scholarly journals Biofilm Microbiome in Extracorporeal Membrane Oxygenator Catheters

2020 ◽  
Author(s):  
Yeuni Yu ◽  
Yun Hak Kim ◽  
Woo Hyun Cho ◽  
HYE JU YEO
Keyword(s):  
Alpha Diversity ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Miseq Sequencing ◽  
Membrane Oxygenator ◽  
Significant Elevation ◽  
Sequencing Platform ◽  
Extracorporeal Membrane Oxygenator ◽  
The Relationship

Abstract Background : To assess the relationship between bacteremia and biofilms in extracorporeal membrane oxygenation (ECMO) catheters.Methods: We evaluated the biofilm microbiome of ECMO catheters from adults with (n = 6) and without bacteremia (n = 15). 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.Results: 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, it was not statistically significant. Also, there was no difference in beta diversity between the two groups. At the genus level, Delftia was more abundant in the non-bacteremic group, but Bacillus, Flavobacterium, CL0-1, Candidatus, and Xiphinematobacter were more abundant in the bacteremic group. In particular, Arthrobacter, SMB53, Neisseria, Candidatus, Ortrobactrum, Candidatus, Rhabdochlamydia, Deefgae, Dyella, Paracoccus, and Pedobacter were more abundant in the bacteremic group. In a network analysis, compared to the non-bacteremic group, the microbiome of the bacteremic group was very complex. Notably, there was a significant elevation in the secretion system of the non-bacteremic group.Conclusions: Biofilm characteristics in ECMO catheters varied according to the presence or absence of bacteremia.

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 Rhizosphere Bacteriobiome of the Husk Tomato Grown in the Open Field in West Siberia

2019 ◽  
Vol 65 (4) ◽  
pp. 147-154
Author(s):  
Natalia B. Naumova ◽  
Oleg A. Savenkov ◽  
Tatiana Y. Alikina ◽  
Marsel R. Kabilov
Keyword(s):  
Open Field ◽  
Relative Abundance ◽  
Hypervariable Region ◽  
West Siberia ◽  
Illumina Miseq ◽  
Shannon Index ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequencing Platform ◽  
Husk Tomato

Abstract The composition and structure of rhizosphere bacteriobiome of the husk tomato (Physalis philadelphica Lam.) plants grown on Phaeozem in the open field in West Siberia, Russia (55°15’ NL, 83°31’ EL) were studied using Illumina MiSeq sequencing of the V3-V4 hypervariable region of 16S rRNA genes. In total 5898 OTUs (Operational Taxonomic Units) were found in the study, representing 20 phyla and 53 identified and 15 non-identified (below the phylum level) classes. The most OTU-rich phyla were Proteobacteria, Acidobacteria and Actinobacteria, their relative abundance in the total number of sequence reads being 26, 22 and 19%, respectively. Bacteroidetes, Gemmatimonadetes and Verrucomicrobia phyla each accounted for 2 ‒ 4%. The rest 14 of the identified phyla were quite negligible, contributing less than 0.5% each. At the OTUs level, the structure was very even and equitable, as only 7 OTUs had relative abundance ranging from 0.5 to 1.1%. The main dominant OTU represented Bradyrhizobiaceae family, implying the importance of nitrogen-fixing bacteria for plant growth and development without any mineral fertilisation. The dominance biodiversity index was very low (0.001), while Shannon index was rather high (7.5). We believe the presented husk tomato rhizosphere bacteriobiome, as the first study using new generation sequencing platform for this species, will help get a better picture of Solanaceae microbiomes in different environments, thus contributing to a more comprehensive understanding of shaping microbial communities by plant roots.

scholarly journals Treatment nonresponse in children receiving silver diamine fluoride for caries: A pilot study

2020 ◽  
Author(s):  
Ryan Richard Ruff ◽  
Bidisha Paul ◽  
Maria A Sierra ◽  
Fangxi Xu ◽  
Yasmi Crystal ◽  
...  
Keyword(s):  
Pilot Study ◽  
Bacterial Species ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Lasso Regression ◽  
Silver Diamine Fluoride ◽  
Operational Taxonomic Units ◽  
Acid Tolerant ◽  
Nonsurgical Therapy

