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  1. Viruses play an important role in ecosystems, including the built environment (BE). While numerous studies have characterized bacterial and fungal microbiomes in the BE, few have focused on the viral microbiom...

    Authors: Aaron J. Prussin II, Pedro J. Torres, John Shimashita, Steven R. Head, Kyle J. Bibby, Scott T. Kelley and Linsey C. Marr

    Citation: Microbiome 2019 7:53

    Content type: Research

    Published on:

  2. Environmental and commensal bacteria maintain a diverse and largely unknown collection of antibiotic resistance genes (ARGs) that, over time, may be mobilized and transferred to pathogens. Metagenomics enables...

    Authors: Fanny Berglund, Tobias Österlund, Fredrik Boulund, Nachiket P. Marathe, D. G. Joakim Larsson and Erik Kristiansson

    Citation: Microbiome 2019 7:52

    Content type: Software

    Published on:

  4. A vaginal microbiota dominated by lactobacilli (particularly Lactobacillus crispatus) is associated with vaginal health, whereas a vaginal microbiota not dominated by lactobacilli is considered dysbiotic. Here we...

    Authors: Charlotte van der Veer, Rosanne Y. Hertzberger, Sylvia M. Bruisten, Hanne L. P. Tytgat, Jorne Swanenburg, Alie de Kat Angelino-Bart, Frank Schuren, Douwe Molenaar, Gregor Reid, Henry de Vries and Remco Kort

    Citation: Microbiome 2019 7:49

    Content type: Research

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  6. Analysis of mixed microbial communities using metagenomic sequencing experiments requires multiple preprocessing and analytical steps to interpret the microbial and genetic composition of samples. Analytical s...

    Authors: Erik L. Clarke, Louis J. Taylor, Chunyu Zhao, Andrew Connell, Jung-Jin Lee, Bryton Fett, Frederic D. Bushman and Kyle Bittinger

    Citation: Microbiome 2019 7:46

    Content type: Software

    Published on:

  7. Evidence from preclinical and clinical studies suggests that interactions among the brain, gut, and microbiota may affect the pathophysiology of irritable bowel syndrome (IBS). As disruptions in central and pe...

    Authors: Jennifer S. Labus, Vadim Osadchiy, Elaine Y. Hsiao, Julien Tap, Muriel Derrien, Arpana Gupta, Kirsten Tillisch, Boris Le Nevé, Cecilia Grinsvall, Maria Ljungberg, Lena Öhman, Hans Törnblom, Magnus Simren and Emeran A. Mayer

    Citation: Microbiome 2019 7:45

    Content type: Research

    Published on:

  9. Species-specific differences in tolerance to infection are exemplified by the high susceptibility of humans to enterohemorrhagic Escherichia coli (EHEC) infection, whereas mice are relatively resistant to this pa...

    Authors: Alessio Tovaglieri, Alexandra Sontheimer-Phelps, Annelies Geirnaert, Rachelle Prantil-Baun, Diogo M. Camacho, David B. Chou, Sasan Jalili-Firoozinezhad, Tomás de Wouters, Magdalena Kasendra, Michael Super, Mark J. Cartwright, Camilla A. Richmond, David T. Breault, Christophe Lacroix and Donald E. Ingber

    Citation: Microbiome 2019 7:43

    Content type: Research

    Published on:

  10. Viruses are important components of microbial communities modulating community structure and function; however, only a couple of tools are currently available for phage identification and analysis from metagen...

    Authors: Tingting Zheng, Jun Li, Yueqiong Ni, Kang Kang, Maria-Anna Misiakou, Lejla Imamovic, Billy K. C. Chow, Anne A. Rode, Peter Bytzer, Morten Sommer and Gianni Panagiotou

    Citation: Microbiome 2019 7:42

    Content type: Methodology

    Published on:

  11. Idiopathic chronic diarrhea (ICD) is a common cause of morbidity and mortality among juvenile rhesus macaques. Characterized by chronic inflammation of the colon and repeated bouts of diarrhea, ICD is largely ...

    Authors: Samuel T. Westreich, Amir Ardeshir, Zeynep Alkan, Mary E. Kable, Ian Korf and Danielle G. Lemay

    Citation: Microbiome 2019 7:41

    Content type: Research

    Published on:

  12. The growth in publically available microbiome data in recent years has yielded an invaluable resource for genomic research, allowing for the design of new studies, augmentation of novel datasets and reanalysis...

