Unveiling Fusarium falciforme: Genome sequencing of a Novel wilt causing pathogen in subabul (Leucaena leucocephala L.) in India
Sahana N. Banakar,
Ratna Karan,
M. K. Prasanna Kumar
и другие.
Microbial Pathogenesis,
Год журнала:
2025,
Номер
200, С. 107281 - 107281
Опубликована: Янв. 5, 2025
Язык: Английский
Viral activity in lake analogs of anoxic early Earth oceans
Microbiome,
Год журнала:
2025,
Номер
13(1)
Опубликована: Апрель 26, 2025
Meromictic
lakes,
with
their
stratified
water
columns,
are
modern
analogs
for
ancient
euxinic
(anoxic
and
sulfidic)
oceans,
where
anaerobic
sulfur-oxidizing
purple
green
sulfur
bacteria
(PSB
GSB)
dominated
as
primary
producers.
Recent
studies
suggest
a
potential
role
of
viruses
in
the
metabolisms
biosignatures
these
bacteria,
but
conclusive
evidence
viral
replication
activity
such
lakes
is
still
lacking.
Here,
we
investigate
upper
mixed
layer
(mixolimnion),
anoxic
bottom
(monimolimnion),
microbial
plate
(a
dense
phototrophic
forming
at
boundary
between
oxygenated
mixolimnion
monimolimnion)
three
meromictic
lakes:
Poison
Lime
Blue
Lakes
(WA,
USA)
Mahoney
Lake
(BC,
CA).
Geochemical
profiles
two
Poison,
which
by
PSB,
show
sharp
chemocline,
whereas
displays
less
steep
chemical
gradient
hosts
mixture
PSB
GSB.
Viral
gene
transcription
epifluorescence
microscopy
revealed
depth-dependent
patterns
activity.
The
strongly
stratified,
PSB-dominated
showed
significant
decrease
virus-to-microbe
ratio
(VMR)
plates,
suggesting
reduced
particle
production
via
lysis.
Metatranscriptome
data
corroborated
this
trend
showing
lower
levels
expression
higher
CRISPR
defense
lysogeny-related
genes,
relatively
high
photosynthesis-related
genes.
Conversely,
third
lake,
harbors
mix
GSB,
exhibited
low
density,
VMR,
transcriptional
significantly
correlated
VMR
plates
layers,
relationship
was
absent
low-density,
oxic
surface
samples.
independent
lines
evidence,
abundances
expression,
lytic
lakes.
This
suggests
that
lysis
may
contribute
to
bacterial
community
structuring
high-density
plates.
Rather,
other
viral-mediated
mechanisms,
lysogeny
auxiliary
metabolic
represent
more
influence
on
physiology
geochemistry.
These
virus-bacteria
interactions
be
consequential
interpretations
left
groups
geologic
record.
Video
Abstract.
Язык: Английский
Non-Intestinal Microbial Signatures in Stool as Predictors of Cancer Immunotherapy Outcome
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Май 11, 2025
Abstract
Despite
advances
in
immunotherapy,
clinical
responses
remain
heterogeneous,
underscoring
the
need
to
elucidate
gut
microbiome’s
role
modulating
therapeutic
efficacy.
We
conducted
a
large-scale
genome-resolved
metagenomic
analysis
of
624
stool
samples
from
11
cohorts
spanning
five
cancer
types
three
continents
identify
conserved
microbial
biomarkers
immunotherapy
response.
Responders
(R;
n
=
362)
exhibited
enrichment
Blautia
species,
linked
acetate
production
CO
2
via
Wood-Ljungdahl
(WL)
pathway,
glycoside
hydrolases
(GH),
and
amino
acid
biosynthesis.
Non-responders
(NR;
262)
showed
increased
oral
(e.g.
Veillonella
parvula,
Dialister
invisus
)
food-derived
taxa
included
opportunistic
species
e.g.
Citrobacter
freundii,
Klebsiella
spp.,
alongside
depletion
gut-resident
microbes
enriched
lipopolysaccharide
biosynthesis
flagellar
assembly
pathways.
