Nature Communications,
Год журнала:
2019,
Номер
10(1)
Опубликована: Март 4, 2019
Abstract
Metagenomic
sequencing
has
greatly
improved
our
ability
to
profile
the
composition
of
environmental
and
host-associated
microbial
communities.
However,
dependency
most
methods
on
reference
genomes,
which
are
currently
unavailable
for
a
substantial
fraction
species,
introduces
estimation
biases.
We
present
an
updated
functionally
extended
tool
based
universal
(i.e.,
reference-independent),
phylogenetic
marker
gene
(MG)-based
operational
taxonomic
units
(mOTUs)
enabling
profiling
>7700
species.
As
more
than
30%
them
could
not
previously
be
quantified
at
this
resolution,
relative
abundance
estimates
mOTUs
accurate
compared
other
methods.
new
feature,
we
show
that
mOTUs,
essential
housekeeping
genes,
demonstrably
well-suited
quantification
basal
transcriptional
activity
community
members.
Furthermore,
single
nucleotide
variation
profiles
estimated
using
reflect
those
from
whole
allows
comparing
strain
populations
(e.g.,
across
different
human
body
sites).
New England Journal of Medicine,
Год журнала:
2016,
Номер
375(24), С. 2369 - 2379
Опубликована: Дек. 14, 2016
The
large
majority
of
studies
on
the
role
microbiome
in
pathogenesis
disease
are
correlative
and
preclinical;
several
have
influenced
clinical
practice.
Cell Research,
Год журнала:
2020,
Номер
30(6), С. 492 - 506
Опубликована: Май 20, 2020
Abstract
The
interplay
between
the
commensal
microbiota
and
mammalian
immune
system
development
function
includes
multifold
interactions
in
homeostasis
disease.
microbiome
plays
critical
roles
training
of
major
components
host’s
innate
adaptive
system,
while
orchestrates
maintenance
key
features
host-microbe
symbiosis.
In
a
genetically
susceptible
host,
imbalances
microbiota-immunity
under
defined
environmental
contexts
are
believed
to
contribute
pathogenesis
multitude
immune-mediated
disorders.
Here,
we
review
microbiome-immunity
crosstalk
their
health
disease,
providing
examples
molecular
mechanisms
orchestrating
these
intestine
extra-intestinal
organs.
We
highlight
aspects
current
knowledge,
challenges
limitations
achieving
causal
understanding
host
immune-microbiome
interactions,
as
well
impact
on
diseases,
discuss
how
insights
may
translate
towards
future
microbiome-targeted
therapeutic
interventions.
Cell,
Год журнала:
2019,
Номер
176(3), С. 649 - 662.e20
Опубликована: Янв. 1, 2019
The
body-wide
human
microbiome
plays
a
role
in
health,
but
its
full
diversity
remains
uncharacterized,
particularly
outside
of
the
gut
and
international
populations.
We
leveraged
9,428
metagenomes
to
reconstruct
154,723
microbial
genomes
(45%
high
quality)
spanning
body
sites,
ages,
countries,
lifestyles.
recapitulated
4,930
species-level
genome
bins
(SGBs),
77%
without
public
repositories
(unknown
SGBs
[uSGBs]).
uSGBs
are
prevalent
(in
93%
well-assembled
samples),
expand
underrepresented
phyla,
enriched
non-Westernized
populations
(40%
total
SGBs).
annotated
2.85
M
genes
SGBs,
many
associated
with
conditions
including
infant
development
(94,000)
or
Westernization
(106,000).
permit
deeper
analyses
increase
average
mappability
metagenomic
reads
from
67.76%
87.51%
(median
94.26%)
65.14%
82.34%
mouth.
thus
identify
thousands
yet-to-be-named
species,
pangenomes
human-associated
microbes,
allow
better
exploitation
technologies.
Nature,
Год журнала:
2017,
Номер
550(7674), С. 61 - 66
Опубликована: Сен. 19, 2017
Abstract
The
characterization
of
baseline
microbial
and
functional
diversity
in
the
human
microbiome
has
enabled
studies
microbiome-related
disease,
diversity,
biogeography,
molecular
function.
National
Institutes
Health
Human
Microbiome
Project
provided
one
broadest
such
characterizations
so
far.
Here
we
introduce
a
second
wave
data
from
study,
comprising
1,631
new
metagenomes
(2,355
total)
targeting
diverse
body
sites
with
multiple
time
points
265
individuals.
We
applied
updated
profiling
assembly
methods
to
provide
personalization.
Strain
identification
revealed
subspecies
clades
specific
sites;
it
also
quantified
species
phylogenetic
under-represented
isolate
genomes.
Body-wide
classified
pathways
into
universal,
human-enriched,
site-enriched
subsets.
Finally,
temporal
analysis
decomposed
variation
rapidly
variable,
moderately
stable
This
study
furthers
our
knowledge
enables
an
understanding
personalized
function
dynamics.
Science Translational Medicine,
Год журнала:
2017,
Номер
9(378)
Опубликована: Фев. 22, 2017
Commensal
skin
bacteria
produce
previously
unknown
antimicrobial
peptides
that
can
inhibit
Staphylococcus
aureus
colonization
of
atopic
dermatitis
subjects.
Pediatric Allergy and Immunology,
Год журнала:
2016,
Номер
27(S23), С. 1 - 250
Опубликована: Май 1, 2016
The
availability
of
allergen
molecules
('components')
from
several
protein
families
has
advanced
our
understanding
immunoglobulin
E
(IgE)-mediated
responses
and
enabled
'component-resolved
diagnosis'
(CRD).
European
Academy
Allergy
Clinical
Immunology
(EAACI)
Molecular
Allergology
User's
Guide
(MAUG)
provides
comprehensive
information
on
important
allergens
describes
the
diagnostic
options
using
CRD.
Part
A
EAACI
MAUG
introduces
molecules,
families,
composition
extracts,
databases,
IgE,
skin,
basophil
tests.
Singleplex
multiplex
IgE
assays
with
components
improve
both
sensitivity
for
low-abundance
analytical
specificity;
to
individual
can
yield
clinical
risks
distinguish
cross-reactivity
true
primary
sensitization.
B
discusses
molecular
aspects
IgE-mediated
allergies
foods
(including
nuts,
seeds,
legumes,
fruits,
vegetables,
cereal
grains,
milk,
egg,
meat,
fish,
shellfish),
inhalants
(pollen,
mold
spores,
mites,
animal
dander),
Hymenoptera
venom.
Diagnostic
algorithms
short
case
histories
provide
useful
workup
allergic
individuals
targeted
C
covers
containing
ubiquitous,
highly
cross-reactive
panallergens
plant
(lipid
transfer
proteins,
polcalcins,
PR-10,
profilins)
sources
(lipocalins,
parvalbumins,
serum
albumins,
tropomyosins)
explains
their
utility.
D
lists
100
molecules.
In
conclusion,
reactions
diseases,
including
rhinoconjunctivitis,
asthma,
food
reactions,
insect
sting
are
discussed
a
novel
perspective.
documents
rapid
progression
allergology
basic
research
its
integration
into
practice,
quantum
leap
in
management
patients.
