scholarly journals Characterization of The Microbiome In Bile From Normal Human Gallbladders

2021 ◽  
Author(s):  
Shin Watanabe ◽  
Tadashi Shinoda ◽  
Masaaki Minagawa ◽  
Mari Toya ◽  
Daisuke Motooka ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Profile Analysis ◽  
Bacterial Flora ◽  
Normal Liver ◽  
Ribosomal Gene ◽  
Gallbladder Bile ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Gene Profile

Abstract Background: Scientists previously believed that bacteria could not grow in bile, which is rich in bacteriostatic compounds such as bile acids. Therefore, the biliary tract was considered to be a sterile environment. However, high-throughput (i.e., amplicon) sequencing analysis methods have recently been used to discover the bacterial flora in gallbladder bile in brain-dead patients with normal gallbladders. In a bacterial flora analysis targeting the 16S ribosomal gene, a specific flora was present in the bile of normal gallbladders. However, these results were not obtained from truly healthy individuals. Therefore, the aim of this study was to analyze the microbial flora of bile collected from pathologically normal gallbladders that were surgically removed from patients with hepatobiliary pancreatic diseases who had normal liver function.Results: All 12 bile samples obtained from the gallbladders had negative culture results, although a bacterial flora was detected in all samples via 16S ribosome gene analysis. The composition of the bacterial flora was very simple, and the Firmicutes, Proteobacteria, and Actinobacteria phyla were identified in all samples. Based on 16S rRNA gene profile analysis, the composition ratio accounted for more than 80% of the total number of reads. The Anaerobacillus, Delftia, Bacillus, Ralstonia, Ochrobactrum, Acidovorax, and Curvibacter genera were detected in all 12 samples. Based on 16S rRNA gene profile analysis, at the genus level, Anaerobacillus and Delftia accounted for 58.62%–87.63% of the identified bacteria in each sample. Conclusions: In this study, the bacterial flora in the gallbladder bile was not diverse. Contrary to previous reports, few bacteria belonging to the Bacteroidetes phylum were detected. The functional significance of the gallbladder bacterial flora requires further investigation.

scholarly journals Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Shantelle Claassen-Weitz ◽  
Sugnet Gardner-Lubbe ◽  
Kilaza S. Mwaikono ◽  
Elloise du Toit ◽  
Heather J. Zar ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Profile Analysis ◽  
Induced Sputum ◽  
Rrna Gene ◽  
Gene Profile

scholarly journals Microbiome of Odontogenic Abscesses

2021 ◽  
Vol 9 (6) ◽  
pp. 1307
Author(s):  
Sebastian Böttger ◽  
Silke Zechel-Gran ◽  
Daniel Schmermund ◽  
Philipp Streckbein ◽  
Jan-Falco Wilbrand ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Oral Microbiome ◽  
Minor Role ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Bacterial Strains ◽  
16S Rrna Gene Analysis ◽  
Odontogenic Infections ◽  
Odontogenic Abscess

Severe odontogenic abscesses are regularly caused by bacteria of the physiological oral microbiome. However, the culture of these bacteria is often prone to errors and sometimes does not result in any bacterial growth. Furthermore, various authors found completely different bacterial spectra in odontogenic abscesses. Experimental 16S rRNA gene next-generation sequencing analysis was used to identify the microbiome of the saliva and the pus in patients with a severe odontogenic infection. The microbiome of the saliva and the pus was determined for 50 patients with a severe odontogenic abscess. Perimandibular and submandibular abscesses were the most commonly observed diseases at 15 (30%) patients each. Polymicrobial infections were observed in 48 (96%) cases, while the picture of a mono-infection only occurred twice (4%). On average, 31.44 (±12.09) bacterial genera were detected in the pus and 41.32 (±9.00) in the saliva. In most cases, a predominantly anaerobic bacterial spectrum was found in the pus, while saliva showed a similar oral microbiome to healthy individuals. In the majority of cases, odontogenic infections are polymicrobial. Our results indicate that these are mainly caused by anaerobic bacterial strains and that aerobic and facultative anaerobe bacteria seem to play a more minor role than previously described by other authors. The 16S rRNA gene analysis detects significantly more bacteria than conventional methods and molecular methods should therefore become a part of routine diagnostics in medical microbiology.

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.

