The species composition of the microbial association involved in industrial tank biooxidation of the concentrate of refractory pyrrhotite-containing pyrite-arsenopyrite gold-arsenic ore of the ...Olympiadinskoe deposit at 39°C was studied by cultural and molecular biological techniques. Pure microbial cultures were isolated, their physiological characteristics were investigated, and their taxonomic position was determined by 16S rRNA gene sequencing. The library of 16S rRNA gene clones obtained from the total DNA isolated from the biomass of the pulp of industrial reactors was analyzed. The diversity of microorganisms revealed by cultural techniques in the association of acidophilic chemolithotrophs (
Acidithiobacillus ferrooxidans, Leptospirillum ferriphilum, Sulfobacillus thermosulfidooxidans, Ferroplasma acidiphilum, Alicyclobacillus tolerans
, and
Acidiphilium cryptum
) was higher than the diversity of the 16S rDNA clone library (
At. ferrooxidans, L. ferriphilum
, and
F. acidiphilum
). The combination of microbiological and molecular biological techniques for the investigation of the biodiversity in natural and anthropogenic microbial communities promotes detection of new phylogenetic microbial groups in these communities.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Quantitative and qualitative composition of the cultivated acidophilic microorganisms obtained from the enrichment cultures on the universal medium inoculated with the samples of Shanuch deposit ...(Kamchatka peninsula) was investigated. The clone library (
N
= 93) containing eubacterial and archaeal 16S rRNA gene insertions was analyzed. DNA sequences were grouped into 5 ribotypes related to four known genera and one family. Most microorganisms (92%) were shown to belong to the genus
Acidithiobacillus
. One more group of microorganisms was identified as belonging to the family
Acetobacteriaceae
(3%); one microorganism was identified as a member of the genus
Acidiphilium
. Apart from eubacteria, the sequences specific for archaea of the genera
Thermococcus
(3%) and
Ferroplasma
(2%) were found; however, these sequences could not be reliably referred to any known species. Quantitative ratio of the microorganisms from the enrichment cultures was determined using real-time PCR. Species-specific test systems were used to determine that the sequences of
A. ferrooxidans, A. thiooxidans
, and
Ferroplasma acidiphilum
present in the samples in the ratio of 62, 4, and 0.14%, respectively.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
For efficient biological treatment of naphthalene in the industrial wastewater, activated anaerobic sludge was collected from a wastewater treatment plant of petroleum industry, and domesticated with ...naphthalene, naphthalene and lactate as electron donors, respectively. When the removal efficiency of naphthalene reached more than 90% in a domestication cycle, degradation kinetics were investigated in batch reactions with naphthalene, naphthalene and lactate as electron donors, respectively. Meanwhile, the microbial DNA was extracted from the sludge with high naphthalene removal efficiency, the 16S rDNA clone library was built up, and the bacterial community was analyzed. The results indicated that the degradation rate of naphthalene in reaction with naphthalene as the sole electron donor was much lower than that with naphthalene and lactate as electron donors. In both domestication modes, the naphthalene concentration and the time followed the first order reaction kinetics model and the kinetic constant K wer
The bacterial communities associated with rotifers (Brachionus plicatilis sp. complex) and their culture water were determined using culture-dependent and -independent methods (16S rRNA gene clone ...library). The bacterial communities determined by the culture-independent method were more diverse than those determined by the culture-dependent method. Although the culture-dependent method indicated the bacterial community of rotifers was relatively similar to that of the culture water, 16S rRNA gene clone library analyses revealed a great difference between the two microbiotas. Our results suggest that most bacteria associated with rotifers are not easily cultured using conventional methods, and that the microbiota of rotifers do not correspond with that of the culture water completely.
Spontaneous fermentation is a traditional and ecologically friendly way to purify silk, but the knowledge of the microbial structure in this system is limited. The fermentation liquids (W1 and W2) ...from two waste silk refining systems were analyzed for their bacterial community and diversity. W1 had higher oil-removing and degumming efficiency than W2, and so was superior for the recovery of waste silk. The bacterial community structures of W1 and W2 were characterized by polymorphisms in the 16S rRNA gene. Two corresponding clone libraries (C1 and C2) were constructed from each system. Using amplified rDNA restriction analysis (ARDRA), 112 randomly selected clones were grouped in 24 operational taxonomic units (OTUs) from C1 and 113 clones were grouped in 20 OTUs from C2. The bacterial diversity of C1 was higher than C2 according to the Shannon–Weaver index. Sequencing and phylogenetic analysis indicated that
Firmicutes
were the most dominant group in both samples, followed by
Bacteroidetes
. Clones related to
Synergistetes
were only found in C1. This investigation expands substantially our knowledge of the bacterial composition and diversity in waste silk refining systems. The results also revealed that the silk-spinning system may harbor a bacterial population structure suitable for metagenomic mining for novel bacterial lipase, esterase, and protease.
