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Lecaudé C, Orieux N, Chuzeville S, Bertry A, Coissac E, Boyer F, Bonin A, Colomb-Boeckler N, Mathieu B, Recour M, Vindret J, Pignol C, Romand S, Petite C, Taberlet P, Charles C, Bel N, Hauwuy A. Deciphering microbial communities of three Savoyard raw milk cheeses along ripening and regarding the cheese process. Int J Food Microbiol 2024; 418:110712. [PMID: 38723541 DOI: 10.1016/j.ijfoodmicro.2024.110712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/26/2024] [Accepted: 04/17/2024] [Indexed: 05/27/2024]
Abstract
Different Savoyard cheeses are granted with PDO (Protected Designation or Origin) and PGI (Protected Geographical Indication) which guarantees consumers compliance with strict specifications. The use of raw milk is known to be crucial for specific flavor development. To unravel the factors influencing microbial ecosystems across cheese making steps, according to the seasonality (winter and summer) and the mode of production (farmhouse and dairy factory ones), gene targeting on bacteria and fungus was used to have a full picture of 3 cheese making technologies, from the raw milk to the end of the ripening. Our results revealed that Savoyard raw milks are a plenteous source of biodiversity together with the brines used during the process, that may support the development of specific features for each cheese. It was shown that rinds and curds have very contrasted ecosystem diversity, composition, and evolution. Ripening stage was selective for some bacterial species, whereas fungus were mainly ubiquitous in dairy samples. All ripening stages are impacted by the type of cheese technologies, with a higher impact on bacterial communities, except for fungal rind communities, for which the technology is the more discriminant. The specific microorganism's abundance for each technology allow to see a real bar-code, with more or less differences regarding bacterial or fungal communities. Bacterial structuration is shaped mainly by matrices, differently regarding technologies while the influence of technology is higher for fungi. Production types showed 10 differential bacterial species, farmhouses showed more ripening taxa, while dairy factory products showing more lactic acid bacteria. Meanwhile, seasonality looks to be a minor element for the comprehension of both microbial ecosystems, but the uniqueness of each dairy plant is a key explicative feature, more for bacteria than for fungus communities.
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Affiliation(s)
- Cresciense Lecaudé
- CERAQ, Centre de ressources pour l'agriculture de qualité et de montagne, 40 Rue du Terraillet, 73190 Saint-Baldoph, France.
| | - Nicolas Orieux
- ENILV, Ecole Nationale des industries du lait et de la viande, 212Rue Anatole France, 74800 La Roche-sur-Foron, France
| | - Sarah Chuzeville
- ACTALIA, Centre technique d'expertise agroalimentaire, Division d'expertise analytique sur le lait et les produits laitiers, 419 Rte des Champs Laitiers, 74800 Eteaux, France
| | - Alicia Bertry
- ACTALIA, Centre technique d'expertise agroalimentaire, Division d'expertise analytique sur le lait et les produits laitiers, 419 Rte des Champs Laitiers, 74800 Eteaux, France
| | - Eric Coissac
- Université Grenoble Alpes, Université Savoie Mont-Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000 Grenoble, France
| | - Frederic Boyer
- Université Grenoble Alpes, Université Savoie Mont-Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000 Grenoble, France
| | - Aurélie Bonin
- Université Grenoble Alpes, Université Savoie Mont-Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000 Grenoble, France
| | - Nelly Colomb-Boeckler
- ACTALIA, Centre technique d'expertise agroalimentaire, Division d'expertise analytique sur le lait et les produits laitiers, 419 Rte des Champs Laitiers, 74800 Eteaux, France
| | - Bruno Mathieu
- Syndicat Interprofessionnel du Reblochon, 28 Rue Louis Haase, 74230 Thônes, France
| | - Manon Recour
- Syndicat Interprofessionnel du Reblochon, 28 Rue Louis Haase, 74230 Thônes, France
| | - Joël Vindret
- sifa syndicat interprofessionnel du fromage abondance, 16 chemin d'Hirmentaz, 74200 Thonon-les-Bains, France
| | - Céline Pignol
- Savoicime, Syndicat Interprofessionnel de la Tomme de Savoie, 10 Allée Jules Vernes, 74150 Rumilly, France
| | - Stéphane Romand
- Syndicat Interprofessionnel du Reblochon, 28 Rue Louis Haase, 74230 Thônes, France
| | - Caroline Petite
- Syndicat Interprofessionnel de la Tome des Bauges, Rue Henri Bouvier, 73630 Le Chatelard, France
| | - Pierre Taberlet
- Université Grenoble Alpes, Université Savoie Mont-Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000 Grenoble, France
| | - Cécile Charles
- CERAQ, Centre de ressources pour l'agriculture de qualité et de montagne, 40 Rue du Terraillet, 73190 Saint-Baldoph, France
| | - Nadège Bel
- ACTALIA, Centre technique d'expertise agroalimentaire, Division d'expertise analytique sur le lait et les produits laitiers, 419 Rte des Champs Laitiers, 74800 Eteaux, France
| | - Agnès Hauwuy
- CERAQ, Centre de ressources pour l'agriculture de qualité et de montagne, 40 Rue du Terraillet, 73190 Saint-Baldoph, France
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Gu HY, Hao SY, Sun ZB, Xu JL, Ren Q, Pan HX. Bosea beijingensis sp. nov., Telluria beijingensis sp. nov. and Agrococcus beijingensis sp. nov., isolated from baijiu mash. Int J Syst Evol Microbiol 2024; 74. [PMID: 38530339 DOI: 10.1099/ijsem.0.006304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Abstract
