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Güley Z, Fallico V, Cabrera-Rubio R, Cotter PD, Beresford T. Identification of Streptococcus infantarius subsp. infantarius as the species primarily responsible for acid production in Izmir Brined Tulum Cheese from the Aegean Region of Türkiye. Food Res Int 2022; 160:111707. [DOI: 10.1016/j.foodres.2022.111707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 07/02/2022] [Accepted: 07/15/2022] [Indexed: 11/04/2022]
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2
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Tarrah A, da Silva Duarte V, Pakroo S, Corich V, Giacomini A. Genomic and phenotypic assessments of safety and probiotic properties of Streptococcus macedonicus strains of dairy origin. Food Res Int 2020; 130:108931. [DOI: 10.1016/j.foodres.2019.108931] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 10/25/2022]
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3
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Khaldi TEM, Kebouchi M, Soligot C, Gomri MA, Kharroub K, Le Roux Y, Roux E. Streptococcus macedonicus strains isolated from traditional fermented milks: resistance to gastrointestinal environment and adhesion ability. Appl Microbiol Biotechnol 2019; 103:2759-2771. [PMID: 30701281 DOI: 10.1007/s00253-019-09651-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/27/2018] [Accepted: 01/15/2019] [Indexed: 12/12/2022]
Abstract
In this study, Streptococcus macedonicus (S. macedonicus) strains were identified from Algerian traditional fermented milks (Lben and Rayeb). Important prerequisites of probiotic interest such as acidity, bile salts tolerance, and adhesion ability to epithelial cells were investigated. A combination of phenotypic (ability to grow on Bile Esculin Azide medium, BEA; on high salt content medium NaCl 6.5%; on alkaline medium pH 9.6) and genotypic approaches (16S rRNA, ITS genes sequencing and MLST technique) allowed to identify four genetically distinct strains of S. macedonicus. These four strains and two references, Streptococcus thermophilus LMD-9 and Lactobacillus rhamnosus GG (LGG), were tested for their capacity to survive at low pH values, and at different concentrations of an equimolar bile salts mixture (BSM). Two different cell lines, Caco-2 TC7 and HT29-MTX, were used for the adhesion study. The results show that S. macedonicus strains selected constitute a distinct genetic entity from the Greek strain S. macedonicus ACA-DC-198. They were able to survive up to pH 3 and could tolerate high concentrations of bile salts (10 mM), unlike LMD-9 and LGG strains. Our strains also display in vitro adhesion similar to the LGG strain on Caco-2 TC7 and higher adhesion than the LMD-9 strain to Caco-2 TC7 and HT29-MTX cell models. This first characterization allows considering S. macedonicus as a potential candidate for possible probiotic effects that need to be investigated.
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Affiliation(s)
- Tedj El Moulouk Khaldi
- Laboratoire Alimentation, Nutrition et Santé (ALNUTS), Institut de la Nutrition, de l'Alimentation et des Technologies Agro Alimentaires (INATAA), Université Frères Mentouri Constantine 1 (UFMC1), Route de Ain El Bey, 25000, Constantine, Algeria
| | | | - Claire Soligot
- INRA, URAFPA, Université de Lorraine, F-54000, Nancy, France
| | - Mohamed Amine Gomri
- Laboratoire Biotechnologie et Qualité des Aliments (BIOQUAL), Equipe Métabolites des Extrêmophiles METEX, Institut de la Nutrition, de l'Alimentation et des Technologies Agro Alimentaires (INATAA), Université Frères Mentouri Constantine 1 (UFMC1), Route de Ain El Bey, 25000, Constantine, Algeria
| | - Karima Kharroub
- Laboratoire Biotechnologie et Qualité des Aliments (BIOQUAL), Equipe Métabolites des Extrêmophiles METEX, Institut de la Nutrition, de l'Alimentation et des Technologies Agro Alimentaires (INATAA), Université Frères Mentouri Constantine 1 (UFMC1), Route de Ain El Bey, 25000, Constantine, Algeria
| | - Yves Le Roux
- INRA, URAFPA, Université de Lorraine, F-54000, Nancy, France
| | - Emeline Roux
- CALBINOTOX, Université de Lorraine, F-54000, Nancy, France.
