Molecular identification and differentiation of Staphylococcus species and strains of cheese origin

Amplified Ribosomal-DNA Restriction Analysis (ARDRA) was used to differentiate among 12 species and 4 subspecies of the genus Staphylococcus. With a universal primer pair a 2.4 kbp PCR-product was amplified, including the 16S rDNA, the 16S-23S rDNA interspacer region, and about 500 bp of the 23S rDNA. Species-specific restriction patterns were found using the restriction enzymes HindIII and XmnI separately. Cheese related staphylococci were clearly differentiated. ARDRA results were in good agreement with results of partial sequencing of the 16S rDNA. ARDRA could fully replace the biochemical identification with ID32 Staph (BioMerieux) which was less reliable when staphylococci of cheese origin were analysed. Genomic restriction digests of cheese-related S. equorum strains by SmaI and SacI gave unique strain-specific restriction patterns which can be used to identify starter staphylococci in a complex microbial environment such as the surface of Red-Smear cheeses.     

Formation of lipolytic enzymes by Brevibacterium linens

When Brevibacterium linens ATCC 9172 was grown in shake flasks, it produced a cell-associated lipase with a specific activity of 152 to 188 U g^–1 cells depending on the composition of the growth medium. There was no growth in media containing tributyrine as the sole carbon source. The cell-associated lipase had maximum activity at pH 8.0 and 37 °C and was strongly inhibited by 3,4-dichloroisocoumarin, an inhibitor specific for serine esterases. Cell-associated activity was released from the cells by treatment with lysozyme. The kinetics of lipase formation was closely related to the amount of biomass formed during growth.     

Biochemical and nucleic acid hybridisation studies on Brevibacterium linens and related strains

Twenty coryneform bacteria identified as Brevibacterium linens or related strains from different private and public collections were studied biochemically in respect to the composition of the cell walls and in respect to the nucleic acid hybridisation. Investigation of the cell walls revealed an identical meso-diaminopimelic acid containing directly cross-linked peptidoglycan type which is not amidated. The characteristic polymers of the polysaccharide moiety of the cell walls were found to be teichoic acids which belong to the poly(glycerolphosphate) and the poly(ribitolphosphate) type. Furthermore a novel mannitol containing teichoic acid is present which is tentatively characterized as poly(mannitolphosphate). Arabinoglactan and ribose as distinctive sugar components together with galactose and glucose in the cell walls of B. linens could not be detected in any strain. The biochemical findings lend support to the view that B. linens and related strains form a distinctive group which is clearly distinguished from all other coryneform bacteria. This is supported by DNA-23S/16S ribosomal ribonucleic acid reassociation studies. Deoxyribonucleic acid-deoxyribonucleic acid homology studies show the incoherency of B. linens which obviously comprises two species.     

Identification and differentiation of species and strains of Arthrobacter and Microbacterium barkeri isolated from smear cheeses with Amplified Ribosmal DNA Restriction Analysis (ARDRA) and pulsed field gel electrophoresis (PFGE)

ARDRA (Amplified Ribosomal-DNA Restriction Analysis) was used to differentiate among species and genera of Arthrobacter and Microbacteria. Species-specific restriction patterns of PCR-products were obtained with NciI for Arthrobacter citreus (DSM 20133T), A. sulfureus (DSM 20167T), A. globiformis (DSM 20124T) and A. nicotianae strains (DSM 20123T, MGE 10D, CA13, CA14, isolate 95293, 95294, and 95299), A. rhombi CCUG 38813T, and CCUG 38812, and Microbacterium barkeri strains (DSM 30123T, MGE 10D, CA12 and CA15, isolate 95292, and isolate 95207). All yellow pigmented coryneforme bacteria isolated from the smear of surface ripened cheeses were identified as either A. nicotianae or M. barkeri strains. Using pulsed field gel electrophoresis (PFGE) strain specific restriction pattern for all Arthrobacter species and Microbacteria tested were obtained with restriction enzymes AscI and SpeI.     

