SUMMARY: GREAT NEWS: My Instagram @patty.carter is posting some of my gut flora supporting microbiome recipes!I will still continue to post recipes on this website (and other posts with direct links to the science) ⇔ I’m adding Instagram because it is a great work around for the Pinterest failure to post the entire description on images posted (at this time, they truncate descriptions when you view them)! Of course, continue contacting me direct for those Pinterest recipes, all of which focus on the healing diet tenets from SCD, PALEO, Mediterranean Diet, and others! The second reason for adding Instagram is that I will post practical insights for integrating microbiome support into your lifestyle effortlessly and seamlessly ⇒ like today’s Instagram post showed my Whole Foods Market food haul, and it linked to the newly published May, 2018 American Gut new findings ♥♥♥ The bottom line, for my Instagram…it is best if you follow me to get the full recipe and practical integration insights, (but you don’t need to) –> just link here @patty.carter! The balance of this website post shares what posted in my Instagram today which included my Whole Foods Market food haul, and the link to the newly published May, 2018 American Gut new findings (which continues to confirm that 30 different vegetables consumed each week is best for microbiome diversity and health) ♥♥♥
Category Archives: Antibiotics & Microbiome
Study Recruiting for Antibiotics, Autism Symptoms
Summary: The 2014 1st International Symposium on the Microbiome in Health and Disease with a Special Focus on Autism brought out anecdotal parent findings that autism symptoms improved or worsened on antibiotics. Baylor College of Medicine study in conjunction with Texas Children’s Hospital, is now investigating those findings! If you have an autistic child, consider enrolling now before they are sick, so you have a test kit if prescribed an antibiotic over the next two years. You would send microbiome samples pre and post the antibiotic. Those are to be evaluated for changes to behavior and the microbiome — the bacteria, yeasts and fungi that also inhabit the gut, as well as examining metabolites (small chemical molecules) found in the GI tract. The study is free to participants and fully paid for by N of One: Autism Research Foundation which is founded by John Rodakis, the father of an autistic son who experienced symptom improvement due to an antibiotic dose Thanksgiving 2012. Participate if you can to increase understanding of Antibiotics, Autism Symptoms which at present, has a gap in the published autism research. This initial data may more effectively sub-type autism and develop and deliver more effective microbial-based interventions.
Lots of children have autism.
Data from 2014, and confirmed in 2016, show 1 in 42 boys and 1 in 189 girls have autism. This is often put as one in 68 children have autism. The prevalence chart below shows the alarming autism increase since 2000. Also startling, the number of children with autism varies widely by community, from 1 in 175 children in areas of Alabama, to 1 in 45 children in areas of New Jersey. See CDC Autism State Report, 2014 and CNN Report, Autism rates now 1 in 68 U.S. children: CDC.
Autistic children’s microbiome metabolites (the exhaust of the gut microbiota) differs compared to children without autism.
Several studies have reported significantly higher oral antibiotic use in children with autism versus typical children (6, 14–17). Antibiotics cause collateral damage to the microbiome. From the 2016 review, The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation: The use of antibiotics heavily disrupts the ecology of the human microbiome (i.e., the collection of cells, genes, and metabolites from the bacteria, eukaryotes, and viruses that inhabit the human body). A dysbiotic microbiome may not perform vital functions such as nutrient supply, vitamin production, and protection from pathogens [3]. Dysbiosis of the microbiome has been associated with a large number of health problems and causally implicated in metabolic, immunological, and developmental disorders, as well as susceptibility to development of infectious diseases [4–11].
Watch Bacteria Become Antibiotic Resistant
SUMMARY: This genius 2 week time-lapse video by Harvard Medical School lab lets you watch bacteria become antibiotic resistant. This experiment is thought to be the first large-scale glimpse of the maneuvers of bacteria as they become superbugs as they encounter increasingly higher doses of antibiotic and adapt to survive — and thrive — in them! Also read what to do if prescribed an antibiotic. Why? Antibiotics severely affect microbial diversity in the gut for months after exposure (4 months for clindamycin, 12 months for ciprofoxacin)… An added bonus of this experiment is the rewriting of lab research tools: The use of a large scale petri plate now opens up new ways for researchers to think about and conduct novel experiments!