Flavobacterium cutihirudinis sp. nov., isolated from the skin of the medical leech Hirudo verbana

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2841-2847 ◽  
Author(s):  
S. P. Glaeser ◽  
H. Galatis ◽  
K. Martin ◽  
P. Kämpfer
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Biochemical Characterization ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Hirudo Verbana

A Gram-staining-negative, non-endospore-forming, yellow-pigmented strain (E89T) was isolated from the skin of the medical leech Hirudo verbana obtained from a leech farm located in Biebertal, Germany. 16S rRNA gene sequencing analysis showed that the isolate was grouped in the genus Flavobacterium . Strain E89T was most closely related to Flavobacterium chilense LM-09-FpT (98.2 %), Flavobacterium chungangense CJ7T (98.1 %), and Flavobacterium oncorhynchi 631-08T (98.1 %). 16S rRNA gene sequence similarities to all other species of the genus Flavobacterium were ≤97.4 %. A menaquinone of the type MK-6 was found to be the predominant respiratory quinone and the polar lipid profile consisted of the major compounds phosphatidylethanolamine, phosphatidylserine, two unidentified aminolipids, one unknown phospholipid and two unknown lipids. The fatty acid profile was composed of iso-C15 : 0, C15 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) found in major amounts and several hydroxylated fatty acids in smaller amounts, among them iso-C15 : 0 3-OH and iso-C17 : 0 3-OH. All these data support the allocation of the isolate in the genus Flavobacterium . Physiological/biochemical characterization and DNA–DNA hybridizations with the type strains of the most closely related species allowed a clear phenotypic and genotypic differentiation of the strain. Based on these data, strain E89T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium cutihirudinis sp. nov. is proposed. The type strain is E89T ( = DSM 25795T = LMG 26922T = CIP 110374T).

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 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 A framework for IS200, 16S rRNA gene and plasmid-profile analysis in Salmonella serogroup D1

1994 ◽  
Vol 41 (2) ◽  
pp. 112-119 ◽  
Author(s):  
J. Stanley ◽  
N. Powell ◽  
C. Jones ◽  
A. P. Burnens
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Profile Analysis ◽  
Plasmid Profile ◽  
Rrna Gene

scholarly journals Molecular Identification of Mycobacterium Species of Public Health Importance in Cattle in Zimbabwe by 16S rRNA Gene Sequencing

2015 ◽  
Vol 9 (1) ◽  
pp. 38-42 ◽  
Author(s):  
Leah Padya ◽  
Nyasha Chin'ombe ◽  
Marcelyn Magwenzi ◽  
Joshua Mbanga ◽  
Vurayai Ruhanya ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Sequences ◽  
Close Relative ◽  
Cow Dung ◽  
Rrna Gene ◽  
Mycobacterium Fortuitum ◽  
Sequencing Analysis ◽  
Public Health Importance ◽  
Detection And Identification

Mycobacteriumspecies are naturally found in the environment as well as in domestic animals such as cattle. So far, more than 150 species ofMycobacterium, some of which are pathogenic, have been identified. Laboratory isolation, detection and identification ofMycobacteriumspecies are therefore critical if human and animal infections are to be controlled. The objective of this study was to identifyMycobacteriumspecies isolated in cattle in Zimbabwe using 16S ribosomal RNA gene amplification and sequencing. A total of 134 cow dung samples were collected throughout Zimbabwe and mycobacteria were isolated by culture. Only 49 culture isolates that were found to be acid-fast bacilli positive by Ziehl-Neelsen staining. The 16S rRNA gene was successfully amplified by PCR in 41 (84%) of the samples. There was no amplification in 8 (16%) of the samples. Out of the 41 samples that showed amplification, 26 (63%) had strong PCR bands and were selected for DNA sequencing. Analysis of the DNA sequences showed that 7 (27%) belonged toMycobacterium neoaurum, 6 (23%) belonged toMycobacterium fortuitum, 3 (12%) toMycobacterium goodii, 2 (1%) toMycobacterium arupense, 2 (1%) toMycobacterium peregrinumorM. septicumand 1 isolate (0.04%) toMycobacterium elephantis. There were 5 (19%) isolates that were non-mycobacteria and identified as Gordonia terrae, a close relative ofMycobacterium. The study therefore provided a molecular basis for detection and identification ofMycobacteriumspecies in animals and humans.

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