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The Microbiome Across Biological Systems

Published March 27, 2020 Calls for Papers Collections

Microbiomes are complex communities of bacteria, fungi, archaea, viruses, and microscopic eukaryotic organisms that can inhabit diverse environments, from the human gut, to soil, to even the atmosphere. These communities can impact an equally wide range of processes, including human brain development, pathogen virulence, and ecosystem nutrient cycling. New technologies and methods for studying microbiomes—their composition, formation, and how they influence their surroundings—are constantly emerging and researchers are only just starting to untangle these complex interactions. PLOS ONE and PLOS Biology are excited to publish a shared Collection on the topic of microbiomes across biological systems.

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PLOS Biology Collection
PLOS ONE Collection

Guest Editors

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Zaid Abdo, CC0

PLOS ONE Dr. Zaid Abdo
April 23, 2019 Guest Editor, PLOS ONE
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Sanjay Chotirmall, CC0

PLOS ONE Dr. Sanjay Chotirmall
April 23, 2019 Guest Editor, PLOS ONE
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Thomas Dawson, CC0

PLOS ONE Dr. Thomas Dawson
April 23, 2019 Guest Editor, PLOS ONE
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Suzanne Ishaq, CC0

PLOS ONE Dr. Suzanne Ishaq
April 23, 2019 Guest Editor, PLOS ONE
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Noelle Noyes, CC0

PLOS ONE Dr. Noelle Noyes
April 23, 2019 Guest Editor, PLOS ONE
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Pankaj Trivedi, CC0

PLOS ONE Dr. Pankaj Trivedi
April 23, 2019 Guest Editor, PLOS ONE

PLOS Biology Collection

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Flooy, CC0

PLOS Biology Framing the discussion of microorganisms as a facet of social equity in human health
November 26, 2019 Suzanne L. Ishaq, Maurisa Rapp, Risa Byerly, Loretta S. McClellan, Maya R. O’Boyle, Anika Nykanen, Patrick J. Fuller, Calvin Aas, Jude M. Stone, Sean Killpatrick, Manami M. Uptegrove, Alex Vischer, Hannah Wolf, Fiona Smallman, Houston Eymann, Simon Narode, Ellee Stapleton, Camille C. Cioffi, Hannah F. Tavalire
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Kevskoot, CC0

PLOS Biology Host-associated microbiomes drive structure and function of marine ecosystems
November 11, 2019 Laetitia G. E. Wilkins, Matthieu Leray, Aaron O’Dea, Benedict Yuen, Raquel S. Peixoto, Tiago J. Pereira, Holly M. Bik, David A. Coil, J. Emmett Duffy, Edward Allen Herre, Harilaos A. Lessios, Noelle M. Lucey, Luis C. Mejia, Douglas B. Rasher, Koty H. Sharp, Emilia M. Sogin, Robert W. Thacker, Rebecca Vega Thurber, William T. Wcislo, Elizabeth G. Wilbanks, Jonathan A. Eisen

PLOS ONE Collection

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10.1371/journal.pone.0230071

PLOS ONE The microbiome of modern microbialites in Bacalar Lagoon, Mexico
March 25, 2020 Alfredo Yanez-Montalvo, Selene Gómez-Acata, Bernardo Águila, Héctor Hernández-Arana, Luisa Falcón
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10.1371/journal.pone.0230170

PLOS ONE The rodent vaginal microbiome across the estrous cycle and the effect of genital nerve electrical stimulation
March 12, 2020 Micah Levy, Christine M. Bassis, Eric Kennedy, Katie E. Yoest, Jill B. Becker, Jason Bell, Mitchell B. Berger, Tim M. Bruns
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10.1371/journal.pone.0229442

PLOS ONE Diel, daily, and spatial variation of coral reef seawater microbial communities
March 11, 2020 Laura Weber, Amy Apprill
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10.1371/journal.pone.0229586

PLOS ONE Changes in key vaginal bacteria among postpartum African women initiating intramuscular depot-medroxyprogesterone acetate
March 5, 2020 Bridget M. Whitney, Brandon L. Guthrie, Sujatha Srinivasan, Kenneth Tapia, Eric Munene Muriuki, Bhavna H. Chohan, Jacqueline M. Wallis, Congzhou Liu, R. Scott McClelland, David N. Fredricks, Alison C. Roxby
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NIAID

PLOS ONE Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut
March 4, 2020 Yonatan Sher, Matthew R. Olm, Tali Raveh-Sadka, Christopher T. Brown, Ruth Sher, Brian Firek, Robyn Baker, Michael J. Morowitz, Jillian F. Banfield
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10.1371/journal.pone.0229204

