Analysis of Whole-Genome as a Novel Strategy for Animal Species Identification
International Journal of Molecular Sciences,
Год журнала:
2024,
Номер
25(5), С. 2955 - 2955
Опубликована: Март 3, 2024
Survival
crises
stalk
many
animals,
especially
endangered
and
rare
animals.
Accurate
species
identification
plays
a
pivotal
role
in
animal
resource
conservation.
In
this
study,
we
developed
an
method
called
Analysis
of
whole-GEnome
(AGE),
which
identifies
by
finding
species-specific
sequences
through
bioinformatics
analysis
the
whole
genome
subsequently
recognizing
these
using
experimental
technologies.
To
clearly
demonstrate
AGE
method,
Cervus
nippon,
well-known
species,
closely
related
elaphus,
were
set
as
model
without
with
published
genomes,
respectively.
By
analyzing
genomes
C.
nippon
obtained
next-generation
sequencing
online
databases,
built
specific
sequence
databases
containing
7,670,140
570,981
sequences,
Then,
specificities
confirmed
experimentally
Sanger
CRISPR-Cas12a
system.
Moreover,
for
11
fresh
samples
35
commercially
available
products,
our
results
complete
agreement
those
other
authoritative
methods,
demonstrating
AGE’s
precision
potential
application.
Notably,
found
mixture
products
successfully
identified
it.
This
study
broadens
horizons
sheds
light
on
conserving
resources.
Язык: Английский
Analysis of Whole-Genome for Identification of Seven Penicillium Species with Significant Economic Value
International Journal of Molecular Sciences,
Год журнала:
2024,
Номер
25(15), С. 8172 - 8172
Опубликована: Июль 26, 2024
The
Язык: Английский
The Role of Quantitative Real-Time PCR in the Invasive Pulmonary Aspergillosis Diagnosis: A Retrospective Study
Microorganisms,
Год журнала:
2025,
Номер
13(2), С. 409 - 409
Опубликована: Фев. 13, 2025
Invasive
pulmonary
aspergillosis
(IPA)
reports
significant
mortality
rates
among
critically
ill
patients.
A
prompt
microbiological
diagnosis
is
essential
to
establish
a
coherent
antifungal
treatment.
Despite
its
low
sensitivity
and
prolonged
turn-around
time,
culture
represents
the
conventional
diagnostic
technique.
Additionally,
galactomannan
detection
may
support
process.
Ultimate
generation
methods,
such
as
real-time
polymerase
chain
reaction
(Real-Time
PCR),
integrated
procedure
improve
overall
laboratory
effectiveness,
especially
regarding
quantitative
Aspergillus
spp.
DNA
detection.
Herein,
we
propose
retrospective
analysis
where
PCR
was
performed
on
respiratory
samples
belonging
patients
with
or
without
probable
aspergillosis.
The
study
enrolled
62
samples,
whose
results
were
compared
indexes.
clinical
general
data
collected
for
all
qPCR
assay
reported
100%
negative
predictive
value,
while
specificity
reached
59.2%
positive
value
76.1%.
Moreover,
IPA
fungal
loads
higher
than
103
in
logarithmic
scale,
non-aspergillosis
episodes
maximum
level
of
103.
We
hypothesized
future
possibility
define
specific
cut-off
distinguishing
colonization
from
infection
cases,
requiring
further
investigations
speculations
about
samples.
Язык: Английский
Biotechnological Potential for Fructooligosaccharides Production and Molecular Characterization of Aspergillus oryzae DIA-ITDAM
Food Biotechnology,
Год журнала:
2025,
Номер
39(1), С. 94 - 114
Опубликована: Янв. 2, 2025
Язык: Английский
Analysis of Whole-Genome for Alternaria Species Identification
Journal of Fungi,
Год журнала:
2025,
Номер
11(3), С. 185 - 185
Опубликована: Фев. 26, 2025
The
genus
Alternaria,
functioning
as
a
saprobe,
endophyte,
and
plant
pathogen,
is
widely
distributed
across
various
natural
human-impacted
environments.
Leaf
spot
black
diseases,
caused
by
Alternaria
species,
are
the
most
prevalent
diseases
within
this
genus,
leading
to
significant
reductions
in
crop
yields
substantial
economic
losses.
To
facilitate
timely
detection
of
species
during
early
stages
infection,
enable
targeted
treatments,
mitigate
associated
damages,
we
employed
identification
method
based
on
Analysis
whole-GEnome
(AGE).
