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Fan G, Sun Q, Sun Y, Liu D, Li S, Li M, Chen Q, Wang F, Moriya O, Itoh T, Kawasaki H, Yu Y, Cai M, Kim SG, Lee JS, Ma J, Wu L. GCM and gcType in 2024: comprehensive resources for microbial strains and genomic data. Nucleic Acids Res 2025; 53:D763-D771. [PMID: 39498510 PMCID: PMC11701616 DOI: 10.1093/nar/gkae1057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Revised: 10/16/2024] [Accepted: 10/22/2024] [Indexed: 01/18/2025] Open
Abstract
Microbial culture collections play a crucial role in the collection, maintenance, and distribution of quality-assured living microbial strains, along with their associated phenotypic and omics data. To enhance the find-able, accessible, interoperable, and re-usable (FAIR) data utilization of microbial resources, the World Data Center for Microorganisms (WDCM) has developed the Global Catalogue of Microorganisms (GCM) and the Global Catalogue of Type Strains (gcType). These platforms provide interactive interfaces for cataloging the holdings of collections, along with detailed annotations of type strain genomes and curated metadata, including ecosystems, growth conditions, and collection locations. The system maximizes the scientific impact of microbial resources and culture collections through an integrated data mining tool that links strain- and species-related information from various public resources. Currently, the GCM and gcType include 574 422 strains from 154 culture collections across 51 countries and regions, along with 25 980 genomes from type species. Additionally, 2 702 655 articles and 103 337 patents are integrated with these microbial resources. The system supports microbial taxonomic research and provides evidence for implementing the Nagoya Protocol in the field of microbial resources and their digital sequence information (DSI). Access is freely available at gcm.wdcm.org and gctype.wdcm.org.
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Affiliation(s)
- Guomei Fan
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- World Data Center for Microorganisms, Beijing 100101, China
- China National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Qinglan Sun
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- World Data Center for Microorganisms, Beijing 100101, China
- China National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Yan Sun
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- World Data Center for Microorganisms, Beijing 100101, China
- China National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Dongmei Liu
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- World Data Center for Microorganisms, Beijing 100101, China
- China National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Shiwen Li
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- World Data Center for Microorganisms, Beijing 100101, China
- China National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Min Li
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- World Data Center for Microorganisms, Beijing 100101, China
- China National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Qi Chen
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- World Data Center for Microorganisms, Beijing 100101, China
- China National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Fang Wang
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- World Data Center for Microorganisms, Beijing 100101, China
- China National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Ohkuma Moriya
- Japan Collection of Microorganisms/ Microbe Division, RIKEN BioResource Research Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan
| | - Takashi Itoh
- Japan Collection of Microorganisms/ Microbe Division, RIKEN BioResource Research Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan
| | - Hiroko Kawasaki
- NITE Biological Resource Center (NBRC), National Institute of Technology and 24 Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Yajing Yu
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Man Cai
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Song-Gun Kim
- Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and 30 Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and 30 Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do 56212, Republic of Korea
| | - Juncai Ma
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- World Data Center for Microorganisms, Beijing 100101, China
- China National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Linhuan Wu
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- World Data Center for Microorganisms, Beijing 100101, China
- China National Microbiology Data Center (NMDC), Beijing 100101, China
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Tovar-Pedraza JM, Solano-Báez AR, Leyva-Mir SG, Tlapal-Bolaños B, Camacho-Tapia M, García-León E, Ayala-Escobar V, Nava-Díaz C, Quezada-Salinas A, Santiago-Santiago V, Beltrán-Peña H, Hernandez-Hernandez MA, Juárez-Cruz KJ, Márquez-Licona G. The Need and Opportunity to Update the Inventory of Plant Pathogenic Fungi and Oomycetes in Mexico. J Fungi (Basel) 2024; 10:395. [PMID: 38921381 PMCID: PMC11204560 DOI: 10.3390/jof10060395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/27/2024] Open
Abstract
Mexico generates specific phytosanitary regulations for each product and origin to prevent the entry of quarantine pests and/or delay their spread within the national territory, including fungi and oomycetes. Phytosanitary regulations are established based on available information on the presence or absence of these pathogens in the country; however, the compilation and precise analysis of reports is a challenging task due to many publications lacking scientific rigor in determining the presence of a taxon of phytosanitary interest in the country. This review evaluated various studies reporting the presence of plant pathogenic fungi and oomycetes in Mexico and concluded that some lists of diseases and phytopathogenic organisms lack technical-scientific basis. Thus, it highlights the need and presents an excellent opportunity to establish a National Collection of Fungal Cultures and a National Herbarium for obligate parasites, as well as to generate a National Database of Phytopathogenic Fungi and Oomycetes present in Mexico, supported by the combination of morphological, molecular, epidemiological, pathogenicity, symptom, and micrograph data. If realized, this would have a direct impact on many future applications related to various topics, including quarantines, risk analysis, biodiversity studies, and monitoring of fungicide resistance, among others.