DNA-DNA homology studies among strains of Arthrobacter and Brevibacterium

Sixteen named strains of Arthrobacter and two strains of Brevibacterium were investigated by nucleic acid hybridisation. The Arthrobacter strains show homology values ranging between 11 and 55% to the type strain A. globiformis DSM 20124 (ATCC 8010), indicating only a low to moderate relationship. Two strains of A. globiformis, DSM 20124 and DSM 20125, exhibit only poor relationship to one another (30%). Among all the Arthrobacter strains the homology data range between 10 to 70% demonstrating separate status of almost all species. Only A. polychromogenes DSM 20136 was found to be a subspecies of A. oxydans DSM 20119. The type strain of A. citreus, DSM 20133 shows a remarkable lack of homology to four other strains of A. citreus, deposited as ATCC 15170, ATCC 17775, ATCC 21040 and ATCC 21348 (11–13%) which themselves can be separated into two groups according to the homology data (24–31%). Each of the two strains of Brevibacterium share high genetic relatedness with one of these A. citreus groups (71 and 73%, respectively). According to the DNA-DNA homology data, most of the species of Arthrobacter can actually be ranged taxonomically as species.Abbreviation DSM German Collection of Microorganisms, Menzinger Strasse 67, D-8000 Munich 19, FRG - ATCC American Type Culture Collection, Rockville, Maryland, U.S.A. - CCM Czechoslovak Collection of Microorganisms, J. E. Purkyne University, Tr. Obracu miru 10, Brno, CSSR - NCIB National Collection of Industrial Bacteria Aberdeen, Scotland     

High cell density cultivation of Brevibacterium linens and formation of proteinases and lipase

Brevibacterium linens forms hydrolytic enzymes which can be used to accelerate the ripening of cheese without causing bitterness. B. linens ATCC 9172 was grown to a high cell density (50 g dry wt l^–1 after 60 h) in a mineral medium containing lactic acid, soy-peptone and ammonium sulphate by applying a continuous feed of nutrients. The maximal activities of l-leucine aminopeptidase and cell-associated proteinase were 286 U l^–1 and 202 U l^–1, respectively. The cell-associated lipolytic activity exhibited a strong and sudden increase at 46 h, resulting in a maximum of 9.5 U g^–1 dry wt; thus the volumetric productivity of proteolytic and lipolytic activity was 4220 U l^–1 h^–1 and 7.3 U l^–1 h^–1, respectively.     

Survival of Brevibacterium linens during nutrient starvation and intracellular changes

The present work reports the survival capacity of a strain of Brevibacterium linens isolated from a French camembert cheese and the ensuing changes in cell composition. Exponentially growing cells were harvested, washed and resuspended with shaking in pH 8.0 buffer at 21°C in the absence of a carbon source. The viability of this strain, assessed with slide cultures, is much less than that of coryneform bacteria isolated from soil samples, even though no cell lysis was detected. Intracellular RNA was rapidly consumed during the first few days although magnesium levels remained high. The quantity of DNA initially increased by 17% within 24 h and then remained stable during the 30 days of the experiment. During the same period, absorbance of the medium at 260 nm reached 2 absorbance units. Reserve polysaccharides in this strain are less abundant than in Arthrobacter and were rapidly consumed. Proteolysis was regular and thus maintained a pool of free amino acids which was greater than 60% of the initial value. There was a parallel accumulation of ammonia in the medium. Catalase activity decreased regularly during the first 80 h whereas the quantity of Adenosine-5-triphosphate (ATP) dropped by 47% in 10 h, stabilizing at less than 10% of its initial value. Cell respiration declined very rapidly and was very low after 24 h.     

