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Gerlicz W, Sypka M, Jodłowska I, Białkowska AM. Isolation, Selection, and Identification of Keratinolytic Bacteria for Green Management of Keratin Waste. Molecules 2024; 29:3380. [PMID: 39064958 PMCID: PMC11280386 DOI: 10.3390/molecules29143380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/11/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
The volume of difficult-to-process keratin waste is increasing as a result of rising global meat production. If not properly managed, this waste can contribute to environmental pollution and pose a threat to human and animal welfare. An interesting and more sustainable alternative is therefore the bioconversion of keratin using microorganisms and their enzymes. This work aimed to isolate bacteria from soil samples and zoonotic keratins and to evaluate their enzymatic capacity to degrade α- and β-keratin wastes. A total of 113 bacterial strains were isolated from environmental samples and subjected to taxonomic identification using the MALDI-TOF MS technique and to a two-step screening for proteolytic and keratinolytic activity. The ability to degrade a β-rich keratin substrate was observed in almost all of the strains isolated from soil and horsehairs. In contrast, when an α-rich keratin substrate was used, the highest levels of hydrolysis were observed only for Ker39, Ker66, Ker85, Ker100, and Ker101. Strains with the highest biodegradation potential were identified using molecular biology methods. Phylogenetic analysis of 16S rDNA gene sequences allowed the assignment of selected keratinolytic microorganisms to the genera Exiguobacterium, Priestia, Curtobacterium, Stenotrophomonas, Bacillus, Kocuria, or Pseudomonas. The results of this study are a promising precursor for the development of new, more sustainable methods of managing keratin waste to produce high-value hydrolysates.
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Affiliation(s)
| | | | | | - Aneta M. Białkowska
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-537 Lodz, Poland; (W.G.); (M.S.); (I.J.)
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2
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Ratnawati SE, Kuuliala L, Verschuere N, Cnockaert M, Vandamme P, Devlieghere F. The exploration of dominant spoilage bacteria in blue mussels (Mytilus edulis) stored under different modified atmospheres by MALDI-TOF MS in combination with 16S rRNA sequencing. Food Microbiol 2024; 118:104407. [PMID: 38049269 DOI: 10.1016/j.fm.2023.104407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/06/2023] [Accepted: 10/20/2023] [Indexed: 12/06/2023]
Abstract
Few studies have addressed species-level identification of spoilage bacteria in blue mussels packed under modified atmospheres (MAs). We investigated the effect of MAs and seasons on the tentative species-level of dominant spoilage bacteria in blue mussels. Summer (s) and winter (w) blue mussels were stored at 4 °C in the atmospheres (%CO2/O2/N2): A40s (30/40/30), B60s (40/60/0), C60s (0/60/40), A40w (30/40/30), and D75w (25/75/0). In total, 122 culturable isolates were obtained at the final stage of shelf life, when mortality was high (56-100%) and total psychrotrophic bacteria counted >7 log CFU g-1. Biochemical properties were analyzed using gram reactions, catalase and oxidase activities, and salt tolerance tests. Culturable isolates were identified through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16 S rRNA gene sequence analysis. Spoilage potential tests were investigated by evaluating protease, lipase, and fermentation activities as well as gas and H2S production. The culturable isolates showed tolerance to varied salt concentrations. Psychromonas arctica, Pseudoalteromonas elyakovii, and Shewanella frigidimarina were dominating in specific MAs. Winter blue mussels resulted in a higher variation of spoilage bacteria, including S. frigidimarina, S. vesiculosa, S. polaris, Micrococcus luteus, Paeniglutamicibacter terrestris sp. nov., and Alteromonas sp.
