Environmental Databases (EMBL)
Table S3. 22 Environmental databases in NCBI
Database(Accessions) / Size (Mbp) / NCBI Accession no / Site of sample
collection / Source of DNA / References
Candidatus Kuenenia stuttgartiensis / 4.2 / CT030148 and CT573071-CT573074 / Dokhaven wastewater treatment plant from Rotterdam, the Netherlands / Reconstruction of the Kuenenia stuttgartiensis genome from the anaerobic ammonium oxidation bioreactor that had been inoculated with nitrification slude from the wastewater treatment plant. Sampling was done one year after inoculation. / Strous et al. 2006
Combined gut microbiome of obese and lean mice / 199.8 / AATF00000000 / Distal gut of genetically obese mice and their lean littermates / Isolation from the distal gut of eight-week old obese and lean mice / Turnbaugh et al. 2006
Methane-Oxidizing Archaea from Deep-Sea Sediments / 123.3 / AY714814 - AY714873 / Eel River Basin off the Mendocino California coastline / Isolation from a 6- to 9-cm-deep sediment pushcore interval / Hallam et al. 2004
North Pacific Subtropical Gyre planktonic microbial community / ~64 / DU731018 - DU796676, DU800850 - DU800864, DQ300508 - DQ300926 / Hawaii open-ocean time-series station ALOHA in the North Pacific Ocean (N22.45 W158) / Planktonic microbial community at different depths (10m to 4000m) / DeLong et al., 2006
Marine metagenome (Global ocean sampling, GOS) / 8072 / AACY00000000 / World’s oceans / Marine microbial community at different world’s oceans / Kannan et al., 2007, Rusch et al., 2007, Yooseph et al., 2007, Venter et al., 2004
Mine drainage metegenome / ~100 / AAWO00000000 / Richmond Mine at Iron Mountain, California / Microbial biofilms in the mine drainage / Lo et al., 2007
Uncultured human fecal virus / N.A. / AAMI00000000, AAMH00000000,
AAMG00000000 / Three fecal samples from two healthy adults in San Diego, California / Enteric RNA viral community from uncultured viruses that were concentrated by tangential flow filtration / Zhang et al., 2006
Uncultured marine RNA virus / N.A. / DQ439712 – DQ439732 / English Bay at Jericho Pier and the Strait of Georgia, British Columbia, Canada / Natural virus communities were concentrated from Sea. / Culley et al., 2006
Acid Mine Drainage Biofilm Community / 76 / AADL00000000 / Richmond Mine at Iron Mountain, California / Microbial biofilms in the acid mine drainage / Ram et al., 2005, Tringe et al., 2005 & Tyson et al., 2004
Human Distal Gut Biome / ~78 / AAQL00000000,
AAQK00000000 / fecal DNAs of two healthy adults / Human intestinal microbiota in the fecal specimens / Gill et al., 2006
Mammuthus primigenius / 28 / CAAM00000000 / Bol'shaya Kolopatkaya River in Russia & Lake Taimyr in Siberia / Extraction of DNA from a 43,000 old mammoth (Mammuthus primigenius) bone and woolly mammoth / Krause et al., 2006 & Poinar et al., 2006
Mediterranean gutless worm symbiont / 204 / AASZ00000000 / Capo di Sant' Andrea, Elba, Italy / Marine oligochaetes Olavius Isolation of algarvenis and Olavius ilvae from silicate sediments in a bay / Woyke et al., 2006
Neanderthal metagenome / 32 / CAAN00000000 / Vindija Cave, Croatia / Extraction of DNA from the Vi-80 Neanderthal bone that was discovered in the layer G3 of Vindija Cave in 1980 / Green et al., 2006
OZ EBPR sludge / 78 / AATN00000000 / Thornside Sewage Treatment Plant in Queensland, Australia / Microbial community in the sludge samples from wastewater treatment plants / Garcia et al., 2006
Soil Sample from Waseca County Farm / 100 / AAFX00000000 / A farm in Waseca Country, Minnesota. / Microbes in surface soil (0-10cm) / Tringe et al. 2005
US EBPR sludge / 98 / AATO00000000 / Nine Springs Wastewater Treatment Plant in Madison, Wisconsin, USA / Microbial community in the sludge samples from wastewater treatment plants / Garcia et al., 2006
Whale Fall Community / 75 / AAFY00000000, AAFZ00000000,
AAGA00000000 / Pacific Ocean, Santa Cruz Basin (N33.30 W119.22) and West Antarctic Peninsula Shelf (S65.10 W64.47) / Microbial community from a rib bone of a gray whale carcass and a whale bone at a depth of 1674m and 560m, respectively / Tringe et al. 2005
N.A.: Not available.
Culley AI et al., Metagenomic analysis of coastal RNA virus communities. Science, 2006 Jun 23;312(5781):1795-8
DeLong EF et al., Community genomics among stratified microbial assemblages in the ocean's interior. Science, 2006 Jan 27;311(5760):496-503
Garcia Martin H et al., Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol, 2006 Oct;24(10):1263-9
Gill SR et al., Metagenomic analysis of the human distal gut microbiome. Science, 2006 Jun 2;312(5778):1355-9
Green RE et al., Analysis of one million base pairs of Neanderthal DNA. Nature, 2006 Nov 16;444(7117):330-6
Hallam SJ et al., Reverse methanogenesis: testing the hypothesis with environmental genomics. Science, 2004 Sep 3;305(5689):1457-62
Lo I et al., Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature, 2007 Mar 29;446(7135):537-41
Kannan N et al., Structural and Functional Diversity of the Microbial Kinome. PLoS Biol, 2007 Mar 13;5(3):e17
Krause J et al., Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature, 2006 Feb 9;439(7077):724-7
Poinar HN et al., Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science, 2006 Jan 20;311(5759):392-4
Ram RJ et al., Community proteomics of a natural microbial biofilm. Science, 2005 Jun 24;308(5730):1915-20
Rusch DB et al., The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol, 2007 Mar 13;5(3):e77
Strous M et al., Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature, 2006 Apr 6;440(7085):790-4
Tringe SG et al., Comparative metagenomics of microbial communities. Science, 2005 Apr 22;308(5721):554-7
Turnbaugh PJ et al., An obesity-associated gut microbiome with increased capacity for energy harvest. Nature, 2006 Dec 21;444(7122):1027-31
Tyson GW et al., Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 2004 Mar 4;428(6978):37-43
Venter JC et al., Environmental genome shotgun sequencing of the Sargasso Sea. Science, 2004 Apr 2;304(5667):66-74
Woyke T et al., Symbiosis insights through metagenomic analysis of a microbial consortium. Nature, 2006 Oct 26;443(7114):950-5
Yooseph S et al., The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families. PLoS Biol, 2007 Mar 13;5(3):e16
Zhang T et al., RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol, 2006 Jan;4(1):e3