The document discusses the human microbiome and its role in health and disease. It begins by defining the microbiota and microbiome. The human microbiome consists of trillions of microorganisms living on and inside the human body, mostly in the gut. When in balance, the gut microbiome aids digestion, produces vitamins, and supports the immune system. However, dysbiosis or imbalance of the gut microbiota has been linked to diseases like inflammatory bowel disease. Large projects like the Human Microbiome Project aim to better understand the microbiome's role in health and disease.

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MICROBIOME IN HEALTH AND DISEASES

2. Outline
• Introduction
• The Human Microbiome
• The Human Microbiome in Health
• The Human Microbiome in Diseases
• Microbiota in Therapy
• The Human Microbiome Project
• Conclusion
• Recommendation
• References
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3. Introduction
• A microbiota is defined as the community of
microorganisms living in a specific environment and a
microbiome is the entire collection of all the genomic
elements of a specific microbiota (Icaza-Chávez, 2014)
• The bacteria, archaea, fungi, and viruses that populate
every facet of our external and internal surfaces compose
what is known as the human microbiome (Netto & Kaul,
2019)
• Humans are colonized at birth by microorganisms that
eventually make up the human microbiome
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4. The Human Microbiome
• More than 100 trillion
microorganisms live on and
within human beings (Wang et
al., 2017)
• The body sites where they are
found include the oral cavity,
skin, airways, gut and
urogenital tract (Argenio &
Salvatore, 2015)
• The bulk of the human
microbiome reside in the gut
and has been implicated mostly
in diseases
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Fig. 1. Bacterial distribution by body site
(Peterson et al., 2009)

5. The Gut Microbiome
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• Sequencing techniques such as 16s rRNA sequencing and
shotgun metagenomics have been used to characterize and
identify bacterial species in the gut microbiota
• The most abundant have been found to be of the phylum
Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria
while Fusobacteria, Cyanobacteria and Verrucomicrobia are
usually less represented (Argenio & Salvatore, 2015)
• Interactions between the host and microbiota as well as
between members of the microbiota help determine a normal
symbiotic gut microbiota

6. The Gut microbiome in Health
• The steady state, abundance,
and diversity of the gut
microbiota are vital to healthy
development from birth to
adulthood (Wei et al., 2019)
• Butyric acid (short chain fatty
acid), a metabolite of the gut
microbiota is used by colon
cells as a source of energy
• Maintenance of the integrity of
the mucosal barrier of the
intestine
(Amon & Sanderson, 2017) Fig. 2. Roles of the gut microbiome in the
control of homeostatic processes (Amon
& Sanderson, 2017)
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7. The Gut microbiome in Health Cont’d
• The gut microbiota has also been linked
availability of tryptophan (an amino acid) in the
body
• This tryptophan is a precursor for the
neurotransmitter Serotonin
• This neurotransmitter plays important role in
mood, anxiety and happiness
(Dehhaghi et al., 2019)
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8. The Gut Microbiome in Diseases
• Studies have shown that diseases linked to the microbiome
occur due to alterations in the constituent of the microbiome
which is known as “Dysbiosis” (Netto & Kaul, 2019)
• Factors such as diet and antibiotics have been found to cause
dysbiosis (Amon & Sanderson, 2017)
• Gut dysbiosis either predisposes an individual to a certain
disease or aids in the pathophysiology of the disease
• A study carried out in murine model showed that germ free
mice had abnormal body development, atrophy in intestinal
walls, low weight organs and an underdeveloped immune
system (Jia & Rajani, 2017)
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9. The Gut Microbiome in Diseases Cont’d
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Fig. 3 Alterations in gut microbiota influencing organ systems in the body leading to diseas
(Amon & Sanderson, 2017)

10. Case study: Inflammatory Bowel Disease (IBD)
• Crohn’s disease and ulcerative colitis are variants of IBD
• The hallmark of these diseases is chronic inflammation of
the gastrointestinal tract
• Some studies have shown that a bacterium with anti-
inflammatory properties, F. prausnitzii, is less abundant in
patients with IBD than in healthy individuals
• It is also hypothesized that disturbed host-microbial
immunologic interactions lead to host recognition of gut
commensals as pathogenic and may mount an inappropriate
inflammatory response which ultimately lead to IBD
(Quigley, 2013)
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11. Microbiota in Therapy
• Probiotics
Live microorganisms such as gram +ve
Lactobacillus spp. and Bifidobacterium spp.
taken in to benefit host health
• Prebiotics
A prebiotic is defined as “a selectively
fermented ingredient that allows specific
changes, both in the composition and/or activity
in the gastrointestinal microbiota that confers
benefits upon host well-being and health” (Netto
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12. Microbiota in Therapy Cont’d.
• Synbiotics refers to a
combination of probiotics
and prebiotics
• Fecal microbial transplant
(FMT)
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Fig. 4 (Credit:

