Abstract
The
prevalence
of
many
chronic
diseases
has
increased
over
the
last
decades.
It
been
postulated
that
dysbiosis
driven
by
environmental
factors
such
as
antibiotic
use
is
shifting
microbiome
in
ways
increase
inflammation
and
onset
disease.
Dysbiosis
can
be
defined
through
loss
or
gain
bacteria
either
promote
health
disease,
respectively.
Here
we
multiple
independent
datasets
to
determine
nature
for
a
cluster
includes
urinary
stone
disease
(USD),
obesity,
diabetes,
cardiovascular
kidney
which
often
exist
co-morbidities.
For
all
states,
individuals
exhibited
statistically
significant
association
with
antibiotics
year
compared
healthy
counterparts.
There
was
also
between
gut
microbiota
composition.
Furthermore,
each
state
associated
microbial
diversity
gut.
Three
genera,
Bacteroides,
Prevotella
,
Ruminococcus
were
most
common
dysbiotic
taxa
terms
being
enriched
depleted
populations
part
operational
taxonomic
units
(OTUs)
within
these
genera.
Results
cross-sectional
analysis
suggest
antibiotic-driven
may
risk
However,
longitudinal
studies
are
needed
confirm
causative
effect
risk.
Nature,
Год журнала:
2019,
Номер
568(7753), С. 499 - 504
Опубликована: Фев. 11, 2019
The
composition
of
the
human
gut
microbiota
is
linked
to
health
and
disease,
but
knowledge
individual
microbial
species
needed
decipher
their
biological
roles.
Despite
extensive
culturing
sequencing
efforts,
complete
bacterial
repertoire
remains
undefined.
Here
we
identify
1,952
uncultured
candidate
by
reconstructing
92,143
metagenome-assembled
genomes
from
11,850
microbiomes.
These
substantially
expand
known
collective
microbiota,
with
a
281%
increase
in
phylogenetic
diversity.
Although
newly
identified
are
less
prevalent
well-studied
populations
compared
reference
isolate
genomes,
they
improve
classification
understudied
African
South
American
samples
more
than
200%.
encode
hundreds
biosynthetic
gene
clusters
possess
distinctive
functional
capacity
that
might
explain
elusive
nature.
Our
work
expands
diversity
bacteria,
which
provides
unprecedented
resolution
for
taxonomic
characterization
intestinal
microbiota.
Frontiers in Cellular and Infection Microbiology,
Год журнала:
2020,
Номер
10
Опубликована: Ноя. 24, 2020
Advances
in
culture-independent
research
techniques
have
led
to
an
increased
understanding
of
the
gut
microbiota
and
role
it
plays
health
disease.
The
intestine
is
populated
by
a
complex
microbial
community
that
organized
around
network
metabolic
interdependencies.
It
now
understood
vital
for
normal
development
functioning
human
body,
especially
priming
maturation
adaptive
immune
system.
Antibiotic
use
can
several
negative
effects
on
microbiota,
including
reduced
species
diversity,
altered
activity,
selection
antibiotic-resistant
organisms,
which
turn
lead
antibiotic-associated
diarrhea
recurrent
Clostridioides
difficile
infections.
There
also
evidence
early
childhood
exposure
antibiotics
gastrointestinal,
immunologic,
neurocognitive
conditions.
increase
recent
years
suggests
these
problems
are
likely
become
more
acute
or
prevalent
future.
Continued
into
structure
function
required
address
this
challenge.
Frontiers in Immunology,
Год журнала:
2020,
Номер
11
Опубликована: Дек. 10, 2020
The
human
microbiota
has
a
fundamental
role
in
host
physiology
and
pathology.
Gut
microbial
alteration,
also
known
as
dysbiosis,
is
condition
associated
not
only
with
gastrointestinal
disorders
but
diseases
affecting
other
distal
organs.
Recently
it
became
evident
that
the
intestinal
bacteria
can
affect
central
nervous
system
(CNS)
inflammation.
tract
are
communicating
through
bidirectional
network
of
signaling
pathways
called
gut-brain
axis,
which
consists
multiple
connections,
including
vagus
nerve,
immune
system,
bacterial
metabolites
products.
During
these
dysregulated
altered
permeability
blood-brain
barrier
(BBB)
neuroinflammation.
However,
numerous
mechanisms
behind
impact
gut
neuro-development
-pathogenesis
remain
poorly
understood.
