Microbiology Spectrum,
Год журнала:
2023,
Номер
11(1)
Опубликована: Янв. 10, 2023
As
a
core
microbe
of
the
human
gut
ecosystem,
Bacteroides
vulgatus
has
been
linked
to
multiple
aspects
metabolic
disorders
in
collection
associative
studies,
which,
while
indicative,
warrants
more
direct
experimental
evidence
verify.
In
this
study,
we
experimentally
demonstrated
that
oral
administration
B.
Bv46
ameliorated
serum
lipid
profile
and
systemic
inflammation
high-fat
diet-induced
hyperlipidemic
rats
microbiome-regulated
manner,
which
appears
be
associated
with
changes
bile
acid
metabolism,
short-chain
fatty
biosynthesis,
metabolomic
profile.
In
recent
decades,
with
the
continuous
development
of
high-throughput
sequencing
technology,
data
volume
in
medical
research
has
increased,
at
same
time,
almost
all
clinical
researchers
have
their
own
independent
omics
data,
which
provided
a
better
condition
for
mining
and
deeper
understanding
gene
functions.
However,
these
large
amounts
many
common
cutting-edge
effective
bioinformatics
methods
still
cannot
be
widely
used.
This
encouraged
establishment
analytical
platforms,
portion
databases
or
platforms
were
designed
to
solve
special
analysis
needs
users,
instance,
MG
RAST,
IMG/M,
Qiita,
BIGSdb,
TRAPR
developed
specific
research,
some
servers
provide
solutions
problems
solutions.
Metascape
was
only
functional
annotations
genes
as
well
function
enrichment
analysis;
BioNumerics
RidomSeqSphere+
perform
multilocus
sequence
typing;
CARD
provides
antimicrobial
resistance
annotations.
Additionally,
web
services
are
outdated,
inefficient
interaction
often
fails
meet
researchers,
such
our
previous
versions
platform.
Therefore,
demand
complete
massive
processing
tasks
urgently
requires
comprehensive
Hence,
we
website
platform,
Sangerbox
3.0
(http://vip.sangerbox.com/),
web-based
tool
On
user-friendly
interface
that
also
supports
differential
analysis,
platform
interactive
customizable
tools,
including
various
kinds
correlation
analyses,
pathway
weighted
network
other
tools
functions,
users
need
upload
corresponding
into
3.0,
select
required
parameters,
submit,
wait
results
after
task
been
completed.
We
established
new
plotting
system
allows
adjust
parameters
image;
moreover,
optimized
performance
enables
large-capacity
vector
maps
on
site.
At
integrated
GEO,
TCGA,
ICGC,
processed
batches,
greatly
reducing
difficulty
obtain
improving
efficiency
bioimformatics
study
users.
Finally,
rich
sources
courses,
offering
share
exchange
knowledge.
Pharmacological Research,
Год журнала:
2021,
Номер
172, С. 105840 - 105840
Опубликована: Авг. 24, 2021
Emerging
evidence
indicates
that
the
gut
microbiota
play
a
crucial
role
in
bidirectional
communication
between
and
brain
suggesting
microbes
may
shape
neural
development,
modulate
neurotransmission
affect
behavior,
thereby
contribute
to
pathogenesis
and/or
progression
of
many
neurodevelopmental,
neuropsychiatric,
neurological
conditions.
This
review
summarizes
recent
data
on
microbiota-gut-brain
axis
pathophysiology
neuropsychiatric
disorders
including
depression,
anxiety,
schizophrenia,
autism
spectrum
disorders,
Parkinson's
disease,
migraine,
epilepsy.
Also,
involvement
co-existing
with
conditions
is
highlighted.
We
discuss
from
both
vivo
preclinical
experiments
clinical
reports
including:
(1)
studies
germ-free
animals,
(2)
exploring
composition
animal
models
diseases
or
humans,
(3)
evaluating
effects
probiotic,
prebiotic
antibiotic
treatment
as
well
(4)
fecal
transplantation.
Frontiers in Plant Science,
Год журнала:
2021,
Номер
12
Опубликована: Март 2, 2021
Plant
secondary
metabolites
(PSMs)
play
many
roles
including
defense
against
pathogens,
pests,
and
herbivores;
response
to
environmental
stresses,
mediating
organismal
interactions.
Similarly,
plant
microbiomes
participate
in
of
the
above-mentioned
processes
directly
or
indirectly
by
regulating
metabolism.
Studies
have
shown
that
plants
can
influence
their
microbiome
secreting
various
and,
turn,
may
also
impact
metabolome
host
plant.
However,
not
much
is
known
about
communications
between
interacting
partners
phenotypic
changes.
In
this
article,
we
review
patterns
potential
underlying
mechanisms
interactions
PSMs
microbiomes.
We
describe
recent
developments
analytical
approaches
methods
field.
