ode All Images Videos Short videos News Forums Web Books Maps Flights Finance undefined undefined undefined 21 sites The gut microbiome refers to the trillions of microorganisms—including bacteria, fungi, viruses, and parasites—that reside in the human digestive tract, primarily the large intestine. Often described as a "supporting organ," it contains over 1,000 species of bacteria and expresses roughly 150 times more genes than the human genome. Is our gut microbiome stable or ever-changing? - Gut ... Why Your Gut Microbiome Matters More Than You Think Why Your Gut Microbiome Matters More Than You Think Core Functions The gut microbiome is essential for survival, performing tasks the human body cannot do alone: Digestion and Nutrition: Breaks down complex carbohydrates and fibers into short-chain fatty acids (SCFAs) like butyrate, which provide energy for colon cells and help regulate metabolism. It also synthesizes essential vitamins, including K, B12, folate, and riboflavin. Immune System Support: Roughly 70–80% of the body's immune cells are located in the gut. Microbes "train" these cells to distinguish between harmless compounds and dangerous pathogens. Pathogen Protection: Beneficial microbes physically occupy space and consume nutrients, preventing harmful bacteria from colonizing the intestinal wall—a process called colonization resistance. Gut-Brain Axis: Microbes produce neurotransmitters (e.g., 95% of the body's serotonin is made in the gut) and signal the brain through the vagus nerve, influencing mood, anxiety, and cognitive function. Factors Influencing the Microbiome An individual's microbiome is unique and shaped by several factors throughout life: Early Life: Initial colonization occurs at birth (influenced by delivery method) and through breastfeeding. Diet: A high-fiber, plant-rich diet promotes diversity, while diets high in sugar and processed fats can favor harmful species. Medications: Antibiotics can significantly reduce microbial diversity and disrupt the balance for weeks or months. Lifestyle: Regular exercise, adequate sleep, and exposure to nature or pets are linked to a healthier, more diverse microbiome. Dysbiosis and Health Conditions Dysbiosis is an imbalance where harmful bacteria outnumber beneficial ones. It has been linked to numerous conditions, though researchers are still determining if it is a cause or a consequence: Digestive Disorders: IBS, IBD (Crohn’s and ulcerative colitis), and C. difficile infections. Metabolic Issues: Obesity, Type 2 diabetes, and non-alcoholic fatty liver disease (NAFLD). Systemic Diseases: Heart disease (via TMAO production), asthma, allergies, and certain autoimmune conditions. Mental Health: Depression, anxiety, and potentially neurodegenerative diseases like Alzheimer's. Ways to Support Gut Health Eat Fiber: Aim for a variety of plant foods (vegetables, fruits, legumes, and whole grains). Incorporate Prebiotics: Foods like garlic, onions, bananas, and oats act as fuel f

1. HUMAN MICROBIOME
IN HEALTH & DISEASE
Dr/ Eman Ahmed Abd-Alrahman
Lecturer of Medical Microbiology and Immunology

3. Outcomes
Defining the term “microbiome” (and other related
terminology)
Current hypothesis around the ways we may be
acquiring our microbes; how it may be changed
due to lifetime exposures and how these
microbial profiles may be similar or vary between
individuals
Know that different body sites have unique
microbiomes
Appreciate the importance of studying the
microbiome (what are the clinical impacts).

4. • The human microbiome can be defined as the
“ecological community of commensal, symbiotic,
and pathogenic microorganisms that share our
body space.
• The microbiota includes helminths, fungi,
protozoa, viruses, bacteria, and archaea.
HUMAN MICROBIOME

5. HUMAN MICROBIOME
• The quantity of microbes in our
bodies number approximately 100
trillion cells, ten times more than
the number of human cells.
• Gut contains 70% of total
microbiota
We are more microbes than human.

6. Gastrointestinal Microbiota
> 1000 bacterial species
 each Individuals have > 160 species
– Firmicutes >250 genera
Lactobacillus, mycoplasma, bacillus, clostridium …
– Bacteroidetes ~ 20 genera
– Actinobacteria
Core Microbiome (18 species shared individuals)
Qin et al Nature 2010, 464:59-65 MetaHIT Consortium
90%

7. THE HUMAN MICROBIOME: MORE THAN
JUST THE GIT
Compositional differences in the microbiome by anatomic site Cho I. and Blaser M. Nat Rev Genet 2012 13(4): 260–270

8. A. González,1 Y. Vázquez-Baeza, R. Knight Cell 158 July 31 2014

9. MMHP: Million Microbiomes from Humans
Project
The Million Microbiomes from Humans Project
(MMHP) was officially launched at the 14th
International Conference on Genomics (ICG-14).
Scientists from China, Sweden, Denmark, France,
and Latvia agreed to collaborate on a large-scale
microbial metagenomic project, aiming to
sequence and analyze one million samples
from the intestine, mouth, skin, reproductive
tract, and other organs in the next three to five
years to construct a microbiome map of the
human body and build the world's largest
database of the human microbiome.
https://db.cngb.org/mmhp/

10. • Human microbiota
begins to be
established even
before birth.
1) Gestation
FACTORS AFFECTING THE ESTABLISHMENT
AND ALTERATION OF HUMAN MICROBIOME

