Host Microbiomes and their Interactions with Immune System

Gerald John A. Paz

Introduction:

The role of microbiota and its interactions in the immune system of the host has been studied with
increasing interest in the past decades. These studies however, had been limited in understanding the
immune regulations that is mediated by the microbiota in the gastrointestinal tract (Gensollen &
Blumberg, 2017). These organisms that are part of the host microbiome is commonly regarded as having
a commensal relationship with the host. However, several studies can highlight the relationship as more
of a symbiotic one rather than commensal (reference). Any imbalances of the immune system and the
microbiome of the host had been associated with various diseases like autoimmune diseases Type 2
DM, obesity, inflammatory bowel disease, colorectal cancer, and allergies (O’Mahony, 2015). This
report will focus on understanding the host immune response as a result of normal immune regulation
elicited by the normal microbiota and the effects of dysbiosis. A bulk of these host-microbiota
interaction is described as it happens in the gastrointestinal tract. The report will also touch some host-
microbiota interaction that happens in other sites for normal microbiota in the human body as
previously studied. Furthermore, this report will also highlight the various approaches in studying the
host microbiota and the applications of the current knowledge in medicine.

Microbiomes are regarded as complex communities of several organisms like bacteria, fungi,
parasites and viruses that normally thrive in the designated areas in the body of the host. It is
estimated that there are 100 trillion cells that comprises the human microbiome (Reference). The
relationship between the human host and its microbiome is regarded as symbiotic. Meaning, both
the host and the microorganisms benefit from each other. It is obvious that the microorganisms
which are part of the normal flora of the host acquire their nutrients coming from the host’s diet.
On the other hand, the host’s immune system is being primed into maintaining the regulatory
pathways involved in tolerating opportunistic pathogens. Adaptive immunity plays a big role in
the host-microbiome interaction particularly in the acquisition of a complex microbiota
(reference).

The alliance between the host immune system and the microbiota is more of the interweaving of
innate and adaptive immunity. This alliance is not a new concept as this was already observed by
Doderlein (1892) in lactobacilli as part of the microbiome of the vaginal ecosystem.

immune system - microbiota alliance:

- interweaving of innate and adaptive immunity
- example: Doderlein (1892) - lacto bacolli as gatekeepers of the vaginal ecosystem [shows that
promotion of human health with microbial partners is not a recent concept]

Basics of host immune and microbiota interaction.

- Composition of the host immune response that is involved in the interaction
 o What are the immune regulatory mechanisms normally elicited by the normal
microbiota?
- Composition of the normal microbiota
o What are the species classified as normal microbiota?
o What is involved in the direct interaction of host immune system and the normal
flora?
o What is involved in the indirect interaction of host immune system and the normal
microbiota?
o What is dysbiosis?
- Containing the microbiota
- the capacity of a given microbe to trigger or promote disease is highly dependent on the
state of activation of the host, the host's genetic predisposition and the localization of the
particular microbe.

- reinforcing barrier immunity and containment of the microbiota itself.

- minimize contact between microorganisms and the epithelial cell surface limits tissue
inflammation and microbial translocation --> Establishment of mucosal firewall.
FIGURE 1
-
- - "demilitarized zone"
- -- in the host gut, the separation of the microbiota and the epithelial cell sruface is important as
explained above and in order to obatin this separation, a "demilitarized zone" is established. this
physical barrier is made up of mucus produced by the goblet cells, antimicrobial peptides
produced by epithelial cell lineages, secreted immunoglobulin A and macrophages. some of
these proteins are alpha defensins and REGIII gamma which has a direct microbicidal effect on
gram positive bacteria.
-

o
o What is the consequence of dysbiosis in the host?

Importance of host microbiome during early development

The intestinal microbiome already plays a significant role during early development. It should be
noted that the fetal gastrointestinal tract is considered to be sterile and the first exposure to these
commensals occur during the passage through the birth canal. This passage determines the
mucosal and systemic immune system for the long term (reference).

