Ferret upper respiratory tract
microbiome in influenza infection
Barb Methe & Elodie Ghedin, JCVI
Adolfo Garcia-Sastre, Mt Sinai, NYC
Questions study would address
• Following Influenza viral infection of the host,
how is the bacterial community structure
affected?
• Can we see a change in the bacterial
community during the course of the infcetion?
• Once the host recovers from viral infection,
how resilient is the bacterial community
structure?
Influenza Genome Project
Pilot to determine best conditions
• 2 uninfected (ferrets “94” and “96”)
– Nasal swab versus nasal wash
– Day 0 and Day 2
– Total specimens: 8
• 2 infected (ferrets “01” and “08”) + 1
uninfected control (“06”)
– Nasal washes only
– Day 0, Day 2, Day 3
– Total specimens: 9
Replicates and controls
• Total of 17 specimens
– 3 technical replicates of 16S amplicons
– 2 regions for each: V1-V3 and V3-V5
– For each round of PCR, 1 positive and 1 negative
control
• Total amplicons (test + controls): 114
• Sequencing: average of 4175 classifiable reads
per sample
Infected versus uninfected ferrets
STUDY 1
Infected V1-V3
Infected V3-V5
Control uninfected ferret: Day 0
Control uninfected ferret: Day 2
Control uninfected ferret: Day 3
V1-V3
V3-V5
Bacteria rank differently depending
on region studied
Infected ferrets: Day 0
Ferret “08”
Ferret “01”
Infected ferrets: Day 2
Ferret “08”
Ferret “01”
Infected ferrets: Day 3
Ferret “08”
Ferret “01”
V1-V3
V3-V5
Summary
• Important differences depending on region
analyzed (V1-V3 vs V3-V5)
• Ferret effect
Nasal Swab versus Wash
STUDY 2
Wash captures more species than swab
V1-V3 vs V3-V5:
Some species overlap and many unique
captured by each region
Conclusions
• Based on the results we have obtained thus far,
the nasal washes are recovering the greatest
diversity using either 16S variable region and are
likely to be the most useful samples going
forward.
• Not surprisingly, each 16S variable region returns
a slightly different result and one can argue for
either region. The V1V3 in general performs
better in the lab and it is the region of the 16S
gene that is evolving faster than the remainder of
the gene (so in theory more discrimination).
Teams
JCVI
Barb Methe
Elodie Ghedin
Kelvin Li
Monika Bihan
Sana Scherbakova
Mt. Sinai
Adolfo GarciaSastre
Rafael Medina
Funding:
NIAID
Infected
V1-V3
V3-V5
Uninfected