Metagenomes used in the statistical analysis by Dinsdale, Edwards, et al. Nature, 2008

This table shows the metadata and links to sources of the data and citations associated with the publicly available metagenome sequences used in the Dinsdale, Edwards, et al., analysis of 87 different metagenomes. The links will take you to the annotated sequences in the metagenomics SEED, CAMERA, and the NCBI Short Read Archve. Please note that all metagenomes are currently available to download via the ftp links, some are available in the meta-RAST, and other links will be added as soon as they become available. Citations for individual metagenomes will also be added as and when they become available.

DNA sequences for all metagenomes are avaialble via anonymous FTP. You may browse the list at ftp.theseed.org or select an individual genome from the list below.

Citation:

For those metagenomes whose annotations are publicly available in the meta-RAST, the link will take you to the new version of the RAST web pages.

We have had extensive press coverage about this work. Here is a selection of the coverage:

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Number in Manuscript 
Name 
Description 
Citation 
Download via FTP 
metaRAST 
NCBI Genome Project 
CAMERA 
Sequence manipulation 
Library Type 
Project 
Contact 
Other Key Words 
Coordinates 
Collection date 
1Soudan Red StuffTotal microbial community taken from the oxidized sediments of the Soudan Mine (Minnesota). The outflow feeding this stream was the BlackSoudMineMic033105 sample. Sequenced at 454 Life Sciences.Edwards et al., BMC Genomics. 2006 20;7:57.4440281.3.fa.gz4440281.317633RedSoudMineMic033105NoneMicrobialSubterraneanRob EdwardsTerrestrial; Subterranean47.819307, -92.24259503/31/2005
2Soudan Black StuffTotal microbial community taken from the reduced sediments of the Soudan Mine (Minnesota). Sequenced at 454 Life Sciences.Edwards et al., BMC Genomics. 2006 20;7:57.4440282.3.fa.gz4440282.317635BlackSoudMineMic033105NoneMicrobialSubterraneanRob EdwardsTerrestrial; Subterranean47.819307, -92.24259503/31/2005
3Low saltern microbes (Pond 11)Microbial community from a "low" salinity saltern in San Diego, CA. Sequenced at 454 Life Sciences. 4440437.3.fa.gz4440437.328359LowSalternSDbayMic0704NoneMicrobialHyper-salineBeltran Rodriguez-BritoLow Salinity; Aquatic32.599040, -117.107356date
4Medium saltern microbes (MB1110)Microbial community from a "medium" salinity saltern in San Diego, CA. Sequenced at 454 Life Sciences. 4440435.3.fa.gz4440435.328377MedSalternSDbayMic111005NoneMicrobialHyper-salineBeltran Rodriguez-BritoLow Salinity; Aquatic32.599040, -117.10735611/10/2005
5Medium saltern microbes (MB1111)Microbial community from a "medium" salinity saltern in San Diego, CA. Sequenced at 454 Life Sciences. 4440434.3.fa.gz4440434.328379MedSalternSDbayMic111105NoneMicrobialHyper-salineBeltran Rodriguez-BritoMedium Salinity; Aquatic32.599040, -117.10735611/11/2005
6Low saltern pond plasmids (TT)Plasmids were enriched from a marine microbial community (COSMIC prep and Plasmid-safe DNase) and sequenced at 454 Life Sciences. 4440090.3.fa.gz4440090.328443LowSalternSDbayPla112205NoneMicrobialHyper-salineTuong TranLow Salinity; Aquatic; Plasmids32.599040, -117.10735611/22/2005
7Medium saltern microbial (MB1128)Total microbial community from a "medium" salinity saltern and sequenced at 454 Life Sciences. 4440416.3.fa.gz4440416.328449MedSalterSDbayMic112805NoneMicrobialHyper-salineBeltran Rodriguez-BritoMedium Salinity; Aquatic32.599040, -117.10735611/28/2005
8High saltern microbial (HB1128)High salinity saltern microbes 4440419.3.fa.gz4440419.328453HighSalternSDbayMic112805NoneMicrobialHyper-salineBeltran Rodriguez-BritoHigh Salinity; Aquatic32.599040, -117.10735611/28/2005
9Salton Sea Bacteria 1Sediment microbial community from the Salton Sea, CA. Sequenced at 454 Life Sciences. 4440329.3.fa.gz4440329.328613SaltonSeaMic082308NoneMicrobialHyper-salineBrandon SwanAquatic33.338864, -115.84164008/23/2006