Identification and differentiation of Lactobacillus, Streptococcus and Bifidobacterium species in fermented milk products with bifidobacteria

The aim of this study was to identify and discriminate bacteria contained in commercial fermented milks with bifidobacteria by the use of amplified ribosomal DNA restriction analysis (ARDRA) and randomly amplified polymorphic DNA (RAPD) techniques. ARDRA of the 16S rDNA gene and RAPD were performed on 13 Lactobacillus strains, 13 Streptococcus and 13 Bifidobacterium strains isolated from commercial fermented milk. Lactobacillus delbrueckii, Streptococcus thermophilus and Bifidobacterium animalis isolates were identified by genus- and species-PCR and also, they were differentiated at genus and species level by ARDRA using MwoI restriction enzyme. The ARDRA technique allowed for the discrimination among these three related genus with the use of only one restriction enzyme, since distinctive profiles were obtained for each genus. Therefore it can be a simple, rapid and useful method for routine identification. Also, RAPD technique allowed the discrimination of all bacteria contained in dairy products, at genus- and strain-level by the performance of one PCR reaction.     

Development of a large scale process for the conversion of polysialogangliosides to monosialotetrahexosylganglioside with a novel strain of <Emphasis Type="Italic">Brevibacterium casei</Emphasis> producing sialidase

A bioconversion process of producing GM1 (monosialotetrahexosylganglioside) on an industrial scale was developed with a novel sialidase-producing strain Brevibacterium casei. The sialidase hydrolyzed polysialogangliosides to produce GM1 but did not act on GM1. When Brevibacterium casei was cultured in a synthetic medium containing crude pig brain gangliosides (10% w/v) at 30°C for 24 h in a 50 l fermenter, most of the polysialogangliosides were converted to GM1. The content of GM1 was increased from 9% in crude gangliosides to 45% with 70% (w/w) yield.     

The dnaJ gene as a novel phylogenetic marker for identification of Vibrio species

The utility of the dnaJ gene for identifying Vibrio species was investigated by analyzing dnaJ sequences of 57 type strains and 22 clinical strains and comparing sequence homologies with those of the 16S rDNA gene and other housekeeping genes (recA, rpoA, hsp60). Among the 57 Vibrio species, the mean sequence similarity of the dnaJ gene (77.9%) was significantly less than that of the 16S rDNA gene (97.2%), indicating a high discriminatory power of the dnaJ gene. Most Vibrio species were, therefore, differentiated well by dnaJ sequence analysis. Compared to other housekeeping genes, the dnaJ gene showed better resolution than recA or rpoA for differentiating Vibrio coralliilyticus from Vibrio neptunius and Vibrio harveyi from Vibrio rotiferianus. Among the clinical strains, all 22 human pathogenic strains, including an atypical strain, were correctly identified by the dnaJ sequence. Our findings suggest that analysis of the dnaJ gene sequence can be used as a new tool for the identification of Vibrio species.     

Utilization of aromatic amino acids as nitrogen sources in Brevibacterium linens: an inducible aromatic amino acid aminotransferase

The first step of the utilization of the aromatic amino acids as sole nitrogen sources by Brevibacterium linens strain 47 was found to be a transamination. The deaminated metabolites of the amino acids were detected in culture supernatants, and the enzyme activity was identified in cell free extracts. The cells contained increased aromatic amino acid aminotransferase activities on growth on the aromatic amino acids as sole nitrogen sources. Two aromatic aminotransferases (AT-I and AT-II) were separated upon diethylaminoethyl-Trisacryl M column chromatography of cell free extracts. Only AT-I was responsible for the increased level of aromatic amino acid aminotransferase activity of induced cells. The results suggested a catabolic role of AT-I in vivo.Abbreviations DNP dinitrophenyl - HPLC high performance liquid chromatography - PLP pyridoxal-5-phosphate     

Three New Species of Brevibacteria,Brevibacterium antiquum sp. nov., Brevibacterium aurantiacum sp. nov., and Brevibacterium permense sp. nov.

