Microbiology,
Journal Year:
2019,
Volume and Issue:
165(12), P. 1252 - 1264
Published: June 11, 2019
The
rationale
of
our
bioprospecting
campaigns
is
that
the
extremobiosphere,
particularly
deep
sea
and
hyper-arid
deserts,
harbours
undiscovered
biodiversity
likely
to
express
novel
chemistry
biocatalysts
thereby
providing
opportunities
for
therapeutic
drug
industrial
process
development.We
have
focused
on
actinobacteria
because
their
frequent
role
as
keystone
species
in
soil
ecosystems
unrivalled
track
record
a
source
bioactive
compounds.Population
numbers
diversity
extremobiosphere
are
traditionally
considered
be
low,
although
they
often
comprise
dominant
bacterial
biota.Recent
metagenomic
evaluation
'the
uncultured
microbial
majority'
has
now
revealed
enormous
taxonomic
among
'dark'
'rare'
samples
diverse
sediments
from
depths
Mariana
Trench
soils
heights
Central
Andes.The
application
innovative
culture
screening
options
emphasize
rigorous
dereplication
at
each
stage
analysis,
strain
prioritization
identify
'gifted'
organisms,
been
deployed
detect
characterize
hit
compounds
sought-after
catalysts
this
hitherto
untapped
resource.The
rewards
include
first-in-a-class
chemical
entities
with
modes
action,
well
growing
seed
bank
represents
potentially
biotechnological
innovation.
Nucleic Acids Research,
Journal Year:
2019,
Volume and Issue:
47(W1), P. W81 - W87
Published: April 17, 2019
Abstract
Secondary
metabolites
produced
by
bacteria
and
fungi
are
an
important
source
of
antimicrobials
other
bioactive
compounds.
In
recent
years,
genome
mining
has
seen
broad
applications
in
identifying
characterizing
new
compounds
as
well
metabolic
engineering.
Since
2011,
the
‘antibiotics
secondary
metabolite
analysis
shell—antiSMASH’
(https://antismash.secondarymetabolites.org)
assisted
researchers
this,
both
a
web
server
standalone
tool.
It
established
itself
most
widely
used
tool
for
analysing
biosynthetic
gene
clusters
(BGCs)
bacterial
fungal
sequences.
Here,
we
present
entirely
redesigned
extended
version
5
antiSMASH.
antiSMASH
adds
detection
rules
encoding
biosynthesis
acyl-amino
acids,
β-lactones,
RiPPs,
RaS-RiPPs,
polybrominated
diphenyl
ethers,
C-nucleosides,
PPY-like
ketones
lipolanthines.
For
type
II
polyketide
synthase-encoding
clusters,
now
offers
more
detailed
predictions.
The
HTML
output
visualization
been
to
improve
navigation
visual
representation
annotations.
We
have
again
improved
runtime
steps,
making
it
possible
deliver
comprehensive
annotations
genomes
within
few
minutes.
A
file
standard
JavaScript
object
notation
(JSON)
format
is
aimed
at
downstream
tools
that
process
results
programmatically.
Nucleic Acids Research,
Journal Year:
2021,
Volume and Issue:
49(W1), P. W29 - W35
Published: April 19, 2021
Abstract
Many
microorganisms
produce
natural
products
that
form
the
basis
of
antimicrobials,
antivirals,
and
other
drugs.
Genome
mining
is
routinely
used
to
complement
screening-based
workflows
discover
novel
products.
Since
2011,
"antibiotics
secondary
metabolite
analysis
shell—antiSMASH"
(https://antismash.secondarymetabolites.org/)
has
supported
researchers
in
their
microbial
genome
tasks,
both
as
a
free-to-use
web
server
standalone
tool
under
an
OSI-approved
open-source
license.
It
currently
most
widely
for
detecting
characterising
biosynthetic
gene
clusters
(BGCs)
bacteria
fungi.
Here,
we
present
updated
version
6
antiSMASH.
antiSMASH
increases
number
cluster
types
from
58
71,
displays
modular
structure
multi-modular
BGCs,
adds
new
BGC
comparison
algorithm,
allows
integration
results
prediction
tools,
more
effectively
detects
tailoring
enzymes
RiPP
clusters.
Natural Product Reports,
Journal Year:
2019,
Volume and Issue:
36(7), P. 960 - 980
Published: Jan. 1, 2019
Covering:
up
to
2019Landmark
advances
in
bioinformatics
tools
have
recently
enhanced
the
field
of
natural
products
research,
putting
today's
product
chemists
enviable
position
being
able
perform
efficient
targeting/discovery
previously
undescribed
molecules
by
expediting
prioritization
isolation
workflow.
Among
these
advances,
MS/MS
molecular
networking
has
appeared
as
a
promising
approach
dereplicate
complex
mixtures,
leading
real
revolution
"art
isolation"
accelerating
pace
research
this
field.
This
review
illustrates
through
selected
cornerstone
studies
new
thinking
drawing
parallel
between
different
underlying
philosophies
behind
use
targeting
products.
Journal of Applied Microbiology,
Journal Year:
2019,
Volume and Issue:
128(3), P. 630 - 657
Published: July 16, 2019
The
prevalence
of
multidrug-resistant
microbial
pathogens
due
to
the
continued
misuse
and
overuse
antibiotics
in
agriculture
medicine
is
raising
prospect
a
return
preantibiotic
days
at
time
diminishing
numbers
drug
leads.
good
news
that
an
increased
understanding
nature
extent
diversity
natural
habitats
coupled
with
application
new
technologies
microbiology
chemistry
opening
up
strategies
search
for
specialized
products
therapeutic
properties.
