Jack A. Gilbert, Ph.D. – Argonne National Lab -Group Leader Microbial Ecology – The Microbiome of Homes, Hospitals and More {Flashback Friday 4-10-2015|Episode 363}

Air Date: 8-19-2016| Episode: 427

Dr Jack A Gilbert earned his Ph.D. from Unilever and Nottingham University, UK in 2002, and received his postdoctoral training at Queens University, Canada…

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Dr. Jack Gilbert

Dr Jack A Gilbert earned his Ph.D. from Unilever and Nottingham University, UK in 2002, and received his postdoctoral training at Queens University, Canada. He subsequently returned to the UK in 2005 to Plymouth Marine Laboratory at a senior scientist until his move to Argonne National Laboratory and the University of Chicago in 2010. Dr Gilbert is Group Leader for Microbial Ecology at Argonne National Laboratory, Associate Professor in the Department of Ecology and Evolution and the Department of Surgery at University of Chicago, Associate Director of the Institute of Genomic and Systems Biology, and Senior Scientist at the Marine Biological Laboratory. Dr. Gilbert uses molecular analysis and sequencing tools to test fundamental hypotheses in ARgone National Labmicrobial ecology. He has authored more than 160 peer reviewed publications and book chapters on metagenomics and approaches to ecosystem ecology (www.gilbertlab.com). He is currently working on generating observational and mechanistic models of microbial communities in natural, urban, built and human ecosystems. He is on the board of the Genomic Standards Consortium is a section editor for PLoS ONE and senior editor for the ISME Journal and Environmental Microbiology. Among other projects, he leads the Earth Microbiome Project Home Microbiome Project Hospital Microbiome Project and co-founded American Gut. In 2014 he was recognized on Crain’s Buisness Chicago’s 40 Under 40 List.

Dr. Gilbert was mentioned in a few interviews recently when we got into discussions on the microbiome of the built environment. He is a prolific researcher and speaker we are thrilled to have been able to schedule him this week.

Z-Man’s Blog:


First he studied entomology (butterflies), then he worked with arctic proteins to make ice cream smoother, now Jack Gilbert, PhD studies the microbiome. Dr. Gilbert works at the Argonne National Lab a non-profit research laboratory operated by the University of Chicago for the Department of Energy (DOE).

Gold NuggetsNuggets mined from today’s broadcast:

  • The human genome is our DNA blueprint. Metagenomics is like going into a forest gathering everything, blending it together and then trying to reconstitute, detangle and tease apart how the microbes work and react.
  • Bacteria are the fabric of the world. We have 100 trillion of them inside us.
  • Microbiome is the microbial community that share our body space. Research money is available to study the microbiome. New research projects are starting daily.
  • Microbes are another organ of the human body. If we can figure out the role they play in our health it will unlock the mystery of why and how we get sick.
  • By numerical count, microbes make up 90% of the cells in our body. The microbes in our bodies weigh 2-3 pounds the same as our brain. Of the total count of microbes in our bodies, bacteria comprise 85%-89%.
  • 99.999% of the bacteria in our bodies are beneficial, they help us develop and train our immune system.
  • The human body evolved to avoid fungi. Most fungi in the human body is not sporinated.
  • Home microbiome. Cleanliness and sterility reduce human exposure to biodiversity resulting in an adverse effect on health is the “hygiene hypothesis”. When we move into a new home we bring our microbiome with us. Microbes transfer both ways: from the built environment to us and from us to the built environment. The baseline microbial signature within a new dwelling changes within a few hours. The vast majority of the microbial transfer is from us to the built environment, comparison of a toy water gun to a firehose. Seven healthy families and ten homes were studied for six weeks mapping the routes of microbial movement.
  • Each human has a unique microbial signature, even identical twins have different microbial signatures.
  • The human body has “real estate” for microbial colonization. When antibiotics are taken available “real estate” opens up providing the opportunity for more organisms and potential new pathogens to colonize.
  • Each cell of skin shed by humans contains 10,000-20,000 bacterial cells.
  • Alcohol hand sanitizer wipes “knock back” microbes for the short term (30 seconds).
  • Any built environment is purposely designed to be a hostile environment for microbes. Excessive sanitation reduces human exposure to microbes and disrupts the symbiotic relationship between humans and their microbiome. Sick building syndrome, autism, Altzheimer’s disease may have microbial origin and roots?
  • Surgery and antibiotics stress microorganism’s pursuit of food causing them to rebel and attack their human host. Keeping the right microbes happy prevents them from becoming dangerous. It’s easy to blame doctors and hospitals for hospital acquired infections, the damaged microbiome of the patient also needs to be considered. Biotherapeutics, also known as biotech drugs or biologics, are therapies derived from living organisms
  • Probiotics is an enormous catchall term we don’t understand. Very few products marketed as probiotics have clinical studies. Medical probiotics are used to treat inflammatory conditions such as irritable bowel. The challenge is how to add the right microbial stuff. Administering probiotics to patients after surgery keeps the body happy by filling available real estate; probiotics after surgery are known to reduce depression.
  • Hand washing is important. Microbial colonization on human hands goes deep. Alcohol based hand sanitizes are preferred as they only sanitize the uppermost surface of the skin where microbes will bounce back quickly. An ingredient used in some antimicrobial hand soaps is known to alter hormone levels of children.
  • Compared to the vast number of bacteria in humans there are few viruses. Resident viruses in humans attack bacteria.
  • Our ignorance about epidemiology is profound. We don’t always understand the mechanism by which we get sick.
  • Babies are born sterile. Microbes from mothers colonize their infants at birth. Human mother’s milk contains beneficial gut bacteria. The microbiome of a child stabilizes at age 3. Built environments provide a purely a human microbiome experience while farms provide a richer experience. The shotgun approach of exposing children to pets and animals is beneficial for young children. Pet dogs enrich the microbiome in homes.
  • Our microbiome is intimately associated with health: influencing brain development, altering hormone levels and weight gain.
  • Microbial cartography, maps understand how to manipulate indoor environments to benefit occupant health.
  • “Cleanliness” is a hard term to define and understand. Advertising depicts an indoor world sterilized with chlorine bleach; the world doesn’t work like that.
  • Industry standards are the result of a politically flawed process.
  • Sampling. Counting the number of cells or CFUs is not a useful measure for determining health of the environment. Culturing misses many organisms. ATP counts may not be appropriate for post remediation verification on restoration projects.
  • The beneficial effects of embedding materials with novel microbial based nano technology is being studied in laboratory animals. Reduction of the incidence of asthma and food allergies in animal studies may lead to human trials. Building suitable microbes into building materials can protect them from attack following water intrusion.
  • Perhaps “building probiotics” can positively manipulate the indoor microbiome?
  • Ergot fungus is known to create hallucinogenic effects. Ghost sightings in old buildings may be attributed to MVOCs from ergot fungus.
  • Hospital patients treated with antibiotics are more prone to pick up nosocomial infections is one takeaway from the hospital microbiome study.

Today’s music: Bacteria (A Song) by Florence Schechter, YouTube

Z-Man signing off