scholarly journals Illumina MiSeq Sequencing for Preliminary Analysis of Microbiome Causing Primary Endodontic Infections in Egypt

2018 ◽  
Vol 2018 ◽  
pp. 1-15 ◽  
Author(s):  
Sally Ali Tawfik ◽  
Marwa Mohamed Azab ◽  
Ali Abdellah Abdelrahman Ahmed ◽  
Dalia Mukhtar Fayyad
Keyword(s):  
Pcr Amplification ◽  
Illumina Miseq ◽  
Oral Microbiome ◽  
University Hospital ◽  
Rrna Gene ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Soil Dna ◽  
Sequencing Platform ◽  
Endodontic Infections

The use of high throughput next generation technologies has allowed more comprehensive analysis than traditional Sanger sequencing. The specific aim of this study was to investigate the microbial diversity of primary endodontic infections using Illumina MiSeq sequencing platform in Egyptian patients. Samples were collected from 19 patients in Suez Canal University Hospital (Endodontic Department) using sterile # 15K file and paper points. DNA was extracted using Mo Bio power soil DNA isolation extraction kit followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized on the basis of the V3 and V4 hypervariable region of the 16S rRNA gene by using paired-end sequencing on Illumina MiSeq device. MOTHUR software was used in sequence filtration and analysis of sequenced data. A total of 1858 operational taxonomic units at 97% similarity were assigned to 26 phyla, 245 families, and 705 genera. Four main phyla Firmicutes, Bacteroidetes, Proteobacteria, and Synergistetes were predominant in all samples. At genus level,Prevotella,Bacillus,Porphyromonas,Streptococcus, andBacteroideswere the most abundant. Illumina MiSeq platform sequencing can be used to investigate oral microbiome composition of endodontic infections. Elucidating the ecology of endodontic infections is a necessary step in developing effective intracanal antimicrobials.

scholarly journals Diversity of the Bacterial Community of Three Soils Revealed by Illumina-Miseq Sequencing of 16S rRNA Gene in the South of Brazzaville, Congo

2020 ◽  
Vol 8 (4) ◽  
pp. 141-149
Author(s):  
Shaloom Teresa MABIALA ◽  
Joseph GOMA-TCHIMBAKALA ◽  
Emerance Jessica Claire D’Assise GOMA-TCHIMBAKALA ◽  
Augustin Aimé LEBONGUY ◽  
Alvychelle Benith BANGA
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
The South

scholarly journals Epizootic ulcerative syndrome causes cutaneous dysbacteriosis in hybrid snakehead (Channa maculata♀ × Channa argus♂)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6674 ◽  
Author(s):  
Zhifei Li ◽  
Guangjun Wang ◽  
Kai Zhang ◽  
Wangbao Gong ◽  
Ermeng Yu ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Illumina Miseq ◽  
Infected Fish ◽  
Rrna Gene ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Host Health ◽  
Channa Argus ◽  
Epizootic Ulcerative Syndrome ◽  
The 16S Rrna Gene

Cutaneous microbiota play an important role in protecting fish against pathogens. Aphanomyces infection causes epizootic ulcerative syndrome (EUS) in fish, and by perturbing the integrity of the cutaneous microbiota, increases the potential for infection by pathogenic bacteria. However, whether the composition of the cutaneous microbiota is altered in fish with EUS, and if so, which species are changed and how this might influence infected fish, is still largely unclear. Considering the importance of cutaneous microbiota in maintaining host health, we hypothesized that Aphanomyces infection significantly enhances the presence of certain bacterial pathogens in the cutaneous microbiota and causes cutaneous dysbacteriosis. To test this hypothesis, we compared the cutaneous microbiota compositions of hybrid snakehead (Channa maculata♀ × Channa argus♂) with and without Aphanomyces infection using Illumina Miseq sequencing of the 16S rRNA gene. Our results showed that the cutaneous microbiota of hybrid snakehead were significantly altered subsequent to EUS infection and that the numbers of potentially pathogenic bacteria classified into the genera Anaerosinus, Anaerovorax, Dorea, and Clostridium were significantly enhanced in the cutaneous microbiota of hybrid snakehead with EUS, whereas bacteria classified into the genera Arthrobacter, Dysgonomonas, Anoxybacillus, Bacillus, Solibacillus, Carnobacterium, Lactococcus, Streptococcus, Achromobacter, Polynucleobacter, Vogesella, and Pseudomonas were significantly reduced. These results imply that treatment for EUS should not only take into consideration the control of Aphanomyces reproduction but should also focus on regulating the cutaneous microbiota of infected fish.

scholarly journals Biofilm microbiome in extracorporeal membrane oxygenator catheters

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257449
Author(s):  
Yeuni Yu ◽  
Yun Hak Kim ◽  
Woo Hyun Cho ◽  
Bong Soo Son ◽  
Hye Ju Yeo
Keyword(s):  
Alpha Diversity ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Membrane Oxygenator ◽  
Sequencing Platform ◽  
Extracorporeal Membrane Oxygenator ◽  
The Difference

