Note: Much of the information included in this piece was derived from two articles published in the May 28th edition of Nature News, a resource published by the medical journal Nature

Even those of us who live under rocks have heard of the Human Genome Project, a massive international scientific research project the aim of which was to understand the genetic makeup of the human species. Its primary goal was to determine the sequence of chemical base pairs which make up DNA and to identify the approximately 25,000 genes of the human genome from both a physical and functional standpoint.

The goal of the Human Genome Project was to understand the genetic makeup of the human species.

A working draft of the genome was released in 2000 and a complete one in 2003, with further analyses yet to be completed and published. Meanwhile, a parallel project was conducted by the private company Celera Genomics. Most of the sequencing was performed in universities and research centers from the United States, Canada and Great Britain.

Most researchers would agree that the Human Genome Project was launched in order to answer the long-standing question, “Who am I?” The goal was to identify and sequence every single human gene. By doing so, many researchers were certain they would uncover causes for most of the chronic diseases that plague humankind. At the project’s start, scientists were faced with a multitude of unknown sequences to decipher and understand. Surely such sequences would offer up answers to disease, and specific genes would be found that would correlate with specific illnesses. In a Gattaca-like environment, people would then be informed early in life that they had “the gene” for MS or “the gene” for breast cancer. Scientists would work fervently to identify and change the expression of such disease-causing genes, finally developing enough gene therapies to eradicate human disease. The above scenario has an abiding appeal, largely because the idea that our genes dictate our health is so temptingly simplistic.

Yet, while striving to answer the question- “Who am I?”- those researchers searching for a purely genetic cause for disease have failed to recognize that the question, “Who am I?” can only be answered after the question “Who are we?” has been clarified and understood.

The question, “Who am I?” can only be answered after the question “Who are we?” has been clarified and understood.As Asher Mullard of Nature Newsdescribes, ‘we’ refers to the wild profusion of bacteria, fungi and viruses that are able to colonize the human body. Such pathogens, and bacteria in particular, number in the trillions. According to one common estimate, the human gut alone contains at least a kilogram of bacteria.

The fact is, at the present moment, human beings serve as communities in which prodigious numbers of bacteria can thrive. Since the average human is currently outnumbered by the pathogens they harbor, the genes produced by these bacteria outnumber human genes as well. According to Mullard, “Between them [the pathogens in our bodies], they harbour millions of genes, compared with the paltry 20,000 estimated in the human genome. To say that you are outnumbered is a massive understatement.”

So by sequencing only human genes, the Human Genome Project has failed to take into account a vast number of bacterial genes that also have the potential to affect the progression of human disease. The fact that many researchers are interpreting genetic data while leaving bacterial genomes and bacteria in general out of the picture is a serious issue.

This is because many of the chronic bacteria we harbor are intraphagocytic – meaning they have developed the ability to live inside the nuclei of our cells. Such pathogens thrive in the cytoplasm, or the liquid surrounding the cellular organelles that allow for DNA replication and repair.

Our DNA sequences are replicated on a regular basis. The process of transcription allows for the synthesis of RNA under the direction of DNA. Since both RNA and DNA use the same “language”, information is simply transcribed, or copied, from one molecule to the other. The result is messenger RNA (mRNA) that carries a genetic message from the DNA to the protein-synthesizing machinery of the cell. In translation, messenger RNA (mRNA) is decoded to produce a specific protein according to the rules specified by the genetic code.

Pathogens in the cytoplasm can likely interfere with the processes of transcription and translation.

Unfortunately, pathogens in the cytoplasm can likely interfere with any number of the many precise steps involved in the transcription and translation processes. Such interference results in genetic mutations, meaning that our DNA is almost certainly altered, over time, by the intracellular pathogens we harbor. The more pathogens a person accumulates, the more his genome is potentially altered.

It is also quite likely that intracellular pathogens disrupt DNA repair mechanisms. Since environmental factors such as UV light result in as many as 1 million individual molecular lesions per cell per day, the potential of intracellular bacteria to interfere with DNA repair mechanisms also greatly interferes with the integrity of the genome and its normal functioning. If the rate of DNA damage exceeds the capacity of the cell to repair it, the accumulation of errors can overwhelm the cell and result in early senescence, apoptosis or cancer. Problems associated with faulty DNA repair functioning result in premature aging, increased sensitivity to carcinogens, and correspondingly increased cancer risk.

“Lifelong persistent symbiosis between the human genome and the microbiota [the large community of chronic pathogens that inhabit the human body] must necessarily result in modification of individual genomes,” states biomedical researcher Trevor Marshall. It must necessarily result in the accumulation of ‘junk’ in the cytosol, it must necessarily cause interactions between DNA repair and DNA transcription activity”, he continues.

