Trends in Microbiology,
Journal Year:
2024,
Volume and Issue:
32(12), P. 1229 - 1240
Published: June 5, 2024
Recent
studies
of
dynamic
interactions
between
epigenetic
modifications
a
host
organism
and
the
composition
or
activity
its
associated
gut
microbiota
suggest
an
opportunity
for
to
shape
microbiome
through
alterations
that
lead
changes
in
gene
expression
noncoding
RNA
activity.
We
use
insights
from
microbiota-induced
review
potential
epigenetically
regulate
microbiome,
which
bidirectional
'epigenome–microbiome
axis'
emerges.
This
axis
embeds
environmentally
induced
variation,
may
influence
adaptive
evolution
host–microbe
interactions.
furthermore
present
our
perspective
on
how
epigenome–microbiome
can
be
understood
investigated
within
holo-omic
framework
with
applications
applied
health
food
sciences.
Abstract
DNA
methylation
serves
as
the
primary
mode
of
epigenetic
regulation
in
prokaryotes,
particularly
through
transcriptional
regulation.
With
rapid
implementation
third‐generation
sequencing
technology,
we
are
currently
experiencing
a
golden
age
bacterial
epigenomics.
However,
there
has
been
lack
comprehensive
research
exploring
versatility
and
consequential
impact
methylome
on
cellular
physiological
functions.
There
is
critical
need
for
user‐friendly
bioinformatics
tool
that
can
effectively
characterize
modification
features
predict
patterns.
To
address
this
gap,
current
study
introduces
Bacmethy,
an
innovative
utilizes
SMRT‐seq
data
offers
range
analytical
modules.
First,
classifies
sites
genome,
highlighting
distinct
regulations
present
under
varying
fractions
location
enrichment.
Furthermore,
enables
us
to
identify
regulatory
region
potential
cis
trans
interactions
between
effectors.
Using
benchmark
sets
our
data,
show
facilitates
understanding
distinctive
traits
modifications
predicts
effects
important
pathological
Bacmethy
code
freely
available,
Docker
image
downloadable.
made
available
web
server
interface
at
https://bacmethy.med.sustech.edu.cn
.
Ecology and Evolution,
Journal Year:
2025,
Volume and Issue:
15(3)
Published: March 1, 2025
ABSTRACT
The
study
of
the
rules
that
govern
relationship
between
phenotypic
plasticity,
genetic
structure,
and
ecological
success
has
traditionally
focused
on
animals,
plants,
a
few
model
microbial
species,
whereas
non‐model
microorganisms
have
received
much
less
attention
in
this
regard.
floral
nectar
angiosperms
is
an
ephemeral,
island‐like
habitat
for
different
highly
adapted
yeasts
bacteria.
growth
depends
their
ability
to
efficiently
use
available
nutrients
tolerate
challenging
physicochemical
conditions,
including
high
osmotic
pressures,
unbalanced
carbon‐to‐nitrogen
ratios,
presence
diverse
defensive
compounds
plant
origin.
production
alternative
states
response
environmental
cues
(i.e.,
plasticity)
or
independently
from
these
(within‐environment
trait
variability)
might
be
particularly
relevant
nectar,
which
rapid
needed
population
persistence
improve
chance
animal‐mediated
dispersal.
In
article,
we
microbiome
as
example
encourage
further
research
causes
consequences
plasticity
within‐environment
variability
microbes.
We
review
previous
work
mechanisms
potential
significance
displayed
by
Additionally,
provide
overview
some
topics
require
attention,
trade‐offs
traits
are
adaptation
dynamic
environments
direct
indirect
effects
fitness
flower‐visiting
other
conclude
microbes
essential
get
better
understanding
community
assembly
establishment
interactions
similar
strongly
selective
habitats.
Frontiers in Veterinary Science,
Journal Year:
2025,
Volume and Issue:
12
Published: March 19, 2025
Avian
pathogenic
Escherichia
coli
(APEC)
causes
colibacillosis
in
poultry,
which
is
a
very
important
disease
worldwide.
Despite
well-documented
genomic
traits
and
diversity
of
APEC,
its
epigenomic
characteristics
are
less
understood.
This
study
utilized
the
high
throughput
long-read
capabilities
Oxford
Nanopore
Technology
(ONT)
to
elucidate
genome
structures
methylation
modifications
three
E.
isolates
avian
origin:
one
intestinal
isolate
from
healthy
wild
bird
two
systemic
clinically
affected
chickens.
Three
complete
genomes,
each
comprising
single
chromosome
multiple
plasmids
were
assembled.
Diverse
virulence-associated
genes,
antimicrobial
resistance
mobile
genetic
elements
integrons
characterized
genomes.
limited
sample
size,
our
whole
sequencing
(WGS)
data
highlighted
significant
among
strains
enriched
repertoire
gene
clusters
related
APEC
pathogenicity.
From
epigenetic
analysis,
modifications,
including
N5-methylcytosine
(5mC),
eight
N6-methyladenine
(6mA)
N4-methylcytosine
(4mC)
modification
motifs
identified
within
all
isolates.
Furthermore,
common
GATC
CCWGG
predominantly
distributed
regulatory
regions,
suggesting
role
transcription
regulation.
opens
avenue
for
future
research
into
pathogenesis,
diagnostic
therapeutic
strategies
considering
analysis.
PLoS Biology,
Journal Year:
2024,
Volume and Issue:
22(9), P. e3002792 - e3002792
Published: Sept. 20, 2024
Adaptation
is
usually
explained
by
beneficial
genetic
mutations
that
are
transmitted
from
parents
to
offspring
and
become
fixed
in
the
adapted
population.
