Skip to main content

Articles

Page 4 of 23

  1. Polintons are large mobile genetic elements found in the genomes of eukaryotic organisms that are considered the ancient ancestors of most eukaryotic dsDNA viruses. Originally considered as transposons, they h...

    Authors: Christopher M. Bellas and Ruben Sommaruga

    Citation: Microbiome 2021 9:13

    Content type: Research

    Published on:

    The Correction to this article has been published in Microbiome 2021 9:30

  2. Proteolysis regulation allows gut microbes to respond rapidly to dynamic intestinal environments by fast degradation of misfolded proteins and activation of regulatory proteins. However, alterations of gut mic...

    Authors: Zhixiang Yan, Feixiang He, Fei Xiao, Huanhuan He, Dan Li, Li Cong, Lu Lin, Huijin Zhu, Yanyan Wu, Ru Yan, Xiaofeng Li and Hong Shan

    Citation: Microbiome 2021 9:12

    Content type: Research

    Published on:

  3. Non-caloric artificial sweeteners (NCAS) are widely used as a substitute for dietary sugars to control body weight or glycemia. Paradoxically, some interventional studies in humans and rodents have shown unfav...

    Authors: Joan Serrano, Kathleen R. Smith, Audra L. Crouch, Vandana Sharma, Fanchao Yi, Veronika Vargova, Traci E. LaMoia, Lydia M. Dupont, Vanida Serna, Fenfen Tang, Laisa Gomes-Dias, Joshua J. Blakeslee, Emmanuel Hatzakis, Scott N. Peterson, Matthew Anderson, Richard E. Pratley…

    Citation: Microbiome 2021 9:11

    Content type: Research

    Published on:

  4. For more than a century, the prenatal environment was considered sterile. Over the last few years, findings obtained with next-generation sequencing approaches from samples of the placenta, the amniotic fluid,...

    Authors: Martin J. Blaser, Suzanne Devkota, Kathy D. McCoy, David A. Relman, Moran Yassour and Vincent B. Young

    Citation: Microbiome 2021 9:8

    Content type: Commentary

    Published on:

  5. A recent study by Rackaityte et al. reported evidence for a low level of bacterial colonization, specifically of Micrococcus luteus, in the intestine of second trimester human fetuses. We have re-analyzed their s...

    Authors: Marcus C. de Goffau, D. Stephen Charnock-Jones, Gordon C. S. Smith and Julian Parkhill

    Citation: Microbiome 2021 9:6

    Content type: Letter to the Editor

    Published on:

  6. Widespread bioinformatic resource development generates a constantly evolving and abundant landscape of workflows and software. For analysis of the microbiome, workflows typically begin with taxonomic classifi...

    Authors: Laura-Jayne Gardiner, Niina Haiminen, Filippo Utro, Laxmi Parida, Ed Seabolt, Ritesh Krishna and James H. Kaufman

    Citation: Microbiome 2021 9:4

    Content type: Short report

    Published on:

  7. An article published in Microbiome in July 2018 uses incorrect definitions of integron integrase IntI1 and of class 1 integrons that affect the interpretation of the data.

    Authors: Paul H. Roy, Sally R. Partridge and Ruth M. Hall

    Citation: Microbiome 2021 9:3

    Content type: Letter to the Editor

    Published on:

  8. The inaugural “Microbiome for Mars” virtual workshop took place on July 13, 2020. This event assembled leaders in microbiome research and development to discuss their work and how it may relate to long-duratio...

    Authors: Michael LaPelusa, Dorit Donoviel, Sergio E. Branzini, Paul E. Carlson Jr, Stephanie Culler, Amrita K. Cheema, Rima Kaddurah-Daouk, Denise Kelly, Isabelle de Cremoux, Rob Knight, Rosa Krajmalnik-Brown, Stephen L. Mayo, Sarkis K. Mazmanian, Emeran A. Mayer, Joseph F. Petrosino and Keith Garrison

    Citation: Microbiome 2021 9:2

    Content type: Meeting report

    Published on:

  9. Targeted amplicon deep sequencing (TADS) has enabled characterization of diverse bacterial communities, yet the application of TADS to communities of parasites has been relatively slow to advance. The greatest...

    Authors: Briana R. Flaherty, Joel Barratt, Meredith Lane, Eldin Talundzic and Richard S. Bradbury

    Citation: Microbiome 2021 9:1

    Content type: Research

    Published on:

  10. Research around the weedkiller Roundup is among the most contentious of the twenty-first century. Scientists have provided inconclusive evidence that the weedkiller causes cancer and other life-threatening dis...