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Linezolid resistance genes and genetic elements enhancing their dissemination in enterococci and streptococci. Plasmid 2018; 99:89-98. [PMID: 30253132 DOI: 10.1016/j.plasmid.2018.09.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 09/21/2018] [Accepted: 09/21/2018] [Indexed: 01/08/2023]
Abstract
Linezolid is considered a last resort drug in treatment of severe infections caused by Gram-positive pathogens, resistant to other antibiotics, such as vancomycin-resistant enterococci (VRE), methicillin-resistant staphylococci and multidrug resistant pneumococci. Although the vast majority of Gram-positive pathogenic bacteria remain susceptible to linezolid, resistant isolates of enterococci, staphylococci and streptococci have been reported worldwide. In these bacteria, apart from mutations, affecting mostly the 23S rRNA genes, acquisition of such genes as cfr, cfr(B), optrA and poxtA, often associated with mobile genetic elements (MGE), plays an important role for resistance. The purpose of this paper is to provide an overview on diversity and epidemiology of MGE carrying linezolid-resistance genes among clinically-relevant Gram-positive pathogens such as enterococci and streptococci.
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Whole-Genome Sequences of Three Streptococcus macedonicus Strains Isolated from Italian Cheeses in the Veneto Region. GENOME ANNOUNCEMENTS 2017; 5:5/50/e01358-17. [PMID: 29242223 PMCID: PMC5730673 DOI: 10.1128/genomea.01358-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the genome sequences of three Streptococcus macedonicus strains isolated from different cheeses in the Veneto region of Italy. The presented data aim at increasing the scarce genomic information available for this species, which is frequently encountered in fermented foods and appears to be a promising technological microorganism.
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6
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Whole-Genome Sequence of the Cheese Isolate Streptococcus macedonicus 679. GENOME ANNOUNCEMENTS 2016; 4:4/5/e01025-16. [PMID: 27660795 PMCID: PMC5034146 DOI: 10.1128/genomea.01025-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
It is well recognized that Streptococcus macedonicus can populate artisanal fermented foods, especially those of dairy origin. However, the safety of S. macedonicus remains to be established. Here, we present the whole-genome sequence of strain 679, which was isolated from a French uncooked semihard cheese made with cow milk.
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Anastasiou R, Driessche GV, Boutou E, Kazou M, Alexandraki V, Vorgias CE, Devreese B, Tsakalidou E, Papadimitriou K. Engineered strains of Streptococcus macedonicus towards an osmotic stress resistant phenotype retain their ability to produce the bacteriocin macedocin under hyperosmotic conditions. J Biotechnol 2015; 212:125-33. [PMID: 26319319 DOI: 10.1016/j.jbiotec.2015.08.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 08/17/2015] [Accepted: 08/20/2015] [Indexed: 12/25/2022]
Abstract
Streptococcus macedonicus ACA-DC 198 produces the bacteriocin macedocin in milk only under low NaCl concentrations (<1.0%w/v). The thermosensitive plasmid pGh9:ISS1 was employed to generate osmotic stress resistant (osmr) mutants of S. macedonicus. Three osmr mutants showing integration of the vector in unique chromosomal sites were identified and the disrupted loci were characterized. Interestingly, the mutants were able to grow and to produce macedocin at considerably higher concentrations of NaCl compared to the wild-type (up to 4.0%w/v). The production of macedocin under hyperosmotic conditions solely by the osmr mutants was validated by the well diffusion assay and by mass spectrometry analysis. RT-PCR experiments demonstrated that the macedocin biosynthetic regulon was transcribed at high salt concentrations only in the mutants. Mutant osmr3, the most robust mutant, was converted in its markerless derivative (osmr3f). Co-culture of S. macedonicus with spores of Clostridium tyrobutyricum in milk demonstrated that only the osmr3f mutant and not the wild-type inhibited the growth of the spores under hyperosmotic conditions (i.e., 2.5%w/v NaCl) due to the production of macedocin. Our study shows how genetic manipulation of a strain towards a stress resistant phenotype could improve bacteriocin production under conditions of the same stress.
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Affiliation(s)
- Rania Anastasiou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | - Gonzalez Van Driessche
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Effrossyni Boutou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimioupolis-Zographou, 157 84 Athens, Greece
| | - Maria Kazou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | - Voula Alexandraki
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | - Constantinos E Vorgias
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimioupolis-Zographou, 157 84 Athens, Greece
| | - Bart Devreese
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Effie Tsakalidou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | - Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece; Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimioupolis-Zographou, 157 84 Athens, Greece.
