shime paper ready - Biology bibliographies - in Harvard style

In-text: (Alberti et al., 2009)

Your Bibliography: Alberti, K., Eckel, R., Grundy, S., Zimmet, P., Cleeman, J., Donato, K., Fruchart, J., James, W., Loria, C. and Smith, S., 2009. Harmonizing the metabolic syndrome: a joint interim statement of the International Diabetes Federation Task Forceon Epidemiology and Prevention; National Heart, Lung, and Blood Institute; American Heart Association; World HeartFederation; International Atherosclerosis Society; and International Association for the Study of Obesity. Obesity and metabolism, (1), p.63.

In-text: (Arora, Sharma and Frost, 2011)

Your Bibliography: Arora, T., Sharma, R. and Frost, G., 2011. Propionate. Anti-obesity and satiety enhancing factor?. Appetite, 56(2), pp.511-515.

In-text: (Chloride channels, 2009)

Your Bibliography: British Journal of Pharmacology, 2009. Chloride channels. 158, pp.S130-S134.

In-text: (Chambers et al., 2014)

Your Bibliography: Chambers, E., Viardot, A., Psichas, A., Morrison, D., Murphy, K., Zac-Varghese, S., MacDougall, K., Preston, T., Tedford, C., Finlayson, G., Blundell, J., Bell, J., Thomas, E., Mt-Isa, S., Ashby, D., Gibson, G., Kolida, S., Dhillo, W., Bloom, S., Morley, W., Clegg, S. and Frost, G., 2014. Effects of targeted delivery of propionate to the human colon on appetite regulation, body weight maintenance and adiposity in overweight adults. Gut, 64(11), pp.1744-1754.

In-text: (Chia et al., 2018)

Your Bibliography: Chia, L., Hornung, B., Aalvink, S., Schaap, P., de Vos, W., Knol, J. and Belzer, C., 2018. Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach. Antonie van Leeuwenhoek, 111(6), pp.859-873.

In-text: (De Weirdt et al., 2017)

Your Bibliography: De Weirdt, R., Hernandez-Sanabria, E., Fievez, V., Mees, E., Geirnaert, A., Van Herreweghen, F., Vilchez-Vargas, R., Van den Abbeele, P., Jauregui, R., Pieper, D., Vlaeminck, B. and Van de Wiele, T., 2017. Mucosa-associated biohydrogenating microbes protect the simulated colon microbiome from stress associated with high concentrations of poly-unsaturated fat. Environmental Microbiology, 19(2), pp.722-739.

In-text: (Derrien and van Hylckama Vlieg, 2015)

Your Bibliography: Derrien, M. and van Hylckama Vlieg, J., 2015. Fate, activity, and impact of ingested bacteria within the human gut microbiota. Trends in Microbiology, 23(6), pp.354-366.

In-text: (Dethlefsen and Relman, 2011)

Your Bibliography: Dethlefsen, L. and Relman, D., 2011. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proceedings of the National Academy of Sciences, 108(Supplement_1), pp.4554-4561.

In-text: (Dethlefsen, Huse, Sogin and Relman, 2008)

Your Bibliography: Dethlefsen, L., Huse, S., Sogin, M. and Relman, D., 2008. The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing. PLoS Biology, 6(11), p.e280.

In-text: (Dugas et al., 2016)

Your Bibliography: Dugas, L., Chorell, E., Plange-Rhule, J., Lambert, E., Cao, G., Cooper, R., Layden, B., Scholten, D., Olsson, T., Luke, A. and Goedecke, J., 2016. Obesity-related metabolite profiles of black women spanning the epidemiologic transition. Metabolomics, 12(3).

In-text: (Economopoulos et al., 2016)

Your Bibliography: Economopoulos, K., Ward, N., Phillips, C., Teshager, A., Patel, P., Mohamed, M., Hakimian, S., Cox, S., Ahmed, R., Moaven, O., Kaliannan, K., Alam, S., Haller, J., Goldstein, A., Bhan, A., Malo, M. and Hodin, R., 2016. Prevention of antibiotic-associated metabolic syndrome in mice by intestinal alkaline phosphatase. Diabetes, Obesity and Metabolism, 18(5), pp.519-527.

