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Dutch Journal of Medical Microbiology Publishes uBiome Science Editor’s Most Recent Microbiome Paper

uBiome, the leading microbial genomics company, is delighted to report the publishing of the latest paper by its Science Editor, Dr. Elisabeth Bik, in the December 2016 issue of the Dutch Journal of Medical Microbiology (Nederlands Tijdschrift voor Medische Microbiologie). Dr. Bik joined uBiome in October 2016 from her previous position at Stanford University School of Medicine and is also editor of the respected daily Microbiome Digest. Her paper, "Friends for Life: Human Microbiota," provides a comprehensive review of the state of the human microbiome.

The review begins by paying credit to Dr. Bik’s fellow countryman, 17th century Dutch scientist Antonie van Leeuwenhoek, who first discovered microbes using his homemade microscopes. Although microbiology began with van Leeuwenhoek, and flourished during the subsequent three centuries, for much of that time, bacteria and viruses were considered mainly pathogenic, largely because of their association with diseases such as cholera, tuberculosis, and smallpox. It has only been fairly recently that we have appreciated how the human body accommodates communities of thousands of different species of microorganisms (mostly living in the large intestine), many of which make important contributions to healthy living.

Dr. Bik’s paper points to a spectacular rise in the number of microbiome research studies over the past twenty years, thanks largely to significant advances in DNA amplification and sequencing techniques. This has led to the possibility of sequencing the complete genomic DNA in a sample, enabling the study of all the genes and their functions (metagenomics), in the process underpinning two large-scale studies of the microbiome: the US Human Microbiome Project and the European MetaHit studies.

The article goes on to recognize that human microbial colonization begins at birth, with the method of delivery making important differences in the microorganisms that an infant encounters. During natural birth, a baby is first exposed to bacteria from its mother’s vagina and rectum, whereas in a Cesarean section, the baby’s first contact is with skin bacteria. Early feeding also influences the microbiome. Breast milk contains bacteria, but formula feeding is sterile. As found in both methods of childbirth and a diet including breast milk, there is evidence that exposure to a certain amount of bacteria in early life is actually beneficial in terms of later health.

Dr. Bik reminds us that the gut microbiome is of significant importance to health. For example, the body itself cannot process important dietary plant carbohydrates and fibers, so it is our intestinal bacteria that take on the task of fermenting and processing them. Our microbes also enable energy extraction. Although germ-free mice eat 30 percent more food than mice with a conventional microbiome, Dr. Bik says they remain thinner. There are also indications that the gut microbiome communicates with the central nervous system through a “Gut-Brain Axis.”

On average, American infants are prescribed between three and six courses of antibiotics before the age of three, precisely at a time when their microbiome are developing. Dr. Bik’s paper explains that broad spectrum antibiotics can permanently damage the microbiome, suggesting that medical practitioners could become increasingly reluctant to prescribe them.

One of the great successes of microbiome research has been the treatment of Clostridium difficile infections using fecal transplants, transferring stool from healthy donors into diseased patients. Statistics show a success rate of over 80 percent after a first treatment, rising to 94 percent after a second procedure.

Dr. Bik reviews ongoing work that investigates possible links between the gut microbiome and autism. Autistic children often have gastrointestinal problems such as diarrhea or constipation, but Dr. Bik’s paper explains that many microbiome/autism papers unfortunately seem to contradict each other. Despite the discrepancies in scientific research, some parents are “self-medicating” their autistic children using fecal transplants.

The paper concludes by suggesting that our lives may be becoming over-sterile, leaving us with low diversity in our gut microbiomes and ill-equipped to support healthy life. We might do well, therefore, to consume more fermented foods and probiotics. Walks in the countryside or garden, or play in sandboxes, would also be beneficial. Better knowledge of the individuality of the human microbiome may also lead to the development of personalized medicine.

Dr. Jessica Richman, CEO and co-founder of uBiome, says: “As one of the world’s leading experts on microbiome research, Elisabeth is a brilliant scientist. She maintains a terrific overview of the science of the microbiome and we’re excited about her most recent work.”

Dr. Zachary Apte, CTO and co-founder of uBiome, adds: “Elisabeth has done a superb job in summarizing both progress in, and prospects for, microbiome research. Her remarkable energy in sifting through enormous volumes of research every day knows no end. Her paper should be celebrated for both its range and clarity.”

Founded in 2012, uBiome is the world’s leading microbial genomics company. uBiome is funded by Y Combinator, Andreessen Horowitz, 8VC, and other leading investors.

uBiome’s mission is to explore important research questions about the microbiome and develop accurate and reliable clinical tests based on the microbiome.

Dr. Bik’s paper in the Nederlands Tijdschrift voor Medische Microbiologie is available online:

Visit the uBiome Blog to read an English translation of the paper:

Julie Taylor
Ph: +1 (415) 212-9214

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