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
Study links common food additives to Crohn's disease, colitis
"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
The dormant blood microbiome in chronic, inflammatory diseases
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)