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Gene Sequence Analysis (gene + sequence_analysis)
Kinds of Gene Sequence Analysis Selected AbstractsGenomic and phenotypic heterogeneity of Acidithiobacillus spp. strains isolated from diverse habitats in ChinaFEMS MICROBIOLOGY ECOLOGY, Issue 2 2008Yong-Qing Ni Abstract The genetic variability among 32 Chinese Acidithiobacillus spp. environmental isolates and four reference strains representing three recognized species of the genus Acidithiobacillus was characterized by using a combination of molecular methods, namely restriction fragment length polymorphisms of PCR-amplified 16S rRNA genes and 16S,23S rRNA gene intergenic spacers, repetitive element PCR, arbitrarily primed PCR and 16S rRNA gene sequence analyses. 16S rRNA gene sequences revealed that all Acidithiobacillus spp. strains could be assigned to seven groups, three of which encompassed the Acidithiobacillus ferrooxidans strains from various parts of the world. A comparative analysis of the phylogenetic Group 1 and 2 was undertaken. Restriction fragment length polymorphism results allowed us to separate the 35 Acidithiobacillus strains into 15 different genotypes. An integrated phenotypic and genotypic analysis indicated that the distribution of A. ferrooxidans strains among the physiological groups were in agreement with their distribution among the genomic groups, and that no clear correlation was found between the genetic polymorphism of the Acidithiobacillus spp. strains and either the geographic location or type of habitats from which the strains were isolated. In addition, five unidentified sulfur-oxidizing isolates may represent one or two novel species of the genus Acidithiobacillus. The results showed that the Chinese Acidithiobacillus spp. isolates exhibited a high degree of genomic and phenotypic heterogeneity. [source] MORPHOLOGY, REPRODUCTION, AND THE 18S rRNA GENE SEQUENCE OF PIHIELLA LIAGORACIPHILA GEN.JOURNAL OF PHYCOLOGY, Issue 5 2003ET SP. Pihiella liagoraciphila gen. et sp. nov. (Rhodophyta) is described for a minute endo/epiphyte that is commonly associated with members of the Liagoraceae ( Nemaliales, Rhodophyta). Algae are discoid or subspherical and grow to a maximum diameter of 400 ,m. Attachment is via isolated elongate rhizoids that penetrate into the loosely filamentous structure of the host or by a pad of several coalesced rhizoids where the host has a more cohesive cortex. Elongate surface hairs are common. Gametophytes are dioecious, the spermatangia arising on surface cells, and carpogonia with elongate trichogynes borne directly on undifferentiated surface supporting cells. Large sporangia form on stalk cells across the upper surface of the plants, these appearing to be either monosporangial or the result of fertilization of the carpogonia and equivalent to undivided zygotosporangia. Carposporophytes and tetrasporangia are unknown. 18S rRNA gene sequence analyses indicate that Pihiella constitutes a clade of long branch length most closely related to the Ahnfeltiales. The unique morphology and reproduction of Pihiella, combined with a substantial genetic divergence from the Ahnfeltiales, suggest that it is sufficiently distinct to warrant placement in a new family and order. We therefore describe the family Pihiellaceae and the order Pihiellales to accommodate the new genus. [source] Evaluation of apoptosis in cytologic specimensDIAGNOSTIC CYTOPATHOLOGY, Issue 9 2010Viktor Shtilbans Ph.D. Abstract A hallmark of neoplasia is dysregulated apoptosis, programmed cell death. Apoptosis is crucial for normal tissue homeostasis. Dysregulation of apoptotic pathways leads to reduced cytocidal responses to chemotherapeutic drugs or radiation and is a frequent contributor to therapeutic resistance in cancer. The literature pertaining to detection of apoptotic pathway constituents in cytologic specimens is reviewed herein. Virtually all methods for detecting apoptosis, including classic cytomorphologic evaluation, TUNEL assay, immunocytochemistry, and gene sequence analysis, may be applied to cytologic samples as well as tissue. Components of both intrinsic and extrinsic apoptotic pathways have been studied, including many reports examining p53 and bcl-2, as well as studies of