bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Nov. 21, 2024
Abstract
The
gut-microbiota-brain
axis
influences
neuroinflammation,
neural
development
and
behaviour
such
as
sociability,
memory
anxiety.
To
study
these
traits
in
vivo
,
especially
during
or
disease,
it
is
crucial
to
analyse
them
over
time
with
multiple
analyses
the
same
animal.
With
a
growing
understanding
of
role
specific
bacteria
neurodegenerative
disease
behaviour,
demand
for
gnotobiotic
mouse
models
has
increased.
However,
maintaining
stable
hygienic
conditions
behavioural
testing
challenging,
exposure
conventional
environments
can
alter
status
mice
affect
behaviour.
We
established
protocols
perform
tests
assessing
memory,
anxiety,
exploration,
learning
recognition
under
axenic
using
flexible
film
isolators.
Our
compared
germ-free
carrying
defined
minimal
moderately
diverse
microbiota.
results
showed
no
effect
microbiota
on
short-
long-term
novel
object
recognition.
we
first
that
colonised
commensal
exhibited
more
anxiety-like
than
mice.
In
addition,
complexity
important,
only
allowing
us
disentangle
contribution
microbial
species
community
interactions
this
phenotype.
This
phenotype
correlated
differences
hippocampal
serum
metabolic
profiles
between
propose
approach
rodent
at
different
physiological
pathological
stages
their
life
without
compromising
hygiene,
thus
promoting
refinement
reduction
used
experiments.
EMBO Molecular Medicine,
Journal Year:
2025,
Volume and Issue:
unknown
Published: Feb. 13, 2025
Abstract
Colorectal
cancer
(CRC)
is
a
major
health
problem,
with
an
alarming
increase
of
early-onset
CRC
(EO-CRC)
cases
among
individuals
under
50
years
age.
This
trend
shows
the
urgent
need
for
understanding
underlying
mechanisms
leading
to
EO-CRC
development
and
progression.
There
significant
evidence
that
gut
microbiome
acts
as
key
player
in
by
triggering
molecular
changes
colon
epithelium,
tumorigenesis.
However,
comprehensive
collection
comparison
methods
study
such
tumor-microbiome
interactions
context
sparse.
review
provides
overview
available
vivo,
ex
vivo
well
vitro
approaches
model
assess
effect
microbes
on
tumor
growth.
By
comparing
advantages
limitations
each
system,
it
highlights
that,
while
no
single
perfect,
suitable
studying
specific
aspects
microbiome-induced
Taken
together,
multifaceted
can
simulate
human
body’s
complexity,
aiding
effective
treatment
prevention
strategies
EO-CRC.
FEBS Journal,
Journal Year:
2025,
Volume and Issue:
unknown
Published: Feb. 24, 2025
The
last
two
decades
have
seen
a
major
increase
in
our
understanding
of
the
role
microbiome
health
and
disease.
We
now
realise
that
these
fellow
travellers
are
really
important
regulators
various
systems
body
across
lifespan.
In
this
Special
Issue,
we
bring
together
collection
articles
from
leading
authors
who
summarise
current
state
art
host-microbe
interactions.
While
celebrate
breakthroughs
science,
also
acknowledge
challenges-variability
microbiota
composition,
complexities
interactions
need
for
standardised
methodologies.
As
research
progresses,
harnessing
power
may
pave
way
novel
diagnostic
therapeutic
strategies,
reaffirming
notion
never
alone-our
microbial
accompany
us
through
life,
better
or
worse.
Practical Neurology,
Journal Year:
2025,
Volume and Issue:
unknown, P. pn - 004400
Published: March 12, 2025
The
gastrointestinal
tract
is
inhabited
by
trillions
of
micro-organisms
that
form
the
gut
microbiome,
which
serves
various
functions
can
influence
neurological
pathways.
It
release
metabolites
could
affect
nervous
system.
bidirectional
communication
between
intestine
and
central
system
known
as
gut–brain
axis.
This
be
impacted
microbiota
in
direct
indirect
ways.
