bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2021,
Volume and Issue:
unknown
Published: July 25, 2021
Abstract
Metagenomics
is
a
powerful
method
for
interpreting
the
ecological
roles
and
physiological
capabilities
of
mixed
microbial
communities.
Yet,
many
tools
processing
metagenomic
data
are
not
designed
to
consider
eukaryotes,
nor
they
built
an
increasing
amount
sequence
data.
EukHeist
automated
pipeline
retrieve
eukaryotic
prokaryotic
metagenome
assembled
genomes
(MAGs)
from
large-scale
datasets.
We
developed
workflow
specifically
process
large
amounts
both
and/or
metatranscriptomic
in
reproducible
fashion.
Here,
we
applied
large-size
fraction
(0.8-2000
µm
)
Tara
Oceans
recover
MAGs,
which
refer
as
TOPAZ
(
Particle-Associated
MAGs).
The
MAGs
consisted
>900
environmentally-relevant
>4,000
bacterial
archaeal
MAGs.
expand
known
marine
phylogenetic
diversity
through
increase
coverage
likely
particle-
host-associated
taxa.
also
demonstrate
approach
infer
putative
functional
mode
recovered
A
global
survey
enabled
identification
cohorts,
driven
by
specific
environmental
factors,
host-microbe
associations.
Importance
Despite
importance
single-celled
organisms
environments,
majority
difficult
cultivate
lab.
Sequencing
genetic
material
extracted
samples
enables
researchers
document
naturally-occurring
protistan
However,
conventional
sequencing
methodologies
cannot
separate
out
individual
organisms.
To
more
completely
capture
entire
genomic
content
community,
can
create
bins
sequences
that
represent
same
organism.
scientists
bin
reads,
show
results
provide
exciting
insights
into
what
communities
present
ocean
play
ecosystem.
Accessible
scalable
computational
tools,
such
EukHeist,
accelerate
meaningful
signatures
datasets,
ultimately
expanding
tree
life.
Human Reproduction Open,
Journal Year:
2023,
Volume and Issue:
2023(3)
Published: Jan. 1, 2023
Abstract
STUDY
QUESTION
How
should
recurrent
implantation
failure
(RIF)
in
patients
undergoing
ART
be
defined
and
managed?
SUMMARY
ANSWER
This
is
the
first
ESHRE
good
practice
recommendations
paper
providing
a
definition
for
RIF
together
with
on
how
to
investigate
causes
contributing
factors,
improve
chances
of
pregnancy.
WHAT
IS
KNOWN
ALREADY
challenge
clinic,
multitude
investigations
interventions
offered
applied
clinical
practice,
often
without
biological
rationale
or
unequivocal
evidence
benefit.
DESIGN,
SIZE,
DURATION
document
was
developed
according
predefined
methodology
recommendations.
Recommendations
are
supported
by
data
from
literature,
if
available,
results
previously
published
survey
expertise
working
group.
A
literature
search
performed
PubMed
Cochrane
focussing
‘recurrent
reproductive
failure’,
‘repeated
failure’.
PARTICIPANTS/MATERIALS,
SETTING,
METHODS
The
Working
Group
Recurrent
Implantation
Failure
included
eight
members
representing
Special
Interest
Groups
Early
Pregnancy,
Reproductive
Endocrinology,
Embryology,
an
independent
chair
expert
statistics.
were
formulated
based
opinion
group,
while
taking
into
consideration
uptake
practice.
draft
then
open
online
peer
review
revised
light
comments
received.
MAIN
RESULTS
AND
THE
ROLE
OF
CHANCE
group
recommends
considering
as
secondary
phenomenon
ART,
it
can
only
observed
IVF,
that
following
description
adopted:
‘RIF
describes
scenario
which
transfer
embryos
considered
viable
has
failed
result
positive
pregnancy
test
sufficiently
specific
patient
warrant
further
and/or
interventions'.
It
agreed
recommended
threshold
cumulative
predicted
chance
identify
purposes
initiating
investigation
60%.
