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Myth vs Truth: Do Antibiotics Ruin Gut Health?

Johnny Delirious • February 12, 2025

Restoring gut bacteria after antibiotics

If you have ever gone on vacation to a tropical paradise the first thing people tell you is “don't drink the water.” Well that is good advise however during an evening of dancing and music we might accidentally eat or drink the wrong thing and have violent diarrhea or vomiting. To stop this digestive trauma, the doctor may prescribe antibiotics and many times this gives some relief, at least we are can start getting back to normal or so we think. The violent digestive trauma is gone but discomfort lingers on and things in a subtle way just don't feel right.


We can't talk about the digestive track in any rational way unless we address the full scope of the microbiome. We have to consider the full recognition of how antibiotics affected gut health. Most people don't realize that our microbiome in our colon provides more the 60% of our immunity response. To once and full all get it back in balance and healthy again we need certain spore biotics, particularly from the Bacillus strain. So in true Dr. Johnny fashion I will give the history and research from Microbiome Labs for a more in-depth discussion of spores.


History of Bacillus Spores


During WWII, more German soldiers stationed in North Africa were dying from dysentery than in battles. The Germans noticed that when the locals became ill, theyfound dried camel dung and consumed it. Yes, they ate it right on the spot. Something in the camel dung was fighting dysentery and other infections, so they took some camel dung back to the pharmaceutical companies in Germany.


Late 1940's - Bacillus clausii was isolated and used as a prescription spore probiotic in Germany (Enterogermina). Primarily used to treat dysentery, chronic upper respiratory infections, and other immune dysfunctions in kids and adults. Enterogermina is still on the market today (made in Italy). Since 1958: Bacti-Subtil (France) also entered the market as a prescription. There are at least 14 well-established spore drugs on the market in Europe, South East Asia, and Latin America, in addition to products used in agriculture and aquaculture.


First forward to today in Florida, Dr. Johnny's home state, when starting in 2005 - Microbiologist, Kiran Krishnan, was tasked with developing the most effective probiotic that not only survives and thrives, but contains probiotic strains native to the gastrointestinal tract. He asked - What would be nature's probiotic? How would we encounter them in nature? What are they and what would they do in the body? The obvious answer - would be something that mimics nature. Kiran and Dr. Tom Bayne realized the incredible potential of Bacillus spores and started the research process to bring Bacillus spores to manufacturing.


2012 - After 7 years, the research team achieved the very difficult task of stabilizing the spores for supplement manufacturing founded Microbiome Labs and MegaSporeBiotic their flagship product entered the market


The reason for spores inherent survivability comes from their bi-phasic life cycle. This means that the Bacillus spores can transition interchangeably from their dormant form to their active form, depending on the environment. In its dormant spore form, Bacillus


will surround itself with an endospore, which is a tough, natural outer shell that protects it from light, harsh temp., lack of oxygen, low PH, gastric barriers, antibiotics, UV radiation, solvents, enzymes, and even high pressures. This key feature is what allows MegaSporeBiotic™ to survive easily through digestion without the need for enteric- coated capsules or refrigeration.


Bacillus spores open in the intestines, tumble around the lining of the gut, then a molecular handshake happens welcoming them into the environment, and they open up.


They become metabolically active and start quorum sensing. They read microbial signatures of bacteria in the environment. Because they have evolved with us, they know which bacteria should and shouldn't be there so they will read their chemical signatures, identify pathogens that are overgrown, sit next to them, and compete with them.


Bacillus Spores in MegaSporeBiotic


  • Bacillus Subtilis Bacillus Licheniformis Bacillus Coagulans Bacillus Clausii Bacillus Indicus HU36
  • Most widely used and well-studied strains in humans are: Spores that modulate the microbiota through quorum sensing.
  • Quorum sensing is a cell-to-cell communication process that enables bacteria to collectively modify behavior in response to changes in the cell density and species composition of the surrounding microbial community.
  • Bacillus spores produce a significant number of antimicrobials that control bacterial overgrowth in the GUT. There are over 17of these antimicrobials.
  • Spores conduct competitive exclusion (CE) of pathogenic organisms to help maintain microbiota balance. CE is accomplished by competing for space and nutrients.
  • Spores have the ability to increase the numbers of important GIT commensals such as Lacto., Bifido., Akkermansia, F. Pauznitzii.
  • This is important when we are achieving Microbiome Balance.


MegaSporeBiotic™ can increase microbial diversity by changing the pH, crowding out unwanted pathogens, and increasing the production of short-chain fatty acids.