caspase inhibitory proteins XIAP and survivin, death receptors and ligands such as Fas, Fas-ligand, and TRAIL. p53 undergoes oncogenic alteration more than any other protein; its immunocytochemical detection almost always connotes loss of its physiologic role as an inducer of apoptosis in response to a damaged genome. Several reports establish cytologic sampling as being as useful as tissue sampling. In one respect cytologic sampling is superior to tissue sampling in particular, by allowing clinicians to repeat sampling of the same tumor before and after administration of therapy; a number of reports use this approach to attempt to predict tumor response by assaying the effect of chemotherapy on the induction of apoptosis. Diagn. Cytopathol. 2010;38:685,697. © 2010 Wiley-Liss, Inc. [source] Phylogenetic analysis of Porphyromonas species isolated from the oral cavity of Australian marsupialsENVIRONMENTAL MICROBIOLOGY, Issue 9 2008Deirdre Mikkelsen Summary Porphyromonas species are frequently isolated from the oral cavity and are associated with periodontal disease in both animals and humans. Black, pigmented Porphyromonas spp. isolated from the gingival margins of selected wild and captive Australian marsupials with varying degrees of periodontal disease (brushtail possums, koalas and macropods) were compared phylogenetically to Porphyromonas strains from non-marsupials (bear, wolf, coyote, cats and dogs) and Porphyromonas gingivalis strains from humans using 16S rRNA gene sequence analysis. The results of the phylogenetic analysis identified three distinct groups of strains. A monophyletic P. gingivalis group (Group 1) contained only strains isolated from humans and a Porphyromonas gulae group (Group 2) was divided into three distinct subclades, each containing both marsupial and non-marsupial strains. Group 3, which contained only marsupial strains, including all six strains isolated from captive koalas, was genetically distinct from P. gulae and may constitute a new Porphyromonas species. [source] Molecular and morphological characterization of the association between bacterial endosymbionts and the marine nematode Astomonema sp. from the BahamasENVIRONMENTAL MICROBIOLOGY, Issue 5 2007Niculina Musat Summary Marine nematode worms without a mouth or functional gut are found worldwide in intertidal sandflats, deep-sea muds and methane-rich pock marks, and morphological studies show that they are associated with endosymbiotic bacteria. While it has been hypothesized that the symbionts are chemoautotrophic sulfur oxidizers, to date nothing is known about the phylogeny or function of endosymbionts from marine nematodes. In this study, we characterized the association between bacterial endosymbionts and the marine nematode Astomonema sp. from coral reef sediments in the Bahamas. Phylogenetic analysis of the host based on its 18S rRNA gene showed that Astomonema sp. is most closely related to non-symbiotic nematodes of the families Linhomoeidae and Axonolaimidae and is not closely related to marine stilbonematinid nematodes with ectosymbiotic sulfur-oxidizing bacteria. In contrast, phylogenetic analyses of the symbionts of Astomonema sp. using comparative 16S rRNA gene sequence analysis revealed that these are closely related to the stilbonematinid ectosymbionts (95,96% sequence similarity) as well as to the sulfur-oxidizing endosymbionts from gutless marine oligochaetes. The closest free-living relatives of these gammaproteobacterial symbionts are sulfur-oxidizing bacteria from the family Chromatiaceae. Transmission electron microscopy and fluorescence in situ hybridization showed that the bacterial symbionts completely fill the gut lumen of Astomonema sp., suggesting that these are their main source of nutrition. The close phylogenetic relationship of the Astomonema sp. symbionts to known sulfur-oxidizing bacteria as well as the presence of the aprA gene, typically found in sulfur-oxidizing bacteria, indicates that the Astomonema sp. symbionts use reduced sulfur compounds as an energy source to provide their hosts with nutrition. [source] Arsenic Binding to Iron(II) Minerals Produced by An Iron(III)-Reducing Aeromonas Strain Isolated from Paddy SoilENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 11 