scholarly journals Seronegative Bacteremic Melioidosis Caused by Burkholderia pseudomallei with Ambiguous Biochemical Profile: Clinical Importance of Accurate Identification by 16S rRNA Gene and groEL Gene Sequencing

2003 ◽  
Vol 41 (8) ◽  
pp. 3973-3977 ◽  
Author(s):  
P. C. Y. Woo ◽  
S. K. P. Lau ◽  
G. K. S. Woo ◽  
A. M. Y. Fung ◽  
A. H. Y. Ngan ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Burkholderia Pseudomallei ◽  
Gene Sequencing ◽  
Clinical Importance ◽  
Rrna Gene ◽  
Biochemical Profile ◽  
Accurate Identification ◽  
Groel Gene

scholarly journals Identification of Mycobacterium smegmatis in Bovine Mastitis

2016 ◽  
Vol 44 (1) ◽  
pp. 4
Author(s):  
Franciele Maboni Siqueira ◽  
Cassiane Elizabete Lopes ◽  
Gustavo Geraldo Snell ◽  
Marcos José Pereira Gomes
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Mycobacterium Smegmatis ◽  
Gene Sequence ◽  
Bovine Mastitis ◽  
Rrna Gene ◽  
Biochemical Profile ◽  
Rrna Gene Sequence ◽  
Accurate Identification

Background: Rapidly growing mycobacteria (RGM) are ubiquitous in the environment, can be isolated from soil and wa­ter, and demonstrate visible growth on culture media within seven days. Mycobacterium smegmatis is an acid-alcohol fast bacterium, which belong to RGM group. The diagnosis of M. smegmatis infections may be quite difficult by conventional methods; therefore, biochemistry associated to nucleic acid-based approaches provided fast and accurate identification. Although this specie may be associated to animals and humans infections, there is few cases description. Nontuberculous mycobacterial bovine mastitis is uncommon, and bovine mastitis by M. smegmatis has been reported but non-confirmed case once in the past. This paper reports M. smegmatis recovered from a cattle with relapsing pyogranulomatous mastitis.Case: Milk samples from an adult Holstein cow showing relapsing pyogranulomatous mastitis history and by pronounced glandular hardening were cultivated and analyzed accordingly to standard milk cultivation protocols. The animal had been subject to several intramammary and parenteral antibiotic therapies protocols without adequate response. After 48 h incubation, a slow and sparse growth of slightly pigmented, shiny and smooth colonies was observed on the blood agar plate. The bacterium isolated was named as strain 55/08. The morphological and biochemical profile were tested, and the ability of the isolate to grow at Lowenstein-Jensen slants was confirmed. The isolated have showed positive reaction to catalase, glucose, sucrose, mannitol and nitrate. The pigment formation was observed for 14 days incubation, and the colonies produce pigment after prolonged time. Gram and Ziehl-Neelsen staining revealed poorly pigmented, irregular, slender Gram-positive and acid fast rods. The staining and biochemical profile showed closed isolated relationship to M. smegmatis. A discriminatory identification based in the 16S rRNA gene sequence analysis was performed. The total DNA from the strain 55/08 was extracted and the partial 16S rRNA sequence was amplified, using prokaryotic universal primer pairs and the extract DNA as template, by PCR assay following the purification and sequencing of the amplicons. A total of 1,443 nucleotides form consensus sequence were alignment to M. smegmatis and other mycobacteria 16S rRNA avail­able sequences. The sequence analysis confirmed the M. smegmatis identification as etiological agent of bovine relapsing pyogranulomatous mastitis. M. smegmatis strain 55/08 partial 16S rRNA gene sequence was submitted to GenBank. The phylogenetic relationship of the strain 55/08 with other mycobacteria was performed in order to confirm the identification of the isolate as M. smegmatis. Discussion: Nontuberculous mycobacteria are uncommon causes of bovine mastitis. Some old reports have described M. smegmatis as etiological agent of mastitis, but without definitive diagnostic. M. smegmatis mammary quarter introduction may be related to the repeated intramammary treatment protocols, because this mycobacteria is related to environmental infections. The relapsing pyogranulomatous mastitis infection could be associated to other bacteria species. However, the phenotypic and molecular characterization which was performed demonstrated the accurate identification of the isolated as M. smegmatis. Milk contaminated by M. smegmatis may be a potential infection source for human and other animal species. This report reinforces the need to optimize quality programs and laboratorial diagnosis to further the accurate microorganism identification in milk samples.Keywords: RGM mycobacteria, relapsing mastitis, M. smegmatis, molecular identification.

