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2010
BIBLIOGRAPHY
Rook GAW. 99th Dahlem conference on infection, inflammation and chronic inflammatory disorders: Darwinian medicine and the “hygiene” or “old friends” hypothesis. Clin Exp Immunol. 2010;160:70–79.
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Kirchner S, Kieu T, Chow C, Casey S, Blumberg B. Prenatal exposure to the environmental obesogen tributyltin predisposes multipotent stem cells to become adipocytes. Mol Endocrinol. 2010;24(3):526–539.
Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, et al. 2010. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One 52e9085; doi:[Online 5 February 2010] doi: 10.1371/journal.pone.0009085.
Lee DH, Steffes MW, Sjodin A, Jones RS, Needham LL, Jacobs DR., Jr Low dose of some persistent organic pollutants predicts type 2 diabetes: a nested case–control study. Environ Health Perspect. 2010;118:1235–1242.
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Charoensawan V, Wilson D, Teichmann SA. Genomic repertoires of DNA-binding transcription factors across the tree of life. Nucleic Acids Research. 2010;38:7364–7377. doi: 10.1093/nar/gkq617.
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Yooseph S, Nealson KH, Rusch DB, McCrow JP, Dupont CL, Kim M, Johnson J, Montgomery R, Ferriera S, Beeson K, Williamson SJ, Tovchigrechko A, Allen AE, Zeigler LA, Sutton G, Eisenstadt E, Rogers Y-H, Friedman R, Frazier M, Venter JC. Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature. 2010;468:60–66. doi: 10.1038/nature09530.
Rusch DB, Martiny AC, Dupont CL, Halpern AL, Venter JC. Characterization of Prochlorococcus clades from iron-depleted oceanic regions. Proceedings of the National Academy of Sciences. 2010;107:16184–16189. doi: 10.1073/pnas.1009513107.
Beszteri B, Temperton B, Frickenhaus S, Giovannoni SJ. Average genome size: a potential source of bias in comparative metagenomics. ISME J. 2010;4:1075–1077. doi: 10.1038/ismej.2010.29.
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer ELL, Eddy SR, Bateman A. The Pfam protein families database. Nucl Acids Res. 2010;38:D211–222. doi: 10.1093/nar/gkp985.
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Oksanen J, Blanchet FG, Kindt R, Legendre P, O'Hara RB, Simpson GL, Solymos P, Stevens MHH, Wagner H. vegan: Community Ecology Package. 2010.
Brown BL, Swan CM. Dendritic network structure constrains metacommunity properties in riverine ecosystems. Journal of Animal Ecology. 2010;79:571–580.
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Heino J, Bini LM, Karjalainen SM, Mykrä H, Soininen J, et al. Geographical patterns of micro-organismal community structure: are diatoms ubiquitously distributed across boreal streams? Oikos. 2010;119:129–137.
Scheckenbach F, Hausmann K, Wylezich C, Weitere M, Arndt H. Large-scale patterns in biodiversity of microbial eukaryotes from the abyssal sea floor. Proceedings of the National Academy of Sciences. 2010;107:115–120.
Bennett JR, Cumming BF, Ginn BK, Smol JP. Broad-scale environmental response and niche conservatism in lacustrine diatom communities. Global Ecology and Biogeography. 2010;19:724–732.
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Anderson MJ, Crist TO, Chase JM, Vellend M, Inouye BD, et al. Navigating the multiple meanings of ß diversity: a roadmap for the practicing ecologist. Ecology Letters. 2010:no-no.
Kraft NJB, Ackerly DD. Functional trait and phylogenetic tests of community assembly across spatial scales in an Amazonian forest. Ecological Monographs. 2010;80:401–422.
Gilbert B, Bennett JR. Partitioning variation in ecological communities: do the numbers add up? Journal of Applied Ecology. 2010;47:1071–1082.
Brook I. (2010). The role of anaerobic bacteria in bacteremia. Anaerobe 16, 183–189. doi: 10.1016/j.anaerobe.2009.12.001.
De Filippo C., Cavalieri D., Di Paola M., Ramazzotti M., Poullet J. B., Massart S., Collini S., Pieraccini G., Lionetti P. (2010). Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl. Acad. Sci. U.S.A. 107, 14691–14696.
Del Rio T. G., Abt B., Spring S., Lapidus A., Nolan M., Tice H., Copeland A., Cheng J.-F., Chen F., Hugenholtz P., Kyrpides N. C., Klenk H.-P., Lucas S. (2010). Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034T). Stand. Genomic Sci. 2, 87–95. doi: 10.4056/sigs.661199.
DeLong E. F., Beja O. (2010). The light-driven proton pump proteorhodopsin enhances bacterial survival during tough times. PLoS Biol. 8, e1000359. doi: 10.1371/journal.pbio.1000359.
