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Decadt H, Weckx S, De Vuyst L. The rotation of primary starter culture mixtures results in batch-to-batch variations during Gouda cheese production. Front Microbiol 2023; 14:1128394. [PMID: 36876114 PMCID: PMC9978159 DOI: 10.3389/fmicb.2023.1128394] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/24/2023] [Indexed: 02/18/2023] Open
Abstract
Industrial production of Gouda cheeses mostly relies on a rotated use of different mixed-strain lactic acid bacteria starter cultures to avoid phage infections. However, it is unknown how the application of these different starter culture mixtures affect the organoleptic properties of the final cheeses. Therefore, the present study assessed the impact of three different starter culture mixtures on the batch-to-batch variations among Gouda cheeses from 23 different batch productions in the same dairy company. Both the cores and rinds of all these cheeses were investigated after 36, 45, 75, and 100 weeks of ripening by metagenetics based on high-throughput full-length 16S rRNA gene sequencing accompanied with an amplicon sequence variant (ASV) approach as well as metabolite target analysis of non-volatile and volatile organic compounds. Up to 75 weeks of ripening, the acidifying Lactococcus cremoris and Lactococcus lactis were the most abundant bacterial species in the cheese cores. The relative abundance of Leuconostoc pseudomesenteroides was significantly different for each starter culture mixture. This impacted the concentrations of some key metabolites, such as acetoin produced from citrate, and the relative abundance of non-starter lactic acid bacteria (NSLAB). Cheeses with the least Leuc. pseudomesenteroides contained more NSLAB, such as Lacticaseibacillus paracasei that was taken over by Tetragenococcus halophilus and Loigolactobacillus rennini upon ripening time. Taken together, the results indicated a minor role of leuconostocs in aroma formation but a major impact on the growth of NSLAB. The relative abundance of T. halophilus (high) and Loil. rennini (low) increased with ripening time from rind to core. Two main ASV clusters of T. halophilus could be distinguished, which were differently correlated with some metabolites, both beneficial (regarding aroma formation) and undesirable ones (biogenic amines). A well-chosen T. halophilus strain could be a candidate adjunct culture for Gouda cheese production.
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Affiliation(s)
- Hannes Decadt
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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2
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Daranas N, Roselló G, Cabrefiga J, Donati I, Francés J, Badosa E, Spinelli F, Montesinos E, Bonaterra A. Biological control of bacterial plant diseases with Lactobacillus plantarum strains selected for their broad-spectrum activity. THE ANNALS OF APPLIED BIOLOGY 2019; 174:92-105. [PMID: 30686827 PMCID: PMC6334523 DOI: 10.1111/aab.12476] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/02/2018] [Accepted: 10/26/2018] [Indexed: 05/06/2023]
Abstract
The use of lactic acid bacteria (LAB) to control multiple pathogens that affect different crops was studied, namely, Pseudomonas syringae pv. actinidiae in kiwifruit, Xanthomonas arboricola pv. pruni in Prunus and Xanthomonas fragariae in strawberry. A screening procedure based on in vitro and in planta assays of the three bacterial pathogens was successful in selecting potential LAB strains as biological control agents. The antagonistic activity of 55 strains was first tested in vitro and the strains Lactobacillus plantarum CC100, PM411 and TC92, and Leuconostoc mesenteroides CM160 and CM209 were selected because of their broad-spectrum activity. The biocontrol efficacy of the selected strains was assessed using a multiple-pathosystem approach in greenhouse conditions. L. plantarum PM411 and TC92 prevented all three pathogens from infecting their corresponding plant hosts. In addition, the biocontrol performance of PM411 and TC92 was comparable to the reference products (Bacillus amyloliquefaciens D747, Bacillus subtilis QST713, chitosan, acibenzolar-S-methyl, copper and kasugamycin) in semi-field and field experiments. The in vitro inhibitory mechanism of PM411 and TC92 is based, at least in part, on a pH lowering effect and the production of lactic acid. Moreover, both strains showed similar survival rates on leaf surfaces. PM411 and TC92 can easily be distinguished because of their different multilocus sequence typing and random amplified polymorphic DNA profiles.
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Affiliation(s)
- Núria Daranas
- Institute of Food and Agricultural Technology‐CIDSAV‐XaRTAUniversity of GironaGironaSpain
| | - Gemma Roselló
- Institute of Food and Agricultural Technology‐CIDSAV‐XaRTAUniversity of GironaGironaSpain
| | - Jordi Cabrefiga
- Institute of Food and Agricultural Technology‐CIDSAV‐XaRTAUniversity of GironaGironaSpain
| | - Irene Donati
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater StudiorumUniversity of BolognaBolognaItaly
| | - Jesús Francés
- Institute of Food and Agricultural Technology‐CIDSAV‐XaRTAUniversity of GironaGironaSpain
| | - Esther Badosa
- Institute of Food and Agricultural Technology‐CIDSAV‐XaRTAUniversity of GironaGironaSpain
| | - Francesco Spinelli
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater StudiorumUniversity of BolognaBolognaItaly
| | - Emilio Montesinos
- Institute of Food and Agricultural Technology‐CIDSAV‐XaRTAUniversity of GironaGironaSpain
| | - Anna Bonaterra
- Institute of Food and Agricultural Technology‐CIDSAV‐XaRTAUniversity of GironaGironaSpain
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3
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Monitoring Viable Cells of the Biological Control Agent Lactobacillus plantarum PM411 in Aerial Plant Surfaces by Means of a Strain-Specific Viability Quantitative PCR Method. Appl Environ Microbiol 2018. [PMID: 29523544 PMCID: PMC5930365 DOI: 10.1128/aem.00107-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A viability quantitative PCR (v-qPCR) assay was developed for the unambiguous detection and quantification of Lactobacillus plantarum PM411 viable cells in aerial plant surfaces. A 972-bp region of a PM411 predicted prophage with mosaic architecture enabled the identification of a PM411 strain-specific molecular marker. Three primer sets with different amplicon lengths (92, 188, and 317 bp) and one TaqMan probe were designed. All the qPCR assays showed good linearity over a 4-log range and good efficiencies but differed in sensitivity. The nucleic acid-binding dye PEMAX was used to selectively detect and enumerate viable bacteria by v-qPCR. The primer set amplifying a 188-bp DNA fragment was selected as the most suitable for v-qPCR. The performance of the method was assessed on apple blossoms, pear, strawberry, and kiwifruit leaves in potted plants under controlled environmental conditions, as well as pear and apple blossoms under field conditions, by comparing v-qPCR population estimations to those obtained by qPCR and specific plate counting on de Man-Rogosa-Sharpe (MRS)-rifampin. The population estimation did not differ significantly between methods when conditions were conducive to bacterial survival. However, under stressful conditions, differences between methods were observed due to cell death or viable-but-nonculturable state induction. While qPCR overestimated the population level, plate counting underestimated this value in comparison to v-qPCR. PM411 attained stable population levels of viable cells on the flower environment under high relative humidity. However, the unfavorable conditions on the leaf surface and the relatively dryness in the field caused an important decrease in the viable population. IMPORTANCE The v-qPCR method in combination with plate counting and qPCR is a powerful tool for studies of colonization and survival under field conditions, to improve formulations and delivery strategies of PM411, and to optimize the dose and timing of spray schedules. It is expected that PEMAX v-qPCR could also be developed for monitoring other strains on plant surfaces not only as biological control agents but also beneficial bacteria useful in the sustainable management of crop production.
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4
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Rodrigues MX, Lima SF, Higgins CH, Canniatti-Brazaca SG, Bicalho RC. The Lactococcus genus as a potential emerging mastitis pathogen group: A report on an outbreak investigation. J Dairy Sci 2016; 99:9864-9874. [PMID: 27743665 DOI: 10.3168/jds.2016-11143] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 08/09/2016] [Indexed: 12/14/2022]
Abstract
The bacterium Lactococcus lactis is widely used in food production and in medical applications, and is considered safe for human and animal use. However, studies have also linked Lactococcus bacteria to infection. For example, certain variants of Lactococcus species have been associated with bovine mastitis (e.g., Lactococcus lactis and Lactococcus garvieae). In this study, we investigated an outbreak of bovine mastitis thought to be associated with Lactococcus bacteria by using microbiological and molecular techniques. We used bacterial isolation, next-generation sequencing, DNA fingerprinting, and other methods to test our hypothesis that Lactococcus microbes were the primary pathogen causing the mastitis outbreak. Twenty-eight Lactococcus isolates were obtained from mastitic milk of 28 dairy cows. The isolates were identified as L. lactis (27 isolates) and L. garvieae (1 isolate). Phylogenetic analysis based on 16S rDNA gene sequence comparison indicated similarity among the L. lactis isolates as well as between the isolates and reference sequences. The DNA fingerprinting analysis based on random amplified polymorphic DNA results of the 27 L. lactis isolates identified different random amplified polymorphic DNA profiles, which suggests they originated from multiple sources. Microbiome analysis determined Lactococcus to be the dominant genus in the majority of the mastitic milk samples, whereas it was found in low relative abundance in healthy milk samples. The Lactococcus genus was detected in all environmental samples tested, and sampling of bulk tank milk corroborated that Lactococcus was not abundant in healthy milk from the same dairy herd. In summary, our findings suggest that Lactococcus bacteria are a potential etiological agent in the mastitis outbreak studied. Further studies should be conducted to understand the importance of Lactococcus, especially L. lactis, as pathogenic microbes in veterinary medicine and food safety.
