Proceedings of the National Academy of Sciences,
Journal Year:
2024,
Volume and Issue:
121(35)
Published: Aug. 22, 2024
From
microbes
to
humans,
organisms
perform
numerous
tasks
for
their
survival,
including
food
acquisition,
migration,
and
reproduction.
A
complex
biological
task
can
be
performed
by
either
an
autonomous
organism
or
cooperation
among
several
specialized
organisms.
However,
it
remains
unclear
how
autonomy
evolutionarily
switch.
Specifically,
whether
cooperative
specialists
repair
deleted
genes
through
direct
genetic
exchange,
thereby
regaining
metabolic
autonomy.
Here,
we
address
this
question
experimentally
evolving
a
mutualistic
microbial
consortium
composed
of
two
that
cooperatively
degrade
naphthalene.
We
observed
genotypes
capable
performing
the
entire
naphthalene
degradation
pathway
evolved
from
dominated
community.
This
evolutionary
transition
was
driven
horizontal
gene
transfer
(HGT)
between
specialists.
evolution
exclusively
in
fluctuating
environment
alternately
supplied
with
pyruvate,
where
mutualism
competition
alternated.
The
naphthalene-supplied
exerted
selective
pressure
favors
expansion
genotypes.
pyruvate-supplied
promoted
coexistence
cell
density
specialists,
increasing
likelihood
HGT.
Using
mathematical
model,
quantitatively
demonstrate
environmental
fluctuations
facilitate
HGT
when
relative
growth
rate
carrying
capacity
allow
enhanced
higher
competitive
environment.
Together,
our
results
exchange
under
specific
conditions,
The Science of The Total Environment,
Journal Year:
2023,
Volume and Issue:
904, P. 166932 - 166932
Published: Sept. 9, 2023
Shifts
in
rhizosphere
soil
microorganisms
of
dominant
plants'
response
to
climate
change
profoundly
impact
mountain
ecosystem
multifunctionality;
relatively
little
is
known
about
the
relationship
between
them
and
how
they
depend
on
long-term
environmental
drivers.
Here,
we
conducted
analyses
microbial
altitudinal
pattern,
community
assembly,
co-occurrence
network
6
plants
six
typical
vegetation
zones
ranging
from
1350
2900
m
(a.s.l.)
Helan
Mountains
by
absolute
quantitative
sequencing
technology,
finally
related
microbiomes
root
zone
multifunctionality
('soil
multifunctionality'
hereafter),
dependence
was
explored.
It
found
that
pattern
bacterial
fungal
diversities
differed
significantly.
Higher
more
potential
interactions
Stipa
breviflora
Carex
coninux
were
at
lowest
highest
altitudes.
Bacterial
α
diversity,
identity
some
taxa,
had
significant
positive
or
negative
effects
multifunctionality.
The
effect
sizes
diversity
greater
than
those
effects.
These
results
indicated
balance
microbes
determines
As
number
phylum
level
increases,
there
will
be
a
net
gain
Our
study
reveals
geographical
climatic
factors
can
directly
modulate
properties
thereby
affecting
driving
multifunctionality,
points
rather
fungi
being
strongly
associated
with
This
work
has
important
ecological
implications
for
predicting
multiple
environment-plant-soil-microorganisms
ecosystems
respond
future
change.
Nature Microbiology,
Journal Year:
2024,
Volume and Issue:
9(3), P. 848 - 863
Published: Feb. 7, 2024
Engineered
microbial
consortia
often
have
enhanced
system
performance
and
robustness
compared
with
single-strain
biomanufacturing
production
platforms.
However,
few
tools
are
available
for
generating
co-cultures
of
the
model
key
industrial
host
Saccharomyces
cerevisiae.
Here
we
engineer
auxotrophic
overexpression
yeast
strains
that
can
be
used
to
create
through
exchange
essential
metabolites.
Using
these
as
modules,
engineered
two-
three-member
using
different
cross-feeding
architectures.
Through
a
combination
ensemble
modelling
experimentation,
explored
how
cellular
(for
example,
metabolite
strength)
environmental
initial
population
ratio,
density
extracellular
supplementation)
factors
govern
dynamics
in
systems.
We
tested
use
toolkit
division
labour
case
study
show
it
enables
tuneable
antioxidant
resveratrol
production.
expect
this
become
useful
resource
variety
applications
synthetic
ecology
biomanufacturing.
Comprehensive Reviews in Food Science and Food Safety,
Journal Year:
2023,
Volume and Issue:
22(3), P. 1902 - 1932
Published: March 7, 2023
Non-gene-editing
microbiome
engineering
(NgeME)
is
the
rational
design
and
control
of
natural
microbial
consortia
to
perform
desired
functions.
