Biology & Life Sciences

Editor’s Picks: Microbiology

Published June 4, 2018 Curated Collections

The study of Microbiology branches into numerous fields, including those highlighted at ASM Microbe 2018 and featured in this special Editor’s Picks collection. PLOS ONE Associate Editor Anna Simonin and PLOS Biology Senior Editor Lauren Richardson have selected recent PLOS articles highlighting the varied research investigating the complexities of microbiology. PLOS welcomes submissions in these fields.

Image Credit: 10.1371/journal.pone.0133085

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Applied & Environmental Science
Ecological & Evolutionary Science
Host-Microbe Biology
Therapeutics & Prevention

Applied & Environmental Science

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10.1371/journal.pone.0191156

PLOS ONE Coral physiology and microbiome dynamics under combined warming and ocean acidification
January 16, 2018 Andréa G. Grottoli, Paula Dalcin Martins, Michael J. Wilkins, Michael D. Johnston, Mark E. Warner, Wei-Jun Cai, Todd F. Melman, Kenneth D. Hoadley, D. Tye Pettay, Stephen Levas, Verena Schoepf
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10.1371/journal.pone.0180442

PLOS ONE Organic farming enhances soil microbial abundance and activity—A meta-analysis and meta-regression
July 12, 2017 Martina Lori, Sarah Symnaczik, Paul Mäder, Gerlinde De Deyn, Andreas Gattinger
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10.1371/journal.pone.0181901

PLOS ONE Soil features in rookeries of Antarctic penguins reveal sea to land biotransport of chemical pollutants
August 16, 2017 Anna C. Santamans, Rafael Boluda, Antonio Picazo, Carlos Gil, Joaquín Ramos-Miras, Pablo Tejedo, Luis R. Pertierra, Javier Benayas, Antonio Camacho
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10.1371/journal.pbio.2003862

PLOS Biology Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice
February 23, 2018 Joseph A. Edwards, Christian M. Santos-Medellín, Zachary S. Liechty, Bao Nguyen, Eugene Lurie, Shane Eason, Gregory Phillips, Venkatesan Sundaresan
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10.1371/journal.pone.0171695

PLOS ONE Plants promote mating and dispersal of the human pathogenic fungus Cryptococcus
February 17, 2017 Deborah J. Springer, Rajinikanth Mohan, Joseph Heitman
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10.1371/journal.pone.0154937

PLOS ONE A Novel Computerized Cell Count Algorithm for Biofilm Analysis
May 3, 2016 Mareike Klinger-Strobel, Herbert Suesse, Dagmar Fischer, Mathias W. Pletz, Oliwia Makarewicz
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10.1371/journal.pone.0148028

PLOS ONE Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis
February 5, 2016 Adam G. Clooney, Fiona Fouhy, Roy D. Sleator, Aisling O’ Driscoll, Catherine Stanton, Paul D. Cotter, Marcus J. Claesson
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10.1371/journal.pone.0140407

PLOS ONE Mushrooms as Rainmakers: How Spores Act as Nuclei for Raindrops
October 28, 2015 Maribeth O. Hassett, Mark W. F. Fischer, Nicholas P. Money
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10.1371/journal.pgen.1005470

PLOS Genetics Recurrent Domestication by Lepidoptera of Genes from Their Parasites Mediated by Bracoviruses
September 15, 2015 Laila Gasmi, Helene Boulain, Jeremy Gauthier, Aurelie Hua-Van, Karine Musset, Agata K. Jakubowska, Jean-Marc Aury, Anne-Nathalie Volkoff, Elisabeth Huguet, Jean-Michel Drezen, Salvador Herrero
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10.1371/journal.pone.0133085

PLOS ONE A CRISPR-Cas9 System for Genetic Engineering of Filamentous Fungi
July 15, 2015 Christina S. Nødvig, Jakob B. Nielsen, Martin E. Kogle, Uffe H. Mortensen

Ecological & Evolutionary Science

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10.1371/journal.pone.0180517

