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Papadimitriou K, Georgalaki M, Anastasiou R, Alexandropoulou AM, Manolopoulou E, Zoumpopoulou G, Tsakalidou E. Study of the Microbiome of the Cretan Sour Cream Staka Using Amplicon Sequencing and Shotgun Metagenomics and Isolation of Novel Strains with an Important Antimicrobial Potential. Foods 2024; 13:1129. [PMID: 38611432 PMCID: PMC11011300 DOI: 10.3390/foods13071129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Staka is a traditional Greek sour cream made mostly from spontaneously fermented sheep milk or a mixture of sheep and goat milk. At the industrial scale, cream separators and starter cultures may also be used. Staka is sometimes cooked with flour to absorb most of the fat. In this study, we employed culture-based techniques, amplicon sequencing, and shotgun metagenomics to analyze the Staka microbiome for the first time. The samples were dominated by Lactococcus or Leuconostoc spp. Most other bacteria were lactic acid bacteria (LAB) from the Streptococcus and Enterococcus genera or Gram-negative bacteria from the Buttiauxella, Pseudomonas, Enterobacter, Escherichia-Shigella, and Hafnia genera. Debaryomyces, Kluyveromyces, or Alternaria were the most prevalent genera in the samples, followed by other yeasts and molds like Saccharomyces, Penicillium, Aspergillus, Stemphylium, Coniospotium, or Cladosporium spp. Shotgun metagenomics allowed the species-level identification of Lactococcus lactis, Lactococcus raffinolactis, Streptococcus thermophilus, Streptococcus gallolyticus, Escherichia coli, Hafnia alvei, Streptococcus parauberis, and Enterococcus durans. Binning of assembled shotgun reads followed by recruitment plot analysis of single reads could determine near-complete metagenome assembled genomes (MAGs). Culture-dependent and culture-independent analyses were in overall agreement with some distinct differences. For example, lactococci could not be isolated, presumably because they had entered a viable but not culturable (VBNC) state or because they were dead. Finally, several LAB, Hafnia paralvei, and Pseudomonas spp. isolates exhibited antimicrobial activities against oral or other pathogenic streptococci, and certain spoilage and pathogenic bacteria establishing their potential role in food bio-protection or new biomedical applications. Our study may pave the way for additional studies concerning artisanal sour creams to better understand the factors affecting their production and the quality.
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Affiliation(s)
- Konstantinos Papadimitriou
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Marina Georgalaki
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (M.G.); (R.A.); (A.-M.A.); (E.M.); (G.Z.); (E.T.)
| | - Rania Anastasiou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (M.G.); (R.A.); (A.-M.A.); (E.M.); (G.Z.); (E.T.)
| | - Athanasia-Maria Alexandropoulou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (M.G.); (R.A.); (A.-M.A.); (E.M.); (G.Z.); (E.T.)
| | - Eugenia Manolopoulou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (M.G.); (R.A.); (A.-M.A.); (E.M.); (G.Z.); (E.T.)
| | - Georgia Zoumpopoulou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (M.G.); (R.A.); (A.-M.A.); (E.M.); (G.Z.); (E.T.)
| | - Effie Tsakalidou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (M.G.); (R.A.); (A.-M.A.); (E.M.); (G.Z.); (E.T.)
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Subspecies Classification and Comparative Genomic Analysis of Lactobacillus kefiranofaciens HL1 and M1 for Potential Niche-Specific Genes and Pathways. Microorganisms 2022; 10:microorganisms10081637. [PMID: 36014054 PMCID: PMC9415760 DOI: 10.3390/microorganisms10081637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
(1) Background: Strains HL1 and M1, isolated from kefir grains, have been tentatively identified, based on their partial 16S rRNA gene sequences, as Lactobacillus kefiranofaciens. The two strains demonstrated different health benefits. Therefore, not only the genetic factors exerting diverse functionalities in different L. kefiranofaciens strains, but also the potential niche-specific genes and pathways among the L. kefiranofaciens strains, should be identified. (2) Methods: Phenotypic and genotypic approaches were employed to identify strains HL1 and M1 at the subspecies level. For the further characterization of the probiotic properties of both strains, comparative genomic analyses were used. (3) Results: Both strains were identified as L. kefiranofaciens subsp. kefirgranum. According to the COG function category, dTDP-rhamnose and rhamnose-containing glycans were specifically detected in the L. kefiranofaciens subsp. Kefirgranum genomes. Three unique genes (epsI, epsJ, and epsK) encoding glycosyltransferase in the EPS gene cluster, and the ImpB/MucB/SamB family protein encoding gene were found in HL1 and M1. The specific ability to degrade arginine via the ADI pathway was found in HL1. The presence of the complete glycogen metabolism (glg) operon in the L. kefiranofaciens strains suggested the importance of glycogen synthesis to enable colonization in kefir grains and extend survival under environmental stresses. (4) Conclusions: The obtained novel information on the potential genes and pathways for polysaccharide synthesis and other functionalities in our HL1 and M1 strains could be applied for further functionality predictions for potential probiotic screening.
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Kouhi F, Mirzaei H, Nami Y, Khandaghi J, Javadi A. Potential probiotic and safety characterisation of enterococcus bacteria isolated from indigenous fermented motal cheese. Int Dairy J 2022. [DOI: 10.1016/j.idairyj.2021.105247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Maitra S, Brestic M, Bhadra P, Shankar T, Praharaj S, Palai JB, Shah MMR, Barek V, Ondrisik P, Skalický M, Hossain A. Bioinoculants-Natural Biological Resources for Sustainable Plant Production. Microorganisms 2021; 10:51. [PMID: 35056500 PMCID: PMC8780112 DOI: 10.3390/microorganisms10010051] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/22/2022] Open
Abstract
Agricultural sustainability is of foremost importance for maintaining high food production. Irresponsible resource use not only negatively affects agroecology, but also reduces the economic profitability of the production system. Among different resources, soil is one of the most vital resources of agriculture. Soil fertility is the key to achieve high crop productivity. Maintaining soil fertility and soil health requires conscious management effort to avoid excessive nutrient loss, sustain organic carbon content, and minimize soil contamination. Though the use of chemical fertilizers have successfully improved crop production, its integration with organic manures and other bioinoculants helps in improving nutrient use efficiency, improves soil health and to some extent ameliorates some of the constraints associated with excessive fertilizer application. In addition to nutrient supplementation, bioinoculants have other beneficial effects such as plant growth-promoting activity, nutrient mobilization and solubilization, soil decontamination and/or detoxification, etc. During the present time, high energy based chemical inputs also caused havoc to agriculture because of the ill effects of global warming and climate change. Under the consequences of climate change, the use of bioinputs may be considered as a suitable mitigation option. Bioinoculants, as a concept, is not something new to agricultural science, however; it is one of the areas where consistent innovations have been made. Understanding the role of bioinoculants, the scope of their use, and analysing their performance in various environments are key to the successful adaptation of this technology in agriculture.
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Affiliation(s)
- Sagar Maitra
- Department of Agronomy, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India; (S.M.); (T.S.); (S.P.); (J.B.P.)
| | - Marian Brestic
- Department of Plant Physiology, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia;
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic;
| | - Preetha Bhadra
- Department of Biotechnology, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India;
| | - Tanmoy Shankar
- Department of Agronomy, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India; (S.M.); (T.S.); (S.P.); (J.B.P.)
| | - Subhashisa Praharaj
- Department of Agronomy, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India; (S.M.); (T.S.); (S.P.); (J.B.P.)
| | - Jnana Bharati Palai
- Department of Agronomy, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakheundi 761 211, India; (S.M.); (T.S.); (S.P.); (J.B.P.)
| | | | - Viliam Barek
- Department of Water Resources and Environmental Engineering, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia;
| | - Peter Ondrisik
- Department of Plant Physiology, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia;
| | - Milan Skalický
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic;
| | - Akbar Hossain
- Bangladesh Wheat and Maize Research Institute, Dinajpur 5200, Bangladesh;
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The Antimicrobial Resistance and Prevalence of Enterococcus Species in Saudi Arabia. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.4.61] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Nel S, Davis SB, Endo A, Dicks LMT. Phylogenetic Analyses of pheS, dnaA and atpA Genes for Identification of Weissella confusa and Weissella cibaria Isolated from a South African Sugarcane Processing Factory. Curr Microbiol 2019; 76:1138-1146. [PMID: 31338566 DOI: 10.1007/s00284-019-01740-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/05/2019] [Indexed: 12/25/2022]
Abstract
A previous study reported on the isolation of 430 polysaccharide (gum)-producing bacteria from a South African sugarcane processing factory and the identification of isolates by comparative 16S rRNA gene sequencing. A large number of isolates (202) belonged to the genus Weissella and clustered with reference strains of Weissella cibaria and Weissella confusa. In this study, we identified 147 strains as W. cibaria and 55 as W. confusa based on phylogenetic analyses of pheS and dnaA gene sequences of representative isolates. We also included atpA gene sequence analysis of Weissella isolates as potential future phylogenetic marker to differentiate amongst strains of W. cibaria and W. confusa.
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Affiliation(s)
- Sanet Nel
- Sugar Milling Research Institute NPC, c/o University of KwaZulu-Natal, Durban, 4041, South Africa.,Department of Microbiology, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Stephen B Davis
- Sugar Milling Research Institute NPC, c/o University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
| | - Leon M T Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch, 7600, South Africa.
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Sanderson H, Ortega-Polo R, McDermott K, Zaheer R, Brown RS, Majury A, McAllister T, Liss SN. Comparison of biochemical and genotypic speciation methods for vancomycin-resistant enterococci isolated from urban wastewater treatment plants. J Microbiol Methods 2019; 161:102-110. [PMID: 31071353 DOI: 10.1016/j.mimet.2019.04.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 11/24/2022]
Abstract
Enterococci species in wastewater including Enterococcus faecalis, Enterococcus faecium, Enterococcus casseliflavus and Enterococcus gallinarum isolates (n = 308) with low or high level vancomycin resistance were determined and compared using a phenotypic method (RapID™ STR system), 16S rRNA sequencing, and multi-locus (atpA, groESL, and pheS) sequence analysis (MLSA). Error rates for the RapID™ STR system were E. faecalis (15.9%), E. faecium (21.5%), and E. casseliflavus/E. gallinarum (56.9%) when referenced to the consensus of all methods tested. Comparison of single nucleotide polymorphism (SNP) distances and phylogenetic trees suggested that the groESL locus delineated species more effectively than other loci. The groESL locus was the most reliable loci for the correct identification of Enterococcus spp., including E. casseliflavus and E. gallinarum, with high congruence compared to the consensus (Adjusted Rand Index = 0.954; Adjusted Wallace Co-efficient = 0.941). All of the methods were compared to whole genome sequencing, which acted as a gold standard, for the isolates from this study and those downloaded from NCBI.
