REVIEW ARTICLE

Human Health and the Microbiota: Interactions

Between Gut Microbes, Hygiene, and The
Immune System
Simon Fukada1*
1

Department of Biology and Technology Mount Royal University, Calgary, Alberta, Canada

*Email Correspondence:
Sfuka591@mtroyal.ca

Keywords:
Helper T cell (Th): Type of lymphocyte that via
cytokines activates parts of adaptive immune
system
Cytokine: proteins secreted by immune cells
Interleukin (IL): Type of Cytokine
T regulatory cell (Treg): Type of T cell which
regulate immune responses
Xenobiotics: unnatural substance found in an
organism
Eosinophil: Type of immune cell that targets
parasites and contributes to allergic disease
Dendritic Cells: Antigen presenting cell
Antigens: Substance that may induce an immune response

Abstract
Background: In the past, much of the scientific research on microbes focused on mechanisms
of infection and disease. This was not in vain, as we gained valuable knowledge about our
immune system, as well as the ability to develop vaccines and antibiotics. However, the
relationship between humans and microbes is complex. These species have been co-evolving
since multicellular organisms evolved on Earth.
Summary: Recently, it is beginning to be appreciated that the majority of relationships between
humans and microbes are beneficial. From this follows an understanding that beneficial
microbes are vital to the normal physiological development of our gut and immune system. This
beneficial relationship between the human host and the multitude of microbial communities
is well established. However, currently in the developed world epidemiological studies are
showing dramatic increases in autoimmunity, allergies, and obesity. It is thus suggested that
within westernized societies hygiene is altering the relationship between the gut and the
human host in a way that makes humans susceptible to conditions not seen in less developed
countries. This understanding advanced the hygiene hypothesis, and more recently the, old
friends hypothesis and disappearing microbiota hypothesis as possible explanations for the
observed epidemiological phenomena. What follows is a review of the relationship between gut
microbes and the hosts immune system, with a focus on how hygiene (antibiotics, chlorination
of water, etc.) is beginning to alter this relationship. This review concludes that a further
understanding of how hygiene affects the relationship between humans and microbes will be
crucial for developing effective therapies considerate of our microbial friends.

Introduction
Bacterial life inhabited earth billions of years before humans evolved.
Therefore, it is well accepted that during the evolution of complex
multi-cellular organisms, the microbial world played a role in influencing the structure and function of humans (1,2). This proposition
is further supported by the evidence that there are an order of magnitude more microbial cells than somatic cells in and on the human
body (3,4). For these reasons, it is common to view the relationship
between the host and most microbes as mutually symbiotic (2,5,6).
The recognized ecologic definition of symbiosis put forth by Anton
de Bary is a prolonged association between two or more organisms of
different species. Mutualistic if both organism benefit and parasitic

56

Fig. 1
This review will explore how
the symbiotic microbes
in our gut, hygiene (e.g.,
increased use of hand
sanitizer, cleaning products,
antibiotics and vaccinations),
and the immune system
interact with each other to
contribute to human health.

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Human Health and the Microbiota: Interactions Between Gut Microbes, Hygiene, and The Immune System

