This blog is a way of sharing the information and resources that have helped me to recover my son Roo from an Autism Spectrum Disorder. What I have learned is to view our symptoms as the results of underlying biological cause, which can be identified and healed. I say "our symptoms" because I also have a neuro-immune disorder called Myalgic Encephalomyelitis.

And, of course, I am not a doctor (although I have been known to impersonate one while doing imaginative play with my son)- this is just our story and information that has been helpful or interesting to us. I hope it is helpful and interesting to you!

Thursday, November 19, 2015

The Microbiome

There are about 10 times more microbial cells in and on our bodies than there are human cells.  These microbes are referred to as the microbiome, which is divided loosely into separate biomes based on location (such as the gut microbiome, the sinus microbiome, etc).  The way that these microbes affect and influence the health and functioning of our bodies has not been understood much in the past, but is increasingly being studied now.  The microbes that live in and on us play many roles, including aiding in digestion, providing certain enzymes and nutrients, regulating out immune system and inflammation, keeping pathological microbes in check, and even regulating the expression of some of our genes. New evidence shows that micro organisms are even the source of some of our genes which have been acquired through a process called horizontal transfer.

There are many factors that influence the health and diversity of our microbiome.  Many medications alter our flora, especially antibiotics, but many others do too such as oral contraception.  What we eat, what personal care products we use, and what we use to clean our homes are also major factors.  Antibiotics can have a devastating effect on the microbiome, something which is only now being appreciated, and which may explain many of the side effects and unintended outcomes of widespread antibiotic use.  A recent article about research being done on the role of the microbiome in autism and other health conditions called Autism's bacteria link gains credence provides a basic introduction to these factors:

"But changes in the past century have altered the microbial balance as societies relied too heavily on antibiotics, disinfectants, C-section deliveries and a diet of refined carbohydrates. Those changes replace inner gardens of helpful bacteria with a harmful mix that makes compounds that in excess can damage the digestive system, brain, immune system, and the way cells metabolize energy.  The damage is likely worse in babies whose brains and immune systems are developing, MacFabe says. But the damage also occurs throughout life."

The Origins of the Microbiome

A fetus growing in it's mother's uterus is sterile until birth, when it is colonized by bacteria.  In a vaginal birth, the baby is colonized by the mother's vaginal and fecal flora.  Babies born by c-section are instead colonized by the bacteria present in the room during birth.  Touching and kissing the baby is another source of flora.  To learn more about this read The infant gut microbiome: New studies on its origins and how it's knocked out of balance.  Once the baby is colonized at birth, the gut flora is further influenced by whether the baby is breastfed or formula fed and when solid food is started and what foods are eaten.

Maternal prenatal stress is associated with the infant intestinal microbiota.
Psychoneuroendocrinology. 2015 Mar;53:233-45
"Results showed that maternal prenatal stress, i.e., either reported stress or elevated basal maternal salivary cortisol concentrations or both, was strongly and persistently associated with the infants' microbiota composition as determined by a phylogenetic microarray. Infants of mothers with high cumulative stress (i.e., high reported stress and high cortisol concentrations) during pregnancy had significantly higher relative abundances of Proteobacterial groups known to contain pathogens (related to Escherichia, Serratia, and Enterobacter), and lower relative abundances of lactic acid bacteria (i.e., Lactobacillus, Lactoccus, Aerococcus) and Bifidobacteria, altogether characteristics of a potentially increased level of inflammation. Furthermore, this aberrant colonization pattern was related to more maternally reported infant gastrointestinal symptoms and allergic reactions. In conclusion, clear links were found between maternal prenatal stress and the infant intestinal microbiota and health. Although causality cannot be concluded, the results suggest a possible mechanism by which maternal prenatal stress influences the offspring development. These results suggest a potential for bacterial interventions to enhance offspring health and development in pregnant women with stress."

How Diet Affects the Microbiome

What an individual eats has a profound impact on the population and diversity of their gut microbiota.  It is also true that there are differences between normal gut flora in groups of people living in vastly different parts of the world and eating vastly different diets.  A study was done comparing the gut flora of children in Europe with that of children in a rural village in Burkina Faso in west Africa that showed how significant these difference can be and suggests that our gut flora have evolved along with us to reflect what we eat.

Study links common food additives to Crohn's disease, colitis
The study being reported on here looked at two emulsifiers commonly used in processed food and their effect on gut health and gut flora, polysorbate 80 and carboxymethylcellulose.

"A key feature of inflammatory bowel diseases and metabolic syndrome is a change in the gut microbiota - the roughly 100 trillion bacteria that inhabit the intestinal tract - in ways that promote inflammation. In mice given emulsifiers, the bacteria were more apt to digest and infiltrate the dense mucus layer that lines and protects the intestines."

