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Stachelska MA, Ekielski A, Karpiński P, Żelaziński T, Kruszewski B. New Genetic Determinants for qPCR Identification and the Enumeration of Selected Lactic Acid Bacteria in Raw-Milk Cheese. Molecules 2024; 29:1533. [PMID: 38611811 PMCID: PMC11013805 DOI: 10.3390/molecules29071533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Lactic acid bacteria (LAB) play an important role in the ripening of cheeses and contribute to the development of the desired profile of aroma and flavor compounds. Therefore, it is very important to monitor the dynamics of bacterial proliferation in order to obtain an accurate and reliable number of their cells at each stage of cheese ripening. This work aimed to identify and conduct a quantitative assessment of the selected species of autochthonous lactic acid bacteria from raw cow's milk cheese by the development of primers and probe pairs based on the uniqueness of the genetic determinants with which the target microorganisms can be identified. For that purpose, we applied real-time quantitative PCR (qPCR) protocols to quantify Lactobacillus delbrueckii subsp. bulgaricus, Streptococcus thermophilus, and Lactococcus lactis subsp. cremoris cells in cheese directly after production and over three-month and six-month ripening periods. While L. lactis subsp. cremoris shows good acidification ability and the ability to produce antimicrobial compounds, L. delbrueckii subsp. bulgaricus has good proteolytic ability and produces exo-polysaccharides, and S. thermophilus takes part in the formation of the diacetyl flavor compound by metabolizing citrate to develop aroma, they all play an important role in the cheese ripening. The proposed qPCR protocols are very sensitive and reliable methods for a precise enumeration of L. delbrueckii subsp. bulgaricus, S. thermophilus, and L. lactis subsp. cremoris in cheese samples.
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Affiliation(s)
- Milena Alicja Stachelska
- Faculty of Computer Science and Technology, University of Lomza, Akademicka 14, 18-400 Lomza, Poland;
| | - Adam Ekielski
- Department of Production Engineering, Institute of Mechanical Engineering, Warsaw University of Life Sciences-SGGW, Nowoursynowska 164, 02-787 Warsaw, Poland; (A.E.); (T.Ż.)
| | - Piotr Karpiński
- Faculty of Computer Science and Technology, University of Lomza, Akademicka 14, 18-400 Lomza, Poland;
| | - Tomasz Żelaziński
- Department of Production Engineering, Institute of Mechanical Engineering, Warsaw University of Life Sciences-SGGW, Nowoursynowska 164, 02-787 Warsaw, Poland; (A.E.); (T.Ż.)
| | - Bartosz Kruszewski
- Department of Food Technology and Assessment, Institute of Food Sciences, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159 C, 02-776 Warsaw, Poland
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Ritschard JS, Schuppler M. The Microbial Diversity on the Surface of Smear-Ripened Cheeses and Its Impact on Cheese Quality and Safety. Foods 2024; 13:214. [PMID: 38254515 PMCID: PMC10814198 DOI: 10.3390/foods13020214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Smear-ripened cheeses are characterized by a viscous, red-orange surface smear on their rind. It is the complex surface microbiota on the cheese rind that is responsible for the characteristic appearance of this cheese type, but also for the wide range of flavors and textures of the many varieties of smear-ripened cheeses. The surface smear microbiota also represents an important line of defense against the colonization with undesirable microorganisms through various types of interaction, such as competitive exclusion or production of antimicrobial substances. Predominant members of the surface smear microbiota are salt-tolerant yeast and bacteria of the phyla Actinobacteria, Firmicutes, and Proteobacteria. In the past, classical culture-based approaches already shed light on the composition and succession of microorganisms and their individual contribution to the typicity of this cheese type. However, during the last decade, the introduction and application of novel molecular approaches with high-resolution power provided further in-depth analysis and, thus, a much more detailed view of the composition, structure, and diversity of the cheese smear microbiota. This led to abundant novel knowledge, such as the identification of so far unknown community members. Hence, this review is summarizing the current knowledge of the diversity of the surface smear microbiota and its contribution to the quality and safety of smear-ripened cheese. If the succession or composition of the surface-smear microbiota is disturbed, cheese smear defects might occur, which may promote food safety issues. Hence, the discussion of cheese smear defects in the context of an increased understanding of the intricate surface smear ecosystem in this review may not only help in troubleshooting and quality control but also paves the way for innovations that can lead to safer, more consistent, and higher-quality smear-ripened cheeses.
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Affiliation(s)
| | - Markus Schuppler
- Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland;
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3
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Öztürk Hİ, Demirci T, Akın N, Oğul A. Elucidation of the initial bacterial community of Ezine PDO cheese using next-generation sequencing. Arch Microbiol 2022; 204:656. [PMID: 36182984 DOI: 10.1007/s00203-022-03272-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 11/30/2022]
Abstract
This study aims to reveal initial bacterial consortia of Ezine PDO cheeses comprehensively by following a metagenomic approach. A total of 8 artisanal Ezine cheese samples were collected from the Bayramiç and Ezine districts of Çanakkale province of Turkey. Ezine cheese was found to contain Firmicutes, Bacteroidetes, and Proteobacteria phyla dominantly. Streptococcus, Lactococcus, and Lactobacillus genera dominated the microbiota with relative abundances of 4.47-56.07%, 7.33-20.34%, and 1.21-25.12%, respectively, followed by Bacteroides and Prevotella genera. Excluding two cheese samples obtained from the Ezine district, the most dominant species was Streptococcus thermophilus (8.24-54.34%). It was also found in greater proportions in the cheeses of the Bayramiç district. Unexpectedly, Lactobacillus graminis (11.50-23.63%) was the most abundant species in two samples collected from the Ezine district. However, lower bacterial diversity was determined in the samples collected from the Bayramiç district. The lowest species richness was 129 OTU-species in the cheeses from the Bayramiç district while the highest species richness was 267 OTU-species in cheeses from the Ezine district. In addition, the Simpson index was the highest in cheeses from the Ezine district, where different species were evenly distributed. Permutational multivariate analysis of variance tests also confirmed that the differences in the structure of bacterial consortia in cheeses from two different districts were statistically significant. This study will provide pioneer data for further investigations on the role of complex bacterial composition in maintaining and improving the quality and safety of Ezine cheese.
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Affiliation(s)
- Hale İnci Öztürk
- Department of Food Engineering, Konya Food and Agriculture University, Konya, 42080, Turkey.
| | - Talha Demirci
- Department of Food Engineering, University of Selcuk, Konya, 42130, Turkey
| | - Nihat Akın
- Department of Food Engineering, University of Selcuk, Konya, 42130, Turkey
| | - Abdullah Oğul
- Panagro Agriculture and Husbandry Food Industrial Corporation, Meram, Konya, 42140, Turkey
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4
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Kumar V, Sarma VV, Thambugala KM, Huang JJ, Li XY, Hao GF. Ecology and Evolution of Marine Fungi With Their Adaptation to Climate Change. Front Microbiol 2021; 12:719000. [PMID: 34512597 PMCID: PMC8430337 DOI: 10.3389/fmicb.2021.719000] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/10/2021] [Indexed: 01/04/2023] Open
Abstract
Climate change agitates interactions between organisms and the environment and forces them to adapt, migrate, get replaced by others, or extinct. Marine environments are extremely sensitive to climate change that influences their ecological functions and microbial community including fungi. Fungi from marine habitats are engaged and adapted to perform diverse ecological functions in marine environments. Several studies focus on how complex interactions with the surrounding environment affect fungal evolution and their adaptation. However, a review addressing the adaptation of marine fungi to climate change is still lacking. Here we have discussed the adaptations of fungi in the marine environment with an example of Hortaea werneckii and Aspergillus terreus which may help to reduce the risk of climate change impacts on marine environments and organisms. We address the ecology and evolution of marine fungi and the effects of climate change on them to explain the adaptation mechanism. A review of marine fungal adaptations will show widespread effects on evolutionary biology and the mechanism responsible for it.
