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Analysis of compositions of microbiomes with bias correction

Author

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  • Huang Lin

    (University of Pittsburgh)

  • Shyamal Das Peddada

    (University of Pittsburgh)

Abstract

Differential abundance (DA) analysis of microbiome data continues to be a challenging problem due to the complexity of the data. In this article we define the notion of “sampling fraction” and demonstrate a major hurdle in performing DA analysis of microbiome data is the bias introduced by differences in the sampling fractions across samples. We introduce a methodology called Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC), which estimates the unknown sampling fractions and corrects the bias induced by their differences among samples. The absolute abundance data are modeled using a linear regression framework. This formulation makes a fundamental advancement in the field because, unlike the existing methods, it (a) provides statistically valid test with appropriate p-values, (b) provides confidence intervals for differential abundance of each taxon, (c) controls the False Discovery Rate (FDR), (d) maintains adequate power, and (e) is computationally simple to implement.

Suggested Citation

  • Huang Lin & Shyamal Das Peddada, 2020. "Analysis of compositions of microbiomes with bias correction," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-17041-7
    DOI: 10.1038/s41467-020-17041-7
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    References listed on IDEAS

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    1. Shyamal D. Peddada & Katherine E. Prescott & Mark Conaway, 2001. "Tests for Order Restrictions in Binary Data," Biometrics, The International Biometric Society, vol. 57(4), pages 1219-1227, December.
    2. Laura Farnan & Anastasia Ivanova & Shyamal D Peddada, 2014. "Linear Mixed Effects Models under Inequality Constraints with Applications," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-8, January.
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    Cited by:

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    2. Huang Lin & Merete Eggesbø & Shyamal Das Peddada, 2022. "Linear and nonlinear correlation estimators unveil undescribed taxa interactions in microbiome data," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    3. Estelle E. Clerc & Jean-Baptiste Raina & Johannes M. Keegstra & Zachary Landry & Sammy Pontrelli & Uria Alcolombri & Bennett S. Lambert & Valerio Anelli & Flora Vincent & Marta Masdeu-Navarro & Andrea, 2023. "Strong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
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    6. M. Büttner & J. Ostner & C. L. Müller & F. J. Theis & B. Schubert, 2021. "scCODA is a Bayesian model for compositional single-cell data analysis," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    7. Karen D. Corbin & Elvis A. Carnero & Blake Dirks & Daria Igudesman & Fanchao Yi & Andrew Marcus & Taylor L. Davis & Richard E. Pratley & Bruce E. Rittmann & Rosa Krajmalnik-Brown & Steven R. Smith, 2023. "Host-diet-gut microbiome interactions influence human energy balance: a randomized clinical trial," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    8. Osama Al-Dalahmah & Michael G. Argenziano & Adithya Kannan & Aayushi Mahajan & Julia Furnari & Fahad Paryani & Deborah Boyett & Akshay Save & Nelson Humala & Fatima Khan & Juncheng Li & Hong Lu & Yu S, 2023. "Re-convolving the compositional landscape of primary and recurrent glioblastoma reveals prognostic and targetable tissue states," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    9. Barbara B. Warner & Bruce A. Rosa & I. Malick Ndao & Phillip I. Tarr & J. Philip Miller & Sarah K. England & Joan L. Luby & Cynthia E. Rogers & Carla Hall-Moore & Renay E. Bryant & Jacqueline D. Wang , 2023. "Social and psychological adversity are associated with distinct mother and infant gut microbiome variations," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    10. Koen Wortelboer & Patrick A. Jonge & Torsten P. M. Scheithauer & Ilias Attaye & E. Marleen Kemper & Max Nieuwdorp & Hilde Herrema, 2023. "Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    11. Bryan P. Brown & Colin Feng & Ramla F. Tanko & Shameem Z. Jaumdally & Rubina Bunjun & Smritee Dabee & Anna-Ursula Happel & Melanie Gasper & Donald D. Nyangahu & Maricianah Onono & Gonasagrie Nair & Th, 2023. "Copper intrauterine device increases vaginal concentrations of inflammatory anaerobes and depletes lactobacilli compared to hormonal options in a randomized trial," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    12. Gertrude Ecklu-Mensah & Candice Choo-Kang & Maria Gjerstad Maseng & Sonya Donato & Pascal Bovet & Bharathi Viswanathan & Kweku Bedu-Addo & Jacob Plange-Rhule & Prince Oti Boateng & Terrence E. Forrest, 2023. "Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: the METS-microbiome study," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    13. Shulei Wang, 2023. "Robust differential abundance test in compositional data," Biometrika, Biometrika Trust, vol. 110(1), pages 169-185.
    14. Jonathan W. Lo & Domenico Cozzetto & James L. Alexander & Nathan P. Danckert & Matthew Madgwick & Naomi Knox & Jillian Yong Xin Sieh & Marton Olbei & Zhigang Liu & Hajir Ibraheim & Jesus Miguens Blanc, 2023. "Immune checkpoint inhibitor-induced colitis is mediated by polyfunctional lymphocytes and is dependent on an IL23/IFNγ axis," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    15. Zachary D. Wallen & Ayse Demirkan & Guy Twa & Gwendolyn Cohen & Marissa N. Dean & David G. Standaert & Timothy R. Sampson & Haydeh Payami, 2022. "Metagenomics of Parkinson’s disease implicates the gut microbiome in multiple disease mechanisms," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    16. Kotaro Soeda & Takayoshi Sasako & Kenichiro Enooku & Naoto Kubota & Naoki Kobayashi & Yoshiko Matsumoto Ikushima & Motoharu Awazawa & Ryotaro Bouchi & Gotaro Toda & Tomoharu Yamada & Takuma Nakatsuka , 2023. "Gut insulin action protects from hepatocarcinogenesis in diabetic mice comorbid with nonalcoholic steatohepatitis," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    17. Jun-Jun She & Wei-Xin Liu & Xiao-Ming Ding & Gang Guo & Jing Han & Fei-Yu Shi & Harry Cheuk-Hay Lau & Chen-Guang Ding & Wu-Jun Xue & Wen Shi & Gai-Xia Liu & Zhe Zhang & Chen-Hao Hu & Yinnan Chen & Chi, 2024. "Defining the biogeographical map and potential bacterial translocation of microbiome in human ‘surface organs’," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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