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
Clinical Microbiology and Infection,
Год журнала:
2018,
Номер
24(4), С. 350 - 354
Опубликована: Янв. 5, 2018
BackgroundWhole
genome
sequence
(WGS)-based
strain
typing
finds
increasing
use
in
the
epidemiologic
analysis
of
bacterial
pathogens
both
public
health
as
well
more
localized
infection
control
settings.AimsThis
minireview
describes
methodologic
approaches
that
have
been
explored
for
WGS-based
and
considers
challenges
pitfalls
data
interpretation.SourcesPersonal
collection
relevant
publications.ContentWhen
applying
WGS
to
study
molecular
epidemiology
pathogens,
genomic
variability
between
strains
is
translated
into
measures
distance
by
determining
single
nucleotide
polymorphisms
core
alignments
or
indexing
allelic
variation
hundreds
thousands
genes,
assigning
types
unique
profiles.
Interpreting
isolate
relatedness
from
these
distances
highly
organism
specific,
attempts
establish
species-specific
cutoffs
are
unlikely
be
generally
applicable.
In
cases
where
polymorphism
gene
do
not
provide
resolution
necessary
accurate
assessment
inclusion
accessory
plasmid
sequences
may
additional
required
discrimination.ImplicationsAs
with
all
analysis,
realizing
full
potential
revolutionary
advances
requires
understanding
dealing
issues
related
fundamental
steps
generation
interpretation.
Philosophical Transactions of the Royal Society B Biological Sciences,
Год журнала:
2017,
Номер
372(1735), С. 20160424 - 20160424
Опубликована: Окт. 23, 2017
In
biological
systems,
evolutionary
innovations
can
spread
not
only
from
parent
to
offspring
(i.e.
vertical
transmission),
but
also
‘horizontally’
between
individuals,
who
may
or
be
related.
Nowhere
is
this
more
apparent
than
in
bacteria,
where
novel
ecological
traits
rapidly
within
and
species
through
horizontal
gene
transfer
(HGT).
This
important
process
predominantly
a
by-product
of
the
infectious
mobile
genetic
elements
(MGEs).
We
will
discuss
conditions
that
favour
by
HGT,
social
consequences
sharing
traits,
how
HGT
shaped
inherent
conflicts
bacteria
MGEs.
article
part
themed
issue
‘Process
pattern
cells
societies’.
Frontiers in Microbiology,
Год журнала:
2021,
Номер
12
Опубликована: Авг. 13, 2021
The
genus
Roseomonas
is
a
significant
group
of
bacteria
which
invariably
great
clinical
and
ecological
importance.
Previous
studies
have
shown
that
the
polyphyletic
in
nature.
Our
present
study
focused
on
generating
lucid
understanding
phylogenetic
framework
for
re-evaluation
reclassification
Roseomonas.
Phylogenetic
based
16S
rRNA
gene
92
concatenated
genes
suggested
heterogeneous,
forming
seven
major
groups.
Existing
species
were
subjected
to
an
array
genomic,
phenotypic,
chemotaxonomic
analyses
order
resolve
heterogeneity.
Genomic
similarity
indices
(
d
DDH
ANI)
indicated
members
well-defined
at
level.
Percentage
Conserved
Proteins
(POCP)
average
Amino
Acid
Identity
(AAI)
values
between
groups
other
interspersing
family
Acetobacteraceae
below
65
70%,
respectively.
pan-genome
evaluation
depicted
was
open
type
shared
958
core
genes.
This
claim
equally
supported
by
phenotypic
differences
Thus,
this
study,
we
propose
re-evaluate
reclassify
six
novel
genera
as
Pararoseomonas
gen.
nov.,
Falsiroseomonas
Paeniroseomonas
Plastoroseomonas
Neoroseomonas
Pseudoroseomonas
nov.