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Affiliation(s)
- Vinit Kumar
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | | | - Kasun M. Thambugala
- Genetics and Molecular Biology Unit, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Jun-Jie Huang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Xiang-Yang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Ge-Fei Hao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
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5
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Fungal diversity in the coastal waters of King George Island (maritime Antarctica). World J Microbiol Biotechnol 2021; 37:142. [PMID: 34322842 DOI: 10.1007/s11274-021-03112-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/14/2021] [Indexed: 12/19/2022]
Abstract
Fungi have been reported as common inhabitants of the maritime waters in Antarctica by studies based on culture-dependent methods. More recently, results obtained using DNA sequencing technologies, revealed that fungal diversity worldwide has been underestimated by culture methods. The present study provides the first characterization of fungal communities in the coastal waters of King George Island (maritime Antarctica) using both culture-dependent and high-throughput sequencing (HTS) methods. HTS demostrated a higher level of fungal diversity than the obtained by culture methods. A high prevalence of basidiomycetous yeasts and ascomycetous filamentous fungi was confirmed by both methods, however, Chythriomycota, Rozellomycota, lichenized fungi and Malassezia spp. were detected only by HTS. Correspondingly, members of some genera, such as Metschnikowia, were only found by culture-dependent methods. Our results confirm that culturing and HTS, should be seen as complementary approaches that enable one to obtain a more comprehensive picture of the composition of microbial communities.
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6
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Viesser JA, de Melo Pereira GV, de Carvalho Neto DP, Favero GR, de Carvalho JC, Goés-Neto A, Rogez H, Soccol CR. Global cocoa fermentation microbiome: revealing new taxa and microbial functions by next generation sequencing technologies. World J Microbiol Biotechnol 2021; 37:118. [PMID: 34131809 DOI: 10.1007/s11274-021-03079-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/25/2021] [Indexed: 12/01/2022]
Abstract
This review provides an overview of the application of next-generation sequencing (NGS) technologies for microbiome analysis of cocoa beans fermentation. The cocoa-producing regions where NGS has been applied include Brazil, Ghana, Ivory Coast, Cameroon, Nicaragua, and Colombia. The data collected were processed by principal component analysis (PCA) and Venn diagrams to perform a multivariate association between microbial diversity and cocoa-producing regions. NGS studies have confirmed the dominance of three major microbial groups revealed by culture-dependent approaches, i.e., lactic acid bacteria, acetic acid bacteria, and yeasts. However, a more complex microbial diversity has been revealed, comprising sub-dominant populations, late-growing species, and uncultivable microorganisms. A total of 99 microbial genera and species were for the first time reported in cocoa beans fermentation, such as Brevibacillus sp., Halomonas meridiana, Methylobacterium sp., Novosphingobium sp., and Paenibacillus pabuli. PCA and Venn diagrams showed that species composition is rarely fixed and often experiences fluctuations of varying degrees and at varying frequencies between different cocoa-producing regions. Understanding these differences will provide further directions for exploring the functional and metabolic activity of rare and abundant taxa, as well as their use as starter cultures to obtain high-quality cocoa beans.
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Affiliation(s)
- Jéssica A Viesser
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Gilberto V de Melo Pereira
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil.
| | | | - Gabriel R Favero
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Júlio Cesar de Carvalho
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Aristóteles Goés-Neto
- Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Hervé Rogez
- Centre for Valorisation of Amazonian Bioactive Compounds (CVACBA), Federal University of Pará, Belém, PA, Brazil
| | - Carlos R Soccol
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
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7
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Xing J, Xu X, Luo X, Zheng R, Mao L, Zhang S, Lu J, Shen J. Characterization of Microbial Community in Cold-Chain Hairtail Fish by High-Throughput Sequencing Technology. J Food Prot 2021; 84:1080-1087. [PMID: 33508135 DOI: 10.4315/jfp-20-393] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/25/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT High-throughput DNA sequencing with the Illumina MiSeq platform was used to analyze the microbial communities in hairtail (Trichiurus haumela) muscle samples to study the diversity and dynamic changes in these communities during cold-chain circulation of these fish. The richness and diversity of the microbial community in hairtail muscle had a transient decline from 0 to 24 h and decreased after the first rise from 24 to 216 h. The diversity and richness of bacteria in cold-chain hairtail reached maximum at 168 h. The Shannon and Simpson diversity indices of the bacteria were 2.96 and 0.16, respectively, and their ACE and Chao1 richness indices were 254.84 and 155.10, respectively. The dominant bacteria belonged to phylum Proteobacteria, class Gammaproteobacteria, order Pseudomonadales, family Pseudomonadaceae, and genus Pseudomonas, and their relative abundances were 80.52, 72.11, 76.68, 23.25, and 53.50%, respectively. These results provide a basis for exploring how to maintain the freshness and predict the shelf life of hairtail. HIGHLIGHTS
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Affiliation(s)
- Jiali Xing
- Ningbo Academy of Product and Food Quality Inspection (Ningbo Fibre Inspection Institute), Ningbo 315048, People's Republic of China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, People's Republic of China
| | - Xiaorong Xu
- Ningbo Academy of Product and Food Quality Inspection (Ningbo Fibre Inspection Institute), Ningbo 315048, People's Republic of China
| | - Xiaohu Luo
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Ruihang Zheng
- Ningbo Academy of Product and Food Quality Inspection (Ningbo Fibre Inspection Institute), Ningbo 315048, People's Republic of China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, People's Republic of China
| | - Lingyan Mao
- Ningbo Academy of Product and Food Quality Inspection (Ningbo Fibre Inspection Institute), Ningbo 315048, People's Republic of China
| | - Shufen Zhang
- Ningbo Academy of Product and Food Quality Inspection (Ningbo Fibre Inspection Institute), Ningbo 315048, People's Republic of China
| | - Jingping Lu
- Ningbo Academy of Product and Food Quality Inspection (Ningbo Fibre Inspection Institute), Ningbo 315048, People's Republic of China
| | - Jian Shen
- Ningbo Academy of Product and Food Quality Inspection (Ningbo Fibre Inspection Institute), Ningbo 315048, People's Republic of China
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8
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Sensitivity and applications of the PCR Single-Strand Conformation Polymorphism method. Mol Biol Rep 2021; 48:3629-3635. [PMID: 33893925 PMCID: PMC8065318 DOI: 10.1007/s11033-021-06349-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/08/2021] [Indexed: 12/14/2022]
Abstract
PCR Single-Strand Conformation Polymorphism is a method used to identify and detect mutations and is now well known for its many applications on living beings. This paper will discuss the experimental details, limitations and sensitivity of the PCR Single-Strand Conformation Polymorphism method in relation to all existing literature available to us until today. Genomic DNA extraction, PCR amplification and Single-Strand Conformation Polymorphism conditions (concentration of polyacrylamide slab gel electrophoresis, dissociation treatment of double- stranded DNA) and comparison with PCR Restriction Fragment Length Polymorphism are presented. Since its discovery in 1989, there have been many variations, innovations, and modifications of the method, which makes it very easy, safe, fast and for this reason widely applied in clinical diagnostic, forensic medicine, biochemical, veterinary, microbiological, food and environmental laboratories. One of the possible applications of the method is the diagnosis and identification of mutations in new strains of coronaviruses, because science needs more tools to tackle the problem of this pandemic. The PCR Single-Strand Conformation Polymorphism method can be applied in many cases provided that control samples are available and the required conditions of the method are achieved.
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9
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Mayo B, Rodríguez J, Vázquez L, Flórez AB. Microbial Interactions within the Cheese Ecosystem and Their Application to Improve Quality and Safety. Foods 2021; 10:602. [PMID: 33809159 PMCID: PMC8000492 DOI: 10.3390/foods10030602] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/09/2021] [Indexed: 12/26/2022] Open
Abstract
The cheese microbiota comprises a consortium of prokaryotic, eukaryotic and viral populations, among which lactic acid bacteria (LAB) are majority components with a prominent role during manufacturing and ripening. The assortment, numbers and proportions of LAB and other microbial biotypes making up the microbiota of cheese are affected by a range of biotic and abiotic factors. Cooperative and competitive interactions between distinct members of the microbiota may occur, with rheological, organoleptic and safety implications for ripened cheese. However, the mechanistic details of these interactions, and their functional consequences, are largely unknown. Acquiring such knowledge is important if we are to predict when fermentations will be successful and understand the causes of technological failures. The experimental use of "synthetic" microbial communities might help throw light on the dynamics of different cheese microbiota components and the interplay between them. Although synthetic communities cannot reproduce entirely the natural microbial diversity in cheese, they could help reveal basic principles governing the interactions between microbial types and perhaps allow multi-species microbial communities to be developed as functional starters. By occupying the whole ecosystem taxonomically and functionally, microbiota-based cultures might be expected to be more resilient and efficient than conventional starters in the development of unique sensorial properties.
