Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.
METAGENOMICSOFMICROORGANISMS
PRESENTED BY-
RAJAT MEHTA
ROLL NO. 1613
COURSE NO. MB-101
DEPARTMENT OF
MICROBIOLOGY
MDU,ROHT...
Introduction
Total number of prokaryotic cells on earth is
about 4-6*10^30.
Less than 1% are culturable.
There is no kn...
VBNC(Viable but nonculturable) microbes
Aeromonas hydrophila
Agrobacterium tumefaciens,
Burkholderia cepacia,
Campylobacte...
HISTORY
• The term “metagenomics” was first used by Jo
Handelsman, Jon Clardy, Robert M. Goodman and first
appeared in pub...
 DNA fragments are extracted directly from
environment and cloned into the plasmid vector.
 A library of environmental D...
TWO APPROACHES FOR
METAGENOMICS
• In sequence-driven
metagenomics, DNA
from the environment of
interest is sequenced
and s...
LIMITATIONS OF TWO APPROACHES
• The sequence driven approach
– limited existing knowledge: if a metagenomic gene does
not ...
TWO APPROACHES FOR METAGENOMIC STUDY
METAGENOME OF EXTREME
HABITATS
• Metagenomic analyses of seawater revealed some
interesting aspects of ocean-dwelling micr...
Marine Genome Sequencing Project –
Measuring the Genetic Diversity of Ocean Microbes in Sargasso Sea
Sorcerer II Data Will...
GUT METAGENOMICS
• The human intestinal microbiota is
composed of 1013 to 1014 microorganisms.
• The greatest number resid...
ACID MINE DRAINAGE
METAGENOME
 coverage of dominant species
 Leptospirillum
Ferroplasma
 Identified genes
 ion transp...
METAGENOMICS APPLICATIONS
• Successful products
• Antibiotics
• Antibiotic resistance pathways
• Anti-cancer drugs
• Degra...
FUTURE OF METAGENOMICS
• To identify new enzymes & antibiotics.
• To assess the effects of age, diet, and pathologic state...
References
• Willey Joanne , Sherwood Linda ,
Woolverton Christopher J., Prescott's Microbiology, 9th
ed,North America:McG...
THANKS
Upcoming SlideShare
Loading in …5
×

metagenomics

2,878 views

Published on

Metagenomics of microorganisms

Published in: Science
  • Login to see the comments

metagenomics

  1. 1. METAGENOMICSOFMICROORGANISMS PRESENTED BY- RAJAT MEHTA ROLL NO. 1613 COURSE NO. MB-101 DEPARTMENT OF MICROBIOLOGY MDU,ROHTAK
  2. 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. 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. 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. 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. 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. 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. 8. TWO APPROACHES FOR METAGENOMIC STUDY
  9. 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. 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. 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. 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. 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. 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. 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. 16. THANKS

×