Year: 2012

Dear Friends

How are recent analytical advances within the field of microbiology bringing our relationship with Mother Nature back centerstage into the practice of medicine?

Part and partial to the practice of medicine is accurately understanding our relationship with the microbial world—that unseen world that became visible through the world of Louis Pasteur.  His work in the late 19th Century brought germ theory into the field of medicine.  His focus was on bad bugs and that they must be killed—pasteurization and hygeine became good medical standards of practice.

But, we have come along way since then.  NIH, through the Human Genome Project, in collaboration with scientists around the world, developed advanced analytical tools in order to map the human genome, and these tools became a platform through which they could take on the analysis of the microbial world that lives in us and on us—the human microbiome.  In 2007 NIH began the Human Microbiome Project with a goal of determining the core microbiome of a healthy human being.

In this week’s Forward Thinking we will share the insights expressed by Gevers D, Knight R, Petrosino J et al. in their paper, The Human Microbiome Project:  A Community Resource for the Healthy Human Microbiome. (2012) PLos Biol 10(8): e1001377.  In particular, we will look at two new analytical tools used in the leading edge of human microbiology—High Throughput 16S Sequencing and Shotgun Metagenomic Analysis.

The bottomline of what we are discovering in that good microorganisms in our gut and on our body are instrumental to our health and wellbeing.  They are partners in our physiological functioning, they are soldiers in our immune systems, they are crucial to our very survival.  To find out more about the tools to analyze who and what these microbial friends of ours are read more.

Dr. Petrosino teams work 2

In the above diagram, taken from Govers D et al, we can see the two methods of analysis—on the left 16S rDNA Amplification and on the right Shotgun Metagenomic reads.  The challenge had been for microbiologist to see the microbes that live in the gastrointestinal tract for example—95% are unculturable outside of the body.  With these new technologies scientists are able to identify and study the bugs in sito.

The procedures are as follows:  First, you take a sample from one of the body sites—for example, the stool which is used for determining the bugs of the GI tract.  Then, researchers pop the cells open and get the total DNA content.  In some samples there will actually be human DNA in there mixed bacterial DNA because of the nature of the body site and how the sample was collected.  Finally, through the use of PCR primers, scientists can amplify (make multiple copies) of the 16S rRNA fragments so that we can sequenced for their bases.  This provides us with the bacterial fingerprint for each organism, for 16S rRNA sequencing takes us down to the species level of bacterial identification.  Much of the work now is to achieve a complete genomic mapping of the bugs in the gut.  The HMP consortium has already completed the sequencing of 1000 organisms, resident to the gastrointestinal tract.

Next, in regards to Shotgun Metagenomic Analysis, scientists take the original sample and just shear it into little pieces.  Then, they sequences the DNA fragments into genes. The low hanging fruit that comes out of the shotgun approach is that you can get the entire gene content of the sample which allows you to map those genes back to the known metabolic pathways that exist in a bacterial cell.  This gives you an idea of the metabolic potential of a given sample.  This allows you to do a basic metabloic reconstruction of the sample.  How well does it metabolize carbohydrates, or polysaccharides, amino acids, etc.  You compare from sample to sample to get an idea of the different metabolic pathway potentials of a give sample.

How does all of the above relate us to Mother Nature?  Mother Nature is the biosphere. The biosphere is the tree of life.  Within the tree of life we are the branches of the evolutionary process and the microbial world our foundation. You could say we are its offspring.  The Human Microbiome Project is making it visibly clear just how marvelously connected we are to the microbial world.  We all Mother Nature, the microbial world and ourselves are one.

A very big hug to you all and Happy Holidays from Dohrea and me!

Sincerely yours, Seann Bardell

Clinical Note:

The BioImmersion Synbiotic Formulas are the Original Synbiotic formula, the Beta-Glucan Synbiotic Formula, the Triple Berry Probiotic Formula, the High ORAC Synbiotic Formula, the Supernatant Synbiotic Formula, the Cranberry Pomegranate Synbiotic Formula and the No. 7 Systemic Booster. They represent the following strains:  L. bulgaricus ATCC pending, DUP 14073, L. helveticus ATCC 7994, L. casei ATCC 393, B. infantis ATCC 15697, B. longum ATCC 15707, L. acidophillus ATCC 4356, S. thermophillus ATCC 19258, L. plantarum ATCC 8014 and L. rhamnosus ATCC 7469.

We will be driving into the research on the different strains, relative to human health.