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Affiliation(s)
- Juan Manuel Tovar-Pedraza
- Laboratorio de Fitopatología, Centro de Investigación en Alimentación y Desarrollo, Coordinación Culiacán, Culiacán 80110, Sinaloa, Mexico;
| | - Alma Rosa Solano-Báez
- Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional, Yautepec 62731, Morelos, Mexico; (A.R.S.-B.); (M.A.H.-H.); (K.J.J.-C.)
| | - Santos Gerardo Leyva-Mir
- Departamento de Parasitología Agrícola, Universidad Autónoma Chapingo, Texcoco 56230, Estado de México, Mexico; (S.G.L.-M.); (B.T.-B.); (M.C.-T.)
| | - Bertha Tlapal-Bolaños
- Departamento de Parasitología Agrícola, Universidad Autónoma Chapingo, Texcoco 56230, Estado de México, Mexico; (S.G.L.-M.); (B.T.-B.); (M.C.-T.)
| | - Moisés Camacho-Tapia
- Departamento de Parasitología Agrícola, Universidad Autónoma Chapingo, Texcoco 56230, Estado de México, Mexico; (S.G.L.-M.); (B.T.-B.); (M.C.-T.)
| | - Elizabeth García-León
- Campo Experimental Valle del Fuerte, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Guasave 81110, Sinaloa, Mexico;
| | - Victoria Ayala-Escobar
- Fitopatología, Colegio de Postgraduados, Campus Montecillo, Texcoco 56230, Estado de México, Mexico; (V.A.-E.); (C.N.-D.)
| | - Cristian Nava-Díaz
- Fitopatología, Colegio de Postgraduados, Campus Montecillo, Texcoco 56230, Estado de México, Mexico; (V.A.-E.); (C.N.-D.)
| | - Andrés Quezada-Salinas
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Tecámac 55740, Estado de México, Mexico;
| | - Víctor Santiago-Santiago
- Departamento de Agronomía, Instituto Tecnológico del Altiplano de Tlaxcala, San Diego Xocoyucán 90122, Tlaxcala, Mexico;
| | - Hugo Beltrán-Peña
- Departamento de Ciencias Biológicas, Unidad Los Mochis, Universidad Autónoma de Occidente, Los Mochis 81223, Sinaloa, Mexico;
| | - Maria Alondra Hernandez-Hernandez
- Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional, Yautepec 62731, Morelos, Mexico; (A.R.S.-B.); (M.A.H.-H.); (K.J.J.-C.)
| | - Karla Jenifer Juárez-Cruz
- Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional, Yautepec 62731, Morelos, Mexico; (A.R.S.-B.); (M.A.H.-H.); (K.J.J.-C.)
| | - Guillermo Márquez-Licona
- Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional, Yautepec 62731, Morelos, Mexico; (A.R.S.-B.); (M.A.H.-H.); (K.J.J.-C.)
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Chaves-González LE, Jaikel-Víquez D, Lozada-Alvarado S, Granados-Chinchilla F. Unveiling the fungal color palette: pigment analysis of Fusarium solani species complex and Curvularia verruculosa clinical isolates. Can J Microbiol 2024; 70:135-149. [PMID: 38232349 DOI: 10.1139/cjm-2023-0181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Fungal species in the Nectriaceae, such as Fusarium spp. (Hypocreales: Nectriaceae), are etiologic agents of hyalohyphomycosis capable of producing violaceous or yellowish pigments under certain conditions, while Curvularia spp. (Pleosporales: Pleosporaceae) are agents of phaeohyphomycosis and typically produce melanin in their cell walls. In nectriaceous and pleosporaceous fungi, these pigments are mainly constituted by polyketides (e.g., azaphilones, naphthoquinones, and hydroxyanthraquinones). Considering the importance of pigments synthesized by these genera, this work focused on the selective extraction of pigments produced by eight Fusarium solani species complex and one Curvularia verruculosa isolate recovered from dermatomycosis specimens, their separation, purification, and posterior chemical analysis. The pigments were characterized through spectral and acid-base analysis, and their maximum production time was determined. Moreover, spectral identification of isolates was carried out to approach the taxonomic specificity of pigment production. Herein we describe the isolation and characterization of three acidic pigments, yellowish and pinkish azaphilones (i.e., coaherin A and sclerotiorin), and a purplish xanthone, reported for the first time in the Nectriaceae and Pleosporaceae, which appear to be synthesized in a species-independent manner, in the case of fusaria.
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Affiliation(s)
- Luis Enrique Chaves-González
- Sección de Micología Médica, Facultad de Microbiología, Sede Central, Ciudad Universitaria Rodrigo Facio, 11501-2060, Universidad de Costa Rica, San José, Costa Rica
- Centro de Investigación en Enfermedades Tropicales, Sede Central, Ciudad Universitaria Rodrigo Facio, 11501-2060, Universidad de Costa Rica, San José, Costa Rica
| | - Daniela Jaikel-Víquez
- Sección de Micología Médica, Facultad de Microbiología, Sede Central, Ciudad Universitaria Rodrigo Facio, 11501-2060, Universidad de Costa Rica, San José, Costa Rica
- Centro de Investigación en Enfermedades Tropicales, Sede Central, Ciudad Universitaria Rodrigo Facio, 11501-2060, Universidad de Costa Rica, San José, Costa Rica
| | - Stefany Lozada-Alvarado
- Laboratorio Clínico y Banco de Sangre, Hospital del Trauma, Sede Central, Ciudad Universitaria Rodrigo Facio, 11501-2060, Universidad de Costa Rica, San José, Costa Rica
| | - Fabio Granados-Chinchilla
- Centro de Investigación en Enfermedades Tropicales, Sede Central, Ciudad Universitaria Rodrigo Facio, 11501-2060, Universidad de Costa Rica, San José, Costa Rica
- Escuela de Química, Facultad de Ciencias Básicas, Sede Central, Ciudad Universitaria Rodrigo Facio, 11501-2060, Universidad de Costa Rica, San José, Costa Rica
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Bertazzoli G, Nerva L, Chitarra W, Fracchetti F, Campedelli I, Moffa L, Sandrini M, Nardi T. A polyphasic molecular approach to characterize a collection of grapevine endophytic bacteria with bioprotective potential. J Appl Microbiol 2024; 135:lxae050. [PMID: 38419289 DOI: 10.1093/jambio/lxae050] [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: 08/17/2023] [Revised: 02/02/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024]
Abstract
AIMS The work presented here was conducted to characterize the biodiversity of a collection of bacterial isolates, mainly wood endophytes, as part of a research project focused on exploring their bioprotective potential for postharvest biological control of fruits. METHODS AND RESULTS This work was the basis for the development of a tailored method combining 16S rDNA sequencing and Rep-PCR to differentiate the isolates and identify them to genus level or below. More than one hundred isolates obtained from wood and roots of different grapevine genotypes were cultured on appropriate growth media and then subjected to the specified multistep molecular identification. CONCLUSIONS We have obtained good dereplication for grapevine-endophytic bacteria, together with reliable genetic identification. Both are essential prerequisites to properly characterize a biome bank and, at the same time, beneficial prerequisites to subsequently perform a correct bioprotection assessment.