PLOS ONE An empirically derived method for measuring human gut microbiome alpha diversity: Demonstrated utility in predicting health-related outcomes among a human clinical sample
March 2, 2020 Sarah L. Hagerty, Kent E. Hutchison, Christopher A. Lowry, Angela D. Bryan
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Philadelphia : New York Lea & Febiger

PLOS ONE Development of Oral Care Chip, a novel device for quantitative detection of the oral microbiota associated with periodontal disease
February 28, 2020 Ai Nozawa, Hiroyuki Oshima, Naoyuki Togawa, Takenori Nozaki, Shinya Murakami
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10.1371/journal.pone.0221543

PLOS ONE Insights on aquatic microbiome of the Indian Sundarbans mangrove areas
February 25, 2020 Paltu Kumar Dhal, Germán A. Kopprio, Astrid Gärdes
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pxfuel

PLOS ONE Characterization of gut microbiomes of household pets in the United States using a direct-to-consumer approach
February 20, 2020 Aashish R. Jha, Justin Shmalberg, Jirayu Tanprasertsuk, LeeAnn Perry, Dan Massey, Ryan W. Honaker
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ShuaiGuo (pixabay.com)

PLOS ONE Comparative study on archaeal diversity in the sediments of two urban landscape water bodies
February 18, 2020 Yuxin Wang, Chaonan Wang
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John Benson

PLOS ONE Cloacal bacterial communities of tree swallows (Tachycineta bicolor): Similarity within a population, but not between pair-bonded social partners
February 11, 2020 Jessica Hernandez, Camilo Escallón, Daniel Medina, Ben Vernasco, Jenifer Walke, Lisa Belden, Ignacio Moore
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10.1371/journal.pone.0228560

PLOS ONE Duckweed hosts a taxonomically similar bacterial assemblage as the terrestrial leaf microbiome
February 6, 2020 Kenneth Acosta, Jenny Xu, Sarah Gilbert, Elizabeth Denison, Thomas Brinkman, Sarah Lebeis, Eric Lam
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CDC / Janice Haney Carr

PLOS ONE Evaluation of the effects of anthelmintic administration on the fecal microbiome of healthy dogs with and without subclinical Giardia spp. and Cryptosporidium canis infections
February 6, 2020 Madeline A. Fujishiro, Jonathan A. Lidbury, Rachel Pilla, Jörg M. Steiner, Michael R. Lappin, Jan S. Suchodolski
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Grulee, Clifford G. (Clifford Groselle), 1880-1962, Philadelphia, London, W. B. Saunders

PLOS ONE Contributions to human breast milk microbiome and enteromammary transfer of Bifidobacterium breve
January 28, 2020 Kattayoun Kordy, Thaidra Gaufin, Martin Mwangi, Fan Li, Chiara Cerini, David J. Lee, Helty Adisetiyo, Cora Woodward, Pia S. Pannaraj, Nicole H. Tobin, Grace M. Aldrovandi
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Eric Erbe, digital colorization by Christopher Pooley, both of USDA, ARS, EMU.

PLOS ONE Effects from diet-induced gut microbiota dysbiosis and obesity can be ameliorated by fecal microbiota transplantation: A multiomics approach
September 23, 2019 Maria Guirro, Andrea Costa, Andreu Gual-Grau, Pol Herrero, Helena Torrell, Lluis Arola, Núria Canela
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National Aeronautics and Space Administration

PLOS ONE Ozone-induced changes in the serum metabolome: Role of the microbiome
August 27, 2019 Youngji Cho, Ross S. Osgood, Lauren N. Bell, Edward D. Karoly, Stephanie A. Shore
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10.1371/journal.pone.0221828

PLOS ONE Dietary inulin alters the gut microbiome, enhances systemic metabolism and reduces neuroinflammation in an APOE4 mouse model
August 28, 2019 Jared D. Hoffman, Lucille M. Yanckello, George Chlipala, Tyler C. Hammond, Scott D. McCulloch, Ishita Parikh, Sydney Sun, Josh M. Morganti, Stefan J. Green, Ai-Ling Lin
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Jim Gathany

PLOS ONE Habitat disturbance and the organization of bacterial communities in Neotropical hematophagous arthropods
September 6, 2019 Kelly L. Bennett, Alejandro Almanza, W. Owen McMillan, Kristin Saltonstall, Evangelina López Vdovenko, Jorge S. Vinda, Luis Mejia, Kaitlin Driesse, Luis F. De León, Jose R. Loaiza
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Riccardoariotti