Aside from the passage in the birth canal, initial exposure to commensals also occur upon
feeding the newborn with colostrum and breastmilk. There is the presence of live microbes and
their metabolites, maternal IgA, and immune cells which secretes cytokines as well. Individually,
the maternal IgA restricts the immune activation and microbial attachment by binding nutritional
and microbial antigens. Metabolites of the microorganisms present in the breast milk particularly
those of Bifidobacterium promotes the expansion of defined constituents of the microbiota. It
was also observed in the laboratory setting the neonatal immune imprinting in which there was
an increase in bacterial translocation in the mouse gut during pregnancy and lactation and
bacterially loaded dendritic cells in the milk.

The developing infant immune system is regarded as immature and tolerogenic, meaning, the
development of T and B lymphocytes is more inclined with favor of regulatory responses. It is
blunted in such a way that the immune system poses high susceptibility to infections but
nevertheless ensures the establishment of the microbiota without excessive inflammation.

MAMPs

Postnatally, the infant microbiome plays a part in the development of secondary lymphoid organs
in the intestines. This was observed in vitro via the utilization of germ-free laboratory animals
and reported a reduction of CD4+ T cells and Plasma cells upon development. Commensals play
a part in the epithelial cell maturation and angiogenesis as well (reference).

Alteration in the maternal microbiome predisposes the offspring in various diseases associated
with dysregulated barrier responses (elaborate).

Microbiota-immune system interaction during development

- fetal GI tract is considered to be sterile and the first exposure to the commensals occur during
the passage through the birth canal which is considered to determine the mucosal and systemic
ummune system for the long term.
- colostrum and breast milk: live microbes, metabolites, IgA and immune cells with cytokines as
well.
-- maternal IgA: restricts immune activation and microbial attachment by binding nutritional and
microbial antigens
-- presence of metabolites: promotes expansion of defined constituents of the microbiota such as
bifidobacterium

-- neonatal immune imprinting: increase in bacterial translocation in the mouse gut during
pregnancy and lactation, and bacterially loaded dendritic cells in the milk.

-- immature and tolerogenic neonatal immune system: blunted inflammatory cytokine production
skewed T and B cell development in favor of regulatory responses. This immune system poses
high susceptibility to infections but can ensure the establishment of the microbiota without overt
inflammation. To avoid or limit mucosal inflammation following colonization with the
microbiota, a defined population of erythroid cells enriched in neonates contributes to the
maintenance of this immunoregulatory environment.

- Microbial-associated molecular patterns (MAMPs).

-- "dialog" between host and the microbiota
-postnatal development:
-- microbiota plays a critical role in secondary lymphoid structure development. Germ- free cells
on that particular experiment showed smaller peyer's patches and reduce CD4 T cells and Plasma
cells.
-- commensals can also contribute to the fortification of the intestinal barrier bu various
mechanism including the promotion of epithelial cell maturation and angiogenesis.

- alteration of the microbiota in mothers or in neonates may predispose to diseases associated

with dysregulated barrier responses

Interaction of host microbiome and the immune system in the gastrointestinal tract

- Which immune regulatory system participates in the interaction with microbiota?

M cells in the intestine actively transports antigen to underlying lymphoid follicles for
immunological processing.

dendritic cells, extend dentrites between epithelial cells in order to sample adherent bacterial
species.

dendritic cells undergo maturation into potent t cell stimulatory effector or regulatory dendritic
cells.

mucosal immune system:

-organized GALT (gut associated lymphoid tissues): peyer's patches, mesenteric lymph nodes,
and solitary lymphoid follicles. does antigen uptake, processing and presentation

- diffused GALT: non-organized individual cells. intra-epithelial lymphocytes (IELs)

Epithelial cells - barrier to antigen translocation; sensors for luminal contents (Toll-like
receptors)

> Mechanism for microbiome and host interactions:

- crosstalk between epithelial and immune cells with the intestinal microbiota.

contact with bacterial-associated structures -> activation receptors -> innate and adaptive
immune responses.

activation ->polarization of T helper cells into TH1, TH2, TH9, TH17 or T regulatory cells
(TREGs)
Microbiome and dietary components may promote the development of distinct dendritic cell
phenotypes by provoking tissues to release mediators involved in polarization.

