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PubMed2005

Monitoring the bacterial population dynamics during fermentation of artisanal Argentinean sausages.

The dynamics of the microbial community responsible for the artisanal fermentation of dry sausage produced in Argentina was investigated by using classical and molecular approaches. The combined use of RAPD analysis with primers M13, XD9, RAPD1 and RAPD2 and 16S rDNA sequencing were applied to the identification and intraspecific differentiation of 100 strains of lactobacilli and Micrococcaceae. DGGE analysis was used to monitor the dynamic changes in population after total microbial DNA was directly extracted from sausages and subjected to PCR using V3f (GC), Bact-0124f-GC and Univ-0515r primers. The sequence analysis of 16S rDNA of the dominant species was also carried out. Lactobacillus sakei and Lactobacillus plantarum were the dominant lactic acid organisms during the fermentation while Staphylococcus saprophyticus represented the dominant species of Micrococcaceae. It was demonstrated that the ripening process of Argentinean artisanal fermented sausage is driven by a limited number of Lactobacillus and Staphylococcus strains selected from environmental microbiota by the ability to best compete under the prevailing conditions of the ecological niche. The identification of dominant communities present in this artisanal fermented sausage can help in the selection of starter cultures consisting in well adapted strains to the particular production technology.

Animals↗
PubMed2004

Molecular phylogeny of songbirds (Passeriformes) inferred from mitochondrial 16S ribosomal RNA gene sequences.

Phylogenetic relationships among the families of passerine birds have been the subject of many debates. These relationships have been investigated by using a number of different character sets, including morphology, proteins, DNA-DNA hybridization, and mitochondrial DNA gene sequences. Our objective was to examine the phylogenetic relationships of a set of passerine songbirds (Oscines) and to test the taxonomic relationships proposed by. We sequenced 1403 aligned bases encompassing the mitochondrial transfer-RNA-Valine and 16S ribosomal RNA genes in 27 species from 14 families (including a Suboscine outgroup). Our results differ in significant ways from the superfamily designations of Sibley and Ahlquist by questioning the monophyly of the Sylvioidea and by placing the Regulidae in the Corvoidea.

Animals↗
PubMed1997

Interspecies sequence differences in the Mip protein from the genus Legionella: implications for function and evolutionary relatedness.

The nucleotide sequence of the mip genes and their inferred amino acid sequences were determined from 35 Legionella species and compared with the published sequences for L. pneumophila, L. micdadei and L. longbeachae. The sequences were 69-97% conserved at the nucleotide level and 82-99% at the amino acid level, with total conservation of amino acids determined to be associated with sites known to be involved in peptidyl prolyl cis-trans isomerase activity. No apparent difference could be determined in the arrangement of amino acids that would predict a functional difference in Mip from species associated with disease and Mip from species isolated only from the environment. Additionally, a phylogenetic comparison of the sequences with published 16S RNA sequences, using both genetic distance and maximum parsimony methods, was performed. Few relationships were apparent that were well supported by both data sets, the most robust being a clade comprising ([(cincinnatiensis, longbeachae, sainthelensi, santicrucis) gratiana] (moravica, quateirensis, shakespearei, worsleiensis) anisa, bozemanii, cherrii, dumoffii, gormanii, jordanis, parisiensis, pneumophila, steigerwaltii, tucsonensis, and wadsworthii).

Amino Acid Sequence↗
PubMed2003

[Nocardia cyriacigeorgici: First report of invasive human infection].

BACKGROUND: Diagnostic laboratories increasingly offer bacterial identification to the species level. The 17 nocardia species known to date differ in their clinical presentation, antibiotic resistance patterns and geographic distribution. The discovery of a new species with pathogenicity for humans calls for the characterization of its clinical and epidemiological properties. PATIENTS AND METHODS: Nocardia isolated from multifocal brain abscesses of an immunocompromised patient were further identified by the analysis of their cellular fatty acids and sequencing of the 16S ribosomal DNA. Quantitative antibiotic resistance testing was performed with E-tests. RESULTS: The 16S ribosomal DNA analysis showed a 99 % homology to Nocardia cyriacigeorgici. This is the first report of this species as an invasive human pathogen. N. cyriacigeorgici was found susceptible for meropenem, amikacin, ceftriaxon and cotrimoxazole. The combination of surgical drainage and antibiotic treatment for 13 months was curative. CONCLUSIONS: N. cyriacigeorgici has the potential to cause invasive infections at least in immunocompromised patients. Comparing clinical and in vitro characteristics with N. asteroides, the main causative agent of nocardial infections in Europe, we found no clinically relevant differences.