So there is increasing evidence that many of the genetic mutations identified by Human Genome Project researchers are largely induced by bacteria and other pathogens. Rather than serving as markers of particular diseases, such mutations generally mark the presence of those pathogens capable of affecting DNA transcription and translation in the nucleus. This is why, in most cases, the “one gene, one disease” hypothesis has failed to hold water. Instead, geneticists are now stuck examining a perplexing number of different mutations, most of which differ so greatly between individuals that no correlations can be made between their presence and any particular illness. The mutations are nothing but genetic “noise,” induced either by random chance or by the pathogens that such researchers fail to factor into the picture.

As Marshall describes, researchers sequencing human DNA samples often make the assumption that only one genome (the human genome) is present, when in reality, their tests are also likely picking up on the loose bits of multiple genomes (bacterial genomes). So if a person’s genome is sequenced once and then sequenced again, will the same DNA sequences be obtained? Probably not, because each individual sequencing will randomly pull various pathogenic genes into the human mix. Thus, what are currently viewed as “disease-causing” mutations are essentially statistical anomalies that vary depending on when and how a person’s genome is sequenced.

Each individual sequencing of a genome will randomly pull various pathogenic genes into the human mix.

If sequenced genomes are currently just a sum of several random parts, then it’s inevitable that an individual’s genome will change throughout life. Because pathogen-induced mutations, random mutations, and mutations that result from faulty DNA repair accumulate over decades, the genome map of a child will be very different from the genome map produced when the same individual is an adult, with differences increasing as people reach their elderly years. Goodbye the world of Gattaca. Right now, if a child’s genome is sequenced at birth, his or her genetic sequences predict nothing about the common chronic diseases they will encounter, and mutations accumulated later in life largely serve to signal the presence of infection. This means that using people’s genomes to define their identity – as envisioned by futuristic movies in which a person’s genome might serve as their passport and destiny – is not feasible at the moment.

This understanding marks a yet to be fully realized paradigm shift in the way the genome is interpreted. It’s hard not to feel sympathy for those individuals paying hefty sums of money to have their genomes sequenced by certain companies that now offer such a service. Customers are provided with a map of their genome in which the majority of observed mutations serve only to inform them that they harbor numerous intracellular pathogens. As Mullard describes, “Observers have started to question whether the human genome can deliver on its once-hyped promises to tackle disease. To take just one example, anyone so inclined can now pay genetic-testing companies for a preliminary rundown of the genetic variations associated with his or her risk of developing cancer, obesity and other conditions. But the risks identified are often so low or unclear that people are questioning whether the information will actually prompt the changes in health behaviour, such as losing weight, that could make them valuable.”

Finally, bacteria enter the picture – the rise of metagenomics and the Human Microbiome Project

The paradigm shift described above, in which genetic mutations are viewed in a new light, has been largely fueled by a new movement in which scientists are now beginning to use molecular technology to detect and sequence bacteria in lieu of simply trying to grow them in the lab. These tools will allow researchers to bypass the need to culture bacteria, exploring the human microbiome by studying genes en masse, rather than studying the organisms themselves.

Recent studies that have used powerful molecular tools rather than standard cultivation techniques have left scientists slack-jawed at the number of bacterial DNA sequences that correspond to bacteria yet to be named or sequenced. A great number of sequences also correspond to bacteria never thought to have the capability of living on or within the human body. It has recently become all too clear that only a fraction of the bacteria capable of infecting humans grow in the lab, and that we have been oblivious to the presence of the majority of pathogens capable of entering our bodies. This realization that we harbor myriad unnamed and unidentified microbes comes at a time when the Human Genome Project is failing to capitalize on its promise to identify root causes for human disease.

Powerful new molecular tools are revealing the number of bacterial DNA sequences that correspond to bacteria yet to be named or sequenced.

As Mullard admits, “The microbes that swarm in and on the human body have always held a certain fascination for researchers. Since so few of them grow in the lab, it has been difficult to work out exactly who these microbial passengers are and how they interact with one another.” Whereas over the past century, standard laboratory culturing techniques have failed to detect the vast number of pathogens capable of infecting human beings, recent advances in molecular technology that allow for the sequencing of bacterial DNA mean that, at long last, we may be able to successfully identify and sequence the bacteria that cause disease.”

The reality is that the plethora of unknown pathogens that colonize the human body are the previously unrecognized puzzle piece behind chronic inflammatory disease. Enter metagenomics, a relatively new field of research that, thanks to advanced molecular techniques, enables researchers to study organisms not easily cultured in a laboratory as well as organisms in their natural environment.

This year marks the tenth birthday of metagenomics. It was a decade ago that Jo Handelsman and her colleagues at the University of Wisconsin in Madison successfully cloned and determined the functional analysis of the collective genomes of previously unculturable soil microorganisms in an attempt to reconstruct and characterize individual community inhabitants. The team coined the word “metagenomics” to explain their techniques and goals. Since the Handelsmam work, the scope of metagenomics has expanded greatly. Teams of researchers across the world have made efforts to describe the bacteria in environments as diverse as the human gut, the air over New York, the Sargasso Sea and honeybee colonies.

