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Latest Articles

  • An Important Role for Purifying Selection in Archaeal Genome Evolution
    Observation | Ecological and Evolutionary Science
    An Important Role for Purifying Selection in Archaeal Genome Evolution

    The evolution of genome complexities is a fundamental question in biology. A hallmark of eukaryotic genome complexity is that larger genomes tend to have more noncoding sequences, which are believed to be minimal in archaeal and bacterial genomes. However, we found that archaeal genomes also possessed this eukaryotic feature while bacterial genomes did not. This could be predicted from our analysis of genetic drift, which showed relaxed...

    Zhe Lyu, Zhi-Gang Li, Fei He, Ziding Zhang
    24 Oct 2017
  • Multi-omics Comparative Analysis Reveals Multiple Layers of Host Signaling Pathway Regulation by the Gut Microbiota
    Editor's Pick Research Article | Host-Microbe Biology
    Multi-omics Comparative Analysis Reveals Multiple Layers of Host Signaling Pathway Regulation by the Gut Microbiota

    Multiple host pathways were affected by its adaptation to the microbiota. We have found significant transcriptome-proteome discordance caused by the microbiota. This discovery leads to the definite conclusion that transcript-level analysis is not sufficient to predict protein levels and their influence on the function of many specific cellular pathways, so only analysis of combinations of the quantitative data determined at different...

    Nathan P. Manes, Natalia Shulzhenko, Arthur G. Nuccio, Sara Azeem, Andrey Morgun, Aleksandra Nita-Lazar
    24 Oct 2017
  • Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring
    Research Article | Host-Microbe Biology
    Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring

    The conservation and management of large whales rely in part upon health monitoring of individuals and populations, and methods generally necessitate invasive sampling. Here, we used a small, unmanned hexacopter drone to noninvasively fly above humpback whales from two populations, capture their exhaled breath (blow), and examine the associated microbiome. In the first extensive examination of the large-whale blow microbiome, we present...

    Amy Apprill, Carolyn A. Miller, Michael J. Moore, John W. Durban, Holly Fearnbach, Lance G. Barrett-Lennard
    10 Oct 2017
  • Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites
    Editor's Pick Research Article | Host-Microbe Biology
    Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites

    Emerging evidence suggests that environmental toxicants may influence inflammation-promoted chronic disease susceptibility during early life. BPA, an environmental endocrine disruptor, can transfer across the placenta and accumulate in fetal gut and liver. However, underlying mechanisms for BPA-induced colonic and liver inflammation are not fully elucidated. In this report, we show how perinatal BPA exposure in rabbits alters gut...

    Lavanya Reddivari, D. N. Rao Veeramachaneni, William A. Walters, Catherine Lozupone, Jennifer Palmer, M. K. Kurundu Hewage, Rohil Bhatnagar, Amnon Amir, Mary J. Kennett, Rob Knight, Jairam K. P. Vanamala
    10 Oct 2017
  • Comparative Metabolomics of <span class="named-content genus-species" id="named-content-1">Mycoplasma bovis</span> and <span class="named-content genus-species" id="named-content-2">Mycoplasma gallisepticum</span> Reveals Fundamental Differences in Active Metabolic Pathways and Suggests Novel Gene Annotations
    Research Article | Molecular Biology and Physiology
    Comparative Metabolomics of Mycoplasma bovis and Mycoplasma gallisepticum Reveals Fundamental Differences in Active Metabolic Pathways and Suggests Novel Gene Annotations

    Mycoplasmas are pathogenic bacteria that cause serious chronic infections in production animals, resulting in considerable losses worldwide, as well as causing disease in humans. These bacteria have extremely reduced genomes and are thought to have limited metabolic flexibility, even though they are highly successful persistent parasites in a diverse number of species. The extent to which different Mycoplasma species are...

