bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: Oct. 24, 2023
Abstract
Background
The
Anna
Karenina
Principle
predicts
that
stability
in
host-associated
microbiomes
correlates
with
health
the
host.
Microbiomes
are
ecosystems,
and
classical
ecological
theory
suggests
predators
impact
ecosystem
stability.
Phages
can
act
as
on
bacterial
species
microbiomes.
However,
our
ability
to
extrapolate
results
from
existing
phages
is
limited
because
some
stage
lysogenic
infections,
a
process
no
precise
analog
ecology.
In
so-called
“temperate”
integrate
into
cells
of
their
hosts
where
they
remain
dormant
prophages
for
many
generations.
Prophages
later
be
induced
by
environmental
conditions,
whereupon
lyse
host
phage
progeny
released.
It
has
been
suggested
biological
timebombs
destabilize
microbial
but
formal
support
this
hypothesis
lacking.
Results
We
studied
effects
temperate
virulent
diversity
computationally
simulated
presence
either
type
microbiome
increased
diversity.
Bacterial
populations
were
more
likely
fluctuate
over
time
when
there
system.
When
disturbed
steady
states,
both
types
affected
return
times,
different
ways.
returned
pre-disturbance
densities
slowly
species,
cycles
engendered
disturbances
dampened
species.
Conclusions
shape
microbiomes,
A
clear
understanding
life
dynamics
needed
predict
role
composition
health,
applications
including
therapy
transplants.
we
present
here
provide
theoretical
foundation
body
work.
Cell Host & Microbe,
Journal Year:
2024,
Volume and Issue:
32(5), P. 727 - 738.e6
Published: April 4, 2024
Many,
if
not
all,
bacteria
use
quorum
sensing
(QS)
to
control
collective
behaviors,
and
more
recently,
QS
has
also
been
discovered
in
bacteriophages
(phages).
Phages
can
produce
communication
molecules
of
their
own,
or
"listen
in"
on
the
host's
processes,
switch
between
lytic
lysogenic
modes
infection.
Here,
we
study
interaction
Vibrio
cholerae
with
phage
VP882,
which
is
activated
by
molecule
DPO.
We
discover
that
induction
VP882
results
binding
transcripts
major
RNA
chaperone
Hfq,
turn
outcompetes
downregulates
host-encoded
small
RNAs
(sRNAs).
itself
encodes
Hfq-binding
sRNAs,
demonstrate
one
these
named
VpdS,
promotes
replication
regulating
host
mRNA
levels.
further
show
sRNAs
antagonize
downregulating
expression
thus
might
be
part
defense
arsenal.
Environmental Microbiome,
Journal Year:
2025,
Volume and Issue:
20(1)
Published: Jan. 13, 2025
Abstract
Background
Viruses
that
infect
prokaryotes
(phages)
constitute
the
most
abundant
group
of
biological
agents,
playing
pivotal
roles
in
microbial
systems.
They
are
known
to
impact
community
dynamics,
ecology,
and
evolution.
Efforts
document
diversity,
host
range,
infection
effects
bacteriophage
on
cell
metabolism
extremely
underexplored.
Phages
classified
as
virulent
or
temperate
based
their
life
cycles.
Temperate
phages
adopt
lysogenic
mode
infection,
where
genome
integrates
into
forming
a
prophage.
Prophages
enable
viral
replication
without
lysis,
often
contribute
novel
beneficial
traits
genome.
Current
phage
research
predominantly
focuses
lytic
phages,
leaving
significant
gap
knowledge
regarding
prophages,
including
biology,
ecological
roles.
Results
Here
we
develop
describe
Prophage-DB,
database
proteins,
associated
metadata
will
serve
resource
for
genomics
ecology.
To
create
database,
identified
characterized
prophages
from
genomes
three
largest
publicly
available
databases.
We
applied
several
state-of-the-art
tools
our
pipeline
annotate
these
viruses,
cluster
them,
taxonomically
classify
detect
respective
auxiliary
metabolic
genes.
In
total,
identify
characterize
over
350,000
35,000
Our
prophage
is
highly
representative
statistical
results
contains
diverse
set
archaeal
bacterial
hosts
which
show
wide
environmental
distribution.
Conclusion
Given
particularly
overlooked
merit
increased
attention
due
vital
implications
microbiomes
hosts,
created
Prophage-DB
advance
understanding
through
comprehensive
characterization
genomes.
propose
valuable
advancing
research,
offering
insights
taxonomy,
relationships,
genes,
Nature,
Journal Year:
2023,
Volume and Issue:
620(7974), P. 625 - 633
Published: July 26, 2023
Most
bacteria
in
the
biosphere
are
predicted
to
be
polylysogens
harbouring
multiple
prophages1-5.