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Stolze Y, Zakrzewski M, Maus I, Eikmeyer F, Jaenicke S, Rottmann N, Siebner C, Pühler A, Schlüter A. Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:14. [PMID: 25688290 PMCID: PMC4329661 DOI: 10.1186/s13068-014-0193-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/22/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Decomposition of biomass for biogas production can be practiced under wet and dry fermentation conditions. In contrast to the dry fermentation technology, wet fermentation is characterized by a high liquid content and a relatively low total solid content. In this study, the composition and functional potential of a biogas-producing microbial community in an agricultural biogas reactor operating under wet fermentation conditions was analyzed by a metagenomic approach applying 454-pyrosequencing. The obtained metagenomic dataset and corresponding 16S rRNA gene amplicon sequences were compared to the previously sequenced comparable metagenome from a dry fermentation process, meeting explicitly identical boundary conditions regarding sample and community DNA preparation, sequencing technology, processing of sequence reads and data analyses by bioinformatics tools. RESULTS High-throughput metagenome sequencing of community DNA from the wet fermentation process applying the pyrosequencing approach resulted in 1,532,780 reads, with an average read length of 397 bp, accounting for approximately 594 million bases of sequence information in total. Taxonomic comparison of the communities from wet and dry fermentation revealed similar microbial profiles with Bacteria being the predominant superkingdom, while the superkingdom Archaea was less abundant. In both biogas plants, the bacterial phyla Firmicutes, Bacteroidetes, Spirochaetes and Proteobacteria were identified with descending frequencies. Within the archaeal superkingdom, the phylum Euryarchaeota was most abundant with the dominant class Methanomicrobia. Functional profiles of the communities revealed that environmental gene tags representing methanogenesis enzymes were present in both biogas plants in comparable frequencies. 16S rRNA gene amplicon high-throughput sequencing disclosed differences in the sub-communities comprising methanogenic Archaea between both processes. Fragment recruitments of metagenomic reads to the reference genome of the archaeon Methanoculleus bourgensis MS2(T) revealed that dominant methanogens within the dry fermentation process were highly related to the reference. CONCLUSIONS Although process parameters, substrates and technology differ between the wet and dry biogas fermentations analyzed in this study, community profiles are very similar at least at higher taxonomic ranks, illustrating that core community taxa perform key functions in biomass decomposition and methane synthesis. Regarding methanogenesis, Archaea highly related to the type strain M. bourgensis MS2(T) dominate the dry fermentation process, suggesting the adaptation of members belonging to this species to specific fermentation process parameters.
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Affiliation(s)
- Yvonne Stolze
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Martha Zakrzewski
- />QIMR Berghofer Medical Research Institute Herston, 300 Herston Road, Brisbane, QLD 4006 Australia
| | - Irena Maus
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Felix Eikmeyer
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Sebastian Jaenicke
- />Bioinformatics Resource Facility, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Nils Rottmann
- />NORTH-TEC Maschinenbau GmbH, Oldenhörn 1, 25821 Bredstedt, Germany
| | - Clemens Siebner
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Alfred Pühler
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Andreas Schlüter
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
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9
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Papadimitriou K, Anastasiou R, Maistrou E, Plakas T, Papandreou NC, Hamodrakas SJ, Ferreira S, Supply P, Renault P, Pot B, Tsakalidou E. Acquisition through horizontal gene transfer of plasmid pSMA198 by Streptococcus macedonicus ACA-DC 198 points towards the dairy origin of the species. PLoS One 2015; 10:e0116337. [PMID: 25584532 PMCID: PMC4293149 DOI: 10.1371/journal.pone.0116337] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 12/05/2014] [Indexed: 12/22/2022] Open
Abstract