Despite the formation of biofilms on catheters for extracorporeal membrane oxygenation (ECMO), some patients do not show bacteremia. To elucidate the specific linkage between biofilms and bacteremia in patients with ECMO, an improved understanding of the microbial community within catheter biofilms is necessary. Hence, we aimed to evaluate the biofilm microbiome of ECMO catheters from adults with (n = 6) and without (n = 15) bacteremia. The microbiomes of the catheter biofilms were evaluated by profiling the V3 and V4 regions of bacterial 16s rRNA genes using the Illumina MiSeq sequencing platform. In total, 2,548,172 reads, with an average of 121,341 reads per sample, were generated. Although alpha diversity was slightly higher in the non-bacteremic group, the difference was not statistically significant. In addition, there was no difference in beta diversity between the two groups. We found 367 different genera, of which 8 were present in all samples regardless of group; Limnohabitans, Flavobacterium, Delftia, Massilia, Bacillus, Candidatus, Xiphinematobacter, and CL0-1 showed an abundance of more than 1% in the sample. In particular, Arthrobacter, SMB53, Neisseria, Ortrobactrum, Candidatus Rhabdochlamydia, Deefgae, Dyella, Paracoccus, and Pedobacter were highly abundant in the bacteremic group. Network analysis indicated that the microbiome of the bacteremic group was more complex than that of the non-bacteremic group. Flavobacterium and CL0.1, which were abundant in the bacteremic group, were considered important genera because they connected different subnetworks. Biofilm characteristics in ECMO catheters varied according to the presence or absence of bacteremia. There were no significant differences in diversity between the two groups, but there were significant differences in the community composition of the biofilms. The biofilm-associated community was dynamic, with the bacteremic group showing very complex network connections within the microbiome.

scholarly journals Pollutant-Removing Biofilter Strains Associated with High Ammonia and Hydrogen Sulfide Removal Rate in a Livestock Wastewater Treatment Facility

2021 ◽  
Vol 13 (13) ◽  
pp. 7358
Author(s):  
Dong-Hyun Kim ◽  
Hyun-Sik Yun ◽  
Young-Saeng Kim ◽  
Jong-Guk Kim
Keyword(s):  
Wastewater Treatment ◽  
Hydrogen Sulfide ◽  
Microbial Community ◽  
Microbial Communities ◽  
Illumina Miseq ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Treatment Facility ◽  
Livestock Wastewater ◽  
Wastewater Treatment Facility

This study analyzed the microbial community metagenomically to determine the cause of the functionality of a livestock wastewater treatment facility that can effectively remove pollutants, such as ammonia and hydrogen sulfide. Illumina MiSeq sequencing was used in analyzing the composition and structure of the microbial community, and the 16S rRNA gene was used. Through Illumina MiSeq sequencing, information such as diversity indicators as well as the composition and structure of microbial communities present in the livestock wastewater treatment facility were obtained, and differences between microbial communities present in the investigated samples were compared. The number of reads, operational taxonomic units, and species richness were lower in influent sample (NLF), where the wastewater enters, than in effluent sample (NL), in which treated wastewater is found. This difference was greater in June 2019 than in January 2020, and the removal rates of ammonia (86.93%) and hydrogen sulfide (99.72%) were also higher in June 2019. In both areas, the community composition was similar in January 2020, whereas the influent sample (NLF) and effluent sample (NL) areas in June 2019 were dominated by Proteobacteria (76.23%) and Firmicutes (67.13%), respectively. Oleiphilaceae (40.89%) and Thioalkalibacteraceae (12.91%), which are related to ammonia and hydrogen sulfide removal, respectively, were identified in influent sample (NLF) in June 2019. They were more abundant in June 2019 than in January 2020. Therefore, the functionality of the livestock wastewater treatment facility was affected by characteristics, including the composition of the microbial community. Compared to Illumina MiSeq sequencing, fewer species were isolated and identified in both areas using culture-based methods, suggesting Illumina MiSeq sequencing as a powerful tool to determine the relevance of microbial communities for pollutant removal.

Analysis of bacterial diversity of Chinese Luzhou-flavor liquor brewed in different seasons by Illumina Miseq sequencing

2016 ◽  
Vol 66 (3) ◽  
pp. 1293-1301 ◽  
Author(s):  
Weining Sun ◽  
Huazhi Xiao ◽  
Qian Peng ◽  
Qiaoge Zhang ◽  
Xingxing Li ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Illumina Miseq ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Different Seasons

scholarly journals Comparing dental plaque microbiome diversity of extrinsic black stain in the primary dentition using Illumina MiSeq sequencing technique

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Lulu Chen ◽  
Qiong Zhang ◽  
Yan Wang ◽  
Keke Zhang ◽  
Jing Zou
Keyword(s):  
Relative Abundance ◽  
Dental Plaque ◽  
Illumina Miseq ◽  
Primary Dentition ◽  
Tooth Surface ◽  
Oral Microbiota ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Cross Sectional ◽  
Sequencing Technique

