Identification by fluorescence spectroscopy of lactic acid bacteria isolated from a small-scale facility producing traditional dry sausages

Three different fluorescence spectra were recorded following excitation at 250 nm (aromatic amino acids+nucleic acids, AAA+NA), 316 nm (NADH) and 380 nm (FAD) for 20 type strain collections of lactic acid bacteria (LAB). Evaluation of the data using principal component analysis and factorial discriminant analysis showed a good discrimination of considered LAB at the genus, species and genus-species level. AAA+NA fluorophores showed the highest percentage of good classification. From AAA+NA spectra recorded on LAB isolated from a small-scale facility producing traditional dry sausages, we succeeded to identify 28 of 29 wild strains. This method allowed us to discriminate between Lactobacillus sakei subsp. carnosus and Lactobacillus sakei subsp. sakei. Thus, intrinsic fluorescence is an economical and powerful tool for the identification of wild LAB isolated from meat and meat products.     

Reagentless identification of human bifidobacteria by intrinsic fluorescence

A new identification method for bifidobacteria species from the human gastrointestinal tract was developed based on the measurement and statistical analysis of the intrinsic fluorescence of aromatic amino acids (AAA) and nucleic acids (NA), following their excitation at 250 nm. The model was constructed by recording the fluorescence spectra of 53 Bifidobacterium strains of 10 different species, including the corresponding type strains, and validated by analyzing the spectra data from nine further problem strains. Principal components analysis (PCA) and factorial discriminant analysis (FDA) of the results showed the technique to distinguish between the isolates at the species level; the Bifidobacterium pseudolongum subspecies (globosum and pseudolongum) could also be distinguished. The proposed method provides a powerful, inexpensive and convenient means of rapidly identifying intestinal bifidobacteria, which could be of help for large probiotic surveys.     

Rapid Identification of Gram Negative Bacteria from Blood Culture Broth Using MALDI-TOF Mass Spectrometry

An important role of the clinical microbiology laboratory is to provide rapid identification of bacteria causing bloodstream infection. Traditional identification requires the sub-culture of signaled blood culture broth with identification available only after colonies on solid agar have matured. MALDI-TOF MS is a reliable, rapid method for identification of the majority of clinically relevant bacteria when applied to colonies on solid media. The application of MALDI-TOF MS directly to blood culture broth is an attractive approach as it has potential to accelerate species identification of bacteria and improve clinical management. However, an important problem to overcome is the pre-analysis removal of interfering resins, proteins and hemoglobin contained in blood culture specimens which, if not removed, interfere with the MS spectra and can result in insufficient or low discrimination identification scores. In addition it is necessary to concentrate bacteria to develop spectra of sufficient quality. The presented method describes the concentration, purification, and extraction of Gram negative bacteria allowing for the early identification of bacteria from a signaled blood culture broth.     

Stable carbon isotope analysis of nucleic acids to trace sources of dissolved substrates used by estuarine bacteria

The natural abundance of stable carbon isotopes measured in bacterial nucleic acids extracted from estuarine bacterial concentrates was used to trace sources of organic matter for bacteria in aquatic environments. The stable carbon isotope ratios of Pseudomonas aeruginosa and nucleic acids extracted from cultures resembled those of the carbon source on which bacteria were grown. The carbon isotope discrimination between the substrate and total cell carbon from bacterial cultures averaged 2.3% +/- 0.6% (n = 13). Furthermore, the isotope discrimination between the substrate and nucleic acids extracted from bacterial cultures was 2.4% +/- 0.4% (n = 10), not significantly different from the discrimination between bacteria and the substrate. Estuarine water samples were prefiltered through 1-micron-pore-size cartridge filters. Bacterium-sized particles in the filtrates were concentrated with tangential-flow filtration and centrifugation, and nucleic acids were then extracted from these concentrates. Hybridization with 16S rRNA probes showed that approximately 90% of the nucleic acids extracted on two sample dates were of eubacterial origin. Bacteria and nucleic acids from incubation experiments using estuarine water samples enriched with dissolved organic matter from Spartina alterniflora and Cyclotella caspia had stable carbon isotope values similar to those of the substrate sources. In a survey that compared diverse estuarine environments, stable carbon isotopes of bacteria grown in incubation experiments ranged from -31.9 to -20.5%. The range in isotope values of nucleic acids extracted from indigenous bacteria from the same waters was similar, -27.9 to -20.2%. Generally, the lack of isotope discrimination between bacteria and nucleic acids that was noted in the laboratory was observed in the field.(ABSTRACT TRUNCATED AT 250 WORDS)     

Stable carbon isotope analysis of nucleic acids to trace sources of dissolved substrates used by estuarine bacteria.

