Analysis of the interaction of Aeromonas caviae, A. hydrophila and A. sobria with mucins

Aeromonas species are known to be involved in human gastrointestinal diseases. These organisms colonize the gastrointestinal tract. Aeromonas hydrophila, A. caviae, and A. sobria have been demonstrated microscopically to adhere to animal cell lines that express mucous receptors, but quantitative studies of adherence to mucosal components such as mucin have not been published to date. Purified bovine submaxillary gland, hog gastric mucin, and fish skin mucin were used as a model to study mucin-binding activity among A. caviae, A. hydrophila, and A. sobria strains. Our findings revealed that binding of radiolabeled and enzyme-conjugated mucins to Aeromonas cells varied depending on the labeling procedure. The highest binding was observed when the three mucin preparations were labeled with horseradish peroxidase. Binding of the various horseradish peroxidase-labeled mucins by A. caviae, A. hydrophila, and A. sobria cells is a common property among Aeromonas species isolated from human infections, diseased fish, and from environmental sources. The proportion of Aeromonas strains which bind the various horseradish peroxidase-labeled mucins was significantly higher for A. hydrophila than for A. caviae and A. sobria. Bacterial cell-surface extracts containing active mucin-binding components recognized the horseradish peroxidase-labeled mucins. The molecular masses of the mucin-binding proteins were estimated by SDS-PAGE and Western blot as follows: A. caviae strain A4812 (95 and 44 kDa); A. hydrophila strain 48748 (97, 45, 33 and 22 kDa); and A. sobria strain 48739 (95 and 43 kDa). Mucin interaction with Aeromonas cells was also studied in terms of growth in mucin-rich media. The culture conditions greatly influence the expression of A. hydrophila mucin-binding activity.     

A cluster of atypical Yersinia strains with a distinctive 16S rRNA signature

Thirty-eight bacterial isolates from raw milk samples in Queensland, Australia were identified as members of the genus Yersinia on the basis of biochemical profile, ability to hybridize with a genus-specific DNA probe, comparative 16S rDNA sequence analysis, and the presence of characteristic 16S rDNA signature nucleotides which occur in all Yersinia spp. Twenty-five of these isolates reacted with typing sera (O:22 or O:58) of Y. enterocolitica; the remainder were non-typable. None of the isolates displayed any of the phenotypic or genetic virulence-associated characteristics of Y. enterocolitica. Comparative 16S rDNA sequence analysis revealed that members of this group appear to represent a new sub-line within the genus Yersinia, most closely related to Y. frederiksenii hybridization group 2 (unnamed genomospecies 2). This finding was confirmed by DNA hybridization studies which indicated that the strains belonged to the unnamed genomospecies, Yersinia frederiksenii genomospecies 2, which is biochemically indistinguishable from Y. frederiksenii (Y. frederiksenii genomospecies 1). A 23-nucleotide 16S rDNA signature stretch which characterised these strains was identified.     

Acyl phosphatidylglycerol: a major phospholipid of Corynebacterium amycolatum

The type strain and several clinical isolates of Corynebacterium amycolatum were examined for lipid composition as a chemotaxonomic character for routine identification. The phospholipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides, together with various unidentified compounds. One of them, accounting for 20–29% of total phospholipids, was purified and characterized as acyl phosphatidylglycerol by chromatographic and spectrometric techniques. The acyl substituents on the phosphatidyl moiety were characterized as tetradecanoyl, pentadecanoyl, hexadecenoyl, hexadecanoyl, heptadecenoyl, heptadecanoyl, octadecenoyl (the major one), and octadecanoyl. The acyl group on the polar head (glycerol) was only octadecenoyl. Phospholipid analysis by thin-layer chromatography of a collection of Corynebacterium strains proved that this compound is widely distributed, although it only represents a minor (2–9%) component among mycolic acid-containing species. Acyl phosphatidylglycerol can be considered as a useful chemical marker for the identification of C. amycolatum in addition to the absence of mycolic acids.     

