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  1. The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we...

    Authors: Riaan F. Rifkin, Surendra Vikram, Jean-Baptiste Ramond, Alba Rey-Iglesia, Tina B. Brand, Guillaume Porraz, Aurore Val, Grant Hall, Stephan Woodborne, Matthieu Le Bailly, Marnie Potgieter, Simon J. Underdown, Jessica E. Koopman, Don A. Cowan, Yves Van de Peer, Eske Willerslev…

    Citation: Microbiome 2020 8:62

    Content type: Research

    Published on:

  2. Gender reassignment surgery is a procedure some transgender women (TW) undergo for gender-affirming purposes. This often includes the construction of a neovagina using existing penile and scrotal tissue and/or...

    Authors: Kenzie D. Birse, Kateryna Kratzer, Christina Farr Zuend, Sarah Mutch, Laura Noël-Romas, Alana Lamont, Max Abou, Emilia Jalil, Valdiléa Veloso, Beatriz Grinsztejn, Ruth Khalili Friedman, Kristina Broliden, Frideborg Bradley, Vanessa Poliquin, Fan Li, Carolyn Yanavich…

    Citation: Microbiome 2020 8:61

    Content type: Research

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  3. The multifaceted interactions between gastrointestinal (GI) helminth parasites, host gut microbiota and immune system are emerging as a key area of research within the field of host-parasite relationships. In ...

    Authors: Alba Cortés, John Wills, Xiaopei Su, Rachel E. Hewitt, Jack Robertson, Riccardo Scotti, Daniel R. G. Price, Yvonne Bartley, Tom N. McNeilly, Lutz Krause, Jonathan J. Powell, Alasdair J. Nisbet and Cinzia Cantacessi

    Citation: Microbiome 2020 8:60

    Content type: Research

    Published on:

  4. The chaperone ClpB, a bacterial protein, is a conformational antigen-mimetic of α-melanocyte-stimulating hormone (α-MSH) implicated in body weight regulation in mice. We here investigated the potential associa...

    Authors: María Arnoriaga-Rodríguez, Jordi Mayneris-Perxachs, Aurelijus Burokas, Vicente Pérez-Brocal, Andrés Moya, Manuel Portero-Otin, Wifredo Ricart, Rafael Maldonado and José-Manuel Fernández-Real

    Citation: Microbiome 2020 8:59

    Content type: Research

    Published on:

  5. The skin micro-environment varies across the body, but all sites are host to microorganisms that can impact skin health. Some of these organisms are true commensals which colonize a unique niche on the skin, w...

    Authors: Collin M. Timm, Kristin Loomis, William Stone, Thomas Mehoke, Bryan Brensinger, Matthew Pellicore, Phillip P.A. Staniczenko, Curtisha Charles, Seema Nayak and David K. Karig

    Citation: Microbiome 2020 8:58

    Content type: Research

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  6. Giant clams and scleractinian (reef-building) corals are keystone species of coral reef ecosystems. The basis of their ecological success is a complex and fine-tuned symbiotic relationship with microbes. While...

    Authors: Isis Guibert, Gael Lecellier, Gergely Torda, Xavier Pochon and Véronique Berteaux-Lecellier

    Citation: Microbiome 2020 8:57

    Content type: Research

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  7. Spaceflight impacts astronauts in many ways but little is known on how spaceflight affects the salivary microbiome and the consequences of these changes on astronaut health, such as viral reactivation. In orde...

    Authors: Camilla Urbaniak, Hernan Lorenzi, James Thissen, Crystal Jaing, Brian Crucian, Clarence Sams, Duane Pierson, Kasthuri Venkateswaran and Satish Mehta

    Citation: Microbiome 2020 8:56

    Content type: Research

    Published on:

  8. The ocean microbiota modulates global biogeochemical cycles and changes in its configuration may have large-scale consequences. Yet, the underlying ecological mechanisms structuring it are unclear. Here, we in...

    Authors: Ramiro Logares, Ina M. Deutschmann, Pedro C. Junger, Caterina R. Giner, Anders K. Krabberød, Thomas S. B. Schmidt, Laura Rubinat-Ripoll, Mireia Mestre, Guillem Salazar, Clara Ruiz-González, Marta Sebastián, Colomban de Vargas, Silvia G. Acinas, Carlos M. Duarte, Josep M. Gasol and Ramon Massana

    Citation: Microbiome 2020 8:55

    Content type: Research

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  9. When maize (Zea mays L.) is grown in the Northern hemisphere, its development is heavily arrested by chilling temperatures, especially at the juvenile phase. As some endophytes are beneficial for plants under str...