scholarly journals Comparison of Illumina Versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota

2020 ◽  
Author(s):  
Astrid. P. Heikema ◽  
Deborah Horst-Kreft ◽  
Stefan A. Boers ◽  
Rick Jansen ◽  
Saskia D. Hiltemann ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Single Species ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Nanopore Sequencing ◽  
Accurate Identification ◽  
Rrna Gene Sequencing

Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumina and nanopore 16S rRNA gene sequencing. We also monitored the progression of nanopore sequencing in the accurate identification of species, using pure, single species cultures, and evaluated the performance of the nanopore EPI2ME 16S data analysis pipeline. Fifty-nine nasal swabs were sequenced using Illumina MiSeq and Oxford Nanopore 16S rRNA gene sequencing technologies. In addition, five pure cultures of relevant bacterial species were sequenced with the nanopore sequencing technology. The Illumina MiSeq sequence data were processed using bioinformatics modules present in the Mothur software package. Albacore and Guppy base calling, a workflow in nanopore EPI2ME and an in house developed bioinformatics script were used to analyze the nanopore data. At genus level, similar bacterial diversity profiles were found, and five main and established genera were identified by both platforms. However, probably due to mismatching of the nanopore sequence primers, the nanopore sequencing platform identified Corynebacterium in much lower abundance compared to Illumina sequencing. Further, when using default settings in the EPI2ME workflow, almost all sequence reads that seem to belong to the bacterial genus Dolosigranulum and a considerable part to the genus Haemophilus were only identified at family level. Nanopore sequencing of single species cultures demonstrated at least 88% accurate identification of the species at genus and species level for 4/5 strains tested, including improvements in accurate sequence read identification when the basecaller Guppy and Albacore, and when flowcell versions R9.4 and R9.2 were compared.

scholarly journals Evaluation of recA Sequences for Identification of Mycobacterium Species

2000 ◽  
Vol 38 (8) ◽  
pp. 2846-2852 ◽  
Author(s):  
Kym S. Blackwood ◽  
Cheng He ◽  
James Gunton ◽  
Christine Y. Turenne ◽  
Joyce Wolfe ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Gene Sequencing ◽  
Genetic Identification ◽  
Rrna Gene ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Accurate Identification

16S rRNA sequence data have been used to provide a molecular basis for an accurate system for identification of members of the genusMycobacterium. Previous studies have shown thatMycobacterium species demonstrate high levels (>94%) of 16S rRNA sequence similarity and that this method cannot differentiate between all species, i.e., M. gastri and M. kansasii. In the present study, we have used the recAgene as an alternative sequencing target in order to complement 16S rRNA sequence-based genetic identification. The recA genes of 30 Mycobacterium species were amplified by PCR, sequenced, and compared with the published recA sequences of M. tuberculosis, M. smegmatis, and M. leprae available from GenBank. By recA sequencing the species showed a lower degree of interspecies similarity than they did by 16S rRNA gene sequence analysis, ranging from 96.2% betweenM. gastri and M. kansasii to 75.7% betweenM. aurum and M. leprae. Exceptions to this were members of the M. tuberculosis complex, which were identical. Two strains of each of 27 species were tested, and the intraspecies similarity ranged from 98.7 to 100%. In addition, we identified new Mycobacterium species that contain a protein intron in their recA genes, similar to M. tuberculosis and M. leprae. We propose thatrecA gene sequencing offers a complementary method to 16S rRNA gene sequencing for the accurate identification of theMycobacterium species.