In
studied
systems,
prophage
induction
from
lysogeny
lysis
is
near-universally
driven
by
DNA-damaging
agents6.
Thus,
how
co-residing
prophages
compete
for
cell
resources
if
they
respond
an
identical
trigger
unknown.
Here
we
discover
regulatory
modules
that
control
independently
of
DNA-damage
cue.
The
bear
little
resemblance
at
sequence
level
but
share
a
logic
having
transcription
factor
activates
expression
neighbouring
gene
encodes
small
protein.
protein
inactivates
master
repressor
lysis,
which
leads
induction.
Polylysogens
harbour
two
exposed
DNA
damage
release
mixed
populations
phages.
Single-cell
analyses
reveal
this
blend
consequence
discrete
subsets
cells
producing
one,
other
or
both
By
contrast,
through
DNA-damage-independent
module
results
only
phage
sensitive
specific
tested,
stimulus
used
induce
determines
productivity.
Considering
lack
potent
agents
natural
habitats,
additional
phage-encoded
sensory
pathways
likely
have
fundamental
roles
phage-host
biology
and
inter-prophage
competition.
Pathogens,
Journal Year:
2024,
Volume and Issue:
13(6), P. 522 - 522
Published: June 20, 2024
The
emergence
of
multidrug-resistant
bacteria
is
undoubtedly
one
the
most
serious
global
health
threats.
One
response
to
this
threat
that
has
been
gaining
momentum
over
past
decade
'phage
therapy'.
According
this,
lytic
bacteriophages
are
used
for
treatment
bacterial
infections,
either
alone
or
in
combination
with
antimicrobial
agents.
However,
ensure
efficacy
and
broad
applicability
phage
therapy,
several
challenges
must
be
overcome.
These
encompass
development
methods
strategies
host
range
manipulation
bypass
resistance
mechanisms
developed
by
pathogenic
bacteria,
as
case
since
advent
antibiotics.
As
our
knowledge
understanding
interactions
between
phages
their
hosts
evolves,
key
issue
define
each
application.
In
article,
we
discuss
factors
affect
how
determines
classification
into
different
categories
action.
For
group,
recent
representative
examples
provided,
together
suggestions
on
groups
can
combat
certain
types
infections.
available
methodologies
expansion,
through
sequential
adaptation
a
new
pathogen
genetic
engineering
techniques,
also
reviewed.
Trends in Microbiology,
Journal Year:
2025,
Volume and Issue:
unknown
Published: Feb. 1, 2025
Mobile
genetic
elements
(MGEs),
like
temperate
bacteriophages
and
conjugative
plasmids,
are
major
vectors
of
virulence
antibiotic
resistance
in
bacterial
populations.
For
reproductive
success,
MGEs
must
balance
horizontal
vertical
transmission.
Yet,
the
cost
transmission
(metabolic
burden
or
host
death)
puts
these
modes
at
odds.
Using
virulence-transmission
trade-off
(VTT)
theory,
we
identify
three
groups
environmental
variables
affecting
between
transmission:
density,
physiology,
competitors.
We
find
that
general
theoretical
predictions
optimal
response
to
cues
align
with
experimental
evidence
on
regulation
by
phages
plasmids.
further
highlight
gaps
theory
experiments,
differences
suggest
areas
for
future
research.
npj Biofilms and Microbiomes,
Journal Year:
2025,
Volume and Issue:
11(1)
Published: March 19, 2025
Gut
microbiome
(GM)
composition
and
function
is
pivotal
for
human
health
disease,
of
which
the
virome's
importance
increasingly
recognised.
However,
prophages
their
induction
patterns
in
infant
gut
remain
understudied.
Here,
we
identified
10645
putative
662
metagenomes
from
1-year-old
children
COPSAC2010
mother-child
cohort
investigated
potential
functions.
No
core
provirome
was
found
as
most
prevalent
vOTU
only
~70%
samples.
The
dominant
cluster
vOTUs
related
to
Bacteroides
phage
Hanky
p00',
it
carried
both
diversity
generating
retroelements
genes
involved
capsular
polysaccharide
synthesis.
Paired
analysis
viromes
same
samples
revealed
that
within
were
induced
unaffected
by
a
range
environmental
perturbers.
In
summary,
are
major
components
may
have
far
reaching
influences
on
its
host.