    Authors: Will PM Rowe, Anna Paola Carrieri, Cristina Alcon-Giner, Shabhonam Caim, Alex Shaw, Kathleen Sim, J. Simon Kroll, Lindsay J. Hall, Edward O. Pyzer-Knapp and Martyn D. Winn

    Citation: Microbiome 2019 7:40

    Content type: Methodology

    Published on:

  13. There are complex interactions between aging, frailty, diet, and the gut microbiota; modulation of the gut microbiota by diet could lead to healthier aging. The purpose of this study was to test the effect of ...

    Authors: Tam T. T. Tran, Fabien J. Cousin, Denise B. Lynch, Ravi Menon, Jennifer Brulc, Jillian R.-M. Brown, Eileen O’Herlihy, Ludovica F. Butto, Katie Power, Ian B. Jeffery, Eibhlís M. O’Connor and Paul W. O’Toole

    Citation: Microbiome 2019 7:39

    Content type: Research

    Published on:

  14. Following publication of the original article [1], the authors identified wrong citations in the maintext.

    Authors: So-Jeong Kim, Jong-Geol Kim, Sang-Hoon Lee, Soo-Je Park, Joo-Han Gwak, Man-Young Jung, Won-Hyung Chung, Eun-Jin Yang, Jisoo Park, Jinyoung Jung, Yoonsoo Hahn, Jang-Cheon Cho, Eugene L. Madsen, Francisco Rodriguez-Valera, Jung-Ho Hyun and Sung-Keun Rhee

    Citation: Microbiome 2019 7:38

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2019 7:29

  15. Pneumonia is common and frequently fatal in HIV-infected patients, due to rampant, systemic inflammation and failure to control microbial infection. While airway microbiota composition is related to local infl...

    Authors: Meera K. Shenoy, Douglas W. Fadrosh, Din L. Lin, William Worodria, Patrick Byanyima, Emmanuel Musisi, Sylvia Kaswabuli, Josephine Zawedde, Ingvar Sanyu, Emily Chang, Serena Fong, Kathryn McCauley, J. Lucian Davis, Laurence Huang and Susan V. Lynch

    Citation: Microbiome 2019 7:37

    Content type: Research

    Published on:

  16. Blastocystis is a common gut eukaryote detected in humans and animals. It has been associated with gastrointestinal disease in the past although recent metagenomic studies also suggest that it is a member of norm...

    Authors: John Anthony Yason, Yi Ran Liang, Chin Wen Png, Yongliang Zhang and Kevin Shyong Wei Tan

    Citation: Microbiome 2019 7:30

    Content type: Research

    Published on:

  17. Metagenomic datasets provide an opportunity to study horizontal gene transfer (HGT) on the level of a microbial community. However, current HGT detection methods cannot be applied to community-level datasets o...

    Authors: Weizhi Song, Bernd Wemheuer, Shan Zhang, Kerrin Steensen and Torsten Thomas

    Citation: Microbiome 2019 7:36

    Content type: Methodology

    Published on:

  18. Microbial communities present in environmental waters constitute a reservoir for antibiotic-resistant pathogens that impact human health. For this reason, a diverse variety of water environments are being anal...

    Authors: Pablo Fresia, Verónica Antelo, Cecilia Salazar, Matías Giménez, Bruno D’Alessandro, Ebrahim Afshinnekoo, Christopher Mason, Gastón H. Gonnet and Gregorio Iraola

    Citation: Microbiome 2019 7:35

    Content type: Research

    Published on:

  19. Early disruption of the microbial community may influence life-long health. Environmental toxicants can contaminate breast milk and the developing infant gut microbiome is directly exposed. We investigated whe...

    Authors: Nina Iszatt, Stefan Janssen, Virissa Lenters, Cecilie Dahl, Hein Stigum, Rob Knight, Siddhartha Mandal, Shyamal Peddada, Antonio González, Tore Midtvedt and Merete Eggesbø

    Citation: Microbiome 2019 7:34

    Content type: Research

    Published on:

  20. Agricultural food production is at the base of food and fodder, with fertilization having fundamentally and continuously increased crop yield over the last decades. The performance of crops is intimately tied ...