PLOS ONE Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages
July 17, 2017 Karen K. Klyczek, J. Alfred Bonilla, Deborah Jacobs-Sera, Tamarah L. Adair, Patricia Afram, Katherine G. Allen, Megan L. Archambault, Rahat M. Aziz, Filippa G. Bagnasco, Sarah L. Ball, Natalie A. Barrett, Robert C. Benjamin, Christopher J. Blasi, Katherine Borst, Mary A. Braun, Haley Broomell, Conner B. Brown, Zachary S. Brynell, Ashley B. Bue, Sydney O. Burke, William Casazza, Julia A. Cautela, Kevin Chen, Nitish S. Chimalakonda, Dylan Chudoff, Jade A. Connor, Trevor S. Cross, Kyra N. Curtis, Jessica A. Dahlke, Bethany M. Deaton, Sarah J. Degroote, Danielle M. DeNigris, Katherine C. DeRuff, Milan Dolan, David Dunbar, Marisa S. Egan, Daniel R. Evans, Abby K. Fahnestock, Amal Farooq, Garrett Finn, Christopher R. Fratus, Bobby L. Gaffney, Rebecca A. Garlena, Kelly E. Garrigan, Bryan C. Gibbon, Michael A. Goedde, Carlos A. Guerrero Bustamante, Melinda Harrison, Megan C. Hartwell, Emily L. Heckman, Jennifer Huang, Lee E. Hughes, Kathryn M. Hyduchak, Aswathi E. Jacob, Machika Kaku, Allen W. Karstens, Margaret A. Kenna, Susheel Khetarpal, Rodney A. King, Amanda L. Kobokovich, Hannah Kolev, Sai A. Konde, Elizabeth Kriese, Morgan E. Lamey, Carter N. Lantz, Jonathan S. Lapin, Temiloluwa O. Lawson, In Young Lee, Scott M. Lee, Julia Y. Lee-Soety, Emily M. Lehmann, Shawn C. London, A. Javier Lopez, Kelly C. Lynch, Catherine M. Mageeney, Tetyana Martynyuk, Kevin J. Mathew, Travis N. Mavrich, Christopher M. McDaniel, Hannah McDonald, C. Joel McManus, Jessica E. Medrano, Francis E. Mele, Jennifer E. Menninger, Sierra N. Miller, Josephine E. Minick, Courtney T. Nabua, Caroline K. Napoli, Martha Nkangabwa, Elizabeth A. Oates, Cassandra T. Ott, Sarah K. Pellerino, William J. Pinamont, Ross T. Pirnie, Marie C. Pizzorno, Emilee J. Plautz, Welkin H. Pope, Katelyn M. Pruett, Gabbi Rickstrew, Patrick A. Rimple, Claire A. Rinehart, Kayla M. Robinson, Victoria A. Rose, Daniel A. Russell, Amelia M. Schick, Julia Schlossman, Victoria M. Schneider, Chloe A. Sells, Jeremy W. Sieker, Morgan P. Silva, Marissa M. Silvi, Stephanie E. Simon, Amanda K. Staples, Isabelle L. Steed, Emily L. Stowe, Noah A. Stueven, Porter T. Swartz, Emma A. Sweet, Abigail T. Sweetman, Corrina Tender, Katrina Terry, Chrystal Thomas, Daniel S. Thomas, Allison R. Thompson, Lorianna Vanderveen, Rohan Varma, Hannah L. Vaught, Quynh D. Vo, Zachary T. Vonberg, Vassie C. Ware, Yasmene M. Warrad, Kaitlyn E. Wathen, Jonathan L. Weinstein, Jacqueline F. Wyper, Jakob R. Yankauskas, Christine Zhang, Graham F. Hatfull
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10.1371/journal.pone.0187461

PLOS ONE Species-specific signatures of the microbiome from Camponotus and Colobopsis ants across developmental stages
November 22, 2017 Manuela Oliveira Ramalho, Odair Correa Bueno, Corrie Saux Moreau
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10.1371/journal.pbio.2003962

PLOS Biology Design of synthetic bacterial communities for predictable plant phenotypes
February 20, 2018 Sur Herrera Paredes, Tianxiang Gao, Theresa F. Law, Omri M. Finkel, Tatiana Mucyn, Paulo José Pereira Lima Teixeira, Isaí Salas González, Meghan E. Feltcher, Matthew J. Powers, Elizabeth A. Shank, Corbin D. Jones, Vladimir Jojic, Jeffery L. Dangl, Gabriel Castrillo
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10.1371/journal.pbio.2005056

PLOS Biology Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria
May 11, 2018 Antoine Frenoy, Sebastian Bonhoeffer
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10.1371/journal.pgen.1006155

PLOS Genetics Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus
July 6, 2016 David Peris, Quinn K. Langdon, Ryan V. Moriarty, Kayla Sylvester, Martin Bontrager, Guillaume Charron, Jean-Baptiste Leducq, Christian R. Landry, Diego Libkind, Chris Todd Hittinger
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10.1371/journal.pbio.2000735

