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Archive

January/February 2018; Volume 3,Issue 1

Research Articles

  • Abiotic Stresses Shift Belowground <em>Populus</em>-Associated Bacteria Toward a Core Stress Microbiome
    Research Article | Host-Microbe Biology
    Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome

    The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for...

    Collin M. Timm, Kelsey R. Carter, Alyssa A. Carrell, Se-Ran Jun, Sara S. Jawdy, Jessica M. Vélez, Lee E. Gunter, Zamin Yang, Intawat Nookaew, Nancy L. Engle, Tse-Yuan S. Lu, Christopher W. Schadt, Timothy J. Tschaplinski, Mitchel J. Doktycz, Gerald A. Tuskan, Dale A. Pelletier, David J. Weston
    23 Jan 2018
  • Signatures of Selection at Drug Resistance Loci in <span class="named-content genus-species" id="named-content-1">Mycobacterium tuberculosis</span>
    Research Article | Ecological and Evolutionary Science
    Signatures of Selection at Drug Resistance Loci in Mycobacterium tuberculosis

    Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is a significant burden on global health. Antibiotic treatment imposes strong selective pressure on M. tuberculosis populations. Identifying the mutations that cause drug resistance in...

    Tatum D. Mortimer, Alexandra M. Weber, Caitlin S. Pepperell
    30 Jan 2018
  • Market Integration Predicts Human Gut Microbiome Attributes across a Gradient of Economic Development
    Editor's Pick Research Article | Host-Microbe Biology
    Market Integration Predicts Human Gut Microbiome Attributes across a Gradient of Economic Development

    Previous research has reported differences in the gut microbiome between populations residing in wealthy versus poorer countries, leading to the assertion that lifestyle changes associated with economic development promote changes in the gut microbiome that promote the proliferation of microbiome-associated diseases. However, a direct relationship between economic development and the gut microbiome has not previously been shown. We...

    Keaton Stagaman, Tara J. Cepon-Robins, Melissa A. Liebert, Theresa E. Gildner, Samuel S. Urlacher, Felicia C. Madimenos, Karen Guillemin, J. Josh Snodgrass, Lawrence S. Sugiyama, Brendan J. M. Bohannan
    27 Feb 2018
  • Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome
    Editor's Pick Research Article | Host-Microbe Biology
    Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome

    The process of reconstructing genomes from environmental sequence data (genome-resolved metagenomics) allows unique insight into microbial systems. We apply this technique to investigate how the antibiotic resistance genes of bacteria affect their ability to flourish in the gut under various conditions. Our analysis reveals that strain-level selection in formula-fed infants drives enrichment of beta-lactamase genes in the gut resistome...

    Sumayah F. Rahman, Matthew R. Olm, Michael J. Morowitz, Jillian F. Banfield
    9 Jan 2018
  • Host-Virus Protein Interaction Network Reveals the Involvement of Multiple Host Processes in the Life Cycle of Hepatitis E Virus
    Research Article | Host-Microbe Biology
    Host-Virus Protein Interaction Network Reveals the Involvement of Multiple Host Processes in the Life Cycle of Hepatitis E Virus

    Hepatitis E virus (HEV) is a pathogen that is transmitted by the fecal-oral route. Owing to the lack of an efficient laboratory model, the life cycle of the virus is poorly understood. During the course of infection, interactions between the viral and host proteins play essential roles, a clear understanding of which is essential to decode the life cycle of the virus. In this study, we identified the direct host interaction partners of...

    Chandru Subramani, Vidya P. Nair, Saumya Anang, Sukhen Das Mandal, Madhu Pareek, Nidhi Kaushik, Akriti Srivastava, Sudipto Saha, Shalimar, Baibaswata Nayak, C. T. Ranjith-Kumar, Milan Surjit
    23 Jan 2018
  • Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria
    Research Article | Novel Systems Biology Techniques
    Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria

    Molecular genetics is indispensable for interrogating the physiology of bacteria. However, the development of a functional genetic system for any given bacterium can be time-consuming. Here, we present a streamlined approach for identifying an effective transposon mutagenesis system for a new bacterium. Our strategy first involves the construction of hundreds of different transposon vector variants, which we term a “magic pool.” The...

    Hualan Liu, Morgan N. Price, Robert Jordan Waters, Jayashree Ray, Hans K. Carlson, Jacob S. Lamson, Romy Chakraborty, Adam P. Arkin, Adam M. Deutschbauer
    16 Jan 2018
  • Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> K-12 Genome
    Research Article | Molecular Biology and Physiology
    Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the Escherichia coli K-12 Genome

    The 91-amino-acid-residue small-subunit omega (the rpoZ gene product) of Escherichia coli RNA polymerase plays a structural role in the formation of RNA polymerase (RNAP) as a chaperone in folding the largest subunit (β′, of 1,407 residues in length), but except for binding of the stringent signal ppGpp, little is known of its role in the control of RNAP...

    Kaneyoshi Yamamoto, Yuki Yamanaka, Tomohiro Shimada, Paramita Sarkar, Myu Yoshida, Neerupma Bhardwaj, Hiroki Watanabe, Yuki Taira, Dipankar Chatterji, Akira Ishihama
    13 Feb 2018
  • Genomewide Transcriptional Responses of Iron-Starved <span class="named-content genus-species" id="named-content-1">Chlamydia trachomatis</span> Reveal Prioritization of Metabolic Precursor Synthesis over Protein Translation
    Research Article | Molecular Biology and Physiology
    Genomewide Transcriptional Responses of Iron-Starved Chlamydia trachomatis Reveal Prioritization of Metabolic Precursor Synthesis over Protein Translation

    By utilizing an experimental approach that monitors the immediate global response of Chlamydia trachomatis to iron starvation, clues to long-standing issues in Chlamydia biology are revealed, including how Chlamydia adapts to this stress. We determined that this pathogen initiates a transcriptional program that prioritizes replenishment of nutrient...