These spores are found all over the environment (soil, vegetation, dust, rocks, aqua- environments, digestive systems of insects, marine life, mammals, humans, etc.) Studies indicate that the environment is simply a vector to transfer the bacteria from host to host, the spores are better suited for life in the GI, but designed to be passed via the environment.


They colonize very effectively in the human gastrointestinal tract and several different animals. The spores in MegaSporeBiotic are part of the normal human commensal flora. They are true commensal organisms and their mechanisms should be noted.


A bottle of megasporebiotic is sitting on a table.

MegaSporeBiotic™ contains five Bacillus spore-forming bacterial strains. Spore- formers surround themselves with a protective coat, so they are naturally designed to navigate digestion with 99.99% survivability. They arrive in the gut, transition from spore to active form, and provide practical reconditioning support.


MegaSporeBiotic™ can support increased microbial diversity, maintain healthy gut barrier and immune function, and support keystone bacterial species that produce valuable short-chain fatty acid (SCFAs) metabolites, including butyrate. SCFAs support many diverse physiological processes necessary for optimal health and well-being.


MegaSporeBiotic™ is the first, truly innovative, multi-spore-based probiotic. Check the Patient Register link to fill out the form and then purchase this powerhouse probiotic.


Mechanisms of Action:



  • Reconditions the gut by increasing microbial diversity
  • Bacillus spores compete with pathogens for space and nutrients and produce antibiotic compounds
  • Encourages the growth of key, health-promoting bacteria such as Akkermansia muciniphila, Lactobacillus, Bifidobacterium, Faecalibacterium prausnitzii, and more.
  • Maintains healthy gut barrier and immune system
  • Supports tight junction proteins 99.9% survival during digestion and does not need to be refrigerated 5 human commensal Bacillus strains that are found in a healthy human gut and colonize the GI tract.
  • May increase butyrate production by up to 40%
  • Gut Model study demonstrates a nearly 30% shift in microbiota population with continuous administration of our bacillus spores
  • First 100% spore-based probiotic clinically shown to improve leaky gut by 60% in just 30 days


30-Day supplementation with MegaSpore resulted in:


  • 42% reduction in circulating LPS following a high-fat meal
  • 24% reduction in triglyceride levels (36% reduction in 90-days), improved gut brain connection and metabolic markers.
  • Supports immune function, improves cytokine balance, reduction in loose stools


A deeper look at the 5 different probiotics in MegaSporeBiotic


Bacterial spores are dormant life forms that can exist in a desiccated and dehydrated state indefinitely. Each spore-forming strain has its own unique set of benefit survivability:


  • Bacillus Indicus, HU36: potent immune stimulation, produces carotenoids (lycopene, astaxanthin, beta-carotene, & lutein) at the site of absorption, most effective antioxidant probiotic strain on the market
  • Bacillus Subtilis, HU58: produces over 24 antibiotics, strongest competitor, produces nattokinase & K2, shown to lower Il-6 & TNF-a, highly important for immune development – GALT, (gut associated lymphoid tissue) strong production of SCFA's (short chain fatty acids)
  • Bacillus Coagulans (SC-208): produces L+optical form of lactic acid, increases nutrient absorption by producing digestive enzymes, increases absorption of BCAA's, improves peristalsis, reduces inflammatory metabolites
  • Bacillus Licheniformis (SL-307): produces antibiotic bacitracin, produces protease, improves protein digestion, produces full spectrum of B vitamins and folic acid
  • Bacillus Clausii (SC-109): antibiotic-resistant during antibiotic use, supports immune function, improves cytokine balance, reduction in loose stools


With MegaSporeBiotic we can be assured that after that round of antibiotics that saved our lives we can eliminate that lingering discomfort with an imbalanced microbiome. Click on the Patient Registration link and purchase MegaSporeBiotic today.