Edwards J. L., Smith D. L., Connolly J., Mcdonald J. E., Cox M. J., Joint I., Edwards C., Mccarthy A. J. (2010). Identification of carbohydrate metabolism genes in the metagenome of a marine biofilm community shown to be dominated by Gammaproteobacteria and Bacteroidetes. Genes 1, 371–384. doi: 10.3390/genes1030371.
Gomez-Pereira P. R., Fuchs B. M., Alonso C., Oliver M. J., Van Beusekom J. E., Amann R. (2010). Distinct flavobacterial communities in contrasting water masses of the north Atlantic Ocean. ISME J. 4, 472–487. doi: 10.1038/ismej.2009.142.
Hehemann J. H., Correc G., Barbeyron T., Helbert W., Czjzek M., Michel G. (2010). Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464, 908–912. doi: 10.1038/nature08937.
Julies E. M., Fuchs B. M., Arnosti C., Brüchert V. (2010). Organic carbon degradation in anoxic organic-rich shelf sediments: biogeochemical rates and microbial abundance. Geomicrobiol. J. 27, 303–314.
Knapp B. A., Seeber J., Rief A., Meyer E., Insam H. (2010). Bacterial community composition of the gut microbiota of Cylindroiulus fulviceps (diplopoda) as revealed by molecular fingerprinting and cloning. Folia Microbiol. (Praha) 55, 489–496. doi: 10.1007/s12223-010-0081-y.
Koropatkin N. M., Smith T. J. (2010). SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules. Structure 18, 200–215. doi: 10.1016/j.str.2009.12.010.
Lail K., Sikorski J., Saunders E., Lapidus A., Del Rio T. G., Copeland A., Tice H., Cheng J.-F., Lucas S., Kyrpides N. C., Klenk H.-P., Chen F. (2010). Complete genome sequence of Spirosoma linguale type strain (1T). Stand. Genomic Sci. 2, 176–185. doi: 10.4056/sigs.741334.
Lee M., Woo S. G., Park J., Yoo S. A. (2010). Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil. Int. J. Syst. Evol. Microbiol. 60, 2577–2582./div>
Leng J., Xie L., Zhu R., Yang S., Gou X., Li S., Mao H. (2010). Dominant bacterial communities in the rumen of Gayals (Bos frontalis ), Yaks (Bos grunniens ) and Yunnan Yellow Cattle (Bos taurs ) revealed by denaturing gradient gel electrophoresis. Mol. Biol. Rep.PMID: 21140219.
Marchesi J. R. (2010). Prokaryotic and eukaryotic diversity of the human gut. Adv. Appl. Microbiol. 72, 43–62.
Martinez I., Kim J., Duffy P. R., Schlegel V. L., Walter J. (2010). Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. PLoS ONE 5, e15046. doi: 10.1371/journal.pone.0015046.
Martinez-Alonso M., Escolano J., Montesinos E., Gaju N. (2010). Diversity of the bacterial community in the surface soil of a pear orchard based on 16S rRNA gene analysis. Int. Microbiol. 13, 123–134.
Matsui H., Kato Y., Chikaraishi T., Moritani M., Ban-Tokuda T., Wakita M. (2010). Microbial diversity in ostrich ceca as revealed by 16S ribosomal RNA gene clone library and detection of novel Fibrobacter species. Anaerobe 16, 83–93. doi: 10.1016/j.anaerobe.2009.07.005.
McCutcheon J. P., Moran N. A. (2010). Functional convergence in reduced genomes of bacterial symbionts spanning 200 my of evolution. Genome Biol. Evol. 2, 708–718.
Michel G., Tonon T., Scornet D., Cock J. M., Kloareg B. (2010a). The cell wall polysaccharide metabolism of the brown alga Ectocarpus siliculosus. Insights into the evolution of extracellular matrix polysaccharides in Eukaryotes. New Phytol. 188, 82–97. doi: 10.1111/j.1469-8137.2010.03374.x.
Michel G., Tonon T., Scornet D., Cock J. M., Kloareg B. (2010b). Central and storage carbon metabolism of the brown alga Ectocarpus siliculosus : insights into the origin and evolution of storage carbohydrates in Eukaryotes. New Phytol. 188, 67–81. doi: 10.1111/j.1469-8137.2010.03345.x.
Middelbos I. S., Vester Boler B. M., Qu A., White B. A., Swanson K. S., Fahey G. C., Jr. (2010). Phylogenetic characterization of fecal microbial communities of dogs fed diets with or without supplemental dietary fiber using 454 pyrosequencing. PLoS ONE 5, e9768. doi: 10.1371/journal.pone.0009768.
Oh H. M., Kang I., Ferriera S., Giovannoni S. J., Cho J. C. (2010). Complete genome sequence of Croceibacter atlanticus HTCC2559(T). J. Bacteriol. 192, 4796–4797. doi: 10.1128/JB.00733-10.
