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metaproteomics

  • Open Access
    High-Throughput Stool Metaproteomics: Method and Application to Human Specimens
    Research Article | Novel Systems Biology Techniques
    High-Throughput Stool Metaproteomics: Method and Application to Human Specimens

    Widely available technologies based on DNA sequencing have been used to describe the kinds of microbes that might correlate with health and disease. However, mechanistic insights might be best achieved through careful study of the dynamic proteins at the interface between the foods we eat, our microbes, and ourselves. Mass spectrometry-based proteomics has the potential to revolutionize our understanding of this complex system, but its...

    Carlos G. Gonzalez, Hannah C. Wastyk, Madeline Topf, Christopher D. Gardner, Justin L. Sonnenburg, Joshua E. Elias
  • Open Access
    Structural and Functional Changes in Prokaryotic Communities in Artificial Pit Mud during Chinese Baijiu Production
    Research Article | Applied and Environmental Science
    Structural and Functional Changes in Prokaryotic Communities in Artificial Pit Mud during Chinese Baijiu Production

    Strong-flavor baijiu (SFB) accounts for more than 70% of all Chinese liquor production. In the Chinese baijiu brewing industry, artificial pit mud (APM) has been widely used since the 1960s to construct fermentation cellars for production of high-quality SFB. To gain insights at the systems level into the mechanisms driving APM prokaryotic taxonomic and functional dynamics and into how this variation is connected with high-quality SFB...

    Mao-Ke Liu, Yu-Ming Tang, Xiao-Jiao Guo, Ke Zhao, Petri Penttinen, Xin-Hui Tian, Xin-Yu Zhang, Dao-Qun Ren, Xiao-Ping Zhang
  • Open Access
    Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities
    Special Issue Perspective | Host-Microbe Biology
    Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities

    Metaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level. Initially, metaproteomics was mainly used to assess the “expressed” metabolism and physiology of microbial community members.

    Manuel Kleiner
  • Open Access
    Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease
    Research Article | Host-Microbe Biology
    Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease

    A majority of current microbiome research relies heavily on DNA analysis. However, as the field moves toward understanding the microbial functions related to healthy and disease states, it is critical to evaluate how changes in DNA relate to changes in proteins, which are functional units of the genome. This study tracked the abundance of genes and proteins as they fluctuated during various inflammatory states in a 4.5-year study of a...

    Robert H. Mills, Yoshiki Vázquez-Baeza, Qiyun Zhu, Lingjing Jiang, James Gaffney, Greg Humphrey, Larry Smarr, Rob Knight, David J. Gonzalez
  • Open Access
    Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome
    Research Article | Applied and Environmental Science
    Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome

    The microbial production of methane or “biogas” is an attractive renewable energy technology that can recycle organic waste into biofuel. Biogas reactors operating with protein-rich substrates such as household municipal or agricultural wastes have significant industrial and societal value; however, they are highly unstable and frequently collapse due to the accumulation of ammonia. We report the discovery of a novel uncultured...

    J. A. Frank, M. Ø. Arntzen, L. Sun, L. H. Hagen, A. C. McHardy, S. J. Horn, V. G. H. Eijsink, A. Schnürer, P. B. Pope
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