New uses for ancient middens: bridging ecological and evolutionary perspectives
Trends in Ecology & Evolution,
Год журнала:
2024,
Номер
39(5), С. 479 - 493
Опубликована: Март 28, 2024
Язык: Английский
Unveiling the co-phylogeny signal between plunderfish Harpagifer spp. and their gut microbiomes across the Southern Ocean
Microbiology Spectrum,
Год журнала:
2024,
Номер
12(4)
Опубликована: Март 5, 2024
Understanding
the
factors
that
sculpt
fish
gut
microbiome
is
challenging,
especially
in
natural
populations
characterized
by
high
environmental
and
host
genomic
complexity.
However,
closely
related
hosts
are
valuable
models
for
deciphering
contribution
of
evolutionary
history
to
assembly,
through
underscoring
phylosymbiosis
co-phylogeny
patterns.
Here,
we
propose
recent
diversification
several
Язык: Английский
Partner fidelity, not geography, drives co-diversification of gut microbiota with hominids
Biology Letters,
Год журнала:
2025,
Номер
21(1)
Опубликована: Янв. 1, 2025
Bacterial
strains
that
inhabit
the
gastrointestinal
tracts
of
hominids
have
diversified
in
parallel
(co-diversified)
with
their
host
species.
The
extent
to
which
co-diversification
has
been
mediated
by
partner
fidelity
between
and
hosts
or
geographical
distance
is
not
clear
due
a
lack
strain-level
data
from
clades
unconfounded
phylogenetic
relationships
distributions.
Here,
I
tested
these
competing
hypotheses
through
meta-analyses
7121
gut
bacterial
genomes
assembled
wild-living
ape
species
subspecies
sampled
throughout
ranges
equatorial
Africa.
Across
phylogeny,
strain
diversification
was
more
strongly
associated
phylogeny
than
geography.
In
total,
approximately
14%
branch
length
showed
significant
evidence
independent
geography,
whereas
only
4%
geography
phylogeny.
Geographically
co-occurring
heterospecific
(
Pan
Gorilla
)
universally
maintained
distinct
co-diversified
strains.
Strains
whose
included
Proteobacteria
known
adopt
free-living
lifestyles
(e.g.
Escherichia
).
These
results
show
driven
primarily
lineages
rather
Язык: Английский
Recent genetic drift in the co-diversified gut bacterial symbionts of laboratory mice
Nature Communications,
Год журнала:
2025,
Номер
16(1)
Опубликована: Март 5, 2025
Laboratory
mice
(Mus
musculus
domesticus)
harbor
gut
bacterial
strains
that
are
distinct
from
those
of
wild
but
whose
evolutionary
histories
unclear.
Here,
we
show
laboratory
have
retained
lineages
diversified
in
parallel
(co-diversified)
with
rodent
species
for
>
25
million
years,
laboratory-mouse
microbiota
(LGM)
these
ancestral
symbionts
experienced
accelerated
accumulation
genetic
load
during
the
past
~
120
years
captivity.
Compared
to
closely
related
wild-mouse
(WGM)
strains,
co-diversified
LGM
displayed
significantly
faster
genome-wide
rates
nonsynonymous
substitutions,
indicating
elevated
drift-a
difference
was
absent
non-co-diversified
symbiont
clades.
Competition
experiments
germ-free
further
indicated
within
clades
reduced
fitness
vivo
compared
WGM
relatives
an
extent
not
observed
Thus,
stochastic
processes
(e.g.,
bottlenecks),
natural
selection
laboratory,
been
predominant
forces
underlying
divergence
between
and
house
mice.
Our
results
conserved
diverse
acquired
novel
mutational
burdens
mice,
providing
rationale
restoring
strain
diversity.
Язык: Английский
Host specificity of gut microbiota associated with social bees: patterns and processes
Microbiology and Molecular Biology Reviews,
Год журнала:
2025,
Номер
unknown
Опубликована: Март 20, 2025
SUMMARYGut
microbes
provide
benefits
to
some
animals,
but
their
distribution
and
effects
across
diverse
hosts
are
still
poorly
described.
There
is
accumulating
evidence
for
host
specificity
(i.e.,
a
pattern
where
different
tend
associate
with
distinct
lineages),
the
causes
consequences
of
this
unclear.
Combining
experimental
tests
in
laboratory
broad
surveys
wild
promising
approach
gaining
comprehensive
mechanistic
understanding
prevalence,
origin,
importance.
Social
bees
represent
an
ideal
testbed
endeavor
because
they
phylogenetically
functionally
diverse,
host-specific,
stable,
tractable
gut
microbiota.
Furthermore,
western
honeybee
(Apis
mellifera)
emerging
model
system
studying
microbiota-host
interactions.
In
review,
we
summarize
data
on
prevalence
strength
social
bee
microbiota
(bumblebees,
stingless
bees,
honeybees),
as
well
potential
proven
ecological
molecular
mechanisms
that
maintain
specificity.
Overall,
found
relatively
strong
likely
results
from
several
processes,
including
filtering
mediated
by
immune
priority
effects.
However,
more
research
needed
multiple
species
confirm
these
findings.
To
help
future
research,
hypotheses
field
propose
comparative
tests.
Finally,
conclude
review
highlighting
need
understand
how
can
influence
health.
