scholarly journals Hidden Microcosmos in Slovak Gold Mine Rozalia – Microbial Gold Miners?

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Lenka MALINIČOVÁ ◽  
Lea NOSÁĽOVÁ ◽  
Ivana TIMKOVÁ ◽  
Peter PRISTAŠ ◽  
Jana SEDLÁKOVÁ-KADUKOVÁ
Keyword(s):  
Protein Profiling ◽  
Gold Mine ◽  
16S Rdna Sequencing ◽  
Bacterial Isolates ◽  
Isolation And Identification ◽  
Physical Chemical ◽  
Rdna Sequencing ◽  
Gold Miners ◽  
Processing Techniques ◽  
Tof Ms

Biogeochemical cycling of gold involves dispersion and reconcentration of gold (Au) due to physical, chemical and biological processesin Earth surface environments. These processes are evocated by a metabolic activity of different microbial taxa but many of them (andalso their biogeochemical potential) are still unexplored. Understanding the gold cycling is necessary for developing innovative, environmentally friendly gold processing techniques. Our experiments were aimed on isolation and identification of heterotrophic bacteriafrom ore and ore storage dump samples collected in Rozália gold mine in Hodruša-Hámre. Using culture-based approach followed bycombination of MALDI-TOF MS protein profiling and 16S rDNA sequencing, 18 different bacterial genera were identified in studiedmicrobiota. The participation of several representatives of these genera in individual gold cycling steps has already been reported. Thereal involvement of bacterial isolates in gold transformation reactions and their biogeochemical potential will be studied in subsequentexperiments.

scholarly journals Comparative analysis of Campylobacter isolates from wild birds and chickens using MALDI-TOF MS, biochemical testing, and DNA sequencing

2018 ◽  
Vol 30 (3) ◽  
pp. 354-361 ◽  
Author(s):  
Samantha J. Lawton ◽  
Allison M. Weis ◽  
Barbara A. Byrne ◽  
Heather Fritz ◽  
Conor C. Taff ◽  
...  
Keyword(s):  
16S Rdna ◽  
Phylogenetic Relationships ◽  
Wild Birds ◽  
16S Rdna Sequencing ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Gene Testing ◽  
Rdna Sequencing ◽  
Biochemical Testing ◽  
Tof Ms

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was compared to conventional biochemical testing methods and nucleic acid analyses (16S rDNA sequencing, hippurate hydrolysis gene testing, whole genome sequencing [WGS]) for species identification of Campylobacter isolates obtained from chickens ( Gallus gallus domesticus, n = 8), American crows ( Corvus brachyrhynchos, n = 17), a mallard duck ( Anas platyrhynchos, n = 1), and a western scrub-jay ( Aphelocoma californica, n = 1). The test results for all 27 isolates were in 100% agreement between MALDI-TOF MS, the combined results of 16S rDNA sequencing, and the hippurate hydrolysis gene PCR ( p = 0.0027, kappa = 1). Likewise, the identifications derived from WGS from a subset of 14 isolates were in 100% agreement with the MALDI-TOF MS identification. In contrast, biochemical testing misclassified 5 isolates of C. jejuni as C. coli, and 16S rDNA sequencing alone was not able to differentiate between C. coli and C. jejuni for 11 sequences ( p = 0.1573, kappa = 0.0857) when compared to MALDI-TOF MS and WGS. No agreement was observed between MALDI-TOF MS dendrograms and the phylogenetic relationships revealed by rDNA sequencing or WGS. Our results confirm that MALDI-TOF MS is a fast and reliable method for identifying Campylobacter isolates to the species level from wild birds and chickens, but not for elucidating phylogenetic relationships among Campylobacter isolates.

scholarly journals MALDI-TOF Mass Spectrometry Fingerprinting Performance Versus 16S rDNA Sequencing to Identify Bacterial Microflora From Seafood Products and Sea Water Samples

2021 ◽  
Vol 8 ◽  
Author(s):  
Thomas Brauge ◽  
Sylvain Trigueros ◽  
Arnaud Briet ◽  
Sabine Debuiche ◽  
Guylaine Leleu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
16S Rdna ◽  
Sea Water ◽  
Species Level ◽  
16S Rdna Sequencing ◽  
Genus Level ◽  
Maldi Tof ◽  
Rdna Sequencing ◽  
Seafood Products ◽  
Tof Ms

