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Rajar, Polona; Dhariwal, Achal; Salvadori, Gabriela ; Junges, Roger; Åmdal, Heidi Aarø & Berild, Dag
[Vis alle 12 forfattere av denne artikkelen]
(2022).
Microbial DNA extraction of high-host content and low biomass samples: optimized protocol for nasopharynx metagenomic studies.
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Low microbial biomass and high human DNA content in nasopharyngeal aspirate samples hinder comprehensive characterization of microbiota and resistome. We obtained samples from premature infants, a group with increased risk of developing respiratory disorders and infections, and consequently frequent exposure to antibiotics. Our aim was to devise an optimal protocol for handling nasopharyngeal aspirates from premature infants, focusing on host DNA depletion and microbiome and resistome characterization. Three depletion and three DNA extraction protocols were compared, using RT-PCR and whole metagenome sequencing to determine the efficiency of human DNA removal, taxonomic profiling and assignment of antibiotic resistance genes. Protocols were tested using mock communities, as well as pooled and individual patient samples. The only extraction protocol to retrieve the expected DNA yield from mock community samples was based on a lytic method to improve Gram positive recovery (MasterPure™). Only samples depleted with MolYsis™ showed satisfactory, but varied reduction in host DNA content, in both pooled and individual patient samples, allowing for microbiome and resistome characterisation (host DNA content from 15% to 98%). PCR results were indicative of achieved microbial enrichment. Despite high human DNA and low microbial biomass content in nasopharynx aspirates of preterm infants, we were able to reduce host DNA content to levels compatible with downstream shotgun metagenomic analysis, including bacterial species identification and coverage of antibiotic resistance genes. Whole metagenomic sequencing of microbes colonizing the nasopharynx may contribute to explaining the possible role of airway microbiota in respiratory conditions and reveal carriage of antibiotic resistance genes.
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Brar, Navdeep Kaur; Dhariwal, Achal; Åmdal, Heidi Aarø; Junges, Roger; Salvadori, Gabriela & Petersen, Fernanda Cristina
(2022).
The Impact of Ampicillin on the Oral Microbiome and Resistome.
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Shekhar, Sudhanshu; Åmdal, Heidi Aarø & Petersen, Fernanda Cristina
(2021).
Vaccination with the commensal Streptococcus mitis expressing pneumococcal serotype 5 capsule elicits IgG/IgA and Th17 responses against Streptococcus pneumoniae.
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Petersen, Fernanda Cristina; Dhariwal, Achal; Bråten, Lars Christian Haugli; Sturød, Kjersti; Junges, Roger & Salvadori, Gabriela
[Vis alle 10 forfattere av denne artikkelen]
(2021).
Off-target impact of long-term amoxicillin treatment.
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Junges, Roger; Sturød, Kjersti; Salvadori, Gabriela ; Åmdal, Heidi Aarø; Chen, Tsute & Petersen, Fernanda Cristina
(2018).
Interspecies activation of a virulent pathway by an oral commensal.
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Salvadori, Gabriela ; Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute; Morrison, Donald A & Petersen, Fernanda Cristina
(2018).
Insights into regulatory pathways of competence development in Streptococcus mitis type strain and SK321
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Salvadori, Gabriela ; Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute; Morrison, Donald A & Petersen, Fernanda Cristina
(2018).
Molecular Characterization of Genetic Competence in Streptococcus mitis .
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Silva, Gabriela Salvadori; Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute & Petersen, Fernanda Cristina
(2015).
Streptococcus mitis response to the competence pheromone.
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Silva, Gabriela Salvadori; Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute & Petersen, Fernanda Cristina
(2015).
Transcriptome analysis of Streptococcus mitis response to the competence pheromone.
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Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute & Petersen, Fernanda Cristina
(2015).
A New Pheromone in Streptococcus mitis Enhances Biofilm Formation.
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Petersen, Fernanda Cristina; Khan, Rabia; Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute & Morrison, Donald A.
(2015).
A new link between the Streptococcus mutans XIP and CSP pheromone pathways revealed by directional RNA-sequencing.
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Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute & Petersen, Fernanda Cristina
(2015).
Characterization of an Rgg/SHP system in Streptococcus mitis that allows communication with Streptococcus pneumoniae.
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Salvadori, Gabriela; Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute & Petersen, Fernanda Cristina
(2015).
Transcriptome response of Streptococcus mitis to the competence pheromone.
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Junges, Roger; Khan, Rabia; Åmdal, Heidi Aarø; Morrison, Donald A. & Petersen, Fernanda Cristina
(2015).
A new link between two Streptococcus mutans pheromones.
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Junges, Roger; Khan, Rabia; Åmdal, Heidi Aarø; Morrison, Donald A. & Petersen, Fernanda Cristina
(2015).
Transcriptome response of Streptoccocus mutans to the sigX-inducing peptide (XIP).
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Salvadori, Gabriela; Junges, Roger; Åmdal, Heidi Aarø; Chen, Tsute & Petersen, Fernanda Cristina
(2015).
Identification of Streptococcus mitis competence pheromone responsive genes by transcriptome analysis.