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Your poop is important to understand because, guess what, we're all full of it. Anyone who says otherwise
doesn't know s**t. We produce over 1,000 pounds of feces every year (approx weight of a concert piano)!
Furthermore, at any given time, four pounds of our poop is made up of bonafide bacteria. Thats right,
bacteria. But not all bacteria is bad. In fact, if it wasn't for the good and the bad - we need 'em both - our
immune systems would be dysfunctional.

most of our immune system is found tied up in our guts. Its known as G.A.L.T or gut associated lymphoid
tissue. What may surprise you is that our guts are also chemically similar to our brains in that they share
similar neurotransmitters. Intestines are loaded with nerves that stimulate the muscles that line your pipes
to move food down the line. So, if our guts ain't happy, nor are we.
There are important factors to consider when you take audit of your poop.
First, pre and probiotics. Although you can't see them with the naked eye in order to audit these buggers, they do
need to be accounted for. Prebiotics are key elements found in foods like onions, garlic, asparagus, and artichoke
which all contain inulin that feed the beneficial probiotics in question. Probiotics are beneficial bacteria -
sometimes called the friendly germs - that help maintain a healthy intestine, where it is believed that up to 80
percent of our immune system lives. There are various tests to help your health care practitioner determine the
health of your poop, including what amount and types of bacteria - good and bad - grow there.
There may be an unhealthy war against bacteria these days. It may be hight time to summon our natural allies. If
we don't pay close attention to the balance of power that is in our guts, then bacteria will learn their way around
our most powerful medical weapons and our most prudent methods of hygeine prevention. Rather than a futile
effort to eradicate 99.99% of germs on our countertop and sparying our fruit and veggie crops with such harsh
pesticides, perhaps we should pay some attention to our own immune systems. Take for example antibiotic
resistant bacteria. They may be small, but they're not "dumb". Bacteria have evolved for billions of years with an
M.O. to survive. And, yet, is is the natural health products that play an important role in slowing the development
of methicillin-resistant Staphylococcus aureus (or MRSA) and similar bacteria. Rather than throwing powerful
antibiotics at nearly everything that presents as an infection - including viral infections, which are not affected by
antibiotics - we should consider using antibacterial and antiseptic herbs, homeopathics and nutraceuticals as a
first line of defence. These are far less likely develop resistant strains. Save antibiotics - which can be life saving -
for when you really need them.
Some excellent modern research shows that probiotics help maintain a healthy intestine by keeping harmful
bacteria and yeasts in the gut under control. Probiotics can be taken as capsules, tablets, beverages, powders,
therapeutic 'yogurts' and other foods. An increasing number of studies support the use of probiotics as a
supplement to antibiotic therapy and even treatment in C.Diff infection which causes sever diarrhea. Sadly, there
was an outbreak of C.Diff infection at a hospital in southern Ontario resulting in one death and eleven more palced
in isolation at the time this article was written. Some probiotics may also help prevent the development of antibiotic
resistance and evidence with daycare children given probiotics suggests a reduction in the number of sick days,
the frequency of respiratory tract infections, and the frequency of related antibiotic treatments.
An interesting recent study suggests that supplementation of infant formulas with probiotics is one approach for
the management of cow's milk allergy. Probiotics have been found to enhance the digestion and absorption of
proteins, fats, calcium and phosphorus. It may also turn out that they can help to overcome lactose intolerance.
Probiotics also help you to fend of colds, bacterial infections, and other diseases. Food, hormones, stress, and
exercise all influence composition and activity of probiotic status in your gut. And other than C.Diff, probiotics also
help prevent and treat Allergies, prevention of Atopic Dermatitis, IBS, IBD, UTIs, Yeast and other Vaginal
infections.
The diagram to the right illustrates the
probiotic layer (green) living on the surface
of a layer of mucus (turquoise). The arrows
indicate their ability to repel yeasts,
bacteria and fungi.
Acidophilus actually looks like this
This friendly bacteria has many helpful
functions and lives as the dominant
species in the small intestine. Here, it
creates an acidic microenvironment next to
the absorption cells, promoting iron
absorption. One of the causes
of anemiacan be damage to this acid layer
as inceliac disease. Many people are
anemic and correcting this lack by taking
acidophilus daily can help promote iron
absorption. A good acidophilus can be
obtained directly from a reputable company
When acidophilus is in a healthy condition,
one may observe projections from the tips
of the bacteria - acidophilus buds. These
are the beginning of new acidophilus cells
which signifies the health of the bacteria.
The following drawing shows an illustration
of the healthy intestinal villi. These finger-
like projections are how we absorb our
food. Probiotic bacteria stand on guard to
protect us from potential bacterial, viral and
yeast invaders. The probiotics are
illustrated in green.
This illustration demonstrates the situation
in which antibiotics have largely killed off
the probiotic bacteria (in green). The tips of
the villi are exposed - a situation created
by using NSAIDS which decrease mucus
production. This leaves the intestine
susceptible to invasion by yeasts and can
lead to a condition called leaky gut.
During a course of antibiotics and for an
extended period afterward it is important to
protect the intestine by taking probiotics .
Don't take the probiotics with the antibiotic
- they just get killed. Take them in between.
Probiotics for marine aquaculture health
Aquaculture is currently the fastest growing food-
production sector in Asian-Pacific countries.