Screening and Molecular Characterization of Cellulase Producing Actinobacteria from Litchi Orchard

2019 ◽  
Vol 13 (1) ◽  
pp. 90-101
Author(s):  
Sanju Kumari ◽  
Utkarshini Sharma ◽  
Rohit Krishna ◽  
Kanak Sinha ◽  
Santosh Kumar
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Biochemical Characterization ◽  
Evolutionary Relationship ◽  
Gene Sequencing ◽  
Cellulase Activity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Background: Cellulolysis is of considerable economic importance in laundry detergents, textile and pulp and paper industries and in fermentation of biomass into biofuels. Objective: The aim was to screen cellulase producing actinobacteria from the fruit orchard because of its requirement in several chemical reactions. Methods: Strains of actinobacteria were isolated on Sabouraud’s agar medium. Similarities in cultural and biochemical characterization by growing the strains on ISP medium and dissimilarities among them perpetuated to recognise nine groups of actinobacteria. Cellulase activity was measured by the diameter of clear zone around colonies on CMC agar and the amount of reducing sugar liberated from carboxymethyl cellulose in the supernatant of the CMC broth. Further, 16S rRNA gene sequencing and molecular characterization were placed before NCBI for obtaining recognition with accession numbers. Results: Prominent clear zones on spraying Congo Red were found around the cultures of strains of three groups SK703, SK706, SK708 on CMC agar plates. The enzyme assay for carboxymethylcellulase displayed extra cellulase activity in broth: 0.14, 0.82 and 0.66 µmol mL-1 min-1, respectively at optimum conditions of 35°C, pH 7.3 and 96 h of incubation. However, the specific cellulase activities per 1 mg of protein did not differ that way. It was 1.55, 1.71 and 1.83 μmol mL-1 min-1. The growing mycelia possessed short compact chains of 10-20 conidia on aerial branches. These morphological and biochemical characteristics, followed by their verification by Bergey’s Manual, categorically allowed the strains to be placed under actinobacteria. Further, 16S rRNA gene sequencing, molecular characterization and their evolutionary relationship through phylogenetics also confirmed the putative cellulase producing isolates of SK706 and SK708 subgroups to be the strains of Streptomyces. These strains on getting NCBI recognition were christened as Streptomyces glaucescens strain SK91L (KF527284) and Streptomyces rochei strain SK78L (KF515951), respectively. Conclusion: Conclusive evidence on the basis of different parameters established the presence of cellulase producing actinobacteria in the litchi orchard which can convert cellulose into fermentable sugar.

scholarly journals Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Janis R. Bedarf ◽  
Naiara Beraza ◽  
Hassan Khazneh ◽  
Ezgi Özkurt ◽  
David Baker ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
False Positive ◽  
Gene Sequencing ◽  
Bacterial Biomass ◽  
16S Rrna Gene Sequencing ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Abstract Background Recent studies suggested the existence of (poly-)microbial infections in human brains. These have been described either as putative pathogens linked to the neuro-inflammatory changes seen in Parkinson’s disease (PD) and Alzheimer’s disease (AD) or as a “brain microbiome” in the context of healthy patients’ brain samples. Methods Using 16S rRNA gene sequencing, we tested the hypothesis that there is a bacterial brain microbiome. We evaluated brain samples from healthy human subjects and individuals suffering from PD (olfactory bulb and pre-frontal cortex), as well as murine brains. In line with state-of-the-art recommendations, we included several negative and positive controls in our analysis and estimated total bacterial biomass by 16S rRNA gene qPCR. Results Amplicon sequencing did detect bacterial signals in both human and murine samples, but estimated bacterial biomass was extremely low in all samples. Stringent reanalyses implied bacterial signals being explained by a combination of exogenous DNA contamination (54.8%) and false positive amplification of host DNA (34.2%, off-target amplicons). Several seemingly brain-enriched microbes in our dataset turned out to be false-positive signals upon closer examination. We identified off-target amplification as a major confounding factor in low-bacterial/high-host-DNA scenarios. These amplified human or mouse DNA sequences were clustered and falsely assigned to bacterial taxa in the majority of tested amplicon sequencing pipelines. Off-target amplicons seemed to be related to the tissue’s sterility and could also be found in independent brain 16S rRNA gene sequences. Conclusions Taxonomic signals obtained from (extremely) low biomass samples by 16S rRNA gene sequencing must be scrutinized closely to exclude the possibility of off-target amplifications, amplicons that can only appear enriched in biological samples, but are sometimes assigned to bacterial taxa. Sequences must be explicitly matched against any possible background genomes present in large quantities (i.e., the host genome). Using close scrutiny in our approach, we find no evidence supporting the hypothetical presence of either a brain microbiome or a bacterial infection in PD brains.