Bifidobacterium infantis 35624 - polarization of TREGs

significant effects of microbial metabolites:

- Production of short chain fatty acids (SCFAs): produced from microbiome fermentation of
dietary fibers
- Butyrate (more potent than acetate or propionate): promotes dendritic cell regulatory activity;
induction of TREG cells and IL-10 secreting T cells.
- histamine: modifies chemokines and cytokine receptors

implications of disturbed host-microbe interactions for disease states

- Type 2 DM, obesity, inflammatory bowel disease, colorectal cancer, and allergies.

Microbiome-associated therapeutics:
- Fecal microbiota transplantation (FMT) - entire microbiome from a healthy individual is
transplanted into a patient; effective for patients with C. difficile

- Inside-out
- Outside-in

Interaction of host microbiome and the immune system in other host microbiome locations
- Lungs
bacterial communities in the lungs:
- resemble what is in the mouth but lower in bacterial burden
- Bacteroides (incl. prevotella), Firmicutes (incl. streptococcus and veillonella),
Proteobacteria and Actinobacteria

Factors that determine the exact composition of lung microbiota:

1. microbial immigratin due to microaspiration of gastric content
2. Microbial elimination
3. Local microbial growth environment (nutrient availability)
-
o The normal flora of the lungs
o Dysbiosis
o Microbiota of the lungs and the gastrointestinal tract
- Skin
- Urogenital tract
- Vaginal – doderlein
Approaches in studying host microbiome and the immune system
- Germ free animals
- 16S rRNA gene profiling.
- Kung meron pa

Current and future trends in studying the importance of the microbiota in human host.
- Microbiome transplant
o Uses
o Proven effects
o Gaps

(Romero et al., 2014)

Vaginal microbiota:

composition and stability of normal pregnant women is different from that of that of non-
pregnant women.

Lactobacillus spp. were the predominant members of the microbial community in normal
pregnancy.

The presence of Lactobacillus spp. is associated with a healthy state and is thought to protect
reproductive age women from non-indigenous pathogens by contributing to the maintenance of a
low vaginal pH (<4.5) through the production of lactic acid.

sex steroid hormones play major roles in driving the composition and stability of the vaginal
microbiota.

approaches to studying microbiome:

16S rRNA gene profiling.

(Belkaid & Hand, 2014)

Role of microbiota in immunity and inflammation

- induction, training and function of the host immune system

- microbiota and immune system: symbiotic relationship
- maintains regulatory pathways involved in tolerating innocuous pathogens (innocuous:
innocent, opportunistic)
- microbiota lacks resilience and diversity required in cases of drug overuse. changes in diet, and
elimination of constitutive partners.

introduction.
- complex communities estimated to be composed of 100 trillion cells including cells of bacteria,
fungi, viruses, and other microbial and eukaryotic species

immune system.
- innate and adaptive components (ability to adapt and respond to highly diverse challenges)

- regulates host homeostasis (sustain and restore regulator of host homeostasis that operates to
sustain and restore tissue function in the context of microbial and environmental encounters)

- adaptive immunity: arm of immune system capable of the acquisition of a complex microbiota.

immune system - microbiota alliance:

- interweaving of innate and adaptive immunity
- example: Doderlein (1892) - lacto bacolli as gatekeepers of the vaginal ecosystem [shows that
promotion of human health with microbial partners is not a recent concept]

Microbiota-immune system interaction during development

- fetal GI tract is considered to be sterile and the first exposure to the commensals occur during
the passage through the birth canal which is considered to determine the mucosal and systemic
ummune system for the long term.
- colostrum and breast milk: live microbes, metabolites, IgA and immune cells with cytokines as
well.
-- maternal IgA: restricts immune activation and microbial attachment by binding nutritional and
microbial antigens
-- presence of metabolites: promotes expansion of defined constituents of the microbiota such as
bifidobacterium
-- neonatal immune imprinting: increase in bacterial translocation in the mouse gut during
pregnancy and lactation, and bacterially loaded dendritic cells in the milk.
-- immature and tolerogenic neonatal immune system: blunted inflammatory cytokine production
skewed T and B cell development in favor of regulatory responses. This immune system poses
high susceptibility to infections but can ensure the establishment of the microbiota without overt
inflammation. To avoid or limit mucosal inflammation following colonization with the
microbiota, a defined population of erythroid cells enriched in neonates contributes to the
maintenance of this immunoregulatory environment.