10Medium salinity microbial (MB1116)Medium salinity saltern microbes 4440425.3.fa.gz4440425.328459MedSalternSDbayMic111605NoneMicrobialHyper-salineBeltran Rodriguez-BritoMedium Salinity; Aquatic32.599040, -117.10735611/16/2005
11Low salinity microbial (LB1128)Low salinity saltern microbes 4440426.3.fa.gz4440426.328461LowSalternSDbayMic112805NoneMicrobialHyper-salineBeltran Rodriguez-BritoLow Salinity; Aquatic32.599040, -117.10735611/28/2005
12Medium viruses (MP1128)Medium salinity saltern viruses 4440427.3.fa.gz4440427.328463MedSalternSDbayVir112805NoneViralHyper-salineBeltran Rodriguez-BritoMedium Salinity; Aquatic32.599040, -117.10735611/28/2005
13Medium viruses (MP1116)Medium salinity saltern viruses 4440428.3.fa.gz4440428.328465MedSalternSDbayVir111605NoneViralHyper-salineBeltran Rodriguez-BritoMedium Salinity; Aquatic32.599040, -117.10735611/16/2005
14High saltern viral (HP1116)High salinity saltern viruses 4440421.3.fa.gz4440421.328457HighSalternSDbayVir111605NoneViralHyper-salineBeltran Rodriguez-BritoHigh Salinity; Aquatic32.599040, -117.10735611/16/2005
15Low saltern (Pond 11) virusesViral community from a "low" salinity saltern in San Diego, CA. Sequenced at 454 Life Sciences. 4440436.3.fa.gz4440436.328353LowSalternSDbayVir0704NoneViralHyper-salineBeltran Rodriguez-BritoLow Salinity; Aquatic32.599040, -117.10735607/2004
16Low saltern (Pond 11) viruses (LP1110)Viral community from a "low" salinity saltern and sequenced at 454 Life Sciences. 4440432.3.fa.gz4440432.328373LowSalternSDbayVir111005NoneViralHyper-salineBeltran Rodriguez-BritoLow Salinity; Aquatic32.599040, -117.10735611/10/2005
17Medium saltern viruses (Pond MP1110)Viral community from a "medium" salinity saltern in San Diego, CA. Sequenced at 454 Life Sciences. 4440431.3.fa.gz4440431.328375MedSalternSDbayVir111005NoneViralHyper-salineBeltran Rodriguez-BritoMedium Salinity; Aquatic32.599040, -117.10735611/10/2005
18Medium saltern viruses (MP1122)Viral community from a "medium" salinity saltern and sequenced at 454 Life Sciences. 4440417.3.fa.gz4440417.328445MedSalternSDbayVir112205NoneViralHyper-salineBeltran Rodriguez-BritoMedium Salinity; Aquatic32.599040, -117.10735611/22/2005
19High saltern viruses (HP1207)Viral community from a "high" salinity saltern and sequenced at 454 Life Sciences. 4440145.4.fa.gz4440145.428447HighSalternSDbayVir120705NoneViralHyper-salineBeltran Rodriguez-BritoHigh Salinity; Aquatic32.599040, -117.10735612/07/2005
20High saltern viral (HP1128)High salinity saltern viruses 4440144.4.fa.gz4440144.428451HighSalternSDbayVir112805NoneViralHyper-salineBeltran Rodriguez-BritoHigh Salinity; Aquatic32.599040, -117.10735611/28/2005
21Low saltern viruses (LP1128)Low salinity saltern viruses 4440420.3.fa.gz4440420.328455LowSalternSDbayVir112805NoneViralHyper-salineBeltran Rodriguez-BritoLow Salinity; Aquatic32.599040, -117.10735611/28/2005
22Salton Sea Phage 1Sediment viral community from the Salton Sea, CA. Sequenced at 454 Life Sciences. 4440327.3.fa.gz4440327.328613SaltonSeaVirOne082308NoneViralHyper-salineBrandon SwanAquatic33.338864, -115.84164008/23/2006
23Salton Sea Phage 3Sediment viral community from the Salton Sea, CA. Sequenced at 454 Life Sciences. 4440328.3.fa.gz4440328.328613SaltonSeaVirTwo082308NoneViralHyper-salineBrandon SwanAquatic33.338864, -115.84164008/23/2006
24Line Islands Kingman Reef B2 bacteriaMicrobial fraction (100-0.45 micron) from water below the boundary layer (e.g., crevices and benthic surfaces) of Kingman Atoll (Northern Line Islands). Sequenced at 454 Life Sciences.Dinsdale et al, PLoS One, 3:e15844440037.3.fa.gz4440037.328343KingLIMic082105NoneMicrobialMarineLiz DinsdaleCoral; Seawater6.38566667, -162.334783308/21/2005
25Line Islands Christmas Reef B3 bacteriaMicrobial fraction (100-0.45 micron) from water below the boundary layer (e.g., crevices and benthic surfaces) of Christmas Atoll (a.k.a., Kirtimati; Northern Line Islands). Sequenced at 454 Life Sciences.Dinsdale et al, PLoS One, 3:e15844440041.3.fa.gz4440041.328347XmasLIMic080505NoneMicrobialMarineLiz DinsdaleCoral; Seawater1.99231667, -157.484066708/05/2005