The baijiu fermentation environment hosts a variety of micro-organisms, some of which still remain uncultured and uncharacterized. In this study, the isolation, cultivation and characterization of three novel aerobic bacterial strains are described. The cells of strain REN20T were Gram-negative, strictly aerobic, motile and grew at 26-37 °C, at pH 6.0-9.0 and in the presence of 0-5.0 % (w/v) NaCl. The cells of strain REN29T were Gram-negative, strictly aerobic, motile and grew at 15-30 °C, at pH 6.0-9.0 and in the presence of 0-10.0 % (w/v) NaCl. The cells of strain REN33T were Gram-positive, strictly aerobic, motile and grew at 15-37 °C, at pH 5.0-10.0 and in the presence of 0-7.0 % (w/v) NaCl. The digital DNA-DNA hybridization and average nucleotide identity by orthology values between type strains in related genera and REN20T (20.3-36.8 % and 79.8-89.9 %), REN29T (20.3-36.8 % and 74.5-88.5 %) and REN33T (22.6-48.6 % and 75.8-84.2 %) were below the standard cut-off criteria for the delineation of bacterial species, respectively. Based on polyphasic taxonomy analysis, we propose three new species, Bosea beijingensis sp. nov. (=REN20T=GDMCC 1.2894T=JCM 35118T), Telluria beijingensis sp. nov. (=REN29T=GDMCC 1.2896T=JCM 35119T) and Agrococcus beijingensis sp. nov. (=REN33T=GDMCC 1.2898T=JCM 35164T), which were recovered during cultivation and isolation from baijiu mash.
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Affiliation(s)
- Hao-Yue Gu
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, PR China
| | - Shu-Yue Hao
- Guizhou Guotai Liquor Group Co. Ltd., Guizhou, PR China
| | - Zhan-Bin Sun
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, PR China
| | - Jia-Liang Xu
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, PR China
| | - Qing Ren
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, PR China
| | - Han-Xu Pan
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, PR China
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Lopes AR, Bunin E, Viana AT, Froufe H, Muñoz-Merida A, Pinho D, Figueiredo J, Barroso C, Vaz-Moreira I, Bellanger X, Egas C, Nunes OC. In silico prediction of the enzymes involved in the degradation of the herbicide molinate by Gulosibacter molinativorax ON4T. Sci Rep 2022; 12:15502. [PMID: 36109598 PMCID: PMC9477822 DOI: 10.1038/s41598-022-18732-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 08/18/2022] [Indexed: 12/01/2022] Open
Abstract
Gulosibacter molinativorax ON4T is the only known organism to produce molinate hydrolase (MolA), which catalyses the breakdown of the thiocarbamate herbicide into azepane-1-carboxylic acid (ACA) and ethanethiol. A combined genomic and transcriptomic strategy was used to fully characterize the strain ON4T genome, particularly the molA genetic environment, to identify the potential genes encoding ACA degradation enzymes. Genomic data revealed that molA is the only catabolic gene of a novel composite transposon (Tn6311), located in a novel low copy number plasmid (pARLON1) harbouring a putative T4SS of the class FATA. pARLON1 had an ANI value of 88.2% with contig 18 from Agrococcus casei LMG 22410T draft genome. Such results suggest that pARLON1 is related to genomic elements of other Actinobacteria, although Tn6311 was observed only in strain ON4T. Furthermore, genomic and transcriptomic data demonstrated that the genes involved in ACA degradation are chromosomal. Based on their overexpression when growing in the presence of molinate, the enzymes potentially involved in the heterocyclic ring breakdown were predicted. Among these, the activity of a protein related to caprolactone hydrolase was demonstrated using heterologous expression. However, further studies are needed to confirm the role of the other putative enzymes.
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Qu JH, Yue YF, Tian HL, Zhou J, Yang BB, Deng L, Qu LB, Wang LF. Agrococcus sediminis sp. nov., an actinobacterium isolated from lake sediment. Int J Syst Evol Microbiol 2020; 70:4986-4992. [PMID: 32762805 DOI: 10.1099/ijsem.0.004371] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strain, designated NS18T, was isolated from sediment sampled at Taihu Lake, PR China. Cells of the isolate were spherical, aerobic, non-motile, Gram-stain-positive and non-endospore-forming. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NS18T clustered in a clade of the genus Agrococcus. Its closest phylogenetic neighbour was Agrococcus lahaulensis DSM 17612T with 98.2 % 16S rRNA gene sequence similarity. The complete genome of NS18T was 2 736 037 bp and its genomic DNA G+C content was 72.8 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain NS18T and A. lahaulensis DSM 17612T based on their whole genomes were 85.1 and 28.7 %, respectively. The major fatty acids were anteiso-C17 : 0 and anteiso-C15 : 0. The predominant menaquinones were MK11 and MK12. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol and two unidentified lipids. The components of the peptidoglycan were Ala, Gly, Asp, Thr and DAB. The whole-cell sugars contained rhamnose, ribose, xylose and glucose. According to the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain NS18T (=NBRC 113859T=MCCC 1K03759T) represents a novel species, for which the name Agrococcus sediminis sp. nov is proposed.
