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Novel Systems Biology Techniques

  • Open Access
    The Generalized Matrix Decomposition Biplot and Its Application to Microbiome Data
    Editor's Pick Methods and Protocols | Novel Systems Biology Techniques
    The Generalized Matrix Decomposition Biplot and Its Application to Microbiome Data

    Biplots that simultaneously display the sample clustering and the important taxa have gained popularity in the exploratory analysis of human microbiome data. Traditional biplots, assuming Euclidean distances between samples, are not appropriate for microbiome data, when non-Euclidean distances are used to characterize dissimilarities among microbial communities. Thus, incorporating information from non-Euclidean distances into a biplot...

    Yue Wang, Timothy W. Randolph, Ali Shojaie, Jing Ma
  • Open Access
    Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China
    Research Article | Novel Systems Biology Techniques
    Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China

    The gut microbiota is believed to be closely related to many important physical functions in the host. Comprehensive data on mammalian gut metagenomes has facilitated research on host-microbiome interaction mechanisms, but less is known about pig gut microbiome, especially the gut microbiome in industrialized feedlot pigs, compared with human microbiome. On the other hand, pig production, as an important source of food, is believed to...

    Chunlai Wang, Peng Li, Qiulong Yan, Liping Chen, Tiantian Li, Wanjiang Zhang, He Li, Changming Chen, Xiuyan Han, Siyi Zhang, Miao Xu, Bo Li, Xiaoxuan Zhang, Hongbo Ni, Yufang Ma, Bo Dong, Shenghui Li, Siguo Liu
  • Open Access
    Simultaneous Tracking of <span class="named-content genus-species" id="named-content-1">Pseudomonas aeruginosa</span> Motility in Liquid and at the Solid-Liquid Interface Reveals Differential Roles for the Flagellar Stators
    Research Article | Novel Systems Biology Techniques
    Simultaneous Tracking of Pseudomonas aeruginosa Motility in Liquid and at the Solid-Liquid Interface Reveals Differential Roles for the Flagellar Stators

    We have established a methodology to enable the movement of individual bacterial cells to be followed within a 3D space without requiring any labeling. Such an approach is important to observe and understand how bacteria interact with surfaces and form biofilm. We investigated the swimming behavior of Pseudomonas aeruginosa, which has two flagellar stators that drive...

    Andrew L. Hook, James L. Flewellen, Jean-Frédéric Dubern, Alessandro M. Carabelli, Irwin M. Zaid, Richard M. Berry, Ricky D. Wildman, Noah Russell, Paul Williams, Morgan R. Alexander
  • Open Access
    Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes
    Research Article | Novel Systems Biology Techniques
    Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes

    Short-read sequencing with Illumina sequencing technology provides an accurate, high-throughput method for characterizing the metabolic potential of microbial communities. Short-read sequences can be assembled and binned into metagenome-assembled genomes, thus shedding light on the function of microbial ecosystems that are important for health, agriculture, and Earth system processes. The work presented here provides an analytical...

    Taylor M. Royalty, Andrew D. Steen
  • Open Access
    A Metabolome- and Metagenome-Wide Association Network Reveals Microbial Natural Products and Microbial Biotransformation Products from the Human Microbiota
    Editor's Pick Research Article | Novel Systems Biology Techniques
    A Metabolome- and Metagenome-Wide Association Network Reveals Microbial Natural Products and Microbial Biotransformation Products from the Human Microbiota

    Experimental advances have enabled the acquisition of tandem mass spectrometry and metagenomics sequencing data from tens of thousands of environmental/host-oriented microbial communities. Each of these communities contains hundreds of microbial features (corresponding to microbial species) and thousands of molecular features (corresponding to microbial natural products). However, with the current technology, it is very difficult to...

    Liu Cao, Egor Shcherbin, Hosein Mohimani
  • Open Access
    Mouse Gut Microbiome-Encoded β-Glucuronidases Identified Using Metagenome Analysis Guided by Protein Structure
    Research Article | Novel Systems Biology Techniques
    Mouse Gut Microbiome-Encoded β-Glucuronidases Identified Using Metagenome Analysis Guided by Protein Structure

    Mice are commonly employed as model organisms of mammalian disease; as such, our understanding of the compositions of their gut microbiomes is critical to appreciating how the mouse and human gastrointestinal tracts mirror one another. GUS enzymes, with importance in normal physiology and disease, are an attractive set of proteins to use for such analyses. Here we show that while the specific GUS enzymes differ at the sequence level, a...

    Benjamin C. Creekmore, Josh H. Gray, William G. Walton, Kristen A. Biernat, Michael S. Little, Yongmei Xu, Jian Liu, Raad Z. Gharaibeh, Matthew R. Redinbo
  • Open Access
    Species Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes
    Research Article | Novel Systems Biology Techniques
    Species Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes

    Gut microbes associate, compete for, and specialize in specific metabolic tasks. These interactions are dictated by the cross-feeding of degradation or fermentation products. However, the individual contribution of microbes to the function of the gut microbiome is difficult to evaluate. It is essential to understand the complexity of microbial interactions and how the presence or absence of specific microorganisms affects the stability...

    Natalia Gutiérrez, Daniel Garrido
  • Open Access
    redbiom: a Rapid Sample Discovery and Feature Characterization System
    Observation | Novel Systems Biology Techniques
    redbiom: a Rapid Sample Discovery and Feature Characterization System

    Although analyses that combine many microbiomes at the whole-community level have become routine, searching rapidly for microbiomes that contain a particular sequence has remained difficult. The software we present here, redbiom, dramatically accelerates this process, allowing samples that contain microbiome features to be rapidly identified. This is especially useful when taxonomic annotation is limited, allowing users to identify...

    Daniel McDonald, Benjamin Kaehler, Antonio Gonzalez, Jeff DeReus, Gail Ackermann, Clarisse Marotz, Gavin Huttley, Rob Knight
  • Open Access
    Quantifying and Understanding Well-to-Well Contamination in Microbiome Research
    Research Article | Novel Systems Biology Techniques
    Quantifying and Understanding Well-to-Well Contamination in Microbiome Research

    Microbiome research has uncovered magnificent biological and chemical stories across nearly all areas of life science, at times creating controversy when findings reveal fantastic descriptions of microbes living and even thriving in what were once thought to be sterile environments. Scientists have refuted many of these claims because of contamination, which has led to robust requirements, including the use of controls, for validating...

    Jeremiah J. Minich, Jon G. Sanders, Amnon Amir, Greg Humphrey, Jack A. Gilbert, Rob Knight
  • Open Access
    Determining Microbial Niche Breadth in the Environment for Better Ecosystem Fate Predictions
    Special Issue Perspective | Novel Systems Biology Techniques
    Determining Microbial Niche Breadth in the Environment for Better Ecosystem Fate Predictions

    Integrated omics applied to microbial communities offers a great opportunity to analyze the niche breadths (i.e., resource and condition ranges usable by a species) of constituent populations, ranging from generalists, with a broad niche breadth, to specialists, with a narrow one. In this context, extracellular metabolomics measurements describe resource spaces available to microbial populations; dedicated analyses of metagenomics data...

    Emilie E. L. Muller

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