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Affiliation(s)
- Giulia Bertazzoli
- CREA - Council for Agricultural Research and Economics, Research Centre for Viticulture and Enology, Conegliano (TV) 31015, Italy
- Microbion Srl, San Giovanni Lupatoto (VR) 37057, Italy
| | - Luca Nerva
- CREA - Council for Agricultural Research and Economics, Research Centre for Viticulture and Enology, Conegliano (TV) 31015, Italy
- CNR, Institute for Sustainable Plant Protection, Torino 10135, Italy
| | - Walter Chitarra
- CREA - Council for Agricultural Research and Economics, Research Centre for Viticulture and Enology, Conegliano (TV) 31015, Italy
- CNR, Institute for Sustainable Plant Protection, Torino 10135, Italy
| | | | | | - Loredana Moffa
- CREA - Council for Agricultural Research and Economics, Research Centre for Viticulture and Enology, Conegliano (TV) 31015, Italy
| | - Marco Sandrini
- CREA - Council for Agricultural Research and Economics, Research Centre for Viticulture and Enology, Conegliano (TV) 31015, Italy
| | - Tiziana Nardi
- CREA - Council for Agricultural Research and Economics, Research Centre for Viticulture and Enology, Conegliano (TV) 31015, Italy
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Anand U, Vaishnav A, Sharma SK, Sahu J, Ahmad S, Sunita K, Suresh S, Dey A, Bontempi E, Singh AK, Proćków J, Shukla AK. Current advances and research prospects for agricultural and industrial uses of microbial strains available in world collections. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156641. [PMID: 35700781 DOI: 10.1016/j.scitotenv.2022.156641] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Microorganisms are an important component of the ecosystem and have an enormous impact on human lives. Moreover, microorganisms are considered to have desirable effects on other co-existing species in a variety of habitats, such as agriculture and industries. In this way, they also have enormous environmental applications. Hence, collections of microorganisms with specific traits are a crucial step in developing new technologies to harness the microbial potential. Microbial culture collections (MCCs) are a repository for the preservation of a large variety of microbial species distributed throughout the world. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are vital for the safeguarding and circulation of biological resources, as well as for the progress of the life sciences. Ex situ conservation of microorganisms tagged with specific traits in the collections is the crucial step in developing new technologies to harness their potential. Type strains are mainly used in taxonomic study, whereas reference strains are used for agricultural, biotechnological, pharmaceutical research and commercial work. Despite the tremendous potential in microbiological research, little effort has been made in the true sense to harness the potential of conserved microorganisms. This review highlights (1) the importance of available global microbial collections for man and (2) the use of these resources in different research and applications in agriculture, biotechnology, and industry. In addition, an extensive literature survey was carried out on preserved microorganisms from different collection centres using the Web of Science (WoS) and SCOPUS. This review also emphasizes knowledge gaps and future perspectives. Finally, this study provides a critical analysis of the current and future roles of microorganisms available in culture collections for different sustainable agricultural and industrial applications. This work highlights target-specific potential microbial strains that have multiple important metabolic and genetic traits for future research and use.
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Affiliation(s)
- Uttpal Anand
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Anukool Vaishnav
- Department of Biotechnology, Institute of Applied Sciences & Humanities, GLA University, Mathura, Uttar Pradesh 281406, India; Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland; Plant-Soil Interaction Group, Agroscope (Reckenholz), Reckenholzstrasse 191, 8046 Zürich, Switzerland
| | - Sushil K Sharma
- National Agriculturally Important Microbial Culture Collection (NAIMCC), ICAR-National Bureau of Agriculturally Important Microorganisms (ICAR-NBAIM), Mau 275 103, Uttar Pradesh, India.
| | - Jagajjit Sahu
- GyanArras Academy, Gothapatna, Malipada, Bhubaneswar, Odisha 751029, India
| | - Sarfaraz Ahmad
- Department of Botany, Jai Prakash University, Saran, Chhapra 841301, Bihar, India
| | - Kumari Sunita
- Department of Botany, Faculty of Science, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh 273009, India
| | - S Suresh
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal 462 003, Madhya Pradesh, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, West Bengal, India
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, Department of Mechanical and Industrial Engineering, University of Brescia, Via Branze, 38, 25123 Brescia, Italy
| | - Amit Kishore Singh
- Department of Botany, Bhagalpur National College, (A Constituent unit of Tilka Manjhi Bhagalpur University), Bhagalpur 812007, Bihar, India
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Kożuchowska 5b, 51-631 Wrocław, Poland.
| | - Awadhesh Kumar Shukla
- Department of Botany, K.S. Saket P.G. College, Ayodhya (affiliated to Dr. Rammanohar Lohia Avadh University, Ayodhya) 224123, Uttar Pradesh, India.