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Affiliation(s)
- Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain; (J.R.); (L.V.); (A.B.F.)
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10
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Samperio S, Guzmán-Herrador DL, May-Cuz R, Martín MC, Álvarez MA, Llosa M. Conjugative DNA Transfer From E. coli to Transformation-Resistant Lactobacilli. Front Microbiol 2021; 12:606629. [PMID: 33643236 PMCID: PMC7905204 DOI: 10.3389/fmicb.2021.606629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/22/2021] [Indexed: 11/13/2022] Open
Abstract
Lactic acid bacteria (LAB) belonging to the genus classically known as Lactobacillus, recently split into 25 different genera, include many relevant species for the food industry. The well-known properties of lactobacilli as probiotics make them an attractive model also for vaccines and therapeutic proteins delivery in humans. However, scarce tools are available to accomplish genetic modification of these organisms, and most are only suitable for laboratory strains. Here, we test bacterial conjugation as a new tool to introduce genetic modifications into many biotechnologically relevant laboratory and wild type lactobacilli. Using mobilizable shuttle plasmids from a donor Escherichia coli carrying either RP4 or R388 conjugative systems, we were able to get transconjugants to all tested Lactocaseibacillus casei strains, including many natural isolates, and to several other genera, including Lentilactobacillus parabuchneri, for which no transformation protocol has been reported. Transconjugants were confirmed by the presence of the oriT and 16S rRNA gene sequencing. Serendipitously, we also found transconjugants into researcher-contaminant Staphylococcus epidermidis. Conjugative DNA transfer from E. coli to S. aureus was previously described, but at very low frequencies. We have purified this recipient strain and used it in standard conjugation assays, confirming that both R388 and RP4 conjugative systems mediate mobilization of plasmids into S. epidermidis. This protocol could be assayed to introduce DNA into other Gram-positive microorganisms which are resistant to transformation.
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Affiliation(s)
- Sara Samperio
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain
| | - Dolores L Guzmán-Herrador
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain
| | - Rigoberto May-Cuz
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain
| | | | | | - Matxalen Llosa
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC-SODERCAN, Santander, Spain
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11
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Lactic acid bacteria diversity and dynamics during ripening of traditional Turkish goatskin Tulum cheese produced in Mut region assessed by culturing and PCR-DGGE. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110701] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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12
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13
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Araújo-Rodrigues H, Tavaria FK, dos Santos MTP, Alvarenga N, Pintado MM. A review on microbiological and technological aspects of Serpa PDO cheese: An ovine raw milk cheese. Int Dairy J 2020. [DOI: 10.1016/j.idairyj.2019.104561] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Evaluation of DNA Extraction Methods for Culture-Independent Real-Time PCR-Based Detection of Listeria monocytogenes in Cheese. FOOD ANAL METHOD 2019. [DOI: 10.1007/s12161-019-01686-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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15
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Joishy TK, Dehingia M, Khan MR. Bacterial diversity and metabolite profiles of curd prepared by natural fermentation of raw milk and back sloping of boiled milk. World J Microbiol Biotechnol 2019; 35:102. [PMID: 31236715 DOI: 10.1007/s11274-019-2677-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/15/2019] [Indexed: 12/19/2022]
Abstract
Preparation of curd vary worldwide due to which its taste, texture and impact on human health also differ. In Assam, curd prepared from raw milk (RMC) is preferred over curd prepared from boiled milk (BMC), a tradition believed to have originated from the Mongoloid customs. Microbial diversity of raw milk (RM), boiled milk (BM), RMC and BMC collected from three farms were investigated by culture dependent and independent techniques. Additionally, metabolite profiles of RMC and BMC were studied by gas chromatography and mass spectroscopy. A total of 59 bacterial isolates were identified from the four different dairy products. In RM, lactic acid bacteria such as Lactococcus, Enterococcus, Lactobacillus and Leuconostoc were obtained along with the environmental bacteria like Bacillus, Staphylococcus, Acetobacter, Chryseobacterium, Streptococcus, Acinetobacter, Kocuria, Klebsiella and Macrococcus. Additionally, Prevotella, Oscillospira, Phascolarctobacterium and Akkermansia were also detected in BM by culture independent technique. In RMC and BMC, Lactococcus, Leuconostoc and Lactobacillus were prevalent. RM and RMC shared Enterococcus, Lactococcus, Streptococcus and Acinetobacter as common bacterial genera. However, no bacterial genus was common in BM and BMC. The correlation analysis revealed that Lactobacillus was negatively correlated to other bacterial genera. Oligotyping analysis revealed that Lactobacillus brevis and L.fermentum were abundant in RMC and BMC, respectively. In metabolomic study, ascorbic acid, dodecanoic acid and hexadecanoic acid were found to be significantly higher in RMC. Presence of different types of probiotics in these curds samples opens a new avenue to understand their effects on human health.
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Affiliation(s)
- Tulsi K Joishy
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India.,Department of Molecular Biology and Biotechnology, Life Sciences Division, Cotton University, Guwahati, Assam, India
| | - Madhusmita Dehingia
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India
| | - Mojibur R Khan
- Molecular Biology and Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India.
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16
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Cao C, Hou Q, Hui W, Kwok L, Zhang H, Zhang W. Assessment of the microbial diversity of Chinese Tianshan tibicos by single molecule, real-time sequencing technology. Food Sci Biotechnol 2019; 28:139-145. [PMID: 30815304 DOI: 10.1007/s10068-018-0460-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/20/2018] [Accepted: 08/29/2018] [Indexed: 11/26/2022] Open
Abstract
Chinese Tianshan tibico grains were collected from the rural area of Tianshan in Xinjiang province, China. Typical tibico grains are known to consist of polysaccharide matrix that embeds a variety of bacteria and yeasts. These grains are widely used in some rural regions to produce a beneficial sugary beverage that is slightly acidic and contains low level of alcohol. This work aimed to characterize the microbiota composition of Chinese Tianshan tibicos using the single molecule, real-time sequencing technology, which is advantageous in generating long reads. Our results revealed that the microbiota mainly comprised of the bacterial species of Lactobacillus hilgardii, Lactococcus raffinolactis, Leuconostoc mesenteroides, Zymomonas mobilis, together with a Guehomyces pullulans-dominating fungal community. The data generated in this work helps identify beneficial microbes in Chinese Tianshan tibico grains.
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Affiliation(s)
- Chenxia Cao
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
| | - Qiangchuan Hou
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
| | - Wenyan Hui
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
| | - Laiyu Kwok
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
| | - Heping Zhang
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
| | - Wenyi Zhang
- 1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
- 2Key Laboratory of Dairy Products Processing, Ministry of Agriculture, P. R. China, Inner Mongolia Agricultural University, Hohhot, 010018 People's Republic of China
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17
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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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18
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Development of a time-effective and highly specific quantitative real-time polymerase chain reaction assay for the identification of Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus in artisanal raw cow’s milk cheese. ACTA VET BRNO 2018. [DOI: 10.2754/avb201887030301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The first objective of this work included the development of real-time polymerase chain reaction (RT-PCR) which is also known as quantitative polymerase chain reaction (qPCR) assays to quantify two species of lactic acid bacteria which play a very important role in cheese ripening: Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus. The second objective was the comparison of qPCR and plate counts of these two species present in raw cow’s milk cheese samples during different stages of ripening. Thirty-three deoxyribonucleic acid (DNA) samples coming from seven different bacterial species, which were phylogenetically related or commonly isolated from raw milk and dairy products, were chosen as positive and negative controls. The qPCR assays showed a high quantification capacity characterised by their linearity (R2 > 0.998), PCR efficiencies which were within the range 78.0–90.0% for L. delbrueckii subsp. bulgaricus, and 93.6–100.5% for S. thermophilus, and quantification limit (103 gene copies/ml for L. delbrueckii subsp. bulgaricus and 10 gene copies/ml for S. thermophilus). The importance of our study is in the monitoring of changes in populations of L. delbrueckii subsp. bulgaricus and S. thermophilus contributing to cheese ripening using the newly designed qPCR assay.
