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"ABSTRACT Sequential membrane filtration as a pre-processing step for microorganism isolation could lead to high quality and integrity DNA that can be stored and stored at ambient temperatures for analysis by culture-independence molecular methods, e. g. , 16s amplicon sequencing. " We investigated the effects of pre-processing sediment samples by sequential membrane filtration for 16s rDNA-based community profiling of sediment-associated microorganisms. These results show that read abundance after these read processing steps were not influenced by sediment processing or absence thereof. Although non- and pre-processed sediment samples were more consistent than published amplicon sequence variants, we found that their shared ASVs represented 74% of both methods'u2019 absolute read abundance. Our findings show the possibility of pre-processing sediment samples for community analysis, as well as the need to continue testing methods to help develop appropriate study designs for sediment-associated microbial community profiling.
Source link: https://doi.org/10.1101/2020.10.21.348342
"The taxonomic coherence and phylogenetic characteristics of 11 planktonic heterocystous cyanobacterial isolates were investigated by researchers in two areas of the rRNA gene, the 16S rRNA gene, and the internal transcribed spacer found between the 16S rRNA and 23S rRNA genes. " The phylogenetic groupings of Anabaena and Aphanizomenon strains within three of these clusters were not always consistent with their generic or specific assignments based on classical morphological classifications, and the high degree of sequence similarity between strains of Anabaenopsis and Cyanospira suggests that they may be assignable to a single species. Multiple rrn operons and ITS regions of variable size were found in the 11 planktonic heterocystous strains' PCR amplicons, as shown by Ribotyping and additional studies.
Source link: https://doi.org/10.1099/00221287-148-2-481
"However, the DNA extraction reagents as well as the PCR reagents may contain residual bacterial DNA, which ultimately leads to false-positive PCR results. " Here, we discuss the findings obtained with a new technique that uses DNA-free reagents for automated DNA extraction and subsequent real time PCR using sterile clinical specimens. A total of 170 clinical specimens were PCR-positive, of which 62 provided an additional benefit to the patient because only the PCR result was positive. The majority of S. epidermidis, S. aureus, and C. acnes were culture-positive but PCR-negative, with many of the S. epidermidis, S. aureus, and C. acnes. Positive specimens were returned to negative specimens in 4 hours and 1 working day. SYBR Green-PCR's unique and unspecific PCR products can be distinguished by Melting-curve analysis, enabling the differentiation of specific and unspecific PCR products. "The added value of PCR in endocarditis cases is evident. ".
Source link: https://doi.org/10.1186/s12866-022-02542-w
"Ticks are parasitic mites that are essential hematophagous ectoparasites of amphibians, reptiles, birds, and mammals. Members of Haemaphysalinae were monophyletic with the primitive Amblyomminae and members of Hyalomminae, which were grouped within the Rhipicephalinae. In soft ticks, the derived phylogeny failed to promote a monophyletic relationship among Ornithodorinae's supporters and argued for Argasinae's location as the Ixodidae's basal, indicating that hard ticks may have arisen from an Argas-like ancestor. This finding, according to earlier reports that hard ticks did not evolve until the late Cretaceous, because the majority of Argas species are obligate bird octoparasites, and this finding supports earlier claims that hard ticks did not evolve until the late Cretaceous.
Source link: https://doi.org/10.1073/pnas.91.21.10034
To develop an effective preservation strategy, you'll need to explore the spoilage microbial community during rainbow trout storage. " The changes in the total bacterial colony and total volatile base nitrogen during rainbow trout storage were investigated here. According to 4. 4 log CFU/g and 14. 5 mg/100 g, respectively, storage at 0 u00b0C can effectively slow down the spoilage process, decreasing from 8. 7 log CFU/g and 18. 7 mg/100 g to 5. 6 log CFU/g and 14. 5 mg/100 g. The number of microbial genera decreased during storage, according to the 16S rDNA high-throughput sequencing results, suggesting that the number of microbial species decreased during storage. This review demonstrated the most prevalent spoilage bacterial species and assessed isolated strains during the storage of rainbow trout, paving the way for further investigation into the spoilage mechanism of rainbow trout and other aquatic products. ".
