References
- Angelo, G., and Van Gilst, M. R. 2009. Starvation protects germline stem cells and extends reproductive longevity in C. elegans. Science 326:954–958.
- Barriere, A., and Felix, M. A. 2006. Isolation of C. elegans and related nematodes. The C. elegans Research Community, ed. WormBook. doi/10.1895/wormbook.1.115.1.
- Clark, L. C., and Hodgkin, J. 2014. Commensals, probiotics and pathogens in the caenorhabditis elegans model. Cell Microbiol 16:27–38.
- Croll, N. A., Smith, J. M., and Zuckerman, B. M. 1977. The aging process of the nematode caenorhabditis elegans in bacterial and axenic culture. Experimental Aging Research 3:175–189.
- Darby, C. 2005. Interactions with microbial pathogens. The C. elegans Research Community, ed., WormBook. doi/10.1895/wormbook.1.21.1.
- Dirksen, P., Assie, A., Zimmermann, J., Zhang, F., Tietje, A. M., Marsh, S. A., Felix, M. A., Shapira, M., Kaleta, C., Schulenburg, H., and Samuel, B. S. 2020. Cembio – the caenorhabditis elegans microbiome resource. G3 (Bethesda) 10:3025–3039.
- Dirksen, P., Marsh, S. A., Braker, I., Heitland, N., Wagner, S., Nakad, R., Mader, S., Petersen, C., Kowallik, V., Rosenstiel, P., Felix, M. A., and Schulenburg, H. 2016. The native microbiome of the nematode caenorhabditis elegans: Gateway to a new host-microbiome model. BMC Biology 14:38.
- Felix, M. A., Braendle, C., and Cutter, A. D. 2014. A streamlined system for species diagnosis in caenorhabditis (nematoda: Rhabditidae) with name designations for 15 distinct biological species. PLoS One 9:e94723.
- Fradin, H., Kiontke, K., Zegar, C., Gutwein, M., Lucas, J., Kovtun, M., Corcoran, D. L., Baugh, L. R., Fitch, D. H. A., Piano, F., and Gunsalus, K. C. 2017. Genome architecture and evolution of a unichromosomal asexual nematode. Current Biology 27:2928–2939.
- Frezal, L., and Felix, M. A. 2015. C. elegans outside the petri dish. Elife 4:e05849.
- Gracida, X., and Eckmann, C. R. 2013. Fertility and germline stem cell maintenance under different diets requires nhr-114/hnf4 in C. elegans. Current Biology 23:607–613.
- Gravato-Nobre, M. J., and Hodgkin, J. 2005. Caenorhabditis elegans as a model for innate immunity to pathogens. Cell Microbiology 7:741–751.
- Grosmaire, M., Launay, C., Siegwald, M., Brugiere, T., Estrada-Virrueta, L., Berger, D., Burny, C., Modolo, L., Blaxter, M., Meister, P., Felix, M. A., Gouyon, P. H., and Delattre, M. 2019. Males as somatic investment in a parthenogenetic nematode. Science 363: 1210–1213.
- Harrington, L. A., and Harley, C. B. 1988. Effect of vitamin E on lifespan and reproduction in caenorhabditis elegans. Mechanisms of Ageing and Development 43:71–78.
- Honda, Y., Tanaka, M., and Honda, S. 2010. Trehalose extends longevity in the nematode caenorhabditis elegans. Aging Cell 9:558–569.
- Huang, C., Xiong, C., and Kornfeld, K. 2004. Measurements of age-related changes of physiological processes that predict lifespan of caenorhabditis elegans. Proceedings of the National Academy of Sciences U S A 101:8084–8089.
- Hughes, S. E., Evason, K., Xiong, C., and Kornfeld, K. 2007. Genetic and pharmacological factors that influence reproductive aging in nematodes. PLoS Genetics 3:e25.
- Hughes, S. E., Huang, C., and Kornfeld, K. 2011. Identification of mutations that delay somatic or reproductive aging of caenorhabditis elegans. Genetics 189:341–356.
- Kadandale, P., and Singson, A. 2004. Oocyte production and sperm utilization patterns in semi-fertile strains of caenorhabditis elegans. BMC Developmental Biology 4:3.
- Kaletsky, R., Moore, R. S., Vrla, G. D., Parsons, L. R., Gitai, Z., and Murphy, C. T. 2020. C. elegans interprets bacterial non-coding RNAs to learn pathogenic avoidance. Nature 586:445–451.
- Kassambara, A., Kosinski, M., and Biecek, P. 2021. survminer. Drawing survival curves using ‘ggplot2’. R package version 0.4.9. Available at: https://CRAN.R-project.org/package=survminer
- Kiontke, K., and Fitch, D. H. 2005. The phylogenetic relationships of caenorhabditis and other rhabditids. The C. elegans Research Community, ed., WormBook. doi/10.1895/wormbook.1.11.1.
- Klass, M. R. 1977. Aging in the nematode caenorhabditis elegans: Major biological and environmental factors influencing life span. Mechanisms of Ageing and Development 6:413–429.
- Kumar, A., Baruah, A., Tomioka, M., Iino, Y., Kalita, M. C., and Khan, M. 2020. Caenorhabditis elegans: A model to understand host-microbe interactions. Cellular and Molecular Life Sciences 77:1229–1249.