    Amanda J. Brinkworth, Mark R. Wildung, Rey A. Carabeo
    13 Feb 2018
  • Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction
    Research Article | Host-Microbe Biology
    Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction

    In the present report, we show that the human fecal microbiota contains promising and universal biomarkers for the noninvasive evaluation of inflammatory bowel disease severity and IFX treatment efficacy, emphasizing the potential ability to mine the gut microbiota as a modality to stratify IBD patients and apply personalized therapy for optimal outcomes.

    Youlian Zhou, Zhenjiang Zech Xu, Yan He, Yunsheng Yang, Le Liu, Qianyun Lin, Yuqiang Nie, Mingsong Li, Fachao Zhi, Side Liu, Amnon Amir, Antonio González, Anupriya Tripathi, Minhu Chen, Gary D. Wu, Rob Knight, Hongwei Zhou, Ye Chen
    30 Jan 2018
  • Prevalence and Source of Fecal and Oral Bacteria on Infant, Child, and Adult Hands
    Research Article | Host-Microbe Biology
    Prevalence and Source of Fecal and Oral Bacteria on Infant, Child, and Adult Hands

    Bacteria live all around us, and we are constantly exposed to them during our everyday lives. Modern standards of hygiene aim to limit exposure to fecal bacteria, and yet bacteria rapidly colonize the gut in early life and following antibacterial treatment. Exposures to fecal and oral microbes provide risk of disease, but are also necessary since commensal microbes play important roles in health. This work establishes that bacteria of...

    Michael Shaffer, Catherine Lozupone
    16 Jan 2018
  • Omics-Based Insights into Flavor Development and Microbial Succession within Surface-Ripened Cheese
    Editor's Pick Research Article | Applied and Environmental Science
    Omics-Based Insights into Flavor Development and Microbial Succession within Surface-Ripened Cheese

    Fermented foods, in particular, surface-ripened cheese, represent a model to explain the metabolic interactions which regulate microbial succession in complex environments. This study explains the role of individual species in a heterogeneous microbial environment, i.e., the exterior of surface-ripened cheese. Through whole-metagenome shotgun sequencing, it was possible to investigate the metabolic potential of the resident...

    A. S. Bertuzzi, A. M. Walsh, J. J. Sheehan, P. D. Cotter, F. Crispie, P. L. H. McSweeney, K. N. Kilcawley, M. C. Rea
    30 Jan 2018
  • Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities
    Research Article | Ecological and Evolutionary Science
    Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities

    Microorganisms living within the rhizospheres of wetland plants significantly contribute to greenhouse gas emissions. Understanding how microbes produce these gases under conditions that have been imposed by human activities (i.e., nitrogen pollution) is important to the development of future management strategies. Our results illustrate that within the rhizosphere of the wetland plant Juncus acutiflorus, physiological...

    Eric R. Hester, Sarah F. Harpenslager, Josepha M. H. van Diggelen, Leon L. Lamers, Mike S. M. Jetten, Claudia Lüke, Sebastian Lücker, Cornelia U. Welte
    30 Jan 2018
  • Zika Virus Alters DNA Methylation of Neural Genes in an Organoid Model of the Developing Human Brain
    Research Article | Host-Microbe Biology
    Zika Virus Alters DNA Methylation of Neural Genes in an Organoid Model of the Developing Human Brain

    Scientific research on human neural stem cells and cerebral organoids has confirmed the congenital neurotropic and neurodestructive nature of the Zika virus. However, the extent to which prenatal ZIKV infection is associated with more subtle brain alterations, such as epigenetic changes, remains ill defined. Here, we address the question of whether ZIKV infection induces DNA methylation changes with the potential to cause brain...

    Sylvie Janssens, Michael Schotsaert, Rahul Karnik, Vinod Balasubramaniam, Marion Dejosez, Alexander Meissner, Adolfo García-Sastre, Thomas P. Zwaka
    6 Feb 2018
  • Transcriptome Profiling Reveals Interplay of Multifaceted Stress Response in <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> on Exposure to Glutathione and Ciprofloxacin
    Editor's Pick Research Article | Molecular Biology and Physiology
    Transcriptome Profiling Reveals Interplay of Multifaceted Stress Response in Escherichia coli on Exposure to Glutathione and Ciprofloxacin

    The emergence and spread of multidrug-resistant bacterial strains have serious medical and clinical consequences. In addition, the rate of discovery of new therapeutic antibiotics has been inadequate in last few decades. Fluoroquinolone antibiotics such as ciprofloxacin represent a precious therapeutic resource in the fight against bacterial pathogens. However, these antibiotics have been gradually losing their appeal due to the...

    Manish Goswami, Akkipeddi Venkat Satya Surya Narayana Rao
    13 Feb 2018

Author Correction

  • Correction for Morton et al., “Uncovering the Horseshoe Effect in Microbial Analyses”
    Author Correction
    Correction for Morton et al., “Uncovering the Horseshoe Effect in Microbial Analyses”
    James T. Morton, Liam Toran, Anna Edlund, Jessica L. Metcalf, Christian Lauber, Rob Knight
    6 Feb 2018
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mSystems: 3 (1)

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volume 3, issue 1
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  • Impact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota Profiling
  • 2019 Novel Coronavirus (COVID-19) Pandemic: Built Environment Considerations To Reduce Transmission
  • Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level
  • Fungal Communities Are Important Determinants of Bacterial Community Composition in Deadwood
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