Intricacies of Assessing the Human Microbiome in Epidemiologic Studies

Overview

Journal Ann Epidemiol

Publisher Elsevier

Specialty Public Health

Date 2016 May 16

PMID 27180112

Citations 32

Authors

Courtney K Robinson

Rebecca M Brotman

Jacques Ravel

Affiliations

Soon will be listed here.

Abstract

Purpose: In the past decade, remarkable relationships have been documented between dysbiosis of the human microbiota and adverse health outcomes. This review seeks to highlight some of the challenges and pitfalls that may be encountered during all stages of microbiota research, from study design and sample collection, to nucleic acid extraction and sequencing, and bioinformatic and statistical analysis.

Methods: Literature focused on human microbiota research was reviewed and summarized.

Results: Although most studies have focused on surveying the composition of the microbiota, fewer have explored the causal roles of these bacteria, archaea, viruses, and fungi in affecting disease states. Microbiome research is in its relatively early years and many aspects remain challenging, including the complexity and personalized aspects of microbial communities, the influence of exogenous and often confounding factors, the need to apply fundamental principles of ecology and epidemiology, the necessity for new software tools, and the rapidly evolving genomic, technological, and analytical landscapes.

Conclusions: Incorporating human microbiome research in large epidemiologic studies will soon help us unravel the intricate relationships that we have with our microbial partners and provide interventional opportunities to improve human health.

Citing Articles

Examining the healthy human microbiome concept.

Joos R, Boucher K, Lavelle A, Arumugam M, Blaser M, Claesson M Nat Rev Microbiol. 2024; 23(3):192-205.

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The salivary microbiome as a diagnostic biomarker of periodontitis: a 16S multi-batch study before and after the removal of batch effects.

Regueira-Iglesias A, Suarez-Rodriguez B, Blanco-Pintos T, Relvas M, Alonso-Sampedro M, Balsa-Castro C Front Cell Infect Microbiol. 2024; 14:1405699.

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A Narrative Review Discussing the Obstetric Repercussions Due to Alterations of Personalized Bacterial Sites Developed within the Vagina, Cervix, and Endometrium.

Doroftei B, Ilie O, Armeanu T, Stoian I, Anton N, Babici R J Clin Med. 2023; 12(15).

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In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea.

Regueira-Iglesias A, Vazquez-Gonzalez L, Balsa-Castro C, Vila-Blanco N, Blanco-Pintos T, Tamames J Microbiome. 2023; 11(1):58.

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Stability of the Fecal and Oral Microbiome over 2 Years at -80°C for Multiple Collection Methods.

Zouiouich S, Byrd D, Hua X, Karwa S, Wan Y, Shi J Cancer Epidemiol Biomarkers Prev. 2023; 32(3):444-451.

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References

Corless C, Guiver M, Borrow R, Edwards-Jones V, Kaczmarski E, Fox A . Contamination and sensitivity issues with a real-time universal 16S rRNA PCR. J Clin Microbiol. 2000; 38(5):1747-52. PMC: 86577. DOI: 10.1128/JCM.38.5.1747-1752.2000. View

Foxman B, Riley L . Molecular epidemiology: focus on infection. Am J Epidemiol. 2001; 153(12):1135-41. DOI: 10.1093/aje/153.12.1135. View

Chou H, Holmes M . DNA sequence quality trimming and vector removal. Bioinformatics. 2001; 17(12):1093-104. DOI: 10.1093/bioinformatics/17.12.1093. View

Grahn N, Olofsson M, Ellnebo-Svedlund K, Monstein H, Jonasson J . Identification of mixed bacterial DNA contamination in broad-range PCR amplification of 16S rDNA V1 and V3 variable regions by pyrosequencing of cloned amplicons. FEMS Microbiol Lett. 2003; 219(1):87-91. DOI: 10.1016/S0378-1097(02)01190-4. View

Ott S, Musfeldt M, Wenderoth D, Hampe J, Brant O, Folsch U . Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut. 2004; 53(5):685-93. PMC: 1774050. DOI: 10.1136/gut.2003.025403. View

Zhou X, Bent S, Schneider M, Davis C, Islam M, Forney L . Characterization of vaginal microbial communities in adult healthy women using cultivation-independent methods. Microbiology (Reading). 2004; 150(Pt 8):2565-2573. DOI: 10.1099/mic.0.26905-0. View

Mohammadi T, Reesink H, Vandenbroucke-Grauls C, Savelkoul P . Removal of contaminating DNA from commercial nucleic acid extraction kit reagents. J Microbiol Methods. 2005; 61(2):285-8. DOI: 10.1016/j.mimet.2004.11.018. View

Schloss P, Handelsman J . Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol. 2005; 71(3):1501-6. PMC: 1065144. DOI: 10.1128/AEM.71.3.1501-1506.2005. View

Margulies M, Egholm M, Altman W, Attiya S, Bader J, Bemben L . Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005; 437(7057):376-80. PMC: 1464427. DOI: 10.1038/nature03959. View

10.

Li W, Godzik A . Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006; 22(13):1658-9. DOI: 10.1093/bioinformatics/btl158. View

11.

DeSantis T, Hugenholtz P, Larsen N, Rojas M, Brodie E, Keller K . Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006; 72(7):5069-72. PMC: 1489311. DOI: 10.1128/AEM.03006-05. View

12.

Ley R, Turnbaugh P, Klein S, Gordon J . Microbial ecology: human gut microbes associated with obesity. Nature. 2006; 444(7122):1022-3. DOI: 10.1038/4441022a. View

13.

Wang Q, Garrity G, Tiedje J, Cole J . Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007; 73(16):5261-7. PMC: 1950982. DOI: 10.1128/AEM.00062-07. View

14.

Huse S, Huber J, Morrison H, Sogin M, Welch D . Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 2007; 8(7):R143. PMC: 2323236. DOI: 10.1186/gb-2007-8-7-r143. View

15.

Turnbaugh P, Ley R, Hamady M, Fraser-Liggett C, Knight R, Gordon J . The human microbiome project. Nature. 2007; 449(7164):804-10. PMC: 3709439. DOI: 10.1038/nature06244. View

16.

Pruesse E, Quast C, Knittel K, Fuchs B, Ludwig W, Peplies J . SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007; 35(21):7188-96. PMC: 2175337. DOI: 10.1093/nar/gkm864. View

17.

Nechvatal J, Ram J, Basson M, Namprachan P, Niec S, Badsha K . Fecal collection, ambient preservation, and DNA extraction for PCR amplification of bacterial and human markers from human feces. J Microbiol Methods. 2007; 72(2):124-32. DOI: 10.1016/j.mimet.2007.11.007. View

18.

Brotman R, Ghanem K, Klebanoff M, Taha T, Scharfstein D, Zenilman J . The effect of vaginal douching cessation on bacterial vaginosis: a pilot study. Am J Obstet Gynecol. 2008; 198(6):628.e1-7. PMC: 2494605. DOI: 10.1016/j.ajog.2007.11.043. View

19.

Liu Z, DeSantis T, Andersen G, Knight R . Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res. 2008; 36(18):e120. PMC: 2566877. DOI: 10.1093/nar/gkn491. View

20.

Holmes E, Wilson I, Nicholson J . Metabolic phenotyping in health and disease. Cell. 2008; 134(5):714-7. DOI: 10.1016/j.cell.2008.08.026. View