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Bacterial diversity of artisanal cheese from the Amazonian region of Brazil during the dry and rainy seasons. Food Res Int 2018; 108:295-300. [PMID: 29735061 DOI: 10.1016/j.foodres.2018.03.060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/18/2018] [Accepted: 03/21/2018] [Indexed: 11/22/2022]
Abstract
The microbiota from artisanal cheeses produced in the Amazonian region is evaluated. Samples of artisanal cheeses were obtained from markets in Conceição do Araguaia and Redenção (Pará, Brazil) over rainy and dry seasons, and their biodiversity was assessed by culture-dependent and culture-independent methods. Mean counts of lactic acid bacteria (LAB) in cheeses ranged from 7.32 to 8.84 log CFU/g, for both seasons. Members of genera Lactobacillus, Lactococcus, Weissella, Enterococcus, Pediococcus, and Leuconostoc were predominant. The amplification of the 16S rRNA V6-V9 region, followed by a temporal temperature-gradient gel electrophoresis (TTGE) and sequencing of the TTGE bands revealed important differences in the microbial composition variability between samples from the two seasons and among cheese samples analyzed. TTGE showed the presence of microorganisms that are frequently found in cheese, such as L. lactis subsp. lactis, as well as other non-usual species, such as Macrococcus caseolyticus and Corynebacterium variabile. Moreover, TTGE analysis revealed the presence of microorganisms that have been isolated from other types of foods (Paralactobacillus selangorenses) along with some not usually found in foods, such as Exiguobacterium acetylicum, plus the presence of pathogenic microorganisms (Granulicatella elegans and Aerococcus sanguinicola). The present molecular approaches combined with culture-dependent methods provided a more detailed description of the microbial ecology of traditional cheeses from the Amazonian region in northern Brazil.
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20
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Ren Z, Tang S, Jiang Y, Jiang M, Zheng S, Liu W, Yang Z, Sang S, Chen Z, Xia T, Yin M. High-Throughput Sequencing Analysis of Endophytic Bacteria Diversity in Fruits of White and Red Pitayas from Three Different Origins. Pol J Microbiol 2018; 67:27-35. [DOI: 10.5604/01.3001.0011.6139] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2017] [Indexed: 01/08/2023] Open
Abstract
Pitaya contains various types of polyphenols, flavonoid and vitamins which are beneficial for health and it is among the most important commercial tropical fruits worldwide. Endophytic bacteria might be beneficial for plant growth and yield. However, bacterial diversity in pitaya is poorly characterized. In this study, fruits of white and red pitayas from three different origins (Thailand, Vietnam and China) were chosen for endophytic bacteria diversity investigation by using Illumina HiSeq second-generation high-throughput sequencing technology. Large number of endophytic bacteria were detected and 22 phyla, 56 classes, 81 orders, 122 families and 159 genera were identified. Endophytic bacteria diversity was uneven among pitaya fruits from different origins and bacteria structure was different between white pitaya group and red pitaya group. Phylum Bacteroidetes, classes Bacteroidia and Coriobacteriia, orders Bacteroidales and Coriobacteriales, families Prevotellaceae, Bacteroidaceae, Ruminococcaceae, Paraprevotellaceae, Rikenellaceae, Alcaligenaceae and Coriobacteriaceae, genera Prevotella, Bacteroides, Roseburia, Faecalibacterium and Sutterella were statistically significant different species (P < 0.05) between white and red pitayas. These findings might be useful for growth improvement, fruit preservation and processing of different pitaya species from different origins.
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Affiliation(s)
- Zhen Ren
- School of Agriculture, Kunming University, Kunming, Yunnan, China
| | - Shukun Tang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Yi Jiang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Mingxing Jiang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Shangyong Zheng
- School of Medicine, Yunnan University, Kunming, Yunnan, China
| | - Wenjing Liu
- School of Medicine, Yunnan University, Kunming, Yunnan, China
| | - Zhili Yang
- School of Medicine, Yunnan University, Kunming, Yunnan, China
| | - Shuping Sang
- School of Medicine, Yunnan University, Kunming, Yunnan, China
| | - Zebin Chen
- School of Agriculture, Kunming University, Kunming, Yunnan, China
| | - Tiyuan Xia
- School of Agriculture, Kunming University, Kunming, Yunnan, China
| | - Min Yin
- School of Medicine, Yunnan University, Kunming, Yunnan, China
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21
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Lactobacillus rossiae strain isolated from sourdough produces putrescine from arginine. Sci Rep 2018; 8:3989. [PMID: 29507315 PMCID: PMC5838238 DOI: 10.1038/s41598-018-22309-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/21/2018] [Indexed: 11/29/2022] Open
Abstract
This work reports a Lactobacillus rossiae strain (L. rossiae D87) isolated from sourdough that synthesizes putrescine - a biogenic amine that raises food safety and spoilage concerns - from arginine via the ornithine decarboxylase (ODC) pathway. The odc and potE genes were identified and sequenced. These genes respectively encode ornithine decarboxylase (Odc), which participates in the decarboxylation of ornithine to putrescine, and the ornithine/putrescine exchanger (PotE), which exchanges ornithine for putrescine. Transcriptional analysis showed that odc and potE form an operon that is regulated transcriptionally by ornithine in a dose-dependent manner. To explore the possible role of the ODC pathway as an acid stress resistance mechanism for this bacterium, the effect of acidic pHs on its transcriptional regulation and on putrescine biosynthesis was analysed. Acidic pHs induced the transcription of the odc-potE genes and the production of putrescine over that seen at neutral pH. Further, putrescine production via the ODC system improved the survival of L. rossiae D87 by counteracting the acidification of the cytoplasm when the cells were subjected to acidic conditions. These results suggest the ODC pathway of L. rossiae D87 provides a biochemical defence mechanism against acidic environments.
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Attar MA, Yavarmanesh M, Mortazavi A, Edalatian Dovom MR, Habibi Najafi MB. Antibacterial effects of Lactococcus lactis isolated from Lighvan cheese regarding the recognition of Nisin, Lacticin and Lactococcin structural genes. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2017.10.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Karabey B, Eroglu D, Vural C, Ozdemir G, Yerlikaya O, Kinik O. Determination of the microbial flora in traditional İzmir Tulum cheeses by Denaturing Gradient Gel Electrophoresis. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2018; 55:956-963. [PMID: 29487437 DOI: 10.1007/s13197-017-3003-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 06/16/2017] [Accepted: 12/18/2017] [Indexed: 10/18/2022]
Abstract
In this study, it was aimed to determine microbial flora members in three traditional Tulum cheeses (C1, C2 and C3) produced in different villages and settlement areas in İzmir, Turkey. For this purpose, culture depended and 16S rRNA based culture independent methods were used. According to the results of culture depended method, Lactococcus spp., Enterococcus spp., Staphylococcus spp., Lactobacillus spp., Pediococcus spp. and yeast-mold were detected in all samples at different levels. In order to determine and identify both of the culturable and non-culturable microorganisms, denaturing gradient gel electrophoresis (DGGE) method was used. DGGE results have shown that there were eight different dominant microorganisms (Streptococcus thermophilus, Lactococcus lactis subs. lactis, Streptococcus infantarius subs. infantarius, Lactobacillus gallinarum, Streptococcus equinus, Enterococcus faecalis, Enterococcus faecium, Lactococcus garvieae) in three regionally cheese samples. Further more, total bacterial loads were monitored with real-time PCR (qPCR) method. According to the results, 3.5 × 108, 3.8 × 108, 8.4 × 108 copy number of DNA was detected in C1, C2 and C3 cheese samples, respectively. This study is the first description for the dynamics of microbial composition of Izmir Tulum cheese after the production and brining processes.
