Frontiers in Microbiology,
Год журнала:
2018,
Номер
9
Опубликована: Май 25, 2018
Metataxonomic
16S
rDNA
based
studies
are
a
commonplace
and
useful
tool
in
the
research
of
microbiome,
but
they
do
not
provide
full
investigative
power
metagenomics
metatranscriptomics
for
revealing
functional
potential
microbial
communities.
However,
use
metagenomic
metatranscriptomic
technologies
is
hindered
by
high
costs
skills
barrier
necessary
to
generate
interpret
data.
To
address
this,
Phylogenetic
Investigation
Communities
Reconstruction
Unobserved
States
(PICRUSt)
was
developed
inferring
an
observed
microbiome
profile,
on
This
allows
inferences
be
made
from
metataxonomic
with
little
extra
work
or
cost,
its
accuracy
relies
availability
completely
sequenced
genomes
representative
organisms
community
being
investigated.
The
rumen
example
traditionally
underrepresented
genome
sequence
databases,
recent
efforts
projects
such
as
Global
Rumen
Census
Hungate
1000
have
resulted
wide
sampling
profiles
almost
500
fully
this
environment.
Using
information,
we
"CowPI,"
focused
version
PICRUSt
provided
wider
scientific
study
microbiome.
We
evaluated
CowPI
using
two
datasets
microbiome:
one
generated
other
rRNA
where
corresponding
data
also
available.
show
that
predicted
better
match
estimates
both
meta-genomic
transcriptomic
than
PICRUSt,
capture
higher
degree
genetic
variation
larger
pangenomes
organisms.
Nonetheless,
whilst
closer
terms
predictive
there
were
differences
when
compared
metatranscriptome
so
recommend,
possible,
should
replace
approaches.
can
accessed
at
http://www.cowpi.org
Nature Communications,
Год журнала:
2024,
Номер
15(1)
Опубликована: Янв. 16, 2024
Abstract
What
a
strain
is
and
how
many
strains
make
up
natural
bacterial
population
remain
elusive
concepts
despite
their
apparent
importance
for
assessing
the
role
of
intra-population
diversity
in
disease
emergence
or
response
to
environmental
perturbations.
To
advance
these
concepts,
we
sequenced
138
randomly
selected
Salinibacter
ruber
isolates
from
two
solar
salterns
assessed
genomes
against
companion
short-read
metagenomes
same
samples.
The
distribution
genome-aggregate
average
nucleotide
identity
(ANI)
values
among
revealed
bimodal
distribution,
with
four-fold
lower
occurrence
between
99.2%
99.8%
relative
ANI
>99.8%
<99.2%,
revealing
“gap”
sequence
space
within
species.
Accordingly,
used
this
gap
define
genomovars
higher
value
>99.99%
shared
gene-content
>99.0%
strains.
Using
thresholds
extrapolating
metagenomic
reads
each
genomovar
uniquely
recruited,
estimated
that
–although
our
represented
about
80%
Sal.
population–
total
one
saltern
pond
composed
5,500
11,000
genomovars,
great
majority
which
appear
be
rare
in-situ.
These
data
also
most
frequently
recovered
isolate
lab
media
was
often
not
abundant
in-situ,
suggesting
cultivation
biases
are
significant,
even
cases
procedures
thought
robust.
methodology
outlined
here
should
represent
useful
guide
future
microdiversity
surveys
additional
microbial
Nature Ecology & Evolution,
Год журнала:
2024,
Номер
8(5), С. 986 - 998
Опубликована: Март 5, 2024
Abstract
Horizontal
gene
transfer,
the
exchange
of
genetic
material
through
means
other
than
reproduction,
is
a
fundamental
force
in
prokaryotic
genome
evolution.
Genomic
persistence
horizontally
transferred
genes
has
been
shown
to
be
influenced
by
both
ecological
and
evolutionary
factors.
However,
there
limited
availability
information
about
species
habitats
from
which
they
were
isolated,
prevented
deeper
exploration
contributions
horizontal
transfer.
Here
we
focus
on
transfers
detected
comparison
individual
trees
tree,
assessing
distribution
gene-exchanging
prokaryotes
across
over
million
environmental
sequencing
samples.
By
analysing
transfer
events,
show
distinct
functional
profiles
for
recent
versus
old
events.
Although
most
are
part
accessory
genome,
earlier
evolution
tend
more
ubiquitous
within
present-day
species.
We
find
that
co-occurring,
interacting
high-abundance
genes.
Finally,
host-associated
specialist
likely
with
species,
whereas
found
different
have
similar
rates
irrespective
their
preferred
habitat.
Our
study
covers
an
unprecedented
scale
integrated
information,
highlighting
broad
eco-evolutionary
trends.
Frontiers in Microbiology,
Год журнала:
2018,
Номер
9
Опубликована: Май 25, 2018
Metataxonomic
16S
rDNA
based
studies
are
a
commonplace
and
useful
tool
in
the
research
of
microbiome,
but
they
do
not
provide
full
investigative
power
metagenomics
metatranscriptomics
for
revealing
functional
potential
microbial
communities.
However,
use
metagenomic
metatranscriptomic
technologies
is
hindered
by
high
costs
skills
barrier
necessary
to
generate
interpret
data.
To
address
this,
Phylogenetic
Investigation
Communities
Reconstruction
Unobserved
States
(PICRUSt)
was
developed
inferring
an
observed
microbiome
profile,
on
This
allows
inferences
be
made
from
metataxonomic
with
little
extra
work
or
cost,
its
accuracy
relies
availability
completely
sequenced
genomes
representative
organisms
community
being
investigated.
The
rumen
example
traditionally
underrepresented
genome
sequence
databases,
recent
efforts
projects
such
as
Global
Rumen
Census
Hungate
1000
have
resulted
wide
sampling
profiles
almost
500
fully
this
environment.
Using
information,
we
"CowPI,"
focused
version
PICRUSt
provided
wider
scientific
study
microbiome.
We
evaluated
CowPI
using
two
datasets
microbiome:
one
generated
other
rRNA
where
corresponding
data
also
available.
show
that
predicted
better
match
estimates
both
meta-genomic
transcriptomic
than
PICRUSt,
capture
higher
degree
genetic
variation
larger
pangenomes
organisms.
Nonetheless,
whilst
closer
terms
predictive
there
were
differences
when
compared
metatranscriptome
so
recommend,
possible,
should
replace
approaches.
can
accessed
at
http://www.cowpi.org