if one is harmed while the other benefits. The relationship is mutually symbiotic in the sense that the microbiota access nutrients not
attainable through host digestive mechanisms and help to guide the
proper development of the hosts immune system (2,3,4,5). In return
the collaborating microbiota gain a safe, nutrient rich ecosystem (2).
Much of the microbiota that consists of bacteria, viruses, fungi, and
other microeukaryotes live symbiotically within the human gastrointestinal tract (2,3,5). Thus, the gut serves as a useful setting to understand the benefits of this symbiotic relationship. In order to maintain
this safe environment it is likely that the gut microbiota evolved to
function closely with our own immune system, which would selectively destroy pathogenic agents and maintain the non-pathogenic
populations (2).
Additionally, the gut microbiota play a vital role in immune homeostasis, or the maintenance of a stable immune system that neither
overreacts or is too passive (5). However, this cooperation between
species can be delicate due to the extreme microbial load present in
the gut. The massive amount of microbes is a constant threat to the
host systemically (7). If a usually symbiotic microbes cost of cooperating becomes higher than the benefit it receives from the host, it has
the potential to become pathogenic and invade systemically (7). Thus,
those with immunodeficient disorders are at risk of infection from
usually symbiotic bacteria, such as, Enterococcus faecalis and Bacteroides fragilis (7). For this reason the immune system must be able to
maintain the balance of many different microbes while not knocking
them out completely (7). The responsibility to differentiate between
pathogens and commensal microbes, and to organize and maintain
the location, in which these microbes inhabit their host, falls to the
hosts immune system (8, 9). The innate immune system seems to be
primarily responsible for this intricate control of the mucosal environment (9). It must both protect against many pathogens as well as
cooperate with innumerable amounts of symbionts. It accomplishes
this by isolating all the microbes to specific locations within the host,
as the symbiotic bacteria are often only symbiotic in the location in
which they harbor, such as the gut, vagina, or skin to name a few (10).
The innate immune system performs this task by sampling at the
molecular level and can be induced by the components of microbial
cell walls alone (11). For example, lipopolysaccharides, and peptidoglycans or microbial-associated molecular patterns (MAMPS), are ligands for pattern recognition receptors (PRR) on innate immune cells,
such as, macrophages, and include tole-like receptors and mannose
receptors (9, 11, 12, 13). More specifically gram-positive bacteria express lipopolysaccharides, and gram negative bacteria express teichoic acids (9). Through the recognition of specific MAMPs it is possible for the innate defence to differentiate between friendly MAMPs
(symbionts) and pathogenic MAMPs or PAMPs (Pathogen associated
molecular patterns) (9). If cells of the innate immune system (Antigen presenting cells) are activated via MAMPs interacting with PRRs,
it is possible for an adaptive immune response to be activated (9).

Volume 9 - Issue 1 - March 2014

Therefore, understanding the symbiotic relationship that the immune system shares with the microbiota may be a powerful tool to
understand and improve human health. However, this relationship
can be frustrated and strengthened with the addition of hygiene (Increased use of hand sanitizers, cleaning products, antibiotics etc.).
This review will begin with an overview of the relationship between
the host and its symbiotic microbes and conclude with a discussion
on how hygiene fits into this relationship.

Evidence for symbiosis

The 20th century focus on pathogenic microbes led to an understanding of immune response to pathogens and medical advances in vaccinations and antibiotics. However, it is now being appreciated that
most interactions humans have with microbes are either commensal
(one organism benefits, while the other receives no benefit, but remains unharmed) or mutually symbiotic, where both organisms benefit in some way (8, 14, 15).
Within a successful host-microbe relationship, microbes may benefit
the host by releasing molecules that inhibit pathologic microbes (8).
This means that in addition to the chemical (e.g., intestinal mucosa
containing immunoglobulins, cytokines, chemokines and antimicrobial peptides) and physical (e.g., gastrointestinal epithelium) barriers
offered by the host immune system, the symbiotic microbes also assist the immune system in this defense (12). Microbes contribute to
the gastrointestinal physical barrier defense by creating competition
for nutrients against the pathogens (8,12), and also by modulating
cytokine production (12).
Microbes may also attain nutrients for the host. Examples include
the digestion of plant material (cellulose or host-derived mucin) by
microbes required for their own growth, which are delivered to the
microbes via the hosts diet (8, 16). In return, the fermentation products can act as an energy source (e.g. butyrate as energy for colonocytes), gene expression regulators, and as inflammatory mediators
to the host (8, 16). Other non-digestible materials such as inulin
and fructo-oligosaccharides ingested by the host can act as energy
sources (prebiotics) for the healthy microbes in our gut as well (16).
Most interactions with microbes are not pathogenic, instead they are
mutually symbiotic.

