bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Фев. 16, 2023
Abstract
Background
While
genome-resolved
metagenomics
has
revolutionized
our
understanding
of
microbial
and
genetic
diversity
in
environmental
samples,
assemblies
short-reads
often
result
incomplete
and/or
highly
fragmented
metagenome-assembled
genomes
(MAGs),
hampering
in-depth
genomics.
Although
Nanopore
sequencing
increasingly
been
used
as
long
reads
greatly
improve
the
assembly
quality
MAGs,
recommended
DNA
quantity
usually
exceeds
recoverable
amount
samples.
Here,
we
evaluated
lower-than-recommended
quantities
for
library
preparation
by
determining
quality,
community
composition,
recovery
MAGs.
Results
We
generated
27
metagenomes
using
commercially
available
ZYMO
mock
varied
input
from
1000
ng
(the
minimum)
down
to
1
eight
steps.
The
remained
stable
across
all
levels.
read
mapping
accuracy,
which
reflects
how
well
match
a
known
reference
genome,
was
consistently
high
libraries.
relative
abundance
species
levels
50
ng.
High-quality
MAGs
(>
95%
completeness,
≤
5%
contamination)
could
be
recovered
35
material.
When
combined
with
publicly
Illumina
community,
low
improved
hybrid
assemblies.
Conclusion
Our
results
show
that
can
substantially
reduced
without
any
adverse
effects
genome
still
bolster
when
short-read
data.
posit
presented
herein
will
enable
studies
low-biomass
environments,
enhancing
microbiome
understanding.
Nature Communications,
Год журнала:
2022,
Номер
13(1)
Опубликована: Июнь 13, 2022
Abstract
The
ESCRT
machinery,
comprising
of
multiple
proteins
and
subcomplexes,
is
crucial
for
membrane
remodelling
in
eukaryotic
cells,
processes
that
include
ubiquitin-mediated
multivesicular
body
formation,
repair,
cytokinetic
abscission,
virus
exit
from
host
cells.
This
system
appears
to
have
simpler,
ancient
origins,
since
many
archaeal
species
possess
homologues
ESCRT-III
Vps4,
the
components
execute
final
scission
reaction,
where
they
been
shown
play
roles
cytokinesis,
extracellular
vesicle
formation
viral
egress.
Remarkably,
metagenome
assemblies
Asgard
archaea,
closest
known
living
relatives
eukaryotes,
were
recently
encode
entire
cascade
involved
remodelling,
including
ubiquitin
itself,
ESCRT-I
ESCRT-II
Vps4.
Here,
we
explore
phylogeny,
structure,
biochemistry
machinery
associated
ubiquitylation
system.
We
provide
evidence
subcomplexes
being
ubiquitin-directed
recruitment
ESCRT-III,
as
it
eukaryotes.
Taken
together,
our
analyses
suggest
a
pre-eukaryotic
origin
ubiquitin-coupled
likely
path
evolution
via
series
gene
duplication
diversification
events.
Nearly
all
organisms
are
hosts
to
multiple
viruses
that
collectively
appear
be
the
most
abundant
biological
entities
in
biosphere.
With
recent
advances
metagenomics
and
metatranscriptomics,
known
diversity
of
substantially
expanded.
Comparative
analysis
these
using
advanced
computational
methods
culminated
reconstruction
evolution
major
groups
enabled
construction
a
virus
megataxonomy,
which
has
been
formally
adopted
by
International
Committee
on
Taxonomy
Viruses.
This
comprehensive
taxonomy
consists
six
realms,
aspired
monophyletic
assembled
based
conservation
hallmark
proteins
involved
capsid
structure
formation
or
genome
replication.
The
different
taxa
differ
host
range
accordingly
ecological
niches.
In
this
review
article,
we
outline
latest
developments
megataxonomy
discoveries
will
likely
lead
reassessment
some
taxa,
particular,
split
three
current
realms
into
two
more
independent
realms.