Background Streptococcus macedonicus is an intriguing streptococcal species whose most frequent source of isolation is fermented foods similarly to Streptococcus thermophilus. However, S. macedonicus is closely related to commensal opportunistic pathogens of the Streptococcus bovis/Streptococcus equinus complex. Methodology/Principal Findings We analyzed the pSMA198 plasmid isolated from the dairy strain Streptococcus macedonicus ACA-DC 198 in order to provide novel clues about the main ecological niche of this bacterium. pSMA198 belongs to the narrow host range pCI305/pWV02 family found primarily in lactococci and to the best of our knowledge it is the first such plasmid to be reported in streptococci. Comparative analysis of the pSMA198 sequence revealed a high degree of similarity with plasmids isolated from Lactococcus lactis strains deriving from milk or its products. Phylogenetic analysis of the pSMA198 Rep showed that the vast majority of closely related proteins derive from lactococcal dairy isolates. Additionally, cloning of the pSMA198 ori in L. lactis revealed a 100% stability of replication over 100 generations. Both pSMA198 and the chromosome of S. macedonicus exhibit a high percentage of potential pseudogenes, indicating that they have co-evolved under the same gene decay processes. We identified chromosomal regions in S. macedonicus that may have originated from pSMA198, also supporting a long co-existence of the two replicons. pSMA198 was also found in divergent biotypes of S. macedonicus and in strains isolated from dispersed geographic locations (e.g. Greece and Switzerland) showing that pSMA198’s acquisition is not a recent event. Conclusions/Significance Here we propose that S. macedonicus acquired plasmid pSMA198 from L. lactis via an ancestral genetic exchange event that took place most probably in milk or dairy products. We provide important evidence that point towards the dairy origin of this species.
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Affiliation(s)
- Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
- * E-mail:
| | - Rania Anastasiou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Eleni Maistrou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Thomas Plakas
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece
| | - Nikos C. Papandreou
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece
| | - Stavros J. Hamodrakas
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece
| | - Stéphanie Ferreira
- Genoscreen, Service of Research, Development and Innovation in Health and Environment, Campus de l’Institut Pasteur, 1 rue du Professeur Calmette, 59000, Lille, France
| | - Philip Supply
- Genoscreen, Service of Research, Development and Innovation in Health and Environment, Campus de l’Institut Pasteur, 1 rue du Professeur Calmette, 59000, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019, Lille, France
- Inserm U1019, F-59019, Lille, France
- CNRS UMR8204, F-59019, Lille, France
- Univ Lille de Nord France, F-59019, Lille, France
| | - Pierre Renault
- INRA, UMR1319 Micalis, Jouy-en-Josas, F-78352, France
- AgroParisTech, UMR Micalis, Jouy-en-Josas, F-78352, France
| | - Bruno Pot
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59019, Lille, France
- Inserm U1019, F-59019, Lille, France
- CNRS UMR8204, F-59019, Lille, France
- Univ Lille de Nord France, F-59019, Lille, France
| | - Effie Tsakalidou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
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Heperkan D, Daskaya-Dikmen C, Bayram B. Evaluation of lactic acid bacterial strains of boza for their exopolysaccharide and enzyme production as a potential adjunct culture. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Mobilizable Rolling-Circle Replicating Plasmids from Gram-Positive Bacteria: A Low-Cost Conjugative Transfer. Microbiol Spectr 2014; 2:8. [PMID: 25606350 DOI: 10.1128/microbiolspec.plas-0008-2013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Conjugation is a key mechanism for horizontal gene transfer in bacteria. Some plasmids are not self-transmissible but can be mobilized by functions encoded in trans provided by other auxiliary conjugative elements. Although the transfer efficiency of mobilizable plasmids is usually lower than that of conjugative elements, mobilizable plasmidsare more frequently found in nature. In this sense, replication and mobilization can be considered as important mechanisms influencing plasmid promiscuity. Here we review the present available information on two families of small mobilizable plasmids from Gram-positive bacteria that replicate via the rolling-circle mechanism. One of these families, represented by the streptococcal plasmid pMV158, is an interesting model since it contains a specific mobilization module (MOBV) that is widely distributed among mobilizable plasmids. We discuss a mechanism in which the promiscuity of the pMV158 replicon is based on the presence of two origins of lagging strand synthesis. The current strategies to assess plasmid transfer efficiency as well as to inhibit conjugative plasmid transfer are presented. Some applications of these plasmids as biotechnological tools are also reviewed.