26Line Islands Palmyra F8 BacteriaMicrobial fraction (100-0.45 micron) from water below the boundary layer (e.g., crevices and benthic surfaces) of Palmyra (Northern Line Islands). Sequenced at 454 Life Sciences.Dinsdale et al., PLoS One, 3:e15844440039.3.fa.gz4440039.328363PalmLIMic081805NoneMicrobialMarineLiz DinsdaleCoral; Seawater5.86683333,-162.1279666708/18/2005
27Line Islands Tabuaeran B1 BacteriaMicrobial fraction (100-0.45 micron) from water below the boundary layer (e.g., crevices and benthic surfaces) of Fanning (a.k.a., Tabuaeran; Northern Line Islands). Sequenced at 454 Life Sciences.Dinsdale et al., PLoS One, 3:e15844440279.3.fa.gz4440279.328367FannLIMic081105Sequences similar to dinoflagellates removedMicrobialMarineLiz DinsdaleCoral; Seawater3.82595000,-159.3495666708/11/2005
28DMSP 1 (MAM.1)Total microbial community from DMSP treated seawater, sequenced at 454 Life Sciences.Mou et al., Nature, 451:708-7114440364.3.fa.gz4440364.319145 NoneMicrobialMarineMary Ann Morancarbohydrate manipulation31.3975, -81.280311/2005
29DMSP 2 (MAM.2)Total microbial community from DMSP treated seawater, sequenced at 454 Life Sciences.Mou et al., Nature, 451:708-7114440360.3.fa.gz4440360.319145 NoneMicrobialMarineMary Ann Morancarbohydrate manipulation31.3975, -81.280311/2005
30VAN 1 (MAM 3)Total microbial community from Vanillate treated seawater, sequenced at 454 Life Sciences. Mou et al., Nature, 451:708-7114440365.3.fa.gz4440365.319145 NoneMicrobialMarineMary Ann Morancarbohydrate manipulation31.3975, -81.280311/2005
31VAN 2 (MAM 4)Total microbial community from Vanillate treated seawater, sequenced at 454 Life Sciences. Mou et al., Nature, 451:708-7114440363.3.fa.gz4440363.319145 NoneMicrobialMarineMary Ann Morancarbohydrate manipulation31.3975, -81.280311/2005
32Marine Phages GOMMultiple viral communities collected by Suttle lab in the Gulf of Mexico. Sequenced at 454 Life Sciences.Angly et al, PLoS Biol. 2006 4(11):e368. 4440304.3.fa.gz4440304.317765GOMVir94to01NoneViralMarineFlorent AnglyBay; Seawater; Aquatic25.571, -92.883; 26.839, -94.999; 27.489, -96.273; 27.547, -96.473; 27.733, -96.841; 27.838, -97.052; 27.467, -97.417; 27.501, -88.402; 27.969, -87.58; 28.562, -87.414; 29.001, -87.297; 26.475, -85.641; 25.313, -84.7206/01/1994 - 07/31/2001
33Marine Phages BBCMultiple viral communities collected by Suttle lab in the regions around British Colombia. Sequenced at 454 Life Sciences.Angly et al, PLoS Biol. 2006 4(11):e368. 4440305.3.fa.gz4440305.317767BBCVir96to04NoneViralMarineFlorent AnglyGulf; Seawater; Aquatic49.849, -124.434; 50.186, -124.857; 50.197, -124.848; 50.028, -124.732; 50.079, -124.714; 49.975, -124.683; 50.005, -124.964; 50.122, -124.904; 49.727, -124.323; 49.828, -124.796; 50.190, -125.142; 48.801, -123.403; 49.558, -123.79; 49.682, -123.847; 49.774, -123.975; 49.731, -123.738; 49.607, -123.803; 50.295, -124.727; 50.116, -125.314; 49.950, -125.138; 49.950, -125.098; 49.455, -123.285; 49.574, -123.253; 49.661, -123.221; 50.059, -125.246; 50.023, -125.208; 50.114, -125.309; 49.978, -125.192; 49.972, -125.179; 48.586, -123.506; 48.604, -123.502; 48.669, -123.502; 50.162, -123.892; 49.733, -124.246; 49.130, -123.467; 49.300, -123.233; 49.328, -123.735; 48.817, -125.13308/01/1996 - 07/31/2004
34Marine Phages ArcticMultiple viral communities collected by Suttle lab in Arctic. Sequenced at 454 Life Sciences.Angly et al, PLoS Biol. 2006 4(11):e368. 4440306.3.fa.gz4440306.317769ArcticVir2002NoneViralMarineFlorent AnglySeawater; Aquatic71.729, -155.157; 72.500, -160; 72.900, -158.8; 72.500, -157; 74.585, -158.492; 74.250, -162.56; 73.667, -164.113; 72.500, -151.333; 70.875, -133.967; 70.367, -133.6; 70.367, -133.6; 69.896, -139.5; 69.400, -138; 70.200, -13709/01/2002 - 10/31/2002
35Marine Phage SAROne viral communities collected by Carlson lab in the Sargasso Sea. Sequenced at 454 Life Sciences.Angly et al, PLoS Biol. 2006 4(11):e368. 4440322.3.fa.gz4440322.317771SARVir063005NoneViralMarineFlorent AnglySeawater; Aquatic32.167, -64.506/30/2005
