The human microbiome

Definition

The term ‘human microbiome refers to the complete set of genes contained in the entire collection of microorganisms that live in the human body.

Importance

Trillions of symbiotic microbial organisms live in and on the surface of the human body. They can be found in and on nearly every part of the body, including the gut, brain, ear, skin, nose, the oral, gastrointestinal, respiratory, urinary and vaginal tracts and the bloodstream. Their genes are now thought to contribute more to human survival than the genes of the human. Such genes, the human microbiome, are, for example, pivotal to the process of aging, digestion, the immune system, the modulation of the central nervous system, and a person’s mood and cognitive ability. This makes the human microbiome an essential organ in the human body. Without it the human body cannot function.

Our microbial community, known as the human microbiota, is made up of bacteria, yeasts and other Eukarya, archaea (primitive single-cell organisms), fungi, protozoa and non-living viruses (bacteriophages). Bacteria comprise the vast bulk of the microorganisms that inhabit our bodies. These are the most studied microbes so far. More than 10,00 bacterial species are estimated to live in the body. According to researchers from the Human Microbiome Project the ratio of bacterial protein-coding genes to human genes is 360:1.(1) The vast majority of the bacteria dwell in the gut. These bacteria play a critical role in the breakdown and absorption of nutrients, help break down starches, sugars and proteins that humans cannot otherwise digest and synthesise essential amino acids and vitamins. They also play a part in fat storage and the production of anti-inflammatory factors.

In addition to the abundance of bacteria, the human microbiota contains a large variety of viruses, including plant derived viruses, eukaryotic viruses and giant viruses. Bacteriophages, or phage for short, are some of the most prevalent viruses. They are a type virus that infects bacteria. Helping to shuttle genes from one bacterium to another, bacteriophages are instrumental to the genetic modification of bacteria, a process that can in turn modify humans. Overall, viruses play an important role in the dynamics of the ecosystem of the microbial community, helping, for example, to enhance microbial resilience to disturbances, immune evasion, maintenance of physiological processes. In addition, they are important to the promotion and prevention of pathogen colonisation.

No human has the same microbiome. It is as unique as a person’s fingerprint. The human microbiome, however, is a dynamic system that alters over the course of a person’s life. Some of the most dramatic changes occur during a person’s infancy and early childhood. Environmental factors and lifestyle habits, such how often a person washes, what they eat, type of clothing they wear, how much time they spend outside, who they interact with and where they live also determine the composition of person’s microbiome. Antibiotics consumption also affects the microbiome.(2)

The human microbiome is now a hot research area. Just how much importance is attached to the area can be gauged by the US$170 million the National Institutes of Health dedicated to the Human Microbiome Project (HMP), set in 2008 and completed in 2017. Research on the human microbiome gained so much momentum in the wake of the HMP that venture capitalists are now investing heavily in microbiome companies. Venture capital investment in such companies grew by 458.5%, to US$114.5 million between 2011 and 2015. This contrasts with venture investment overall for this period which only grew 103.4%, to $75.29 billion. Microbiome investment continued to grow in 2016. By September 2016 microbiome companies had raised US$ 616.9 million in venture capital. Many pharmaceutical companies, including Pfizer and Roche, are also strongly investing in the area.(3, 4) Microbiome companies range from research-based firms that specialise in the collection of data for potential partnerships with pharmaceutical companies to those that develop microbiome drugs, devices, probiotics and prebiotics. Some companies also provide direct-to-consumer services in the way of microbiome sequencing. Together these companies are becoming an important sector in the biotechnology industry.

Discovery

The diversity of the human microbiome was first observed by Antonie van Leewenhoek, a Dutch merchant. In the early 1680s he noted a striking difference between microbes found in samples taken from the mouth versus those in faecal stools. This was based on samples he took from himself and collected from healthy and sick family members, which he examined under a microscope.(5,6) Reflecting the prevailing attitude at the time that disease was associated with bad smells or the equilibrium of a person’s humours, van Leewenhoek did not make any connection between the microbes and health.

