Microbiome: The Organisms In and On Us All

You and Whose Army?

It’s been said you are the average of the five people you spend the most time with.

We’ll come back to that, but perhaps more accurately, you are the sum total of the hundreds of trillions of microbes who live on and inside your body. Your own body cells count, but are far outnumbered by the microscopic species you cohabit with.

And that’s true for your dog or cat or significant other, animal or human.

As research progresses in the field now called the microbiome, or the populations of microbes intimately associated with you or your animal, we are learning all kinds of interesting things.

For example:

  • You and your dog share common bacteria, fungi and viruses, especially on your skin.
  • In a normal situation, the relationship is a commensal one: the bugs get a “house” to live in, and you derive benefits from them. Win-win.
  • The diversity of these bugs both in and on you is very high when you are healthy.
  • In diseased people and dogs, the diversity of microbe species falls.
  • More flora exposure in early life, even from birth, makes healthier offspring.

Let’s look at some of what’s known in this fascinating world of who’s in and on us and our animals.

Got Skin in The Game? So Does Your Dog

You might guess that, if you kiss your dog frequently, you and your dog might share a lot of gut microbes. While that’s true to a certain extent, the real sharing was found in the skin flora you both have.

Makes sense, right? You’re petting, wrestling with, tick examining and brushing your dog multiple times a day. Close skin contact is bound to make sharing of external organisms common.

The breakthrough in understanding this came fairly recently when genetic sequencing took over from culturing the skin as a means of seeing “who’s living there?” In the days of swabbing skin and rolling that swab across a petri dish full of a growth medium, very few species were found.

Now, that swab is looked at with a whole new eye, called gene sequencing. And way more species are apparent that reside on our skin.

The skin flora, when in good balance, does nice things for us, much like the good guy gut populations do. They modulate the immune response and they prevent colonization of potentially pathogenic (disease causing) microbes.

Scary Skin Shifts

You’ve maybe heard these fear-inducing words,

He’s got a staph infection and we need to put him on these antibiotics for two weeks.”

Staph? Oh God, isn’t that the bug in the hospitals that’s now called MRSA and kills people? Like a lot?

Yes, MRSA stands for methicillin resistant staph aureus, and it can kill people.

But staphylococcus is a common bacteria on everyone’s skin. It’s considered “normal flora,” until it morphs into this antibiotic resistant form, and that’s usually when the body is sick with some disease first.

[As an aside, that whole antibiotic resistance fear? It goes away with homeopathy. Get the patient well, the bacteria pack up and leave, rather quickly.]

Our overuse of antibiotics as a society holds a lot of the blame here.

That’s the first drug Dr. WhiteCoat usually reaches for, and often for the darnedest reasons. And, the feeding of antibiotics to livestock, especially in CAFOs, are no small players in creating resistant microbes that antibiotics can no longer kill.

Recent research shows that allergic dogs and atopic people have fewer species of beneficial organisms on their skin. It’s unclear whether that’s cause or effect, but it’s clearly abnormal.

Interestingly, the bugs who live inside of you and your pet and even your spouse are more likely similar among related family members that they are in those who you cohabit with. That was a surprise to me.

Diversity: A Damned Good Thing

Just as society is richer and more creative and substantive from a wide variety of thoughts and customs and cultures, so it’s the case with the population of microbes in or on the body. We can measure this diversity of species more easily now with the gene analysis methods.

Just to remind you of the good that comes from our healthy gut dwellers alone, they:

  • aid digestion and the extraction of energy from consumed food
  • are responsible for B vitamins, vitamin K, and the production of amino acids and fatty acids
  • nourish the cells they live close to, the lining cells of the gut wall or enterocytes
  • help immunity (some say that the gut has MOST of the immune system)
  • offer a barrier against pathogens invading

It turns out that diversity is greatly depressed when an animal or human is ill. Both show less species when chronic diarrhea or inflammatory bowel disease is present. Even obesity in people is associated with a lack in species of microbes.

C-Section? Get Flora!