“We can look at the metagenomic analysis so much more deeply, at such a better cost,” says Jane Peterson, associate director of the Division of Extramural Research of the National Human Genome Research Institute in Bethesda, Maryland, which recently launched a five-year initiative to explore the human microbiome.

The five-year initiative is one of several massive projects striving to characterize what is referred to as the human microbiome, the name given to the collection of microorganisms living in and on the human body. The goal of the project is as ambitious as it is exciting – to detect and name every type of bacterial species that is currently capable of inhabiting the human body.

The project is perhaps the best example of a new, and long overdue, shift in thinking among many medical researchers. At long last, microbiome scientists are vastly more interested in studying and identifying the pathogens that inhabit the human body rather than simply examining human genes.

Microbiome scientists are vastly more interested in studying and identifying the pathogens that inhabit the human body rather than simply examining human genes.

Late last year, the US National Institutes of Health (NIH) pledged US$ 115 million to identify and characterize the human microbiome, Also last year, the European Commission and various research institutes committed €20 million (US$31 million) for similar research. Smaller research teams with similar goals are also pledging lesser sums of money towards research that hopes to contribute to a greater understanding of the microbiome. These teams are situated in countries as diverse as China, Canada, Japan, Singapore and Australia.

Since the human microbiome is so diverse, it’s not surprising that an array of different research teams are needed to tackle divergent areas of the project. The NIH’s five-year Human Microbiome Project will spend much of its money identifying where certain bacteria in the body are located. They also plan to compile a reference set of genetic sequences that correspond to each bacterial species.

Although one-quarter of the project’s money has been earmarked to examine the role of the microbiome in health and disease, the Human Microbiome Project will do little to assess the function of microbes during its first year, although it may focus on the topic later. It’s serendipitous that the “health and disease” aspect of the project has been put off, since it’s only a matter of time before the medical community realizes that biomedical researcher Trevor Marshall has already largely elucidated how the intraphagocytic, metagenomic, microbiota of bacteria that cause chronic inflammatory disease are able to survive in the body and evade the immune system. Ideally, the money now dedicated towards examining the role of the human microbiome in disease could be used to pursue research projects related to Marshall’s discoveries.

Since the vast number of bacteria and other pathogens that cause human disease have yet to even be discovered and documented, the primary goal of the Human Microbiome Project is to build up a research community and generate a sequence resource, akin to that developed during the Human Genome Project, so that questions about bacteria and specific disease-causing mechanisms can be tackled at a later date.

Under the most ideal of circumstances, the money now dedicated towards examining the role of the human microbiome in disease could be used to pursue research projects related to Marshall’s discoveries.This year, researchers will collect samples of feces plus swabs from the vagina, mouth, nose and skin of 250 volunteers. 250 people may seem like a small number of subjects for such a massive project, but when one understands that the DNA of every single one of the trillions of pathogens harbored by each subject will be analyzed, it’s easy to see that such an undertaking is actually a monumental task.

How do you effectively study such a vast and unknown community? The ultimate goal is to sequence the complete genomes of hundreds of bacterial species and deposit them in a shared database. Most of the research teams involved in the project will be sequencing short, variable stretches of DNA that code for components of bacterial proteins in order to roughly identify which bacteria are present in each person and how many bacterial species volunteers have in common. Once an estimate of diversity has been attained, the researchers plan to mine deeper by using shotgun sequencing – a molecular technique that will allow them to analyze many short pieces of DNA from all over the microbes’ genomes and reveal which genes are present.

In shotgun sequencing, DNA is broken up randomly into numerous small segments with the goal of creating multiple overlapping sequences.

In shotgun sequencing, DNA is broken up randomly into numerous small segments. The DNA sequence of each fragment is subsequently identified. The process is then repeated in order to create multiple overlapping sequences of DNA. When enough overlapping sequences have been generated a computer program is able to assemble the ends of the overlapping sequences into a contiguous sequence.

Microbiome researchers will initially use shotgun sequencing data from a few bacterial species that can already be grown, and piece together their whole genomes by putting overlapping fragments in order. The Human Microbiome Project plans to provide 600 “reference genomes.” The European project will do another 100, and other sequencing efforts by the NIH and elsewhere will make additional contributions. The hope is that enough research teams are able to set up a broad enough reference database. Then, researchers will be able to predict the genetic capabilities of many currently unculturable species (many of which are in an L-form and/or biofilm-like state) solely on the basis of similarities with known genes.

