Avid Bioservices Inc (CDMO)

[biopharm]

Microbial signatures bring Biomarkers via PS Targeting

If we analyze all authors and all research published and how fast we are moving towards Biomarkers ....you shall notice the Sandia National Labs funded Peregrine study may be very relevant to PS Targeting and how it opens the doors to massive data that will lead to astronomical biomarkers data

Peregrine RNA-Seq library

Stanley A. Langevin, † Zachary W. Bent, † Owen D. Solberg, Deanna J. Curtis, Pamela D. Lane, Kelly P. Williams, Joseph S. Schoeniger, Anupama Sinha, Todd W. Lane, and Steven S. Branda*
Biotechnology and Bioengineering; Sandia National Laboratories; Livermore, CA USA
†These authors contributed equally.
*Correspondence to: Steven S. Branda, Email: vog.aidnas@adnarbs

Received 2012 Dec 20;
Revised 2013 Feb 15;
Accepted 2013 Mar 13.

Peregrine
A rapid and unbiased method to produce strand-specific RNA-Seq libraries from small quantities of starting material
Stanley A. Langevin, Zachary W. Bent, [...], and Steven S. Branda

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3710357/

..Early_nasopharyngeal_microbial_signature_associated_with_severe_influenza_in_children_a_retrospective_pilot_study

Early nasopharyngeal microbial signature associated with severe influenza in children: a retrospective pilot study

Article in Journal of General Virology · September 2017
DOI: 10.1099/jgv.0.000920

Stanley Langevin

Maxime Pichon at University Hospital of Lyon, France
Maxime Pichon
15.01University Hospital of Lyon, France

Elise Smith at University of Washington Seattle
Elise Smith
12.58University of Washington Seattle

Juliet Morrison
Not on ResearchGate

Zachary Bent
Not on ResearchGate

Richard Green
Not on ResearchGate

Kristi Leigh Barker at NanoString Technologies
Kristi Leigh Barker
25.76NanoString Technologies

Owen Solberg
Not on ResearchGate
Yves Gillet at Centre Hospitalier Universitaire de Lyon
Yves Gillet
30.75Centre Hospitalier Universitaire de Lyon

Etienne Javouhey
Not on ResearchGate

Bruno Lina at Claude Bernard University Lyon 1
Bruno Lina
45.33Claude Bernard University Lyon 1

Michael G. Katze
Not on ResearchGate

Laurence Josset at University of Washington Seattle
Laurence Josset
29.95University of Washington Seattle


Abstract
A few studies have highlighted the importance of the respiratory microbiome in modulating the frequency and outcome of viral respiratory infections. However, there are insufficient data on the use of microbial signatures as prognostic biomarkers to predict respiratory disease outcomes. In this study, we aimed to evaluate whether specific bacterial community compositions in the nasopharynx of children at the time of hospitalization are associated with different influenza clinical outcomes. We utilized retrospective nasopharyngeal (NP) samples (n=36) collected at the time of hospital arrival from children who were infected with influenza virus and had been symptomatic for less than 2 days. Based on their clinical course, children were classified into two groups: patients with mild influenza, and patients with severe respiratory or neurological complications. We implemented custom 16S rRNA gene sequencing, metagenomic sequencing and computational analysis workflows to classify the bacteria present in NP specimens at the species level. We found that increased bacterial diversity in the nasopharynx of children was strongly associated with influenza severity. In addition, patients with severe influenza had decreased relative abundance of Staphylococcus aureus and increased abundance of Prevotella (including P. melaninogenica), Streptobacillus, Porphyromonas, Granulicatella (including G. elegans), Veillonella (including V. dispar), Fusobacterium and Haemophilus in their nasopharynx. This pilot study provides proof-of-concept data for the use of microbial signatures as prognostic biomarkers of influenza outcomes. Further large prospective cohort studies are needed to refine and validate the performance of such microbial signatures in clinical settings.

https://www.researchgate.net/publication/319481762_Early_nasopharyngeal_microbial_signature_associated_with_severe_influenza_in_children_a_retrospective_pilot_study