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Affiliation(s)
- Jian-Hang Qu
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450000, Henan Province, PR China
| | - Yi-Fei Yue
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450000, Henan Province, PR China
| | - Hai-Long Tian
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450000, Henan Province, PR China
| | - Jia Zhou
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450000, Henan Province, PR China
| | - Bang-Bang Yang
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450000, Henan Province, PR China
| | - Lei Deng
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450000, Henan Province, PR China
| | - Ling-Bo Qu
- State Key Laboratory of Motor Vehicle Biofuel Technology, Nanyang 473000, Henan Province, PR China
| | - Lin-Feng Wang
- State Key Laboratory of Motor Vehicle Biofuel Technology, Nanyang 473000, Henan Province, PR China
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Complete Genome Sequence of Agrococcus sp. Strain SGAir0287, Isolated from Tropical Air Collected in Singapore. Microbiol Resour Announc 2019; 8:8/32/e00616-19. [PMID: 31395637 PMCID: PMC6687924 DOI: 10.1128/mra.00616-19] [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
Agrococcus sp. strain SGAir0287 was isolated from tropical air samples collected in Singapore. Assembled using single-molecule real-time (SMRT) sequencing and MiSeq reads, the genome consists of one circular chromosome of 3,084,767 bp. The entire genome has 2,870 protein-coding genes, 45 tRNAs, and 3 rRNAs.
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Ritschard JS, Amato L, Kumar Y, Müller B, Meile L, Schuppler M. The role of the surface smear microbiome in the development of defective smear on surface-ripened red-smear cheese. AIMS Microbiol 2018; 4:622-641. [PMID: 31294238 PMCID: PMC6613336 DOI: 10.3934/microbiol.2018.4.622] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/20/2018] [Indexed: 01/05/2023] Open
Abstract
The complex smear microbiota colonizing the surface of red-smear cheese fundamentally impacts the ripening process, appearance and shelf life of cheese. To decipher the prokaryotic composition of the cheese smear microbiome, the surface of a semi-hard surface ripened cheese was studied post-ripening by culture-based and culture-independent molecular approaches. The aim was to detect potential bacterial alterations in the composition of the cheese smear microbiota resulting from cheese storage in vacuum film-prepackaging, which is often accompanied by the development of a surface smear defect. Next-generation sequencing of amplified 16S rRNA gene fragments revealed an unexpected high diversity of a total of 132 different genera from the domains Bacteria and Archaea on the cheese surface. Beside typical smear organisms, our study revealed the presence of several microorganisms so far not associated with cheese, but related to milk, farm and cheese dairy environments. A 16S ribosomal RNA based analysis from total RNA identified the major metabolically active populations in the cheese surface smear as Actinobacteria of the genera Corynebacterium, Brevibacterium, Brachybacterium and Agrococcus. Comparison of data on a higher phylogenetic level revealed distinct differences in the composition of the cheese smear microbiome from the different samples. While the proportions of Proteobacteria and Bacteroidetes were increased in the smear of prepacked samples and in particular in defective smear, staphylococci showed an opposite trend and turned out to be strongly decreased in defective smear. In conclusion, next-generation sequencing of amplified 16S rRNA genes and 16S rRNA from total RNA extracts provided a much deeper insight into the bacterial composition of the cheese smear microbiota. The observed shifts in the microbial composition of samples from defect surface smear suggest that certain members of the Proteobacteria contribute to the observed negative organoleptic properties of the surface smear of cheese after prepacking in plastic foil.
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Affiliation(s)
- Jasmine S Ritschard
- Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Lea Amato
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Yadhu Kumar
- Eurofins GATC Biotech AG, Jakob-Stadler-Platz 7, 78467 Konstanz, Germany
| | - Britta Müller
- Eurofins GATC Biotech AG, Jakob-Stadler-Platz 7, 78467 Konstanz, Germany
| | - Leo Meile
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Markus Schuppler
- Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
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White RA, Gavelis G, Soles SA, Gosselin E, Slater GF, Lim DSS, Leander B, Suttle CA. The Complete Genome and Physiological Analysis of the Microbialite-Dwelling Agrococcus pavilionensis sp. nov; Reveals Genetic Promiscuity and Predicted Adaptations to Environmental Stress. Front Microbiol 2018; 9:2180. [PMID: 30374333 PMCID: PMC6196244 DOI: 10.3389/fmicb.2018.02180] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 08/24/2018] [Indexed: 12/15/2022] Open
Abstract
Members of the bacterial genus Agrococcus are globally distributed and found across environments so highly diverse that they include forests, deserts, and coal mines, as well as in potatoes and cheese. Despite how widely Agrococcus occurs, the extent of its physiology, genomes, and potential roles in the environment are poorly understood. Here we use whole-genome analysis, chemotaxonomic markers, morphology, and 16S rRNA gene phylogeny to describe a new isolate of the genus Agrococcus from freshwater microbialites in Pavilion Lake, British Columbia, Canada. We characterize this isolate as a new species Agrococcus pavilionensis strain RW1 and provide the first complete genome from a member of the genus Agrococcus. The A. pavilionensis genome consists of one chromosome (2,627,177 bp) as well as two plasmids (HC-CG1 1,427 bp, and LC-RRW783 31,795 bp). The genome reveals considerable genetic promiscuity via mobile elements, including a prophage and plasmids involved in integration, transposition, and heavy-metal stress. A. pavilionensis strain RW1 differs from other members of the Agrococcus genus by having a novel phospholipid fatty acid iso-C15:1Δ4, β-galactosidase activity and amygdalin utilization. Carotenoid biosynthesis is predicted by genomic metabolic reconstruction, which explains the characteristic yellow pigmentation of A. pavilionensis. Metabolic reconstructions of strain RW1 genome predicts a pathway for releasing ammonia via ammonification amino acids, which could increase the saturation index leading to carbonate precipitation. Our genomic analyses suggest signatures of environmental adaption to the relatively cold and oligotrophic conditions of Pavilion Lake microbialites. A. pavilionensis strain RW1 in modern microbialites has an ecological significance in Pavilion Lake microbialites, which include potential roles in heavy-metal cycling and carbonate precipitation (e.g., ammonification of amino acids and filamentation which many trap carbonate minerals).