- Microbial-associated molecular patterns (MAMPs).

-- "dialog" between host and the microbiota

-postnatal development:
-- microbiota plays a critical role in secondary lymphoid structure development. Germ- free cells
on that particular experiment showed smaller peyer's patches and reduce CD4 T cells and Plasma
cells.
-- commensals can also contribute to the fortification of the intestinal barrier bu various
mechanism including the promotion of epithelial cell maturation and angiogenesis.

- alteration of the microbiota in mothers or in neonates may predispose to diseases associated

with dysregulated barrier responses

Containing the microbiota

- the capacity of a given microbe to trigger or promote disease is highly dependent on the state of
activation of the host, the host's genetic predisposition and the localization of the particular
microbe.

- reinforcing barrier immunity and containment of the microbiota itself.

- minimize contact between microorganisms and the epithelial cell surface limits tissue
inflammation and microbial translocation --> Establishment of mucosal firewall. FIGURE 1

- "demilitarized zone"
-- in the host gut, the separation of the microbiota and the epithelial cell sruface is important as
explained above and in order to obatin this separation, a "demilitarized zone" is established. this
physical barrier is made up of mucus produced by the goblet cells, antimicrobial peptides produced by
epithelial cell lineages, secreted immunoglobulin A and macrophages. some of these proteins are alpha
defensins and REGIII gamma which has a direct microbicidal effect on gram positive bacteria.

(O’Mahony, 2015)

M cells in the intestine actively transports antigen to underlying lymphoid follicles for
immunological processing.

dendritic cells, extend dentrites between epithelial cells in order to sample adherent bacterial
species.

dendritic cells undergo maturation into potent t cell stimulatory effector or regulatory dendritic
cells.

mucosal immune system:

-organized GALT (gut associated lymphoid tissues): peyer's patches, mesenteric lymph nodes,
and solitary lymphoid follicles. does antigen uptake, processing and presentation

- diffused GALT: non-organized individual cells. intra-epithelial lymphocytes (IELs)

Epithelial cells - barrier to antigen translocation; sensors for luminal contents (Toll-like
receptors)

Mechanism for microbiome and host interactions:

- crosstalk between epithelial and immune cells with the intestinal microbiota.

contact with bacterial-associated structures -> activation receptors -> innate and adaptive
immune responses.

activation ->polarization of T helper cells into TH1, TH2, TH9, TH17 or T regulatory cells
(TREGs)

Microbiome and dietary components may promote the development of distinct dendritic cell
phenotypes by provoking tissues to release mediators involved in polarization.

Bifidobacterium infantis 35624 - polarization of TREGs

significant effects of microbial metabolites:

- Production of short chain fatty acids (SCFAs): produced from microbiome fermentation of
dietary fibers
- Butyrate (more potent than acetate or propionate): promotes dendritic cell regulatory activity;
induction of TREG cells and IL-10 secreting T cells.
- histamine: modifies chemokines and cytokine receptors

implications of disturbed host-microbe interactions for disease states

- Type 2 DM, obesity, inflammatory bowel disease, colorectal cancer, and allergies.

