The
microbial
gut
communities
of
fish
are
receiving
increased
attention
for
their
relevance,
among
others,
in
a
growing
aquaculture
industry.The
members
these
often
split
into
resident
(long-term
colonisers
specialised
to
grow
and
adhere
the
gut)
transient
(short-term
originated
from
food
items
surrounding
water)
microorganisms.Separating
two
small
impeded
by
size
fragility
gastrointestinal
tract.With
aim
testing
whether
it
is
possible
recover
distinct
species
using
simple
sampling
technique,
we
used
16S
amplicon
sequencing
paired
intestinal
wall
digesta
samples
three
Cyprinodontiformes
fish.We
examined
diversity
compositional
variation
recovered
communities,
joint
distribution
modelling
identify
microbes
that
most
likely
be
part
community.For
all
found
was
significantly
lower
compared
community
composition
between
sample
types
different.Across
eight
unique
families
bacteria
enriched
wall,
encompassing
89
ASVs
samples.We
conclude
characterise
different
potentially
through
separately
analysing
encourage
researchers
aware
procedures
microbiome
characterization
will
capture
parts
this
should
taken
consideration
when
reporting
results
such
studies
on
fish.
Nature Communications,
Год журнала:
2023,
Номер
14(1)
Опубликована: Март 17, 2023
Abstract
Spatial
analysis
of
microbiomes
at
single
cell
resolution
with
high
multiplexity
and
accuracy
has
remained
challenging.
Here
we
present
spatial
profiling
a
microbiome
using
sequential
error-robust
fluorescence
in
situ
hybridization
(SEER-FISH),
highly
multiplexed
accurate
imaging
method
that
allows
mapping
microbial
communities
micron-scale.
We
show
RNA
can
be
increased
significantly
by
rounds
probe
dissociation.
Combined
error-correction
strategies,
demonstrate
SEER-FISH
enables
taxonomic
identification
complex
communities.
Using
composed
diverse
bacterial
taxa
isolated
from
plant
rhizospheres,
apply
to
quantify
the
abundance
each
taxon
map
biogeography
on
roots.
At
micron-scale,
identify
clustering
cells
multiple
species
rhizoplane.
Under
treatment
metabolites,
find
re-organization
colonization
along
root
alterations
association
among
taxa.
Taken
together,
provides
useful
for
ecology
situ.
Comprehensive Reviews in Food Science and Food Safety,
Год журнала:
2024,
Номер
23(4)
Опубликована: Июнь 12, 2024
Abstract
Consumers
are
attracted
to
traditional
fermented
foods
due
their
unique
flavor
and
nutritional
value.
However,
the
fermentation
technique
can
no
longer
accommodate
requirements
of
food
industry.
Traditional
produce
hazardous
compounds,
off‐odor,
anti‐nutritional
factors,
reducing
product
stability.
The
microbial
system
complexity
resulting
from
open
process
has
made
it
challenging
regulate
these
problems
by
modifying
behaviors.
Synthetic
communities
(SynComs)
have
been
shown
simplify
complex
allow
for
targeted
design
communities,
which
applied
in
processing
foods.
Herein,
we
describe
theoretical
information
SynComs,
particularly
physiological
processes
interactions.
This
paper
discusses
current
approaches
creating
including
designing,
building,
testing,
learning,
with
typical
applications
fundamental
techniques.
Based
on
various
innovation
demands,
potential
application
SynComs
enhancing
quality
highlighted.
showed
superior
performance
regulating
using
interaction
core
microorganisms
reduce
compounds
improve
flavor.
Additionally,
presented
status
future
perspectives
improving
Nature Microbiology,
Год журнала:
2024,
Номер
9(9), С. 2262 - 2277
Опубликована: Июнь 25, 2024
The
exchange
of
mobile
genetic
elements
(MGEs)
facilitates
the
spread
functional
traits
including
antimicrobial
resistance
within
bacterial
communities.
Tools
to
spatially
map
MGEs
and
identify
their
hosts
in
complex
microbial
communities
are
currently
lacking,
limiting
our
understanding
this
process.
Here
we
combined
single-molecule
DNA
fluorescence
situ
hybridization
(FISH)
with
multiplexed
ribosomal
RNA-FISH
enable
simultaneous
visualization
both
taxa.