In-text: (El Hage, Hernandez-Sanabria and Van de Wiele, 2017)

Your Bibliography: El Hage, R., Hernandez-Sanabria, E. and Van de Wiele, T., 2017. Emerging Trends in “Smart Probiotics”: Functional Consideration for the Development of Novel Health and Industrial Applications. Frontiers in Microbiology, 8.

In-text: (Feng et al., 2017)

Your Bibliography: Feng, Z., Long, W., Hao, B., Ding, D., Ma, X., Zhao, L. and Pang, X., 2017. A human stool-derived Bilophila wadsworthia strain caused systemic inflammation in specific-pathogen-free mice. Gut Pathogens, 9(1).

In-text: (Fernandes et al., 2014)

Your Bibliography: Fernandes, J., Su, W., Rahat-Rozenbloom, S., Wolever, T. and Comelli, E., 2014. Adiposity, gut microbiota and faecal short chain fatty acids are linked in adult humans. Nutrition & Diabetes, 4(6), pp.e121-e121.

In-text: (Flint, Duncan, Scott and Louis, 2014)

Your Bibliography: Flint, H., Duncan, S., Scott, K. and Louis, P., 2014. Links between diet, gut microbiota composition and gut metabolism. Proceedings of the Nutrition Society, 74(01), pp.13-22.

In-text: (Francino, 2016)

Your Bibliography: Francino, M., 2016. Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances. Frontiers in Microbiology, 6.

In-text: (GOLDHILL, ROSE and PERCY, 1996)

Your Bibliography: GOLDHILL, J., ROSE, K. and PERCY, W., 1996. Effects of Antibiotics on Epithelial Ion Transport in the Rabbit Distal Colon In-vitro. Journal of Pharmacy and Pharmacology, 48(6), pp.651-656.

In-text: (Grunert et al., 2016)

Your Bibliography: Grunert, O., Hernandez-Sanabria, E., Vilchez-Vargas, R., Jauregui, R., Pieper, D., Perneel, M., Van Labeke, M., Reheul, D. and Boon, N., 2016. Mineral and organic growing media have distinct community structure, stability and functionality in soilless culture systems. Scientific Reports, 6(1).

In-text: (Halcox and Quyyumi, 2005)

Your Bibliography: Halcox, J. and Quyyumi, A., 2005. Metabolic Syndrome: Overview and Current Guidelines. Cardiology Board Review Manual, [online] 11, pp.1-12. Available at: <http://turner-white.com/pdf/brm_Card_V11P1.pdf> [Accessed 10 May 2018].

In-text: (Hernandez-Sanabria et al., 2010)

Your Bibliography: Hernandez-Sanabria, E., Guan, L., Goonewardene, L., Li, M., Mujibi, D., Stothard, P., Moore, S. and Leon-Quintero, M., 2010. Correlation of Particular Bacterial PCR-Denaturing Gradient Gel Electrophoresis Patterns with Bovine Ruminal Fermentation Parameters and Feed Efficiency Traits. Applied and Environmental Microbiology, 76(19), pp.6338-6350.

In-text: (Hosseini, Grootaert, Verstraete and Van de Wiele, 2011)

Your Bibliography: Hosseini, E., Grootaert, C., Verstraete, W. and Van de Wiele, T., 2011. Propionate as a health-promoting microbial metabolite in the human gut. Nutrition Reviews, 69(5), pp.245-258.

In-text: (Jin et al., 2016)

Your Bibliography: Jin, Y., Wu, Y., Zeng, Z., Jin, C., Wu, S., Wang, Y. and Fu, Z., 2016. From the Cover: Exposure to Oral Antibiotics Induces Gut Microbiota Dysbiosis Associated with Lipid Metabolism Dysfunction and Low-Grade Inflammation in Mice. Toxicological Sciences, 154(1), pp.140-152.

