Probiotics, Antibiotics and Arsenic

Adapt to Survive - The Arsenic Files 6

Disclaimer: We are not medical doctors. Nothing in this article constitutes medical advise. This article is intended for entertainment purposes only. If you are experiencing health issues please contact your qualified medical provider.

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The rise of alternative medicine

Health advise today literally never stops. We are told to eat fewer eggs, stop drink wine, eat much less meat, start eating insects, don’t swim, do swim, don’t go out in the sun, do go out in the sun. We are given antibiotics that 50 years later we are forced to reduce because of ‘resistance’, then we are given multiple new drugs to cure this or the other ailment. Many of us decided to ‘cure’ ailments our own way, but even then the profiteers are lying in wait, failing to explain the minuteae of the way their supplements work is only a bare shadow of the miracles the human body can perform when given the right sustenance.

The same applies to lifestyle, belief systems, friendships and family. As we go along we believe that a magic cure exists to remedy a creeping sense of loss of control. The toxicity enters our lives and bodies. We burn bridge after bridge attempting to hold on to the one or two things we believe are helping us survive. At every turn we try to find something that will ‘just make it feel better’. Invariably any addition to the already swirling soup will make little difference and may sometimes even make things much worse.

Allopathic sceptics are being carefully nurtured towards an alternative pathway of healthcare, one that we pay for quite happily, and is not always good. As every individual on earth has unique fingerprints, so too do we have completely unique microbiomes. One size really does not fit all. The library of brands of minerals, vitamins, superfood supplements and probiotics are estimated to be worth $151 billion globally per year in 2021 and growing.

Origins of Probiotics

One small but growing part of that industry is probiotics. Scientists of the 1800’s knew much of the existence of bacteria and their role in infection. Gut bacteria however were not recognised as potentially important to health until the 1900’s. The work of Russian scientist Elie Metchnikoff at the Pasteur Institute in Paris on Lactobacillus Bulgaricus and Minoru Shirota in Japan on the bacteria population control of lactic acid, brought the field in to focus.

The term probiotic, coined in 1965, means ‘live microorganisms which, when administered in adequate amounts, confer a health benefit on the host’ according to the World Health Organisation and the Food and Agriculture Organisation. The definition excludes metabolites or bi-products from the activity of the bacteria, and therefore also antibiotics.

Strains from the Lactobacillus group are of ‘probiotic’ importance, along with other lactic acid producing bacteria including enterococcus and streptococcus. On closer inspection it seems lactic acid bacteria produce acetate, propionate and butyrate and other bi-products when digesting dietary fibre, which help the gut and body remain healthy. Lactic acid producing bacteria were also shown to have a positive effect on the culturing of more beneficial bacteria communities, in turn reducing pathogenic bacteria populations.

Obesity or preferential weight gain?

Multiple research papers consider the possibility that the population in the gut may contribute to obesity, cardiovascular diseases and diabetes. If this is the case, anything that unsettles gut balance would be a potential causative factor. Livestock farming highlights some of the mechanisms involved in weight gain.

Strains of Lactobacillus acidophilus (L. acidophilus) are used in livestock management to increase final weights of animals before sale. In Europe antibiotics were used as growth promoters until they were banned in 2006. At this point farmers turned to probiotics. This paper on L. Acidophilus administration found that pigs responded with an increase average weight gain per day compared to controls and that populations of E.Coli were reduced. For humans, however, L. Acidophilus is promoted as a supplement that may help weight loss. Puzzling.

In the paper ‘Comparative meta-analysis of the effect of Lactobacillus species on weight gain in humans and animals’ this whole marketing premise is thrown in to question. The analysis found not only did L. acidophilus promote weight gain, but so did other bacteria we often find in the pathogenic group, namely Staphylococcus aureus, Escherichia coli (E. coli), Faecalibacterium prausnitzii. The strains of bacteria used specifically for animal weight gain in farming are L. acidophilus, L. plantarum, L. casei, L. reuteri, and L. fermentum.

Lactobacillus strains overall did not show a tendency to weight gain, so researchers then looked at individual strains. L. Acidophilus results showed a significant weight gain of 1.5 kg in a 70kg man. There were no human results for L. fermentum though showed a higher proportional weight gain in ducks, chicks and pigs to the acidophilus strain. L. plantarum showed significant weight loss in animal studies which is strange as some strains are shown to cause weight gain in calves. L. ingluvievi also showed weight gain in animal trials. In L. gasseri the calculations for weight loss in obese humans was 6kg.

