microbiome2 -- overview

this is the second of two blogs on the microbiome, inspired by a recent review that highlighted several other health-related data besides the non-caloric artificial sweeteners (see microbiome review nejm2016 in dropbox, or Lynch SV. N Engl J Med 2016;375:2369). 

Details:

​ -- the microbiome is huge, with 9.9 million microbial genes represented, as found from studying 1200 people in the US, China, and Europe. And it has >1000 species of microbes

-- Although the microbiome was previously felt to develop after birth, bacteria are found in the placentas of healthy mothers, in the amniotic fluid of preterm infants, and in meconium. And, the mode of infant delivery does influence postnatal microbial exposure: intravaginal delivery does seem to confer an infant microbiome taxonomically similar to the maternal gut and vaginally microbiota. Also the infant microbiome does become more similar to the adult one with the cessation of breast-feeding, and over the years bacterial diversity and functional capacity expand. The microbiome becomes less diverse in elderly, which could reflect coexisting conditions and age-related declines in immunocompetence.

-- Things that affect the microbiome include sex, age, diet, exposure to antimicrobial agents, changes in stool consistency, PPIs and other meds, travel, malnutrition, exercise (the effect of exercise on the microbiome is pretty clear in mice, not so clear in humans, since it is hard to sort out the effect of exercise vs different diets in those who exercise more).  Also, host genetic features, host immune response, xenobiotics (including antibiotics), other drugs, infections, diurnal rhythms (see below), and environmental microbial exposures.

-- Clostridium difficile infections

    -- this is probably the most advanced and practicable microbiome application. See http://gmodestmedblogs.blogspot.com/search/label/c%20difficile  for many studies and analyses. However about 90% of patients affected with severe, recurrent antibiotic-resistant C. difficile infections respond to fecal microbial transplants

-- Effects on immunity:

    -- there are data that the infant microbiota at one month of age is significantly related to allergy in two-year-old children and to asthma in four-year-old children. Several of the products of the higher risk microbiota are associated with subclinical inflammation, which precedes childhood disease. Also other studies have found that children born by cesarean section, who do have differences in their microbiota, are more likely to develop type I diabetes, celiac disease, asthma, hospitalizations for gastroenteritis, and allergic rhinitis.

-- obesity/metabolic syndrome/insulin resistance/diabetes

    -- there are several studies finding that there are significant differences in the microbiome between obese and lean human subjects, with a decrease in Bacteroidetes and an increase in Firmicutes species in obese individuals. Studies have shown that taking microbiome samples from pairs of identical human twins, one lean and one obese, and placing them into genetically identical baby mice, have found that the mice with the microbiota from the obese twin develops more weight gain and more body fat, along with a less diverse microbiome, than those from the lean twin. Also, interestingly, women in their third trimester of pregnancy have an altered microbiome, which, when transplanted into mice, leads to more obesity, and that pro-obesity microbiome is more efficient in extracting energy from food [one common clinical issue with overweight/obese patients is that they may often eat much less than others but still do not lose weight, which has been shown in several studies, and attributed to their being more efficient in metabolizing foods. But perhaps this is mediated through the microbiome???]

    -- some proteins elaborated by E. coli stimulate glucagon-like peptide-1 (GLP-1) secretion, which could augment glycemic control in diabetics, where this hormone is less active than in nondiabetics. In addition, E. coli can elaborate peptide YY (produced in the ileum in response to feeding), which can activate anoxeretic pathways in the brain, mediating satiety.

-- atherosclerosis/cerebral artery occlusion

    -- there are pretty convincing studies that eating red meat leads to changes in the gut microbiota, which leads to increase production of trimethylamine-N-oxide (TMAO), which is a very strong risk factor for human atherosclerotic disease. And feeding meat to vegetarians does not increase TMAO until there are these microbiota changes from recurrent red meat diets. See blogs listed below for more details. Also, experimental data on mice show that  cerebral arterial occlusion leads to 60% less damage in those with microbiota which are sensitive to antibiotics; mice given probiotics have less impairment after spinal cord injury.

