Metagenomics of microorganisms

1. METAGENOMICSOFMICROORGANISMS
PRESENTED BY-
RAJAT MEHTA
ROLL NO. 1613
COURSE NO. MB-101
DEPARTMENT OF
MICROBIOLOGY
MDU,ROHTAK

2. Introduction
Total number of prokaryotic cells on earth is
about 4-6*10^30.
Less than 1% are culturable.
There is no known cultural conditions for the
rest 99% but they are reffered as viable.
 Metagenomics is the study of genomic material
obtained directly from the environment, instead
of from culture.
Metagenomics is also reffered as environmental
genomics, ecogenomics or community
genomics.eg. Seawater,soil,the human gut,acid
mines,human feces etc.

3. VBNC(Viable but nonculturable) microbes
Aeromonas hydrophila
Agrobacterium tumefaciens,
Burkholderia cepacia,
Campylobacter jejuni,
Enterobacter aerogenes,
Enterobacter cloacae,
Enterococcus faecalis,
Escherichia coli (including EHEC),
Helicobacter pylori,
Klebsiella pneumoniae,
Legionella pneumophila,
Listeria monocytogenes,
Mycobacterium tuberculosis,
Pseudomonas aeruginosa,
Salmonella typhi,
Salmonella typhimurium,
Shigella dysenteriae,
Shigella flexneri,
Shigella sonnei,
Streptococcus faecalis,
Vibrio alginolyticus,
Vibrio cholerae,
Vibrio harveyi,
Vibrio parahaemolyticus,
Vibrio vulnificus

4. HISTORY
• The term “metagenomics” was first used by Jo
Handelsman, Jon Clardy, Robert M. Goodman and first
appeared in publications in 1998.
• Anton van Leeuwenhoek was first metagenomicst who
directly studied organisms from pond water and his own
teeth.
• Norman Pace proposed the idea of cloning DNA directly
from environmental samples in 1985.
• Recently, Kevin Chen and Lior Pachter defined
metagenomics as "the application of modern genomics
technique without the need for isolation and lab
cultivation of individual species.

5.  DNA fragments are extracted directly from
environment and cloned into the plasmid vector.
 A library of environmental DNA fragments can be
maintained and amplified.
 Certain genes may be obtained by PCR amplification of
DNA fragments derived from the environmental
sample.
 A stable source of nucleotide sequence is generated
that reflects the diversity of microbes growing in
nature.
 Nucleotides are then sequenced and analyzed or
expressed in a microbial host and screened for a
specific function such as production of antimicrobial
compound .
STEPS TO METAGENOMICS

6. TWO APPROACHES FOR
METAGENOMICS
• In sequence-driven
metagenomics, DNA
from the environment of
interest is sequenced
and subjected to
computational analysis.
• The metagenomic
sequences are used to
compare taxonomic
relationship between
organisms in sample.
• In‘function-driven
metagenomics’, the gene
products from the
cloned plasmids in the
bacterial cells can be
used to compare the
metabolic relationship
between community or
to search for new
enzymes,vitamins,antibi-
otics or chemicals of
therapeutic or industrial
use.

7. LIMITATIONS OF TWO APPROACHES
• The sequence driven approach
– limited existing knowledge: if a metagenomic gene does
not look like a gene of known function deposited in the
databases, then little can be learned about the gene or
its product from sequence alone.
• The function driven approach
– most genes from organisms in wild communities cannot
be expressed easily by a given surrogate host
Therefore, the two approaches are complementary and
should be pursued in parallel.

8. TWO APPROACHES FOR METAGENOMIC STUDY

9. METAGENOME OF EXTREME
HABITATS
• Metagenomic analyses of seawater revealed some
interesting aspects of ocean-dwelling microorganisms.
• More than one million genes were sequenced and
deposited in the public databases.
• Groups of bacteria that were not previously known to
transduce light energy appear to contain genes for such
a function eg. Rhodopsin.
• Metagenomic analysis of the biofilm led to the
computer-based reconstruction of the genomes of some
of the community members.
• A model for the cycling of carbon, nitrogen and metals in
the acid mine drainage environment was developed.

10. Marine Genome Sequencing Project –
Measuring the Genetic Diversity of Ocean Microbes in Sargasso Sea
Sorcerer II Data Will Double Number
of Proteins in GenBank!
Specify
Ocean Data
Each Sample
~2000
Microbial
Species
One Million Microbes
Ten Million Viruses
Per Cubic Centimeter
of Ocean Water
BY J.Craig Venter
and Hamilton
Smith

11. GUT METAGENOMICS
• The human intestinal microbiota is
composed of 1013 to 1014 microorganisms.
• The greatest number residing in the distal
gut.
• They synthesize essential amino acids and
vitamins and process
components,otherwise indigestible
contributions to our diet.
• The distal gut and fecal microbiota was
dominated by two bacterial divisions, the
Bacteroidetes and the Firmicutes and by
one methanogenic archaeon,
Methanobrevibacter smithii.

12. ACID MINE DRAINAGE
METAGENOME
 coverage of dominant species
 Leptospirillum
Ferroplasma
 Identified genes
 ion transport
 iron-oxidation
 carbon fixation
 N2-fixation genes found only in
a minor community member
Leptospirillum

13. METAGENOMICS APPLICATIONS
• Successful products
• Antibiotics
• Antibiotic resistance pathways
• Anti-cancer drugs
• Degradation pathways
– Lipases, amylases, nucleases, hemolytic
• Transport proteins
• Ecology and Environment
• Energy
• Bioremediation
• Biotechnology
• Agriculture
• Biodefence

14. FUTURE OF METAGENOMICS
• To identify new enzymes & antibiotics.
• To assess the effects of age, diet, and pathologic states
(e.g., inflammatory bowel diseases, obesity, and
cancer) on the distal gut microbiome of humans living in
different environments.
• Study of more exotic habitats .
• Study antibiotic resistance in soil microbes.
• Improved bioinformatics will quicken analysis for library
profiling .
• Investigating ancient DNA remnants.
• Discoveries such as phylogenic tags (rRNA genes, etc) will
give momentum to the growing field.
• Learning novel pathways will lead to knowledge about
the current nonculturable bacteria to then culture these
systems,

15. References
• Willey Joanne , Sherwood Linda ,
Woolverton Christopher J., Prescott's Microbiology, 9th
ed,North America:McGraw Hill,2014.
• Jeffrey C. Pommerville,Alcamo’s Fundamental of
MICROBIOLOGY, Tenth ed,Burlington:Jones and Bartlett
publisher(2014)
• https://en.wikipedia.org/wiki/Metagenomics
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC18210
61/
• http://www.ncbi.nlm.nih.gov/pmc/articles/PMC42993
32/
• http://www.hindawi.com/journals/isrn/2013/703813/

16. THANKS