Microbiome,
Journal Year:
2015,
Volume and Issue:
3(1)
Published: Dec. 1, 2015
Each
day
people
are
exposed
to
millions
of
bioaerosols,
including
whole
microorganisms,
which
can
have
both
beneficial
and
detrimental
effects.
The
next
chapter
in
understanding
the
airborne
microbiome
built
environment
is
characterizing
various
sources
microorganisms
relative
contribution
each.
We
identified
following
eight
major
categories
bacteria,
viruses,
fungi
environment:
humans;
pets;
plants;
plumbing
systems;
heating,
ventilation,
air-conditioning
mold;
dust
resuspension;
outdoor
environment.
Certain
species
associated
with
certain
sources,
but
full
potential
source
characterization
apportionment
has
not
yet
been
realized.
Ideally,
future
studies
will
quantify
detailed
emission
rates
from
each
identify
indoor
air
microbiome.
This
information
could
then
be
used
probe
fundamental
relationships
between
specific
human
health,
design
interventions
improve
building
health
or
even
provide
evidence
for
forensic
investigations.
Science,
Journal Year:
2014,
Volume and Issue:
346(6212), P. 954 - 959
Published: Nov. 20, 2014
Human
skin,
the
body's
largest
organ,
functions
as
a
physical
barrier
to
bar
entry
of
foreign
pathogens,
while
concomitantly
providing
home
myriad
commensals.
Over
human's
life
span,
keratinized
skin
cells,
immune
and
microbes
all
interact
integrate
processes
maintaining
skin's
under
homeostatic
healthy
conditions
also
multiple
stresses,
such
wounding
or
infection.
In
this
Review,
we
explore
intricate
interactions
cells
on
surface
within
associated
appendages
regulate
orchestrated
maturation
in
context
both
host
physiological
changes
environmental
challenges.
Systematic Biology,
Journal Year:
2018,
Volume and Issue:
68(2), P. 365 - 369
Published: Aug. 23, 2018
Next
generation
sequencing
(NGS)
technologies
have
led
to
a
ubiquity
of
molecular
sequence
data.
This
data
avalanche
is
particularly
challenging
in
metagenetics,
which
focuses
on
taxonomic
identification
sequences
obtained
from
diverse
microbial
environments.
Phylogenetic
placement
methods
determine
how
these
fit
into
an
evolutionary
context.
Previous
implementations
phylogenetic
algorithms,
such
as
the
algorithm
(EPA)
included
RAxML,
or
PPLACER,
are
being
increasingly
used
for
this
purpose.
However,
due
steady
progress
NGS
technologies,
current
face
substantial
scalability
limitations.
Herein,
we
present
EPA-NG,
complete
reimplementation
EPA
that
substantially
faster,
offers
distributed
memory
parallelization,
and
integrates
concepts
both,
RAxML-EPA
PPLACER.
EPA-NG
can
be
executed
standard
shared
memory,
well
systems
(e.g.,
computing
clusters).
To
demonstrate
placed
$1$
billion
metagenetic
reads
Tara
Oceans
Project
onto
reference
tree
with
3748
taxa
just
under
$7$
h,
using
2048
cores.
Our
performance
assessment
shows
outperforms
PPLACER
by
up
factor
$30$
sequential
execution
mode,
while
attaining
comparable
parallel
efficiency
systems.
We
further
show
parallelization
scales
available
AGPLv3
license:
https://github.com/Pbdas/epa-ng.
Virulence,
Journal Year:
2016,
Volume and Issue:
8(3), P. 352 - 358
Published: Oct. 13, 2016
Many
species
of
fungi
have
been
detected
in
the
healthy
human
gut;
however,
nearly
half
all
taxa
reported
only
found
one
sample
or
study.
Fungi
capable
growing
and
colonizing
gut
are
limited
to
a
small
number
species,
mostly
Candida
yeasts
family
Dipodascaceae
(Galactomyces,
Geotrichum,
Saprochaete).
Malassezia
filamentous
fungus
Cladosporium
potential
colonizers;
more
work
is
needed
clarify
their
role.
Other
commonly-detected
come
from
diet
environment
but
either
cannot
do
not
colonize
(Penicillium
Debaryomyces
which
common
on
fermented
foods
grow
at
body
temperature),
while
still
others
dietary
environmental
sources
(Saccharomyces
cerevisiae,
fermentation
agent
sometime
probiotic;
Aspergillus
ubiquitous
molds)
yet
likely
impact
ecology.
The
mycobiome
appears
less
stable
than
bacterial
microbiome,
subject
factors.
mSystems,
Journal Year:
2018,
Volume and Issue:
3(6)
Published: Oct. 30, 2018
The
eHOMD
(
http://www.ehomd.org
)
is
a
valuable
resource
for
researchers,
from
basic
to
clinical,
who
study
the
microbiomes
and
individual
microbes
in
body
sites
human
aerodigestive
tract,
which
includes
nasal
passages,
sinuses,
throat,
esophagus,
mouth,
lower
respiratory
health
disease.
an
actively
curated,
web-based,
open-access
resource.
provides
following:
(i)
species-level
taxonomy
based
on
grouping
16S
rRNA
gene
sequences
at
98.5%
identity,
(ii)
systematic
naming
scheme
unnamed
and/or
uncultivated
microbial
taxa,
(iii)
reference
genomes
facilitate
metagenomic,
metatranscriptomic,
proteomic
studies
(iv)
convenient
cross-links
other
databases
(e.g.,
PubMed
Entrez).
By
facilitating
assignment
of
species
names
sequences,
vital
enhancing
clinical
relevance
gene-based
microbiome
studies,
as
well
metagenomic
studies.
