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Rook GAW. Review series on helminths, immune modulation and the hygiene hypothesis: The broader implications of the hygiene hypothesis. Immunology. 2009;126:3–11.
Costello EK, et al. Bacterial community variation in human body habitats across space and time. Science. 2009;326:1694–1697.
Grice EA, et al. NISC Comparative Sequencing Program Topographical and temporal diversity of the human skin microbiome. Science. 2009;324:1190–1192.
Lloyd CM, Hawrylowicz CM. Regulatory T cells in asthma. Immunity. 2009;31:438–449.
Conrad ML, et al. Maternal TLR signaling is required for prenatal asthma protection by the nonpathogenic microbe Acinetobacter lwoffii F78. J Exp Med. 2009;206:2869–2877.
Sjögren YM, Jenmalm MC, Böttcher MF, Björkstén B, Sverremark-Ekström E. Altered early infant gut microbiota in children developing allergy up to 5 years of age. Clin Exp Allergy. 2009;39:518–526.
Akdis M. Immune tolerance in allergy. Curr Opin Immunol. 2009;21:700–707.
Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol. 2009;9:313–323.

Schloss PD, et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537–7541.

Earth Policy Institute Natural Systems. Data Center, 2009.
Ezeonu CS, Onwurah INE. Effect of crude oil contamination on Chlorophyll content in Zea mays L. International Journal of Biology and Biotechnology. 2009;6(4):299–301.
Taylor D, Gregory J, Jones M, Fosbery R. AS and A Level Biology. International Examinations Textbook. 2nd edition. University of Cambridge; 2009. The use of microorganisms to extract heavy metals from low grade ores.
U.S. Department of Energy, Office of Science. Systems Biology for Energy and Environment: Biohydrogen Production, 2009.
The third wave in Biotechnology: a primer on industrial biotechnology.2009.
Armougom F, Henry M, Vialettes B, Raccah D, Raoult D. 2009. Monitoring bacterial community of human gut microbiota reveals an increase in Lactobacillus in obese patients and methanogens in anorexic patients. PLoS One 49e7125; doi:[Online 23 September 2009] doi: 10.1371/journal.pone.0007125.
Cani PD, Lecourt E, Dewulf EM, Sohet FM, Pachikian BD, Naslain D, et al. Gut microbiota fermentation of prebiotics increases satietogenic and incretin gut peptide production with consequences for appetite sensation and glucose response after a meal. Am J Clin Nutr. 2009;90(5):1236–1243.
Clayton TA, Baker D, Lindon JC, Everett JR, Nicholson JK. Pharmacometabonomic identification of a significant host–microbiome metabolic interaction affecting human drug metabolism. Proc Natl Acad Sci USA. 2009;106(34):14728–14733.
Fenton SE, Reiner JL, Nakayama SF, Delinsky AD, Stanko JP, Hines EP, et al. Analysis of PFOA in dosed CD-1 mice. Part 2. Disposition of PFOA in tissues and fluids from pregnant and lactating mice and their pups. Reprod Toxicol. 2009;27(3–4):365–372.
Finkelstein EA, Trogdon JG, Cohen JW, Dietz W. Annual medical spending attributable to obesity: payer-and service-specific estimates. Health Aff (Millwood) 2009;28(5):w822–w831.
Heindel JJ, vom Saal FS. Role of nutrition and environmental endocrine disrupting chemicals during the perinatal period on the aetiology of obesity. Mol Cell Endocrinol. 2009;304(1–2):90–96.
Hines EP, White SS, Stanko JP, Gibbs-Flournoy EA, Lau C, Fenton SE. Phenotypic dichotomy following developmental exposure to perfluorooctanoic acid (PFOA) in female CD-1 mice: low doses induce elevated serum leptin and insulin, and overweight in mid-life. Mol Cell Endocrinol. 2009;304(1–2):97–105.
Lopez-Espinosa MJ, Freire C, Arrebola JP, Navea N, Taoufiki J, Fernandez MF, et al. Nonylphenol and octylphenol in adipose tissue of women in Southern Spain. Chemosphere. 2009;76(6):847–852.
Lundin JI, Alexander BH, Olsen GW, Church TR. Ammonium perfluorooctanoate production and occupational mortality. Epidemiology. 2009;20(6):921–928.
