Metagenomic Biomarker Discovery and Explanation

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2011 Jun 28

PMID 21702898

Citations 6829

Authors

Nicola Segata

Jacques Izard

Levi Waldron

Dirk Gevers

Larisa Miropolsky

Wendy S Garrett

Curtis Huttenhower

Affiliations

Soon will be listed here.

Abstract

This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.

Citing Articles

Influences of gestational diabetes mellitus on the changes in the vaginal microbiota from antepartum to postpartum.

Liao Y, Liu T, Zeng X, Xiao B, Xiao M, Zhu Y BMC Pregnancy Childbirth. 2025; 25(1):290.

PMID: 40089657 DOI: 10.1186/s12884-025-07411-8.

The comparison of gut microbiota between different types of epilepsy in children.

Fang S, Hu N, Zhou C, You J, Wu L, Pan X Microb Cell Fact. 2025; 24(1):64.

PMID: 40082906 PMC: 11908097. DOI: 10.1186/s12934-025-02684-2.

High-throughput workflow for cultivation and characterization of gut microbiota strains with anti-inflammatory properties and metabolite signature associated with gut-brain communication.

dokic J, Dinic M, Sokovic Bajic S, Bisenic A, Mitrovic H, Jakovljevic S Sci Rep. 2025; 15(1):8741.

PMID: 40082612 PMC: 11906651. DOI: 10.1038/s41598-025-93180-5.

Investigation of the female genital tract microbiome and its association with hydrosalpinx in women undergoing salpingectomy.

Yagel Y, Motro Y, Green S, Klapper-Goldstein H, Pardo E, Moran-Gilad J Arch Gynecol Obstet. 2025; .

PMID: 40082312 DOI: 10.1007/s00404-025-07944-5.

Evaluation of gut microbiota alterations following orlistat administration in obese mice.

Xue C, Wang T, Chen Y, Zhang H, Wang H, Li Q Front Endocrinol (Lausanne). 2025; 15:1337245.

PMID: 40078888 PMC: 11896870. DOI: 10.3389/fendo.2024.1337245.

References

Clarke R, Ressom H, Wang A, Xuan J, Liu M, Gehan E . The properties of high-dimensional data spaces: implications for exploring gene and protein expression data. Nat Rev Cancer. 2007; 8(1):37-49. PMC: 2238676. DOI: 10.1038/nrc2294. View

Preidis G, Versalovic J . Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era. Gastroenterology. 2009; 136(6):2015-31. PMC: 4108289. DOI: 10.1053/j.gastro.2009.01.072. View

Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M . Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010; Chapter 19:Unit 19.10.1-21. PMC: 4264107. DOI: 10.1002/0471142727.mb1910s89. View

Mitra S, Klar B, Huson D . Visual and statistical comparison of metagenomes. Bioinformatics. 2009; 25(15):1849-55. DOI: 10.1093/bioinformatics/btp341. View

Overbeek R, Begley T, Butler R, Choudhuri J, Chuang H, Cohoon M . The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005; 33(17):5691-702. PMC: 1251668. DOI: 10.1093/nar/gki866. View

Gobet A, Quince C, Ramette A . Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets. Nucleic Acids Res. 2010; 38(15):e155. PMC: 2926624. DOI: 10.1093/nar/gkq545. View

Godon J, Moriniere J, Moletta M, Gaillac M, Bru V, Delgenes J . Rarity associated with specific ecological niches in the bacterial world: the 'Synergistes' example. Environ Microbiol. 2005; 7(2):213-24. DOI: 10.1111/j.1462-2920.2004.00693.x. View

White J, Nagarajan N, Pop M . Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol. 2009; 5(4):e1000352. PMC: 2661018. DOI: 10.1371/journal.pcbi.1000352. View

Dethlefsen L, McFall-Ngai M, Relman D . An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature. 2007; 449(7164):811-8. PMC: 9464033. DOI: 10.1038/nature06245. View

10.

Parks D, Beiko R . Identifying biologically relevant differences between metagenomic communities. Bioinformatics. 2010; 26(6):715-21. DOI: 10.1093/bioinformatics/btq041. View

11.

Wei X, Li K . Exploring the within- and between-class correlation distributions for tumor classification. Proc Natl Acad Sci U S A. 2010; 107(15):6737-42. PMC: 2872377. DOI: 10.1073/pnas.0910140107. View

12.

Turnbaugh P, Ley R, Mahowald M, Magrini V, Mardis E, Gordon J . An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006; 444(7122):1027-31. DOI: 10.1038/nature05414. View

13.

Sokol H, Seksik P, Furet J, Firmesse O, Nion-Larmurier I, Beaugerie L . Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis. 2009; 15(8):1183-9. DOI: 10.1002/ibd.20903. View

14.

Veiga P, Gallini C, Beal C, Michaud M, Delaney M, DuBois A . Bifidobacterium animalis subsp. lactis fermented milk product reduces inflammation by altering a niche for colitogenic microbes. Proc Natl Acad Sci U S A. 2010; 107(42):18132-7. PMC: 2964251. DOI: 10.1073/pnas.1011737107. View

15.

Khoruts A, Dicksved J, Jansson J, Sadowsky M . Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea. J Clin Gastroenterol. 2010; 44(5):354-60. DOI: 10.1097/MCG.0b013e3181c87e02. View

16.

Hilbert F, Scherwitzel M, Paulsen P, Szostak M . Survival of Campylobacter jejuni under conditions of atmospheric oxygen tension with the support of Pseudomonas spp. Appl Environ Microbiol. 2010; 76(17):5911-7. PMC: 2935043. DOI: 10.1128/AEM.01532-10. View

17.

Hamady M, Knight R . Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res. 2009; 19(7):1141-52. PMC: 3776646. DOI: 10.1101/gr.085464.108. View

18.

Sartor R . Mechanisms of disease: pathogenesis of Crohn's disease and ulcerative colitis. Nat Clin Pract Gastroenterol Hepatol. 2006; 3(7):390-407. DOI: 10.1038/ncpgasthep0528. View

19.

Young C, Sharma R, Handfield M, Mai V, Neu J . Biomarkers for infants at risk for necrotizing enterocolitis: clues to prevention?. Pediatr Res. 2009; 65(5 Pt 2):91R-97R. PMC: 2929681. DOI: 10.1203/PDR.0b013e31819dba7d. View

20.

Garrett W, Lord G, Punit S, Lugo-Villarino G, Mazmanian S, Ito S . Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system. Cell. 2007; 131(1):33-45. PMC: 2169385. DOI: 10.1016/j.cell.2007.08.017. View