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Affiliation(s)
- Burcin Karabey
- 1Department of Biology, Basic and Industrial Microbiology Section, Faculty of Science, Ege University, Bornova, Izmir, Turkey
| | - Didem Eroglu
- 1Department of Biology, Basic and Industrial Microbiology Section, Faculty of Science, Ege University, Bornova, Izmir, Turkey
| | - Caner Vural
- 1Department of Biology, Basic and Industrial Microbiology Section, Faculty of Science, Ege University, Bornova, Izmir, Turkey
| | - Guven Ozdemir
- 1Department of Biology, Basic and Industrial Microbiology Section, Faculty of Science, Ege University, Bornova, Izmir, Turkey
| | - Oktay Yerlikaya
- 2Department of Dair Technology, Faculty of Agriculture, Ege University, Bornova, Izmir, Turkey
| | - Ozer Kinik
- 2Department of Dair Technology, Faculty of Agriculture, Ege University, Bornova, Izmir, Turkey
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24
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Effect of High-Pressure Processing on Quality and Microbiological Properties of a Fermented Beverage Manufactured from Sweet Whey Throughout Refrigerated Storage. FOOD BIOPROCESS TECH 2018. [DOI: 10.1007/s11947-018-2078-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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25
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Frantzen CA, Kleppen HP, Holo H. Lactococcus lactis Diversity in Undefined Mixed Dairy Starter Cultures as Revealed by Comparative Genome Analyses and Targeted Amplicon Sequencing of epsD. Appl Environ Microbiol 2018; 84:e02199-17. [PMID: 29222100 PMCID: PMC5772235 DOI: 10.1128/aem.02199-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/10/2017] [Indexed: 12/20/2022] Open
Abstract
Undefined mesophilic mixed (DL) starter cultures are used in the production of continental cheeses and contain unknown strain mixtures of Lactococcus lactis and leuconostocs. The choice of starter culture affects the taste, aroma, and quality of the final product. To gain insight into the diversity of Lactococcus lactis strains in starter cultures, we whole-genome sequenced 95 isolates from three different starter cultures. Pan-genomic analyses, which included 30 publically available complete genomes, grouped the strains into 21 L. lactis subsp. lactis and 28 L. lactis subsp. cremoris lineages. Only one of the 95 isolates grouped with previously sequenced strains, and the three starter cultures showed no overlap in lineage distributions. The culture diversity was assessed by targeted amplicon sequencing using purR, a core gene, and epsD, present in 93 of the 95 starter culture isolates but absent in most of the reference strains. This enabled an unprecedented discrimination of starter culture Lactococcus lactis and revealed substantial differences between the three starter cultures and compositional shifts during the cultivation of cultures in milk.IMPORTANCE In contemporary cheese production, standardized frozen seed stock starter cultures are used to ensure production stability, reproducibility, and quality control of the product. The dairy industry experiences significant disruptions of cheese production due to phage attacks, and one commonly used countermeasure to phage attack is to employ a starter rotation strategy, in which two or more starters with minimal overlap in phage sensitivity are used alternately. A culture-independent analysis of the lactococcal diversity in complex undefined starter cultures revealed large differences between the three starter cultures and temporal shifts in lactococcal composition during the production of bulk starters. A better understanding of the lactococcal diversity in starter cultures will enable the development of more robust starter cultures and assist in maintaining the efficiency and stability of the production process by ensuring the presence of key bacteria that are important to the characteristics of the product.
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Affiliation(s)
- Cyril A Frantzen
- Laboratory of Microbial Gene Technology and Food Microbiology, Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Hans Petter Kleppen
- Laboratory of Microbial Gene Technology and Food Microbiology, Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- ACD Pharmaceuticals AS, Leknes, Norway
| | - Helge Holo
- Laboratory of Microbial Gene Technology and Food Microbiology, Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- TINE SA, Oslo, Norway
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26
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Stachelska MA. Identification of Lactobacillus delbrueckii and Streptococcus thermophilus Strains Present in Artisanal Raw Cow Milk Cheese Using Real-time PCR and Classic Plate Count Methods. Pol J Microbiol 2017; 66:491-499. [DOI: 10.5604/01.3001.0010.7041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The aim of this paper was to detect Lactobacillus delbrueckii and Streptococcus thermophilus using real-time quantitative PCR assay in 7-day ripening cheese produced from unpasteurised milk. Real-time quantitative PCR assays were designed to identify and enumerate the chosen species of lactic acid bacteria (LAB) in ripened cheese. The results of molecular quantification and classic bacterial enumeration showed a high level of similarity proving that DNA extraction was carried out in a proper way and that genomic DNA solutions were free of PCR inhibitors. These methods revealed the presence of L. delbrueckii and S. thermophilus. The real-time PCR enabled quantification with a detection of 101–103 CFU/g of product. qPCR-standard curves were linear over seven log units down to 101 copies per reaction; efficiencies ranged from 77.9% to 93.6%. Cheese samples were analysed with plate count method and qPCR in parallel. Compared with the classic plate count method, the newly developed qPCR method provided faster and species specific identification of two dairy LAB and yielded comparable quantitative results.
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Affiliation(s)
- Milena A. Stachelska
- Institute of Food Technology and Gastronomy, Lomza State University of Applied Sciences, Lomza, Poland
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27
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Bacterial diversity of the Colombian fermented milk "Suero Costeño" assessed by culturing and high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons. Food Microbiol 2017; 68:129-136. [PMID: 28800820 DOI: 10.1016/j.fm.2017.07.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 06/13/2017] [Accepted: 07/16/2017] [Indexed: 11/22/2022]
Abstract
"Suero Costeño" (SC) is a traditional soured cream elaborated from raw milk in the Northern-Caribbean coast of Colombia. The natural microbiota that characterizes this popular Colombian fermented milk is unknown, although several culturing studies have previously been attempted. In this work, the microbiota associated with SC from three manufacturers in two regions, "Planeta Rica" (Córdoba) and "Caucasia" (Antioquia), was analysed by means of culturing methods in combination with high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons. The bacterial ecosystem of SC samples was revealed to be composed of lactic acid bacteria belonging to the Streptococcaceae and Lactobacillaceae families; the proportions and genera varying among manufacturers and region of elaboration. Members of the Lactobacillus acidophilus group, Lactocococcus lactis, Streptococcus infantarius and Streptococcus salivarius characterized this artisanal product. In comparison with culturing, the use of molecular in deep culture-independent techniques provides a more realistic picture of the overall bacterial communities residing in SC. Besides the descriptive purpose, these approaches will facilitate a rational strategy to follow (culture media and growing conditions) for the isolation of indigenous strains that allow standardization in the manufacture of SC.
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28
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Sánchez-Gamboa C, Hicks-Pérez L, Gutiérrez-Méndez N, Heredia N, García S, Nevárez-Moorillón GV. Seasonal influence on the microbial profile of Chihuahua cheese manufactured from raw milk. INT J DAIRY TECHNOL 2017. [DOI: 10.1111/1471-0307.12423] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Cristina Sánchez-Gamboa
- Facultad de Ciencias Biológicas; Universidad Autónoma de Nuevo León; Ave. Pedro de Alba s/n; Ciudad Universitaria; 66451 San Nicolás de los Garza Nuevo León México
| | - Liliana Hicks-Pérez
- Facultad de Ciencias Químicas; Universidad Autónoma de Chihuahua; Circuito Universitario S/N; Campus Universitario II 31125 Chihuahua Chihuahua México
| | - Néstor Gutiérrez-Méndez
- Facultad de Ciencias Químicas; Universidad Autónoma de Chihuahua; Circuito Universitario S/N; Campus Universitario II 31125 Chihuahua Chihuahua México
| | - Norma Heredia
- Facultad de Ciencias Biológicas; Universidad Autónoma de Nuevo León; Ave. Pedro de Alba s/n; Ciudad Universitaria; 66451 San Nicolás de los Garza Nuevo León México
| | - Santos García
- Facultad de Ciencias Biológicas; Universidad Autónoma de Nuevo León; Ave. Pedro de Alba s/n; Ciudad Universitaria; 66451 San Nicolás de los Garza Nuevo León México
| | - Guadalupe V Nevárez-Moorillón
- Facultad de Ciencias Químicas; Universidad Autónoma de Chihuahua; Circuito Universitario S/N; Campus Universitario II 31125 Chihuahua Chihuahua México
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29
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Mehri I, Lajnef R, Rejab AB, Khessairi A, Cherif H, Ouzari H, Hassen A. Biofilms in bioremediation and wastewater treatment: characterization of bacterial community structure and diversity during seasons in municipal wastewater treatment process. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:3519-3530. [PMID: 27878485 DOI: 10.1007/s11356-016-8090-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/09/2016] [Indexed: 05/02/2023]
Abstract
The bacterial community structure and diversity were assessed at the scale of rotating biodisk procedure (RB) in a semi-industrial pilot plant. As well, the Salmonella community was particularly monitored, and the effects of ultraviolet (UV-C254) on the bacterial community were studied. The identification of dominant bacteria revealed the presence of beneficial and useful species that could play an important role in the process of wastewater purification. Several species as Enterobacter agglomerans, Cronobacter sakazakii, and Pantoea agglomerans known for their bioremediation activities were revealed in the majority of biofilm samples. Common detection of Salmonella community provides evidence that the RB system did not seriously affect Salmonella. Furthermore, the investigation on the (UV)-C254 inactivation of the whole bacterial community, in secondary treated wastewater, showed variable UV resistance results. No Salmonella detection was registered at a dose of around 1440 mW s cm-2 since a total disappearance of Salmonella was recorded.
