Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes
Genome biology,
Год журнала:
2024,
Номер
25(1)
Опубликована: Апрель 15, 2024
As
most
viruses
remain
uncultivated,
metagenomics
is
currently
the
main
method
for
virus
discovery.
Detecting
in
metagenomic
data
not
trivial.
In
past
few
years,
many
bioinformatic
identification
tools
have
been
developed
this
task,
making
it
challenging
to
choose
right
tools,
parameters,
and
cutoffs.
all
these
measure
different
biological
signals,
use
algorithms
training
reference
databases,
imperative
conduct
an
independent
benchmarking
give
users
objective
guidance.
Язык: Английский
The Potential Harmful Effects of Genetically Engineered Microorganisms (GEMs) on the Intestinal Microbiome and Public Health
Microorganisms,
Год журнала:
2024,
Номер
12(2), С. 238 - 238
Опубликована: Янв. 23, 2024
Gut
luminal
dysbiosis
and
pathobiosis
result
in
compositional
biodiversified
alterations
the
microbial
host
co-metabolites.
The
primary
mechanism
of
bacterial
evolution
is
horizontal
gene
transfer
(HGT),
acquisition
new
traits
can
be
achieved
through
exchange
mobile
genetic
elements
(MGEs).
Introducing
genetically
engineered
microbes
(GEMs)
might
break
harmonized
balance
intestinal
compartment.
present
objectives
are:
1.
To
reveal
role
played
by
GEMs’
transfers
changing
landscape
enteric
microbiome
eubiosis
2.
expand
on
potential
detrimental
effects
those
changes
human
genome
health.
A
search
articles
published
PubMed/MEDLINE,
EMBASE,
Scielo
from
2000
to
August
2023
using
appropriate
MeSH
entry
terms
was
performed.
exchanges
induce
multiple
diseases.
GEMs
change
long-term
natural
pro-
or
eukaryotic
cell
inhabitants.
worldwide
regulatory
authority’s
safety
control
not
enough
protect
public
Viability,
biocontainment,
many
other
aspects
are
only
partially
controlled
harmful
consequences
for
health
should
avoided.
It
important
remember
that
prevention
most
cost-effective
strategy
primum
non
nocere
focus.
Язык: Английский
Interactions and evolutionary relationships among bacterial mobile genetic elements
Nature Reviews Microbiology,
Год журнала:
2025,
Номер
unknown
Опубликована: Март 11, 2025
Язык: Английский
Shotgun and Hi-C Sequencing Datasets for Binning Wheat Rhizosphere Microbiome
Scientific Data,
Год журнала:
2025,
Номер
12(1)
Опубликована: Март 1, 2025
Abstract
Binning
is
a
crucial
process
in
metagenomics
studies,
where
sequenced
reads
are
combined
to
form
longer
contigs
and
assigned
individual
genomes.
Conventional
methods,
such
as
shotgun
binning,
rely
on
similarity
measurements
abundance
profiles
across
multiple
samples.
However,
cost
constraints
for
sequencing
limited
sample
collection
capacity
hinder
their
effectiveness.
High-throughput
chromosome
conformation
capture
(Hi-C),
DNA
proximity
ligation
technique,
has
been
adapted
accurately
bin
metagenome-assembled
genomes
(MAGs)
from
single
sample,
addressing
challenges
like
chimeric
MAGs.
In
this
study,
we
generated
over
190
Gb
of
metagenomic
data
wheat
rhizospheres
grown
two
highly
calcareous
soils
South
Australian
region
compared
conventional
Hi-C
binning
methods.
Two
metagenomes
libraries
were
generated,
assembling
1089
MAGs
39
bacterial
one
archaeal
taxon,
including
94
based
bins.
performed
using
only
short
read
sequences
was
prone
high
contamination,
while
the
addition
improved
MAG
quality
identified
mobile
element-host-infection
interaction.
This
dataset
provides
important
tools
studying
microbial
communities
rhizosphere
soils.
Язык: Английский
Metagenomics as a Transformative Tool for Antibiotic Resistance Surveillance: Highlighting the Impact of Mobile Genetic Elements with a Focus on the Complex Role of Phages
Antibiotics,
Год журнала:
2025,
Номер
14(3), С. 296 - 296
Опубликована: Март 12, 2025
Extensive
use
of
antibiotics
in
human
healthcare
as
well
agricultural
and
environmental
settings
has
led
to
the
emergence
spread
antibiotic-resistant
bacteria,
rendering
many
infections
increasingly
difficult
treat.
Coupled
with
limited
development
new
antibiotics,
rise
antimicrobial
resistance
(AMR)
caused
a
major
health
crisis
worldwide,
which
calls
for
immediate
action.
Strengthening
AMR
surveillance
systems
is,
therefore,
crucial
global
national
efforts
combating
this
escalating
threat.
This
review
explores
potential
metagenomics,
sequenced-based
approach
analyze
entire
microbial
communities
without
need
cultivation,
transformative
rapid
tool
improving
strategies
compared
traditional
cultivation-based
methods.
We
emphasize
importance
monitoring
mobile
genetic
elements
(MGEs),
such
integrons,
transposons,
plasmids,
bacteriophages
(phages),
relation
their
critical
role
facilitating
dissemination
determinants
via
horizontal
gene
transfer
(HGT)
across
diverse
environments
clinical
settings.