36Line Islands Kingman Reef B2 phageViral fraction from water below the boundary layer (e.g., crevices and benthic surfaces) of Kingman Atoll (Northern Line Islands). Sequenced at 454 Life Sciences.Dinsdale et al, PLoS One, 3:e15844440036.3.fa.gz4440036.328345KingLIVir082105NoneViralMarineLiz DinsdaleCoral; Seawater6.38566667, -162.334783308/21/2005
37Line Islands Christmas Reef B3 phageViral fraction from water below the boundary layer (e.g., crevices and benthic surfaces) of Christmas Atoll (a.k.a., Kirtimati; Northern Line Islands). Sequenced at 454 Life Sciences.Dinsdale et al, PLoS One, 3:e15844440038.3.fa.gz4440038.328349XmasLIVir080505NoneViralMarineLiz DinsdaleCoral; Seawater1.99231667, -157.484066708/05/2005
38Line Islands Palmyra F8 PhageViral fraction from water below the boundary layer (e.g., crevices and benthic surfaces) of Palmyra (Northern Line Islands). Sequenced at 454 Life Sciences.Dinsdale et al., PLoS One, 3:e15844440040.3.fa.gz4440040.328365PalmLIVir081805NoneViralMarineLiz DinsdaleCoral; Seawater5.86683333,-162.1279666708/18/2005
39Line Islands Tabuaeran B1 PhageViral fraction from water below the boundary layer (e.g., crevices and benthic surfaces) of Fanning (a.k.a., Tabuaeran; Northern Line Islands). Sequenced at 454 Life Sciences.Dinsdale et al., PLoS One, 3:e15844440280.3.fa.gz4440280.328369FannLIVir081105NoneViralMarineLiz DinsdaleCoral; Seawater3.82595000,-159.3495666708/11/2005
40Tampa Bay phage from induction experimentTampa Bay phage from induction experiment 4440102.3.fa.gz4440102.328619 NoneViralMarineMya BreitbartInduced Phage27.761504, -82.632981date
41Skan Bay Phage 1Skan Bay, Unalaska Island core phage 9/27/06 4440330.3.fa.gz4440330.328619SkanBayAKVir092706NoneViralMarineBrandon SwanAquatic33.338864, -115.84164009/27/2006
42Tilapia pond microbesMicrobial community isolated from the Tilapia pond at Kent SeaTech (Salton Sea, CA). Sequencing was done at 454 Life Sciences. 4440440.3.fa.gz4440440.328387TilPondKentSTMic1105NoneMicrobialFreshwaterChristelle DesnuesFish; Tilapia33.537594, -116.09775111/2005
43Healthy Tilapia pond microbesMicrobial community isolated from the Tilapia pond at Kent SeaTech (Salton See, CA). Sequencing was done at 454 Life Sciences. 4440413.3.fa.gz4440413.328405TilPondKentSTMic050406NoneMicrobialFreshwaterChristelle DesnuesFish; Tilapia, pond33.537594, -116.09775105/04/2006
44Healthy Prebead tank microbesMicrobial community isolated from the Prebead pond at Kent SeaTech (Salton Sea, CA). Sequencing was done at 454 Life Sciences. 4440411.3.fa.gz4440411.328407PrePondKentSTMic050406NoneMicrobialFreshwaterChristelle DesnuesFish; Tilapia, pond33.537594, -116.09775105/04/2006
45Tpond microbe 3Microbial community isolated from the Tilapia pond at Kent SeaTech (Salton Sea, CA). Sequencing was done at 454 Life Sciences. 4440422.3.fa.gz4440422.328603TilPondKentSTMic0806NoneMicrobialFreshwaterChristelle DesnuesFish; Tilapia, pond33.537594, -116.09775108/2006
46Tpond phage 3Viral community isolated from the Tilapia pond at Kent SeaTech (Salton Sea, CA). Sequencing was done at 454 Life Sciences. 4440424.3.fa.gz4440424.328601TilPondKentSTVir0806NoneViralFreshwaterChristelle DesnuesFish; Tilapia, pond33.537594, -116.09775108/2006
47Healthy Tilapia pond phagesViral community isolated from the Tilapia pond at Kent SeaTech (Salton Sea, CA). Sequencing was done at 454 Life Sciences. 4440412.3.fa.gz4440412.328409TilPondKentSTVir050406NoneViralFreshwaterChristelle DesnuesFish; Tilapia, pond33.537594, -116.09775105/04/2006
48Healthy Prebead tank phagesViral community isolated from the Prebead pond at Kent SeaTech (Salton Sea, CA). Sequencing was done at 454 Life Sciences. 4440414.3.fa.gz4440414.328411PrePondKentSTVir050406NoneViralFreshwaterChristelle DesnuesFish; Tilapia, pond33.537594, -116.09775105/04/2006