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Whole-Genome Sequence of Streptococcus macedonicus Strain 33MO, Isolated from the Curd of Morlacco Cheese in the Veneto Region (Italy). GENOME ANNOUNCEMENTS 2014; 2:2/4/e00746-14. [PMID: 25103758 PMCID: PMC4125769 DOI: 10.1128/genomea.00746-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A genetic characterization of Streptococcus macedonicus is important to better understand the characteristics of this lactic acid bacterium, frequently detected in fermented food bacteria communities. This report presents the draft genome sequence description of strain 33MO, the first publicly available genome sequence of an Italian S. macedonicus isolate.
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Arioli S, Guglielmetti S, Amalfitano S, Viti C, Marchi E, Decorosi F, Giovannetti L, Mora D. Characterization of tetA-like gene encoding for a major facilitator superfamily efflux pump in Streptococcus thermophilus. FEMS Microbiol Lett 2014; 355:61-70. [PMID: 24766488 DOI: 10.1111/1574-6968.12449] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 04/07/2014] [Accepted: 04/22/2014] [Indexed: 11/26/2022] Open
Abstract
Efflux pumps are membrane proteins involved in the active extrusion of a wide range of structurally dissimilar substrates from cells. A multidrug efflux pump named TetA belonging to the major facilitator superfamily (MFS) of transporters was identified in the Streptococcus thermophilus DSM 20617(T) genome. The tetA-like gene was found in the genomes of a number of S. thermophilus strains sequenced to date and in Streptococcus macedonicus ACA-DC 198, suggesting a possible horizontal gene transfer event between these two Streptococcus species, which are both adapted to the milk environment. Flow cytometry (single-cell) analysis revealed bistable TetA activity in the S. thermophilus population, and tetA-like gene over-expression resulted in a reduced susceptibility to ethidium bromide, tetracycline, and other toxic compounds even when the efflux pump was over-expressed in a strain naturally lacking tetA-like gene.
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Affiliation(s)
- Stefania Arioli
- Department of Food Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
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14
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Papadimitriou K, Anastasiou R, Mavrogonatou E, Blom J, Papandreou NC, Hamodrakas SJ, Ferreira S, Renault P, Supply P, Pot B, Tsakalidou E. Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex. BMC Genomics 2014; 15:272. [PMID: 24713045 PMCID: PMC4051162 DOI: 10.1186/1471-2164-15-272] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 04/01/2014] [Indexed: 12/21/2022] Open
Abstract
Background Within the genus Streptococcus, only Streptococcus
thermophilus is used as a starter culture in food fermentations.
Streptococcus macedonicus though, which belongs to the
Streptococcus bovis/Streptococcus equinus complex
(SBSEC), is also frequently isolated from fermented foods mainly of dairy
origin. Members of the SBSEC have been implicated in human endocarditis and
colon cancer. Here we compare the genome sequence of the dairy isolate
S. macedonicus ACA-DC 198 to the other SBSEC genomes in order
to assess in silico its potential adaptation to milk and its
pathogenicity status. Results Despite the fact that the SBSEC species were found tightly related based on
whole genome phylogeny of streptococci, two distinct patterns of evolution
were identified among them. Streptococcus macedonicus, Streptococcus
infantarius CJ18 and Streptococcus pasteurianus ATCC 43144
seem to have undergone reductive evolution resulting in significantly
diminished genome sizes and increased percentages of potential pseudogenes
when compared to Streptococcus gallolyticus subsp.
gallolyticus. In addition, the three species seem to have lost
genes for catabolizing complex plant carbohydrates and for detoxifying toxic
substances previously linked to the ability of S. gallolyticus to
survive in the rumen. Analysis of the S. macedonicus genome
revealed features that could support adaptation to milk, including an extra
gene cluster for lactose and galactose metabolism, a proteolytic system for
casein hydrolysis, auxotrophy for several vitamins, an increased ability to
resist bacteriophages and horizontal gene transfer events with the dairy
Lactococcus lactis and S. thermophilus as potential
donors. In addition, S. macedonicus lacks several
pathogenicity-related genes found in S. gallolyticus. For example,
S. macedonicus has retained only one (i.e. the pil3)
of the three pilus gene clusters which may mediate the binding of S.
gallolyticus to the extracellular matrix. Unexpectedly, similar
findings were obtained not only for the dairy S. infantarius CJ18,
but also for the blood isolate S. pasteurianus ATCC 43144. Conclusions Our whole genome analyses suggest traits of adaptation of S.
macedonicus to the nutrient-rich dairy environment. During this
process the bacterium gained genes presumably important for this new
ecological niche. Finally, S. macedonicus carries a reduced number
of putative SBSEC virulence factors, which suggests a diminished pathogenic
potential.
