Volume 13 • Number 7 • July 2012

This special issue may be too technical for some; but, if you have been reading this newsletter on a regular basis you will do fine. It covers a most stunning issue of the Journal Science, a publication of the American Association for the Advancement of Science. This journal is widely ranked in the top 5 of ALL scientific journals; it is not a medical journal per se, which makes its report on THE GUT MICROBIOTA all the more compelling. The journal is aware that this issue is a GAME CHANGER; they have made it available in its entirety if you contact them before August 15th 2012. Therein you will read (only quotes below) about the immune system in the gut, cancer links, and many other “connections” to your health. But, perhaps the most compelling is the association between gut organisms and obesity.

Obesity is also addressed in a June issue of the Journal of the American Medical Association. Both publications cover neglected areas of obesity, which is sadly blanketed under the worn out refrain of “calories in = calories out.” This dogmatic and oversimplified view may get most people in the ballpark, but not to home plate. “Weight Loss and Weight Loss Maintenance[1] demonstrates that foods may have the same calories, but some are more fattening than others, a fact that the New England Journal of Medicine covered last year.[2]

Why are we not implementing such simple principles, despite strong evidence available to all? Could it be that Big Pharma and Big Food care more about their profits than your health? Two glaring examples of these concerns are the lawsuit against Pfizer for colluding to keep Generic Lipitor, which will be much cheaper, from being available to you, and the European Union ruling that France cannot “discriminate” against GMO farm products. ~Hugo Rodier, MD

From the Cover of the Journal Science June 8th 2012.

“Human intestinal bacteria: The human gut is teeming with symbiotic microbes that interact with their host to maintain health. A joint Science and Science Translational Medicine special section explores advances in microbial ecology, microbial and host metabolisms, and interactions between gut microbes and the host immune system. Complementary articles discuss how to apply this knowledge to boost health and nutrition, combat infectious disease, and control non communicable diseases such as obesity and diabetes.”

“We are on the threshold of making profound discoveries about the microorganisms with which we share our bodies, indeed whose cell count vastly outnumbers our own. In Science‘s 2005 special section Gut: The Inner Tube of Life, we saw hints of the important relationships we have with the microbial inhabitants of our guts. Since then, next-generation DNA sequencing and functional studies have begun to reveal how crucial these inhabitants are for our evolution, development, metabolism, immune defense, and susceptibility to a multiplicity of infectious diseases.”

“Science and Science Translational Medicine have joined forces to resume the exploration of our inner tube and its microbiota. As Gordon points out, investigations into gut microbiota draw from many fields: ecology, genomics, metabolomics, immunology, and public health. A gathering of diverse minds and ideas will drive the development of new therapies for treating intractable infections, scourges of the developing world such as malnutrition, and lifelong inflammatory diseases, such as Crohn’s disease and colitis, as well as offering options for relieving the burden of metabolic diseases, including obesity and type II diabetes.”

“These joint special sections in Science and Science Translational Medicine still provide only a distant view of our inner world. The next decade will see a revolution in understanding our microbial symbionts and how they can be manipulated for therapeutic benefits that will bring true inner world peace.”

The editors suggest the following Related Resources on Science sites:

  • Interactions Between Commensal Fungi and the C-Type Lectin Receptor Dectin-1 Influence Colitis .Science 8 June 2012: 13141317.Published online 6 June 2012
  • Innate Lymphoid Cells Promote Anatomical Containment of Lymphoid-Resident Commensal Bacteria .Science 8 June 2012: 13211325.Published online 6 June 2012
  • Report Regulated Virulence Controls the Ability of a Pathogen to Compete with the Gut Microbiota .Science 8 June 2012: 13251329.Published online 10 May 2012
  • The Application of Ecological Theory Toward an Understanding of the Human MicrobiomeScience 8 June 2012: 12551262.Published online 6 June 2012

“The human-microbial ecosystem plays a variety of important roles in human health and disease. Each person can be viewed as an island-like “patch” of habitat occupied by microbial assemblages formed by the fundamental processes of community ecology: dispersal, local diversification, environmental selection, and ecological drift. Community assembly theory, and metacommunity theory in particular, provides a framework for understanding the ecological dynamics of the human microbiome, such as compositional variability within and between hosts. We explore three core scenarios of human microbiome assembly: development in infants, representing assembly in previously unoccupied habitats; recovery from antibiotics, representing assembly after disturbance; and invasion by pathogens, representing assembly in the context of invasive species. Judicious application of ecological theory may lead to improved strategies for restoring and maintaining the microbiota and the crucial health-associated ecosystem services that it provides.”

  • Virulence or Competition? Science 8 June 2012: 12381239.Published online 10 May 2012

“The human gastrointestinal tract harbors trillions of bacterial cells belonging to more than 1000 species (1), and there are 10 times as many bacterial cells within the gastrointestinal tract as there are human cells within our bodies (2). The gastrointestinal microbiota plays essential roles in human nutrition, physiology, development, immunity, and behavior, such that disrupting the structure and balance of this community leads to dysbiosis and disease (35). This important balance between host and microbiota can be severely disrupted by environmental stimuli. One of the most common insults to the microbiota that induces dysbiosis is infectious diseases. On page 1325 of this issue, Kamada et al. (6) propose that competition between resident microbes and pathogens is influenced by the expression of virulence factors by pathogens and by the nutritional requirements of both populations. These dynamics can steer the survival, colonization, and clearance of pathogens in the gut.”