The natural abundance of stable carbon isotopes measured in bacterial nucleic acids extracted from estuarine bacterial concentrates was used to trace sources of organic matter for bacteria in aquatic environments. The stable carbon isotope ratios of Pseudomonas aeruginosa and nucleic acids extracted from cultures resembled those of the carbon source on which bacteria were grown. The carbon isotope discrimination between the substrate and total cell carbon from bacterial cultures averaged 2.3% +/- 0.6% (n = 13). Furthermore, the isotope discrimination between the substrate and nucleic acids extracted from bacterial cultures was 2.4% +/- 0.4% (n = 10), not significantly different from the discrimination between bacteria and the substrate. Estuarine water samples were prefiltered through 1-micron-pore-size cartridge filters. Bacterium-sized particles in the filtrates were concentrated with tangential-flow filtration and centrifugation, and nucleic acids were then extracted from these concentrates. Hybridization with 16S rRNA probes showed that approximately 90% of the nucleic acids extracted on two sample dates were of eubacterial origin. Bacteria and nucleic acids from incubation experiments using estuarine water samples enriched with dissolved organic matter from Spartina alterniflora and Cyclotella caspia had stable carbon isotope values similar to those of the substrate sources. In a survey that compared diverse estuarine environments, stable carbon isotopes of bacteria grown in incubation experiments ranged from -31.9 to -20.5%. The range in isotope values of nucleic acids extracted from indigenous bacteria from the same waters was similar, -27.9 to -20.2%. Generally, the lack of isotope discrimination between bacteria and nucleic acids that was noted in the laboratory was observed in the field.(ABSTRACT TRUNCATED AT 250 WORDS)     

Thin layer chromatographic determination of organic acids for rapid identification of bifidobacteria at genus level

This study presents a simple and fast method for the identification of bifidobacteria using a thin layer chromatographic (TLC) analysis of the short chain fatty acids in a culture broth. When the chromatogram was sprayed with the indicator solution (methyl red-bromophenol blue in 70% ethanol), lactic acid exhibited two red spots, and acetic acid, propionic acid, and butyric acid all produced blue spots. Succinic acid and citric acid produced yellow and dark yellow spot, respectively. In addition, these organic acids showed different R(f) values. The total time taken to analyze the organic acids in the 10 bacterial culture broths using the proposed method was approximately 50 min. The proposed TLC method was used to analyze the organic acids in culture broths of the following strains, five Bifidobacterium species. (Bifidobacterium longum, B. breve, B. infantis, B. bifidum, and B. adolescentis) and five other lactic acid bacteria strains (Lactobacillus casei, L. bulgaricus, L. acidophilus, Streptococcus thermophilus, and S. lactis). Both spots of lactic acid and acetic acid were detected on all the TLC plates from the five bifidobacterial culture broths. The five other lactic acid bacterial culture broths, however, only exhibited lactic acid spots. Accordingly, the proposed TLC method would appear to be a useful tool for rapid identification of Bifidobacterium spp. at the genus level.     

Identification and validation of reference genes to study the gene expression in Gluconacetobacter diazotrophicus grown in different carbon sources using RT-qPCR

Species of the family Pasteurellaceae play an important role as primary or opportunistic animal pathogens. In veterinary diagnostic laboratories identification of this group of bacteria is mainly done by phenotypic assays while genetic identification based on housekeeping genes is mostly used for research and particularly important diagnostic samples. MALDI-TOF MS seems to represent a promising alternative to the currently practiced cumbersome, phenotypic diagnostics carried out in many veterinary diagnostic laboratories. We therefore assessed its application for animal associated members of the family Pasteurellaceae. The Bruker Biotyper 3.0 database was complemented with reference spectra of clinically relevant as well as commensal animal Pasteurellaceae species using generally five strains per species or subspecies and tested for its diagnostic potential with additional, well characterized field isolates. About 250 strains comprising 15 genera and more than 40 species and subspecies were included in the study, covering most representatives of the family. A high discrimination at the genus and species level was observed. Problematic discrimination was only observed with some closely related species and subspecies. MALDI-TOF MS was shown to represent a highly potent method for the diagnosis of this group of animal pathogens, combining speed, precision and low running costs.     

