Microbes and Microbiota: Benefits and Risks

Poster Winner Questions Assumption of Womb Sterility

Scientists around the world debate evidence: sterile womb or bacterial colonization in utero? Learn how 21st century methods for detecting microbes help separate hypotheses, facts

 Credit:  Edgard Garrido/Reuters ;   Willard, 2018 ; articles/d41586-018-00664-8

Credit: Edgard Garrido/Reuters;
Willard, 2018; articles/d41586-018-00664-8

I learned a new term from poster winner Shantelle Claassen-Weitz (meconium, baby’s first ‘feces’). A new world of clinical studies opened on research into natural microbes (the microbiota) in health and disease. Her poster was a highlight of my first blog.

I selected the four studies listed as Key References below to highlight Shantelle’s work and raise questions about separating assumptions or hypotheses from scientific facts.

In the decade following the first report that meconium was not sterile, many studies, including Shantelle’s from University of Capetown, continue to document bacteria in meconium of healthy babies that differ from their mother’s microbiota (gut, milk, skin, vagina) and from subsequent fecal samples from the same babies sampled weeks after birth. Journalist Cassandra Willard (2018) quotes scientists on both sides of the debate.

For more than a century, generations of humans believed the ‘dogma of a sterile womb’ and now consider that detection of microbes in amniotic fluid, placenta, and meconium in multiple studies represents ‘sloppy science’ or contamination. The assumption of sterility seems largely based on the limitations of traditional microbiology. Apparent sterility may reflect our lack of knowledge about what microbes are present and how to grow them in pure culture media, in test tubes and on agar plates. Thus, our inability to provide optimal nutrient and culture conditions for the unknown microbes present in healthy humans perpetuates the myth that microbes are absent.

The game changer for microbiologists in the 21st century is the ability to rely not just on growing single microbial species in pure culture, but to also apply sophisticated new tools and methodologies (including genomics, metagenomics, metabolomics) to detect our trillions of microbial partners in the human microbiome and determine their functions in complex communities within and outside the human body. This report by an American Academy of Microbiologists colloquium is written for a wide audience and conveys the beauty and complexity of the human microbiome and its influences on our health and well being.

Microbiologists coined the term ‘Microbiome Revolution’ because these new methods for analyzing whole communities of microbes are providing startling insights, radically different from what could be learned from traditional culturing of individual microbes. Researchers around the world are applying these new methods in controlled studies that are generating evidence of microbes transferred from mother to baby in breastmilk, and likely in the womb as well.

The study by Pannara and colleagues analyzed microbiome data from 107 mother-infant pairs sampled over time. During the first 30 days of life, 15% of bacteria in infant feces were mapped to breastmilk, and 6% to maternal skin. This study did not sample meconium or environmental microbes as a source of the infant fecal microbiota. However, microbes in the environment are associated with infant microbiota as demonstrated in a study cited by Dietert (2018); the microbiota of infants from 36 mothers treated with intrapartum antibiotics were enriched in environmental strains typical of hospital environments and associated with inflammation. Antibiotics and other drugs affect not only humans, but also their microbiota and their babies, potentially increasing risk of infectious disease and inflammation.

The study by Stinson and colleagues points out significant technical challenges with microbial analysis of meconium. They note that the International Human Microbiome Standards consortium provides two standardized methods for extracting microbial DNA from feces, but no standardized or optimized method for extracting DNA from meconium, a unique substance. Meconium has a tar-like consistency, is difficult to dissolve for analysis, and has high concentrations of inhibitors that interfere with extraction and analysis of DNA. Unlike feces that contain waste products from digestion, meconium includes no digestion products, rather bile acids, pancreatic secretions, human epithelial cells, and residue of swallowed amniotic fluid. The Stinson study tested a set of meconium samples using 5 different DNA extraction kits and procedures, and the choice of extraction kit greatly impacted the ability to extract and detect bacterial DNA from meconium. Some of the conflicting studies in the literature are likely explained by methods not optimized for meconium.

Past assumptions and hypotheses based on what we thought we knew about microbes from culturing are being overturned and updated as 21st century biology and medicine advance. The assumption of sterility of the womb may be disproved once methodology issues are resolved, just as the assumption that human breast tissue was sterile is now rejected.

Why would nursing mothers be interested in learning more about the human microbiome including genes from our microbial partners, the ‘Microbiome Revolution’, and the breastmilk microbiota? Learning about the benefits of our microbiome and microbiota can inform the choices that you make for yourself and your baby to live healthy lives. The work of my colleague Rodney Dietert, an immunotoxicologist at Cornell University in upstate NY, provides opportunities to consider more holistic, ecological approaches to health of infants, children, and adults. These two books are recommended for your reading.


If you live in upstate NY, plan to join the Upstate NY Society for Risk Analysis (SRA) for a lecture and discussion at Cornell University on Tuesday afternoon, October 23rd in Lecture Hall 2 of the College of Veterinary Medicine from 4:30 - 6 pm. Rodney will present highlights of his 2018 paper in the pediatric journal NeoReviews listed below in Key References. SRA President-Elect Katherine McComas, a renown risk communication researcher at Cornell, will serve as rapporteur. More information on this event will be available on this blog, on Facebook, and at the Upstate NY SRA website.

Why would risk practitioners and decision makers be interested in these scientific advances in knowledge of our microbial partners? As assumptions of sterility for breast tissue and the womb are being challenged by 21st century science, risk communicators acknowledge that germophobia, based on emotionality and fear of microbes as germs, grossly oversimplifies the evidence. The 20th century assumptions of health benefits for sterile air, food, and water are certainly not supported by scientific studies conducted in the past decade. Guidance and policies about health of our milk and our babies based on fear of microbes naturally present do not serve public good or promote healthy living. Unbiased risk practitioners emphasize that emotionality is best balanced by processes that engage all those with a ‘stake’ in the decisions (stakeholders, including skeptics from all positions) and build trust and fairness (other key elements of risk communication) by open, objective public deliberation of the evidence for both benefits and risks of microbes.

I invite you to follow and subscribe to this blog (It’s free!) to continue to learn more about the microbiota all around us, with emphasis on fresh unprocessed (raw) and pasteurized milks from humans and cows.

Key References