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Affiliation(s)
- S E Ratnawati
- Research Unit Food Microbiology and Food Preservation (FMFP), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - L Kuuliala
- Research Unit Food Microbiology and Food Preservation (FMFP), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; Research Unit Knowledge-based Systems (KERMIT), Department of Data Analysis and Mathematical Modelling, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Belgium
| | - N Verschuere
- Research Unit Food Microbiology and Food Preservation (FMFP), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - M Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - P Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - F Devlieghere
- Research Unit Food Microbiology and Food Preservation (FMFP), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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3
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Bielen A, Babić I, Vuk Surjan M, Kazazić S, Šimatović A, Lajtner J, Udiković-Kolić N, Mesić Z, Hudina S. Comparison of MALDI-TOF mass spectrometry and 16S rDNA sequencing for identification of environmental bacteria: a case study of cave mussel-associated culturable microorganisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:21752-21764. [PMID: 38393570 DOI: 10.1007/s11356-024-32537-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/15/2024] [Indexed: 02/25/2024]
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is routinely used as a rapid and cost-effective method for pathogen identification in clinical settings. In comparison, its performance in other microbiological fields, such as environmental microbiology, is still being tested, although isolates of environmental microbes are essential for in-depth in vivo studies of their biology, including biotechnological applications. We investigated the applicability of MALDI-TOF MS for the identification of bacterial isolates from a highly oligotrophic environment - Dinaric Karst caves, which likely harbor specific microorganisms. We cultured bacteria from the shell surface of the endemic mussel Congeria jalzici, one of the three known cave mussels in the world that lives in the Dinaric karst underground. The bacterial isolates were obtained by swabbing the shell surface of mussels living in microhabitats with different amounts of water: 10 air-exposed mussels, 10 submerged mussels, and 10 mussels in the hygropetric zone. A collection of 87 pure culture isolates was obtained, mostly belonging to the phylum Bacillota (72%), followed by Pseudomonadota (16%), Actinomycetota (11%), and Bacteroidota (1%). We compared the results of MALDI-TOF MS identification (Bruker databases DB-5989 and version 11, v11) with the results of 16S rDNA-based phylogenetic analysis, a standard procedure for bacterial identification. Identification to the genus level based on 16S rDNA was possible for all isolates and clearly outperformed the results from MALDI-TOF MS, although the updated MALDI-TOF MS database v11 gave better results than the DB-5989 version (85% versus 62%). However, identification to the species-level by 16S rDNA sequencing was achieved for only 17% of isolates, compared with 14% and 40% for the MALDI-TOF MS databases DB-5989 and v11 database, respectively. In conclusion, our results suggest that continued enrichment of MALDI-TOF MS libraries will result with this method soon becoming a rapid, accurate, and efficient tool for assessing the diversity of culturable bacteria from different environmental niches.
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Affiliation(s)
- Ana Bielen
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia.
| | - Ivana Babić
- Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
| | - Marija Vuk Surjan
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | | | - Ana Šimatović
- Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
| | - Jasna Lajtner
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | | | - Zrinka Mesić
- Oikon Ltd., Trg Senjskih Uskoka 1-2, 10020, Zagreb, Croatia
| | - Sandra Hudina
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
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Lukhele T, Msagati TAM. Evaluating the microcystin-LR-degrading potential of bacteria growing in extreme and polluted environments. Arch Microbiol 2023; 205:213. [PMID: 37129688 PMCID: PMC10154260 DOI: 10.1007/s00203-023-03554-4] [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: 02/15/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
Inhabitants of extreme and polluted environments are attractive as candidates for environmental bioremediation. Bacteria growing in oil refinery effluents, tannery dumpsite soils, car wash effluents, salt pans and hot springs were screened for microcystin-LR biodegradation potentials. Using a colorimetric BIOLOG MT2 assay; Arthrobacter sp. B105, Arthrobacter junii, Plantibacter sp. PDD-56b-14, Acinetobacter sp. DUT-2, Salinivibrio sp. YH4, Bacillus sp., Bacillus thuringiensis and Lysinibacillus boronitolerans could grow in the presence of microcystin-LR at 1, 10 and 100 µg L-1. Most bacteria grew optimally at 10 µg L-1 microcystin-LR under alkaline pH (8 and 9). The ability of these bacteria to use MC-LR as a growth substrate depicts their ability to metabolize the toxin, which is equivalent to its degradation. Through PCR screening, these bacteria were shown to lack the mlr genes implying possible use of a unique microcystin-LR degradation pathway. The study highlights the wide environmental and taxonomic distribution of microcystin-LR degraders.
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Affiliation(s)
- Thabile Lukhele
- Institute for Nanotechnology and Water Sustainability, College of Science Engineering and Technology, University of South Africa, Florida Science Campus, Johannesburg, South Africa.