For most folks, antibiotic resistance is conceptual and abstract. Most don’t understand why there now is a push for judicious use of antibiotics. For those details, see WHO, World Health Organization Vows To Combat Drug Resistance, with more here, and here for WHO pdf.
“Getting more people to understand how quickly bacteria evolve antibiotic resistance might help people understand why they shouldn’t be prescribed antibiotics. The drug resistance is not some abstract threat. It’s real.” —Tami Lieberman, member of Alm Lab, an evolutionary microbiologist at MIT. As quoted in WATCH: Bacteria Invade Antibiotics And Transform Into Superbugs.
In humans, antibiotics severely affect microbial diversity in the gut for months after exposure and enrich genes associated with antibiotic resistance, One course of antibiotics disrupts gut microbiome for a year, 2015, explains:
- Microbiome diversity in feces was significantly reduced for up to 4 months for clindamycin and up to 12 months for ciprofloxacin. Contrast this to microorganisms in the oral cavity and saliva which showed signs of recovery in as little as a few weeks after drug exposure.
- Amoxicillin had no significant effect on microbiome diversity in either the gut or oral cavity, but it was associated with the greatest number of antibiotic-resistant genes.
- Researchers saw a decline in the abundance of health-associated species that produce butyrate, a substance that inhibits inflammation, cancer formation and stress in the gut.
“Certainly we cannot live or survive without antibiotics; that’s out of the question. But there are situations when we should not use them, like when there are no evidence-based reasons.”
—One course of antibiotics disrupts gut microbiome for a year, 2015,
Practically, be vigilant and advocate for yourself when in the situation where antibiotics are being prescribed.
Ask for delay on starting the antibiotic until the culture results are in. In the very least, make sure the least broad spectrum antibiotic possible is prescribed. Many doctors will now agree.
What to do if taking ANTIBIOTICS, MICROBIOME
Summary: Antibiotics carpet bomb the microbiome. Here’s important things to do if you must take an antibiotic as noted in this article by Dr. Robynne Chutkan, MD and gastroenterologist, see bio below. I’ve adapted the list to include the How-To-Do details. Realize that the gist of the steps below you should ALWAYS be doing, not just during times you take antibiotics. But be particularly diligent and persistent following these steps if you must take an antibiotic in order to try to counteract the antibiotics, microbiome, nuke! For even more guidance on what to do before and after taking antibiotics, Dr. Mark Hyman’s recommendations from his article, Here’s the Downside of Antibiotics Your Doctor Might Not Tell You, has been added. Last, the studies looking at antibiotics and Culturelle, VSL #3, and Saccharomyces boulardii or Florastor(®), as well as their precautions, are included.
A word of caution concerning the FODMAP and Resistant Starch prong on the below gut preservation list:
FODMAP and resistant starch are part of the preservation strategy since both build up the diversity and richness of the microbiome. This is especially important for antibiotic dosing as the antibiotics nuke the microbiome; Caution though with FODMAPs… many with gut dysfunction have a hard time eating those. If you haven’t been eating FODMAPs, start slow and see if your gut can tolerate them. The goal of the FODMAP diet is to learn your individual tolerance for FODMAPs and NOT to eliminate them from your diet. Healing the gut using healing diet tenets and lifestyle supports the microbiome and will increase what you can consume FODMAP wise!