Creating the database will not be a simple task. According to Peer Bork, a biochemist who heads the European project’s computational center at the European Molecular Biology Laboratory in Heidelberg, Germany, even if many reference sequences are created, fitting together DNA fragments in order to identify unknown species, “is pretty hairy from a computational biology analysis point of view. Even with the immense power of supercomputers to process the sequencing data, it will take some clever analysis to compare the millions of sequence reads that span thousands of species between hundreds of ‘healthy’ and unhealthy people.”

Many different research teams will be working simultaneously in order to build a map of human bacteria.

Yet, the scientists involved in the project appear intent on capitalizing on their promise to sequence the microbiome. Furthermore, each research team will still be allowed to pursue their own pet projects. “Talented people are doing what they think is the most important research to do, rather than being forced to do what somebody else has decided would be the best,” says Ehrlich.

As touched on above, one of the main scientists pushing forward the metagenomics movement is Marshall. Although not directly involved in the Microbiome Project at the moment, decades of in silico and clinical research have allowed the biomedical researcher to create a treatment regimen that effectively kills the intraphagocytic, metagenomic bacteria that microbiome researchers will be identifying in greater detail.[1]

While at first glance it may seem counterintuitive that Marshall’s work has demonstrated how to kill the microbiome before the bacteria that comprise it have even been fully sequenced, one must keep in mind that all bacteria possess certain characteristics. Every bacterial species has a 70S ribosome – a protein region that must be functioning if the pathogen is to survive. Whether or not a species has been named, identified, cultured, or sequenced, if its 70S ribosome is blocked, as it is by the pulsed, low-dose antibiotics championed by Marshall, it will be weakened so greatly that it cannot survive in the presence of an activated immune system.

Every bacterial species has a 70S ribosome – a protein region that must be functioning if the pathogen is to survive.

So Marshall’s treatment protocol – dubbed the Marshall Protocol – already exists, and can kill the pathogens that Microbiome researchers will be identifying. As it perfuses the mainstream, Marshall’s research (when fully appreciated) will represent a quantum leap forward for microbiome researchers. After all, the microbiome community should be quite pleasantly surprised to find out that the disease-causing bacteria they sequence can already be killed.

However, at the moment, patients on the Marshall Protocol have little knowledge of exactly what chronic pathogens they are killing. In a sense, such knowledge isn’t of utmost importance, as specific names are not needed to induce recovery. Yet it would certainly be of great interest for researchers working with various aspects of the Marshall Pathogenesis to possess a greater understanding of the bacterial species any one patient is killing, and what species of bacteria can generally be associated with specific symptoms.

Thus, the database that the Microbiome project intends to provide promises to be uniquely helpful for researchers working on MP-related projects. Such researchers will be able to use the database to get a much clearer idea of exactly which chronic pathogens cause inflammatory disease, the substances created by these pathogens that may lead to receptor blockage, and exactly which bacteria are killed by different antibiotic combinations. As more knowledge is built about the specific pathogens that cause inflammatory disease, other drugs besides the MP antibiotics may be developed that also target them effectively, adding to an already powerful arsenal to render them dead.

Of course, using the Microbiome database to identify the presence and species of bacteria targeted by the Marshall Protocol will require numerous researchers to perform shotgun sequencing of the bacteria in the tissues of patients with many forms of chronic disease. Sequences derived from such patients can be compared with the database in order to match DNA sequences with those of specific bacterial species.

If periodic shotgun sequencing studies are performed as a patient progresses through the MP, they will undoubtedly reveal that MP patients have high bacterial loads at the onset of treatment and greatly reduced bacterial loads after several years of therapy.Even better, shotgun sequencing can be used to convince skeptics of the MP’s validity. If periodic shotgun sequencing studies are performed as a patient progresses through the MP, they will undoubtedly reveal that MP patients have high bacterial loads at the onset of treatment and greatly reduced bacterial loads after several years of therapy. Absence of bacteria would, of course, correlate with disease resolution and cure. Such data would provide even the greatest skeptic with the proof necessary to confirm that the MP does indeed reverse inflammatory disease and successfully kill chronic idiopathic bacteria.

The few shotgun sequencing studies performed to date have already helped Marshall flesh out certain aspects of the Marshall Pathogenesis. A recent shotgun sequencing study that detected the species of bacteria present on prosthetic hip joints allowed him to identify (using molecular software) that the chronic pathogen Flavobacter, creates a lipid capable of dysregulating the Vitamin D Receptor (VDR). The discovery finally provided proof of concept for the fact that many of the chronic pathogens we harbor almost certainly increase their survival by creating similar ligands that block the ability of the VDR to activate components of the innate immune response.

The fact that same study also found hydrothermal heat vent bacteria (which clearly cannot be killed by boiling) on the joints reinforces just how much we have yet to discover about the pathogens capable of inhabiting our bodies. Other pathogens detected by the research team include species such as Lysobacter, Methylobacterium, and Eubacteria. “None of these species were previously expected to exist in man” states Marshall. “These are species nobody is looking for, they are not picked up by PCR testing and nobody is culturing them.”