Amikacin↗
PubMed2004

Lymphadenitis cervicalis due to Mycobacterium interjectum in immunocompetent children.

UNLABELLED: This report presents two cases of cervical lymphadenitis due to Mycobacterium interjectum in healthy young children, identified by sequencing of the 16S rRNA gene. Surgical resection combined with chemotherapy resulted in cure. CONCLUSION: The attention of clinicians needs to be drawn to an emerging mycobacterial pathogen which might be overlooked or misidentified in routine laboratory testing.

Cheek↗
PubMed1997

Use of amplification and sequencing of the 16S rRNA gene to diagnose Mycoplasma pneumoniae osteomyelitis in a patient with hypogammaglobulinemia.

A splenectomized patient with hypogammaglobulinemia who was hospitalized because of a high-grade fever subsequently developed osteomyelitis. Although pus cultures were repeatedly sterile, polymerase chain reaction (PCR) analysis with use of 16S rRNA gene primers with a broad specificity detected bacterial DNA in pus samples. Subsequent nucleotide base determination of the amplified DNA demonstrated that the detected DNA was derived from Mycoplasma pneumoniae. The results were confirmed by a PCR assay with use of M. pneumoniae-specific primers. Our findings confirm the usefulness of 16S rRNA gene amplification and analysis in the rapid and specific diagnosis of infectious osteomyelitis and reaffirm the role of such methods in detecting fastidious or uncultivable pathogens.

Adult↗
PubMed2004

Phylogenetic diversity of drinking water bacteria in a distribution system simulator.

AIMS: To characterize the composition of microbial populations in a distribution system simulator (DSS) by direct sequence analysis of 16S rDNA clone libraries. METHODS AND RESULTS: Bacterial populations were examined in chlorinated distribution water and chloraminated DSS feed and discharge water. Bacterial strains isolated from DSS discharge water on R2A medium were identified using 16S rDNA sequence analysis. The majority of the bacteria identified were alpha-proteobacteria, ranging from approx. 34% in the DSS discharge water to 94% of the DSS isolates. Species richness estimators Chao1 and ACE (abundance-based coverage estimators) indicated that the chlorinated distribution water sample was representative of the total population diversity, while the chloraminated DSS feed water sample was dominated by Hyphomicrobium sp. sequences. The DSS discharge water contained the greatest diversity of alpha-, beta-, gamma-proteobacteria, with 36% of the sequences being operational taxonomic units (OTUs, sequences with >97.0% homology). CONCLUSIONS: This work demonstrated the dominance of alpha-proteobacteria in distribution system water under two different disinfectant residuals. The shift from chlorine to monochloramine residual may have played a role in bacterial population dynamics. SIGNIFICANCE AND IMPACT OF THE STUDY: Accurate identification of bacteria present in treated drinking water is needed in order to better determine the risk of regrowth of potentially pathogenic organisms within distribution systems.

Base Sequence↗
PubMed2001

Multitude and temporal variability of ecological niches as indicated by the diversity of cultivated bacterioplankton.

The diversity of cultured planktonic bacteria was analyzed. Bacterial strains were isolated from a eutrophic lake (Zwischenahner Meer, Niedersachsen, Germany) at three different sampling dates (October 1997, April and May 1998). Phylogenetic diversity was assessed by polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), and sequencing of 16S rRNA gene fragments. Enterobacterial repetitive intergenic consensus (ERIC)-PCR revealed a high genomic diversity within the strain collections, which exceeded the diversity of the 16S rRNA gene sequences considerably. The composition of each of the three strain collections was unique since strains isolated at different dates always exhibited different ERIC-PCR fingerprints. Growth tests with 59 different carbon substrates demonstrated that even strains with identical ERIC-PCR fingerprints, isolated on one sampling date, differed in their physiology. The culturable fraction investigated in the present study constituted a relatively small fraction (</=15%) of the whole bacterioplankton assemblage. Nevertheless, the high physiological diversity in this fraction already indicates that a multitude of different ecological niches must exist in the planktonic environment. The majority of strains isolated in April prior to the decay of the phytoplankton bloom were members of the Cytophaga-Flavobacterium group. One month later, not a single strain of this group could be isolated. When a group-specific PCR-DGGE technique was employed, rapid shifts in the diversity of non-cultured Cytophaga-Flavobacteria also became evident. Based on the rapid shifts in the composition of cultivated as well as some non-cultivated bacteria, the ecological niches in the planktonic habitat must undergo rapid temporal changes.

Journal Article↗
PubMed2006

Common evolutionary origin of planktonic and benthic nitrogen-fixing oscillatoriacean cyanobacteria from tropical oceans.

