Scientific advances in genetics over recent years mean that we know a lot more about the microbes that live in and on us in their trillions.
Many countries have invested a lot into research toward understanding the interactions within the human body's ecosystem and their relevance to health and disease.
The two terms microbiota and microbiome are often used to mean the same thing - you will often see them used interchangeably. There is a subtle difference between the meanings, however, and so this article will distinguish between the two.
Here are some key points about the human body's microbial populations. More detail is found in the article.
- The human microbiota is made up of trillions of cells - including bacteria, viruses and funguses - and they outnumber our own cells tenfold.
- The biggest populations of microbe reside in our gut - the gut microbiota. Other habitats include the skin.
- The microbial cells - and their genetic material, the microbiome - live with us in an innate relationship that is vital to normal health, although some species are also opportunistic pathogens that can invade us and cause disease.
- The microorganisms living inside the gastrointestinal tract - also known as the gut flora - amount to as much as 4 pounds of biomass, with every individual having a unique mix of species.
- The microbiota is important in nutrition, immunity and effects on the brain and behavior. It is implicated in numerous diseases when the normal individual balance of microbes is disturbed.
What are the human microbiota and microbiome?1-3
The human microbiota comprises the populations of microbial species that live on or in the human body - the commensal bacteria, viruses and funguses (and other single-celled animals such as archaea and protists) that call our bodies home.
Each of us harbors anywhere between 10 trillion and 100 trillion microbial cells in a symbiotic relationship that, in the normal healthy state, suits both them and us. Estimates vary, but there could be over 1,000 different species of microorganism making up the human microbiota.
All of the genes inside these microbial cells, meanwhile, are what constitute the microbiome.
In a similar way to deciphering the human genome - by sequencing all of our genes - the microbiome has been subject to intensive efforts to unravel all its genetic information.
The following video about the human ecosystem has been produced by the Genetic Science Learning Center of the University of Utah, Salt Lake City.
It is a good introduction to the various habitats for different types of microbe in and around our body, including the differences between the dry environment of the forearm and the wet and oily environment of the armpit.
The total of microbes in the human microbiota may be highly numerous in terms of cell numbers and species, but the microbes are so small that, while they outnumber human cells, they make up only about 2-3% of our total body weight.
Ongoing research over the past decade has elucidated the genetic diversity of these communities, which varies according to site.
A study published by the Human Microbiome Project Consortium in the journal Nature in 2012 found that:
- Samples of mouth and stool microbial communities are particularly diverse
- In contrast, samples from vaginal sites show particularly simple microbial communities.
The study characterized the great diversity of the human microbiome across a large group of healthy Western people but asks numerous questions that may be answered by further genetic research. How do microbial populations within each of us vary across our lifetimes, and are patterns of healthy colonization mirrored by disease-causing microbes?
"How large a role does host immunity or genetics play in shaping patterns of diversity, and how do the patterns observed in this North American population compare to those around the world?" the authors write. Some answers are provided by more recent findings covered on page 2.
This paper in the September 2015 issue of the journal Endocrinology looked into the question of whether "disruptions to the vaginal ecosystem could be a contributing factor in significant and long-term consequences for the offspring."
Bacterial populations in the eyes of contact lens wearers were more typical of the eyelid skin flora than of the eye surface of non-lens wearers' eyes in this research presented in May 2015.
Why is the human microbiota important?4-10
The microorganisms that have evolved alongside us and form such an integral part of human life perform a range of roles. They are implicated in both health and disease, and research has found links between our bacterial populations, whether normal or disturbed, and the following diseases:
Microorganisms such as bacteria are vital for health as well playing roles in disease.
- Celiac disease
- Heart disease
- Multiple sclerosis
The human microbiome has an influence on the following four broad areas of importance to our health: nutrition, immunity, behavior and disease.
In addition to helping themselves to energy from the food we eat, gut microbes are essential to the availability of nutrients for ourselves. Gut bacteria help us break down complex molecules in meats and vegetables, for example. Without the aid of gut bacteria, plant cellulose is indigestible.
Gut microbes may also have an influence on our cravings and feelings of being full after eating via their metabolic activities.
The diversity of our microbiota is related to the diversity of our diet, and adolescents trying out a wide variety of foods display a more varied gut microbiota than adults who follow a distinct dietary pattern.
