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.
Journal for ImmunoTherapy of Cancer,
Год журнала:
2021,
Номер
9(12), С. e003334 - e003334
Опубликована: Дек. 1, 2021
The
gut
microbiome
is
associated
with
the
response
to
immunotherapy
for
different
cancers.
However,
impact
of
on
hepatobiliary
cancers
receiving
remains
unknown.
This
study
aims
investigate
relationship
between
and
clinical
anti-programmed
cell
death
protein
1
(PD-1)
in
patients
advanced
cancers.Patients
unresectable
hepatocellular
carcinoma
or
biliary
tract
who
have
progressed
from
first-line
chemotherapy
(gemcitabine
plus
cisplatin)
were
enrolled.
Fresh
stool
samples
collected
before
during
anti-PD-1
treatment
analyzed
metagenomic
sequencing.
Significantly
differentially
enriched
taxa
prognosis
identified.
Kyoto
Encyclopedia
Genes
Genomes
database
MetaCyc
further
applied
annotate
explore
potential
mechanism
influencing
cancer
immunotherapy.In
total,
65
included
this
study.
Seventy-four
significantly
benefit
(CBR)
group
40
non-clinical
(NCB)
group.
Among
these
taxa,
higher
abundance
Lachnospiraceae
bacterium-GAM79
Alistipes
sp
Marseille-P5997,
which
CBR
group,
achieved
longer
progression-free
survival
(PFS)
overall
(OS)
than
lower
abundance.
Higher
Ruminococcus
calidus
Erysipelotichaceae
bacterium-GAM147
was
also
observed
better
PFS.
In
contrast,
worse
PFS
OS
found
Veillonellaceae,
NCB
Functional
annotation
indicated
that
energy
metabolism
while
amino
acid
metabolism,
may
modulate
addition,
immunotherapy-related
adverse
events
affected
by
diversity
relative
abundance.We
demonstrate
Taxonomic
signatures
responders
are
effective
biomarkers
predict
immunotherapy,
might
provide
a
new
therapeutic
target
immunotherapy.
Abstract
Revealing
the
roles
of
biotic
factors
in
driving
community
assembly,
which
is
crucial
for
understanding
biodiversity
and
ecosystem
functions,
a
fundamental
but
infrequently
investigated
subject
microbial
ecology.
Here,
combining
cross‐biome
observational
study
with
an
experimental
microcosm
study,
we
provided
evidence
to
reveal
major
(i.e.,
soil
fungi
cross‐kingdom
species
associations)
determining
bacterial
biogeography
assembly
complex
terrestrial
ecosystems
arid
regions
northwest
China.
The
results
showed
that
fungal
richness
mediates
balance
processes
communities,
stochastic
decreased
increasing
richness.
Our
further
suggest
predicted
increase
aridity
conditions
due
climate
change
will
reduce
α‐diversity,
particularly
desert
soils
subsurface
layer,
induce
more
negative
associations.
Together,
our
represents
significant
advance
linking
mechanisms
underlying
biogeographic
patterns
under
land‐use
scenarios.
OmicStudio
focuses
on
speed,
quality
together
with
flexibility.
Generally,
can
not
only
meet
the
users'
demand
of
ordinary
bioinformatics
data
analysis,
statistics,
and
visualization,
but
also
provides
them
freedom
mining
beyond
developer's
framework.
Additionally,
unlimited
to
aesthetics,
users
get
more
elegant
graphs
through
customizing.
Available
online
https://www.omicstudio.cn.
ISME Communications,
Год журнала:
2022,
Номер
2(1)
Опубликована: Окт. 6, 2022
Abstract
The
many
microbial
communities
around
us
form
interactive
and
dynamic
ecosystems
called
microbiomes.
Though
concealed
from
the
naked
eye,
microbiomes
govern
influence
macroscopic
systems
including
human
health,
plant
resilience,
biogeochemical
cycling.
