metagenome all kinds of fun

Microbial diversity

Much of the interest in metagenomics comes from the discovery that the vast majority of microorganisms had previously gone unnoticed. Traditional microbiological methods relied upon laboratory cultures of organisms. Surveys of ribosomal RNA (rRNA) genes taken directly from the environment revealed that cultivation based methods find less than 1% of the bacteria and archaea species in a sample.[3]

Gene surveys

Shotgun sequencing and screens of clone libraries reveal genes present in environmental samples. This provides information both on which organisms are present and what metabolic processes are possible in the community. This can be helpful in understanding the ecology of a community, particularly if multiple samples are compared to each other.[31]

Environmental genomes

Shotgun metagenomics also is capable of sequencing nearly complete microbial genomes directly from the environment.[14] Because the collection of DNA from an environment is largely uncontrolled, the most abundant organisms in an environmental sample are most highly represented in the resulting sequence data. To achieve the high coverage needed to fully resolve the genomes of underrepresented community members, large samples, often prohibitively so, are needed. On the other hand, the random nature of shotgun sequencing ensures that many of these organisms will be represented by at least some small sequence segments. Due to the limitations of microbial isolation methods, the vast majority of these organisms would go unnoticed using traditional culturing techniques.

1.

Metagenomic analysis of stress genes in microbial mat communities from Antarctica and the High Arctic.

Varin T, Lovejoy C, Jungblut AD, Vincent WF, Corbeil J.

Appl Environ Microbiol. 2011 Nov 11. [Epub ahead of print]

PMID:
22081564
[PubMed - as supplied by publisher]

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2.

A Method for Metagenomics of Helicobacter pylori from Archived Formalin-Fixed Gastric Biopsies Permitting Longitudinal Studies of Carcinogenic Risk.

Zheng Z, Andersson AF, Ye W, Nyrén O, Normark S, Engstrand L.

PLoS One. 2011;6(10):e26442. Epub 2011 Oct 21.

PMID:
22031833
[PubMed - in process]
Free PMC Article

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3.

Metagenomic Profile of the Bacterial Communities Associated with Ixodes ricinus Ticks.

Carpi G, Cagnacci F, Wittekindt NE, Zhao F, Qi J, Tomsho LP, Drautz DI, Rizzoli A, Schuster SC.

PLoS One. 2011;6(10):e25604. Epub 2011 Oct 13.

PMID:
22022422
[PubMed - in process]
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4.

Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome.

Berg Miller ME, Yeoman CJ, Chia N, Tringe SG, Angly FE, Edwards RA, Flint HJ, Lamed R, Bayer EA, White BA.

Environ Microbiol. 2011 Oct 17. doi: 10.1111/j.1462-2920.2011.02593.x. [Epub ahead of print]

PMID:
22004549
[PubMed - as supplied by publisher]

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5.

Comparative analysis of hydrogen-producing bacterial biofilms and granular sludge formed in continuous cultures of fermentative bacteria.

Chojnacka A, Błaszczyk MK, Szczęsny P, Nowak K, Sumińska M, Tomczyk-Żak K, Zielenkiewicz U, Sikora A.

Bioresour Technol. 2011 Nov;102(21):10057-64. Epub 2011 Aug 22.

PMID:
21908188
[PubMed - in process]

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6.

Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools.

Li RW, Connor EE, Li C, Baldwin Vi RL, Sparks ME.

Environ Microbiol. 2011 Sep 12. doi: 10.1111/j.1462-2920.2011.02543.x. [Epub ahead of print]

PMID:
21906219
[PubMed - as supplied by publisher]

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7.

A Molecular Enrichment Strategy Based on cpn60 for Detection of Epsilon-Proteobacteria in the Dog Fecal Microbiome.

Chaban B, Links MG, Hill JE.

Microb Ecol. 2011 Sep 1. [Epub ahead of print]

PMID:
21881944
[PubMed - as supplied by publisher]

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8.

A 'universal' type II chaperonin PCR detection system for the investigation of Archaea in complex microbial communities.