In
context,
strengths
limitations
current
bioinformatic
tools
designed
detect
AMR-associated
MGEs
metagenomic
datasets,
including
emerging
predictive
machine
learning
models,
are
evaluated.
Moreover,
controversial
phages
transmission
is
discussed
alongside
phage
therapy
promising
alternative
conventional
antibiotic
treatment.
Язык: Английский
The long-chain flavodoxin FldX1 improves the biodegradation of 4-hydroxyphenylacetate and 3-hydroxyphenylacetate and counteracts the oxidative stress associated to aromatic catabolism in Paraburkholderia xenovorans
Biological Research,
Год журнала:
2024,
Номер
57(1)
Опубликована: Апрель 1, 2024
Abstract
Background
Bacterial
aromatic
degradation
may
cause
oxidative
stress.
The
long-chain
flavodoxin
FldX1
of
Paraburkholderia
xenovorans
LB400
counteracts
reactive
oxygen
species
(ROS).
aim
this
study
was
to
evaluate
the
protective
role
in
P.
during
4-hydroxyphenylacetate
(4-HPA)
and
3-hydroxyphenylacetate
(3-HPA).
Methods
functionality
evaluated
p2-
fldX1
that
overexpresses
FldX1.
effects
on
were
studied
measuring
growth
hydroxyphenylacetates,
4-HPA
3-HPA,
ROS
formation.
hydroxyphenylacetates
(HPAs)
proteome
(LC–MS/MS)
gene
expression
(qRT-PCR)
quantified.
Bioaugmentation
with
strain
4-HPA-polluted
soil
assessed,
(HPLC),
4-HPA-degrading
bacteria,
plasmid
stability.
Results
exposure
increased
formation
compared
3-HPA
or
glucose.
showed
an
control
WT-p2.
Strain
degraded
faster
than
Both
WT-p2
cells
grown
displayed
more
changes
comparison
glucose-grown
cells.
Several
enzymes
involved
detoxification,
including
AhpC2,
AhpF,
AhpD3,
KatA,
Bcp,
CpoF1,
Prx1
Prx2,
upregulated
by
hydroxyphenylacetates.
Downregulation
organic
hydroperoxide
resistance
(Ohr)
DpsA
proteins
observed.
A
downregulation
genes
encoding
scavenging
(
katE
sodB
),
gstA
trxB
observed
cells,
suggesting
prevents
antioxidant
response.
More
20
membrane
proteins,
porins
transporters,
both
strains
An
recombinant
microcosms
.
In
soil,
overexpressing
a
lower
loss,
strain,
contributes
bacterial
fitness.
Overall,
these
results
suggest
is
attractive
bacterium
for
its
application
bioremediation
processes
compounds.
Conclusions
improved
capability
degrade
liquid
culture
protecting
against
degradation-associated
Язык: Английский
An eco-evolutionary perspective on antimicrobial resistance in the context of One Health.
iScience,
Год журнала:
2024,
Номер
28(1), С. 111534 - 111534
Опубликована: Дек. 5, 2024
Язык: Английский
Jaeger: an accurate and fast deep-learning tool to detect bacteriophage sequences
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Сен. 24, 2024
ABSTRACT
Viruses
are
integral
to
every
biome
on
Earth,
yet
we
still
need
a
more
comprehensive
picture
of
their
identity
and
global
distribution.
Global
metagenomics
sequencing
efforts
revealed
the
genomic
content
tens
thousands
environmental
samples,
however
identifying
viral
sequences
in
these
datasets
remains
challenging
due
vast
diversity.
Here,
address
bacteriophage
unlabeled
data.
In
recent
benchmarking
paper,
observed
that
existing
deep-learning
tools
show
high
true
positive
rate,
but
may
also
produce
many
false
positives
when
confronted
with
divergent
sequences.
To
tackle
this
challenge,
introduce
Jaeger,
novel
method
designed
specifically
for
genome
fragments.
Extensive
IMG/VR
database
real-world
metagenomes
reveals
Jaeger’s
consistent
sensitivity
(0.87)
precision
(0.92).
Applying
Jaeger
over
16,000
metagenomic
assemblies
from
MGnify
yielded
five
million
putative
phage
contigs.
On
average,
is
around
20
times
faster
than
other
state-of-the-art
methods.
available
at
https://github.com/MGXlab/Jaeger
.
Язык: Английский
Graphite: painting genomes using a colored de Bruijn graph
NAR Genomics and Bioinformatics,
Год журнала:
2024,
Номер
6(4)
Опубликована: Июль 2, 2024
Abstract
The
recent
growth
of
microbial
sequence
data
allows
comparisons
at
unprecedented
scales,
enabling
the
tracking
strains,
mobile
genetic
elements,
or
genes.
Querying
a
genome
against
large
reference
database
can
easily
yield
thousands
matches
that
are
tedious
to
interpret
and
pose
computational
challenges.
We
developed
Graphite
uses
colored
de
Bruijn
graph
(cDBG)
paint
query
genomes,
selecting
local
best
along
full
length.
By
focusing
on
genomic
match
each
region,
reduces
number
while
providing
most
promising
leads
for
forensics.
When
applied
hundreds
Campylobacter
genomes
we
found
extensive
gene
sharing,
including
previously
undetected
C.
coli
plasmid
matched
jejuni
chromosome.
Together,
painting
using
cDBGs
as
enabled
by
Graphite,
reveal
new
biological
phenomena
mitigating
hurdles.
Язык: Английский