The Inhabited Body — Primer Bibliography

References for companion primer chapters, sorted by chapter. Reference identifiers use the format REF:shortname for in-text citation. All DOIs verified via PubMed and/or web search, April 2026.

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

Verification Notes

References verified against PubMed metadata (April 2026). All DOIs confirmed to resolve to the cited titles with matching authors, journals, volumes, and page numbers.

Issues found and corrected:

1. [REF:sender2016] — Title in the bibliography was listed as "Revised estimates for the number of human and bacteria cells in the body." The actual PubMed title is "Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans." Corrected above.

1. [REF:zheludev2024] — Page range updated from "6521–6536" to "6521–6536.e18" to reflect the extended online supplement pages.

1. [REF:gram1884] — DOI added: 10.1055/s-0029-1209285 (via Thieme).

1. [REF:hooke1665] — No DOI exists for this 1665 work. Project Gutenberg URL added for digital access.

1. [REF:schwann1839] — No DOI exists. Internet Archive URL added for digital access.

1. [REF:margulis1970] — No DOI exists (book). ISBN added: 978-0-300-01353-5.

1. [REF:alberts2022] — No DOI exists (textbook). ISBN added: 978-0-393-88482-1.

1. [REF:cavalier-smith1987] — No DOI available for this book chapter. Noted in entry.

1. [REF:lederberg2001] — Not indexed in PubMed (published in The Scientist, a trade magazine). URL added.

1. [REF:lagier2016] — The original citation (Lagier et al. 2016, Nature Microbiology) is listed as a "Retracted Publication" in PubMed. Replaced with [REF:lagier2018]: Lagier et al. (2018), "Culturing the human microbiota and culturomics," Nature Reviews Microbiology, 16, 540–550 — a comprehensive review by the same group that covers the same material.

1. [REF:lane2015] — Title corrected to match PubMed: "The unseen world: reflections on Leeuwenhoek (1677) 'Concerning little animals'." (previously listed as The Unseen World: Reflections on Leeuwenhoek without the subtitle).

1. Chapters 3–6 — All references were present in the individual chapter files but missing from this consolidated bibliography. Now added.