| | - Titus Alfred Makudali Msagati
- Institute for Nanotechnology and Water Sustainability, College of Science Engineering and Technology, University of South Africa, Florida Science Campus, Johannesburg, South Africa
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5
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Boonstra M, Fouz B, van Gelderen B, Dalsgaard I, Madsen L, Jansson E, Amaro C, Haenen O. Fast and accurate identification by MALDI-TOF of the zoonotic serovar E of Vibrio vulnificus linked to eel culture. JOURNAL OF FISH DISEASES 2023; 46:445-452. [PMID: 36656662 DOI: 10.1111/jfd.13756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Vibrio vulnificus is a zoonotic pathogen that can cause death by septicaemia in farmed fish (mainly eels) and humans. The zoonotic strains that have been isolated from diseased eels and humans after eel handling belong to clade E (or serovar E (SerE)), a clonal complex within the pathovar (pv.) piscis. The aim of this study was to evaluate the accuracy of MALDI-TOF mass spectrometry (MS) in the identification of SerE, using the other two main pv. piscis-serovars (SerA and SerI) from eels as controls. MALDI-TOF data were compared with known serologic and genetic data of five pv. piscis isolates or strains, and with the non pv. piscis reference strain. Based on multiple spectra analysis, we found serovar-specific peaks that were of ~3098 Da and ~ 4045 Da for SerE, of ~3085 Da and ~ 4037 Da for SerA, and of ~3085 Da and ~ 4044 Da for SerI. Therefore, our results demonstrate that MALDI-TOF can be used to identify SerE and could also help in the identification of the other serovars of the species. This means that zoonosis due to V. vulnificus could be prevented by using MALDI-TOF, as action can be taken immediately after the isolation of a possible zoonotic V. vulnificus strain.
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Affiliation(s)
- Mirjam Boonstra
- National Reference Laboratory for Fish Diseases, Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands
| | - Belén Fouz
- Instituto Universitario BIOTECMED, University of Valencia, Valencia, Spain
| | - Betty van Gelderen
- National Reference Laboratory for Fish Diseases, Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands
| | - Inger Dalsgaard
- DTU Aqua, Technical University of Denmark, National Institute of Aquatic Resources, Section for Fish and Shellfish Diseases, Kgs. Lyngby, Denmark
| | - Lone Madsen
- DTU Aqua, Technical University of Denmark, National Institute of Aquatic Resources, Section for Fish and Shellfish Diseases, Kgs. Lyngby, Denmark
| | - Eva Jansson
- SVA, Department of Animal Health and Antimicrobial Strategies, Uppsala, Sweden
| | - Carmen Amaro
- Instituto Universitario BIOTECMED, University of Valencia, Valencia, Spain
| | - Olga Haenen
- National Reference Laboratory for Fish Diseases, Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands
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Besson M, Alison J, Bjerge K, Gorochowski TE, Høye TT, Jucker T, Mann HMR, Clements CF. Towards the fully automated monitoring of ecological communities. Ecol Lett 2022; 25:2753-2775. [PMID: 36264848 PMCID: PMC9828790 DOI: 10.1111/ele.14123] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/09/2022] [Accepted: 09/06/2022] [Indexed: 01/12/2023]
Abstract
High-resolution monitoring is fundamental to understand ecosystems dynamics in an era of global change and biodiversity declines. While real-time and automated monitoring of abiotic components has been possible for some time, monitoring biotic components-for example, individual behaviours and traits, and species abundance and distribution-is far more challenging. Recent technological advancements offer potential solutions to achieve this through: (i) increasingly affordable high-throughput recording hardware, which can collect rich multidimensional data, and (ii) increasingly accessible artificial intelligence approaches, which can extract ecological knowledge from large datasets. However, automating the monitoring of facets of ecological communities via such technologies has primarily been achieved at low spatiotemporal resolutions within limited steps of the monitoring workflow. Here, we review existing technologies for data recording and processing that enable automated monitoring of ecological communities. We then present novel frameworks that combine such technologies, forming fully automated pipelines to detect, track, classify and count multiple species, and record behavioural and morphological traits, at resolutions which have previously been impossible to achieve. Based on these rapidly developing technologies, we illustrate a solution to one of the greatest challenges in ecology: the ability to rapidly generate high-resolution, multidimensional and standardised data across complex ecologies.
