Nature Microbiology,
Год журнала:
2021,
Номер
6(4), С. 499 - 511
Опубликована: Фев. 1, 2021
Abstract
The
herbivore
digestive
tract
is
home
to
a
complex
community
of
anaerobic
microbes
that
work
together
break
down
lignocellulose.
These
microbiota
are
an
untapped
resource
strains,
pathways
and
enzymes
could
be
applied
convert
plant
waste
into
sugar
substrates
for
green
biotechnology.
We
carried
out
more
than
400
parallel
enrichment
experiments
from
goat
faeces
determine
how
substrate
antibiotic
selection
influence
membership,
activity,
stability
chemical
productivity
gut
communities.
assembled
719
high-quality
metagenome-assembled
genomes
(MAGs)
unique
at
the
species
level.
More
90%
these
MAGs
previously
unidentified
microorganisms.
Microbial
consortia
dominated
by
fungi
outperformed
bacterially
in
terms
both
methane
production
extent
cellulose
degradation,
which
indicates
have
important
role
release.
Metabolic
pathway
reconstructions
737
bacteria,
archaea
suggest
cross-domain
partnerships
between
methanogens
enabled
acetate,
formate
methane,
whereas
mainly
produced
short-chain
fatty
acids,
including
propionate
butyrate.
Analyses
carbohydrate-active
enzyme
domains
present
each
consortium
bacteria
employ
mostly
complementary
hydrolytic
strategies.
division
labour
among
anaerobes
degrade
biomass
harnessed
industrial
bioprocessing.
Oxford University Press eBooks,
Год журнала:
2018,
Номер
unknown
Опубликована: Фев. 15, 2018
Abstract
Environmental
DNA
(eDNA),
i.e.
released
in
the
environment
by
any
living
form,
represents
a
formidable
opportunity
to
gather
high-throughput
and
standard
information
on
distribution
or
feeding
habits
of
species.
It
has
therefore
great
potential
for
applications
ecology
biodiversity
management.
However,
this
research
field
is
fast-moving,
involves
different
areas
expertise
currently
lacks
approaches,
which
calls
an
up-to-date
comprehensive
synthesis.
monitoring
covers
current
methods
based
eDNA,
with
particular
focus
“eDNA
metabarcoding”.
Intended
scientists
managers,
it
provides
background
allow
design
sound
experiments.
revisits
all
steps
necessary
produce
high-quality
metabarcoding
data
such
as
sampling,
metabarcode
design,
optimization
PCR
sequencing
protocols,
well
analysis
large
datasets.
All
these
are
presented
discussing
challenges
eDNA-based
approaches
infer
parameters
ecological
processes.
The
last
chapters
book
review
how
been
used
so
far
unravel
novel
patterns
diversity
space
time,
detect
species,
answer
new
questions
various
ecosystems
organisms.
constitutes
essential
reading
graduate
students,
researchers
practitioners
who
do
not
have
strong
molecular
genetics
willing
use
eDNA
biomonitoring.
Frontiers in Microbiology,
Год журнала:
2018,
Номер
9
Опубликована: Май 1, 2018
The
gut
microbiome
is
a
community
of
host-associated
symbiotic
microbes
that
fulfills
multiple
key
roles
in
host
metabolism,
immune
function,
and
tissue
development.
Given
the
ability
to
impact
fitness,
there
increasing
interest
studying
wild
animals
better
understand
these
communities
context
ecology
evolution.
Human
research
protocols
are
well
established,
but
wildlife
still
developing
field.
Currently,
no
standardized
set
best
practices
guiding
collection
samples
from
wildlife.
Gut
microflora
typically
sampled
either
by
fecal
collection,
rectal
swabbing,
or
destructively
sampling
intestinal
contents
animal.
Studies
rarely
include
more
than
one
technique
comparison
methods
currently
exists
for
mammal.
Although
some
studies
have
hypothesized
nested
subset
microbiome,
this
hypothesis
has
not
been
formally
tested
system.
To
address
issues,
we
examined
guano
(feces)
distal
mucosa
17
species
free-ranging
bats
Lamanai,
Belize,
using
16S
rRNA
amplicon
sequencing
compare
microbial
across
sample
types.
We
found
diversity
composition
intestine
differed
substantially.
In
addition,
conclude
signatures
evolution
retained
microbiomes
based
on
mucosal
samples,
samples.
Conversely,
signal
diet
These
results
suggest
interchangeable,
two
microbiotas
record
different
information
about
which
they
isolated.
Nature Communications,
Год журнала:
2019,
Номер
10(1)
Опубликована: Май 16, 2019
Abstract
Multiple
factors
modulate
microbial
community
assembly
in
the
vertebrate
gut,
though
studies
disagree
as
to
their
relative
contribution.
One
cause
may
be
a
reliance
on
captive
animals,
which
can
have
very
different
gut
microbiomes
compared
wild
counterparts.
To
resolve
this
disagreement,
we
analyze
new,
large,
and
highly
diverse
animal
distal
16
S
rRNA
microbiome
dataset,
comprises
80%
animals
includes
members
of
Mammalia,
Aves,
Reptilia,
Amphibia,
Actinopterygii.
We
decouple
effects
host
evolutionary
history
diet
diversity
show
that
each
factor
modulates
aspects
diversity.
Moreover,
particular
taxa
associated
with
phylogeny
or
Mammalia
stronger
signal
cophylogeny.
Finally,
find
environmental
filtering
microbe-microbe
interactions
differ
among
clades.
These
findings
provide
robust
assessment
processes
driving
intestine.
The
trillions
of
microbes
living
in
the
gut—the
gut
microbiota—play
an
important
role
human
biology
and
disease.
While
much
has
been
done
to
explore
its
diversity,
a
full
understanding
our
microbiomes
demands
evolutionary
perspective.
In
this
review,
we
compare
from
populations,
placing
them
context
humanity’s
near
distant
animal
relatives.
We
discuss
potential
mechanisms
generate
host-specific
microbiome
configurations
consequences
disrupting
those
configurations.
Finally,
propose
that
broader
phylogenetic
perspective
is
useful
for
underlying
human–microbiome
interactions.
In
this
comprehensive
survey
of
microbiomes
>900
species,
including
315
mammals
and
491
birds,
we
find
a
striking
convergence
the
birds
animals
that
fly.
nonflying
mammals,
diet
short-term
evolutionary
relatedness
drive
microbiome,
many
microbial
species
are
specific
to
particular
kind
mammal,
but
flying
break
pattern
with
microbes
shared
across
different
little
correlation
either
or
hosts.
This
finding
suggests
adaptation
flight
breaks
long-held
relationships
between
hosts
their
microbes.
