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Latest Articles

  • Genomes of Gut Bacteria from <em>Nasonia</em> Wasps Shed Light on Phylosymbiosis and Microbe-Assisted Hybrid Breakdown
    Research Article
    Genomes of Gut Bacteria from Nasonia Wasps Shed Light on Phylosymbiosis and Microbe-Assisted Hybrid Breakdown

    Animal and plant hosts often establish intimate relationships with their microbiomes. In varied environments, closely related host species share more similar microbiomes, a pattern termed phylosymbiosis.

    Karissa L. Cross, Brittany A. Leigh, E. Anne Hatmaker, Aram Mikaelyan, Asia K. Miller, Seth R. Bordenstein
    6 Apr 2021
  • Targeted Manipulation of Abundant and Rare Taxa in the <em>Daphnia magna</em> Microbiota with Antibiotics Impacts Host Fitness Differentially
    Research Article
    Targeted Manipulation of Abundant and Rare Taxa in the Daphnia magna Microbiota with Antibiotics Impacts Host Fitness Differentially

    Understanding the contributions of rare and abundant taxa to host fitness is an outstanding question in host microbial ecology. In this study, we use the model zooplankton Daphnia magna and its relatively simple cohort of bacterial taxa to disentangle the roles of distinct taxa in host life history metrics, using a suite of antibiotics to selectively reduce the abundance of functionally important taxa.

    Reilly O. Cooper, Janna M. Vavra, Clayton E. Cressler
    6 Apr 2021
  • The Gut Microbiome in Autism: Study-Site Effects and Longitudinal Analysis of Behavior Change
    Research Article
    The Gut Microbiome in Autism: Study-Site Effects and Longitudinal Analysis of Behavior Change

    Autism spectrum disorder (ASD) is a brain developmental disorder with varying behavioral symptom severity both across individuals and within individuals over time. There have been promising but also inconsistent literature results regarding how the gut microbiota (microbiome) may be involved.

    Jennifer Fouquier, Nancy Moreno Huizar, Jody Donnelly, Cody Glickman, Dae-Wook Kang, Juan Maldonado, Rachel A. Jones, Kimberly Johnson, James B. Adams, Rosa Krajmalnik-Brown, Catherine Lozupone
    6 Apr 2021
  • Finding Needles in Haystacks and Inferring Their Function: Challenges and Successes in Beneficial Symbiosis Research
    Commentary
    Finding Needles in Haystacks and Inferring Their Function: Challenges and Successes in Beneficial Symbiosis Research

    Symbioses between hosts and beneficial microbes are key drivers of biological innovation and diversity. While a range of systems have emerged that provide foundational insights into how symbioses function and evolve, we still have a limited understanding of the vast diversity of organisms that engage in such interactions.

    Gordon M. Bennett, Elizabeth Heath-Heckman, E. Maggie Sogin
    6 Apr 2021
  • The Role of the Microbiome in Autism: All That We Know about All That We Don’t Know
    Commentary
    The Role of the Microbiome in Autism: All That We Know about All That We Don’t Know

    Autism spectrum disorder (ASD) is an overly complex disorder influenced by both genetic and environmental factors. Numerous microbial diversity surveys conducted over the past decade have attempted to link specific ASD biomarkers to gastrointestinal tract disturbances, but results generated across cohorts and studies remain inconsistent.

    Maude M. David
    6 Apr 2021
  • Children with Autism and Their Typically Developing Siblings Differ in Amplicon Sequence Variants and Predicted Functions of Stool-Associated Microbes
    Research Article
    Children with Autism and Their Typically Developing Siblings Differ in Amplicon Sequence Variants and Predicted Functions of Stool-Associated Microbes

    Autism spectrum disorder (ASD), which now affects 1 in 59 children in the United States, is known to have comorbidity with gut disorders of a variety of types; however, the link to the microbiome remains poorly characterized. Recent work has provided compelling evidence to link the gut microbiome to the autism phenotype in mouse models, but identification of specific taxa associated with autism has suffered replicability issues in...

    Maude M. David, Christine Tataru, Jena Daniels, Jessey Schwartz, Jessica Keating, Jarrad Hampton-Marcell, Neil Gottel, Jack A. Gilbert, Dennis P. Wall
    6 Apr 2021
  • BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities
    Methods and Protocols
    BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities

    The failure of current universal taxonomic databases to support the rapidly expanding field of bee microbiota research has led to many investigators relying on “in-house” reference sets or manual classification of sequence reads (usually based on BLAST searches), often with vague identity thresholds and subjective taxonomy choices. This time expensive, error- and bias-prone process lacks standardization, cripples the potential for...

    Brendan A. Daisley, Gregor Reid
    6 Apr 2021
  • Bridging Rare and Abundant Bacteria with Ecosystem Multifunctionality in Salinized Agricultural Soils: from Community Diversity to Environmental Adaptation
    Research Article
    Bridging Rare and Abundant Bacteria with Ecosystem Multifunctionality in Salinized Agricultural Soils: from Community Diversity to Environmental Adaptation

    Soil salinization is a worldwide environmental problem and threatens plant productivity and microbial diversity. Understanding the generation and maintenance of microbial diversity is essential to estimate soil tillage potential via investigating ecosystem multifunctionality.

    Wenjie Wan, Song Liu, Xiang Li, Yonghui Xing, Wenli Chen, Qiaoyun Huang
    30 Mar 2021
  • Dynamic Bayesian Networks for Integrating Multi-omics Time Series Microbiome Data
    Methods and Protocols
    Dynamic Bayesian Networks for Integrating Multi-omics Time Series Microbiome Data

    While a number of large consortia collect and profile several different types of microbiome and genomic time series data, very few methods exist for joint modeling of multi-omics data sets. We developed a new computational pipeline, PALM, which uses dynamic Bayesian networks (DBNs) and is designed to integrate multi-omics data from longitudinal microbiome studies.

    Daniel Ruiz-Perez, Jose Lugo-Martinez, Natalia Bourguignon, Kalai Mathee, Betiana Lerner, Ziv Bar-Joseph, Giri Narasimhan
    30 Mar 2021
  • Systems Biology behind Immunoprotection of Both Sheep and Goats after Sungri/96 PPRV Vaccination
    Research Article
    Systems Biology behind Immunoprotection of Both Sheep and Goats after Sungri/96 PPRV Vaccination

    Peste des petits ruminants (PPR) by PPR virus (PPRV) is an World Organisation for Animal Health (OIE)-listed acute, contagious transboundary viral disease of small ruminants. The attenuated Sungri/96 PPRV vaccine used all over India against this PPR provides long-lasting robust innate and adaptive immune response.

    Sajad Ahmad Wani, Manas Ranjan Praharaj, Amit R. Sahu, Raja Ishaq Nabi Khan, Shikha Saxena, Kaushal Kishor Rajak, Dhanavelu Muthuchelvan, Aditya Sahoo, Bina Mishra, Raj Kumar Singh, Bishnu Prasad Mishra, Ravi Kumar Gandham
    30 Mar 2021

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