MacNeil J, Steenland NK, Shankar A, Ducatman A. A cross-sectional analysis of type II diabetes in a community with exposure to perfluorooctanoic acid (PFOA). Environ Res. 2009;109(8):997–1003.
Meinl W, Sczesny S, Brigelius-Flohe R, Blaut M, Glatt H. Impact of gut microbiota on intestinal and hepatic levels of phase 2 xenobiotic-metabolizing enzymes in the rat. Drug Metab Dispos. 2009;37(6):1179–1186.
Palmer JR, Herbst AL, Noller KL, Boggs DA, Troisi R, Titus-Ernstoff L, et al. 2009. Urogenital abnormalities in men exposed to diethylstilbestrol in utero: a cohort study. Environ Health 837; doi:[Online 18 August 2009] doi: 10.1186/1476-069X-8-37.
Possemiers S, Grootaert C, Vermeiren J, Gross G, Marzorati M, Verstraete W, et al. The intestinal environment in health and disease—recent insights on the potential of intestinal bacteria to influence human health. Curr Pharm Des. 2009;15(18):2051–2065.
Rahman MM, Ng JC, Naidu R. Chronic exposure of arsenic via drinking water and its adverse health impacts on humans. Environ Geochem Health. 2009;31(suppl 1):189–200.
Rignell-Hydbom A, Lidfeldt J, Kiviranta H, Rantakokko P, Samsioe G, Agardh CD, et al. 2009. Exposure to p,p’-DDE: a risk factor for type 2 diabetes. PLoS One 410e7503; doi:[Online 19 October 2009] doi: 10.1371/journal.pone.0007503.
Rowland IR. The role of the gastrointestinal microbiota in colorectal cancer. Curr Pharm Des. 2009;15(13):1524–1527.
Turnbaugh PJ, Gordon JI. The core gut microbiome, energy balance and obesity. J Physiol. 2009;587(Pt 17):4153–4158.
Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. A core gut microbiome in obese and lean twins. Nature. 2009a;457(7228):480–484.
Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. 2009b. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 1(6):6ra14.
Turyk M, Anderson H, Knobeloch L, Imm P, Persky V. Organochlorine exposure and incidence of diabetes in a cohort of Great Lakes sport fish consumers. Environ Health Perspect. 2009a;117:1076–1082.
uryk M, Anderson HA, Knobeloch L, Imm P, Persky VW. Prevalence of diabetes and body burdens of polychlorinated biphenyls, polybrominated diphenyl ethers, and p,p’-diphenyldichloroethene in Great Lakes sport fish consumers. Chemosphere. 2009b;75(5):674–679.
Wiegand H, Boesch-Saadatmandi C, Regos I, Treutter D, Wolffram S, Rimbach G. Effects of quercetin and catechin on hepatic glutathione-S transferase (GST), NAD(P)H quinone oxidoreductase 1 (NQO1), and antioxidant enzyme activity levels in rats. Nutr Cancer. 2009;61(5):717–722.
Wilson ID. Drugs, bugs, and personalized medicine: pharmacometabonomics enters the ring. Proc Natl Acad Sci USA. 2009;106(34):14187–14188.
Wilson ID, Nicholson JK. The role of gut microbiota in drug response. Curr Pharm Des. 2009;15(13):1519–1523.
Wecker P, Klockow C, Ellrott A, Quast C, Langhammer P, Harder J, Glöckner FO. Transcriptional response of the model planctomycete Rhodopirellula baltica SH1(T) to changing environmental conditions. BMC Genomics. 2009;10:410. doi: 10.1186/1471-2164-10-410.
Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB. Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci USA. 2009;106:1374–1379. doi: 10.1073/pnas.0808022106.
Lauro FM, McDougald D, Thomas T, Williams TJ, Egan S, Rice S, DeMaere MZ, Ting L, Ertan H, Johnson J, Ferriera S, Lapidus A, Anderson I, Kyrpides N, Munk AC, Detter C, Han CS, Brown MV, Robb FT, Kjelleberg S, Cavicchioli R. The genomic basis of trophic strategy in marine bacteria. Proc Natl Acad Sci USA. 2009;106:15527–15533. doi: 10.1073/pnas.0903507106.
Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inform. 2009;23:205–211.
Eddy SR. HMMER3 beta test: User's guide. 2009.
