scholarly journals Bacterial composition of nasal discharge in children based on highly accurate 16S rRNA gene sequencing analysis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Kaoru Haro ◽  
Midori Ogawa ◽  
Mitsumasa Saito ◽  
Koichi Kusuhara ◽  
Kazumasa Fukuda
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Nasal Discharge ◽  
Rrna Gene ◽  
Respiratory Pathogens ◽  
Sequencing Analysis ◽  
Bacterial Cells ◽  
Rrna Gene Sequencing

AbstractNasopharyngeal colonization by bacteria is a prerequisite for progression to respiratory disease and an important source of horizontal spread within communities. We aimed to perform quantitative analysis of the bacterial cells and reveal the microbiota of the nasal discharge in children at the species level based on highly accurate 16S rRNA gene sequencing. This study enrolled 40 pediatric patients with rhinorrhea. The bacterial cells in the nasal discharge were counted by epifluorescence microscopic analysis. The microbiota was analyzed by using the 16S rRNA gene clone library sequencing method. We demonstrated that a high abundance (median 2.2 × 107 cells/mL) of bacteria was contained in the nasal discharge of children. Of the 40 samples, 37 (92.5%) were dominated by OTUs corresponding to Haemophilus aegyptius/influenzae, Moraxella catarrhalis/nonliquefaciens, or Streptococcus pneumoniae. These samples showed higher cell abundance and lower alpha diversity than the remaining three samples in which the other bacteria coexisted. In addition, 12 sequences with low homology to type strains were considered as previously unknown bacterial lineages. In conclusion, the nasal discharge of most young children contains a large amount of respiratory pathogens and several unknown bacteria, which could not only cause endogenous infection but also be a source of transmission to others.

scholarly journals First case of an invasive Bacteroides dorei infection detected in a patient with a mycotic aortic aneurysm—raising a rebellion of major indigenous bacteria in humans: a case report and review

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Takayuki Matsuoka ◽  
Takuya Shimizu ◽  
Tadanori Minagawa ◽  
Wakiko Hiranuma ◽  
Miki Takeda ◽  
...  
Keyword(s):  
Aortic Aneurysm ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Resected Specimen ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
First Case ◽  
Rrna Gene Sequencing

Abstract Background Bacteroides dorei is an anaerobic gram-negative bacterium first described in 2006. Because of the high similarity in mass spectra between B. dorei and Bacteroides vulgatus, discriminating between these species is arduous in clinical practice. In recent decades, 16S rRNA gene sequencing has been a complementary method for distinguishing taxonomically close bacteria, including B. dorei and B. vulgatus, at the genus and species levels. Consequently, B. dorei has been shown to contribute to some diseases, including type 1 autoimmune diabetes mellitus and atherosclerotic diseases. However, there are no reports on invasive infectious diseases caused by B. dorei. This report describes the first case of direct invasion and colonisation of human tissue by B. dorei, thus providing a warning regarding the previously proposed application of B. dorei as a live biotherapeutic for atherosclerotic diseases. Case presentation A 78-year-old Japanese man complained of intermittent chest/back pain and was diagnosed with a mycotic thoracic aortic aneurysm by enhanced computed tomography on admission. Despite strict blood pressure control and empirical antibiotic therapy, the patient’s condition worsened. To prevent aneurysmal rupture and eliminate infectious foci, the patient underwent surgical treatment. The resected specimen was subjected to tissue culture and 16S rRNA gene sequencing analysis to identify pathogenic bacteria. A few days after the surgery, culture and sequencing results revealed that the pathogen was B. dorei/B. vulgatus and B. dorei, respectively. The patient was successfully treated with appropriate antibacterial therapy and after improvement, was transferred to another hospital for rehabilitation on postoperative day 34. There was no recurrence of infection or aneurysm after the patient transfer. Conclusions This report describes the first case of invasive infectious disease caused by B. dorei, casting a shadow over its utilisation as a probiotic for atherosclerotic diseases.