Aquaculture farming is a main production activity of
poor coastal communities because of its high profit for
food export and excellent natural conditions
yearround for culture. However, there is a serious
problem with microbial disease outbreaks, leading to an
annual total loss of millions of $ in shrimp culture. A
major bacterial disease of shrimps is vibriosis, which is
caused by Vibrio species. Owing to the problem of
antibiotic resistance and subsequent reluctance of
using antibiotics, the usage of beneficial bacteria as
probiotic biocontrol agents is becoming increasingly
popular. A few species of microorganisms, such as
lactic acid bacteria and Bacillus species, are
attempted as probionts against pathogenic Vibrio.
Some commercial probiotics are currently available, but
all of them are either very expensive for farmers or
unsuitable for local cultured conditions.
A fraction of ingested probiotics are able to interact with intestinal epithelial cells (IECs) and dendritic cells
(DCs), depending on the presence of a dynamic mucus layer. Probiotics can occasionally encounter DCs
through two routes: DCs residing in the lamina propria sample luminal bacterial antigens by passing their
dendrites between IECs into the gut lumen
118
, and DCs can also interact directly with bacteria that have gained
access to the dome region of the gut-associated lymphoid tissue (GALT) through specialized epithelial cells,
termed microfold or M cells
119
. The interaction of the host cells with microorganism-associated molecular
patterns (MAMPs) that are present on the surface macromolecules of probiotic bacteria will induce a certain
molecular response. The host pattern recognition receptors (PRRs) that can perceive probiotic signals include
Toll-like receptors (TLRs) and the C type lectin DC-specific intercellular adhesion molecule 3-grabbing non-
integrin (DC-SIGN). Some molecular responses of IECs depend on the subtype of cell, for example, Paneth
cells produce defensins and goblet cells produce mucus. Important responses of DCs against probiotics include
the production of cytokines, major histocompatibility complex molecules for antigen presentation, and co-
stimulatory molecules that polarize T cells into T helper or CD4
+
CD25
+
regulatory T cells in the mesenteric
lymph nodes (MLNs) or subepithelial dome of the GALT. IFN, interferon-; IL, interleukin; TGFb; transforming
growth factor-.
Interaction of probiotic bacteria with IECs and DCs from the
GALT.
Schematic diagram illustrating potential or known mechanisms whereby probiotic bacteria
might impact on the microbiota. These mechanisms include (1) competition for dietary
ingredients as growth substrates, (2) bioconversion of, for example, sugars into
fermentation products with inhibitory properties, (3) production of growth substrates, for
example, EPS or vitamins, for other bacteria, (4) direct antagonism by bacteriocins, (5)
competitive exclusion for binding sites, (6) improved barrier function, (7) reduction of
inflammation, thus altering intestinal properties for colonization and persistence within,
and (8) stimulation of innate immune response (by unknown mechanisms). IEC: epithelial
cells, DC: dendritic cells, T:T-cells
The intestinal environment modulates cellular differentiation in
the immune system to control defence against pathogens and
tolerance to commensal species. Tolerance depends, among
other things, on appropriate innate defence mechanisms that
limit microbial entry into intestinal tissues. Intestinal epithelial
cells provide a physical barrier between the luminal
microorganisms and the underlying intestinal tissues to
control homeostasis and tolerance. Specialized epithelial cells
produce a mucus layer (goblet cells) and secrete antimicrobial
proteins (Paneth cells) that limit bacterial exposure to the
epithelial cells. Production of large amounts of secretory
immunoglobulin A (sIgA) by B cells provides additional
protection from the luminal microbiota. Innate microbial
sensing by epithelial cells, dendritic cells (DCs) and
macrophages is mediated through pattern recognition
receptors (PRRs) such as Toll-like receptors (TLRs).
Activation of PRRs on innate immune cells normally induces
pathways that mediate microbial killing and activate pro-
inflammatory T helper 1 (T
H
1) and T
H
17 cells and adaptive
immune cells. During the maintenance of homeostasis and
immune tolerance, however, activation of PRRs on
macrophages and DCs in the intestinal lamina propria does
not result in secretion of pro-inflammatory cytokines. DCs
instead present antigen to T cells in the Peyer's patches and
mesenteric lymph nodes, and this can lead to differentiation of
regulatory T (T
Reg
) cell populations that are regulated by
interleukin-10 (IL-10), transforming growth factor- (TGF )
and retinoic acid. Factors secreted by epithelial cells in the
intestinal environment can contribute to tolerance of intestinal
immune cells.FM, follicular mantle; GC, germinal centre; IFN,
interferon-; M cell, microfold cell.
Mechanisms of host defence against and tolerance to intestinal
microorganisms
Probiotics are friendly
microorganisms inhabiting our
digestive tract that aid digestion and
may confer additional health benefits.
Prebiotics are non-living, non-
digestible carbs that serve as food for
Probiotics
Probiotics are, for the most part,
bacteria that reside in our intestinal
tract. Other types of probiotics are
yeast. Probiotics get into our
intestines from foods we eat or
supplements. There are many types
of probiotics, and each one
behaves a bit differently in our gut.
Although the term probiotics is
relatively new, weve been ingesting
them for thousands of years. Any
food that is cultured or fermented
has probiotics
On to prebiotics. Unlike probitoics, these
are not alive. Most prebiotics are some
form of fiber. Our body does not digest
fiber, but the bacteria in our gut, including
the probiotics, digest the fiber. Feeding
these helpful bacteria keeps them doing
what they are supposed to do in order to
help our health
Synbiotics are defined as products containing both Prebiotic(s) and Probiotic(s).
The presence of Prebiotic(s) has a beneficial effect on both the stability of the
Probiotic(s) in the product and its survival after introduction in the gastro-intestinal
tract, throughout the presence of the Prebiotic.