Consider that each species of bacteria detected in the above study has about 1,000 – 4,000 genes. So together they create about 100,000 genes that are active in the body, yet are not even contemplated by the vast majority of mainstream researchers. And those are only the pathogens detected by one molecular analysis.

A continued focus on gut bacteria

As previously discussed, the European Commission has launched a four-year initiative, called Metagenomics of the Human Intestinal Tract (MetaHIT). The project, which contains many different initiatives, overlaps somewhat with the American initiative in the sense that the European team is required to sequence bacterial genomes for a database. American and European results will be put in the same database, one which is freely available for anyone interested in sequencing and identifying bacterial DNA. And who isn’t?

But Tract (Meta HIT) has a different goal than the American Microbiome Project. It will focus on better understanding of the bacteria that inhabit the gut and how they contribute to obesity and inflammatory bowel disease. And, according to Mullard, whereas the Human Microbiome Project is initially comparing people’s microbiota on a species level, MetaHIT aims to find differences in microbial genes and the proteins they express without necessarily worrying about which species they came from.

The bacterium, Entercoccus faecalis, which lives in the human gut, is just one type of microbe that will be studied as part of NIH’s Human Microbiome Project.

“We don’t care if the name of the bacteria isEnterobacter or Salmonella. We want to know if there is an enzyme producing carbohydrates, an enzyme producing gas or an enzyme degrading proteins,” explains Francisco Guarner, a gastroenterologist at Vall D’Hebron University Hospital in Barcelona, Spain. We want to “examine associations between bacterial genes and human phenotypes,” says Dusko Ehrlich, coordinator of MetaHIT and head of microbial genetics at INRA, the French agricultural research agency in Jouy-en-Josas.

This is similar to the approach currently taken by Marshall who is more interested in the observable characteristics of the bacteria, including how they respond to different antibiotics and what substances they produce, than in identifying individual species.

A handful of projects have already tried to characterize the bacteria that cause bowel disease and obesity, including research by Jeff Gordon at Washington University in St. Louis, who found different compositions of bacteria in obese and lean subjects (for details, see my article on obesity). Then, there was the 2006 project by Steven Gill and colleagues at the Institute for Genomic Research in Rockville, Maryland, who threw around some then-hefty numbers when they carried out such a metagenomic analysis of the microbes in two people’s intestines. After 2,062 polymerase chain reactions and 78 million base pairs, the team provided only the briefest of glimpses into the genetic underpinnings of the human gut’s microbes.

According to Mullard, these first surveys involved too few individuals and sampled too few microbes, usually from only the gut or the mouth, to provide an adequate description of the microbiome. But things have changed in the past few years. A few million foreign genes no longer sound so daunting in the face of advanced genetic-sequencing methods that are capable of crunching monumental amounts of numbers. As with the American Microbiome project, thanks to certain cutting-edge technologies, researchers can assess hundreds of millions of base pairs in just a few hours.

A few million foreign genes no longer sound so daunting in the face of advanced genetic-sequencing methods that are capable of crunching monumental amounts of numbers.

An in-depth analysis by Tract (MetaHIT) researchers of exactly what microbes inhabit the gut and what substances they produce will only enhance the knowledge already derived from Marshall’s work, which shows that chronic bacteria in the gut or elsewhere survive largely because they have evolved mechanisms to block the activity of certain receptors that would otherwise activate pathways that would inhibit their survival. A better understanding of what substances gut bacteria create may help Marshall and other scientists identify other ligands that dysregulate the VDR or other receptors.

Combining data derived from Tract (MetaHIT) with that derived from Marshall’s work will also provide an opportunity to better understand exactly what the mass microbes in our gut are up to. Historically, researchers have understood that a great number of bacteria thrive in the gut. However, in the absence of enough data showing how pathogens in the gut survive, or how gut bacteria contribute to disease, they have only been able to guess at the role of the gut microbial community.

Such researchers have proven to be optimists. Over the past decades, the vast majority of them have concluded that, if bacteria are present in large numbers in the gut, they must be doing something helpful. That, or gut bacteria have been assumed to be commensal – helping the human gut in some way and in turn obtaining nutrients from the host. Yet nature shows that commensal relationships are not necessarily the rule. Sure, you’ll find mites on certain birds or orchids growing on trees. But in the majority of cases where two species interact, one usually takes advantage of the other. Furthermore, considering what we already know about bacteria, they are almost always guilty of exploiting the resources of their host. So it may be wishful thinking to assume that the bacteria in our guts are largely friendly helpers.