Antibiotics, microbiome and preservation — adapted from this article by Dr. Robynne Chutkan, MD
1. Take a probiotic during and after antibiotics (continue for at least one month after finishing antibiotics). [Consume the probiotic two hours before and two hours after the antibiotic.] Probiotics containing strains of Lactobacillus and Bifidobacterium are the most useful, as well as those containing the beneficial yeast Saccharomyces boulardii. Note though that bifidobacterium, in the SCD/GAPS world, seems to be contradicted due to overgrowth concerns and here. It’s controversial however; UMass IBD-AID permits this strain; see An anti-inflammatory diet as treatment for inflammatory bowel disease: a case series report. Whole food probiotics to consider for a crowding out pathogen purpose to help preserve the beneficial microbiome constituency, are lactose-free SCD yogurt, live sauerkrauts, Kimchi, pickles, etc. such as:
If you ask your doctor about CDiff risk with the antibiotic being prescribed, often they’ll tell you it is rare (not true by the way; it’s currently an epidemic, read the post ANTIBIOTIC RESISTANCE AND MICROBIOME COMPETITIVE CROWDING OUT CONCEPTS) and then they’ll immediately prescribe Florastor(®) (which likely won’t be covered by you insurance but it costs under $20 in my area). Also concerning, only 9.6% of academic medical centers stocked Culturelle and Florastor according to this study which is detailed below. Florastor(®) is S.Boulardii, which actually is a yeast, not a bacteria. The article, Saccharomyces boulardii CNCM I-745 supports regeneration of the intestinal microbiota after diarrheic dysbiosis – a review, is extraordinarily important . It has a gut mucosal focus, and anyone thinking about taking S.boulardii should read it… more than once… to realize the potential of this yeast. This article, along with other Saccharomyces boulardii or Florastor(®) studies, is excerpted below as is information on Saccharomyces boulardii or Florastor(®) precautions.
2. Eat PREBIOTIC foods (called FODMAPs and RESISTANT STARCH) to support your gut microbes. Foods high in fiber and resistant starch feed your microbes and help to promote species diversity and richness, which can decrease dramatically after a course of antibiotics. A Convenient FODMAPs Food list from =&0=& and from Monash University “Low FODMAP Diet” book and app (by Sue Shepherd and Dr. Peter Gibson, MD) follows. “High” FODMAP foods promote species diversity and richness. The limits noted are threshold levels where consumption above those levels, may not be tolerable for some.
• High-FODMAPs protein: Legumes (chickpeas, broad beans, butter beans, kidney beans), lentils over ½ cup. Low-FODMAPs protein: Meat, fish, chicken, tofu ( I don’t recommend soy especially if you are a Westerner since many lack the microbial bacterial enzymes to properly digest soy).
• High-FODMAPs vegetables: Garlic, leeks, onions, asparagus, cabbage, brussels sprouts, beets, artichokes, sugar snap peas, peas over 1/3 cup, celery, sweet corn, mushrooms, sweet potatoes over ½ cup, cauliflower, broccoli, cooked and then cooled potatoes, spinach over 15 leaves, zucchini over ¾ cup. Low-FODMAPs vegetables: Green beans, carrots, cucumbers, lettuce, tomatoes.
Antibiotic Resistance: Obama White House Today Convenes First Antibiotic Summit
SUMMARY: This is an incredibly timely followup to my last post, ANTIBIOTIC RESISTANCE AND MICROBIOME COMPETITIVE CROWDING OUT CONCEPTS. Copied below is the press coverage, issued just minutes ago, of:
Today: Obama White House Convenes (one day) First Antibiotic Summit focusing on “Forum on Antibiotic Stewardship” .
I can’t say enough about the real risk for acquiring an antibiotic resistant infection as explained in my last post, ANTIBIOTIC RESISTANCE AND MICROBIOME COMPETITIVE CROWDING OUT CONCEPTS, especially given that the average American has lost 1/3 of their diversity. Another study estimates 1 in 4 have 40% less bacteria (see prior post link for references). This post also provided maps that showed individual state antibiotic use and resistance risk:
Antibiotic resistance is an issue that you need to be aware of as antibacterials do not necessarily neutralize these strains. CDiff is one such example, as a virulent, antibiotic-resistant strain of CDiff now causes close to 500,000 new cases and 30,000 deaths a year in the United States alone. –Wide Use of Antibiotics Allows C. Diff to Flourish.
The only cure at the moment is Fecal microbiota transplantation [which] has >90 percent cure for antibiotic resistant CDiff. In the US, only after repeated antibiotic failure (thus confirming that the CDiff strain is in fact antibiotic resistant) is FMT allowed to be administered in order to implant a new donor microbiome. More details can be found in PRESERVE & RESTORE LOSS OF MICROBIOME DIVERSITY IS AGGRESSIVE PREVENTATIVE MEDICINE.
