links to headings within this page (incomplete)

   oxalates are really a biofilm problem and not a genetic issue

   lactic acid bacteria supplementation reduces urinary oxalate

   lead causes kidney stones


   catherine tamaro's summary of the low oxalate diet


'all roads lead to biofilm'

its just looking like this whole oxalate issue is just a particular manifestion of the usual low glutathione, impaired bile production/enzymes, toxicity problems

"Unabsorbed fat and bile acids may react with calcium in the intestinal lumen, limiting the amount of free calcium binding with oxalate and thereby raising intestinal oxalate absorption leading to hyperoxaluria."

the above quote from the study titled "Fat malabsorption induced by gastrointestinal lipase inhibitor leads to an increase in urinary oxalate excretion."  pubmed

since the interest in oxalates seems to be driven by scd types its a stong confimation that scd has some big holes in, scd does not resolve biofilm issues

catherine tamaro writes that protease (12 virastop a day) and lipase (6 lypo a day) enzymes and melatonin have helped with her kidney pain (ed. note, included for interest, i do not regard catherines protocol as successful)

"For any parents who are doing the K2 protocol and feeling achey kidneys, I just wanted to post that about a week or so ago I started taking high doses of protease and lipase enzymes between meals, to get rid of some of the "sludge" and my kidneys definitely feel better."

"The other thing that really helped my kidneys was using high-dose melatonin. Over about a 2-month period I went all the way up to the 20 mg used in the sarcoidosis study, and it helped immensely."

melatonin promotes thymic peptides   pubmed

"Further more, excess vitamin E completely prevented calcium oxalate deposition, by preventing peroxidative injury and restoring renal tissue antioxidants and glutathione redox balance"

vit e, calcium oxalate  study

so oxidative stress is huge factor in calcium oxlate deposition on susceptible tissue like kidney tubules


catherine tamaro replies to a mom on the vitamin k board (may 2007):

M. writes:

I was concerned about giving my son the mineral supp that our DAN had prescribed, but I finally caved and gave him some. Now, this was not a huge Calcium Citrate dose, just small amounts, but after about a week and a half, he was doing horribly and several behaviours that we had not seen in a while came back.....But no one that has been around him this week could deny the change in him after pulling the Calcium and adding the K2. Why do you suppose we don't see the crystals?

Catherine replies:

This falls into the category of “Every child is different.” For instance, I have never seen sandy stools in either of my sons even though I have been reading about the sand on internet lists for years. Also, not all the oxalate has bonded with calcium to form crystals - much of the oxalate coming out is in the form of oxalic acid, unbound to calcium. Oxalic acid gets stored in cells and is the “leftover” after the K2-activated proteins pull the calcium away from the CaOx crystal. Oxalic acid is what the kidneys filter into urine and what the intestines secrete into the stool. It could be that your son might not have too many large crystals in his kidney tubules (which is good!), or that they will start coming later, or only with more K2. One thing you might try is to freeze the sample, then defrost it – the colder the liquid gets, the more the solids precipitate out.


rose writes:

Should I be concerned that the only OAT test my son had done 3 years ago showed oxalic acid in the normal range? His arabinose was high (65.35 <47) , as well as 3 very high Fatty Acid Metabolites (the worst being acetoacetic 276.92 <10) & very high Hippuric Acid (938.27 <10-400). I know this test may be irrelevant as it is a few years old but it's all I have to go by right now. Has anyone else seen these types of readings & still seen improvements with the Vit K Protocol?

kathy replies:

They changed the normal range. dylan's and mine were marked "normal" at 78 and 48, now anything over 37 is too high. They found out they weren't normal after all... reference ranges changed, test remained the same.

catherine tamaro writes:

RE: [VitaminK] Canadian charges + Organic Acid test

Kathy is right about the oxalic acid reference range. Bill Shaw at Great Plains is finding that about 1 out of 3 kids with autism has high urinary oxalic acid. OxThera Corp is getting reports from clinics regarding children with high urinary oxalates who don't have any of the known genetic faults that cause internal production, meaning there is probably a metabolic pathway leading to oxalate production that hasn't been figured out yet.