This
review
explores
premise
harsh
environmental
conditions
extreme
biomes,
notably
deserts,
permafrost
soils
deep-sea
sediments
select
micro-organisms,
especially
actinobacteria,
cyanobacteria
fungi,
potential
synthesize
druggable
molecules.
There
evidence
over
past
decade
micro-organisms
adapted
life
are
rich
source
metabolites.
Extreme
by
their
very
tend
be
fragile
hence
there
need
conserve
those
known
hot-spots
novel
gifted
needed
drive
discovery
campaigns
innovative
biotechnology.
also
provides
overview
microbial-derived
molecules
biological
activities
focusing
on
period
from
2010
until
2018,
this
186
structures
were
isolated
129
representatives
taxa
recovered
habitats.
Proceedings of the National Academy of Sciences,
Journal Year:
2022,
Volume and Issue:
119(42)
Published: Oct. 10, 2022
Bacterial
secondary
metabolites
are
a
major
source
of
antibiotics
and
other
bioactive
compounds.
In
microbial
communities,
these
molecules
can
mediate
interspecies
interactions
responses
to
environmental
change.
Despite
the
importance
in
human
health
ecology,
little
is
known
about
their
roles
regulation
context
multispecies
communities.
simplified
model
rhizosphere
composed
Bacillus
cereus
,
Flavobacterium
johnsoniae
Pseudomonas
koreensis
we
show
that
dynamics
metabolism
depend
on
community
species
composition
interactions.
Comparative
metatranscriptomics
metametabolomics
reveal
abundance
transcripts
biosynthetic
gene
clusters
(BGCs)
metabolomic
molecular
features
differ
between
monocultures
or
dual
cultures
tripartite
community.
both
two-
three-member
cocultures,
P.
modified
expression
BGCs
for
zwittermicin,
petrobactin,
B.
F.
johnsoniae,
whereas
BGC
transcriptional
response
itself
was
minimal.
Pairwise
cocultures
with
displayed
unique
appear
be
derivatives
lokisin,
suggesting
metabolic
handoffs
species.
Deleting
koreenceine,
another
metabolite,
altered
transcript
metabolite
profiles
across
community,
including
substantial
up-regulation
petrobactin
bacillibactin
koreenceine
represses
siderophore
production.
Results
from
this
bacterial
chemical
output
identity
capacity
coculture
partners,
microbiome
may
shape
nature.
Nucleic Acids Research,
Journal Year:
2023,
Volume and Issue:
52(D1), P. D586 - D589
Published: Oct. 30, 2023
Abstract
Many
microorganisms
produce
natural
products
that
are
frequently
used
in
the
development
of
medicines
and
crop
protection
agents.
Genome
mining
has
evolved
into
a
prominent
method
to
access
this
potential.
antiSMASH
is
most
popular
tool
for
task.
Here
we
present
version
4
database,
providing
biosynthetic
gene
clusters
detected
by
7.1
publicly
available,
dereplicated,
high-quality
microbial
genomes
via
an
interactive
graphical
user
interface.
In
4,
database
contains
231
534
high
quality
BGC
regions
from
592
archaeal,
35
726
bacterial
236
fungal
available
at
https://antismash-db.secondarymetabolites.org/.
Nucleic Acids Research,
Journal Year:
2019,
Volume and Issue:
unknown
Published: Oct. 10, 2019
Microbial
secondary
metabolism
is
a
reservoir
of
bioactive
compounds
immense
biotechnological
and
biomedical
potential.
The
biosynthetic
machinery
responsible
for
the
production
these
metabolites
(SMs)
(also
called
natural
products)
often
encoded
by
collocated
groups
genes
gene
clusters
(BGCs).
High-throughput
genome
sequencing
both
isolates
metagenomic
samples
combined
with
development
specialized
computational
workflows
enabling
systematic
identification
BGCs
discovery
novel
SMs.
In
order
to
advance
exploration
microbial
its
diversity,
we
developed
largest
publicly
available
database
predicted
experimentally
verified
BGCs,
Integrated
Genomes
Atlas
Biosynthetic
Clusters
(IMG-ABC)
(https://img.jgi.doe.gov/abc-public).
Here
describe
first
major
content
update
IMG-ABC
knowledgebase,
since
initial
release
in
2015,
refreshing
BGC
prediction
pipeline
latest
version
antiSMASH
(v5)
as
well
presenting
data
context
underlying
environmental
metadata
sourced
from
GOLD
(https://gold.jgi.doe.gov/).
This
has
greatly
improved
quality
expanded
types
compared
previous
version.
Accounts of Chemical Research,
Journal Year:
2021,
Volume and Issue:
54(6), P. 1374 - 1384
Published: Feb. 18, 2021
The
total
synthesis
of
structurally
complex
natural
products
has
challenged
and
inspired
generations
chemists
remains
an
exciting
area
active
research.
Despite
their
history
as
privileged
bioactivity-rich
scaffolds,
the
use
in
drug
discovery
waned.
This
shift
is
driven
by
relatively
low
abundance
hindering
isolation
from
sources
challenges
presented
synthesis.
Recent
developments
biocatalysis
have
resulted
application
enzymes
for
construction
molecules.
From
inception
Narayan
lab
2015,
we
focused
on
harnessing
exquisite
selectivity
alongside
contemporary
small
molecule-based
approaches
to
enable
concise
chemoenzymatic
routes
products.We
various
families
that
perform
selective
oxidation
reactions.
For
example,
targeted
xyloketal
through
a
strategy
relies
chemo-
site-selective
biocatalytic
hydroxylation.
Members
family
are
characterized
polycyclic
ketal
cores
demonstrate
potent
neurological
activity.
We
envisioned
assembling
representative
product
(xyloketal
D)
involving
biocatalytically
generated