49Tilapia pondViral community isolated from the Tilapia pond at Kent SeaTech (Salton Sea, CA). Sequencing was done at 454 Life Sciences. 4440439.3.fa.gz4440439.328361TpondKentSTVir1105NoneViralFreshwaterChristelle DesnuesFish; Tilapia33.537594, -116.09775111/2005
50Porites compressa time zero bacteriaMicrobes collected from whole Porites compressa tissue extracts taken directly off the reef at the Hawai'i Marine Laboratory Refuge Point Reef. Corals were collected 3 meters apart and at 3 meters depth and rinsed extensively in filtered autoclaved seawater before processing. Metagenome consists of 45 amplified coral microbe DNA samples combined in equal amounts for sequencing at 454 Life Sciences. 4440380.3.fa.gz4440380.328427T0PortComHawMic022306Sequences similar to dinoflagellates removedMicrobialCoralBecky Vega ThurberExperimental Treatments21.434025, -157.78782202/23/2006
51Porites compressa control treated bacteriaMicrobes collected from whole Porites compressa tissue extracts taken from an aquarium control experiment that consisted of 5 liters of ambient seawater that was changed every 24 hours. Metagenome consisted of 36 amplified microbial viral DNA samples that were collected at 1 (n =9), 4 (n =9), 16 (n =9), and 64 (n =9) hours during the experiment. DNA samples were pooled in equal amounts for sequencing at 454 Life Sciences. 4440378.3.fa.gz4440378.328429ConPorCompHawMic0206Sequences similar to dinoflagellates removedMicrobialCoralBecky Vega ThurberExperimental Treatments21.434025, -157.78782202/23/2006 - 02/25/2006
52Porites compressa temperature treated bacteriaMicrobes collected from whole Porites compressa tissue extracts taken from a temperature stressor experiment that consisted of 5 liters of 30oC seawater that was changed every 24 hours. Metagenome consisted of 36 amplified coral microbial DNA samples that were collected at 1 (n =9), 4 (n =9), 16 (n =9), and 64 (n =9) hours during the experiment. DNA samples were pooled in equal amounts for sequencing at 454 Life Sciences. 4440373.3.fa.gz4440373.328431TempPorCompHawMic0206Sequences similar to dinoflagellates removedMicrobialCoralBecky Vega ThurberExperimental Treatments21.434025, -157.78782202/23/2006 - 02/25/2006
53Porites compressa DOC treated microbesMicrobes collected from whole Porites compressa tissue extracts taken from a dissolved organic carbon (DOC) stressor experiment that consisted of 5 liters of ambient seawater with 125 mg of additional glucose (25 mg / L) that was changed every 24 hours. Metagenome consisted of 36 amplified coral microbial DNA samples that were collected at 1 (n =9), 4 (n =9), 16 (n =9), and 64 (n =9) hours during the experiment. DNA samples were pooled in equal amounts for sequencing at 454 Life Sciences. 4440372.3.fa.gz4440372.328433DOCPorCompHawMic0206Sequences similar to dinoflagellates removedMicrobialCoralBecky Vega ThurberExperimental Treatments21.434025, -157.78782202/23/2006 - 02/25/2006
54Porites compressa pH treated microbesMicrobes collected from whole Porites compressa tissue extracts taken from a reduced pH stressor experiment that consisted of 5 liters of seawater with molecular grade HCl added to a final pH 6.8 that was changed every 24 hours. Metagenome consisted of 36 amplified coral microbial DNA samples that were collected at 1 (n =9), 4 (n =9), 16 (n =9), and 64 (n =9) hours during the experiment. DNA samples were pooled in equal amounts for sequencing at 454 Life Sciences. 4440379.3.fa.gz4440379.328435pHPorCompHawMic0206Sequences similar to dinoflagellates removedMicrobialCoralBecky Vega ThurberExperimental Treatments21.434025, -157.78782202/23/2006 - 02/25/2006
55Porites compressa nutrient treated microbesMicrobes collected from whole Porites compressa tissue extracts taken from a nutrient stressor experiment that consisted of 5 liters of ambient seawater with additional 10 mM excess of each: nitrate (Ca(NO3)2), nitrite (NaNO2), ammonium (NH4Cl), and phosphate (KH2PO4) that was changed every 24 hours. Metagenome consisted of 36 amplified coral microbial DNA samples that were collected at 1 (n =9), 4 (n =9), 16 (n =9), and 64 (n =9) hours during the experiment. DNA samples were pooled in equal amounts for sequencing at 454 Life Sciences. 4440381.3.fa.gz4440381.328437NutPorCompHawMic0206Sequences similar to dinoflagellates removedMicrobialCoralBecky Vega ThurberExperimental Treatments21.434025, -157.78782202/23/2006 - 02/25/2006