2009Xin-Jun Wang Abstract An iron-reducing bacterial strain was isolated from a paddy soil and identified as a member of the Aeromonas group by 16S rRNA gene sequence analysis. When the cells were growing with dissolved Fe(III) as the electron acceptor in the presence of As(V), Fe(II) minerals (siderite and vivianite) were formed and dissolved. As was removed efficiently from solution. When the cells were growing with the Fe(III) hydroxide mineral (ferrihydrite) as the electron acceptor in the presence of As(V), ferrihydrite was reduced and dissolved As(V) concentrations decreased sharply. The present study results demonstrated first that members of the Aeromonas group can reduce Fe(III) in paddy soils and second that iron reduction does not necessarily lead to arsenic mobilization. However, As immobilization can occur in environments that contain significant concentrations of counterions such as bicarbonate and phosphate. [source] Isolation and identification of equol-producing bacterial strains from cultures of pig faecesFEMS MICROBIOLOGY LETTERS, Issue 1 2008Zhuo-Teng Yu Abstract Transformation of daidzein to equol was compared during fermentation of three growth media inoculated with faeces from Erhualian piglets, but equol was produced from only one medium, M1. Two equol-producing strains (D1 and D2) were subsequently isolated using medium M1. Both strains were identified as Eubacterium sp., on the basis of morphological and physiological characteristics, and 16S rRNA gene sequence analysis showed that strains D1 and D2 were most closely related to previously characterized daidzein-metabolizing bacteria isolated from human faecal and rumen samples, respectively. This suggests that the ability to metabolize daidzein can be found among bacteria present within the mammalian intestine. The results provided the first account of conversion of daidzein directly to equol by bacterial species from farm animals. These strains may be of importance to the improvement of animal performance, and the use of medium M1 could provide a simple way to isolate bacterial strains capable of transforming daidzein into equol. [source] Application of recA and rpoB sequence analysis on phylogeny and molecular identification of Geobacillus speciesJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2009F.Y. Weng Abstract Aims:, Some Geobacillus species have highly similar 16S rRNA gene sequences, making 16S rDNA sequence analysis-based identification problematic. To overcome this limitation, recA and rpoB sequence analysis was evaluated as an alternative for distinguishing Geobacillus species. Methods and Results:, The phylogram of 16S rRNA gene sequences inferred from the neighbour-joining method showed that nine clusters of Geobacillus species were characterized with bootstrap values >90%. The recA and rpoB sequences of 10 reference strains in clusters V, VIb and VIc were amplified and sequenced using consensus primers. Alignment of recA sequences in clusters V, VIb and VIc revealed three types of recA genes, consistent with the putative amino acid sequences and in vivo recA splicing analysis. The phylogram constructed from rpoB sequences showed more divergence than that constructed from 16S rRNA gene sequences. Conclusions:,recA and rpoB sequence analysis differentiated closely-related Geobacillus species and provided direct evidence for reclassifying some species dubiously categorized as Geobacilli. Additionally, this study revealed three types of recA genes in the different Geobacillus species. Significance and Impact of the Study:, This study highlights the advantage of recA and rpoB sequence analysis to supplement 16S rRNA gene sequence analysis for efficient and convenient determination of Geobacillus species. [source] Phylogenetic analysis by 16S rDNA gene sequence comparison of avian taxa of Bisgaard and characterization and description of two new taxa of PasteurellaceaeJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2003H. Christensen Abstract Aims: Characterization and classification of members of Pasteurellaceae isolated from birds by extended phenotypic characterization and 16S rDNA gene sequence comparison. Methods and Results: A total of 95 avian isolates were subjected to extended phenotypic characterization. Thirteen