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Affiliation(s)
- Marc Besson
- School of Biological SciencesUniversity of BristolBristolUK,Sorbonne Université CNRS UMR Biologie des Organismes Marins, BIOMBanyuls‐sur‐MerFrance
| | - Jamie Alison
- Department of EcoscienceAarhus UniversityAarhusDenmark,UK Centre for Ecology & HydrologyBangorUK
| | - Kim Bjerge
- Department of Electrical and Computer EngineeringAarhus UniversityAarhusDenmark
| | - Thomas E. Gorochowski
- School of Biological SciencesUniversity of BristolBristolUK,BrisEngBio, School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | - Toke T. Høye
- Department of EcoscienceAarhus UniversityAarhusDenmark,Arctic Research CentreAarhus UniversityAarhusDenmark
| | - Tommaso Jucker
- School of Biological SciencesUniversity of BristolBristolUK
| | - Hjalte M. R. Mann
- Department of EcoscienceAarhus UniversityAarhusDenmark,Arctic Research CentreAarhus UniversityAarhusDenmark
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7
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Mann C, Downard KM. Analysis of bacterial biotyping datasets with a mass-based phylonumerics approach. Anal Bioanal Chem 2022; 414:3411-3417. [DOI: 10.1007/s00216-022-03961-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/04/2022] [Accepted: 02/04/2022] [Indexed: 11/01/2022]
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8
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LaMontagne MG, Tran PL, Benavidez A, Morano LD. Development of an inexpensive matrix-assisted laser desorption-time of flight mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize. PeerJ 2021; 9:e11359. [PMID: 34123583 PMCID: PMC8166240 DOI: 10.7717/peerj.11359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/06/2021] [Indexed: 12/14/2022] Open
Abstract
Many endophytes and rhizobacteria associated with plants support the growth and health of their hosts. The vast majority of these potentially beneficial bacteria have yet to be characterized, in part because of the cost of identifying bacterial isolates. Matrix-assisted laser desorption-time of flight (MALDI-TOF) has enabled culturomic studies of host-associated microbiomes but analysis of mass spectra generated from plant-associated bacteria requires optimization. In this study, we aligned mass spectra generated from endophytes and rhizobacteria isolated from heritage and sweet varieties of Zea mays. Multiple iterations of alignment attempts identified a set of parameters that sorted 114 isolates into 60 coherent MALDI-TOF taxonomic units (MTUs). These MTUs corresponded to strains with practically identical (>99%) 16S rRNA gene sequences. Mass spectra were used to train a machine learning algorithm that classified 100% of the isolates into 60 MTUs. These MTUs provided >70% coverage of aerobic, heterotrophic bacteria readily cultured with nutrient rich media from the maize microbiome and allowed prediction of the total diversity recoverable with that particular cultivation method. Acidovorax sp., Pseudomonas sp. and Cellulosimicrobium sp. dominated the library generated from the rhizoplane. Relative to the sweet variety, the heritage variety c ontained a high number of MTUs. The ability to detect these differences in libraries, suggests a rapid and inexpensive method of describing the diversity of bacteria cultured from the endosphere and rhizosphere of maize.
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Affiliation(s)
- Michael G LaMontagne
- Department of Biology and Biotechnology, University of Houston, Clear Lake, Houston, Texas, United States
| | - Phi L Tran
- Department of Biology and Biotechnology, University of Houston, Clear Lake, Houston, Texas, United States
| | - Alexander Benavidez
- Department of Natural Sciences, University of Houston, Downtown, Houston, Texas, United States
| | - Lisa D Morano
- Department of Natural Sciences, University of Houston, Downtown, Houston, Texas, United States
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Vidal LMR, Venas TM, Gonçalves ARP, Mattsson HK, Silva RVP, Nóbrega MS, Azevedo GPR, Garcia GD, Tschoeke DA, Vieira VV, Thompson FL, Thompson CC. Rapid screening of marine bacterial symbionts using MALDI-TOF MS. Arch Microbiol 2020; 202:2329-2336. [PMID: 32529508 DOI: 10.1007/s00203-020-01917-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/14/2020] [Accepted: 05/16/2020] [Indexed: 11/30/2022]
Abstract
Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) is a rapid, cost-effective and high-throughput method for bacteria characterization. However, most previous studies focused on clinical isolates. In this study, we evaluated the use of MALDI-TOF MS as a rapid screening tool for marine bacterial symbionts. A set of 255 isolates from different marine sources (corals, sponge, fish and seawater) was analyzed using cell lysates to obtain a rapid grouping. Cluster analysis of mass spectra and 16S rRNA showed 18 groups, including Vibrio, Bacillus, Pseudovibrio, Alteromonas and Ruegeria. MALDI-TOF distance similarity scores ≥ 60% and ≥ 70% correspond to ≥ 98.7% 16S rRNA gene sequence similarity and ≥ 95% pyrH gene sequence similarity, respectively. MALDI-TOF MS is a useful tool for Vibrio species groups' identification.