Vaginal birth, the natural delivery of young through the birth canal, is the first place the newborns get seriously inoculated with flora.

They leave the womb sterile but by their first breath, babies are covered with colonies of bacteria that get their immune systems primed, their digestive systems off to a good start, and even help shape their growing brain.

Those babies delivered by Cesarean section are more prone to autoimmune diseases. While not yet studied in the dog, it would make sense that they’d have a similar deficit.

Minimally, you’d want to liberally dose probiotics to these youngsters from a very young age. It would even make sense to rub in some of mom’s lochia, the vaginal discharge that appears after birth for a spell.

Raise Your Kids with Dogs!

Remember the Amish study showing way less allergies in these kids growing up on the farm? Well, similar findings have emerged showing that dog-owning families have way more diverse microbes than those families without a dog in their lives.

Human kids are experiencing higher rates of eczema, for reasons unknown. (Well, I can take an educated guess, seeing what I do in pets. How about the concurrent rising rates of childhood vaccines!).

When kids have the chronic skin eruptions of eczema, they are more prone to other immune based diseases like asthma and food allergies.

We see asthma in cats and food allergies in both dogs and cats. And we’re vaccinating them a lot more than just 30 years ago. Hmmm.

Kids raised with dogs have less eczema, even if they tested allergic to dogs!

Cat-allergic kids actually showed the opposite: their risk of eczema, asthma and food allergies significantly increased, growing up with a cat. Normal, non-allergic kids were no worse from cats being present, however.

So, here’s further evidence that exposure to “germs” early in life is a good thing. Get that boy out of that bubble! Toss that germ killing soap and toothpaste into the trash! Go play in the dirt!

Practically Speaking

Among the many papers I read for this post, one thing was repeatedly made clear: the flora in and on our bodies and those of our animals is a boon for all of us.

Many researchers said how little we actually know about this young field. For example, how much species interactions among these trillions of microbes affects us and our loved ones.

Still largely unknown.

It all makes me more confident than ever that I dumped antibiotics so many years ago. I’d urge you to think of the potential for microbiome disruption and its consequences with these ever present drugs.

You can say no. Call your homeopathic vet instead.

Who Are You Hanging With?

To close, I just want to put in a plug for being careful who you choose to hang out with. If your eyes are opened to the damage that conventional medicine does to your animals and/or your kids, you will be far happier and more productive if you associate with people who’ve also had paradigm shifts like yours.

You can’t get a good discussion of vaccine damage going with the average person on the street now.

So many have bought into a very slanted view from the pro-Big Pharma media that, instead of being seen as a thoughtful person who’s studied the risk/benefit ratio on vaccines, you’ll be condemned as a selfish anti-vaxxer that’s somehow risking the lives of innocent children!

If someone can’t get enough of your amazingly wondrous Vital Animal at the dog park, but backs away when you tell them how he got this way (raw diet! few or no vaccines! no flea poisons! no heartworm poisons!), you know that person’s not part of your pack.

Don’t waste any more breath. Move on.

To that end, I’ve formed the Vital Animal Pack, which you can join for free, where I envision a healthy and conscious group growing, who’ll have each other’s backs and who can entertain thoughtful discussions of the health challenges of our day. We’re having some great comments come through on the blog, certainly.

Be careful who you are close to, and, as much as you can, surround yourself with those who have already firmly decided the Natural Path is the only reasonable one to take.

And did you just put your hand in your dog’s mouth? C’mere, I’d like to shake your hand!

Tell us in the comments if your “germ phobias” have subsided a bit since being on this path, and who is shaping who you are these days.

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  1. Suzan Lieberman on June 17, 2017 at 6:14 pm

    Someone is our SA group has a dog that was just diagnosed with MRSA, the Conventional Vet put dog on 30 days of Sulfamethoxazole, this is the 3rd antibiotic the dog has been on, not counting the antibiotics he was on for SA. She was trying to go all natural, had dog on raw, and supplements, the dog was thriving, and now the MRSA. Also, dog now has a bad SA flare up. Do you have any suggestions? Thank you for your time.