    Y. Masukagami, D. P. De Souza, S. Dayalan, C. Bowen, S. O’Callaghan, K. Kouremenos, B. Nijagal, D. Tull, K. A. Tivendale, P. F. Markham, M. J. McConville, G. F. Browning, F. M. Sansom
    10 Oct 2017
  • Thiamine Acquisition Strategies Impact Metabolism and Competition in the Gut Microbe <span class="named-content genus-species" id="named-content-1">Bacteroides thetaiotaomicron</span>
    Research Article | Host-Microbe Biology
    Thiamine Acquisition Strategies Impact Metabolism and Competition in the Gut Microbe Bacteroides thetaiotaomicron

    Variation in the ability of gut microbes to transport, synthesize, and compete for vitamin B1 (thiamine) is expected to impact the structure and stability of the microbiota, and ultimately this variation may have both direct and indirect effects on human health. Our study identifies the diverse strategies employed by gut Bacteroidetes to acquire thiamine. We demonstrate how the presence or absence of thiamine...

    Zachary A. Costliow, Patrick H. Degnan
    26 Sep 2017
  • The Induction of Oxalate Metabolism <em>In Vivo</em> Is More Effective with Functional Microbial Communities than with Functional Microbial Species
    Research Article | Host-Microbe Biology
    The Induction of Oxalate Metabolism In Vivo Is More Effective with Functional Microbial Communities than with Functional Microbial Species

    Oxalate is a central component in 80% of kidney stones. While mammals do not possess the enzymes to degrade oxalate, many gastrointestinal bacteria are efficient oxalate degraders. We examined the role of cohesive microbial networks for oxalate metabolism, using Sprague-Dawley rats as a model host. While the transplantation of oxalate-degrading bacteria alone to the Sprague-Dawley hosts did increase oxalate metabolism, fecal transplants...

    Aaron W. Miller, Colin Dale, M. Denise Dearing
    26 Sep 2017
  • Functional Changes in the Gut Microbiome Contribute to Transforming Growth Factor β-Deficient Colon Cancer
    Editor's Pick Research Article | Host-Microbe Biology
    Functional Changes in the Gut Microbiome Contribute to Transforming Growth Factor β-Deficient Colon Cancer

    Most research on the gut microbiome in colon cancer focuses on taxonomic changes at the genus level using 16S rRNA gene sequencing. Here, we develop a new methodology to integrate DNA and RNA data sets to examine functional shifts at the species level that are important to tumor development. We uncover several metabolic pathways in the microbiome that, when perturbed by host genetics and H. hepaticus inoculation, contribute to...

    Scott G. Daniel, Corbie L. Ball, David G. Besselsen, Tom Doetschman, Bonnie L. Hurwitz
    26 Sep 2017
  • Systematic Discovery of Archaeal Transcription Factor Functions in Regulatory Networks through Quantitative Phenotyping Analysis
    Research Article | Novel Systems Biology Techniques
    Systematic Discovery of Archaeal Transcription Factor Functions in Regulatory Networks through Quantitative Phenotyping Analysis

    To ensure survival in the face of stress, microorganisms employ inducible damage repair pathways regulated by extensive and complex gene networks. Many archaea, microorganisms of the third domain of life, persist under extremes of temperature, salinity, and pH and under other conditions. In order to understand the cause-effect relationships between the dynamic function of the stress network and ultimate physiological consequences, this...

    Cynthia L. Darnell, Peter D. Tonner, Jordan G. Gulli, Scott C. Schmidler, Amy K. Schmid
    19 Sep 2017
  • Proteomes of <em>Lactobacillus delbrueckii</em> subsp. <em>bulgaricus</em> LBB.B5 Incubated in Milk at Optimal and Low Temperatures
    Research Article | Applied and Environmental Science
    Proteomes of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5 Incubated in Milk at Optimal and Low Temperatures

    Lactobacillus delbrueckii subsp. bulgaricus has a long history of use in yogurt production. Although commonly cocultured with Streptococcus salivarius subsp. thermophilus in milk, fundamental knowledge of the adaptive responses of L. delbrueckii subsp. bulgaricus to the dairy environment and the consequences of those responses on the use of L. delbrueckii subsp. ...

    Xiaochen Yin, Michelle R. Salemi, Brett S. Phinney, Velitchka Gotcheva, Angel Angelov, Maria L. Marco
    19 Sep 2017

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