    Authors: Stien Beirinckx, Tom Viaene, Annelies Haegeman, Jane Debode, Fien Amery, Steven Vandenabeele, Hilde Nelissen, Dirk Inzé, Raul Tito, Jeroen Raes, Caroline De Tender and Sofie Goormachtig

    Citation: Microbiome 2020 8:54

    Content type: Research

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  10. Recent evidence has linked the gut microbiome to host behavior via the gut–brain axis [1–3]; however, the underlying mechanisms remain unexplored. Here, we determined the links between host genetics, the gut micr...

    Authors: Jian-Hua Mao, Young-Mo Kim, Yan-Xia Zhou, Dehong Hu, Chenhan Zhong, Hang Chang, Colin J. Brislawn, Sarah Fansler, Sasha Langley, Yunshan Wang, B. Y. Loulou Peisl, Susan E. Celniker, David W. Threadgill, Paul Wilmes, Galya Orr, Thomas O. Metz…

    Citation: Microbiome 2020 8:53

    Content type: Research

    Published on:

    The Correction to this article has been published in Microbiome 2020 8:73

  11. Bacteriophages, the viruses infecting bacteria, are biological entities that can control their host populations. The ecological relevance of phages for microbial systems has been widely explored in aquatic env...

    Authors: Lucas P. P. Braga, Aymé Spor, Witold Kot, Marie-Christine Breuil, Lars H. Hansen, João C. Setubal and Laurent Philippot

    Citation: Microbiome 2020 8:52

    Content type: Research

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  12. The newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently incre...

    Authors: Renmao Tian, Daliang Ning, Zhili He, Ping Zhang, Sarah J. Spencer, Shuhong Gao, Weiling Shi, Linwei Wu, Ya Zhang, Yunfeng Yang, Benjamin G. Adams, Andrea M. Rocha, Brittny L. Detienne, Kenneth A. Lowe, Dominique C. Joyner, Dawn M. Klingeman…

    Citation: Microbiome 2020 8:51

    Content type: Research

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  13. Following publication of the original article [1], the authors reported an error in Fig. 2. The original Fig. 2 has been incorrectly replaced with the Supplementary Fig. 2. The correct Fig. 2 is presented here.

    Authors: Abigail J. S. Armstrong, Michael Shaffer, Nichole M. Nusbacher, Christine Griesmer, Suzanne Fiorillo, Jennifer M. Schneider, C. Preston Neff, Sam X. Li, Andrew P. Fontenot, Thomas Campbell, Brent E. Palmer and Catherine A. Lozupone

    Citation: Microbiome 2020 8:50

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2018 6:198

  14. Myxobacteria are micropredators in the soil ecosystem with the capacity to move and feed cooperatively. Some myxobacterial strains have been used to control soil-borne fungal phytopathogens. However, interacti...

    Authors: Xianfeng Ye, Zhoukun Li, Xue Luo, Wenhui Wang, Yongkai Li, Rui Li, Bo Zhang, Yan Qiao, Jie Zhou, Jiaqin Fan, Hui Wang, Yan Huang, Hui Cao, Zhongli Cui and Ruifu Zhang

    Citation: Microbiome 2020 8:49

    Content type: Research

    Published on:

  16. The Arctic and Antarctic are the two most geographically distant bioregions on earth. Recent sampling efforts and following metagenomics have shed light on the global ocean microbial diversity and function, ye...

    Authors: Shunan Cao, Weipeng Zhang, Wei Ding, Meng Wang, Shen Fan, Bo Yang, Andrew Mcminn, Min Wang, Bin-bin Xie, Qi-Long Qin, Xiu-Lan Chen, Jianfeng He and Yu-Zhong Zhang

    Citation: Microbiome 2020 8:47

    Content type: Research

    Published on:

    The Correction to this article has been published in Microbiome 2020 8:77

  18. Chronic infection and concomitant airway inflammation is the leading cause of morbidity and mortality for people living with cystic fibrosis (CF). Although chronic infection in CF is undeniably polymicrobial, ...

    Authors: Leah Cuthbertson, Alan W. Walker, Anna E. Oliver, Geraint B. Rogers, Damian W. Rivett, Thomas H. Hampton, Alix Ashare, J. Stuart Elborn, Anthony De Soyza, Mary P. Carroll, Lucas R. Hoffman, Clare Lanyon, Samuel M. Moskowitz, George A. O’Toole, Julian Parkhill, Paul J. Planet…

    Citation: Microbiome 2020 8:45

    Content type: Research

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  19. The impact of the gut microbiota on host physiology and behavior has been relatively well established. Whether changes in microbial composition affect brain structure and function is largely elusive, however. ...