    Authors: Antonio Suppa, Jouni Kvist, Xiaojing Li, Vignesh Dhandapani, Hanan Almulla, Antoine Y. Tian, Stephen Kissane, Jiarui Zhou, Alessio Perotti, Hayley Mangelson, Kyle Langford, Valeria Rossi, James B. Brown and Luisa Orsini

    Citation: Microbiome 2020 8:170

    Content type: Research

    Published on:

  11. An amendment to this paper has been published and can be accessed via the original article.

    Authors: Hong-Yi Li, Hang Wang, Hai-Tao Wang, Pei-Yong Xin, Xin-Hua Xu, Yun Ma, Wei-Ping Liu, Chang-Yun Teng, Cheng-Liang Jiang, Li-Ping Lou, Wyatt Arnold, Lauren Cralle, Yong-Guan Zhu, Jin-Fang Chu, Jack A. Gilbert and Zhi-Jian Zhang

    Citation: Microbiome 2020 8:169

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2018 6:187

  12. The key effects of intestinal microbiota in animal health have led to an increasing interest in manipulating these bacterial populations to improve animal welfare. The aquaculture sector is no exception and in...

    Authors: M. Carla Piazzon, Fernando Naya-Català, Erick Perera, Oswaldo Palenzuela, Ariadna Sitjà-Bobadilla and Jaume Pérez-Sánchez

    Citation: Microbiome 2020 8:168

    Content type: Research

    Published on:

  13. Early microbial colonization triggers processes that result in intestinal maturation and immune priming. Perinatal factors, especially those associated with birth, including both mode and place of delivery are...

    Authors: M. Selma-Royo, M. Calatayud Arroyo, I. García-Mantrana, A. Parra-Llorca, R. Escuriet, C. Martínez-Costa and M. C. Collado

    Citation: Microbiome 2020 8:167

    Content type: Research

    Published on:

  14. Taxonomic profiles of vaginal microbial communities can be sorted into a discrete number of categories termed community state types (CSTs). This approach is advantageous because collapsing a hyper-dimensional ...

    Authors: Michael T. France, Bing Ma, Pawel Gajer, Sarah Brown, Michael S. Humphrys, Johanna B. Holm, L. Elaine Waetjen, Rebecca M. Brotman and Jacques Ravel

    Citation: Microbiome 2020 8:166

    Content type: Research

    Published on:

  15. Female genital tract (FGT) inflammation is an important risk factor for HIV acquisition. The FGT microbiome is closely associated with inflammatory profile; however, the relative importance of microbial activi...

    Authors: Arghavan Alisoltani, Monalisa T. Manhanzva, Matthys Potgieter, Christina Balle, Liam Bell, Elizabeth Ross, Arash Iranzadeh, Michelle du Plessis, Nina Radzey, Zac McDonald, Bridget Calder, Imane Allali, Nicola Mulder, Smritee Dabee, Shaun Barnabas, Hoyam Gamieldien…

    Citation: Microbiome 2020 8:165

    Content type: Research

    Published on:

  16. The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more susta...

    Authors: Oscar Mencía-Ares, Raúl Cabrera-Rubio, José Francisco Cobo-Díaz, Avelino Álvarez-Ordóñez, Manuel Gómez-García, Héctor Puente, Paul D. Cotter, Fiona Crispie, Ana Carvajal, Pedro Rubio and Héctor Argüello

    Citation: Microbiome 2020 8:164

    Content type: Research

    Published on:

  17. Lake Baikal is the largest body of liquid freshwater on Earth. Previous studies have described the microbial composition of this habitat, but the viral communities from this ecosystem have not been characteriz...

    Authors: F. H. Coutinho, P. J. Cabello-Yeves, R. Gonzalez-Serrano, R. Rosselli, M. López-Pérez, T. I. Zemskaya, A. S. Zakharenko, V. G. Ivanov and F. Rodriguez-Valera

    Citation: Microbiome 2020 8:163

    Content type: Research

    Published on:

  18. The capability of gut microbiota in degrading foods and drugs administered orally can result in diversified efficacies and toxicity interpersonally and cause significant impact on human health. Production of a...

    Authors: Wei-Kai Wu, Suraphan Panyod, Po-Yu Liu, Chieh-Chang Chen, Hsien-Li Kao, Hsiao-Li Chuang, Ying-Hsien Chen, Hsin-Bai Zou, Han-Chun Kuo, Ching-Hua Kuo, Ben-Yang Liao, Tina H. T. Chiu, Ching-Hu Chung, Angela Yu-Chen Lin, Yi-Chia Lee, Sen-Lin Tang…

    Citation: Microbiome 2020 8:162

    Content type: Research

    Published on:

  19. The microbiota presents a compartmentalized distribution across different gut segments. Hence, the exogenous microbiota from a particular gut segment might only invade its homologous gut location during microb...

    Authors: Na Li, Bin Zuo, Shimeng Huang, Benhua Zeng, Dandan Han, Tiantian Li, Ting Liu, Zhenhua Wu, Hong Wei, Jiangchao Zhao and Junjun Wang

    Citation: Microbiome 2020 8:161

    Content type: Research

    Published on:

  20. Interest for the study of gut mycobiota in relation with human health and immune homeostasis has increased in the last years. From this perspective, new tools to study the immune/fungal interface are warranted...

