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Pace.indoor air2011
1. Ribosomal RNA Surveys of Human-
Occupied Indoor Environments
Norm Pace
CU-Boulder
nrpace@colorado.edu
2. Outline
• The microbial world is a complex place -
How to make sense of “diversity”?
• The molecular view of the natural microbial
world.
• Sampling the indoor environment – aerosols.
4. Making Sense of Sequences:
Molecular Phylogeny
1. Align sequences so that “homologous” residues
are juxtaposed.
2. Count the number of differences between pairs of
sequences; this is some measure of “evolutionary
distance” that separates the organisms.
3. Calculate the “tree”, the relatedness map, that most
accurately represents all the pairwise differences.
9. E.g. Gene contents of different
“strains” of “Escherichia coli”
Strain B
Strain A
Strain C
10. Indoor Microbiology Project (sponsored by A.P. Sloan Fndn.)
Laura Baumgartner
• NYC Subway system aerosols (7 stations, 3 connected
sites, multiple seasons.
Piret Koll
• School aerosols (3 in Denver–Boulder area)
• Homeless shelter aerosols (2 in Denver–Boulder area)
• Health setting aerosols (2 hospitals, 1 clinic in CO)
• Hotel HVAC (1, Atlanta)
• Office building aerosols (2, Atlanta)
• University setting aerosols (3 in TX, several in CO)
Kim Ross
• Municipal water distribution, source-to-POU (many
samples in Boulder and Centennial systems, some
overlap with a concurrent 454 source water survey.
Kristen Peterson
• Public swimming facility aerosols and biofilms (5 in CO,
2 in TX)
13. What
are
we
finding
generally?
•
The
microbiology
of
the
human
environment
phylogene:cally
is
rela:vely
simple,
mainly
only
~5
of
~100
known
phyla.
Few
“candidate
phyla”
in
~100K
sequences.
•
Sequences
are
seldom
iden:cal
to
a
previously
determined
sequence,
but
many
“bin”
with
cultured
species
at
the
“genus”
level
(95%)
or
even
“species”
level
(97%).
•
Every
site
sampled
differs
in
the
detail,
but
generali:es
emerge
for
each
kind
of
environment.
•
Indoor
aerosol
microbiology
is
significantly/mainly
human-‐shed
microbiology.
•
Water
microbiology
is
idiosyncra:c
with
source
and
system,
and
in
some
seSngs
is
of
poten:al
health
concern.