The filamentous cyanobacteria belonging to the genus Hydrocoleum (Blennothrix) are among the most common mat-forming cyanobacteria in tropical oceans. We present here the evidence that these benthic cyanobacteria are morphologically and phylogenetically very close to the planktonic species of Trichodesmium. Genetic relationship was established independently with regard to sequences of the 16S rRNA gene, nifH gene, and phycocyanin and phycoerythrin intergenic spacers. The species of both genera formed a common distinct branch in phylogenetically reconstructed cyanobacterial trees, suggesting that the main constituents of cyanobacterial benthos and plankton have an early common origin and both represent major contributors to nitrogen budget of tropical oceans today as in the distant geological past.

Animals↗
PubMed1997

Granulocytic ehrlichiosis in two dogs in Switzerland.

This case report describes two dogs with granulocytic ehrlichiosis. Dog 1 was a male Labrador retriever with clinical signs of lymphosarcoma. Dog 2 was a female Airedale terrier, whose clinical signs included apathy, pyrexia, diarrhea, and abdominal pain. Examination of blood smears revealed Ehrlichia organisms in the neutrophils of both dogs. There was thrombocytopenia in both dogs, and dog 2 also had leukopenia. In both dogs, bands of identical length were amplified from DNA of leukocytes via nested PCR. The bands had identical nucleotide sequences, which differed from the gene sequences of Ehrlichia equi and E. phagocytophila in three and two positions, respectively. Interestingly, the nucleotide sequence of the 16S rRNA was 100% homologous to that of a human granulocytic ehrlichia.

Animals↗
PubMed2001

Biochemical identification and characterization of DNA groups within the Proteus vulgaris complex.

We placed 43 isolates belonging to the Proteus vulgaris complex into proposed DNA groups (genomovars) using five previously recommended tests (tests for esculin hydrolysis, production of acid from salicin, L-rhamnose fermentation, and elaboration of DNase and lipase). On the basis of the results of these five tests, 49% of the isolates fell into DNA groups 5 and 6, 37% fell into DNA group 2, and the remaining 14% fell into DNA groups 3 and 4. Sequencing of the 16S rRNA genes of 11 members of DNA groups 5 and 6 indicated that 10 of these isolates (91%) could be unambiguously assigned to one of these two genomospecies. Overall expression of selected enzymatic and virulence-associated characteristics did not differ significantly among DNA groups.

Bacterial Typing Techniques↗
PubMed2005

Isolation, characterization, and identification of Geobacillus thermodenitrificans HRO10, an alpha-amylase and alpha-glucosidase producing thermophile.

Thermophilic and amylolytic aerobic bacteria were isolated from soil through a selective enrichment procedure at 60 degrees C with starch as the carbon source. One of the isolates designated as HRO10 produced glucose aside from limit dextrin as the only hydrolysis product from starch and was characterized in detail. The starch-degrading enzymes produced by strain HRO10 were determined to be alpha-amylase and alpha-glucosidase. Whereas the alpha-amylase activity was detected exclusively in the culture supernatant, alpha-glucosidase occurred intracellular, extracellular, or on the surface of the bacteria depending on the growth phase. The optimum temperature and pH required for the growth of strain HRO10 were about 50 degrees C and pH 6.5 to 7.5. The strain used different carbohydrates as the carbon source, but the maximum production of alpha-amylase occurred when 1.0% (w/v) starch or dextrin was used. The use of organic vs. inorganic nitrogen favored the production of alpha-amylase in strain HRO10. The metal ions Li+, Mg2+, and Mn2+ stimulated the production of both enzymes. Identification of strain HRO10 by physiological and molecular methods including sequencing of the 16S rDNA showed that this strain belongs to the species Geobacillus thermodenitrificans. Biochemically, strain HRO10 differs from the type strain DSM 465 only in its ability to hydrolyze starch.

Bacillaceae↗
PubMed2004

Phylogenetic study and identification of Vibrio splendidus-related strains based on gyrB gene sequences.