Both work together in a synergistic way more efficiently promoting the probiotics'
benefits.
Prebiotics are selectively fermented, dietary ingredients that result in specific changes in
the composition and/or activity of the gastrointestinal micro flora thus conferring benefits
upon host health. Unlike probiotics, a prebiotic targets the micro flora already present within
the ecosystem, it acts as a 'food' for the target microbes.


The most widely accepted prebiotics are FOS (fructo- oligosaccharides) and GOS (galacto-
oligosaccharides). FOS and GOS occur naturally in foods such as asparagus, garlic,
artichoke, onion, wheat and oat, as well as soybean. However, it would take a large quantity
of these foods for their active oligosaccharides to exert a useful prebiotic effect. A more
realistic method involves fortifying popular foodstuffs with defined amounts of prebiotics.
Thus, you will find that prebiotic compounds are added to many foods including yogurts,
cereals, breads, biscuits, milk desserts, nutritional supplement bars, ice-creams, spreads,
drinks, water, infant formula, as well as to some animal foods.
There are over 400 distinct species of microorganisms that inhabit the various
regions of the adult human digestive tract, making up nearly two kg of total body
weight. This includes harmful as well as useful bacteria.Pro: Biotics are foods or
concentrates of live organisms that contribute to a healthy microbial environment
and suppress the potential harmful microbes. Probiotics can be bacteria, molds or
yeast. But most probiotics are bacteria. Among bacteria, lactic acid bacteria are
more popular. The first recorded probiotic was fermented milk.
The strategy is based on interfering with
pathogenreceptor or toxinreceptor
interactions by engineering the expression of
host-receptor mimics on the surface of a
harmless bacterium, so that this 'designer
probiotic' strain (blue) can bind and
neutralize toxins in the gut lumen or interfere
with the adherence of pathogens (white) to
the intestinal epithelium.
Overview of the anti-C. difficile potential of designer probiotics.
Sleator R D , and Hill C J Med Microbiol 2008;57:793-794
Overview of the anti-C. difficile potential of designer probiotics. Bacteriocin produced by the
probiotic (dark shading) can lyse invading C. difficile cells (light shading) (a), while
heterologously expressed receptor mimics on the surface of probiotic cells can antagonize
pathogen adherence to the host (b) and neutralize toxin production (c).
Influence of Streptococcus salivarius probiotics in the oral cavity. Health benefits can occur through the
direct inhibition and exclusion of pathogens, modulation of the human immune system to reduce pathogen-
induced inflammation or by 'priming' the immune system to respond rapidly to viral or bacterial infection.
the microbiota can be viewed as a
metabolic organ exquisitely tuned to our
physiology that performs function we have
not had to evolve on our own
Backhed et al. 2004. PNAS 101:15718-
15723
Figure 1: The Human Body and number of
bacteria present in the total microflora.
Probiotics and Beneficial Effects in the
Intestine. Depiction of the interactions
between beneficial bacteria (left side),
their secreted factors, pathogens, and
the intestinal mucosa (right side).
Potential beneficial effects of probiotics
are listed. Only two host cell types are
shown, intestinal epithelial cells and
macrophages although other cell types
including dendritic cells, lymphocytes,
myofibroblasts, and neutrophils
comprise the intestinal mucosa. The
arrows indicate the release and
possible distribution of secreted factors
derived from probiotics.
Diseases
influenced by gut
microbial
metabolism. The
variety of systemic
diseases that are
directly influenced
by gut microbial
metabolism and its
influence on other
mammalian
pathways, such as
the innate immune
system, are shown.
Specifically
highlighted are the
metabolic pathways
involved in drug
metabolism and
obesity that are
directly influenced
by the gut microbial
content. Ags,
antigens; C. bolteae,
Clostridium bolteae;
DCs; dendritic cells;
SCFA, short-chain
fatty acid; TLR, toll-
like receptor.
Ensuring identity: Comprehensive identity validation

