From molecules to dynamic biological communities View Full Text


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Article Info

DATE

2013-02-05

AUTHORS

Daniel McDonald, Yoshiki Vázquez-Baeza, William A. Walters, J. Gregory Caporaso, Rob Knight

ABSTRACT

Microbial ecology is flourishing, and in the process, is making contributions to how the ecology and biology of large organisms is understood. Ongoing advances in sequencing technology and computational methods have enabled the collection and analysis of vast amounts of molecular data from diverse biological communities. While early studies focused on cataloguing microbial biodiversity in environments ranging from simple marine ecosystems to complex soil ecologies, more recent research is concerned with community functions and their dynamics over time. Models and concepts from traditional ecology have been used to generate new insight into microbial communities, and novel system-level models developed to explain and predict microbial interactions. The process of moving from molecular inventories to functional understanding is complex and challenging, and never more so than when many thousands of dynamic interactions are the phenomena of interest. We outline the process of how epistemic transitions are made from producing catalogues of molecules to achieving functional and predictive insight, and show how those insights not only revolutionize what is known about biological systems but also about how to do biology itself. Examples will be drawn primarily from analyses of different human microbiota, which are the microbial consortia found in and on areas of the human body, and their associated microbiomes (the genes of those communities). Molecular knowledge of these microbiomes is transforming microbiological knowledge, as well as broader aspects of human biology, health and disease. More... »

PAGES

241-259

References to SciGraph publications

  • 2006-12. An obesity-associated gut microbiome with increased capacity for energy harvest in NATURE
  • 2011-09-08. Using network analysis to explore co-occurrence patterns in soil microbial communities in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2011-05-30. Moving pictures of the human microbiome in GENOME BIOLOGY
  • 2011-12-01. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2012-08-14. Categorization of the gut microbiota: enterotypes or gradients? in NATURE REVIEWS MICROBIOLOGY
  • 2012-05-09. Human gut microbiome viewed across age and geography in NATURE
  • 2012-09-12. Diversity, stability and resilience of the human gut microbiota in NATURE
  • 2011-03-24. Marine bacterial, archaeal and protistan association networks reveal ecological linkages in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2012-07-13. Gut microbiota composition correlates with diet and health in the elderly in NATURE
  • 1986. The Analysis of Natural Microbial Populations by Ribosomal RNA Sequences in ADVANCES IN MICROBIAL ECOLOGY
  • 2007-10-17. The Human Microbiome Project in NATURE
  • 2008-09-09. Human colonic microbiota associated with diet, obesity and weight loss in INTERNATIONAL JOURNAL OF OBESITY
  • 2011-08-18. Defining seasonal marine microbial community dynamics in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2012-03-21. Gut microbial 'enterotypes' become less clear-cut in NATURE
  • 2011-04-20. Enterotypes of the human gut microbiome in NATURE
  • 2011-11-10. The Western English Channel contains a persistent microbial seed bank in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2010-03-22. Environmental distribution of prokaryotic taxa in BMC MICROBIOLOGY
  • 2010-05-06. Soil bacterial and fungal communities across a pH gradient in an arable soil in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2010. The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010. in ENVIRONMENTAL MICROBIOME
  • 2009-10-22. Global ecological patterns in uncultured Archaea in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2008-11-30. A core gut microbiome in obese and lean twins in NATURE
  • 2003-05. Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis in NATURE
  • 2010-03. A human gut microbial gene catalogue established by metagenomic sequencing in NATURE
  • 2008-10-09. Next-generation DNA sequencing in NATURE BIOTECHNOLOGY
  • 2012-06-13. Structure, Function and Diversity of the Healthy Human Microbiome in NATURE
  • 2012-06-07. Unlocking the potential of metagenomics through replicated experimental design in NATURE BIOTECHNOLOGY
  • 2009-12. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea in NATURE
  • 2011-06-30. Saliva microbiomes distinguish caries-active from healthy human populations in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2010-03-12. Review of software for space-time disease surveillance in INTERNATIONAL JOURNAL OF HEALTH GEOGRAPHICS
  • 2012-07-26. Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2009-08-09. Accurate determination of microbial diversity from 454 pyrosequencing data in NATURE METHODS
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    http://scigraph.springernature.com/pub.10.1007/s10539-013-9364-4

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    http://dx.doi.org/10.1007/s10539-013-9364-4

    DIMENSIONS

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    PUBMED

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