A Novel Sparse Compositional Technique Reveals Microbial Perturbations

Abstract

By accounting for the sparse compositional nature of microbiome data sets, robust Aitchison PCA can yield high discriminatory power and salient feature ranking between microbial niches. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/DEICODE ; additionally, a QIIME 2 plugin is provided to perform this analysis at https://library.qiime2.org/plugins/q2-deicode .

References 54

1. 1.

   Kuczynski J, Liu Z, Lozupone C, McDonald D, Fierer N, Knight R 2010 Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat Methods 7:813–819. doi:.

   Not in our library10.1038/nmeth.1499 (opens in a new tab)

2. 2.

   Hamady M, Knight R 2009 Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res 19:1141–1152. doi:.

   Not in our library10.1101/gr.085464.108 (opens in a new tab)

3. 3.

   Morton JT, Toran L, Edlund A, Metcalf JL, Lauber C, Knight R 2017 Uncovering the horseshoe effect in microbial analyses. mSystems 2:e00166-16. doi:.

   Not in our library10.1128/msystems.00166-16 (opens in a new tab)

4. 4.

   Greig-Smith P 1980 The development of numerical classification and ordination. Vegetatio 42:1–9. doi:.

   Not in our library10.1007/bf00048864 (opens in a new tab)

5. 5.

   Potvin C, Roff DA 1993 Distribution-free and robust statistical methods: viable alternatives to parametric statistics. Ecology 74:1617–1628. doi:.

   Not in our library10.2307/1939920 (opens in a new tab)

6. 6.

   Tabachnick BG, Fidell LS 2013 Using multivariate statistics: Pearson new international edition. Pearson Education Limited, London, United Kingdom.

   Not in our library

7. 7.

   Ginter JL, Thorndike RM 1979 Correlational procedures for research. J Mark Res 16:600. doi:.

   Not in our library10.2307/3150840 (opens in a new tab)

8. 8.

   Lozupone C, Knight R 2005 UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228–8235. doi:.

   Not in our library10.1128/aem.71.12.8228-8235.2005 (opens in a new tab)

9. 9.

   Lozupone CA, Hamady M, Kelley ST, Knight R 2007 Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73:1576–1585. doi:.

   Not in our library10.1128/aem.01996-06 (opens in a new tab)

10. 10.

    Pawlowsky-Glahn V, Egozcue JJ, Tolosana-Delgado R 2015 Modeling and analysis of compositional data. John Wiley & Sons, New York, NY.

    Not in our library

11. 11.

    Martín-Fernández JA, Palarea-Albaladejo J, Olea RA 2011 Dealing with zeros. Monogr Stat Appl Probab 44:43–58.

    Not in our library

12. 12.

    Silverman JD, Roche K, Mukherjee S, David LA 2018 Naught all zeros in sequence count data are the same. bioRxiv https://www.biorxiv.org/content/early/2018/11/26/477794.

    Not in our library10.1016/j.csbj.2020.09.014 (opens in a new tab)

13. 13.

    Candès EJ, Li X, Ma Y, Wright J 2011 Robust principal component analysis? J ACM 58:1–37. doi:.

    Not in our library10.1145/1970392.1970395 (opens in a new tab)

14. 14.

    Tipping ME, Bishop CM 1999 Probabilistic principal component analysis. J R Stat Soc B 61:611–622. doi:.

    Not in our library10.1111/1467-9868.00196 (opens in a new tab)

15. 15.

    Jiang B, Ma S, Causey J, Qiao L, Hardin MP, Bitts I, Johnson D, Zhang S, Huang X 2016 Corrigendum: SparRec: an effective matrix completion framework of missing data imputation for GWAS. Sci Rep 6:37365. doi:.

    Not in our library10.1038/srep37365 (opens in a new tab)

16. 16.

    Cai T, Tony Cai T, Zhang A 2016 Structured matrix completion with applications to genomic data integration. J Am Stat Assoc 111:621–633. doi:.

    Not in our library10.1080/01621459.2015.1021005 (opens in a new tab)

17. 17.
    Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible · 2014

    No notice
18. 18.

    Wu JR, Macklaim JM, Genge BL, Gloor GB 2017 Finding the centre: corrections for asymmetry in high-throughput sequencing datasets. arXiv 1704.01841 [q-bio.QM]. https://arxiv.org/abs/1704.01841.

    Not in our library

19. 19.

    Fierer N, Lauber CL, Zhou N, McDonald D, Costello EK, Knight R 2010 Forensic identification using skin bacterial communities. Proc Natl Acad Sci U S A 107:6477–6481. doi:.