We
then
discuss
correspondence
between
distribution
among
niches,
as
well
abundance
versus
cells
habitats.
across
environments
appears
primarily
determined
ranges,
i.e.
virome
is
shaped
composition
biome
given
habitat,
itself
affected
abiotic
factors.
Nature Microbiology,
Год журнала:
2023,
Номер
8(2), С. 231 - 245
Опубликована: Янв. 19, 2023
Abstract
‘
Candidatus
Methanophagales’
(ANME-1)
is
an
order-level
clade
of
archaea
responsible
for
anaerobic
methane
oxidation
in
deep-sea
sediments.
The
diversity,
ecology
and
evolution
ANME-1
remain
poorly
understood.
In
this
study,
we
use
metagenomics
on
hydrothermal
samples
to
expand
diversity
uncover
the
effect
virus–host
dynamics.
Phylogenetic
analyses
reveal
a
deep-branching,
thermophilic
family,
Methanospirareceae’,
closely
related
short-chain
alkane
oxidizers.
Global
phylogeny
near-complete
genomes
show
that
hydrogen
metabolism
within
ancient
trait
was
vertically
inherited
but
differentially
lost
during
lineage
diversification.
Metagenomics
also
uncovered
16
undescribed
virus
families
so
far
exclusively
targeting
archaea,
showing
unique
structural
replicative
signatures.
expansive
virome
contains
metabolic
gene
repertoire
can
influence
host
through
virus-mediated
displacement.
Our
results
suggest
evolutionary
continuum
between
oxidizers
underscore
effects
viruses
dynamics
methane-driven
ecosystems.
Proceedings of the National Academy of Sciences,
Год журнала:
2022,
Номер
119(5)
Опубликована: Янв. 25, 2022
Viruses
are
a
distinct
type
of
replicators
that
encode
structural
proteins
encasing
virus
genomes
in
virions.
For
some
the
widespread
capsid
and
other
major
components
virions,
likely
ancestors
encoded
by
cellular
life
forms
identifiable.
In
particular,
one
most
common
proteins,
with
single
jelly-roll
(SJR)
fold,
appears
to
have
evolved
from
particular
family
carbohydrate-binding
proteins.
However,
double
protein
(DJR-MCP),
hallmark
enormously
diverse
viruses
kingdom
Nature Microbiology,
Год журнала:
2022,
Номер
7(7), С. 948 - 952
Опубликована: Июнь 27, 2022
Asgard
archaea
have
recently
been
identified
as
the
closest
archaeal
relatives
of
eukaryotes.
Their
ecology,
and
particularly
their
virome,
remain
enigmatic.
We
reassembled
closed
chromosome
Candidatus
Odinarchaeum
yellowstonii
LCB_4,
through
long-range
PCR,
revealing
CRISPR
spacers
targeting
viral
contigs.
found
related
viruses
in
genomes
diverse
prokaryotes
from
geothermal
environments,
including
other
archaea.
These
open
research
avenues
into
ecology
evolution
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY,
Год журнала:
2023,
Номер
73(5)
Опубликована: Май 9, 2023
Microbiology
Society
journals
contain
high-quality
research
papers
and
topical
review
articles.
We
are
a
not-for-profit
publisher
we
support
invest
in
the
microbiology
community,
to
benefit
of
everyone.
This
supports
our
principal
goal
develop,
expand
strengthen
networks
available
members
so
that
they
can
generate
new
knowledge
about
microbes
ensure
it
is
shared
with
other
communities.
Systematic and Applied Microbiology,
Год журнала:
2024,
Номер
47(4), С. 126525 - 126525
Опубликована: Июнь 15, 2024
Asgardarchaeota,
commonly
referred
to
as
Asgard
archaea,
is
a
candidatus
phylum-rank
archaeal
clade
that
includes
the
closest
relatives
of
eukaryotes.
Despite
their
prevalence
in
scientific
literature,
name
Asgardarchaeota
lacks
nomenclatural
validation.
Here,
we
describe
novel
high-quality
metagenome-assembled
genome
(MAG),
AB3033_2