13. The Human Microbiome Project (HMP)
• It is an initiative launched in 2008 and sponsored
by the National Human Genome Research Institute
(NHGRI), a part of the National Institutes of
Health (NIH)
• It has been carried out over ten years and two
phases to provide resources, methods, and
discoveries that link interactions between humans
and their microbiomes to health-related outcomes
(The integrative HMP research consortium, 2019)
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14. The Human Microbiome Project contd.
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Fig. 5. The first and second phases of the NIH Human
Microbiome Project (The integrative HMP research
consortium, 2019)

15. The Human Microbiome Project Cont’d.
• Some key findings from HMP 1 include:
 The microbiome varies among individuals
 Diet, environment, host genetics, and early microbial
exposure affect the diversity of the microbiome
 There is niche specialization of the microbiota both
within and among individuals
 Estimation of about 81-99% of the genera, enzyme
families and community configuration occupied by the
healthy microbiome
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16. The African Collaborative Centre for
Microbiome and Genomics Research
(ACCME)
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17. Conclusion
• Several studies have shown the importance of the
human microbiome in maintaining health and also in
diseases.
However, questions such as
 What are the specific microbial-host interactions that
bring about the disease outcomes
 How the microbiome affect a person’s response to
medications
 How can these findings be used in clinical settings for
diagnosis
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18. Recommendations
• Research which will help elucidate the specific
mechanism of action of the microbiomes in
disease outcome need to be carried out
• A Human Microbiome Project initiative needs to
be conducted in African countries in order to
relate the human microbiome in these regions to
diseases of public health impact there such as
Malaria
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19. References
• Amon, P., & Sanderson, I. (2017). What is the microbiome? Archives of Disease
in Childhood: Education and Practice Edition, 102(5), 258–261.
https://doi.org/10.1136/archdischild-2016-311643
• Argenio, V. D., & Salvatore, F. (2015). Clinica Chimica Acta The role of the gut
microbiome in the healthy adult status. Clinica Chimica Acta, 451, 97–102.
• Dehhaghi, M., Kazemi, H., Panahi, S., & Guillemin, G. J. (2019).
Microorganisms , Tryptophan Metabolism , and Kynurenine Pathway : A
Complex Interconnected Loop Influencing Human Health Status. International
Journal of Tryptophan Research, 12, 1–10.
https://doi.org/10.1177/1178646919852996
• Icaza-Chávez, M. E. (2014). Gut microbiota in health and disease ଝ. Integrative
Medicine Research, 78(4), 240–248.
https://doi.org/10.1016/j.rgmxen.2014.02.009
• Jia, W., & Rajani, C. (2017). Gut Microbial Metabolism in Health and Disease. In
Nutrition in the Prevention and Treatment of Disease (Fourth Edition).
https://doi.org/10.1016/B978-0-12-802928-2.00038-2
• Ley, R. E. (2010). Obesity and the human microbiome. Current Opinion in
Gastroenterology, 26(1), 5–11. https://doi.org/10.1097/MOG.0b013e328333d751
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20. References
• Quigley, E. M. M. (2013). Gut bacteria in health and disease. Gastroenterology and
Hepatology, 9(9), 560–569.
• Sekirov, I., Russell, S. L., Antunes, L. C. M., & Finlay, B. B. (2010). Gut Microbiota in
Health and Disease Gut Microbiota in Health and Disease. Physiol Rev, 90, 859–904.
https://doi.org/10.1152/physrev.00045.2009
• The integrative HMP research consortium. (2019). The Integrative Human Microbiome
Project. Perspective, 569, 641–648. https://doi.org/10.1038/s41586-019-1238-8
• Valles-colomer, M., Falony, G., Darzi, Y., Tigchelaar, E. F., Wang, J., Tito, R. Y., …
Raes, J. (2019). microbiota in quality of life and depression. Nature Microbiology.
https://doi.org/10.1038/s41564-018-0337-x
• Wang, B., Yao, M., Lv, L., Ling, Z., & Li, L. (2017). The Human Microbiota in Health
and Disease. Engineering, 3, 71–82.
• Wei, M. Y., Shi, S., Liang, C., Meng, Q. C., Hua, J., Zhang, Y. Y., … Yu, X. J. (2019).
The microbiota and microbiome in pancreatic cancer: More influential than expected.
Molecular Cancer, 18(1), 1–15. https://doi.org/10.1186/s12943-019-1008-0
• https://www.sciencealert.com/fda-stops-fecal-transplant-trials-after-one-led-to-fatal-
infection
• https://www.fda.gov/news-events/fda-brief/fda-brief-fda-warns-about-potential-risk-
serious-infections-caused-multi-drug-resistant-organisms
• www.h3accme.com
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