Temporary dietary fiber depletion prompts rapid and lasting gut microbiota restructuring in mice
Microbiology Spectrum,
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 5, 2025
ABSTRACT
Long-term
alterations
of
the
gut
microbiota
and
host
symbiosis
after
a
dietary
perturbation
remain
insufficiently
understood
characterized.
In
this
study,
we
investigate
impact
temporary
fiber
depletion
in
mice
that
received
diet
with
reduced
content
(RFD)
for
3
weeks
followed
by
return
to
standard
chow
6
weeks,
compared
only
diet.
Fiber
deprivation
was
accompanied
reduction
diversity
an
increase
mucolytic
sulfate-reducing
bacteria.
The
activities
enzymes
targeting
glycans
from
mucus
were
increased
accordingly,
while
those
plant
fibers
decreased.
On
side,
report
transiently
higher
quantities
DNA
feces
during
RFD
suggesting
impaired
barrier
function.
Six
diet,
lasting
changes
composition
observed,
as
exemplified
replacement
durably
depleted
amplicon
sequence
variants
close
Duncaniella
dubosii
other
members
Muribaculaceae
family.
observation
two
distinct
microbial
communities
under
identical
environmental
alimentary
conditions
at
end
experiment
suggests
existence
alternative
stable
states.
IMPORTANCE
article,
authors
explore
on
microbiota-host
mouse
model.
More
importantly,
they
examine
resilience
intestinal
(chow)
Some
measured
parameters
(intestinal
impairment
bacterial
glycan-degrading
enzymatic
activities)
returned
control
values.
However,
not
case
richness—the
number
different
bacteria
observed—which
remained
reduced.
Among
related
bacteria,
some
groups
receded
undetected
until
others
saw
their
abundance
replacement.
find
little
can
cause
transition
state,
i.e.,
change
composition.
Язык: Английский
Living on the edge: Mucus-associated microbes in the colon
Mucosal Immunology,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 1, 2025
The
colonic
mucus
layer
acts
as
a
physicochemical
barrier
to
pathogen
invasion
and
habitat
for
mucus-associated
microbes.
This
mucosal
microbiome
plays
crucial
role
in
moderating
production,
maintaining
integrity,
shaping
the
host
immune
response.
However,
unchecked
mucin
foraging
may
render
vulnerable
disease.
To
better
understand
these
dynamics
layer,
it
is
essential
advance
fundamental
knowledge
on
how
commensals
bind
utilize
well
their
interactions
with
both
microbial
neighbors.
We
present
an
overview
of
approaches
surveying
bacteria
assessing
mucin-utilizing
capacity,
alongside
discussion
limitations
existing
methods.
Additionally,
we
highlight
diet
secretory
immunoglobulin
A
interact
bacterial
community
colon.
Insights
into
this
subset
can
guide
therapeutic
strategies
optimally
support
modulate
integrity.
Язык: Английский
Next-generation IgA-SEQ allows for high-throughput, anaerobic, and metagenomic assessment of IgA-coated bacteria
Microbiome,
Год журнала:
2024,
Номер
12(1)
Опубликована: Окт. 21, 2024
The
intestinal
microbiota
plays
a
significant
role
in
maintaining
systemic
and
homeostasis,
but
can
also
influence
diseases
such
as
inflammatory
bowel
disease
(IBD)
cancer.
Certain
bacterial
species
within
the
tract
chronically
activate
immune
system,
leading
to
low-grade
inflammation.
As
result,
plasma
cells
produce
high
levels
of
secretory
antigen-specific
immunoglobulin
A
(IgA),
which
coats
immunostimulatory
bacteria.
This
IgA
response
against
bacteria
may
be
associated
with
maintenance
homeostasis
health,
well
disease.
Unraveling
this
dichotomy
identifying
is
crucial
for
understanding
relationship
between
their
health
IgA-SEQ
technology
has
successfully
identified
immunostimulatory,
IgA-coated
from
fecal
material.
However,
original
time-consuming
limited
downstream
applications.
In
study,
we
aimed
develop
next-generation,
high-throughput,
magnet-based
sorting
approach
(ng-IgA-SEQ)
overcome
limitations
protocol.
Язык: Английский
Long-term fasting remodels gut microbial metabolism and host metabolism
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Апрель 19, 2024
Abstract
Long-term
fasting
has
become
a
promising
research
subject
for
its
potential
of
treating
and
preventing
metabolic
diseases.
However,
little
is
known
about
impact
on
the
functional
capacity
gut
microbiome
combined
effect
serum
metabolome.
Here,
we
demonstrate
extensive
remodelling
microbial
ecosystem
in
humans
(n=92)
after
an
average
9.8
days
(∼250
kcal
/
day).
Fasting
transiently
affected
relative
abundance
majority
bacterial
species
(306
decreased
210
increased
out
772).
Species
changes
could
largely
be
explained
by
their
genomic
repertoire
carbohydrate-active
enzymes
(CAZymes),
which
were
investigated
here
first
time.
induced
CAZyme
families,
depleting
families
with
dietary
fibre
substrates
increasing
host-derived
glycan
substrates.
Likewise,
observed
metabolome,
382
721
metabolites
significantly
(246
136
decreased).
In-depth
metagenome-metabolome
co-variation
analysis
suggested
Oscillibacter
to
key
producers
indole-3-propionic
acid,
crucial
metabolite
cardiometabolic
health.
Together,
our
results
provide
unprecedented
view
long-term
composition
function.
