Abstract
Natural
ecosystems
harbor
a
huge
reservoir
of
taxonomically
diverse
microbes
that
are
important
for
plant
growth
and
health.
The
vast
diversity
soil
microorganisms
their
complex
interactions
make
it
challenging
to
pinpoint
the
main
players
life
support
functions
can
provide
plants,
including
enhanced
tolerance
(a)biotic
stress
factors.
Designing
simplified
microbial
synthetic
communities
(SynComs)
helps
reduce
this
complexity
unravel
molecular
chemical
basis
interplay
specific
microbiome
functions.
While
SynComs
have
been
successfully
employed
dissect
or
reproduce
microbiome-associated
phenotypes,
assembly
reconstitution
these
often
based
on
generic
abundance
patterns
taxonomic
identities
co-occurrences
but
only
rarely
informed
by
functional
traits.
Here,
we
review
recent
studies
designing
reveal
common
principles
discuss
multidimensional
approaches
community
design.
We
propose
strategy
tailoring
design
integration
high-throughput
experimental
assays
with
strains
computational
genomic
analyses
capabilities.
Nature Communications,
Год журнала:
2025,
Номер
16(1)
Опубликована: Янв. 21, 2025
Abstract
Bacterial
type
VI
secretion
systems
(T6SSs)
are
puncturing
molecular
machines
that
transport
effector
proteins
to
kill
microbes,
manipulate
eukaryotic
cells,
or
facilitate
nutrient
uptake.
How
and
why
T6SS
effectors
differ
within
a
species
is
not
fully
understood.
Here,
we
applied
population
genetics
the
T6SSs
in
global
of
opportunistic
pathogen
Pseudomonas
aeruginosa
.
We
reveal
varying
occurrence
up
four
distinct
machines.
Moreover,
define
conserved
core
effectors,
likely
critical
for
biology
P.
,
accessory
can
exhibit
mutual
exclusivity
between
strains.
By
ancestral
reconstruction,
observed
dynamic
changes
gain
loss
genes
species’
evolutionary
history.
Our
work
highlights
potential
importance
intraspecific
diversity
bacterial
ecology
evolution.
Scientific Reports,
Год журнала:
2024,
Номер
14(1)
Опубликована: Март 19, 2024
Abstract
Klebsiella
aerogenes
is
an
emergent
pathogen
associated
with
outbreaks
of
carbapenem-resistant
strains.
To
date,
studies
focusing
on
K.
have
been
small-scale
and/or
geographically
restricted.
Here,
we
analyzed
the
epidemiology,
resistome,
virulome,
and
plasmidome
this
species
based
561
genomes,
spanning
all
continents.
Furthermore,
sequenced
four
new
strains
from
Brazil
(mostly
Amazon
region).
Dozens
STs
occur
worldwide,
but
pandemic
clones
ST93
ST4
prevailed
in
several
countries.
Almost
genomes
were
clinical,
however,
most
them
did
not
carry
ESBL
or
carbapenemases,
instead,
they
carried
chromosomal
alterations
(
omp
36,
amp
D,
G,
R)
resistance
to
β-lactams.
Integrons
also
identified,
presenting
gene
cassettes
yet
reported
bla
IMP,
VIM,
GES).
Considering
virulence
loci,
yersiniabactin
colibactin
operons
found
ICEKp10
element,
which
disseminated
STs,
as
well
incomplete
salmochelin
cluster.
In
contrast,
aerobactin
hypervirulence
trait
was
observed
only
one
ST432
genome.
Plasmids
common,
mainly
ColRNAI
replicon,
some
carrying
genes
mcr
,
TEM,
NDM,
KPC,
VIM)
(EAST1,
sen
B).
Interestingly,
172
different
presented
putative
plasmids
containing
colicin
gene.
Molecular Systems Biology,
Год журнала:
2024,
Номер
20(6), С. 702 - 718
Опубликована: Апрель 24, 2024
Abstract
The
type
VI
secretion
system
(T6SS)
is
an
important
mediator
of
microbe–microbe
and
microbe–host
interactions.
Gram-negative
bacteria
use
the
T6SS
to
inject
effectors
(T6Es),
which
are
usually
proteins
with
toxic
activity,
into
neighboring
cells.
Antibacterial
have
cognate
immunity
that
neutralize
self-intoxication.
