Microbiome Research Reports,
Год журнала:
2024,
Номер
3(2)
Опубликована: Март 27, 2024
Background:
The
role
of
the
urobiome
in
health
and
disease
remains
an
understudied
area
compared
to
rest
human
microbiome.
Enhanced
culturing
techniques
next-generation
sequencing
technologies
have
identified
as
untapped
source
potentially
novel
antimicrobials.
aim
this
study
was
screen
for
genes
encoding
bacteriocin
production.
Methods:
genomes
181
bacterial
isolates
were
screened
silico
presence
gene
clusters
using
mining
tool
BAGEL4
secondary
metabolite
screening
antiSMASH7.
Results:
From
these
isolates,
initial
263
areas
interest
identified,
manually
annotated,
evaluated
potential
clusters.
This
resulted
32
containing
80
clusters,
which
72%
class
II,
13.75%
III,
8.75%
I,
5%
unclassified
bacteriocins.
Conclusion:
Overall,
53
variants
discovered,
including
nisin,
gassericin,
ubericin,
colicins.
Briefings in Bioinformatics,
Год журнала:
2024,
Номер
25(4)
Опубликована: Май 23, 2024
Abstract
How
to
resolve
the
metabolic
dark
matter
of
microorganisms
has
long
been
a
challenging
problem
in
discovering
active
molecules.
Diverse
omics
tools
have
developed
guide
discovery
and
characterization
various
microbial
metabolites,
which
make
it
gradually
possible
predict
overall
metabolites
for
individual
strains.
The
combinations
multi-omic
analysis
effectively
compensates
shortcomings
current
studies
that
focus
only
on
single
or
broad
class
metabolites.
In
this
review,
we
systematically
update,
categorize
sort
out
different
prediction
last
five
years
appeal
combination
understanding
nature
microbes.
First,
provide
general
survey
updated
databases,
webservers,
software
based
genomics,
transcriptomics,
proteomics,
metabolomics,
respectively.
Then,
discuss
essentiality
integration
multi-omics
data
strains
communities,
as
well
stressing
other
techniques,
such
systems
biology
methods
data-driven
algorithms.
Finally,
identify
key
challenges
trends
developing
more
comprehensive
diverse
contribute
human
health
disease
treatment.
Antimicrobial
peptides
(AMPs)
are
short,
usually
cationic
with
an
amphiphilic
structure,
which
allows
them
to
easily
bind
and
interact
the
cellular
membranes
of
viruses,
bacteria,
fungi,
other
pathogens.
Bacterial
AMPs,
or
bacteriocins,
can
be
produced
from
Gram-negative
Gram-positive
bacteria
via
ribosomal
synthesis
eliminate
competing
organisms.
AMPs
vital
in
addressing
increasing
antibiotic
resistance
various
pathogens,
potentially
serving
as
alternative
ineffective
antibiotics.
Bacteriocins
have
a
narrow
spectrum
action,
making
highly
specific
antibacterial
compounds
that
target
particular
bacterial
This
review
covers
two
main
groups
bacteriocins
by
their
modes
classification,
sources
positive
effects
they
play
on
human
body,
limitations
future
perspectives
Journal of Advanced Research,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 1, 2025
Antimicrobial
peptides
(AMPs)
present
a
promising
avenue
to
combat
the
growing
threat
of
antibiotic
resistance.
The
ruminant
gastrointestinal
microbiome
serves
as
unique
ecosystem
that
offers
untapped
potential
for
AMP
discovery.
Organic & Biomolecular Chemistry,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 1, 2025
We
heterologously
produced
a
type
II
lasso
peptide
gene
cluster
that
was
mined
from
Streptacidiphilus
jiangxiensis
in
E.
coli
.
Streptacidin
is
the
first
documented
to
maintain
its
3D
structure
with
methionine
as
steric
lock.
Microbial Cell Factories,
Год журнала:
2025,
Номер
24(1)
Опубликована: Янв. 31, 2025
Antibiotics
have
been
saving
countless
lives
from
deadly
infectious
diseases,
which
we
now
often
take
for
granted.
However,
are
currently
witnessing
a
significant
rise
in
the
emergence
of
multidrug-resistant
(MDR)
bacteria,
making
these
infections
increasingly
difficult
to
treat
hospitals.