Fourier transform infrared (FTIR) spectroscopy for identifying Lactobacillus species

Abstract Fourier Transform infrared (FTIR) spectroscopy can be used to identify microorganisms. This study describes the influence of culture conditions on FTIR spectra and the discrimination of Lactobacillus species found in breweries. Fifty three Lactobacillus strains were analysed by FTIR spectroscopy and identification at the species level was correct for 94% of the strains, and at the strain level for 91% of the strains.     

Spectral Irradiance and Distribution of Pigments in a Highly Layered Marine Microbial Mat

The spectral irradiance from 400 to 1,100 nm was measured with depth in the intertidal sand mats at Great Sippewissett Salt Marsh, Mass. These mats contained at least four distinct layers, composed of cyanobacteria, purple sulfur bacteria containing bacteriochlorophyll a (Bchl a), purple sulfur bacteria containing Bchl b, and green sulfur bacteria. Spectral irradiance was measured directly by layering sections of mat on a cosine receptor. Irradiance was also approximated by using a calibrated fiber-optic tip. With the tip, irradiance measurements could be obtained at depth intervals less than 250 μm. The irradiance spectra were correlated qualitatively and quantitatively with the distribution of the diverse chlorophyll pigments in this mat and were compared with spectra recorded in plain sand lacking pigmented phototrophs. We found that the shorter wavelengths (400 to 550 nm) were strongly attenuated in the top 2 mm of the mat. The longer wavelengths (red and near infrared) penetrated to much greater depths, where they were attenuated by Bchl a, b, and c-containing anoxygenic phototrophic bacteria. The specific attenuation bands in the irradiance spectra correlated with the specific in vivo absorption bands of the Bchl-protein complexes in the bacteria. We concluded that the pigments in the phototrophs had a profound affect on the light environment within the mat. It seems likely that the diverse Bchl-protein complexes found in the anoxygenic phototrophs evolved in dense mat environments as a result of competition for light.     

HPLC analysis of free amino acids and amino acids of total proteins in cultured cells: an application to the study of rat Sertoli cell protein metabolism.

A simple, rapid and, sensitive HPLC method, coupled with fluorometric detection, has been worked out and employed to determine the intracellular free amino acid concentrations and the amino acid composition of total proteins in rat Sertoli cell primary culture. Sertoli cells were isolated enzymatically from testes of 20- and 28-day-old rats and cultured at 32 degrees C in Eagle's minimum essential medium. On the second day of culture, cell monolayers were quickly rinsed with ice-cold saline, immediately frozen in liquid nitrogen, accurately harvested, and homogenized in 10% trichloroacetic acid. Tissue free amino acids were determined in the acidic soluble fraction following neutralization, while the precipitate was hydrolyzed for the evaluation of the fractional content of amino acids into total proteins. Amino acid samples were derivatized with o-phthaldialdehyde/3-mercaptopropionic acid and resolved by a linear one-step acetonitrile gradient in 12.5 mM sodium phosphate buffer, pH 7.2, employing a 5-microns particle size reversed-phase column. Fluorescence was monitored with excitation at 330 nm and emission at 450 nm. Under these conditions all major physiological amino acids could be satisfactory separated, identified, and subsequently quantified with the aid of standards. The run time was about 50 min; the linearity was excellent over a large range of concentrations (1-800 pmol) and the lower limit of sensitivity appeared to be 0.5 pmol. This method permits us to demonstrate age-dependent modifications in the intracellular amino acid pool and to adequately evaluate the process of protein synthesis in cultured Sertoli cells.(ABSTRACT TRUNCATED AT 250 WORDS)     

Study of the structure of the histidine decarboxylase of Micrococcus sp. n. by the method of circular dichroism]