scholarly journals Fastidious Gram-Negatives: Identification by the Vitek 2 Neisseria-Haemophilus Card and by Partial 16S rRNA Gene Sequencing Analysis

2010 ◽  
Vol 4 (1) ◽  
pp. 123-131 ◽  
Author(s):  
Jens JØrgen Christensen ◽  
Brita Bruun ◽  
Ute Wolff Sönksen ◽  
Lisbeth Nielsen ◽  
Annemarie Hesselbjerg ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Vitek 2 ◽  
Rrna Gene Sequencing

scholarly journals Spontaneous peritonitis and bacteremia caused by Streptococcus equinus: Value of 16S rRNA gene sequencing analysis

2017 ◽  
Vol 2 (1) ◽  
Author(s):  
John Dotis ◽  
Nikoleta Printza ◽  
Stella Stabouli ◽  
Efthymia Petinaki ◽  
Fotios Papachristou
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Rrna Gene Sequencing ◽  
Streptococcus Equinus

scholarly journals Bacterial Communities in Serpa Cheese by Culture Dependent Techniques, 16S rRNA Gene Sequencing and High-throughput Sequencing Analysis

2018 ◽  
Vol 83 (5) ◽  
pp. 1333-1341 ◽  
Author(s):  
Maria Teresa P. Gonçalves ◽  
María José Benito ◽  
María de Guía Córdoba ◽  
Conceição Egas ◽  
Almudena V. Merchán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Rrna Gene Sequencing ◽  
Culture Dependent

scholarly journals Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur

GigaScience ◽  
2018 ◽  
Vol 8 (2) ◽  
Author(s):  
Saskia D Hiltemann ◽  
Stefan A Boers ◽  
Peter J van der Spek ◽  
Ruud Jansen ◽  
John P Hays ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Rrna Gene Sequencing ◽  
User Friendly

scholarly journals MinION™, a portable long-read sequencer, enables rapid vaginal microbiota analysis in a clinical setting

2021 ◽  
Author(s):  
Shinnosuke Komiya ◽  
Yoshiyuki Matsuo ◽  
So Nakagawa ◽  
Yoshiharu Morimoto ◽  
Kirill Kryukov ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Vaginal Microbiota ◽  
Full Length ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Sample Collection ◽  
Rrna Gene Sequencing

AbstractIt has been suggested that the local microbiota in the reproductive organs is relevant to women’s health and may also affect pregnancy outcomes. Analysis of partial 16S ribosomal RNA (rRNA) gene sequences generated by short-read sequencers has been used to identify vaginal and endometrial microbiota, but it requires a long time to obtain the results, making it unsuitable for the rapid analysis of small samples in a clinical context. We demonstrated a simple workflow using the nanopore sequencer MinION™ that allows high-resolution and rapid differentiation of vaginal microbiota. Vaginal samples collected from 18 participants were subjected to DNA extraction and full-length 16S rRNA gene sequencing with MinION™. The principal coordinate analysis showed no differences in the bacterial compositions regardless of the sample collection method. The vaginal microbiota results could be reported within 2 days of specimen receipt. Although bacterial vaginosis (BV) was not diagnosed by the Nugent score in any cases, groups with both healthy and BV-like vaginal microbiota were clearly characterized by MinION™ sequencing. We conclude that full-length 16S rRNA gene sequencing analysis with MinION™ provides a rapid means for identifying vaginal bacteria with higher resolution. Species-level profiling of human vaginal microbiota by MinION™ sequencing can allow the analysis of associations with conditions such as genital infections, endometritis, and threatened miscarriage.

scholarly journals Bacterial communities in two Antarctic ice cores analyzed by 16S rRNA gene sequencing analysis

Polar Science ◽  
2010 ◽  
Vol 4 (2) ◽  
pp. 215-227 ◽  
Author(s):  
Takahiro Segawa ◽  
Kazunari Ushida ◽  
Hideki Narita ◽  
Hiroshi Kanda ◽  
Shiro Kohshima
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Gene Sequencing ◽  
Ice Cores ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Rrna Gene Sequencing
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