permaculture

["Lawrence F. London, Jr." <lfl@intrex.net>]

-------- Original Message --------
Subject:        Re: [SANET-MG] Genetically Engineered Crops May Produce
Herbicide Inside Our Intestines
Date:   Fri, 2 Jun 2006 10:52:00 -0400
From:   Steve Gilman <sgilman@NETHEAVEN.COM>
To:     SANET-MG@LISTS.IFAS.UFL.EDU

    In response to Dale's post, I include the attached article which
reports on research concerning the diverse microbial population that
constitutes the human colon microbiome -- and how our digestion and
well-being depends on colonization by beneficial organisms to keep
pathogens and interlopers in check. The article also speculates that the
diversity in the human gut is as complex as the sea or soil, and a new
science of metagenomics has arisen to study genomic ecosystem
interactions. Finally.

    Such complexities in the soil ecosystem have been revealed in soil
foodweb research, particularly regarding the role of plant root exudates
which feed and colonize beneficial soil microorganisms for the plant's
nourishment, protection and health. I recall a study a few years ago
that showed the persistence of transgenic strains of Bt in soil
ecosystems, from GM corn crops. The transgenic strain was still alive
and well in the soil after 8 months, whereupon the study ended...

    Sure, Bt is a natural soil organism -- but the more virulent GM
strain isn't, although it is very much at home in the soil ecosystem.
There's always been a question about mutation effects in the soil
foodweb. From the studies I've come across this whole question lies
conveniently beyond the purview of the Biotech industry. Ditto with
potential effects on the human microbiome.

    Ratcheting things up a few notches -- already in widespread release
in test plots (and how far beyond?) are pharm crops -- transgenic
biopharmaceuticals with an even greater potential to wreck havoc on our
immune systems, etc. Though Not substantially equivalent, these
inherently unstable transgenes are similar enough to be the wolf in
sheep's clothing -- environmental contaminants that can sneak through
defenses and interfere with gene expression -- preventing them from
turning on when needed or expressing them when they should be silent.
Numerous new metabolic pathways are created with a high probability of
unintended consequences. Welcome to the Brave New World.

    These are valid questions, not fear mongering. Thanks to the Reagan
era deregulation climate which spawned the Biotech Industry as we know
it, FDA, EPA and USDA only have pieces of oversight, with NO power to
require research into deeper health and safety questions. Meanwhile
patent-protected riches beckon. Finally, despite the industry's claims
of safety, absence of proof is not proof of absence.

Steve Gilman
Ruckytucks Farm

*Gut reaction: researchers define the colon’s genome (From Food Safety Net)*
June 1, 2006
The Institute for Genomic Research (TIGR)
Rockville, MD—For the first time, scientists have defined the collective
genome of the human gut, or colon. Up to 100 trillion microbes,
representing more than 1,000 species, make up a motley “microbiome” that
allows humans to digest much of what we eat, including some vitamins,
sugars, and fiber.
In a study published in the June 2 issue of Science, scientists at The
Institute for Genomic Research (TIGR) and their colleagues describe and
analyze the colon microbiome, which includes more than 60,000
genes--twice as many as found in the human genome. Some of these
microbial genes code for enzymes that humans need to digest food,
suggesting that bacteria in the colon co-evolved with their human host,
to mutual benefit.
“The GI tract has the most abundant, diverse population of bacteria in
the human body,” remarks lead author Steven Gill, a molecular biologist
formerly at TIGR and now at the State University of New York in Buffalo.
“We’re entirely dependent on this microbial population for our
well-being. A shift within this population, often leading to the absence
or presence of beneficial microbes, can trigger defects in metabolism
and development of diseases such as inflammatory bowel disease.”
As in studies of other animals, the scientists began by collecting
droppings. They collected fecal samples from two anonymous, healthy
adults who’d gone without antibiotics or other medications for a year
prior to the study. The researchers created DNA libraries based on the
samples, generating a total of 65,059 and 74,462 sequence reads,
respectively, from the two subjects. They found evidence for several
hundred bacterial phylotypes, most falling into two divisions of
bacteria known as Firmicutes and Actinobacteria. In addition, a
microbial organism known as a methanogenic archaeon, Methanobrevibacter
smithii, was prominent.
To assess the diversity of the colon microbiome, the researchers used
two strategies. First, they matched their gut microbial DNA sequences up
to two databases, one containing 16s rDNA gene sequences and the other
containing non-redundant protein sequences. Second, they compared the
colon-culled sequences to two previously sequenced human gut organisms:
a bacterium, Bifidobacterium longum, and the archaeal microbe M.
smithii. These known organisms showed striking similarity to much of the
microbiome residents.
Based on the sequence comparisons, the researchers conclude that the
human GI tract hosts multiple strains of B. longum, and a majority of
its archaeal species is related M. smithii. How many unique bacterial
genera or species exist in the colon community? By comparison to the
outside world, Gill suspects the human gut is at least as complex as our
soils or seas. With the evidence at hand, the researchers have described
greater diversity in the human gut than researchers have reported for
samples of acid mine drainage.
These microbes are busy, too. The new study shows that resident microbes
in the colon actively synthesize vitamins and break down plant sugars,
such as xylan and cellobiose (similar to cellulose), which humans could
not otherwise digest because we lack the necessary enzymes. Cellobiose,
for instance, is a key component of plant cell walls and thus is found
in most edible plants, such as apples and carrots.
The new study advances the growing field of metagenomics, or the study
of many genomes found in a given ecosystem. Scientists at TIGR and
elsewhere have recently scooped up whole environmental samples, from
soil to sea, to study the diverse genomes contained within them. The
idea is to survey a complex community in one fell swoop, examining how
whole ecosystems of genomes respond to environmental perturbations—and,
in the case of humans, how microbial ecosystems contribute to health and
disease.
“This study is an important first step toward identifying microbial
differences between healthy people and those with conditions ranging
from Crohn’s Disease to cancer,” says co-author Karen Nelson of TIGR,
who has previously studied the guts of termites and other animals. “We
might compare different individuals, with different diets, for instance.”
More broadly, the new work could become the opening salvo of a Human
Microbiome Project that defines the microbial side of ourselves,
suggests co-author Jeffrey Gordon, a microbiologist at Washington
University in St. Louis. Gordon envisions such a project pursuing
fundamental questions. How different are our microbiomes? Should
differences in our microbiomes be viewed, along with our immune and
nervous systems, as features of our biology that are affected by our
individual environmental exposures? How is the human microbiome evolving
as a function of our changing diets, lifestyle, and biosphere? Finally,
how might we alter these microbial communities for better health in a
person or population?
The current study was funded by the Defense Advanced Research Projects
Agency and the Office of Naval Research.
The Institute for Genomic Research is a not-for-profit center dedicated
to deciphering and analyzing genomes. Since 1992, TIGR, based in
Rockville, Md., has been a genomics leader, conducting research critical
to medicine, agriculture, energy, the environment and biodefense.