High hippuric acid may be a general marker for high inflammation.

my comment:

the pathway is oxlate production by biofilm

took a whole capsule of vrp K2 over the weekend, it was a blast, a bit much i think ;o)

bit laxative too, can see why scd'ers use it


scd is a low cysteine/cystine diet since it excludes whey in any form, even as part of milk and the yogurts may also be low cysteine with the bacteria metabolising some of the cysteine

cysteine is important for reducing the formation of oxalate

so a low oxalate diet would reduce the effects from the scd induced cysteine deficiency

low vitamin d may be a factor for oxalate formation


there appears to be a difference between the oxalate content of food and bioavaliabilty of the oxalates

low oxalate is a medical diet for kidney stones that has been around since the 90's, how successful i don't know, i would assume not successful as it seems to have dropped from sight except for susan owens promotion of it recently

the theory is that oxalates combine with calcium to form stones

its far better to promote the sulphur processing pathways that metabolise oxalate, than attempt to restrict oxalate, which, given that the oxalate levels ingested is a function of both the bioavaliability and amount in foods, is difficult to estimate in the first place.

an exception to this could be rhubarb which is high in oxalate and medium or large amounts in combination with vitamin K2 may cause urethral irritation

the low oxalate diet has been around long enough that eliane gotschall would have been aware of it but obviously wasn't that interested in it

some or most people really don't have the digestive enzymes for nuts in the quantities eaten today, so removing nuts is of benefit by reducing fermentative load, not because of their relatively high and bioavaliable oxalate content.

also nuts contain enzyme inhibitors.

chard, collards, spinach, kale and silverbeet are necessary because of high vitamin k content but are hard on the gut so should be eaten in moderate quanties and occasionally, rather than every day which is what can happen with the ease of just chucking them into food processors

a particular issue with scd is that given the elimination of grains and potatoes, other foods are looked for and in some cases chard, collards, spinach, kale and silverbeet are considerably overused and they are very hard on the gut.

the LOD (low oxalate diet), by eliminating the high oxalate chard, collards, spinach, kale and silverbeet, appears to assist but the reasoning is wrong since malign biofilm is the primary problem and all that is required is that these vegs be used in moderation and cooked adequately, perhaps once every two days for their needed high vitamin k content.


brinkley et al, university of texas southwestern medical school, dallas

“We extended the study of oxalate bioavailability by testing 7 additional food items: brewed tea, tea with milk, turnip greens, okra, peanuts and almonds. Nine normal subjects ingested a large serving of each of these items. The bioavailable oxalate was calculated from the increment in urinary oxalate during 8 hours after ingestion and bioavailability was determined as the percentage of total oxalate content in a given food item represented by bioavailable oxalate.

Brewed tea and tea with milk, with a high oxalate content, had a low bioavailable oxalate level (1.17 and 0.44 mg. per load) because of the low oxalate availability (bioavailability of 0.08 and 0.03%).

Turnip greens, with a satisfactory oxalate bioavailability (5.8%), had a negligible effect on urinary oxalate excretion, since oxalate content was relatively low (12 mg. per load).

Okra, with a moderate oxalate content (264 mg. per load) had a negligible bioavailable oxalate (0.28 mg. per load).

Only peanuts and almonds provided a moderate increase in oxalate excretion (3 to 5 mg. per load) due to the modest oxalate content (116 and 131 mg. per load) and oxalate bioavailability (3.8 and 2.8%).

Thus, the ability of various oxalate-rich foods to augment urinary oxalate excretion depends not only on oxalate content but on the bioavailability.”


an abmd post (june 06) by R.

Related to the oxalate issue, I found these passages in a book called "Let's Get Well" written by Adele Davis a loooong time ago, but many things she said have come to fruition, i.e. she was among the first to notice the relationship between folic acid deficiency in mothers and birth defects in babies (1965)

Adelle Davis, worked with Bernard Rimland to develop the B6 formula he used with the first attempt to ameliorate autistic symptoms in children.

"The amino acid glycine, improperly utilized when vitamin B6 is undersupplied, changes into oxalic acid, which forms stones and also often causes sharp oxalate crystals to damate the kidneys. Radioatively labeled glycine, given to stone formers, can be recovered as oxalic acid, in healthy persons it can be found only in body protein. When experimental animals are deficient in vitamin B6, the more glycine given them, the greater is the urinary excretion of oxalic acid, this excretion immediately DECREASES if the vitamin is given with the glycine.

Individuals are often given diets excluding dozens of excellent fruits and vegetables because they contain some oxalic acid. Unfortunately, oxalate stones are still formed even when no oxalic acid whatsoever is obtained in the diet. If fruits and vegetables are restricted, more proteins are eaten; therefore, the need for vitamin B6 and the intake of glycine both increase while the magnesium intake decreases; thus the stage is set for more stones to form.

