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Thread: Your microbiome and you

  1. #1 Your microbiome and you 
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    http://www.nytimes.com/2013/05/19/ma...=fb-share&_r=0

    This makes very interesting reading and I think its a very positive direction for health-care/medicine to be going in. Although considering how many bacteria there are, it will take a lot of unravelling. I think our current obsessions with anti-bacterial everything isn't doing us any good at all and the general perception to bacteria will need a lot of tweaking.


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    My mind is blown.
    It turns out that we are only 10 percent human: for every human cell that is intrinsic to our body, there are about 10 resident microbes — including commensals (generally harmless freeloaders) and mutualists (favor traders) and, in only a tiny number of cases, pathogens. To the extent that we are bearers of genetic information, more than 99 percent of it is microbial. And it appears increasingly likely that this “second genome,” as it is sometimes called, exerts an influence on our health as great and possibly even greater than the genes we inherit from our parents. But while your inherited genes are more or less fixed, it may be possible to reshape, even cultivate, your second genome.
    I recall that as my baby acquired new sets of microbes (e.g. first time wading in a pond, first visit to petting zoo, etc.) his "aura" would change. Maybe better say "scent" or "taste" though these weren't perceptions I could link to any physical sense. I'm wondering if, like pheromones, there could be some exchanges between the microbes of different people, that is information we're subtly aware of.


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    Well - to suggest a crackpot theory.......... I have often wondered if our biome is the "magical" entity that people feel aware of and lots call god (in one different form or another). Certainly there has been research that shows the biome of fruit flies can be responsible for speciation. A group of flies were split and fed different foods and so over time developed different biome's and then wouldn't mate any more. Once they were fed the same diets they began to mate again - will go off and get the reference/article. But the suggestion there was that they were repelled by the scent.

    And the smell of human sweat is the result of bacteria so it makes sense that different bacteria would smell differently........ hmmm food for thought indeed.
    "And we should consider every day lost on which we have not danced at least once. And we should call every truth false which was not accompanied by at least one laugh" Nietzsche.
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    See here for articles:The hologenome: A new view of evolution - life - 14 January 2013 - New Scientist (this was a Dr Jefferson) and here Gut bacteria change the sexual preferences of fruit flies : Not Exactly Rocket Science
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  6. #5  
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    Quote Originally Posted by LuciDreaming View Post
    wondered if our biome is the "magical" entity that people feel aware of and lots call god
    Christ means "the anointed one". He bore an exceptional biome aura.

    Quote Originally Posted by LuciDreaming View Post
    the biome of fruit flies can be responsible for speciation
    This helps explain how populations of humans remain exclusive even in the same city. Obviously, they eat different foods. More privately, they may engage in purification washing including group inoculation by dunking in a common bath forbidden to outsiders. The plainest example of how this works is with the Hebrews in Egypt, who refused to drink Egyptian beer but rather untreated water, so they were infested as untouchables with the same parasite (dracunculus medinensis); ultimately this condition got them cast out of the country.

    Quote Originally Posted by LuciDreaming View Post
    the smell of human sweat is the result of bacteria so it makes sense that different bacteria would smell differently
    Ever seen women mob around a newborn to "smell the baby". I've observed some behave as if they were getting high on it. Maybe some biome-pheromone at work there? My own was born at height of summer and no matter what we did he always smelled like a gerbil nest... in a good way.


    Hmm.. "you may kiss the bride" = "you may exchange microbes"?
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    Quote Originally Posted by Pong View Post
    Christ means "the anointed one". He bore an exceptional biome aura.
    Quote Originally Posted by Pong View Post
    Ever seen women mob around a newborn to "smell the baby". I've observed some behave as if they were getting high on it. Maybe some biome-pheromone at work there? My own was born at height of summer and no matter what we did he always smelled like a gerbil nest... in a good way.
    Hmm.. "you may kiss the bride" = "you may exchange microbes"?
    From egg snatching rats to this. You say some of the damndest things...
    Well, you know what to do with the Christs Aura comment.
    "evidence of any aura" etc. etc.
    Women sniffing babies. Getting high off the fumes.

