The Inhabited Body — Primer Bibliography

References for companion primer chapters, sorted by chapter. Reference identifiers use the format REF:shortname for in-text citation.

Primer Ch. 1 — The Living World: Life's Major Domains

• [REF:woese1977] Woese, C.R. & Fox, G.E. (1977). Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences, 74(11), 5088–5090. DOI: 10.1073/pnas.74.11.5088

• [REF:woese1990] Woese, C.R., Kandler, O. & Wheelis, M.L. (1990). Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences, 87(12), 4576–4579. DOI: 10.1073/pnas.87.12.4576

• [REF:louca2019] Louca, S., Mazel, F., Doebeli, M. & Parfrey, L.W. (2019). A census-based estimate of Earth's bacterial and archaeal diversity. PLOS Biology, 17(2), e3000106. DOI: 10.1371/journal.pbio.3000106

• [REF:locey2016] Locey, K.J. & Lennon, J.T. (2016). Scaling laws predict global microbial diversity. Proceedings of the National Academy of Sciences, 113(21), 5970–5975. DOI: 10.1073/pnas.1521291113

• [REF:spang2015] Spang, A. et al. (2015). Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature, 521(7551), 173–179. DOI: 10.1038/nature14447

• [REF:zheludev2024] Zheludev, I.N. et al. (2024). Viroid-like colonists of human microbiomes. Cell, 187(23), 6521–6536.e18. DOI: 10.1016/j.cell.2024.09.033

• [REF:lederberg2001] Lederberg, J. & McCray, A.T. (2001). 'Ome sweet 'omics — a genealogical treasury of words. The Scientist, 15(7), 8. URL: https://www.the-scientist.com/ome-sweet-omics-a-genealogical-treasury-of-words-54889

• [REF:sender2016] Sender, R., Fuchs, S. & Milo, R. (2016). Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell, 164(3), 337–340. DOI: 10.1016/j.cell.2016.01.013

Primer Ch. 2 — The Cell: Life's Basic Unit

• [REF:hooke1665] Hooke, R. (1665). Micrographia: or Some Physiological Descriptions of Minute Bodies Made by Magnifying Glasses. London: Royal Society. URL: https://www.gutenberg.org/ebooks/15491

• [REF:schwann1839] Schwann, T. (1839). Mikroskopische Untersuchungen über die Uebereinstimmung in der Struktur und dem Wachsthum der Thiere und Pflanzen. Berlin: Verlag der Sander'schen Buchhandlung. [English translation: Microscopical Researches into the Accordance in the Structure and Growth of Animals and Plants, 1847.] URL: https://archive.org/details/b29287455

• [REF:virchow1855] Virchow, R. (1855). Cellular-Pathologie. Archiv für pathologische Anatomie und Physiologie und für klinische Medicin, 8(1), 3–39. DOI: 10.1007/BF01935312

• [REF:gram1884] Gram, H.C. (1884). Ueber die isolirte Färbung der Schizomyceten in Schnitt- und Trockenpräparaten. Fortschritte der Medicin, 2, 185–189. DOI: 10.1055/s-0029-1209285

• [REF:sagan1967] Sagan, L. [later Margulis] (1967). On the origin of mitosing cells. Journal of Theoretical Biology, 14(3), 225–274. DOI: 10.1016/0022-5193(67)90079-390079-3)

• [REF:margulis1970] Margulis, L. (1970). Origin of Eukaryotic Cells. New Haven: Yale University Press. ISBN: 978-0-300-01353-5.

• [REF:shih2006] Shih, Y.-L. & Rothfield, L. (2006). The bacterial cytoskeleton. Microbiology and Molecular Biology Reviews, 70(3), 729–754. DOI: 10.1128/MMBR.00017-06

• [REF:bianconi2013] Bianconi, E. et al. (2013). An estimation of the number of cells in the human body. Annals of Human Biology, 40(6), 463–471. DOI: 10.3109/03014460.2013.807878

• [REF:blattner1997] Blattner, F.R. et al. (1997). The complete genome sequence of Escherichia coli K-12. Science, 277(5331), 1453–1462. DOI: 10.1126/science.277.5331.1453

• [REF:international2004] International Human Genome Sequencing Consortium (2004). Finishing the euchromatic sequence of the human genome. Nature, 431(7011), 931–945. DOI: 10.1038/nature03001

• [REF:alberts2022] Alberts, B. et al. (2022). Molecular Biology of the Cell, 7th edition. New York: W.W. Norton. ISBN: 978-0-393-88482-1.