The
applications
these
new
increased
our
understanding
relationships
Though
current
studies
primarily
focused
on
model
organisms,
results
obtained
so
far
should
help
future
agriculturally
important
facilitate
development
manipulate
PSMs–microbiome
with
predictive
outcomes
for
sustainable
crop
productions.
Abstract
Data
visualization
plays
a
crucial
role
in
illustrating
results
and
sharing
knowledge
among
researchers.
Though
many
types
of
tools
are
widely
used,
most
them
require
enough
coding
experience
or
designed
for
specialized
usages,
not
free.
Here,
we
present
ImageGP,
platform
biology
chemistry
data
illustration.
ImageGP
could
generate
generalized
plots
like
lines,
bars,
scatters,
boxes,
sets,
heatmaps,
histograms
with
the
common
input
content
user‐friendly
interface.
Normally
plotting
using
only
needs
few
mouse
clicks.
For
some
plots,
one
to
just
paste
click
submit
get
results.
Additionally,
supplies
up
26
parameters
meet
customizable
requirements.
also
contains
volcano
plot,
functional
enrichment
plot
omics‐data
analysis,
other
four
functions
microbiome
analysis.
Since
2017,
has
been
running
nearly
5
years
serving
336,951
visits
from
all
over
world.
Together,
(
http://www.ehbio.com/ImageGP/
)
is
an
effective
efficient
tool
experimental
researchers
comprehensively
visualize
interpret
generated
wet‐lab
dry‐lab.
Journal of Clinical Investigation,
Год журнала:
2022,
Номер
132(7)
Опубликована: Март 31, 2022
Next-generation
sequencing
(NGS)
technology
has
advanced
our
understanding
of
the
human
microbiome
by
allowing
for
discovery
and
characterization
unculturable
microbes
with
prediction
their
function.
Key
NGS
methods
include
16S
rRNA
gene
sequencing,
shotgun
metagenomic
RNA
sequencing.
The
choice
which
methodology
to
pursue
a
given
purpose
is
often
unclear
clinicians
researchers.
In
this
Review,
we
describe
fundamentals
NGS,
focus
on
We
also
discuss
pros
cons
each
as
well
important
concepts
in
data
variability,
study
design,
clinical
metadata
collection.
further
present
examples
how
studies
have
disease
pathophysiology
across
diverse
contexts,
including
development
diagnostics
therapeutics.
Finally,
share
insights
might
be
integrated
into
advance
research
care
coming
years.
The
network
analysis
has
attracted
increasing
attention
and
interest
from
ecological
academics,
thus
it
is
of
great
necessity
to
develop
more
convenient
powerful
tools.
For
that
reason,
we
have
developed
an
R
package,
named
"ggClusterNet,"
complete
display
the
in
easier
manner.
In
ten
layout
algorithms
are
designed
better
modules
microbiome
(randomClusterG,
PolygonClusterG,
PolygonRrClusterG,
ArtifCluster,
randSNEClusterG,
PolygonModsquareG,
PolyRdmNotdCirG,
model_Gephi.2,
model_igraph,
model_maptree).
convenience
users,
many
functions
related
microbial
analysis,
such
as
corMicor(),
net_properties(),
node_properties(),
ZiPiPlot(),
random_Net_compate(),
integrated
mining.
Furthermore,
pipeline
function
network.2()
corBionetwork()
also
added
for
quick
achievement
or
bipartite
well
their
in-depth
ggClusterNet
publicly
available
via
GitHub
(https://github.com/taowenmicro/ggClusterNet/)
Gitee
(https://gitee.com/wentaomicro/ggClusterNet)
users'
access.
A
description
usages
can
be
found
on
manuscript's
page
(https://github.com/taowenmicro/ggClusterNet/wiki).
Journal of Integrative Plant Biology,
Год журнала:
2022,
Номер
64(2), С. 230 - 243
Опубликована: Янв. 14, 2022
The
root
microbiome
refers
to
the
community
of
microbes
living
in
association
with
a
plant's
roots,
and
includes
mutualists,
pathogens,
commensals.
Here
we
focus
on
recent
advances
study
commensal
which
is
major
research
object
microbiome-related
researches.
With
rapid
development
new
technologies,
plant-commensal
interactions
can
be
explored
unprecedented
breadth
depth.
Both
soil
environment
host
plant
drive
assembly.
bulk
seed
bank
potential
commensals,
plants
use
exudates
immune
responses
build
healthy
microbial
communities
from
available
microbes.
extends
functional
system
by
participating
variety
processes,
including
nutrient
absorption,
growth
promotion,
resistance
biotic
abiotic
stresses.
Plants
their
microbiomes
have
evolved
adaptation
strategies
over
time.
However,
there
still
huge
gap
our
understanding
regulatory
mechanisms
interactions.
In
this
review,
summarize
assembly
effects
these
development,
look
at
prospects
for
promoting
sustainable
agricultural
through
microbiome.