Ring dichroism spectra (RD) of histidine decarboxylase (HDC) from Micrococcus sp. n. at the regions of peptide bonds (200-240 nm) and aromatic amino acids (250-300 nm) absorption are studied. The treatment of RD spectra according to methods of Greenfield-Fasman, Saksena-Vetlaufer and Mayer permits to conclude that at the pH range within 4-8 the content of ordered structures of alpha-helix type comprises 20%, that of beta-structure type-40%, while the rest 40% are represented with polypeptide chain in a disordered globular state. When pH is varied from 1 to 12, the content of alpha-helices decreases from 17 to 5%. There are two distinct dichroic bands in the spectrum of aromatic chromophores absorption (at 270 and 290 nm), the former containing tirosine, tryptophane and phenylalanine residues and the latter being induced with triptophane residues. The study of HDC RD spectra at the regions of peptide bonds and aromatic acids absorption at different temperatures has shown that a part of triptophane, tyrosine and phenylalanine residues is in an ordered structure of the alpha-helix type. The HDC undergoes irreversible changes under heating to 70 degrees and in 8 M urea. 5 M guanidine chloride eliminates the ordered HDC structure, while sodium dodecylsulphate at concentrations up to 1% does not affect the enzyme structure.     

Reliable and rapid identification of Listeria monocytogenes and Listeria species by artificial neural network-based Fourier transform infrared spectroscopy

Differentiation of the species within the genus Listeria is important for the food industry but only a few reliable methods are available so far. While a number of studies have used Fourier transform infrared (FTIR) spectroscopy to identify bacteria, the extraction of complex pattern information from the infrared spectra remains difficult. Here, we apply artificial neural network technology (ANN), which is an advanced multivariate data-processing method of pattern analysis, to identify Listeria infrared spectra at the species level. A hierarchical classification system based on ANN analysis for Listeria FTIR spectra was created, based on a comprehensive reference spectral database including 243 well-defined reference strains of Listeria monocytogenes, L. innocua, L. ivanovii, L. seeligeri, and L. welshimeri. In parallel, a univariate FTIR identification model was developed. To evaluate the potentials of these models, a set of 277 isolates of diverse geographical origins, but not included in the reference database, were assembled and used as an independent external validation for species discrimination. Univariate FTIR analysis allowed the correct identification of 85.2% of all strains and of 93% of the L. monocytogenes strains. ANN-based analysis enhanced differentiation success to 96% for all Listeria species, including a success rate of 99.2% for correct L. monocytogenes identification. The identity of the 277-strain test set was also determined with the standard phenotypical API Listeria system. This kit was able to identify 88% of the test isolates and 93% of L. monocytogenes strains. These results demonstrate the high reliability and strong potential of ANN-based FTIR spectrum analysis for identification of the five Listeria species under investigation. Starting from a pure culture, this technique allows the cost-efficient and rapid identification of Listeria species within 25 h and is suitable for use in a routine food microbiological laboratory.     

Simple liquid chromatography-electrospray ionization mass spectrometry method for the routine determination of salmon calcitonin in serum

A simple liquid chromatography-electrospray ionization mass spectrometry (LC-ESI-MS) method was developed for the quantification of salmon calcitonin (sCT) in serum. Serum samples from rats and dogs were deproteinized and freeze-dried. The residue was then reconstituted with 57% acetonitrile in water containing 0.1% trifluoroacetic acid and 0.005% benzalkonium chloride. A 20-microl aliquot of the reconstituted solution was injected onto a polymer based RP-C18 column, The outlet was connected to an ion-trap mass spectrometer equipped with an ESI source, and spectra were recorded in a positive-ion, selected-ion monitoring mode. The limit of quantification of the method was 10 ng/ml. Biexponential curves were observed for the temporal serum concentration of sCT following intravenous administration of sCT to rats (100 microg/kg) and dogs (250 microg/kg), resulting in reasonable pharmacokinetic parameters. The present method appears applicable to routine analysis of serum sCT in pharmacokinetic studies with good selectivity, accuracy and precision.     

Bovine lens crystallins do contain helical structure: a circular dichroism study.