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Affiliation(s)
- M X Rodrigues
- Department of Agroindustry, Food and Nutrition, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP13418-900, Brazil
| | - S F Lima
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - C H Higgins
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - S G Canniatti-Brazaca
- Department of Agroindustry, Food and Nutrition, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP13418-900, Brazil
| | - R C Bicalho
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853.
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Kelleher P, Murphy J, Mahony J, van Sinderen D. Next-generation sequencing as an approach to dairy starter selection. DAIRY SCIENCE & TECHNOLOGY 2015; 95:545-568. [PMID: 26798445 PMCID: PMC4712225 DOI: 10.1007/s13594-015-0227-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/25/2015] [Accepted: 04/02/2015] [Indexed: 02/06/2023]
Abstract
Lactococcal and streptococcal starter strains are crucial ingredients to manufacture fermented dairy products. As commercial starter culture suppliers and dairy producers attempt to overcome issues of phage sensitivity and develop new product ranges, there is an ever increasing need to improve technologies for the rational selection of novel starter culture blends. Whole genome sequencing, spurred on by recent advances in next-generation sequencing platforms, is a promising approach to facilitate rapid identification and selection of such strains based on gene-trait matching. This review provides a comprehensive overview of the available methodologies to analyse the technological potential of candidate starter strains and highlights recent advances in the area of dairy starter genomics.
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Affiliation(s)
- Philip Kelleher
- School of Microbiology, University College Cork, Cork, Ireland
| | - James Murphy
- School of Microbiology, University College Cork, Cork, Ireland
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, Cork, Ireland
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6
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Cavanagh D, Fitzgerald GF, McAuliffe O. From field to fermentation: the origins of Lactococcus lactis and its domestication to the dairy environment. Food Microbiol 2014; 47:45-61. [PMID: 25583337 DOI: 10.1016/j.fm.2014.11.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/22/2014] [Accepted: 11/01/2014] [Indexed: 11/18/2022]
Abstract
Lactococcus lactis is an organism of substantial economic importance, used extensively in the production of fermented foods and widely held to have evolved from plant strains. The domestication of this organism to the milk environment is associated with genome reduction and gene decay, and the acquisition of specific genes involved in protein and lactose utilisation by horizontal gene transfer. In recent years, numerous studies have focused on uncovering the physiology and molecular biology of lactococcal strains from the wider environment for exploitation in the dairy industry. This in turn has facilitated comparative genome analysis of lactococci from different environments and provided insight into the natural phenotypic and genetic diversity of L. lactis. This diversity may be exploited in dairy fermentations to develop products with improved quality and sensory attributes. In this review, we discuss the classification of L. lactis and the problems that arise with phenotype/genotype designation. We also discuss the adaptation of non-dairy lactococci to milk, the traits associated with this adaptation and the potential application of non-dairy lactococci to dairy fermentations.
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Affiliation(s)
- Daniel Cavanagh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; Department of Microbiology, University College Cork, Co. Cork, Ireland.
| | | | - Olivia McAuliffe
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.
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7
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New insights into Lactococcus lactis diacetyl- and acetoin-producing strains isolated from diverse origins. Int J Food Microbiol 2013; 160:329-36. [DOI: 10.1016/j.ijfoodmicro.2012.10.023] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 09/17/2012] [Accepted: 10/24/2012] [Indexed: 11/21/2022]
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8
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Khemariya P, Singh S, Nath G, Gulati AK. Diversity analysis of dairy and non-dairy strains of Lactococcus lactis ssp. lactis by multilocus sequence analysis (MLSA). ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0563-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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9
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Abstract
We report the complete genome sequence of Lactococcus lactis subsp. cremoris A76, a dairy strain isolated from a cheese production outfit. Genome analysis detected two contiguous islands fitting to the L. lactis subsp. lactis rather than to the L. lactis subsp. cremoris lineage. This indicates the existence of genetic exchange between the diverse subspecies, presumably related to the technological process.
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10
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Cascade cell lyses and DNA extraction for identification of genes and microorganisms in kefir grains. J DAIRY RES 2011; 79:26-32. [PMID: 22008413 DOI: 10.1017/s0022029911000677] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Kefir is a dairy product popular in many countries in Central Europe, especially in Poland and other countries of Eastern and Northern Europe. This type of fermented milk is produced by a complex population of symbiotic bacteria and yeasts. In this work, conditions for DNA extraction, involving disruption of kefir grains and a cascade of cell lysis treatments, were established. Extraction procedure of total microbial DNA was carried out directly from fresh kefir grains. Using different lysis stringency conditions, five DNA pools were obtained. Genetic diversity of DNA pools were validated by RAPD analysis, which showed differences in patterns of amplified DNA fragments, indicating diverse microbial composition of all the analysed samples. These DNA pools were used for construction of genomic DNA libraries for sequencing. As much as 50% of the analysed nucleotide sequences showed homology to sequences from bacteria belonging to the Lactobacillus genus. Several sequences were similar to sequences from bacteria representing Lactococcus, Oenococcus, Pediococcus, Streptococcus and Leuconostoc species. Among homologues of yeast proteins were those from Candida albicans, Candida glabrata, Kluyveromyces lactis and Saccharomyces cerevisiae. In addition, several sequences were found to be homologous to sequences from bacteriophages.
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11
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Ponnusamy K, Jose S, Savarimuthu I, Michael G, Redenbach M. Genetic diversity study of Chromobacterium violaceum isolated from Kolli hills by amplified ribosomal DNA restriction analysis (ARDRA) and random amplified polymorphic DNA (RAPD). Lett Appl Microbiol 2011; 53:341-9. [DOI: 10.1111/j.1472-765x.2011.03115.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Pavlidou S, Bozoudi D, Hatzikamari M, Tzanetakis N, Litopoulou-Tzanetaki E. Differentiation of Lactococci from 2 Greek Cheeses with Protected Designation of Origin by Phenotypic Criteria and RAPD-PCR. J Food Sci 2011; 76:M175-83. [DOI: 10.1111/j.1750-3841.2011.02043.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Siezen RJ, Bayjanov JR, Felis GE, van der Sijde MR, Starrenburg M, Molenaar D, Wels M, van Hijum SAFT, van Hylckama Vlieg JET. Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays. Microb Biotechnol 2011; 4:383-402. [PMID: 21338475 PMCID: PMC3818997 DOI: 10.1111/j.1751-7915.2011.00247.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Lactococcus lactis produces lactic acid and is widely used in the manufacturing of various fermented dairy products. However, the species is also frequently isolated from non-dairy niches, such as fermented plant material. Recently, these non-dairy strains have gained increasing interest, as they have been described to possess flavour-forming activities that are rarely found in dairy isolates and have diverse metabolic properties. We performed an extensive whole-genome diversity analysis on 39 L. lactis strains, isolated from dairy and plant sources. Comparative genome hybridization analysis with multi-strain microarrays was used to assess presence or absence of genes and gene clusters in these strains, relative to all L. lactis sequences in public databases, whereby chromosomal and plasmid-encoded genes were computationally analysed separately. Nearly 3900 chromosomal orthologous groups (chrOGs) were defined on basis of four sequenced chromosomes of L. lactis strains (IL1403, KF147, SK11, MG1363). Of these, 1268 chrOGs are present in at least 35 strains and represent the presently known core genome of L. lactis, and 72 chrOGs appear to be unique for L. lactis. Nearly 600 and 400 chrOGs were found to be specific for either the subspecies lactis or subspecies cremoris respectively. Strain variability was found in presence or absence of gene clusters related to growth on plant substrates, such as genes involved in the consumption of arabinose, xylan, α-galactosides and galacturonate. Further niche-specific differences were found in gene clusters for exopolysaccharides biosynthesis, stress response (iron transport, osmotolerance) and bacterial defence mechanisms (nisin biosynthesis). Strain variability of functions encoded on known plasmids included proteolysis, lactose fermentation, citrate uptake, metal ion resistance and exopolysaccharides biosynthesis. The present study supports the view of L. lactis as a species with a very flexible genome.
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Affiliation(s)
- Roland J Siezen
- Kluyver Centre for Genomics of Industrial Fermentation, NIZO food research, P.O. Box 20, 6710 BA Ede, the Netherlands.