We evaluated the performance of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) associated with the Bruker BioTyperTM V7.0.0 database for the identification of 713 bacterial strains isolated from seafood products and sea water samples (ANSES B3PA collection) under culture conditions that may have been significantly different from those used to create the reference spectrum vs. the 16S rDNA sequencing. We identified 78.8% of seafood isolates with 46.7% at the species level (Bruker score above 2) and 21.2% (Bruker score between 1.7 and 2) at the genus level by the two identification methods, except for 3.8% of isolates with a difference of identification between the two methods (Bruker score between 1.7 and 2). There were 41.9% isolates (Bruker score below 1.7) with the identification at the genus level. We identified 94.4% of seafood isolates with 16S rDNA sequencing. The MALDI-TOF allowed a better strain identification to the species level contrary to the 16s rDNA sequencing, which allowed an identification mainly to the genus level. MALDI-TOF MS in association with the Bruker database and 16S rDNA sequencing are powerful tools to identify a wide variety of bacteria from seafood but require further identification by biochemical, molecular technique or other conventional tests.

scholarly journals Contraception: Influence on Vaginal Microbiota and Identification of Vaginal Lactobacilli Using MALDI-TOF MS and 16S rDNA Sequencing

2018 ◽  
Vol 12 (1) ◽  
pp. 218-229 ◽  
Author(s):  
Sonia E. Fosch ◽  
Cecilia A. Ficoseco ◽  
Antonella Marchesi ◽  
Silvina Cocucci ◽  
Maria E. F. Nader-Macias ◽  
...  
Keyword(s):  
16S Rdna ◽  
Oral Contraceptive Pill ◽  
Vaginal Microbiota ◽  
16S Rdna Sequencing ◽  
Contraceptive Methods ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Vaginal Lactobacilli ◽  
Rdna Sequencing ◽  
Tof Ms

Background:The vaginal microbiome is influenced by a wide variety of factors, including contraceptive methods.Aim:To evaluate the effect of contraceptive methods on vaginal microbiota and to compare MALDI-TOF MS and 16S rDNA sequencing for lactobacilli identification.Patients and Methods:One hundred and one (101) women consulting for birth control were included in a prospective study. Their vaginal content was sampled and analyzed once before they started using the contraceptive method of their choice, and twice after the initiation of contraception, at three months (94/101 women attended) and at six months (89/101 women attended). The relative frequencies of yeasts and trichomonas were analyzed. MALDI-TOF MS and 16S rDNA sequence analysis were applied for the identification of lactobacilli in their vaginal microbiota. The following contraceptive methods were assessed: Combined Oral Contraceptive Pill (COCP), Condom (CON) and The Rhythm Method (RHYT). McNemar’s statistical test was applied.Results:A statistically significant association between COCP and normal microbiota was observed after three months (p< 0.01) and after six months (p< 0.0001), when the vaginal microbiota was modified. At six months, inflammatory reaction was detected in 3/7 women in the CON group, while 6/7 patients using RHYT showed the same state. Yeast colonization increased with the COCP. Identification of lactobacilli by MALDI-TOF MS analysis compared to 16S rDNA sequencing yielded 92.9% concordant results.Lactobacillus gasseriandL. crispatuswere the predominant species.Conclusion:The pattern of vaginal states was significantly modified. Hormone administration apparently corrected the alterations and retained a normal vaginal state. MALDI-TOF MS has the potential of being an accurate tool for the identification of vaginal lactobacilli speciesL. murinuswas for the first time isolated from the vagina.