The Microbiome in Health and Disease

In this study Foxp3 T Cells Regulate Immunoglobulin A Selection and Facilitate Diversification of Bacterial Species Responsible for Immune Homeostasis (you can read about what this study means here) it is found that:

"They discovered that the immune system "sees" and responds differently to different bacterial communities. Rich and balanced bacterial communities seem to be perceived as "self" and induce a quick maturation of the immune system and gut responses (induction of regulatory T cells and IgA), while a poor and unbalanced bacterial community is apparently perceived as "non-self" and induces responses aimed at eliminating it (T cells with inflammatory properties and IgG or IgE responses)."

Understanding an individual's microbiome is part of the emerging paradigm shift going on in medicine right now to individualized medicine, which is an approach to understanding and treating disease based on an individual's genetics, microbiome, environmental factors, and any other factors that influence the health of an individual.  In this new paradigm, rather than classifying patients together by diagnosis and then treating each of them with the same methods it is a way to individualize treatment to the individual's specific needs.  This brief interview from a medical conference held in 2015 on the cutting edge research in digestive disease gives a little more detail on how this paradigm shift relates to the gut and it's microbiome.

Restoring Microbial Balance Key to Keeping Sinuses Healthy
"A new study by Dr. Goldberg and colleagues likewise concludes that the health of our sinus cavities, once thought to be largely sterile, may be highly dependent on the composition of their microbial residents...Beyond a significant decrease in the diversity of microorganisms among the patients, the researchers found a noticeable drop in a group of bacteria known as Lactobacilli, long associated with maintaining health in the gut. Concurrently, the researchers saw an increase in a little-known potential pathogen called Corynebacterium tuberculostearicum..."Central to the concept that we’re putting forward is that there is a protective mechanism in a normal sinus that comes about as a result of the microbiome,” Dr. Goldberg said."

The dormant blood microbiome in chronic, inflammatory diseases
"A number of recent, sequence-based and ultramicroscopic studies have uncovered an authentic blood microbiome in a number of non-communicable diseases. The chief origin of these microbes is the gut microbiome (especially when it shifts composition to a pathogenic state, known as 'dysbiosis'). Another source is microbes translocated from the oral cavity. 'Dysbiosis' is also used to describe translocation of cells into blood or other tissues. To avoid ambiguity, we here use the term 'atopobiosis' for microbes that appear in places other than their normal location. Atopobiosis may contribute to the dynamics of a variety of inflammatory diseases. Overall, it seems that many more chronic, non-communicable, inflammatory diseases may have a microbial component than are presently considered, and may be treatable using bactericidal antibiotics or vaccines."

Gut dysbiosis and detection of "live gut bacteria" in blood of Japanese patients with type 2 diabetes
"Mounting evidence indicates that the gut microbiota are an important modifier of obesity and diabetes...The counts of the Clostridium coccoides group, Atopobium cluster, and Prevotella (obligate anaerobes) were significantly lower, while the counts of total Lactobacillus (facultative anaerobes) were significantly higher in fecal samples of diabetic patients than in those of control subjects. Especially, the counts of Lactobacillus reuteri and Lactobacillus plantarum subgroups were significantly higher. Gut bacteria were detected in blood at a significantly higher rate in diabetic patients than in control subjects (28% vs. 4%, P < 0.01), and most of these bacteria were Gram-positive...The high rate of gut bacteria in the circulation suggests translocation of bacteria from the gut to the bloodstream."

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease
"Inflammatory bowel diseases (IBDs), including Crohn’s disease (CD), are genetically linked to host pathways that implicate an underlying role for aberrant immune responses to intestinal microbiota. However, patterns of gut microbiome dysbiosis in IBD patients are inconsistent among published studies. Using samples from multiple gastrointestinal locations collected prior to treatment in new-onset cases, we studied the microbiome in the largest pediatric CD cohort to date. An axis defined by an increased abundance in bacteria which include Enterobacteriaceae, Pasteurellacaea, Veillonellaceae, and Fusobacteriaceae, and decreased abundance in Erysipelotrichales, Bacteroidales, and Clostridiales, correlates strongly with disease status. Microbiome comparison between CD patients with and without antibiotic exposure indicates that antibiotic use amplifies the microbial dysbiosis associated with CD. Comparing the microbial signatures between the ileum, the rectum, and fecal samples indicates that at this early stage of disease, assessing the rectal mucosal-associated microbiome offers unique potential for convenient and early diagnosis of CD."
It has recently been discovered that certain parasites are able to modulate the immune system of the host by communicating with the host's microbiome.  Some of these parasites are being used therapeutically to treat inflammatory and allergic disorders, although it was not fully understood why the treatment was effective.  Here findings are discussed that show that the parasites are inducing the microbes of the gut to produce certain short-chain fatty acids that modulate the immune system.

In addition, a compromised immune system can alter the microbiome of the gut, leading to intestinal disease such as Inflammatory Bowel Disease.

Study Finds Gut Bacteria Help Prevent Post Traumatic Stress Disorder (PTSD)