bacterial strains selected from main phenotypic clusters and isolated from parrot, parakeet, budgerigar, partridge, pheasant, chicken, duck, hawk and gull were subsequently characterized by 16S rDNA gene sequencing. Eight of the sequenced strains were classified with six taxa of Bisgaard of which two (34 and 40) have not been published before, and the properties of four others (14, 22, 26 and 32) changed upon the characterization of these new isolates. Of the remaining strains, one was identified as a phenotypic variant in maltose and dextrin of Pasteurella gallinarum another as a trehalose positive variant of taxon 3 of Bisgaard. The remaining three strains sequenced were not closely related to existing taxa of Pasteurellaceae. However, they were found to belong to the Avian cluster with 92,97% 16S rDNA gene sequence similarity. Conclusion: The study allowed the classification of bacteria isolated from birds by the integrated use of extended phenotypic characterization and 16S rDNA gene sequence analysis. Only the application of 16S rDNA gene sequencing allows a correct identification of variant strains. Significance and Impact of the Study: The description of new taxa within the bacterial family Pasteurellaceae will subsequently allow additional isolates of these taxa to be identified and improve the diagnosis and epidemiological understanding of bacteria causing disease in birds. [source] Marine biogeographical structure in two highly dispersive gastropods: implications for trans-Tasman dispersalJOURNAL OF BIOGEOGRAPHY, Issue 4 2007Jonathan M. Waters Abstract Aim, Recent genetic and ecological studies of marine invertebrate species with planktotrophic larvae have inferred high rates of gene flow across wide oceanic barriers. We therefore aim to test for the genetic signature of long-distance dispersal in two widespread and abundant marine gastropod taxa. Location, The intertidal and shallow subtidal zones of southern Australia and New Zealand (NZ), which house similar marine invertebrate assemblages despite being separated by the 2000-km-wide Tasman Sea. Methods, We used mtDNA cytochrome oxidase I gene sequence analysis of two gastropod genera exhibiting trans-Tasman distributions, namely Austrolittorina (Littorinidae) (139 specimens; 28 localities) and Scutus (Fissurellidae) (154 specimens; 32 localities). The cool-temperate Australian (A. unifasciata; S. antipodes) and NZ (A. antipodum; S. breviculus) taxa within each genus are morphologically similar but of uncertain taxonomic status. Results, The mtDNA analyses indicate major trans-Tasman genetic discontinuities for both gastropod genera, with no evidence of recent or ongoing intercontinental gene flow. Although both Scutus and Austrolittorina show significant east,west structure within southern Australia , consistent with recent studies of regional marine phylogeography , neither taxon exhibits significant differentiation within NZ. Main conclusions, Morphologically conserved but biogeographically disjunct gastropod populations may exhibit striking phylogeographic discontinuities, even when dispersal abilities appear to be high. On the basis of these data we reject recent calls for the synonymy of NZ and Australian lineages. [source] ISOLATION AND IDENTIFICATION OF A NOVEL ASPERGILLUS JAPONICUS JN19 PRODUCING ,-FRUCTOFURANOSIDASE AND CHARACTERIZATION OF THE ENZYMEJOURNAL OF FOOD BIOCHEMISTRY, Issue 6 2006LI-MEI WANG ABSTRACT A novel strain, Aspergillus sp. JN19, producing,-fructofuranosidase (FFase), was isolated from soil. According to the physiological and biochemical characteristics and its 18S rDNA gene sequence analysis, it was identified as Aspergillus japonicus. The optimal conditions for production of fructofuranosidase by A. japonicus JN-19 were investigated. The initial concentration of sucrose was 15 to 18%. Yeast extract was the best nitrogen source. K2HPO4 was effective in increasing enzyme production. The enzyme activity was increased to about 1.3 times by addition of 0.2% carboxymethylcellulose in the medium. The highest FFase activity was 55.42 U/mL at pH 5.5 and 30C, and production yield of fructooligosaccharides was 55.8%. Some characteristics of purified FFase were also studied. [source] Affinities of the freshwater red