Interestingly,
part
NR-associated
originated
non-intestinal
niches
(oral/food),
which
may
correlate
with
reduced
load
large
intestine.
These
findings
redefine
dietary
interventions
as
dual-edged:
while
carbon
sources
such
fiber
processed
by
GH
or
WL
pathway
supports
beneficial
immune
system,
pathogen-free
food
sourcing
is
critical
avoid
introducing
microbes.
Our
work
establishes
resident-to-transient
ratio
novel
predictive
biomarker
positions
keystone
genus
for
next-generation
probiotics
targeting
metabolism-immune
crosstalk.
By
integrating
taxonomic,
functional,
ecological
axes,
this
study
provides
roadmap
microbiome-guided
precision
nutrition
optimize
outcomes.
While
non-responders
exhibit
microbiota
food/oral
commensals,
Faecalibacterium
prausnitzii
-
shows
context-dependent
associations,
strain-level
variations
potentially
A
blood
group
antigen
N-acetylgalactosamine
utilization,
highlighting
its
conditional
prognostic
value
metagenomics
personalized
therapy.
Язык: Английский
MerCat2: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from omics data
Bioinformatics Advances,
Год журнала:
2024,
Номер
4(1)
Опубликована: Янв. 1, 2024
Abstract
Motivation
MerCat2
(“Mer—Catenate2”)
is
a
versatile,
parallel,
scalable
and
modular
property
software
package
for
robustly
analyzing
features
in
omics
data.
Using
massively
parallel
sequencing
raw
reads,
assembled
contigs,
protein
sequences
from
any
platform
as
input,
performs
k-mer
counting
of
length
k,
resulting
feature
abundance
counts
tables,
quality
control
reports,
metrics,
graphical
representation
(i.e.
principal
component
analysis
(PCA)).
Results
allows
direct
data
properties
database-independent
manner
that
initializes
all
data,
which
other
profilers
assembly-based
methods
cannot
perform.
represents
an
integrated
tool
to
illuminate
within
sample
rapid
cross-examination
comparisons.
Availability
implementation
written
Python
distributed
under
BSD-3
license.
The
source
code
freely
available
at
https://github.com/raw-lab/mercat2.
compatible
with
3
on
Mac
OS
X
Linux.
can
also
be
easily
installed
using
bioconda:
mamba
create
-n
mercat2
-c
conda-forge
bioconda
Язык: Английский
Genome Annotation and Analysis
Elsevier eBooks,
Год журнала:
2024,
Номер
unknown
Опубликована: Янв. 1, 2024
Язык: Английский
NFixDB (Nitrogen Fixation DataBase)—a comprehensive integrated database for robust ‘omics analysis of diazotrophs
NAR Genomics and Bioinformatics,
Год журнала:
2024,
Номер
6(2)
Опубликована: Апрель 4, 2024
Biological
nitrogen
fixation
is
a
fundamental
biogeochemical
process
that
transforms
molecular
into
biologically
available
via
diazotrophic
microbes.
Diazotrophs
anaerobically
fix
using
the
nitrogenase
enzyme
which
arranged
in
three
different
gene
clusters:
(i)
molybdenum
(
Язык: Английский
Viral activity in lake analogs of anoxic early Earth oceans
Research Square (Research Square),
Год журнала:
2024,
Номер
unknown
Опубликована: Сен. 25, 2024
Abstract
Background
Meromictic
lakes,
with
their
stratified
water
columns,
are
modern
analogs
for
ancient
euxinic
(anoxic
and
sulfidic)
oceans,
where
anaerobic
sulfur-oxidizing
purple
green
sulfur
bacteria
(PSB
GSB)
dominated
as
primary
producers.
Recent
studies
suggest
a
potential
role
of
viruses
in
the
metabolisms
biosignatures
these
bacteria,
but
conclusive
evidence
viral
replication
activity
such
lakes
is
still
lacking.