This is the season for giving and in this article collected by The Global Oneness Project called Radical Generosity, Paul Van Slambrouck explores the diversity of gift economy projects around the globe.  It is very thought provoking and inspiring.  Everyone can do it, all can participate.  Check it out.

 

Human Microbiome Project I

December 7, 2012


Can you name this Beautiful Creature?

 

Dear Friends

In 2012, we have completed HMP I.  Now it’s on to HMP II. What the heck am I talking about?  Glad you asked!

The Human Microbiome Project (HMP) consortium in 2012 completed their five year plan (HMP I) to put in place the groundworkings of technologies and research to provide a platform from which to dive into the mysteries of interplay between our human cells and our microbial cells, whom when our health is good, exist as friends and fellow soldiers, fighting the good fight to keep our bodies well. How can we use the genomic power of the microbiome to heal us?  Representing a gene pool 100 fold that of our own human cells, how can we proactively influence all that gene power to be used to our healthful advantage? Where do probiotics come in?  Which probiotics? When? These questions and many more will be answered in HMP II.

Nature JournalOn June 14, Nature along with PLoS came out with two major consortium papers on the human microbiome resulting from their five years of research.  These were followed by 20+ companion studies published in prestigious journals.  They highlighted a broad analysis of the microbiomes of over 200 healthy adult men and women, the largest such study to date.  So this is definately a time and the season for us to give a toast to their grounding breaking, paradigm shifting, utterly amazing work.

Thanks to YouTube, we have a recording of a live broadcast back in June of a public meeting where some of the key research luminaries are sharing, in a panel discussion format, via questions and answers, highlights on some of the findings for their landmark studies.  It is worth watching.  One realizes how much we know and at the same time how little we know when it comes to the microbiome of the human body.

On the panel representating the NIH/HMP consortium are Lita Proctor PhD from the National Human Genome Research Institute/NIH, Rob Knight PhD from the University of Colorado, Rick Bushman PhD from the University of Pennsylvania, Janet Jansson PhD from the Lawrence Berkeley National Laboratory, Univeristy of California (Berkeley), Larry Forney PhD from the University of Idaho, Ashlee Earl PhD from the Broad Institute and moderator Stanley Maloy PhD from San Diego State University.  Here my friends it is:  The Latest News from the Human Microbiome Project.

So, I’ll stop myself here from expanding on the points they made, and simply point you in the direction of the link above.  It really is worth looking at, even a couple of times, as it’s even better the second time if you know what I mean. Why not hear it first hand.

One of the closing questions from the audience was, “you have a lot of data about sequences but how do we go about relating sequences to function?”  One of the panalists jokingly said, “Well, that’s a question for HMP II.”  It’s true, they are seeing a lot of genes in this massive pool of sequences in the digestive tract, and the work to know if those genes are expressed or not, is truly the next step.  This takes us back to the field of proteomics and looking at the interplay of proteins in the mileau of our bodies ecosystems.  That without question is one of the lead-edge waves of medical research that will be hitting our shores.  It should be very exciting.
Sincerely yours,
Seann Bardell

Clinical Note:

The BioImmersion Synbiotic Formulas are the Original Synbiotic formula, the Beta-Glucan Synbiotic Formula, the Triple Berry Probiotic Formula, the High ORAC Synbiotic Formula, the Supernatant Synbiotic Formula, the Cranberry Pomegranate Synbiotic Formula and the No. 7 Systemic Booster.They represent the following strains:  L. bulgaricus ATCC pending, DUP 14073, L. helveticus ATCC 7994, L. casei ATCC 393, B. infantis ATCC 15697, B. longum ATCC 15707, L. acidophillus ATCC 4356, S. thermophillus ATCC 19258, L. plantarum ATCC 8014 and L. rhamnosus ATCC 7469.

We will be driving into the research on the different strains, relative to human health.

The Last Quiz Answer:

This gorgeous creature, the red-sided garter snake of the Interlake Region of Manitoba Canada, is one of between 100,000 to 150,000 just emerging simulateiously from their winter dens in late Spring—a swarming mass of snakes, making for one of the world’s largest congregation of any vertebrate species.

As an undergraduate in zoology, we had a garter snake in a big aquarium, living with a rattlesnake and a big king snake.  An amazing thing happened one afternoon as a bunch of us students were watching the snakes. The rattlesnake decide to eat the garter snake, swallowing it head first.  Apparently the king snake thought it was a good idea and swallowed the garter snake tail first.  So there they were, the rattle snake and king snake slowly ingorging the poor garter snake and moment by moment drawing closer to each other—kind of a game of chicken.  We wondered what would be happening when they met in the middle.  What do you think?  As we all watched in amazement, including our professor, the two diners got within an inch of each other, and then all of a sudden the rattle snake began disgorging his prey.  The King snake was the winner.  Snakes are carnivores, and obviously they can be cannibalistic too.