Legendre P, Mi XC, Ren HB, Ma KP, Yu MJ, et al. Partitioning beta diversity in a subtropical broad-leaved forest of China. Ecology. 2009;90:663–674.
Rominger A, Miller T, Collins S. Relative contributions of neutral and niche-based processes to the structure of a desert grassland grasshopper community. Oecologia. 2009;161:791–800.
Chase JM, Biro EG, Ryberg WA, Smith KG. Predators temper the relative importance of stochastic processes in the assembly of prey metacommunities. Ecology Letters. 2009;12:1210–1218.
Graham CH, Parra JL, Rahbek C, McGuire JA. Phylogenetic structure in tropical hummingbird communities. Proceedings of the National Academy of Sciences. 2009;106:19673–19678.
Winter M, Schweiger O, Klotz S, Nentwig W, Andriopoulos P, et al. Plant extinctions and introductions lead to phylogenetic and taxonomic homogenization of the European flora. Proceedings of the National Academy of Sciences. 2009;106:21721–21725.
Soininen J, Weckstrom J. Diatom community structure along environmental and spatial gradients in lakes and streams. Fundamental and Applied Limnology. 2009;174:205–213.
Gotelli NJ, Anderson MJ, Arita HT, Chao A, Colwell RK, et al. Patterns and causes of species richness: a general simulation model for macroecology. Ecology Letters. 2009;12:873–886.
. Ricotta C, Burrascano S. Testing for differences in beta diversity with asymmetric dissimilarities. Ecological Indicators. 2009;9:719–724.
Kembel SW. Disentangling niche and neutral influences on community assembly: Assessing the performance of community phylogenetic structure tests. Ecology Letters 2009.
Cantarel B. L., Coutinho P. M., Rancurel C., Bernard T., Lombard V., Henrissat B. (2009). The carbohydrate-active enzymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37, D233–D238.
Gihring T. M., Humphrys M., Mills H. J., Huettel M., Kostka J. E. (2009). Identification of phytodetritus-degrading microbial communities in sublittoral Gulf of Mexico sands. Limnol. Oceanogr. 54, 1073–1083.
Han C., Spring S., Lapidus A., Del Rio T. G., Tice H., Copeland A., Cheng J.-F., Lucas S., Chen F., Nolan M., Bruce D., Hugenholtz P., Kyrpides N. C., Klenk H.-P., Detter J. C. (2009). Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3T). Stand. Genomic Sci. 1, 54–62. doi: 10.4056/sigs.22138.
Hildebrandt M. A., Hoffmann C., Sherrill-Mix S. A., Keilbaugh S. A., Hamady M., Chen Y. Y., Knight R., Ahima R. S., Bushman F., Wu G. D. (2009). High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology 137, 1716–1724, e 1711.–1712.
Kim H.-J., Miller A. J., Mcgowan J., Carter M. L. (2009). Coastal phytoplankton blooms in the Southern California Bight. Prog. Oceanogr. 82, 137–147.
Lang E., Lapidus A., Chertkov O., Brettin T., Detter J. C., Han C., Copeland A., Del Rio T. G., Nolan M., Chen F., Hugenholtz P., Göker M., Rohde M., Kyrpides N. C., Klenk H.-P. (2009). Complete genome sequence of Dyadobacter fermentans type strain (NS114T). Stand. Genomic Sci. 1, 133–140. doi: 10.4056/sigs.19262
Lauber C. L., Hamady M., Knight R., Fierer N. (2009). Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 75, 5111–5120.
Lopez-Sanchez M. J., Neef A., Peretó J., Patiño-Navarrete R., Pignatelli M., Latorre A., Moya A. (2009). Evolutionary convergence and nitrogen metabolism in Blattabacterium strain Bge, primary endosymbiont of the cockroach Blattella germanica. PLoS Genet. 5, e1000721. doi: 10.1371/journal.pgen.1000721.
Lu J., Santo Domingo J. W., Hill S., Edge T. A. (2009). Microbial diversity and host-specific sequences of Canada goose feces. Appl. Environ. Microbiol. 75, 5919–5926.
Martens E. C., Koropatkin N. M., Smith T. J., Gordon J. I. (2009). Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm. J. Biol. Chem. 284, 24673–24677.
