Jump to ContentJump to Main Navigation
Show Summary Details

LaboratoriumsMedizin - Journal of Laboratory Medicine

Offizielles Organ der Deutschen Vereinten Gesellschaft für Klinische Chemie und Laboratoriumsmedizin e.V. (DGKL) und affiliiert mit der Österreichischen Gesellschaft für Laboratoriumsmedizin und Klinische Chemie (ÖGLMKC)

Editor-in-Chief: Schuff-Werner, Peter

Editorial Board Member: Ahmad-Nejad, Parviz / Bidlingmaier, Martin / Borucki, Katrin / Karsten, Conrad / Fraunberger, Peter / Ghebremedhin, Beniam / Holdenrieder, Stefan / Kiehntopf, Michael / Klein, Hanns-Georg / Klouche, Mariam / Kohse, Klaus P. / Kratzsch, Jürgen / Luppa, Peter B. / März, Winfried / Nebe, Carl Thomas / Orth, Matthias / Ruf, Andreas / Sack, Ulrich / Steimer, Werner / Weber, Bernard / Wieland, Eberhard / Tumani, Hayrettin / Zettl, Uwe K.

6 Issues per year

IMPACT FACTOR 2015: 0.104
5-year IMPACT FACTOR: 0.180

SCImago Journal Rank (SJR) 2014: 0.151
Source Normalized Impact per Paper (SNIP) 2014: 0.172
Impact per Publication (IPP) 2014: 0.313

See all formats and pricing
Volume 37, Issue 6 (Nov 2013)


Developments and insights into the analysis of the human microbiome

Entwicklungen und Erkenntnisse in der Analyse des humanen Mikrobioms

Ovidiu Rücker
  • Corresponding author
  • IMGM Laboratories GmbH, Martinsried, Germany
  • Email:
/ Alexandra Dangel
  • IMGM Laboratories GmbH, Martinsried, Germany
/ Hanns-Georg Klein
  • IMGM Laboratories GmbH, Martinsried, Germany
  • Center for Human Genetics and Laboratory Medicine Dr. Klein & Dr. Rost, Martinsried, Germany
Published Online: 2013-08-29 | DOI: https://doi.org/10.1515/labmed-2013-0018


The intense research focused on the human microbiome during the last years has shed some light on this mostly uncharacterized part of the human body. The constantly improving sequencing technologies have additionally eased the process of collecting a large amount of genome data from metagenomics samples. Using these methods, large studies with sufficient number of subjects have started to reveal the implications of our microbiome in health and disease. Here, we present a review on the last developments of sequencing technology together with an overview on the findings in this fast-evolving field of science.


In den letzten Jahren haben sich immer mehr wissenschaftliche Untersuchungen auf das humane Mikrobiom konzentriert, um diesen noch meist unbekannten Teil des menschlichen Körpers intensiver zu durchleuchten. Die konstante Verbesserung der verfügbaren Sequenziertechnologien hat weiterhin die Verfügbarkeit von großen Mengen an genomischen Daten deutlich erleichtert. Hiermit konnten große Studien mit einer genügend großen Anzahl an Probanden beginnen zu beschreiben, welche Auswirkungen unser Mikrobiom nicht nur in Verbindung mit Krankheiten sondern auch auf unseren gesunden Körper hat. In diesem Übersichtsartikel beschreiben wir die neuesten Entwicklungen in den Sequenziertechnologien zusammen mit einer Darstellung neuester Erkenntnisse aus diesem Forschungsbereich, welcher sich immer schneller entwickelt.

Reviewed publication: KleinH.-G.

Keywords: human metagenome; Illumina; metagenomics; next-generation sequencing (NGS); Roche; 16S rRNA; humanes Metagenom; Illumina; Metagenomik; next generation sequencing (NGS); Roche; 16S rRNA


  • 1.

    Thomas T, Gilbert J, Meyer F. Metagenomics – a guide from sampling to data analysis. Microb Inform Exp 2012;2:3. [Crossref]

  • 2.

    Metzker ML. Sequencing technologies – the next generation. Nat Rev Genet 2010;11:31–46. [Crossref] [Web of Science]

  • 3.

    Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, et al. Microbial diversity in the deep sea and the underexplored “rare biosphere.” PNAS 2006;103:12115–20. [Crossref]

  • 4.

    Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci USA 2011;108:4516–22. [Crossref]

  • 5.

    Whiteley AS, Jenkins S, Waite I, Kresoje N, Payne H, Mullan B, et al. Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform. J Microbiol Methods 2012;91:80–8. [Web of Science] [Crossref]

  • 6.

    Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, Scheutz F, et al. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 2011;365:709–17. [Web of Science]

  • 7.

    Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucl Acids Res 2013;41:e1. [Crossref]

  • 8.

    Altermann E. Tracing lifestyle adaptation in prokaryotic genomes. Front Microbiol 2012;3:48. [Crossref] [Web of Science]

  • 9.

    Harris SR, Clarke IN, Seth-Smith HMB, Solomon AW, Cutcliffe LT, Marsh P, et al. Whole genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing. Nat Genet 2012;44:413–S1. [Crossref] [Web of Science]

  • 10.

    Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D, et al. Experimental and analytical tools for studying the human microbiome. Nat Rev Genet 2011;13:47–58. [Web of Science] [Crossref]

  • 11.

    Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial community variation in human body habitats across space and time. Science 2009;326:1694–7. [Web of Science]

  • 12.

    Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, et al. Structure, function and diversity of the healthy human microbiome. Nature 2012;486:207–14. [Web of Science]

  • 13.

    Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010;464:59–65. [Web of Science]

  • 14.

    Sommer F, Bäckhed F. The gut microbiota – masters of host development and physiology. Nat Rev Micro 2013;11:227–38. [Web of Science] [Crossref]

  • 15.

    Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature 2012;486:222–7. [Web of Science]

  • 16.

    Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, et al. Enterotypes of the human gut microbiome. Nature 2011;473:174–80. [Web of Science]

  • 17.

    Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, et al. Topographical and temporal diversity of the human skin microbiome. Science 2009;324:1190–2. [Web of Science]

  • 18.

    Findley K, Oh J, Yang J, Conlan S, Deming C, Meyer JA, et al. Topographic diversity of fungal and bacterial communities in human skin. Nature [Internet] 2013 [cited 2013 May 27]; advance online publication. Available from: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12171.html.

  • 19.

    Wylie KM, Weinstock GM, Storch GA. Emerging view of the human virome. Transl Res 2012;160:283–90. [Web of Science]

  • 20.

    Didelot X, Bowden R, Wilson DJ, Peto TEA, Crook DW. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet 2012;13:601–12. [Web of Science] [Crossref]

  • 21.

    Buttigieg PL, Hankeln W, Kostadinov I, Kottmann R, Yilmaz P, Duhaime MB, et al. Ecogenomic perspectives on domains of unknown function: correlation-based exploration of marine metagenomes. PLoS One 2013;8:e50869. [Crossref] [Web of Science]

  • 22.

    Hirsch PR, Mauchline TH. Who’s who in the plant root microbiome? Nat Biotechnol 2012;30:961–2. [Crossref] [Web of Science]

  • 23.

    Fouts DE, Szpakowski S, Purushe J, Torralba M, Waterman RC, MacNeil MD, et al. Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen. PLoS One 2012;7:e48289. [Web of Science] [Crossref]

  • 24.

    Temperton B, Giovannoni SJ. Metagenomics: microbial diversity through a scratched lens. Curr Opin Microbiol 2012;15:605–12. [Web of Science] [Crossref]

  • 25.

    Zarco M, Vess T, Ginsburg G. The oral microbiome in health and disease and the potential impact on personalized dental medicine. Oral Dis 2012;18:109–20. [Web of Science] [Crossref]

  • 26.

    Blaser MJ, Falkow S. What are the consequences of the disappearing human microbiota? Nat Rev Micro 2009;7:887–94. [Web of Science] [Crossref]

  • 27.

    Frank DN, Pace NR. Gastrointestinal microbiology enters the metagenomics era. Curr Opin Gastroenterol 2008;24:4–10. [Crossref] [Web of Science]

  • 28.

    Devaraj S, Hemarajata P, Versalovic J. The human gut microbiome and body metabolism: implications for obesity and diabetes. Clin Chem 2013;59:617–28. [Crossref] [Web of Science]

  • 29.

    Lakhdari O, Cultrone A, Tap J, Gloux K, Bernard F, Ehrlich SD, et al. Functional metagenomics: a high throughput screening method to decipher microbiota-driven NF-κB modulation in the human gut. PLoS One 2010;5:e13092. [Crossref] [Web of Science]

  • 30.

    Li E, Hamm CM, Gulati AS, Sartor RB, Chen H, Wu X, et al. Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. PLoS One 2012;7:e26284.

  • 31.

    Schmieder R, Edwards R. Insights into antibiotic resistance through metagenomic approaches. Future Microbiol 2012;7:73–89. [Crossref] [Web of Science]

  • 32.