In-text: (Kaur, Yawar, Kumar and Suresh, 2013)

Your Bibliography: Kaur, S., Yawar, M., Kumar, P. and Suresh, K., 2013. Hungatella effluvii gen. nov., sp. nov., an obligately anaerobic bacterium isolated from an effluent treatment plant, and reclassification of Clostridium hathewayi as Hungatella hathewayi gen. nov., comb. nov. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 64(Pt 3), pp.710-718.

In-text: (Knoop, McDonald, Kulkarni and Newberry, 2015)

Your Bibliography: Knoop, K., McDonald, K., Kulkarni, D. and Newberry, R., 2015. Antibiotics promote inflammation through the translocation of native commensal colonic bacteria. Gut, 65(7), pp.1100-1109.

In-text: (Lê Cao, Boitard and Besse, 2011)

Your Bibliography: Lê Cao, K., Boitard, S. and Besse, P., 2011. Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems. BMC Bioinformatics, 12(1), p.253.

In-text: (LI, SHIMIZU and KIMURA, 2017)

Your Bibliography: LI, X., SHIMIZU, Y. and KIMURA, I., 2017. Gut microbial metabolite short-chain fatty acids and obesity. Bioscience of Microbiota, Food and Health, 36(4), pp.135-140.

In-text: (Maldonado-Gómez et al., 2016)

Your Bibliography: Maldonado-Gómez, M., Martínez, I., Bottacini, F., O’Callaghan, A., Ventura, M., van Sinderen, D., Hillmann, B., Vangay, P., Knights, D., Hutkins, R. and Walter, J., 2016. Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome. Cell Host & Microbe, 20(4), pp.515-526.

In-text: (McOrist, Abell, Cooke and Nyland, 2008)

Your Bibliography: McOrist, A., Abell, G., Cooke, C. and Nyland, K., 2008. Bacterial population dynamics and faecal short-chain fatty acid (SCFA) concentrations in healthy humans. British Journal of Nutrition, 100(01).

In-text: (Miller, Keane and O’Toole, 2005)

Your Bibliography: Miller, B., Keane, C. and O’Toole, M., 2005. In: Miller-Keane Encyclopedia & Dictionary of Medicine, Nursing & Allied Health, 7th ed. Elsevier.

In-text: (Miquilena-Colina et al., 2011)

Your Bibliography: Miquilena-Colina, M., Lima-Cabello, E., Sanchez-Campos, S., Garcia-Mediavilla, M., Fernandez-Bermejo, M., Lozano-Rodriguez, T., Vargas-Castrillon, J., Buque, X., Ochoa, B., Aspichueta, P., Gonzalez-Gallego, J. and Garcia-Monzon, C., 2011. Hepatic fatty acid translocase CD36 upregulation is associated with insulin resistance, hyperinsulinaemia and increased steatosis in non-alcoholic steatohepatitis and chronic hepatitis C. Gut, 60(10), pp.1394-1402.

In-text: (MITCHELL, 1966)

Your Bibliography: MITCHELL, P., 1966. CHEMIOSMOTIC COUPLING IN OXIDATIVE AND PHOTOSYNTHETIC PHOSPHORYLATION. Biological Reviews, 41(3), pp.445-501.

In-text: (Molly, Vande Woestyne and Verstraete, 1993)

Your Bibliography: Molly, K., Vande Woestyne, M. and Verstraete, W., 1993. Development of a 5-step multi-chamber reactor as a simulation of the human intestinal microbial ecosystem. Applied Microbiology and Biotechnology, 39(2), pp.254-258.

In-text: (Moore, Chaudhary and Akinyemiju, 2017)

Your Bibliography: Moore, J., Chaudhary, N. and Akinyemiju, T., 2017. Metabolic Syndrome Prevalence by Race/Ethnicity and Sex in the United States, National Health and Nutrition Examination Survey, 1988–2012. Preventing Chronic Disease, 14.