It is the Christmas Season. See in the video below the most precious gift we can give?

“Come rain or shine, 88-year-old Bermudian Johny Barnes devotes 6 hours every day to an endearing traffic ritual that has made him one of the islands most cherished citizens- Click on Mr. Happy Man.”                    

©2005 – 2012 BioImmersion Inc. All Rights Reserved

 

Origin of the Human Proteome

November 29, 2012


Can you name this Beautiful Creature?

 

Dear Friends

Over the past two weeks, within our Forward Thinking newsletters, we have begun to the roll out the exciting news regarding the bugs that live in us and on us (our human microbiome) and their influence over our state of health or disease.  Two weeks ago we defined the human microbiome, and last week we began to look at some of the conclusions derived from the five years of research on the human microbiome just concluded by the Human Microbiome Project consortium (HMP).

Exposing my 60’s roots, I used the phase mind-blowing to describe some of the statements coming forth from the HMP scientists regarding their findings.

We humans are mostly microbes (Greenblum S. et al. Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease Proc Natl Acad Sci USA 2012 January 10; 109(2):592-599).

I’ll bet, if you’ve ever focused on the question, who am I or what am I, your answer was never a collection of human cells and microbial cells.  But my friends, that is exactly what the elite HMP scientists are saying that we in fact are.

There are 6 major sites on and in our bodies—the gastrointestinal tract, skin, nasal, oral, airways and urogenital—where microbes have intimate contact with our human cell. The microbial genes produce proteins that interact with the proteins produced by our human cells, thereby jointly providing the protein building blocks for our body’s physiological metabolic pathways, for messenger molecules, receptor sites, neurotransmitters, hormones, enzymes, etc.

Our digestive system, our nervous systems, our immune system, all body systems for that matter depend on the proteins produced by a healthy microbiome.  For example, what is most interesting to consider is that the microbiome of our gastrointestinal tract produces three times more unique proteins than do our human cells.  How this mix of proteins combine together to make for a healthy functioning body is the intense focus of the HMP—the study of the proteome.  The proteome being defined as the entire complement of proteins in a given area.  Proteomics, the science of proteins, is very much part of the leading edge for medical research today.

Next week we focus on a paper by Cho and Blaser entitled, The Human Microbiome:  at the interface of health and disease.  One of the key thoughts coming from their paper is redundancy rules.  Stay tuned.
Sincerely yours,
Seann Bardell

Clinical Note:

The BioImmersion Synbiotic Formulas are the Original Synbiotic formula, the Beta-Glucan Synbiotic Formula, the Triple Berry Probiotic Formula, the High ORAC Synbiotic Formula, the Supernatant Synbiotic Formula, the Cranberry Pomegranate Synbiotic Formula and the No. 7 Systemic Booster.They represent the following strains:  L. bulgaricus ATCC pending, DUP 14073, L. helveticus ATCC 7994, L. casei ATCC 393, B. infantis ATCC 15697, B. longum ATCC 15707, L. acidophillus ATCC 4356, S. thermophillus ATCC 19258, L. plantarum ATCC 8014 and L. rhamnosus ATCC 7469.

We will be driving into the research on the different strains, relative to human health.

The Last Quiz Answer:

This amazing creature is a Giant African Bullfrog, Pyxicephalus adspersus, always ready for its next meal. And, they will eat just about anything—spiders, rodents, birds, snakes, other frogs—anything they can get their huge mouth around.  Plus they have teeth-like projections called odontoids, that feel like broken glass.  

They are found throughout southern, central and eastern Africa, and are the worlds second largest frog species, reaching a weight of five pounds and a length of almost a foot.  They can jump 12 feet.

The last two weeks in Green Facts we’ve been focusing on our global climate crisis.  It is very clear that if we continue on in our current course of trashing our planet we will in the immediate future be facing our planet’s Sixth Mass Extinction.  We must take strong action now!

The following video takes us to the core of our problem and solicits the power of the big guns, bringing in the biosphere itself to make the necessary corrections to save us.  Enjoy this brilliant presentation:  Most Powerful Geologic Force.  (Scroll down towards the bottom of this linked page to find the presentation)                 

                     ©2005 – 2012 BioImmersion Inc. All Rights Reserved

 


Can you name this Beautiful Creature?