    Authors: Zhi-Bo Zhao, Ji-Zheng He, Stefan Geisen, Li-Li Han, Jun-Tao Wang, Ju-Pei Shen, Wen-Xue Wei, Yun-Ting Fang, Pei-Pei Li and Li-Mei Zhang

    Citation: Microbiome 2019 7:33

    Content type: Research

    Published on:

  23. Polynyas in the Southern Ocean are regions of intense primary production, mainly by Phaeocystis antarctica. Carbon fixed by phytoplankton in the water column is transferred to higher trophic levels, and finally, ...

    Authors: So-Jeong Kim, Jong-Geol Kim, Sang-Hoon Lee, Soo-Je Park, Joo-Han Gwak, Man-Young Jung, Won-Hyung Chung, Eun-Jin Yang, Jisoo Park, Jinyoung Jung, Yoonsoo Hahn, Jang-Cheon Cho, Eugene L. Madsen, Francisco Rodriguez-Valera, Jung-Ho Hyun and Sung-Keun Rhee

    Citation: Microbiome 2019 7:29

    Content type: Research

    Published on:

    The Correction to this article has been published in Microbiome 2019 7:38

  24. Bacteria within family S24-7 (phylum Bacteroidetes) are dominant in the mouse gut microbiota and detected in the intestine of other animals. Because they had not been cultured until recently and the family classi...

    Authors: Ilias Lagkouvardos, Till R. Lesker, Thomas C. A. Hitch, Eric J. C. Gálvez, Nathiana Smit, Klaus Neuhaus, Jun Wang, John F. Baines, Birte Abt, Bärbel Stecher, Jörg Overmann, Till Strowig and Thomas Clavel

    Citation: Microbiome 2019 7:28

    Content type: Research

    Published on:

  25. Aquaculture is on the rise worldwide, and the use of antibiotics is fostering higher production intensity. However, recent findings suggest that the use of antibiotics comes at the price of increased antibioti...

    Authors: Johan S. Sáenz, Tamires Valim Marques, Rafael Simões Coelho Barone, José Eurico Possebon Cyrino, Susanne Kublik, Joseph Nesme, Michael Schloter, Susanne Rath and Gisle Vestergaard

    Citation: Microbiome 2019 7:24

    Content type: Research

    Published on:

  26. Host microbiomes play a role in hormone production and subsequent fertility in humans, but this is less well understood in non-model organisms. This is of particular relevance to species in zoo-based conservat...

    Authors: Rachael E. Antwis, Katie L. Edwards, Bryony Unwin, Susan L. Walker and Susanne Shultz

    Citation: Microbiome 2019 7:27

    Content type: Research

    Published on:

  27. Fungal infections are a significant cause of mortality and morbidity in hospitalized preterm infants, yet little is known about eukaryotic colonization of infants and of the neonatal intensive care unit as a p...

    Authors: Matthew R. Olm, Patrick T. West, Brandon Brooks, Brian A. Firek, Robyn Baker, Michael J. Morowitz and Jillian F. Banfield

    Citation: Microbiome 2019 7:26

    Content type: Research

    Published on:

  28. Increased autoreactive antibodies have been reported in HIV disease; however, the mechanism accounting for autoantibody induction in HIV remains unknown.

    Authors: Zhenwu Luo, Min Li, Yongxia Wu, Zhefeng Meng, Lisa Martin, Lumin Zhang, Elizabeth Ogunrinde, Zejun Zhou, Shenghui Qin, Zhuang Wan, Maria Anna Julia Westerink, Stephanie Warth, Hui Liu, Ping Jin, David Stroncek, Quan-Zhen Li…

    Citation: Microbiome 2019 7:25

    Content type: Research

    Published on:

  29. Studies of the cystic fibrosis (CF) lung microbiome have consistently shown that lung function decline is associated with decreased microbial diversity due to the dominance of opportunistic pathogens. However,...

    Authors: Robert A. Quinn, Sandeep Adem, Robert H. Mills, William Comstock, Lindsay DeRight Goldasich, Gregory Humphrey, Alexander A. Aksenov, Alexei V. Melnik, Ricardo da Silva, Gail Ackermann, Nuno Bandeira, David J. Gonzalez, Doug Conrad, Anthony J. O’Donoghue, Rob Knight and Pieter C. Dorrestein

    Citation: Microbiome 2019 7:23

    Content type: Research

    Published on:

  30. Following publication of the original article [1], the authors reported a typographic error in the type of master mix kit used, the text should read as: “The qPCR was performed using Fast SYBR Green Master Mix...

