Scientia Agricola,
Год журнала:
2014,
Номер
71(6), С. 528 - 539
Опубликована: Дек. 1, 2014
A
plethora
of
microbial
cells
is
present
in
every
gram
soil,
and
microbes
are
found
extensively
plant
animal
tissues.
The
mechanisms
governed
by
microorganisms
the
regulation
physiological
processes
their
hosts
have
been
studied
light
recent
findings
on
microbiomes.
In
plants,
components
these
microbiomes
may
form
distinct
communities,
such
as
those
inhabiting
rhizosphere,
endosphere
phyllosphere.
each
niches,
"microbial
tissue"
established
by,
responds
to,
specific
selective
pressures.
Although
there
no
clear
picture
overall
role
microbiome,
substantial
evidence
that
communities
involved
disease
control,
enhance
nutrient
acquisition,
affect
stress
tolerance.
this
review,
we
first
summarize
features
compose
microbiome
further
a
series
studies
describing
underpinning
factors
shape
phylogenetic
functional
plant-associated
communities.
We
advocate
idea
understanding
which
plants
select
interact
with
direct
effect
development
health,
lead
to
establishment
novel
microbiome-driven
strategies,
can
cope
more
sustainable
agriculture.
ABSTRACT
Grapevine
is
a
well-studied,
economically
relevant
crop,
whose
associated
bacteria
could
influence
its
organoleptic
properties.
In
this
study,
the
spatial
and
temporal
dynamics
of
bacterial
communities
with
grapevine
organs
(leaves,
flowers,
grapes,
roots)
soils
were
characterized
over
two
growing
seasons
to
determine
vine
cultivar,
edaphic
parameters,
developmental
stage
(dormancy,
flowering,
preharvest),
vineyard.
Belowground
differed
significantly
from
those
aboveground,
yet
leaves,
grapes
shared
greater
proportion
taxa
soil
than
each
other,
suggesting
that
may
serve
as
reservoir.
A
subset
microorganisms,
including
root
colonizers
enriched
in
plant
growth-promoting
related
functional
genes,
selected
by
grapevine.
addition
selective
pressure,
structure
microbiota
was
influenced
pH
C:N
ratio,
changes
leaf-
grape-associated
correlated
carbon
showed
interannual
variation
even
at
small
scales.
Diazotrophic
bacteria,
e.g.,
Rhizobiaceae
Bradyrhizobium
spp.,
more
abundant
samples
specific
vineyards.
Vine-associated
microbial
assemblages
myriad
factors
shape
their
composition
structure,
but
majority
organ-associated
originated
soil,
distribution
reflected
highly
localized
biogeographic
vineyard
management.
IMPORTANCE
play
roles
productivity
disease
resistance
host
plant.
Also,
on
have
potential
properties
wine,
contributing
regional
terroir.
Understanding
these
provide
insights
into
management
practices
craft
individual
wine
We
show
serves
key
source
vine-associated
vineyard-specific
can
native
microbiome
preharvest.
PLoS Computational Biology,
Год журнала:
2021,
Номер
17(11), С. e1009581 - e1009581
Опубликована: Ноя. 8, 2021
Nucleotide
sequence
and
taxonomy
reference
databases
are
critical
resources
for
widespread
applications
including
marker-gene
metagenome
sequencing
microbiome
analysis,
diet
metabarcoding,
environmental
DNA
(eDNA)
surveys.
Reproducibly
generating,
managing,
using,
evaluating
nucleotide
creates
a
significant
bottleneck
researchers
aiming
to
generate
custom
databases.
Furthermore,
database
composition
drastically
influences
results,
lack
of
standardization
limits
cross-study
comparisons.
To
address
these
challenges,
we
developed
RESCRIPt,
Python
3
software
package
QIIME
2
plugin
reproducible
generation
management
databases,
dedicated
functions
that
streamline
creating
from
popular
sources,
evaluating,
comparing,
interactively
exploring
qualitative
quantitative
characteristics
across
highlight
the
breadth
capabilities
provide
several
examples
working
with
profiling
(SILVA,
Greengenes,
NCBI-RefSeq,
GTDB),
eDNA
metabarcoding
surveys
(BOLD,
GenBank),
as
well
genome
comparison.
We
show
bigger
is
not
always
better,
standardized
taxonomies
those
focus
on
type
strains
have
advantages,
though
may
be
appropriate
all
use
cases.
Most
appear
benefit
some
curation
(quality
filtering),
clustering
appears
detrimental
quality.
