World Journal of Gastroenterology,
Journal Year:
2015,
Volume and Issue:
21(29), P. 8787 - 8787
Published: Jan. 1, 2015
Relation
between
the
gut
microbiota
and
human
health
is
being
increasingly
recognised.It
now
well
established
that
a
healthy
flora
largely
responsible
for
overall
of
host.The
normal
comprises
two
major
phyla,
namely
Bacteroidetes
Firmicutes.Though
in
an
infant
appears
haphazard,
it
starts
resembling
adult
by
age
3
years.Nevertheless,
there
exist
temporal
spatial
variations
microbial
distribution
from
esophagus
to
rectum
all
along
individual's
life
span.Developments
genome
sequencing
technologies
bioinformatics
have
enabled
scientists
study
these
microorganisms
their
function
microbehost
interactions
elaborate
manner
both
disease.The
imparts
specific
host
nutrient
metabolism,
xenobiotic
drug
maintenance
structural
integrity
mucosal
barrier,
immunomodulation,
protection
against
pathogens.Several
factors
play
role
shaping
microbiota.They
include
(1)
mode
delivery
(vaginal
or
caesarean);
(2)
diet
during
infancy
(breast
milk
formula
feeds)
adulthood
(vegan
based
meat
based);
(3)
use
antibiotics
antibiotic
like
molecules
are
derived
environment
commensal
community.A
concern
long-term
alteration
horizontal
transfer
resistance
genes
could
result
reservoir
organisms
with
multidrug
resistant
gene
pool.
PLoS ONE,
Journal Year:
2013,
Volume and Issue:
8(4), P. e61217 - e61217
Published: April 22, 2013
Background
The
analysis
of
microbial
communities
through
DNA
sequencing
brings
many
challenges:
the
integration
different
types
data
with
methods
from
ecology,
genetics,
phylogenetics,
multivariate
statistics,
visualization
and
testing.
With
increased
breadth
experimental
designs
now
being
pursued,
project-specific
statistical
analyses
are
often
needed,
these
difficult
(or
impossible)
for
peer
researchers
to
independently
reproduce.
vast
majority
requisite
tools
performing
reproducibly
already
implemented
in
R
its
extensions
(packages),
but
limited
support
high
throughput
microbiome
census
data.
Results
Here
we
describe
a
software
project,
phyloseq,
dedicated
object-oriented
representation
R.
It
supports
importing
variety
common
formats,
as
well
techniques.
These
include
calibration,
filtering,
subsetting,
agglomeration,
multi-table
comparisons,
diversity
analysis,
parallelized
Fast
UniFrac,
ordination
methods,
production
publication-quality
graphics;
all
manner
that
is
easy
document,
share,
modify.
We
show
how
apply
functions
other
packages
phyloseq-represented
data,
illustrating
availability
large
number
open
source
discuss
use
phyloseq
reproducible
research,
practice
fields
still
rare
highly
parallel
have
made
available
materials
necessary
completely
reproduce
figures
included
this
article,
an
example
best
practices
research.
Conclusions
project
new
open-source
package,
freely
on
web
both
GitHub
Bioconductor.
Science,
Journal Year:
2011,
Volume and Issue:
334(6052), P. 105 - 108
Published: Sept. 2, 2011
Diet
strongly
affects
human
health,
partly
by
modulating
gut
microbiome
composition.
We
used
diet
inventories
and
16S
rDNA
sequencing
to
characterize
fecal
samples
from
98
individuals.
Fecal
communities
clustered
into
enterotypes
distinguished
primarily
levels
of
Bacteroides
Prevotella.
Enterotypes
were
associated
with
long-term
diets,
particularly
protein
animal
fat
(Bacteroides)
versus
carbohydrates
(Prevotella).
A
controlled-feeding
study
10
subjects
showed
that
composition
changed
detectably
within
24
hours
initiating
a
high-fat/low-fiber
or
low-fat/high-fiber
diet,
but
enterotype
identity
remained
stable
during
the
10-day
study.
Thus,
alternative
states
are
diet.