This work deals with the taxonomic study of orange-pigmented bacteria isolated from permafrost sediments, rice plots, and soils contaminated with wastes from the chemical and salt industries that were assigned to the genus Brevibacterium on the basis of phenotypic characteristics, as well as of some strains described previously as Brevibacterium linens. The study revealed three genomic species, whose members and the type strains of the closest species of Brevibacterium had DNA similarity levels between 24 and 59%. The strains of the genomic species differed from each other and from the known species of Brevibacterium in some physiological and biochemical characteristics, as well as in the sugar and polyol composition of their teichoic acids. The 16S rDNA sequence analysis confirmed the assignment of the environmental isolates to the genus Brevibacterium and showed the phylogenetic distinction of the three genomic species. The results obtained in this study allow three new Brevibacterium species to be described: Brevibacterium antiquum (type strain VKM Ac-2118^T = UCM Ac-411^T), Brevibacterium aurantiacum (type strain VKM Ac-2111^T = NCDO 739^T = ATCC 9175^T), and Brevibacterium permense (type strain VKM Ac-2280^T = UCM Ac-413^T).     

The use of neural networks to aid in microorganism identification: a case study ofHaemophilus species identification

The adipamidase of a mutant strainBrevibacterium sp. R312 involved in the degradation of adiponitrile to adipic acid was purified. Its N-terminal amino acid sequence was shown to be identical toBrevibacterium sp. R312 enantio-selective amidase andRhodococcus sp. N-774 amidase.     

MALDI-TOF mass spectrometry as a tool for differentiation of Bradyrhizobium species: Application to the identification of Lupinus nodulating strains

Genus Bradyrhizobium includes slow growing bacteria able to nodulate different legumes as well as species isolated from plant tumours. The slow growth presented by the members of this genus and the phylogenetic closeness of most of its species difficults their identification. In the present work we applied for the first time Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) to the analysis of Bradyrhizobium species after the extension of MALDI Biotyper 2.0 database with the currently valid species of this genus. With this methodology it was possible to identify strains belonging to phylogenetically closely related species of genus Bradyrhizobium allowing the discrimination among species with rrs gene identities higher than 99%. The application of MALDI-TOF MS to strains isolated from nodules of different Lupinus species in diverse geographical locations allowed their correct identification when comparing with the results of rrs gene and ITS analyses. The nodulation of Lupinus gredensis, an endemic species of the west of Spain, by B. canariense supports the European origin of this species.     

Sequence analysis of the Brevibacterium lactofermentum trp operon

Summary Brevibacterium lactofermentum, a Gram-positive bacterium, is a commercially important amino acid producer. In this organism, the tryptophan biosynthetic enzymes are encoded within a 7725 bp HapII-BamHI fragment. Seven open reading frames were identified as trp genes by complementation tests with various B. lactofermentum and Escherichia coli tryptophan auxotrophs. Following the nomenclature established for E. coli and Serratia marcescens, the B. lactofermentum trp genes were designated trpL, trpE, trpG, trpD, trpC (including the trpF domain), trpB, and trpA. The organization of these genes is identical to that in S. marcescens. The nucleotide sequences of the putative ribosome-binding sites for the B. lactofermentum trp genes resemble those of E. coli and Bacillus subtilis. Computer analysis revealed that the trp enzymes of B. lactofermentum resemble the enzymes of the Gram-negative E. coli more closely than those of the Gram-positive B. subtilis.Abbreviations bp base pairs - kb kilobases     

