The dawn of the revolution that will allow us to precisely describe how microbiomes function
Journal of Proteomics,
Год журнала:
2025,
Номер
316, С. 105430 - 105430
Опубликована: Март 11, 2025
The
community
of
microorganisms
inhabiting
a
specific
environment,
such
as
the
human
gut
-
including
bacteria,
fungi,
archaea,
viruses,
protozoa,
and
others
is
known
microbiota.
A
holobiont,
in
turn,
refers
to
an
integrated
ecological
unit
where
microbial
communities
function
interact
with
their
host,
thus
more
integrative
concept.
To
understand
processes
involved,
diversity
present
must
be
identified
molecular
components
quantified,
especially
proteins.
Indeed,
proteins
through
roles
catalytic
units,
structural
components,
signaling
molecules
are
main
drivers
biological
processes.
Metagenomics
has
significantly
expanded
what
we
know
about
genetic
material
microbiota,
revealing
functional
potential;
metabolomics
delivers
overall
snapshot
metabolites
produced
by
community.
But
metaproteomics
offers
complementary
approach
explore
microbiome
holobiont
functionality
focusing
on
active
pathways
from
each
taxon.
Significant
recent
advances
high-resolution
tandem
mass
spectrometry
have
greatly
catalog
peptide
sequences
accessible
sample,
creating
conditions
for
unprecedented
taxonomical
profiling,
while
also
providing
accurate
biomass
quantification,
detailed
protein
characterization,
greater
capacity
monitor
abundance
distinguish
host
biomarkers.
By
integrating
artificial
intelligence
into
pipeline,
extended
datasets
can
now
efficiently
mined
gain
comprehensive
view
complex
systems,
paving
way
next-generation
metaproteomics.
In
this
perspective,
I
discuss
transformative
potential
methodology.
We
cusp
remarkable
omic
revolution
that
promises
uncover
intricate
workings
microbiomes
producing
vast
array
new
knowledge
multiple
applications.
SIGNIFICANCE:
Metaproteomics
provides
powerful
lens
investigate
identifying
quantifying
within
Recent
breakthroughs
dramatically
repertoire
detectable
per
sample.
This
progress
enables
taxonomic
resolution
identification,
precise
monitoring,
unique
identification
commentary,
delve
distinctive
features
make
tool.
advancements
argue
primary
challenge
analyzing
samples
shifting
data
acquisition
interpretation.
With
integration
intelligence,
believe
poised
become
next
Big
Thing
research,
unlocking
profound
insights
ecosystem
dynamics.
Язык: Английский
Evaluation of imputation and imputation-free strategies for differential abundance analysis in metaproteomics data
Briefings in Bioinformatics,
Год журнала:
2025,
Номер
26(2)
Опубликована: Март 1, 2025
Abstract
For
metaproteomics
data
derived
from
the
collective
protein
composition
of
dynamic
multi-organism
systems,
proportion
missing
values
and
dimensions
exceeds
that
observed
in
single-organism
experiments.
Consequently,
evaluations
differential
analysis
strategies
other
mass
spectrometry
(MS)
(such
as
proteomics
metabolomics)
may
not
be
directly
applicable
to
data.
In
this
study,
we
systematically
evaluated
five
imputation
methods
[sample
minimum,
quantile
regression,
k-nearest
neighbors
(KNN),
Bayesian
principal
component
(bPCA),
random
forest
(RF)]
six
imputation-free
(moderated
t-test,
two-part
Wilcoxon
test,
semiparametric
abundance
analysis,
with
Bayes
shrinkage
estimation
variance
method,
Mixture)
for
simulated
metaproteomic
datasets
based
on
both
data-dependent
acquisition
MS
experiments
emerging
data-independent
The
simulation
comprised
588
scenarios
by
considering
impacts
sample
size,
fold
change
between
case
control,
value
ratio
at
nonrandom.
Compared
methods,
KNN,
bPCA,
RF
performed
poorly
a
high
missingness
large
size
resulted
false-positive
risk.
We
made
empirical
recommendations
balance
sensitivity
control
false
positives.
moderated
t-test
was
optimal
low
ratio.
test
recommended
small
or
comprehensive
our
study
can
provide
guidance
metaproteomics.
Язык: Английский
A Non‐Metaproteomics Researchers’ View on Metaproteomics in Microbiome Research
PROTEOMICS,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 27, 2025
ABSTRACT
Metaproteomics,
an
emerging
field
among
the
omic
techniques,
holds
great
promise
for
unraveling
function
of
microbiomes
in
host
health
and
our
environment.
Metaproteomics
can
also
be
a
valuable
addition
to
multiomics
studies
microbiome,
complementing
genome‐resolved
metagenomics,
metatranscriptomics,
metabolomics.
The
potential
advancements
from
metaproteomics
research
touch
breadth
disciplines,
including
ecology,
biochemistry,
immunology,
medical
microbiology,
cell
physiology,
medicine,
could
lead
both
fundamental
applied
discoveries.
However,
there
are
significant
roadblocks
widespread
adoption
microbiome
researchers.
In
this
Viewpoint
article,
we
highlight
pivotal
role
by
showcasing
its
advantages,
exploring
opportunities
overcome
challenges,
paving
way
broader
as
mainstream
technique.
We
hope
that
recommendations
provided
article
will
inspire
new,
beneficial
collaborations
between
proteomics
experts,
algorithm
infrastructure
developers,
biochemists,
biologists,
microbiologists,
enabling
construction
knowledge
base
have
immediate
direct
impact
on
Язык: Английский