There
has
been
a
suggested
connection
microbiome
many
disorders,
including
epilepsy,
Alzheimer’s
disease,
Parkinson’s
disease
multiple
sclerosis.
explored
human
animal
studies.
While
no
microbial
biomarkers
have
identified
yet,
alterations
several
taxa
to
associated
with
states.
potential
modulate
function
sparked
clinical
trials
using
gut-altering
treatments,
some
positive
preliminary
results.
medRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Aug. 3, 2024
ABSTRACT
The
gut
microbiota
is
widely
implicated
in
host
health
and
disease,
inspiring
translational
efforts
to
implement
our
growing
body
of
knowledge
clinical
settings.
However,
the
need
characterize
by
its
genomic
content
limits
feasibility
rapid,
point-of-care
diagnostics.
produces
a
diverse
array
xenobiotic
metabolites
that
disseminate
into
tissues,
including
volatile
organic
compounds
(VOCs)
may
be
excreted
breath.
We
hypothesize
breath
contains
microbe-derived
VOCs
inform
composition
metabolic
state
microbiota.
To
explore
this
idea,
we
compared
volatilome
fecal
microbiomes
27
healthy
children
found
VOC
correlated
with
microbiomes.
experimentally
interrogate
finding,
devised
method
for
capturing
exhaled
from
gnotobiotic
mice.
Breath
volatiles
are
then
profiled
gas-chromatography
mass-spectrometry
(GC-MS).
Using
novel
methodology,
murine
profile
markedly
shaped
also
find
produced
microbes
pure
culture
can
identified
vivo
mice
monocolonized
same
bacteria.
Altogether,
studies
identify
support
mechanism
which
bacterial
metabolism
directly
contributes
mammalian
profiles.
Pakistan Journal of Health Sciences,
Journal Year:
2024,
Volume and Issue:
unknown, P. 02 - 12
Published: Aug. 31, 2024
The
human
gut
is
a
densely
populated
organ
system
that
bears
hundreds
of
microbial
species,
including
bacteria,
viruses,
and
various
protozoans.
microbiome
expresses
enormous
functional
diversity
based
on
community
collection.
However,
this
has
remained
unexplored
for
long
time,
but
in
the
recent
past
researches
have
revealed
its
immense
significance
host
metabolism
immunity.
Gut
microbiota
metabolize
undigested
substances
release
metabolites
response
to
significant
effect
immune
system.
balance
stability
within
body
are
achieved
maintained
through
complex
interaction
between
mucosal
Upon
loss
control
by
system,
dysbiosis
occurs,
modulation
community,
which
leads
different
disorders,
inflammatory
bowel
disease
colorectal
cancer.
Moreover,
also
associated
with
autoimmune
diseases
such
as
rheumatoid
arthritis,
diabetes
mellitus,
multiple
sclerosis.
Despite
intricate
mechanism
diseases,
therapeutic
strategies
utilized
treat
chronic
prebiotics
treatment,
personalized
probiotics
therapy,
fecal
transplantation,
narrow-spectrum
antibiotic
treatment.
This
review
discusses
how
association
becomes
dysregulated,
outcomes
form
interventions
cope
it.
Frontiers in Microbiology,
Journal Year:
2024,
Volume and Issue:
15
Published: Nov. 11, 2024
Our
understanding
of
the
role
gut
microbes
in
human
health
and
disease
has
come
a
long
way
since
John
M.
Whipps
colleagues
first
defined
term
'microbiome'.
Since
early
2000s,
with
gradual
lowering
cost
commercial
DNA
sequencing,
science
been
flooded
16S
rRNA
data.
Unfortunately,
despite
plethora
preclinical
clinical
publications
on
gutliver
axis,
majority
our
microbiota-liver
reciprocal
interaction
basically
remains
limited
to
correlation
analysis.
The
most
exciting
part
such
metagenomic
studies
is
sheer
amount
'big
data'
generated
which
rather
easy
correlate
physiological
variables;
bigger
data
number
independent
variables,
more
chances
find
'significant'
associations.