However,
mutation
analysis
alone
not
sufficient
fully
explain
adaptive
processes,
several
studies
report
existence
of
nongenetic
(or
epigenetic)
inheritance
can
enable
adaptation
new
environments.
In
present
work,
we
tested
hypothesis
role
DNA
methylation,
a
form
epigenetic
modification,
plant
pathogen
Ralstonia
pseudosolanacearum
host
during
experimental
evolution.
Using
SMRT-seq
technology,
analyzed
methylomes
31
experimentally
evolved
clones
obtained
after
serial
passages
on
5
different
species
300
generations.
Comparison
with
methylome
ancestral
clone
revealed
list
50
differential
methylated
sites
(DMSs)
at
GTWWAC
motif.
Gene
expression
39
genes
targeted
these
DMSs
limited
correlation
between
methylation
corresponding
genes.
Only
1
gene
showed
correlation,
RSp0338
encoding
EpsR
regulator
protein.
The
MSRE-qPCR
used
as
an
alternative
approach
for
analysis,
also
found
2
upstream
RSp0338.
site-directed
mutagenesis,
demonstrated
contribution
adaptation.
As
appeared
very
early
evolution,
hypothesize
such
fast
changes
allow
rapid
stem
environment.
addition,
change
remains
stable
least
100
generations
outside
thus
contribute
long-term
plant.
To
our
knowledge,
this
first
study
showing
direct
link
bacterial
variation
Genes,
Journal Year:
2024,
Volume and Issue:
15(12), P. 1599 - 1599
Published: Dec. 14, 2024
Background/Objectives:
Aging
is
a
natural
physiological
process
involving
biological
and
genetic
pathways.
Growing
evidence
suggests
that
alterations
in
the
epigenome
during
aging
result
transcriptional
changes,
which
play
significant
role
onset
of
age-related
diseases,
including
cancer,
cardiovascular
disease,
diabetes,
neurodegenerative
disorders.
For
this
reason,
epigenetic
diseases
have
been
reviewed,
major
extrinsic
factors
influencing
these
identified.
In
addition,
gut
microbiome
its
metabolites
as
modifiers
has
addressed.
Results:
Long-term
exposure
to
such
air
pollution,
diet,
drug
use,
environmental
chemicals,
microbial
infections,
physical
activity,
radiation,
stress
provoke
changes
host
through
several
endocrine
immune
pathways,
potentially
accelerating
process.
Diverse
studies
reported
plays
critical
regulating
brain
cell
functions
DNA
methylation
histone
modifications.
The
interaction
between
genes
serves
source
adaptive
variation,
contributing
phenotypic
plasticity.
However,
molecular
mechanisms
signaling
pathways
driving
are
still
not
fully
understood.
Conclusions:
Extrinsic
potential
inducers
alterations,
may
important
implications
for
longevity.
an
effector
gene
expression
modifications,
while
bidirectional
interactions
with
underexplored
roles
non-bacterial
microorganisms
fungi
viruses
highlight
need
further
research.
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: June 3, 2024
Abstract
Non-genetic
sources
of
phenotypic
variation,
such
as
the
epigenome
and
microbiome,
could
be
important
contributors
to
adaptive
variation
for
species
with
low
genetic
diversity.
However,
little
is
known
about
complex
interaction
between
these
factors
diversity
host,
particularly
in
wild
populations.
Here,
we
examine
skin
microbiome
composition
two
closely-related
mangrove
killifish
different
mating
systems
(self-fertilising
outcrossing)
under
sympatric
allopatric
conditions.
This
allows
us
partition
influence
genotype
environment
on
their
(previously
described)
epigenetic
profiles.
We
find
community
are
strongly
shaped
by
and,
a
lesser
extent,
species-specific
influences.
Heterozygosity
alpha
diversity,
but
not
associated
fluctuating
asymmetry
traits
related
performance
(vision)
behaviour
(aggression).
Our
study
identifies
that
proportion
differentiation
unrelated
evidence
an
associative
relationship
suggests
both
mechanisms
potentially
contribute
Fish
performance
is
influenced
by
their
genotype
and
environment.
For
populations
with
low
genetic
diversity,
adaptation
to
environmental
change
can
be
compromised,
but
it
has
been
suggested
that
the
microbiome
act
as
an
additional
source
of
variability.
Early
rearing
conditions
particularly
important
for
fish
development
behaviour,
due
dependence
on
conditions.
This
thesis
explored
interactions
between
environment
(diet
enrichment)
metabolic
rate
(gut,
skin)
using
captive
wild
naturally
inbred
mangrove
killifishes
(Kryptolebias
sp.),
where
exploratory
behaviour
closed
respirometry
were
used
test
killifish
diversity
analyses
performed
in
both
killifishes.
Behavioural
trials
self-fertilizing
marmoratus)
indicated
a
significant
effect
strain
(environmental
enrichment
diet)
activity
measurements.
Incubation
time
also
had
substantial
role
diversity.
Gut-microbiome
alpha
was
shaped
strain,
diet,
hatching
K.
marmoratus
diet
physical
enrichment.
An
intergenerational
influence
detected
K.armoratus,
parental
found
offspring
activity.
Gut-microbial
comparisons
parents
identified
Vibrionaceae
dominant
colonizers
laboratory
reared
marmoratus.
A
over
composition
distribution
observed.
The
interaction
own
environments
suggests
long-term
effects
(gut)
microbiome.
In
wild,
results
from
outcrossing
ocelatus
self-fertilising
hermaphroditus
community
skin
strongly
species
host
at
different
levels.
study
first-time
evidence
relationship
epigenetic
these
populations,
suggesting
mechanisms
could
potential
sources
variability
global
findings
this
origins
(laboratory
natural
conditions)
highlighted
importance
shaping
