Illumina, Inc. · NASDAQ:ILMN
Illumina — Conference Presentation (2014)
89 slides from Illumina's conference presentation, 2014
Slide 1: Slide 1
Slide 2: Postdoc / Senior technical officer (EMBL Heidelberg Bork group)
• • Postdoc / Senior technical officer (EMBL Heidelberg Bork group) •
Slide 3: Metabolic pathway
Metabolic pathway http://www.kegg.jp/
Slide 4: Slide 4
Slide 5: Nature, Volume 464 Number 7285
Nature, Volume 464 Number 7285
Slide 6: 1. 2. 3.
1. 2. 3.
Slide 7: 2 kg 100T cells
2 kg 100T cells
Slide 8: Slide 8
Slide 9: DGGE
DGGE http://en.wikipedia.org/wiki/Community_Fingerprinting
Slide 10: T-RFLP
T-‐RFLP http://nodens.ceab.csic.es/t-rfpred/method
Slide 11: DNA sequencing history, 2004
2004 atgaaacgcatta gcaccaccattac caccaccatcacc attaccacaggta acggtgcgggct J.C. Venter et al, Science, vol. 304, no. 5667, pp. 66–74, 2004.
Slide 12: DNA
atgaaacgcatta gcaccaccattac caccaccatcacc attaccacaggta acggtgcgggct DNA
Slide 13: Slide 13
Slide 14: Japanese_01
Japanese_01 Atneritdm Ot SpanishgOe
Slide 15: DNA
atgaaacgcatta gcaccaccattac caccaccatcacc attaccacaggta acggtgcgggct DNA
Slide 16: Analysis workflow
te 1 By ZUR Wi Aa— Bee keenunes HUT IL NABI 1. BERIc Sibi 2 nea DNABCR DNABd5I) 4 -SOAPdonevo2 2 Metaveve! 3.1DBAUD WEFT R: 1. MeiaCenehrnotator 2! MetaGeneMark RTF: 1. 16s 2, Universal ‘ingle cooy gene ots Bare Keo cog RATT T tax tovel I sequencing depth FARR SamMIh: | BOAR NSRR UT BR WXs7—sLE ERED
Slide 17: Analysis workflow
Rte 1 By ZUR Wi Aa— Bee keenunes HUT IL BNABRE 1. BERIc Sibi 2 nea PCR ARaRRE: SAI 2.vivs posy yy) Vlumina 2. lon Prete 3.454 Rech: DNABCA DNABC5I) Peasy 4 -SOAPdonevo2 2 Metaveves ‘SripBAUO 2! MetaGeneMark Bare Keo cog WicAZy REE FARR SamMIh: | BOAR NSRR UT BR WXs7—sLE ERED ignewen ® PACT el |. FIV
Slide 18: 16S rRNA gene
16S rRNA gene 0 500 1000 1500 bp 1 ee ee CO RR: S< OLDE CHIRGEORU RR EE FRR: HEOLMEPT OME CHA ORR
Slide 19: • • • •
• • • •
Slide 20: Analysis workflow
Rte 1 By ZUR Wi Aa— Bee keenunes HUT IL BNABRE 1. BERIc Sibi 2 nea PCR ARaRRE: SAI 2.vivs posy yy) Vlumina 2. lon Prete 3.454 Rech: DNABCA DNABC5I) Peasy 4 -SOAPdonevo2 2 Metaveves ‘SripBAUO 2! MetaGeneMark Bare Keo cog WicAZy REE FARR SamMIh: | BOAR NSRR UT BR WXs7—sLE ERED ignewen ® PACT el |. FIV
Slide 21: Metagenome sequencing
Metagenome sequencing http://catalog.takara-bio.co.jp/
Slide 22: DNA
• • DNA • •
Slide 23: Analysis workflow
Rte 1 By ZUR Wi Aa— Bee keenunes HUT IL BNABRE 1. BERIc Sibi 2 nea PCR ARaRRE: SAI 2.vivs posy yy) Vlumina 2. lon Prete 3.454 Rech: DNABCA DNABC5I) Peasy 4 -SOAPdonevo2 2 Metaveves ‘SripBAUO 2! MetaGeneMark Bare Keo cog WicAZy REE FARR SamMIh: | BOAR NSRR UT BR WXs7—sLE ERED ignewen ® PACT el |. FIV
Slide 24: Sequencing platforms: Illumina, Life Technologies
Ilumina Miseq, Hiseq Life technologies Ion proton, Ion PGM
Slide 25: Illumina MiSeq
Illumina Miseq Output Read Number Read Length 15 Gb 25m 2x300 bp
Slide 26: DNA
atgaaacgcatta gcaccaccattac caccaccatcacc attaccacaggta acggtgcgggct DNA
Slide 27: Analysis workflow
1 By ZUR Wi Aa— Bee keenunes NABI 1. BERIc Sibi 2 nea DNAs Gi: 2 yoy: Tilmna 2. lon Proton 3454 Recha Peasy 4 -SOAPdonevo2 2 Metaveve! 3.1DBAUD WEFT R: 1. MeiaCenehrnotator 2! MetaGeneMark RTF: 1. 16s 2, Universal ‘ingle cooy gene 37 Bare Keo cog RATT T tax tovel I sequencing depth Sama: | BOAR NSRR
Slide 28: •
•
Slide 29: Slide 29
Slide 30: Analysis workflow
