noninvasive-sampling-mucosal-lining-fluid-for-quantification-vivo

Noninvasive Sampling of Mucosal Lining Fluid for the Quantification of <em>In Vivo</em> Upper Airway Immune-mediator Levels

This protocol describes noninvasive sampling of undisturbed upper airway mucosal lining fluid. It also details the extraction procedure used prior to the ...

University of Copenhagen

Delivery by means of cesarean section has been associated with increased risk of childhood immune-mediated diseases, suggesting a role of early bacterial colonization patterns for immune maturation.

Cesarean section changes neonatal gut colonization.

There is an immense scientific interest in the human microbiome and its effects on human physiology, health, and disease. A common approach for examining bacterial communities is high-throughput sequencing of 16S rRNA gene hypervariable regions, aggregating sequence-similar amplicons into operational taxonomic units (OTUs). Strategies for detecting differential relative abundance of OTUs between sample conditions include classical statistical approaches as well as a plethora of newer methods, many borrowing from the related field of RNA-seq analysis. This effort is complicated by unique data characteristics, including sparsity, sequencing depth variation, and nonconformity of read counts to theoretical distributions, which is often exacerbated by exploratory and/or unbalanced study designs. Here, we assess the robustness of available methods for (1) inference in differential relative abundance analysis and (2) beta-diversity-based sample separation, using a rigorous benchmarking framework based on large clinical 16S microbiome datasets from different sources.

Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies.

Reduced intake of n-3 long-chain polyunsaturated fatty acids (LCPUFAs) may be a contributing factor to the increasing prevalence of wheezing disorders. We assessed the effect of supplementation with n-3 LCPUFAs in pregnant women on the risk of persistent wheeze and asthma in their offspring.

Fish Oil-Derived Fatty Acids in Pregnancy and Wheeze and Asthma in Offspring.

The airways of healthy humans harbor a distinct microbial community. Perturbations in the microbial community have been associated with disease, yet little is known about the formation and development of a healthy airway microbiota in early life. Our goal was to understand the establishment of the airway microbiota within the first 3 months of life. We investigated the hypopharyngeal microbiota in the unselected COPSAC2010 cohort of 700 infants, using 16S rRNA gene sequencing of hypopharyngeal aspirates from 1 week, 1 month, and 3 months of age.

The developing hypopharyngeal microbiota in early life.

To study the association between antibiotic intake in pregnancy and the development of otitis media and placement of ventilation tubes (VTs) in the offspring under the hypothesis that antibiotics in pregnancy may alter the offspring's propensity for disease.

Antibiotics in Pregnancy Increase Children's Risk of Otitis Media and Ventilation Tubes.

Although the pathogenesis of hidradenitis suppurativa (HS) remains enigmatic, several factors point to potential involvement of the cutaneous microbiome. Insight into the cutaneous microbiome in HS using next-generation sequencing may provide novel data on the microbiological diversity of the skin.

Article	Year
Cesarean section changes neonatal gut colonization. The Journal of allergy and clinical immunology\| PubMed ID: 27045582	2016
Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies. Microbiome\| PubMed ID: 27884206	2016
Fish Oil-Derived Fatty Acids in Pregnancy and Wheeze and Asthma in Offspring. The New England journal of medicine\| PubMed ID: 28029926	2016
The developing hypopharyngeal microbiota in early life. Microbiome\| PubMed ID: 28038686	2016
Antibiotics in Pregnancy Increase Children's Risk of Otitis Media and Ventilation Tubes. The Journal of pediatrics\| PubMed ID: 28088397	2017
The Follicular Skin Microbiome in Patients With Hidradenitis Suppurativa and Healthy Controls. JAMA dermatology\| PubMed ID: 28538949	2017

Jonathan Thorsen

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