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Hosseini H, Al-Jabri HM, Moheimani NR, Siddiqui SA, Saadaoui I. Marine microbial bioprospecting: Exploitation of marine biodiversity towards biotechnological applications-a review. J Basic Microbiol 2022; 62:1030-1043. [PMID: 35467037 DOI: 10.1002/jobm.202100504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/14/2022] [Accepted: 04/07/2022] [Indexed: 11/09/2022]
Abstract
The increase in the human population causes an increase in the demand for nutritional supplies and energy resources. Thus, the novel, natural, and renewable resources became of great interest. Here comes the optimistic role of bioprospecting as a promising tool to isolate novel and interesting molecules and microorganisms from the marine environment as alternatives to the existing resources. Bioprospecting of marine metabolites and microorganisms with high biotechnological potentials has gained wide interest due to the variability and richness of the marine environment. Indeed, the existence of extreme conditions that increases the adaptability of marine organisms, especially planktons, allow the presence of interesting biological species that are able to produce novel compounds with multiple health benefits and high economical value. This review aims to provide a comprehensive overview of marine microbial bioprospecting as a growing field of interest. It emphasizes functional bioprospecting that facilitates the discovery of interesting metabolites. Marine bioprospecting was also discussed from a legal aspect for the first time, focusing on the shortcomings of international law. We also summarized the challenges facing bioprospecting in the marine environment including economic feasibility issues.
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Affiliation(s)
- Hoda Hosseini
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Hareb M Al-Jabri
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar.,Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Navid R Moheimani
- Algae R&D Centre, Harry Buttler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Simil A Siddiqui
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Imen Saadaoui
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar.,Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
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Assessing effectiveness of Komagataeibacter strains for producing surface-microstructured cellulose via guided assembly-based biolithography. Sci Rep 2021; 11:19311. [PMID: 34588564 PMCID: PMC8481549 DOI: 10.1038/s41598-021-98705-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/07/2021] [Indexed: 02/08/2023] Open
Abstract
In this study, a medical device made of surface microstructured bacterial cellulose was produced using cellulose-producing acetic acid bacteria wild-type strains in combination with guided assembly-based biolithography. The medical device aims at interfering with the cell's focal adhesion establishment and maturation around implantable devices placed in soft tissues by the symmetrical array on its surface. A total of 25 Komagataeibacter strains was evaluated over a three-step selection. In the first step, the ability of strains to produce a suitable bacterial cellulose layer with high production yield was examined, then nine strains, with a uniform and smooth layer of bacterial cellulose, were cultured in a custom-made silicone bioreactor and finally the characteristics of the symmetrical array of topographic features on the surface were analysed. Selected strains showed high inter and intra species variability in bacterial cellulose production. The devices obtained by K2G30, K1G4, DSM 46590 (Komagataeibacter xylinus), K2A8 (Komagataeibacter sp.) and DSM 15973T (Komagataeibacter sucrofermentas) strains were pouched-formed with hexagonal surface pattern required for reducing the formation of fibrotic tissue around devices, once they are implanted in soft tissues. Our findings revealed the effectiveness of the selected Komagataeibacter wild-type strains in producing surface microstructured bacterial cellulose pouches for making biomedical devices.
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Cocuzza CE, Martinelli M, Perdoni F, Giubbi C, Vinetti MEA, Calaresu E, Frugoni S, Scaturro M, Ricci ML, Musumeci R. Antibiotic Susceptibility of Environmental Legionella pneumophila Strains Isolated in Northern Italy. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18179352. [PMID: 34501942 PMCID: PMC8431511 DOI: 10.3390/ijerph18179352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 11/17/2022]
Abstract
Legionella pneumophila is ubiquitous in aquatic environments and responsible for severe pneumonia in humans through inhalation of aerosol containing Legionella spp. Macrolides and fluoroquinolones are frequently used antimicrobials, but treatment failures are increasingly being reported. As susceptibility testing is not routinely performed, this study aimed to determine the minimum inhibitory concentrations (MICs) on 58 environmental Legionella pneumophila strains (24 of serogroup 1 and 34 of non-serogroup 1) isolated in Northern Italy. MICs of azithromycin, erythromycin, ciprofloxacin, levofloxacin, and rifampicin were determined by the microdilution method using buffered yeast extract broth supplemented with α-ketoglutarate (BYEα). Seventy-five percent of Legionella pneumophila isolates showed MIC values below the tentative highest MICs indicated by the European Committee on Antimicrobial Susceptibility Testing (EUCAST); rifampicin was the most active agent with MIC90 values below 0.008 mg/L. Interestingly, one isolate was tested and found to be PCR-positive for the azithromycin LpeAB active efflux system, further confirmed by the reserpine/resazurin microtiter assay. In conclusion, this study has provided additional susceptibility data for environmental Legionella pneumophila isolates from Northern Italy demonstrating, in general, low MICs values for the tested antimicrobials, although one strain tested was shown to possess the LpeAB resistance determinant, indicating that future surveillance studies are warranted.
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Affiliation(s)
- Clementina Elvezia Cocuzza
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (M.M.); (F.P.); (C.G.); (M.E.A.V.); (E.C.); (S.F.); (R.M.)
- MicroMiB Biorepository, University of Milano-Bicocca, Associated Member of the JRU MIRRI-IT, Via Cadore, 20900 Monza, Italy
- Correspondence: ; Tel.: +39-335-627-2830
| | - Marianna Martinelli
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (M.M.); (F.P.); (C.G.); (M.E.A.V.); (E.C.); (S.F.); (R.M.)