Mavrommatis K., Gronow S., Saunders E., Land M., Lapidus A., Copeland A., Del Rio T. G., Nolan M., Lucas S., Chen F., Tice H., Cheng J.-F., Bruce D., Goodwin L., Pitluck S., Pati A., Ivanova N., Chen A., Palaniappan K., Chain P., Hauser L., Chang Y.-J., Jeffries C. D., Brettin T., Detter J. C., Han C., Bristow J., Göker M., Rohde M., Eisen J. A., Markowitz V., Kyrpides N. C., Klenk H.-P., Hugenholtz P. (2009). Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845T). Stand. Genomic Sci. 1, 101–109. doi: 10.4056/sigs.15195.
McBride M. J., Xie G., Martens E. C., Lapidus A., Henrissat B., Rhodes R. G., Goltsman E., Wang W., Xu J., Hunnicutt D. W., Staroscik A. M., Hoover T. R., Cheng Y. Q., Stein J. L. (2009). Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Appl. Environ. Microbiol. 75, 6864–6875.
. Nasidze I., Li J., Quinque D., Tang K., Stoneking M. (2009a). Global diversity in the human salivary microbiome. Genome Res. 19, 636–643. doi: 10.1101/gr.084616.108.
Nasidze I., Quinque D., Li J., Li M., Tang K., Stoneking M. (2009b). Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches. Anal. Biochem. 391, 64–68. doi: 10.1016/j.ab.2009.04.034.
. Nolan M., Tindall B. J., Pomrenke H., Lapidus A., Copeland A., Glavina Del Rio T., Lucas S., Chen F., Tice H., Cheng J. F., Saunders E., Han C., Bruce D., Goodwin L., Chain P., Pitluck S., Ovchinikova G., Pati A., Ivanova N., Mavromatis K., Chen A., Palaniappan K., Land M., Hauser L., Chang Y. J., Jeffries C. D., Brettin T., Göker M., Bristow J., Eisen J. A., Markowitz V., Hugenholtz P., Kyrpides N. C., Klenk H. P., Detter J. C. (2009). Complete genome sequence of Rhodothermus marinus type strain (R-10). Stand. Genomic Sci. 1, 283–290. doi: 10.4056/sigs.46736.
Oh H. M., Giovannoni S. J., Lee K., Ferriera S., Johnson J., Cho J. C. (2009). Complete genome sequence of Robiginitalea biformata HTCC2501. J. Bacteriol. 191, 7144–7145. doi: 10.1128/JB.01191-09.
Sabree Z. L., Kambhampati S., Moran N. A. (2009). Nitrogen recycling and nutritional provisioning by Blattabacterium, the cockroach endosymbiont. Proc. Natl. Acad. Sci. U.S.A. 106, 19521–19526.
. Turnbaugh P. J., Ridaura V. K., Faith J. J., Rey F. E., Knight R., Gordon J. I. (2009). The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci. Transl. Med. 1, 6ra14.
Woyke T., Xie G., Copeland A., Gonzalez J. M., Han C., Kiss H., Saw J. H., Senin P., Yang C., Chatterji S., Cheng J. F., Eisen J. A., Sieracki M. E., Stepanauskas R. (2009). Assembling the marine metagenome, one cell at a time. PLoS ONE 4, e5299. doi: 10.1371/journal.pone.0005299.
Zhou J. P., Huang Y., Mo M. (2009). Phylogenetic analysis on the soil bacteria distributed in karst forest. Braz. J. Microbiol. 40, 827–837.
Mika KB, Imamura G, Chang C, Conway V, Fernandez G, Griffith JF, Kampalath RA, Lee CM, Lin CC, Moreno R. Pilot-and bench-scale testing of faecal indicator bacteria survival in marine beach sand near point sources. J. Appl. Microbiol. 2009;107(1):72–84.
Yamahara KM, Walters SP, Boehm AB. Growth of enterococci in unaltered, unseeded beach sands subjected to tidal wetting. Appl. Environ. Microbiol. 2009;75(6):1517–1524.
Walters SP, Yamahara KM, Boehm AB. Persistence of nucleic acid markers of health-relevant organisms in seawater microcosms: Implications for their use in assessing risk in recreational waters. Water Res. 2009;43:4929–4939.