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Affiliation(s)
- Ines Mehri
- Water Research and Technology Centre (CERTE), Borj Cédria Technology Park, P.O. BOX 273, Soliman, 8020, Tunisia
| | - Rim Lajnef
- Water Research and Technology Centre (CERTE), Borj Cédria Technology Park, P.O. BOX 273, Soliman, 8020, Tunisia
| | - Asma Ben Rejab
- Water Research and Technology Centre (CERTE), Borj Cédria Technology Park, P.O. BOX 273, Soliman, 8020, Tunisia
| | - Amel Khessairi
- Water Research and Technology Centre (CERTE), Borj Cédria Technology Park, P.O. BOX 273, Soliman, 8020, Tunisia
| | - Hanene Cherif
- Water Research and Technology Centre (CERTE), Borj Cédria Technology Park, P.O. BOX 273, Soliman, 8020, Tunisia
| | - Hadda Ouzari
- Laboratoire Microorganisme and Biomolécules Actives, Département de Biologie, Faculté des Sciences de Tunis, Campus Universitaire, 2092, Tunis, Tunisia
| | - Abdennaceur Hassen
- Water Research and Technology Centre (CERTE), Borj Cédria Technology Park, P.O. BOX 273, Soliman, 8020, Tunisia
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Zhong Z, Hou Q, Kwok L, Yu Z, Zheng Y, Sun Z, Menghe B, Zhang H. Bacterial microbiota compositions of naturally fermented milk are shaped by both geographic origin and sample type. J Dairy Sci 2016; 99:7832-7841. [DOI: 10.3168/jds.2015-10825] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 04/02/2016] [Indexed: 11/19/2022]
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31
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Pega J, Rizzo S, Pérez C, Rossetti L, Díaz G, Ruzal S, Nanni M, Descalzo A. Effect of the addition of phytosterols and tocopherols on Streptococcus thermophilus robustness during industrial manufacture and ripening of a functional cheese as evaluated by qPCR and RT-qPCR. Int J Food Microbiol 2016; 232:117-25. [DOI: 10.1016/j.ijfoodmicro.2016.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 04/08/2016] [Accepted: 06/03/2016] [Indexed: 10/21/2022]
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Danezis GP, Tsagkaris AS, Brusic V, Georgiou CA. Food authentication: state of the art and prospects. Curr Opin Food Sci 2016. [DOI: 10.1016/j.cofs.2016.07.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Šuranská H, Raspor P, Uroić K, Golić N, Kos B, Mihajlović S, Begović J, Šušković J, Topisirović L, Čadež N. Characterisation of the yeast and mould biota in traditional white pickled cheeses by culture-dependent and independent molecular techniques. Folia Microbiol (Praha) 2016; 61:455-463. [PMID: 27027646 DOI: 10.1007/s12223-016-0455-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 03/02/2016] [Indexed: 11/28/2022]
Abstract
Artisanal white pickled cheese of Western Serbia is a product of complex microbial community which detection by culture-dependent method only is hampered by its limitations. Thus, in the present study, we used a culture-independent, semi-quantitative technique based on construction of an internal transcribed spacer (ITS)-clone library from metagenomic DNA. This approach, based on direct DNA extraction followed by amplification of fungal internal transcribed regions (ITS) cloned into plasmid and restricted by endonucleases, revealed greater species richness in analysed cheeses and their by-products (17 species in total) compared to the more commonly used techniques of the culture-dependent method (8 species) and LSU-DGGE (10 species). The most frequently occurring yeast species which are commonly associated with cheeses production were Debaryomyces hansenii, Kluyveromyces lactis and Candida zeylanoides. On the other hand, Yarrowia lipolytica and Galactomyces geotrichum were detected only in one cheese sample. Moreover, some species, mainly moulds (Filobasidium globisporum, Cladosporium sp., Aspergillus sp. or Alternaria sp.) were identified only by culture-independent methods. The discrepancies between the techniques were confirmed by low correlation factor and by different indices of general biodiversity and dominance of species. The ITS-clone library approach provides the opportunity to analyse complex fungal communities associated with food products.
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Affiliation(s)
- Hana Šuranská
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia.,Institute of Food Science and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Peter Raspor
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Ksenija Uroić
- Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Nataša Golić
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Blaženka Kos
- Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Sanja Mihajlović
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Jelena Begović
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Jagoda Šušković
- Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Ljubiša Topisirović
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Neža Čadež
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia.
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Chombo-Morales P, Kirchmayr M, Gschaedler A, Lugo-Cervantes E, Villanueva-Rodríguez S. Effects of controlling ripening conditions on the dynamics of the native microbial population of Mexican artisanal Cotija cheese assessed by PCR-DGGE. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2015.09.044] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Puerari C, Magalhães-Guedes KT, Schwan RF. Bacaba beverage produced by Umutina Brazilian Amerindians: Microbiological and chemical characterization. Braz J Microbiol 2015; 46:1207-16. [PMID: 26691483 PMCID: PMC4704630 DOI: 10.1590/s1517-838246420140964] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 03/30/2015] [Indexed: 11/22/2022] Open
Abstract
Bacaba chicha is a beverage prepared by the indigenous Umutina people from the bacaba fruit (Oenocarpus bacaba), a purple berry that is rich in fat and carbohydrates, as well as a source of phenolic compounds. In this study, samples of bacaba chicha beverage were collected, and the microbial community was assessed using culture-dependent and -independent techniques. The nutritional composition and metabolite profiles were analyzed, and species belonging to lactic acid bacteria (LAB) and yeasts were detected. The LAB group detected by culture-dependent analysis included Enterococcus hormaechei and Leuconostoc lactis. Polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) detected additional Propionibacterium avidum, Acetobacter spp., and uncultured bacteria. Pichia caribbica and Pichia guilliermondii were detected in a culture-dependent method, and Pichia caribbica was confirmed by PCR-DGGE analysis. The pH value of the beverage was 6.2. The nutritional composition was as follows: 16.47 ± 0.73 g 100 mL-1 dry matter, 2.2 ± 0.0 g 100 mL-1 fat, 3.36 ± 0.44 g 100 mL-1 protein, and 10.87 ± 0.26 g 100 mL-1 carbohydrate. The metabolites detected were 2.69 g L-1 succinic acid, 0.9 g L-1 acetic acid, 0.49 g L-1 citric acid, 0.52 g L-1 ethanol, and 0.4 g L-1 glycerol. This is the first study to identify microbial diversity in bacaba chicha spontaneous fermentation. This study is also the starting step in the immaterial record of this Brazilian indigenous beverage prepared from bacaba fruit.
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Affiliation(s)
- Cláudia Puerari
- Departamento de Ciência de Alimentos, Universidade Federal de Lavras, Lavras, MG, Brazil
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Abosereh NA, Ghani SAE, Gomaa RS, Fouad MT. Molecular Identification of Potential Probiotic Lactic Acid Bacteria Strains Isolated from Egyptian Traditional Fermented Dairy Products. ACTA ACUST UNITED AC 2015. [DOI: 10.3923/biotech.2016.35.43] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Wang J, Sun C, Liu C, Yang Y, Lu W. Comparison of vaginal microbial community structure in healthy and endometritis dairy cows by PCR-DGGE and real-time PCR. Anaerobe 2015; 38:1-6. [PMID: 26551525 DOI: 10.1016/j.anaerobe.2015.11.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 08/31/2015] [Accepted: 11/03/2015] [Indexed: 10/22/2022]
Abstract
The normal vaginal microflora provides protection against infections of the reproductive tract. Previous studies have focused on the isolation and screening of probiotic strains from the vagina of cows; however, the vaginal microflora of postpartum cows is poorly characterized. The present study was conducted to evaluate and characterize the vaginal microflora of healthy postpartum cows in relation to postpartum cows with endometritis by using PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE) and Real-time PCR. The study population comprised 5 healthy cows and 5 cows with endometritis. The results indicated that the vaginal bacterial microflora of healthy postpartum cows was dominated by Lactobacillus sakei subsp. and Weissella koreensis, while there were no dominant bacterial species in the vaginal microflora of postpartum cows with endometritis. Common microorganisms such as Bacteroides spp., Fusobacterium spp., Enterococcus spp., Prevotella spp., Clostridium perfringens strains, and Escherichia coli were detected in both groups of cows by Real-time PCR. The bacterial diversity in the vagina of cows with endometritis was significantly higher than that in healthy cows. The results indicated that the vaginal microflora of cows with endometritis was more diverse and lacked dominant bacterial species as compared to that of the healthy cows, suggesting that disruption of the normal vaginal microflora may contribute to the onset of endometritis. This microbial community analysis provided information that might be used to develop probiotics to treat endometritis in cows; however, further investigation is needed.