    Authors: Anouk C. Tengeler, Sarita A. Dam, Maximilian Wiesmann, Jilly Naaijen, Miranda van Bodegom, Clara Belzer, Pieter J. Dederen, Vivienne Verweij, Barbara Franke, Tamas Kozicz, Alejandro Arias Vasquez and Amanda J. Kiliaan

    Citation: Microbiome 2020 8:44

    Content type: Research

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  20. Bathyarchaeota, a newly proposed archaeal phylum, is considered as an important driver of the global carbon cycle. However, due to the great diversity of them, there is limited genomic information that accurat...

    Authors: Jie Pan, Zhichao Zhou, Oded Béjà, Mingwei Cai, Yuchun Yang, Yang Liu, Ji-Dong Gu and Meng Li

    Citation: Microbiome 2020 8:43

    Content type: Research

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  21. Limiting microbial growth during drinking water distribution is achieved either by maintaining a disinfectant residual or through nutrient limitation without using a disinfectant. The impact of these contrasti...

    Authors: Zihan Dai, Maria C. Sevillano-Rivera, Szymon T. Calus, Q. Melina Bautista-de los Santos, A. Murat Eren, Paul W. J. J. van der Wielen, Umer Z. Ijaz and Ameet J. Pinto

    Citation: Microbiome 2020 8:42

    Content type: Research

    Published on:

  22. New antibiotic resistance determinants are generally discovered too late, long after they have irreversibly emerged in pathogens and spread widely. Early discovery of resistance genes, before or soon after the...

    Authors: Maria-Elisabeth Böhm, Mohammad Razavi, Nachiket P. Marathe, Carl-Fredrik Flach and D. G. Joakim Larsson

    Citation: Microbiome 2020 8:41

    Content type: Research

    Published on:

  23. Following publication of the original article [1], the authors reported that an affiliation of the first author was missing.

    Authors: Vinicius S. Kavagutti, Adrian-Ştefan Andrei, Maliheh Mehrshad, Michaela M. Salcher and Rohit Ghai

    Citation: Microbiome 2020 8:40

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2019 7:135

  24. The abundance and diversity of antibiotic resistance genes (ARGs) in the human respiratory microbiome remain poorly characterized. In the context of influenza virus infection, interactions between the virus, t...

    Authors: Lingdi Zhang, Christian V. Forst, Aubree Gordon, Gabrielle Gussin, Adam B. Geber, Porfirio J. Fernandez, Tao Ding, Lauren Lashua, Minghui Wang, Angel Balmaseda, Richard Bonneau, Bin Zhang and Elodie Ghedin

    Citation: Microbiome 2020 8:39

    Content type: Research

    Published on:

  26. Resident soil microbiota play key roles in sustaining the core ecosystem processes of terrestrial Antarctica, often involving unique taxa with novel functional traits. However, the full scope of biodiversity a...

    Authors: Eden Zhang, Loïc M. Thibaut, Aleks Terauds, Mark Raven, Mark M. Tanaka, Josie van Dorst, Sin Yin Wong, Sally Crane and Belinda C. Ferrari

    Citation: Microbiome 2020 8:37

    Content type: Research

    Published on:

  28. There are a variety of bioinformatic pipelines and downstream analysis methods for analyzing 16S rRNA marker-gene surveys. However, appropriate assessment datasets and metrics are needed as there is limited gu...

    Authors: Nathan D. Olson, M. Senthil Kumar, Shan Li, Domenick J. Braccia, Stephanie Hao, Winston Timp, Marc L. Salit, O. Colin Stine and Hector Corrada Bravo

    Citation: Microbiome 2020 8:35

    Content type: Methodology

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  29. Apicomplexans are the causative agents of major human diseases such as malaria and toxoplasmosis. A novel group of apicomplexans, recently named corallicolids, have been detected in corals inhabiting tropical ...

    Authors: Samuel A. Vohsen, Kaitlin E. Anderson, Andrea M. Gade, Harald R. Gruber-Vodicka, Richard P. Dannenberg, Eslam O. Osman, Nicole Dubilier, Charles R. Fisher and Iliana B. Baums

    Citation: Microbiome 2020 8:34

    Content type: Research

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  30. Human-targeted drugs may exert off-target effects or can be repurposed to modulate the gut microbiota. However, our understanding of such effects is limited due to a lack of rapid and scalable assay to compreh...