    Authors: Efrem S. Lim, Cynthia Rodriguez and Lori R. Holtz

    Citation: Microbiome 2019 7:22

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2018 6:87

  31. How and when a newborn is first colonized by microbes continues to be of great interest due to its broad implications on human health and disease. Payne et al. express their opinion about our recent study in w...

    Authors: Efrem S. Lim, Cynthia Rodriguez and Lori R. Holtz

    Citation: Microbiome 2019 7:21

    Content type: Correspondence

    Published on:

    The Letter to the Editor to this article has been published in Microbiome 2019 7:20

  32. A recent publication by Lim et al. 2018 (Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community) strongly concluded that the microbiome of amniotic fluid primarily origin...

    Authors: M. S. Payne, J. A. Keelan and L. F. Stinson

    Citation: Microbiome 2019 7:20

    Content type: Letter to the Editor

    Published on:

    The Correspondence to this article has been published in Microbiome 2019 7:21

  33. Disruption of the gut microbiota homeostasis may induce low-grade inflammation leading to obesity-associated diseases. A major protective mechanism is to use the multi-layered mucus structures to keep a safe d...

    Authors: Yiran Liang, Jing Zhan, Donghui Liu, Mai Luo, Jiajun Han, Xueke Liu, Chang Liu, Zheng Cheng, Zhiqiang Zhou and Peng Wang

    Citation: Microbiome 2019 7:19

    Content type: Research

    Published on:

  34. The gut microbiome plays a fundamental role in the human host’s overall health by contributing key biological functions such as expanded metabolism and pathogen defense/immune control. In a healthy individual,...

    Authors: J. Alfredo Blakeley-Ruiz, Alison R. Erickson, Brandi L. Cantarel, Weili Xiong, Rachel Adams, Janet K. Jansson, Claire M. Fraser and Robert L. Hettich

    Citation: Microbiome 2019 7:18

    Content type: Research

    Published on:

  35. Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replic...

    Authors: Adrian Fritz, Peter Hofmann, Stephan Majda, Eik Dahms, Johannes Dröge, Jessika Fiedler, Till R. Lesker, Peter Belmann, Matthew Z. DeMaere, Aaron E. Darling, Alexander Sczyrba, Andreas Bremges and Alice C. McHardy

    Citation: Microbiome 2019 7:17

    Content type: Software

    Published on:

  36. Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. Howe...

    Authors: Ke Yu, Shan Yi, Bing Li, Feng Guo, Xingxing Peng, Zhiping Wang, Yang Wu, Lisa Alvarez-Cohen and Tong Zhang

    Citation: Microbiome 2019 7:16

    Content type: Research

    Published on:

  37. Understanding the spatial distributions and ecological diversity of soil archaeal communities in agricultural ecosystems is crucial for improvements in crop productivity. Here, we conducted a comprehensive, co...

    Authors: Shuo Jiao, Yiqin Xu, Jie Zhang and Yahai Lu

    Citation: Microbiome 2019 7:15

    Content type: Research

    Published on:

  38. Soil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces that occurs worldwide, but little is known about the interaction...

    Authors: Wencong Shi, Mingcong Li, Guangshan Wei, Renmao Tian, Cuiping Li, Bing Wang, Rongshan Lin, Chunyu Shi, Xiuli Chi, Bo Zhou and Zheng Gao

    Citation: Microbiome 2019 7:14

    Content type: Research

    Published on:

  39. Arugula is a traditional medicinal plant and popular leafy green today. It is mainly consumed raw in the Western cuisine and known to contain various bioactive secondary metabolites. However, arugula has been ...

    Authors: Tomislav Cernava, Armin Erlacher, Jung Soh, Christoph W. Sensen, Martin Grube and Gabriele Berg

    Citation: Microbiome 2019 7:13

    Content type: Research

    Published on:

  41. The current view suggests that in low-temperature acidic environments, archaea are significantly less abundant than bacteria. Thus, this study of the microbiome of Parys Mountain (Anglesey, UK) sheds light on ...

