Frontiers in Microbiology,
Journal Year:
2021,
Volume and Issue:
12
Published: March 23, 2021
Metagenomics
is
a
segment
of
conventional
microbial
genomics
dedicated
to
the
sequencing
and
analysis
combined
genomic
DNA
entire
environmental
samples.
The
most
critical
step
metagenomic
data
reconstruction
individual
genes
genomes
microorganisms
in
communities
using
assemblers
–
computational
programs
that
put
together
small
fragments
sequenced
generated
by
instruments.
Here,
we
describe
challenges
assembly,
wide
spectrum
applications
which
assemblies
were
used
better
understand
ecology
evolution
ecosystems,
present
one
efficient
assemblers,
SPAdes
was
upgraded
become
applicable
for
metagenomics.
Scientific Reports,
Journal Year:
2021,
Volume and Issue:
11(1)
Published: Feb. 4, 2021
Abstract
In
this
paper
we
compared
taxonomic
results
obtained
by
metataxonomics
(16S
rRNA
gene
sequencing)
and
metagenomics
(whole
shotgun
metagenomic
to
investigate
their
reliability
for
bacteria
profiling,
studying
the
chicken
gut
as
a
model
system.
The
experimental
conditions
included
two
compartments
of
gastrointestinal
tracts
sampling
times.
We
relative
abundance
distributions
with
sequencing
strategies
then
tested
capability
distinguish
conditions.
showed
that
16S
detects
only
part
microbiota
community
revealed
sequencing.
Specifically,
when
sufficient
number
reads
is
available,
Shotgun
has
more
power
identify
less
abundant
taxa
than
Finally,
genera
detected
are
biologically
meaningful,
being
able
discriminate
between
much
both
strategies.
Science,
Journal Year:
2020,
Volume and Issue:
369(6503), P. 582 - 587
Published: June 8, 2020
The
coronavirus
disease
2019
(COVID-19)
pandemic
caused
by
severe
acute
respiratory
syndrome
2
(SARS-CoV-2)
has
spread
globally,
with
>365,000
cases
in
California
as
of
17
July
2020.
We
investigated
the
genomic
epidemiology
SARS-CoV-2
Northern
from
late
January
to
mid-March
2020,
using
samples
36
patients
spanning
nine
counties
and
Grand
Princess
cruise
ship.
Phylogenetic
analyses
revealed
cryptic
introduction
at
least
seven
different
lineages
into
California,
including
epidemic
WA1
strains
associated
Washington
state,
lack
a
predominant
lineage
limited
transmission
among
communities.
Lineages
outbreak
clusters
two
were
defined
single
base
substitution
viral
genome.
These
findings
support
contact
tracing,
social
distancing,
travel
restrictions
contain
other
states.
Journal of Clinical Investigation,
Journal Year:
2022,
Volume and Issue:
132(7)
Published: March 31, 2022
Next-generation
sequencing
(NGS)
technology
has
advanced
our
understanding
of
the
human
microbiome
by
allowing
for
discovery
and
characterization
unculturable
microbes
with
prediction
their
function.
Key
NGS
methods
include
16S
rRNA
gene
sequencing,
shotgun
metagenomic
RNA
sequencing.
The
choice
which
methodology
to
pursue
a
given
purpose
is
often
unclear
clinicians
researchers.
In
this
Review,
we
describe
fundamentals
NGS,
focus
on
We
also
discuss
pros
cons
each
as
well
important
concepts
in
data
variability,
study
design,
clinical
metadata
collection.
further
present
examples
how
studies
have
disease
pathophysiology
across
diverse
contexts,
including
development
diagnostics
therapeutics.
Finally,
share
insights
might
be
integrated
into
advance
research
care
coming
years.
Critical Reviews in Microbiology,
Journal Year:
2019,
Volume and Issue:
45(5-6), P. 668 - 685
Published: Nov. 2, 2019
Metagenomic
next-generation
sequencing
(mNGS)
is
increasingly
being
applied
in
clinical
laboratories
for
unbiased
culture-independent
diagnosis.
Whether
it
can
be
a
next
routine
pathogen
identification
tool
has
become
topic
of
concern.
We
review
the
current
implementation
this
new
technology
infectious
disease
diagnostics
and
discuss
feasibility
transforming
mNGS
into
diagnostic
test.
Since
2008,
numerous
studies
from
over
20
countries
have
revealed
practicality
work-up
undiagnosed
diseases.
performs
well
identifying
rare,
novel,
difficult-to-detect
coinfected
pathogens
directly
samples
presents
great
potential
resistance
prediction
by
antibiotic
genes,
providing
evidence
that
used
to
guide
treatment
options
improve
stewardship.
Many
physicians
recognized
as
last
resort
method
address
infection
problems.
Although
several
hurdles,
such
workflow
validation,
quality
control,
standardisation,
data
interpretation,
remain
before
implemented
routinely
laboratories,
they
are
temporary
overcome
rapidly
evolving
technologies.
With
more
validated
workflows,
lower
cost
turnaround
time,
simplified
interpretation
criteria,
will
widely
accepted
practice.
Overall,
landscape
microbiology
ensure
properly
utilised
diagnosis,
both
microbiologists
should
thorough
understanding
power
limitations
method.