56Porites astreoides microbial extractionMicrobes were separated from Porites astreoides tissues using Percoll gradients. The metagenomic library contains sequences from fungi (presumably spores), bacteria, viruses, and the coral mitochondria. Sequenced at 454 Life Sciences.Wegley, et al Environ Microbiol. 2007 9(11):2707-19. 4440319.3.fa.gz4440319.328371BocasPAMic092105removed dinoflagellates and mitochindriaMicrobialCoralLinda Wegleycoral holobiont; nutrient cycling9.351608, -82.25671709/21/2005
57Porites compressa time zero virusesViruses collected from whole Porites compressa tissue extracts taken directly off the reef at the Hawai'i Marine Laboratory Refuge Point Reef. Corals were collected 3 meters apart and at 3 meters depth and rinsed extensively in filtered autoclaved seawater before processing. Metagenome consists of 45 amplified coral viral DNA samples combined in equal amounts for sequencing at 454 Life Sciences. 4440376.3.fa.gz4440376.328415T0PortComHawVir022306NoneViralCoralBecky Vega ThurberExperimental Treatments21.434025, -157.78782202/23/2006
58Porites compressa control treated virusesViruses collected from whole Porites compressa tissue extracts taken from an aquarium control experiment that consisted of 5 liters of ambient seawater that was changed every 24 hours. Metagenome consisted of 36 amplified coral viral DNA samples that were collected at 1 (n =9), 4 (n =9), 16 (n =9), and 64 (n =9) hours during the experiment. DNA samples were pooled in equal amounts for sequencing at 454 Life Sciences. 4440374.3.fa.gz4440374.328417ConPorCompHawVir0206NoneViralCoralBecky Vega ThurberExperimental Treatments21.434025, -157.78782202/23/2006 - 02/25/2006
59Porites compressa DOC treated virusesViruses collected from whole Porites compressa tissue extracts taken from a dissolved organic carbon (DOC) stressor experiment that consisted of 5 liters of ambient seawater with 125 mg of additional glucose (25 mg / L) that was changed every 24 hours. Metagenome consisted of 36 amplified coral viral DNA samples that were collected at 1 (n =9), 4 (n =9), 16 (n =9), and 64 (n =9) hours during the experiment. DNA samples were pooled in equal amounts for sequencing at 454 Life Sciences. 4440370.3.fa.gz4440370.328421DOCPorCompVirHaw0206NoneViralCoralBecky Vega ThurberExperimental Treatments21.434025, -157.78782202/23/2006 - 02/25/2006
60Porites compressa pH treated virusesViruses collected from whole Porites compressa tissue extracts taken from a reduced pH stressor experiment that consisted of 5 liters of seawater with molecular grade HCl added to a final pH 6.8 that was changed every 24 hours. Metagenome consisted of 36 amplified coral viral DNA samples that were collected at 1 (n =9), 4 (n =9), 16 (n =9), and 64 (n =9) hours during the experiment. DNA samples were pooled in equal amounts for sequencing at 454 Life Sciences. 4440371.3.fa.gz4440371.328423pHPorCompHawVir0206NoneViralCoralBecky Vega ThurberExperimental Treatments21.434025, -157.78782202/23/2006 - 02/25/2006
61Porites compressa nutrient treated virusesViruses collected from whole Porites compressa tissue extracts taken from a nutrient stressor experiment that consisted of 5 liters of ambient seawater with additional 10 mM excess of each: nitrate (Ca(NO3)2), nitrite (NaNO2), ammonium (NH4Cl), and phosphate (KH2PO4) that was changed every 24 hours. Metagenome consisted of 36 amplified coral viral DNA samples that were collected at 1 (n =9), 4 (n =9), 16 (n =9), and 64 (n =9) hours during the experiment. DNA samples were pooled in equal amounts for sequencing at 454 Life Sciences. 4440377.3.fa.gz4440377.328425NutPorCompHawVir0206NoneViralCoralBecky Vega ThurberExperimental Treatments21.434025, -157.78782202/23/2006 - 02/25/2006