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Affiliation(s)
- Livia M R Vidal
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Tainá M Venas
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Aline R P Gonçalves
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Hannah K Mattsson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Raphael V P Silva
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Maria S Nóbrega
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gustavo P R Azevedo
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gizele D Garcia
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Departamento de Ensino de Graduação, Campus UFRJ - Macaé Professor Aloisio Teixeira, Universidade Federal do Rio de Janeiro (UFRJ), Macaé, RJ, Brazil
| | - Diogo A Tschoeke
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Biomedical Engineer Program - COPPE (UFRJ), Rio de Janeiro, Brazil
| | - Verônica V Vieira
- Interdisciplinary Medical Research Laboratory, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane C Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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10
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de Oliveira BFR, Cavalcanti MD, de Oliveira Nunes S, Lobo LA, Domingues RMCP, Muricy G, Laport MS. Paraclostridium is the Main Genus of Anaerobic Bacteria Isolated from New Species of the Marine Sponge Plakina in the Brazilian Southeast Coast. Curr Microbiol 2019; 76:713-722. [DOI: 10.1007/s00284-019-01684-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/01/2019] [Indexed: 02/05/2023]
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11
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Evaluation of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) for the Identification of Group B Streptococcus. BMC Res Notes 2019; 12:85. [PMID: 30764872 PMCID: PMC6376729 DOI: 10.1186/s13104-019-4119-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/06/2019] [Indexed: 01/14/2023] Open
Abstract
Objective Group B Streptococcus (GBS) is a leading cause of neonatal meningitis and sepsis worldwide. Intrapartum antibiotics given to women carrying GBS are an effective means of reducing disease in the first week of life. Rapid and reliable tests are needed to accurately identify GBS from these women for timely intrapartum antibiotic administration to prevent neonatal disease. Many laboratories now use matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) by direct plating or cell lysis for the identification of GBS isolates. The cell lysis step increases time to results for clinical samples and is more complex to perform. Therefore, we seek to evaluate the sensitivity and specificity of the quicker and more rapid direct plating method in identifying GBS. Results We directly compared swab isolates analysed by both direct plating and cell lysis method and demonstrated that direct plating has a sensitivity and specificity of 0.97 and 1, respectively, compared to an additional cell lysis step. We demonstrated that MALDI-TOF MS can be successfully used for batch processing by the direct plating method which saves time. These results are reassuring for laboratories worldwide who seek to identify GBS from swabs samples as quickly as possible.
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12
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Duarte LN, Coelho FJRC, Oliveira V, Cleary DFR, Martins P, Gomes NCM. Characterization of bacterioplankton communities from a hatchery recirculating aquaculture system (RAS) for juvenile sole (Solea senegalensis) production. PLoS One 2019; 14:e0211209. [PMID: 30682196 PMCID: PMC6347143 DOI: 10.1371/journal.pone.0211209] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 01/09/2019] [Indexed: 12/18/2022] Open
Abstract
There is a growing consensus that future technological developments of aquaculture systems should account for the structure and function of microbial communities in the whole system and not only in fish guts. In this study, we aimed to investigate the composition of bacterioplankton communities of a hatchery recirculating aquaculture system (RAS) used for the production of Senegalese sole (Solea senegalensis) juveniles. To this end, we used a 16S rRNA gene based denaturing gradient gel electrophoresis (DGGE) and pyrosequencing analyses to characterize the bacterioplankton communities of the RAS and its water supply. Overall, the most abundant orders were Alteromonadales, Rhodobacterales, Oceanospirillales, Vibrionales, Flavobacteriales, Lactobacillales, Thiotrichales, Burkholderiales and Bdellovibrionales. Although we found a clear distinction between the RAS and the water supply bacterioplankton communities, most of the abundant OTUs (≥50 sequences) in the hatchery RAS were also present in the water supply. These included OTUs related to Pseudoalteromonas genus and the Roseobacter clade, which are known to comprise bacterial members with activity against Vibrio fish pathogens. Overall, in contrast to previous findings for sole grow-out RAS, our results suggest that the water supply may influence the bacterioplankton community structure of sole hatchery RAS. Further studies are needed to investigate the effect of aquaculture practices on RAS bacterioplankton communities and identification of the key drivers of their structure and diversity.
