Sunday, January 6, 2013

The Scientific Evidence Against Bacteria. 1

Here I have cut and paste extracts from various sites. The sites are linked below the extracts. I have used bold text, underlines and italics to highlight the points I want to make. Otherwise, the content has not been touched. Certain complete statements have been juxtaposed for efficient usage of space. This conceals gaps in the narrative, as a visit to the link will reveal. These gaps could not be depicted here. The large bold numbered titles are mine and do not belong to the extracts and links indicated. Always check with the original post if there is any doubt about whatever is presented here. Reading Resources were linked in the previous post.

The gut alone has about 100 trillion of them. If conditions are favorable, a population of bacteria can double every 20 minutes or so. The body has 22,000 human genes compared to 8 million bacterial genes.

"The human gut is filled with large numbers of a wide variety of bacteria; clearly those that cause disease must rank high on the priority list of those to be studied, but the picture emerging from new research is that pathogens and beneficial bacteria are not necessarily mutually exclusive organisms. A microbe’s effects on the human body can depend on conditions."

"P. aeruginosa and C. difficile are common residents of human bodies and under normal circumstances are benign. So what turns them into enemies? Most of the time, says John Alverdy, an intestinal and critical-care surgeon at the University of Chicago, bacteria “have to have a reason to hurt you.” Surgery is just such a reason. A surgical patient’s normal metabolism is altered; usually nutrients are provided intravenously instead of through the digestive system, so in a patient being fed by an IV drip, the gut bacteria perceive their sustenance disappearing. A decline in available nutrients alarms them. And surgery triggers the release of stress compounds that bacteria also sense, Alverdy says. Chemotherapy and radiation have similar effects. When threatened, bacteria become defensive, often producing toxins that make the host even sicker. They also tend to speed up their acquisition of and purging of genes when under external selection pressure, of which antibiotics are an obvious and powerful example". ( )
 "Now, a new study suggests that gut bacteria can even mess with the mind, altering brain chemistry and changing mood and behavior.
In recent years, researchers have become increasingly interested in how gut bacteria might influence the brain and behavior, says John Cryan, a neuroscientist at University College Cork in Ireland. So far, most of the work has focused on how pathogenic bugs influence the brain by releasing toxins or stimulating the immune system, Cryan says. One recent study suggested that even benign bacteria can alter the brain and behavior, but until now there has been very little work in this area, Cryan says".


"Anaerobic bacteria are prevalent among the bacterial populations of the human body, particularly on mucous membrane surfaces. The major sites with a rich anaerobic normal microflora are the mouth, the gastrointestinal tract and the female genital tract."

"Your gut bacteria are very vulnerable to your lifestyle. If you eat a lot of sugar and refined grains for instance, your gut bacteria are going to be compromised because sugar feeds bad bacteria and yeast. Your gut bacteria are also very sensitive to:
Processed foods Antibiotics Chlorinated/fluoridated drinking water
Antibacterial soap Agricultural chemicals Pollution

It's really no wonder that poor gut health is more the norm than the exception these days, especially in the Western world. The good news though, is that you CAN optimize your bacterial population rather easily, and any damage to your intestines can also be reversed.  Dr. Campbell-McBride's GAPS Nutritional Program is designed to heal and restore the integrity and function of your gut lining. I highly recommend it, particularly if you suffer from any form of autoimmunity- and inflammatory disease, such as:
Multiple sclerosis Type 1 diabetes Rheumatoid arthritis Osteoarthritis
Lupus Crohn's disease Ulcerative colitis Chronic skin conditions
Kidney problems Urinary conditions Allergic and atopic conditions Degenerative conditions
Chronic fatigue syndrome Fibromyalgia Myalgic encephalomyelitis (ME) Inflammatory bowel diseases