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Genes but not genomes reveal bacterial domestication of Lactococcus lactis. PLoS One 2010; 5:e15306. [PMID: 21179431 PMCID: PMC3003715 DOI: 10.1371/journal.pone.0015306] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 11/05/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The population structure and diversity of Lactococcus lactis subsp. lactis, a major industrial bacterium involved in milk fermentation, was determined at both gene and genome level. Seventy-six lactococcal isolates of various origins were studied by different genotyping methods and thirty-six strains displaying unique macrorestriction fingerprints were analyzed by a new multilocus sequence typing (MLST) scheme. This gene-based analysis was compared to genomic characteristics determined by pulsed-field gel electrophoresis (PFGE). METHODOLOGY/PRINCIPAL FINDINGS The MLST analysis revealed that L. lactis subsp. lactis is essentially clonal with infrequent intra- and intergenic recombination; also, despite its taxonomical classification as a subspecies, it displays a genetic diversity as substantial as that within several other bacterial species. Genome-based analysis revealed a genome size variability of 20%, a value typical of bacteria inhabiting different ecological niches, and that suggests a large pan-genome for this subspecies. However, the genomic characteristics (macrorestriction pattern, genome or chromosome size, plasmid content) did not correlate to the MLST-based phylogeny, with strains from the same sequence type (ST) differing by up to 230 kb in genome size. CONCLUSION/SIGNIFICANCE The gene-based phylogeny was not fully consistent with the traditional classification into dairy and non-dairy strains but supported a new classification based on ecological separation between "environmental" strains, the main contributors to the genetic diversity within the subspecies, and "domesticated" strains, subject to recent genetic bottlenecks. Comparison between gene- and genome-based analyses revealed little relationship between core and dispensable genome phylogenies, indicating that clonal diversification and phenotypic variability of the "domesticated" strains essentially arose through substantial genomic flux within the dispensable genome.
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Bove CG, De Dea Lindner J, Lazzi C, Gatti M, Neviani E. Evaluation of genetic polymorphism among Lactobacillus rhamnosus non-starter Parmigiano Reggiano cheese strains. Int J Food Microbiol 2010; 144:569-72. [PMID: 21131087 DOI: 10.1016/j.ijfoodmicro.2010.11.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 11/05/2010] [Accepted: 11/09/2010] [Indexed: 10/18/2022]
Abstract
Parmigiano Reggiano (PR) is an Italian cooked, long-ripened cheese made with unheated cow's milk and natural whey starter. The microflora is involved in the manufacturing of this cheese, arising from the natural whey starter, the raw milk and the environment. Molecular studies have shown that mesophilic non-starter lactic acid bacteria (NSLAB) are the dominant microflora present during the ripening of PR. In this study, a characterisation of Lactobacillus rhamnosus isolated from a single PR manufacturing and ripening process is reported, using a combination of genotypic fingerprinting techniques (RAPD-PCR and REP-PCR). The intraspecies heterogeneity evidenced for 66 strains is correlated to their abilities to adapt to specific environmental and technological conditions. The detection of biotypes that correlate with specific moments in cheese ripening or differential development throughout this process suggests that these strains may have specific roles closely linked to their peculiar technological properties.
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Affiliation(s)
- Claudio Giorgio Bove
- Dipartimento di Genetica, Biologia dei microrganismi, Antropologia, Evoluzione, Università degli Studi di Parma, Viale Usberti 11/A, 43100 Parma, Italy
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16
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Kelly WJ, Ward LJH, Leahy SC. Chromosomal diversity in Lactococcus lactis and the origin of dairy starter cultures. Genome Biol Evol 2010; 2:729-44. [PMID: 20847124 PMCID: PMC2962554 DOI: 10.1093/gbe/evq056] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A large collection of Lactococcus lactis strains, including wild-type isolates and dairy starter cultures, were screened on the basis of their phenotype and the macrorestriction patterns produced from pulsed-field gel electrophoresis (PFGE) analysis of SmaI digests of genomic DNA. Three groups of dairy starter cultures, used for different purposes in the dairy industry, and a fourth group made up of strains isolated from the environment were selected for analysis of their chromosomal diversity using the endonuclease I-CeuI. Chromosome architecture was largely conserved with each strain having six copies of the rRNA genes, and the chromosome size of individual strains ranged between 2,240 and 2,688 kb. The origin of L. lactis strains showed the greatest correlation with chromosome size, and dairy strains, particularly those with the cremoris phenotype, had smaller chromosomes than wild-type strains. Overall, this study, coupled with analysis of the sequenced L. lactis genomes, provides evidence that defined strain dairy starter cultures have arisen from plant L. lactis strains. Adaptation of these strains to the dairy environment has involved loss of functions resulting in smaller chromosomes and acquisition of genes (usually plasmid associated) that facilitate growth in milk. We conclude that dairy starter cultures generally and the industrially used cremoris and diacetylactis phenotype strains in particular comprise a specialized group of L. lactis strains that have been selected to become an essential component of industrial processes and have evolved accordingly, so that they are no longer fit to survive outside the dairy environment.
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Affiliation(s)
- William J Kelly
- Rumen Microbial Genomics, AgResearch Limited, Grasslands Research Center, Palmerston North, New Zealand.
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MILLS SUSAN, O’SULLIVAN ORLA, HILL COLIN, FITZGERALD GERALD, ROSS RPAUL. The changing face of dairy starter culture research: From genomics to economics. INT J DAIRY TECHNOL 2010. [DOI: 10.1111/j.1471-0307.2010.00563.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Cukrowska B, Motyl I, Kozáková H, Schwarzer M, Górecki RK, Klewicka E, Śliżewska K, Libudzisz Z. Probiotic Lactobacillus strains: in vitro and in vivo studies. Folia Microbiol (Praha) 2010; 54:533-7. [DOI: 10.1007/s12223-009-0077-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Revised: 11/19/2009] [Indexed: 11/29/2022]
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19
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Characterization and safety evaluation of enterococci isolated from Spanish goats' milk cheeses. Int J Food Microbiol 2009; 132:24-32. [DOI: 10.1016/j.ijfoodmicro.2009.03.010] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 02/19/2009] [Accepted: 03/17/2009] [Indexed: 11/19/2022]
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20
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López I, Torres C, Ruiz-Larrea F. Genetic typification by pulsed-field gel electrophoresis (PFGE) and randomly amplified polymorphic DNA (RAPD) of wild Lactobacillus plantarum and Oenococcus oeni wine strains. Eur Food Res Technol 2007. [DOI: 10.1007/s00217-007-0755-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Rademaker JLW, Herbet H, Starrenburg MJC, Naser SM, Gevers D, Kelly WJ, Hugenholtz J, Swings J, van Hylckama Vlieg JET. Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting. Appl Environ Microbiol 2007; 73:7128-37. [PMID: 17890345 PMCID: PMC2168189 DOI: 10.1128/aem.01017-07] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The diversity of a collection of 102 lactococcus isolates including 91 Lactococcus lactis isolates of dairy and nondairy origin was explored using partial small subunit rRNA gene sequence analysis and limited phenotypic analyses. A subset of 89 strains of L. lactis subsp. cremoris and L. lactis subsp. lactis isolates was further analyzed by (GTG)(5)-PCR fingerprinting and a novel multilocus sequence analysis (MLSA) scheme. Two major genomic lineages within L. lactis were found. The L. lactis subsp. cremoris type-strain-like genotype lineage included both L. lactis subsp. cremoris and L. lactis subsp. lactis isolates. The other major lineage, with a L. lactis subsp. lactis type-strain-like genotype, comprised L. lactis subsp. lactis isolates only. A novel third genomic lineage represented two L. lactis subsp. lactis isolates of nondairy origin. The genomic lineages deviate from the subspecific classification of L. lactis that is based on a few phenotypic traits only. MLSA of six partial genes (atpA, encoding ATP synthase alpha subunit; pheS, encoding phenylalanine tRNA synthetase; rpoA, encoding RNA polymerase alpha chain; bcaT, encoding branched chain amino acid aminotransferase; pepN, encoding aminopeptidase N; and pepX, encoding X-prolyl dipeptidyl peptidase) revealed 363 polymorphic sites (total length, 1,970 bases) among 89 L. lactis subsp. cremoris and L. lactis subsp. lactis isolates with unique sequence types for most isolates. This allowed high-resolution cluster analysis in which dairy isolates form subclusters of limited diversity within the genomic lineages. The pheS DNA sequence analysis yielded two genetic groups dissimilar to the other genotyping analysis-based lineages, indicating a disparate acquisition route for this gene.