It would take another two centuries before scientists began to understand the link between microbes and disease. This was fueled by the work of Louis Pasteur, a French chemist, and Robert Koch, a German physician, who initiated the development of new tools for growing and studying microbes in relation to infectious disease during the late 19th century. The science of medical microbiology was greatly aided by the creation of shallow lidded dishes (the Petri dish) and adoption of agar, a solid growth medium, which together transformed the process for cultivating bacteria in the laboratory. A number of techniques were also developed in this period for growing viruses, including their cultivation in fertile hen eggs, introduced in 1898. Alongside the advances made in the cultivation of microorganisms, their identification also became easier with improvements to the magnification of microscopes.(7) The process of identification was also helped by the emergence of new staining techniques. Previously organisms had been characterised by studying their shape and movement.(8)

The very first link made between a specific organism and a particular disease was made by Koch. In 1876 he demonstrated that Bacillus anthracis, a type of bacteria, was responsible for anthrax, a deadly disease. He went on to determine the microbial causes of two other infectious diseases - tuberculosis and cholera. By 1930 microbiologists had worked out that bacteria were the cause of more than a dozen diseases. This included those that were responsible for gonorrhea, dysentery and whooping cough.(8)

Researchers were not confined to identifying disease-causing microorganisms. Some also explored the interrelationship between non-pathogenic microorganisms and the host.(9) As early as 1901 Eli Metchkinoff, a Russian zoologist and immunologist, pointed to the possibility of using living microbes (probiotics) to enhance intestinal microbiota so as to promote good health.(10) Soon after this Arthur I Kendall, an American bacteriologist, began investigating normal intestinal flora and the conditions they needed to maintain and reproduce themselves. In 1909 he showed the effect of diet on the composition of intestinal bacteria in monkeys and the impact this had on their health.(11)

The characterisation of microorganisms remained a labour intensive process and beset with difficulties for much of the early twentieth century. One of the key problems was the fact that most staining techniques could only distinguish broad groups of bacteria. The only way to identify a specific species was to culture a sample. Detection was done by placing samples on a plate and assessing their growth on different culture media, the morphological characteristics of colonies and an organism's metabolic production or consumption. Given that only a handful of species could be easily grown in the laboratory, this approach was severely limited. Furthermore, the number of organisms in a sample counted under the microscope never matched the number of colonies grown on an agar plate.(9, 11)

A new chapter opened up for studying microbes in the 1950s with the development of germ-free animals.(8) These are animals carefully removed from their mother’s womb, using surgery to avoid contact with microorganisms in the mother’s vagina and skin, and then raised in a sterile environment with sterile food and water. Once created a germ-free mother will give birth to naturally germ-free offspring. With germ-free animals scientists now had the means to study host-microbe and microbe-microbe interactions through the deliberate introduction of selected microorganisms or microbial populations into the animals.(8)

One of the first microbiologists to take advantage of germ-free animals was Rene Dubos at the Rockefeller Institute for Medical Research (later renamed Rockefeller University). By the mid-1950s he had come to the conclusion that not all microbes living in the body were harmful and were part of a well-defined ecosystem and that it took certain conditions to transform microbes into virulent pathogens that cause disease.(12) This was informed by his earlier research to understand the mechanisms of immunological resistance to tuberculosis. Because microbes can inhibit and enhance each other’s growth and behaviour, Dubos emphasised the need to go beyond studying each microbe in isolation and to look at the whole ecosystem. This meant looking at how different organisms communicate with each other and interact with and alter the environment. With most microbes still unknown, this was not an easy task.(8)

From the late 1950s Dubos began a series of experiments with colleagues that involved introducing different mixtures of bacteria into previously germ-free mice to study how they each colonised the gut. This required the team devising new quantitative techniques to count the anaerobic bacterial flora in the gut and a new culture media to grow specific intestinal bacteria.(8, 13) By the mid-1960s Dubos’ group had discovered many different indigenous flora in the gut. Many of the microbe species they showed were far from accidental or inert intruders as researchers had previously assumed. Indeed, they appeared to be essential to the physiology and health of the gastrointestinal tract. The Dubos laboratory also demonstrated there to be an important relationship between diet, stress and antimicrobials in the health and growth of the microbes, which in turn had multiple effects on the health of the host. For example, germ-free female mice that were fed a low quality protein diet during their prenatal period were found to produce offspring with low levels of dopamine and norepinephrine in their brains.(14, 15)