We have a similar scenario in the Bifidobacterium family. Some promoting weight gain and others promoting weight loss. Results possibly dependent on the health and weight status of the person being treated. In this paper on weight gain in malnourished children of Bangladesh, Bifidobacterium infantis was administered to 3-24 month old children. A live US donor B. Infantis EVC001, an infant-adapted microbe, was given with resulting weight gain and reduction of intestinal inflammation.

In Neonatal intensive care unit (NICU) studies in the US, preterm babies were found to have increased pathogenic gut populations. Feeding of the same B. Infantis EVC001 improved quantities of bifidobacteria, reduced enterococcus strains (which include E. Coli and Klebsiella), leading to apparently better use of human milk oligosaccharides. Recent work suggests babies develop gut bacteria in utero. The potential of feotal bacterial populations potentially being affected by toxins and pathogens before birth is for later discussion.

Why do these specific strains of bacteria lead to weight gain and potentially unwanted weight gain in adults? Also how does weight gain and HGT relate to our study on arsenic? From previous research we know bacteria can message and send out molecules to other bacteria in the immediate community and evolve genetically according to their environment.

Genetic Arsenic protection

A ‘gene cassette’ is an encapsulated single strand of DNA instruction which can be recombined in to the DNA of other bacteria. Some of these instructions tell bacteria how to detoxify metals, metalloids and chemicals. The passing of this cassette from a bacteria to the larger community to be taken up by other bacteria is called ‘horizontal gene transfer’ (HGT). Initially thought unique to bacteria, research has identified this process in protazoa, other parasites, fungi, animals and humans and remarkably across species. Scientists even theorise the ABO blood group gene was transferred to humans from bacteria.

Some bacteria hold a series of genes that allow them to process and/or store arsenic. This gene cluster is called the Ars Operon. As well as antibiotics and probiotics farmers have used and some still use arsenic based compounds in feed to increase sale weight. It is suggested here that probiotic supplementation leads to stronger, heavier animals without antibiotic resistance.

In older studies most arsenic was said to be removed from the body after 48 hours through urine and the remaining amounts over weeks/months from the liver. As research develops that assumption is constantly challenged. It is recognised that arsenic can be stored throughout the body including in fat (adipose) and muscle tissue.

Brown adipose tissue is found in the back of the neck, above the clavicle area, between the shoulder blades and in the adrenal area above the kidneys. Beige adipose tissue is distributed throughout the body together with white fat around the heart, organs, in and around the abdominal cavity, thighs and buttocks.

In studies on how arsenic influences brown and beige fat, factors controlling the way fat is used and stored were altered. Perilipin protein levels, that played a key role in maintaining control of fat deposits was particularly affected. The protein has a number of cysteine residues which contain sulphur atoms, a binding target for arsenic. In addition, mitochondria, as the energy converters of brown adipose tissue cells, are also affected by the presence of arsenic, meaning energy production through the citric acid (Krebs) cycle is impaired. The effects of arsenic on metabolism are wide ranging.

Antibiotics and Mitochondria

The broad spectrum antibiotic Azythromycin, developed from Actinomycetales bacteria found naturally in the gut and mouth, halts bacterial growth and reproduction. It also inhibits brown and beige fatty tissue function in animals accumulating in fatty tissue, inhibiting mitochondrial respiration and increasing reactive oxygen species (ROS). Administration of Azythromycin leads to damage of the metabolic pathways, logically causing weight gain. Tetracylines have also been shown to impair mitochondrial function.

Excessive antibiotic use allows bacteria to adapt to survive

In this article, we find incredibly that mitochondria seem to be part bacteria and part host. The evolutionary formation of mitochondria involved the symbiotic fusing of an α-proteobacterium and an amitochondriate cell. Cell nuclei have absorbed much of the genetic information in to our DNA, but mitochondria have kept parts of the bacterial DNA and coding machinery. This may explain why antibiotics would also have a detrimental effect on mitochondria. Other antibiotics put in livestock feed to increase weight included penicillin, streptomycin and bactrican.

It is also possible that mitochondria, if we consider their residual bacterial genes, have developed similar operons for detoxification to bacteria. This might allow them to process and/or store arsenic retaining a contaminated cellular function. As the mitochondria are shown to increase if the Sonic hedgehog pathway is activated due to arsenic’s displacement of zinc, this theory seems quite feasible.