    Maybe some women can weigh in on this. I did my time as a single dad with an infant and he was a good lookin' baby, too.
    Never had them flock to sniff.
    They cuddled, petted and cooed- but whiff him out? Maybe I missed it.
    Now, occasionally one might check the diaper because flocks of women were sure that a mere man couldn't possibly keep his son properly diapered... Is that sniffing to get high?

    And while I'm grousing... you have any idea how often they would reproachfully ask, "But where's his mother? He Needs his mother!"
    Like I'm supposed to have a good answer for that. "She left me three packs of diapers, a bottle of estrogen and a breast pump and ran off with the French Foreign Legion."
    Because, you know, a mere man couldn't possibly handle a child.

    Grflptz snarl

    Be back later. I need to go kill something and eat it.
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    I don't know about flock around to sniff them but I don't know anyone who doesn't like the smell of babies (but I don't know everyone so I could be wrong). I also don't want to mislead here as I am not suggesting that a specific biome makes some people "god-like" at all. Rather I think possibly the action of the biome on the human system maybe the action that gives some people the feeling they are being "guided by another's hand" - in non-religious terms when you don't feel "yourself" and don't know why or feel you cant quite control your actions whether that is speech, thought or movement.

    Modern day humans have difficulties interpreting the feelings that arise in their own bodies and I wonder if some of those feelings gave rise to our ancestors starting to think there was some higher power guiding their actions. I say this because a lot of illness is accompanied by the feeling of not being totally in control of your own actions - I experienced this first hand when I was on some rather harsh treatment a couple of years back. It is a most dislocating experience to suddenly feel that your mouth (or something other part) is running on auto-pilot - most times we can snap in and out of automatic and focused responses with no trouble but when that becomes difficult it feels like some-one has stopped you doing it. Also because of peripheral nerve damage I found I got clumsy because the signal from eye to hand and back again was fuzzy, so I broke lots of crockery when washing dishes because I would bang them against the tap instead of running them under it - but it felt like my movement and aim was good but it had somehow been deflected at the last second. How you interpret that feeling of course depends on your circumstances.

    Anyway - I got a long way from the biome there but essentially my thought is a change of biome can effect a change of behaviour that leads to some people interpreting their actions are guided by some-one else and they call that some-one else god (in my case I called it a virus and the treatment for it). Pure speculation of course but not too crackpot I hope.
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    I usually grow sensible of a distinct prickly sensation in my flesh, before developing symptoms normally associated with a cold or flu. Sometimes the infection fizzles short of real symptoms but then I learn by others I'm exposed to that something's going around. This prickly feeling is nearly identical to the physical component of moderate schizophrenia I had when younger. I suppose that both are "noise"; the difference being one originates from irritated tissue, the other is faulty processing of a clean signal.


    "A change of biome" why not just say "an infection" if this will do? It's a plausible idea since there are infections that alter a host's behavour in specific ways to help the infection spread, and any feeling caused by an infection will affect behaviour somehow (like crushing your head under a pillow and moaning). Your experience shows that one viral infection produced a specific mind-altering cocktail of toxins. Wouldn't be surprising if other hosts felt the same.

    Ah, now I remember the "Miserable flu" that went around near the turn of the millennium. Half the folks I know got it, I got it. The funny thing about the Miserable (don't know the official name) was physical symptoms were so faint in most people they might not realize they were ill. However - the infection somehow made people feel sad and irritable. They'd get a slight fever and the flu would run its course - which meant a week of feeling perfectly healthy physically, but crappy psychologically.
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    I think its important to state what something is as accurately as possible - to my mind what you call something matters. Although I agree with you, it is an infection of sorts but not always in the sense of illness. For example a change of gut bacteria will make you smell different to other individuals and it doesn't have to make you ill to change your behaviour. If an overgrowth of one type of bacteria led to a surge say in dopamine production or uptake then your behaviour will change without illness. To me the word infection doesn't quite cover those instances and worse implies its something bad to be stopped when that's not always the case either.
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    Yeah, our vocabulary regarding microbes is rooted in ignorance. I prefer "inoculation" to mean addition of anything benign, or unknown, besides the common usage "this will help you." The virus you had, I call an infection because you decided to treat it. If some cult likes to spike their Kool-Aid with the mind-altering virus, I'd call it inoculation.
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    More research showing the possible influence of the microbiome in the development of mental health:
    Gut Bacteria Regulate Happiness | Neuroscience News
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    The abundance of these unicellular organisms in human bodies and its importance for general human health, makes me wonder:
    Are we human cells who carry bacteria, or are we human cells carried by bacteria?
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    Quote Originally Posted by Cogito Ergo Sum View Post
    The abundance of these unicellular organisms in human bodies and its importance for general human health, makes me wonder:
    Are we human cells who carry bacteria, or are we human cells carried by bacteria?
    I rather hypothesize that humans are simply ambulatory systems for micro-organisms. We are dependent on them for our existence yet most of them are quite capable of utilizing other hosts.