Identification of Pediococcus acidilactici and Pediococcus pentosaceus based on 16S rRNA and ldhD gene-targeted multiplex PCR analysis

A multiplex PCR assay that can readily and unambiguously identify Pediococcus acidilactici and Pediococcus pentosaceus strains was developed to give an easy-to-read profile based on the amplification of a 16S rRNA gene fragment, specific for each species, and a d-lactate dehydrogenase gene fragment specific for Pediococcus acidilactici strains.     

Sex identification of parrots,toucans, and curassows by PCR: Perspectives for wild and captive population studies

Methods for the identification of the sex of bird species without external sexual dimorphism are specially important in field studies and for captive breeding of endangered taxa. We confirmed the accuracy of a polymerase chain reaction (PCR)-based method to identify the sex in three disparate avian orders that included 31 species of parrot, two species of toucan, and eight species of curassow, for which many individuals were previously sexed. In each case, two DNA fragments were amplified in females and one in males with the use of a single set of primers. This method was also tested on unsexed birds of 13 other species of parrot and five species of toucan. The same kind of polymorphism was detected in each. The PCR products of parrots and toucans could be separated in simple agarose gels, while the curassows' products could only be distinguished in acrylamide gels. An advantage of this DNA test is that samples of blood or feathers can be easily collected and stored at room temperature, which is of particular importance for studies of wild birds. Zoo Biol 17:415–423, 1998. © 1998 Wiley-Liss, Inc.     

贵州苗岭地区野猪肠道菌群结构与功能分析

野猪是当前南方山地森林生态系统中数量激增的主要有蹄类.为揭示贵州苗岭地区野猪肠道细菌的群落结构、多样性及菌群功能,本研究采用16SrRNA高通量测序技术检测了 4头野猪胃肠道(胃、回肠、结肠和直肠)的细菌群落,共获得1 268 577条有效序列.经质控过滤,所有序列归类于1 019个OTU,包含19门292属.在门分类...     

A sequence-specific DNA-binding protein interacts with the xlnC upstream region of Streptomyces sp. strain EC3

Abstract With the recent resolution of the crystal structures of several bacterial porins, it is worthwhile to define the generality of their organization throughout the Enterobacteriaceae. The distribution of specific epitopes was analysed among various Gram-negative bacterial porins using anti-peptide antibodies specific to exposed, transmembrane spanning, or pore-forming regions of Escherichia coli porins. Anti-peptide antibodies which recognized the exposed epitopes indicated a great variability among the bacterial porins analysed. Interestingly, an antigenic site located in the internal loop L3 constricting the pore diameter was present in the majority of the bacterial porins tested. Two epitopes located in domains involved in subunit interaction were also highly conserved. The presence of these common peptides suggested a conservation of specific regions involved in the functional organization of the enterobacterial porins.     

Characterization of sulphate-reducing bacterial populations within marine and estuarine sediments with different rates of sulphate reduction

