Natural Product Reports,
Год журнала:
2019,
Номер
37(4), С. 566 - 599
Опубликована: Дек. 11, 2019
We
review
known
evolutionary
mechanisms
underlying
the
overwhelming
chemical
diversity
of
bacterial
natural
products
biosynthesis,
focusing
on
enzyme
promiscuity
and
evolution
enzymatic
domains
that
enable
metabolic
traits.
Bioinformatics,
Год журнала:
2017,
Номер
33(20), С. 3202 - 3210
Опубликована: Июнь 16, 2017
Nonribosomally
synthesized
peptides
(NRPs)
are
natural
products
with
widespread
applications
in
medicine
and
biotechnology.
Many
algorithms
have
been
developed
to
predict
the
substrate
specificities
of
nonribosomal
peptide
synthetase
adenylation
(A)
domains
from
DNA
sequences,
which
enables
prioritization
dereplication,
integration
other
data
types
discovery
efforts.
However,
insufficient
training
a
lack
clarity
regarding
prediction
quality
impeded
optimal
use.
Here,
we
introduce
prediCAT,
new
phylogenetics-inspired
algorithm,
quantitatively
estimates
degree
predictability
each
A-domain.
We
then
systematically
benchmarked
all
on
newly
gathered,
independent
test
set
434
A-domain
showing
that
active-site-motif-based
outperform
whole-domain-based
methods.
Subsequently,
SANDPUMA,
powerful
ensemble
based
trained
versions
high-performing
algorithms,
significantly
outperforms
individual
Finally,
deployed
SANDPUMA
systematic
investigation
7635
Actinobacteria
genomes,
suggesting
NRP
chemical
diversity
is
much
higher
than
previously
estimated.
has
integrated
into
widely
used
antiSMASH
biosynthetic
gene
cluster
analysis
pipeline
also
available
as
an
open-source,
standalone
tool.SANDPUMA
freely
at
https://bitbucket.org/chevrm/sandpuma
docker
image
https://hub.docker.com/r/chevrm/sandpuma/
under
GNU
Public
License
3
(GPL3)[email protected]
or
[email protected]
Bioinformatics
online.
The
understanding
of
the
roles
gut
bacteria
in
fitness
and
vectorial
capacity
mosquitoes
that
transmit
malaria,
is
improving;
however,
factors
shaping
composition
structure
such
bacterial
communities
remain
elusive.
In
this
study,
a
high-throughput
16S
rRNA
gene
sequencing
was
conducted
to
understand
effect
developmental
stage,
feeding
status,
species,
geography
on
microbiota
two
main
Colombian
malaria
vectors,
Anopheles
nuneztovari
darlingi.
results
revealed
mosquito
followed
by
geographical
location,
are
more
important
determinants
than
species
or
adult
status.
Further,
they
showed
major
filter
for
environmental
colonization.
sampling
design
analytical
approach
study
allowed
untangle
influence
simultaneously
Latin-American
essential
aspect
vector
biocontrol
strategies.
Tropical
peatlands,
which
play
a
crucial
role
in
the
maintenance
of
different
ecosystem
services,
are
increasingly
drained
for
agriculture,
forestry,
peat
extraction
and
human
settlement
purposes.
The
present
study
investigated
differences
between
natural
sites
tropical
peatland
community
structure
soil
bacteria
archaea
their
potential
to
perform
nitrogen
transformation
processes.
results
indicate
significant
dissimilarities
bacterial
archaeal
communities
as
well
nirK,
nirS,
nosZ,
nifH
amoA
gene-possessing
microbial
communities.
reduced
denitrification
N
Polymers,
Год журнала:
2021,
Номер
13(12), С. 1989 - 1989
Опубликована: Июнь 17, 2021
Rubber
is
an
essential
part
of
our
daily
lives
with
thousands
rubber-based
products
being
made
and
used.