Язык: Английский
Bridging Ecology and Microbiomes: Applying Ecological Theories in Host-associated Microbial Ecosystems
Current Clinical Microbiology Reports,
Год журнала:
2025,
Номер
12(1)
Опубликована: Апрель 15, 2025
Abstract
Purpose
of
Review
This
review
explores
the
application
classical
ecological
theory
to
host-associated
microbiomes
during
initial
colonization,
maintenance,
and
recovery.
We
discuss
unique
challenges
applying
these
theories
host
factors
consider
going
forward.
Recent
Findings
studies
community
ecology
principles
continue
demonstrate
a
role
for
both
selective
stochastic
processes
in
shaping
microbiomes.
However,
frameworks
developed
describe
dynamics
homeostasis
do
not
necessarily
apply
diseased
or
highly
perturbed
states,
where
large
variations
can
potentially
lead
alternate
stable
states.
Summary
Despite
providing
valuable
insights,
has
some
challenges.
The
integration
host-specific
factors,
such
as
genotype
immune
models
is
crucial
understanding
microbiome
assembly
stability,
which
could
improve
our
ability
predict
outcomes
health.
Язык: Английский
Ecology and Evolution of the Social Microbiome
Annual Review of Ecology Evolution and Systematics,
Год журнала:
2024,
Номер
55(1), С. 89 - 114
Опубликована: Авг. 1, 2024
Animals
with
close
social
relationships
often
have
similar
microbiomes.
These
socially
structured
microbiomes
can
arise
through
multiple
mechanisms
that
are
difficult
to
disentangle,
including
transmission
between
partners
or
via
structured,
shared
environments.
Here,
we
review
evidence
for
and
propose
methods
differentiate
the
give
rise
them.
We
discuss
evolutionary
implications
of
these
both
hosts
their
microbiomes,
possibility
selects
host-specialized
conclude
by
identifying
outstanding
questions
related
evolution.
identify
new
underutilized
approaches
like
longitudinal
study
designs,
strain-sharing
analysis,
culture-based
characterization
address
questions.
Язык: Английский
Recent genetic drift in the co-diversified gut bacterial symbionts of laboratory mice
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Авг. 14, 2024
Laboratory
mice
(Mus
musculus
domesticus)
harbor
gut
bacterial
strains
that
are
distinct
from
those
of
wild
mice1
but
whose
evolutionary
histories
poorly
understood.
Understanding
the
divergence
laboratory-mouse
microbiota
(LGM)
wild-mouse
(WGM)
is
critical,
because
LGM
and
WGM
have
been
previously
shown
to
differentially
affect
mouse
immune-cell
proliferation2,3,
infection
resistance4,
cancer
progression2,
ability
model
drug
outcomes
for
humans5.
Here,
we
show
laboratory
retained
symbiont
lineages
diversified
in
parallel
(co-diversified)
with
rodent
species
>
25
million
years,
these
ancestral
symbionts
experienced
accelerated
accumulation
genetic
load
during
past
~
120
years
captivity.
Compared
closely
related
strains,
co-diversified
displayed
significantly
faster
genome-wide
rates
fixation
nonsynonymous
mutations,
indicating
elevated
drift,
a
difference
was
absent
non-co-diversified
clades.
Competition
experiments
germ-free
further
indicated
within
clades
reduced
fitness
vivo
compared
relatives
an
extent
not
observed
Thus,
stochastic
processes
(e.g.,
bottlenecks),
natural
selection
laboratory,
predominant
forces
underlying
between
house
mice.
Our
results
conserved
diverse
acquired
novel
mutational
burdens
mice,
providing
rationale
restoring
strain
diversity.
Язык: Английский
Comparative Genomics Reveals Three Genetic Groups of the Whitefly Obligate Endosymbiont Candidatus Portiera aleyrodidarum
Insects,
Год журнала:
2023,
Номер
14(11), С. 888 - 888
Опубликована: Ноя. 17, 2023
Maternally
inherited
obligate
endosymbionts
codiverge
with
their
invertebrate
hosts
and
reflect
host's
evolutionary
history.
Whiteflies
(Hemiptera:
Aleyrodidae)
harbor
one
endosymbiont,
Candidatus
Portiera
aleyrodidarum
(hereafter
Portiera).
was
anciently
acquired
by
whitefly
has
been
coevolving
its
host
ever
since.
Uncovering
the
divergence
of
provides
a
fundamental
basis
for
inspecting
coevolutionary
processes
between
bacteria
hosts.
To
illustrate
lineages
across
different
species,
we
sequenced
genome
from
Aleyrodes
shizuokensis
conducted
comparative
analysis
on
basic
features
gene
evolution
bacterial
genomes
five
genera,
namely
Aleurodicus,
Aleyrodes,
Bemisia,
Pealius,
Trialeurodes.
The
results
indicated
that
Bemisia
possessed
significantly
larger
genomes,
fewer
coding
sequences
(CDSs),
lower
density.
Their
arrangement
differed
notably
those
other
genera.
phylogeny
nine
resembled
Moreover,
were
classified
into
three
distinct
genetic
groups
based
distance,
Aleurodicus
(Aleurodicinae),
(Aleyrodinae),
another
Trialeurrodes
(Aleyrodinae).
Synonymous
nonsynonymous
rate
analyses,
parity
rule
2
plot
neutrality
effective
number
codons
analyses
supported
distinction
groups.
Our
distant
exhibit
genomic
contents,
implying
codivergence
endosymbionts.
This
work
will
enhance
our
understanding
coevolution
Язык: Английский