Abstract Background Extrinsic black stain (EBS) is characterized by discrete dark dots or lines on the tooth surface. The relationship between EBS and oral microbiota in children remains elusive. The aim of this study was to compare dental plaque microbiome in EBS children with that in EBS-free children in the primary dentition. Methods The Illumina MiSeq sequencing technique was utilized in the cross-sectional pilot study to investigate the diversity and composition of the supragingival plaque microbiota from 10 EBS-positive and 10 EBS-free children. The results were analysed with nonparametric Mann-Whitney U test, Pearson Chi-Square test, Fisher’s Exact test and one-way ANOVA tests. Results We identified 13 different phyla, 22 classes, 33 orders, 54 families, 105 genera, and 227 species from a total of 52,646 high-quality sequences. Between two groups, no statistical differences were observed in the estimators of community richness and diversity at 97% similarity, as well as in the Unweighted Unifrac principal co-ordinates analysis (PCoA). At the species level, higher level of relative abundance of Actinomyces naeslundii and lower level of relative abundance of a species belonging to Candidate_division_TM7 was observed in dental plaque of EBS-positive subjects, compared to dental plaque of EBS-free subjects (P < 0.05). This indicated that some species might be involved in the EBS process. Conclusion Changes in dental plaque microbiota is possibly relevant to the process of EBS in the primary dentition.

Developmental validation of a Nextera XT mitogenome Illumina MiSeq sequencing method for high-quality samples

2018 ◽  
Vol 34 ◽  
pp. 25-36 ◽  
Author(s):  
Michelle A. Peck ◽  
Kimberly Sturk-Andreaggi ◽  
Jacqueline T. Thomas ◽  
Robert S. Oliver ◽  
Suzanne Barritt-Ross ◽  
...  
Keyword(s):  
Illumina Miseq ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
High Quality ◽  
Sequencing Method ◽  
Developmental Validation

scholarly journals Changes in the Soil Microbiome in Eggplant Monoculture Revealed by High-Throughput Illumina MiSeq Sequencing as Influenced by Raw Garlic Stalk Amendment

2019 ◽  
Vol 20 (9) ◽  
pp. 2125 ◽  
Author(s):  
Muhammad Imran Ghani ◽  
Ahmad Ali ◽  
Muhammad Jawaad Atif ◽  
Muhammad Ali ◽  
Bakht Amin ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput ◽  
Soil Microbial Communities ◽  
Illumina Miseq ◽  
Soil Microbiome ◽  
Plant Residues ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Community Structures ◽  
Microbial Community Structures

The incorporation of plant residues into soil can be considered a keystone sustainability factor in improving soil structure function. However, the effects of plant residue addition on the soil microbial communities involved in biochemical cycles and abiotic stress phenomena are poorly understood. In this study, experiments were conducted to evaluate the role of raw garlic stalk (RGS) amendment in avoiding monoculture-related production constraints by studying the changes in soil chemical properties and microbial community structures. RGS was applied in four different doses, namely the control (RGS0), 1% (RGS1), 3% (RGS2), and 5% (RGS3) per 100 g of soil. The RGS amendment significantly increased soil electrical conductivity (EC), N, P, K, and enzyme activity. The soil pH significantly decreased with RGS application. High-throughput Illumina MiSeq sequencing revealed significant alterations in bacterial community structures in response to RGS application. Among the 23 major taxa detected, Anaerolineaceae, Acidobacteria, and Cyanobacteria exhibited an increased abundance level. RGS2 increased some bacteria reported to be beneficial including Acidobacteria, Bacillus, and Planctomyces (by 42%, 64%, and 1% respectively). Furthermore, internal transcribed spacer (ITS) fungal regions revealed significant diversity among the different treatments, with taxa such as Chaetomium (56.2%), Acremonium (4.3%), Fusarium (4%), Aspergillus (3.4%), Sordariomycetes (3%), and Plectosphaerellaceae (2%) showing much abundance. Interestingly, Coprinellus (14%) was observed only in RGS-amended soil. RGS treatments effectively altered soil fungal community structures and reduced certain known pathogenic fungal genera, i.e., Fusarium and Acremonium. The results of the present study suggest that RGS amendment potentially affects the microbial community structures that probably affect the physiological and morphological attributes of eggplant under a plastic greenhouse vegetable cultivation system (PGVC) in monoculture.

Illumina MiSeq sequencing and network analysis the distribution and co-occurrence of bacterioplankton in Danjiangkou Reservoir, China

2020 ◽  
Vol 202 (4) ◽  
pp. 859-873 ◽  
Author(s):  
Zhao-Jin Chen ◽  
Ge Xu ◽  
Chuan-Yu Ding ◽  
Bao-Hai Zheng ◽  
Yan Chen ◽  
...  
Keyword(s):  
Network Analysis ◽  
Illumina Miseq ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Danjiangkou Reservoir
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