PLOS Biology Three-dimensional preservation of cellular and subcellular structures suggests 1.6 billion-year-old crown-group red algae
March 14, 2017 Stefan Bengtson, Therese Sallstedt, Veneta Belivanova, Martin Whitehouse
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10.1371/journal.pone.0155080

PLOS ONE Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development
May 4, 2016 Ryan H. Hansen, Andrea C. Timm, Collin M. Timm, Amber N. Bible, Jennifer L. Morrell-Falvey, Dale A. Pelletier, Michael L. Simpson, Mitchel J. Doktycz, Scott T. Retterer
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10.1371/journal.pbio.1002191

PLOS Biology Biofilm Formation As a Response to Ecological Competition
July 7, 2015 Nuno M. Oliveira, Esteban Martinez-Garcia, Joao Xavier, William M. Durham, Roberto Kolter, Wook Kim, Kevin R. Foster
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10.1371/journal.pone.0125356

PLOS ONE Estimating Bacterial Diversity for Ecological Studies: Methods, Metrics, and Assumptions
April 25, 2015 Julia Birtel, Jean-Claude Walser, Samuel Pichon, Helmut Bürgmann, Blake Matthews
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10.1371/journal.pone.0109696

PLOS ONE Evolutionary Strategies of Viruses, Bacteria and Archaea in Hydrothermal Vent Ecosystems Revealed through Metagenomics
October 2, 2014 Rika E. Anderson, Mitchell L. Sogin, John A. Baross

Host-Microbe Biology

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10.1371/journal.pone.0179628

PLOS ONE Skin microbiota in frogs from the Brazilian Atlantic Forest: Species, forest type, and potential against pathogens
July 5, 2017 Ananda Brito de Assis, Cristine Chaves Barreto, Carlos Arturo Navas
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10.1371/journal.pone.0192003

PLOS ONE The Mexican bean beetle (Epilachna varivestis) regurgitome and insights into beetle-borne virus specificity
January 29, 2018 Cassidy R. Gedling, Charlotte M. Smith, Christophe M. R. LeMoine, Bryan J. Cassone
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10.1371/journal.pbio.2000862

PLOS Biology Commensal bacteria and essential amino acids control food choice behavior and reproduction
April 25, 2017 Ricardo Leitão-Gonçalves, Zita Carvalho-Santos, Ana Patrícia Francisco, Gabriela Tondolo Fioreze, Margarida Anjos, Célia Baltazar, Ana Paula Elias, Pavel M. Itskov, Matthew D. W. Piper, Carlos Ribeiro
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10.1371/journal.pbio.2003467

PLOS Biology Disentangling metabolic functions of bacteria in the honey bee gut
December 12, 2017 Lucie Kešnerová, Ruben A. T. Mars, Kirsten M. Ellegaard, Michaël Troilo, Uwe Sauer, Philipp Engel
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10.1371/journal.ppat.1005536

PLOS Pathogens Wolbachia Blocks Viral Genome Replication Early in Infection without a Transcriptional Response by the Endosymbiont or Host Small RNA Pathways
April 18, 2016 Stephanie M. Rainey, Julien Martinez, Melanie McFarlane, Punita Juneja, Peter Sarkies, Aleksei Lulla, Esther Schnettler, Margus Varjak, Andres Merits, Eric A. Miska, Francis M. Jiggins, Alain Kohl
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10.1371/journal.pone.0154632

PLOS ONE Triclosan Exposure Is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish
May 18, 2016 Christopher A. Gaulke, Carrie L. Barton, Sarah Proffitt, Robert L. Tanguay, Thomas J. Sharpton
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10.1371/journal.pone.0155362

PLOS ONE Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing
May 9, 2016 Emily Vogtmann, Xing Hua, Georg Zeller, Shinichi Sunagawa, Anita Y. Voigt, Rajna Hercog, James J. Goedert, Jianxin Shi, Peer Bork, Rashmi Sinha
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10.1371/journal.pone.0152836

PLOS ONE The Effects of Plant Virus Infection on Polarization Reflection from Leaves
April 19, 2016 Daniel J. Maxwell, Julian C. Partridge, Nicholas W. Roberts, Neil Boonham, Gary D. Foster
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10.1371/journal.pone.0153294