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CEKLJ, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Bacterial populations common to healthy human guts may play important roles in human health. A new strategy for discovering genomic sequences as markers for these bacteria was developed using ...Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR fingerprinting. Structural features within microbial communities are compared with ERIC-PCR followed by DNA hybridization to identify genomic fragments shared by samples from healthy human individuals. ERIC-PCR profiles of fecal samples from 12 diseased or healthy human and piglet subjects demonstrated stable, unique banding patterns for each individual tested. Sequence homology of DNA fragments in bands of identical size was examined between samples by hybridization under high stringency conditions with DIG-labeled ERIC-PCR products derived from the fecal sample of one healthy child. Comparative analysis of the hybridization profiles with the original agarose fingerprints identified three predominant bands as signatures for populations associated with healthy human guts with sizes of 500, 800 and 1000 bp. Clone library profiling of the three bands produced 17 genome fragments, three of which showed high similarity only with regions of the
Bacteroides thetaiotaomicron genome, while the remainder were orphan sequences. Association of these sequences with healthy guts was validated by sequence-selective PCR experiments, which showed that a single fragment was present in all 32 healthy humans and 13 healthy piglets tested. Two fragments were present in the healthy human group and in 18 children with non-infectious diarrhea but not in eight children with infectious diarrhea. Genome fragments identified with this novel strategy may be used as genome-specific markers for dynamic monitoring and sequence-guided isolation of functionally important bacterial populations in complex communities such as human gut microflora.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
The phylogenetic composition of bacterioplankton communities in Lake Tanganyika was studied by sequencing 16S rRNA gene clones. Four clone libraries were constructed from oxic epilimnion and anoxic ...hypolimnion samples collected during the dry season of 2002 in the northern and southern basins. Clone library analysis revealed a bacterial community composition (BCC) differing from previously studied freshwater systems and clear differences between both epi- and hypolimnion and the northern and southern basins. We detected few representatives of the Actinobacteria, Bacteroidetes, Cyanobacteria, and Alpha- and Betaproteobacteria commonly found in freshwater environments in temperate and cold regions, but observed a remarkably high number of clones belonging to Chloroflexi and Gammaproteobacteria. This was especially the case in the hypolimnion, but also in the epilimnion in the south of the lake, which suggests that the BCC may be influenced by seasonal upwelling. In total, nearly half of the detected operational taxonomical units were not closely related to bacteria previously observed in freshwater environments. Even in the epilimnetic clone libraries, genotypes commonly reported from oxic freshwater environments (e.g. ACK4, LD12, Sta2-30) were rare or absent.
A hot spring in the solfataric field of Pisciarelli (Naples – Italy) was analysed for Archaeal diversity. Total DNA was extracted from the environment, archaeal 16S rRNA genes were amplified with ...Archaea specific primers, and a clone library consisting of 201 clones was established. The clones were grouped in 10 different groups each representing a specific band pattern using restriction fragment length polymorphism (RFLP). Members of all 10 groups were sequenced and phylogenetically analyzed. Surprisingly, a high abundance of clones belonging to non-thermophilic Crenarchaeal clusters were detected together with the thermophilic archaeon
Acidianus infernus in this thermophilic environment. Neither
Sulfolobus species nor other hyperthermophilic Crenarchaeota were detected in the clone library. The relative abundance of the sequenced clones was confirmed by terminal restriction fragment analyses. Amplification of 16S rRNA genes from Archaea transferred from the surrounding environment was considered negligible because DNA from non-thermophilic Crenarchaeota incubated under conditions similar to the solfatara could not be PCR amplified after 5
min.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Pneumonia is the fourth leading cause of death in Japan. Accurate and rapid detection of the causative pathogen(s) is necessary and important for appropriate antimicrobial treatment, especially in ...patients with rapidly progressive pneumonia or immunocompromised patients. Conventional methods, such as cultivations, detection of urinary antigens or PCR amplification of specific genes, inevitably require the precise presumption of potential pathogens in each case, and pneumonia caused by unanticipated microorganisms might lead to inadequate antimicrobial treatments and unfortunate consequences. We herein report an immunocompromised female patient (69 years old) with fulminant pneumonia caused by Legionella (L.) pneumophila serogroup 8. Ordinary cultivation methods and urinary antigen detection failed to identify the causative organisms. Accordingly, DNA was extracted from the bronchoalveolar lavage fluid and used for the PCR-based cloning of the bacterial 16S rRNA gene. Sequencing analysis of the isolated clones revealed the predominance of L. pneumophila. Based on this information, the patient received an appropriate and successful antimicrobial treatment. In addition, L. pneumophila serogroup 8 was identified with culturing the bronchoalveolar lavage fluid and serotyping with L. pneumophila antisera. The 16S rRNA gene sequencing analysis can reveal the potential pathogens without any presumption about the organism, and can evaluate the kinds and ratio of bacterial species in each specimen. In conclusion, this cultivation-independent method is a potential diagnostic modality for pneumonia, especially in patients with rapidly progressive pneumonia or those who are immunocompromised.
Bacteroides spp. represent a prominent bacterial group in human intestinal microbiota with roles in symbiosis and pathogenicity; however, the detailed composition of this group in human feces has yet ...to be comprehensively characterized. In this study, the molecular diversity of
Bacteroides spp. in human fecal microbiota was analyzed from a seven-member, four-generation Chinese family using
Bacteroides spp. group-specific 16S rRNA gene clone library analysis. A total of 549 partial 16S rRNA sequences amplified by
Bacteroides spp.-specific primers were classified into 52 operational taxonomic units (OTUs) with a 99% sequence identity cut-off. Twenty-three OTUs, representing 83% of all clones, were related to 11 validly described
Bacteroides species, dominated by
Bacteroides coprocola,
B. uniformis, and
B. vulgatus. Most of the OTUs did not correspond to known species and represented hitherto uncharacterized bacteria. Relative to 16S rRNA gene universal libraries, the diversity of
Bacteroides spp. detected by the group-specific libraries was much higher than previously described. Remarkable inter-individual differences were also observed in the composition of
Bacteroides spp. in this family cohort. The comprehensive observation of molecular diversity of
Bacteroides spp. provides new insights into potential contributions of various species in this group to human health and disease.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
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