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Affiliation(s)
- Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, Athens 118 55, Greece.
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15
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Diversity of gram-positive catalase-negative cocci in sheep bulk tank milk by comparative 16S rDNA sequence analysis. Int Dairy J 2014. [DOI: 10.1016/j.idairyj.2013.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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Shibata Y, Tien LHT, Nomoto R, Osawa R. Development of a multilocus sequence typing scheme for Streptococcus gallolyticus. MICROBIOLOGY-SGM 2013; 160:113-122. [PMID: 24131946 DOI: 10.1099/mic.0.071605-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Streptococcus gallolyticus is often found as a member of the normal gut microflora in various animals. However, it has been reported to cause mastitis in cattle, septicaemia in pigeons, and meningitis, septicaemia and endocarditis in humans. However, little is known about the epidemiology and crucial virulence factors of S. gallolyticus. To help address these issues, we developed a multilocus sequence typing (MLST) scheme for S. gallolyticus. Seven housekeeping gene fragments were sequenced from each of 58 S. gallolyticus isolates collected from diverse origins and sources. The MLST scheme had good discriminatory ability. The 63 strains, including the 5 whole genome sequenced strains examined, resolved into 57 sequence types (STs), with 52 STs represented by only a single strain. With respect to the identification of S. gallolyticus subspecies (i.e. S. gallolyticus subsp. gallolyticus, S. gallolyticus subsp. pasteurianus and S. gallolyticus subsp. macedonicus), the results of biochemical tests and DNA-DNA hybridization were in high concordance with those of the MLST scheme. The MLST scheme developed in this study may be a useful tool capable of replacing the conventional methods used for S. gallolyticus subspecies identification. The results of this study suggest that the biology and virulence of two pathogenic S. gallolyticus subspecies (i.e. S. gallolyticus subsp. gallolyticus and S. gallolyticus subsp. pasteurianus) are very different. The MLST scheme offers researchers a valuable typing tool that will promote further investigation of the epidemiology of S. gallolyticus.
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Affiliation(s)
- Yusuke Shibata
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, Rokko-dai 1-1, Nada-ku, Kobe, 657-8501, Japan
| | - Le Hong Thuy Tien
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, Rokko-dai 1-1, Nada-ku, Kobe, 657-8501, Japan
| | - Ryohei Nomoto
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, Rokko-dai 1-1, Nada-ku, Kobe, 657-8501, Japan
| | - Ro Osawa
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, Rokko-dai 1-1, Nada-ku, Kobe, 657-8501, Japan
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17
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Jans C, Kaindi DWM, Böck D, Njage PMK, Kouamé-Sina SM, Bonfoh B, Lacroix C, Meile L. Prevalence and comparison of Streptococcus infantarius subsp. infantarius and Streptococcus gallolyticus subsp. macedonicus in raw and fermented dairy products from East and West Africa. Int J Food Microbiol 2013; 167:186-95. [PMID: 24131584 DOI: 10.1016/j.ijfoodmicro.2013.09.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 08/12/2013] [Accepted: 09/14/2013] [Indexed: 01/25/2023]
Abstract