 

Dear Friends

In 2007 the Human Microbiome Project was launched by NIH.  After the successful mapping of the human genome by NIH’s Human Genome Project, the next logical genetic mapping, relevant to human health, was thought to be the mapping of the human microbiome.

The Human Microbiome is the full collection of microbes (bacteria, fungi, virus, etc) that naturally exist on and within the human body. (NIH)

This past June 2012, in Nature, the Human Microbiome Project came out with the first part of the reports on their five years of research into the human microbiome.  In an introductory piece, entitled Learning about who we are, Dr. David Relman (from the Departments of Medicine, Microbiology and Immunology at Stanford University) proclaimed:

We owe much of our biology and our individuality to the microbes that live on and in our bodies—a realization that promises to radically alter the principles and practice of medicine, public health and basic science.

Two HMP studies are in this issue, one by Huttenhower et al entitle, Structure, function and diversity of the healthy human mirobiome, and the other by Methe’ et al, Human gut microbiome viewed across age and geography.  These together with 15 other papers, published simultaneously elsewhere, comprise the first reports of the HMP consortium research groups.

Two hundred and forty-two healthy adults in the US had three samples taken from 15 sites for men and 18 sites for women, over a period of 22 months, generating a total of 11,174 samples.  Through metagenomic analysis of these samples they were able to determine the following:

  • There was substantial variation in both the diversity and the composition of the microbial communites at differnet sites within the same general body region.
  • They discovered that taxonomic and genetic diversity was greatest in mouth and stool samples.
  • The relative representation of taxa and genes in each habitat varies considerably between individuals.
  • The most common cause for exclusion of people from the HMP was chronic gum disease, a condition that is increasingly regarded as normal in developed countries.
  • Populations living in less-developed regions of the world have markedly different microbiomes from those living in the US.
  • The relative abundance of microbial genes associated with certain physiological pathways varied less between samples for the same habitat than did the relative abundance of taxa.
  • This suggests that there is functional redundancy between microbial community members. 

There is obviouly much, much more to say, but right now I want to stop and say, 

Both Dohrea and I wish for you the very best on this Thanksgiving Holiday!

Sincerely yours,
Seann Bardell

Clinical Note:

The BioImmersion Synbiotic Formulas are the Original Synbiotic formula, the Beta-Glucan Synbiotic Formula, the Triple Berry Probiotic Formula, the High ORAC Synbiotic Formula, the Supernatant Synbiotic Formula, the Cranberry Pomegranate Synbiotic Formula and the No. 7 Systemic Booster.They represent the following strains:  L. bulgaricus ATCC pending, DUP 14073, L. helveticus ATCC 7994, L. casei ATCC 393, B. infantis ATCC 15697, B. longum ATCC 15707, L. acidophillus ATCC 4356, S. thermophillus ATCC 19258, L. plantarum ATCC 8014 and L. rhamnosus ATCC 7469.

Next week we will get into the research on the different strains, relative to human health.

The Last Quiz Answer:

This creature immerging from the sandis a Sahara Chameleon.  There are approximately 80 living species of chameleons, all but four living in Africa.  The largest is the size of a domestic cat, the smallest at about the length of two short fingernails.

They are famous for their projectile tongues, independent eye movement, preheensile tail and grasping feet.  When they spot an insect,  their usual prey, they rock back and forth adjusting their position for maximal striking accuracy—dinner is served.

Our voices have the power to change the world.  

Last week at this time there was the 24 hour continuous broadcast over the internet from around the world called the Dirty Climate Report.  The theme was dirty energy makes for a dirty climate.  Click here now on this link: Climate Reality Project.org.  It’s not too late to add your voice!!!

                

                     ©2005 – 2012 BioImmersion Inc. All Rights Reserved

 


Can you name this Beautiful Creature?

 

Dear Friends

In 2003, the probiotic market in the U.S. was valued at $952 million.  Five years later it had grown by 160% to one billion, 527 million.  By 2015 it is projected to be at $3.1 billion.  Definately a growth industry, and rightly so.

The awareness that a healthy gut flora is manditory for a truly healthy body and robust longevity, and the consensus that a good probiotic formula can facilitate the building of a healthy gut flora has spread from beyond the holsitic medical community to the hollowed medical research centers of the National Institute of Health (NIH).