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Characterization of spontaneous phage-resistant variants of Streptococcus thermophilus by randomly amplified polymorphic DNA analysis and identification of phage-resistance mechanisms. Int Dairy J 2007. [DOI: 10.1016/j.idairyj.2007.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Psoni L, Kotzamanidis C, Yiangou M, Tzanetakis N, Litopoulou-Tzanetaki E. Genotypic and phenotypic diversity of Lactococcus lactis isolates from Batzos, a Greek PDO raw goat milk cheese. Int J Food Microbiol 2007; 114:211-20. [PMID: 17241681 DOI: 10.1016/j.ijfoodmicro.2006.09.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2006] [Revised: 07/17/2006] [Accepted: 09/19/2006] [Indexed: 10/23/2022]
Abstract
The genotypic and phenotypic variability of 40 Lactococcus lactis isolates obtained from three cheese-making trials of Batzos cheese made one in each, winter, spring and summer was investigated. RAPD-PCR, plasmid profiling and PFGE were used to study the genetic variability and distinguish closely related isolates. Results showed a high degree of heterogeneity among strains. According to PFGE data, all strains except one were clustered together (at a similarity level of approximately 50%) with the L. lactis subsp. lactis reference strain and eleven groups of isolates consisting of 2-8 strains each were distinguished. Plasmid profiling results revealed that there were eight isolates lacking plasmids and nine having unique plasmids. Twenty-three isolates were allocated into six groups. There was an interesting similarity between the plasmid profiling groups and those formed according to PFGE. Clustering of strains according to RAPD-PCR was in agreement with results obtained by both plasmid profiling and PFGE for the majority of the strains. In addition, results obtained by molecular methods indicate a grouping of most of the strains according to the season of cheese production. All strains inhibited the growth of Escherichia coli O157:H7. Their ability to affect the growth of Yersinia enterocolitica, Staphylococcus aureus, Bacillus cereus, Listeria monocytogenes and Enterococcus faecalis was strain dependent. In 42.5% of the isolates high acidifying ability in milk after 24 h was recorded and these were isolates, mainly, from fresh cheese. The 75% of the isolates from winter cheese exhibited higher Lys- than Leu-aminopeptidase activity while the approximately 67% of the isolates from summer cheese showed higher Leu- than Lys-aminopeptidase activity. Their caseinolytic activity after growth in milk for 24 h was significant with preference for alpha(s)-casein degradation. The majority (90%) of the strains formed methanethiol from methionine and this ability was strain dependent. These results suggest that among the wild lactococcal population from Batzos cheese there are interesting strains appropriate to be used as starters for the dairy industry.
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Affiliation(s)
- L Psoni
- Laboratory of Food Microbiology and Hygiene, Faculty of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
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Tailliez P, Pagès S, Ginibre N, Boemare N. New insight into diversity in the genus Xenorhabdus, including the description of ten novel species. Int J Syst Evol Microbiol 2007; 56:2805-2818. [PMID: 17158981 DOI: 10.1099/ijs.0.64287-0] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We investigated the diversity of a collection of 76 Xenorhabdus strains, isolated from at least 27 species of Steinernema nematodes and collected in 32 countries, using three complementary approaches: 16S rRNA gene sequencing, molecular typing and phenotypic characterization. The 16S rRNA gene sequences of the Xenorhabdus strains were highly conserved (similarity coefficient >95 %), suggesting that the common ancestor of the genus probably emerged between 250 and 500 million years ago. Based on comparisons of the 16S rRNA gene sequences, we identified 13 groups and seven unique sequences. This classification was confirmed by analysis of molecular typing profiles of the strains, leading to the classification of new isolates into the Xenorhabdus species described previously and the description of ten novel Xenorhabdus species: Xenorhabdus cabanillasii sp. nov. (type strain USTX62(T)=CIP 109066(T)=DSM 17905(T)), Xenorhabdus doucetiae sp. nov. (type strain FRM16(T)=CIP 109074(T)=DSM 17909(T)), Xenorhabdus griffiniae sp. nov. (type strain ID10(T)=CIP 109073(T)=DSM 17911(T)), Xenorhabdus hominickii sp. nov. (type strain KE01(T)=CIP 109072(T)=DSM 17903(T)), Xenorhabdus koppenhoeferi sp. nov. (type strain USNJ01(T)=CIP 109199(T)=DSM 18168(T)), Xenorhabdus kozodoii sp. nov. (type strain SaV(T)=CIP 109068(T)=DSM 17907(T)), Xenorhabdus mauleonii sp. nov. (type strain VC01(T)=CIP 109075(T)=DSM 17908(T)), Xenorhabdus miraniensis sp. nov. (type strain Q1(T)=CIP 109069(T)=DSM 17902(T)), Xenorhabdus romanii sp. nov. (type strain PR06-A(T)=CIP 109070(T)=DSM 17910(T)) and Xenorhabdus stockiae sp. nov. (type strain TH01(T)=CIP 109067(T)=DSM 17904(T)). The Xenorhabdus strains studied here had very similar phenotypic patterns, but phenotypic features nonetheless differentiated the following species: X. bovienii, X. cabanillasii, X. hominickii, X. kozodoii, X. nematophila, X. poinarii and X. szentirmaii. Based on phenotypic analysis, we identified two major groups of strains. Phenotypic group G(A) comprised strains able to grow at temperatures of 35-42 degrees C, whereas phenotypic group G(B) comprised strains that grew at temperatures below 35 degrees C, suggesting that some Xenorhabdus species may be adapted to tropical or temperate regions and/or influenced by the growth and development temperature of their nematode host.
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Affiliation(s)
- Patrick Tailliez
- Institut National de la Recherche Agronomique, Unité d'Ecologie Microbienne des Insectes et Interactions hôte-Pathogène, Université Montpellier II, Place Eugène Bataillon, Case courrier 54, Bâtiment 24, 34095 Montpellier CEDEX 5, France
| | - Sylvie Pagès
- Institut National de la Recherche Agronomique, Unité d'Ecologie Microbienne des Insectes et Interactions hôte-Pathogène, Université Montpellier II, Place Eugène Bataillon, Case courrier 54, Bâtiment 24, 34095 Montpellier CEDEX 5, France
| | - Nadège Ginibre
- Institut National de la Recherche Agronomique, Unité d'Ecologie Microbienne des Insectes et Interactions hôte-Pathogène, Université Montpellier II, Place Eugène Bataillon, Case courrier 54, Bâtiment 24, 34095 Montpellier CEDEX 5, France
| | - Noël Boemare
- Institut National de la Recherche Agronomique, Unité d'Ecologie Microbienne des Insectes et Interactions hôte-Pathogène, Université Montpellier II, Place Eugène Bataillon, Case courrier 54, Bâtiment 24, 34095 Montpellier CEDEX 5, France
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Guglielmotti DM, Reinheimer JA, Binetti AG, Giraffa G, Carminati D, Quiberoni A. Characterization of spontaneous phage-resistant derivatives of Lactobacillus delbrueckii commercial strains. Int J Food Microbiol 2006; 111:126-33. [DOI: 10.1016/j.ijfoodmicro.2006.04.035] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Revised: 03/16/2006] [Accepted: 04/27/2006] [Indexed: 11/26/2022]
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van Hylckama Vlieg JET, Rademaker JLW, Bachmann H, Molenaar D, Kelly WJ, Siezen RJ. Natural diversity and adaptive responses of Lactococcus lactis. Curr Opin Biotechnol 2006; 17:183-90. [PMID: 16517150 DOI: 10.1016/j.copbio.2006.02.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Revised: 01/31/2006] [Accepted: 02/20/2006] [Indexed: 10/24/2022]
Abstract
Lactococcus lactis is the primary model organism for lactic acid bacteria (LAB) and is widely used in the production of fermented dairy products. In recent years there has been increasing interest in strains isolated from non-dairy environments, as these exhibit a high metabolic diversity and have unique flavour-forming activities. Recent progress has been made in understanding the natural diversity and adaptive responses of L. lactis from dairy and non-dairy origins. Genome sequencing and comparative genomics have also had an impact on understanding natural diversity within the species, and have provided new opportunities for industrial strain development.
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Affiliation(s)
- Johan E T van Hylckama Vlieg
- NIZO Food Research, Kluyver Centre for Genomics of Industrial Fermentation, PO Box 20, 6710 BA Ede, The Netherlands.
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Quénée P, Lepage E, Kim WS, Vergnaud G, Gruss A. Minisatellite polymorphism as a tool to distinguish closely related Lactococcus lactis strains. FEMS Microbiol Lett 2005; 248:101-9. [PMID: 15963663 DOI: 10.1016/j.femsle.2005.05.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2005] [Revised: 03/11/2005] [Accepted: 05/16/2005] [Indexed: 11/25/2022] Open
Abstract
Genome plasticity is considered as a means for bacteria to adapt to their environment. Plasticity in tandem repeat sequences on bacterial genomes has been recently exploited to trace the epidemiology of pathogens. Here, we examine the utility of minisatellite (i.e., a repeat unit of six nucleotides or more) typing in non-pathogenic food bacteria of the species Lactococcus lactis. Thirty-four minisatellites identified on the sequenced L. lactis ssp. lactis strain IL1403 genome were first analyzed in 10 closely related ssp. lactis strains, as determined by randomly amplified polymorphic DNA (RAPD). The selected tandem repeats varied in length, percent identity between repeats, and locations. We showed that: (i) the greatest polymorphism was in orfs encoding exported proteins or in intergenic regions; (ii) two thirds of minisatellites were little- or non-variable, despite as much as 90% identity between tandem repeats; and (iii) dendrograms based on either RAPD or minisatellite analyses were similar. Seven minisatellites identified in this study are potentially useful for lactococcal typing. We then asked whether tandem repeats in L. lactis were stable upon very long-term (up to two years) storage. Despite large rearrangements previously reported in derivative strains, just one of 10 minisatellites tested underwent an alteration, suggesting that tandem repeat rearrangements probably occur during active DNA replication. We conclude that multiple locus minisatellite analysis can be a valuable tool to follow lactococcal strain diversity.