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Affiliation(s)
- Jun Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Chengtao Sun
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Chang Liu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Yujiang Yang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Wenfa Lu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China.
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Abstract
The history of cheese manufacture is a "natural history" in which animals, microorganisms, and the environment interact to yield human food. Part of the fascination with cheese, both scientifically and culturally, stems from its ability to assume amazingly diverse flavors as a result of seemingly small details in preparation. In this review, we trace the roots of cheesemaking and its development by a variety of human cultures over centuries. Traditional cheesemakers observed empirically that certain environments and processes produced the best cheeses, unwittingly selecting for microorganisms with the best biochemical properties for developing desirable aromas and textures. The focus of this review is on the role of fungi in cheese ripening, with a particular emphasis on the yeast-like fungus Geotrichum candidum. Conditions that encourage the growth of problematic fungi such as Mucor and Scopulariopsis as well as Arachnida (cheese mites), and how such contaminants might be avoided, are discussed. Bethlehem cheese, a pressed, uncooked, semihard, Saint-Nectaire-type cheese manufactured in the United Sates without commercial strains of bacteria or fungi, was used as a model for the study of stable microbial succession during ripening in a natural environment. The appearance of fungi during a 60-day ripening period was documented using light and scanning electron microscopy, and it was shown to be remarkably reproducible and parallel to the course of ripening of authentic Saint-Nectaire cheese in the Auvergne region of France. Geotrichum candidum, Mucor, and Trichothecium roseum predominate the microbiotas of both cheese types. Geotrichum in particular was shown to have high diversity in different traditional cheese ripening environments, suggesting that traditional manufacturing techniques selected for particular fungi. This and other studies suggest that strain diversity arises in relation to the lore and history of the regions from which these types of cheeses arose.
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Abstract
Cheese is an ideal environment to serve as a model for the behavior of microbes in complex communities and at the same time allow detailed genetic analysis. Linking organisms, and their genes, to their role in the environment becomes possible in the case of cheese since cheese microbial communities have been "in culture" for thousands of years, with the knowledge of how to grow these organisms passed down by generations of cheesemakers. Recent reviews have described several emerging approaches to link molecular systems biology to ecosystem-scale processes, known as ecosystems biology. These approaches integrate massive datasets now available through high-throughput sequencing technologies with measurements of ecosystem properties. High-throughput datasets uncover the "parts list" (e.g., the species and all the genes within each species) of an ecosystem as well as the molecular basis of interactions within this parts list. Novel computational frameworks make it possible to link species and their interactions to ecosystem properties. Applying these approaches across multiple temporal and spatial scales makes it possible to understand how changes in the parts lists over space and time lead to changes in ecosystems processes. By manipulating the species present within model systems, we can test hypotheses related to the role of microbes in ecosystem function. Due to the tractability of cheese microbial communities, we have the opportunity to use an ecosystems biology approach from the scale of individual microbial cells within a cheese to replicated cheese microbial communities across continents. Using cheese as a model microbial ecosystem can provide a way to answer important questions concerning the form, function, and evolution of microbial communities.
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Alves J, Niguma NH, de Oliveira TC. Detection of Salmonella
spp. in Eight Complex Food Matrices Using Polymerase Chain Reaction Assay. J Food Saf 2015. [DOI: 10.1111/jfs.12194] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juliane Alves
- Department of Food Science and Technology; Londrina State University; Rodovia Celso Garcia Cid, PR 445, Km 380, Campus Universitário, Caixa Postal 10.011 CEP 86057-970 Londrina Paraná Brazil
| | - Natália H. Niguma
- Department of Food Science and Technology; Londrina State University; Rodovia Celso Garcia Cid, PR 445, Km 380, Campus Universitário, Caixa Postal 10.011 CEP 86057-970 Londrina Paraná Brazil
| | - Tereza C.R.M. de Oliveira
- Department of Food Science and Technology; Londrina State University; Rodovia Celso Garcia Cid, PR 445, Km 380, Campus Universitário, Caixa Postal 10.011 CEP 86057-970 Londrina Paraná Brazil
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Liu W, Zheng Y, Kwok LY, Sun Z, Zhang J, Guo Z, Hou Q, Menhe B, Zhang H. High-throughput sequencing for the detection of the bacterial and fungal diversity in Mongolian naturally fermented cow's milk in Russia. BMC Microbiol 2015; 15:45. [PMID: 25887414 PMCID: PMC4345014 DOI: 10.1186/s12866-015-0385-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 02/12/2015] [Indexed: 11/10/2022] Open
Abstract
Background Traditional fermented dairy products are major components of the typical Mongolian diet since ancient times. However, almost all the previous studies on the microbial composition of traditional Mongolian fermented dairy products analyzed food samples from the Chinese Mongolian region and Mongolia but not the Russian Mongolian region. In this study, the bacterial and fungal community diversity of nineteen naturally fermented cow’s milk (NFCM) samples from local Mongolian families residing in Kalmykia and Chita of Russia was investigated with pyrosequencing. Results Firmicutes and Ascomycota were the predominant phyla respectively for bacteria and fungi. The abundance of the bacterial phylum Acidobacteria was considerably different between the samples from the two regions. At genus level, Lactobacillus and Pichia were the predominating bacterial and fungal genera, respectively, while six bacterial genera significantly differed between the Kalmykia (enrichment of Aeromonas, Bacillus, Clostridium, Streptococcus, Vogesella) and Chita (enrichment of Lactococcus) samples. The results of principal coordinate analysis (PCoA) based on the bacterial or fungal composition of the Kalmykia and Chita samples revealed a different microbiota structure between the samples collected in these two locations. The redundancy analysis (RDA) identified 60 bacterial and 21 fungal OTUs as the key variables responsible for such microbiota structural difference. Conclusions Our results suggest that structural differences existed in the microbiota of NFCM between Kalmykia and Chita. The difference in geographic environment may be an important factor influencing the microbial diversity of NFCM made by the Mongolians in Russia. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0385-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China. .,Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, 150030, P. R. China.
| | - Yi Zheng
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China. .,Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, 150030, P. R. China.
| | - Jiachao Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Zhuang Guo
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Qiangchuan Hou
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Bilige Menhe
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China. .,Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, 150030, P. R. China.
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Temporal and spatial differences in microbial composition during the manufacture of a continental-type cheese. Appl Environ Microbiol 2015; 81:2525-33. [PMID: 25636841 DOI: 10.1128/aem.04054-14] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine-salted continental-type cheese in cheeses produced early and late in the production day. Differences in the microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that cheeses produced late in the day had a more diverse microbial population than their early equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were initially found to have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the genera Thermus, Pseudoalteromonas, and Bifidobacterium, not routinely associated with a continental-type cheese produced from pasteurized milk, were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high-throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition.
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Chalermwatanachai T, Velásquez LC, Bachert C. The microbiome of the upper airways: focus on chronic rhinosinusitis. World Allergy Organ J 2015; 8:3. [PMID: 25624972 PMCID: PMC4306241 DOI: 10.1186/s40413-014-0048-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 11/20/2014] [Indexed: 01/27/2023] Open
Abstract
Upper airway diseases including allergic rhinitis, chronic rhinosinusitis with or without polyps, and cystic fibrosis are characterized by substantially different inflammatory profiles. Traditionally, studies on the association of specific bacterial patterns with inflammatory profiles of diseases had been dependent on bacterial culturing. In the past 30 years, molecular biology methods have allowed bacterial culture free studies of microbial communities, revealing microbiota much more diverse than previously recognized including those found in the upper airway. At presence, the study of the pathophysiology of upper airway diseases is necessary to establish the relationship between the microbiome and inflammatory patterns to find their clinical reflections and also their possible causal relationships. Such investigations may elucidate the path to therapeutic approaches in correcting an imbalanced microbiome. In the review we summarized techniques used and the current knowledge on the microbiome of upper airway diseases, the limitations and pitfalls, and identified areas of interest for further research.