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Affiliation(s)
- Haley Sanderson
- School of Environmental Studies, Queen's University, Kingston, Ontario K7L 3N6, Canada; Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta T1J 4P4, Canada
| | - Rodrigo Ortega-Polo
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta T1J 4P4, Canada; Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta T1K 6T5, Canada
| | | | - Rahat Zaheer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta T1J 4P4, Canada
| | - R Stephen Brown
- School of Environmental Studies, Queen's University, Kingston, Ontario K7L 3N6, Canada; Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Anna Majury
- School of Environmental Studies, Queen's University, Kingston, Ontario K7L 3N6, Canada; Public Health Ontario, Kingston, Ontario K7L 3K3, Canada
| | - Tim McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta T1J 4P4, Canada.
| | - Steven N Liss
- School of Environmental Studies, Queen's University, Kingston, Ontario K7L 3N6, Canada; Department of Biology, Ryerson University, Toronto, Ontario M5B 2K3, Canada.
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Abstract
The genus Enterococcus comprises a ubiquitous group of Gram-positive bacteria that are of great relevance to human health for their role as major causative agents of health care-associated infections. The enterococci are resilient and versatile species able to survive under harsh conditions, making them well adapted to the health care environment. Two species cause the majority of enterococcal infections: Enterococcus faecalis and Enterococcus faecium Both species demonstrate intrinsic resistance to common antibiotics, such as virtually all cephalosporins, aminoglycosides, clindamycin, and trimethoprim-sulfamethoxazole. Additionally, a remarkably plastic genome allows these two species to readily acquire resistance to further antibiotics, such as high-level aminoglycoside resistance, high-level ampicillin resistance, and vancomycin resistance, either through mutation or by horizontal transfer of genetic elements conferring resistance determinants.
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Affiliation(s)
- Mónica García-Solache
- Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Louis B Rice
- Department of Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
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Evaluation of the infB and rpsB gene fragments as genetic markers intended for identification and phylogenetic analysis of particular representatives of the order Lactobacillales. Arch Microbiol 2018; 200:1427-1437. [PMID: 30039323 DOI: 10.1007/s00203-018-1554-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/28/2018] [Accepted: 07/17/2018] [Indexed: 10/28/2022]
Abstract
Detailed differentiation, classification, and phylogenetic analysis of the order Lactobacillales are performed using molecular techniques that involve the comparison of whole genomes, multilocus sequence analysis, DNA-DNA hybridisation, and 16S rRNA sequencing. Despite the wide application of the latter two techniques, issues associated with them are extensively discussed. Although complete genomic analyses are the most appropriate for phylogenetic studies, they are time-consuming and require high levels of expertise. Many phylogenetic/identification markers have been proposed for enterococci, lactobacilli, streptococci, and lactobacilli. However, none have been established for vagococci and some genera within the order Lactobacillales. The objective of the study was to find novel alternative housekeeping genes for classification, typing, and phylogenetic analysis of selected genera within the order Lactobacillales. We designed primers flanking variable regions of the infB (504 nt) and rpsB (333 nt) genes and amplified and sequenced them in 56 strains of different genera within the order Lactobacillales. Statistical analysis and characteristics of the gene regions suggested that they could be used for taxonomic purposes. Phylogenetic analyses, including assessment of (in)congruence between individual phylogenetic trees indicated the possibility of using the concatenation of the two genes as an alternative tool for the evaluation of phylogeny compared with the 16S rRNA gene representing the standard phylogenetic marker of prokaryotes. Moreover, infB, rpsB regions and their concatenate were phylogenetically consistent with two widely applied alternative genetic markers in taxonomy of particular Lactobacillales genera encoding the 60 kDa chaperonin protein (GroEL-hsp60) and phenylalanyl-tRNA synthetase, alpha subunit (pheS).
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Zhu S, Lin D, Xiong S, Wang X, Xue Z, Dong B, Shen X, Ma X, Chen J, Yang J. Carnobacterium antarcticum sp. nov., a psychrotolerant, alkaliphilic bacterium isolated from sandy soil in Antarctica. Int J Syst Evol Microbiol 2018; 68:1672-1677. [PMID: 29616891 DOI: 10.1099/ijsem.0.002727] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, alkaliphilic, psychrotolerant, facultative anaerobe, designated CP1T, was isolated from sandy soil near the Davis Station in Antarctica. The short-rod-shaped cells displayed Gram-positive staining and did not form spores. Strain CP1T was able to grow at temperatures between 4 and 36 °C, pH 6.0-9.5, and in the presence of up to 5.0 % (w/v) NaCl. 16S rRNA gene and multilocus (pheS, rpoA, and atpA) sequence analysis revealed Carnobacterium mobile DSM 4848T and Carnobacterium iners LMG 26642T as the closest relatives (97.4 and 97.1 % 16S rRNA gene sequence similarity, respectively). The genomic G+C content was 38.1 mol%, and DNA-DNA hybridization with DSM 4848T revealed 32.4±3.4 % similarity. The major fatty acid components were C14 : 0 and C16 : 1ω9c. The cell wall contained meso-diaminopimelic acid and was of peptidoglycan type A1γ. Based on physiological, genotypic and biochemical characteristics, strain CP1T represents a novel species of the genus Carnobacterium for which the name Carnobacterium antarcticum sp. nov. is proposed. The type strain is CP1T (=DSM 103363T=CGMCC 1.15643T).
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Affiliation(s)
- Sidong Zhu
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Danqiu Lin
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Shangling Xiong
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Xing Wang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Zehao Xue
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Bingxia Dong
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Xudong Shen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Xiangdong Ma
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University, Wuhan 430062, PR China
| | - Jigang Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Jifang Yang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
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Rose K, Agius J, Hall J, Thompson P, Eden JS, Srivastava M, Tiernan B, Jenkins C, Phalen D. Emergent multisystemic Enterococcus infection threatens endangered Christmas Island reptile populations. PLoS One 2017; 12:e0181240. [PMID: 28727845 PMCID: PMC5519069 DOI: 10.1371/journal.pone.0181240] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 06/28/2017] [Indexed: 11/19/2022] Open
Abstract
Multisystemic infections with a morphologically unusual bacterium were first observed in captive critically endangered Lister’s geckos (Lepidodactylus listeri) on Christmas Island in October 2014. Since then the infection was identified in another captive critically endangered lizard species, the blue-tailed skink (Cryptoblepharus egeriae) and two species of invasive geckos; the four clawed gecko (Gehyra mutilata) and Asian house gecko (Hemidactylus frenatus), in a wide geographic range across the east side of the island. The Gram and periodic acid-Schiff positive cocci to diplococci have a propensity to form chains surrounded by a matrix, which ultrastructurally appears to be formed by fibrillar capsular projections. The bacterium was associated with severe and extensive replacement of tissues, but minimal host inflammatory response. Attempts to grow the organism in culture and in embryonated eggs were unsuccessful. Molecular characterisation of the organism placed it as a novel member of the genus Enterococcus. Disease Risk Analyses including this organism should now be factored into conservation management actions and island biosecurity.
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Affiliation(s)
- Karrie Rose
- Taronga Conservation Society Australia, Sydney, New South Wales, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- * E-mail:
| | - Jessica Agius
- Faculty of Veterinary Science, Sydney School of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Jane Hall
- Taronga Conservation Society Australia, Sydney, New South Wales, Australia
| | - Paul Thompson
- Taronga Conservation Society Australia, Sydney, New South Wales, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, the University of Sydney, Sydney, New South Wales, Australia
| | - Mukesh Srivastava
- Elizabeth Macarthur Agricultural Institute, New South Wales Department of Primary Industries, Camden, New South Wales, Australia
| | - Brendan Tiernan
- Christmas Island National Park, Drumsite, Territory of Christmas Island, Australia
| | - Cheryl Jenkins
- Elizabeth Macarthur Agricultural Institute, New South Wales Department of Primary Industries, Camden, New South Wales, Australia
| | - David Phalen
- Faculty of Veterinary Science, Sydney School of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
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Bonacina J, Suárez N, Hormigo R, Fadda S, Lechner M, Saavedra L. A genomic view of food-related and probiotic Enterococcus strains. DNA Res 2017; 24:11-24. [PMID: 27773878 PMCID: PMC5381348 DOI: 10.1093/dnares/dsw043] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 08/18/2016] [Indexed: 11/22/2022] Open
Abstract
The study of enterococcal genomes has grown considerably in recent years. While special attention is paid to comparative genomic analysis among clinical relevant isolates, in this study we performed an exhaustive comparative analysis of enterococcal genomes of food origin and/or with potential to be used as probiotics. Beyond common genetic features, we especially aimed to identify those that are specific to enterococcal strains isolated from a certain food-related source as well as features present in a species-specific manner. Thus, the genome sequences of 25 Enterococcus strains, from 7 different species, were examined and compared. Their phylogenetic relationship was reconstructed based on orthologous proteins and whole genomes. Likewise, markers associated with a successful colonization (bacteriocin genes and genomic islands) and genome plasticity (phages and clustered regularly interspaced short palindromic repeats) were investigated for lifestyle specific genetic features. At the same time, a search for antibiotic resistance genes was carried out, since they are of big concern in the food industry. Finally, it was possible to locate 1617 FIGfam families as a core proteome universally present among the genera and to determine that most of the accessory genes code for hypothetical proteins, providing reasonable hints to support their functional characterization.