    Authors: Leyuan Li, Zhibin Ning, Xu Zhang, Janice Mayne, Kai Cheng, Alain Stintzi and Daniel Figeys

    Citation: Microbiome 2020 8:33

    Content type: Research

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  31. Recently, increasing evidence supports that some complex diseases are not attributed to a given pathogen, but dysbiosis in the host intestinal microbiota (IM). The full intestinal ecosystem alterations, rather...

    Authors: Zhijian Huang, Shenzheng Zeng, Jinbo Xiong, Dongwei Hou, Renjun Zhou, Chengguang Xing, Dongdong Wei, Xisha Deng, Lingfei Yu, Hao Wang, Zhixuan Deng, Shaoping Weng, Satapornvanit Kriengkrai, Daliang Ning, Jizhong Zhou and Jianguo He

    Citation: Microbiome 2020 8:32

    Content type: Research

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  33. There is an important need for the development of fast and robust methods to quantify the diversity and temporal dynamics of microbial communities in complex environmental samples. Because tandem mass spectrom...

    Authors: Olivier Pible, François Allain, Virginie Jouffret, Karen Culotta, Guylaine Miotello and Jean Armengaud

    Citation: Microbiome 2020 8:30

    Content type: Methodology

    Published on:

  34. The gut microbiota has the potential to influence the efficacy of cancer therapy. Here, we investigated the contribution of the intestinal microbiome on treatment outcomes in a heterogeneous cohort that includ...

    Authors: Yoshitaro Heshiki, Ruben Vazquez-Uribe, Jin Li, Yueqiong Ni, Scott Quainoo, Lejla Imamovic, Jun Li, Maria Sørensen, Billy K. C. Chow, Glen J. Weiss, Aimin Xu, Morten O. A. Sommer and Gianni Panagiotou

    Citation: Microbiome 2020 8:28

    Content type: Research

    Published on:

  35. Plant health is intimately influenced by the rhizosphere microbiome, a complex assembly of organisms that changes markedly across plant growth. However, most rhizosphere microbiome research has focused on frac...

    Authors: Wu Xiong, Yuqi Song, Keming Yang, Yian Gu, Zhong Wei, George A. Kowalchuk, Yangchun Xu, Alexandre Jousset, Qirong Shen and Stefan Geisen

    Citation: Microbiome 2020 8:27

    Content type: Research

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  36. Antibiotic-resistant pathogens pose high risks to human and animal health worldwide. In recent years, the role of gut microbiota as a reservoir of antibiotic resistance genes (ARGs) in humans and animals has b...

    Authors: Jian Cao, Yongfei Hu, Fei Liu, Yanan Wang, Yuhai Bi, Na Lv, Jing Li, Baoli Zhu and George F. Gao

    Citation: Microbiome 2020 8:26

    Content type: Research

    Published on:

  38. Following publication of the original article [1], the authors reported an error on the legend of of P.damicornis in Fig. 1.

    Authors: Eslam O. Osman, David J. Suggett, Christian R. Voolstra, D. Tye Pettay, Dave R. Clark, Claudia Pogoreutz, Eugenia M. Sampayo, Mark E. Warner and David J. Smith

    Citation: Microbiome 2020 8:24

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2020 8:8

  39. The rumen contains a myriad of microbes whose primary role is to degrade and ferment dietary nutrients, which then provide the host with energy and nutrients. Rumen microbes commonly attach to ingested plant m...

    Authors: Mi-Young Won, Linda B. Oyama, Stephen J. Courtney, Christopher J. Creevey and Sharon A. Huws

    Citation: Microbiome 2020 8:23

    Content type: Research

    Published on:

  40. Methanogenesis, a biological process mediated by complex microbial communities, has attracted great attention due to its contribution to global warming and potential in biotechnological applications. The curre...

    Authors: Xinyu Zhu, Stefano Campanaro, Laura Treu, Rekha Seshadri, Natalia Ivanova, Panagiotis G. Kougias, Nikos Kyrpides and Irini Angelidaki

    Citation: Microbiome 2020 8:22

    Content type: Research

    Published on:

  41. Metagenomics and single cell genomics provide a window into the genetic repertoire of yet uncultivated microorganisms, but both methods are usually taxonomically untargeted. The combination of fluorescence in ...