  • Host-Gut Microbiota Metabolic Interactions , Science 8 June 2012: 12621267.Published online 6 June 2012

“The composition and activity of the gut microbiota co-develop with the host from birth and is subject to a complex interplay that depends on the host genome, nutrition, and life-style. The gut microbiota is involved in the regulation of multiple host metabolic pathways, giving rise to interactive host-microbiota metabolic, signaling, and immune-inflammatory axes that physiologically connect the gut, liver, muscle, and brain. A deeper understanding of these axes is a prerequisite for optimizing therapeutic strategies to manipulate the gut microbiota to combat disease and improve health.”

  • Is It Time for a Metagenomic Basis of Therapeutics? Science 8 June 2012: 12531255.Published online 6 June 2012

“The trillions of microbes associated with the human body are a key part of a comprehensive view of pharmacology. A mechanistic understanding of how the gut microbiota directly and indirectly affects drug metabolism is beginning to emerge.”

  • Taking Stock of the Human Microbiome and Disease .Science 8 June 2012: 12461247.Published online 6 June 2012

“Our bodies, inside and out, are teeming with trillions of microbes. Most of them are our friends, helping us to digest food, strengthen our immune systems, and keep dangerous enemy pathogens from invading our tissues and organs. Evidence is building that this resident community of microbes, called the microbiome, plays a major role in health and disease. When the normal composition of the microbiome is thrown off balance, researchers say, the human host can get into serious trouble-especially because the 5 million to 8 million different microbial genes in our bodies vastly outnumber the 20,000 or so human genes. Indeed, recent research has implicated microbiome imbalances in disorders as diverse as cancer, obesity, inflammatory bowel disease, psoriasis, asthma, and possibly even autism.”

  • Interactions Between the Microbiota and the Immune System .Science 8 June 2012: 12681273.Published online 6 June 2012 Science 8 June 2012;336: 1268

“The large numbers of microorganisms that inhabit mammalian body surfaces have a highly coevolved relationship with the immune system. Although many of these microbes carry out functions that are critical for host physiology, they nevertheless pose the threat of breach with ensuing pathologies. The mammalian immune system plays an essential role in maintaining homeostasis with resident microbial communities, thus ensuring that the mutualistic nature of the host-microbial relationship is maintained. At the same time, resident bacteria profoundly shape mammalian immunity. Here, we review advances in our understanding of the interactions between resident microbes and the immune system and the implications of these findings for human health.”

  • Honor Thy Gut: SymbiontsRedux .Science 8 June 2012: 12511253.Published online 6 June 2012

“Exploring our gut microbial communities with new tools is allowing us to revisit old questions; to develop new concepts about our evolution, postnatal development, systems physiology, individuality, and definitions of health; and to further delineate the impact of our changing life-styles. It is also allowing us to envision exciting new ways for addressing global health problems. This area is inherently interdisciplinary, offering a wealth of opportunities to create new fields, partnerships, and educational initiatives. It is captivating to the public and carries substantial expectations. As such, participating scientists need to sponsor proactive, solution-focused discussions of its societal implications.”

  • News: My Microbiome and Me .Science 8 June 2012: 12481250.Published online 6 June 2012

“In 2004, microbiologists showed a link between obesity and gut microbiota in mice. To find out whether that link extended to humans, microbiologist Zhao Liping adopted a regimen involving Chinese yam and bitter melon-fermented prebiotic foods that are believed to change the growth of bacteria in the digestive system-and monitored not just his weight loss but also the microbes in his gut. When he combined these prebiotics with a diet based on whole grains, he lost 20 kilograms in 2 years. His blood pressure, heart rate, and cholesterol level came down. Faecalibacterium prausnitzii-a bacterium with anti-inflammatory properties-flourished, increasing from an undetectable percentage to 14.5% of his total gut bacteria. The changes persuaded him to focus on the microbiome’s role in his transformation. He started with mice but has since expanded his research to humans.”

  • EDITORIAL: Tackling the MicrobiomeScience 8 June 2012: 1209.Published online 6 June 2012

“Microorganisms represent the majority of life on earth, populating a wide range of niches on its surface, underground, in the oceans, in the atmosphere, and both on and inside all multicellular organisms. This “microbiome” will clearly play a critical role as humans struggle to deal with society’s major challenges-health care, agriculture, energy, and the environment. As one example, the human gut microbiome contributes 36% of the small molecules that are found in human blood, and it also plays a major role in creating susceptibility to certain human diseases. In recent years, a variety of microbial communities have been characterized through such efforts as the Human Microbiome Project and the Earth Microbiome Project. But mapping these trillions upon trillions of microbes and analyzing the vast amounts of data that are accumulating will require new integrative approaches aimed at understanding how microorganisms function and are interrelated.”

See pictures of the journals discussed below.


[1] J. of the American Medical Association 2012;307:2617

[2]Changes in Diet and Lifestyle and Long-Term Weight Gain in Women and Men,”

NEJM 2011;364:2392

Hugo Rodier, MD is an integrative physician based in Draper, Utah who specializes in healing chronic disease at the cellular level by blending proper nutrition, lifestyle changes, & allopathic practices when necessary.

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