Primer Ch. 3 — The Code of Life: DNA, RNA, and Proteins

• [REF:piovesan2019] Piovesan, A. et al. (2019). On the length, weight and GC content of the human genome. BMC Research Notes, 12, 106. DOI: 10.1186/s13104-019-4137-z

• [REF:watson1953] Watson, J.D. & Crick, F.H. (1953). Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature, 171(4356), 737–738. DOI: 10.1038/171737a0

• [REF:crick1970] Crick, F. (1970). Central dogma of molecular biology. Nature, 227(5258), 561–563. DOI: 10.1038/227561a0

• [REF:nirenberg1961] Nirenberg, M.W. & Matthaei, J.H. (1961). The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides. Proceedings of the National Academy of Sciences, 47(10), 1588–1602. DOI: 10.1073/pnas.47.10.1588

• [REF:crick1961] Crick, F.H., Barnett, L., Brenner, S. & Watts-Tobin, R.J. (1961). General nature of the genetic code for proteins. Nature, 192, 1227–1232. DOI: 10.1038/1921227a0

• [REF:jacob1961] Jacob, F. & Monod, J. (1961). Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology, 3, 318–356. DOI: 10.1016/s0022-2836(61)80072-780072-7)

• [REF:kariko2005] Karikó, K., Buckstein, M., Ni, H. & Weissman, D. (2005). Suppression of RNA recognition by Toll-like receptors: the impact of nucleoside modification and the evolutionary origin of RNA. Immunity, 23(2), 165–175. DOI: 10.1016/j.immuni.2005.06.008

• [REF:encode2012] ENCODE Project Consortium (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57–74. DOI: 10.1038/nature11247

• [REF:venter2001] Venter, J.C. et al. (2001). The sequence of the human genome. Science, 291(5507), 1304–1351. DOI: 10.1126/science.1058040

• [REF:international2004] International Human Genome Sequencing Consortium (2004). Finishing the euchromatic sequence of the human genome. Nature, 431(7011), 931–945. DOI: 10.1038/nature03001

• [REF:schmiedel2015] Schmiedel, J.M. et al. (2015). MicroRNA control of protein expression noise. Science, 348(6230), 128–132. DOI: 10.1126/science.aaa1738

• [REF:alberts2022] Alberts, B. et al. (2022). Molecular Biology of the Cell, 7th edition. New York: W.W. Norton. ISBN: 978-0-393-88482-1.

Primer Ch. 4 — The Fungal Kingdom

• [REF:baldauf1993] Baldauf, S.L. & Palmer, J.D. (1993). Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins. Proceedings of the National Academy of Sciences, 90(24), 11558–11562. DOI: 10.1073/pnas.90.24.11558

• [REF:cavalier-smith1987] Cavalier-Smith, T. (1987). The origin of Fungi and pseudofungi. In: Rayner, A.D.M., Brasier, C.M. & Moore, D. (eds) Evolutionary Biology of the Fungi. Cambridge University Press, pp. 339–353. [No DOI available for this book chapter.]

• [REF:parfrey2011] Parfrey, L.W., Lahr, D.J.G., Knoll, A.H. & Katz, L.A. (2011). Estimating the timing of early eukaryotic diversification with multigene molecular clocks. Proceedings of the National Academy of Sciences, 108(33), 13624–13629. DOI: 10.1073/pnas.1110633108

• [REF:gow2017] Gow, N.A.R., Latge, J.-P. & Munro, C.A. (2017). The fungal cell wall: structure, biosynthesis, and function. Microbiology Spectrum, 5(3), FUNK-0035-2016. DOI: 10.1128/microbiolspec.FUNK-0035-2016

• [REF:naranjo-ortiz2019] Naranjo-Ortiz, M.A. & Gabaldón, T. (2019). Fungal evolution: diversity, taxonomy and phylogeny of the Fungi. Biological Reviews, 94(6), 2101–2137. DOI: 10.1111/brv.12550

• [REF:goffeau1996] Goffeau, A. et al. (1996). Life with 6000 genes. Science, 274(5287), 546–567. DOI: 10.1126/science.274.5287.546

• [REF:sudbery2004] Sudbery, P., Gow, N. & Berman, J. (2004). The distinct morphogenic states of Candida albicans. Trends in Microbiology, 12(7), 317–324. DOI: 10.1016/j.tim.2004.05.008

• [REF:bongomin2017] Bongomin, F., Gago, S., Oladele, R.O. & Denning, D.W. (2017). Global and multi-national prevalence of fungal diseases — estimate precision. Journal of Fungi, 3(4), 57. DOI: 10.3390/jof3040057

