Soil
microorganisms
play
a
key
role
in
nutrient
cycling,
carbon
sequestration,
and
other
important
ecosystem
processes,
yet
their
response
to
seasonal
dry-wet
alternation
remains
poorly
understood.
Here,
we
collected
120
soil
samples
from
dry-hot
valleys
(DHVs,
~
1100
m
a.s.l.),
transition
(~
2000
a.s.l.)
alpine
zones
3000
along
the
Jinsha
River
southwest
China
during
both
wet
dry
seasons.
Our
aims
were
investigate
bacterial
microbiome
across
these
zones,
with
specific
focus
on
difference
between
ISME Communications,
Год журнала:
2024,
Номер
4(1)
Опубликована: Янв. 1, 2024
Abstract
Perturbations
and
modulations
during
early
life
are
vital
to
affect
gut
microbiome
assembly
establishment.
In
this
study,
we
assessed
how
microbial
communities
shifted
calf
diarrhea
with
probiotic
yeast
supplementation
(Saccharomyces
cerevisiae
var.
boulardii,
SCB)
determined
the
key
bacterial
taxa
contributing
shifts
using
a
total
of
393
fecal
samples
collected
from
84
preweaned
calves
an
8-week
trial.
Our
results
revealed
that
patterns
differed
between
healthy
diarrheic
at
6-
trial,
being
stochastic-driven
deterministic-driven.
The
two-state
Markov
model
SCB
had
higher
possibility
shift
deterministic-
in
calves.
Furthermore,
23
21
genera
were
specific
ecotypes
SCB-responsive
(SCB-fed
did
not
exhibit
diarrhea)
nonresponsive
occurred
calves,
respectively.
Among
these
ecotypes,
area
under
receiver
operating
characteristic
curve
Blautia
Ruminococcaceae
UCG
014,
two
unidentified
family,
highest
predictiveness
for
while
Prevotellaceae,
Blautia,
Escherichia-Shigella
most
predictive
SCB-nonresponsive
study
suggests
perturbations
serving
as
deterministic
factors
influenced
critical
patterns,
which
sheds
light
on
mechanisms
community
establishment
neonatal
life.
Abstract
Background
Functional
redundancy
(FR)
is
widely
present,
but
there
no
consensus
on
its
formation
process
and
influencing
factors.
Taxonomically
distinct
microorganisms
possessing
genes
for
the
same
function
in
a
community
lead
to
within-community
FR,
assemblies
of
different
communities
playing
functional
roles
are
termed
between-community
FR.
We
proposed
two
formulas
respectively
quantify
degree
within
between
analyzed
FR
degrees
carbohydrate
degradation
functions
global
environment
samples
using
genetic
information
glycoside
hydrolases
(GHs)
encoded
by
prokaryotes.
Results
Our
results
revealed
that
GHs
each
multiple
taxonomically
prokaryotes
community,
enzyme-encoding
further
almost
any
pairs.
The
within-
between-FR
primarily
affected
alpha
beta
diversities,
respectively,
also
environmental
factors
(e.g.,
pH,
temperature,
salinity).
prokaryotic
determined
deterministic
Conclusions
conclude
stabilized
characteristic.
This
study
helps
determine
provides
new
insights
into
relationships
biodiversity
ecosystem
functions.
Frontiers in Industrial Microbiology,
Год журнала:
2024,
Номер
2
Опубликована: Апрель 25, 2024
Climate
change
and
pollution
drive
the
need
for
fossil
fuel
alternatives.
Dark
fermentation
offers
promise
through
use
of
microbial
consortia
to
convert
organic
matter
into
hydrogen
gas.
Persisting
challenges
like
instability
low
yields
may
stem
from
reduced
diversity
anaerobic
digestion
communities
that
serve
as
inoculum
undergo
aggressive
pretreatments
culturing
conditions.
This
study
explores
impact
loss
on
function,
focusing
biogas
production
stability.
Two
treatments,
with
without
pretreatment,
were
tested
12
replicate
bioreactors
each,
resulting
in
differing
levels.
Microbial
assessed
via
16S
amplicon
sequencing,
monitoring
production,
volatile
fatty
acids,
testing
invasion
susceptibility.
The
two
treatments
exhibited
divergent
assembly
functional
trajectories,
although
replicates
within
each
treatment
ultimately
converged
similar
compositions
stable
levels
production.
Heat-treated
showed
a
91.5%
increase
but
higher
susceptibility
compared
non-treated.
Non-treated
unique
species
associations
(e.g.
Ethanoligenens
harbinense
Enterococcus
olivae
),
distinct
commonly
studied
Clostridium
group.
These
findings
provide
insights
effects
stability,
elucidating
differences
across
taxonomic
stability
well
Moreover,
identification
novel
bacterial
groups
associated
suggests
promising
directions
future
research
enhance
control
design
dark
fermentation.
Frontiers in Microbiology,
Год журнала:
2024,
Номер
15
Опубликована: Июль 8, 2024
Growing
evidence
has
suggested
a
strong
link
between
gut
microbiota
and
host
fitness,
yet
our
understanding
of
the
assembly
mechanisms
governing
remains
limited.