Investigating human microbiota was made immeasurably easier by the arrival of DNA amplification and sequencing techniques in the 1980s. These made it possible to characterise microbes based on their genetic profile without having to first culture the organism in question. Research in this area was also aided by the adoption of ribosomal RNA genes as molecular markers in the mid-1980s, pioneered by Carl Woese and Norman Pace. The markers provided the means to define the evolutionary relationships between microbial communities. Armed with the new techniques, scientists now had the ability to more accurately characterise and quantify what types of microbes were present in any given community and determine their biological functions for the first time. Such work was boosted by the introduction of new sequencing machines from the late 1990s. These increased the capacity for DNA sequencing and sped-up and reduced the cost of the process. The coevolution of computational tools also opened up the ability to analyse the ever-increasing amount of data generated. By 2005 DNA technology had advanced so much that most scientists could now economically and efficiently sequence the DNA of an entire microbial community in a sample. This helped shift research away from examining the properties of single types of organisms in isolation to looking at the whole network of entire communities.(8, 16)

A new phase for understanding the human microbiome opened up with the creation of the Human Microbiome Project in 2007. This was a series of coordinated projects that were launched by a consortium of nearly 80 universities and scientific institutions from different parts of the world. Funded by NIH, the Project was designed to understand the microbial components of the human’s genetic and metabolic landscape and their role in a person’s normal physiology and susceptibility to disease. By 2012 HMP researchers had worked out the normal composition of bacteria in a healthy Western population. This involved the purification and analysis of all human and microbial DNA in 5,000 samples taken from the mouth, nose, skin, and vaginal sites of 242 healthy American volunteers. The was a huge undertaking that could not have been achieved without the sharp reduction in the cost of sequencing DNA. Overall the researchers managed to identify 81 to 99 per cent of the more than 10,000 microbial species calculated to inhabit the human ecosystem. Their achievement was remarkable given that only a few hundred bacterial species had ever been isolated before.(1)

HMP researchers also conducted a number of studies to look at the link between the microbiome and disease. One found that the diversity of bacterial species decreased dramatically in a woman’s vagina in preparation for birth. Another showed a fivefold increase in viral DNA in nasal samples taken from children with fevers compared to children without fevers. A number of projects were also undertaken to investigate the relationship of the microbiome in specific disorders, including Crohn’s disease, ulcerative colitis, esophageal cancer, acme, psoriasis, atopic dermatitis and immunodeficiency.

In 2014 the NIH funded a second phase of research, called the Integrative Microbiome Project, designed to deepen the understanding of how the microbiome affects disease. This is directed towards understanding the role of the microbiome in pregnancy and preterm birth, inflammatory bowel disease and type 2 diabetes.

Application

Studying the human microbiome is helping researchers to understand how the body responds to different diets, diseases and drugs. Such work is seen as an important key to personalised medicine. Most of the work on the human microbiome todate has concentrated on microorganisms - particularly bacteria - that live in the gut.

Some of the earliest impact of the research was seen in the treatment of chronic gastritis, a condition that if left can cause duodenal ulcers and stomach cancer. In 1982 the Australian scientists Barry Marshall and Robin Warren showed that the presence of Helicobacter pylori, a type of bacteria, in the stomach could cause chronic gastritis. Their finding ended decades of medical teaching that bacteria could not live in the acidic environment of the stomach and the belief that peptic ulcers were caused by stress, spicy foods and too much acid. Marshall demonstrated the link by drinking a broth containing Helicobacter pylori. He developed symptoms five days later. Thanks to this work peptic ulcers can now be treated with a short course of antibiotics and acid secretion inhibitors.

Another area where the microbiome has proven important has been in the treatment of patients infected with Clostridium difficile, a type of bacterium that can take over a patient’s gastrointestinal tract when antibiotics reduce or eliminate resident microbes. Some patients will recover from the infection once they stop taking antibiotics. Many, however, many do not and about 20% of those who recover go on to have recurrent infections. This is a serious problem because C. difficile infections (CDI) can result in severe diarrhoea and dehydration, and is a major cause of morbidity and mortality in the elderly and in immunocompromised patients.