62Porites compressa temperature treated virusesViruses collected from whole Porites compressa tissue extracts taken from a temperature stressor experiment that consisted of 5 liters of 30oC seawater that was changed every 24 hours. Metagenome consisted of 36 amplified coral viral DNA samples that were collected at 1 (n =9), 4 (n =9), 16 (n =9), and 64 (n =9) hours during the experiment. DNA samples were pooled in equal amounts for sequencing at 454 Life Sciences. 4440375.3.fa.gz4440375.328419TempPorCompHawVir0206Sequences similar to organelles removedViralCoralBecky Vega ThurberExperimental Treatments21.434025, -157.78782202/23/2006 - 02/25/2006
63Rios Mesquites Stromatolites bacteriaMicrobial community isolated from the Rios Mesquites microbiolite in Cuatro Cienagas, Mexico. Sequenced at 454 Life Sciences. 4440060.3.fa.gz4440060.328351RMStromCCMexMic072205NoneMicrobialMicrobialitesMya BreitbartMarine26.985876, -102.06639007/22/2005
64Highborne Cay stromatolite bacteriaMicrobial community isolated from Highborne Cay microbiolite in the Bahamas. Sequenced at 454 Life Sciences 4440061.3.fa.gz4440061.328383HBCStromBahamasMic011105NoneMicrobialMicrobialitesChristelle DesnuesMarine24.709876, -76.82252101/11/2005
65Pozas Azule II stromatolite microbesMicrobial community isolated from Pozas Azules II stromatolite in Mexico. Sequenced at 454 life Sciences. 4440067.3.fa.gz4440067.328385PAStromBahamasMic072205NoneMicrobialMicrobialitesMya BreitbartMarine26.985876, -102.06639007/22/2005
66Pozas Azules Stromatolites phagesViral community isolated from the Pozas Azules microbiolite in Cuatro Cienagas, Mexico. Sequenced at 454 Life Sciences.Desnues, C. M. et al. Nature, In press.4440320.3.fa.gz4440320.328355PAStromCCMexVir072205NoneViralMicrobialitesMya BreitbartMarine26.985876, -102.06639007/22/2005
67Rios Mesquites Stromatolites phagesViral community isolated from the Rios Mesquites microbiolite in Cuatro Cienagas, Mexico. Sequenced at 454 Life Sciences.Desnues, C. M. et al. Nature, In press.4440321.3.fa.gz4440321.328357RMStromCCMexVir072205NoneViralMicrobialitesMya BreitbartMarine26.985876, -102.06639007/22/2005
68Highborne Cay Stromatolite phageViral community isolated from Highborne Cay microbiolite in the Bahamas. Sequenced at 454 Life SciencesDesnues, et al Nature, In press.4440323.3.fa.gz4440323.328381HBCStromBahamasVir011105NoneViralMicrobialitesChristelle DesnuesMarine24.709876, -76.82252101/11/2005
69Healthy slime bacteriaMicrobial community isolated from the slime layer of hybrid striped bass from Kent SeaTech (Salton Sea, CA). The fish showed no sign of disease. Sequencing was done at 454 Life Sciences. 4440059.3.fa.gz4440059.328393FishHealSlimKentSTMic050406NoneMicrobialFish-associatedChristelle DesnuesFish; Tilapia33.537594, -116.09775105/04/2006
70Morbid slime bacteriaMicrobial community isolated from the slime layer of hybrid striped bass from Kent SeaTech (Salton Sea, CA). The fish were sick at time of sampling. Sequencing was done at 454 Life Sciences. 4440066.3.fa.gz4440066.328395FishMorSlimKentSTMic050406NoneMicrobialFish-associatedChristelle DesnuesFish; Tilapia33.537594, -116.09775105/04/2006
71Healthy gut bacteriaMicrobial community isolated from the gut contents of hybrid striped bass from Kent SeaTech (Salton Sea, CA). The fish showed no sign of disease. Sequencing was done at 454 Life Sciences. 4440055.3.fa.gz4440055.328389FishHealGutKentSTMic050406NoneMicrobialFish-associatedChristelle DesnuesFish; Tilapia33.537594, -116.09775105/04/2006
72Morbid gut bacteriaMicrobial community isolated from the gut contents of hybrid striped bass from Kent SeaTech (Salton Sea, CA). The fish were sick at time of sampling. Sequencing was done at 454 Life Sciences. 4440056.3.fa.gz4440056.328391FishMorGutKentSTMic050406NoneMicrobialFish-associatedChristelle DesnuesFish; Tilapia33.537594, -116.09775105/04/2006