Here,
we
collected
invasive
native
freshwater
snails
coexisting
at
four
independent
sites
in
Guangdong,
China.
We
used
high-throughput
sequencing
to
study
processes
their
microbiota.
Our
results
revealed
significant
differences
diversity
composition
snails.
Specifically,
exhibited
lower
alpha
fewer
enriched
bacteria,
with
phylogenetic
signal
identified
microbes
that
were
or
depleted.
Both
normalized
stochasticity
ratio
(pNST)
phylogenetic-bin-based
null
model
analysis
(iCAMP)
showed
process
was
more
deterministic
compared
snails,
primarily
driven
by
homogeneous
selection.
The
linear
mixed-effects
negative
correlation
(homogeneous
selection)
snail
microbiota,
especially
where
explained
most
variance.
This
indicates
selection
acts
as
filter
for
specific
microbial
lineages,
constraining
Overall,
suggests
assembly-mediated
lineage
filtering
is
potential
mechanism
maintaining
Comprehensive Reviews in Food Science and Food Safety,
Год журнала:
2025,
Номер
24(1)
Опубликована: Янв. 1, 2025
Abstract
The
global
food
system
faces
numerous
challenges,
creating
an
urgent
need
for
sustainable
reform.
Functional
microbiome
assemblies
offer
transformative
potential
by
endowing
microbial
foods
with
diverse,
beneficial
characteristics.
These
can
dynamically
influence
specific
systems,
positioning
them
as
a
promising
approach
reshaping
production.
However,
the
current
applications
and
types
of
in
remain
limited,
lack
effective
screening
regulatory
methods.
This
review
introduces
functions
practical
approaches
implementing
systems
alongside
future
directions
enhancing
their
applications.
Several
ecological
studies
evaluated
how
to
regulate
functional
output
revealed
that
environmental
conditions,
which
shape
niche
species
survival,
significantly
influenced
microbiomes.
Building
on
this
theoretical
foundation,
presents
model
comprising
gene
codes,
corresponding
outputs.
is
illustrated
examples
explore
mechanisms
assemblies.
By
highlighting
roles
outputs
examining
environments
induce
modulate
functions,
provides
roadmap
address
emerging
challenges
sustainability.
ISME Communications,
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 17, 2025
Resolving
the
ecological
drivers
mediating
diversity
patterns
of
microbial
communities
across
space
and
through
time
is
a
central
issue
in
ecology.
Both
regional
species
pools
local
community
assembly
contribute
to
spatial
turnover
biodiversity.
In
this
study,
we
extended
concept
pool
temporal,
investigated
seasonal
dynamics
intertidal
microbiomes
four
domains/kingdoms
(bacteria,
archaea,
fungi,
protists).
The
results
showed
that
variations
β-diversity
were
primarily
governed
by
processes
rather
than
temporal
pools.
Different
structured
different
processes,
with
homogeneous
selection
as
major
process
for
all
them.
Additionally,
bacteria
fungi
critically
shaped
drift,
protists
drift
dispersal.
Among
various
factors,
temperature
was
important
shaping
β-diversity.
fluctuation
strongly
associated
protists,
resulting
high
composition.
This
study
demonstrated
dynamic
β-variations
microbiomes,
expanding
our
understanding
from
Microbiology Spectrum,
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 24, 2025
ABSTRACT
Growing
interest
in
the
impact
of
microbial
balance
on
health
has
driven
studies
ecological
processes
shaping
skin
microbiota.
Skin
diseases,
which
alter
skin’s
local
environment,
can
disrupt
structure
and
interact
with
disease
itself.
However,
research
assembly
diseased
remains
limited.
In
this
study,
we
applied
models
to
characterize
microbiota
acne
patients,
considering
duration
both
pores
surfaces
using
bacterial
amplicon
sequencing.
Our
results
revealed
a
significant
shift
diversity
surface
patients
long-term
acne.
Further
community
analyses
showed
transition
from
healthy
skin.
Microbial
communities
controls
individuals
short-duration
were
primarily
by
heterogeneous
selection,
whereas
drift
dominated
process
long-duration
groups.
Using
Sloan
neutral
model,
classified
sequence
variants
(ASVs)
into
high-effect
low-effect
groups
based
relative
abundance
sample
occurrence.
High-effect
ASVs,
likely
exerting
greater
influence,
predominantly
represented
Cutibacterium
across
all
acne-affected
groups,
while
Staphylococcus
became
enriched
among
ASVs
Functional
profiling
further
demonstrated
that
significantly
motility-related
pathways.
Additionally,
observed
reduction
network
complexity
as
increased.
Overall,
dynamics
may
offer
valuable
insights
mechanisms
underlying
onset
persistence.
IMPORTANCE
The
plays
critical
role
development,
yet
governing
during
progression
remain
poorly
understood.
Previous
focused
factors
such
severity,
location,
relation
structure,
little
attention
given
communities.
investigate
influencing
varying
durations
examined
functions
ecologically
important
non-neutral
(ASVs).
findings
reveal
deterministic
increased,
potentially
contributing
pathogenicity
These
contribute
deeper
understanding
indicate
targeting
these
or
their
associated
serve
basis
for
future
therapeutic
strategies.