Evolution of normal host Immunity

Host immunity evolved in the presence of the microbiota. Due to a
technique known as 16S ribosomal RNA gene sequencing much more
accurate records of gut microbes can now be established when compared to only using culture based studies (8, 11, 16). 16S ribosomal
RNA gene sequencing is beneficial taxonomically because it is found
within most bacteria, has a conserved function and is large enough

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Human Health and the Microbiota: Interactions Between Gut Microbes, Hygiene, and The Immune System

to be detected (17). From 16S ribosomal RNA gene sequencing, it has

been shown that microbial communities consist of a few phyla (8,
11, 16). Examples include Firmicutes, Bacteroidetes, Actinobacteria,
Proteobacteria, Chlamydiae, Cyanobacteria, Defferribacteres, Deinococcusthermus, Fusobacteria, Spirochaetes, Verrucomicrobia (8, 11).
Although, at first glance this may not seem like a lot of variation, at
a species and strain level there is much diversity (8). This is thought
to be due the many years of co-evolution between microbes and
humans, resulting in only the successful symbionts persisting and
evolving within the human gastrointestinal tract ecosystem (11).
In order to elucidate the interactions between the microbiota and
the host, a technique called gnotobiology is commonly used (11).
Gnotobiology is the study of germ-free animals while observing the
consequences when re-colonized with certain microbes (11, 17). A
germ free animal is one aseptically derived such that it has never
had a microbiota. These studies have shown that the microbiota tremendously influence the hosts immune system, intestinal epithelial
cells, metabolism of materials present in gut, absorption of nutrients
and even endocrine function (11). One example of the microbiotas
effects on the intestinal epithelial cells comes from studies involving Bacteroides thetaiotamicron. When germ-free mice were populated
with only these microbes and transcriptional responses were observed with DNA microarrays, complement reactive protein-ductin
receptor expression was observed (11). This receptor is known to
aid in epithelial repair (11). However, it is important to remember
that mono-colonization studies are limited in their interpretation
because it is the net function of microbial communities that drives
host function.
Without the microbiota present in the gut the host organism suffers
in the way of undeveloped tissues, underdeveloped immune function, malnutrition, and a serious vulnerability to infection (11). As
demonstrated by germ-free animal experiments, a reduction in IgA
antibodies, smaller Peyers patches, and a reduced number of T cells
has been found, all important contributors to a normal immune system (17). Furthermore, without the continuous presence of microbes
in the gut, the antimicrobial substances usually ubiquitously present
that act as part of the innate defense to control not only pathogens
but all microbial populations are drastically reduced (17). All these
changes culminate to produce an underdeveloped, immature immune system. This is demonstrated by evidence showing that with
germ free mice, secondary immune organs (i.e. spleen and lymph
nodes) also contain underdeveloped lymphoid follicles and reduced
B and T cell populations (17, 10). Thus, the host immune system requires the presence of microbes in the gut to develop properly.

Where does hygiene fit in?

Now that the importance of the host-microbe relationship has been
established, how hygiene gets involved can be explored. In 1989, Dav-