- MicroMiB Biorepository, University of Milano-Bicocca, Associated Member of the JRU MIRRI-IT, Via Cadore, 20900 Monza, Italy
| | - Federica Perdoni
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (M.M.); (F.P.); (C.G.); (M.E.A.V.); (E.C.); (S.F.); (R.M.)
- MicroMiB Biorepository, University of Milano-Bicocca, Associated Member of the JRU MIRRI-IT, Via Cadore, 20900 Monza, Italy
| | - Chiara Giubbi
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (M.M.); (F.P.); (C.G.); (M.E.A.V.); (E.C.); (S.F.); (R.M.)
| | - Maria Erica Alessandra Vinetti
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (M.M.); (F.P.); (C.G.); (M.E.A.V.); (E.C.); (S.F.); (R.M.)
| | - Enrico Calaresu
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (M.M.); (F.P.); (C.G.); (M.E.A.V.); (E.C.); (S.F.); (R.M.)
| | - Sergio Frugoni
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (M.M.); (F.P.); (C.G.); (M.E.A.V.); (E.C.); (S.F.); (R.M.)
| | - Maria Scaturro
- National Reference Laboratory for Legionella, Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Roma, Italy; (M.S.); (M.L.R.)
| | - Maria Luisa Ricci
- National Reference Laboratory for Legionella, Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Roma, Italy; (M.S.); (M.L.R.)
| | - Rosario Musumeci
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (M.M.); (F.P.); (C.G.); (M.E.A.V.); (E.C.); (S.F.); (R.M.)
- MicroMiB Biorepository, University of Milano-Bicocca, Associated Member of the JRU MIRRI-IT, Via Cadore, 20900 Monza, Italy
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9
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Ijoma GN, Heri SM, Matambo TS, Tekere M. Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi. J Fungi (Basel) 2021; 7:700. [PMID: 34575737 PMCID: PMC8464691 DOI: 10.3390/jof7090700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 12/14/2022] Open
Abstract
Identifying and adopting industrial applications for proteins and enzymes derived from fungi strains have been at the focal point of several studies in recent times. To facilitate such studies, it is necessary that advancements and innovation in mycological and molecular characterisation are concomitant. This review aims to provide a detailed overview of the necessary steps employed in both qualitative and quantitative research using the omics technologies that are pertinent to fungi characterisation. This stems from the understanding that data provided from the functional characterisation of fungi and their metabolites is important towards the techno-economic feasibility of large-scale production of biological products. The review further describes how the functional gaps left by genomics, internal transcribe spacer (ITS) regions are addressed by transcriptomics and the various techniques and platforms utilised, including quantitive reverse transcription polymerase chain reaction (RT-qPCR), hybridisation techniques, and RNA-seq, and the insights such data provide on the effect of environmental changes on fungal enzyme production from an expressional standpoint. The review also offers information on the many available bioinformatics tools of analysis necessary for the analysis of the overwhelming data synonymous with the omics approach to fungal characterisation.
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Affiliation(s)
- Grace N. Ijoma
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa; (S.M.H.); (T.S.M.)
| | - Sylvie M. Heri
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa; (S.M.H.); (T.S.M.)
| | - Tonderayi S. Matambo
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa; (S.M.H.); (T.S.M.)
| | - Memory Tekere
- Department of Environmental Science, College of Agricultural and Environmental Science, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa;
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10
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Regassa H, Bose D, Mukherjee A. Review of Microorganisms and Their Enzymatic Products for Industrial Bioprocesses. Ind Biotechnol (New Rochelle N Y) 2021. [DOI: 10.1089/ind.2021.0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Hailemeleak Regassa
- Faculty of Applied Sciences & Biotechnology, Shoolini University of Biotechnology & Management Sciences, Solan, Himachal Pradesh, India
| | - Debajyoti Bose
- Faculty of Applied Sciences & Biotechnology, Shoolini University of Biotechnology & Management Sciences, Solan, Himachal Pradesh, India
| | - Alivia Mukherjee
- Department of Chemical and Biological Engineering, University of Saskatchewan, Saskatoon, SK, Canada
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11
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Autochthonous Natural Starter Cultures: A Chance to Preserve Biodiversity and Quality of Pecorino Romano PDO Cheese. SUSTAINABILITY 2021. [DOI: 10.3390/su13158214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
During Pecorino Romano PDO cheese production, scotta (residual whey from ricotta cheese manufacturing) or siero (whey) can be integrated with autochthonous starters, natural and composed of an indefinite number of species and strains, or commercial selected starters to obtain scotta/siero-innesto. In this study, three biodiverse autochthonous natural starter cultures (SR30, SR56, and SR63) belonging to the Agris Sardegna BNSS microbial collection, composed of different strains belonging to the species Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, Enterococcus faecium, and Limosilactobacillus reuteri were lyophilized and combined into two starter mixes (A and B). The scotta/siero-innesto and the Pecorino Romano obtained using natural starters were compared with those obtained using commercial selected starters during three seasons of the cheesemaking campaign. Different pH and microbial compositions for the scotta/siero-innesto obtained using natural or commercial starters were found, attributable to their different biodiversity. The six-month-ripened cheese microbiota was influenced mostly by the season of cheesemaking, whereas physico-chemical and sensory analyses did not highlight differences among the products obtained. In general, no effect attributable to the type of scotta/siero-innesto used was observed, allowing the conclusion that natural starter cultures can be used also in industrial-scale production, ensuring high stability in the technological performances and preserving the microbial, chemical, and sensory characteristics of Pecorino Romano PDO cheese.