Notably,
gut-liver
axis
derived
from
microbiome,
not
microbiota.
Therefore,
conclusions
obtained
through
microbiome-related
often
do
reflect
causation,
are
representative
universal
phenomenon,
there
almost
no
true
microbial
markers
dysbiosis
linked
chronic
liver
disease.Translational
potentials
pre-clinical
associations
prediction
treatment
have
much
successful
enormous
numbers
interventional
observational
studies.
In
fact,
relevance
utilizing
rodents'
signatures
diseases
criticized
due
massive
difference
between
both
species,
attributed
gastrointestinal
biogeography
genetic
makeup
(Nguyen
et
al.,
2015).
Especially
high-fat
diet
model
metabolic
disease,
lack
consistency
good
bad
microbes.
also
associated
strains
belonging
probiotics
(e.g.,
Lactobacillus)
commensals
Akkermansia,
Faecalibacterium)
(Dey
Ray
Chaudhuri,
2023).
Added
this
fact
that
confounding
results
chemicalinduced
models
physiologically
mostly
irrelevant
(Dey,
2020)
germ-free
mice
possess
innate
defect
various
processes
(Jans
Vereecke,
2024).
Clinical
progression
distinct
terms
timeline,
cellular
phenotype,
pathological
complexity,
immune
responses,
machinery
(Liu
2013).
Further,
general
differences
animal
as
biological
makeup,
organ
anatomy,
functional
capacity),
extent
complexity
specificity,
co-influence
comorbidities),
ability
perform
controlled
experiments,
predictive
validity,
etc.
make
it
challenging
conclude
phenotypes
based
Although
emerging
reports
vitro
distal
intestine
(Qi
2023),
these
given
their
host
nature.
Due
advent
culturomics
techniques
studies,
patterns
were
initially
considered
conditions,
Firmicutesto-Bacteroides
ratio,
enrichment
energy-harvesting
specific
functions,
seem
be
falling
apart.
For
instance,
-proteobacteria
presence
lipopolysaccharide
(LPS)
previously
thought
simply
cause
hepatic
inflammation.
However,
identified
LPS-TLR4-inflammation
cannot
generalized
huge
LPS
structure
dictating
response
(Picarello,
2022),
luminal
LPS-supplying
Bacteroides,
displays
an
immunosuppressive
characteristics
(d'Hennezel
2017).
Today,
being
strongly
recognized
good,
bad,
ugly
nature
microbiota
conditionspecific.
Factors
availability
preferred
nutrients,
pathoadaptive
mutations,
evade
mucosal
critical
factors
define
species
commensal
or
pathobiont
2023;Dey,
bottom
line
proper
definition
eubiosis
features.
only
one
aspect
universally
accepted
loss
diversity
when
we
talk
about
diversity,
it's
community
effects,
causation
by
single
species.A
recent
systematic
review
meta-analysis
54
indicated
substantial
inter-study
heterogeneity
taxonomic
identification,
inflammation-inducing
genera
closely
non-alcoholic
fatty
but
provide
long-term
risk
value
(Su
To
date,
than
100
cross-sectional
identify
predominant
yet
absolute
core
microbiome
related
progressive
identified.
longitudinal
superior
informed
pathogenesis
can
former
one,
few
undertaken
order
link
health.
One
study
Kyoto
(Japan)
evaluated
alterations
pre-transplantation
two
months
post-surgery
38
transplant
patients
(Kato
Data
show
initial
decline
later
increase
along
overall
Enterobacteriaceae,
Streptococcaceae,
Bifidobacteriaceae,
while
depletion
abundance
Lactobacillaceae,
Enterococcaceae,
Clostridiaceae,
Peptostreptococcaceae
Ruminococcaceae
was
noted.
authors
acknowledged
variations
antibiotic
regimes,
food,
synbiotics,
patient
donors
underlying
diseases)
likely
influence
study's
findings.