This isn’t to say that there aren’t species of gut bacteria that can provide a benefit to their host. Yet increasing evidence points to the fact that the vast majority of gut bacteria are actually responsible for causing many bowel diseases previously considered to be of “unknown” cause. When faced with the large number of different inflammatory bowel diseases and the fact that a tremendous number of uncharacterized bacteria inhabit the gut, it’s logical that there’s a connection between the two phenomena. Of course, Marshall’s in silico work, as well as data derived from the MP study site shows that patients who kill large numbers of gut bacteria end up recovering from a number of bowel diseases, providing a good deal of support for the above hypothesis.

This all invokes the rather controversial question, “Do humans really need gut bacteria?” Those patients to spend long periods of time on the MP have killed a great deal of their gut bacteria, yet seem to have GI tracts that function properly. Marshall has conceded that “good” gut bacteria could potentially exist, but as of yet, he has simply seen no evidence of a species that offers humans a benefit.

Then again, whether or not a certain species of gut bacteria may be considered “helpful” may depend on a person’s set of circumstances.Then again, as Marshall describes, whether or not a certain species of gut bacteria may be considered “helpful” may depend on a person’s set of circumstances. It’s widely accepted that some gut bacteria help metabolize carbohydrates, causing people to absorb about 15-20% more of the energy from the carbohydrates they ingest. In a country like the United States, where the majority of people are well-fed, or in many cases over-fed, the presence of such bacteria in the gut might provide a distinct disadvantage. People who have access to enough food are usually seeking to lose weight and, in such cases, the presence of bacteria that glean more energy from carbohydrates would contribute to weight gain. The average American would probably be better off without such species in the gut.

But what about people in developing countries who face food shortages and are often limited to eating just the amount of food they need to survive? Under such circumstances, the presence of a bacterial species in the gut that gleans more energy from carbohydrates would be seen as a great advantage, allowing people to acquire more energy from a smaller portion of food. In a world where even the developed world may face food shortages in the future, one can never tell if someday such bacteria would provide a benefit to the entire population.

Scanning electron microscope images of B. thetaiotaomicron, a prominent human gut bacterium, and the intestine.

Yet, possibilities like the one discussed above still don’t answer the questions of whether humans actually need gut bacteria. Bacteria and humans (or our ape-like ancestors) have evolved in tandem for millennia. Are pathogens’ ability to inhabit our bodies an evolutionary adaptation that serves to benefit both humans and bacteria, or is it possible that the ability of microbes to persist in the human body is largely an evolutionary victory for bacteria won at our expense? As more and more diseases are linked to bacteria previously considered innocuous, the latter is becoming an increasingly plausible possibility.

Compare the human body to planet Earth. Creatures including human beings have evolved to live on our planet, yet does the Earth need the presence of such animals to survive? Most people would agree that the Earth would manage just fine without human beings. Although a handful of humans may strive to enhance certain aspects of our natural surroundings, the vast majority of mankind is depleting the Earth’s resources, leading to massive problems such as climate change, pollution, and an accumulation of fake chemicals in our water and food supply. So if we compare the bacteria that inhabit our guts and bodies to the people that inhabit our planet, it’s plausible that both might be better off without alien inhabitants.

Of course, some animals may be seen as beneficial to Earth. The earthworm restores the resiliency of soil, or the honey bee carries pollen from flower to flower. Yet even under these potentially beneficial circumstances, one can still question whether the Earth could maintain a state of homeostasis on it’s own without such help, or quickly evolve different ways to manage without such aid.

Furthermore, there is no question that any bacteria, whether friend or foe, places a burden on the innate immune system. With trillions of bacteria to keep track of, the innate immune system is constantly at work, prioritizing which bacteria to attack and determining where immune system cells should be located. In fact, researchers estimate that 70 percent of the immune system is located in and around the gut. Imagine if gut bacterial load was reduced to the point where much of this burden was lifted? The innate immune system would certainly be able to divert much more strength towards killing pathogens in other tissues as well new pathogens attempting to enter the body. Of course, as of now, such a scenario would only be possible if a person were to remain on low, pulsed antibiotics for a lifetime. Without the help of antibiotics, it seems reasonable to conclude the innate immune system would be over-burdened by the task of keeping the body bacteria-free.

We may be asked to embrace the reality the gut bacteria are not just “friendly” helpers.

Some may argue that probiotics are beneficial bacteria yet, as described in this article. An alternate hypothesis about how they provide palliation must also be factored into the picture.

All this means that Tract (MetaHIT) researchers, MP researchers, and scientists studying gut bacteria in the light of new molecular technology may be facing a paradigm shift in the way gut microbes are perceived. Rather than viewing the majority of them as “friends,” we may unfortunately have to face the fact that many of them are enemies, or at least not necessary for our well-being. It still remains unclear if humans would want to be completely bacteria-free if the option existed, but the possibility that a person would be in better health without bacteria is nevertheless an intriguing possibility. Or perhaps in the future, humans will be able to pick and choose the bacteria that will inhabit their guts, in order to harbor certain species that fit their specific needs.