Without contact with the microorganisms that colonize us from birth, our adaptive immunity would not exist. Adaptive immunity is the part of our immune system that learns how to respond to microbes after first encountering them, enabling a more rapid defense against disease-causing organisms.
Scientists have found profoundly ill effects in germ-free rodents - rodents that are sterile of microorganisms - and an underdeveloped immunity is among them.
The microbiota also has relevance to autoimmune conditions and allergies, which can be more likely to develop when early microbial exposures are disturbed.
Scientists have found intimate relationships between the brain and the gut microbiota.
Because of its involvement in digestion, the microbiota can also affect the brain. Some have even called the gut microbiota a "second brain."
Small molecules released by the activity of gut bacteria trigger the response of nerves in the gastrointestinal tract.
Links have also been observed between the gut microbiome and brain disorders such as depression and autistic spectrum disorder (ASD).
Gastrointestinal bacterial populations have provided insights into gut conditions such as the inflammatory bowel diseases (IBD) of Crohn's disease and ulcerative colitis. Low diversity in the gut microbiota has been linked to IBD as well as obesity and type 2 diabetes.
The nature of the gut microbiota has been linked to metabolic syndrome, and dietary modification has shown an effect on this cluster of risk factors via prebiotics, probiotics and other supplements.
Gut microbes and their genetics affect our energy balance, and brain development and function. As a result, research into the effects of gut microbes on the developing brain and diet-related disorders is ongoing.
Antibiotic disturbance of the microbiota can lead to disease, including the emergence of infections that display antibiotic resistance.
The innate microbiota also plays an important role in resisting intestinal overgrowth of externally introduced populations that would otherwise cause disease - the "good" bacteria compete with the "bad," with some even releasing anti-inflammatory compounds.
What is the gut microbiota?5,11
In 1996, Dr. Rodney Berg of Louisiana State University's microbiology and immunology department wrote about the gut microbiota, summing up its "profound" importance at a time when it was termed the microflora of the gut.
"The indigenous gastrointestinal tract microflora has profound effects on the anatomical, physiological and immunological development of the host," Dr. Berg wrote, in a paper published in Trends in Microbiology.
The paper adds:
"The indigenous microflora stimulates the host immune system to respond more quickly to pathogen challenge and, through bacterial antagonism, inhibits colonization of the GI tract by overt exogenous pathogens."
This symbiotic relationship is of benefit to us, and the presence of this normal flora includes microorganisms that are so ubiquitous in our environment that they inhabit practically all animals from the same habitat.
However, these native microbes also include harmful bacteria that, as Berg puts it, "can translocate across the mucosal barrier to cause systemic infection in debilitated hosts."
In summary, there are beneficial bacteria in the gut and there are harmful bacteria that can cross into our wider body systems and can cause local infections of the GI tract. These infections include food poisoning and other GI diseases that result in diarrhea and vomiting.
The gut microbiota:
- Comprises tens of trillions of microbial cells, collectively weighing up to 2 kg (4.4 pounds)
- Is host to hundreds of different bacterial species - over a thousand have been identified
- Contains over 3 million genes - the gut microbiome has 150 times more genes than the human body does
- Is unique to each person - we all share a third of the microbes present, but the rest constitute our individual microbiota.
New findings on the microbiome7,10
Huge investment has gone into research about the body's microbial populations and their genetics, exploring links with health and disease.
The National Institutes of Health (NIH) launched the Human Microbiome Project in 2007, a research project that aims to characterize our microbial species and their relationships to health by producing large, publicly available datasets from genetic studies.
Europe and China have also collaborated to launch a similar program, the Metagenomics of the Human Intestinal Tract project (MetaHIT). In 2013, another Europe-funded project was launched, dubbed MyNewGut.
Most of the microorganisms living with us are found in the gastrointestinal system, and this is also where most new discoveries are being made. Key examples are listed under the following recent developments.
This recent paper reviews the way in which diseases such as type 2 diabetes, obesity and inflammatory bowel disease (IBD) may be linked to reductions in the richness of the gastrointestinal microbiota.
A study published in February found that maternal obesity did not influence the child's gut microbial diversity and that solid foods became the major influence once an infant reached 9 months old.
Changes in gut bacteria could lead to earlier diagnosis of type 2 diabetes, according to findings from identical twins published in Genome Medicine in February 2016.
A study published in November 2015 underlines the need to use antibiotics only when strictly needed.