PLOS ONE Metabolomic profiling of oxalate-degrading probiotic Lactobacillus acidophilus and Lactobacillus gasseri
September 23, 2019 Casey A. Chamberlain, Marguerite Hatch, Timothy J. Garrett
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Rocky Mountain Laboratories, NIAID, NIH

PLOS ONE Gut microbiome diversity is associated with sleep physiology in humans
October 7, 2019 Robert P. Smith, Cole Easson, Sarah M. Lyle, Ritishka Kapoor, Chase P. Donnelly, Eileen J. Davidson, Esha Parikh, Jose V. Lopez, Jaime L. Tartar
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10.1371/journal.pone.0222881

PLOS ONE Framework for rational donor selection in fecal microbiota transplant clinical trials
October 10, 2019 Claire Duvallet, Caroline Zellmer, Pratik Panchal, Shrish Budree, Majdi Osman, Eric J. Alm
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10.1371/journal.pone.0222527

PLOS ONE Bacterial diversity in Icelandic cold spring sources and in relation to the groundwater amphipod Crangonyx islandicus
October 2, 2019 Ragnhildur Guðmundsdóttir, Agnes-Katharina Kreiling, Bjarni Kristófer Kristjánsson, Viggó Þór Marteinsson, Snæbjörn Pálsson
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10.1371/journal.pone.0222962

PLOS ONE Optimizing bacterial DNA extraction in urine
September 24, 2019 Matthew M. Munch, Laura C. Chambers, Lisa E. Manhart, Dan Domogala, Anthony Lopez, David N. Fredricks, Sujatha Srinivasan
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10.1371/journal.pone.0223543

PLOS ONE Extensive culturomics of 8 healthy samples enhances metagenomics efficiency
October 21, 2019 Ami Diakite, Grégory Dubourg, Niokhor Dione, Pamela Afouda, Sara Bellali, Issa Isaac Ngom, Camille Valles, Matthieu Million, Anthony Levasseur, Frédéric Cadoret, Jean-Christophe Lagier, Didier Raoult
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Alton N. Sparks, Jr., University of Georgia, Bugwood.org

PLOS ONE Microbiome profiling of the onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae)
September 30, 2019 Suresh J. Gawande, Sivalingam Anandhan, Ashish Ingle, Praveen Roylawar, Kiran Khandagale, Tushar Gawai, Alana Jacobson, Ramasamy Asokan, Major Singh
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10.1371/journal.pone.0223680

PLOS ONE Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools
December 12, 2019 Xiaofang Jiang, Andrew Brantley Hall, Ramnik J. Xavier, Eric J. Alm
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Renee Grayson

PLOS ONE Honey bee microbiome associated with different hive and sample types over a honey production season
November 8, 2019 Sladjana Subotic, Andrew M. Boddicker, Vy M. Nguyen, James Rivers, Christy E. Briles, Annika C. Mosier
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Ben Mills

PLOS ONE Sildenafil citrate long-term treatment effects on cardiovascular reactivity in a SHR experimental model of metabolic syndrome
November 7, 2019 Yosra Doghri, Fabien Chetaneau, Moez Rhimi, Aicha Kriaa, Valérie Lalanne, Chantal Thorin, Emmanuelle Maguin, M. Yassine Mallem, Jean-Claude Desfontis
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keisotyo

PLOS ONE Host plants influence the composition of the gut bacteria in Henosepilachna vigintioctopunctata
October 18, 2019 Jing Lü, Wei Guo, Shimin Chen, Mujuan Guo, Baoli Qiu, Chunxiao Yang, Tengxiang Lian, Huipeng Pan
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Bart van Dorp

PLOS ONE Evaluating rectal swab collection method for gut microbiome analysis in the common marmoset (Callithrix jacchus)
November 7, 2019 Stephen C. Artim, Alexander Sheh, Monika A. Burns, James G. Fox
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10.1371/journal.pone.0225481

PLOS ONE Microvesicles from Lactobacillus reuteri (DSM-17938) completely reproduce modulation of gut motility by bacteria in mice
January 7, 2020 Christine L. West, Andrew M. Stanisz, Yu-Kang Mao, Kevin Champagne-Jorgensen, John Bienenstock, Wolfgang A. Kunze
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JIRCAS Library from Tsukuba, Japan

PLOS ONE Long-term high-grain diet altered the ruminal pH, fermentation, and composition and functions of the rumen bacterial community, leading to enhanced lactic acid production in Japanese Black beef cattle during fattening
November 26, 2019 Toru Ogata, Hiroki Makino, Naoki Ishizuka, Eiji Iwamoto, Tatsunori Masaki, Kentaro Ikuta, Yo-Han Kim, Shigeru Sato
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CDC/ Joe Miller