scholarly journals The mutL Gene as a Genome-Wide Taxonomic Marker for High Resolution Discrimination of Lactiplantibacillus plantarum and Its Closely Related Taxa

2021 ◽  
Vol 9 (8) ◽  
pp. 1570
Author(s):  
Chien-Hsun Huang ◽  
Chih-Chieh Chen ◽  
Yu-Chun Lin ◽  
Chia-Hsuan Chen ◽  
Ai-Yun Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Target Genes ◽  
Marker Genes ◽  
Rrna Gene ◽  
Accurate Identification ◽  
Discrimination Power ◽  
Sequence Identity ◽  
Genome Wide ◽  
A Genome

The current taxonomy of the Lactiplantibacillus plantarum group comprises of 17 closely related species that are indistinguishable from each other by using commonly used 16S rRNA gene sequencing. In this study, a whole-genome-based analysis was carried out for exploring the highly distinguished target genes whose interspecific sequence identity is significantly less than those of 16S rRNA or conventional housekeeping genes. In silico analyses of 774 core genes by the cano-wgMLST_BacCompare analytics platform indicated that csbB, morA, murI, mutL, ntpJ, rutB, trmK, ydaF, and yhhX genes were the most promising candidates. Subsequently, the mutL gene was selected, and the discrimination power was further evaluated using Sanger sequencing. Among the type strains, mutL exhibited a clearly superior sequence identity (61.6–85.6%; average: 66.6%) to the 16S rRNA gene (96.7–100%; average: 98.4%) and the conventional phylogenetic marker genes (e.g., dnaJ, dnaK, pheS, recA, and rpoA), respectively, which could be used to separat tested strains into various species clusters. Consequently, species-specific primers were developed for fast and accurate identification of L. pentosus, L. argentoratensis, L. plantarum, and L. paraplantarum. During this study, one strain (BCRC 06B0048, L. pentosus) exhibited not only relatively low mutL sequence identities (97.0%) but also a low digital DNA–DNA hybridization value (78.1%) with the type strain DSM 20314T, signifying that it exhibits potential for reclassification as a novel subspecies. Our data demonstrate that mutL can be a genome-wide target for identifying and classifying the L. plantarum group species and for differentiating novel taxa from known species.

scholarly journals Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Francesco Durazzi ◽  
Claudia Sala ◽  
Gastone Castellani ◽  
Gerardo Manfreda ◽  
Daniel Remondini ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Shotgun Sequencing ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Experimental Conditions ◽  
Rrna Gene Sequencing

AbstractIn this paper we compared taxonomic results obtained by metataxonomics (16S rRNA gene sequencing) and metagenomics (whole shotgun metagenomic sequencing) to investigate their reliability for bacteria profiling, studying the chicken gut as a model system. The experimental conditions included two compartments of gastrointestinal tracts and two sampling times. We compared the relative abundance distributions obtained with the two sequencing strategies and then tested their capability to distinguish the experimental conditions. The results showed that 16S rRNA gene sequencing detects only part of the gut microbiota community revealed by shotgun sequencing. Specifically, when a sufficient number of reads is available, Shotgun sequencing has more power to identify less abundant taxa than 16S sequencing. Finally, we showed that the less abundant genera detected only by shotgun sequencing are biologically meaningful, being able to discriminate between the experimental conditions as much as the more abundant genera detected by both sequencing strategies.

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