Degradation of dibenzothiophene by Brevibacterium sp.DO

Dibenzothiophene, a polycyclic aromatic sulfur heterocycle, represents as a model compound the organic sulfur integrated in the macromolecular coal matrix. A pure culture of a Brevibacterium species was isolated, which is able to use dibenzothiophene as sole source of carbon, sulfur and energy for growth. During dibenzothiophene utilization sulfite was released in a stoichiometrical amount and was further oxidized to sulfate. Three metabolites of dibenzothiophene degradation were isolated and identified as dibenzothiophene-5-oxide, dibenzothiophene-5-dioxide and benzoate by cochromatography, UV spectroscopy and gas chromatographymass spectrometry analyses. Based on the identified metabolites a pathway for the degradation of dibenzothiophene by Brevibacterium sp. DO is proposed.Non-standard abbreviations DBT dibenzothiophene - PASH polycyclic aromatic sulfur heterocycle - PAH polycyclic aromatic hydrocarbons - GC-MS gas chromatography-mass spectrometry - HPLC high pressure liquid chromatography - IC ion chromatography     

Membrane fluidity in glutamic acid-producing bacteria Brevibacterium sp. ATCC 13869

The bacterial secretion of glutamate was studied through plasma membrane fluidity, measured by anisotropy using the fluorophore TMA-DPH incorporated in the lipid part of the cell membrane. Cells of Brevibacterium sp. ATCC 13869 (wild type) were switched from the biotin-limited, producing state to the biotin-supplemented, non-producing state, and back. The following conclusions could be drawn: 1. It was not possible to detect any change in anisotropy by switching the cells from biotin-limited biotin-supplemented, as well as from biotin-supplemented, to biotin-limited, media. 2. The anisotropy value in the glutamic acid fermentation remains constant during the lag, exponential, growth, production and stationary phases. 3. The treatment of cells with a neutral synthetic polyester of ethylene-and propyleneoxide with soya oil-fatty acids increased the anisotropy values, indicating incorporation of the surfactant. 4. Glutamate secretion is not coupled with membrane fluidity, so a leak providing a general fluidization of the membrane could not be detected.     

Cell Wall Teichoic Acids of Two Brevibacterium Strains

Structurally identical teichoic acids were detected in cell walls of two soil isolates assigned to Brevibacterium linens based on phylogenetic data. Both cell walls contain unsubstituted 1,3-poly(glycerol phosphate) and poly(glycosylglycerol phosphate). Repeating units of the latter--alpha-D-GlcpNAc-(1-->4)-beta-D-Galp-(1-->1)-Gro--are bound by phosphodiester bonds including OH-3 of galactose and OH-3 of glycerol. Some of the N-acetylglucosamine residues have 4,6-pyruvic acid acetal, amounts of the latter in the two strains being unequal. Species-specificity of the structures of teichoic acids in the genus Brevibacterium is discussed.     

dnaJ and gyrB gene sequence relationship among species and strains of genus Streptococcus

The dnaJ and gyrB nucleotide sequences were determined for members of the genus Streptococcus. The average similarity between the species tested was 76.4% (69.7-100%) for dnaJ and 75.9 (70.1-98.7%) for gyrB. These data indicated that the dnaJ and gyrB genes are more divergent and more discriminatory than the 16S rDNA gene. Furthermore, the variation in the dnaJ nucleotide sequences among the mitis group was greater than that of the gyrB nucleotide sequences, especially between Streptococcus pneumoniae and Streptococcus mitis. Subsequently, the high discrimination power of dnaJ within the mitis group was confirmed. Thus, we conclude that the dnaJ and gyrB genes are efficient alternative targets for the classification of the genus Streptococcus, and that dnaJ is suitable for phylogenetic analysis of closely related Streptococcus strains.     

Molecular differentiation of Keratinomyces (Trichophyton) species

The taxonomy of the form-genus Keratinomyces (Trichophyton) within the group of the dermatophytes is based on morphological features which remain insufficient for the distinction of these anamorphic species. The three species included in the genus Keratinomyces, namely K. ajelloi, K. ceretanicus and K. longifusus were examined by means of their mitochondrial-like DNA diversity and compared to few other dermatophytes. The analysis of the mtDNA restriction fragments confirmed that the three species are different and well separate from the other dermatophytes.