A number of methods have now been developed for dealing with CDI. One involves the transfer of fecal material from a healthy donor into a patient. This approach was first used to treat a patient with pseudomembranous colitis in 1958,(19) but was not adopted on a wide-scale until the 2000s when the number of patients suffering CDIs reached epidemic proportions and microbial sequencing had taken off. The treatment aims to increase the diversity of the intestinal flora and alter the activity of their metabolic pathways so that the patient can resist attack by C. difficile bacteria. The use of fecal microbiota transplantation in CDI patients became so popular that in 2014 the US Food and Drug Administration issued guidelines to regulate the therapy so as to prevent unscreened and potentially dangerous fecal samples flooding the market. Any donor now has to be screened for pathogens to prevent recipients getting sicker. Most donor material was initially acquired from a patient’s friend or family member which the clinician then processed. Now treatment can be done using donations from stool banks.(20)

In addition to the use of fecal microbiota transplantation, phage therapy is also being explored as a treatment for CDI. One of the advantages of using phages as therapeutic agents is that they are self-replicating and have highly specific interactions with their bacterial hosts. They also have minimal impact on non-target bacteria or body tissue. Phages thus can be used to infect and kill specific pathogenic bacteria. The use of phages to treat bacterial infections in humans goes back for nearly a century.(21) Nonetheless, the method has certain challenges. One of the major problems is finding the right phage for treating CDI. This is difficult because of the diversity of C. difficile bacteria and ever-constant emergence of novel stains in clinical settings.(22)

Over the past twenty years some research conducted by Jeffrey Gordon and colleagues at Washington University in St. Louis has also revealed important connections between between gut microflora and obesity. This was uncovered through a series of experiments with mice. In one study they demonstrated that germ-free mice were more likely to gain weight when given transplants of gut microbes from mice with genetic or dietary obesity than when given gut microbes from lean mice. Another experiment involved transplanting into germ-free mice gut microbes taken from four sets of human twins, each pair with one lean and one obese twin. From this the team found that the mice that received the microbes from obese twins got fat whereas those given microbes from the lean twin did not. This effect, however, only happened when the mice were housed separately. As soon they were housed together, all the mice remained lean, suggesting that the mice that received obese microbes transplants acquired microbes from the lean mice.(8)

A number of human, animal and in vivo studies have also begun to show that gut bacteria can determine how a cancer patient responds to some chemotherapies and immunotherapies. Based on this some clinicians have begun trying to restore the equilibrium of a patient’s gut microbiome wrecked by radiation and chemotherapy by giving them fecal microbiota that was collected from them prior to treatment.(18)

Issues

A plethora of conditions are now thought to be linked to disturbances of gut microflora. This includes not only obesity but also diabetes, autism, anxiety, cardiovascular problems and autoimmune disorders. Most of the work carried out in this area, however, has so far only shown associations rather than cause and effect. Also it is not certain whether such links are due of a secondary effect rather than a direct cause of disease. Drawing conclusions is further hampered by the fact that most of the evidence we now have originates from experiments with germ-free mice rather than with humans.

While challenges remain, research on the human microbiome continues apace. Every year we see unprecedented growth of data collected in this area, aided by advances in whole genome sequencing and the ability to transplant and watch human microbial communities in mice with higher efficiency. All of this is providing greater insights into the human microbiome and with it the means to manipulate it to improve health in the future. Targeted antibiotic use to eradicate select microbes, probiotics and prebiotics to expand beneficial bacteria, the use of fecal microbiota transplants to restore bacterial communities, and the use of genetic modified phages are just some of the methods now being explored for medical purposes.

This profile was written by Lara Marks, September 2018..

References

1) NIH, ‘NIH Human Microbiome Project defines normal bacterial makeup of the body’, (13 June 2012), https://www.nih.gov/news-events/news-releases/nih-human-microbiome-project-defines-normal-bacterial-makeup-body.

2) P Amon, I Sanderson, ‘What is the microbiome’, BMJ: Archives of Disease in Childhood -- Education & Practice Edition, (Feb 2017), DOI 10.1136/archdischild-2016-311643, https://ep.bmj.com/content/102/5/257.

3) B Gormley, ‘Microbiome companies attract big investments’, The Wall Street Journal, 18 Sept 2016.

4) E Branch, ‘New ventures in the microbiome’, Pharma’s Almanac, 8 May 2017, https://www.pharmasalmanac.com/articles/new-ventures-in-the-microbiome.

