rod-shaped non-toxigenic organism isolated from Crimean lake silt. It is unique in forming spores from which about twelve large, flat, ribbon-like appendages emanate. These ribbon-like structures, about 4.5 microm long and 0.45 microm wide, are assembled from smaller fibrils with 5 nm diameter spherical heads attached to thin tails about 1-2 nm in diameter and about 40 nm in length. The appendages have four major components, a glycoprotein with a collagen-like region, two proteins each of which contains two conserved domains of unknown function, and an ortholog of the Bacillus subtilis spore morphogenetic protein SpoVM. Genes for three of these and other, possibly related proteins, cluster on two chromosome fragments. Here we report that C. taeniosporum is saccharolytic, non-proteolytic, and produces both acetic and butyric acid fermentation products. It synthesizes alpha-D-glucosidase and N-acetyl-beta,D-glucoseaminidase constitutively. These physiological properties are similar to those of the C. botulinum Group II. Genotypically, C. taeniosporum is also closely related to the same Group II, based on 16S rDNA sequences. C. taeniosporum differs from typical C. botulinum Group II strains because it is non-toxigenic and in forming the ribbon-like spore appendages. These major differences among otherwise closely related organisms suggest lateral transfer of genes for appendage synthesis and for toxigenicity.
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MESH Headings
- Bacterial Typing Techniques
- Clostridium/classification
- Clostridium/genetics
- Clostridium/isolation & purification
- Clostridium/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Genes, rRNA
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Spores, Bacterial/ultrastructure
- Water Microbiology
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Affiliation(s)
- Arun V Iyer
- Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas, One University Station A5000, Austin, Texas 78712-0162, USA.
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O-Thong S, Prasertsan P, Intrasungkha N, Dhamwichukorn S, Birkeland NK. Improvement of biohydrogen production and treatment efficiency on palm oil mill effluent with nutrient supplementation at thermophilic condition using an anaerobic sequencing batch reactor. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2007.05.002] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Validation list no. 113. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2007; 57:1. [PMID: 17220429 DOI: 10.1099/ijs.0.64923-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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List of changes in taxonomic opinion no. 5. Notification of changes in taxonomic opinion previously published outside the IJSEM. Int J Syst Evol Microbiol 2007; 57:4-5. [PMID: 17220431 DOI: 10.1099/ijs.0.64924-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Bacteriological Code deals with the nomenclature of prokaryotes. This may include existing names (the Approved Lists of Bacterial Names) as well as new names and new combinations. In this sense the Code is also dealing indirectly with taxonomic opinions. However, as with most codes of nomenclature there are no mechanisms for formally recording taxonomic opinions that do not involve the creation of new names or new combinations. In particular, it would be desirable for taxonomic opinions resulting from the creation of synonyms or emended descriptions to be made widely available to the public. In 2004, the Editorial Board of the International Journal of Systematic and Evolutionary Microbiology (IJSEM) agreed unanimously that it was desirable to cover such changes in taxonomic opinions (i.e. the creation of synonyms or the emendation of circumscriptions) previously published outside the IJSEM, and to introduce a List of Changes in Taxonomic Opinion [Notification of changes in taxonomic opinion previously published outside the IJSEM; Euzéby et al. (2004). Int J Syst Evol Microbiol 54, 1429-1430]. Scientists wishing to have changes in taxonomic opinion included in future lists should send one copy of the pertinent reprint or a photocopy or a PDF file thereof to the IJSEM Editorial Office or to the Lists Editor. It must be stressed that the date of proposed taxonomic changes is the date of the original publication not the date of publication of the list. Taxonomic opinions included in the List of Changes in Taxonomic Opinion cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission. The names that are to be used are those that are the "correct names" (in the sense of Principle 6) in the opinion of the bacteriologist, with a given circumscription, position and rank. A particular name, circumscription, position and rank does not have to be adopted in all circumstances. Consequently, the List of Changes in Taxonomic Opinion must be considered as a service to bacteriology and it has no "official character", other than providing a centralized point for registering/indexing such changes in a way that makes them easily accessible to the scientific community.
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