1. Post-Genomic Microbiology Francisco Rodriguez-Valera

2. Outline How has genomics improved the power of Microbiology to understand microbes? What new concepts and paradigms have been advanced? Future challenges 3. Outline How has genomics improved the power of Microbiology to understand microbes? What new concepts and paradigms have been advanced? Future challenges 4. r-strategists Fast growers Easy to retrieve in pure culture Not very abundant in the environment Sporadic blooms E.g. Roseobacter, AlteromonasK-strategists slow growers Dificult to retrieve in pure culture Very abundant in the environment Steady numbers E.g. Pelagibacter, Prochlorococcus 5. Growth curve of Pelagibacter ubique SAR 11 6. The square archaeon Haloquadratum walsbyi ! 1 mmHASH-Agarose plates plus Na-Pyruvate and 0.01% YEWE GOT IT !!! Strain HBSQ001 7. Extract 5 g of DNA (100 ml liquid culture) 1/24th of Illumina lane 1.5 Gbp (500x a 3Mbp genome 350!! Assembly??? Annotation YES 8. What do you learn from the genome 9. Ghai et al, NSR 2013 10. What do you learn from the genome General features (Size, GC content, tetranucleotide frequencies, coding density, etc) 11. Genomic taxonomy DNA-DNA hybridization>70% 16S rRNA >97% similarity ANI >95% Synteny over the core genome 12. Some Alteromonas genomes Flagella glycosylationO-chainO-chain relatedAlteromonas australica 98,6%Alt170ANI75,0%A. macleodii 80,7%AltATCC 82,6%Alt199 1.0 Mbp2.0 Mbp3.0 Mbp4.0 Mbp 13. What do you learn from the genome General features (Size, GC content, tetranucleotide frequencies, coding density, etc) Precise phylogenetic/taxonomic placement 14. Ivars et al, ISME J 2008 15. What do you learn from the genome General features (Size, GC content, tetranucleotide frequencies, coding density, etc) Precise phylogenetic/taxonomic placement Predictions for metabolism (e.g transporters) Prediction for ecology (survival strategies, environmental parameters, motility) 16. Figure 4 Put genomes in the picture Genome recruitment 40000% identity30000% identityNumber of hits3500010010034252 9080908025000 20000Prochlorococcus marinus subsp. pastoris CCMP198670 05000001000000Candidatus Pelagibacter sp. HTCC721170 015000005000001000000150000015000 10000 5432 5000 024651561150914721421119610701048 17. Evapora. Ratio (Vi/Vo)36-70 g/lCarbonate Domain 70-140 g/lIntermediate 140-220 g/lGypsum Domain 220-290 g/lDiatoms Cyanobacteria Green AlgaeHalite Domain >290 g/lHaloarchaea Sulphur Phototrophic Bacteria Artenia Salina DunaliellaNo life 18. Na+ driven respiratory chain or transport unusual in freshwater or soils Rhodopsins or photolyases Transporters Motility Low pI halophiles 19. What do you learn from the genome General features (Size, GC content, tetranucleotide frequencies, coding density, etc) Precise phylogenetic/taxonomic placement Predictions for metabolism (e.g transporters) Prediction for ecology (survival strategies, environmental parameters, motility) 20. SCIENTIFIC ASPECTS Hybrid cluster PKS-NRPS in pAMDE1 21. What do you learn from the genome General features (Size, GC content, tetranucleotide frequencies, coding density, etc) Precise phylogenetic/taxonomic placement Predictions for metabolism (e.g transporters) Prediction for ecology (survival strategies, environmental parameters, motility) Biotechnological potential 22. Mutreja et al 23. 3-4 SNPs/year/geno meCholera in Haiti comes from Nepal 24. SCIENTIFIC ASPECTS Alteromonas macleodii from the deep Mediterranean 25. Outline How has genomics improved the power of Microbiology to understand microbes? What new concepts and paradigms have been advanced? Future challenges 26. THE BACTERIAL PAN-GENOME: a new paradigm in Microbiology Welch et al, 2002Pan-genomeCore genomeFlexible genome 27. The Bacterial PAN-GENOMEEscherichia coli K12 genome 4721 genesEscherichia coli core-genome 2167genesEscherichia coli PAN-GENOME 139.000 gene families (293 genomes) 28. ProkaryotesEukaryotesIntra-species variation1 genome is NOT enough to represent the speciesPANGENOME 29. 95% ANI >95% Synteny over the core genome 30. METAGENOMIC ISLANDS GOS marine metagenomes GENOMIC ISLANDSO-chain LPSGiant proteinPiliExo-polysaccharideEXTRACELLULAR COMPONENTS IN GENOMIC ISLANDSTransporters OtherProchlorococcus marinus MED4Prochlorococcus marinus MIT9301Pelagibacter ubique HTCC1062% sim.100% Pelagibacter ubique HTCC1062(1308759 bp)Burkholderia sp. 383 chr.1Synechococcus sp. WH812Pili Giant Exoprotein polysaccharide relatedO-chain LPSPili TransportersShewanella sp. MR-4Aeromonas hydrophila subs. hydrophila ATCC 796650%Pelagibacter ubique HTCC1002contigs% sim.100%50% Transmembrane/ Outer membrane proteinsO-chain LPSPili TransportersRespiratory system Fe transporterGiant protein Pili Solar salter metagenomesPelagibacter ubique HTCC7211 100%O-chain LPSPiliZn transporter, Phosphonate and Phosphate metabolismPiliO-chain LPSSalinibacter ruber DSM 1385510095Haloquadratum walsbyi DSM 1679095 Y Axis Title50%Y Axis Title% sim.10090 85 8090 85 80Exo-polysaccharide75 050000075Cell surface0 500000 1000000 1500000 2000000 2500000 3000000 3500000 glycoproteinsX Axis Title10000001500000X Axis Title2000000Cell surface 2500000 3000000 glycoproteins 31. H. walsbyi is a unique species Num. Mbp over 95% id (in 70% length) = 398.8 A 100 95%id90 85 80 75 246810121416182022242628Haloquadratum walsbyi HSBQ001 chr. (3132494 bp)BMetagenomeHouse-keeping genesCAtpB SecYNum. Seqs.Num. Seqs.Tef2%id398.8MpRadA%id30 32. Low recruiting genes (MGIs and islets) Coding for exposed features: O-chain of LPS, glycoproteins etc, pili, flagella Transporters Sensors and regulators (behaviour) Sub-niche specialization e.g. microaerophilic growth 33. constant diversityCell SurfaceNiche 34. constant diversityO-chainTransport 35. constant diversity 36. Outline How has genomics improved the power of Microbiology to understand microbes? What new concepts and paradigms have been advanced? Future challenges 37. Third generation* Microbiology Know (rather than the meager 0.1%) Know their (rather than a single strain) Understand their in nature (rather than in the lab) Understand their contribution to the*First generationPhysiology 1865-1952 Second generation Molecular Biology 1952-1995 Third generationGenomics and Metagenomics 1995- 38. Questions please