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John Hopkins Medicine suggests 5 foods to improve your digestion, they are Whole Grains, Leafy Greens, Lean Protein, Low Fructose Fruits(berries), Avocado. Well Dr Johnny totally agrees that fits right into the Mediterranean Diet from ancient Greek Health Wisdom which is the core of The Master Survivor Program. According to UC Davis; “The Mediterranean diet is a well- researched way of eating that can help improve overall health. It focuses on whole, plant-based foods and healthy fats. These are scientifically proven to reduce the risk of chronic conditions like heart disease.” They continue: “The Mediterranean diet consists of many foods found in regions that border the Mediterranean Sea. These types of foods provide a variety of vitamins and nutrients that nourish our body. Food groups that are part of the Mediterranean diet include: Fruits and vegetables Nuts and seeds, including almonds, walnuts, sunflower seeds, and pumpkin seeds Beans and legumes, such as lentils, chickpeas, black beans, and kidney beans Whole grains like whole wheat bread, quinoa, brown rice, and whole wheat pasta Fish and seafood Healthy fats and oils, including extra virgin olive oil and avocado and nut oils” This is exactly what Dr. Johnny has been promoting for over 40 years to all of his patients and they maintain a healthy gut. In fact, when you submit your hair sample, Dr. Johnny will run the analysis in the lab and produce your hair tissue mineral analysis (HTMA) report. This is why America needs the Master Survivor Program more than ever. The HTMA is number one starting point and it provides a road map for better health. In the report you will have a detailed and comprehensive outline of the foods you eat and it follows the Mediterranean Diet all taken from your chemistry. Therefore weight loss is easier for the ones on a diet and if you are in sport competition your Performance Benefits are enormous. I want to give you six points of how it helps the athlete and those wanting to get in better shape mentally and physically. Following the HTMA road map will improve Mental Clarity and Focus The brain is a chemical organ, and requires a vast array of nutrients for proper functioning. All toxic metals interfere with the central nervous system, leading to impaired mental functioning. These toxic metals can be elimination following the road map of the HTMA . This will be correcting biochemical imbalances and leads to improved mental focus and functioning. Coordination, clarity, awareness, judgment and a quick response time are a major part of all athletic performance. Balancing the mineral levels in all the cells including the brain by following the diet and supplement schedule will be the edge you need to have a better workout or win that race. Following the HTMA road map will provide Prevention of Injury and Burnout Chronic fatigue and burnout physiology are common conditions among athletes and people who push themselves past their limits. Particularly later in the season, Colds, flu, pneumonia and other illnesses will plague many athletes, especially those who travel and train and work out hard. The HTMA report identifies your stress level and shows ways to improve that using food. By correcting the stress levels before things go down hill will help you recover quicker, get more rest and maintain that competitive edge. Following the HTMA road map will create a Strong Immune System and provide more Resistance to Infection Nutritional imbalances cause weak joints, tendons and ligaments, excessive inflammation and muscle tears. Properly balancing body chemistry can help avoid injuries by maintaining stronger and more flexible ligaments, tendons and muscles. Staying on the HTMA schedule will keep balanced mineral ratios and speed recovery from fractures, sprains, strains and muscle fatigue. Following the HTMA road map will bring Improved Recovery from Workouts and Injuries A low sodium/potassium ratio and/or an abnormal phosphorus level is associated with excessive protein breakdown or catabolism. A chronic catabolic state can impair or even prevent the normal healing of sports injuries. The body requires many nutrients for healing injuries, including zinc, manganese, copper, calcium, magnesium and a variety of vitamins all in their proper balance. With the corrected nutrition amounts and combinations, healing results improve rapidly. Following the HTMA road map will show the Safe Use of Dietary Supplements getting only what your body needs. Most athletes take a variety of nutritional supplements, some of which are unnecessary, incorrect, or may be dangerous. One problem is they maybe getting too much of two or more vitamins or minerals. A thorough assessment and analysis of the athlete's diet, nutrient mineral balance, and toxic load provides important parameters to help determine the correct supplementation needed to balance and enhance body chemistry. Only the HTMA can tell the exact amounts of foods and supplements you need. Following the HTMA road map is the best Weight Management tool because the body will balance out on its own and get your weight under your control. Stubborn problems with food cravings and weight control plague some athletes, because they have too much of some elements and not enough of others. Consequently, professional athletes have shorter life spans and eat a lot of calories while training, but then when they stop training hard they keep eating the same way and stay out of balance. The HTMA provides specific data that when followed can assist with both weight gain and weight loss as well as eliminating the arthritis and joint problems by offering a scientific and individualized plan solving the problem safely and effectively. Many of my patients don't realize that we also do the hair tissue analysis HTMA on horses and dogs. So if you are worried about your fury four legged member of the family; your dog or horses when they compete in shows or races there is no better way to keep them in the winner's circle than following their diet and supplement schedule of their HTMA . Both canine and equine hair can be tested at my lab and if the HTMA is followed then your four legged loved one will have shiny healthy coats and quick responses to commands because their stress has been minimized. Some of my four legged clients have won AKA blue ribbons and have placed in the top 10 of the Breeder's Cup. The price for canine and equine HTMA is $250 and you get a comprehensive report. Most of my tell me that their dog and horse are all natural and refuse to give them vaccines. With analysis of the mineral profile we can determine what is lacking and what is needed. The HTMA is the most valuable diagnostic to find the right foods to help you and your dog or horse. For the owners following the HTMA, they will adhering closer to the Mediterranean Diet and have a healthy gut.
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