1 By ZUR Wi Aa— Bee keenunes NABI 1. BERIc Sibi 2 nea DNAs Gi: 2 yoy: Tilmna 2. lon Proton 3454 Recha Peasy 4 -SOAPdonevo2 2 Metaveve! 3.1DBAUD WEFT R: 1. MeiaCenehrnotator 2! MetaGeneMark RTF: 1. 16s 2, Universal ‘ingle cooy gene 37 Bare Keo cog RATT T tax tovel I sequencing depth Sama: | BOAR NSRR
Slide 31: Soap de novo 2 / Velvet / IDBA-UD
• Soap de novo 2 / Velvet / IDBA-‐UD •
Slide 32: MetaGeneMark / MetaGeneAnnotator
• MetaGeneMark / MetaGeneAnnotator A
Slide 33: Analysis workflow
1 By ZUR Wi Aa— Bee keenunes NABI 1. BERIc Sibi 2 nea DNAs Gi: 2 yoy: Tilmna 2. lon Proton 3454 Recha Peasy 4 -SOAPdonevo2 2 Metaveve! 3.1DBAUD WEFT R: 1. MeiaCenehrnotator 2! MetaGeneMark RTF: 1. 16s 2, Universal ‘ingle cooy gene 37 Bare Keo cog RATT T tax tovel I sequencing depth Sama: | BOAR NSRR
Slide 34: Whole genome vs 16S rRNA
• Whole • 16SrRNA • • • •
Slide 35: Slide 35
Slide 36: Slide 36
Slide 37: Slide 37
Slide 38: Slide 38
Slide 39: Enterotype principal component plot
Veillonella Catenibacterium Alkaliphilus Akkermansia Helicobacter Geobacter ● JP.AD.7 Leuconostoc Bacteroides Ruminococcaceae Staphylococcus Bacteroides Parabacteroides Prevotella JP.AD.1 Eggerthella Peptostrepto coccaceae ● ●JP.AD.9 Clostridiales Desulfovibrio Holdemania ● FR.AD.3 Lactobacillus ● J
Slide 40: Enterotype principal component plot
Veillonella Catenibacterium Alkaliphilus Akkermansia Helicobacter Geobacter ● JP.AD.7 Leuconostoc Bacteroides Ruminococcaceae Staphylococcus Bacteroides Parabacteroides Prevotella JP.AD.1 Eggerthella Peptostrepto coccaceae ● ●JP.AD.9 Clostridiales Desulfovibrio Holdemania ● FR.AD.3 Lactobacillus ● J
Slide 41: Enterotype principal component plot
Veillonella Catenibacterium Alkaliphilus Akkermansia Helicobacter Geobacter ● JP.AD.7 Leuconostoc Bacteroides Ruminococcaceae Staphylococcus Bacteroides Parabacteroides Prevotella JP.AD.1 Eggerthella Peptostrepto coccaceae ● ●JP.AD.9 Clostridiales Desulfovibrio Holdemania ● FR.AD.3 Lactobacillus ● J
Slide 42: Large-scale gut metagenome studies
2011 2014 124 330 1267 1,000 Junhua Li et al, Nature Biotechnology 32, 834–841 (2014) Junjie Qin et al, Nature 464, 59-65 (4 March 2010)
Slide 43: Analysis workflow
1 By ZUR Wi Aa— Bee keenunes NABI 1. BERIc Sibi 2 nea DNAs Gi: 2 yoy: Tilmna 2. lon Proton 3454 Recha Peasy 4 -SOAPdonevo2 2 Metaveve! 3.1DBAUD WEFT R: 1. MeiaCenehrnotator 2! MetaGeneMark RTF: 1. 16s 2, Universal ‘ingle cooy gene 37 Bare Keo cog RATT T tax tovel I sequencing depth Sama: | BOAR NSRR
Slide 44: Gut bacteria associated with disease
• → Emmanuelle Le Chatelier et al, Nature 500,541–546(29 August 2013) • → Junjie Qin et al, Nature 490,55–60 (4 October 2012) • → Bacteroides fragilis, Fusobacterium Nucleatum Zeller G et al, Mol Syst Biol. 2014 Nov 28;
Slide 45: SCFA
-‐> SCFA
Slide 46: 1. 2. 3.
1. 2. 3.
Slide 47: SCFA
-‐> SCFA
Slide 48: Symbiotic relationship and intestinal flora balance
Symbiotic relationship Pathogenicity Balance of intestinal flora Bacterial counts per gram feces 10*-10" 108-108 0-10¢ Bacterial group Bacteroides Eubacteria Anaerobic streptococci Bifidobacteria Escherichia coli Streptococci Lactobacilli Veillonella Proteus Pseudomonas aeruginosa AMPH 193% 2005 Fun
Slide 49: Stool samples from HMP
139 stool samples from HMP enzymes, 1914468 other proteins, 13092134 Data from “A framework for human microbiome research. Nature 486, 215–21 (2012).”