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Affiliation(s)
- Julieta Bonacina
- Laboratorio de Genética y Biología Molecular, CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán (T4000ILC), Tucumán, Argentina
| | - Nadia Suárez
- Laboratorio de Genética y Biología Molecular, CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán (T4000ILC), Tucumán, Argentina
| | - Ricardo Hormigo
- Laboratorio de Genética y Biología Molecular, CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán (T4000ILC), Tucumán, Argentina
| | - Silvina Fadda
- Laboratorio de Genética y Biología Molecular, CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán (T4000ILC), Tucumán, Argentina
| | - Marcus Lechner
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, 35037 Marburg, Germany
| | - Lucila Saavedra
- Laboratorio de Genética y Biología Molecular, CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán (T4000ILC), Tucumán, Argentina
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Development of a Rapid Identification Method for the Differentiation of Enterococcus Species Using a Species-Specific Multiplex PCR Based on Comparative Genomics. Curr Microbiol 2017; 74:476-483. [PMID: 28229213 DOI: 10.1007/s00284-017-1210-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 02/02/2017] [Indexed: 10/20/2022]
Abstract
Enterococci are lactic acid bacteria that are commonly found in food and in animal gut. Since 16 S ribosomal RNA (rRNA) sequences, genetic markers for bacterial identification, are similar among several Enterococcus species, it is very difficult to determine the correct species based on only 16 S rRNA sequences. Therefore, we developed a rapid method for the identification of different Enterococcus species using comparative genomics. We compared 38 genomes of 13 Enterococcus species retrieved from the National Center of Biotechnology Information database and identified 25,623 orthologs. Among the orthologs, four genes were specific to four Enterococcus species (Enterococcus faecalis, Enterococcus faecium, Enterococcus hirae, and Enterococcus durans). We designed species-specific primer sets targeting the genes and developed a multiplex PCR using primer sets that could distinguish the four Enterococcus species among the nine strains of Enterococcus species that were available locally. The multiplex PCR method also distinguished the four species isolated from various environments, such as feces of chicken and cow, meat of chicken, cow, and pigs, and fermented soybeans (Cheonggukjang and Doenjang). These results indicated that our novel multiplex PCR using species-specific primers could identify the four Enterococcus species in a rapid and easy way. This method will be useful to distinguish Enterococcus species in food, feed, and clinical settings.
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14
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Harada T, Dang VC, Nguyen DP, Nguyen TAD, Sakamoto M, Ohkuma M, Motooka D, Nakamura S, Uchida K, Jinnai M, Yonogi S, Kawahara R, Kanki M, Kawai T, Kumeda Y, Yamamoto Y. Enterococcus saigonensis sp. nov., isolated from retail chicken meat and liver. Int J Syst Evol Microbiol 2016; 66:3779-3785. [DOI: 10.1099/ijsem.0.001264] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tetsuya Harada
- Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
| | - Van Chinh Dang
- Institute of Public Health, 159 Hung Phu, District 8, Ward 8, Ho Chi Minh City, Vietnam
| | - Do Phuc Nguyen
- Institute of Public Health, 159 Hung Phu, District 8, Ward 8, Ho Chi Minh City, Vietnam
| | - Thi Anh Dao Nguyen
- Institute of Public Health, 159 Hung Phu, District 8, Ward 8, Ho Chi Minh City, Vietnam
| | - Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kotaro Uchida
- Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
| | - Michio Jinnai
- Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
| | - Shinya Yonogi
- Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
| | - Ryuji Kawahara
- Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
| | - Masashi Kanki
- Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
| | - Takao Kawai
- Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
| | - Yuko Kumeda
- Osaka Prefectural Institute of Public Health, Osaka 537-0025, Japan
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15
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Flandrois JP, Perrière G, Gouy M. leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences. BMC Bioinformatics 2015; 16:251. [PMID: 26264559 PMCID: PMC4531848 DOI: 10.1186/s12859-015-0692-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 07/31/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Estimating the phylogenetic position of bacterial and archaeal organisms by genetic sequence comparisons is considered as the gold-standard in taxonomy. This is also a way to identify the species of origin of the sequence. The quality of the reference database used in such analyses is crucial: the database must reflect the up-to-date bacterial nomenclature and accurately indicate the species of origin of its sequences. DESCRIPTION leBIBI(QBPP) is a web tool taking as input a series of nucleotide sequences belonging to one of a set of reference markers (e.g., SSU rRNA, rpoB, groEL2) and automatically retrieving closely related sequences, aligning them, and performing phylogenetic reconstruction using an approximate maximum likelihood approach. The system returns a set of quality parameters and, if possible, a suggested taxonomic assigment for the input sequences. The reference databases are extracted from GenBank and present four degrees of stringency, from the "superstringent" degree (one type strain per species) to the loosely parsed degree ("lax" database). A set of one hundred to more than a thousand sequences may be analyzed at a time. The speed of the process has been optimized through careful hardware selection and database design. CONCLUSION leBIBI(QBPP) is a powerful tool helping biologists to position bacterial or archaeal sequence commonly used markers in a phylogeny. It is a diagnostic tool for clinical, industrial and environmental microbiology laboratory, as well as an exploratory tool for more specialized laboratories. Its main advantages, relatively to comparable systems are: i) the use of a broad set of databases covering diverse markers with various degrees of stringency; ii) the use of an approximate Maximum Likelihood approach for phylogenetic reconstruction; iii) a speed compatible with on-line usage; and iv) providing fully documented results to help the user in decision making.
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Affiliation(s)
- Jean-Pierre Flandrois
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard - Lyon 1, 43 bd. du 11 Novembre 1918, Villeurbanne, 69622, France.
| | - Guy Perrière
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard - Lyon 1, 43 bd. du 11 Novembre 1918, Villeurbanne, 69622, France.
| | - Manolo Gouy
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard - Lyon 1, 43 bd. du 11 Novembre 1918, Villeurbanne, 69622, France.
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16
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Zuo FL, Feng XJ, Chen LL, Chen SW. Identification and partial characterization of lactic acid bacteria isolated from traditional dairy products produced by herders in the western Tianshan Mountains of China. Lett Appl Microbiol 2014; 59:549-56. [PMID: 25082064 DOI: 10.1111/lam.12313] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 07/03/2014] [Accepted: 07/28/2014] [Indexed: 11/26/2022]
Abstract
UNLABELLED Thirty strains of lactic acid bacteria (LAB) were isolated from herders' traditional dairy products collected from Xinjiang, China. The species Lactobacillus, Lactococcus, Enterococcus, Pediococcus and Leuconostoc were identified by 16S ribosomal RNA gene sequencing analysis and conventional observation. The strains' fermentation characteristics, including milk acidification, proteolysis, autolysis, antimicrobial activity and diacetyl production, were assayed and compared. Strains NL24 and NL31 showed the highest proteolytic activity-2·75 and 2·08 mmol Phe l(-1) milk, respectively. Strains C, NL41, SW2, Z3-11, NL42 and Z2-91 had high autolytic activity. In addition, most of the wild strains produced diacetyl, half of them to high levels. This study provides a clue to LAB biodiversity in traditional dairy foods produced by herders in the western Tianshan Mountains. High-performing strains should be further evaluated for practical application in value-added fermented dairy products. SIGNIFICANCE AND IMPACT OF THE STUDY Our results reveal a certain variety of lactic acid bacteria (LAB) in traditional dairy products from Xinjiang. Some of the LAB strains, such as Lactobacillus rhamnosus NL24 and Lactobacillus paracasei SW2, possess excellent functional properties and have the potential for application in indigenous fermented dairy products. Performance of the newly isolated strains in cheese or yogurt manufacturing was further evaluated. Application of the high-performing strains to enrich the flavour of fermented dairy products is highly desirable and holds great commercial potential.
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Affiliation(s)
- F L Zuo
- Key Laboratory of Functional Dairy Science of Chinese Ministry of Education and Municipal Government of Beijing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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17
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Staley C, Dunny GM, Sadowsky MJ. Environmental and animal-associated enterococci. ADVANCES IN APPLIED MICROBIOLOGY 2014; 87:147-86. [PMID: 24581391 DOI: 10.1016/b978-0-12-800261-2.00004-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Enterococci are generally commensal bacteria inhabiting the gastrointestinal tract of humans and animals. They have, however, been implicated as the etiological agent of a variety of illnesses and nosocomial infections. In addition to pathogenic potential, there is growing concern regarding the incidence of antibiotic resistance and genetic exchange among Enterococcus spp. within and among a variety of animal hosts. While primarily considered an enteric group, extra-enteric habitats in which enterococci persist and potentially grow have been studied for decades. Although many biotic (e.g., predation) and abiotic (e.g., sunlight, nutrients, and salinity) stressors have been thought to limit the success of enterococci in these secondary habitats, a growing body of evidence suggests that certain strains may become naturalized to environmental habitats. Enterococci have also been used for decades as indicators of fecal contamination in recreational waters where increased concentrations of this group have been linked to the incidence of illness in humans following recreational use of these waters. Persistence of enterococci in secondary habitats, however, suggests that their presence in ambient waters may prove to be a poor indicator of actual risks to public health. In this chapter, we provide a review of the existing body of literature concerning animal host associations, genetic exchange is reviewed, and emphasis is placed on the growing body of evidence for the persistence and growth of enterococci in secondary habitats.
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Affiliation(s)
- Christopher Staley
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Gary M Dunny
- Department of Microbiology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA; Department of Soil, Water and Climate, University of Minnesota, St. Paul, Minnesota, USA.
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18
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Reybroeck W, De Vleeschouwer M, Marchand S, Sinnaeve D, Heylen K, De Block J, Madder A, Martins JC, Heyndrickx M. Cyclic lipodepsipeptides produced by Pseudomonas spp. naturally present in raw milk induce inhibitory effects on microbiological inhibitor assays for antibiotic residue screening. PLoS One 2014; 9:e98266. [PMID: 24853676 PMCID: PMC4031126 DOI: 10.1371/journal.pone.0098266] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/30/2014] [Indexed: 11/23/2022] Open
Abstract
Two Pseudomonas strains, identified as closely related to Pseudomonas tolaasii, were isolated from milk of a farm with frequent false-positive Delvotest results for screening putative antibiotic residues in raw milk executed as part of the regulatory quality programme. Growth at 5 to 7°C of these isolates in milk resulted in high lipolysis and the production of bacterial inhibitors. The two main bacterial inhibitors have a molecular weight of 1168.7 and 1140.7 Da respectively, are heat-tolerant and inhibit Geobacillus stearothermophilus var. calidolactis, the test strain of most of the commercially available microbiological inhibitor tests for screening of antibiotic residues in milk. Furthermore, these bacterial inhibitors show antimicrobial activity against Staphylococcus aureus, Bacillus cereus and B. subtilis and also interfere negatively with yoghurt production. Following their isolation and purification with RP-HPLC, the inhibitors were identified by NMR analysis as cyclic lipodepsipeptides of the viscosin group. Our findings bring to light a new challenge for quality control in the dairy industry. By prolonging the refrigerated storage of raw milk, the keeping quality of milk is influenced by growth and metabolic activities of psychrotrophic bacteria such as pseudomonads. Besides an increased risk of possible spoilage of long shelf-life milk, the production at low temperature of natural bacterial inhibitors may also result in false-positive results for antibiotic residue screening tests based on microbial inhibitor assays thus leading to undue production loss.
