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16S rRNA Sequencing - Europe PMC

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Last Updated: 10 November 2022

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Comparison of iSeq and MiSeq as the two platforms for 16S rRNA sequencing in the study of the gut of rat microbiome.

The 16S ribosomal RNA regions' DNA sequencing of the 16S ribosomal RNA regions is a culture-free method used to detect and analyze Procaryota living within a population. In 20 fecal rat samples, the most significant similarities and differences of 16S microbiome sequencing were described. According to 16S Metagenomic Sequencing Library Preparation for the 16S' V3 and V4 regions, genetic libraries were developed according to 16S Metagenomic Sequencing Library Preparation. Compared to MiSeq, the species richness achieved using iSeq technology was lower than MiSeq. Beginning from the order to the species level, alpha diversity in iSeq was lower for iSeq than for MiSeq. On two experimental platforms, statistically significant differences in microbiota diversity varied from the class level to the species level in samples sequences. KEY POINTS: u2022 iSeq's unique design enables sequencing times to be reduced three times when compared to the MiSeq.

Source link: https://europepmc.org/article/MED/36322250


16S rRNA gene sequencing of stool samples collected from patients with latent tuberculosis infection before, during, and two months after treatment with 3HP or 4R

Objective: We present 16s rRNA gene sequencing and sample results from a pilot observational cohort study to investigate the gut microbiota response in patients with latent tuberculosis infection treated with a three- to four-month course of a rifamycin-based regimen. Six LTBI patients were followed for 5 u2013 6 months, according to data description. In addition, phosphate buffer washes of the LTBI participants' stool samples were tested by a validated LC-MS assay to determine concentrations of the parent and partially active metabolite rifamycins.

Source link: https://europepmc.org/article/PPR/PPR564826


Statistical Evaluation of Metaproteomics and 16S rRNA Amplicon Sequencing Techniques for Study of Gut Microbiota Establishment in Infants with Cystic Fibrosis.

Infants with cystic fibrosis can be identified but not asymptomatic infants can be identified. Both the small amount of feces available and the low microorganism load in the gut microbiota study make choosing the right omic technique for gut microbiota research extremely important. In a small sample size sample, our aim was to compare the results between 16S rRNA amplicon sequencing and metaproteomics by a robust statistical analysis that included both presence and abundance of taxa in order to describe the gradual establishment of the gut microbiota during the first year of life in a small sample size sample. By amplicon sequencing, the taxonomic assignments were similar, with some discrepancies identified in the abundance detection, mainly the lower predicted relative abundance of Bifidobacterium and the increased predicted relative abundance of certain Firmicutes and Proseobacteria. The CF gut microbiota is characterized by significant enrichment of Ruminococcus gnavus, the expression of certain virulent bacterial characteristics, and the detection of human inflammation-related proteins in the first months of life. Both techniques revealed an aberrant microbiota in our tiny cohort of infants with CF during their first year of life, dominated by the enrichment of R. gnavus in a human inflammatory environment. Our research shows that the two methods are similar in terms of microorganism detection, but alpha diversity analysis yields contradictory results. On the other hand, we have also investigated newborns with cystic fibrosis, for whom we have described the establishment of an intestinal ecosystem marked by the host's inflammatory response and the enrichment of Ruminococcus gnavus.

Source link: https://europepmc.org/article/MED/36255300


Nanopore Sequencing Using the Full-Length 16S rRNA Gene for Detection of Blood-Borne Bacteria in Dogs Reveals a Novel Species of Hemotropic Mycoplasma.

Diagnosis of VBB infections can be difficult due to the poor number of bacteria in the blood, widespread coinfections, and the wide variety of common, emerging, and potentially new VBB species encountered. We detail the first use of a nanopore-based sequencing technique developed on the Oxford Nanopore Technologies MinION device to clearly deciprate the "hemobacteriome" from canine blood by sequencing of the full-length 16S RNA gene. Utilizing the ability of the ONT MinION device to sequence long read lengths provides an excellent alternative diagnostic method by which the hemobacteriome can be precisely identified to the species level in a way that has been previously unobtainable using short reads. IMPORTANCE In many regions around the globe, blood- and vector-borne bacteria can cause severe diarrhea and even lethal for dogs. Accurate diagnosis of all the bacterial pathogens infecting a canine host is vital, because coinfections are common and growing, and novel pathogens that can go undetected by traditional diagnostic procedures are often unknown. As the long read lengths of current short-read technologies could not achieve, deep sequencing using Oxford Nanopore Technologies devices provides a solution. We developed a system that used the ONT' MinION sequencer to precisely identify and classify a wide range of VBB from canine blood with a similar sensitivity to that of commonly used diagnostics such as qPCR.

Source link: https://europepmc.org/article/MED/36250862


Metabonomics and 16S rRNA gene sequencing to study the therapeutic mechanism of Danggui Sini decoction on collagen-induced rheumatoid arthritis rats with Cold Bi syndrome.

Rheumatoid arthritis is an autoimmune disorder characterized by persistent joint inflammation. The emergence of rheumatoid arthritis is directly related to the alterations of intestinal microbiome and its metabolites. RA can be effectively treated with the Danggui Sini decoction, a Traditional Chinese medicine prescription from the Treatise on Febrile Diseases. According to the findings of 16 S RNA gene sequencing, eight microbes were presentably at the genus level, and DSD severely affected six of them. According to the results of targeting SCFAs, six SCFAs in feces increased significantly in RA, according to the study, while five SCFAs' DSD treatment had decreased significantly. DSD, according to our report, may influence RA's metabolic disorder by affecting intestinal microbiome and its metabolites. It also provides a framework for future study into the use of gut microbes therapeutic to treat RA.

Source link: https://europepmc.org/article/MED/36270097


Incipiently social carpenter bees (Xylocopa) host distinctive gut bacterial communities and display geographical structure as revealed by full-length PacBio 16S rRNA sequencing.

Here, we compare the crop and gut microbiomes of two distinctly social carpenter bee species, Xylocopa sonorina and Xylocopa tabaniformis, from multiple geographic locations within each species' range. The crop bacterial community of X. sonorina was almost entirely composed of Apilactobacillus with occasional abundant nectar bacteria. Among bee populations, Bombilactobacillus and Bombiscardovia showed variation in amplicon sequence variants, but not in Lactobacillus, indicating that some bacterial species in the gut may be characterized by different processes. We conclude that these Xylocopa species host a distinct microbiome that is similar to that of previously described social corbiculate apids, which means that further investigation into the bee microbiome and its drivers is warranted.

Source link: https://europepmc.org/article/MED/36239475


Species-level respiratory microbiome profiling for etiologic diagnosis of children pneumonia using full length 16S rRNA gene sequencing.

Methods of Comparison Using full-length 16S RNA gene sequencing, the bronchoalveolar lavage fluid bacterial community of the Mycobactera pneumoniae pneumonia and the pathogen negative pneumonia patients were compared. In the MP patients, distinctive bacterial populations were found in two groups and lower u03b1-diversity was observed, indicating the lower abundance microbiota compositions. MP patients were treated with Mycoplasma and Mycoplasma pneumoniae, which was both genus and species specific.

Source link: https://europepmc.org/article/MED/36241528

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions

* Please keep in mind that all text is summarized by machine, we do not bear any responsibility, and you should always check original source before taking any actions