  2. Helen Terry on August 4, 2015 at 12:55 pm

    Dr. Will,
    Thanks for this article and forum for sharing. My herd does not have a place to just be dogs – the property I’m on is unfenced. Maybe it’s time to fence it in? They so long to be outside and our nightly walks are full of sniffing, marking and more sniffing. I have endless deer (taking carrots out of my hand and fingers – the buck know this is a safe zone) but maybe should figure out something at the back door for land they can dig in – rest in – walk in – many composted leaves? I’m presuming the scholopendra heros will scamper when they feel the land rumbling? The deer are walking through it, and my alpha dog continually wants to eat deer scat…time for a change?

  3. Gay on August 4, 2015 at 2:02 am

    Our family does a lot of fermenting to support our microbiome, veggies, fruits, raw milk kefir, water kefir, Kombucha, sourdough, etc. I’ve read that just like we let veggies basically “spoil” using their natural bacteria to ferment to support our digestive systems, dogs gain beneficial bacterial flora from raw meat that is starting to spoil. Supposedly that is why they can burry meat/bones and go eat it a week later. Does anyone know any more about this? I know that there are some die hard fermenters that do this with meat on purpose and eat it. They claim to get much energy and healing from it. I’ve heard it called “high meat.” I’ve eaten some unusual fermented foods but I don’t know if I could get myself to eat that. I have seen our dog find a piece of meat from a previous meal (she is fed outside) that has been around a while and eat it with great pleasure and no ill effects. I put away or throw away any uneaten food but I swear sometimes she will hide it so she can go back after it’s “ripened” and eat it.

    • Will Falconer, DVM on August 4, 2015 at 4:15 am

      Oh, Gay, this is the first time anyone’s mentioned this to me, and it makes perfect sense! The soil is a motherlode of beneficial bacteria, yeasts, etc, and there are lines of product now sold for people around this understanding.
      I’ve never thought of the “why” of this instinct of burying, but now I get it: it’s inoculation and culturing at work! Very cool.
      Thanks for sharing this knowledge.

      • Kim Hudson on August 4, 2015 at 7:14 am

        Juliet de Bairacli-Levy’s Handbook for the Cat & Dog talks about this. I highly recommend her book, its what introduced me to natural rearing. Green Thank you for a beautiful educational article Will. So appreciate your work!! Blessings, Kim

      • Gay on August 9, 2015 at 8:01 pm

        It does make sense, Dr Falconer. I’ll feel better now that I’ve run it by you when I “catch” her eating her treasures! Thanks Kim for the book recommendation. I’ve looked at that book before but have not yet purchased a copy. It’s now gone to the top of my wish list!

  4. Madeleine Innocent on August 3, 2015 at 8:36 pm

    I often wonder why vets and doctors have such long training periods when all they dish out is antibiotics and steroids. Couldn’t they learn that in a day? OK, I’m being mean, but…

    • Will Falconer, DVM on August 3, 2015 at 9:20 pm

      Part of it is societal in my mind, Madeleine. We want those symptoms gone NOW, never mind the long term disasters that come from that approach. We’ve got enough generations of misunderstanding now that suppressed symptoms is the goal. We’ve mostly lost track of what true healing looks like.

  5. jill on August 3, 2015 at 4:58 pm

    I fully agree with this article! Since ive started the “natural route” for my pets, and me, over 15 years ago..no vaxs, chemicals of any kind in or on us, no unnecessary baths, and raw diet for the dogs/cats/ferrets, i have not had a cold or stomach bug since, nothing! Not one. I also bath “as needed” … with plain goat milk soap. When needed i bath my service dog with spa mud to clean his coat, shed out dead hair and cleanse his pores..no shampoo. He has no doggie odor anyways!
    I am briefly living with my elderly folks, both who smoke and dad drinks vodka at night. Mother has copd/asthma/allergies high bp, cholesterol ect and on loads of drugs. Dad has heart disease and is on cholesterol meds. Both bath daily in anti-bacterial stuff. They also get the flu and pneumonia shots yearly, and both get the flu 2-3x yearly! They have ironically become healthier since me and my “filthy” animals have moved in! Thankfully they smoke only in their bedroom/bathroom, and i keep myself and my animals FAR away from their room, but the house still reeks of a cheap bar.
    Hopefully their bad health stays on them.. and away from me and my crew!