Streptococcus infantarius subsp. infantarius (Sii) and Streptococcus gallolyticus subsp. macedonicus are members of the Streptococcus bovis/Streptococcus equinus complex (SBSEC) associated with human infections. SBSEC-related endocarditis was furthermore associated with rural residency in Southern Europe. SBSEC members are increasingly isolated as predominant species from fermented dairy products in Europe, Asia and Africa. African variants of Sii displayed dairy adaptations to lactose metabolism paralleling those of Streptococcus thermophilus including genome decay. In this study, the aim was to assess the prevalence of Sii and possibly other SBSEC members in dairy products of East and West Africa in order to identify their habitat, estimate their importance in dairy fermentation processes and determine geographic areas affected by this potential health risk. Presumptive SBSEC members were isolated on semi-selective M17 and SM agar media. Subsequent genotypic identification of isolates was based on rep-PCR fingerprinting and SBSEC-specific16S rRNA gene PCR assay. Detailed identification was achieved through application of novel primers enhancing the binding stringency in partial groES/groEL gene amplification and subsequent DNA sequencing. The presence of S. thermophilus-like lacS and lacZ genes in the SBSEC isolates was determined to elucidate the prevalence of this dairy adaptation. Isolates (n = 754) were obtained from 72 raw and 95 fermented milk samples from Côte d'Ivoire and Kenya on semi-selective agar media. Colonies of Sii were not detected from raw milk despite high microbial titers of approximately 10(6)CFU/mL on M17 agar medium. However, after spontaneous milk fermentation Sii was genotypically identified in 94.1% of Kenyan samples and 60.8% of Kenyan isolates. Sii prevalence in Côte d'Ivoire displayed seasonal variations in samples from 32.3% (June) to 40.0% (Dec/Jan) and isolates from 20.5% (June) to 27.7% (Dec/Jan) present at titers of 10(6)-10(8)CFU/mL. lacS and lacZ genes were detected in all Kenyan and 25.8% (June) to 65.4% (Dec/Jan) of Ivorian Sii isolates. Regional differences in prevalence of Sii and dairy adaptations were observed, but no clear effect of dairy animal, fermentation procedure and climate was revealed. Conclusively, the high prevalence of Sii in Kenya, Côte d'Ivoire in addition to Somalia, Sudan and Mali strongly indicates a pivotal role of Sii in traditional African dairy fermentations potentially paralleling that of typical western dairy species S. thermophilus. Putative health risks associated with the consumption of high amounts of live Sii and potential different degrees of evolutionary adaptation or ecological colonization require further epidemiologic and genomic investigations, particularly in Africa.
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Affiliation(s)
- Christoph Jans
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
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18
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Quigley L, O'Sullivan O, Stanton C, Beresford TP, Ross RP, Fitzgerald GF, Cotter PD. The complex microbiota of raw milk. FEMS Microbiol Rev 2013; 37:664-98. [PMID: 23808865 DOI: 10.1111/1574-6976.12030] [Citation(s) in RCA: 471] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 06/14/2013] [Accepted: 06/18/2013] [Indexed: 12/15/2022] Open
Abstract
Here, we review what is known about the microorganisms present in raw milk, including milk from cows, sheep, goats and humans. Milk, due to its high nutritional content, can support a rich microbiota. These microorganisms enter milk from a variety of sources and, once in milk, can play a number of roles, such as facilitating dairy fermentations (e.g. Lactococcus, Lactobacillus, Streptococcus, Propionibacterium and fungal populations), causing spoilage (e.g. Pseudomonas, Clostridium, Bacillus and other spore-forming or thermoduric microorganisms), promoting health (e.g. lactobacilli and bifidobacteria) or causing disease (e.g. Listeria, Salmonella, Escherichia coli, Campylobacter and mycotoxin-producing fungi). There is also concern that the presence of antibiotic residues in milk leads to the development of resistance, particularly among pathogenic bacteria. Here, we comprehensively review these topics, while comparing the approaches, both culture-dependent and culture-independent, which can be taken to investigate the microbial composition of milk.