    Humans are their best bet for getting off-planet and spreading to other solar systems.
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    That's a really interesting perspective CES and Sheherezade - I'd not considered that.
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    I was called away last night before I finished reading on this thread. That is a very interesting link you posted, LuciDreaming. From the article you linked to, the following, for those who may not take the time to click it...

    APC scientists have shown that brain levels of serotonin, the ‘happy hormone’ are regulated by the amount of bacteria in the gut during early life. Their research is being published today in the leading international psychiatry journal, Molecular Psychiatry.
    This research shows that normal adult brain function depends on the presence of gut microbes during development. Scientists at the APC used a germ-free mouse model to show that the absence of bacteria during early life significantly affected serotonin concentrations in the brain in adulthood. Serotonin, the major chemical involved in the regulation of mood and emotion, is altered in times of stress, anxiety and depression and most clinically effective antidepressant drugs work by targeting this neurochemical.
    The research also highlighted that the influence is sex dependent, with more marked effects in male compared with female animals. Finally, when the scientists colonised the animals with bacteria prior to adulthood, they found that many of the central nervous system changes, especially those related to serotonin, could not be reversed indicating a permanent imprinting of the effects of absence of gut flora on brain function.
    Emphasis and underline of last sentence added by me. If true, this serves to reinforce the importance of nutrition and explains why remedial measures do not seem to be effective in many cases if they are applied too late. Once the damage is done, the prior full potential can never be realized.
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    Quote Originally Posted by scheherazade View Post
    Humans are their best bet for getting off-planet and spreading to other solar systems.

    Some people have hypothesized that meteorites and comets have brought the necessary components to Earth, in order to let abiogenesis take place.
    Together with the fact that bacteria are simply dependent on the human bodies because we (as you have already pointed out) can travel to other worlds,
    I come up with the hypothesis that bacteria are on 3.5 billion year old quest to find a spacecraft that can bring them... home.
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    Quote Originally Posted by Cogito Ergo Sum View Post
    Quote Originally Posted by scheherazade View Post
    Humans are their best bet for getting off-planet and spreading to other solar systems.

    Some people have hypothesized that meteorites and comets have brought the necessary components to Earth, in order to let abiogenesis take place.
    Together with the fact that bacteria are simply dependent on the human bodies because we (as you have already pointed out) can travel to other worlds,
    I come up with the hypothesis that bacteria are on 3.5 billion year old quest to find a spacecraft that can bring them... home.
    Good point, in that inert matter is a far easier medium to work with than the vagaries and inherent frailty of human biology.

    Still, it begs the question of the origins of comets and meteorites. If the bacteria arrived here by such means, is there a home world to return to?
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    Is there any way to get a "reload" of all the "good" gut bacteria without going the fecal route? My mate has Hepatitis (supposedly under control by injections every few years) and I don't know if there is a risk of infection. We do not share bodily fluids of any kind, BTW.
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    Quote Originally Posted by scheherazade View Post

    Good point, in that inert matter is a far easier medium to work with than the vagaries and inherent frailty of human biology.

    Still, it begs the question of the origins of comets and meteorites. If the bacteria arrived here by such means, is there a home world to return to?