The
discovery
and
development
new
antibiotic
has
slowed,
largely
due
reduced
profitability,
as
antibiotics
lose
effectiveness
quickly
pathogenic
bacteria
evolve
into
MDR
strains.
To
address
this
challenge,
metabolic
engineering
recently
become
crucial
developing
efficient
enzymes
cell
factories
capable
producing
both
existing
wide
range
derivatives
analogs.
In
paper,
review
recent
tools
strategies
synthetic
biology
production
antibiotics,
their
derivatives,
analogs,
along
with
representative
examples.
These
offer
promising
potential
revitalize
providing
renewed
hope
humanity's
fight
against
bacteria.
ACS Synthetic Biology,
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 25, 2025
Human
health
is
greatly
influenced
by
the
gut
microbiota
and
imbalance
can
lead
to
development
of
diseases.
It
widely
acknowledged
that
interaction
bacteria
within
competitive
ecosystems
their
specialized
metabolites,
which
act,
e.g.,
as
antibacterials
or
siderophores.
However,
our
understanding
occurrence
impact
such
natural
products
in
human
microbiome
remains
very
limited.
As
arylthiazole
siderophores
are
an
emerging
family
growth-promoting
molecules
pathogenic
bacteria,
we
analyzed
a
metagenomic
data
set
from
thereby
identified
bil-BGC,
originates
uncultured
Bilophila
strain.
Through
gene
synthesis
BGC
assembly,
heterologous
expression
mutasynthetic
experiments,
discovered
bilothiazoles
A–F.
While
established
activities
related
indicate
involvement
metal-binding
-uptake,
could
promote
growth
strains,
also
found
antibiotic
activity
for
some
bilothiazoles.
This
supported
biosensor-experiments,
where
C
E
show
PrecA-suppressing
activity,
while
bilothiazole
F
induces
PblaZ,
biosensor
characteristic
β-lactam
antibiotics.
These
findings
serve
starting
point
investigating
role
pathogenicity
species
gut.
Chemical Reviews,
Год журнала:
2025,
Номер
unknown
Опубликована: Март 21, 2025
Synthetic
biology
has
played
an
important
role
in
the
renaissance
of
natural
products
research
during
post-genomics
era.
The
development
and
integration
new
tools
have
transformed
workflow
product
discovery
engineering,
generating
multidisciplinary
interest
field.
In
this
review,
we
summarize
recent
developments
biosynthesis
from
three
different
aspects.
First,
advances
bioinformatics,
experimental,
analytical
to
identify
associated
with
predicted
biosynthetic
gene
clusters
(BGCs)
will
be
covered.
This
followed
by
extensive
review
on
heterologous
expression
bacterial,
fungal
plant
organisms.
native
host-independent
paradigm
identification,
pathway
characterization,
enzyme
is
where
synthetic
most
prominent
role.
Lastly,
strategies
engineer
pathways
for
structural
diversification
complexity
generation
discussed,
including
assembly-line
megasynthase
precursor-directed
modification,
combinatorial
biosynthesis.
Nature Communications,
Год журнала:
2025,
Номер
16(1)
Опубликована: Март 28, 2025
The
human
microbiome
produces
diverse
metabolites
that
influence
host
health,
yet
the
chemical
landscape
of
ribosomally
synthesized
and
post-translationally
modified
peptides
(RiPPs)-a
versatile
class
bioactive
compounds-remains
underexplored.
Here,
we
conduct
a
large-scale
biosynthetic
analysis
306,481
microbial
genomes
from
human-associated
microbiomes,
uncovering
broad
array
yet-to-be-discovered
RiPPs.
These
RiPPs
are
distributed
across
various
body
sites
but
show
specific
enrichment
in
gut
oral
microbiome.
Big
data
omics
reveals
numerous
RiPP
families
inversely
related
to
diseases,
suggesting
their
potential
protective
effects
on
health.
For
proof
principle
study,
apply
synthetic-bioinformatic
natural
product
(syn-BNP)
approach
chemically
synthesize
nine
autoinducing
(AIPs)
for
vitro
ex
vivo
assay.
Our
findings
reveal
five
AIPs
effectively
inhibit
biofilm
formation
disease-associated
pathogens.
Furthermore,
when
testing
microbiota
mice
with
inflammatory
bowel
disease,
observe
two
can
regulate
community
reduce
harmful
species.
highlight
vast
regulating
communities
maintaining
emphasizing
therapeutic
development.