73Healthy slime virusesViral community isolated from the slime layer of hybrid striped bass from Kent SeaTech (Salton Sea, CA). The fish showed no sign of disease. Sequencing was done at 454 Life Sciences. 4440065.3.fa.gz4440065.328401FishHealSlimKentSTVir050406NoneViralFish-associatedChristelle DesnuesFish; Tilapia33.537594, -116.09775105/04/2006
74Morbid slime virusesViral community isolated from the slime layer of hybrid striped bass from Kent SeaTech (Salton Sea, CA). The fish were sick at time of sampling. Sequencing was done at 454 Life Sciences. 4440064.3.fa.gz4440064.328403FishMorSlimKentSTVir050406NoneViralFish-associatedChristelle DesnuesFish; Tilapia33.537594, -116.09775105/04/2006
75Pooled PlanktonicTotal microbial community from cow rumens 4440357.3.fa.gz4440357.328611 NoneMicrobialTerrestrial animal associatedBryan WhiteCattle; Rumen; Farm
7680F6Total microbial community from cow rumens 4440356.3.fa.gz4440356.328605 NoneMicrobialTerrestrial animal associatedBryan WhiteCattle; Rumen; Farm
77640F6Total microbial community from cow rumens 4440355.3.fa.gz4440355.328607 NoneMicrobialTerrestrial animal associatedBryan WhiteCattle; Rumen; Farm
78710F6Total microbial community from cow rumens 4440387.3.fa.gz4440387.328609 NoneMicrobialTerrestrial animal associatedBryan WhiteCattle; Rumen; Farm
79Lean MiceTotal microbial community from lean mice. This is the sample that I called 164. It is from the Turnbaugh experimentTurnbaugh et al., Nature. 2006 444(7122):1027-31.4440463.3.fa.gz4440463.317401 NoneMicrobialTerrestrial animal-associatedPeter TurnbaughMice; Intestine; Lean Mice
80Obese MiceTotal microbial community from obese mice. This is the sample that I called 165. It is from the Turnbaugh experimentTurnbaugh et al., Nature. 2006 444(7122):1027-31.4440464.3.fa.gz4440464.317401 NoneMicrobialTerrestrial animal-associatedPeter TurnbaughMice; Intestine; Obese Mice
81Chicken Cecum BTotal microbial community from chicken cecum 4440367.3.fa.gz4440367.328599 NoneMicrobialTerrestrial animal associatedBryan WhiteChicken Intestine; Farm
82Chicken Cecum ATotal microbial community from chicken cecum 4440368.3.fa.gz4440368.328597 NoneMicrobialTerrestrial animal associatedBryan WhiteChicken Intestine; Farm
83CF Lung Sputum VirusesViral community isolated from the sputum of Cystic Fibrosis patient in a non-exacerbated state. Subject tests positive for Pseudomonas aeruginosa. Third sequencing. Sequenced at 454 Life Sciences. Human DNA contamination. 4440441.3.fa.gz4440441.328441CFLungSDPat001Rep3Vir050506Sequences similar to human DNA removedViralTerrestrial animal-associatedMike FurlanLungs; Cystic Fibrosis32.777580, -117.07132405/05/2006
84Health Lung Sputum VirusesViral community isolated from the sputum of an asymptomatic patient.Third sequencing. Sequenced at 454 Life Sciences. Human DNA contamination. 4440442.4.fa.gz4440442.428439HealSputSDRep3Vir070706Sequences similar to human DNA removedViralTerrestrial animal-associatedMike FurlanLungs; Cystic Fibrosis32.777580, -117.07132407/07/2006
85Mosquito DNA 1Viral community isolated from mixed species mosquitoes collected at Buena Vista Lagoon in Oceanside, CA. Sequenced at the Genome Institute of Singapore. 4440052.3.fa.gz4440052.328413MosqISDVir01252006NoneViralMosquitoDana HallInsect32.934670, -117.26055901/25/2006
86Mosquito DNA 2Mung bean nuclease digestion of DNA isolated from viral community in Mosquito DNA II sample. Sequenced at the Genome Institute of Singapore. Quality scores can be found at Genome Institute of Singapore. 4440053.3.fa.gz4440053.328467MosqDigSDVir060606NoneViralMosquitoDana HallInsect33.462526, -117.08065306/06/2006
87Mosquito DNA 3Viral community isolated from mixed species mosquitoes collected in Mission Valley in San Diego, CA. Sequenced at the Genome Institute of Singapore. Quality scores can be found at Genome Institute of Singapore. 4440054.3.fa.gz4440054.328469MosqIISDVir060606NoneViralMosquitoDana HallInsect33.462526, -117.08065306/06/2006
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