When
couple
have
not
had
successful
certain
number
embryo
transfers
associated
greater
than
60%,
they
counselled
treatment
options.
term
defines
actions
considered.
Nineteen
when
suspected,
13
interventions.
colour-coded
whether
investigations/interventions
(green),
(orange),
recommended,
i.e.
routinely
(red).
LIMITATIONS,
REASONS
FOR
CAUTION
While
awaiting
studies
trials,
identifying
individual
restrict
treatments
those
clear
indicating
their
likely
WIDER
IMPLICATIONS
FINDINGS
article
provides
advice
but
also
highlights
need
research.
research,
well-conducted,
will
key
making
progress
management
RIF.
FUNDING/COMPETING
INTEREST(S)
meetings
technical
support
this
project
funded
ESHRE.
N.M.
declared
consulting
fees
ArtPRED
(The
Netherlands)
Freya
Biosciences
(Denmark);
Honoraria
lectures
Gedeon
Richter,
Merck,
Abbott,
IBSA;
being
co-founder
Verso
Biosense.
He
Co-Chief
Editor
Biomedicine
Online
(RBMO).
D.C.
Associate
Human
Reproduction
Update,
honoraria
Organon,
IBSA,
Fairtility;
attending
Cooper
Surgical,
Fujifilm
Irvine
Scientific.
G.G.
he
his
institution
received
financial
non-financial
lectures,
workshops,
advisory
roles,
travelling
Ferring,
Gedeon-Richter,
PregLem,
Vifor,
MSD,
Coopersurgical,
ObsEVA,
ReprodWissen.
journals
Archives
Obstetrics
Gynecology
Online,
Chief
Journal
Gynäkologische
Endokrinologie.
involved
guideline
developments
quality
control
national
international
level.
G.L.
Vianex/Organon,
MSD.
immediate
past
Coordinator
Endocrinology
been
Guideline
Development
fertility
authorities.
D.J.M.
Open
statistical
Advisor
Online.
B.T.
shareholder
Reprognostics
she
her
roles
Exeltis,
Merck
Serono,
Bayer,
Teva,
Theramex
Novartis,
Astropharm,
Ferring.
other
authors
nothing
disclose.
DISCLAIMER
Good
Practice
(GPR)
represents
views
ESHRE,
consensus
between
relevant
stakeholders
scientific
available
at
time
preparation.
GPRs
used
information
educational
purposes.
They
interpreted
setting
standard
care
deemed
inclusive
all
proper
methods
care,
exclusive
reasonably
directed
obtaining
same
results.
do
replace
application
judgement
each
presentation,
variations
locality
facility
type.
Furthermore,
constitute
imply
endorsement,
favouring,
any
technologies
International Journal of Molecular Sciences,
Journal Year:
2022,
Volume and Issue:
23(1), P. 485 - 485
Published: Jan. 1, 2022
Changes
in
the
female
genital
tract
microbiome
are
consistently
correlated
to
gynecological
and
obstetrical
pathologies,
dysbiosis
can
impact
reproductive
outcomes
during
fertility
treatment.
Nonetheless,
a
consensus
regarding
physiological
core
inside
uterine
cavity
has
not
been
reached
due
myriad
of
study
limitations,
such
as
sample
size
experimental
design
variations,
influence
endometrial
bacterial
communities
on
human
reproduction
remains
debated.
Understanding
healthy
microbiota
how
changes
its
composition
affect
would
potentially
allow
personalized
treatment
through
management
assisted
therapies,
ultimately
leading
improvement
clinical
outcomes.
Here,
we
review
current
knowledge
it
relates
conception.
Nature Communications,
Journal Year:
2025,
Volume and Issue:
16(1)
Published: Jan. 14, 2025
The
gut
microbiome
significantly
impacts
human
health,
yet
cultivation
challenges
hinder
its
exploration.
Here,
we
combine
deep
whole-metagenome
sequencing
with
culturomics
to
selectively
enrich
for
taxa
and
functional
capabilities
of
interest.
Using
a
modified
commercial
base
medium,
50
growth
modifications
were
evaluated,
spanning
antibiotics,
physico-chemical
conditions,
bioactive
compounds.