58

id Strachan observed a huge increase in the amount of allergies such

as hay fever and could not explain this huge increase with genetics
alone, and thus, the hygiene hypothesis was born (19,21,26). If genetics alone could not explain this increase, then the environment must
also be playing a role (21). He suggested that although increased hygiene (e.g. increased antibiotic use, vaccinations, and better cleaning
procedures such as, pasteurization, sewage treatment and chlorination) has made great contributions to human health, it also altered
our immune system such that we are more susceptible to the development of allergy and autoimmune disease (26). This hygiene hypothesis was advanced because such increases in allergies were not
seen in undeveloped countries where hygiene was less controlled
(22). Additionally, epidemiological studies in 1998 showed that atopic
diseases such as asthma afflicted one in five children, with the numbers reaching epidemic levels today (22). Furthermore, autoimmune
diseases such as type 1 diabetes, rheumatoid arthritis, and multiple
sclerosis have also had an increased prevalence in developed countries as compared to undeveloped countries (22). In other words, the
hygiene hypothesis suggests that the increased hygiene has altered
the symbiotic relationship between the host and the microbiota to
such an extent that the hosts immune system becomes reactive to
the host and harmless antigens.
It is important to note that the interactions occurring are complex,
and with so many compounding variables it is difficult to say with
certainty that the rise in allergy and autoimmune diseases is truly
a result of increased antibiotic use and hygienic practices. For example, opponents to the hygiene hypothesis suggest that perhaps
the increase in autoimmune diseases may be simply due to better
techniques for diagnosing such conditions in the developed world
(22). Nevertheless, with epidemiological studies showing a difference
between prevalence of allergies and autoimmune diseases between
developed and undeveloped countries, combined with the clear difference in hygiene and medical practices, the hygiene hypothesis is
worth considering (26).
One of the first mechanisms put forward to explain the observation
of increased allergies and autoimmunity in Westernized societies is
an imbalance between Th1 and Th2 cells, to key immune cells known
to play a role in both autoimmunity and allergy respectfully (26).
This hypothesis was explained by the knowledge that most allergies
are associated with an increase of the immunoglobulin E (IgE) antibody, which is secreted by B cells via assistance from Th2 cells (22).
In undeveloped countries where early childhood infection is common, antigen-presenting cells such as dendritic cells promote Th1
differentiation through secretion of IL-12 and IL-18 (20). However, in
developed countries where early childhood infection is low, Th1 differentiation is also low. Because Th1 and Th2 cells can inhibit each
others differentiation, a loss of Th1 cells may lead to a skewed Th2
population of cells in the body resulting in inappropriate production
of IgE and development of allergic disease (22).

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Human Health and the Microbiota: Interactions Between Gut Microbes, Hygiene, and The Immune System

This hypothesis may be too simple, as there are many paradoxes that
cannot be explained. For example, in undeveloped countries there
are also high levels of parasitic infection as well as bacterial and viral
infections. Parasites such as intestinal helminths, or worms, elicit a
potent Th2 response. Another paradox also presents itself with the
increased prevalence of autoimmune diseases observed in developed
countries. This is because autoimmune diseases are known to be associated with an inappropriate Th1 response, and if there are truly a
lower number of Th1 cells due to less infection, there should not be
an increase in autoimmune diseases (20, 21, 22).
Due to the above conflicts, researchers began to explore the possibility that T regulatory (Treg) cells, an immune cell responsible for the
down regulation of inflammation, may be responsible for the protection observed in undeveloped countries (20, 21, 25, 26). Perhaps
helminths do increase the Th2 response and also induce Treg cells to
secrete interlukin-10, a potent anti-inflammatory cytokine to assist
in their own survival within the host (20, 25). However, the confusion
only deepens with more conflicting evidence. With some groups suggesting findings that helminths offer protection from allergies with
increased interlukin-10 production (20, 25), while others groups have
reported no difference in cytokine production (23). To further convolute the investigation, a report done in the United States surveying
approximately 20,000 Americans on physician diagnosed autoimmune and allergic disorders found that an increase in allergy was
positively associated with an increase in autoimmune disease (24).
This data weaken the hypothesis that an imbalance in Th1 and Th2
cells provokes allergy and autoimmune disease (21). Although this
explanation is now out of date, it was one of the first attempts made
to explain the phenomena of the hygiene hypothesis.
Since then other suggestions have been put forward with an updated
understanding of the hygiene hypothesis. Currently it is defined as
the idea that the increased incidence of allergic and autoimmune diseases in developed countries may be linked to a lack of exposure to
microbes in early childhood. This allowed for the old friends hypothesis, another possible explination for the increased prevelance of autoimmunity and allergy in developed countries (21, 25, 26). The old
friends hypothesis suggestes that in undeveloped countries, chronic
exposure to pathogens, including parasites that can establish themselves in the host, induces a chronic and harmful aggressive immune
response that can damage healthy host tissue (21, 25). The immune
system has adapted by up regulating the number of dendritic cells
able to sample antigens from these chronic pathogens (21, 25, 26).
As a result of this increased sampling, dendritic cells enhance the
differentiation and/or function of Treg cells to these pathogens (i.e.,
Old Friends). These Tregs are constantly present, and thus, prevent
damaging immune responses (21, 25, 26). Quite coincidentally, with
increased number of dendritic cells sampling antigens, they also
sample self-antigens and allergens more often as well, and similar
to their response to the continuous exposure to Old Friends there
is a corresponding up regulation of Treg cells towards self-antigens

