This document summarizes Norm Pace's research on surveying microbial communities in indoor human environments using ribosomal RNA sequencing. It describes sampling aerosols from various indoor locations like subway stations, schools, hospitals, hotels, offices and universities. It finds that indoor microbiomes are dominated by a few bacterial phyla and many sequences are closely related to known species. Environments differ in their microbial makeup but human-associated microbes predominate indoors. Showerhead biofilms frequently contain potential pathogens like Mycobacterium avium. The research is providing insights into the diversity and distribution of microbes people encounter.

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.

3. Kim Ross
Kim Ross

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.

5. You are here -->

6. “Metagenomics”

7. Sample  DNA  rDNA PCR library  clone  sequence
“ “ “  Next-gen multiplex

8. Expansion of the Bacterial Tree

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)

11. Sampling aerosols: NON-TRIVIAL!

12. Evolution of the Sceptor Industries Omni 3000

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.

14. How similar are our samples to the Human Microbiome?

15. Where in the home? -
Any place moist
Who’s in your showerhead?

16. Examples of Showerhead Biofilm Swab
Results
VSM5Q1u
showerhead swab
N=85
Streptococcus oralis BSD2Q1u
Dietzia maris showerhead swab
Staphylococcus Moraxella osloensis Chlamydiae
N=81
capitis 1%
Staphylococcus Novel Group
2%
epidermidis
Mycobacterium Methylococcaceae
Sphingomonas 2%
yanoikuyae avium
Flavobacterium
Blastomonas 2%
Methylocystis
natatoria Mycobacterium 34%
gordonae
7%
Escherichia coli Bacillus
7%
Delftia acidovorans Mycobacterium
gordonae Bacteroidetes
11%
Mycobacterium other Sphingomonas
Methylobacterium Uncultured Beta Proteo
16%
sp. 13%
Mycobacterium avium Positive M. avium Negative
-cause of MAC pulmonary infections
-have seen in 35/54 Showerheads
analyzed

17. Water/Showerhead Swab Comparison
VPM5W1u,
water from pipe pre-showerhead
N=86
Escherichia coli
Novosphingobium
lentum VSM5Q1u
Mycobacterium avium showerhead swab
Mycobacterium N=85
gordonae Methylobacter
psychrophilus Streptococcus oralis
Blastomonas natatoria
Dietzia maris
Dir. of Water Flow
Moraxella osloensis
Staphylococcus capitis
Staphylococcus
epidermidis
Methylobacterium sp.
Sphingomonas yanoikuyae Mycobacterium avium
Blastomonas natatoria
Mycobacterium
gordonae
VSM5W1u, Escherichia coli
Legionella waltersii
water collected post-showerhead
Blastomonas natatoria
N=90
Bdellovibrio
Delftia acidovorans
bacteriovorus Mycobacterium gordonae
Rhodobacter blastica
Mycobacterium other
Sphingomonas sp. Methylobacterium sp.
Novosphingobium sp.
Methylobacterium sp.
Methylobacter
psychrophilus

18. The End
nrpace@colorado.edu