Boehm AB, Yamahara KM, Love DC, Peterson BM, McNeill K, Nelson KL. Covariation and Photoinactivation of Traditional and Novel Indicator Organisms and Human Viruses at a Sewage-Impacted Marine Beach. Environ. Sci. Technol. 2009;43(21):8046–8052.
National Resource Defense Council (NRDC) Testing the Waters 2009: A guide to water quality at vacation beaches.
Clark CD, De Bruyn WJ, Jones JG. Photochemical production of hydrogen peroxide in size-fractionated Southern California coastal waters. Chemosphere. 2009;76:141–146.
Boehm AB, Griffith J, McGee C, Edge TA, Solo-Gabriele HM, Whitman R, Cao Y, Getrich M, Jay JA, Ferguson D, et al. Faecal indicator bacteria enumeration in beach sands. J. Appl. Microbiol. 2009;107(5):1740–1750.
Whitman RL, Przybyla-Kelly K, Shively DA, Nevers MB, Byappanahalli MN. Hand-mouth transfer and potential for exposure to E. coli and F (+) coliphage in beach sand, Chicago, Illinois. J. Water Health. 2009;7(4):623–629.
Heaney CD, Sams E, Wing S, Marshall S, Brenner K, Dufour AP, Wade TJ. Contact With Beach Sand Among Beachgoers and Risk of Illness. Am. J. Epidemiol. 2009;170(2):164–172.
Goodwin KD, Pobuda M. Performance of CHROMagarTM Staph aureus and CHROMagarTM MRSA for detection of Staphylococcus aureus in seawater and beach sand–Comparison of culture, agglutination, and molecular analyses. Water Res. 2009;43(19):4802–4811.
Soge OO, Meschke JS, No DB, Roberts MC. Characterization of methicillin-resistant Staphylococcus aureus and methicillin-resistant coagulase-negative Staphylococcus spp. isolated from US West Coast public marine beaches. J. Antimicrob. Chemother. 2009;64(6):1148–1155.
Smith CJ, Osborn AM. Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology. FEMS Microb. Ecol. 2009;67(1):6–20.
Banfield JF, Young M. Microbiology. Variety the spice of life – in microbial communities. Science. 2009;326:1198–1199.
Blazewicz J, Bryja M, Figlerowicz M, Gawron P, Kasprzak M, et al. Whole genome assembly from 454 sequencing output via modified DNA graph concept. Comput Biol Chem. 2009;33:224–230.
Brady SF, Simmons L, Kima JH, Schmidt EW. Metagenomic approaches to natural products from free-living and symbiotic organisms. Nat Prod Rep. 2009;26:1488–1503.
Caron DA, Worden AZ, Countway PD, Demir E, Heidelberg KB. Protists are microbes too: a perspective. ISME J. 2009a;3:4–12.
Caron DA, Gast RJ, Countway PD, Heidelberg KB. Microbial eukaryote ecology: questions of diversity and biogeography. Microbe. 2009b;4:71–77.
Chan EY. Next-generation sequencing methods: impact of sequencing accuracy on SNP discovery. Methods Mol Biol. 2009;578:95–111.
Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, et al. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol. 2009;10:R32.
Hewson I, Poretsky RS, Beinart RA, White A, Shi T, Bench SR, et al. In situ transcriptomic analysis of the globally important keystone N-2-fixing taxon Crocosphaera watsonii. ISME J. 2009;3:618–631.
Poretsky RS, Gifford S, Rinta-Kanto J, Vila-Costa M, Moran MA. Analyzing gene expression from marine microbial communities using environmental transcriptomics. J Vis Exp. 2009;18:1086.
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Shi Y, Tyson GW, DeLong EF. Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature. 2009;459:266–269.
Temperton B, Field D, Oliver A, Tiwari B, Mühling M, Joint I, Gilbert JA. Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing. ISME J. 2009;3:792–796.
Wilkening J, Wilke A, Desai N, Meyer F. Using clouds for metagenomics: a case study. IEEE Cluster. 2009;2009:1–6.
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Yanmei S, Tyson GW, DeLong EF. Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature. 2009;459:266–269.
Zhang H, DiBaise JK, Zuccolo A, Kudrna D, Braidotti M, Yu Y, et al. Human gut microbiota in obesity and after gastric bypass. Proc Natl Acad Sci USA. 2009;106(7):2365–2370.


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