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Affiliation(s)
- Wim Reybroeck
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Science Unit, Melle, Belgium
| | - Matthias De Vleeschouwer
- Ghent University (UGent), Department of Organic Chemistry, NMR and Structure Analysis Unit, Gent, Belgium
- Ghent University (UGent), Department of Organic Chemistry, Organic and Biomimetic Chemistry Research Unit, Gent, Belgium
| | - Sophie Marchand
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Science Unit, Melle, Belgium
| | - Davy Sinnaeve
- Ghent University (UGent), Department of Organic Chemistry, NMR and Structure Analysis Unit, Gent, Belgium
| | - Kim Heylen
- Ghent University (UGent), Department of Biochemistry and Microbiology, Laboratory of Microbiology, Gent, Belgium
| | - Jan De Block
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Science Unit, Melle, Belgium
| | - Annemieke Madder
- Ghent University (UGent), Department of Organic Chemistry, Organic and Biomimetic Chemistry Research Unit, Gent, Belgium
| | - José C. Martins
- Ghent University (UGent), Department of Organic Chemistry, NMR and Structure Analysis Unit, Gent, Belgium
| | - Marc Heyndrickx
- Institute for Agricultural and Fisheries Research (ILVO), Technology and Food Science Unit, Melle, Belgium
- Ghent University (UGent), Department of Pathology, Bacteriology and Poultry Diseases, Merelbeke, Belgium
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19
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Killer J, Havlík J, Vlková E, Rada V, Pechar R, Benada O, Kopečný J, Kofroňová O, Sechovcová H. Lactobacillus rodentium sp. nov., from the digestive tract of wild rodents. Int J Syst Evol Microbiol 2014; 64:1526-1533. [DOI: 10.1099/ijs.0.054924-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three strains of regular, long, Gram-stain-positive bacterial rods were isolated using TPY, M.R.S. and Rogosa agar under anaerobic conditions from the digestive tract of wild mice (Mus musculus). All 16S rRNA gene sequences of these isolates were most similar to sequences of
Lactobacillus gasseri
ATCC 33323T and
Lactobacillus johnsonii
ATCC 33200T (97.3 % and 97.2 % sequence similarities, respectively). The novel strains shared 99.2–99.6 % 16S rRNA gene sequence similarities. Type strains of
L. gasseri
and
L. johnsonii
were also most related to the newly isolated strains according to rpoA (83.9–84.0 % similarities), pheS (84.6–87.8 %), atpA (86.2–87.7 %), hsp60 (89.4–90.4 %) and tuf (92.7–93.6 %) gene sequence similarities. Phylogenetic studies based on 16S rRNA, hsp60, rpoA, atpA and pheS gene sequences, other genotypic and many phenotypic characteristics (results of API 50 CHL, Rapid ID 32A and API ZYM biochemical tests; cellular fatty acid profiles; cellular polar lipid profiles; end products of glucose fermentation) showed that these bacterial strains represent a novel species within the genus
Lactobacillus
. The name Lactobacillus rodentium sp. nov. is proposed to accommodate this group of new isolates. The type strain is MYMRS/TLU1T ( = DSM 24759T = CCM 7945T).
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Affiliation(s)
- J. Killer
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Kamýcká 129, Prague 6 – Suchdol 165 21, Czech Republic
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 – Krč 142 20, Czech Republic
| | - J. Havlík
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Kamýcká 129, Prague 6 – Suchdol 165 21, Czech Republic
| | - E. Vlková
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Kamýcká 129, Prague 6 – Suchdol 165 21, Czech Republic
| | - V. Rada
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Kamýcká 129, Prague 6 – Suchdol 165 21, Czech Republic
| | - R. Pechar
- Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Kamýcká 129, Prague 6 – Suchdol 165 21, Czech Republic
| | - O. Benada
- Department of Biology, Faculty of Science, J. E. Purkyně University in Ustí nad Labem, Za Válcovnou 1000/8, 400 96 Ústí nad Labem, Czech Republic
- Laboratory of Molecular Structure Characterization, Institute of Microbiology, Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 – Krč 142 20, Czech Republic
| | - J. Kopečný
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 – Krč 142 20, Czech Republic
| | - O. Kofroňová
- Laboratory of Molecular Structure Characterization, Institute of Microbiology, Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 – Krč 142 20, Czech Republic
| | - H. Sechovcová
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 – Krč 142 20, Czech Republic
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20
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Vagococcus entomophilus sp. nov., from the digestive tract of a wasp (Vespula vulgaris). Int J Syst Evol Microbiol 2014; 64:731-737. [DOI: 10.1099/ijs.0.054940-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three unknown Gram-stain-positive, catalase-negative, facultatively anaerobic and coccus-shaped strains of bacteria were isolated from the digestive tracts of wasps (Vespula vulgaris). Analysis of 16S rRNA gene sequences revealed that these strains had identical sequences and showed that
Vagococcus salmoninarum
, with 96.2 % sequence similarity, was the closest phylogenetic neighbour. Further analyses based on hsp60 and pheS gene sequences of representatives of the family Enteroccocaceae and genotypic and phenotypic characterization using (GTG)5-PCR fingerprintings, EcoRI ribotyping, DNA G+C content, whole-cell protein profiling, cellular fatty acid profiles analysis and extensive biotyping confirmed that the investigated strains were representatives of a novel bacterial species within the genus Vagoccocus for which the name Vagoccocus entomophilus sp. nov. is proposed. The type strain is VOSTP2T ( = DSM 24756T = CCM 7946T).
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21
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Rahkila R, De Bruyne K, Johansson P, Vandamme P, Björkroth J. Reclassification of Leuconostoc gasicomitatum as Leuconostoc gelidum subsp. gasicomitatum comb. nov., description of Leuconostoc gelidum subsp. aenigmaticum subsp. nov., designation of Leuconostoc gelidum subsp. gelidum subsp. nov. and emended description of Leuconostoc gelidum. Int J Syst Evol Microbiol 2014; 64:1290-1295. [PMID: 24431060 DOI: 10.1099/ijs.0.058263-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the present study we investigated the taxonomic status of 20 lactic acid bacteria (LAB) originating from packaged meat. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the genus Leuconostoc with Leuconostoc gelidum, Leuconostoc inhae and Leuconostoc gasicomitatum as the closest phylogenetic relatives. The novel strains shared more than 70 % DNA-DNA relatedness with type and reference strains of both L. gelidum and L. gasicomitatum. The DNA-DNA relatedness values between L. gelidum type and reference strains and L. gasicomitatum type and reference strains were also above 70 %, showing that all these strains belonged to the same species. Sequence analyses of concatenated atpA, pheS, and rpoA genes demonstrated that the novel strains as well as type and reference strains of L. gelidum and L. gasicomitatum are phylogenetically closely related, but form three clearly separated subgroups. Numerical analysis of HindIII ribopatterns and phenotypic tests supported this subdivision. Based on the data presented in this study, we propose to reclassify Leuconostoc gasicomitatum as Leuconostoc gelidum subsp. gasicomitatum comb. nov. (type strain, LMG 18811(T) = DSM 15947(T)). The novel strains isolated in the present study represent a novel subspecies, for which the name Leuconostoc gelidum subsp. aenigmaticum subsp. nov. is proposed, with POUF4d(T) ( = LMG 27840(T) = DSM 19375(T)) as the type strain. The proposal of these two novel subspecies automatically creates the subspecies Leuconostoc gelidum subsp. gelidum subsp. nov. (type strain, NCFB 2775(T) = DSM 5578(T)). An emended description of Leuconostoc gelidum is also provided.
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Affiliation(s)
- Riitta Rahkila
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Katrien De Bruyne
- Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Per Johansson
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Peter Vandamme
- Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Johanna Björkroth
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
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22
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Lactobacillus apis sp. nov., from the stomach of honeybees (Apis mellifera), having an in vitro inhibitory effect on the causative agents of American and European foulbrood. Int J Syst Evol Microbiol 2014; 64:152-157. [DOI: 10.1099/ijs.0.053033-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was performed on Gram-stain-positive, catalase-negative and regular rod-shaped bacterial strains R4BT and R4C, isolated from the stomachs of honeybees. 16S rRNA gene sequence analysis revealed that the phylogenetic position of the novel strains was within the genus
Lactobacillus
; the highest sequence similarity to R4BT was shown by
Lactobacillus acidophilus
BCRC 10695T (93.6 %). Lower sequence similarities were found to other obligately homofermentative lactobacilli. A PCR–DGGE method could detect the sequence of the 16S rRNA gene of strain R4BT at different developmental stages of honeybees occurring in two different locations in the Czech Republic. The distinctiveness of the strains from other lactobacilli was also confirmed by analysis of sequences of other phylogenetic markers applicable to the taxonomy of the genus
Lactobacillus
, ribotyping and rep-PCR analysis. The DNA G+C content of strain R4BT was 41.3 mol%. The predominant cellular fatty acids of strain R4BT were C18 : 1ω9c, summed C19 : 1ω6c/C19 : 0 cyclo ω10c, C16 : 0, summed C18 : 1ω7c/C18 : 1ω6c and summed C16 : 1ω7c/C16 : 1ω6c. The major polar lipids of strain R4BT were glycolipids, lipids and phospholipids. Phenotypic and phylogenetic characteristics also confirmed the independent status of the strains at the species level. Interestingly, strain R4BT was able to inhibit growth in vitro of
Paenibacillus larvae subsp. larvae
(causal agent of American foulbrood in honeybees) and
Melissococcus plutonius
(causal agent of European foulbrood). The name Lactobacillus apis sp. nov. is proposed for this novel taxon; the type strain is R4BT ( = CCM 8403T = LMG 26964T).