We
downloaded
148
genomes,
including
31
from
NCBI
GenBank
database.
Through
bioinformatics
analysis,
constructed
specific-target
sequence
library
selected
representative
per
species.
specific
target
sequences
seven
exemplary
were
subsequently
used
for
validation
rapid
detection,
utilizing
Sanger
sequencing
CRISPR-Cas12a
technology,
respectively.
results
demonstrated
that
our
accurately
identified
Additionally,
combining
Enzymatic
Recombinase
Amplification
(ERA)
with
CRISPR-Cas12a,
achieved
precise
genomic
DNA
samples,
limit
low
0.01
ng/µL
30
min.
Therefore,
AGE
proves
be
highly
robust
efficient
offering
broad
potential
applications.
Язык: Английский
Genomic Characterization and Functional Evaluation of Eurotium cristatum EC-520: Impacts on Colon Barrier Integrity, Gut Microbiota, and Metabolite Profile in Rats
Foods,
Год журнала:
2025,
Номер
14(9), С. 1569 - 1569
Опубликована: Апрель 29, 2025
Eurotium
cristatum
(EC),
the
dominant
fungus
in
Fuzhuan
brick
tea,
has
significant
applications
food
fermentation
and
pharmaceutical
industries,
exhibiting
probiotic
properties,
but
further
investigation
of
its
intestinal
benefits
is
required.
This
study
characterized
EC-520
strain
through
whole
genome
sequencing
evaluated
effects
on
rat
colons
using
histomorphology,
16S
rRNA
sequencing,
untargeted
metabolomics.
The
genomic
analysis
revealed
that
possessed
a
28.37
Mb
distantly
related
to
Aspergillus
flavus.
results
demonstrated
significantly
increased
abundance
Bacteroidota
(p
<
0.05)
while
decreasing
Proteobacteria
Firmicutes/Bacteroidota
ratio
(the
F/B
ratio);
at
genus
level,
it
elevated
Muribaculaceae
Clostridia_UCG-014
reducing
harmful
bacteria.
metabolomic
showed
also
altered
tryptamine,
caproic
acid,
isocaproic
erucic
acid
0.05).
Additionally,
Spearman’s
correlation
Muribaculaceae_unclassified
Clostridia_UCG-014_unclassified
were
positively
correlated
with
acid.
Therefore,
this
suggested
enhanced
colon
barrier
Clostridia_UCG-014_unclassified,
thus
promoting
secretion
tryptamine
affecting
release
5-hydroxytryptamine
(5-HT).
It
promoted
certain
fatty
acids,
enhancing
balance
colonic
microbiota.
provides
new
view
for
comprehensive
understanding
EC’s
regulatory
role
colon.
Язык: Английский
Strain Typing (Bacterial, Viral, Fungal, and Mycobacterial)
Опубликована: Май 19, 2025
Язык: Английский
MALDI TOF-MS for microbial identification and diagnosis
Elsevier eBooks,
Год журнала:
2024,
Номер
unknown, С. 43 - 57
Опубликована: Янв. 1, 2024
Biodegradation of petroleum hydrocarbon and related molecular microbiology analysis of some fungal species
Alexandria Journal of Agricultural Research,
Год журнала:
2024,
Номер
0(0), С. 0 - 0
Опубликована: Июль 24, 2024
Petroleum
hydrocarbon
contamination
is
one
of
the
main
environmental
challenges.
Bioremediation
using
fungi
(Mycoremediation)
best
method
to
overcome
this
problem.
Consequently,
current
study
aimed
investigate
tolerance
four
fungal
isolates
petroleum
and
estimate
level
production
cellulase
Mn
peroxidase
enzymes
involved
in
oil
biodegradation.
The
were
identified
as
Fusarium
solani,
Trichoderma
harzianum,
Aspergillus
terreus,
flavus
by
rDNA
sequencing
ITS1
-5.8
S
rRNA-ITS2
region.
A
test
was
conducted
solid
minimal
media
(MM)
containing
different
concentrations
diesel
oil,
growth
rate
dose
inhibition
response
percentage
(DIRP)
values
recorded.
Treated
non-treated
Bushnell
Haas
(BH)
broth
used
ability
secret
target
enzymes.
results
showed
that
T.
harzianum
had
highest
towards
followed
A.
flavus.
Diesel
induced
gene-overexpression
for
producer
peroxidase.
Finally,
all
isolates,
especially
can
adapt
high
hydrocarbon.
Thus,
they
be
successfully
bioremediation
Язык: Английский