Whole-metagenome
identified
medium
additives,
like
caffeine,
that
enhance
often
associated
healthier
subjects
(e.g.,
Lachnospiraceae,
Oscillospiraceae,
Ruminococcaceae).
We
also
explore
the
impact
on
composition
cultured
communities
establish
link
between
preference
microbial
phylogeny.
Leveraging
these
insights,
demonstrate
combinations
media
can
further
targeted
enrichment
metabolic
functions,
such
as
Collinsella
aerofaciens,
or
strains
harboring
biochemical
pathways
involved
in
dopamine
metabolism.
This
streamlined,
scalable
approach
unlocks
potential
selective
enrichment,
advancing
research
by
understanding
different
parameters
microbes.
Frontiers in Reproductive Health,
Journal Year:
2022,
Volume and Issue:
4
Published: Aug. 9, 2022
The
intricate
interactions
between
the
host
cells,
bacteria,
and
immune
components
that
reside
in
female
reproductive
tract
(FRT)
are
essential
maintaining
homeostasis.
Much
of
our
current
knowledge
surrounding
FRT
microbiota
relates
to
vaginal
microbiota,
where
‘health’
has
long
been
associated
with
low
bacterial
diversity
Lactobacillus
dominance.
This
concept
recently
challenged
as
women
can
have
a
diverse
microbial
composition
absence
symptomatic
disease.
structures
upper
(the
endocervix,
uterus,
Fallopian
tubes,
ovaries)
distinct,
lower
biomass
microbiotas
than
vagina;
however,
existence
permanent
at
these
sites
is
disputed.
During
homeostasis,
balance
exists
bacteria
system
maintains
quiescence.
Alterations
system,
or
local
environment
may
result
perturbances
defined
dysbiosis.
inflammatory
signature
perturbed
“dysbiotic”
characterized
by
elevated
concentrations
pro-inflammatory
cytokines
cervical
fluid.
It
appears
homeostasis
be
disrupted
two
different
mechanisms:
first,
shift
toward
increased
trigger
inflammation,
second,
immunity
altered
some
manner,
which
disrupts
response
an
environmental
change.
dysbiosis
negative
effects
on
health.
review
will
examine
increasing
evidence
for
involvement
inflammation
gynecologic
conditions
such
endometriosis,
infertility,
endometrial
ovarian
cancer;
precise
mechanisms
involved
remains
speculative
present.
While
only
their
infancy,
use
antibiotics
probiotics
therapeutically
alter
being
studied
discussed
herein.
Our
understanding
intimate
relationship
its
early
days,
more
research
needed
deepen
mechanistic
this
assess
how
present
harnessed
assist
diagnosis
treatment
conditions.
Computational and Structural Biotechnology Journal,
Journal Year:
2022,
Volume and Issue:
20, P. 1541 - 1553
Published: Jan. 1, 2022
The
presence
of
microbial
communities
in
the
reproductive
tract
has
been
revealed,
and
this
resident
microbiota
is
involved
maintenance
health.
Intentional
modulation
via
probiotics
proposed
as
a
possible
strategy
to
enhance
health
reduce
risk
diseases.
male
seminal
suggested
an
important
factor
that
influences
couple's
health,
pregnancy
outcomes,
offspring
Probiotics
have
reported
play
role
fertility
affect
mothers
offspring.
While
female
more
complicated
identified
both
upper
lower
systems,
they
together
contribute
maintenance.
shown
regulatory
effects
on
tract,
thereby
contributing
homeostasis
influencing
Further,
through
transmission
bacteria
or
other
indirect
mechanisms,
parent's
probiotic
intervention
influence
infant
gut
colonization
immunity
development,
with
potential
consequences.
In
vitro
vivo
studies
explored
mechanisms
underlying
benefits
administration
intervention,
array
positive
results,
such
composition,
regulation
metabolism,
promotion
epithelial
barrier,
improvement
immune
function,
observed.