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12
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Design of a New Fermented Beverage from Medicinal Plants and Organic Sugarcane Molasses via Lactic Fermentation. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11136089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Functional beverages obtained using medicinal plants and fermented with lactic acid bacteria are gaining much interest from the scientific community, driven by the growing demand for food and beverages with beneficial properties. In this work, three different batches of medicinal plants and organic sugarcane molasses, named FB-lc, FB-sp and FB-lcsp, were prepared and fermented by using Lactobacillus acidophilus ATCC 43121, Bifidobacterium breve B632 and a mix of both strains’ culture, respectively. The three fermented beverages revealed a high level of polyphenols (expressed as gallic acid equivalent), ranging from 182.50 to 315.62 µg/mL. The highest content of flavonoids (152.13 µg quercetin equivalent/mL) and tannins (93.602 µg catechin equivalent/mL) was detected in FB-lcsp trial. The IR spectroscopy analysis showed a decrease in sugar (pyranose forms, D-glucopyranose and rhamnosides). In addition, the aromatic compounds of the fermented beverages, detected by GC-MS headspace analysis, showed twenty-four interesting volatile compounds, which could give positive aroma attributes to the flavor of the beverages. The highest antioxidant activity was observed in the beverage obtained by the mix culture strains. Accordingly, the production of these beverages can be further investigated for considering their well-being effects on human health.
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13
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Chessa L, Paba A, Daga E, Dupré I, Comunian R. Biodiversity and Safety Assessment of Half-Century Preserved Natural Starter Cultures for Pecorino Romano PDO Cheese. Microorganisms 2021; 9:1363. [PMID: 34201694 PMCID: PMC8305336 DOI: 10.3390/microorganisms9071363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/22/2022] Open
Abstract
The use of biodiverse autochthonous natural starter cultures to produce typical and PDO cheeses contributes to establishing a link between products and territory of production, which commercial starters, constituted by few species and strains, are not able to. The purpose of this work was the assessment of biodiversity, at strain level, and safety of natural scotta-innesto cultures whose use is mandatory for the Pecorino Romano PDO cheese manufacturing, according to its product specification. The biodiversity of three scotta-innesto, collected in the 1960s and preserved in lyophilised form, was assessed by molecular biotyping using both PFGE and (GTG)5 rep-PCR profiling on 209 isolates belonging to Streptococcus thermophilus (30), Lactobacillus delbrueckii subsp. lactis (72), Enterococcus faecium (87), and Limosilactobacillus reuteri (20), revealing high biodiversity, at the strain level, in the cultures. The cultures' safety was proved through a new approach assessing phenotypic and molecular antibiotic resistance of the cultures in toto, instead of single strains, while the safety of Enterococcus faecium isolates was investigated according to EFSA guidelines. The use of natural biodiverse cultures for the production of microbial starters for typical and PDO cheeses, such as Pecorino Romano, could be an opportunity for recovering the cheese microbiota biodiversity lost during years of commercial starters use.
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Affiliation(s)
- Luigi Chessa
- Agris Sardegna, Agenzia Regionale per la Ricerca in Agricoltura, Associated Member of the JRU MIRRI-IT, Loc. Bonassai, SS291 km 18.600, 07100 Sassari, Italy; (A.P.); (E.D.); (I.D.); (R.C.)
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14
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Effectiveness of 0.66% Povidone-Iodine Eye Drops on Ocular Surface Flora before Cataract Surgery: A Nationwide Microbiological Study. J Clin Med 2021; 10:jcm10102198. [PMID: 34069600 PMCID: PMC8160713 DOI: 10.3390/jcm10102198] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/10/2021] [Accepted: 05/14/2021] [Indexed: 01/04/2023] Open
Abstract
A multicenter, nonrandomized, prospective, controlled study was conducted to evaluate, as perioperative prophylactic treatment, the anti-infective effectiveness of 0.66% povidone-iodine eye drops (IODIM®) against the bacterial flora of the conjunctival surface of patients who undergo cataract surgery. Eye drops containing 0.66% povidone-iodine were applied to the eye undergoing cataract surgery; the untreated contralateral eye was used as control. One hundred and twenty patients set to receive unilateral cataract surgery were enrolled in 5 Italian Ophthalmology Centers and pretreated for three days with 0.66% povidone-iodine eye drops. The contralateral eye, used as control, was left untreated. Conjunctival swabs of both eyes were collected at the baseline visit and after three days of treatment, just before the cataract surgery. A qualitative and quantitative microbiological analysis of bacterial presence was evaluated by means of bacterial culture, followed by identification. Methicillin resistance determination was also performed on staphylococci isolates. Bacterial load before and after treatment of the eye candidate for cataract surgery was evaluated and compared to the untreated eye. A reduction or no regrowth on the culture media of the bacterial load was observed in 100% of the study subjects. A great heterogenicity of bacterial species was found. The 0.66% povidone-iodine eye drops, used for three days prior to cataract surgery, were effective in reducing the conjunctival bacterial load. The 0.66% povidone-iodine eye drops (IODIM®) might represent a valid perioperative prophylactic antiseptic adjuvant treatment to protect the ocular surface from microbial contamination in preparation of the surgical procedure.