    Not in our library10.1073/pnas.1000162107 (opens in a new tab)

20. 20.

    Kullback S, Leibler RA 1951 On information and sufficiency. Ann Math Statist 22:79–86. doi:.

    Not in our library10.1214/aoms/1177729694 (opens in a new tab)

21. 21.
    The sponge microbiome project · 2017

    No notice
22. 22.
    Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome · 2018

    No notice
23. 23.

    Dollhopf SL, Hashsham SA, Tiedje JM 2001 Interpreting 16S rDNA T-RFLP data: application of self-organizing maps and principal component analysis to describe community dynamics and convergence. Microb Ecol 42:495–505. doi:.

    Not in our library10.1007/s00248-001-0027-7 (opens in a new tab)

24. 24.

    Aggarwal CC, Hinneburg A, Keim DA 2001 On the surprising behavior of distance metrics in high dimensional space, p 420–434. In Database theory—ICDT 2001. Springer, Berlin, Germany.

    Not in our library

25. 25.

    Aitchison J, Greenacre M 2002 Biplots of compositional data. J R Stat Soc C 51:375–392. doi:.

    Not in our library10.1111/1467-9876.00275 (opens in a new tab)

26. 26.
    Balances: a New Perspective for Microbiome Analysis · 2018

    No notice
27. 27.

    Feng G, Sun W, Zhang F, Karthik L, Li Z 2016 Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei. Sci Rep 6:24966. doi:.

    Not in our library10.1038/srep24966 (opens in a new tab)

28. 28.

    Usher KM 2008 The ecology and phylogeny of cyanobacterial symbionts in sponges. Mar Ecol 29:178–192. doi:.

    Not in our library10.1111/j.1439-0485.2008.00245.x (opens in a new tab)

29. 29.

    Diaz MC, Ward BB 1997 Sponge-mediated nitrification in tropical benthic communities. Mar Ecol Prog Ser 156:97–107. doi:.

    Not in our library10.3354/meps156097 (opens in a new tab)

30. 30.

    Moitinho-Silva L, Díez-Vives C, Batani G, Esteves AIS, Jahn MT, Thomas T 2017 Integrated metabolism in sponge-microbe symbiosis revealed by genome-centered metatranscriptomics. ISME J 11:1651. doi:.

    Not in our library10.1038/ismej.2017.25 (opens in a new tab)

31. 31.

    Waterbury BJ 1986 Biological and ecological characterization of the marine unicellular cyanobacterium Synechococcus. Can Bull Fish Aquat Sci 214:71–120.

    Not in our library

32. 32.

    Erwin PM, Thacker RW 2008 Cryptic diversity of the symbiotic cyanobacterium Synechococcus spongiarum among sponge hosts. Mol Ecol 17:2937–2947. doi:.

    Not in our library10.1111/j.1365-294x.2008.03808.x (opens in a new tab)

33. 33.
    Functional Intestinal Bile Acid 7α-Dehydroxylation by Clostridium scindens Associated with Protection from Clostridium difficile Infection in a Gnotobiotic Mouse Model · 2016

    No notice
34. 34.
    The gut microbiome in atherosclerotic cardiovascular disease · 2017

    No notice
35. 35.
    Intestinal Colonization by a <i>Lachnospiraceae</i> Bacterium Contributes to the Development of Diabetes in Obese Mice · 2014

    No notice
36. 36.

    Greenacre M, Lewi P 2009 Distributional equivalence and subcompositional coherence in the analysis of contingency tables, ratio-scale measurements and compositional data. J Classif 26:29–54.

    Not in our library

37. 37.
    A phylogenetic transform enhances analysis of compositional microbiota data · 2017

    No notice
38. 38.

    Palarea-Albaladejo J, Martín-Fernández JA 2015 zCompositions—R package for multivariate imputation of left-censored data under a compositional approach. Chemometrics Intell Lab Syst 143:85–96. doi:.

    Not in our library10.1016/j.chemolab.2015.02.019 (opens in a new tab)

39. 39.

    Keshavan RH, Montanari A 2010 Regularization for matrix completion, p 1503–1507. In 2010 IEEE International Symposium on Information Theory. https://ieeexplore.ieee.org/document/5513563.

    Not in our library

40. 40.

    Lauber CL, Hamady M, Knight R, Fierer N 2009 Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75:5111–5120. doi:.

    Not in our library10.1128/aem.00335-09 (opens in a new tab)

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