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Affiliation(s)
- Richard Allen White
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Greg Gavelis
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Sarah A Soles
- School of Geography and Earth Sciences, McMaster University, Hamilton, ON, Canada
| | - Emma Gosselin
- Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Greg F Slater
- School of Geography and Earth Sciences, McMaster University, Hamilton, ON, Canada
| | - Darlene S S Lim
- Bay Area Environmental Research Institute, Petaluma, CA, United States.,NASA Ames Research Center, Moffett Field, CA, United States
| | - Brian Leander
- Bay Area Environmental Research Institute, Petaluma, CA, United States
| | - Curtis A Suttle
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada.,Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, Vancouver, BC, Canada.,Canadian Institute for Advanced Research, Toronto, ON, Canada
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Young AJ, Nock CJ. Molecular Detection of Diverse Leifsonia Strains Associated With Sugarcane. PLANT DISEASE 2017; 101:1422-1431. [PMID: 30678587 DOI: 10.1094/pdis-01-17-0016-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Leifsonia xyli subsp. xyli, causal agent of ratoon stunting disease (RSD) of sugarcane (Saccharum interspecific hybrids), is the most well-known member of the Microbacteriaceae genus Leifsonia. However, the presence of other Leifsonia strains associated with sugarcane has not been reported. A total of 697 Australian and 40 Indonesian sugarcane fields were screened by leaf sheath biopsy (LSB) PCR using primers specific for L. xyli subsp. xyli, in addition to primers designed to amplify DNA from other members of the genus Leifsonia. While L. xyli subsp. xyli was detected in 126 fields, a total of 37 distinct and novel Leifsonia and non-Leifsonia strains were detected in 116 fields. Representatives of these strains were also detected in multiple samples of expressed xylem sap. Sequencing and phylogenetic analyses demonstrated the presence of a broad complex of novel Leifsonia strains, in addition to strains closely related to the recently erected Cnuibacter genus. Attempts to isolate Leifsonia strains were unsuccessful; however, one strain related to Cnuibacter was recovered from expressed xylem sap. Among the genetically diverse lineages discovered, identical genotypes were present in multiple sugarcane varieties growing in disparate regions in different years, strongly suggesting an ongoing association with sugarcane. The epidemiological significance of these strains is unknown, but there is evidence that they can interfere with serological and microscopic RSD diagnostics, and there is the potential that they may represent new and distinct pathologies of sugarcane.
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Affiliation(s)
- Anthony J Young
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland, Australia
| | - Catherine J Nock
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
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Kuwano A, Niwa H, Arai K. New methods for isolation of keratolytic bacteria inducing intractable hoof wall cavity ( Gidoh) in a horse; double screening procedures of the horn powder agar-translucency test and horn zymography. J Equine Sci 2017; 28:19-25. [PMID: 28400703 PMCID: PMC5383627 DOI: 10.1294/jes.28.19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/23/2017] [Indexed: 11/01/2022] Open
Abstract
To establish a new system to isolate keratolytic bacteria from the hoof wall cavity (Gidoh) of a racehorse, we invented the horn powder agar-translucency (HoPAT) test and horn zymography (HZ). Using routine bacteriological techniques and these methods, we isolated five strains of keratolytic soil bacteria, which were then identified by means of 16S ribosomal RNA (rRNA) gene sequencing analysis. The findings from the study on the horse suggested that Brevibacterium luteolum played the main role in the local fragility of the hoof, eventually forming a Gidoh in coordination with four other strains of keratolytic bacteria. The double screening procedures of the HoPAT test and HZ were useful and easy techniques for isolating the keratolytic bacteria from the horn lesions.