-- cancer

    -- in mice, specific gut bacteria (most clearly shown for Bifidobacterium) enhance the efficacy of cancer immunotherapy, delaying melanoma growth. Human data has shown that certain microbiota species (B. Thetaiotaomicron or B. fragilis) can improve the effects of anti-tumor therapy targeting cytotoxic T-lymphocytes-associated antigen 4.

--Autism

    -- there are even some suggestive data that the microbiome may play a role in autism spectrum disorders. MIA mice, a maternal immune activation mouse model, exhibits autistic-like behavior, gut microbiome dysbiosis, increased gut mucosal permeability, and an increase in 4-ethylphenylsulfate (4EPS, a metabolite of gut bacteria). Injection of 4EPS into healthy, normal mice results in anxiety. And, feeding the MIA strain of mice a strain of Bacteroides fragilis normalized these adverse gut changes and decreased behavioral abnormalities, associated with decreasing circulating 4EPS levels. There are other neuropsych issues potentially related to the microbiome: gut bacteria can produce several neurotransmitters (eg norepinephrine, serotonin, dopamine, GABA, acetylcholine), and can change emotional behavior of mice (which seems to be related to central GABA receptor expression).

-- Other diseases with suggestive data of a linkage to microbiome dysbiosis include inflammatory bowel disease, kwashiorkor, juvenile rheumatoid arthritis, and multiple sclerosis. Also, in mice, stress leads to altered microbiota (less Bacteroides and more Clostridia), and in humans undergoing bariatric surgery, there are huge differences in the microbiome by either the Roux-en-Y gastric bypass or vertical banded gastroplasty, and this microbiome transplanted into germ-free mice leads to reduced fat deposition, suggesting that these microbiome changes themselves might play a direct role in decreasing adiposity (see gastric bypass and microbiome changes cellmetab2015 in dropbox, or Tremaroli V. Cell Metabolism2015; 22:228)​. And perhaps the changes in the microbiome, through the gut-brain relationship is part of the reason for the documented improvement in memory noted after bariatric surgery.

--diurnal rhythms (see microbiome and diurnal changes cell2014 in dropbox, or Thaiss CA. Cell. 2014; 159: 514): the gut microbiota has diurnal variations that reflect feeding rhythms; humans with jet lag have dysbiosis; this jet lag leads to  microbiome changes promoting glucose intolerance and obesity and are transferable to germ-free mice.

Commentary:

-- we should approach these studies on the microbiome with caution: some of the most impressive studies were done in animals in highly controlled conditions, and predictions in humans based on the studies is always fraught. For example, in general the use of probiotics in human adults has not shown as dramatic a response as found in rodents. (Although an interesting study of human neonatal probiotic supplementation in the first month of life was associated with a 60% reduction in the risk of pancreatic islet cell autoimmunity, a precursor to type 1 diabetes, before school-age). In addition, a stool sample may not be an adequate proxy for the microbial content of the entire GI tract. And, most of these studies have focused primarily on bacterial species in the microbiota, not taking into account the many other types of microorganisms found or their complex interactions.

-- one concern I have in general is our tendency towards reductionism. The microbiome appears to be a quite complex organ, composed of many different varieties of organisms which undoubtedly interact with each other in complex ways, and which are influenced by many known and undoubtedly unknown external cues (diet, antibiotic use, etc, etc). So, for example, simply attempting to manipulate that microbiome through the introduction of one species or another of probiotics (ie, our usual medical fix) may not deal with the complexity of this situation.

--there have been a slew of other blogs on the microbiome over the years. see http://gmodestmedblogs.blogspot.com/search/label/microbiome  . one particularly interesting finding in one of the blogs was that one of metformin's major action might be in its effects on the microbiome (see http://gmodestmedblogs.blogspot.com/2014/10/heart-failure-microbiome.html , which also reviews some of the TMAO data.

-- So, although I am pretty convinced of the importance of a healthy microbiome, it does seem to me that the major initiative should be around lifestyle changes overall: a healthy diet (and specifically one which is predominantly vegetarian), adequate exercise, perhaps adequate sleep (would be great to have more data on the effect of sleep patterns overall on the microbiome and if changing those patterns changes the microbiome), and minimizing exposure to unnecessary antibiotics (both in humans and in animals that make it into our food chain).