MALDI-Biotyper as a tool to identify polymer producer bacteria

Karolski, Bruno; Cardoso, Letícia Oliveira Bispo; Gracioso, Louise Hase; Nascimento, Cláudio Augusto Oller do; Perpétuo, Elen Aquino

doi:10.1016/j.mimet.2018.09.016

Cited by 9 publications

(5 citation statements)

References 19 publications

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“…The technique has also been increasingly used in the field of environmental microbiology in the recent years. Examples include the identification of microbes isolated from sewage sludge [57]; marine sponges [58]; soils contaminated with organic compounds [59]; the study of microbial diversity in hot water ponds in the Yamunotri landscape, Himalaya [60]; and its use to identify polymer producer bacteria [61]. Some studies showed however that MALDI-TOF MS technique may have a lower discriminatory power for strains of closely related species [62] or may incorrectly identify rare or unknown species that are not contained in the reference entries of commercial databases.…”

Section: Microbiological Studymentioning

confidence: 99%

Towards the Development of Sustainable Ground Improvement Techniques—Biocementation Study of an Organic Soil

et al. 2021

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Ongoing research effort is dedicated to the development of innovative, superior and cost-effective ground improvement techniques to mitigate natural and man-made hazards while minimising waste and other environmental impacts. In this context, the nature-based process of biocementation of soils has been proposed as a potentially more sustainable technique than conventional chemical ground improvement practices. This paper focuses on the biocementation of an organic soil of the UK railway network. Having recently proven the feasibility of biocementing this soil using indigenous ureolytic bacteria, in this paper, the authors perform a parametric study to identify treatments successful in increasing the strength of the soil. Selected treatments are then applied to the soil to assess its volume change during consolidation, secondary compression and shrinkage upon drying. The results show that, depending on the treatments used, biocementation has increased the unconfined compressive strength by up to 81% compared to that of the control samples. For selected treatments and the range of water contents tested (55–33%), shrinkage upon drying reduced by 16%, while the volumetric strains of the soil upon 1-D compression reduced by 32–47%. This was reflected in the values of the coefficient of volume compressibility and the coefficient of secondary compression (the latter either reduced by up to an order of magnitude or secondary compression was not observed altogether in the testing period). Overall, the results proved that biocementation improved considerably the mechanical properties of the organic soil, which gives promise for addressing the settlement problems of this soil.

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Section: Microbiological Studymentioning

confidence: 99%

Towards the Development of Sustainable Ground Improvement Techniques—Biocementation Study of an Organic Soil

et al. 2021

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“…1). This follows previous work in this area examining horseradish soil (19), arctic seawater (20), spacecraft organisms (21), and polymer-producing bacteria (22). Because the primary application for Biotyper instrumentation is in clinical settings, current reference libraries lack coverage of environmental strains for most genera.…”

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confidence: 93%

Custom Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometric Database for Identification of Environmental Isolates of the Genus Burkholderia and Related Genera

Fergusson

Coloma

Valentine

et al. 2020

Appl Environ Microbiol

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Success of discovery programs for microbial natural products is dependent on quick and concise discrimination between isolates from diverse environments. However, laboratory isolation and identification of priority genera using current 16S rRNA PCR-based methods are both challenging and time-consuming. An emerging strategy for rapid isolate discrimination is protein fingerprinting via matrix-assisted laser desorption ionization (MALDI) mass spectrometry. Using our in-house environmental isolate repository, we have created a main spectral (MSP) library for the Bruker Biotyper MALDI mass spectrometer that contains 95 entries, including Burkholderia, Caballeronia, Paraburkholderia, and other environmentally related genera. The library creation required the acquisition of over 2,250 mass spectra, which were manually reviewed for quality control and consolidated into a single reference library using a commercial software platform. We tested the effectiveness of the reference library by analyzing 49 environmental isolate strains using two different sample preparation methods. Overall, this approach correctly identified all strains to the genus level provided that suitable reference spectra were present in the MSP library. In this study, we present a fast, accurate method for taxonomic assignment of environmentally derived bacteria from the order Burkholderiales, providing a valuable alternative to traditional PCR-based methods. The MSP library described in the manuscript is available for use. IMPORTANCE The Gram-negative proteobacterial order Burkholderiales has emerged as a promising source of novel natural products in recent years. This order includes the genus Burkholderia and the newly defined genera Caballeronia and Paraburkholderia. However, development of this resource has been hampered by difficulties with rapid and selective isolation of Burkholderiales strains from the environment. Environmental metagenome sequencing has revealed that the potential for natural products is not evenly distributed throughout the microbial world. Thus, large but targeted microbial isolate libraries are needed to effectively explore the chemical potential of natural products. To study these organisms efficiently, methods to quickly identify isolates to the genus level are required. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is already used in clinical settings to reliably identify unknown bacterial pathogens. We have adapted similar methodology using the MALDI Biotyper instrument to rapidly identify environmental isolates of Burkholderia, Caballeronia, and Paraburkholderia for downstream natural product discovery.

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“…Em trabalhos anteriores realizados com a espécie Methylopila foi comprovada a capacidade desta em acumular PHB (DORONINA et al, 2000;LI et al, 2011). Esta capacidade também foi evidenciada quando a cepa foi cultivada sob condições de estresse, em meio de cultivo sem nitrogênio e com excesso de carbono (KAROLSKI et al, 2018). No entanto, a fim de aumentar a quantidade de biomassa e otimizar as condições de acúmulo, neste trabalho foram testados dois meios de culturas diferentes, descritos anteriormente, usando metanol como principal fonte de carbono.…”

Section: 1avaliação Da Capacidade De Acúmulo De Phb Da Cepa Mcsubhunclassified

“…Além disso, o trabalho que isolou o micro-organismo estudado, cepa MCSUBH validou a técnica rápida, com custo reduzido, para comprovar a produção de PHB por dessorção/ionização a laser assistida por matriz técnica (MALDI-Biotyper)(KAROLSKI et al, 2018), conhecida por identificar bactérias com base em uma única colônia isolada. através das vias metabólicas do carbono.…”

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Produção de copolímeros do tipo P(3HB-co-3HV) por >i<Methylopila >/i<>i<oligotropha>/i< (cepa MCSUBH) isolada do manguezal de Cubatão-SP

Silva

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Produção de copolímeros do tipo P(3HB-co-3HV) por Methylopila oligotropha (cepa MCSUBH) isolada do manguezal de Cubatão-SP.São Paulo P(3HB-co-3HV) apenas quando o ácido valérico foi fornecido como co-substrato na presença de metanol. Além disso, foram testadas diferentes estratégias para a produção do copolímero como: tempo de cultivo, concentração de metanol e concentração de nitrogênio. A produção de P(3HB-co-3HV) variou entre 0,49 e 2,41g.L -1 com diferentes frações molares de ácido 3hidroxivalérico (3HV) (entre 1,86-20 mol%)Palavras chaves: Copolímeros. Poli(3-hidroxibutirato-co-3-hidroxivalerato). Metilotrófica.Metanol. Ácido Valérico.

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MALDI-Biotyper as a tool to identify polymer producer bacteria

Cited by 9 publications

References 19 publications

Towards the Development of Sustainable Ground Improvement Techniques—Biocementation Study of an Organic Soil

Towards the Development of Sustainable Ground Improvement Techniques—Biocementation Study of an Organic Soil

Custom Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometric Database for Identification of Environmental Isolates of the Genus Burkholderia and Related Genera

Produção de copolímeros do tipo P(3HB-co-3HV) por >i<Methylopila >/i<>i<oligotropha>/i< (cepa MCSUBH) isolada do manguezal de Cubatão-SP

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