We
mapped
bacteriophage
(AMR)
plasmids
identified
host
taxa
human
oral
biofilms.
This
revealed
distinct
clusters
AMR
prophage,
coinciding
densely
packed
regions
bacteria.
Our
data
suggest
spatial
heterogeneity
results
heterogeneous
MGE
distribution
community,
resulting
from
horizontal
gene
transfer
hotspots
or
expansion
MGE-carrying
strains.
approach
can
help
advance
study
phage
ecology
FEMS Microbiology Reviews,
Год журнала:
2024,
Номер
48(2)
Опубликована: Фев. 28, 2024
Abstract
Microbiomes
are
foundational
components
of
the
environment
that
provide
essential
services
relating
to
food
security,
carbon
sequestration,
human
health,
and
overall
well-being
ecosystems.
Microbiota
exert
their
effects
primarily
through
complex
interactions
at
interfaces
with
plant,
animal,
hosts,
as
well
within
soil
environment.
This
review
aims
explore
ecological,
evolutionary,
molecular
processes
governing
establishment
function
microbiome–host
relationships,
specifically
critical
One
Health—a
transdisciplinary
framework
recognizes
health
outcomes
people,
animals,
plants,
tightly
interconnected.
Within
context
Health,
core
principles
underpinning
microbiome
assembly
will
be
discussed
in
detail,
including
biofilm
formation,
microbial
recruitment
strategies,
mechanisms
attachment,
community
succession,
effect
these
have
on
host
health.
Finally,
this
catalogue
recent
advances
microbiology
ecology
methods
can
used
profile
interfaces,
particular
attention
multi-omic,
advanced
imaging,
modelling
approaches.
These
technologies
for
delineating
general
specific
functions,
mapping
interconnectivity
across
varying
spatial
temporal
scales,
predictive
frameworks
guide
development
targeted
microbiome-interventions
deliver
Health
outcomes.
Cell Host & Microbe,
Год журнала:
2023,
Номер
31(4), С. 464 - 471
Опубликована: Апрель 1, 2023
Just
as
mammals
have
coevolved
with
the
intestinal
bacterial
communities
that
are
part
of
microbiota,
helminths
represent
an
important
selective
force
on
their
mammalian
host.
The
complex
interaction
between
helminths,
microbes,
and
host
is
likely
determinant
mutual
fitness.
immune
system
in
particular
a
critical
interface
both
this
crosstalk
often
determines
balance
tolerance
resistance
against
these
widespread
parasites.
Hence,
there
many
examples
how
microbiota
can
influence
tissue
homeostasis
homeostatic
immunity.
Understanding
processes
at
cellular
molecular
level
exciting
area
research
we
seek
to
highlight
review
will
potentially
guide
future
treatment
approaches.
Environmental Science & Technology,
Год журнала:
2021,
Номер
56(8), С. 4691 - 4701
Опубликована: Ноя. 18, 2021
Bacteriophages
(phages)
are
an
underutilized
biological
resource
with
vast
potential
for
pathogen
control
and
microbiome
editing.
Phage
research
commercialization
have
increased
rapidly
in
biomedical
agricultural
industries,
but
adoption
has
been
limited
elsewhere.
Nevertheless,
converging
advances
DNA
sequencing,
bioinformatics,
microbial
ecology,
synthetic
biology
now
poised
to
broaden
phage
applications
beyond
toward
the
manipulation
of
communities
defined
functional
improvements.
Enhancements
sequencing
combined
network
analysis
make
it
feasible
identify
disrupt
associations
elicit
desirable
shifts
community
structure
or
function,
indirectly
modulate
species
abundance,
target
hub
keystone
achieve
broad
shifts.
Sequencing
bioinformatic
advancements
also
facilitating
use
temperate
phages
safe
gene
delivery
applications.
Finally,
integration
stands
create
novel
chassis
modular
genetic
components.
While
some
fundamental,
regulatory,
barriers
widespread
remain,
many
major
challenges
that
impeded
field
workable
solutions.
Thus,
a
new
dawn
phage-based
(chemical-free)
precise
biocontrol
editing
is
on
horizon
enhance,
suppress,
activities
important
public
health,
food
security,
more
sustainable
energy
production
water
reuse.