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Burgos MJG, Aguayo MCL, Pulido RP, Gálvez A, López RL. Multilocus sequence typing and antimicrobial resistance in Enterococcus faecium isolates from fresh produce. Antonie van Leeuwenhoek 2013; 105:413-21. [DOI: 10.1007/s10482-013-0073-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Accepted: 11/07/2013] [Indexed: 02/07/2023]
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24
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Huch M, De Bruyne K, Cleenwerck I, Bub A, Cho GS, Watzl B, Snauwaert I, Franz CMAP, Vandamme P. Streptococcus rubneri sp. nov., isolated from the human throat. Int J Syst Evol Microbiol 2013; 63:4026-4032. [PMID: 23749274 DOI: 10.1099/ijs.0.048538-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The novel, Gram-stain-positive, ovoid, lactic acid bacterial isolates LMG 27205, LMG 27206, LMG 27207(T) and MRI-F 18 were obtained from throat samples of healthy humans. 16S rRNA gene sequence analyses indicated that these isolates belong to the genus Streptococcus, specifically the Streptococcus mitis group, with Streptococcus australis and Streptococcus mitis as the nearest neighbours (99.45 and 98.56 % 16S rRNA gene sequence similarity to the respective type strains). Genotypic fingerprinting by fluorescent amplified fragment length polymorphism (FAFLP) and pulsed-field gel electrophoresis (PFGE), DNA-DNA hybridizations, comparative sequence analysis of pheS, rpoA and atpA and physiological and biochemical tests revealed that these bacteria formed a taxon well separated from its nearest neighbours and other species of the genus Streptococcus with validly published names and, therefore, represent a novel species, for which the name Streptococcus rubneri sp. nov. is proposed, with LMG 27207(T) ( = DSM 26920(T)) as the type strain.
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Affiliation(s)
- Melanie Huch
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Safety and Quality of Fruit and Vegetables, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Katrien De Bruyne
- Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Achim Bub
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Physiology and Biochemistry of Nutrition, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Gyu-Sung Cho
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Safety and Quality of Fruit and Vegetables, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Bernhard Watzl
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Physiology and Biochemistry of Nutrition, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Isabel Snauwaert
- Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Charles M A P Franz
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Safety and Quality of Fruit and Vegetables, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Peter Vandamme
- Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
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Padilla C, Lobos O. Virulence, bacterocin genes and antibacterial susceptibility in Enterococcus faecalis strains isolated from water wells for human consumption. SPRINGERPLUS 2013; 2:43. [PMID: 23449751 PMCID: PMC3579423 DOI: 10.1186/2193-1801-2-43] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 01/31/2013] [Indexed: 11/10/2022]
Abstract
The objectives of this study were to detect genes for virulence and bacteriocins in addition to studying the antimicrobial susceptibility of 78 strains of E. faecalis isolated from water wells for human consumption. The virulence and bacteriocin genes of 78 E. faecalis were amplified by PCR and visualized in agarose gels. The antimicrobial susceptibility was determined through diffusion agar tests and the MIC through microdilution. It was observed that the major percentage of virulence genes in the E. faecalis strains corresponds to aggA (93.5%). The bacteriocin gene entA (64.1%) is the most frequently detected. The studied strains exhibited different virulence and bacteriocin genes, and an important antibacterial resistance. The most common resistant phenotype (n = 14) corresponds to tetracycline and chloramphenicol and the less frequent (n = 2) to ciprofloxacin and moxifloxacin. Eight different genetic profiles were observed for virulence y bacteriocin genes. It was determined a statistical association between the bacterial resistance and some of the genetic profiles detected.
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Affiliation(s)
- Carlos Padilla
- Departamento de Microbiología, Universidad de Talca, Talca Camino Lircay s/n, Talca, Chile
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Niemi RM, Ollinkangas T, Paulin L, Švec P, Vandamme P, Karkman A, Kosina M, Lindström K. Enterococcus rivorum sp. nov., from water of pristine brooks. Int J Syst Evol Microbiol 2012; 62:2169-2173. [DOI: 10.1099/ijs.0.038257-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A significant number of
Enterococcus
strains from pristine waters of two brooks in Finland formed a distinct cluster on the basis of whole-cell protein fingerprinting by one-dimensional SDS-PAGE. The strains shared the following characteristics. Cells were ovoid, Gram-positive-staining and non-spore-forming, appearing singly or in pairs or chains. They were facultatively anaerobic and catalase-negative. Growth in broth containing 6.5 % NaCl or at 45 °C was weak or absent. Production of D antigen was variable. The strains tolerated 60 °C for 30 min, 40 % bile and tellurite, hydrolysed aesculin strongly and gelatin weakly, produced no acid from hippurate and did not reduce it, grew weakly at 10 °C, showed a strong reaction for the Voges–Proskauer test and produced acid from methyl α-d-glucoside, mannitol, sorbitol and sucrose, with weak or no production of acid from methyl α-d-mannoside, l-arabinose, gluconate and l-xylose. Several of the strains were selected for identification on the basis of sequencing of almost the whole 16S rRNA gene and partial atpA and pheS genes and of (GTG)5-PCR fingerprints. Partial atpA and pheS gene sequencing was also performed for those type strains of
Enterococcus
species without available sequences in the database. The pristine brook isolates formed a novel species, for which the name Enterococcus rivorum sp. nov. (type strain S299T = HAMBI 3055T = LMG 25899T = CCM 7986T) is proposed. On the basis of 16S rRNA gene sequence similarity, E. rivorum sp. nov. is related to the
Enterococcus faecalis
genogoup. It is distinguished from described
Enterococcus
species on the basis of 16S rRNA, atpA and pheS gene sequences and whole-cell protein and (GTG)5-PCR fingerprints. It is most closely related to
E. faecalis
, but DNA–DNA hybridization confirms it to represent a novel species.
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Affiliation(s)
- R. Maarit Niemi
- Finnish Environment Institute, Ecosystem Change, PO Box 140, FI-00251 Helsinki, Finland
| | - Tuula Ollinkangas
- Finnish Environment Institute, Ecosystem Change, PO Box 140, FI-00251 Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, PO Box 56, FI-00014 Helsinki, Finland
| | - Pavel Švec
- Masaryk University, Faculty of Science, Department of Experimental Biology, Czech Collection of Microorganisms (CCM), Tvrdého 14, Brno 60200, Czech Republic
| | - Peter Vandamme
- Laboratory of Bacteriology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Antti Karkman
- Department of Food and Environmental Sciences, Division of Microbiology, University of Helsinki, PO Box 56, FI-00014 Helsinki, Finland
| | - Marcel Kosina
- Masaryk University, Faculty of Science, Department of Experimental Biology, Czech Collection of Microorganisms (CCM), Tvrdého 14, Brno 60200, Czech Republic
| | - Kristina Lindström
- Department of Food and Environmental Sciences, Division of Microbiology, University of Helsinki, PO Box 56, FI-00014 Helsinki, Finland
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Bigwood T, Hudson JA, Cooney J, McIntyre L, Billington C, Heinemann JA, Wall F. Inhibition of Listeria monocytogenes by Enterococcus mundtii isolated from soil. Food Microbiol 2012; 32:354-60. [PMID: 22986201 DOI: 10.1016/j.fm.2012.07.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 07/23/2012] [Accepted: 07/30/2012] [Indexed: 11/15/2022]
Abstract
Two bacterial isolates with inhibitory activity against Listeria monocytogenes and Enterococcus faecalis were obtained from soil. Genotypic and phenotypic characterization identified them as Enterococcus mundtii, a species whose ability to compete with L. monocytogenes is relatively unexplored compared to other members of the genus. The thermal stability of the inhibitory factor and its sensitivity to proteolytic enzymes indicate that it is most likely a bacteriocin. Both isolates grew at comparable rates to L. monocytogenes at 5 °C and 10 °C in vitro. One isolate killed L. monocytogenes when it reached concentrations of 10(6)-10(8) CFU ml(-1). Minimum inocula of 10(6) and 10(5) CFU ml(-1) of E. mundtii were required to reduce and maintain L. monocytogenes concentrations beneath the level of detection at 5 °C and 10 °C, respectively. In situ experiments at 5 °C showed that E. mundtii inhibited the growth of L. monocytogenes on vacuum-packed cold smoked salmon during its four week shelf life. E. mundtii could, therefore, control the growth of L. monocytogenes at low temperatures, indicating a potential application in controlling this pathogen in chilled foods. To control growth of Listeria, the concentration of E. mundtii needs to be high, but it is possible that a purified bacteriocin could be used to achieve the same effect.
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Affiliation(s)
- T Bigwood
- Food Safety Programme, Institute of Environmental Science and Research Ltd (ESR), Christchurch Science Centre, PO Box 29-181, Ilam, Christchurch, New Zealand.
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Ao X, Zhang X, Zhang X, Shi L, Zhao K, Yu J, Dong L, Cao Y, Cai Y. Identification of lactic acid bacteria in traditional fermented yak milk and evaluation of their application in fermented milk products. J Dairy Sci 2012; 95:1073-84. [PMID: 22365191 DOI: 10.3168/jds.2011-4224] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 11/14/2011] [Indexed: 11/19/2022]
Abstract
In this study, 53 strains of lactic acid bacteria (LAB) isolated from Xueo, a traditional fermented yak milk in the western Sichuan Plateau of China, were identified and their use in fermented milk was evaluated. All gram-positive and catalase-negative strains were divided into 6 groups at the level of 87% similarity using amplified ribosomal DNA restriction analysis. These groups were identified as 6 species using 16S rDNA sequence analysis and atpA gene analysis. The dominant LAB strains in Xueo were Enterococcus durans, Lactobacillus fermentum, and Lactobacillus paracasei, accounting for 45.3, 22.6, and 17.0% of isolates, respectively. Milk fermented with most of the representative strains was high in quality, exhibiting relatively high viscosity, moderate acidity, good sensory quality, and high counts of viable LAB. Fermented milk of E. durans SCA16 and L. fermentum SCA52 achieved the highest scores for overall sensory quality. Most strains displayed antimicrobial activity against at least 1 of 9 spoilage microorganisms. Lactic acid was the main factor inhibiting the growth of spoilage bacteria, and H(2)O(2) was also inhibitory to some extent. Excluding the influence of acid and H(2)O(2), strains SCA52 (L. fermentum) and SCA7 (Lactobacillus plantarum) were antagonistic against some of the indicators, suggesting that the 2 strains may produce a bacteriocin-like substance. Therefore, the development of superior strains isolated from Xueo to ferment milk with similar flavor and texture to Xueo is expected.