Язык: Английский
Unraveling interindividual differences and functional consequences of gut microbial metabolism of immunosuppressants
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Март 28, 2024
Abstract
A
major
challenge
in
kidney
transplantation
(KT)
is
the
large
interpatient
variability
pharmacokinetics
of
immunosuppressive
drugs.
Here,
we
explored
role
gut
microbiome
interindividual
variation
drug
metabolism.
Analysis
38
fecal
communities,
including
10
from
KT
recipients,
and
45
bacterial
species
against
25
drugs,
revealed
significant
drug-specific
differences
Notably,
15
16
immunosuppressants
tested
were
metabolized
by
at
least
one
microbial
community,
found
specific
species,
such
as
Bacteroides
uniformis
,
to
be
potent
metabolizers.
We
identified
18
different
metabolites
for
two
previously
undescribed
sirolimus
everolimus.
Our
study
reveals
functional
impact
metabolism
on
key
immunosuppressants,
inactivation
tacrolimus,
activation
potential
increase
toxicity
mycophenolate
mofetil
(MMF),
shows
that
metabolite
methylprednisolone
exhibits
a
2.6-fold
epithelial
permeability
compared
parent
drug.
Through
gain-of-function
genetic
screen
B.
enzyme
BACUNI_RS05305
responsible
MMF
activation.
Using
machine
learning
model
community
metabolism,
abundance
features
prevalent
predicted
biotransformation
some
drugs
well,
while
others,
priori
experimental
information
genes
protein
structures
led
improved
predictions.
research
highlights
explain
therapies
sets
stage
clinical
trials
identify
microbiome-encoded
signatures
predictive
patients.
Язык: Английский
Health benefits of a five-day at-home modified fasting program: a randomised controlled trial
medRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Ноя. 4, 2024
ABSTRACT
Background
Fasting
has
been
shown
to
be
one
of
the
most
cost-effective
methods
improve
cardiometabolic
health.
We
studied
a
5-day
hypocaloric
(∼600
kcal/day)
and
ketogenic,
modified
fasting
program
(MFP)
for
at-home
interventions.
hypothesised
that
this
MFP
induces
metabolic
changes
comparable
5
days
prolonged
(75-250kcal/day).
Methods
tested
in
two-arm
randomised
controlled
trial
where
sixty-four
healthy
subjects
were
or
control
group.
Serum
biochemistry
analyses
questionnaires
allowed
determining
effects
on
risk
factors.
Emotional
well-being,
possible
side
physical
activity
assessed
with
questionnaires.
Biological
pathways
processes
explored
nuclear
magnetic
resonance
blood
metabolomics
gut
metagenomics
analyses.
Results
participants
(n=32)
experienced
weight
loss
(−3.1
±
1.1
kg)
persisting
month
after
intervention.
The
induced
significant,
but
transient
reductions,
systolic
(−6.4
11.5
mmHg)
diastolic
(−4.4
7.7
pressure,
glucose
levels,
HbA1c
coagulation
led
greater
reductions
BMI
(p=0.006),
pressure
(p
=
0.009),
cholesterol
0.02),
LDL
0.02)
individuals
at
diseases
compared
individuals.
Total
cholesterol,
LDL-C
HDL-C
levels
continued
decreasing
during
food
reintroduction.
also
increased
emotional
well-being.
Blood
revealed
significant
decrease
chronic
inflammation
markers.
Shotgun
microbiome
showed
trends
relative
abundance
majority
bacterial
species
their
genomic
repertoire
carbohydrate-active
enzymes
(CAZymes).
This
reflected
families
metabolising
dietary
fibre
substrates
an
increase
host-derived
glycan
substrates.
Comparing
previous
cohort’s
similar
changes.
Conclusion
is
safe
effectively
improves
health
well-being
It
offers
benefits
those
observed
clinic.
practised
home,
widely
accessible
compatible
individuals’
everyday
life.
Язык: Английский
Exclusive cataloging of near-complete genomes unveils novel functional insights into the human gut microbiome
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 11, 2024
Abstract
Understanding
the
human
gut
microbiome
requires
comprehensive
genomic
catalogs,
yet
many
existing
ones
lack
geographic
diversity
and
include
numerous
medium-quality
metagenome-assembled
genomes
(MAGs)
missing
up
to
50%
of
regions,
potentially
leading
inaccurate
functional
insights
into
microbiome.
To
address
these
limitations,
we
developed
an
enhanced
Human
Reference
Gut
Microbiome
(HRGM2),
a
catalog
near-complete
(NC)
MAGs
(completeness
≥90%
contamination
≤5%)
isolate
(collectively
‘NC
genomes’)
with
extensive
sampling.
HRGM2
comprises
155,211
non-redundant
NC
from
4,824
prokaryotic
species
across
41
countries,
representing
66%
increase
in
genome
count
boost
over
genome-based
Unified
Gastrointestinal
Genome
catalog.
Extensive
sampling
Africa
revealed
previously
undetectable
Africa-associated
phyla,
highlighting
microbial
links
between
humans
environment.
Given
high
complexity
microbiota,
DNA-based
profiling
using
outperforms
marker-based
accuracy.
Profiling
protein
annotations
provides
reliable
Notably,
exclusive
use
genomes,
enhances
assessments
microbiota
metabolic
capacities
supports
genome-scale
models
(GEMs)
entire
microbiota.
These
findings
offer
novel
perspectives
on
microbiome,
achievable
only
through
high-quality
cataloging.
Язык: Английский