Microorganisms,
Год журнала:
2018,
Номер
6(3), С. 75 - 75
Опубликована: Июль 23, 2018
Akkermansia
muciniphila
is
a
mucin-degrading
bacterium
of
the
phylum
Verrucomicrobia.
Its
abundance
in
human
intestinal
tract
inversely
correlated
to
several
disease
states.
A.
resides
mucus
layer
large
intestine,
where
it
involved
maintaining
integrity.
We
explore
presence
Akkermansia-like
spp.
based
on
its
16S
rRNA
sequence
and
metagenomic
signatures
body
so
as
understand
colonization
pattern
time
space.
were
detected
colonic
samples
early
few
weeks
after
birth
likely
could
be
maintained
throughout
life.
The
sites
sequences
(including
Verrucomicrobia
and/or
found
literature)
apart
from
colon
included
milk,
oral
cavity,
pancreas,
biliary
system,
small
appendix.
function
these
may
differ
that
mucosal
colon.
present
appendix
or
milk
play
role
re-colonization
breast-fed
infants,
respectively.
In
conclusion,
even
though
most
abundantly
colon,
along
digestive
indicates
this
might
have
more
functions
than
those
currently
known.
Nucleic Acids Research,
Год журнала:
2023,
Номер
51(W1), С. W115 - W121
Опубликована: Май 1, 2023
Carbohydrate
active
enzymes
(CAZymes)
are
made
by
various
organisms
for
complex
carbohydrate
metabolism.
Genome
mining
of
CAZymes
has
become
a
routine
data
analysis
in
(meta-)genome
projects,
owing
to
the
importance
bioenergy,
microbiome,
nutrition,
agriculture,
and
global
carbon
recycling.
In
2012,
dbCAN
was
provided
as
an
online
web
server
automated
CAZyme
annotation.
dbCAN2
(https://bcb.unl.edu/dbCAN2)
further
developed
2018
meta
combine
multiple
tools
improved
also
included
CGC-Finder,
tool
identifying
gene
clusters
(CGCs)
(meta-)genomes.
We
have
updated
dbCAN3
with
following
new
functions
components:
(i)
dbCAN-sub
profile
Hidden
Markov
Model
database
(HMMdb)
substrate
prediction
at
subfamily
level;
(ii)
searching
against
experimentally
characterized
polysaccharide
utilization
loci
(PULs)
known
glycan
substates
dbCAN-PUL
CGC
(iii)
majority
voting
method
consider
all
predicted
from
(iv)
browsing
visualization
results
on
website.
summary,
not
only
inherits
dbCAN2,
but
integrates
three
methods
prediction.
Cell Host & Microbe,
Год журнала:
2019,
Номер
26(5), С. 666 - 679.e7
Опубликована: Окт. 10, 2019
Prevotella
copri
is
a
common
human
gut
microbe
that
has
been
both
positively
and
negatively
associated
with
host
health.
In
cross-continent
meta-analysis
exploiting
>6,500
metagenomes,
we
obtained
>1,000
genomes
explored
the
genetic
population
structure
of
P.
copri.
encompasses
four
distinct
clades
(>10%
inter-clade
divergence)
propose
constitute
complex,
all
were
confirmed
by
isolate
sequencing.
These
are
nearly
ubiquitous
co-present
in
non-Westernized
populations.
Genomic
analysis
showed
substantial
functional
diversity
complex
notable
differences
carbohydrate
metabolism,
suggesting
multi-generational
dietary
modifications
may
be
driving
reduced
prevalence
Westernized
Analysis
ancient
metagenomes
highlighted
patterns
presence
consistent
modern
populations
clade
delineation
time
pre-dating
migratory
waves
out
Africa.
findings
reveal
exhibits
high
underrepresented
Western-lifestyle
Microorganisms,
Год журнала:
2018,
Номер
6(3), С. 75 - 75
Опубликована: Июль 23, 2018
Akkermansia
muciniphila
is
a
mucin-degrading
bacterium
of
the
phylum
Verrucomicrobia.
Its
abundance
in
human
intestinal
tract
inversely
correlated
to
several
disease
states.
A.
resides
mucus
layer
large
intestine,
where
it
involved
maintaining
integrity.
We
explore
presence
Akkermansia-like
spp.
based
on
its
16S
rRNA
sequence
and
metagenomic
signatures
body
so
as
understand
colonization
pattern
time
space.
were
detected
colonic
samples
early
few
weeks
after
birth
likely
could
be
maintained
throughout
life.
The
sites
sequences
(including
Verrucomicrobia
and/or
found
literature)
apart
from
colon
included
milk,
oral
cavity,
pancreas,
biliary
system,
small
appendix.
function
these
may
differ
that
mucosal
colon.
present
appendix
or
milk
play
role
re-colonization
breast-fed
infants,
respectively.
In
conclusion,
even
though
most
abundantly
colon,
along
digestive
indicates
this
might
have
more
functions
than
those
currently
known.
