The document provides a brief history of metagenomics, beginning in the 17th century when Antonie van Leeuwenhoek first observed microbes using microscopes. Key developments included the definition of microbial communities, techniques for culturing microorganisms, and the realization that culture-based techniques did not capture total microbial diversity. The field of metagenomics emerged in the late 20th century with developments like PCR, sequencing of 16S rRNA, and shotgun sequencing of environmental samples without culturing. This led to insights into uncultured microbes and their roles in environments like acid mine drainage. Global metagenomic sampling projects helped discover thousands of new microbial species.

1. BRIEF HISTORY AND
DEVELOPMENT OF
METAGENOMICS

2. • Leeuwenhoek made microscopes consisting of a
single high-quality lens of very short focal length.
• In 1674 he likely observed protozoa for the first time
and several years later bacteria.
• The first report of microbes made by Leeuwenhoek
and their oral organisms in 1676.
• In his notebook, he wrote “I didn’t clean my teeth for
three days and then took the material that had
lodged in small amounts on the gums above my front
teeth. . . . I found a few living animalcules.”
• The microbes sketched in his notebook are now
known as some of the most abundant bacteria in the
oral cavity, including cocci, fusiform bacteria, and
spirochetes

3. • Begon, M., Harper, J. L., and Townsend, C. R.
(1986) defines “microbial communities” as the
set of organisms coexisting in the same space
and time.
• Robert Koch in 1888, started using nutrients in a
solid phase to cultivate and isolate
microorganisms. Ultimately, these isolation
techniques helped scientists to understand the
microorganisms' physiologies
• Soon, the microscope became the principal tool
to study microorganisms and their interactions.
Development of practical staining techniques
such as Gram, Ziehl–Neelsen significantly
improved the resolution of microscopy
techniques.

4. • The number of observed microorganisms in a
microscope did not correspond with number of
microorganism obtained in culture plates.
• Winogradsky in1931 emulated environments for
culture media production that resembled native
growing conditions . His ideas and his contribution
to ecology revolutionized microbiology and gave
birth to a new concept named “microbial ecology,”
which refers to the study of microorganisms and
their environmental roles.

6. • In the late 1977, Carl Woese proposed the
use of ribosomal RNA genes as molecular
markers for life classification.
• The three-domains of Carl Woese’s
Classification system include archaea,
bacteria, eukaryote, and six kingdoms are
Archaebacteria (ancient bacteria),
Eubacteria (true bacteria), Protista, Fungi,
Plantae, Animalia.
• This classification system divides the life
based on the differences in the 16S
ribosomal RNA (rRNA) structure and as
well as the cell’s membrane lipid structure
and its sensitivity to antibiotics.

7. • This idea in conjunction with the Sanger automated
sequencing method revolutionized the study and classification
of microorganisms.
• The polymerase chain reaction (PCR), rRNA genes cloning and
sequencing, fluorescent in situ hybridization (FISH), denaturing
gradient gel electrophoresis (DGGE and TGGE), restriction-
fragment length polymorphism, and terminal restriction-
fragment length polymorphism (T-RFLP) granted access to a
“new uncultured world” of microbial communities
• Kary Mullis develops PCR in 1980.
• The 16S rRNA amplicon sequencing technique is based on the
amplification of small fragments of one or two hypervariable
regions of the 16S rRNA gene. The sequences of these
fragments are then obtained and compared with reference
sequences in curted databases for taxonomic identification.

8. • Yet, as the century went on it became clear that culturing techniques were not
keeping up with the immense diversity of microbes. James T. Staley and Allan
Konopka 1985 first deemed the problem as, “The Great Plate Count Anomaly”.
• Norman Pace proposed the idea of cloning DNA directly from environmental
samples in 1985.
• The first report was published by Pace and colleagues in 1991 which reported
non fuctional genes.
• Healy reported the metagenomic isolation of functional genes from
"zoolibraries" constructed from a complex culture of environmental organisms
grown in the laboratory on dried grasses in 1995.
• The term metagenomics was first coined by Jo Handelsman in her 1998 work
• After leaving the Pace laboratory, Edward DeLong continued in the field and
has published work that has largely laid the groundwork for environmental
phylogenies based on signature 16S sequences, beginning with his group's
construction of libraries from marine samples.

9. • In 2002, Mya Breitbart & Forest Rohwer, and colleagues used
shotgun sequencing to show that 200 liters of seawater
contains over 5000 different viruses.
• In 2003, Craig Venter led the Global Ocean Sampling Expedition
(GOS), circumnavigating the globe and collecting metagenomic
samples throughout the journey. All of these samples are
sequenced using shotgun sequencing, in hopes that new
genomes (and therefore new organisms) would be identified.
The pilot project, conducted in the Sargasso Sea, found DNA
from nearly 2000 different species, including 148 types of
bacteria never before seen.
• Venter has circumnavigated the globe and thoroughly explored
the West Coast of the United States, and completed a two-year
expedition to explore the Baltic, Mediterranean and Black Seas.
Analysis of the metagenomic data collected during this journey
revealed two groups of organisms, one composed of taxa
adapted to environmental conditions of 'feast or famine', and a
second composed of relatively fewer but more abundantly and
widely distributed taxa primarily composed of plankton.

10. • DNA isolated from an acid mine drainage system was
sequenced in 2004 by Gene Tyson, Jill Banfield, and
colleagues at the University of California, Berkeley, and
the Joint Genome Institute.
• The first sequences of an environmental sample obtained
with high-throughput sequencing, in this instance
massively parallel pyrosequencing created by 454 Life
Sciences, were published in 2005 by Stephan C. Schuster
and colleagues at Penn State University.

12. REFERENCES
• Alejandra Escobar-Zepeda, Arturo Vera-Ponce de León, and
Alejandro Sanchez-Flores, (2015) The Road to Metagenomics:
From Microbiology to DNA Sequencing Technologies and
Bioinformatics
• K. Kuramitsu, Xuesong He, Renate Lux,Maxwell H. Anderson,
and Wenyuan Shi2 (2005) Interspecies Interactions within Oral
Microbial Communities Howard
• Britannica, The Editors of Encyclopaedia. "Antonie van
Leeuwenhoek". Encyclopedia Britannica, 20 Oct. 2021,
https://www.britannica.com/biography/Antonie-van-
Leeuwenhoek.
• The biology notes, Sourav Pan(2020) Three-domain system (Carl
Woese’s Classification)
• Slideshare, Surendra Rawat (2014) Metagenomics

13. Thank You