Fixing the microbiome and cell damage

Alastair Crisp and team, University of Cambridge, did genome sequencing on 40 different animal species. They found hundreds of genes that appeared to have originated in bacteria, archaea, fungi, and plants. HGT has also been observed in repair of human DNA double strand breaks. Scientists found exosomes carried DNA repair genes to cells, directly hampering their CRISPR gene editing study. It is not too far a leap to theorise that bacterial ‘gene cassettes’ could be swept up by exosomes in the gut to deliver resistance genes to human cells and mitochondria.

Gut bacteria produce molecules with bacteriocidal functions. Acetate has been shown in concentration to be able to control populations of metalloid/heavy metal resistant E. Coli and reduce gut inflammation However, as E. Coli also produces acetate, when populations are thriving due to an arsenic rich environment, the increased acetate causes a reduction of non resistant bacteria. An increase in pathogenic bacteria in the microbiome corresponds to an increase in acetate production, causing metabolic syndrome. Signalling by acetate to the parasympathetic nervous system leads to increased insulin secretion, increased hunger hormone, abnormal appetite and food consumption and obesity.

This creates a vicious cycle that seems to resolve only with the removal of the arsenic and excess E. Coli through diarrhoea, vomiting and involuntary fasting. Fasting has also been shown to rebalance the microbiome and trigger increases of mitochondria in white fat, causing it to beige or brown, leading to rebalancing of fatty tissues. It has also been shown to reduce E.coli populations and pro-inflammatory factors while propionate and butyrate producing bacteria increased.

Butyrate, one bi-product of lactic acid bacteria digestion of fibre, suppresses appetite and prevents diet related obesity. Propionate also reduces the formation of fat in animal studies. Considering both of these are produced concurrently to acetate, it makes little sense that specific probiotic strains can lead to such substantial weight gain. So what is going on?

Suspect strains

When we consume probiotics we are only taking in a very a very narrow range of bacteria, usually from the following groups: Lactobacillus acidophilus, casei, bulgaricus, reuteri, rhamnosus, fermentum and plantarum, Bifidumbacterium breve, longum, infantis, lactis, animalis and bifidum. Bacillus subtilis, Enterrococus faecium, lactococcus lactis and two species of Saccharomyces – cerevisiae and boulardii.

As it is unlikely that the normal bacteria functions should be able to promote weight gain we though we would check something else. Had any of these bacteria acquired detoxification operons using ‘gene cassettes’ and horizontal gene transfer? Had they acquired any for detoxification of arsenate in to arsenite, which might be causing issues in brown and beige adipose mitochondria.

Of the bacteria listed we found an erm(X) resistance gene to erythromycin across Bifidobacterium species, specifically B. longum. This study found that the resistance could be transferred across the species to different strains. Also in Bifidobacterium longum, the Ars operon genes arsC1, arsB1, arsB2 and arsR were all present but arsA was not. ArsB1 and arsB2 are both relate to ‘efflux pumps’, which remove arsenic metabolites from the bacteria after processing. ArsC1 is the gene which codes the reduction of arsenate to arsenite, ArsR is the gene which control the switching on and off of the ars operon.

Arsenate (V) causes significant disruption in red blood cells, where Arsenite (III) does not. Whilst arsenite is deemed to be more toxic, arsenate can also cause just as many issues as we have seen throughout the Arsenic Files series. This review of arsenic resistance across a wide range of bacteria details the effects of different arsenic species. Some bacteria even use arsenic as an electron donor or receptor in different processes within the bacterial cell.

The arsM operon makes up one of the many arsenic reduction operons and is present in many species of animal, plant, bacteria and other microbes. It is this gene which allows us to metabolise and excrete arsenic. It is possibly the most widely transferred ars operon gene between species. Theory claims the arsM gene was transferred in response to at least 6 significant earth events.

Lactobacillus plantarum carries an unusual version of the ars operon with an arsRDDB cluster. It does not carry the arsC gene, which is responsible for reducing arsenate to arsenite, which possibly makes it more of a candidate for arsenic removal from the gut. The arsD gene has cysteine pairs (remembering that cysteine has one sulphur atom per molecule), so it is likely the pair of sulphur atoms acts as a binder to any arsenic present, enabling easier removal from the gut. It is also responsible, as the arsR operon for switching the operon on and off depending on whether arsenic is present. Given some strains of L. plantarum promote weight gain, they may have subsequently acquired the arsC gene.