In-text: (Morrison and Preston, 2016)

Your Bibliography: Morrison, D. and Preston, T., 2016. Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism. Gut Microbes, 7(3), pp.189-200.

In-text: (Müller, Canfora and Blaak, 2018)

Your Bibliography: Müller, M., Canfora, E. and Blaak, E., 2018. Gastrointestinal Transit Time, Glucose Homeostasis and Metabolic Health: Modulation by Dietary Fibers. Nutrients, 10(3), p.275.

In-text: (Nicolson, 2007)

Your Bibliography: Nicolson, G., 2007. Metabolic syndrome and mitochondrial function: Molecular replacement and antioxidant supplements to prevent membrane peroxidation and restore mitochondrial function. Journal of Cellular Biochemistry, 100(6), pp.1352-1369.

In-text: (Nolan et al., 2017)

Your Bibliography: Nolan, P., Carrick-Ranson, G., Stinear, J., Reading, S. and Dalleck, L., 2017. Prevalence of metabolic syndrome and metabolic syndrome components in young adults: A pooled analysis. Preventive Medicine Reports, 7, pp.211-215.

In-text: (Oksanen et al., 2007)

Your Bibliography: Oksanen, J., Kindt, R., Legendre, P., O’Hara, B. and H Stevens, M., 2007. The vegan package. Community ecology package, 10, pp.631-637.

In-text: (Olle, 2013)

Your Bibliography: Olle, B., 2013. Medicines from microbiota. Nature Biotechnology, 31(4), pp.309-315.

In-text: (Ottman et al., 2017)

Your Bibliography: Ottman, N., Davids, M., Suarez-Diez, M., Boeren, S., Schaap, P., Martins dos Santos, V., Smidt, H., Belzer, C. and de Vos, W., 2017. Genome-Scale Model and Omics Analysis of Metabolic Capacities of Akkermansia muciniphila Reveal a Preferential Mucin-Degrading Lifestyle. Applied and Environmental Microbiology, 83(18), pp.e01014-17.

In-text: (Ouwehand, 2017)

Your Bibliography: Ouwehand, A., 2017. A review of dose-responses of probiotics in human studies. Beneficial Microbes, 8(2), pp.143-151.

In-text: (Paschold et al., 2012)

Your Bibliography: Paschold, A., Jia, Y., Marcon, C., Lund, S., Larson, N., Yeh, C., Ossowski, S., Lanz, C., Nettleton, D., Schnable, P. and Hochholdinger, F., 2012. Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents. Genome Research, 22(12), pp.2445-2454.

In-text: (Possemiers, Verthe, Uyttendaele and Verstraete, 2004)

Your Bibliography: Possemiers, S., Verthe, K., Uyttendaele, S. and Verstraete, W., 2004. PCR-DGGE-based quantification of stability of the microbial community in a simulator of the human intestinal microbial ecosystem. FEMS Microbiology Ecology, 49(3), pp.495-507.

In-text: (Psichas et al., 2014)

Your Bibliography: Psichas, A., Sleeth, M., Murphy, K., Brooks, L., Bewick, G., Hanyaloglu, A., Ghatei, M., Bloom, S. and Frost, G., 2014. The short chain fatty acid propionate stimulates GLP-1 and PYY secretion via free fatty acid receptor 2 in rodents. International Journal of Obesity, 39(3), pp.424-429.

In-text: (Reichardt et al., 2014)

Your Bibliography: Reichardt, N., Duncan, S., Young, P., Belenguer, A., McWilliam Leitch, C., Scott, K., Flint, H. and Louis, P., 2014. Phylogenetic distribution of three pathways for propionate production within the human gut microbiota. The ISME Journal, 8(6), pp.1352-1352.

In-text: (Ren, Pulakat, Whaley-Connell and Sowers, 2010)

Your Bibliography: Ren, J., Pulakat, L., Whaley-Connell, A. and Sowers, J., 2010. Mitochondrial biogenesis in the metabolic syndrome and cardiovascular disease. Journal of Molecular Medicine, 88(10), pp.993-1001.