Source link: https://doi.org/10.1155/2022/5367984
"Strains of Legionella pneumophila were identified as having products of 900 and 530 bp, and L. birminghamensis had 1,390, 960, and 380 bp. L. pneumophila was the name of two environmental isolates. Strain LLAP-3, a symbiont of amoebae, could not be identified with any Legionella sp. ".
Source link: https://doi.org/10.1128/jcm.33.9.2377-2381.1995
"ABSTRACT "ABSTRACT" says that cystic fibrosis patients' leading cause of morbidity and mortality in cystic fibrosis patients is repeated bacterial respiratory infections. The 16S ribosomal DNA gene PCR products were amplified from extracted nucleic acids, with evaluations by terminal restriction fragment length polymorphism, length heterogeneity PCR, and sequencing of individual cloned PCR samples to identify these groups. 12 distinct T-RFLP profiles were found with between 3 and 32 T-RFLP bands when using the same loading of PCR samples. Five patients were tested for a total of 103 16S rRNA gene clones. P. aeruginosa was the most commonly recognized species, according to P. aeruginosa. The remaining 17 clones contained eight other bacterial species, including eight other bacterial species found within the remaining 17 clones. In conclusion, T-RFLP analysis coupled with 16S rRNA gene sequencing is a useful way to determine the composition and diversity of the bacterial community in specimens collected from CF patients. ".
Source link: https://doi.org/10.1128/jcm.41.8.3548-3558.2003
"ABSTRACT" is a document that describes clinical Mycobacterium isolates. The MicroSeq 500 16S rDNA Bacterial Sequencing Kit, a 500-bp sequence-based identification system, was tested for its ability to recognize clinical Mycobacterium isolates. " The organism's identity was determined by comparing the 16S rDNA sequence to the MicroSeq database, which is largely composed of type strain sequence sequences. Discordant results were determined by hsp65 gene sequence analysis and, in some cases repeat phenotypic identification, AccuProbe rRNA hybridization, or high-performance liquid chromatography of mycolic acids. The MicroSeq identity was discovered for 93 isolates, consistent with the previously reported identity. The original identification of 18 isolates was contradictory with the MicroSeq analysis. Both isolates failed to establish definitive phenotypic identification, but the MicroSeq assay was able to successfully identify one of these isolates. The MicroSeq identification system is a fast and convenient way to identify Mycobacterium spp.
Source link: https://doi.org/10.1128/jcm.38.1.246-251.2000
"ABSTRACT The Canary Islands, Spain, nine strains of symbiotic nitrogen-fixing bacteria isolated from nodules of tagasaste and other endemic woody legumes are described in a phylogenetic analysis. Bradyrhizobium japonicum USDA 110 sp. 4 and Bradyrhizobium sp. investigated the Canarian isolates with four tetrameric endonucleases, grouped the Canarian isolates with the two reference strains, Bradyrhizobium sp. 3 and Bradyrhizobium sp. Moreover, we show that IGS RFLPs and even dissimilar rep-PCR fingerprints can be grouped into phylogenetically sound groupings by combining them with 16S rDNA RFLPs in computer-assisted cluster analysis of electrophoretic data. Three new DNA sequences were found, one of which had not been described previously, and all of them belonged to the B. japonicum/Rhodopseudomonas rDNA cluster, one of which was not previously reported, and they were all related to the B. japonicum/Rhodopseudomonas rDNA cluster. "No one of the Canarian isolates nodulated Glycine max or Leucaena leucocephala, according to a spokesperson, but all noddedulated Acacia pendula, C. proliferus, Macroptilium atropurpureum, and Vigna unguiculata. ".
Source link: https://doi.org/10.1128/aem.64.6.2096-2104.1998
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