Biome 101 | Microbiome Report

BIOME FACTS

The microbiome is defined as all the bacteria, viruses, fungi, archaea, and eukaryotes that inhabit the human body. Collectively referred to as the “second human genome”.

The gut microbiome in particular is now being considered a separate “organ” with distinct metabolic and immune activity.

The two major areas of microbiota investigation include taxonomic diversity to identify “who” is there and functional metagenomics to figure out what they are doing.

There are 10x the number of microbial cells in the human gut than in the whole human body, totaling roughly 100 trillion microbes representing as many as 5,000 different species and weighing approximately 2 kilograms

Until the entry of next generation sequencing in 2005 and the birth of metagenomics, the ability to measure the vast community of microbiota in the human GI tract was not possible since most of the bacteria which reside in the gut are anaerobic and unable to be grown via culture

Our understanding of the “normal” microbiome patterns, including what constitutes a healthy versus diseased pattern is still in its infancy. Only a few associations have been established in human studies thus far.

The Human Microbiome Project, funded and directed by the NIH from 2007-2015 and the American Gut Project are the two major studies in the US aiming to characterize the composition and diversity of the human microbiome and establish a dataset library of human microbial communities. For a fee of $99, anyone can participate in the American Gut Project to get their gut microbiome sequenced http://humanfoodproject.com/americangut/.

Though once thought that the fetal intrauterine environment and GI tract were sterile, the evidence of microbes in meconium suggests that the microbiome may develop sometime during fetal development.3 The neonatal microbiome is further influenced by delivery type (vaginal versus C-section) and feeding type (breast milk versu formula) and continues to develop until age 2-3 years when the gut micobiota stabilizes and resembles that of adults.

Antibiotic therapy alters the patterns of gut microbiota and when given early in life (infancy and childhood) may shift the bacterial profile towards one that promotes obesity, metabolic abnormalities and/or autoimmune diseases. This relationship is seen in livestock animals given low-dose antibiotics to enhance growth and weight gain, so this relationship in humans is also being explored.

“Normal” gut microbiota in healthy persons include such pathogenic strains as E. coli and Enterococci – but as of yet, there is no clear distinction of which are the good versus the bad bacteria,4 or if some have both roles.

Gut bacteria are involved in harvesting energy from food, balancing the good versus bad bacterial composition, manufacturing neurotransmitters such as serotonin, enzymes and vitamins like vitamin K and are involved with immune and metabolic functions.

The gut microbiome of Americans and most other Westernized, industrialized populations is less diverse and dominated by different bacterial species than that of people from rural, less developed populations. Diet plays a role, but a general shift away from natural environments with little exposure to soil, animals, and other environmental microbes seems to be impacting the gut microbiome in potentially detrimental ways. Children raised in homes with pets have less risk of allergic diseases and new evidence is demonstrating a link with gut microbiome patterns. Exposure to dogs seems to alter the gut microbiome to be protective against allergic airway issues and respiratory viruses.5 So, Lucy was wrong and a dog kiss a day may help keep bad things away!