Herein,
we
review
state
art
system
its
reproduction,
well
beneficial
their
contributions
prevention
associated
Reproduction,
Journal Year:
2022,
Volume and Issue:
163(5), P. R81 - R96
Published: Feb. 23, 2022
Microbiome
or
microbiota
is
essential
to
regulate
many
mammalian
physiological
processes,
including
reproduction.
Like
other
organs
tissues,
the
upper
female
reproductive
tract
used
be
considered
as
devoid
of
microorganisms;
however,
a
non-infection-related
bacterial
community
was
discovered
in
uterus
from
humans
and
mammals,
its
composition
related
success.
The
dysbiosis
endometrial
associated
with
benign
malign
uterine
diseases.
Hence,
this
review
addressed
current
knowledge
about
alterations
their
association
common
diseases,
polyposis,
endometriosis,
myomatosis,
hyperplasia,
cancer.
There
specific
endometrium
most-analyzed
However,
constant
finding
consists
reduced
abundance
Firmicutes
Lactobacillus
,
while
there
an
increased
Proteobacteria
(such
Escherichia
coli
Enterococcus
),
Bacteroidetes
(
Prevotella
for
example),
Actinobacteria
(as
Gardnerella
contrast
healthy
endometrium.
Besides,
we
discussed
future
usefulness
components
biomarkers
diagnose
diseases
probable
clinical
outcomes.
In
addition,
analyzed
potential
use
probiotics
since
they
could
provide
alternative
complement
existing
therapies.
Frontiers in Cellular and Infection Microbiology,
Journal Year:
2022,
Volume and Issue:
12
Published: Dec. 16, 2022
Every
year,
millions
of
women
are
affected
by
genital
tract
disorders,
such
as
bacterial
vaginosis
(BV),
endometrial
cancer,
polycystic
ovary
syndrome
(PCOS),
endometriosis,
and
uterine
fibroids
(UFs).
These
disorders
pose
a
significant
economic
burden
on
healthcare
systems
have
serious
implications
for
health
fertility
outcomes.
This
review
explores
the
relationships
between
gut,
vaginal,
dysbiosis
pathogenesis
various
diseases
female
tract.
In
recent
years,
reproductive
clinicians
scientists
focused
microbiome
to
investigate
its
role
in
prevention
diseases.
Recent
studies
microbiomes
identified
patterns
composition
changes
across
individuals'
lives
associated
with
specific
healthy
diseased
states,
particularly
regarding
effects
estrogen-gut
axis
estrogen-driven
(such
UFs)
estrogen
deficiency
PCOS).
Furthermore,
this
discusses
contribution
vitamin
D
gut
altered
metabolism
well
how
these
play
key
roles
UFs.
More
research
influences
is
vital.
Reproductive BioMedicine Online,
Journal Year:
2022,
Volume and Issue:
45(5), P. 1021 - 1031
Published: June 17, 2022
Is
the
composition
of
endometrial
or
vaginal
microbiota
associated
with
recurrent
pregnancy
loss
(RPL)?Endometrial
and
samples
were
collected
from
47
women
two
more
consecutive
losses
39
healthy
control
without
a
history
loss,
between
March
2018
December
2020
at
Helsinki
University
Hospital,
Helsinki,
Finland.
The
compositions
microbiota,
analysed
using
16S
rRNA
gene
amplicon
sequencing,
compared
RPL
women,
individual
samples.
mycobiota
was
internal
transcribed
spacer
1
sequencing
for
descriptive
summary.
models
adjusted
body
mass
index,
age
parity.
False
discovery
rate-corrected
P-values
(q-values)
used
to
define
nominal
statistical
significance
q
<
0.05.Lactobacillus
crispatus
less
abundant
in
controls
(mean
relative
abundance
17.2%
versus
45.6%,
=
0.04).
Gardnerella
vaginalis
group
than
both
(12.4%
5.8%,
0.001)
(8.7%
5.7%,
0.002)
microbial
correlated
strongly
(R
0.85,
P
0.001).
Fungi
detected
22%
36%
samples.Dysbiosis
reproductive
tract
is
may
represent
novel
risk
factor
losses.