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Affiliation(s)
- X Ao
- Sichuan Agricultural University, Yaan, Sichuan 625000, China
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Ferrario C, Ricci G, Borgo F, Rollando A, Fortina MG. Genetic investigation within Lactococcus garvieae revealed two genomic lineages. FEMS Microbiol Lett 2012; 332:153-61. [DOI: 10.1111/j.1574-6968.2012.02591.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 04/24/2012] [Accepted: 05/03/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Chiara Ferrario
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche; Sezione di Microbiologia Industriale; Università degli Studi di Milano; Milan; Italy
| | - Giovanni Ricci
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche; Sezione di Microbiologia Industriale; Università degli Studi di Milano; Milan; Italy
| | - Francesca Borgo
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche; Sezione di Microbiologia Industriale; Università degli Studi di Milano; Milan; Italy
| | - Alessandro Rollando
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche; Sezione di Microbiologia Industriale; Università degli Studi di Milano; Milan; Italy
| | - Maria Grazia Fortina
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche; Sezione di Microbiologia Industriale; Università degli Studi di Milano; Milan; Italy
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Borgo F, Ferrario C, Ricci G, Fortina MG. Genotypic intraspecies heterogeneity of Enterococcus italicus: data from dairy environments. J Basic Microbiol 2012; 53:20-8. [PMID: 22581461 DOI: 10.1002/jobm.201100464] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 11/26/2011] [Indexed: 11/08/2022]
Abstract
The diversity of a collection of 19 Enterococcus italicus strains isolated from different dairy sources was explored using a molecular polyphasic approach, comprising random amplification of polymorphic DNA (RAPD-PCR), repetitive element PCR (REP-PCR), plasmid profiling and ribotyping. The data obtained showed a high-level of biodiversity, not always correlated to the niche of isolation. Particularly, REP-PCR with primer BOXA1R and plasmid profiling allowed the best discrimination at strain level. Exploiting the genome shotgun sequence of the type strain of the species, available in public database, genes related to insertion sequences present on enterococcal Pathogenic Islands (ISEf1, IS905), determinants related to virulence factors (codifying for hemolysin and cell wall surface proteins), exogenously DNA (conjugal transfer protein, replication plasmid protein, pheromone shutdown protein, phage integrase/recombinase) and penicillin binding proteins system were detected. The presence of most of these genes seemed a common genetic trait in the Enterococcus genus, sur gene (cell wall surface protein) was only detected in strains of E. italicus. To our knowledge, this is the first time that specific primers, with the expection of the species-specific probe targeted to 16S rRNA gene, have been designed for this species.
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Affiliation(s)
- Francesca Borgo
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Sezione di Microbiologia Industriale, Università degli Studi di Milano, Milan, Italy.
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Identification of enterococci from broiler products and a broiler processing plant and description of Enterococcus viikkiensis sp. nov. Appl Environ Microbiol 2010; 77:1196-203. [PMID: 21183650 DOI: 10.1128/aem.02412-10] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In two previous studies dealing with lactic acid bacteria (LAB) from modified-atmosphere-packaged (MAP) broiler products and a broiler processing plant, several isolates remained unidentified. According to 16S rRNA gene sequence analysis, 36 isolates were assigned to the genus Enterococcus. Numerical analysis of combined HindIII and EcoRI ribopatterns of these isolates resulted in species-specific clusters that were congruent with the clusters obtained by both DNA-directed RNA polymerase subunit A (rpoA) and phenylalanyl-tRNA synthetase α chain (pheS) housekeeping gene analyses. In the analyses, a group of five isolates distinct from any known enterococcal species clustered together. The five isolates were positioned in the Enterococcus avium group, with E. devriesei being the closest phylogenetic neighbor. The DNA-DNA hybridization levels with E. devriesei ranged from 28.8 to 54.3% and indicated that these strains represented a novel species. The name Enterococcus viikkiensis sp. nov. is proposed, with strain DSM 24043(T) (LMG 26075(T)) being the type strain. Our study demonstrated that the identification of enterococci within the E. avium phylogenetic group demands polyphasic taxonomic approaches. The rpoA and pheS gene similarities (99.0 to 99.2% and 94.3 to 95.4%, respectively) between E. viikkiensis and its closest phylogenetic neighbor, E. devriesei, were higher than those previously reported within the enterococci. In addition, the phenotypic profiles of the species in the E. avium group were also highly similar, and some traits were found to be misleading for enterococci, such as E. viikkiensis does not grow at 45°C. The numerical analysis of combined HindIII and EcoRI ribopatterns was of considerable assistance in distinguishing enterococcal species within the E. avium group.
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Watanabe S, Kobayashi N, Quiñones D, Hayakawa S, Nagashima S, Uehara N, Watanabe N. Genetic diversity of the low-level vancomycin resistance gene vanC-2/vanC-3 and identification of a novel vanC subtype (vanC-4) in Enterococcus casseliflavus. Microb Drug Resist 2010; 15:1-9. [PMID: 19216682 DOI: 10.1089/mdr.2009.0856] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An intrinsic low-level vancomycin resistance (VanC phenotype) in Enterococcus casseliflavus is conferred by either of two subtypes of vanC genes, that is, vanC-2 or vanC-3, which are genetically closely related. To know genetic diversity of vanC-2/C-3 genes among E. casseliflavus, nucleotide sequences of vanC-2/C-3 and other genetic components in vanC gene cluster (vanXYc, vanTc, vanRc, and vanSc) were analyzed for nine clinical isolates and four standard strains that showed low-level vancomycin resistance. While the vanC-2/C-3 gene sequences showed 93-100% identities among the strains examined, two genetic groups were discriminated by phylogenetic analysis: one closely related to the previously reported vanC-2 or vanC-3 genes (vanC-2/C-3 genotype) with 98-100% identity, and the other distinct from the vanC-2/C-3 genotype (93-95% identity). The latter group found in three clinical isolates was considered as a new subtype of vanC and tentatively designated as vanC-4. Between strains with the vanC-2/C-3 genotype and those with vanC-4, vanXYc genes were also genetically discriminated with 92-93% identity. Similar sequence diversity was observed for vanTc, vanRc, and vanSc (88-93% identity). Clonal relatedness among the E. casseliflavus strains was investigated by phylogenetic analysis of atpA gene. While among E. casseliflavus strains with vanC-2/C-3 genotype, extremely high sequence identities of atpA were found (98.7% or higher), these strains showed slightly lower identity to those with vanC-4 (94-96%). These two groups of E. casseliflavus strains were also discriminated by genotyping with arbitrarily primed PCR. These findings indicated that among E. casseliflavus there are at least two genetic lineages with the distinct vanC genes, that is, a single subtype including previously known vanC-2/C-3, and a novel subtype vanC-4.
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Affiliation(s)
- Shojiro Watanabe
- Department of Hygiene, Sapporo Medical University School of Medicine, Chuo-ku, Sapporo, Japan
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Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island. BMC Genomics 2010; 11:239. [PMID: 20398277 PMCID: PMC2858755 DOI: 10.1186/1471-2164-11-239] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 04/14/2010] [Indexed: 02/07/2023] Open
Abstract
Background The Gram-positive bacterium Enterococcus faecium is an important cause of nosocomial infections in immunocompromized patients. Results We present a pyrosequencing-based comparative genome analysis of seven E. faecium strains that were isolated from various sources. In the genomes of clinical isolates several antibiotic resistance genes were identified, including the vanA transposon that confers resistance to vancomycin in two strains. A functional comparison between E. faecium and the related opportunistic pathogen E. faecalis based on differences in the presence of protein families, revealed divergence in plant carbohydrate metabolic pathways and oxidative stress defense mechanisms. The E. faecium pan-genome was estimated to be essentially unlimited in size, indicating that E. faecium can efficiently acquire and incorporate exogenous DNA in its gene pool. One of the most prominent sources of genomic diversity consists of bacteriophages that have integrated in the genome. The CRISPR-Cas system, which contributes to immunity against bacteriophage infection in prokaryotes, is not present in the sequenced strains. Three sequenced isolates carry the esp gene, which is involved in urinary tract infections and biofilm formation. The esp gene is located on a large pathogenicity island (PAI), which is between 64 and 104 kb in size. Conjugation experiments showed that the entire esp PAI can be transferred horizontally and inserts in a site-specific manner. Conclusions Genes involved in environmental persistence, colonization and virulence can easily be aquired by E. faecium. This will make the development of successful treatment strategies targeted against this organism a challenge for years to come.
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Global spread of the hyl(Efm) colonization-virulence gene in megaplasmids of the Enterococcus faecium CC17 polyclonal subcluster. Antimicrob Agents Chemother 2010; 54:2660-5. [PMID: 20385861 DOI: 10.1128/aac.00134-10] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Enterococcus faecium has increasingly been reported as a nosocomial pathogen since the early 1990s, presumptively associated with the expansion of a human-associated Enterococcus faecium polyclonal subcluster known as clonal complex 17 (CC17) that has progressively acquired different antibiotic resistance (ampicillin and vancomycin) and virulence (esp(Efm), hyl(Efm), and fms) traits. We analyzed the presence and the location of a putative glycoside hydrolase hyl(Efm) gene among E. faecium strains obtained from hospitalized patients (255 patients; outbreak, bacteremic, and/or disseminated isolates from 23 countries and five continents; 1986 to 2009) and from nonclinical origins (isolates obtained from healthy humans [25 isolates], poultry [30], swine [90], and the environment [55]; 1999 to 2007). Clonal relatedness was established by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Plasmid analysis included determination of content and size (S1-PFGE), transferability (filter mating), screening of Rep initiator proteins (PCR), and location of vanA, vanB, ermB, and hyl(Efm) genes (S1/I-CeuI hybridization). Most E. faecium isolates contained large plasmids (>150 kb) and showed variable contents of van, hyl(Efm), or esp(Efm). The hyl(Efm) gene was associated with megaplasmids (170 to 375 kb) of worldwide spread (ST16, ST17, and ST18) or locally predominant (ST192, ST203, ST280, and ST412) ampicillin-resistant CC17 clones collected in the five continents since the early 1990s. All but one hyl(Efm)-positive isolate belonged to the CC17 polyclonal subcluster. The presence of hyl(Efm) megaplasmids among CC17 from Europe, Australia, Asia, and Africa since at least the mid-1990s was documented. This study further demonstrates the pandemic expansion of particular CC17 clones before acquisition of vancomycin resistance and putative virulence traits and describes the presence of megaplasmids in most of the contemporary E. faecium isolates with different origins.