Such
feats
have
attracted
interest
scientific
community,
which
has
recently
turned
to
machine
learning
deep
methods
interrogate
microbiome
elucidate
relationships
between
its
composition
function.
Here,
we
provide
an
overview
of
how
latest
studies
harness
inductive
prowess
artificial
intelligence
methods.
We
start
by
highlighting
that
data
–
being
compositional,
sparse,
high-dimensional
necessitates
special
treatment.
then
introduce
traditional
novel
discuss
their
strengths
applications.
Finally,
outlook
pipelines,
focusing
on
bottlenecks
considerations
address
them.
It
is
difficult
for
beginners
to
learn
and
use
amplicon
analysis
software
because
there
are
so
many
tools
choose
from,
all
of
them
need
multiple
steps
operation.
Herein,
we
provide
a
cross-platform,
open-source,
community-supported
pipeline
EasyAmplicon.
EasyAmplicon
has
most
the
modules
needed
an
analysis,
including
data
quality
control,
merging
paired-end
reads,
dereplication,
clustering
or
denoising,
chimera
detection,
generation
feature
tables,
taxonomic
diversity
compositional
biomarker
discovery,
publication-quality
visualization.
includes
more
than
30
cross-platform
R
packages
commonly
used
in
field.
All
integrated
into
RStudio,
which
reduces
learning
costs,
keeps
flexibility
process,
facilitates
personalized
analysis.
The
maintained
updated
by
authors
editors
WeChat
official
account
"Meta-genome."
Our
team
will
regularly
release
latest
tutorials
both
Chinese
English,
read
feedback
from
users,
help
GitHub.
can
be
deployed
on
various
platforms,
installation
time
less
half
hour.
On
ordinary
laptop,
whole
process
dozens
samples
completed
within
3
h.
available
at
GitHub
(https://github.com/YongxinLiu/EasyAmplicon)
Gitee
(https://gitee.com/YongxinLiu/EasyAmplicon).
The
increasing
application
of
meta-omics
approaches
to
investigate
the
structure,
function,
and
intercellular
interactions
microbial
communities
has
led
a
surge
in
available
data.
However,
this
abundance
human
environmental
microbiome
data
exposed
new
scalability
challenges
for
existing
bioinformatics
tools.
In
response,
we
introduce
Wekemo
Bioincloud-a
specialized
platform
-omics
studies.
This
offers
comprehensive
analysis
solution,
specifically
designed
alleviate
tool
selection
users
face
expanding
sets.
As
now,
Bioincloud
been
regularly
equipped
with
22
workflows
65
visualization
tools,
establishing
itself
as
user-friendly
widely
embraced
studying
diverse
Additionally,
enables
online
modification
vector
outputs,
registration-independent
personalized
dashboard
system
ensures
privacy
traceability.
is
freely
at
https://www.bioincloud.tech/.
Cell Reports Medicine,
Год журнала:
2023,
Номер
4(1), С. 100884 - 100884
Опубликована: Янв. 1, 2023
•Intratumoral
microbes
have
been
revealed
to
exist
in
many
cancers•Intratumoral
affect
the
host
immune
and
tumor
chemotherapy•The
characteristics
roles
of
intratumoral
tumors
were
summarized•Exploring
biomarkers
for
diagnosis,
treatment,
prognosis
It
is
estimated
that
future,
number
new
cancer
cases
worldwide
will
exceed
19.3
million
recorded
2020,
deaths
10
million.
Cancer
remains
leading
cause
human
mortality
lagging
socioeconomic
development.
Intratumoral
types,
including
pancreatic,
colorectal,
liver,
esophageal,
breast,
lung
cancers.
microorganisms
not
only
system,
but
also
effectiveness
chemotherapy.
This
review
concentrates
on
various
tumors.
In
addition,
potential
therapies
targeting
microbes,
as
well
main
challenges
currently
delaying
these
therapies,
are
explored.
Furthermore,
we
briefly
summarize
existing
technical
methods
used
characterize
microbes.
We
hope
provide
ideas
exploring
targets
prognostication.