In-text: (Rojo et al., 2017)

Your Bibliography: Rojo, D., Méndez-García, C., Raczkowska, B., Bargiela, R., Moya, A., Ferrer, M. and Barbas, C., 2017. Exploring the human microbiome from multiple perspectives: factors altering its composition and function. FEMS Microbiology Reviews, 41(4), pp.453-478.

In-text: (Silva and Bloom, 2012)

Your Bibliography: Silva, A. and Bloom, S., 2012. Gut Hormones and Appetite Control: A Focus on PYY and GLP-1 as Therapeutic Targets in Obesity. Gut and Liver, 6(1), pp.10-20.

In-text: (Smillie et al., 2018)

Your Bibliography: Smillie, C., Sauk, J., Gevers, D., Friedman, J., Sung, J., Youngster, I., Hohmann, E., Staley, C., Khoruts, A., Sadowsky, M., Allegretti, J., Smith, M., Xavier, R. and Alm, E., 2018. Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation. Cell Host & Microbe, 23(2), pp.229-240.e5.

In-text: (Storey and Tibshirani, 2003)

Your Bibliography: Storey, J. and Tibshirani, R., 2003. Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences, 100(16), pp.9440-9445.

In-text: (Strahl and Hamoen, 2010)

Your Bibliography: Strahl, H. and Hamoen, L., 2010. Membrane potential is important for bacterial cell division. Proceedings of the National Academy of Sciences, 107(27), pp.12281-12286.

In-text: (Tolhurst et al., 2011)

Your Bibliography: Tolhurst, G., Heffron, H., Lam, Y., Parker, H., Habib, A., Diakogiannaki, E., Cameron, J., Grosse, J., Reimann, F. and Gribble, F., 2011. Short-Chain Fatty Acids Stimulate Glucagon-Like Peptide-1 Secretion via the G-Protein-Coupled Receptor FFAR2. Diabetes, 61(2), pp.364-371.

In-text: (Truchado et al., 2017)

Your Bibliography: Truchado, P., Hernandez-Sanabria, E., Salden, B., Van den Abbeele, P., Vilchez-Vargas, R., Jauregui, R., Pieper, D., Possemiers, S. and Van de Wiele, T., 2017. Long chain arabinoxylans shift the mucosa-associated microbiota in the proximal colon of the simulator of the human intestinal microbial ecosystem (M-SHIME). Journal of Functional Foods, 32, pp.226-237.

In-text: (Turroni et al., 2012)

Your Bibliography: Turroni, F., Peano, C., Pass, D., Foroni, E., Severgnini, M., Claesson, M., Kerr, C., Hourihane, J., Murray, D., Fuligni, F., Gueimonde, M., Margolles, A., De Bellis, G., O’Toole, P., van Sinderen, D., Marchesi, J. and Ventura, M., 2012. Diversity of Bifidobacteria within the Infant Gut Microbiota. PLoS ONE, 7(5), p.e36957.

In-text: (Van den Abbeele et al., 2012)

Your Bibliography: Van den Abbeele, P., Roos, S., Eeckhaut, V., MacKenzie, D., Derde, M., Verstraete, W., Marzorati, M., Possemiers, S., Vanhoecke, B., Van Immerseel, F. and Van de Wiele, T., 2012. Incorporating a mucosal environment in a dynamic gut model results in a more representative colonization by lactobacilli. Microbial Biotechnology, 5(1), pp.106-115.

In-text: (Vonaesch, Anderson and Sansonetti, 2018)

Your Bibliography: Vonaesch, P., Anderson, M. and Sansonetti, P., 2018. Pathogens, microbiome and the host: emergence of the ecological Koch's postulates. FEMS Microbiology Reviews,.

In-text: (Yajima, 1988)

Your Bibliography: Yajima, T., 1988. Luminal propionate-induced secretory response in the rat distal colon in vitro. The Journal of Physiology, 403(1), pp.559-575.