11. Jiménez et al. (2008) Res Microbiol. 159(3):187-93; Jiménez E
et al. (2005). Curr Microbiol. 51(4):270-4
HOW THE HUMAN MICROBIOTA IS
STABLISHED AND ALTERED

12.  Prenatal antibiotic
treatment
 Maternal prenatal
stress
 Gestational duration
 Maternal diabetes
status
FACTORS AFFECTING THE ESTABLISHMENT
AND ALTERATION OF HUMAN MICROBIOME

13. • One of the largest influences on the establishment of the
infant’s microbiota is the mode of delivery ,whether the
baby is delivered vaginally or not .
2) Mode of delivery
FACTORS AFFECTING THE ESTABLISHMENT
AND ALTERATION OF HUMAN MICROBIOME

14. FACTORS AFFECTING THE ESTABLISHMENT
AND ALTERATION OF HUMAN MICROBIOME
Lactobacillus
& Prevotella Corynebacte
rium,
& Propioniba
cterium

15. FACTORS AFFECTING THE ESTABLISHMENT
AND ALTERATION OF HUMAN MICROBIOME
3) Breast feeding
• Lactobacillus and Bifidobacterium
species are more dominant in
breast feeding infants that
essential for the breakdown of
maternal milk oligosaccharides into
short-chain fatty acids.
• short-chain fatty acids is essential
for the immune system maturation
and integrity of gut

17. Low
er fecal
diversity
in
breast-fed
infants
Bifidobacterim
Ma, J., Li, Z., Zhang, W. et al. Comparison of gut microbiota in exclusively breast-fed and
formula-fed babies: a study of 91 term infants. Sci Rep 10, 15792 (2020).

19. • The gut microbiota has essential roles in degradation of
dietary components, producing compounds that support
host nutrition, the maturation of the immune system, and
the prevention of colonization of invading pathogens.
FACTORS AFFECTING THE ESTABLISHMENT
AND ALTERATION OF HUMAN MICROBIOME
4) Dietary content

20. Dietary shifts, including the
introduction of high-fat, low-fibre
diets, have a significant impact
on microbiota composition,
metabolome and diversity.
Low-fibre diets lacking complex
polysaccharides impair the
protective barrier functions
conferred by the microbiota
against pathogens. .
FACTORS AFFECTING THE ESTABLISHMENT
AND ALTERATION OF HUMAN MICROBIOME

22. FACTORS AFFECTING THE ESTABLISHMENT
AND ALTERATION OF HUMAN MICROBIOME
5) Antibiotic intake
The antibiotics has a
compromising effect on microbial
community and leading to changes
in host health.
These impacts can be transient or
permanent, causing irreversible
damage to gut microbiota.
These changes in the gut microbial
are various between individuals
depending on its duration, the
number of doses, antibiotic class,
host age, genetic susceptibility, and
lifestyle.

23. CONSEQUENCES OF ANTIBIOTIC-INDUCED
MICROBIOTA CHANGES FOR HEALTH AND DISEASE

26. Surrounding environment (e.g., sanitation, urban vs.
rural, geographic factors)
Caregiving structure (e.g., extended family
involvement).
 Ethnicity and cultural practices.
FACTORS AFFECTING THE ESTABLISHMENT
AND ALTERATION OF HUMAN MICROBIOME
5) Others

27. Relationship between Host and Microbes
(beneficial to both)
Germ free mouse models( complete absence bacteria in the
gut )
Defective gut associated/mesenteric lymphoid tissue, low
levels IgA.
• Immune response devolopment
• Cover body spaces.
• Mitigate intestinal pathogens
• Maintain tissue homeostasis
• Facilitate fermentation of dietary fiber (inulin, pectin…)
• Metabolic end products and therapeutic drug processing
• Signaling among cells and organ systems
• Butyrate: Energy for gut epithelial cells
• Acetate and Propionate: Lipogenesis and Gluconeogenesis

28. Does a compromised Microbiome lead to
Disease?
Koch’s Postulates
Be present in all cases of
the disease.
Be isolated from diseased
patients .
Cause disease when
reintroduced to a healthy
susceptible animal model.
Be isolated again from the new
host.
V.P. Singh et al. / Clinical Microbiology and Infection
(2016)

29. Microbiome and disease

34. Modification of gut microbiota
• Prebiotic: Chemical that induces the growth or activity of
microorganisms that potentially contribute to well-being of
the host (HMOs in infants) – Increase number or activity
of bifidobacteria.
– Bran sources
– Raw foods:raw garlic, leek, onion, chicory root and
banana
• Probiotic: Ingested microorganism(s) associated with
beneficial effects to humans and animals
– Lacctobacillus (50 species), Bifidobacteria (30 species),
Sacchoaroyces boulardii, Streptococcus thermophilus&
Enterococcus faecium

35. Fecal Microbial Transplantation
Fecal Microbial Transplantation durably alters gut
microbiota
Goal: Restore phylogenetic diversity
C. difficile infection
– Severe or recurrent infection
– Mean cure rate 80-90% (>500 cases)
119 FMT clinical trials (mostly C. diff) have been submitted
to FDA Kelly et al Gastroenterology 2015;149:223 –237

36. November 30, 2022

37. Assessment of microbial community profiling
using 16S rRNA gene sequencing