NO healthful foods should be avoided but to prevent protein imbalance, complete proteins should be eaten with all the incomplete ones; and gelatin, which supplies such an excess of glycine that it can increase formation, should be give a wide birth." (Davis, 1965, pg252-253)

She also goes on to state that when too little fruits and vegetables are eaten, a potassium deficiency ensues causing the urine to be so alkaline as to disable a person's ability to absorb minerals.

my comment:

the low oxalate diet does seem to correct some weaknesses of scd (though the low oxalate diet is itself not that coherent biochemically and too short of vitamin k imo), but the scd emphasis on gelatine/collagen without b6 may be exposing scd'ers to excess oxlate formation

i have always noticed how much better a whole carcass broth like wallaby broth is than store bought gelatine and that would be in part due to the high level of b vits that would be in the broth water.

basically jelly/collagen is designed to be eaten in broth which includes co- factors like b6, thiamine and magnesium and if you don't have these co-factors you get excess conversion of glycine to oxalate

store bought jelly lacks these co-factors, though other portions of the meal may provide them

a comment by susan owens:

Yes, oxalates are an end product of metabolism, but not only relating to glycine, but also relating to fat and carbohydrate and hydroxyproline metabolism. It is very important to have adequate B6, but also adequate thiamine, magnesium, and pantothenic acid and cysteine in order to prevent excess formation of oxalate.

I do think that there are some vegetables now billed as healthy that may actually be problems for most people. It is interesting to see how foods like spinach, which were not eaten much in the past, became considered a health food due to some PR that was pretty intense (Popeye!) when the benefit (iron) was later found to be much exaggerated.


an abmd poster (september 06) asks:

If the diet shows improvements for 1-2 months and is followed by a regression that continues for 6, 8 months and more, would you advise a parent to continue with the diet? How long is it reasonable to expect a "temporary" regression to last?

my comment:

this sorta matches what i figure, the root issue is low cysteine and those whey borne amino acids that scd and gfcf excludes, and overdoing kale, spinach and silverbeet

but of course they still need the cysteine and without some kale, spinach or silverbeet, vitamin k which is fat soluble gets run down


if you look at wikipedia 'calcium oxalate' and 'oxalic acid' you can actually get some sense

mineral precipitates can be formed as the result of biofilm action

so i think its similar to all wilhelms bruha about gall bladder cleanses when the biofilm was making them as fast as he could get rid of them

vitamin k is not going to remove biofilm either

the core issue of the kerfuffle is the catch 22 problem of scd that eliminates whey, so removing branced amino acids and cysteine which the body uses to help regulate oxalate metabolism

scd tries to compensate for this by emphasising yogurt to provide some of these amino acids, but these amino acids do get degraded in yogurt and the supply is not enough



the lactic acid bacteria may partly consume dietary oxalate, partly displace the gut flora that make it, (especially fungi making oxalate acid), and also provide reduced toxic load from the better gut flora so the normal body pathways can process oxalates more effectively

i think biofilm is especially prevalent where you get liquid to tissue interfaces like the baldder or kidneys or gall bladder and obviously the intestine as well


Use of a probiotic to decrease enteric hyperoxaluria.

Lieske JC, Goldfarb DS, De Simone C, Regnier C.

Division of Nephrology and Hypertension, Mayo Clinic, Mayo Hyperoxaluria Center, and Mayo Complementary and Integrative Medicine Program, Rochester, Minnesota 55905, USA.

BACKGROUND: Patients with inflammatory bowel disease have a 10- to 100-fold increased risk of nephrolithiasis, with enteric hyperoxaluria being the major risk factor for these and other patients with fat malabsorptive states. Endogenous components of the intestinal microflora can potentially limit dietary oxalate absorption. METHODS: Ten patients were studied with chronic fat malabsorption, calcium oxalate stones, and hyperoxaluria thought to be caused by jejunoileal bypass (1) and Roux-en-Y gastric bypass surgery for obesity (4), dumping syndrome secondary to gastrectomy (2), celiac sprue (1), chronic pancreatitis (1), and ulcerative colitis in remission (1). For 3 months, patients received increasing doses of a lactic acid bacteria mixture (Oxadrop), VSL Pharmaceuticals), followed by a washout month. Twenty-four-hour urine collections were performed at baseline and after each month. RESULTS: Mean urinary oxalate excretion fell by 19% after 1 month (1 dose per day, P < 0.05), and oxalate excretion remained reduced by 24% during the second month (2 doses per day, P < 0.05). During the third month on 3 doses per day oxalate excretion increased slightly, so that the mean was close to the baseline established off treatment. Urinary oxalate again fell 20% from baseline during the washout period. Calcium oxalate supersaturation was reduced while on Oxadrop, largely due to the decrease in oxalate excretion, although mean changes did not reach statistical significance. CONCLUSION: Manipulation of gastrointestinal (GI) flora can influence urinary oxalate excretion to reduce urinary supersaturation levels. These changes could have a salutary effect on stone formation rates. Further studies will be needed to establish the optimal dosing regimen.