Slide 50: Enzyme ratio in 2800 genomes
Enzyme ra\o in 2800 genomes 70 60 50 Enzyme Raio/ % 40 30 20 10 0 0 2000 4000 6000 8000 10000 12000 Protein Number
Slide 51: Stool samples from HMP
139 stool samples from HMP enzymes, 1914468 ? other proteins, 13092134 Data from “A framework for human microbiome research. Nature 486, 215–21 (2012).”
Slide 52: Slide 52
Slide 53: SCFA
-‐> SCFA
Slide 54: HMP
HMP enzymes, 1914468 ? other proteins, 13092134 Data from “A framework for human microbiome research. Nature 486, 215–21 (2012).”
Slide 55: Curcumin, Dihydrocurcumin, Tetrahydrocurcumin
• • – – – Curcumin – – Dihydrocurcumin Tetrahydrocurcumin
Slide 56: Curcumin medicinal properties
Curcumin has a range of medicinal properties including antioxidant, anti-inflammatory, anticancer and analgesic. Discovery of the curcumin metabolic pathway involving a unique enzyme in an intestinal microorganism. Proc Natl Acad Sci U S A. 2011 Apr 19;108(16):6615-20.
Slide 57: Curcumin metabolic pathway
Curcumin has a range of medicinal properties including antioxidant, anti-inflammatory, anticancer and analgesic. Discovery of the curcumin metabolic pathway involving a Curcumin unique enzyme in an intestinal microorganism. Proc Natl Acad Sci U S A. 2011 Apr 19;108(16):6615-20. Dihydrocurcumin Tetra
Slide 58: Curcumin metabolic pathway
Curcumin has a range of medicinal properties including antioxidant, anti-inflammatory, anticancer and analgesic. Discovery of the curcumin metabolic pathway involving a Curcumin unique enzyme in an intestinal microorganism. Proc Natl Acad Sci U S A. 2011 Apr 19;108(16):6615-20. Dihydrocurcumin Tetra
Slide 59: Curcumin metabolic pathway
Curcumin has a range of medicinal properties including antioxidant, anti-inflammatory, anticancer and analgesic. Discovery of the curcumin metabolic pathway involving a Curcumin unique enzyme in an intestinal microorganism. Proc Natl Acad Sci U S A. 2011 Apr 19;108(16):6615-20. GI:327134017 Dihydroc
Slide 60: mit a
- HL mit a ttt)
Slide 61: Food, Drug, Secretion
Food Drug Secretion Others
Slide 62: EnteroPathway reactions and modules
EnteroPathway KEGG Total Gene known Gene unknown Reac\ons 59 343 2411 2813 Modules 136 217 353 2014/5/23!
Slide 63: •
•
Slide 64: Secretion
Secretion
Slide 65: 1. 2. 3.
1. 2. 3.
Slide 66: EnteroPathway reactions and modules
EnteroPathway KEGG Total Gene known Gene unknown Reac\ons 59 + 78 265 2411 2813 Modules 136 217 353 2014/5/23!
Slide 67: Future works
Future works • – • Web tool
Slide 68: 1. 2. 3.
1. 2. 3.
Slide 69: Japanese Consortium for Human Microbiome
Japanese Consortium for Human Micro! “=A JCHMOZ3EA a —7 Japanese Consortium for Human Microbiome
Slide 70: 130
130
Slide 71: Slide 71
Slide 72: Slide 72
Slide 73: Slide 73
Slide 74: Cloud sourcing, Cloud funding
a large scale scientific study open to everyone Cloud sourcing, Cloud funding = http://my.microbes.eu/
Slide 75: my.microbes.eu
• 1000 • http://my.microbes.eu/
Slide 76: epee
a , epee HAAMAMMOSSAE ZOERGHISYbIt—L |
Slide 77: Slide 77
Slide 78: Peer Bork@EMBL & SFR
Peer Bork@ttc & SFR
Slide 79: Analysis approach
• – – DNA – • (16S) – In house • – – – KEGG/COG/CAZy
Slide 80: BBG Y TILBH/IN—hF— (Bee BA)
1 BBG Y TILBH/IN—hF— (Bee BA) on ‘om CARR, ARRIBNBE)
Slide 81: ABPDATFTOVYIIb
ABPDATFTOVYIIb EMAAR YZ DATASRAE 1S @ (USAR Y 2) LA $e) (RTA) th LARA RITOYIIb ON AHIR LEE $B) GRISEA) My.microbes FOYI7b Ste (RRIZAFRS) WR ha) (RTA)
Slide 82: 5000
= 5000
Slide 83: ?
?
Slide 84: ? ! ! !
? ! ! !
Slide 85: =
=
Slide 86: Japanese Consortium for Human Microbiome
Japanese Consortium for Human Micro! “=A JCHMOZ3EA a —7 Japanese Consortium for Human Microbiome
Slide 87: www.jchm.jp
www.jchm.jp
Slide 88: jchm
Japan jchm
Slide 89: DBCLS, EMBL, Peer Bork
DBCLS EMBL Peer Bork