Chaban B, Hill JE.

ISME J. 2011 Jul 21. doi: 10.1038/ismej.2011.96. [Epub ahead of print]

PMID:
21776031
[PubMed - as supplied by publisher]

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9.

Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass.

Gladden JM, Allgaier M, Miller CS, Hazen TC, VanderGheynst JS, Hugenholtz P, Simmons BA, Singer SW.

Appl Environ Microbiol. 2011 Aug 15;77(16):5804-12. Epub 2011 Jul 1.

PMID:
21724886
[PubMed - in process]

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10.

Metagenomic comparison of direct and indirect soil DNA extraction approaches.

Delmont TO, Robe P, Clark I, Simonet P, Vogel TM.

J Microbiol Methods. 2011 Sep;86(3):397-400. Epub 2011 Jun 25.

PMID:
21723887
[PubMed - in process]

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11.

Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat.

Liu Z, Klatt CG, Wood JM, Rusch DB, Ludwig M, Wittekindt N, Tomsho LP, Schuster SC, Ward DM, Bryant DA.

ISME J. 2011 Aug;5(8):1279-90. doi: 10.1038/ismej.2011.37. Epub 2011 Jun 23.

PMID:
21697962
[PubMed - indexed for MEDLINE]

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12.

Going deeper: metagenome of a hadopelagic microbial community.

Eloe EA, Fadrosh DW, Novotny M, Zeigler Allen L, Kim M, Lombardo MJ, Yee-Greenbaum J, Yooseph S, Allen EE, Lasken R, Williamson SJ, Bartlett DH.

PLoS One. 2011;6(5):e20388. Epub 2011 May 24.

PMID:
21629664
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13.

Comparative fecal metagenomics unveils unique functional capacity of the swine gut.

Lamendella R, Domingo JW, Ghosh S, Martinson J, Oerther DB.

BMC Microbiol. 2011 May 15;11:103.

PMID:
21575148
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14.

Uncultured archaea dominate in the thermal groundwater of Uzon Caldera, Kamchatka.

Mardanov AV, Gumerov VM, Beletsky AV, Perevalova AA, Karpov GA, Bonch-Osmolovskaya EA, Ravin NV.

Extremophiles. 2011 May;15(3):365-72. Epub 2011 Apr 22.

PMID:
21512891
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15.

Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads.

Bartram AK, Lynch MD, Stearns JC, Moreno-Hagelsieb G, Neufeld JD.

Appl Environ Microbiol. 2011 Jun;77(11):3846-52. Epub 2011 Apr 1. Erratum in: Appl Environ Microbiol. 2011 Aug;77(15):5569.

PMID:
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16.

Metagenomics.

Gilbert JA, Laverock B, Temperton B, Thomas S, Muhling M, Hughes M.

Methods Mol Biol. 2011;733:173-83.

PMID:
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17.

Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities.

Stewart FJ, Sharma AK, Bryant JA, Eppley JM, DeLong EF.

Genome Biol. 2011;12(3):R26. Epub 2011 Mar 22.

PMID:
21426537
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18.

Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements.

Kristiansson E, Fick J, Janzon A, Grabic R, Rutgersson C, Weijdegård B, Söderström H, Larsson DG.

PLoS One. 2011 Feb 16;6(2):e17038.

PMID:
21359229
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19.

Comparative metagenomics of microbial traits within oceanic viral communities.

Sharon I, Battchikova N, Aro EM, Giglione C, Meinnel T, Glaser F, Pinter RY, Breitbart M, Rohwer F, Béjà O.

ISME J. 2011 Jul;5(7):1178-90. doi: 10.1038/ismej.2011.2. Epub 2011 Feb 10.

PMID:
21307954
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20.

Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice.

Kellermayer R, Dowd SE, Harris RA, Balasa A, Schaible TD, Wolcott RD, Tatevian N, Szigeti R, Li Z, Versalovic J, Smith CW.

FASEB J. 2011 May;25(5):1449-60. Epub 2011 Jan 12.

PMID:
21228220
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