Microbiome-associated therapeutics:
- Fecal microbiota transplantation (FMT) - entire microbiome from a healthy individual is
transplanted into a patient; effective for patients with C. difficile

(Aline et al., 2017)

bacterial communities in the lungs:

- resemble what is in the mouth but lower in bacterial burden
- Bacteroides (incl. prevotella), Firmicutes (incl. streptococcus and veillonella), Proteobacteria
and Actinobacteria

Factors that determine the exact composition of lung microbiota:

1. microbial immigratin due to microaspiration of gastric content
2. Microbial elimination
3. Local microbial growth environment (nutrient availability)

(Mandell, Bennett, & Dolin, 2005)

Normal indigenous microbial flora

- Protects the host from “pathogenic” organisms

o Competition for the same nutrients: interference
o Competition for the same receptors on host cells: tropism
o Production of secreted products, such as bacteriocins (antibiotics), that are toxic to
other organisms
[first three: to limit the quantity or dominance of any one species.
o Production of volatile fatty acids or other metabolites that are toxic to competing
microbes
o Continual stimulation of the immune system to maintain low but constant levels of class
II histocompatibility (HLA-DR) molecule expression on macrophages and other antigen
presenting cells
o Stimulation of cross-reactive immune factors, such as “natural” antibodies.
- Divided into two:
o Normal resident flora and regularly found and if perturbed
o A microbial flora that may colonize the host transiently for periods ranging from hours
to weeks.

Importance of normal flora:

 - Keeps the immune system “primed” and more rapid and efficient in its response to invading
microorganisms

Indigenous oral flora

- Overall, Streptococcus, Peptostreptococcus, Veillonella, Lactobacillus, Corynebacterium and

Actinomyces account for more than 80% of the total cultivatable normal flora.

Microbial flora in normal lungs

(Tanner, Kressirer, & Faller, 2016)

2008 National Institutes of Health - Human Microbiome Project

- studied the microbiomes of the oral, gut, nasal, vaginal and skin body sites.

(Gottschick et al., 2017)

Female urine microbiota:

A recent study identified six urotypes in the healthy
midstream FUM; they were dominated in abundance by Lactobacillus, Gardnerella, Sneathia,
Staphylococcus or Enterobacteriaceae or consisted of highly diverse micro- biota [5].

Male urine microbiota:

There are only a few studies on the male urine microbiota (MUM). The healthy MUM is
character- ized by genera such as Lactobacillus, Sneathia, Veillo- nella, Corynebacterium
(Meisel et al., 2018)Prevotella, Streptococcus and Ureaplasma, and these are also found on
urethral swabs [13, 14]

Urethra and bladder thus harbor microbial communities distinct from the vagina. The high
abundance of BV related species in the urine of both men and women suggests that urine may act
as a reservoir of pathogens and contribute to recurrence.
Trial
(Meisel et al., 2018)

differentially expressed genes were enriched for those related to immunity and epidermal
differentiation and development. Those microbially regulated genes have critical roles in
epidermal barrier formation.

Results:
- commensal microbiota modulate the cutaneous transcriptome
- cutaneous immune response genes are differentially regulated by resident microbiota
- analysis of skin immune cell populations supports gene expression findings.
- epidermal differentiation is regulated by the commensal microbiota.
-- there are genes having an enhanced expression through the presence of the normal microbiota.
E.coli has the tendency to enhance the expression of genes that codes for the development of
psoriasis

- colonization state shifts gene expression networks for epidermal differentiation and
development processes.

- DEGs under microbial regulation are common to the skin and gastrointestinal tract

different skin resident microbes can control expression of antimicrobial peptides [61]. Cutaneous
IL-1 signaling has also been shown to be augmented by the commensal microbiota, subsequently
promoting effector T cell func- tions [6]. Commensal microbes are also responsible for ac-
cumulation of regulatory T cells via a Ccl20-Ccr6 axis in neonatal skin [15]. The

Upregulation of innate immunity genes in the presence of microbes could be associated with the
higher levels of IL-1α observed in SPF compared to GF skin. It is important to note that these
expression differences are not accompan- ied by an increase in overall inflammation, supporting
the role of the microbiome in priming the cutaneous immune response.

characterization of
genes that are transcriptionally modulated by the micro- biome in both the gut and the skin,
suggesting that while microbiota across different tissues induce niche-specific gene expression
changes, they also stimulate similar host-immune responses. A

skin microbiome mediates two fundamental processes at the transcriptional level in the skin: the
immune response and epidermal develop- ment and differentiation