    Although I am aware of the vastness of the universe and the possible worlds that might reside 'in' it,
    I am reluctant to accept that there is a place X that harboured the ancestors of the current terrestrial bacteria for two reasons:
    1. There is no evidence for it.
    2. It solely postpones the questions about the origin of terrestrial life.
    Ergo, I do not think that there is a home to return to.
    Unless when you are a Prometheus​ fan.
    "The only safe rule is to dispute only with those of your acquaintance of whom you know that they possess sufficient intelligence and self-respect not to advance absurdities; to appeal to reason and not to authority, and to listen to reason and yield to it; and, finally, to be willing to accept reason even from an opponent, and to be just enough to bear being proved to be in the wrong."

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    Quote Originally Posted by WorldCitizenUSA View Post
    Is there any way to get a "reload" of all the "good" gut bacteria without going the fecal route? My mate has Hepatitis (supposedly under control by injections every few years) and I don't know if there is a risk of infection. We do not share bodily fluids of any kind, BTW.
    Have you done a probiotic search lately? The number of products has expanded in number and complexity and I believe everyone should maintain a supply of whatever is the best product for those times when you have to take antibiotics. After your 10 days or two weeks on antibiotics most of your gut bacteria will have experienced a major extinction event. You can help get the good bacteria growing back faster by using a probiotic supplement, and this very much beats letting any old bacteria re-populate your gut as it can cause many problems that will be hard not only to identify but to treat.

    It's only been recently that they discovered stomach ulcers were caused by a bacterial infection and maybe some viruses had a part in that. I often wonder how many of those people used antibiotics and then just let any old bacteria grow back? I knew people that had most of their stomachs removed because of bleeding ulcers, and they thought it was just a bad case of nerves and stress causing the problem.
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    Quote Originally Posted by Cogito Ergo Sum View Post
    Quote Originally Posted by scheherazade View Post

    Good point, in that inert matter is a far easier medium to work with than the vagaries and inherent frailty of human biology.

    Still, it begs the question of the origins of comets and meteorites. If the bacteria arrived here by such means, is there a home world to return to?

    Although I am aware of the vastness of the universe and the possible worlds that might reside 'in' it,
    I am reluctant to accept that there is a place X that harboured the ancestors of the current terrestrial bacteria for two reasons:
    1. There is no evidence for it.
    2. It solely postpones the questions about the origin of terrestrial life.

    Ergo, I do not think that there is a home to return to.
    Unless when you are a Prometheus​ fan.
    It really has nothing to do with a home to go back to. It's about survival, the best way to survive the longest is to survive in as many places as possible. The do not have all your eggs in one basket example says it best.
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    Quote Originally Posted by Bad Robot View Post
    Have you done a probiotic search lately? The number of products has expanded in number and complexity and I believe everyone should maintain a supply of whatever is the best product for those times when you have to take antibiotics. After your 10 days or two weeks on antibiotics most of your gut bacteria will have experienced a major extinction event. You can help get the good bacteria growing back faster by using a probiotic supplement, and this very much beats letting any old bacteria re-populate your gut as it can cause many problems that will be hard not only to identify but to treat.
    I'm taking medication that seems to kill off the good ones, leaving embarrassing stomach issues in its wake. Yes, I have tried several different probiotic supplements but none are a cure... I have to continue taking them indefinitely. Each time I stop taking the probiotics by stomach attacks me.

    What I hope for is a more permanent solution, a cure not a treatment. Currently, I eat yogurt once or twice a day and take twice the recommended dose of probiotic in gummy bear form (seems to work far better than the pills, almost as good as the chocolate coated probiotic which I can never find in the stores nearby). There may be no better answer as I will be on this medication (for Anxiety and Panic Attacks) probably for the rest of my life. That being the case, the meds will keep killing my biota every day so I'll have to try to repopulate them day after day. It's frustrating to say the least.
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    Originally posted by WorldCitizenUSA:

    There may be no better answer as I will be on this medication (for Anxiety and Panic Attacks) probably for the rest of my life. That being the case, the meds will keep killing my biota every day so I'll have to try to repopulate them day after day. It's frustrating to say the least.
    There is at least one other potential solution.

