Critical Reviews in Microbiology,
Journal Year:
2024,
Volume and Issue:
unknown, P. 1 - 40
Published: Jan. 25, 2024
Microbial
communities
thrive
through
interactions
and
communication,
which
are
challenging
to
study
as
most
microorganisms
not
cultivable.
To
address
this
challenge,
researchers
focus
on
the
extracellular
space
where
communication
events
occur.
Exometabolomics
interactome
analysis
provide
insights
into
molecules
involved
in
dynamics
of
their
interactions.
Advances
sequencing
technologies
computational
methods
enable
reconstruction
taxonomic
functional
profiles
microbial
using
high-throughput
multi-omics
data.
Network-based
approaches,
including
community
flux
balance
analysis,
aim
model
molecular
within
between
communities.
Despite
these
advances,
challenges
remain
computer-assisted
biosynthetic
capacities
elucidation,
requiring
continued
innovation
collaboration
among
diverse
scientists.
This
review
provides
current
state
future
directions
elucidation
studying
mSystems,
Journal Year:
2023,
Volume and Issue:
8(2)
Published: March 21, 2023
Microbial
consortia
drive
essential
processes,
ranging
from
nitrogen
fixation
in
soils
to
providing
metabolic
breakdown
products
animal
hosts.
However,
it
is
challenging
translate
the
composition
of
microbial
into
their
emergent
functional
capacities.
Metabolic Engineering,
Journal Year:
2023,
Volume and Issue:
79, P. 1 - 13
Published: June 25, 2023
Many
studies
have
demonstrated
that
the
gut
microbiota
is
associated
with
human
health
and
disease.
Manipulation
of
microbiota,
e.g.
supplementation
probiotics,
has
been
suggested
to
be
feasible,
but
subject
limited
therapeutic
efficacy.
To
develop
efficient
microbiota-targeted
diagnostic
strategies,
metabolic
engineering
applied
construct
genetically
modified
probiotics
synthetic
microbial
consortia.
This
review
mainly
discusses
commonly
adopted
strategies
for
in
microbiome,
including
use
silico,
vitro,
or
vivo
approaches
iterative
design
construction
engineered
Especially,
we
highlight
how
genome-scale
models
can
advance
our
understanding
microbiota.
Also,
recent
applications
microbiome
as
well
discuss
important
challenges
opportunities.
BioEssays,
Journal Year:
2023,
Volume and Issue:
45(10)
Published: Aug. 9, 2023
Abstract
Microbial
systems
biology
has
made
enormous
advances
in
relating
microbial
physiology
to
the
underlying
biochemistry
and
molecular
biology.
By
meticulously
studying
model
microorganisms,
particular
Escherichia
coli
Saccharomyces
cerevisiae
,
increasingly
comprehensive
computational
models
predict
metabolic
fluxes,
protein
expression,
growth.
The
modeling
rationale
is
that
cells
are
constrained
by
a
limited
pool
of
resources
they
allocate
optimally
maximize
fitness.
As
consequence,
expression
proteins
at
expense
others,
causing
trade‐offs
between
cellular
objectives
such
as
instantaneous
growth,
stress
tolerance,
capacity
adapt
new
environments.
While
current
remarkably
predictive
for
E.
S.
when
grown
laboratory
environments,
this
may
not
hold
other
growth
conditions
microorganisms.
In
contribution,
we
therefore
discuss
relationship
rate,
resources,
long‐term
We
uses
limitations
models,
rapidly
changing
adverse
propose
classify
strategies
based
on
Grimes's
CSR
framework.
Microbial Biotechnology,
Journal Year:
2024,
Volume and Issue:
17(1)
Published: Jan. 1, 2024
Abstract
Building
models
is
essential
for
understanding
the
functions
and
dynamics
of
microbial
communities.
Metabolic
built
on
genome‐scale
metabolic
network
reconstructions
(GENREs)
are
especially
relevant
as
a
means
to
decipher
complex
interactions
occurring
among
species.
Model
reconstruction
increasingly
relies
metagenomics,
which
permits
direct
characterisation
naturally
communities
that
may
contain
organisms
cannot
be
isolated
or
cultured.
In
this
review,
we
provide
an
overview
field
modelling
its
increasing
reliance
synergy
with
metagenomics
bioinformatics.
We
survey
assigning
reconstructing
networks
from
(meta‐)genomes,
present
variety
mathematical
fundamentals
foster
dynamics.
emphasise
scaling
model
construction
large
communities,
two
important
bottlenecks
in
applicability
these
models.
give
current
state
art
metagenome
sequencing
bioinformatics
analysis,
focusing
genomes
Metagenomics
benefits
tremendously
third‐generation
sequencing,
discuss
opportunities
long‐read
strain‐level
eukaryotic
metagenomics.
aim
at
providing
algorithmic
support,
together
tool
application
resources,
permit
bridging
gap
between
modelling.
Critical Reviews in Microbiology,
Journal Year:
2024,
Volume and Issue:
unknown, P. 1 - 40
Published: Jan. 25, 2024
Microbial
communities
thrive
through
interactions
and
communication,
which
are
challenging
to
study
as
most
microorganisms
not
cultivable.
To
address
this
challenge,
researchers
focus
on
the
extracellular
space
where
communication
events
occur.
Exometabolomics
interactome
analysis
provide
insights
into
molecules
involved
in
dynamics
of
their
interactions.
Advances
sequencing
technologies
computational
methods
enable
reconstruction
taxonomic
functional
profiles
microbial
using
high-throughput
multi-omics
data.
Network-based
approaches,
including
community
flux
balance
analysis,
aim
model
molecular
within
between
communities.
Despite
these
advances,
challenges
remain
computer-assisted
biosynthetic
capacities
elucidation,
requiring
continued
innovation
collaboration
among
diverse
scientists.
This
review
provides
current
state
future
directions
elucidation
studying
