Applied and Environmental Microbiology,
Journal Year:
2025,
Volume and Issue:
unknown
Published: April 30, 2025
ABSTRACT
Within-species
diversity
of
microorganisms
in
food
systems
significantly
shapes
community
function.
While
next-generation
sequencing
(NGS)
methods
have
advanced
our
understanding
microbiomes
at
the
level,
it
is
essential
to
recognize
importance
within-species
variation
for
and
predicting
functional
activities
these
communities.
This
review
highlights
substantial
observed
among
microbial
species
its
implications
their
functionality.
We
discuss
a
selection
key
fermented
foods
systems,
highlighting
examples
strain-level
influence
on
quality
safety.
present
comprehensive
roadmap
methodologies
aimed
uncovering
this
often
overlooked
underlying
diversity.
Technologies
like
long-read
marker-gene
or
shotgun
metagenome
offer
enhanced
resolution
communities
insights
into
potential
individual
strains
should
be
integrated
with
techniques
such
as
metabolomics,
metatranscriptomics,
metaproteomics
link
structure
activities.
Furthermore,
interactions
between
viruses
microbes
that
contribute
strain
stability
are
also
critical
consider.
article
existing
research
emphasizes
incorporating
studies
harness
full
potential,
advance
fundamental
science,
foster
innovation.
International Journal of Molecular Sciences,
Journal Year:
2023,
Volume and Issue:
24(4), P. 3950 - 3950
Published: Feb. 16, 2023
Our
skin
is
the
largest
organ
of
body,
serving
as
an
important
barrier
against
harsh
extrinsic
environment.
Alongside
preventing
desiccation,
chemical
damage
and
hypothermia,
this
protects
body
from
invading
pathogens
through
a
sophisticated
innate
immune
response
co-adapted
consortium
commensal
microorganisms,
collectively
termed
microbiota.
These
microorganisms
inhabit
distinct
biogeographical
regions
dictated
by
physiology.
Thus,
it
follows
that
perturbations
to
normal
homeostasis,
occurs
with
ageing,
diabetes
disease,
can
cause
microbial
dysbiosis
increase
infection
risk.
In
review,
we
discuss
emerging
concepts
in
microbiome
research,
highlighting
pertinent
links
between
cutaneous
repair.
Moreover,
address
gaps
current
knowledge
highlight
key
areas
requiring
further
exploration.
Future
advances
field
could
revolutionise
way
treat
associated
ageing
other
pathologies.
Genome Medicine,
Journal Year:
2023,
Volume and Issue:
15(1)
Published: June 14, 2023
Advances
in
clinical
genetic
testing,
including
the
introduction
of
exome
sequencing,
have
uncovered
molecular
etiology
for
many
rare
and
previously
unsolved
disorders,
yet
more
than
half
individuals
with
a
suspected
disorder
remain
after
complete
evaluation.
A
precise
diagnosis
may
guide
treatment
plans,
allow
families
to
make
informed
care
decisions,
permit
participate
N-of-1
trials;
thus,
there
is
high
interest
developing
new
tools
techniques
increase
solve
rate.
Long-read
sequencing
(LRS)
promising
technology
both
increasing
rate
decreasing
amount
time
required
diagnosis.
Here,
we
summarize
current
LRS
technologies,
give
examples
how
they
been
used
evaluate
complex
variation
identify
missing
variants,
discuss
future
applications
LRS.
As
costs
continue
decrease,
will
find
additional
utility
space
fundamentally
changing
pathological
variants
are
discovered
eventually
acting
as
single-data
source
that
can
be
interrogated
multiple
times
service.
Frontiers in Molecular Biosciences,
Journal Year:
2024,
Volume and Issue:
10
Published: Jan. 19, 2024
The
human
gastrointestinal
(gut)
microbiome
plays
a
critical
role
in
maintaining
host
health
and
has
been
increasingly
recognized
as
an
important
factor
precision
medicine.
High-throughput
sequencing
technologies
have
revolutionized
-omics
data
generation,
facilitating
the
characterization
of
gut
with
exceptional
resolution.
analysis
various
data,
including
metatranscriptomics,
metagenomics,
glycomics,
metabolomics,
holds
potential
for
personalized
therapies
by
revealing
information
about
functional
genes,
microbial
composition,
glycans,
metabolites.
This
multi-omics
approach
not
only
provided
insights
into
diseases
but
also
facilitated
identification
biomarkers
diagnosis,
prognosis,
treatment.
Machine
learning
algorithms
emerged
powerful
tools
extracting
meaningful
from
complex
datasets,
more
recently
applied
to
metagenomics
via
efficiently
identifying
signatures,
predicting
disease
states,
determining
therapeutic
targets.
Despite
these
rapid
advancements,
several
challenges
remain,
such
key
knowledge
gaps,
algorithm
selection,
bioinformatics
software
parametrization.
In
this
mini-review,
our
primary
focus
is
while
recognizing
that
other
can
enhance
understanding
diversity
organisms
how
they
interact
host.
We
aim
explore
current
intersection
multi-omics,
medicine,
machine
advancing
microbiome.
A
multidisciplinary
promise
improving
patient
outcomes
era
we
unravel
intricate
interactions
between
health.
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: March 11, 2024
Abstract
Metagenomic
binning
is
an
essential
technique
for
genome-resolved
characterization
of
uncultured
microorganisms
in
various
ecosystems
but
hampered
by
the
low
efficiency
tools
adequately
recovering
metagenome-assembled
genomes
(MAGs).
Here,
we
introduce
BASALT
(
B
inning
A
cross
a
S
eries
ssemb
l
ies
T
oolkit)
and
refinement
short-
long-read
sequencing
data.
employs
multiple
binners
with
thresholds
to
produce
initial
bins,
then
utilizes
neural
networks
identify
core
sequences
remove
redundant
bins
refine
non-redundant
bins.
Using
same
assemblies
generated
from
Critical
Assessment
Metagenome
Interpretation
(CAMI)
datasets,
produces
up
twice
as
many
MAGs
VAMB,
DASTool,
or
metaWRAP.
Processing
lake
sediment
dataset,
~30%
more
than
metaWRAP,
including
21
unique
class-level
prokaryotic
lineages.
Functional
annotations
reveal
that
can
retrieve
47.6%
opening-reading
frames
These
results
highlight
robust
handling
metagenomic
data
BASALT.
BMC Bioinformatics,
Journal Year:
2024,
Volume and Issue:
25(1)
Published: Jan. 11, 2024
Long
reads
have
gained
popularity
in
the
analysis
of
metagenomics
data.
Therefore,
we
comprehensively
assessed
classification
tools
on
species
taxonomic
level.
We
analysed
kmer-based
tools,
mapping-based
and
two
general-purpose
long
mappers.
evaluated
more
than
20
pipelines
which
use
either
nucleotide
or
protein
databases
selected
13
for
an
extensive
benchmark.
prepared
seven
synthetic
datasets
to
test
various
scenarios,
including
presence
a
host,
unknown
related
species.
Moreover,
used
available
sequencing
data
from
three
well-defined
mock
communities,
dataset
with
abundance
varying
0.0001
20%
six
real
gut
microbiomes.