Comparison of MALDI-TOF MS Biotyper and 16S rDNA sequencing for the identification of Pseudomonas species isolated from fish

2019 ◽  
Vol 132 ◽  
pp. 313-318 ◽  
Author(s):  
Miroslava Kačániová ◽  
Alīna Klūga ◽  
Attila Kántor ◽  
Juraj Medo ◽  
Jana Žiarovská ◽  
...  
Keyword(s):  
16S Rdna ◽  
16S Rdna Sequencing ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Rdna Sequencing ◽  
Pseudomonas Species ◽  
Tof Ms

scholarly journals Isolation and identification of guaiacol producing Alicyclobacillus fastidiosus strains from orchards in Poland

2021 ◽  
Author(s):  
Barbara Sokolowska ◽  
Marzena Połaska ◽  
Agnieszka Dekowska
Keyword(s):  
Hot Springs ◽  
Biochemical Properties ◽  
Flavor Compounds ◽  
Natural Environments ◽  
16S Rdna Sequencing ◽  
Isolation And Identification ◽  
Acidophilic Bacteria ◽  
Rdna Sequencing ◽  
Spoilage Bacteria ◽  
Orchard Soils

The genus Alicyclobacillus comprises a group of Gram-positive, thermo-acidophilic bacteria that are capable of producing highly resistant endospores during unfavorable environmental conditions. The members of this genus inhabit natural environments, including hot springs and soils. The main reason behind the spoilage of final commercial fruit products by Alicyclobacillus is the contamination of fruits with soil at the time of harvesting. Some of the Alicyclobacillus species, including Alicyclobacillus acidoterrestris, are categorized as spoilage bacteria due to their ability to produce off-flavor compounds (e.g., guaiacol and halophenols) that adversely affect the taste and aroma of beverages. In our study, Alicyclobacillus species were isolated from Polish orchard soils and fruits and were subjected to 16S rDNA sequencing. The results of the analysis showed that the isolated strains belonged to A. acidoterrestris and Alicyclobacillus fastidiosus species. All the three isolated strains of A. fastidiosus (f1, f2, f3) exhibited similar morphological and biochemical properties as the strain described in the literature. However, these isolated strains were able to produce guaiacol at temperatures of 20°C, 25°C, and 45°C. Thus, the strains of A. fastidiosus discovered in the present study can be included in the group of spoilage species as they possessed the gene responsible for the production of guaiacol.

scholarly journals Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing

2014 ◽  
Vol 14 (1) ◽  
Author(s):  
Annette Carola Anderson ◽  
Mohamed Sanunu ◽  
Christian Schneider ◽  
Andreas Clad ◽  
Lamprini Karygianni ◽  
...  
Keyword(s):  
16S Rdna ◽  
Species Level ◽  
16S Rdna Sequencing ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Ms Analysis ◽  
Rdna Sequencing ◽  
Level Identification ◽  
Tof Ms

scholarly journals Identification of airborne bacteria by 16S rDNA sequencing, MALDI-TOF MS and the MIDI microbial identification system

Aerobiologia ◽  
2015 ◽  
Vol 31 (3) ◽  
pp. 271-281 ◽  
Author(s):  
Else Marie Fykse ◽  
Torbjörn Tjärnhage ◽  
Tarmo Humppi ◽  
Vilde Sørvik Eggen ◽  
Andre Ingebretsen ◽  
...  
Keyword(s):  
16S Rdna ◽  
Identification System ◽  
Airborne Bacteria ◽  
16S Rdna Sequencing ◽  
Maldi Tof Ms ◽  
Microbial Identification ◽  
Maldi Tof ◽  
Rdna Sequencing ◽  
Microbial Identification System ◽  
Tof Ms

Rapid Identification of Microorganisms Isolated from Pickled Vegetables by MALDI-TOF Mass Spectrometry

2013 ◽  
Vol 712-715 ◽  
pp. 494-497
Author(s):  
Zhi Lei Tan ◽  
Yu Qiao Wei ◽  
Shuang Liang ◽  
Ran Zhang ◽  
Miao Liu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
16S Rdna ◽  
Leuconostoc Mesenteroides ◽  
16S Rdna Sequencing ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Rdna Sequencing ◽  
Pickled Vegetables ◽  
Food Bacteria ◽  
Tof Ms