There
several
involved
CNS
homeostasis
Among
those,
inflammasome
pathway
been
linked
to
neuroinflammatory
conditions
such
sclerosis,
Alzheimer’s
Parkinson’s
diseases,
anxiety
depressive-like
disorders.
complex
assembles
upon
cell
activation
due
exposure
microbes,
danger
signals,
or
stress
lead
production
pro-inflammatory
cytokines
(interleukin-1β
interleukin-18)
pyroptosis.
Evidences
suggest
there
reciprocal
influence
brain.
how
this
precisely
working
yet
be
discovered.
Herein,
we
discuss
status
knowledge
open
questions
field
focusing
on
function
products
cells
during
healthy
inflammatory
conditions,
neuropsychiatric
In
particular,
focus
innate
mechanism
certain
microbes.
Nature Communications,
Год журнала:
2022,
Номер
13(1)
Опубликована: Янв. 17, 2022
Identifying
differentially
abundant
microbes
is
a
common
goal
of
microbiome
studies.
Multiple
methods
are
used
interchangeably
for
this
purpose
in
the
literature.
Yet,
there
few
large-scale
studies
systematically
exploring
appropriateness
using
these
tools
interchangeably,
and
scale
significance
differences
between
them.
Here,
we
compare
performance
14
differential
abundance
testing
on
38
16S
rRNA
gene
datasets
with
two
sample
groups.
We
test
amplicon
sequence
variants
operational
taxonomic
units
(ASVs)
Our
findings
confirm
that
identified
drastically
different
numbers
sets
significant
ASVs,
results
depend
data
pre-processing.
For
many
number
features
correlate
aspects
data,
such
as
size,
sequencing
depth,
effect
size
community
differences.
ALDEx2
ANCOM-II
produce
most
consistent
across
agree
best
intersect
from
approaches.
Nevertheless,
recommend
researchers
should
use
consensus
approach
based
multiple
to
help
ensure
robust
biological
interpretations.
Many
available,
but
it
lacks
systematic
comparison
among
authors
groups,
show
results.
Nature Communications,
Год журнала:
2018,
Номер
9(1)
Опубликована: Июль 3, 2018
The
human
gut
microbiome
has
been
associated
with
many
health
factors
but
variability
between
studies
limits
exploration
of
effects
them.
Gut
microbiota
profiles
are
available
for
>2700
members
the
deeply
phenotyped
TwinsUK
cohort,
providing
a
uniform
platform
such
comparisons.
Here,
we
present
association
analyses
38
common
diseases
and
51
medications
within
cohort.
We
describe
several
novel
associations,
highlight
associations
across
multiple
diseases,
determine
which
have
greatest
microbiota.
These
results
provide
reference
future
its
role
in
health.
JAMA Psychiatry,
Год журнала:
2021,
Номер
78(12), С. 1343 - 1343
Опубликована: Сен. 15, 2021
Evidence
of
gut
microbiota
perturbations
has
accumulated
for
multiple
psychiatric
disorders,
with
signatures
proposed
as
potential
biomarkers.
However,
no
attempts
have
been
made
to
evaluate
the
specificity
these
across
range
conditions.
The
human
gut
microbiome
is
a
complex
ecosystem,
densely
colonised
by
thousands
of
microbial
species.
It
varies
among
individuals
and
depends
on
host
genotype
environmental
factors,
such
as
diet
antibiotics.
In
this
review,
we
focus
stability
resilience
essential
ecological
characteristics
the
its
relevance
for
health.
Microbial
diversity,
metabolic
flexibility,
functional
redundancy,
microbe–microbe
host–microbe
interactions
seem
to
be
critical
maintaining
resilience.
equilibrium
ecosystem
can
disrupted
perturbations,
antibiotic
therapy,
causing
significant
decreases
in
richness
diversity
well
impacting
As
consequence,
unbalanced
states
or
even
unhealthy
stable
develop,
potentially
leading
supporting
diseases.
Accordingly,
strategies
have
been
developed
manipulate
order
prevent
revert
caused
including
faecal
microbiota
transplantation,
supplementation
with
probiotics
non-digestible
carbohydrates,
more
extensive
dietary
modifications.
Nevertheless,
an
increasing
number
studies
has
evidenced
interindividual
variability
extent
direction
response
which
attributed
unique
each
individual’s
microbiome.
From
clinical,
translational
perspective,
ability
improve
prior
restore
afterwards,
would
offer
benefits.
To
effective,
therapeutic
approach
will
likely
need
personalised
subgroup-based
understanding
individual
genetics,
diet,
other
factors
that
might
involved.