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Affiliation(s)
- Lisa Quigley
- Teagasc Moorepark Food Research Centre, Fermoy, Cork, Ireland
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19
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Jans C, Follador R, Hochstrasser M, Lacroix C, Meile L, Stevens MJA. Comparative genome analysis of Streptococcus infantarius subsp. infantarius CJ18, an African fermented camel milk isolate with adaptations to dairy environment. BMC Genomics 2013; 14:200. [PMID: 23521820 PMCID: PMC3640971 DOI: 10.1186/1471-2164-14-200] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 03/13/2013] [Indexed: 12/14/2022] Open
Abstract
Background Streptococcus infantarius subsp. infantarius (Sii) belongs to the Streptococcus bovis/Streptococcus equinus complex associated with several human and animal infections. Sii is a predominant bacterium in spontaneously fermented milk products in Africa. The genome sequence of Sii strain CJ18 was compared with that of other Streptococcus species to identify dairy adaptations including genome decay such as in Streptococcus thermophilus, traits for its competitiveness in spontaneous milk fermentation and to assess potential health risks for consumers. Results The genome of Sii CJ18 harbors several unique regions in comparison to Sii ATCC BAA-102T, among others an enlarged exo- and capsular polysaccharide operon; Streptococcus thermophilus-associated genes; a region containing metabolic and hypothetical genes mostly unique to CJ18 and the dairy isolate Streptococcus gallolyticus subsp. macedonicus; and a second oligopeptide transport operon. Dairy adaptations in CJ18 are reflected by a high percentage of pseudogenes (4.9%) representing genome decay which includes the inactivation of the lactose phosphotransferase system (lacIIABC) by multiple transposases integration. The presence of lacS and lacZ genes is the major dairy adaptation affecting lactose metabolism pathways also due to the disruption of lacIIABC. We constructed mutant strains of lacS, lacZ and lacIIABC and analyzed the resulting strains of CJ18 to confirm the redirection of lactose metabolism via LacS and LacZ. Natural competence genes are conserved in both Sii strains, but CJ18 contains a lower number of CRISPR spacers which indicates a reduced defense capability against alien DNA. No classical streptococcal virulence factors were detected in both Sii strains apart from those involved in adhesion which should be considered niche factors. Sii-specific virulence factors are not described. Several Sii-specific regions encoding uncharacterized proteins provide new leads for virulence analyses and investigation of the unclear association of dairy and clinical Sii with human diseases. Conclusions The genome of the African dairy isolate Sii CJ18 clearly differs from the human isolate ATCC BAA-102T. CJ18 possesses a high natural competence predisposition likely explaining the enlarged genome. Metabolic adaptations to the dairy environment are evident and especially lactose uptake corresponds to S. thermophilus. Genome decay is not as advanced as in S. thermophilus (10-19%) possibly due to a shorter history in dairy fermentations.
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Affiliation(s)
- Christoph Jans
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, ETH Zurich, Zurich, CH 8092, Switzerland
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20
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Macedovicin, the second food-grade lantibiotic produced by Streptococcus macedonicus ACA-DC 198. Food Microbiol 2013; 33:124-30. [DOI: 10.1016/j.fm.2012.09.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 07/14/2012] [Accepted: 09/19/2012] [Indexed: 11/20/2022]
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21
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O'Sullivan DJ, Giblin L, McSweeney PLH, Sheehan JJ, Cotter PD. Nucleic acid-based approaches to investigate microbial-related cheese quality defects. Front Microbiol 2013; 4:1. [PMID: 23346082 PMCID: PMC3549567 DOI: 10.3389/fmicb.2013.00001] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 01/02/2013] [Indexed: 01/14/2023] Open
Abstract
The microbial profile of cheese is a primary determinant of cheese quality. Microorganisms can contribute to aroma and taste defects, form biogenic amines, cause gas and secondary fermentation defects, and can contribute to cheese pinking and mineral deposition issues. These defects may be as a result of seasonality and the variability in the composition of the milk supplied, variations in cheese processing parameters, as well as the nature and number of the non-starter microorganisms which come from the milk or other environmental sources. Such defects can be responsible for production and product recall costs and thus represent a significant economic burden for the dairy industry worldwide. Traditional non-molecular approaches are often considered biased and have inherently slow turnaround times. Molecular techniques can provide early and rapid detection of defects that result from the presence of specific spoilage microbes and, ultimately, assist in enhancing cheese quality and reducing costs. Here we review the DNA-based methods that are available to detect/quantify spoilage bacteria, and relevant metabolic pathways in cheeses and, in the process, highlight how these strategies can be employed to improve cheese quality and reduce the associated economic burden on cheese processors.
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Affiliation(s)
- Daniel J. O'Sullivan
- Food Bioscience Department, Teagasc Food Research CentreFermoy, Ireland
- School of Food and Nutritional Sciences, University College CorkCork, Ireland
| | - Linda Giblin
- Food Bioscience Department, Teagasc Food Research CentreFermoy, Ireland
| | | | | | - Paul D. Cotter
- Food Bioscience Department, Teagasc Food Research CentreFermoy, Ireland
- Alimentary Pharmabiotic Centre, University College CorkCork, Ireland
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22
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Nelson OW, Garrity GM. Genome sequences published outside of Standards in Genomic Sciences, March-April 2012. Stand Genomic Sci 2012. [PMCID: PMC3387800 DOI: 10.4056/sigs.2836114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.
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Affiliation(s)
- Oranmiyan W. Nelson
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
| | - George M. Garrity
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
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