• [REF:lockhart2017] Lockhart, S.R. et al. (2017). Simultaneous emergence of multidrug-resistant Candida auris on 3 continents confirmed by whole-genome sequencing and epidemiological analyses. Clinical Infectious Diseases, 64(2), 134–140. DOI: 10.1093/cid/ciw691

• [REF:tedersoo2018] Tedersoo, L. et al. (2018). High-level classification of the Fungi and a tool for evolutionary ecological analyses. Fungal Diversity, 90, 135–159. DOI: 10.1007/s13225-018-0401-0

• [REF:hawksworth2017] Hawksworth, D.L. & Lücking, R. (2017). Fungal diversity revisited: 2.2 to 3.8 million species. Microbiology Spectrum, 5(4), FUNK-0052-2016. DOI: 10.1128/microbiolspec.FUNK-0052-2016

• [REF:brown2006] Brown, G.D. (2006). Dectin-1: a signalling non-TLR pattern-recognition receptor. Nature Reviews Immunology, 6(1), 33–43. DOI: 10.1038/nri1745

• [REF:li2021] Li, Y. et al. (2021). A genome-scale phylogeny of the kingdom Fungi. Current Biology, 31(8), 1653–1665.e5. DOI: 10.1016/j.cub.2021.01.074

Primer Ch. 5 — Viruses and Their Strange Relatives

• [REF:suttle2007] Suttle, C.A. (2007). Marine viruses — major players in the global ecosystem. Nature Reviews Microbiology, 5(10), 801–812. DOI: 10.1038/nrmicro1750

• [REF:shkoporov2019] Shkoporov, A.N. & Hill, C. (2019). Bacteriophages of the human gut: the "known unknown" of the microbiome. Cell Host & Microbe, 25(2), 195–209. DOI: 10.1016/j.chom.2019.01.017

• [REF:baltimore1970] Baltimore, D. (1970). RNA-dependent DNA polymerase in virions of RNA tumour viruses. Nature, 226(5252), 1209–1211. DOI: 10.1038/2261209a0

• [REF:temin1970] Temin, H.M. & Mizutani, S. (1970). RNA-dependent DNA polymerase in virions of Rous sarcoma virus. Nature, 226(5252), 1211–1213. DOI: 10.1038/2261211a0

• [REF:barresinoussi1983] Barré-Sinoussi, F. et al. (1983). Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science, 220(4599), 868–871. DOI: 10.1126/science.6189183

• [REF:zheludev2024] Zheludev, I.N. et al. (2024). Viroid-like colonists of human microbiomes. Cell, 187(23), 6521–6536.e18. DOI: 10.1016/j.cell.2024.09.033

• [REF:alberts2022] Alberts, B. et al. (2022). Molecular Biology of the Cell, 7th edition. New York: W.W. Norton. ISBN: 978-0-393-88482-1.

Primer Ch. 6 — How We Study What We Can't See

• [REF:lane2015] Lane, N. (2015). The unseen world: reflections on Leeuwenhoek (1677) 'Concerning little animals'. Philosophical Transactions of the Royal Society B, 370(1666), 20140344. DOI: 10.1098/rstb.2014.0344

• [REF:blevins2010] Blevins, S.M. & Bronze, M.S. (2010). Robert Koch and the 'golden age' of bacteriology. International Journal of Infectious Diseases, 14(9), e744–e751. DOI: 10.1016/j.ijid.2009.12.003

• [REF:staley1985] Staley, J.T. & Konopka, A. (1985). Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annual Review of Microbiology, 39, 321–346. DOI: 10.1146/annurev.mi.39.100185.001541

• [REF:woese1977] Woese, C.R. & Fox, G.E. (1977). Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences, 74(11), 5088–5090. DOI: 10.1073/pnas.74.11.5088

• [REF:hmp2012] Human Microbiome Project Consortium (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207–214. DOI: 10.1038/nature11234

• [REF:qin2010] Qin, J. et al. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464(7285), 59–65. DOI: 10.1038/nature08821

• [REF:knight2018] Knight, R. et al. (2018). Best practices for analysing microbiomes. Nature Reviews Microbiology, 16(7), 410–422. DOI: 10.1038/s41579-018-0029-9

• [REF:lagier2018] Lagier, J.-C. et al. (2018). Culturing the human microbiota and culturomics. Nature Reviews Microbiology, 16, 540–550. DOI: 10.1038/s41579-018-0041-0