"Vitamin K inhibits the formation of calcium oxalate stones by synthesising urinary proteins essential to kidney function. Vegetarians, whose diets are often high in vitamin K, have a low incidence of kidney stones. Vitamin K is also necessary for the regulation of calcium in bone turnover and mineralisation. Vitamin K intakes much higher than the current recommendations improve bone formation as well as bone density."

also from the same page

X rays and radiation increase vitamin K requirements

so oxidative condtions increase the need for vitamin k

it does sound like vitamin K moves calcium and other minerals out of the body into bone

there will be synergies with vitamin d and other minerals

the problem is if you have a biofilm established in the gut or kidneys or kidney tubules then this biofilm is going to be making factors that dramatically increase mineral precipitation/oxalate stones

so you have this basic issue of the immune system failing to keep these biofilms form forming which is the central issue scd addresses, but unlike the gut where you can to some degree starve the biofilm, you can't do that for biofilm in the kidneys and tubules, and the deficency of whey proteins that scd enforces accelerates this mineral precipation issue

a good biofilm web site

the thing to realise is biofilms can be free floating like capsules in the stomach, or attached to a flexiable walls like kidney tubules or the intestine or attached to rigid surfaces like plaque on teeth of body implants

bacteria in these colonies have an incredible ability to turn on different genes for different adaptive features



China Villages Battle Lead, Zinc Poisoning 2006.11.29

Residents of at least two regions in China’s poorer provinces of Gansu and Guangxi say they are being poisoned with lead and zinc waste being pumped into their water supply by local mining groups.

Jiang Wenjian, a resident of Guo’an village in Guangxi’s Teng county, told RFA’s Cantonese service that around 100,000 people were affected by the pollution of the river by nearby lead and zinc mines, which had a daily output of 20 tonnes.

“There are now three operations extracting lead and zinc from ore in this region, with a daily output of 20 tonnes. All of the waste flows into the nearby rivers.”

“The river in Dali is the main river for the whole region, with about 100,000 people relying on it for drinking water. It also flows into other areas, so perhaps even more than that have been affected,” Jiang said.

All of the drinking water available to the 3,000 people in our village is polluted, and the fish have all died. “A lot of people are getting sick. The doctors say it’s down to the drinking water too. A couple of people had kidney disease and have died. About 30 percent of people have kidney stones,” he said.

if you used extra fertilizer, you could still get crops to grow. Now, nothing will grow at all in the fields.



Kidney stones have repeatedly been produced in magnesium-deficient animals. Total serum magnesium and erythrocyte magnesium levels may be low in recurrent stone formers. Perhaps 5% of stone formers have hypomagnesiuria, and the urine of over 25% of stone formers has a lowered magnesium to calcium ratio. The hypomagnesiuria appears to be due to inadequate magnesium intake, as magnesium absorption following supplementation appears to be normal.

Supplementation with magnesium salts may inhibit stone formation, even in patients without magnesium deficiency. Magnesium decreases the urinary saturation of calcium oxalate by combining with urinary oxalate to form soluble magnesium oxalate so long as it is administered with meals. In some studies, magnesium has been combined with vitamin B6 with good results.



Here is catherine's position on the Low Oxalate Diet:

1. It is unhealthy because of all the fruits and vegetables that get eliminated.

2. The indiscriminate use of calcium is a truly terrible idea, because children with autism already have a problem managing calcium and adding supplemental calcium makes that problem worse.

3. It is irrelevant, because the main source of oxalates appears to be internal synthesis, not dietary consumption.

4. The "dumping" symptoms are actually indications of elevated calcium and hypothyroidism and parents should not be inducing those symptoms in their children.

andrew's comments:

catherine tamaro seems to be coming along a bit with supplementing iodine, her intelligence has distinctly improved, the same cannot be said for susan owens (a promoter of the low oxalate diet and the nemesis of catherine tamaro)

its interesting to compare catherine tamaro's approach with mine, her's is test tube chemistry which takes as primary the reactions between chemical compounds in a test tube, but mine has the organic processes of biofilm as primary which is a whole different ball game since bioflm processes are enzymatic and hugely more sophisticated, complex, and recursive, and actually knowing lot about chemistry doesn't help you much at all, as is the case for most biochemical processes

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