Here,
we
applied
novel
structural
bioinformatic
tools
perform
systematic
discovery
functional
annotation
T6Es
their
from
a
dataset
17,920
T6SS-encoding
bacterial
genomes.
Using
clustering,
identified
517
putative
T6E
families,
outperforming
sequence-based
clustering.
We
developed
logistic
regression
model
reliably
quantify
protein–protein
interaction
new
T6E-immunity
pairs,
yielding
candidate
for
231
out
families.
used
sensitive
structure-based
yielded
annotations
51%
again
annotation.
Next,
validated
four
pairs
using
basic
experiments
in
E.
coli
.
In
particular,
showed
Pfam
domain
DUF3289
homolog
Colicin
M
DUF943
acts
as
its
protein.
Furthermore,
discovered
SleB,
lytic
transglycosylase,
specific
glutamate
catalytic
residue.
Overall,
this
study
applies
pair
discovery,
provides
extensive
database
annotated
pairs.
Frontiers in Microbiology,
Год журнала:
2024,
Номер
14
Опубликована: Янв. 8, 2024
Campylobacteriosis,
a
prevalent
foodborne
gastrointestinal
infection
in
Europe,
is
primarily
caused
by
Campylobacter
jejuni
and
coli
,
with
rising
global
concerns
over
antimicrobial
resistance
these
species.
This
study
comprehensively
investigates
133
human-origin
spp.
strains
(102
C.
31
)
collected
Italy
from
2013
to
2021.
The
predominant
Multilocus
Sequence
Typing
Clonal
complexes
(CCs)
were
ST-21
CC
ST-206
ST-828
.
Ciprofloxacin
tetracycline
resistance,
mainly
attributed
GyrA
(T86I)
mutation
tet
(O)
presence,
prevalent,
while
erythromycin
was
associated
23S
rRNA
gene
(A2075G),
particularly
exhibiting
multidrug-resistant
pattern
CipTE.
Notable
disparities
virulence
factors
among
observed,
higher
abundance
compared
Notably,
specific
sequence
types,
including
ST-21,
ST-5018,
ST-1263,
demonstrated
significantly
elevated
counts
of
genes.
finding
underscores
the
significance
considering
both
species
strain-level
variations
factor
profiles,
shedding
light
on
potential
differences
pathogenicity
clinical
outcomes
distinct
lineages.
plasmids
classified
into
three
groups
comprising
pVir-like
pTet-like
families,
diversity
importance
early
detection
through
Whole
Genome
Sequencing
identify
emergent
virulence,
resistance/virulence
plasmids,
new
markers.
approach
provides
actionable
public
health
data,
supporting
development
robust
surveillance
programs
Italy.
Molecular Plant Pathology,
Год журнала:
2024,
Номер
25(1)
Опубликована: Янв. 1, 2024
Stenotrophomonas
rhizophila
CFBP13503
is
a
seedborne
commensal
bacterial
strain,
which
efficiently
transmitted
to
seedlings
and
can
outcompete
the
phytopathogenic
bacterium
Xanthomonas
campestris
pv.
(Xcc8004).
The
type
VI
secretion
system
(T6SS),
an
interference
contact-dependent
mechanism,
critical
component
of
interbacterial
competition.
involvement
T6SS
S.
in
inhibition
Xcc8004
growth
seed-to-seedling
transmission
was
assessed.
cluster
nine
putative
effectors
were
identified.
Deletion
two
structural
genes,
hcp
tssB,
abolished
competitive
advantage
against
vitro.
population
sizes
these
species
monitored
after
inoculation
radish
seeds
with
mixtures
either
wild-type
(wt)
strain
or
isogenic
mutant.
A
significant
decrease
size
observed
during
confrontation
wt
comparison
T6SS-deletion
mutants
germinated
seedlings.
We
found
that
distribution
among
835
genomes
genus
scarce.
In
contrast,
all
available
genomes,
clusters
are
widespread
mainly
belong
group
i4.
conclusion,
involved
antibiosis
reduces
seedling
radish.
this
complex
could
make
it
possible
exploit
strains
as
biocontrol
agents
X.
campestris.
Nucleic Acids Research,
Год журнала:
2024,
Номер
53(D1), С. D871 - D877
Опубликована: Окт. 29, 2024
Abstract
With
the
escalating
crisis
of
bacterial
multidrug
resistance,
anti-virulence
therapeutic
strategies
have
emerged
as
a
highly
promising
alternative
to
conventional
antibiotic
treatments.