alga Audouinella macrospora (Florideophyceae, Rhodophyta) and related forms based on ssu rrna gene sequence analysis and pit plug ultrastructureJOURNAL OF PHYCOLOGY, Issue 2 2000Curt M. Pueschel Small subunit rDNA sequencing and transmission electron microscopy were performed to clarify the ordinal affinities of Audouinella macrospora (Wood) Sheath et Burkholder isolates 3394, 3395, and 3603, as well as Chantransia sp. isolate 3585. Culture 3603 is known to produce thalli of Batrachospermum -like morphology under certain culture conditions. Sequence analyses unequivocally placed the three Audouinella macrospora isolates in a clade with Batrachospermum macrosporum Montagne of the Batrachospermales, and Chantransia sp. was found to have affinities with B. louisianae Skuja and B. virgato-decaisneanum Sirodot. The pit plugs of the Audouinella macrospora cultures 3394 and 3395 were nearly identical in size and structure, having thickened plug caps and no cap membranes. Both of these features agree with those of the Batrachospermaceae, with the latter feature showing batrachospermacean rather than acrochaetioid affinities. Pit plugs in the chantransia phase of 3603 were similar, but the plug caps were less well developed. The Batrachospermum phase generated from 3603 had pit plugs that were variable in diameter, according to location in the thallus, thus reflecting the more variable cell size in this phase. Dome-like outer caps, considered typical of Batrachospermum, were present between cells of the determinate lateral filaments. The pit plugs of Chantransia sp. had prominent, dome-like outer caps, but the plug cores were strikingly and consistently smaller in diameter than those of the A. macrospora chantransia cultures, suggesting that plug diameter may be of systematic value in some contexts. [source] Fungal endophytes from Dioscorea zingiberensis rhizomes and their antibacterial activityLETTERS IN APPLIED MICROBIOLOGY, Issue 1 2008L. Xu Abstract Aims:, The aim of the study was to isolate and characterize the endophytic fungi from the rhizomes of the Chinese traditional medicinal plant Dioscorea zingiberensis and to detect their antibacterial activities. Methods and Results:, After strict sterile sample preparation, nine fungal endophytes were isolated from rhizomes of the Chinese traditional medicinal plant D. zingiberensis. The endophytes were classified by morphological traits and internal transcribed spacer (ITS) rRNA gene sequence analysis. Their ITS rDNA sequences were 99,100% identical to Nectria, Fusarium, Rhizopycnis, Acremonium and Penicillium spp. respectively. Of these, the most frequent genera were Fusarium and Nectria. One isolate, Dzf7, was unclassified on the basis of its low sequence similarity. The next closest species was Alternaria longissima (c. 92·4% sequence similarity). Endophyte isolate Dzf5 showed the closest sequence similarity (c. 99·5%) to an uncultured soil fungus (DQ420800) obtained from Cedar Creek, USA. Bioassays using a modified broth dilution test were used to detect the antibacterial activity of n -butanol extracts of both mycelia and culture filtrates of D. zingiberensis showed biological activity against Bacillus subtilis, Staphylococcus haemolyticus, Escherichia coli and Xanthomonas vesicatoria. Minimal inhibitory concentration (MIC) values of the extracts were between 31·25 ,g ml,1 and 125 ,g ml,1. Conclusions:, Endophytic fungus Dzf2 (c. 99·8% sequence similarity to Fusarium redolens) isolated from D. zingiberensis rhizome showed the most potent antibacterial activities. Significance and Impact of the Study:, Endophytic fungi isolated from D. zingiberensis may be used as potential producers of antibacterial natural products. [source] Description and Phylogenetic Relationships of Spumochlamys perforata n. sp. and Spumochlamys bryora n. sp. (Amoebozoa, Arcellinida)THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 6 2009ALEXANDER KUDRYAVTSEV ABSTRACT. Spumochlamys perforata n. sp. and Spumochlamys bryora n. sp. were isolated and described from dry epiphytic moss. The morphology and ultrastructure of both species clearly demonstrate that they belong to the genus Spumochlamys (family Microchlamyiidae). They differ from its only described member, Spumochlamys iliensis (as well as from species of Microchlamys), in the relief of the dorsal surface of the test, revealed by scanning electron microscopy, which can represent a good characteristic for species identification. They also differ in the structure of the dorsal part of the test wall (especially S. perforata). Small subunit ribosomal DNA-based molecular phylogenetic analyses show that Spumochlamys is a deeply branching lineage of the Arcellinida, without any close affinities. Actin gene sequence analysis places this genus within the Tubulinea, close to two other arcellinid lineages but without forming a monophyletic group with them. These data together strongly suggest that the lack of resolution in the arcellinid molecular phylogenies is due to serious undersampling of taxa, a limited number of sequence data, and high divergence rates in most of the species. [source] Molecular Characterization of the Obligate Endosymbiont "Caedibacter macronucleorum"Fokin and Görtz, 1993 and of its Host Paramecium duboscqui Strain Ku4-8THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 6 2006MARTINA SCHRALLHAMMER ABSTRACT. Bacterial endosymbionts of protozoa were often described as new species by protozoologists mainly on the basis of few morphological characters and partly by host specificity. Many of these species have never been validated by prokaryotic microbiologists whose taxonomic rules are quite different from those of protozoologists, who use the Zoological Code of Nomenclature. "Caedibacter macronucleorum"Fokin and Görtz 1993, an endosymbiont of Paramecium duboscqui, belongs to this category. Here we provide the molecular characterization of this organism and of its host P. duboscqui strain Ku4-8. Bacterial 16S rRNA gene sequence analysis proved that "C. macronucleorum" belongs to the Alphaproteobacteria. It is closely related to Caedibacter caryophilus but not to Caedibacter taeniospiralis, which belongs to the Gammaproteobacteria. "Caedibacter macronucleorum" and C. caryophilus 16S rRNA genes show a similarity value of 99%. This high 16S rRNA sequence similarity and the lack of a specific oligonucleotide probe for distinguishing the two endosymbionts do not allow validating "C. macronucleorum" as a provisional taxon (Candidatus). Nevertheless, "C. macronucleorum" and C. caryophilus can be easily discriminated on the basis of a highly variable stretch of nucleotides that interrupts the 16S rRNA genes of both organisms. [source] Identification of gut-associated amylase, cellulase and protease-producing bacteria in three species of Indian major carpsAQUACULTURE RESEARCH, Issue 10 2010Arun Kumar Ray Abstract Isolation and enumeration of amylase, cellulase and protease-producing autochthonous bacteria in the proximal intestine (PI) and distal intestine (DI) of three species of Indian major carps, catla (Catla catla), mrigal (Cirrhinus mrigala) and rohu (Labeo rohita), were investigated using the conventional culture-based technique. Population levels of amylolytic strains were the highest in the PI of catla and the lowest in the DI of rohu. The highest viable count of cellulase and protease-producing bacteria was recorded in the DI and PI of mrigal respectively. Among the bacteria isolated, 10 strains (five from PI and five from DI) were selected as potent enzyme producers according to a quantitative enzyme assay. The chosen strains were further identified by 16S rRNA gene sequence analysis. The five strains isolated from catla showed high similarity to Citrobacter sp. clone W2, Enterobacter sp. JA24, Bacillus coagulans strain TR, uncultured bacterial clone Hel3bc04 and Bacillus cereus strain UST2006-BC004. The four strains isolated from mrigal were most closely related to Bacillus sp. KCd2, uncultured bacterial clone Hel3bd09, B. cereus strain BU040901-020 and Citrobacter freundii strain YRL11, while the strain isolated from rohu probably belonged to Bacillus sp. GV. [source] Antagonistic activity of bacterial isolates from intestinal microbiota of Atlantic cod, Gadus morhua, and an investigation of their immunomodulatory capabilitiesAQUACULTURE RESEARCH, Issue 2 2010Christopher Marlowe A Caipang Abstract In an effort to identify potential probionts, four bacterial strains obtained from the intestinal tract of wild-caught