    Have you given up on identifying the cause of your anxiety and panic attacks? Just yesterday, a friend showed up, and confided that she had experienced a panic attack at work, it being a fast paced workplace, she still the newest salaried employee and one of her immediate supervisors taken down by health issues at the busiest time of the year. She managed to hold it together but was frightened by the experience, which was new to her, although she is a type 1 diabetic and is good at dealing with her blood sugars.

    She is already floating her resume because she can see that the salary and benefits at this job might not be worth the danger to her health.

    I am from old school thinking in that I believe in seeking the source of a problem and only treating the symptoms until a permanent or better solution can be found.

    My sympathies for what you must be dealing with.
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    Quote Originally Posted by WorldCitizenUSA View Post
    Quote Originally Posted by Bad Robot View Post
    Have you done a probiotic search lately? The number of products has expanded in number and complexity and I believe everyone should maintain a supply of whatever is the best product for those times when you have to take antibiotics. After your 10 days or two weeks on antibiotics most of your gut bacteria will have experienced a major extinction event. You can help get the good bacteria growing back faster by using a probiotic supplement, and this very much beats letting any old bacteria re-populate your gut as it can cause many problems that will be hard not only to identify but to treat.
    I'm taking medication that seems to kill off the good ones, leaving embarrassing stomach issues in its wake. Yes, I have tried several different probiotic supplements but none are a cure... I have to continue taking them indefinitely. Each time I stop taking the probiotics by stomach attacks me.

    What I hope for is a more permanent solution, a cure not a treatment. Currently, I eat yogurt once or twice a day and take twice the recommended dose of probiotic in gummy bear form (seems to work far better than the pills, almost as good as the chocolate coated probiotic which I can never find in the stores nearby). There may be no better answer as I will be on this medication (for Anxiety and Panic Attacks) probably for the rest of my life. That being the case, the meds will keep killing my biota every day so I'll have to try to repopulate them day after day. It's frustrating to say the least.
    I too have seemingly permanent digestive problems from 6 months Hep C treatment plus a trial protease inhibitor. The problem is that there are a class of bacteria in the stomach called bacteroides that cannot survive outside of the human gut, not even for a second, so once they are gone they are gone. The only way to replenish them is through faecal transplant which I would gladly do if it were available to me but it isn't. There isn't a probiotic or prebiotic available that can replace these particular ones at all.
    You can find more info here. Fermentation in the gut and CFS - DoctorMyhill
    "And we should consider every day lost on which we have not danced at least once. And we should call every truth false which was not accompanied by at least one laugh" Nietzsche.
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    Quote Originally Posted by WorldCitizenUSA View Post
    I'm taking medication that seems to kill off the good ones, leaving embarrassing stomach issues in its wake. Yes, I have tried several different probiotic supplements but none are a cure... I have to continue taking them indefinitely. Each time I stop taking the probiotics by stomach attacks me.

    What I hope for is a more permanent solution, a cure not a treatment. Currently, I eat yogurt once or twice a day and take twice the recommended dose of probiotic in gummy bear form (seems to work far better than the pills, almost as good as the chocolate coated probiotic which I can never find in the stores nearby). There may be no better answer as I will be on this medication (for Anxiety and Panic Attacks) probably for the rest of my life. That being the case, the meds will keep killing my biota every day so I'll have to try to repopulate them day after day. It's frustrating to say the least.
    I do sympathize with your problem, it can be really frustrating when the best doctors don't have a good fix for your problem. I would recommend you continue to research your particular problem and any closely related problems. Make it a point to always have new questions for your doctor visits. It seems to me that this particular field of medicine is starting to get a lot of attention and advancements will start coming at a faster pace now. It might even be fun if you can read about something new before your doctor does. Good luck.
    Last edited by Bad Robot; June 17th, 2013 at 09:31 PM.
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    Quote Originally Posted by WorldCitizenUSA View Post
    Quote Originally Posted by Bad Robot View Post
    Have you done a probiotic search lately? The number of products has expanded in number and complexity and I believe everyone should maintain a supply of whatever is the best product for those times when you have to take antibiotics. After your 10 days or two weeks on antibiotics most of your gut bacteria will have experienced a major extinction event. You can help get the good bacteria growing back faster by using a probiotic supplement, and this very much beats letting any old bacteria re-populate your gut as it can cause many problems that will be hard not only to identify but to treat.
    I'm taking medication that seems to kill off the good ones, leaving embarrassing stomach issues in its wake. Yes, I have tried several different probiotic supplements but none are a cure... I have to continue taking them indefinitely. Each time I stop taking the probiotics by stomach attacks me.