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Willems RJL, van Schaik W. Transition of Enterococcus faecium from commensal organism to nosocomial pathogen. Future Microbiol 2009; 4:1125-35. [DOI: 10.2217/fmb.09.82] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The Gram-positive species Enterococcus faecium has long been thought of as a harmless commensal of the mammalian GI tract. In the last two decades, however, E. faecium has become an important cause of nosocomial bacteremias. These infections are often difficult to treat owing to the resistance of E. faecium to a large number of antibiotics. In this article, we review the recent transition of E. faecium from commensal to nosocomial pathogen. We focus on population biology-based studies, which suggest that several clonal populations of E. faecium are mostly responsible for causing infections. We also discuss the role of the accessory genome of E. faecium in contributing to the infectious phenotype and examine the role that surface proteins of E. faecium may have in colonization and infection.
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Affiliation(s)
- Rob JL Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Room G04.614, 3584 CX Utrecht, The Netherlands
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Room G04.614, 3584 CX Utrecht, The Netherlands
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Viau E, Peccia J. Evaluation of the enterococci indicator in biosolids using culture-based and quantitative PCR assays. WATER RESEARCH 2009; 43:4878-4887. [PMID: 19781735 DOI: 10.1016/j.watres.2009.09.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 08/18/2009] [Accepted: 09/06/2009] [Indexed: 05/28/2023]
Abstract
The utility of the enterococci indicator for measuring biosolids quality was evaluated in biosolids from 22 U.S. wastewater treatment facilities. Enterococci were enumerated using 23S rRNA quantitative PCR (qPCR) and membrane filtration with mEI-agar culture analyses in biosolids collected after mesophilic anaerobic digestion (MAD, class B, 13 treatment plants), composting (class A, 10 treatment plants), and temperature-phased anaerobic digestion (TPAD, class A, six treatment plants). Enterococci qPCR and culture values were not significantly different for a given treatment (P>0.05, paired t-test) and both assays showed differences in biosolid treatment effectiveness-anaerobic digestion treatments averaged 5-5.5log genomic units (GU) and colony forming units (CFU)/dry g while composting decreased enterococci on average to 3.7logGU and 3.8logCFU/dry g. Only in class A TPAD biosolids dewatered with a belt-filter press were culture values significantly lower than qPCR values (1.7logCFU/dryg vs. 5GU/dryg). Further investigation of compost inactivation was compared for enterococci and other fecal indicators (n=5 treatment plants)-the enterococci indicator was more resistant to compost treatment than fecal coliforms, with reductions averaging only 1-2.5 logs for enterococci, male-specific coliphages, and sulfite-reducing Clostridia while 5-log reductions were observed for fecal coliforms. Lastly, biosolid isolates from culture-based methods were identified using DNA sequencing-these results revealed that non-enterococci, including Bacillus spp. and Vagococcus spp., were commonly isolated from compost and TPAD biosolids using mEI agar. Given the equivalency of culture- and qPCR-based enterococci concentrations in biosolids and the more conservative inactivation noted for both assays during class A composting, the use of enterococci qPCR monitoring could bypass non-specificity issues with culture-based methods while providing an improved description of pathogen fate in biosolids.
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Affiliation(s)
- Emily Viau
- Department of Chemical Engineering, Environmental Engineering Program, Yale University, New Haven, CT 06520, USA
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Detection and quantification of Enterococcus gilvus in cheese by real-time PCR. Syst Appl Microbiol 2009; 32:514-21. [DOI: 10.1016/j.syapm.2009.07.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Indexed: 11/20/2022]
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39
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Development and validation of a species-independent functional gene microarray that targets lactic acid bacteria. Appl Environ Microbiol 2009; 75:6488-95. [PMID: 19684161 DOI: 10.1128/aem.01055-09] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
During the last few years, genome-related information has become available for many microorganisms, including important food-related bacteria. Lactic acid bacteria (LAB) are important industrially in the production of fermented foods such as dairy products, sausages, sourdoughs, and vegetables. Despite their limited metabolic capacity, LAB contribute considerably to important characteristics of fermented foods, such as flavor and texture. In the present study, a species-independent functional gene microarray was developed that targets 406 genes that play key roles in the production of sugar catabolites, bacteriocins, exopolysaccharides, and aromas, in probiotic and biosafety characteristics, and in the stress response. Also, genes linked to negative traits, such as antibiotic resistance and virulence, are represented. As LAB ecosystems contain a variety of species, there was a more global focus on these specific functional properties. Thus, an algorithm was used to design gene-specific oligonucleotides that preferably hybridize with multiple LAB species, thereby allowing controlled cross-hybridization. For proof of concept, the microarray composed of 2,269 30-mer oligonucleotides focused on LAB species that are prevalent in sourdough ecosystems. Validation hybridizations using DNA and RNA from 18 LAB strains, covering 86% of all the oligonucleotides, showed that there were wide ranges in intensity and high reproducibility between microarrays.
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40
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Cottyn B, Heylen K, Heyrman J, Vanhouteghem K, Pauwelyn E, Bleyaert P, Van Vaerenbergh J, Höfte M, De Vos P, Maes M. Pseudomonas cichorii as the causal agent of midrib rot, an emerging disease of greenhouse-grown butterhead lettuce in Flanders. Syst Appl Microbiol 2009; 32:211-25. [PMID: 19157742 DOI: 10.1016/j.syapm.2008.11.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Bacterial midrib rot of greenhouse-grown butterhead lettuce (Lactuca sativa L. var. capitata) is an emerging disease in Flanders (Belgium) and fluorescent pseudomonads are suspected to play an important role in the disease. Isolations from infected lettuces, collected from 14 commercial greenhouses in Flanders, yielded 149 isolates that were characterized polyphasically, which included morphological characteristics, pigmentation, pathogenicity tests by both injection and spraying of lettuce, LOPAT characteristics, FAME analysis, BOX-PCR fingerprinting, 16S rRNA and rpoB gene sequencing, as well as DNA-DNA hybridization. Ninety-eight isolates (66%) exhibited a fluorescent pigmentation and were associated with the genus Pseudomonas. Fifty-five of them induced an HR+ (hypersensitive reaction in tobacco leaves) response. The other 43 fluorescent isolates were most probably saprophytic bacteria and about half of them were able to cause rot on potato tuber slices. BOX-PCR genomic fingerprinting was used to assess the genetic diversity of the Pseudomonas midrib rot isolates. The delineated BOX-PCR patterns matched quite well with Pseudomonas morphotypes defined on the basis of colony appearance and variation in fluorescent pigmentation. 16S rRNA and rpoB gene sequence analyses allowed most of the fluorescent isolates to be allocated to Pseudomonas, and they belonged to either the Pseudomonas fluorescens group, Pseudomonas putida group, or the Pseudomonas cichorii/syringae group. In particular, the isolates allocated to this latter group constituted the vast majority of HR+ isolates and were identified as P. cichorii by DNA-DNA hybridization. They were demonstrated by spray-inoculation tests on greenhouse-grown lettuce to induce the midrib rot disease and could be re-isolated from lesions of inoculated plants. Four HR+ non-fluorescent isolates associated with one sample that showed an atypical midrib rot were identified as Dickeya sp.
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Affiliation(s)
- Bart Cottyn
- Plant-Crop Protection, Institute for Agricultural and Fisheries Research (ILVO), Burg. Van Gansberghelaan 96, B-9820 Merelbeke, Belgium.
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41
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Marchand S, Heylen K, Messens W, Coudijzer K, De Vos P, Dewettinck K, Herman L, De Block J, Heyndrickx M. Seasonal influence on heat-resistant proteolytic capacity of Pseudomonas lundensis and Pseudomonas fragi, predominant milk spoilers isolated from Belgian raw milk samples. Environ Microbiol 2009; 11:467-82. [PMID: 19196277 DOI: 10.1111/j.1462-2920.2008.01785.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Psychrotolerant bacteria and their heat-resistant proteases play a major role in the spoilage of UHT-processed dairy products. Summer and winter raw milk samples were screened for the presence of such bacteria. One hundred and three proteolytic psychrotolerant bacteria were isolated, characterized by API tests, rep-PCR fingerprint analysis and evaluated for heat-resistant protease production. Twenty-nine strains (representing 79% of the complete collection) were further identified by 16S rRNA gene sequencing, rpoB gene sequencing and DNA-DNA hybridizations. A seasonal inter- and intra-species influence on milk spoilage capacity (e.g. growth rate and/or protease production) was demonstrated. Moreover, this polyphasic approach led to the identification of Pseudomonas fragi and Pseudomonas lundensis (representing 53% of all isolates) as predominant producers of heat-resistant proteases in raw milk. The role of Pseudomonas fluorescens, historically reported as important milk spoiler, could not unequivocally be established. The use of more reliable identification techniques and further revision of the taxonomy of P. fluorescens will probably result in a different perspective on its role in the milk spoilage issue.
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Affiliation(s)
- Sophie Marchand
- Institute for Agricultural and Fisheries Research, Technology and Food Unit (ILVO-T&V), Melle, Belgium.
