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microbial ecology

  • Open Access
    Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria
    Research Article | Ecological and Evolutionary Science
    Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria

    Due to the promiscuous exchange of genetic material and asexual reproduction, delineating microbial species (and, by extension, populations) remains challenging. Because of this, the vast majority of microbial studies assessing population structure often compare divergent strains from disparate environments under varied selective pressures. Here, we investigated the population structure within a single bacterial ecotype, a unit...

    Alexander B. Chase, Philip Arevalo, Eoin L. Brodie, Martin F. Polz, Ulas Karaoz, Jennifer B. H. Martiny
  • Open Access
    Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons
    Editor's Pick Research Article | Ecological and Evolutionary Science
    Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons

    Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly...

    Tess E. Brewer, Emma L. Aronson, Keshav Arogyaswamy, Sharon A. Billings, Jon K. Botthoff, Ashley N. Campbell, Nicholas C. Dove, Dawson Fairbanks, Rachel E. Gallery, Stephen C. Hart, Jason Kaye, Gary King, Geoffrey Logan, Kathleen A. Lohse, Mia R. Maltz, Emilio Mayorga, Caitlin O’Neill, Sarah M. Owens, Aaron Packman, Jennifer Pett-Ridge, Alain F. Plante, Daniel D. Richter, Whendee L. Silver, Wendy H. Yang, Noah Fierer
  • Open Access
    Reply to Sun et al., “Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy”
    Author Reply | Applied and Environmental Science
    Reply to Sun et al., “Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy”
    Xiaoquan Su, Gongchao Jing, Daniel McDonald, Honglei Wang, Zengbin Wang, Antonio Gonzalez, Zheng Sun, Shi Huang, Jose Navas, Rob Knight, Jian Xu
  • Open Access
    Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures
    Research Article | Ecological and Evolutionary Science
    Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures

    Humans leave behind a microbial trail, regardless of intention. This may allow for the identification of individuals based on the “microbial signatures” they shed in built environments. In a shared living environment, these trails intersect, and through interaction with common surfaces may become homogenized, potentially confounding our ability to link individuals to their associated microbiota. We sought to understand the factors that...

    Miles Richardson, Neil Gottel, Jack A. Gilbert, Simon Lax
  • Open Access
    Fecal Short-Chain Fatty Acids Are Not Predictive of Colonic Tumor Status and Cannot Be Predicted Based on Bacterial Community Structure
    Observation | Host-Microbe Biology
    Fecal Short-Chain Fatty Acids Are Not Predictive of Colonic Tumor Status and Cannot Be Predicted Based on Bacterial Community Structure

    Considering that colorectal cancer is the third leading cancer-related cause of death within the United States, it is important to detect colorectal tumors early and to prevent the formation of tumors. Short-chain fatty acids (SCFAs) are often used as a surrogate for measuring gut health and for being anticarcinogenic because of their anti-inflammatory properties. We evaluated the fecal SCFA concentrations of a cohort of individuals...

    Marc A. Sze, Begüm D. Topçuoğlu, Nicholas A. Lesniak, Mack T. Ruffin, Patrick D. Schloss
  • Open Access
    The Impact of Anthelmintic Treatment on Human Gut Microbiota Based on Cross-Sectional and Pre- and Postdeworming Comparisons in Western Kenya
    Research Article | Clinical Science and Epidemiology
    The Impact of Anthelmintic Treatment on Human Gut Microbiota Based on Cross-Sectional and Pre- and Postdeworming Comparisons in Western Kenya

    The gut microbiome is an important factor in human health. It is affected by what we eat, what medicines we take, and what infections we acquire. In turn, it affects the way we absorb nutrients and whether we have excessive intestinal inflammation. Intestinal worms may have an important impact on the composition of the gut microbiome. Without a complete understanding of the impact of mass deworming programs on the microbiome, it is...

    Alice V. Easton, Mariam Quiñones, Ivan Vujkovic-Cvijin, Rita G. Oliveira, Stella Kepha, Maurice R. Odiere, Roy M. Anderson, Yasmine Belkaid, Thomas B. Nutman
  • Open Access
    Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease
    Research Article | Host-Microbe Biology
    Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease

    Oral health has substantial economic importance, with over $100 billion spent on dental care in the United States annually. The microbiome plays a critical role in oral health, yet remains poorly classified. To address the question of how microbial diversity and function in the oral cavities of children relate to caries diagnosis, we surveyed the supragingival plaque biofilm microbiome in 44 juvenile twin pairs. Using shotgun sequencing...

    Josh L. Espinoza, Derek M. Harkins, Manolito Torralba, Andres Gomez, Sarah K. Highlander, Marcus B. Jones, Pamela Leong, Richard Saffery, Michelle Bockmann, Claire Kuelbs, Jason M. Inman, Toby Hughes, Jeffrey M. Craig, Karen E. Nelson, Chris L. Dupont
  • Open Access
    Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome
    Research Article | Host-Microbe Biology
    Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome

    Colorectal cancer is a leading cause of cancer-related death in the United States and worldwide. Its risk and severity have been linked to colonic bacterial community composition. Although human-specific viruses have been linked to other cancers and diseases, little is known about colorectal cancer virus communities. We addressed this knowledge gap by identifying differences in colonic virus communities in the stool of colorectal cancer...

    Geoffrey D. Hannigan, Melissa B. Duhaime, Mack T. Ruffin, Charlie C. Koumpouras, Patrick D. Schloss
  • Open Access
    Identifying and Predicting Novelty in Microbiome Studies
    Research Article | Applied and Environmental Science
    Identifying and Predicting Novelty in Microbiome Studies

    We introduce two concepts to quantify the novelty of a microbiome. The first, the microbiome novelty score (MNS), allows identification of microbiomes that are especially different from what is already sequenced. The second, the microbiome attention score (MAS), allows identification of microbiomes that have many close neighbors, implying that considerable scientific attention is devoted to their study. By computing a microbiome focus...

    Xiaoquan Su, Gongchao Jing, Daniel McDonald, Honglei Wang, Zengbin Wang, Antonio Gonzalez, Zheng Sun, Shi Huang, Jose Navas, Rob Knight, Jian Xu
  • Open Access
    Research Article
    Novel Insights into Selection for Antibiotic Resistance in Complex Microbial Communities
    Aimee K. Murray, Lihong Zhang, Xiaole Yin, Tong Zhang, Angus Buckling, Jason Snape, William H. Gaze

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