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Affiliation(s)
- Atsutoshi Kuwano
- Equine Research Institute, Japan Racing Association, Tochigi 329-0412, Japan; Current affiliation: Japan Farriery Association, Tokyo 105-0004, Japan
| | - Hidekazu Niwa
- Equine Research Institute, Japan Racing Association, Tochigi 329-0412, Japan
| | - Katsuhiko Arai
- Department of Tissue Physiology, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
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Biodiversity of the Surface Microbial Consortia from Limburger, Reblochon, Livarot, Tilsit, and Gubbeen Cheeses. Microbiol Spectr 2015; 2:CM-0010-2012. [PMID: 26082119 DOI: 10.1128/microbiolspec.cm-0010-2012] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Comprehensive collaborative studies from our laboratories reveal the extensive biodiversity of the microflora of the surfaces of smear-ripened cheeses. Two thousand five hundred ninety-seven strains of bacteria and 2,446 strains of yeasts from the surface of the smear-ripened cheeses Limburger, Reblochon, Livarot, Tilsit, and Gubbeen, isolated at three or four times during ripening, were identified; 55 species of bacteria and 30 species of yeast were found. The microfloras of the five cheeses showed many similarities but also many differences and interbatch variation. Very few of the commercial smear microorganisms, deliberately inoculated onto the cheese surface, were reisolated and then mainly from the initial stages of ripening, implying that smear cheese production units must have an adventitious "house" flora. Limburger cheese had the simplest microflora, containing two yeasts, Debaryomyces hansenii and Geotrichum candidum, and two bacteria, Arthrobacter arilaitensis and Brevibacterium aurantiacum. The microflora of Livarot was the most complicated, comprising 10 yeasts and 38 bacteria, including many gram-negative organisms. Reblochon also had a very diverse microflora containing 8 yeasts and 13 bacteria (excluding gram-negative organisms which were not identified), while Gubbeen had 7 yeasts and 18 bacteria and Tilsit had 5 yeasts and 9 bacteria. D. hansenii was by far the dominant yeast, followed in order by G. candidum, Candida catenulata, and Kluyveromyces lactis. B. aurantiacum was the dominant bacterium and was found in every batch of the 5 cheeses. The next most common bacteria, in order, were Staphylococcus saprophyticus, A. arilaitensis, Corynebacterium casei, Corynebacterium variabile, and Microbacterium gubbeenense. S. saprophyticus was mainly found in Gubbeen, and A. arilaitensis was found in all cheeses but not in every batch. C. casei was found in most batches of Reblochon, Livarot, Tilsit, and Gubbeen. C. variabile was found in all batches of Gubbeen and Reblochon but in only one batch of Tilsit and in no batch of Limburger or Livarot. Other bacteria were isolated in low numbers from each of the cheeses, suggesting that each of the 5 cheeses has a unique microflora. In Gubbeen cheese, several different strains of the dominant bacteria were present, as determined by pulsed-field gel electrophoresis, and many of the less common bacteria were present as single clones. The culture-independent method, denaturing gradient gel electrophoresis, resulted in identification of several bacteria which were not found by the culture-dependent (isolation and rep-PCR identification) method. It was thus a useful complementary technique to identify other bacteria in the cheeses. The gross composition, the rate of increase in pH, and the indices of proteolysis were different in most of the cheeses.
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11
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Almeida M, Hébert A, Abraham AL, Rasmussen S, Monnet C, Pons N, Delbès C, Loux V, Batto JM, Leonard P, Kennedy S, Ehrlich SD, Pop M, Montel MC, Irlinger F, Renault P. Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products. BMC Genomics 2014; 15:1101. [PMID: 25496341 PMCID: PMC4320590 DOI: 10.1186/1471-2164-15-1101] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 12/04/2014] [Indexed: 11/10/2022] Open
Abstract
Background Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial communities are still not well understood. Metagenomic analysis of these communities by high throughput shotgun sequencing is a promising approach to characterize their genomic and functional profiles. Such analyses, however, critically depend on the availability of appropriate reference genome databases against which the sequencing reads can be aligned. Results We built a reference genome catalog suitable for short read metagenomic analysis using a low-cost sequencing strategy. We selected 142 bacteria isolated from dairy products belonging to 137 different species and 67 genera, and succeeded to reconstruct the draft genome of 117 of them at a standard or high quality level, including isolates from the genera Kluyvera, Luteococcus and Marinilactibacillus, still missing from public database. To demonstrate the potential of this catalog, we analysed the microbial composition of the surface of two smear cheeses and one blue-veined cheese, and showed that a significant part of the microbiota of these traditional cheeses was composed of microorganisms newly sequenced in our study. Conclusions Our study provides data, which combined with publicly available genome references, represents the most expansive catalog to date of cheese-associated bacteria. Using this extended dairy catalog, we revealed the presence in traditional cheese of dominant microorganisms not deliberately inoculated, mainly Gram-negative genera such as Pseudoalteromonas haloplanktis or Psychrobacter immobilis, that may contribute to the characteristics of cheese produced through traditional methods. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1101) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Pierre Renault
- Institut National de la Recherche Agronomique, UMR 1319 MICALIS, 78352 Jouy-en-Josas, France.
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Kim SJ, Ahn JH, Weon HY, Hamada M, Suzuki KI, Kwon SW. Diaminobutyricibacter tongyongensis gen. nov., sp. nov. and Homoserinibacter gongjuensis gen. nov., sp. nov. belong to the family Microbacteriaceae. J Microbiol 2014; 52:527-33. [PMID: 24535740 DOI: 10.1007/s12275-014-3278-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 09/11/2013] [Accepted: 09/11/2013] [Indexed: 10/25/2022]
Abstract
Two bacterial strains, KIS66-7(T) and 5GH26-15(T), were isolated from soil samples collected in the South Korean cities of Tongyong and Gongju, respectively. Both strains were aerobic, Gram-stain-positive, mesophilic, flagellated, and rodshaped. A phylogenetic analysis revealed that both strains belonged to the family Microbacteriaceae of the phylum Actinobacteria. The 16S rRNA gene sequence of strain KIS66-7(T) had the highest similarities with those of Labedella gwakjiensis KSW2-17(T) (97.3%), Cryobacterium psychrophilum DSM 4854T (97.2%), Leifsonia lichenia 2Sb(T) (97.2%), Leifsonia naganoensis JCM 10592(T) (97.0%), and Cryobacterium mesophilum MSL-15(T) (97.0%). Strain 5GH26-15(T) showed the highest sequence similarities with Leifsonia psychrotolerans LI1T (97.4%) and Schumannella luteola KHIAT (97.1%). The 16S rRNA gene sequence from KIS66-7(T) exhibited 96.4% similarity with that from 5GH26-15(T). Strain KIS66-7(T) contained a B2γ type peptidoglycan structure with D-DAB as the diamino acid; MK-13, MK-12, and MK-14 as the respiratory quinones; ai-C15:0, ai-C17:0, and i-C16:0 as the major cellular fatty acids; and diphosphatidylglycerol, phatidylglycerol, and glycolipids as the predominant polar lipids. Strain 5GH26-15T had a B2β type peptidoglycan structure with D-DAB as the diamino acid; MK-14 and MK-13 as the respiratory quinones; ai-C15:0, i-C16:0, and ai-C{vn17:0} as the major cellular fatty acids; and diphosphatidylglycerol, phatidylglycerol, and glycolipids as the predominant polar lipids. Both strains had low DNA-DNA hybridization values (<40%) with closely related taxa. Based on our polyphasic taxonomic characterization, we propose that strains KIS66-7(T) and 5GH26-15(T) represent novel genera and species, for which we propose the names Diaminobutyricibacter tongyongensis gen. nov., sp. nov. (type strain KIS66-7(T)=KACC 15515(T)=NBRC 108724(T)) and Homoserinibacter gongjuensis gen. nov., sp. nov. (type strain 5GH26-15(T)=KACC 15524(T)=NBRC 108755(T)) within the family Microbacteriaceae.