Arsenite resistance has been amplified in vitro (in a petri dish enviroment) to Lactobacillus acidophillus. Though scientists are not entirely sure what the amplified arsH operon does, it does seem to have the ability to reduce quinones, which is peculiar given the use of quinone based drugs to treat a number of different illness. As L. acidophilus has been used to clear arsenic from water sources, we could assume that this arsH gene allows the bacteria to accumulate arsenic. It is unclear to what degree it can continue doing that before the bacteria is ‘full’. Might it then adapt further to reduce arsenate for efflux if there is a high level of toxicity in the immediate environment, or has it already adapted?

Bacteria adapt to survive

Looking at the use of arsenic as a growth mediator before switching to antibiotics and now probiotics, the ability of bacteria to adapt to toxins in the right environment, may well have conferred a full complement of arsenic resistance to L. acidophilus in livestock over time. The source of human dietary acidophilus may well be cultured from animals whose bacterial complement already has this resistance. Are bacteria strains screened for the presence of the arsC gene particularly?

It seems that all bacteria can receive ‘gene cassettes’ from the public goods pool, transforming or changing DNA profile through transduction. If one strain of bifidobacteria can acquire resistance to arsenic, so can others. There seems to be no real way to predict which strains will acquire which genes. It is unclear over what time period these genes can be conferred in the wild though laboratory experiments seem to suggest that horizontal gene transfer can occur quickly with extreme exposure. According to the paper ‘Assessing the benefits of horizontal gene transfer by laboratory evolution and genome sequencing’ high populations of certain strains of bacteria seemed to have a positive effect on horizontal gene transfer, working together with natural selection. Success of transfer was also likely due to the lack of other competitive gene mutations, as strains were restricted to the E. coli group.

There is a significant amount of cooperation but also conflict between bacteria species. The recombination of a foreign gene code may or may not be beneficial to the host bacteria and could result in the demise of species to the benefit of others. However, it seems that the transfer of genes is largely beneficial, increasing chances of survival in adverse environments.

Antibiotic resistance is an example of the speed at which bacteria can adapt. Azythromycin was launched in 1980 and warnings were issue in 2013 about cardiac problems apparently precipitated by the antibiotic. In 2015 a strain of ‘gonorrhea’ bacteria was found to be strongly resistant. A spate of broad antibiotic resistance suddenly appeared in the 1980’s despite penicillin being available since the 1940’s (which may give us some clues as to when our environmental exposure to arsenic increased). Alexander Fleming warned early on that bacteria could to make these genetic mutations.

We adapt to survive

The health of the human, animal, plant, microbe and environment very much depends on adaption. The ability for the microbial communities within and around us to co-exist very much depends on the environment we find ourselves in. Toxicity, as we are seeing with arsenic, encourages surges in populations of deleterous strains of bacteria, leading to an imbalanced gut microbiome, fewer available nutrients and reduced overall health of the host. Can a broad selection of uncontaminated sources of food nutrients support and protect the existing microbiome even more effectively than the stab-in-the-dark application of supplements and probiotics? Some people think so.

Increased populations of a few probiotic strains from supplementation may be fertile ground for horizontal gene transfer in an arsenic rich environment. The experiment on E. coli found that the large population made it the easier for operons to transfer. Flooding the gut with a narrow selection of bacteria at a time when arsenic is present in large quantities, could be like putting these strains in a petri dish along with the arsenic and the ‘gene cassette’ tools they can use to protect themselves. Good for the bacteria in question, not so good for the host.

It may well, therefore, be beneficial for us to take probiotics only in a time of absolute need, to vary the probiotic strains each time and to limit the course to a short period. In effect, treating probiotics in exactly the same way we do antibiotics, may prolong the usefulness of this tool in our personal healthcare box. Or alternatively we could protect and nurture the already huge population of bacteria in our bodies with uncontaminated and wholesome nutrients.

Thank you to the Emergency New Channel and Twitter followers for your feedback on probiotics and diet. It has been crucial to understanding where some of the issues may have originated. Thanks also as always to Seb, Loretta and Elayne.

Next up we will do a little more digging in to how antibiotics work, look at some more natural nutrients essential to keeping our bodies healthy and more conditions related to arsenic exposure.