- Le, T. S., Nguyen, T. T. H., Huong, B. T., Nguyen, H. G., Ha, B. H., Nguyen, V. S., Nguyen, M. H., Nguyen, H. H., and Wang, J. 2021. Cultivation of caenorhabditis elegans on new cheap monoxenic media without peptone. Journal of Nematology 53.
- Liu, H., Wang, X., Wang, H. D., Wu, J., Ren, J., Meng, L., Wu, Q., Dong, D., Kao, T. Y., Ge, Q., Wu, Z. X., Yuh, C. H., and Shan, G. 2012. Escherichia coli noncoding RNAs can affect gene expression and physiology of caenorhabditis elegans. Nature Communications 3:1073.
- Luo, S., Shaw, W. M., Ashraf, J., and Murphy, C. T. 2009. TGF-β Sma/Mab signaling mutations uncouple reproductive aging from somatic aging. PLoS Genetics 5:e1000789.
- MacNeil, L. T., Watson, E., Arda, H. E., Zhu, L. J., and Walhout, A. J. 2013. Diet-induced developmental acceleration independent of tor and insulin in C. elegans. Cell 153:240–252.
- Madhu, B., Salazar, A., and Gumienny, T. 2019. Caenorhabditis elegans egg-laying and brood-size changes upon exposure to serratia marcescens and staphylococcus epidermidis are independent of DBL-1 signaling. MicroPublication Biology 2019.
- Maklakov, A. A., and Immler, S. 2016. The expensive germline and the evolution of ageing. Current Biology 26:R577–R586.
- Morgulis, A., Coulouris, G., Raytselis, Y., Madden, T. L., Agarwala, R., and Schaffer, A. A. 2008. Database indexing for production megablast searches. Bioinformatics 24:1757–1764.
- Onken, B., and Driscoll, M. 2010. Metformin induces a dietary restriction-like state and the oxidative stress response to extend C. elegans healthspan via AMPK, LKB1, and SKN-1. PLoS One 5:e8758.
- Pukkila-Worley, R., and Ausubel, F. M. 2012. Immune defense mechanisms in the caenorhabditis elegans intestinal epithelium. Current Opinion in Immunology 24:3–9.
- R Core Team. 2017. R: A language and environment for statistical computing. R foundation for statistical computing.
- Sambrook, J., and Russell, D. W. (2001). Molecular cloning, a laboratory manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
- Samuel, B. S., Rowedder, H., Braendle, C., Felix, M. A., and Ruvkun, G. 2016. Caenorhabditis elegans responses to bacteria from its natural habitats. Proceedings of the National Academy of Sciences U S A 113:E3941–E3949.
- Scharf, A., Pohl, F., Egan, B. M., Kocsisova, Z., and Kornfeld, K. 2021. Reproductive aging in caenorhabditis elegans: From molecules to ecology. Frontiers in Cell and Developmental Biology 9:718522.
- Schulenburg, H., and Felix, M. A. 2017. The natural biotic environment of caenorhabditis elegans. Genetics 206:55–86.
- Shaham, S. 2006. Methods in cell biology. WormBook. V. Ambros, ed. WormBook, The C. elegans Research Community. http://www.wormbook.org.
- Stiernagle, T. 2006. Maintenance of C. elegans. Wormbook. WormBook, The C. elegans Research Community: 1–11. doi/10.1895/wormbook.1.101.1.
- Stuhr, N. L., and Curran, S. P. 2020. Bacterial diets differentially alter lifespan and healthspan trajectories in C. elegans. Communications Biology 3:653.
- Templeman, N. M., Cota, V., Keyes, W., Kaletsky, R., and Murphy, C. T. 2020. CREB non-autonomously controls reproductive aging through hedgehog/patched signaling. Developmental Cell 54:92–105.
- Templeman, N. M., and Murphy, C. T. 2018. Regulation of reproduction and longevity by nutrient-sensing pathways. Journal of Cell Biology 217:93–106.
- Vingataramin, L., and Frost, E. H. 2015. A single protocol for extraction of gDNA from bacteria and yeast. Biotechniques 58:120–125.
- Wang, M. C., Oakley, H. D., Carr, C. E., Sowa, J. N., and Ruvkun, G. 2014. Gene pathways that delay caenorhabditis elegans reproductive senescence. PLoS Genetics 10:e1004752.
- Zecic, A., Dhondt, I., and Braeckman, B. P. 2019. The nutritional requirements of caenorhabditis elegans. Genes & Nutrition 14:15.
- Zhang, F., Berg, M., Dierking, K., Felix, M. A., Shapira, M., Samuel, B. S., and Schulenburg, H. 2017a. Caenorhabditis elegans as a model for microbiome research. Frontiers in Microbiology 8:485.
- Zhang, J., Holdorf, A. D., and Walhout, A. J. 2017b. C. Elegans and its bacterial diet as a model for systems-level understanding of host-microbiota interactions. Current Opinion in Biotechnology 46:74–80.
- Zhang, Z., Schwartz, S., Wagner, L., and Miller, W. 2000. A greedy algorithm for aligning DNA sequences. Journal of Computational Biology 7:203–214.
- Zimmermann, J., Obeng, N., Yang, W., Pees, B., Petersen, C., Waschina, S., Kissoyan, K. A., Aidley, J., Hoeppner, M. P., Bunk, B., Sproer, C., Leippe, M., Dierking, K., Kaleta, C., and Schulenburg, H. 2020. The functional repertoire contained within the native microbiota of the model nematode caenorhabditis elegans. The ISME Journal 14:26–38.