Anti-virulence
compounds
are
specifically
designed
target
virulence
factors
(VFs),
disarming
pathogens
without
affecting
growth
and
thus
reduce
selective
pressure
for
resistance
development.
However,
due
complexity
pathogenesis,
no
small
molecules
been
approved
clinical
use
far,
despite
documentation
hundreds
potential
candidates.
To
provide
valuable
reference
resources
drug
design,
repurposing,
selection,
factor
database
(VFDB,
http://www.mgc.ac.cn/VFs/)
has
systematically
collected
public
data
on
through
extensive
literature
mining,
further
integrated
this
information
with
its
existing
knowledge
VFs.
date,
VFDB
curated
comprehensive
dataset
902
across
17
superclasses
reported
by
262
studies
worldwide.
By
cross-linking
current
VFs
relevant
(e.g.
classification,
chemical
structure,
molecular
targets
mechanisms
action),
aims
bridge
gap
between
chemists
microbiologists,
providing
crucial
insights
development
innovative
effective
antibacterial
therapies
combat
infections
address
resistance.
Frontiers in Microbiology,
Год журнала:
2023,
Номер
14
Опубликована: Авг. 17, 2023
The
type
VI
secretion
system
(T6SS)
is
a
contact-dependent
contractile
multiprotein
apparatus
widely
distributed
in
Gram-negative
bacteria.
These
systems
can
deliver
different
effector
proteins
into
target
bacterial
and/or
eukaryotic
cells,
contributing
to
the
environmental
fitness
and
virulence
of
many
pathogens.
Salmonella
harbors
five
T6SSs
encoded
genomic
islands.
T6SS
Pathogenicity
Island
6
(SPI-6)
contributes
competition
with
host
microbiota
its
interaction
infected
cells.
Despite
relevance,
information
regarding
total
number
within
SPI-6
distribution
among
enterica
serotypes
limited.
In
this
work,
we
performed
bioinformatic
comparative
genomics
analyses
gene
cluster
expand
our
knowledge
repertoire
global
these
effectors
Salmonella.
analysis
curated
dataset
60
genomes
from
Secret6
database
revealed
presence
23
new
putative
effector/immunity
protein
(E/I)
modules.
were
concentrated
variable
regions
1
3
(VR1-3)
cluster.
VR1-2
enriched
candidate
predicted
peptidoglycan
hydrolase
activity,
while
VR3
was
Rhs
family
C-terminal
extensions
DNase,
RNase,
deaminase,
or
ADP-ribosyltransferase
activity.
A
known
NCBI
that
are
differentially
serotypes.
While
some
present
over
200
serotypes,
others
found
less
than
dozen.
hierarchical
clustering
identified
distinct
profiles
effectors,
highlighting
diversity
repertoires
enterica.
existence
suggests
combinations
may
have
differential
impact
on
pathogenic
potential
strains.
Proteins
secreted
by
Gram-negative
bacteria
are
tightly
linked
to
the
virulence
and
adaptability
of
these
microbes
environmental
changes.
Accurate
identification
such
proteins
can
facilitate
investigations
infections
diseases
caused
bacterial
pathogens.
However,
current
bioinformatic
methods
for
predicting
substrate
have
limited
computational
efficiency
application
scope
on
a
genome-wide
scale.
Here,
we
propose
novel
deep-learning-based
framework-DeepSecE-for
simultaneous
inference
multiple
distinct
groups
produced
bacteria.
DeepSecE
remarkably
improves
their
classification
from
nonsecreted
using
pretrained
protein
language
model
transformer,
achieving
macro-average
accuracy
0.883
5-fold
cross-validation.
Performance
benchmarking
suggests
that
achieves
competitive
performance
with
state-of-the-art
binary
predictors
specialized
individual
types
substrates.
The
attention
mechanism
corroborates
salient
patterns
motifs
at
N
or
C
termini
sequences.
Using
this
pipeline,
further
investigate
prediction
taxonomic
distribution
across
~1,000
genomes.
present
analysis
demonstrates
has
major
potential
discovery
disease-associated
in
diverse
range
An
online
web
server
is
also
publicly
available
predict
explore
various
via
input
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