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Affiliation(s)
- Pascal Quénée
- Recherches Laitières et Génétique Appliquée-URLGA, Institute National de la Recherche Agronomique, Jouy en Josas Cedex, France
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Bernardet JF, Vancanneyt M, Matte-Tailliez O, Grisez L, Tailliez P, Bizet C, Nowakowski M, Kerouault B, Swings J. Polyphasic study of Chryseobacterium strains isolated from diseased aquatic animals. Syst Appl Microbiol 2005; 28:640-60. [PMID: 16156122 DOI: 10.1016/j.syapm.2005.03.016] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Members of most Chryseobacterium species occur in aquatic environments or food products, while strains of some other species are pathogenic to humans and animals. A collection of 52 Chryseobacterium sp. strains isolated from diseased fish, one frog isolate and 22 reference strains were included in a polyphasic taxonomy study. Fourteen clusters of strains were delineated following the comparison of whole-cell protein profiles. Most of these clusters were confirmed when the phenotypic and RAPD profiles and the 16S rRNA gene sequences were compared. Fatty acid composition helped differentiate the Chryseobacterium strains from members of related genera. None of the fish isolates could be allocated to the two species previously reported from fish but two isolates belonged to C. joostei, while the frog isolate was identified as Elizabethkingia meningoseptica, a human pathogen previously included in the genus Chryseobacterium. Three clusters grouping from 3 to 13 isolates will probably constitute the core of new Chryseobacterium species but all other isolates occupied separate or uncertain positions in the genus. This study further demonstrated the overall high similarity displayed by most Chryseobacterium strains whatever the technique used and the resulting difficulty in delineating new species in the genus. Members of this bacterial group should be considered potential emergent pathogens in various fish and frog species, farming conditions and geographical areas.
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Affiliation(s)
- J F Bernardet
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires, Jouy-en-Josas, France.
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Bolotin A, Quinquis B, Sorokin A, Ehrlich DS. Recent genetic transfer between Lactococcus lactis and enterobacteria. J Bacteriol 2004; 186:6671-7. [PMID: 15375152 PMCID: PMC516620 DOI: 10.1128/jb.186.19.6671-6677.2004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome sequence of Lactococcus lactis revealed that the ycdB gene was recently exchanged between lactococci and enterobacteria. The present study of ycdB orthologs suggests that L. lactis was probably the gene donor and reveals three instances of gene transfer to enterobacteria. Analysis of ycdB gene transfer between two L. lactis subspecies, L. lactis subsp. lactis and L. lactis subsp. cremoris, indicates that the gene can be mobilized, possibly by conjugation.
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Affiliation(s)
- Alexander Bolotin
- Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy en Josas, France.
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30
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Lepage E, Marguet E, Geslin C, Matte-Tailliez O, Zillig W, Forterre P, Tailliez P. Molecular diversity of new Thermococcales isolates from a single area of hydrothermal deep-sea vents as revealed by randomly amplified polymorphic DNA fingerprinting and 16S rRNA gene sequence analysis. Appl Environ Microbiol 2004; 70:1277-86. [PMID: 15006744 PMCID: PMC368356 DOI: 10.1128/aem.70.3.1277-1286.2004] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Members of the Thermococcales are anaerobic Archaea belonging to the kingdom Euryarchaea that are studied in many laboratories as model organisms for hyperthermophiles. We describe here a molecular analysis of 86 new Thermococcales isolates collected from six different chimneys of a single hydrothermal field located in the 13 degrees N 104 degrees W segment of the East Pacific ridge at a depth of 2,330 m. These isolates were sorted by randomly amplified polymorphic DNA (RAPD) fingerprinting into nine groups, and nine unique RAPD profiles were obtained. One RAPD group corresponds to new isolates of Thermococcus hydrothermalis, whereas all other groups and isolates with unique profiles are different from the 22 reference strains included in this study. Analysis of 16S rRNA gene sequences of representatives of each RAPD group and unique profiles showed that one group corresponds to Pyrococcus strains, whereas all the other isolates are Thermococcus strains. We estimated that our collection may contain at least 11 new species. These putative species, isolated from a single area of hydrothermal deep-sea vents, are dispersed in the 16S rRNA tree among the reference strains previously isolated from diverse hot environments (terrestrial, shallow water, hydrothermal vents) located around the world, suggesting that there is a high degree of dispersal of Thermococcales: About one-half of our isolates contain extrachromosomal elements that could be used to search for novel replication proteins and to develop genetic tools for hyperthermophiles.
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Affiliation(s)
- Elodie Lepage
- Unité de Recherches Laitières et Génétique Appliquée, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy-en-Josas, France
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Ward LJH, Heap HA, Kelly WJ. Characterization of closely related lactococcal starter strains which show differing patterns of bacteriophage sensitivity. J Appl Microbiol 2004; 96:144-8. [PMID: 14678167 DOI: 10.1046/j.1365-2672.2003.02134.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To characterize a group of closely related Lactococcus lactis subsp. lactis casein starter strains used commercially, which differ in their sensitivity to bacteriophages isolated from the same industrial environment. METHODS AND RESULTS Nine strains of L. lactis, six of which had been used as starter cultures for lactic casein manufacture, were shown to be closely related by pulsed-field gel electrophoresis and total DNA profiles. Nineteen phages which propagated on one or more of these starter strains were isolated from industrial casein whey samples. The phages were all small isometric-headed and could be divided into five groups on the basis of host range on the nine strains. Most of the phages did not give a PCR product with primers designed to detect the two most common lactococcal small isometric phage species (936 and P335). The hosts could be divided into six groups depending on their phage sensitivity. Plasmids encoding genes for the cell envelope associated PI-type proteinase, lactose metabolism and specificity subunits of a type I restriction/modification system were identified. CONCLUSIONS This work demonstrates how isolates of the same starter strain may come to be regarded as separate cultures because of their different origins, and how these closely related strains may differ in some of their industrially relevant characteristics. SIGNIFICANCE AND IMPACT OF THE STUDY This situation may be very common among lactococci used as dairy starter cultures, and implies that the dairy industry worldwide depends on a small number of different strains.
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Affiliation(s)
- L J H Ward
- Fonterra Research Centre, Palmerston North, New Zealand
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Lin M, Payne DA, Schwarz JR. Intraspecific diversity of Vibrio vulnificus in Galveston Bay water and oysters as determined by randomly amplified polymorphic DNA PCR. Appl Environ Microbiol 2003; 69:3170-5. [PMID: 12788713 PMCID: PMC161529 DOI: 10.1128/aem.69.6.3170-3175.2003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2002] [Accepted: 03/24/2003] [Indexed: 11/20/2022] Open
Abstract
Randomly amplified polymorphic DNA (RAPD) PCR was used to analyze the temporal and spatial intraspecific diversity of 208 Vibrio vulnificus strains isolated from Galveston Bay water and oysters at five different sites between June 2000 and June 2001. V. vulnificus was not detected during the winter months (December through February). The densities of V. vulnificus in water and oysters were positively correlated with water temperature. Cluster analysis of RAPD PCR profiles of the 208 V. vulnificus isolates revealed a high level of intraspecific diversity among the strains. No correlation was found between the intraspecific diversity among the isolates and sampling site or source of isolation. After not being detected during the winter months, the genetic diversity of V. vulnificus strains first isolated in March was 0.9167. Beginning in April, a higher level of intraspecific diversity (0.9933) and a major shift in population structure were observed among V. vulnificus isolates. These results suggest that a great genetic diversity of V. vulnificus strains exists in Galveston Bay water and oysters and that the population structure of this species is linked to changes in environmental conditions, especially temperature.
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Affiliation(s)
- Meilan Lin
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, Texas 77551, USA
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Nardi M, Fiez-Vandal C, Tailliez P, Monnet V. The EstA esterase is responsible for the main capacity of Lactococcus lactis to synthesize short chain fatty acid esters in vitro. J Appl Microbiol 2003; 93:994-1002. [PMID: 12452955 DOI: 10.1046/j.1365-2672.2002.01793.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS Esters of short-chain fatty acids and alcohols participate significantly in the overall flavour of foods. The capacity of the lactic acid bacterium Lactococcus lactis to synthesize such esters is known even though the enzymes involved in the process are not well identified. The objective of our work is to determine whether the esterase is responsible for the whole capacity of L. lactis to synthesize esters in vitro. METHODS AND RESULTS A negative mutant for the esterase was constructed and its capacity to synthesize short chain fatty acid esters from different substrate couples was compared to that of the wild type. We observed that the esterase is responsible for the main ester synthesis activity of L. lactis in vitro. However, in the presence of some substrates, the esterase negative mutant still synthesizes low amounts of esters. CONCLUSIONS In favourable environmental conditions, the L. lactis esterase is responsible for the main ester synthesizing activity, even though another pathway for ester synthesis probably exists. SIGNIFICANCE AND IMPACT OF THE STUDY Since esters are potent aroma compounds, esterase is probably a key enzyme in the development of food flavour.