As living organisms, probiotics continually modify their own metabolism and composition in response to genetic and environmental
factors. Consequently, conventional testing methods predicated on metabolism and composition produce variable and unreliable
results. Genotyping, the exemplary method of modern microbial taxonomy, excludes these factors to precisely authenticate genus
and species according to DNA sequence. Since this genetic method can only validate genus and species, a second method is
required for strain verification. Fatty acid methyl ester (FAME) analysis examines the profile of fatty acids in a probiotic and searches
for a match among 2,000 strain-specific reference profiles. This comprehensive identity validation of all Pure Encapsulations
Probiotics, as part of our patent-pending product process, is conducted through independent laboratories equipped with the most
advanced microbial identification technology and expertise.

Ensuring viability: The Pure Probiotic Initiative*

Bacteria are delicate organisms that are particularly sensitive to temperature and moisture. To properly optimize these parameters,
handling and manufacturing procedures must include strict specifications that extend beyond the scope of standard GMP
compliance. Pure Encapsulations' patent-pending manufacturing process focuses on the vulnerability of probiotics at the most critical
steps. Based on a model that minimizes the cooperative impact of the three most important factorstemperature, humidity and
timingthe process maximizes viability from the moment of raw material receipt through the date of finished product expiration. It is
widely recognized that control of ambient temperature supports probiotic survival. Of equal importance is avoidance of sudden and
severe temperature shifts, such as those resulting from freezing and thawing. Circumventing these fluctuations during production is a
focal point of the Pure Encapsulations process (Figure 1). Operating within a defined temperature range, together with rigorous
observance of time limits for sensitive operations such as blending, enhances probiotic resistance to another threatmoisture.*
Lab Exploration of Survival of Probiotic
Cultures Inside Human Digestive Tract
Scientists often model complex biological phenomena in vitro , mimicking conditions found in living organisms. To
develop our own in vitro model for testing the survival of bacteria from probiotic supplements. To decide which factors
are important for survival of bacteria in a chosen portion of the human digestive tract. Create in vitro models of organs
such as stomach and/or intestines and expose a probiotic supplement to conditions mimicking the chosen portion of the
human digestive tract, and measure the effect of those conditions on the survival of bacteria found in the supplement.
Can focus on conditions such as low pH found in stomach or pancreatic enzymes found in the upper intestine.

What does it takes to design and carry out a meaningful in vitro experiment in order to model and investigate a complex
biological phenomenon survival of bacterial inside the digestive tract.

Learning objectives
Develop a specific research question to investigate survival of probiotics inside the human digestive tract.
Explain major factors that influence survival of probiotic cultures in the human digestive tract.
Develop their own model for testing survival of probiotic cultures inside the human digestive tract.
Calculate and analyze the survival of bacterial cultures in their model system.
Interested in more Research?
Statement of Purpose:
to contribute to the advancement of probiotics and gastrointestinal microbiota
research in the United States.
Grant Program Objectives
To stimulate innovative research relevant to the field of gastrointestinal
microbiota in the United States
To impact academic and career development of young investigators in the
United States and attract them into the field of probiotics and gastrointestinal
microbiota
To provide preliminary data for future funding from NIH and other funding
sources
http://www.probioticsresearch.com/grantprogram.as
p
Human Microbiome Project
In conclusion