Traditional
NgeME
approaches
use
selected
environmental
variables
force
Spontaneous
food
fermentation,
oldest
kind
traditional
NgeME,
transforms
foods
into
various
fermented
products
using
networks.
In
spontaneous
fermentation
microbiotas
(SFFMs)
are
typically
formed
controlled
manually
by
establishment
limiting
factors
in
small
batches
with
little
mechanization.
However,
limitation
generally
leads
trade-offs
between
efficiency
quality
fermentation.
Modern
based
on
synthetic
ecology
have
been
developed
designed
communities
explore
assembly
mechanisms
target
functional
enhancement
SFFMs.
This
has
greatly
improved
our
understanding
microbiota
control,
but
such
still
shortcomings
compared
NgeME.
Here,
we
comprehensively
describe
research
strategies
for
SFFMs
modern
We
discuss
ecological
principles
two
enhance
how
best
SFFM.
also
review
recent
applied
theoretical
propose
an
integrated
vitro
model
bridge
gaps
Computational and Structural Biotechnology Journal,
Journal Year:
2024,
Volume and Issue:
23, P. 1990 - 2000
Published: April 22, 2024
Microbial
communities
are
shaped
by
the
complex
interactions
among
organisms
and
environment.
Genome-scale
metabolic
models
(GEMs)
can
provide
deeper
insights
into
complexity
ecological
properties
of
various
microbial
communities,
revealing
their
intricate
interactions.
Many
researchers
have
modified
GEMs
for
based
on
specific
needs.
Thus,
need
to
be
comprehensively
summarized
better
understand
trends
in
development.
In
this
review,
we
key
developments
deciphering
designing
using
different
GEMs.
A
timeline
selected
highlights
indicated
that
area
is
evolving
from
single-strain
level
community
level.
Then,
outlined
a
framework
constructing
communities.
We
also
resources
static
dynamic
community-level
focused
role
external
environmental
intracellular
shaping
assembly
Finally,
discussed
challenges
future
directions
GEMs,
focusing
integration
with
quorum
sensing
mechanisms,
ecology
interactions,
machine
learning
algorithms,
automatic
modeling,
all
which
contribute
consortia-based
applications
fields.
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: Sept. 17, 2024
Microbial
communities
exhibit
intricate
interactions
underpinned
by
metabolic
dependencies.
To
elucidate
these
dependencies,
we
present
a
workflow
utilizing
random
matrix
theory
on
metagenome-assembled
genomes
to
construct
co-occurrence
and
complementarity
networks.
We
apply
this
approach
temperature
gradient
hot
spring,
unraveling
the
interplay
between
thermal
stress
cooperation.
Our
analysis
reveals
an
increase
in
frequency
of
with
rising
temperatures.
Amino
acids,
coenzyme
A
derivatives,
carbohydrates
emerge
as
key
exchange
metabolites,
forming
foundation
for
syntrophic
which
commensalistic
take
greater
proportion
than
mutualistic
ones.
These
exchanges
are
most
prevalent
phylogenetically
distant
species,
especially
archaea-bacteria
collaborations,
crucial
adaptation
harsh
environments.
Furthermore,
identify
significant
positive
correlation
basal
metabolite
genome
size
disparity,
potentially
signifying
means
streamlined
leverage
cooperation
metabolically
richer
partners.
This
phenomenon
is
also
confirmed
another
composting
system
has
similar
wide
range
fluctuations.
provides
feasible
way
decipher
mechanisms
underlying
microbial
interactions,
our
findings
suggested
environmental
regulates
cooperative
strategies
thermophiles,
while
dependencies
have
been
hardwired
into
their
during
co-evolutions.
mLife,
Journal Year:
2022,
Volume and Issue:
1(4), P. 382 - 398
Published: Nov. 3, 2022
Although
the
accomplishments
of
microbiome
engineering
highlight
its
significance
for
targeted
manipulation
microbial
communities,
knowledge
and
technical
gaps
still
limit
applications
in
biotechnology,
especially
environmental
use.
Addressing
challenges
refractory
pollutants
fluctuating
conditions
requires
an
adequate
understanding
theoretical
achievements
practical
engineering.
Here,
we
review
recent
cutting-edge
studies
on
strategies
their
classical
bioremediation.
Moreover,
a
framework
is
summarized
combining
both
top-down
bottom-up
approaches
toward
improved
applications.
A
strategy
to
engineer
microbiomes
use,
which
avoids
build-up
toxic
intermediates
that
pose
risk
human
health,
suggested.
We
anticipate
highlighted
will
be
beneficial
address
difficult
such
as
degrading
multiple
sustain
performance
engineered
situ
with
indigenous
microorganisms
under
conditions.