Volume 9 - Issue 1 - March 2014

and allergens as well (21, 25). Hence, the lower prevalence of autoimmune disease and allergies in undeveloped countries as compared
to developed countries can be explained by dendritic cells increased
presentation of self-antigens (21). Therefore it has been suggested
that increased prevalence of allergy and autoimmunity may be the
result of humans being able to adapt to their changing environment
with technology much faster than our genetics are able to keep up
(21). However, this hypothesis is not widely accepted on its own. To
make this explanation more plausible it must be explained with the
disappearing microbiota hypothesis (27, 28). In this hypothesis it is
suggested that although antibiotics are a powerful tool we have to
fight infection they also destroy the hosts symbiotic microbial communities (27). This collateral damage to the hosts symbiotic microbes
is then hindered in its recovery by chlorination and pasteurization
etc. that not only destroy pathogenic microbes but symbiotic ones in
our environment as well (27). This lack of symbiotic microbes in the
environment makes it difficult for the host to repopulate its benifical microbial communities (27, 28). One example of a disappearing
microbe is Helicobacter pylori, a microbe found in our stomachs (27,
28). Thus, this pattern of collateral damage to our microbiota and
lack of symbiotic microbes in our environment slowly depletes our
stores of healthy microbes (Hunter). The consequences of this are
not only allergy and autoimmunity but obesity as well (27, 28). A
key difference between the disappearing microbiota hypothesis and
the previous two explanations put forward is that in the disappearing microbiota hypothesis emphasis is put on the lack of exposure
to healthy microbes while the other two put emphasis on the lack of
exposure to infectious disease (28).
These three hypotheses together prove that a complete mechanism
to explain the epidemiological observation of increased autoimmunity and allergy in developed countries is not simple. However, they
clearly outline the fact our increased hygiene in developed countries
is altering the hosts relationship with symbiotic microbes. Moreover, this altered relationship is affecting the hosts immune system. I
do not want to suggest that the use of antibiotics and hygienic practices such as chlorination of water are negative and thus should be
stopped. The purpose here is to call attention and emphasize that
the majority of our interactions with microbes is not pathogenic, and
that we should be cautious and considerate of our microbial friends.

Conclusion
Over billions of years, we have co-evolved with the microbes that call
us home. The gastrointestinal microbiota, a complex and dynamic
ecosystem, is home to trillions of harmless microbes. These microbes
are essential to the normal development and function of our immune
system, and pivotal in absorbing nutrients and vitamins. Gnotobiotic animal studies have demonstrated the devastating effects on the
hosts ability to defend itself against various pathogens when the microbial community composition is altered.

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Human Health and the Microbiota: Interactions Between Gut Microbes, Hygiene, and The Immune System

It is clear that there is still much to learn. The mechanisms of

the three hypotheses have proven to be elaborate, representing
a challenge to find solid experimental evidence to explain the
epidemiological patterns being observed, especially with regard to
allergy and autoimmunity. Despite the complexity, it is clear that
with a better understanding of our symbiotic relationship with
microbes and our hygiene may affect the function of our immune
system, it will be possible to incorporate better therapies for various
ailments, and improve the quality of life for residents in both
developing and developed countries.

Acknowledgments
Tremendous thanks to Dr. Trevor Day for his editorial advice,
valuable discussion, guidance and continuing support throughout
the process of writing this review.

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