Natural
rubber
undergoes
chemical
processes
structural
modifications,
while
synthetic
rubber,
mainly
synthetized
from
petroleum
by-products
are
difficult
to
degrade
safely
sustainably.
The
most
prominent
group
biological
degraders
Actinobacteria.
degrading
Actinobacteria
contain
genes
or
oxygenase
known
as
latex
clearing
protein
(lcp).
a
polymer
consisting
isoprene,
each
containing
one
double
bond.
degradation
first
takes
place
when
lcp
enzyme
cleaves
the
isoprene
bond,
breaking
them
down
into
sole
carbon
energy
source
be
utilized
by
bacteria.
grow
in
diverse
environments,
gene
strains
have
been
detected
various
sources
including
soil,
water,
human,
animal,
plant
samples.
This
review
entails
occurrence,
physiology,
biochemistry,
molecular
characteristics
respect
its
ability,
discusses
possible
technological
applications
based
on
activity
for
treating
waste
more
environmentally
responsible
manner.
Molecules,
Год журнала:
2021,
Номер
26(15), С. 4504 - 4504
Опубликована: Июль 26, 2021
The
current
review
aims
to
summarise
the
biodiversity
and
biosynthesis
of
novel
secondary
metabolites
compounds,
phylum
Actinobacteria
diverse
range
produced
that
vary
depending
on
its
ecological
environments
they
inhabit.
creates
a
wide
bioactive
substances
can
be
great
value
public
health
pharmaceutical
industry.
literature
analysis
process
for
this
was
conducted
using
VOSviewer
software
tool
visualise
bibliometric
networks
most
relevant
databases
from
Scopus
database
in
period
between
2010
22
March
2021.
Screening
exploring
available
relating
extreme
ecosystems
inhabit
identify
new
strains
major
microorganism
class,
producing
unique
compounds.
knowledge
gained
these
studies
is
intended
encourage
scientists
natural
product
discovery
field
characterise
containing
various
gene
clusters
with
potential
clinical
applications.
It
evident
adapted
survive
represent
an
important
source
have
large
number
metabolite
biosynthetic
clusters.
They
synthesise
thousands
subordinate
different
biological
actions
such
as
anti-bacterial,
anti-parasitic,
anti-fungal,
anti-virus,
anti-cancer
growth-promoting
These
are
highly
significant
economically
due
their
applications
food,
nutrition
industries
thus
support
our
communities’
well-being.
PLoS ONE,
Год журнала:
2022,
Номер
17(1), С. e0262039 - e0262039
Опубликована: Янв. 12, 2022
Insights
into
biodiversity
and
trophic
webs
are
important
for
understanding
ecosystem
functions.
Although
the
surfaces
of
glaciers
one
most
productive
biologically
diverse
parts
cryosphere,
links
between
top
consumers,
their
diet
microbial
communities
poorly
understood.
In
this
study,
first
time
we
investigated
relationships
bacteria,
fungi
other
microeukaryotes
as
they
relate
to
tardigrades,
microscopic
metazoans
that
consumers
in
cryoconite,
a
rich
biogenic
sediment
found
on
glacier
surfaces.
Using
metabarcoding
(16S
rDNA
ITS1
fungi,
18S
microeukaryotes),
analyzed
community
structures
cryoconite
compared
them
with
both
fully
fed
starved
tardigrades.
The
structure
each
group
(bacteria,
microeukaryotes)
were
similar
within
host
(cryoconite,
tardigrades
tardigrades),
differed
significantly
groups,
indicated
by
redundancy
analyses.
relative
number
operational
taxonomic
units
(ZOTUs,
OTUs)
Shannon
index
Species
indicator
analysis
highlighted
taxa
typical
(potential
commensals),
like
bacteria
genera
Staphylococcus
Stenotrophomonas,
well
(likely
part
tardigrade
diet;
Flavobacterium
sp.,
Preussia
algae
Trebouxiophyceae
sp.).
Tardigrades
and,
being
hosts
microbes,
presence
can
enrich
microbiome
glaciers.