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Affiliation(s)
- Soo-Jin Kim
- Agricultural Microbiology Division, National Academy of Agricultural Science, Rural Development Administration, Suwon, 441-707, Republic of Korea
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First draft genome sequence from a member of the genus agrococcus, isolated from modern microbialites. GENOME ANNOUNCEMENTS 2013; 1:1/4/e00391-13. [PMID: 23814108 PMCID: PMC3695436 DOI: 10.1128/genomea.00391-13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the first draft genome sequence from a member of the genus Agrococcus, isolated from cold thrombolytic microbialites within Pavilion Lake, British Columbia, Canada. The draft genome assembly for Agrococcus pavilionensis strain RW-1 has a size of 2,878,403 bp with a G+C content of 72.56%.
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Jang YH, Kim SJ, Tamura T, Hamada M, Weon HY, Suzuki KI, Kwon SW, Kim WG. Lysinimonas soli gen. nov., sp. nov., isolated from soil, and reclassification of
Leifsonia kribbensis
Dastager et al. 2009 as Lysinimonas kribbensis sp. nov., comb. nov. Int J Syst Evol Microbiol 2013; 63:1403-1410. [DOI: 10.1099/ijs.0.042945-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, non-motile rod, designated strain SGM3-12T, was isolated from paddy soil in Suwon, Republic of Korea. 16S rRNA gene sequence analysis revealed that the strain represented a novel member of the family
Microbacteriaceae
. The nearest phylogenetic neighbour was
Leifsonia kribbensis
MSL-13T (97.4 % 16S rRNA gene sequence similarity). Strain SGM3-12T and
Leifsonia kribbensis
MSL-13T formed a distinct cluster within the family
Microbacteriaceae
. Strain SGM3-12T contained MK-12(H2) and MK-11(H2) as the predominant menaquinones with moderate amounts of MK-12 and MK-11; anteiso-C15 : 0 and iso-C16 : 0 as the major cellular fatty acids (>10 % of total); and diphosphatidylglycerol, phosphatidylglycerol and unidentified glycolipids as the polar lipids. The peptidoglycan type of the isolate was B1δ with l-Lys as the diagnostic cell-wall diamino acid. On the basis of these results, strain SGM3-12T represents a novel species within a new genus, for which the name Lysinimonas soli gen. nov., sp. nov. is proposed (the type strain of the type species is SGM3-12T = KACC 13362T = NBRC 107106T). It is also proposed that
Leifsonia kribbensis
be transferred to this genus as Lysinimonas kribbensis comb. nov. (the type strain is MSL-13T = DSM 19272T = JCM 16015T = KACC 21108T = KCTC 19267T).
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Affiliation(s)
- Yun-Hee Jang
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Soo-Jin Kim
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Tomohiko Tamura
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Moriyuki Hamada
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Hang-Yeon Weon
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Ken-ichiro Suzuki
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Soon-Wo Kwon
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Wan-Gyu Kim
- Korean Agricultural Culture Collection (KACC), National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
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15
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Kim SJ, Jang YH, Hamada M, Tamura T, Ahn JH, Weon HY, Suzuki KI, Kwon SW. Homoserinimonas aerilata gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an air sample in Korea. J Microbiol 2012; 50:673-9. [DOI: 10.1007/s12275-012-2096-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 04/23/2012] [Indexed: 11/24/2022]
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Larpin-Laborde S, Imran M, Bonaïti C, Bora N, Gelsomino R, Goerges S, Irlinger F, Goodfellow M, Ward AC, Vancanneyt M, Swings J, Scherer S, Guéguen M, Desmasures N. Surface microbial consortia from Livarot, a French smear-ripened cheese. Can J Microbiol 2011; 57:651-60. [PMID: 21815832 DOI: 10.1139/w11-050] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The surface microflora (902 isolates) of Livarot cheeses from three dairies was investigated during ripening. Yeasts were mainly identified by Fourier transform infrared spectroscopy. Geotrichum candidum was the dominating yeast among 10 species. Bacteria were identified using Biotype 100 strips, dereplicated by repetitive extragenic palindromic PCR (rep-PCR); 156 representative strains were identified by either BOX-PCR or (GTG)(5)-PCR, and when appropriate by 16S rDNA sequencing and SDS-PAGE analysis. Gram-positive bacteria accounted for 65% of the isolates and were mainly assigned to the genera Arthrobacter , Brevibacterium , Corynebacterium , and Staphylococcus . New taxa related to the genera Agrococcus and Leucobacter were found. Yeast and Gram-positive bacteria strains deliberately added as smearing agents were sometimes undetected during ripening. Thirty-two percent of the isolates were Gram-negative bacteria, which showed a high level of diversity and mainly included members of the genera Alcaligenes , Hafnia , Proteus , Pseudomonas , and Psychrobacter . Whatever the milk used (pasteurized or unpasteurized), similar levels of biodiversity were observed in the three dairies, all of which had efficient cleaning procedures and good manufacturing practices. It appears that some of the Gram-negative bacteria identified should now be regarded as potentially useful in some cheese technologies. The assessment of their positive versus negative role should be objectively examined.