AbstractObjectives: Silver diamine fluoride (SDF) is a nonsurgical therapy for the arrest and prevention of dental caries with demonstrated clinical efficacy. Approximately 20% of children receiving SDF fail to respond to treatment. The objective of this study was to develop a predictive model of treatment nonresponse using machine learning. Methods: An observational pilot study (N=20) consisting of children with and without active decay and who did and did not respond to silver diamine fluoride provided salivary samples and plaque from infected and contralateral sites. 16S rRNA genes from samples were amplified and sequenced on an Illumina Miseq and analyzed using QIIME. The association between operational taxonomic units and treatment nonresponse was assessed using lasso regression and artificial neural networks. Results: Bivariate group comparisons of bacterial abundance indicate a number of genera were significantly different between nonresponders and those who responded to SDF therapy. No differences were found between nonresponders and caries-active subjects. Prevotella pallens and Veillonella denticariosi were retained in full lasso models and combined with clinical variables in a six-input multilayer perceptron. Discussion: The acidogenic and acid-tolerant nature of retained bacterial species may overcome the antimicrobial effects of SDF. Further research to validate the model in larger external samples is needed.

scholarly journals Sputum Microbiome Composition in Patients With Squamous Cell Lung Carcinoma

2021 ◽  
Author(s):  
E. D. Baranova ◽  
V. G. Druzhinin ◽  
L. V. Matskova ◽  
P. S. Demenkov ◽  
V. P . Volobaev ◽  
...  
Keyword(s):  
Squamous Cell ◽  
Inflammatory Responses ◽  
Alpha Diversity ◽  
Taxonomic Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Cell Lung Carcinoma ◽  
Microbiome Composition ◽  
Β Diversity ◽  
Genome Damage

Abstract Recent findings indicate that the microbiome can have a significant impact on the development of lung cancer by inducing inflammatory responses, causing dysbiosis and generating genome damage. The aim of this study was to search for bacterial markers of squamous cell carcinoma (LUSC). In the study, the taxonomic composition of the sputum microbiome of 40 men with untreated LUSC was compared with 40 healthy controls. Next Generation sequencing of bacterial 16S rRNA genes was used to determine the taxonomic composition of the respiratory microbiome. There was no differences in alpha diversity between the LUSC and control groups. Meanwhile, differences in the structure of bacterial communities (β diversity) among patients and controls differed significantly in sputum samples (pseudo-F = 1.65; p = 0.026). Only Streptococcus, Bacillus, Gemella and Haemophilus were found to be significantly increased in patients with LUSC compared to the control subjects, while 19 bacterial genera were significantly reduced, indicating a decrease in beta diversity in the microbiome of patients with LUSC. From our study, Streptococcus (Streptococcus agalactiae) emerges as the most likely LUSC biomarker, but more research is needed to confirm this assumption.

scholarly journals A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2492 ◽  
Author(s):  
Catherine M. Burke ◽  
Aaron E. Darling
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
Single Molecule ◽  
Illumina Miseq ◽  
Full Length ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Bacterial Taxonomy

BackgroundThe bacterial 16S rRNA gene has historically been used in defining bacterial taxonomy and phylogeny. However, there are currently no high-throughput methods to sequence full-length 16S rRNA genes present in a sample with precision.ResultsWe describe a method for sequencing near full-length 16S rRNA gene amplicons using the high throughput Illumina MiSeq platform and test it using DNA from human skin swab samples. Proof of principle of the approach is demonstrated, with the generation of 1,604 sequences greater than 1,300 nt from a single Nano MiSeq run, with accuracy estimated to be 100-fold higher than standard Illumina reads. The reads were chimera filtered using information from a single molecule dual tagging scheme that boosts the signal available for chimera detection.ConclusionsThis method could be scaled up to generate many thousands of sequences per MiSeq run and could be applied to other sequencing platforms. This has great potential for populating databases with high quality, near full-length 16S rRNA gene sequences from under-represented taxa and environments and facilitates analyses of microbial communities at higher resolution.

scholarly journals The effect of carbon subsidies on marine planktonic niche partitioning and recruitment during biofilm assembly

2015 ◽  
Author(s):  
Chuck Pepe-Ranney ◽  
Ed Hall
Keyword(s):  
Heterotrophic Bacteria ◽  
Alpha Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Competitive Balance ◽  
Community Membership ◽  
Resource Space ◽  
Plankton Communities ◽  
Planktonic Communities