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Affiliation(s)
- Thanit Chalermwatanachai
- Department of Oto-Rhino-Laryngology, The Upper Airways Research Laboratory (URL), Ghent University Hospital, Ghent, 9000 Belgium ; Department of Otolaryngology, Phramongkutklao Hospital and College of Medicine, Royal Thai Army, Bangkok, 10400 Thailand
| | - Leydi Carolina Velásquez
- Department of Oto-Rhino-Laryngology, The Upper Airways Research Laboratory (URL), Ghent University Hospital, Ghent, 9000 Belgium ; Basic Biomedical Sciences Department, Health Faculty, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Claus Bachert
- Department of Oto-Rhino-Laryngology, The Upper Airways Research Laboratory (URL), Ghent University Hospital, Ghent, 9000 Belgium ; Division of ENT Diseases, Clintec, Karolinska Institutet, Stockholm, Sweden
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Detection and viability of Lactococcus lactis throughout cheese ripening. PLoS One 2014; 9:e114280. [PMID: 25503474 PMCID: PMC4266610 DOI: 10.1371/journal.pone.0114280] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 11/09/2014] [Indexed: 02/07/2023] Open
Abstract
Recent evidences highlighted the presence of Lactococcus lactis during late cheese ripening. For this reason, the role of this microorganism, well known as dairy starter, should be reconsidered throughout cheese manufacturing and ripening. Thus, the main objective of this study was to develop a RT-qPCR protocol for the detection, quantification and determination of the viability of L. lactis in ripened cheese samples by direct analysis of microbial nucleic acids. Standard curves were constructed for the specific quantification of L. lactis in cheese matrices and good results in terms of selectivity, correlation coefficient and efficiency were obtained. Thirty-three ripened cheeses were analyzed and, on the basis of RNA analysis, twelve samples showed 106 to 108 CFU of L. lactis per gram of product, thirteen from 103 to 105 CFU/g, and in eight cheeses, L. lactis was not detected. Traditional plating on M17 medium led to loads ranging from 105 to 109 CFU/g, including the cheese samples where no L. lactis was found by RT-qPCR. From these cheeses, none of the colonies isolated on M17 medium was identified as L. lactis species. These data could be interpreted as a lack of selectivity of M17 medium where colony growth is not always related to lactococcal species. At the same time, the absence or low abundance of L. lactis isolates on M17 medium from cheese where L. lactis was detected by RT-qPCR support the hypothesis that L. lactis starter populations are mainly present in viable but not culturable state during ripening and, for this reason, culture-dependent methods have to be supplemented with direct analysis of cheese.
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Castellote J, Fraud S, Irlinger F, Swennen D, Fer F, Bonnarme P, Monnet C. Investigation of Geotrichum candidum gene expression during the ripening of Reblochon-type cheese by reverse transcription-quantitative PCR. Int J Food Microbiol 2014; 194:54-61. [PMID: 25461609 DOI: 10.1016/j.ijfoodmicro.2014.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/21/2014] [Accepted: 11/10/2014] [Indexed: 12/12/2022]
Abstract
Cheese ripening involves the activity of various bacteria, yeasts or molds, which contribute to the development of the typical color, flavor and texture of the final product. In situ measurements of gene expression are increasingly being used to improve our understanding of the microbial flora activity in cheeses. The objective of the present study was to investigate the physiology and metabolic activity of Geotrichum candidum during the ripening of Reblochon-type cheeses by quantifying mRNA transcripts at various ripening times. The expression of 80 genes involved in various functions could be quantified with a correct level of biological repeatability using a set of three stable reference genes. As ripening progresses, a decrease in expression was observed for genes involved in cell wall organization, translation, vesicular mediated transport, and in cytoskeleton constituents and ribosomal protein genes. There was also a decrease in the expression of mitochondrial F1F0 ATP synthase and plasma membrane H(+) ATPase genes. Some genes involved in the catabolism of lactate, acetate and ethanol were expressed to a greater extent at the beginning of ripening. During the second part of ripening, there was an increased expression of genes involved in the transport and catabolism of amino acids, which could be attributed to a change in the energy source. There was also an increase in the expression of genes involved in autophagy and of genes possibly involved in lifespan determination. Quantification of mRNA transcripts may also be used to produce bioindicators relevant for cheesemaking, for example when considering genes encoding enzymes involved in the catabolism of amino acids.
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Affiliation(s)
- Jessie Castellote
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, 78850 Thiverval-Grignon, France; AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, 78850 Thiverval-Grignon, France
| | | | - Françoise Irlinger
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, 78850 Thiverval-Grignon, France; AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, 78850 Thiverval-Grignon, France
| | - Dominique Swennen
- INRA, UMR1319 Micalis, 78850 Thiverval-Grignon, France; AgroParisTech, UMR1319 Micalis, 78850 Thiverval-Grignon, France
| | - Frédéric Fer
- INRA, UMR1319 Micalis, 78850 Thiverval-Grignon, France; INRA, UMR518 Mathématiques et Informatique Appliquées, 75005 Paris, France
| | - Pascal Bonnarme
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, 78850 Thiverval-Grignon, France; AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, 78850 Thiverval-Grignon, France
| | - Christophe Monnet
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, 78850 Thiverval-Grignon, France; AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, 78850 Thiverval-Grignon, France.
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Mei J, Guo Q, Wu Y, Li Y. Microbial diversity of a Camembert-type cheese using freeze-dried Tibetan kefir coculture as starter culture by culture-dependent and culture-independent methods. PLoS One 2014; 9:e111648. [PMID: 25360757 PMCID: PMC4216126 DOI: 10.1371/journal.pone.0111648] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 10/01/2014] [Indexed: 12/11/2022] Open
Abstract
The biochemical changes occurring during cheese ripening are directly and indirectly dependent on the microbial associations of starter cultures. Freeze-dried Tibetan kefir coculture was used as a starter culture in the Camembert-type cheese production for the first time. Therefore, it's necessary to elucidate the stability, organization and identification of the dominant microbiota presented in the cheese. Bacteria and yeasts were subjected to culture-dependent on selective media and culture-independent polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) analysis and sequencing of dominant bands to assess the microbial structure and dynamics through ripening. In further studies, kefir grains were observed using scanning electron microscopy (SEM) methods. A total of 147 bacteria and 129 yeasts were obtained from the cheese during ripening. Lactobacillus paracasei represents the most commonly identified lactic acid bacteria isolates, with 59 of a total of 147 isolates, followed by Lactococcus lactis (29 isolates). Meanwhile, Kazachstania servazzii (51 isolates) represented the mainly identified yeast isolate, followed by Saccharomyces cerevisiae (40 isolates). However, some lactic acid bacteria detected by sequence analysis of DGGE bands were not recovered by plating. The yeast S. cerevisiae and K. servazzii are described for the first time with kefir starter culture. SEM showed that the microbiota were dominated by a variety of lactobacilli (long and curved) cells growing in close association with a few yeasts in the inner portion of the grain and the short lactobacilli were observed along with yeast cells on the exterior portion. Results indicated that conventional culture method and PCR-DGGE should be combined to describe in maximal detail the microbiological composition in the cheese during ripening. The data could help in the selection of appropriate commercial starters for Camembert-type cheese.
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Affiliation(s)
- Jun Mei
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Qizhen Guo
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Yan Wu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Yunfei Li
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
- * E-mail:
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Ringø E, Andersen R, Sperstad S, Zhou Z, Ren P, Breines EM, Hareide E, Yttergård GJ, Opsal K, Johansen HM, Andreassen AK, Kousha A, Godfroid J, Holzapfel W. Bacterial Community of Koumiss from Mongolia Investigated by Culture and Culture-Independent Methods. FOOD BIOTECHNOL 2014. [DOI: 10.1080/08905436.2014.964253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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