PLOS ONE Comparative analysis of the vaginal microbiome of pregnant women with either Trichomonas vaginalis or Chlamydia trachomatis
December 12, 2019 Simon Chengo Masha, Collins Owuor, Joyce Mwongeli Ngoi, Piet Cools, Eduard J. Sanders, Mario Vaneechoutte, Tania Crucitti, Etienne P. de Villiers
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CDC/ C. Goldsmith, P. Feorino, E. L. Palmer, W. R. McManus

PLOS ONE Human gut microbiota is associated with HIV-reactive immunoglobulin at baseline and following HIV vaccination
December 23, 2019 Jacob A. Cram, Andrew J. Fiore-Gartland, Sujatha Srinivasan, Shelly Karuna, Giuseppe Pantaleo, Georgia D. Tomaras, David N. Fredricks, James G. Kublin
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Yun Y, Srinivas G, Kuenzel S, Linnenbrink M, Alnahas S, et al. (2014) Environmentally Determined Differences in the Murine Lung Microbiota and Their Relation to Alveolar Architecture. PLOS ONE 9(12): e113466.

PLOS ONE Airway microbiome composition correlates with lung function and arterial stiffness in an age-dependent manner
November 26, 2019 Shuen Yee Lee, Micheál Mac Aogáin, Kai Deng Fam, Kar Ling Chia, Nur A’tikah Binte Mohamed Ali, Margaret M. C. Yap, Eric P. H. Yap, Sanjay H. Chotirmall, Chin Leong Lim
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Angelo Popovic

PLOS ONE The diversity and abundance of fungi and bacteria on the healthy and dandruff affected human scalp
December 18, 2019 Sally G. Grimshaw, Adrian M. Smith, David S. Arnold, Elaine Xu, Michael Hoptroff, Barry Murphy
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Isani M, Bell BA, Delaplain PT, Bowling JD, Golden JM, et al. (2018) Lactobacillus murinus HF12 colonizes neonatal gut and protects rats from necrotizing enterocolitis. PLOS ONE 13(6): e0196710.

PLOS ONE Impact of oral probiotic Lactobacillus acidophilus vaccine strains on the immune response and gut microbiome of mice
December 12, 2019 Zaid Abdo, Jonathan LeCureux, Alora LaVoy, Bridget Eklund, Elizabeth P. Ryan, Gregg A. Dean
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Marco Verch

PLOS ONE The effect of carbohydrate sources: Sucrose, invert sugar and components of mānuka honey, on core bacteria in the digestive tract of adult honey bees (Apis mellifera)
December 4, 2019 Michelle A. Taylor, Alastair W. Robertson, Patrick J. Biggs, Kate K. Richards, Daniel F. Jones, Shanthi G. Parkar
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Pacific Southwest Region from Sacramento, US

PLOS ONE California condor microbiomes: Bacterial variety and functional properties in captive-bred individuals
December 11, 2019 Lindsey Jacobs, Benjamin H. McMahon, Joel Berendzen, Jonathan Longmire, Cheryl Gleasner, Nicolas W. Hengartner, Momchilo Vuyisich, Judith R. Cohn, Marti Jenkins, Andrew W. Bartlow, Jeanne M. Fair
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10.1371/journal.pone.0225933

PLOS ONE Host-mediated microbiome engineering (HMME) of drought tolerance in the wheat rhizosphere
December 4, 2019 Michael D. Jochum, Kelsey L. McWilliams, Elizabeth A. Pierson, Young-Ki Jo
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Ed Uthman

PLOS ONE Helicobacter pylori antibody and pepsinogen testing for predicting gastric microbiome abundance
December 4, 2019 Saemi Choi, Jae Gon Lee, A-reum Lee, Chang Soo Eun, Dong Soo Han, Chan Hyuk Park
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CDC/ Dr. V.R. Dowell

PLOS ONE Sharing of gut microbial strains between selected individual sets of twins cohabitating for decades
December 5, 2019 Hyunmin Koo, Joseph A. Hakim, David K. Crossman, Elliot J. Lefkowitz, Casey D. Morrow
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Jody O'Connor

PLOS ONE An inter-island comparison of Darwin’s finches reveals the impact of habitat, host phylogeny, and island on the gut microbiome
December 13, 2019 Wesley T. Loo, Rachael Y. Dudaniec, Colleen M. Cavanaugh, Sonia Kleindorfer
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10.1371/journal.pone.0226835

PLOS ONE Effect of endometriosis on the fecal bacteriota composition of mice during the acute phase of lesion formation
December 30, 2019 Josefine Hantschel, Severin Weis, Karl-Herbert Schäfer, Michael D. Menger, Matthias Kohl, Markus Egert, Matthias W. Laschke
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CDC/ Janice Carr/ Deepak Mandhalapu, M.H.S.