PLOS ONE Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults
April 10, 2016 Carolin A. Kolmeder, Jarkko Salojärvi, Jarmo Ritari, Mark de Been, Jeroen Raes, Gwen Falony, Sara Vieira-Silva, Riina A. Kekkonen, Garry L. Corthals, Airi Palva, Anne Salonen, Willem M. de Vos
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10.1371/journal.pone.0140301

PLOS ONE Genome-Wide Association Studies of the Human Gut Microbiota
November 3, 2015 Emily R. Davenport, Darren A. Cusanovich, Katelyn Michelini, Luis B. Barreiro, Carole Ober, Yoav Gilad
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10.1371/journal.pone.0121329

PLOS ONE Bacteria Isolated from Bats Inhibit the Growth of Pseudogymnoascus destructans, the Causative Agent of White-Nose Syndrome
April 8, 2015 Joseph R. Hoyt, Tina L. Cheng, Kate E. Langwig, Mallory M. Hee, Winifred F. Frick, A. Marm Kilpatrick

Therapeutics & Prevention

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10.1371/journal.pone.0186269

PLOS ONE Efficacy of chemical disinfectants for the containment of the salamander chytrid fungus Batrachochytrium salamandrivorans
October 12, 2017 Pascale Van Rooij, Frank Pasmans, Yanaika Coen, An Martel
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10.1371/journal.pone.0186169

PLOS ONE Cysteamine-mediated clearance of antibiotic-resistant pathogens in human cystic fibrosis macrophages
October 5, 2017 Chandra L. Shrestha, Kaivon D. Assani, Hannah Rinehardt, Florentina Albastroiu, Shuzhong Zhang, Richard Shell, Amal O. Amer, Larry S. Schlesinger, Benjamin T. Kopp
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10.1371/journal.pbio.2001586

PLOS Biology History of antibiotic adaptation influences microbial evolutionary dynamics during subsequent treatment
August 8, 2017 Phillip Yen, Jason A. Papin
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10.1371/journal.ppat.1006292

PLOS Pathogens The blood DNA virome in 8,000 humans
March 22, 2017 Ahmed Moustafa, Chao Xie, Ewen Kirkness, William Biggs, Emily Wong, Yaron Turpaz, Kenneth Bloom, Eric Delwart, Karen E. Nelson, J. Craig Venter, Amalio Telenti
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10.1371/journal.pone.0151219

PLOS ONE Global Economic Burden of Norovirus Gastroenteritis
April 26, 2016 Sarah Bartsch, Benjamin Lopman, Sachiko Ozawa, Aron Hall, Bruce Lee
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10.1371/journal.pcbi.1004857

PLOS Computational Biology Integrating Antimicrobial Therapy with Host Immunity to Fight Drug-Resistant Infections: Classical vs. Adaptive Treatment
April 14, 2016 Erida Gjini, Patricia H. Brito
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10.1371/journal.ppat.1005531

PLOS Pathogens Reversal of the Progression of Fatal Coronavirus Infection in Cats by a Broad-Spectrum Coronavirus Protease Inhibitor
March 29, 2016 Yunjeong Kim, Hongwei Liu, Anushka C. Galasiti Kankanamalage, Sahani Weerasekara, Duy H. Hua, William C. Groutas, Kyeong-Ok Chang, Niels C. Pedersen
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10.1371/journal.pone.0136486

PLOS ONE Castanea sativa (European Chestnut) Leaf Extracts Rich in Ursene and Oleanene Derivatives Block Staphylococcus aureus Virulence and Pathogenesis without Detectable Resistance
August 19, 2015 Cassandra L. Quave, James T. Lyles, Jeffery S. Kavanaugh, Kate Nelson, Corey P. Parlet, Heidi A. Crosby, Kristopher P. Heilmann, Alexander R. Horswill
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10.1371/journal.pbio.1002198

PLOS Biology Imperfect Vaccination Can Enhance the Transmission of Highly Virulent Pathogens
July 25, 2015 Andrew F. Read, Susan J. Baigent, Claire Powers, Lydia B. Kgosana, Luke Blackwell, Lorraine P. Smith, David A. Kennedy, Stephen W. Walkden-Brown, Venugopal K. Nair
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10.1371/journal.pone.0122283

PLOS ONE Rational Design of Antibiotic Treatment Plans: A Treatment Strategy for Managing Evolution and Reversing Resistance
May 6, 2015 Portia M. Mira, Kristina Crona, Devin Greene, Juan C. Meza, Bernd Sturmfels, Miriam Barlow

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