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Affiliation(s)
- Sandra Larpin-Laborde
- Université de Caen Basse-Normandie, Unité des Microorganismes d'Intérêt Laitier et Alimentaire, E.A. 3213, IFR 146 ICORE, 14032 Caen CEDEX, France
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Dhanjal S, Kaur I, Korpole S, Schumann P, Cameotra SS, Pukall R, Klenk HP, Mayilraj S. Agrococcus carbonis sp. nov., isolated from soil of a coal mine. Int J Syst Evol Microbiol 2010; 61:1253-1258. [PMID: 20601492 DOI: 10.1099/ijs.0.024745-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An actinobacterial strain, designated G4(T), isolated from a coal mine was subjected to polyphasic taxonomic characterization. Cells were Gram-stain-positive, yellow-pigmented, non-motile and non-spore-forming cocci. This organism possessed a type B peptidoglycan with diaminobutyric acid as diagnostic diamino acid. The major respiratory quinones were MK-9, MK-10 and MK-11. The major fatty acids were anteiso-C(15 : 0) (41.6 %) and anteiso-C(17 : 0) (32.8 %). The predominant cellular polar lipids were diphosphatidylglycerol and phosphatidylglycerol. Cell wall sugars comprised galactose, glucose, ribose and rhamnose. 16S rRNA gene sequence analysis of strain G4(T) showed high similarity with Agrococcus baldri (98.9 %), Agrococcus citreus (97.8 %), Agrococcus jenensis (97.3 %) and Agrococcus terreus (97.0 %). Sequence similarity with the type strains of the other species of the genus Agrococcus was less than 97.0 %. The DNA-DNA relatedness of strain G4(T) with the type strains of Agrococcus baldri, Agrococcus citreus, Agrococcus jenensis and Agrococcus terreus was less than 70 %. On the basis of the physiological, biochemical and chemotaxonomic characteristics, strain G4(T) should be classified as the type strain of a novel species of the genus Agrococcus, for which the name Agrococcus carbonis sp. nov. is proposed. The type strain is G4(T) ( = MTCC 10213(T) = DSM 22965(T)).
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Affiliation(s)
- Soniya Dhanjal
- Division of Environmental Biotechnology and Microbial Biochemistry, Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Ishwinder Kaur
- MTCC - Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Chandigarh 160 036, India
| | - Suresh Korpole
- MTCC - Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Chandigarh 160 036, India
| | - Peter Schumann
- DSMZ - German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Swaranjit Singh Cameotra
- Division of Environmental Biotechnology and Microbial Biochemistry, Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Rüdiger Pukall
- DSMZ - German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- DSMZ - German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Shanmugam Mayilraj
- MTCC - Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Chandigarh 160 036, India
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Zhang JY, Liu XY, Liu SJ. Agrococcus terreus sp. nov. and Micrococcus terreus sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2009; 60:1897-1903. [PMID: 19783614 DOI: 10.1099/ijs.0.013235-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains, DNG5T and V3M1T, isolated from forest soil of the Changbai mountains in China, were characterized using a polyphasic approach. Analysis of their 16S rRNA gene sequences indicated that strains DNG5T and V3M1T were phylogenetically related to members of the genus Agrococcus (96.0-98.4% similarity) and Micrococcus (96.7-98.0% similarity), respectively, within the order Actinomycetales. Strains DNG5T and V3M1T were Gram-stain-positive and strictly aerobic and formed yellow colonies on LB agar. Cells of strain DNG5T were short, non-motile rods, 0.4-0.5x0.8-1.0 microm. Strain DNG5T contained MK-10 and MK-11 as the major respiratory quinones and anteiso-C15:0 (49.2%) and iso-C16:0 (22.4%) as the major fatty acids. The diamino acid in the peptidoglycan of strain DNG5T was 2,4-diaminobutyric acid and the murein was of the acetyl type. Cells of strain V3M1T were cocci, 0.6-0.7 microm in diameter. The cell-wall peptidoglycan of strain V3M1T contained the amino acids lysine, glutamic acid, alanine and glycine. Strain V3M1T contained MK-7, MK-7(H2), MK-8 and MK-8(H2) as respiratory quinones and anteiso-C15:0 (78.2%) and iso-C15:0 (13.1%) as the major cellular fatty acids. The DNA G+C contents of strains DNG5T and V3M1T were 75.9 and 67.2 mol%, respectively. The DNA-DNA relatedness of strain DNG5T to Agrococcus jejuensis DSM 22002T, A. jenensis JCM 9950T, A. baldri JCM 12132T and A. citreus JCM 12398T was 58.3, 43.9, 36.1 and 54.1%, respectively. The DNA-DNA relatedness of strain V3M1T to Micrococcus luteus CGMCC 1.2299T, M. antarcticus CGMCC 1.2373T and M. lylae CGMCC 1.2300T was 57.5, 45.4 and 39.0%, respectively. Combining phenotypic and genotypic traits, strain DNG5T represents a novel species of the genus Agrococcus, for which the name Agrococcus terreus sp. nov. is proposed, with DNG5T (=CGMCC 1.6960T =NBRC 104260T) as the type strain. Strain V3M1T represents a novel species of the genus Micrococcus, for which the name Micrococcus terreus sp. nov. is proposed, with V3M1T (=CGMCC 1.7054T =NBRC 104258T) as the type strain.