In 2008, NIH established the Human Microbiome Project (HMP) to study the significance, in health and in disease, of the vast number of microbes that intimately associate themselves with our human bodies.   HMP is focusing their research on four major dwelling places for these human associated microbial communities— the ecosystems of the GI tract, the respiratory tract, the urogenital tract (in women), and the skin.

The gastrointestinal tract (from the mouth to the anus) is the largest and most diverse of the microbial ecosystems, comprised of 100 trillion organisms (mostly bacterial), that is 10 times more one-celled microbial organisms in the lumin of our gut than the total human cell mass of our body, which is at 10 trillion.

Where doctors had previously isolated only a few hundred bacterial species from the body, HMP researchers now calculate that more than 10,000 microbial species occupy the human ecosystem. Moreover, researchers calculate that they have identified between 81 and 99 percent of all microorganismal genera in healthy adults.

HMP researchers also reported that this plethora of microbes contribute more genes responsible for human survival than humans contribute. Where the human genome carries some 22,000 protein-coding genes, researchers estimate that the human microbiome contributes some 8 million unique protein-coding genes or 360 times more bacterial genes than human genes. (MacDougall, R. NIH Human Microbiome Project defines normal bacterial makeup of the body.  NIH News, June 13, 2012)

Actually, each human gene is capable of producing three different proteins where as each bacterial gene only can produce one protein, so that helps the totals a bit for human derived proteins—now its 66,000 to 8,000,000 bacterial proteins.  As they say it is mind blowing.

Just think, genes produce proteins, and proteins are the building blocks of metabolic pathways, enzymes, receptor site molecules, messenger molecules, structural molecules, neurotransmitters and hormones.  The new understanding is that the collection of proteins that run our bodies comes not only from our human cells but also from our microbial selves, our own unique microbiome.  The sum total of our human cell genome and our microbial genome is called our metagenome.  Our gut is awash with proteins from our human cells and microbials cell.

Our adult bodies harbor 10 times more microbial cells than human cells. Their genomes (the microbiome’s) endows us with physiological capacities that we have not had to evolve on our own and thus are both a manifestation of who we are genetically and metabolically and a reflection of our state of well being. (NIH)

This brings us  to the door of the probiotic product world, a door that we will open over the next couple of weeks.  In the last few years alone there has been alone 482 peer-reviewed papers published regarding  lactobacillus and human health, catalogued within the US National Library of Medicine at NIH.  Stay tuned.
Sincerely yours,
Seann Bardell

Clinical Note:

The BioImmersion Synbiotic Formulas are the Original Synbiotic formula, the Beta-Glucan Synbiotic Formula, the Triple Berry Probiotic Formula, the High ORAC Synbiotic Formula, the Supernatant Synbiotic Formula, the Cranberry Pomegranate Synbiotic Formula and the No. 7 Systemic Booster.They represent the following strains:  L. bulgaricus ATCC pending, DUP 14073, L. helveticus ATCC 7994, L. casei ATCC 393, B. infantis ATCC 15697, B. longum ATCC 15707, L. acidophillus ATCC 4356, S. thermophillus ATCC 19258, L. plantarum ATCC 8014 and L. rhamnosus ATCC 7469.

Next week we will get into the research on the different strains, relative to human health.

The Last Quiz Answer:

Check out the Orangutan Foundation International. There mission is to support the conservation, protection, and understanding of orangutans and their rain forest habitat while caring for ex-captive orangutan orphans as they make their way back to the forest.

Furthermore, OFI educates the public, school children, and governments about orangutans, tropical rain forests, and the issues surrounding orangutan and forest conservation and protection.  Our support can help them save the orangutans, and save their magnificient jungle habitat in Borneo.

I went to The 350.org National Tour opening last Wednesday night in Seattle at the Benaroya Hall.  There were 2000 people there.  I’m way in the back right corner.  It is a critically important movement.

On Thursday they were going to Portland, Friday to Berkley, Saturday to San Francisco and Palo Alto and Sunday to LA. This week they will be doing the East Coast.

The Lecture is entitled Do The Math.  It is very important for you to go if you can. Check out their calendar and agenda.  Here we are:

Do the Math Tour 3

P.S.  Have you wondered what Al Gore is doing?  Well wonder no more.  Beginning this evening, Wednesday night Nov. 14th at 8:00pm EST, Gore et al is rolling out The Dirty Weather Report International.  It’s 24 hours of non stop commentary on the world man-made weather crisis.  Tune in on line by going to Climate Reality Project.org.  If it’s Nov. 15th, it is happening live right now.
                   
 ©2005 – 2012 BioImmersion Inc. All Rights Reserved