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42
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De Bruyne K, Franz CMAP, Vancanneyt M, Schillinger U, Mozzi F, de Valdez GF, De Vuyst L, Vandamme P. Pediococcus argentinicus sp. nov. from Argentinean fermented wheat flour and identification of Pediococcus species by pheS, rpoA and atpA sequence analysis. Int J Syst Evol Microbiol 2009; 58:2909-16. [PMID: 19060081 DOI: 10.1099/ijs.0.65833-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, small coccus-shaped lactic acid bacterium, strain LMG 23999(T), was isolated from Argentinean wheat flour. 16S rRNA gene sequence analysis revealed that the phylogenetic position of the novel strain was within the genus Pediococcus, with Pediococcus stilesii, Pediococcus pentosaceus and Pediococcus acidilactici as its closest relatives (97.7, 97.3 and 96.9 % gene sequence similarity, respectively). Fluorescent amplified fragment length polymorphism fingerprinting of whole genomes and whole-cell protein electrophoresis confirmed the unique taxonomic status of the novel strain. DNA-DNA hybridizations, DNA G+C content determination, comparative sequence analysis of the pheS, rpoA and atpA genes and physiological and biochemical characterization demonstrated that strain LMG 23999(T) (=CCUG 54535(T)=CRL 776(T)) represents a novel species for which the name Pediococcus argentinicus sp. nov. is proposed. Multi-locus sequence analysis based on pheS, rpoA and atpA genes was found to be a suitable method for the identification of species of the genus Pediococcus.
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43
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Martín B, Corominas L, Garriga M, Aymerich T. Identification and tracing ofEnterococcusspp. by RAPD-PCR in traditional fermented sausages and meat environment. J Appl Microbiol 2009; 106:66-77. [DOI: 10.1111/j.1365-2672.2008.03976.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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44
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Coorevits A, De Jonghe V, Vandroemme J, Reekmans R, Heyrman J, Messens W, De Vos P, Heyndrickx M. Comparative analysis of the diversity of aerobic spore-forming bacteria in raw milk from organic and conventional dairy farms. Syst Appl Microbiol 2008; 31:126-40. [DOI: 10.1016/j.syapm.2008.03.002] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2007] [Indexed: 11/16/2022]
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45
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Martín B, Garriga M, Aymerich T. Identification of Enterococcus species by melting curve analysis of restriction fragments. J Microbiol Methods 2008; 75:145-7. [PMID: 18558446 DOI: 10.1016/j.mimet.2008.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 04/01/2008] [Accepted: 05/05/2008] [Indexed: 11/16/2022]
Abstract
A new method for the identification of Enterococcus species has been developed. It combines PCR amplification of sodA gene and 16S-23S intergenic spacer region with restriction enzyme digestion followed by a melting curve analysis of the restriction fragments (MCARF). All strains analyzed were correctly identified by MCARF. This method was proved to be a reliable enterococcal identification tool.
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Affiliation(s)
- Belén Martín
- Institute for Food and Agricultural Research and Technology (IRTA), Finca Camps i Armet, E-17121 Monells, Spain
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46
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Naser SM, Dawyndt P, Hoste B, Gevers D, Vandemeulebroecke K, Cleenwerck I, Vancanneyt M, Swings J. Identification of lactobacilli by pheS and rpoA gene sequence analyses. Int J Syst Evol Microbiol 2008; 57:2777-2789. [PMID: 18048724 DOI: 10.1099/ijs.0.64711-0] [Citation(s) in RCA: 219] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aim of this study was to evaluate the use of the phenylalanyl-tRNA synthase alpha subunit (pheS) and the RNA polymerase alpha subunit (rpoA) partial gene sequences for species identification of members of the genus Lactobacillus. Two hundred and one strains representing the 98 species and 17 subspecies were examined. The pheS gene sequence analysis provided an interspecies gap, which in most cases exceeded 10 % divergence, and an intraspecies variation of up to 3 %. The rpoA gene sequences revealed a somewhat lower resolution, with an interspecies gap normally exceeding 5 % and an intraspecies variation of up to 2 %. The combined use of pheS and rpoA gene sequences offers a reliable identification system for nearly all species of the genus Lactobacillus. The pheS and rpoA gene sequences provide a powerful tool for the detection of potential novel Lactobacillus species and synonymous taxa. In conclusion, the pheS and rpoA gene sequences can be used as alternative genomic markers to 16S rRNA gene sequences and have a higher discriminatory power for reliable identification of species of the genus Lactobacillus.
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Affiliation(s)
- Sabri M Naser
- Department of Biology and Biotechnology, Faculty of Sciences, An-Najah National University, Nablus, Palestine
| | - Peter Dawyndt
- Department of Applied Mathematics, Biometrics and Process Control, Ghent University, Coupure links 653, Ghent 9000, Belgium.,Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Bart Hoste
- BCCMTM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Dirk Gevers
- Bioinformatics and Evolutionary Genomics, Ghent University/VIB, Technologiepark 927, Ghent 9052, Belgium.,Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
| | | | - Ilse Cleenwerck
- BCCMTM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Marc Vancanneyt
- BCCMTM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Jean Swings
- BCCMTM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium.,Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, Ghent 9000, Belgium
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47
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De Bruyne K, Schillinger U, Caroline L, Boehringer B, Cleenwerck I, Vancanneyt M, De Vuyst L, Franz CMAP, Vandamme P. Leuconostoc holzapfelii sp. nov., isolated from Ethiopian coffee fermentation and assessment of sequence analysis of housekeeping genes for delineation of Leuconostoc species. Int J Syst Evol Microbiol 2008; 57:2952-2959. [PMID: 18048756 DOI: 10.1099/ijs.0.65292-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, ovoid lactic acid bacterium, strain LMG 23990(T), was isolated from Ethiopian coffee fermentation. 16S rRNA gene sequence analysis indicated that the novel strain belongs to the genus Leuconostoc, with Leuconostoc citreum and Leuconostoc lactis as the closest neighbours (99.6 and 99.0 % 16S rRNA gene sequence similarity, respectively). Genotypic fingerprinting by fluorescent amplified fragment length polymorphism, whole-cell protein electrophoresis, DNA-DNA hybridizations, comparative sequence analysis of pheS, rpoA, atpA, and physiological and biochemical tests allowed us to differentiate strain LMG 23990(T) from all established Leuconostoc species. Strain LMG 23990(T) (=CCUG 54536(T)) therefore represents a novel species, for which the name Leuconostoc holzapfelii sp. nov. is proposed.
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Affiliation(s)
- Katrien De Bruyne
- Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Ulrich Schillinger
- Federal Research Centre for Nutrition and Food, Institute of Hygiene and Toxicology, Haid-und-Neu-Strasse 9, D-76131 Karlsruhe, Germany
| | - Lily Caroline
- Federal Research Centre for Nutrition and Food, Institute of Hygiene and Toxicology, Haid-und-Neu-Strasse 9, D-76131 Karlsruhe, Germany
| | - Benjamin Boehringer
- Federal Research Centre for Nutrition and Food, Institute of Hygiene and Toxicology, Haid-und-Neu-Strasse 9, D-76131 Karlsruhe, Germany
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Marc Vancanneyt
- BCCM/LMG Bacteria Collection, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Applied Biological Sciences and Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Charles M A P Franz
- Federal Research Centre for Nutrition and Food, Institute of Hygiene and Toxicology, Haid-und-Neu-Strasse 9, D-76131 Karlsruhe, Germany
| | - Peter Vandamme
- Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
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48
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Biosafety assessment of probiotics used for human consumption: recommendations from the EU-PROSAFE project. Trends Food Sci Technol 2008. [DOI: 10.1016/j.tifs.2007.07.013] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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49
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Thompson CC, Thompson FL, Vicente ACP, Swings J. Phylogenetic analysis of vibrios and related species by means of atpA gene sequences. Int J Syst Evol Microbiol 2007; 57:2480-2484. [DOI: 10.1099/ijs.0.65223-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We investigated the use of atpA gene sequences as alternative phylogenetic and identification markers for vibrios. A fragment of 1322 bp (corresponding to approximately 88 % of the coding region) was analysed in 151 strains of vibrios. The relationships observed were in agreement with the phylogeny inferred from 16S rRNA gene sequence analysis. For instance, the Vibrio cholerae, Vibrio
halioticoli, Vibrio
harveyi and Vibrio
splendidus species groups appeared in the atpA gene phylogenetic analyses, suggesting that these groups may be considered as separate genera within the current Vibrio genus. Overall, atpA gene sequences appeared to be more discriminatory for species differentiation than 16S rRNA gene sequences. 16S rRNA gene sequence similarities above 97 % corresponded to atpA gene sequences similarities above 80 %. The intraspecies variation in the atpA gene sequence was about 99 % sequence similarity. The results showed clearly that atpA gene sequences are a suitable alternative for the identification and phylogenetic study of vibrios.
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Affiliation(s)
- Cristiane C. Thompson
- Department of Genetics, Federal University of Rio de Janeiro, Brazil
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | | | - Jean Swings
- Laboratory of Microbiology and BCCM/LMG Bacteria Collection, Ghent University, Belgium
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50
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Leisner JJ, Laursen BG, Prévost H, Drider D, Dalgaard P. Carnobacterium: positive and negative effects in the environment and in foods. FEMS Microbiol Rev 2007; 31:592-613. [PMID: 17696886 PMCID: PMC2040187 DOI: 10.1111/j.1574-6976.2007.00080.x] [Citation(s) in RCA: 227] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The genus Carnobacterium contains nine species, but only C. divergens and C. maltaromaticum are frequently isolated from natural environments and foods. They are tolerant to freezing/thawing and high pressure and able to grow at low temperatures, anaerobically and with increased CO2 concentrations. They metabolize arginine and various carbohydrates, including chitin, and this may improve their survival in the environment. Carnobacterium divergens and C. maltaromaticum have been extensively studied as protective cultures in order to inhibit growth of Listeria monocytogenes in fish and meat products. Several carnobacterial bacteriocins are known, and parameters that affect their production have been described. Currently, however, no isolates are commercially applied as protective cultures. Carnobacteria can spoil chilled foods, but spoilage activity shows intraspecies and interspecies variation. The responsible spoilage metabolites are not well characterized, but branched alcohols and aldehydes play a partial role. Their production of tyramine in foods is critical for susceptible individuals, but carnobacteria are not otherwise human pathogens. Carnobacterium maltaromaticum can be a fish pathogen, although carnobacteria are also suggested as probiotic cultures for use in aquaculture. Representative genome sequences are not yet available, but would be valuable to answer questions associated with fundamental and applied aspects of this important genus.
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Affiliation(s)
- Jørgen J Leisner
- Department of Veterinary Pathobiology, Faculty of Life Sciences, University of Copenhagen, Grønnegårdsvej 15, DK-1870 Frederiksberg C., Denmark.
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