The fact that the Microbiome project and Tract (MetaHIT) plan to generate so much new information on bacteria means that collaboration between the two groups and other smaller groups involved in bacterial sequencing is important. According to Bork, when all the projects are running at speed, reams of data will be generated worldwide. But because different groups are using different techniques to collect samples, extract DNA and annotate data, the data sets could be difficult to compare.

Enter the as-yet-unlaunched International Human Microbiome Consortium. Scientists from several international projects, including the Human Microbiome Project and MetaHIT, have been meeting since late 2005 to figure out how to collaborate on a range of issues such as the compatibility of data and which bacteria to sequence for the reference database. The group is already setting up infrastructure and “beginning to address the tough questions,” says Weinstock. But according to Nathan Blow of Nature News, it is too early to say how well the Consortium will foster collaboration. Its official launch, scheduled for this past April, was postponed for six months to allow the NIH and the European Commission to overcome bureaucratic difficulties.

Another issue being addressed by the Consortium is that of intellectual property. As with other genomic projects, members of the Consortium will be expected to release sequence data into the public domain as soon as they are generated. But according to Blow, this doesn’t necessarily preclude disputes over intellectual property if, for instance, a particular bacterial gene proves to be a useful diagnostic marker for a disease. Another unresolved question is whether a laboratory can have one project that abides by the Consortium’s regulations, and another that doesn’t. “There are grey areas, and I feel that until we have a test case, they will have to be watched very carefully,” says Bhagirath Singh of the Canadian Institute of Health Research, who is helping to develop the Canadian Microbiome Initiative.

It’s increasingly important for researchers and doctors to start pulling information out of individual laboratories and individual clinic records so that we may compile it.Intellectual privacy and patent issues aside, optimism for the collaboration still runs high, and having a database of bacterial sequences that is available to other research teams and perhaps even the public would be a great step forward in a medical movement that many believe needs a pick-me-up. It’s increasingly important for researchers and doctors to start pulling information out of individual laboratories and individual clinic records so that we may compile it. Patterns and associations can be detected much more easily when large groups of data are gathered simultaneously and made accessible to as many people as possible. The computer open-source movement, which has spread to many other fields, has seen incredible success in areas where research and data are openly shared. Access to open-source databases will almost certainly augment the pace of major medical discoveries – a pace that, MP aside, can often seem as if it’s at a current standstill.

Participants from microbiome projects around the world have expressed the desire to join and attend the Consortium. Like bulls ready to race down the streets of Pamplona, such research teams will be competing with each other as the search to sequence the microbiome moves forward. After all, each group wants credit for identifying as many new species of bacteria as possible.

“The intention is to work together,” says George Weinstock, a geneticist at Washington University in St Louis, who is helping to organize the Human Microbiome Project, “but for the moment it is more about working in parallel until we can understand how to work together”. Apparently some European researchers feel at a disadvantage because MetaHIT’s operating budget is only a quarter the size of the Human Microbiome Project’s. “This is giving a huge advantage to the Americans,” Guarner says. “They are going to be quicker and they have more equipment.”

Then again, other members of MetaHIT feel that they actually have an edge because money for their project has already been distributed and data collection is under way, whereas the Human Microbiome Project will not announce many of its funding decisions until later this year. “We have an advantage already, we have a show on the road,” says Willem de Vos, a microbiologist at Wageningen University in the Netherlands and a member of MetaHIT.

Color-enhanced scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells

For example, in Denmark, a team led by Oluf Pedersen at the Steno Diabetes Centre in Copenhagen is collecting fecal samples from 120 obese volunteers and 60 controls to tease out specific microbial genes that might contribute to obesity. A similar-sized study in Spain, led by Guarner, will compare the microbiotas of patients with inflammatory bowel disease with those of genetically matched controls and examine the effect of drugs.

Others feel that the sharing of data will simply allow the most ingenious teams to get ahead. “If it is an international consortium, it doesn’t matter where the data are generated,” Bork adds. “For example, we can be the pirates here, sitting at the end in Europe, and use American data to make the discoveries.”

As Blow describes, given the number of separate projects, all at such an early stage, it’s almost impossible to make out where the starting line lies or who exactly is edging ahead. But for many of us, the potentially intense competition among microbiome researchers is a welcome change to the increasing number of “consensus conferences” in which researchers with the same opinions fail to consider alternate lines of thinking and generate novel hypotheses. Competition has the potential to speed up output, allowing for a medical community that may stall less and deliver more. Furthermore, when faced with talented competitors, researchers are more likely to consider new hypotheses and break from the norm in order to gain an edge over an opposing team.