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Affiliation(s)
- Jia-Yue Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xing-Yu Liu
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, Beijing 100088, PR China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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19
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Schmidt VSJ, Mayr R, Wenning M, Glockner J, Busse HJ, Scherer S. Bavariicoccus seileri gen. nov., sp. nov., isolated from the surface and smear water of German red smear soft cheese. Int J Syst Evol Microbiol 2009; 59:2437-43. [DOI: 10.1099/ijs.0.006601-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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20
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Behrendt U, Schumann P, Ulrich A. Agrococcus versicolor sp. nov., an actinobacterium associated with the phyllosphere of potato plants. Int J Syst Evol Microbiol 2008; 58:2833-8. [DOI: 10.1099/ijs.0.2008/001610-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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21
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Lee SD. Agrococcus jejuensis sp. nov., isolated from dried seaweed. Int J Syst Evol Microbiol 2008; 58:2297-300. [DOI: 10.1099/ijs.0.65731-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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22
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Rea MC, Görges S, Gelsomino R, Brennan NM, Mounier J, Vancanneyt M, Scherer S, Swings J, Cogan TM. Stability of the biodiversity of the surface consortia of Gubbeen, a red-smear cheese. J Dairy Sci 2008; 90:2200-10. [PMID: 17430918 DOI: 10.3168/jds.2006-377] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A total of 1,052 bacteria and 828 yeasts were isolated from the surface flora of 6 batches of Gubbeen cheese made in 1996-1997 and 2002-2003. Stability of the microflora was evaluated over time and also during ripening at 4, 10, and 16 d (batches 4, 5, and 6) or at 4, 16, 23, and 37 d (batches 1, 2, and 3). Bacteria were identified using pulsed-field gel electrophoresis, repetitive extragenic palindromic-PCR, and 16S rRNA gene sequencing, and yeasts were identified by Fourier transform infrared spectroscopy. The bacteria included at least 17 species, of which the most common were Staphylococcus saprophyticus (316 isolates), Corynebacterium casei (248 isolates), Brevibacterium aurantiacum (187 isolates), Corynebacterium variabile (146 isolates), Microbacterium gubbeenense (55 isolates), Staphylococcus equorum/cohnii (31 isolates), and Psychrobacter spp. (26 isolates). The most common yeasts were Debaryomyces hansenii (624 isolates), Candida catenulata (135 isolates), and Candida lusitaniae (62 isolates). In all batches of cheese except batch 2, a progression of bacteria was observed, with staphylococci dominating the early stages of ripening and coryneforms the later stages. No progression of yeast was found. Pulsed-field gel electrophoresis showed that several different strains of the 5 important species of bacteria were present, but generally only one predominated. The commercial strains used for smearing the cheese were recovered, but only in very small numbers early in ripening. Four species, B. aurantiacum, C. casei, C. variabile, and Staph. saprophyticus, were found on all batches of cheese, but their relative importance varied considerably. The results imply that significant variation occurs in the surface microflora of cheese.
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Affiliation(s)
- M C Rea
- Moorepark Food Research Centre, Teagasc, Fermoy, Ireland
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Growth characteristics of Brevibacterium, Corynebacterium, Microbacterium, and Staphylococcus spp. isolated from surface-ripened cheese. Appl Environ Microbiol 2007; 73:7732-9. [PMID: 17921266 DOI: 10.1128/aem.01260-07] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The growth characteristics of five bacteria, Brevibacterium aurantiacum 1-16-58, Corynebacterium casei DPC 5298(T), Corynebacterium variabile DPC 5310, Microbacterium gubbeenense DPC 5286(T), and Staphylococcus saprophyticus 4E61, all of which were isolated from the surface of smear cheese, were studied in complex and chemically defined media. All of the coryneforms, except M. gubbeenense, grew in 12% salt, while B. aurantiacum and S. saprophyticus grew in 15% salt. All five bacteria assimilated lactate in a semisynthetic medium, and none of the coryneform bacteria assimilated lactose. Glucose assimilation was poor, except by S. saprophyticus and C. casei. Five to seven amino acids were assimilated by the coryneforms and 12 by S. saprophyticus. Glutamate, phenylalanine, and proline were utilized by all five bacteria, whereas utilization of serine, threonine, aspartate, histidine, alanine, arginine, leucine, isoleucine, and glycine depended on the organism. Growth of C. casei restarted after addition of glutamate, proline, serine, and lactate at the end of the exponential phase, indicating that these amino acids and lactate can be used as energy sources. Pantothenic acid was essential for the growth of C. casei and M. gubbeenense. Omission of biotin reduced the growth of B. aurantiacum, C. casei, and M. gubbeenense. All of the bacteria contained lactate dehydrogenase activity (with both pyruvate and lactate as substrates) and glutamate pyruvate transaminase activity but not urease activity.
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