Different strains related to Vibrio splendidus have been associated with infection of aquatic animals. An epidemiological study of V. splendidus strains associated with Crassostrea gigas mortalities demonstrated genetic diversity within this group and suggested its polyphyletic nature. Recently 4 species, V. lentus, V. chagasii, V. pomeroyi and V. kanaloae, phenotypically related to V. splendidus, have been described, although biochemical methods do not clearly discriminate species within this group. Here, we propose a polyphasic approach to investigate their taxonomic relationships. Phylogenetic analysis of V. splendidus-related strains was carried out using the nucleotide sequences of 16S ribosomal DNA (16S rDNA) and gyrase B subunit (gyrB) genes. Species delineation based on 16S rDNA-sequencing is limited because of divergence between cistrons, roughly equivalent to divergence between strains. Despite a high level of sequence similarity, strains were separated into 2 clades. In the phylogenetic tree constructed on the basis of gyrB gene sequences, strains were separated into 5 independent clusters containing V. splendidus, V. lentus, V. chagasii-type strains and a putative new genomic species. This phylogenetic grouping was almost congruent with that based on DNA-DNA hybridisation analysis. V. pomeroyi, V. kanaloae and V. tasmaniensis-type strains clustered together in a fifth clade. The gyrB gene-sequencing approach is discussed as an alternative for investigating the taxonomy of Vibrio species.

Animals↗
PubMed2004

[Evaluation of bacterial flora in contaminated soil as a countermeasure against H2S gas production].

Gas productions in illegal dumping sites and waste landfills have caused serious problems. The gas production was induced by bacterial flora inhabited soils. In order to construct a culture independent evaluation system of the soil bacteria, bacterial communities were analyzed quantitatively and qualitatively, about 16 soil samples at 4 sites, both using culture and culture-independent methods. The real time PCR method was developed for counting total bacterial number. Sequencing analysis of 16S rDNA amplified by a direct PCR method revealed that non-spore forming sulfate reducing bacteria and sulfur-oxidizing bacteria were detected at a similar frequency at an illegal dumping site near mountains. On the other hand, spore-forming sulfate reducing bacteria and Clostridium sp. were mainly detected in deep samples at reclaimed landfills from the sea, whereas sulfur-oxidizing bacteria was hardly detected. The result regarding sulfate-reducing bacteria was confirmed also by an anaerobic culture method. Culture-independent molecular analyses of soil bacteria would give us useful information for prediction of gas production and for the evaluation of soil equilibrium.

Air Pollution↗
PubMed2004

Biodiversity of human faecal bacteria isolated from phytic acid enriched chemostat fermenters.

BACKGROUND: Myo-inositol hexaphosphate (IP6) or phytic acid is found mostly in cereals and legumes and is thought to possess anti-carcinogenic properties. AIM: To isolate and identify faecal bacteria capable of phytic acid metabolism and to assess the effectiveness of prebiotics (dietary oligosaccharides, metabolised by selective colonic bacteria) in preserving the integrity of phytic acid. METHODS: Faecal samples from three volunteers were used in continuous culture experiments under varying conditions of pH, substrate concentration and dilution rates, seventy three different isolates cultured at steady state were then screened for phytic acid metabolism and identified through partial sequencing of their 16S rRNA genes (16S ribosomal ribonucleic acid). Utilisation of phytic acid was also assessed in a continuous culture system enriched with prebiotic fructooligosaccharides (FOS). RESULTS: Bacteroides spp., Clostridium spp. and facultatively anaerobic bacteria generally appeared to maintain viable counts in the presence of phytic acid. Bifidobacterium spp. and Lactobacillus spp. appeared less able to maintain viable counts in the presence of phytic acid. These results were confirmed by an increase in viable counts of Bacteroides spp., Clostridium spp. and a decrease in viable counts of Bifidobacterium spp. and Lactobacillus spp. once phytic acid was introduced to a FOS enriched continuous culture. CONCLUSIONS: The phytate metabolising biodiversity from the human large intestine does not appear to encompass major bacterial genera associated with beneficial or benign health effects (e.g. Lactobacillus spp. and Bifidobacterium spp).

Bacteria↗
PubMed2005

[Identification of Vibrio campbellii isolated from cultured pacific oyster].

Four bacterial strains were isolated from cultured pacific oyster (Crassostrea gigia) in September 2003 at coast of Fujian province. Their morphological, physiological and biochemical characteristics and 16S rRNA sequence were analyzed. And the relationship between reproduction of the bacterium and NaCl concentrations, pH and temperature were also determined. The results showed that four strains were gram-negative rods with a single polar flagellum, glucose fermented without gas production, oxidase positive, required sodium ions for growth, no pigment, non-luminescence; They grew well on TCBS-plate as green colonies and were sensitive to the vibriostratic agent O/129. Therefore, it was confirmed that the strains belonged to the genus of Vibrio. The sequence analysis of 16S rRNA gene of SXS1 isolation and comparison with that of other related vibrios- showed that SXS1 was very close to Vibrio campbellii. The similarities was 99%. The distribution of V. campbellii in environment and its relationship to the diseases of aquaculture animals were discussed.

Animals↗