Competition has the potential to speed up output, allowing for a medical community that may stall less and deliver more.Then again, the fact that trillions of bacterial genomes must be sequenced means that at the current moment there is plenty of work for each research team and multiple ways for every research team to excel. With trillions of microbes to sift through, most researchers feel that there is more than enough of the microbiome to go around. “There’s so much to learn, so much we don’t know and so many adventures,” Gordon says. “There’s enough room for everyone.”

A core microbiome?

How many different bacterial species the microbiome project will uncover remains anyone’s guess. But according to Blow, many of the researchers involved with the project have one impending question.

Is there a core human microbiome?

“One of the things that is obsessing microbiologists is: ‘What is the size of the core microbiome?,’” says Jeremy Nicholson, a biological chemist who studies microbes and metabolism at Imperial College in London.

By core microbiome, researchers like Nicholson are referring to a hypothesized number of bacteria that every person might harbor. For example, if some bacteria are shown to have a beneficial effect on human health, then perhaps everybody needs a certain number of these pathogens to survive. Then again, if all people harbor certain bacterial species, such pathogens may be seen in a different light. If a “core microbiome” is established, then perhaps the bacteria that comprise it contribute a process that happens to every human being. That process is aging.

As Marshall and colleagues discussed at the recent “Understanding Aging: Biomedical and Bioengineering Approaches” conference at UCLA, it’s entirely possible that the bacteria we harbor are able to infect our stem cells – cells found in all adult tissues that act as a repair system for the body by replenishing other more specialized cells. But as people age, stem cells often lose their ability to repair and heal. If bacteria infect the stem cells, it has been hypothesized that they may expedite the rate at which they lose their resiliency, thus accelerating the aging process.

A stem cell derived from the skin.

Remember the above discussion about how certain microbes can allow people to glean 15% more energy from the carbohydrates they consume? While beneficial under some circumstances, Marshall warns that if such a bacterial species can infect nearby stem cells, they will contribute to the aging processes in the gut.

Several studies support the possibility that chronic bacteria can infect the stem cells. A team of German researchers recently showed that patients who had suffered a heart attack (an event most likely caused by chronic bacterial forms in the heart and blood vessels) had stem cells which were only about half as effective at repairing the heart tissue as stem cells transplanted from healthy 20 year-old males. This supports the view that infected stem cells lack many of the healing properties maintained by their healthy counterparts.

Dr Emil Wirosko, one of the foremost experts on L-form bacteria, died before he could publish on the subject. But according to his colleagues, Wirosko believed L-form bacteria are able to infect stem cells.

Then there are telomeres – DNA sequences on the ends of chromosomes that are gradually lost as cells replicate. As they shorten, a cell can no longer divide and becomes inactive or dies – meaning that the length of a person’s telomeres plays a role in how quickly they will age. The fact that people with heart disease, Alzheimer’s, cancer, and other illnesses have been shown to lose telomere sequences at a faster rate than their healthy counterparts suggests that the bacteria involved in causing such diseases may also have an effect on telomere length.[2] As Marshall describes, if pathogens do directly alter our DNA, then the weakened DNA at the ends of telomeres provides some of the easiest genetic material for them to mutate.

The weakened DNA at the ends of telomeres might provide some of the easiest genetic material for bacteria to mutate.

Once again then, the question is posed: What might occur if humans were to become largely bacteria-free? Might they age at a slower rate? The possibility is tantalizing. Data from people on the Marshall Protocol, who are gradually reducing their bacterial loads, will prove to be increasingly insightful in this regard as time wears on.

As previously discussed, the sequencing of the human genome alone does not allow for the Gattaca-like world described earlier in which humans could be identified and catalogued by their unique DNA sequences. Ironically, the human Microbiome Project and Marshall’s work might make that world more of a reality. If it turns out that the bacteria we harbor are a source of disease and a burden on the innate immune system, then the population will seek (like those people on the MP) to eliminate at least the majority of them.

If sequencing procedures then no longer detect bacterial genes along with human genes, it may be possible to sequence a more fully human genome. One must still factor in DNA mutated by other environmental factors or by chance, but nevertheless, we would be closest to actually answering the question “Who am I?”

Will we ever enter a Gattacca-type world?

Perhaps then, after people have eliminated much of their bacterial load, genetic information will prove to be a more valuable human fingerprint, ethical issues aside.

In the meantime, an optimal environment to better the health of humankind will be one in which controversial hypotheses such as that described above are at least put on the table, and new ideas that challenge current paradigms are embraced rather than rejected. Under such conditions scientists can fully live out Mullard’s advice to, “Celebrate their quest to map, catalogue, and understand the human microbiome for the inspiring saga it is.”


  1. Marshall, T. G. (2006d). Molecular mechanisms driving the current epidemic of chronic disease. []
  2. Cawthon, R.M., Smith, K.R., O’Brien, E., Sivatchenko, A., & Kerber, R.A. (2003). Association between telomere length in blood and mortality in people aged 60 years or older. Lancet, 361(9355), 393-5. []