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Affiliation(s)
- Letícia N. Duarte
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | | | - Vanessa Oliveira
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | | | - Patrícia Martins
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - Newton C. M. Gomes
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
- * E-mail:
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13
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Jang KS, Kim YH. Rapid and robust MALDI-TOF MS techniques for microbial identification: a brief overview of their diverse applications. J Microbiol 2018; 56:209-216. [PMID: 29492868 DOI: 10.1007/s12275-018-7457-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/23/2018] [Accepted: 01/24/2018] [Indexed: 10/25/2022]
Abstract
in mass spectrometry have enabled the investigation of various biological systems by directly analyzing diverse sets of biomolecules (i.e., proteins, lipids, and carbohydrates), thus making a significant impact on the life sciences field. Over the past decade, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been widely utilized as a rapid and reliable method for the identification of microorganisms. MALDI-TOF MS has come into widespread use despite its relatively low resolving power (full width at half maximum, FWHM: < 5,000) and its incompatibility with tandem MS analysis, features with which other high-resolution mass spectrometers are equipped. Microbial identification is achieved by searching databases containing mass spectra of peptides and proteins extracted from microorganisms of interest, using scoring algorithms to match analyzed spectra with reference spectra. In this paper, we give a brief overview of the diverse applications of rapid and robust MALDI-TOF MS-based techniques for microbial identification in a variety of fields, such as clinical diagnosis and environmental and food monitoring. We also describe the fundamental principles of MALDI-TOF MS. The general specifications of the two major MS-based microbial identification systems available in the global market (BioTyper® and VITEK® MS Plus) and the distribution of these instruments in Republic of Korea are also discussed. The current review provides an understanding of this emerging microbial identification and classification technology and will help bacteriologists and cell biologists take advantage of this powerful technique.
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Affiliation(s)
- Kyoung-Soon Jang
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea. .,Department of Bio-Analytical Science, University of Science and Technology, Daejeon, 34113, Republic of Korea.
| | - Young Hwan Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea.,Department of Bio-Analytical Science, University of Science and Technology, Daejeon, 34113, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
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14
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Kambouris ME, Manoussopoulos Y, Kantzanou M, Velegraki A, Gaitanis G, Arabatzis M, Patrinos GP. Rebooting Bioresilience: A Multi-OMICS Approach to Tackle Global Catastrophic Biological Risks and Next-Generation Biothreats. ACTA ACUST UNITED AC 2018; 22:35-51. [DOI: 10.1089/omi.2017.0185] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Manousos E. Kambouris
- Department of Pharmacy, University of Patras, Rio Patras, Greece
- Department of Food Technology, ATEI of Thessaly, Karditsa, Greece
| | - Yiannis Manoussopoulos
- Plant Protection Division of Patras, Institute of Industrial and Forage Plants, Patras, Greece
| | - Maria Kantzanou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Aristea Velegraki
- Department of Microbiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios Gaitanis
- Department of Skin and Venereal Diseases, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Michalis Arabatzis
- First Department of Dermatology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
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15
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Vithanage NR, Bhongir J, Jadhav SR, Ranadheera CS, Palombo EA, Yeager TR, Datta N. Species-Level Discrimination of Psychrotrophic Pathogenic and Spoilage Gram-Negative Raw Milk Isolates Using a Combined MALDI-TOF MS Proteomics–Bioinformatics-based Approach. J Proteome Res 2017; 16:2188-2203. [DOI: 10.1021/acs.jproteome.6b01046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Nuwan R. Vithanage
- College
of Health and Biomedicine, Victoria University, Werribee, Victoria 3030, Australia
- Advanced
Food Systems, Victoria University, Werribee, Victoria 3030, Australia
| | - Jeevana Bhongir
- College
of Health and Biomedicine, Victoria University, Werribee, Victoria 3030, Australia
| | - Snehal R. Jadhav
- Faculty
of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia
| | - Chaminda S. Ranadheera
- College
of Health and Biomedicine, Victoria University, Werribee, Victoria 3030, Australia
- Advanced
Food Systems, Victoria University, Werribee, Victoria 3030, Australia
| | - Enzo A. Palombo
- Faculty
of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia
| | - Thomas R. Yeager
- College
of Engineering and Science, Victoria University, Melbourne, Victoria 8001, Australia
- Institute
for Sustainability and Innovation, Victoria University, Werribee, Victoria 3030, Australia
- Advanced
Food Systems, Victoria University, Werribee, Victoria 3030, Australia
| | - Nivedita Datta
- College
of Health and Biomedicine, Victoria University, Werribee, Victoria 3030, Australia
- Institute
for Sustainability and Innovation, Victoria University, Werribee, Victoria 3030, Australia
- Advanced
Food Systems, Victoria University, Werribee, Victoria 3030, Australia
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