“Initially
we didn’t give it any name, it was just called ‘the new virus'. Then I was
like, Oh okay, maybe I can use this opportunity to advertise my computer tool.
And basically that’s how it got the name crAssphage.”
Dr Bas Dutilh, a bioinformatician
at Radboud University Medical Centre in the Netherlands explaining how
crAssphage got its name
Turns
out there’s a war going on in your stomach, which is a battlefield between Bacteroides
Strain of Bacteria and crAssphage Virus.
It’s
the bad Bacteria vs Bacteriophage, those Bacteria killing Viruses that I wrote
about awhile back in my blog article entitled
“Bacteriophage
Therapy from former USSR State Georgia is a potential treatment against
Super-bug Bacteria - Hansel and Gretel Witch Hunters Panacea to eradicate
Bacterial infections”.
The
Bacteriophage in this case is the crAssphage, a bacteriophage discovered by Dr
Bas Dutilh, a bioinformatician at Radboud University Medical Centre in the
Netherlands as explained in “A Common
Virus Is Eating Your Gut Bacteria”, published 8/02/2014 @ 1:06PM by JV
Chamary, Forbes.
It
gets its rather odd name from the fact that he developed a computer program
called crAss (short for 'Cross Assembly') that reassembles the Genetic material
harvested from feces into separate genomes and Genes associated with a
particular organism, as fecal Bacteria genetic information will be all mixed up
on exit from the anus.
His
work, which was published in the Journal of Nature in the article “A
highly abundant bacteriophage discovered in the unknown sequences of human
faecal metagenomes” published 24 July 2014, Nature
is part of a collaborative decade long effort by geneticists to determine the
Genetic sequence of Bacteria, viruses and other organisms living in your
Stomach, Small Intestine and Large Intestine.
This
US$170 million project, called the Human
Microbiome Project, involves extracting the Bacteria from some 242 adults across
the world at five (5) locations on their bodies:
1. Mouth
2. Nose
3. Skin
4. Urogenital
Tracts i.e. urine
5. Gastrointestinal
tracts i.e. Fecal matter
This
sample is then killed via pasteurization, most likely via vacuum pyrolysis. Using
traditional Genome sequencing techniques combined with advanced algorithms such
as crAss, the different protein and DNA fragments are reassembled into Genes.
These Genes are then grouped into Genomes and thus the Genome Sequence is
determined for each Bacteria and virus in the stomach. It was using this method
that Dr Bas Dutilh made his discovery.
But
how does Dr Bas Dutilh computational tool crAss work? And what's so important
about the crAssphage Virus anyway?
Dr Bas Dutilh’s crAss
at work - crAssphage Virus saves you from Colorectal Cancer
First,
a quick primer on how Dr Bas Dutilh computational tool crAss works!
In
Dr Bas Dutilh study, his team worked with researchers at San Diego State University
who assisted with the analysis of the fecal matter from 12 persons.
Since
the DNA material is part of a massive mixture of genetic material known as a
metagenome, the program looks for common pieces across the various samples,
like similar fitting pieces in a mixed up set of Lego pieces. If the same
Genetic material turns up in different metagenome samples from the 12, then
it's safe to say they're part of the same organism.
Confirmation
of what eventually became known as crAssphage was done via further DNA analysis
on one of the twelve samples.
Based
on his work, the crAssphage virus is now fully sequenced and is known to have a
genome with 80 Genes and a total of 97,000 Base pairs. Even more interesting is
that the proteins that these based pairs encode for are proteins that allow the
crAssphage to take over a Bacteria but also specifies which Bacteria it
attacks, in this case the of Bacteroides Strain of Bacteria.
Most
of the Bacteroides Strain of Bacteria are good and bad Bacteria as described in
“Bacteroides: the
Good, the Bad, and the Nitty-Gritty” by Hannah M. Wexler, Clinical Microbiology Review.
The
Bacteroides Strain of Bacteria and constitute some 50% of the population of Bacteria
in your stomach as explained in the study “Structure,
function and diversity of the healthy human microbiome”, published 14 June
2012, Nature. They are a part of the
Probiotics that help with healthy digestion of certain types of animal
proteins, very leafy and starchy foods and the production of roughage for the
easy passage of stool.
Because
they are often killed off by certain antibiotics such as in the case of the
treatment of a Clostridium difficile
infection, enemas had to be done to replace these good Bacteria in what's effectively
a fecal transplant as described in my blog
article entitled “University
of Calgary develops Fecal Transplant to repopulate the Large Intestine after a
Clostridium difficile treatment - How to cure diarrhoea, cramping and bloating
after eating infected food”.
crAssphage hates
Bacteroides fragilis - GM love-hate relationship against other Bacteria
The
crAssphage bacteriophage specifically attacks the Bacteroides fragilis, a bacterium with a toxic coating that is
suspected of causing Colorectal Cancer as stated in “Enterotoxigenic Bacteroides
fragilis: a Rogue among Symbiotes” by Cynthia L. Sears, Clinical Microbiology Reviews.
By
attacking this particular bad member of the Bacteroides Strain of Bacteria,
it's helping to keep Colorectal Cancer at bay. Now that Dr Bas Dutilh has
identified the genome of this particular crAssphage bacteriophage, it can also
be cultured or extracted from healthy donors and possibly used in enemas or
fecal transplant to treat early stages of Colorectal Cancer.
Additionally,
the researchers found that this beneficial bacteriophage was in 74% of the 466
fecal metagenomes from across the world, particularly in US, Europe and South
Korea participants in the study. This suggests, even without the completion of
the US$170 million Human Microbiome
Project, that the crAssphage bacteriophage is a common organism living in
the stomachs of many humans worldwide.
In
fact, the abundance of crAssphage Virus and Bacteroides
fragilis that it targets became obvious when the crAssphage DNA was
compared against 151 metagenomes in the Human
Microbiome Project. They found that in their database of 3000 bacterial
genomes, the correlation between bacterium DNA that matched what the crAssphage
Virus DNA that determined which bacterium it was targeting, which is called the
CRISPR Sequence, indicated that the Bacteroides family of Bacteria were the top
of its hitlist!
However,
despair not, as GM (Genetic Modification) comes to the rescue!
This
crAssphage bacteriophage has a bright future as a delivery mechanism for
vitamins and minerals not to mention being genetically modified to also attack
other Bacteria such as Anthrax, Escherichia Coli, Cholera, Malaria or other
bacterium as described in my blog article entitled
“Bacteriophage
Therapy from former USSR State Georgia is a potential treatment against
Super-bug Bacteria - Hansel and Gretel Witch Hunters Panacea to eradicate
Bacterial infections”.
So
much for pharmaceutical usages, as Big Pharmaceutical companies may not like
the idea of a virus that could potentially cure a lot of illnesses caused by Bacteria
that's so easily harvested and administered. Still a cure for so many bacterial
infections makes Bacteriophages the number probiotic alternative to antibiotics
that are increasingly resistant to drugs.
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