Confounding
variables
relative
among
limitations.
line,
relatively
National
Institutes
Health,
USA,
investigated
hepatitis
C
patients,
taking
into
account
varied
degrees
fibrosis
severity
(Ali
investigation
done
six
after
HCV
undetectable
(n=23)
before
(n=29)
attaining
durable
virologic
response.
suggest
increased
correlated
Anaerostipes
hadrus,
Bacteroides
vulgatus
portal
inflammation
HCV.
A
prolonged
Methanobrevibacter
smithii
may
beneficial
effect
indicators
disease.
made
possible
compare
HCV-infected
individuals
supposedly
improved
viral
clearance
state,
they
unable
report
healthy
controls
unavailability
samples.
Another
Stanford
examines
composition
at
body
site
(including
gut)
multi-omics,
immunological,
hepatic)
(n=86)
over
6-year
period
comprehend
dynamic
microbiomes
throughout
illness
(Zhou
Despite,
identifying
compositional
parameters
metabolites,
temporal
measured
liver-specific
transaminases).
Emerging
although
claims
causative
effects
oral
including
(Gupta
Dey,
till
date.
Thus,
dynamics
under
course
remission
largely
unknown.Beyond
data,
fundamental
difficulty
analyzing
large-scale
big-data
lie
high
dimensionality
(Advani
Ganguli,
2016).
classically
designed
small
carefully
selected
(V)
test
hypothesis,
large
measurements
(M)
for
each
variable.
measurement
density
very
(M/V
→
∞).
Such
datasets
referred
low-dimensional,
classical
statistics
operates
within
framework.
contrast
scenario,
technological
capacity
high-throughput
sequencing
led
different
statistical
regime.
It
commonplace
simultaneously
measure
many
hundreds
taxa
individual
level.
constraints
time
resources,
simultaneous
measurements.
M
V
large,
(M/V)
smaller
conventional
experiments.
dimensional,
i.e.,
consist
points
high-dimensional
space.
Microbiome
thousands
gut.
Hence,
requires
us
employ
machine
learning
(ML)
approaches
dissect
dataset.
Utilizing
enhances
complex
host-microbe
reciprocal,
helping
tracking
monitoring
valuable
personalized
medicine.In
years,
ML
widely
used
shed
light
how
impact
diseases.
These
biomarkers
(Ruuskanen
2021;Zhang
2021;Liu
2022;Park
nature,
suffer
First,
extremely
difficult
detect
sets
useful
insight
translational
value.
High
dimensional
analysis
PCA,
ICA,
t-SNE,
reducing
detecting
patterns.
resulting
axes
represent
linear
combinations
features
abundance),
interpreting
making
experimental
predictions
(Donoho
Tanner,
2009)
(Furchtgott
Identifying
becomes
even
proportion
relevant
decreases,
higher
levels
2009).
decades
research
shown
This
indicate
subset
accurate
computational
inferences.
need
develop
novel
methods
sparse
datasets.The
second
challenge
extract
meaningful
predict
outcomes
guide
implications
Building
describing
networks
involve
parameters.
cases
remain
completely
unknown.
As
Von
Neumann
once
said:
"with
four
I
fit
elephant,
five
him
wiggle
his
trunk."
challenges
involving
clearly
exacerbated
simplest
would
require
available
always
never
constrain
space
completely.
Given
under-constrained
problem,
exist
infinite
successfully
replicate
underconstrained
proven
challenging.
Moreover,
trained
Western
Chinese
generalize
populations,
limiting
applicability.
Often
employed
population
size.
Some
suffered
absence
lifestyle
information
diet,
socioeconomic
status,
tobacco,
alcoholism,
etc.).
Also,
some
case,
clinical,
metabolomic
profiles,
hampered
garnering
comprehensive
causal
aspects
disease.The
its
function
character
disorders
well
captured
investigations.
We
using
cutting-edge
conjunction
address
issues.
imperative
then
train
models.
By
addressing
limitations
building
new
approaches,
fully
harness
potential
deepen
microbiome's
other
areas.
doing
this,
pinpoint
certain
advancement
development
potent
preventative
therapeutic
approaches.
reach
full
potential,
must
included.