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Affiliation(s)
- M Nardi
- Unité de Biochimie et Structure des Protéines, Institut National de la Recherche Agronomique, 78352 Jouy-en-Josas cedex, France
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Matte-Tailliez O, Lepage E, Tenenhaus M, Tailliez P. Use of predictive modeling for Propionibacterium strain classification. Syst Appl Microbiol 2002; 25:386-95. [PMID: 12421076 DOI: 10.1078/0723-2020-00129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Computed data analysis of biochemical or molecular profiles is currently used in studies of microbial taxonomy, epidemiology, and microbial diversity. We assessed the use of Partial Least Squares (PLS) regression for multivariate data analysis in bacteriology. We identified clear relationships between RAPD profiles of propionibacteria strains and their species classification, autolytic capacities, and their origins. The PLS regression also predicted species identity of some strains with RAPD profiles partially related to those of reference strains. The PLS analysis also allowed us to identify key characteristics to use to classify strains. PLS regression is particularly well adapted to i) describing a collection of bacterial isolates, ii) justifying bacterial groupings using several sets of data, and iii) predicting phenotypic characters of strains that have been classified by routine typing methods.
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Affiliation(s)
- Oriane Matte-Tailliez
- Institut National de la Recherche Agronomique, Unité de Recherches Laitières et Génétique Appliquée, Collection CNRZ de bactéries lactiques et de bactéries propioniques, Jouy-en-Josas, France.
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Samarzija D, Sikora S, Redzepović S, Antunac N, Havranek J. Application of RAPD analysis for identification of Lactococcus lactis subsp. cremoris strains isolated from artisanal cultures. Microbiol Res 2002; 157:13-7. [PMID: 11911609 DOI: 10.1078/0944-5013-00126] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Randomly amplified polymorphic DNA (RAPD) was used for identification of Lactococcus lactis subsp. cremoris strains isolated 40 years ago from various dairy homemade products. Total genomic DNAs from six randomly chosen isolates and the reference strain Lactococcus lactis subsp. cremoris NIZO B64 were amplified using four different 10-mer primers. Although most RAPD fragments were common to all six isolates, a sufficient number of polymorphic fragments were also detected that allowed clear distinction of the isolates and the reference strain. The results indicate that RAPD analysis could be a useful and efficient method to distinguish Lactococcus lactis subsp. cremoris at the strain level and to detect genetic diversity.
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Affiliation(s)
- D Samarzija
- Dairy Department, Faculty of Agriculture, University of Zagreb, Croatia.
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Marcille F, Gomez A, Joubert P, Ladiré M, Veau G, Clara A, Gavini F, Willems A, Fons M. Distribution of genes encoding the trypsin-dependent lantibiotic ruminococcin A among bacteria isolated from human fecal microbiota. Appl Environ Microbiol 2002; 68:3424-31. [PMID: 12089024 PMCID: PMC126812 DOI: 10.1128/aem.68.7.3424-3431.2002] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fourteen bacterial strains capable of producing a trypsin-dependent antimicrobial substance active against Clostridium perfringens were isolated from human fecal samples of various origins (from healthy adults and children, as well as from adults with chronic pouchitis). Identification of these strains showed that they belonged to Ruminococcus gnavus, Clostridium nexile, and Ruminococcus hansenii species or to new operational taxonomic units, all from the Clostridium coccoides phylogenetic group. In hybridization experiments with a probe specific for the structural gene encoding the trypsin-dependent lantibiotic ruminococcin A (RumA) produced by R. gnavus, seven strains gave a positive response. All of them harbored three highly conserved copies of rumA-like genes. The deduced peptide sequence was identical to or showed one amino acid difference from the hypothetical precursor of RumA. Our results indicate that the rumA-like genes have been disseminated among R. gnavus and phylogenetically related strains that can make up a significant part of the human fecal microbiota.
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Affiliation(s)
- F Marcille
- Unité d'Ecologie et de Physiologie du Système Digestif, Institut National de la Recherche Agronomique, 78352 Jouy-en-Josas Cedex, France
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Gente S, Desmasures N, Panoff JM, Guéguen M. Genetic diversity among Geotrichum candidum strains from various substrates studied using RAM and RAPD-PCR. J Appl Microbiol 2002; 92:491-501. [PMID: 11872125 DOI: 10.1046/j.1365-2672.2002.01553.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS Assessment of genetic diversity within the species Geotrichum candidum and development of tools to trace the strains that play an important role in the agro food industry. METHODS AND RESULTS RAM-PCR and RAPD-PCR techniques were assessed for their ability to discriminate 57 strains of various morphotypes, substrates and geographical origin. The techniques were complementary and, when combined, allowed us to discriminate isolates. Moreover, we established a link between a taxon and its occupation of an ecological niche, which should not be confused with the substrate of isolation. CONCLUSIONS We observed a high degree of diversity, which could be linked to the variety of the ecological niches chosen and to the high degree of morphological polymorphism encountered within the species. SIGNIFICANCE AND IMPACT OF THE STUDY Used in combination, RAM-PCR and RAPD-PCR permit traceability and monitoring systems for G. candidum strains during food processing.
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Affiliation(s)
- S Gente
- Laboratoire de Microbiologie Alimentaire EA 3213, Institut de Biochimie et Biologie Appliquée, Université de Caen Basse-Normandie, Esplanade de la Paix, 14032 Caen cedex, France
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Bouton Y, Guyot P, Beuvier E, Tailliez P, Grappin R. Use of PCR-based methods and PFGE for typing and monitoring homofermentative lactobacilli during Comté cheese ripening. Int J Food Microbiol 2002; 76:27-38. [PMID: 12038575 DOI: 10.1016/s0168-1605(02)00006-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study investigated the genotypic characteristics of selected and wild homofermentative thermophilic lactobacilli strains during ripening of Comté cheeses, made into two cheese plants. Both amplification and restriction analysis of the 16S rRNA gene (PCR-ARDRA) and classical biochemical tests were used to identify isolates. Diversity within homofermentative lactobacilli was not found in their species composition since the same two species Lactobacillus helveticus and L. delbrueckii susbp. lactis were isolated from cheeses. In cheeses made with natural whey starter, it appeared that the most likely sources of L. helveticus and L. delbrueckii susbp. lactis were the starter and raw milk, respectively. The examination of RAPD profiles of lactobacilli strains revealed 19 RAPD groups among 50 isolates, which were different from selected starter strains. Using RAPD, REP-PCR, and PFGE to identify selected starter strains during cheese ripening, we showed that L. helveticus decreased quickly while L. delbrueckii susbp. lactis sustained high viability during ripening. The use of selected L. delbrueckii susbp. lactis strains diminished the genetic diversity among strains isolated from cheese, probably in preventing the raw milk microflora from growing.
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Affiliation(s)
- Yvette Bouton
- Comité Interprofessionnel du Comté, Poligny, France.
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Gusils C, Cuozzo S, Sesma F, González S. Examination of adhesive determinants in three species of Lactobacillus isolated from chicken. Can J Microbiol 2002; 48:34-42. [PMID: 11888161 DOI: 10.1139/w01-122] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The microbial adhesion process includes passive forces; electrostatic interactions; hydrophobic, steric forces; lipoteichoic acids; and specific structures, such as external appendages (lectins) and (or) extracellular polymers. In a previous work, we showed that Lactobacillus animalis, L. fermentum, and L. fermentum ssp. cellobiosus had lectinlike proteic structures on their surfaces and high hydrophobicity values on the cell surface of L. fermentum ssp. cellobiosus. Here, we examined the presence of the bacterial forces or structures that could be involved in the interaction between bacteria and epithelial cells. Lactobacillus animalis and L. fermentum possessed a net negative surface charge, whereas L. fermentum ssp. cellobiosus showed similar affinity to both cationic and anionic exchange resins, aggregated in the presence of ammonium sulfate, and had high affinity (75.4%) to a hydrophobic matrix. Only L. animalis was shown to have ribitol teichoic acids in the cell wall. The amount of polysaccharides from cell walls varied between different strains, with L. fermentum ssp. cellobiosus having the highest concentration. Lectin extracts obtained from lactobacilli did not possess sugar residues, thereby demonstrating the proteic nature of the superficial surface structures of three strains. The lactic acid bacteria studied here showed different surface determinants, which could be involved in the interactions between these lactobacilli and intestinal epithelial cells.