Bacterial pathogens operate by attacking crucial intracellular pathways in their hosts. These pathogens usually target more than one intracellular pathway and often interact at several points in each of these pathways to commandeer them fully.19 These well-documented strategies include, to cite just several among many examples:
  • modulation of programmed host-cell death, known as apoptosis, to facilitate survival in the host;20 21 22 delayed apoptosis is a common feature of chronic inflammatory diseases; for more, see discussion of granuloma
  • modulation of vesicular traffic, a strategy which provides a protective niche within host cells, including in macrophages and neutrophils, which normally kill bacteria23
  • modulation of membrane traffic as is the case with the Legionnaire's bacterium Legionella pneumophila 24
  • modulation of macrophage cytokine production25
  • secretion of proteins, which are similar in effect to substances known to be toxic to humans26
  • creation of virulence factors which suppress MAMPs (Microbial Associated Molecular Patterns)27
  • Ehrlichia/anaplasma (EA) are an obscure group of obligate parasitic intracellular pathogens that intracellularly excrete a substance called host transcriptional protein, which can alter transcription in cell division. Infection with EA may lead to changes in transcription in proliferating cells, and contribute to illnesses such as leukemia, systemic lupus erythematosus, myelodysplastic disease, multiple sclerosis, amyotrophic lateral sclerosis, and rheumatoid arthritis.28
  • creation of ligands such as Capnine which bind, block, and downregulate the Vitamin D Receptor;29 Alzheimer's may be a case where bacteria stimulate the body's production of the antimicrobial peptide amyloid-beta to dramatically suppress VDR activity30
Bacterial pathogens have used many clever strategies to exploit the interior of host cells to their benefit, by manipulating intracellular trafficking pathways or targeting specific intracellular niches. The challenge facing the cell-mediated immune system is to detect and eliminate these pathogens.
M.S. Glickman and E.G. Pamer 31
Conversely, harmful bacteria may deregulate genes mediating energy metabolism, and can produce toxins that mutate DNA, affecting the nervous and immune systems. The outcome is various forms of chronic disease, including obesity, diabetes and even cancers.32 33 34
"Pathogenic bacteria have a variety of ways of disrupting the activity of and causing damage to human genes.
  • Horizontal gene transferBacteria can insert their DNA into human DNA.
  • Interruption of transcription and translation of DNA and RNA Intracellular pathogens, which inhabit the cytoplasm, can interfere with the steps involved in the transcription and translation processes. Such interference results in genetic mutations, meaning that human DNA is almost certainly altered, over time. The more pathogens people accumulate, the more their genome is potentially altered.
  • Disruption of DNA repair mechanisms – Since environmental factors such as exposure to ultraviolet light result in as many as one 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."

    "The Marshall Pathogenesis describes how microbes persist intraphagocytically – that is, inside the phagocytes. For example, Enterobacter hormaechei can infect skin cells,15 but where it can really wreak havoc is in infecting the very cells charged with ingesting bacteria."   


    "The following are virulence factors that promote bacterial colonization of the host .
    1. The ability to use motility and other means to contact host cells and disseminate within a host.
    2. The ability to adhere to host cells and resist physical removal.
    3. The ability to invade host cells.
    4. The ability to compete for iron and other nutrients.
    5. The ability to resist innate immune defenses such as phagocytosis and complement.
    6. The ability to evade adaptive immune defenses."
    "Some bacteria, such as Pseudomonas aeruginosa, are able to produce toxins and enzymes that kill host cells only when iron concentrations are low. In this way the bacteria can gain access to the iron that was in those cells.
    Staphylococcus aureus, on the other hand, produces surface adhesins that bind to extracellular matrix proteins and polysaccharides surrounding host cell tissue, including fibronectin, collagen, laminin, hyaluronic acid, and elastin.  S. aureus proteases and hyaluronidase then dissolve these components of the extracellular matrix providing food for the bacteria and enabling the bacteria to spread."

    "Researchers called this phenomenon quorum-sensing -- the bacteria communicate to determine the size of their community.
    But how? It turns out that the bacteria emit autoinducers, or signaling molecules similar to pheromones. The concentration of autoinducers in any given area indicates the size of the population. But bacteria don't just communicate with their own kind -- in recent years, scientists have determined that bacteria have a receptor for species-specific autoinducers, as well as a receptor for the signals sent out by all other kinds of bacteria. Not only does this indicate that many species of bacteria beyond the bioluminescent ones have the capability to communicate, it means that all bacteria in close proximity are probably chatting it up. Much like we account for our loved ones at the end of the day, the bacteria are taking roll as well.
    Why does this matter? Knowing how bacteria communicate could impact how we fight disease. Many bacteria begin to wreak havoc on the human body only once there are enough to overwhelm the immune system. Instead of waiting for bacteria to attack us, drug manufacturers are interested in developing a way to scramble the wires of bacterial communication before it starts. That way, bacteria will never know that they've achieved the kind of threshold necessary to establish an infection in the body."

    Bacteria, however, can communicate to evade anti-biotics!

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