*****************************************************


We are not entirely human, germ gene experts argue - Yahoo! News
<http://news.yahoo.com/s/nm/bacteria_dc;_ylt=Ao0Zt3w4h0B45NW_o7gyMgVhr7sF;_ylu=X3oDMTBhcmljNmVhBHNlYwNtcm5ld3M->
By Maggie Fox, Health and Science Correspondent Thu Jun 1, 2:13 PM ET

WASHINGTON (Reuters) - We may not be entirely human, gene experts said on Thursday after studying the DNA of hundreds of 
different kinds of bacteria in the human gut.

Bacteria are so important to key functions such as digestion and the immune system that we may be truly symbiotic 
organisms -- relying on one another for life itself, the scientists write in Friday's issue of the journal Science.

Their findings suggest that studying bacteria native to our bodies may provide important clues to disease, nutrition, 
obesity and how well drugs will work in individuals, said the team at The Institute for Genomic Research, commonly known 
as TIGR, in Maryland.

"We are somehow like an amalgam, a mix of bacteria and human cells. There are some estimates that say 90 percent of the 
cells on our body are actually bacteria," Steven Gill, a molecular biologist formerly at TIGR and now at the State 
University of New York in Buffalo, said in a telephone interview.

"We're entirely dependent on this microbial population for our well-being. A shift within this population, often leading 
to the absence or presence of beneficial microbes, can trigger defects in metabolism and development of diseases such as 
inflammatory bowel disease."

Scientists have long known that at least 50 percent of human feces, and often more, is made up of bacteria from the gut. 
Bacteria start to colonize the intestines and colon shortly after birth, and adults carry up to 100 trillion microbes, 
representing more than 1,000 different species.

They are not just freeloading. They help humans to digest much of what we eat, including some vitamins, sugars, and 
fiber. They also synthesize vitamins that people cannot.

"Humans have evolved for million of years with these bacteria. And they provide 
essential functions," Gill said.

GERM SURPRISE

Gill and his team sequenced the DNA in feces donated by three adults. They found a surprising amount of it came from 
bacteria.

They compared the gene sequences to those from known bacteria and to the human genome and found this so-called colon 
microbiome -- the entire sum of genetic material from microbes in the lower gut -- includes more than 60,000 genes.

That is twice as many as found in the human genome.

"Of all the DNA sequences in that material, only 1 to 5 percent of it was not 
bacterial," Gill said.

"We were surprised."

They also found a surprising number of Archaea, also known as archaebacteria, which are genetically distinct from 
bacteria but which are also one-celled organisms often found in extreme environments such as hot springs.

The donors were healthy adults. None had taken antibiotics for a year, as these drugs are known to disturb the bacteria 
in the body.

Gill said his team hopes now to make a comparison of the gut bacteria from 
different people.

"The ideal study would be to compare 20 people, 30 people from different ethnic backgrounds, different diets, drinkers, 
smokers, and so on, because I think there are going to be distinct differences," Gill said.

These bacteria almost certainly help break down drugs that people take and studying the effects of different populations 
of the microbes might provide clues to treating different people with various medications.

The next study will focus on the bacteria in the mouth, Gill said. There are at least 800 species in the mouth and maybe 
more, Gill said.