    Authors: Aleksei A. Korzhenkov, Stepan V. Toshchakov, Rafael Bargiela, Huw Gibbard, Manuel Ferrer, Alina V. Teplyuk, David L. Jones, Ilya V. Kublanov, Peter N. Golyshin and Olga V. Golyshina

    Citation: Microbiome 2019 7:11

    Content type: Research

    Published on:

  42. Helminth parasites represent a significant threat to the health of human and animal populations, and there is a growing need for tools to treat, diagnose, and prevent these infections. Recent work has turned t...

    Authors: Christopher A. Gaulke, Mauricio L. Martins, Virginia G. Watral, Ian R. Humphreys, Sean T. Spagnoli, Michael L. Kent and Thomas J. Sharpton

    Citation: Microbiome 2019 7:10

    Content type: Research

    Published on:

  43. Bile salt hydrolase plays an important role in bile acid-mediated signaling pathways, which regulate lipid absorption, glucose metabolism, and energy homeostasis. Several reports suggest that changes in the co...

    Authors: Ziwei Song, Yuanyuan Cai, Xingzhen Lao, Xue Wang, Xiaoxuan Lin, Yingyun Cui, Praveen Kumar Kalavagunta, Jun Liao, Liang Jin, Jing Shang and Jing Li

    Citation: Microbiome 2019 7:9

    Content type: Research

    Published on:

  44. Water springs provide important ecosystem services including drinking water supply, recreation, and balneotherapy, but their microbial communities remain largely unknown. In this study, we characterized the sp...

    Authors: Renato Pedron, Alfonso Esposito, Irene Bianconi, Edoardo Pasolli, Adrian Tett, Francesco Asnicar, Mario Cristofolini, Nicola Segata and Olivier Jousson

    Citation: Microbiome 2019 7:8

    Content type: Research

    Published on:

  45. A westernized diet comprising a high caloric intake from animal fats is known to influence the development of pathological inflammatory conditions. However, there has been relatively little focus upon the impl...

    Authors: Vanessa Las Heras, Adam G. Clooney, Feargal J. Ryan, Raul Cabrera-Rubio, Pat G. Casey, Cara M. Hueston, Jorge Pinheiro, Justine K. Rudkin, Silvia Melgar, Paul D. Cotter, Colin Hill and Cormac G. M. Gahan

    Citation: Microbiome 2019 7:7

    Content type: Research

    Published on:

  46. Microorganisms are responsible for fermentation within the rumen and have been reported to contribute to the variation in feed efficiency of cattle. However, to what extent the breed affects the rumen microbio...

    Authors: Fuyong Li, Thomas C. A. Hitch, Yanhong Chen, Christopher J. Creevey and Le Luo Guan

    Citation: Microbiome 2019 7:6

    Content type: Research

    Published on:

  47. In the recent years, the holobiont concept has emerged as a theoretical and experimental framework to study the interactions between hosts and their associated microbial communities in all types of ecosystems....

    Authors: Jean-Christophe Simon, Julian R. Marchesi, Christophe Mougel and Marc-André Selosse

    Citation: Microbiome 2019 7:5

    Content type: Commentary

    Published on:

  49. Endolithic microbes in coral skeletons are known to be a nutrient source for the coral host. In addition to aerobic endolithic algae and Cyanobacteria, which are usually described in the various corals and form a...

    Authors: Shan-Hua Yang, Kshitij Tandon, Chih-Ying Lu, Naohisa Wada, Chao-Jen Shih, Silver Sung-Yun Hsiao, Wann-Neng Jane, Tzan-Chain Lee, Chi-Ming Yang, Chi-Te Liu, Vianney Denis, Yu-Ting Wu, Li-Ting Wang, Lina Huang, Der-Chuen Lee, Yu-Wei Wu…

    Citation: Microbiome 2019 7:3

    Content type: Research

    Published on:

  50. The gut microbiota evolves from birth and is in early life influenced by events such as birth mode, type of infant feeding, and maternal and infant antibiotics use. However, we still have a gap in our understa...

    Authors: Huanzi Zhong, John Penders, Zhun Shi, Huahui Ren, Kaiye Cai, Chao Fang, Qiuxia Ding, Carel Thijs, Ellen E. Blaak, Coen D. A. Stehouwer, Xun Xu, Huanming Yang, Jian Wang, Jun Wang, Daisy M. A. E. Jonkers, Ad A. M. Masclee…

    Citation: Microbiome 2019 7:2

    Content type: Research

    Published on:

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