In order to settle a recent discussion on the secondary structure of lens crystallins, we have measured the circular dichroism (CD) spectra of alpha-, beta(H)-, and beta(L)-crystallin from 178 to 250 nm and of gamma-crystallin from 168 to 250 nm. The results were analysed by means of a newly developed algorithm that almost doubles the reliability of secondary structure prediction and that allows discrimination between alpha- and 3(10)-helical, and between extended and polyproline beta-type structure. The results indicate that the crystallins studied contain a non-negligible amount of alpha-helical structure, although at least 50% of it is in the form of single and/or distorted loops. In alpha-crystallin, which is related to the chaperones, the helical content is lower than in beta- and gamma-crystallin. In some cases, the helices may play a role in DNA binding by the crystallins.     

Optimization of MALDI-TOF MS for strain level differentiation of Arthrobacter isolates

Matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been shown to be a rapid and sensitive method for characterization of bacteria, but it has not yet become a routine microbiological procedure. Currently there are no standardized protocols that would allow development of large libraries of reproducible protein profiles from a broad range of microorganisms to use for identification purposes. Important variables that may affect spectrum quality are MALDI matrices, solvents, cell growth condition, and culture age. In the present study our aim was to: (1) to determine optimal sample preparation and MALDI conditions for discrimination at the strain level; (2) to determine if changes in growth cycle correlated with MALDI spectrum changes; and (3) to compare level of isolate discrimination based on their MALDI spectra versus their 16S rRNA gene sequence. Using 16 strains of the Gram positive bacterium Arthrobacter, optimal spectra were obtained using two-layer sample application of intact cells grown on solid surface overlaid with a matrix consisting of sinapinic acid (SA) or alpha-cyano-hydroxy-cinnaminic acid (CHCA) in 50:50 acetonitrile:water solvent with 2% trifluoroacetic acid. Spectrum changes paralleled the coccus-rod-coccus growth cycle indicative of Arthrobacter. Strain differences based on their MALDI profiles (using Pearson coefficient and UPGMA) corresponded with their 16S rRNA gene phylogeny but it had greater discrimination.     

Cryospectrokinetic evidence for the mode of reversible binding of neocarzinostatin chromophore to poly(deoxyadenylic-thymidylic acid)

The spectra of neocarzinostatin (NCS) chromophore during its reversible association with poly(dA-dT).poly(dA-dT) [poly(dA-dT)] were recorded (at intervals of 17 ms or more) by a cryospectroscopic method. Examination of the spectral changes of a drug during its interaction with DNA has not been previously reported. Such studies indicate binding of chromophore to poly(dA-dT) is a two-step process in which the spectral properties of the intermediate poly(dA-dT). NCS chromophore species closely resemble those of the final equilibrium species. On the basis of cryokinetic studies (at single wavelengths) carried out at low temperature (2 degrees C), the following proposed mechanism of the DNA-drug (PD) interaction was quantitated: (Formula: see text). In analogy with the other reports on the kinetics of drug-DNA interaction, (PD)I and (PD)II could represent externally bound and intercalated complexes, respectively. However, since the spectra of (PD)I and (PD)II are closely similar, it can also be proposed that (PD)I and (PD)II represent two forms of an intercalated complex. The rate and equilibrium constant for each step were determined by examining the kinetics of the forward and reverse reactions. This was accomplished by determining the polynucleotide concentration dependence of the apparent fast and slow first-order rate constants observed during a double-exponential increase in transmittance (at 330 nm) associated with the binding and the apoprotein-induced dissociation rate constant of the chromophore from poly(dA-dT). The opportunity to use apoprotein, instead of a detergent, to follow the kinetics of the reverse reaction provides a novel approach to these studies.(ABSTRACT TRUNCATED AT 250 WORDS)     

Comparison of the spectral emission of lux recombinant and bioluminescent marine bacteria

The purpose of the present paper was to study the influence of bacteria harbouring the luciferase‐encoding Vibrio harveyi luxAB genes upon the spectral emission during growth in batch‐culture conditions. In vivo bioluminescence spectra were compared from several bioluminescent strains, either naturally luminescent (Vibrio fischeri and Vibrio harveyi) or in recombinant strains (two Gram‐negative Escherichia coli::luxAB strains and a Gram‐positive Bacillus subtilis::luxAB strain). Spectral emission was recorded from 400 nm to 750 nm using a highly sensitive spectrometer initially devoted to Raman scattering. Two peaks were clearly identified, one at 491–500 nm (± 5 nm) and a second peak at 585–595 (± 5 nm) with the Raman CCD. The former peak was the only one detected with traditional spectrometers with a photomultiplier detector commonly used for spectral emission measurement, due to their lack of sensitivity and low resolution in the 550–650 nm window. When spectra were compared between all the studied bacteria, no difference was observed between natural or recombinant cells, between Gram‐positive and Gram‐negative strains, and growth conditions and growth medium were not found to modify the spectrum of light emission. Copyright © 2003 John Wiley & Sons, Ltd.     

