Abstract
The study of complexity of metagenome populations is crucial in understanding different microbial communities. The potential number of microbes in the environment is much higher than our knowledge. However, most metagenomic projects only contain tens to hundreds of samples. Most of the microbes can hardly be sampled under such small sample size. Thus, there are many “dark matters” that never been observed. Here in this study, we proposed a statistical model, named SAM (Species Appearance Model), which uses only one to two hundred samples to optimize the parameters, and estimate the potential richness of dark matters when the data size is much higher. An index named ESS (Estimated saturated sample size) were also proposed as an indicator of the complexity of the metagenome population. In the dataset of the American Gut Project (AGP), SAM can precisely predict the OTU richness of pan metagenome with more than 1000 samples using only 200 samples. The ESS of AGP is ~25,000, which means the AGP population is very complex. Using our SAM model, researchers can estimate and decide how many samples they need to collect when initiating a new metagenomic project. Different ESS values of different metagenomic populations can also serve as a guidance of understanding their different complexities.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Lundberg, J.O., Weitzberg, E., Cole, J.A., Benjamin, N.: Nitrate, bacteria and human health. Nat. Rev. Microbiol. 2(7), 593–602 (2004)
Relman, D.A.: Microbial genomics and infectious diseases. N. Engl. J. Med. 365(4), 347–357 (2011)
Loman, N.J., et al.: A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. JAMA 309(14), 1502–1510 (2013)
Kamada, N., Chen, G.Y., Inohara, N., Nunez, G.: Control of pathogens and pathobionts by the gut microbiota. Nat. Immunol. 14(7), 685–690 (2013)
Gallo, R.L., Hooper, L.V.: Epithelial antimicrobial defence of the skin and intestine. Nat. Rev. Immunol. 12(7), 503–516 (2012)
Kramer, P., Bressan, P.: Humans as superorganisms: how microbes, viruses, imprinted genes, and other selfish entities shape our behavior. Perspect. Psychol. Sci. 10(4), 464–481 (2015)
Rakoff-Nahoum, S., Foster, K.R., Comstock, L.E.: The evolution of cooperation within the gut microbiota. Nature 533(7602), 255–259 (2016)
Coyte, K.Z., Schluter, J., Foster, K.R.: The ecology of the microbiome: networks, competition, and stability. Science 350(6261), 663–666 (2015)
Cho, I., Blaser, M.J.: The human microbiome: at the interface of health and disease. Nat. Rev. Genet. 13(4), 260–270 (2012)
Clemente, J.C., Ursell, L.K., Parfrey, L.W., Knight, R.: The impact of the gut microbiota on human health: an integrative view. Cell 148(6), 1258–1270 (2012)
Dinan, T.G., Stilling, R.M., Stanton, C., Cryan, J.F.: Collective unconscious: how gut microbes shape human behavior. J. Psychiatr. Res. 63, 1–9 (2015)
Bravo-Blas, A., Wessel, H., Milling, S.: Microbiota and arthritis: correlations or cause? Curr. Opin. Rheumatol. 28(2), 161–167 (2016)
David, L.A., et al.: Diet rapidly and reproducibly alters the human gut microbiome. Nature 505(7484), 559–563 (2014)
Morris, A., et al.: Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am. J. Respir. Crit. Care Med. 187(10), 1067–1075 (2013)
Devaraj, S., Hemarajata, P., Versalovic, J.: The human gut microbiome and body metabolism: implications for obesity and diabetes. Clin. Chem. 59(4), 617–628 (2013)
Bouter, K.E., van Raalte, D.H., Groen, A.K., Nieuwdorp, M.: Role of the gut microbiome in the pathogenesis of obesity and obesity-related metabolic dysfunction. Gastroenterology 152(7), 1671–1678 (2017)
Tilg, H., Kaser, A.: Gut microbiome, obesity, and metabolic dysfunction. J. Clin. Invest. 121(6), 2126–2132 (2011)
Qin, J., et al.: A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490(7418), 55–60 (2012)
Qin, N., et al.: Alterations of the human gut microbiome in liver cirrhosis. Nature 513(7516), 59–64 (2014)
Saulnier, D.M., et al.: Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology 141(5), 1782–1791 (2011)
Human Microbiome Project C: Structure, function and diversity of the healthy human microbiome. Nature 486(7402), 207–214 (2012)
Qin, J., et al.: A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464(7285), 59–65 (2010)
Bonder, M.J., et al.: The effect of host genetics on the gut microbiome. Nat. Genet. 48(11), 1407–1412 (2016)
Turpin, W., et al.: Association of host genome with intestinal microbial composition in a large healthy cohort. Nat. Genet. 48(11), 1413–1417 (2016)
Falony, G., et al.: Population-level analysis of gut microbiome variation. Science 352(6285), 560–564 (2016)
McDonald, D., Birmingham, A., Knight, R.: Context and the human microbiome. Microbiome 3, 52 (2015)
Lloyd, K.G., Steen, A.D., Ladau, J., Yin, J., Crosby, L.: Phylogenetically novel uncultured microbial cells dominate earth microbiomes. mSystems 3(5) (2018)
Lapierre, P., Gogarten, J.P.: Estimating the size of the bacterial pan-genome. Trends Genet. 25(3), 107–110 (2009)
Collins, R.E., Higgs, P.G.: Testing the infinitely many genes model for the evolution of the bacterial core genome and pangenome. Mol. Biol. Evol. 29(11), 3413–3425 (2012)
Acknowledgements
This work is a continuation of the author’s doctoral research. The author thanks Prof. Xuegong Zhang for his inspirations about this work. This work was supported by the National Key Research and Development Project 2018YFC0910400.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this paper
Cite this paper
Cui, H. (2019). Estimation of Potential Richness of Dark Matters in “Pan Metagenome” Using Species Appearance Model. In: Chen, H., Zeng, D., Yan, X., Xing, C. (eds) Smart Health. ICSH 2019. Lecture Notes in Computer Science(), vol 11924. Springer, Cham. https://doi.org/10.1007/978-3-030-34482-5_1
Download citation
DOI: https://doi.org/10.1007/978-3-030-34482-5_1
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-34481-8
Online ISBN: 978-3-030-34482-5
eBook Packages: Computer ScienceComputer Science (R0)