PLOS ONE Transfer of skin microbiota between two dissimilar autologous microenvironments: A pilot study
December 30, 2019 Benji Perin, Amin Addetia, Xuan Qin
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Dr. Holdeman, USCDCP

PLOS ONE Association between baseline abundance of Peptoniphilus, a Gram-positive anaerobic coccus, and wound healing outcomes of DFUs
January 24, 2020 Kyung R. Min, Adriana Galvis, Katherine L. Baquerizo Nole, Rohita Sinha, Jennifer Clarke, Robert S. Kirsner, Dragana Ajdic
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10.1371/journal.pone.0227053

PLOS ONE Intra-host symbiont diversity in eastern Pacific cold seep tubeworms identified by the 16S-V6 region, but undetected by the 16S-V4 region
January 15, 2020 Corinna Breusing, Maximilian Franke, Curtis Robert Young
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Kris-Mikael Krister

PLOS ONE The effect of diet on the gastrointestinal microbiome of juvenile rehabilitating green turtles (Chelonia mydas)
January 15, 2020 Jennifer C. G. Bloodgood, Sonia M. Hernandez, Anitha Isaiah, Jan S. Suchodolski, Lisa A. Hoopes, Patrick M. Thompson, Thomas B. Waltzek, Terry M. Norton
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Science of Parkinsons, CC BY

PLOS ONE Coronary artery disease is associated with an altered gut microbiome composition
January 29, 2020 Takumi Toya, Michel T. Corban, Eric Marrietta, Irina E. Horwath, Lilach O. Lerman, Joseph A. Murray, Amir Lerman
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Webandi, CC0

PLOS ONE OGG1 deficiency alters the intestinal microbiome and increases intestinal inflammation in a mouse model
January 14, 2020 Holly Simon, Vladimir Vartanian, Melissa H. Wong, Yusaku Nakabeppu, Priyanka Sharma, R. Stephen Lloyd, Harini Sampath
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Anna Frodesiak

PLOS ONE The variability of bacterial communities in both the endosphere and ectosphere of different niches in Chinese chives (Allium tuberosum)
January 16, 2020 Yuxin Wang, Chaonan Wang, Yizhu Gu, Pingzhi Wang, Weitang Song, Jinhai Ma, Xiaofei Yang
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10.1371/journal.pone.0227707

PLOS ONE Assessment of peritoneal microbial features and tumor marker levels as potential diagnostic tools for ovarian cancer
January 9, 2020 Ruizhong Miao, Taylor C. Badger, Kathleen Groesch, Paula L. Diaz-Sylvester, Teresa Wilson, Allen Ghareeb, Jongjin Anne Martin, Melissa Cregger, Michael Welge, Colleen Bushell, Loretta Auvil, Ruoqing Zhu, Laurent Brard, Andrea Braundmeier-Fleming
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Jynto

PLOS ONE Differential effects of synthetic psychoactive cathinones and amphetamine stimulants on the gut microbiome in mice
January 24, 2020 Mariana Angoa-Pérez, Branislava Zagorac, Andrew D. Winters, Jonathan M. Greenberg, Madison Ahmad, Kevin R. Theis, Donald M. Kuhn
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10.1371/journal.pone.0227819

PLOS ONE Microbiota in foods from Inuit traditional hunting
January 14, 2020 Aviaja L. Hauptmann, Petronela Paulová, Lars Hestbjerg Hansen, Thomas Sicheritz-Pontén, Gert Mulvad, Dennis S. Nielsen
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Arallyn!

PLOS ONE Microbiome signatures in neonatal central line associated bloodstream infections
January 16, 2020 Mohan Pammi, Santosh Thapa, Miriam Balderas, Jessica K. Runge, Alamelu Venkatachalam, Ruth Ann Luna
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CDC/ Dr. Norman Jacobs

PLOS ONE Pharyngeal microbiome alterations during Neisseria gonorrhoeae infection
January 16, 2020 Antonella Marangoni, Camilla Ceccarani, Tania Camboni, Clarissa Consolandi, Melissa Salvo, Valeria Gaspari, Antonietta D’Antuono, Matteo Belletti, Maria Carla Re, Marco Severgnini, Claudio Foschi
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Judy Gallagher

PLOS ONE The gut bacterial communities across six grasshopper species from a coastal tallgrass prairie
January 30, 2020 Melani Muratore, Chelse Prather, Yvonne Sun

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