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Affiliation(s)
- C Gusils
- Centro de Referencias para Lactobacilos (CERELA-CONICET), and Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Argentina
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McGrath S, Fitzgerald GF, van Sinderen D. Identification and characterization of phage-resistance genes in temperate lactococcal bacteriophages. Mol Microbiol 2002; 43:509-20. [PMID: 11985726 DOI: 10.1046/j.1365-2958.2002.02763.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The sie2009 gene, which is situated between the genes encoding the repressor and integrase, on the lysogeny module of the temperate lactococcal bacteriophage Tuc2009, was shown to mediate a phage-resistance phenotype in Lactococcus lactis against a number of bacteriophages. The Sie2009 protein is associated with the cell membrane and its expression leaves phage adsorption, transfection and plasmid transformation unaffected, but interferes with plasmid transduction, as well as phage replication. These observations indicate that this resistance is as a result of DNA injection blocking, thus representing a novel superinfection exclusion system. A polymerase chain reaction (PCR)-based strategy was used to screen a number of lactococcal strains for the presence of other prophage-encoded phage-resistance systems. This screening resulted in the identification of two such systems, without homology to sie2009, which were shown to mediate a phage-resistance phenotype similar to that conferred by sie2009. To our knowledge, this is the first description of a phage-encoded super-infection exclusion/injection blocking mechanism in the genus Lactococcus.
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Affiliation(s)
- Stephen McGrath
- National Food Biotechnology Centre, University College Cork, Ireland
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42
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Letort C, Juillard V. Development of a minimal chemically-defined medium for the exponential growth of Streptococcus thermophilus. J Appl Microbiol 2001; 91:1023-9. [PMID: 11851809 DOI: 10.1046/j.1365-2672.2001.01469.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS The present work aimed to define a minimal chemically-defined medium which could sustain the growth of most (if not all) strains of Streptococcus thermophilus. METHODS AND RESULTS A minimal medium containing 20 components, including one carbohydrate source, six amino acids, two metallic ions, six vitamins and urea allowed for growth of 13 out of 15 Strep. thermophilus strains. Growth of the two last strains required the presence of additional amino acids, the number of which depended on the strain. Growth rates of the strains in the minimal medium ranged from 0.38 to 0.64 h(-1), and final populations were about 10(8) cfu ml(-1). CONCLUSIONS Streptococcus thermophilus appears much less demanding than other lactic acid bacteria. SIGNIFICANCE AND IMPACT OF THE STUDY The definition of such a growth medium will be very useful for metabolic flux studies as well as peptide transport studies.
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Affiliation(s)
- C Letort
- Unité de Recherches Laitières et Génétique Appliquée, INRA, Jouy-en-Josas, France
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Bringel F, Quénée P, Tailliez P. Polyphasic investigation of the diversity within Lactobacillus plantarum related strains revealed two L. plantarum subgroups. Syst Appl Microbiol 2001; 24:561-71. [PMID: 11876364 DOI: 10.1078/0723-2020-00061] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The diversity of 140 strains related to Lactobacillus plantarum was investigated using a polyphasic approach combining two molecular techniques: randomly amplified polymorphic DNA fingerprinting (RAPD) and Southern hybridisation with a pyr probe on BglI digests of chromosomal DNA, as well as phenotypic characterization. The RAPD technique allowed us to classify a subset of 60 representative strains into four groups. One group belonged to Lactobacillus paraplantarum, the second to Lactobacillus pentosus and the two remaining groups to L. plantarum (G(L)p1 and G(L)p2). The Southern hybridisation technique (F. Bringel, M.-C. Curk and J.-C. Hubert, Int. J. Syst. Bacteriol. 46: 588-594, 1996) revealed nine groups of profiles (I to IX). Results indicated an excellent convergence between RAPD and hybridisation classifications for more than 93% (56/60) of the strains studied. When we compared the fermentation patterns of the L. plantarum strains, three differences were found. Melezitose fermentation was not fermented by the G(L)p2 RAPD group, unlike the G(L)p1 RAPD group which included L. plantarum type strain NCIMB11974T. Second, alpha-methyl-D-mannoside was fermented by a majority of the strains of the G(L)p1 RAPD group but by none of the strains in the G(L)p2 RAPD group. Third, dulcitol was catabolized by nearly half of the strains of the G(L)p2 RAPD group but by none of the strains in the G(L)p1 RAPD group. Molecular diversity within L. plantarum was confirmed using Southern profiles, PCR amplification and subsequent sequencing of these PCR products. A 773 bp sequence overlapping the pyrDF genes showed high homology: at least 97% identical in L. plantarum strains (V to IX) and 99.9% identical in hybridisation groups VII and VIII. The same G-T transversion which destroyed the pyrF BglI site was found in 11 strains (hybridisation groups VI, VII and VIII). DNA rearrangements were identified downstream from the pyr genes, by PCR amplification and Southern hybridisation profile analysis in three strains of hybridisation groups VIII and IX, two of which also harboured the G-T transversion.
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Affiliation(s)
- F Bringel
- Laboratoire de Microbiologie et de Génétique, Université Louis-Pasteur Strasbourg-I, CNRS, France.
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Schönhuber W, Le Bourhis G, Tremblay J, Amann R, Kulakauskas S. Utilization of tmRNA sequences for bacterial identification. BMC Microbiol 2001; 1:20. [PMID: 11560762 PMCID: PMC55692 DOI: 10.1186/1471-2180-1-20] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2001] [Accepted: 09/07/2001] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Ribosomal RNA molecules are widely used for phylogenetic and in situ identification of bacteria. Nevertheless, their use to distinguish microorganisms within a species is often restricted by the high degree of sequence conservation and limited probe accessibility to the target in fluorescence in situ hybridization (FISH). To overcome these limitations, we examined the use of tmRNA for in situ identification. In E. coli, this stable 363 nucleotides long RNA is encoded by the ssrA gene, which is involved in the degradation of truncated proteins. RESULTS Conserved sequences at the 5'- and 3'-ends of tmRNA genes were used to design universal primers that could amplify the internal part of ssrA from Gram-positive bacteria having low G+C content, i.e. genera Bacillus, Enterococcus, Lactococcus, Lactobacillus, Leuconostoc, Listeria, Streptococcus and Staphylococcus. Sequence analysis of tmRNAs showed that this molecule can be used for phylogenetic assignment of bacteria. Compared to 16S rRNA, the tmRNA nucleotide sequences of some bacteria, for example Listeria, display considerable divergence between species. Using E. coli as an example, we have shown that bacteria can be specifically visualized by FISH with tmRNA targeted probes. CONCLUSIONS Features of tmRNA, including its presence in phylogenetically distant bacteria, conserved regions at gene extremities and a potential to serve as target for FISH, make this molecule a possible candidate for identification of bacteria.
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Affiliation(s)
- Wilhelm Schönhuber
- Lehrstuhl für Mikrobielle Ökologie, Universität Konstanz, Fach M654, Universitätsstrasse 10, D-78457 Konstanz, Germany
- Max-Planck-Institut für Marine Mikrobiologie, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Guenhael Le Bourhis
- Unité de Recherches Laitières et de Génétique Appliquée, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy-en-Josas, France
- Laboratoire de Pharmacologie des Agents Anticancéreux, Institut Bergonié, 229, Cours de l'Argonne, 33076 Bordeaux, France
| | - Josselyne Tremblay
- Unité de Recherches Laitières et de Génétique Appliquée, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy-en-Josas, France
| | - Rudolf Amann
- Max-Planck-Institut für Marine Mikrobiologie, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Saulius Kulakauskas
- Unité de Recherches Laitières et de Génétique Appliquée, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy-en-Josas, France
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Obis D, Guillot A, Mistou MY. Tolerance to high osmolality of Lactococcus lactis subsp. lactis and cremoris is related to the activity of a betaine transport system. FEMS Microbiol Lett 2001; 202:39-44. [PMID: 11506905 DOI: 10.1111/j.1574-6968.2001.tb10777.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Lactococcus lactis strains from the subsp. cremoris are described as more sensitive to osmotic stress than subsp. lactis strains. We examined the relation between osmotic tolerance and the activity of the betaine transporter BusA among 34 strains of L. lactis. The cremoris strains that showed reduced growth at high osmolality failed to accumulate betaine. The nature of the defect was found to vary among cremoris strains: lack of the busA encoding region, absence of synthesis or synthesis of an inactive form of BusA. The results suggest that the selection of strains well fitted to the dairy production lead to the loss of an otherwise efficient adaptation mechanism.