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15
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Yeasts and Lactic Acid Bacteria for Panettone Production: An Assessment of Candidate Strains. Microorganisms 2021; 9:microorganisms9051093. [PMID: 34069676 PMCID: PMC8160612 DOI: 10.3390/microorganisms9051093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 12/15/2022] Open
Abstract
The recovery of yeasts and lactic acid bacteria (LAB) involved in sourdough fermentation is the first step in the selection of starters with suitable technological aptitude and capable of producing desired aromas and/or aromatic precursors. In this work, two sourdoughs samples (MA and MB) and the derived doughs (samples A and B) were collected from a bakery during artisanal Panettone manufacture. Yeasts and bacteria were isolated at different fermentation steps on selective agar media. A total of 77 isolates were obtained and characterized. Representative strains of yeasts and LAB were identified by sequencing the D1/D2 domain of the 26S rRNA and the 16S rRNA genes, respectively. Moreover, the volatile organic compounds (VOCs) produced in the collected samples were detected and correlated to the species found in the same samples. The results highlighted the occurrence of Kazachstania humilis in both samples A and B, while Saccharomyces cerevisiae strains were detected only in samples B. Among LAB, Fructilactobacillus sanfranciscensis was the main species detected in both sourdoughs. Furthermore, strains belonging to the species Lactiplantibacillus plantarum, Furfurilactobacillus rossiae, Lactobacillus parabuchneri, Leuconostoc citreum, and Leuconostoc mesenteroides were assessed in the dough samples.
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16
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Functional and Healthy Features of Conventional and Non-Conventional Sourdoughs. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11083694] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sourdough is a composite ecosystem largely characterized by yeasts and lactic acid bacteria which are the main players in the fermentation process. The specific strains involved are influenced by several factors including the chemical and enzyme composition of the flour and the sourdough production technology. For many decades the scientific community has explored the microbiological, biochemical, technological and nutritional potential of sourdoughs. Traditionally, sourdoughs have been used to improve the organoleptic properties, texture, digestibility, palatability, and safety of bread and other kinds of baked products. Recently, novel sourdough-based biotechnological applications have been proposed to meet the demand of consumers for healthier and more natural food and offer new inputs for the food industry. Many researchers have focused on the beneficial effects of specific enzymatic activities or compounds, such as exopolysaccharides, with both technological and functional roles. Additionally, many studies have explored the ability of sourdough lactic acid bacteria to produce antifungal compounds for use as bio-preservatives. This review provides an overview of the fundamental features of sourdoughs and their exploitation to develop high value-added products with beneficial microorganisms and/or their metabolites, which can positively impact human health.
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17
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Microbial Resources, Fermentation and Reduction of Negative Externalities in Food Systems: Patterns toward Sustainability and Resilience. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7020054] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
One of the main targets of sustainable development is the reduction of environmental, social, and economic negative externalities associated with the production of foods and beverages. Those externalities occur at different stages of food chains, from the farm to the fork, with deleterious impacts to different extents. Increasing evidence testifies to the potential of microbial-based solutions and fermentative processes as mitigating strategies to reduce negative externalities in food systems. In several cases, innovative solutions might find in situ applications from the farm to the fork, including advances in food matrices by means of tailored fermentative processes. This viewpoint recalls the attention on microbial biotechnologies as a field of bioeconomy and of ‘green’ innovations to improve sustainability and resilience of agri-food systems alleviating environmental, economic, and social undesired externalities. We argue that food scientists could systematically consider the potential of microbes as ‘mitigating agents’ in all research and development activities dealing with fermentation and microbial-based biotechnologies in the agri-food sector. This aims to conciliate process and product innovations with a development respectful of future generations’ needs and with the aptitude of the systems to overcome global challenges.
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18
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Haghighi H, Gullo M, La China S, Pfeifer F, Siesler HW, Licciardello F, Pulvirenti A. Characterization of bio-nanocomposite films based on gelatin/polyvinyl alcohol blend reinforced with bacterial cellulose nanowhiskers for food packaging applications. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2020.106454] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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19
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Kombucha Tea as a Reservoir of Cellulose Producing Bacteria: Assessing Diversity among Komagataeibacter Isolates. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11041595] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bacterial cellulose (BC) is receiving a great deal of attention due to its unique properties such as high purity, water retention capacity, high mechanical strength, and biocompatibility. However, the production of BC has been limited because of the associated high costs and low productivity. In light of this, the isolation of new BC producing bacteria and the selection of highly productive strains has become a prominent issue. Kombucha tea is a fermented beverage in which the bacteria fraction of the microbial community is composed mostly of strains belonging to the genus Komagataeibacter. In this study, Kombucha tea production trials were performed starting from a previous batch, and bacterial isolation was conducted along cultivation time. From the whole microbial pool, 46 isolates were tested for their ability to produce BC. The obtained BC yield ranged from 0.59 g/L, for the isolate K2G36, to 23 g/L for K2G30—which used as the reference strain. The genetic intraspecific diversity of the 46 isolates was investigated using two repetitive-sequence-based PCR typing methods: the enterobacterial repetitive intergenic consensus (ERIC) elements and the (GTG)5 sequences, respectively. The results obtained using the two different approaches revealed the suitability of the fingerprint techniques, showing a discrimination power, calculated as the D index, of 0.94 for (GTG)5 rep-PCR and 0.95 for ERIC rep-PCR. In order to improve the sensitivity of the applied method, a combined model for the two genotyping experiments was performed, allowing for the ability to discriminate among strains.
