The human microbiome and endangered bacteria

Each and every part of us harbours its own microbial ecosystem. This ecosystem carries some 100 billion cells, known as the microbiota. They started inhabiting our bodies 200,000 years ago, and since then we have evolved side by side to configure a balanced system in which microbes can survive in perfect harmony, provided no perturbations occur.

A number of standard methods exist for decoding their identities and genetic content. Sequencing of the 16S subunit of the bacterial ribosome from DNA reveals that there are over 5,000 species of microbes living at one with us, and that only a minor fraction, about 2%, is common to most people. By sequencing this gene from RNA, we know that not all the microbes inhabiting our bodies are active but just one in every five. Sequencing of the microbial DNA or RNA reveals that about eight million microbial genes collaborate with our genes and that only one out of 33 (or 3%) is common to most people.

Our microbiomes and their microbial products configure our innate and acquired immune system. They control the ingress of invaders, with the exception of disease, and regulate our metabolism. Therefore, imbalances in microbial and effector microbial products (genes, proteins, and molecules) may have consequences on our health.

The human microbiome is in constant evolution due to modern practices and natural factors

From birth, we establish an intimate symbiotic relationship with our microbiota. Initially the microorganisms are transferred and the relationship is maintained from one generation to the next through the birth canal. After delivery, the number of bacteria in a person’s microbiome begins to increase while simultaneously beginning to receive external influences. These perturbations may be directly linked to today’s lifestyle or to natural situations. The last 150 years have witnessed modern practices that include antibiotic and medicine intake, caesarean-section births or diets, alongside issues related to aging, confrontation with pathogens or illnesses. These factors, and many others, may have strong impacts on our microbes, even though they are highly resilient to changes. These impacts must be investigated in order to answer the question of whether changes in our microbiota are the cause or the consequence of a certain health status.

Microbes form part of us and are affected just as we are

It is highly likely that our bodies and our microbes are constantly adapting to new environments and situations together. Thus, we evolve to reach a balanced situation in which beneficial microorganisms, which keep us healthy, are favoured while pathogens are controlled.

Not all microbes are affected equally during perturbations

We have recently listed different factors (diseases, antibiotics, and others) reported to produce alterations in the microbes inhabiting our innards. They include at least 105 common or rare diseases or disorders, 68 antibiotic treatments either as a single antibiotic or cocktails, and 22 other types of factors. Illnesses produce alterations in 231 out 5,000 bacterial species inhabiting our body; antibiotics in 42 species; and other types of factors such as alcohol or tobacco consumption, medicines, and diet, to mention but a few, affect 130 species. Not all the microbes inhabiting our organism are influenced equally; however, all perturbations have one thing in common: they affect a group of bacteria essential for our bodies to work properly. These include the well-known Bifidobacterium, Lactobacillus, and Faecalibacterium, which should be considered as among the most super-sensitive species.

A step towards resolving or avoiding microbial imbalances that relate to disease and health

A growing amount of evidence has demonstrated the correlation between microorganisms that commonly keep us actively healthy, which are highly vulnerable. Thus, future actions in medicine should consider not only our protection but also prevention of the negative influences wrought by today’s lifestyle, modern practices, and other natural factors on our microbes. Options include the design of new probiotic foods enriched in some of these bacteria, special diets, or therapies favouring their growth.

Featured image credit: dna-microscopic-cell-gene-helix by typographyimages. CC0 Public Domain via Pixabay.