5) A van Leeuwenhoek, ‘An abstract of a Letter from Antonie van Leeuwenhoek’ Sep. 12, 1683

6) A van Leeuwenhoek, ‘About animals in the scrurf of the teeth’, Philosophical Transactions of the Royal Society of London, 14 (1684), 568–74.

7) M Wainwright, J Lederberg, ‘History of microbiology’, Encyclopedia of Microbiology, vol 2 (1992), https://profiles.nlm.nih.gov/ps/access/bbabon.pdf.

8) JJ Houtman, ‘The human microbiome, Your own personal ecosystem’, FASEB, 24 March 2015, https://www.faseb.org/Portals/2/PDFs/opa/2015/Breakthroughs%20In%20Bioscience%20Human%20Microbiome.pdf.

9) RK Aziz, ‘A hundred-year-old insight into the gut microbiome!’, Gut Pathogens, 1, 21 (2009), http://doi.org/10.1186/1757-4749-1-21.

10) E Metchnikoff, ‘The Wilde Medal and Lecture of the Manchester Literary and Philosophical Society. Br Med J, 1 (1901), 1027–28.

11) AI Kendall, ‘Some observations on the study of the intestinal bacteria’,Journal of Biological Chemistry, 6(1909), 499-507. R K Zzir, ‘A hundred-year old insight into gut microbiome’, Gut Pathology, 1 (2009), 21, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2797815/.

12) M Honigsbaumm, ‘Rene Dubos, tuberculosis, and the ecological facets of virulence’, History and Philosophy of the Life Sciences, 39/3 (2017), 15.

13) F Sangodeyi, ‘Rene Dubos and the emerging science of human microbial ecology’, unpublished paper, Harvard University, 2012, http://rockarch.org/publications/resrep/sangodeyi.pdf.

14) Rene Dubos, Russell Schaedler, and Dwayne Savage, ‘The Indigenous Flora of the Gastrointestinal Tract,’ Disease of the Colon and Rectum, 10 (1966), 23-33. Delivered June 21, 1966, p. 23.

15) R Dubos, RW Schaedler, ‘Some biological effects of the digestive flora’, Am J Med Sci, 244 (1962), 265–71.

16) XC Morgan, C Huttenhower (2012) Chapter 12: Human Microbiome Analysis. PLoS Comput Biol 8(12): e1002808. https://doi.org/10.1371/journal.pcbi.1002808species.

17) J L Alexander, et al, ‘Gut microbiota modulation of chemotherapy efficacy and toxicity’, Nature, 14 (June 2017), 356-65.

18) LM Proctor, ‘The Human Microbiome: A True Story about You and Trillions of Your Closest (Microscopic) Friends’, Action Bioscience, Sept 2013, http://www.actionbioscience.org/genomics/the_human_microbiome.html.

19) B Eiseman, W Silen, GS Bascom, AJ Kauvar, ‘Fecal enema as an adjunct in the treatment of pseudomembranous enterocolitis’, Surgery, 44/5 (Nov 1958), 854-9.

20) B Brookshire, ‘To regulate fecal transplants, FDA has to first answer a serious question: What is poop?’, Science News, 18 May 2018, https://www.sciencenews.org/blog/scicurious/fecal-transplants-regulation.

21) ST Abedon, SJ Kuhl, BG Blasdel, EM Kutter, ‘Phage treatment of human infections’, Bacteriophage, 1/2 (March/April 2011), 66-85.

22) KR Hargreaves, MRJ Clokie, ‘Clostridium difficile phages: still difficult?’, Microbiology (28 April 2014), https://doi.org/10.3389/fmicb.2014.00184.

The human microbiome: timeline of key events

Science links: Science home | Cancer immunotherapy | CRISPR-Cas9 | DNA | DNA extraction | DNA polymerase | DNA Sequencing | Epigenetics | Faecal microbiota transplant | Gene therapy | Immune checkpoint inhibitors | Infectious diseases | Messenger RNA (mRNA) | Monoclonal antibodies | Nanopore sequencing | Organ-on-a-chip | p53 Gene | PCR | Phage display | Phage therapy | Plasmid | Recombinant DNA | Restriction enzymes | Stem cells | Transgenic animals |