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20
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Borisova AL, Pokrovskaya MS, Meshkov AN, Metelskaya VA, Shatalova AM, Drapkina OM. ISO 20387 biobanking standard. Analysis of requirements and experience of implementation. Klin Lab Diagn 2021; 65:587-592. [PMID: 33245646 DOI: 10.18821/0869-2084-2020-65-9-587-592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Currently one of the most important problems facing biobanking specialists is the standardization of biobanks operation. Close attention is paid to this issue by international biobanking organizations, such as ISBER and BBMRI-ERIC, which develop regulatory documentation in this area. The article provides examples of standardization tools - implementation of the ISO 9001 quality standard and ISBER Best Practices. General information about the development, scope, and structure of the ISO 20387 standard is provided. The standard does not provide ready-made solutions and does not contain specific requirements for storage temperature or biosamples processing in biobanks, allowing each biobank to adapt its own management system to existing conditions and needs. The standard contains requirements for both the organization of the biobanking and the supporting processes - personnel competence; requirements for biological safety; infrastructure management, including equipment used by the biobank, environmental parameters that affect the storage of biomaterial. The standard contains requirements for the quality management system of biobank, as a necessary element of the organization of any biorepository. At the initiative of the Russian National Association of biobanks and biobanking specialists (NASBIO), development of the Russian standard GOST R ISO 20387 «Biotechnology. Collection and storage of biological samples in biobanks. General requirements» is included in the plan of the National Standardization Program for 2020 by order of Rosstandart No. 2612 of 11/01/2019. Implementing quality standards is a long and painstaking process that requires the involvement of all employees and certain resources. However, the effectiveness of strict compliance exceeds the cost of developing, implementing and maintaining management systems, as it significantly increases the confidence of researchers in the work of biobanks, guarantees high quality of biospecimens and associated data, and creates opportunities for cooperation, both at the national and international level, based on the application of common quality standards in the work.
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Affiliation(s)
- A L Borisova
- FSI National Medical Research Center for Therapy and Preventive Medicine of the Ministry of Healthcare of the Russian Federation
| | - M S Pokrovskaya
- FSI National Medical Research Center for Therapy and Preventive Medicine of the Ministry of Healthcare of the Russian Federation
| | - A N Meshkov
- FSI National Medical Research Center for Therapy and Preventive Medicine of the Ministry of Healthcare of the Russian Federation
| | - V A Metelskaya
- FSI National Medical Research Center for Therapy and Preventive Medicine of the Ministry of Healthcare of the Russian Federation
| | - A M Shatalova
- FSI National Medical Research Center for Therapy and Preventive Medicine of the Ministry of Healthcare of the Russian Federation
| | - O M Drapkina
- FSI National Medical Research Center for Therapy and Preventive Medicine of the Ministry of Healthcare of the Russian Federation
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21
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Preservation, Characterization and Exploitation of Microbial Biodiversity of Agri-Food and Environmental Interest. Microorganisms 2020; 8:microorganisms8121938. [PMID: 33297349 PMCID: PMC7762223 DOI: 10.3390/microorganisms8121938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 11/23/2022] Open
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22
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Selection of Wine Saccharomyces cerevisiae Strains and Their Screening for the Adsorption Activity of Pigments, Phenolics and Ochratoxin A. FERMENTATION-BASEL 2020. [DOI: 10.3390/fermentation6030080] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ochratoxin A is a dangerous mycotoxin present in wines and is considered the principal safety hazard in the winemaking process. Several authors have investigated the ochratoxin A adsorption ability of Saccharomyces cerevisiae yeasts, and specifically selected strains for this desired trait. In the present work, a huge selection of wine yeasts was done starting from Portuguese, Spanish and Italian fermenting musts of different cultivars. Firstly, 150 isolates were collected, and 99 non-redundant S. cerevisiae strains were identified. Then, the strains were screened following a multi-step approach in order to select those having primary oenological traits, mainly (a) good fermentation performance, (b) low production of H2S and (c) low production of acetic acid. The preselected strains were further investigated for their adsorption activity of pigments, phenolic compounds and ochratoxin A. Finally, 10 strains showed the desired features. The goal of this work was to select the strains capable of absorbing ochratoxin A but not pigments and phenolic compounds in order to improve and valorise both the quality and safety of red wines. The selected strains are considered good candidates for wine starters, moreover, they can be exploited to obtain a further enhancement of the specific adsorption/non-adsorption activity by applying a yeast breeding approach.
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23
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Vinegar production from Citrus bergamia by-products and preservation of bioactive compounds. Eur Food Res Technol 2020. [DOI: 10.1007/s00217-020-03549-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Significant advancements in biotechnology have resulted in the development of numerous fundamental bioprocesses, which have consolidated research and development and industrial progress in the field. These bioprocesses are used in medical therapies, diagnostic and immunization procedures, agriculture, food production, biofuel production, and environmental solutions (to address water-, soil-, and air-related problems), among other areas. The present study is a first approach toward the identification of scientific and technological bioprocess trajectories within the framework of sustainability. The method included a literature search (Scopus), a patent search (Patentscope), and a network analysis for the period from 2010 to 2019. Our results highlight the main technological sectors, countries, institutions, and academic publications that carry out work or publish literature related to sustainability and bioprocesses. The network analysis allowed for the identification of thematic clusters associated with sustainability and bioprocesses, revealing different related scientific topics. Our conclusions confirm that biotechnology is firmly positioned as an emerging knowledge area. Its dynamics, development, and outcomes during the study period reflect a substantial number of studies and technologies focused on the creation of knowledge aimed at improving economic development, environmental protection, and social welfare.
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Abstract
Industrial biotechnology is a continuously expanding field focused on the application of microorganisms to produce chemicals using renewable sources as substrates. Currently, an increasing interest in new versatile processes, able to utilize a variety of substrates to obtain diverse products, can be observed. A robust microbial strain is critical in the creation of such processes. Lactic acid bacteria (LAB) are used to produce a wide variety of chemicals with high commercial interest. Lactic acid (LA) is the most predominant industrial product obtained from LAB fermentations, and its production is forecasted to rise as the result of the increasing demand of polylactic acid. Hence, the creation of new ways to revalorize LA production processes is of high interest and could further enhance its economic value. Therefore, this review explores some co-products of LA fermentations, derived from LAB, with special focus on bacteriocins, lipoteichoic acid, and probiotics. Finally, a multi-product process involving LA and the other compounds of interest is proposed.
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