Pena A., Teeling H., Huerta-Cepas J., Santos F., Yarza P., Brito-Echeverría J., Lucio M., Schmitt-Kopplin P., Meseguer I., Schenowitz C., Dossat C., Barbe V., Dopazo J., Rosselló-Mora R., Schüler M., Glöckner F. O., Amann R., Gabaldón T., Antón J. (2010). Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains. ISME J. 4, 882–895. doi: 10.1038/ismej.2010.6.
Pope P. B., Denman S. E., Jones M., Tringe S. G., Barry K., Malfatti S. A., Mchardy A. C., Cheng J. F., Hugenholtz P., Mcsweeney C. S., Morrison M. (2010). Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proc. Natl. Acad. Sci. U.S.A. 107, 14793–14798.
Purushe J., Fouts D. E., Morrison M., White B. A., Mackie R. I., Coutinho P. M., Henrissat B., Nelson K. E. (2010). Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii : insights into their environmental niche. Microb. Ecol. 60, 721–729.
Qin Q. L., Zhang X. Y., Wang X. M., Liu G. M., Chen X. L., Xie B. B., Dang H. Y., Zhou B. C., Yu J., Zhang Y. Z. (2010). The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation. BMC Genomics 11, 247. doi: 10.1186/1471-2164-11-247.
Redford A. J., Bowers R. M., Knight R., Linhart Y., Fierer N. (2010). The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ. Microbiol. 12, 2885–2893.
Salaun S., Kervarec N., Potin P., Haras D., Piotto M., La Barre S. (2010). Whole-cell spectroscopy is a convenient tool to assist molecular identification of cultivatable marine bacteria and to investigate their adaptive metabolism. Talanta 80, 1758–1770. doi: 10.1016/j.talanta.2009.10.020.
Schmitz-Esser S., Tischler P., Arnold R., Montanaro J., Wagner M., Rattei T., Horn M. (2010). The genome of the amoeba symbiont “Candidatus Amoebophilus asiaticus ” reveals common mechanisms for host cell interaction among amoeba-associated bacteria. J. Bacteriol. 192, 1045–1057. doi: 10.1128/JB.01379-09
Sonnenburg E. D., Zheng H., Joglekar P., Higginbottom S. K., Firbank S. J., Bolam D. N., Sonnenburg J. L. (2010). Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell 141, 1241–1252. doi: 10.1016/j.cell.2010.05.005.
Sonnenburg J. L. (2010). Microbiology: genetic pot luck. Nature 464, 837–838. doi: 10.1038/464837a.
Turnbaugh P. J., Henrissat B., Gordon J. I. (2010). Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66, 1261–1264.
Zhu Y., Suits M. D., Thompson A. J., Chavan S., Dinev Z., Dumon C., Smith N., Moremen K. W., Xiang Y., Siriwardena A., Williams S. J., Gilbert H. J., Davies G. J. (2010). Mechanistic insights into a Ca2 -dependent family of alpha-mannosidases in a human gut symbiont. Nat. Chem. Biol. 6, 125–132.s
Feng F, Goto D, Yan T. Effects of autochthonous microbial community on the die-of of fecal indicators in tropical beach sand. FEMS Microb. Ecol. 2010;74(10):214–225.
Fleisher JM, Fleming LE, Solo-Gabriele HM, Kish JK, Sinigalliano CD, Plano L, Elmir SM, Wang JD, Withum K, Shibata T, et al. The BEACHES Study: health effects and exposures from nonpoint source microbial contaminants in subtrobical recreational marine waters. Intl. J. Epidemiol. 2010 Advance Access published on June 3, 2010.
Abdelzaher AM, Wright ME, Ortega C, Solo-Gabriele HM, Miller G, Elmir S, Newman X, Shih P, Alfredo Bonilla J, Bonilla T, et al. Presence of Pathogens and Indicator Microbes at a Non-Point Source Subtropical Recreational Marine Beach. Appl. Environ. Microbiol. 2010;76(3):724–732.
Craft JA, Gilbert JA, Temperton B, Dempsey KE, Ashelford K, Tiwari B, et al. Pyrosequencing of Mytilus galloprovincialis cDNAs: tissue-specific expression patterns. PLoS ONE. 2010;5:e8875.
Glöckner FO, Joint I. Marine microbial genomics in Europe: current status and perspectives. Microb Biotechnol. 2010;3:523–530.
Joint I, Mühling M, Querellou J. Culturing marine bacteria – an essential prerequisite for biodiscovery. Microb Biotechnol. 2010;3:564–575.
Metzker ML. Sequencing technologies- the next generation. Nat Rev Genet. 2010;11:31–46.
Sargis RM, Johnson DN, Choudhury RA, Brady MJ. 2010. Environmental endocrine disruptors promote adipogenesis in the 3T3-L1 cell line through glucocorticoid receptor activation. Obesity (Silver Spring) 1871283–1288.1288; doi:[Online 19 November 2009] doi: 10.1038/oby.2009.419.

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