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Affiliation(s)
- D Obis
- Unité de Recherche de Biochimie et Structure des Protéines, Institut National de la Recherche Agronomique, 78352 Cedex, Jouy-en-Josas, France
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46
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Duwat P, Sourice S, Cesselin B, Lamberet G, Vido K, Gaudu P, Le Loir Y, Violet F, Loubière P, Gruss A. Respiration capacity of the fermenting bacterium Lactococcus lactis and its positive effects on growth and survival. J Bacteriol 2001; 183:4509-16. [PMID: 11443085 PMCID: PMC95345 DOI: 10.1128/jb.183.15.4509-4516.2001] [Citation(s) in RCA: 180] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oxygen is a major determinant of both survival and mortality of aerobic organisms. For the facultative anaerobe Lactococcus lactis, oxygen has negative effects on both growth and survival. We show here that oxygen can be beneficial to L. lactis if heme is present during aerated growth. The growth period is extended and long-term survival is markedly improved compared to results obtained under the usual fermentation conditions. We considered that improved growth and survival could be due to the capacity of L. lactis to undergo respiration. To test this idea, we confirmed that the metabolic behavior of lactococci in the presence of oxygen and hemin is consistent with respiration and is most pronounced late in growth. We then used a genetic approach to show the following. (i) The cydA gene, encoding cytochrome d oxidase, is required for respiration and plays a direct role in oxygen utilization. cydA expression is induced late in growth under respiration conditions. (ii) The hemZ gene, encoding ferrochelatase, which converts protoporphyrin IX to heme, is needed for respiration if the precursor, rather than the final heme product, is present in the medium. Surprisingly, survival improved by respiration is observed in a superoxide dismutase-deficient strain, a result which emphasizes the physiological differences between fermenting and respiring lactococci. These studies confirm respiratory metabolism in L. lactis and suggest that this organism may be better adapted to respiration than to traditional fermentative metabolism.
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Affiliation(s)
- P Duwat
- Génétique Appliquée-URLGA, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy en Josas, France
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Trébaol G, Manceau C, Tirilly Y, Boury S. Assessment of the genetic diversity among strains of Xanthomonas cynarae by randomly amplified polymorphic DNA analysis and development of specific characterized amplified regions for the rapid identification of X. cynarae. Appl Environ Microbiol 2001; 67:3379-84. [PMID: 11472907 PMCID: PMC93031 DOI: 10.1128/aem.67.8.3379-3384.2001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2001] [Accepted: 05/31/2001] [Indexed: 11/20/2022] Open
Abstract
The randomly amplified polymorphic DNA (RAPD) method was used to investigate the genetic diversity in Xanthomonas cynarae, which causes bacterial bract spot disease of artichoke. This RAPD analysis was also intended to identify molecular markers characteristic of this species, in order to develop PCR-based markers which can be used to detect this pathogenic bacterium in artichoke fields. Among the 340 RAPD primers tested, 40 were selected on their ability to produce reproducible and reliable fingerprints in our genetic background. These 40 primers produced almost similar patterns for the 37 X. cynarae strains studied, different from the fingerprints obtained for other Xanthomonas species and other xanthomonad-like bacteria isolated from artichoke leaves. Therefore, X. cynarae strains form a homogeneous genetic group. However, a little DNA polymorphism within this species was observed and the collection of X. cynarae isolates was divided into two groups (one containing three strains, the second one including all other strains). Out of seven RAPD markers characteristic of X. cynarae that were cloned, four did not hybridize to the genomic DNA of strains belonging to other Xanthomonas species. These four RAPD markers were converted into PCR markers (specific characterized amplified regions [SCARs]); they were sequenced, and a PCR primer pair was designed for each of them. Three derived SCARs are good candidates to develop PCR-based tests to detect X. cynarae in artichoke fields.
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Affiliation(s)
- G Trébaol
- B.B.V., Penn ar Prat, 29250 Saint Pol de Léon, France
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48
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Moschetti G, Blaiotta G, Villani F, Coppola S, Parente E. Comparison of statistical methods for identification of Streptococcus thermophilus, Enterococcus faecalis, and Enterococcus faecium from randomly amplified polymorphic DNA patterns. Appl Environ Microbiol 2001; 67:2156-66. [PMID: 11319095 PMCID: PMC92850 DOI: 10.1128/aem.67.5.2156-2166.2001] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2000] [Accepted: 02/18/2001] [Indexed: 11/20/2022] Open
Abstract
Thermophilic streptococci play an important role in the manufacture of many European cheeses, and a rapid and reliable method for their identification is needed. Randomly amplified polymorphic DNA (RAPD) PCR (RAPD-PCR) with two different primers coupled to hierarchical cluster analysis has proven to be a powerful tool for the classification and typing of Streptococcus thermophilus, Enterococcus faecium, and Enterococcus faecalis (G. Moschetti, G. Blaiotta, M. Aponte, P. Catzeddu, F. Villani, P. Deiana, and S. Coppola, J. Appl. Microbiol. 85:25-36, 1998). In order to develop a fast and inexpensive method for the identification of thermophilic streptococci, RAPD-PCR patterns were generated with a single primer (XD9), and the results were analyzed using artificial neural networks (Multilayer Perceptron, Radial Basis Function network, and Bayesian network) and multivariate statistical techniques (cluster analysis, linear discriminant analysis, and classification trees). Cluster analysis allowed the identification of S. thermophilus but not of enterococci. A Bayesian network proved to be more effective than a Multilayer Perceptron or a Radial Basis Function network for the identification of S. thermophilus, E. faecium, and E. faecalis using simplified RAPD-PCR patterns (obtained by summing the bands in selected areas of the patterns). The Bayesian network also significantly outperformed two multivariate statistical techniques (linear discriminant analysis and classification trees) and proved to be less sensitive to the size of the training set and more robust in the response to patterns belonging to unknown species.
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Affiliation(s)
- G Moschetti
- Dipartimento di Scienza degli Alimenti, Università degli Studi di Napoli Federico II, 80055 Portici, Italy
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De Angelis M, Corsetti A, Tosti N, Rossi J, Corbo MR, Gobbetti M. Characterization of non-starter lactic acid bacteria from Italian ewe cheeses based on phenotypic, genotypic, and cell wall protein analyses. Appl Environ Microbiol 2001; 67:2011-20. [PMID: 11319075 PMCID: PMC92830 DOI: 10.1128/aem.67.5.2011-2020.2001] [Citation(s) in RCA: 153] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2000] [Accepted: 01/16/2001] [Indexed: 11/20/2022] Open
Abstract
Non-starter lactic acid bacteria (NSLAB) were isolated from 12 Italian ewe cheeses representing six different types of cheese, which in several cases were produced by different manufacturers. A total of 400 presumptive Lactobacillus isolates were obtained, and 123 isolates and 10 type strains were subjected to phenotypic, genetic, and cell wall protein characterization analyses. Phenotypically, the cheese isolates included 32% Lactobacillus plantarum isolates, 15% L. brevis isolates, 12% L. paracasei subsp. paracasei isolates, 9% L. curvatus isolates, 6% L. fermentum isolates, 6% L. casei subsp. casei isolates, 5% L. pentosus isolates, 3% L. casei subsp. pseudoplantarum isolates, and 1% L. rhamnosus isolates. Eleven percent of the isolates were not phenotypically identified. Although a randomly amplified polymorphic DNA (RAPD) analysis based on three primers and clustering by the unweighted pair group method with arithmetic average (UPGMA) was useful for partially differentiating the 10 type strains, it did not provide a species-specific DNA band or a combination of bands which permitted complete separation of all the species considered. In contrast, sodium dodecyl sulfate-polyacrylamide gel electrophoresis cell wall protein profiles clustered by UPGMA were species specific and resolved the NSLAB. The only exceptions were isolates phenotypically identified as L. plantarum and L. pentosus or as L. casei subsp. casei and L. paracasei subsp. paracasei, which were grouped together. Based on protein profiles, Italian ewe cheeses frequently contained four different species and 3 to 16 strains. In general, the cheeses produced from raw ewe milk contained a larger number of more diverse strains than the cheeses produced from pasteurized milk. The same cheese produced in different factories contained different species, as well as strains that belonged to the same species but grouped in different RAPD clusters.
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Affiliation(s)
- M De Angelis
- Dipartimento di Scienze degli Alimenti, Sezione di Microbiologia Agro-alimentare, Università degli Studi di Perugia, Via S. Costanzo, Perugia, Italy
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50
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Giraffa G, Rossetti L, Neviani E. An evaluation of chelex-based DNA purification protocols for the typing of lactic acid bacteria. J Microbiol Methods 2000; 42:175-84. [PMID: 11018274 DOI: 10.1016/s0167-7012(00)00172-x] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
An easy and rapid protocol to extract DNA to be used as template for polymerase chain reaction (PCR) fingerprinting experiments from cultivable lactic acid bacteria (LAB) is proposed. Different procedures for rapid extraction of DNA by chelex (iminodiacetid acid) ionic resin were compared. Factors affecting the quality and reproducibility of PCR fingerprinting profiles were also investigated. Two out of three chelex-based protocols allowed to obtain DNA samples which, after PCR amplification, provided electrophoretic patterns comparable with those obtained by classical lysozyme and phenol-chloroform DNA extraction. A good level of reproducibility and consistency of the InstaGene procedure was verified. The procedure is fast, practical, and the DNA is of quality similar to that obtained by phenol-chloroform extraction. Although applied to a little number of LAB strains, chelex-based protocols are potentially applicable to a vast array of organisms and/or biological materials.
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Affiliation(s)
- G Giraffa
- Istituto Sperimentale Lattiero Caseario, Via A. Lombardo 11, 26900 Lodi, Italy.
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