The influence of resource availability on planktonic and biofilm microbial community membership is poorly understood. Heterotrophic bacteria derive some to all of their organic carbon (C) from photoautotrophs while simultaneously competing with photoautotrophs for inorganic nutrients such as phosphorus (P) or nitrogen (N). Therefore, C inputs have the potential to shift the competitive balance of aquatic microbial communities by increasing the resource space available to heterotrophs (more C) while decreasing the resource space available to photoautotrophs (less mineral nutrients due to increased competition from heterotrophs). To test how resource dynamics affect membership of planktonic communities and assembly of biofilm communities we amended a series of flow-through mesocosms with C to alter the availability of C among treatments. Each mesocosm was fed with unfiltered seawater and incubated with sterilized microscope slides as surfaces for biofilm formation. The highest C treatment had the highest planktonic heterotroph abundance, lowest planktonic photoautotroph abundance, and highest biofilm biomass. We surveyed bacterial 16S rRNA genes and plastid 23S rRNA genes to characterize biofilm and planktonic community membership and structure. Regardless of resource additions, biofilm communities had higher alpha diversity than planktonic communities in all mesocosms. Heterotrophic plankton communities were distinct from heterotrophic biofilm communities in all but the highest C treatment where heterotrophic plankton and biofilm communities resembled each other after 17 days. Unlike the heterotrophs, photoautotrophic plankton communities were different than photoautotrophic biofilm communities in composition in all treatments including the highest C treatment. Our results suggest that although resource amendments affect community membership and structure, microbial lifestyle (biofilm versus planktonic) has a stronger influence on community composition.

scholarly journals Distribution of Hydrogen-Producing Bacteria in Tibetan Hot Springs, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Li Ma ◽  
Geng Wu ◽  
Jian Yang ◽  
Liuqin Huang ◽  
Dorji Phurbu ◽  
...  
Keyword(s):  
Community Structure ◽  
Hydrogen Production ◽  
16S Rrna ◽  
High Throughput Sequencing ◽  
Hot Springs ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
The Tibetan Plateau

Investigating the distribution of hydrogen-producing bacteria (HPB) is of great significance to understanding the source of biological hydrogen production in geothermal environments. Here, we explored the compositions of HPB populations in the sediments of hot springs from the Daggyai, Quzhuomu, Quseyongba, and Moluojiang geothermal zones on the Tibetan Plateau, with the use of Illumina MiSeq high-throughput sequencing of 16S rRNA genes and hydA genes. In the present study, the hydA genes were successfully amplified from the hot springs with a temperature of 46–87°C. The hydA gene phylogenetic analysis showed that the top three phyla of the HPB populations were Bacteroidetes (14.48%), Spirochaetes (14.12%), and Thermotogae (10.45%), while Proteobacteria were absent in the top 10 of the HPB populations, although Proteobacteria were dominant in the 16S rRNA gene sequences. Canonical correspondence analysis results indicate that the HPB community structure in the studied Tibetan hot springs was correlated with various environmental factors, such as temperature, pH, and elevation. The HPB community structure also showed a spatial distribution pattern; samples from the same area showed similar community structures. Furthermore, one HPB isolate affiliated with Firmicutes was obtained and demonstrated the capacity of hydrogen production. These results are important for us to understand the distribution and function of HPB in hot springs.

Microbial diversity and community structure in agricultural soils suffering from 4 years of Pb contamination

2018 ◽  
Vol 64 (5) ◽  
pp. 305-316 ◽  
Author(s):  
Fengqiu An ◽  
Zhan Diao ◽  
Jialong Lv
Keyword(s):  
Heavy Metal ◽  
Physicochemical Properties ◽  
Agricultural Soils ◽  
Microbial Community Composition ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Resistant Bacteria ◽  
Available Phosphorus ◽  
Highly Correlated

Heavy metal pollution has become a widespread environmental problem due to rapid economic development. The phylogenetic diversity and structure of microbial communities in lead (Pb)-contaminated Lou soils were investigated using Illumina MiSeq sequencing of 16S rRNA genes. The presence of Pb2+ in soil showed weak impact on the diversity of soil bacteria community, but it influenced the abundance of some genera of bacteria, as well as soil physicochemical properties. We found significant differences in the relative abundances of heavy-metal-resistant bacteria such as Bacillus, Streptococcus, and Arthrobacter at the genus level. Available Pb and total Pb negatively correlated with soil organic matter but positively affected available phosphorus. The abundance of main bacteria phyla was highly correlated with total Pb. The relative abundance of Gemmatimonadetes, Nitrospirae, and Planctomycetes was negatively correlated with total Pb. Collectively, Pb influences both the microbial community composition and physicochemical properties of soil.

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