The document discusses the human microbiome and microbiome signatures. It defines key terms like microbiota, microbiome, and microbiome signatures. The gut microbiome contains trillions of microbes belonging to over 1000 unique species. The microbiome plays important roles in metabolism, immune function, and preventing pathogenic infection. Changes in the gut microbiome have been linked to various diseases. Studying the microbiome involves both culture-dependent and culture-independent methods like metagenomics, which uses high-throughput DNA sequencing without culturing to characterize microbial communities.

1. MBB611/607 MEDICAL
BIOTECHNOLOGY/APPLIED
BIOTECHNOLOGY
ASSIGNMENT AND SEMINARS
TOPIC3: MICROBIOME SIGNATURE
AND APPLICATION
STUDENT NAME: BARAKA L NGINGO
Msc one health molecular biology
REG NUMBER: MOH/D/2018/0041
INSTRUCTOR: Prof MACHANGU R.
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2. Outline
Introduction
 Microbiota Microbiome and
Microbiome signature
Review on microbiota and microbiome
Microbiome roles or applications
How to study microbiome
Conclusion
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3. Introduction
• Definitions
Microbiota: collective microorganisms
residing in an environmental niche.
Microbiome 1: the collective genome of
the microbiota
Microbiome 2: microorganisms that,
under normal conditions, exist in
symbiotic and pathogenic harmony with
their host or environment.
‘‘ Microbiota is largely synonymous to
microbiome’’ 3

4. Human microbiome
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SOURCE: GOOGLE IMAGES

5. Example: The gut microbiome means
collective genome of microbes inhabiting
the gut including bacteria, archaea,
viruses, and fungi.
Microbiome signatures are set of genes,
proteins or other variables that can be
used as a marker for particular
microbiota.
Eg 16s rRNA, molecular barcode genes
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6. Microbiome anatomical sites,
dominant phyla and linked effect
6SOURCE: GOOGLE IMAGE

7. The gastrointestinal microbiome
 Characteristics
• 1014 microorganisms (~1012/ml)
• Approximately 10 times more than human cells
• Collective genome (microbiome): 4 × 106 genes
• Between 300-1000 unique species
• Mostly bacteria, but also fungi, protozoa and
archaea
 Considered to be ‘‘the forgotten organ’’
• Important metabolic activities
• Eg. Fermentation, vitamin synthesis, bile acid
breakdown
• Emerging evidence of key role in host immune
function 7

8. Microbiome cont.
The colonization of the intestine begins
at birth and influenced by vaginal or C-
section birth.
Microbiota changes with exposure to
various environmental factors during
maturation.
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9. Microbiome cont.
Each individual has a unique microbiota,
though approximately one-third of the species
are common across most humans.
Human microbiome are influenced by hygiene,
diet, geographical locations, and host
genotype, antibiotics, sex hormones and age.
The microbiota has coevolved with the human
body and is critical to human health
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10. The gastrointestinal microbiome: Role
in health and disease
 Metabolism
• Fermentation, vitamin synthesis
 Suppression of pathogenic microbes
• Eg. Clostridium difficile managed by competitive exclusion
 Host immune function
• Key to development and function of mucosal immune
system
• Expression of host toll like receptors, important for host
repair of injury inducive damage (eg radiation)
• Modulation of immune system during development to
prevent allergies
 Regulation of intestinal endocrine functions
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11. The gastrointestinal microbiome: Role
in health and disease cont.
 Emerging evidence for
complex role in disease
states
• Changes in the gut
microbiome have been
linked to inflammatory
bowel disease (IBD),
obesity, type 2 diabetes,
aging, cancer, Tumor
formation, Colitis and
Mood/Cognitive
disorders
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12. Microbiome and inflammation
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SOURCE: Taneja, V. (2017). Microbiome. Principles of Gender-Specific
Medicine, 569–583. doi:10.1016/b978-0-12-803506-1.00027-9

13. How to study the microbiome
 1. Culture dependent microbiology
• Culturing and DNA sequencing by Sanger (1977) using
SSU rRNA genes
 2.Culture independent approach microbiology
• Without culturing (anaerobic microbiota has been
difficult to culture)
• Use of metagenomics and other omics approaches
without culturing (unculturable bacteria)
• Went beyond use of SSU rRNA and molecular barcode
genes into whole genome sequencing
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14. 16s based Vs shotgun metagenomics
approach
14
SOURCE: GOOGLE IMAGES

15. How to study the microbiome cont.
 Main tool is high throughput DNA sequencing
technology
 DNA extracted, sequenced, identified and then
cross referenced to inter taxonomy and/or
function
15SOURCE: GOOGLE IMAGES

16. 16SOURCE: GOOGLE IMAGES

17. Conclusion
A combination of omics data including
metagenomic, metabolomic,
transcriptomic, and proteomics will help
define types and the function of the gut
microbiome in link with nature of
disease.
Can also be used is assessment of health
status, studying coevolution and
forecasting health of an individuals
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18. References
 Edward ishiguro, Natasha Haskey and Kristina Campbell
(2018) Chapter 1. An overview of the human
microbiome.ISBN 9780128105412. Page 1-16
 Handelsman, J., 2004. Metagenomics: application of
genomics to uncultured microorganisms. Microbiol. Mol. Biol.
Rev. 68 (4), 669–685. Available from:
http://www.ncbi.nlm.nih.gov/pubmed/15590779.
 Taneja, V. (2017). Microbiome. Principles of Gender-Specific
Medicine, 569–583. doi:10.1016/b978-0-12-803506-1.00027-
9
 Veena Taneja, (2017). Microbiome in Principles of Gender-
Specific Medicine (Third Edition),
 Yongqun He. (2015). Bacterial Whole-Genome Determination
and Applications, in Molecular Medical Microbiology (Second
Edition),
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