Sensitive and rapid method for the simultaneous quantification of five antidepressants with their respective metabolites in plasma using high-performance liquid chromatography with diode-array detection

A high-performance liquid chromatographic method with diode array detection (HPLC-DAD) has been developed for the simultaneous separation and quantification of imipramine, amitriptyline, maprotiline, fluoxetine, clomipramine and their respective metabolites using a 500-μl plasma sample and clovoxamine as the internal standard. The substances were eluted on a Symmetry C₁₈ 5-μm column (250×4.6 mm, I.D.). Full UV spectra from 200 to 450 nm were recorded on-line during the entire analysis and were automatically compared to spectra stored in a library. The quantification was performed at 226, 254, and 400 nm. Peak height ratios were linear over a concentration range of 10–3000 ng/ml: the correlation coefficient (r) was better than 0.998 for all substances at each wavelength. Acceptable coefficients of variation are demonstrated for both within-run and day-to-day assays. The method is simple, highly specific and currently being used for drug monitoring and toxicological studies in children and adult patients.     

高产油小球藻的筛选及其油脂分析

小球藻广泛分布于各种生境,特别是淡水环境中,适应性强。其同化产物主要是淀粉,但在环境胁迫条件下可显著积累中性脂,其脂肪酸类型主要为C16和C18,适合作为生物柴油的原料。我们从中国部分地区水体中分离纯化到若干株小球藻,通过薄层层析比较分析了21株产油小球藻的油脂含量,筛选到一株三酰基甘油含量较高的藻株Chlorella sp.NMX37N。其适宜生长温区为15—35℃,在25℃时生长速率最快,比生长速率为0.53/d,生长的最适光强为250μmol photons/(m2.s)。批量培养实验显示,藻细胞的三酰基甘油含量随培养时间延长而增加,并在培养的稳定期达到最大值,此时培养液中氮基本被耗尽。在批量培养条件下培养Chlorella sp.NMX37N约40d,藻细胞中总脂含量可达到33%左右,与此相比通过两步培养方式,将培养至对数后期(约20d)的藻细胞缺氮处理48h后,得到的总脂产率相当。通过两步培养方式可以大大缩短培养时间,使得该藻细胞快速有效积累油脂。另外,气相色谱分析显示,该藻的总脂和三酰基甘油的脂肪酸均以C16∶0和C18∶2为主,占总脂肪酸的70%以上,且不含C20以上的长链脂肪酸,可以作为优质的生物柴油原料。     

Fourier-transform infrared microspectroscopy,a novel and rapid tool for identification of yeasts

Fourier-transform infrared (FT-IR) microspectroscopy was used in this study to identify yeasts. Cells were grown to microcolonies of 70 to 250 micro m in diameter and transferred from the agar plate by replica stamping to an IR-transparent ZnSe carrier. IR spectra of the replicas on the carrier were recorded using an IR microscope coupled to an IR spectrometer, and identification was performed by comparison to reference spectra. The method was tested by using small model libraries comprising reference spectra of 45 strains from 9 genera and 13 species, recorded with both FT-IR microspectroscopy and FT-IR macrospectroscopy. The results show that identification by FT-IR microspectroscopy is equivalent to that achieved by FT-IR macrospectroscopy but the time-consuming isolation of the organisms prior to identification is not necessary. Therefore, this method also provides a rapid tool to analyze mixed populations. Furthermore, identification of 21 Debaryomyces hansenii and 9 Saccharomyces cerevisiae strains resulted in 92% correct identification at the strain level for S. cerevisiae and 91% for D. hansenii, which demonstrates that the resolution power of FT-IR microspectroscopy may also be used for yeast typing at the strain level.