Matrix-assisted laser desorption/ionization time-off light mass spectrometry (MALDI-TOF MS) is increasingly used as a microbial diagnostic method for species identification of pathogens. However, MALDI-TOF MS identification of food bacteria was seldom reported. Ten strains isolated from different pickled vegetables were rapid identified by MALDI-TOF MS. The results of MALDI-TOF MS were confirmed by 16S rDNA sequencing method. Different score values in MALDI-TOF MS revealed nineLeuconostoc mesenteroides and oneStaphylococcus.Identification success at the species and genus levels was 90% (9/10) and 100% (10/10), respectively.16S rDNA sequencing results showed that nine stains were identified asLeuconostoc mesenteroides and one wasStaphylococcus saprophyticus.Results obtained demonstrate that MALDI-TOFMS is a promising method for discriminating and identifying food bacteria.

scholarly journals Mycobacterium parmense sp. nov.

2004 ◽  
Vol 54 (4) ◽  
pp. 1123-1127 ◽  
Author(s):  
Franco Fanti ◽  
Enrico Tortoli ◽  
Leslie Hall ◽  
Glenn D. Roberts ◽  
Reiner M. Kroppenstedt ◽  
...  
Keyword(s):  
Lymph Node ◽  
Type Strain ◽  
Cervical Lymph Node ◽  
16S Rdna Sequencing ◽  
Mycobacterial Species ◽  
Isolation And Identification ◽  
Rdna Sequencing ◽  
Lipid Pattern ◽  
Slow Growing ◽  
Mycobacterium Simiae

The isolation and identification of a novel, slow-growing, scotochromogenic, mycobacterial species is reported. A strain, designated MUP 1182T, was isolated from a cervical lymph node of a 3-year-old child. MUP 1182T is alcohol- and acid-fast, with a lipid pattern that is consistent with those of species that belong to the genus Mycobacterium. It grows slowly at 25–37 °C, but does not grow at 42 °C. The isolate was revealed to be biochemically distinct from previously described mycobacterial species: it has urease and Tween hydrolysis activities and lacks nitrate reductase, 3-day arylsulfatase and β-glucosidase activities. Comparative 16S rDNA sequencing showed that isolate MUP 1182T represents a novel, slow-growing species that is related closely to Mycobacterium lentiflavum and Mycobacterium simiae. On the basis of these findings, the name Mycobacterium parmense sp. nov. is proposed, with MUP 1182T (=CIP 107385T=DSM 44553T) as the type strain.

scholarly journals Influence of High Hydrostatic Pressure on the Identification of Lactobacillus by MALDI-TOF MS- Preliminary Study

2020 ◽  
Vol 8 (6) ◽  
pp. 813
Author(s):  
Joanna Bucka-Kolendo ◽  
Barbara Sokołowska ◽  
Stanisław Winiarczyk
Keyword(s):  
Mass Spectrum ◽  
Hydrostatic Pressure ◽  
16S Rdna ◽  
High Hydrostatic Pressure ◽  
Protein Profile ◽  
16S Rdna Sequencing ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Rdna Sequencing ◽  
Tof Ms

In the present study, we assessed the ability of MALDI-TOF MS (matrix-assisted laser desorption ionization time-of-flight mass spectrometry) to identify microbial strains subjected to high hydrostatic pressure (HHP) as a stress factor. Protein changes induced by HHP can affect the identification of microorganisms when the identification technique is based on the protein profile. We evaluated two methods, namely MALDI-TOF MS and 16S rDNA sequencing, as a valuable tool to identify Lactobacillus species isolated from spoiled food, juices and beers. The data obtained from the protein mass fingerprint analysis of some of the lactobacilli strains showed differences in unpressured and pressured mass spectrum profiles (MSPs), which influenced the results of the identification. Four out of 13 strains (30%) showed different MSP results for unpressured and pressured samples and these results did not overlap with the 16S rDNA identification results. The 16S rDNA sequencing method revealed that five unpressured strains (38%) and four pressured strains (40%) were identified correctly by MALDI-TOF MS. Both methods showed compatible results in 38% of unpressured strains and in 30% of pressured strains. Stress factors, cultivation methods or the natural environment from which the bacteria were derived can affect their protein profile and thus change the mass spectrum. It is necessary to expand the database with a wide range of mass spectra dedicated to a high-throughput study of the microorganisms derived from different environments.

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