Results
Here,
we
investigate
upper
mixed
layer
(mixolimnion),
microbial
plate,
anoxic
bottom
(monimolimnion)
three
meromictic
lake
columns:
Poison
Lake
Lime
Blue
(WA,
USA),
Mahoney
(BC,
CA).
Geochemical
profiles
two
Poison,
which
heavily
by
PSB,
show
sharp
chemocline,
whereas
displays
less
steep
chemical
gradient
hosts
mixture
PSB
GSB.
Viral
gene
transcription
epifluorescence
microscopy
counts
revealed
depth-dependent
patterns
activity.
The
strongly
stratified,
PSB-dominated
showed
significant
decrease
virus-to-microbe
ratio
(VMR)
plates,
suggesting
reduced
particle
production
via
lysis.
Metatranscriptome
data
corroborated
this
trend
showing
lower
levels
expression
relatively
high
photosynthesis-related
genes.
Conversely,
third
lake,
harbors
mix
GSB,
exhibited
low
density,
VMR,
transcriptional
significantly
correlated
VMR
plates
layers,
relationship
was
absent
low-density,
oxic
surface
samples.
Conclusions
independent
lines
evidence,
abundances
expression,
lytic
lakes.
This
suggests
that
lysis
may
contribute
to
bacterial
community
structuring
high-density
plates.
Rather,
other
viral-mediated
mechanisms,
auxiliary
metabolic
genes,
represent
more
influence
on
physiology
geochemistry.
These
virus-bacteria
interactions
be
consequential
interpretations
left
groups
geologic
record.
Язык: Английский
Unlocking the genomic repertoire of a cultivated megaphage
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 20, 2024
Abstract
Megaphages
are
bacteriophages
(i.e.,
phages)
with
exceptionally
large
genomes
that
ecosystem
cosmopolitans,
infect
various
bacterial
hosts,
and
have
been
discovered
across
metagenomic
datasets
globally.
To
date,
almost
all
megaphages
evaded
cultivation,
only
phage
G
being
in
active
culture
for
over
50
years.
We
examined
multiomics
this
five
decades
long
cultivated
history
from
nine
different
laboratories
lab
variants
to
the
modern
era.
In
work,
we
resolved
complete
genomes,
particle
proteome,
de
novo
methylome,
used
artificial
intelligence
(AI)
annotate
genome
of
G.
Phage
is
one
largest
phages
a
size
>0.6
µm,
about
half
width
host
cell,
499
kbp,
non-permuted,
linear
has,
uniquely
among
known
phages,
two
pairs
ends.
Its
closest
relative
Moose
W30-1
which
was
metagenomically
assembled
without
cultivation
moose
rumen
sample.
has
>650
protein-coding
open
reading
frames
(ORFs),
>65%
hypothetical
proteins
no
function,
rest
geared
towards
nucleic
acid
replication
(e.g.,
helicases,
polymerases,
endonucleases)
structural
nature
capsid,
tail,
portal,
terminase).
The
encodes
35
kbp
stretch
66
ORFs
any
functional
homology,
cryptic
genomic
region
roughly
lambda.
an
expansive
repertoire
auxiliary
metabolic
genes
(AMGs)
acquired
its
host,
including
phoH
,
ftsZ
UvsX/RecA-like,
gyrA,
gyrB
,and
DHFR
.
Furthermore,
AMGs
could
manipulate
sporulation
(
sspD,
RsfA,
spoK
)
antiviral
escape
anti-CBass
nuclease
Anti-Pycsar
protein).
proteomics
found
>15%
protein
were
present
either
wild-type
or
mutant
G,
involved
UvsX/RecA-like
),
sporulation,
as
well
portal).
methylome
localized
limited
supervised
machine
learning
HMMs)
unable
resolve
region,
but
AI.
This
hot
spot
methylation
at
32%,
where
many
functions
ORF
still
unknown.
Our
study
represents
doorway
into
complexity
megaphage,
highlighting
continuous
first
time.
Язык: Английский