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:
Elizabeth A. Dinsdale, Robert A. Edwards, Dana Hall, Florent Angly, Mya
Breitbart, Jennifer M. Brulc, Michael Furlan, Christelle Desnues,
Matthew Haynes, Linlin Li, Lauren McDaniel, Mary Ann Moran, Karen E.
Nelson, Christina Nilsson, Robert Olson, John Paul, Beltran Rodriguez
Brito, Yijun Ruan, Brandon K. Swan, Rick Stevens, David L. Valentine,
Rebecca Vega-Thurber, Linda Wegley, Bryan A. White, and Forest Rohwer.
Functional Metagenomic Profiling of Nine Biomes. Nature 452, 629-632 (3 April 2008). Available online.
Total
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.
Microbial
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.
Microbial
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.
Microbial
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.
Microbial
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.
Viral
fraction from water below the boundary layer (e.g., crevices and
benthic surfaces) of Kingman Atoll (Northern Line Islands). Sequenced
at 454 Life Sciences.
Viral
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.
Viral
fraction from water below the boundary layer (e.g., crevices and
benthic surfaces) of Palmyra (Northern Line Islands). Sequenced at 454
Life Sciences.
Viral
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.
Microbes
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.
Microbes
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.
Microbes
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.
Microbes
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.
Microbes
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.
Microbes
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.
Microbes
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.
Viruses
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.
Viruses
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.
Viruses
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.
Viruses
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.
Viruses
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.
Viruses
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.
Microbial
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.
Microbial
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.
Microbial
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.
Microbial
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.
Viral
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.
Viral
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.
Viral
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.
Viral
community isolated from mixed species mosquitoes collected at Buena
Vista Lagoon in Oceanside, CA. Sequenced at the Genome Institute of
Singapore.
Mung
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.
Viral
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.