    Bakken JS, Borody T, Brandt LJ, Brill JV, Demarco DC, Franzos MA, et al. Treating clostridium difficile infection with fecal microbiota transplantation. Clin Gastroenterol Hepatol 2011;9:1044–9. [Web of Science] [Crossref]

  • 33.

    Brandt LJ, Aroniadis OC, Mellow M, Kanatzar A, Kelly C, Park T, et al. Long-term follow-up of colonoscopic fecal microbiota transplant for recurrent Clostridium difficile infection. Am J Gastroenterol 2012;107:1079–87. [Web of Science] [Crossref]

  • 34.

    Markova A, Mostow EN. US skin disease assessment: ulcer and wound care. Dermatol Clin 2012;30:107–111, ix. [Crossref] [Web of Science]

  • 35.

    Rhoads DD, Cox SB, Rees EJ, Sun Y, Wolcott RD. Clinical identification of bacteria in human chronic wound infections: culturing vs. 16S ribosomal DNA sequencing. BMC Infect Dis 2012;12:321. [Web of Science] [Crossref]

  • 36.

    Holmes E, Li JV, Marchesi JR, Nicholson JK. Gut microbiota composition and activity in relation to host metabolic phenotype and disease risk. Cell Metab 2012;16:559–64. [Web of Science] [Crossref]

  • 37.

    Belda-Ferre P, Cabrera-Rubio R, Moya A, Mira A. Mining virulence genes using metagenomics. PLoS One 2011;6:e24975. [Crossref] [Web of Science]

  • 38.

    Baker S, Holt KE, Clements ACA, Karkey A, Arjyal A, Boni MF, et al. Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission. Open Biol 2011;1:110008. [Crossref] [Web of Science]

  • 39.

    Law J, Jovel J, Patterson J, Ford G, O’keefe S, Wang W, et al. Identification of hepatotropic viruses from plasma using deep sequencing: a next generation diagnostic tool. PLoS One 2013;8:e60595. [Crossref] [Web of Science]

  • 40.

    Wylie KM, Mihindukulasuriya KA, Sodergren E, Weinstock GM, Storch GA. Sequence analysis of the human virome in febrile and afebrile children. PLoS One 2012;7:e27735. [Web of Science] [Crossref]

  • 41.

    Reyes A, Semenkovich NP, Whiteson K, Rohwer F, Gordon JI. Going viral: next generation sequencing applied to human gut phage populations. Nat Rev Microbiol 2012;10:607–17. [Web of Science] [Crossref]

  • 42.

    Delwart E. A Roadmap to the Human Virome. PLoS Pathog 2013;9(2):e1003146. doi:10.1371/journal.ppat.1003146. [Crossref] [Web of Science]

  • 43.

    Merget B, Koetschan C, Hackl T, Forster F, Dandekar T, Muller T, et al. The ITS2 database. J Vis Exp 2012.

  • 44.

    Liu L, Li Y, Li S, Hu N, He Y, Pong R, et al. Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012;2012:251364. [Web of Science]

  • 45.

    Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 2012;13:341. [Crossref] [Web of Science]

  • 46.

    Willner D, Daly J, Whiley D, Grimwood K, Wainwright CE, Hugenholtz P. Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples. PLoS One 2012;7:e34605. [Crossref] [Web of Science]

  • 47.

    Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008;74:2461–70. [Web of Science] [Crossref]

  • 48.

    Knight R, Jansson J, Field D, Fierer N, Desai N, Fuhrman JA, et al. Unlocking the potential of metagenomics through replicated experimental design. Nat Biotechnol 2012;30:513–20. [Web of Science] [Crossref]

  • 49.

    Huggett JF, Laver T, Tamisak S, Nixon G, O’Sullivan DM, Elaswarapu R, et al. Considerations for the development and application of control materials to improve metagenomic microbial community profiling. Accred Qual Assur 2013;18:77–83. [Crossref] [Web of Science]

  • 50.

    Raes J, Foerstner KU, Bork P. Get the most out of your metagenome: computational analysis of environmental sequence data. Curr Opin Microbiol 2007;10:490–8. [Web of Science] [Crossref]

About the article

Correspondence: Dr. Ovidiu Rücker, IMGM Laboratories GmbH, Lochhamer Str. 29, 82152 Martinsried, Germany, Tel.: +49 89 89557840, Fax: +49 89 89557841, E-Mail:

Received: 2013-06-05

Accepted: 2013-07-22

Published Online: 2013-08-29

Published in Print: 2013-11-01

Citation Information: LaboratoriumsMedizin, ISSN (Online) 1439-0477, ISSN (Print) 0342-3026, DOI: https://doi.org/10.1515/labmed-2013-0018. Export Citation

Comments (0)

Please log in or register to comment.
Log in