    Authors: Anissa Grieb, Robert M. Bowers, Monike Oggerin, Danielle Goudeau, Janey Lee, Rex R. Malmstrom, Tanja Woyke and Bernhard M. Fuchs

    Citation: Microbiome 2020 8:21

    Content type: Research

    Published on:

  42. Plant-associated microbiomes, which are shaped by host and environmental factors, support their hosts by providing nutrients and attenuating abiotic and biotic stresses. Although host genetic factors involved ...

    Authors: Hyun Kim, Kiseok Keith Lee, Jongbum Jeon, William Anthony Harris and Yong-Hwan Lee

    Citation: Microbiome 2020 8:20

    Content type: Research

    Published on:

  43. The upper gastrointestinal tract plays a prominent role in human physiology as the primary site for enzymatic digestion and nutrient absorption, immune sampling, and drug uptake. Alterations to the small intes...

    Authors: Said R. Bogatyrev, Justin C. Rolando and Rustem F. Ismagilov

    Citation: Microbiome 2020 8:19

    Content type: Research

    Published on:

  44. Cell-free DNA (cfDNA) in blood, urine, and other biofluids provides a unique window into human health. A proportion of cfDNA is derived from bacteria and viruses, creating opportunities for the diagnosis of in...

    Authors: Philip Burnham, Nardhy Gomez-Lopez, Michael Heyang, Alexandre Pellan Cheng, Joan Sesing Lenz, Darshana M. Dadhania, John Richard Lee, Manikkam Suthanthiran, Roberto Romero and Iwijn De Vlaminck

    Citation: Microbiome 2020 8:18

    Content type: Short report

    Published on:

  45. Bacteriophages (phages) are the most numerous biological entities on Earth and play a crucial role in shaping microbial communities. Investigating the bacteriophage community from soil will shed light not only...

    Authors: Pauline C. Göller, Jose M. Haro-Moreno, Francisco Rodriguez-Valera, Martin J. Loessner and Elena Gómez-Sanz

    Citation: Microbiome 2020 8:17

    Content type: Methodology

    Published on:

  46. Microorganisms in activated sludge (AS) play key roles in the wastewater treatment processes. However, their ecological behaviors and differences from microorganisms in other environments have mainly been stud...

    Authors: Lin Ye, Ran Mei, Wen-Tso Liu, Hongqiang Ren and Xu-Xiang Zhang

    Citation: Microbiome 2020 8:16

    Content type: Research

    Published on:

  47. Dietary effects on the gut microbiome play key roles in the pathophysiology of inflammatory disorders, metabolic syndrome, obesity, and behavioral dysregulation. Often overlooked in such studies is the conside...

    Authors: Kathleen E. Morrison, Eldin Jašarević, Christopher D. Howard and Tracy L. Bale

    Citation: Microbiome 2020 8:15

    Content type: Short report

    Published on:

  48. The eco-evolutionary processes ruling post-disturbance microbial assembly remain poorly studied, particularly in host-microbiome systems. The community recovery depends not only on the type, duration, intensit...

    Authors: Bachar Cheaib, Hamza Seghouani, Umer Zeeshan Ijaz and Nicolas Derome

    Citation: Microbiome 2020 8:14

    Content type: Research

    Published on:

  49. Roux-en-Y gastric bypass (RYGB) surgery is a last-resort treatment to induce substantial and sustained weight loss in cases of severe obesity. This anatomical rearrangement affects the intestinal microbiota, b...

    Authors: Sven-Bastiaan Haange, Nico Jehmlich, Ute Krügel, Constantin Hintschich, Dorothee Wehrmann, Mohammed Hankir, Florian Seyfried, Jean Froment, Thomas Hübschmann, Susann Müller, Dirk K. Wissenbach, Kang Kang, Christian Buettner, Gianni Panagiotou, Matthias Noll, Ulrike Rolle-Kampczyk…

    Citation: Microbiome 2020 8:13

    Content type: Research

    Published on:

  50. The capacity of reef-building corals to tolerate (or adapt to) heat stress is a key factor determining their resilience to future climate change. Changes in coral microbiome composition (particularly for micro...

    Authors: Eslam O. Osman, David J. Suggett, Christian R. Voolstra, D. Tye Pettay, Dave R. Clark, Claudia Pogoreutz, Eugenia M. Sampayo, Mark E. Warner and David J. Smith

    Citation: Microbiome 2020 8:8

    Content type: Research

    Published on:

    The Correction to this article has been published in Microbiome 2020 8:24

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