CDiff infections had mainly been thought to be hospital acquired, however, Wide Use of Antibiotics Allows C. Diff to Flourish, and CDC investigates deadly bacteria’s link to doctors’ offices revealed the increased prevalence of infection from “a 2013 study, where researchers found C. diff present in six out of seven outpatient clinics tested in Ohio,including on patients’ chairs and examining tables... patients should wash their hands after visiting the doctor’s office — with soap and water, because alcohol-based gels don’t get rid of C.diff.”
Antibioitics associated with CDiff includes: “Ampicillin, amoxicillin, cephalosporins, clindamycin and fluoroquinolones are the antibiotics that are most frequently associated with the disease, but almost all antibiotics have been associated with infection.” –Wide Use of Antibiotics Allows C. Diff to Flourish
Maja Rupnik wrote in The New England Journal of Medicine:
“The healthy gut microbiota has three features: a large number of micro-organisms, a large number of different species, and an increased representation of certain bacterial phyla and a decreased representation of other phyla. The disruption of any of these features can result in increased susceptibility to the growth of C. difficile… Even after infected individuals recover, about 5 percent continue to harbor the toxic strain in their stool for six months, and if they take another antibiotic during that time, the illness can recur.”
US Antibiotic Resistance and WHO
SUMMARY: Antibiotic resistance is invisible to most of us until you, a family member, or an acquaintance acquires such an infection. You can check out the slides below to see state by state, US Antibiotic Resistance Risk and state Antibiotic Use. erhaps the most reasonable mechanism to prevent antibiotic need in the first place, is explained in the post PRESERVE & RESTORE LOSS OF MICROBIOME DIVERSITY IS AGGRESSIVE PREVENTATIVE MEDICINE. These concepts are especially important given that the average American has lost 1/3 of their microbiome diversity, as estimated by Dr. Maria Gloria Dominguez-Bello as seen on this interview for the film “Microbirth.” Another study estimates 1 in 4 have 40% less bacteria (see This Danish study, or read the scientific article here).
This post teaches that the WHO, and the United States, this month took their first steps to recognize the invisible threat of antibiotic resistance, which missed the microbiome connection. You can comment to the US Request for [Microbiome] Information and help bring this to the forefront. Of course their goal of providing alternate antibiotics to wage the war on antibiotic resistance is wrought with difficulties due to the antibiotic pipeline:
- About 2000, numerous companies withdrew from antibiotic manufacturing, and the number of new antibiotics in development dropped from dozens to three.
- And the cost: The report, Review on Antimicrobial Resistance, estimates that we need 15 new antibiotics over 10 years, of which four would have to be truly new formulas (two broad-spectrum, or capable of attacking a number of bacteria, and two narrow-spectrum), while the remainder could be incremental improvements on existing formulas. It estimates the effort would require between $16 billion and $37 billion over that decade—huge amounts, but as the report points out, the global market for antibiotics now earns $40 billion every year, while resistance costs just the United States $20 billion per year in excess healthcare costs. Read more here and here, and the problem of the antibiotic pipeline, if interested.
⇒⇒Also covered last in this post, for background, is who actually lives in your gut and why it is difficult to know who truly is living in your gut. There are four dominant phyla that comprise the intestinal commensal microbiota of humans. These include Firmicutes and Bacteroidetes, which normally account for >90% of the bacterial populations in the colon, as well as Actinobacteria and Proteobacteria. The intestinal commensal populations are altered when comparing certain disease with non-disease. In addition, when some of these gut players are reduced, skewed, or absent there is health ramifications even beyond disease —for example, acetaminophen is toxic to the liver.
WHO commits unanimously to tackle antibiotic resistance
The annual World Health Assembly is the meeting of health minsters from 194 countries that serves as the decision-making body for the World Health Organization (WHO). For the first time, the global crisis of antibiotic resistance was addressed; the delegates committed unanimously to tackling the issue; WHO Director-General Dr. Margaret Chan’s welcome speech, May 2015:
“This is a unique time in history where economic progress is actually increasing threats to health instead of reducing them… As the century progressed, more and more first- and second-line antimicrobials failed. The pipeline of replacement products ran dry, raising the spectre of a post-antibiotic era in which common infections will once again kill. A draft global action plan on antimicrobial resistance is on your agenda. I urge you to adopt it.”