Atlantic cod, Gadus morhua, were tested for their antagonistic activity against Vibrio anguillarum and Aeromonas salmonicida, two of the most common bacterial pathogens in cod aquaculture, using a well-diffusion agar assay at two incubation temperatures: 13 and 20 °C. The tested bacteria exhibited dissimilarity in their inhibitory action against the target pathogens , an enhanced activity was particularly observed for strains GP11 and GS11 at the highest incubation temperature. Based on the 16S ribosomal DNA gene sequence analysis, the strains showed high similarity to Psychrobacter sp. (strain GP11), Shewanella sp. (GS11), Photobacterium sp. (GP31) and Vibrio sp. (GV11). The incubation of Atlantic cod head kidney cells with the heat-inactivated probiotic strains resulted in the differential expression of immune-response genes that are related to bacterial defence and inflammation. Thus, the gut-derived bacterial strains have probiotic potential and their possible immunomodulatory capabilities could be determined under in vitro conditions. [source] Isolation and identification of Alicyclobacillus acidocaldarius by 16S rDNA from mango juice and concentrateINTERNATIONAL JOURNAL OF FOOD SCIENCE & TECHNOLOGY, Issue 7 2005Pieter A. Gouws Summary In this study we investigate the spoilage of ultra high temperature UHT mango juice as well as a carbonated fruit juice blend to identify organisms contributing to the spoilage. The mango concentrate, the final product, as well as the other ingredients used during manufacturing, were tested for the presence of Alicyclobacillus by polymerase chain reaction (PCR) and sequencing analyses. Microbiological examination of the mango pureé and spoiled fruit juices, using YSG agar [yeast extract 2 g, glucose 1 g, soluble starch 2 g, pH 3.7 (adjust with 2N H2SO4), H2O 1000 mL, bacto agar 15 g] incubated at 55 °C, detected sporeforming, acid dependent and thermotolerant bacteria. The hyper variable region of the 16S rDNA was amplified. The nucleotide sequence of the PCR fragments was determined using the ABI Prism 310 automated DNA sequencer and the collected sequencing data were analysed and compared with the non-redundant database using NCBI-BLAST. Alicyclobacillus acidocaldarius were isolated and identified by 16S rDNA gene sequences analyses. The results indicated that the mango purče, as well as the final product of mango juice and the fruit juice blend, were positive for Alicyclobacillus. The preventative measures of low pH, pasteurization of mango juice and the subsequent use of aseptic packaging were not regarded as sufficient to prevent the outgrowth of Alicyclobacillus spoilage organisms. [source] Genetic diversity assessment of anoxygenic photosynthetic bacteria by distance-based grouping analysis of pufM sequencesLETTERS IN APPLIED MICROBIOLOGY, Issue 6 2007Y.H. Zeng Abstract Aim:, To assess how completely the diversity of anoxygenic phototrophic bacteria (APB) was sampled in natural environments. Methods and Results:, All nucleotide sequences of the APB marker gene pufM from cultures and environmental clones were retrieved from the GenBank database. A set of cutoff values (sequence distances 0·06, 0·15 and 0·48 for species, genus, and (sub)phylum levels, respectively) was established using a distance-based grouping program. Analysis of the environmental clones revealed that current efforts on APB isolation and sampling in natural environments are largely inadequate. Analysis of the average distance between each identified genus and an uncultured environmental pufM sequence indicated that the majority of cultured APB genera lack environmental representatives. Conclusions:, The distance-based grouping method is fast and efficient for bulk functional gene sequences analysis. The results clearly show that we are at a relatively early stage in sampling the global richness of APB species. Periodical assessment will undoubtedly facilitate in-depth analysis of potential biogeographical distribution pattern of APB. Significance and Impact of the Study:, This is the first attempt to assess the present understanding of APB diversity in natural environments. The method used is also useful for assessing the diversity of other functional genes. [source] | |||||||||||||||||||||||||