    • Will Falconer, DVM on August 3, 2015 at 7:11 pm

      My goodness, Jill, you’ve got a first hand family comparison study going there! I hope you can stay compassionate and healthy while you’re living in the mix.

  6. Stacey Zanella on August 3, 2015 at 12:12 pm

    Always enjoy your posts and gorgeous photos Doc. The Coyote turd made me laugh out loud 🙂
    I took my pack on a trail hike recently to get away from toxic park grasses, unruly dogs and their people. I have to say it was nice and we were certainly alone, except for tons of poison oak along the trails. But it felt like we had been on a cattle drive, we were so hot and dusty. Baths for all! Enjoyed ourselves very much.

    • Will Falconer, DVM on August 3, 2015 at 3:04 pm

      Sounds great Stacey. You gotta cut loose sometimes and change it up.

  7. Tricia on August 3, 2015 at 11:02 am

    This all makes so much sense. I think over-bathing falls into this topic as well.
    The dog stinks and has skin allergies – so owners bathe at least once a week sometimes every other day and it gets worse and worse.
    The skin biome is pretty robust in a healthy dog. You honestly don’t need to soap up a dog to keep him smelling nice and hotspot free.

    • John Sturgess on August 3, 2015 at 11:43 am

      Skin Allergies,,, -> Thank you Dr White Coat with all the antibiotics and steroids, lets not address the underlying cause but lets just mask it and let the issue at hand resurface it self as something else.. God for bid that A Vet fesses up and admits that steroids and antibiotic over use is the major cause of so called skin allergies. Let me retrace, My dog was on antibiotics for 24 of a 45 day window as well as Prednisone for 10 days of that period. Low and behold he now has pustules popping up left and right all over his neck and legs,, Yea Hotspots… So what did the Vet say its his food he has a Food Allergy.
      DUH,,, 3yrs Ive owned this dog, no skin allergies showed up NONE. No Flea or Heart Worm Meds given, no topicals , no dryer sheets used in house no floor cleaner but vinegar and h2o , no smokers in house and the yard doesn’t get sprayed with chems also.
      He eats Raw gets Ester C, FIsh Oil, Vit E, Probiotics, Joint Supplements and Coconut oil daily…
      They all want to point the finger elsewhere but never accept responsibility.

      • Will Falconer, DVM on August 3, 2015 at 12:36 pm

        Best place to point you John, is a post called Itchy Skin Wins Big: Vets Scratch Their Heads. Likely the missing piece of the puzzle for you.
        That, and the services of a vet homeopath to undo the damage done. See my Resources page for the AVH list and get someone from there to help get to cure.
        Your dog shows a very strong vital force, popping out pustules after all the suppressive drug therapy. Strong vf = good prognosis for homeopathy to cure.

        • dar on August 3, 2015 at 7:00 pm

          A pal’s 10 yr old terrier had hot spots,etc…she was so far gone that she was semi transparent…whipped out the epsom salts, bicarb,ac vinegar & warm h20: every time the dog came into the house post-pee, it’s raw,hairless&bloody belly was wiped with the mix& at bedtime the cc oil was applied…one week later, not only was the dog still alive, but the belly skin had healed & ALL the fur had grown back…knock me over with a feather!

          • Will Falconer, DVM on August 3, 2015 at 7:08 pm

            Hey Dar,
            So, mixing vinegar and bicarb used to be quite a show as a kid. How’d you keep that brew from leaving the container?

    • Will Falconer, DVM on August 3, 2015 at 12:31 pm

      Right on, Tricia. And thats not even touching the “anti-” shampoos that kill yeast or are drying out sebum, etc.
      Good catch.

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