Finally,
demonstrate
extensibility
RESCRIPt
workflows
comparison
global
hepatitis
genomes.
provides
tools
democratize
process
acquisition
management,
enabling
reproducibly
transparently
create
materials
diverse
research
applications.
released
under
permissive
BSD-3
license
at
https://github.com/bokulich-lab/RESCRIPt
.
AIMS Microbiology,
Год журнала:
2020,
Номер
6(1), С. 1 - 32
Опубликована: Янв. 1, 2020
Saccharomyces
cerevisiae
is
the
best
studied
eukaryote
and
a
valuable
tool
for
most
aspects
of
basic
research
on
eukaryotic
organisms.
This
due
to
its
unicellular
nature,
which
often
simplifies
matters,
offering
combination
facts
that
nearly
all
biological
functions
found
in
eukaryotes
are
also
present
well
conserved
S.
cerevisiae.
In
addition,
it
easily
amenable
genetic
manipulation.
Moreover,
unlike
other
model
organisms,
cerevisiae
concomitantly
great
importance
various
biotechnological
applications,
some
date
back
several
thousands
years.
cerevisiae's
usefulness
resides
unique
characteristics,
i.e.,
fermentation
capacity,
accompanied
by
production
alcohol
CO2
resilience
adverse
conditions
osmolarity
low
pH.
Among
prominent
applications
involving
use
ones
food,
beverage
-especially
wine-
biofuel
industries.
review
focuses
exactly
function
these
alone
or
conjunction
with
useful
microorganisms
involved
processes.
Furthermore,
potential
reservoir
wild,
environmental,
isolates
examined
under
perspective
their
such
applications.
Journal of Clinical Investigation,
Год журнала:
2017,
Номер
127(7), С. 2829 - 2841
Опубликована: Май 21, 2017
Chronic
liver
disease
with
cirrhosis
is
the
12th
leading
cause
of
death
in
United
States,
and
alcoholic
accounts
for
approximately
half
all
deaths.
alcohol
consumption
associated
intestinal
bacterial
dysbiosis,
yet
we
understand
little
about
contribution
fungi,
or
mycobiota,
to
disease.
Here
have
demonstrated
that
chronic
administration
increases
mycobiota
populations
translocation
fungal
β-glucan
into
systemic
circulation
mice.
Treating
mice
antifungal
agents
reduced
overgrowth,
decreased
translocation,
ameliorated
ethanol-induced
Using
bone
marrow
chimeric
mice,
found
induces
inflammation
via
C-type
lectin-like
receptor
CLEC7A
on
Kupffer
cells
possibly
other
marrow-derived
cells.
Subsequent
IL-1β
expression
secretion
contributed
hepatocyte
damage
promoted
development
We
observed
alcohol-dependent
patients
displayed
diversity
Candida
overgrowth.
Compared
healthy
individuals
non-alcohol-related
cirrhosis,
had
increased
exposure
immune
response
mycobiota.
Moreover,
levels
extraintestinal
correlated
mortality.
Thus,
an
altered
products.
Manipulating
mycobiome
might
be
effective
strategy
attenuating
alcohol-related
ABSTRACT
Regionally
distinct
wine
characteristics
(
terroir
)
are
an
important
aspect
of
production
and
consumer
appreciation.
Microbial
activity
is
integral
part
production,
grape
microbiota
present
regionally
defined
patterns
associated
with
vineyard
climatic
conditions,
but
the
degree
to
which
these
microbial
associate
chemical
composition
unclear.
Through
a
longitudinal
survey
over
200
commercial
fermentations,
we
demonstrate
that
both
metabolite
profiles
distinguish
viticultural
area
designations
individual
vineyards
within
Napa
Sonoma
Counties,
California.
Associations
among
fermentation
suggest
new
links
between
microbiota,
performance,
properties.
The
bacterial
fungal
consortia
composed
from
winery
sources,
correlate
finished
wines
predict
abundances
in
using
machine
learning
models.
use
postharvest
as
early
predictor
unprecedented
potentially
poses
paradigm
for
quality
control
agricultural
products.
These
findings
add
further
evidence
.
IMPORTANCE
Wine
multi-billion-dollar
global
industry
crucial
aspects
quality.
Terroir
feature
appreciation
culture,
many
factors
contribute
nebulous.
We
show
exhibit
regional
composition,
suggesting
microbiome
may
influence
In
addition
enriching
our
understanding
how
growing
region
properties
interact,
this
provide
economic
incentive
enological
practices
maintain
biodiversity.
