Last Updated on May 27, 2015 by Patricia Carter

Summary:   Eric Alm’s MIT lab gene sequencing shows microbiome changes from diet & environment (antibiotics and international travel.) Changes to microbiome due to antibiotic was permanent.

I am the ninth viewer of this Microbiome Manipulation via Diet and Environment (YouTube), Eric Alm, PhD, MIT.  It doesn’t get much more current than that!  The study Dr. Alm discusses (daily stool sequencing for one year for several participants) can be read at Host lifestyle affects human microbiota on daily timescales. 

Dr. Eric Alm is one of my favorite researchers; our paths first crossed with Eric Alm: A year in the life of my gut microbiome (2012 GET Conference) (YouTube) which is re-discussed in the second section of his most recently published YouTube.  The 2012 GET Conference provides more insight though, if desired, into the second Pearl listed below.

Pearls from Dr. Eric Alm’s newest YouTube are:

1. Our biome reflects the state of health of the human host.  This leaves the potential for exploiting the biome to develop new diagnostics.  Dr. Alm in collaboration with Athos Bousvanos, Children’s Hospital of Boston:  A certain bacterial biome “community” could accurately diagnose IBD in a pediatric population thereby potentially eliminating the need for more invasive diagnostic testing such as colonoscopy.  No one species stood out with the exception of e-coli, however the sensitivity of accuracy for e-coli was terrible at only 10 to 20% accuracy.
2. Diet and environment can influence and affect the biome, sometimes permanently with stability and resilience in maintaining the new altered biome composition:
   • Antibiotic exposure caused loss and total extinction permanently of certain bacterial species.  
   • International travel transiently altered the biome (immediate biome change-up upon arrival at international destination which reverted back to the pre-travel biome almost immediately upon return to originating country).
3. The biome can influence the state of the host.  1.6 million years of Patient data was evaluated to identify the factors that led to long term weight gain and obesity.  Conclusion: For each additional serving of yogurt per day, not only was there no weight gain, but 1.5 pounds was lost over 4 years.  Changes in Diet and Lifestyle and Long-Term Weight Gain in Women and Men, New England Journal of Medicine, 2011  Investigating if probiotic accounted for health benefit: histological study confirmed mice fed lactobacillus reuteri laced water grew active antigen hair follicles whereas those on Western Diet had dead follicles.  Lactobacillus reuteri is a probiotic component of Activa yogurt which was used in their prior mouse weight study.
4. Dr. Eric Alm, “We have to think carefully about our sub-therapeutic antibiotic treatments because even if the microbes that are antibiotic resistant don’t thrive in our human guts, we are showing that their genes can actually freely move between themselves and bacteria that do thrive in our human gut.”  This is a most concerning finding discussed beginning at 15:10.  Dr. Alm’s motivation for this work came via the “sushi paper”, “Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota”, Nature 2010.  This paper found “seaweeds with associated marine bacteria may have been the route by which novel CAZymes were acquired in human gut bacteria, and that contact with non-sterile food may be a general factor in CAZyme diversity in human gut microbes.”  Dr. Alm’s lab then found evidence of more than 80,000 – 100% identical DNA transferred into totally radically different species involving 11,000 proteins.  Further study concluded that 60% off diagonal transfers to and from our food and our livestock includes at least one antibiotic resistant gene.  

I still need to digest the ramifications of Pearl 4 but the “transfers of genes” finding definitely supports the “Whole Health Pillar” of minimizing toxins which includes diet and environment.

Complicated stuff indeed!