Viable counts of sulphate-reducing bacteria, able to use a range of different growth substrates were determined in sediments from two Sea Lochs (Etive and Eil) and an estuarine site (Tay), in Scotland. The composition of the sulphate-reducing bacterial population, in terms of substrate utilization, broadly corresponded to the in situ substrates for sulphate reduction and concentration of substrates at each site. Addition of acetate, lactate, propionate, butyrate, hydrogen and glutamate/serine (20 mM) to replicate slurries from each site resulted in stimulation of the corresponding population of sulphate-reducing bacteria and the in situ rates of sulphate reduction. The metabolism of the added substrates and changes in bacterial phospholipid fatty acids (PLFA) were quantified. With the exception of acetate and hydrogen, added substrates were incompletely oxidised, producing a mixture of further substrates, which predominantly were sequentially oxidised, and resulted in the stimulation of a mixed population of sulphate-reducing bacteria. There were significant changes in the PLFA of slurries with added substrate compared to controls. Acetate was completely removed at all sites and the small increase in even chain PLFA together with the absence of stimulation of any other biomarker, indicated that acetate was oxidised by sulphate-reducing bacteria distinctly different from those using other substrates. A biomarker for Desulfobacter, 10 Methyl 16:0, was not stimulated in any of the acetate slurries or in slurries where acetate was produced. Biomarkers for the propionate utilizing Desulfobulbus sp (17:1w6, 15:1w6) were always stimulated in propionate slurries and also in lactate slurries, where partial lactate fermentation produced propionate and acetate. In lactate and glutamate / serine slurries from the Tay estuary and lactate and hydrogen slurries from Loch Etive the biomarker for Desulfovibrio sp (i17:1w7) as well as those for Desulfobulbus were stimulated. This provides direct evidence for the significance of Desulfovibrio sp. within sediment slurries and demonstrates the competitive interaction between members of this genus and Desulfobulbus sp. for lactate, hydrogen and amino acid metabolism. At the estuarine site, sulphate reduction was limited at higher sulphate concentrations (about 3.5 mM) than the Sea Loch sites (<2 mM) and this had a significant effect on propionate and butyrate metabolism, as well as on methane production. These results demonstrate that although the sulphate-reducing bacterial population at each site could metabolise identical substrates, the types of sulphate-reducing bacteria involved and their sulphate thresholds were characteristically different.     

Biooxidation of a gold-bearing pyrite-arsenopyrite concentrate

Abstract: Two years of BIOX pilot plant data have been examined for steady state conditions and then correlated using logistic kinetics. It was found that the logistic equation not only predicted the performance of individual stages but also the degree of biooxidation across the entire cascade of bioreactors. It was found that the rate constant was 1.3 day^-1 in the first three stages and 0.3 day^-1 in the fourth stage. The maximum removal constant was 0.90 in stage 1 and 0.99 in the remaining stages. Plant retention time ranged from 4 to 12 days with corresponding sulphide oxidation varying from 82 to 98% respectively, and primary stage removal rates varying from 8.9 to 4.4 kg m^-3 day^-l, respectively. In addition, batch biooxidation data were obtained. The biooxidation rate was found to be about half that for the continuous bioreactors. This is in agreement with the findings of several other workers. The specific rates of bioxidation of pyrite and arsenopyrite were very similar for the bulk concentrate at about 0.15 day^-1. However, it was significant that the biooxidation of arsenopyrite in the mixed mineral preceded that of pyrite, suggesting a sequential mechanism. Gold liberation was found to be linearly related to arsenopyrite biooxidation but oxidation of pyrite appears to be preferential in the gold-rich regions.     

Structural Insights into Higher Order Assembly and Function of the Bacterial Microcompartment Protein PduA

Bacterial microcompartments are large proteinaceous assemblies that are found in the cytoplasm of some bacteria. These structures consist of proteins constituting a shell that houses a number of enzymes involved in specific metabolic processes. The 1,2-propanediol-utilizing microcompartment is assembled from seven different types of shell proteins, one of which is PduA. It is one of the more abundant components of the shell and intriguingly can form nanotubule-like structures when expressed on its own in the cytoplasm of Escherichia coli. We propose a model that accounts for the size and appearance of these PduA structures and underpin our model using a combinatorial approach. Making strategic mutations at Lys-26, Val-51, and Arg-79, we targeted residues predicted to be important for PduA assembly. We present the effect of the amino acid residue substitution on the phenotype of the PduA higher order assemblies (transmission electron microscopy) and the crystal structure of the K26D mutant with one glycerol molecule bound to the central pore. Our results support the view that the hexamer-hexamer interactions seen in PduA crystals persist in the cytoplasmic structures and reveal the profound influence of the two key amino acids, Lys-26 and Arg-79, on tiling, not only in the crystal lattice but also in the bacterial cytoplasm. Understanding and controlling PduA assemblies is valuable in order to inform manipulation for synthetic biology and biotechnological applications.