    What I hope for is a more permanent solution, a cure not a treatment. Currently, I eat yogurt once or twice a day and take twice the recommended dose of probiotic in gummy bear form (seems to work far better than the pills, almost as good as the chocolate coated probiotic which I can never find in the stores nearby). There may be no better answer as I will be on this medication (for Anxiety and Panic Attacks) probably for the rest of my life. That being the case, the meds will keep killing my biota every day so I'll have to try to repopulate them day after day. It's frustrating to say the least.
    I see a couple of problems that will irritate your condition in your post there - gummy bears and chocolate. I would strongly suggest you revise the amount of sugars you have in your diet and by sugars I mean - fruit, fruit juices, grains (wheat, oats, corn etc), fizzy drinks, dairy products and chocolate/sweets - all these will ferment in your stomach to produce an overgrowth of the bacteria that cause problems like flatulence and aside from that, it wont do your anxiety any good either.
    "And we should consider every day lost on which we have not danced at least once. And we should call every truth false which was not accompanied by at least one laugh" Nietzsche.
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    Thank you (several of you) for your well wishes. I am continuing my search for a better treatment. Some of the medications I've tried have had such painful or worrysome side effects that I'm a little leery of continued experimentation. I've heard that therapy sessions with a Psychologist can potentially reduce anxiety and panic attacks but as I have been living in silent misery with these symptoms for over 30 years before seeking treatment (it got worse and worse with each passing decade). So I wonder if I am beyond the point of no return with my mental illness. But I haven't given up.

    As for my digestive troubles, thank you LucidDreaming for the information. I have been trying to remove meat from my diet for over 4 years now and am down to fish and chicken only. Man, I sure do miss pork chops!
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    Quote Originally Posted by WorldCitizenUSA View Post
    Thank you (several of you) for your well wishes. I am continuing my search for a better treatment. Some of the medications I've tried have had such painful or worrysome side effects that I'm a little leery of continued experimentation. I've heard that therapy sessions with a Psychologist can potentially reduce anxiety and panic attacks but as I have been living in silent misery with these symptoms for over 30 years before seeking treatment (it got worse and worse with each passing decade). So I wonder if I am beyond the point of no return with my mental illness. But I haven't given up.

    As for my digestive troubles, thank you LucidDreaming for the information. I have been trying to remove meat from my diet for over 4 years now and am down to fish and chicken only. Man, I sure do miss pork chops!
    I've heard that when you eliminate sugar from your diet, the suffering it causes last about two weeks. I need to do that myself, but I've just been trying to cut down without completely stopping and even that's some what tough. Sometimes I want to drink a coke so bad it hurts. Sorry but the pork stays. I have to have bacon and eggs at least once a month and I could never say no to some baby back ribs.
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    In my humble opinion WorldCitizen cutting meat out is the worst thing you can do for your body. I realise this flies against prevailing wisdoms but you only have to look at the general state of health of the people in Westernised countries to realise there is something going amiss with Western dietary advice. High fat, medium protein and low to med carb is the optimal macronutrient ratio. Having said that I'm not a doctor and I wouldn't suggest you radically alter your diet without consulting one first.

    I didn't find any problems when I cut out sugar BR but then I was ill anyway so probably wouldn't have noticed any other effects. Sugar is a bit of a double whammy unfortunately in that its addictive and it makes you hungry. I think its harder to cut down slowly but we all do these things differently. Good luck.
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    "And we should consider every day lost on which we have not danced at least once. And we should call every truth false which was not accompanied by at least one laugh" Nietzsche.
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    Western Veterinarians seem to have a handle on it.
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