    Authors: Alicia Moreno-Sabater, Gaelle Autaa, Delphine Sterlin, Amenie Jerbi, Remy Villette, Johanna B. Holm, Christophe Parizot, Sameh Selim, Yaye Senghor, Pascale Ghillani-Dalbin, Claude Bachmeyer, Christophe Hennequin, Guy Gorochov and Martin Larsen

    Citation: Microbiome 2020 8:159

    Content type: Methodology

    Published on:

  21. Horizontal gene transfer (HGT) plays a central role in microbial evolution. Our understanding of the mechanisms, frequency, and taxonomic range of HGT in polymicrobial environments is limited, as we currently ...

    Authors: Manuel Kleiner, Brian Bushnell, Kenneth E. Sanderson, Lora V. Hooper and Breck A. Duerkop

    Citation: Microbiome 2020 8:158

    Content type: Research

    Published on:

  22. Cooling towers are a major source of large community-associated outbreaks of Legionnaires’ disease, a severe pneumonia. This disease is contracted when inhaling aerosols that are contaminated with bacteria fro...

    Authors: Kiran Paranjape, Émilie Bédard, Deeksha Shetty, Mengqi Hu, Fiona Chan Pak Choon, Michèle Prévost and Sébastien P. Faucher

    Citation: Microbiome 2020 8:157

    Content type: Research

    Published on:

  23. The human microbiota are complex systems with important roles in our physiological activities and diseases. Sequencing the microbial genomes in the microbiota can help in our interpretation of their activities...

    Authors: Lu Zhang, Xiaodong Fang, Herui Liao, Zhenmiao Zhang, Xin Zhou, Lijuan Han, Yang Chen, Qinwei Qiu and Shuai Cheng Li

    Citation: Microbiome 2020 8:156

    Content type: Research

    Published on:

  24. Genome-centric approaches are widely used to investigate microbial compositions, dynamics, ecology, and interactions within various environmental systems. Hundreds or even thousands of genomes could be retriev...

    Authors: Lei Liu, Yulin Wang, You Che, Yiqiang Chen, Yu Xia, Ruibang Luo, Suk Hang Cheng, Chunmiao Zheng and Tong Zhang

    Citation: Microbiome 2020 8:155

    Content type: Research

    Published on:

  25. The microbiota plays an important role in HIV pathogenesis in humans. Microbiota can impact health through several pathways such as increasing inflammation in the gut, metabolites of bacterial origin, and micr...

    Authors: Anna J. Jasinska, Tien S. Dong, Venu Lagishetty, William Katzka, Jonathan P. Jacobs, Christopher A. Schmitt, Jennifer Danzy Cramer, Dongzhu Ma, Willem G. Coetzer, J. Paul Grobler, Trudy R. Turner, Nelson Freimer, Ivona Pandrea and Cristian Apetrei

    Citation: Microbiome 2020 8:154

    Content type: Research

    Published on:

  26. Chronic immune-mediated diseases are rapidly expanding and notoriously difficult to cure. Altered relatively stable intestinal microbiota configurations are associated with several of these diseases, and with ...

    Authors: Maarten Van de Guchte, Sebastian D. Burz, Julie Cadiou, Jiangbo Wu, Stanislas Mondot, Hervé M. Blottière and Joël Doré

    Citation: Microbiome 2020 8:153

    Content type: Research

    Published on:

  27. The discovery of membrane-enclosed, metabolically functional organelles in Bacteria has transformed our understanding of the subcellular complexity of prokaryotic cells. Biomineralization of magnetic nanoparticle...

    Authors: Wei Lin, Wensi Zhang, Greig A. Paterson, Qiyun Zhu, Xiang Zhao, Rob Knight, Dennis A. Bazylinski, Andrew P. Roberts and Yongxin Pan

    Citation: Microbiome 2020 8:152

    Content type: Research

    Published on:

  28. The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant t...

    Authors: Célio Dias Santos-Júnior, Hugo Sarmento, Fernando Pellon de Miranda, Flávio Henrique-Silva and Ramiro Logares

    Citation: Microbiome 2020 8:151

    Content type: Research

    Published on:

  29. The extraordinarily resistant bacterium Deinococcus radiodurans withstands harsh environmental conditions present in outer space. Deinococcus radiodurans was exposed for 1 year outside the International Space Sta...

    Authors: Emanuel Ott, Yuko Kawaguchi, Denise Kölbl, Elke Rabbow, Petra Rettberg, Maximilian Mora, Christine Moissl-Eichinger, Wolfram Weckwerth, Akihiko Yamagishi and Tetyana Milojevic

    Citation: Microbiome 2020 8:150

    Content type: Research

    Published on:

  30. Recent increases in understanding the ecological and evolutionary roles of microbial communities have underscored the importance of their hosts’ biology. Yet, little is known about gut microbiota dynamics duri...

    Authors: Andreas Härer, Julián Torres-Dowdall, Sina J. Rometsch, Elizabeth Yohannes, Gonzalo Machado-Schiaffino and Axel Meyer

    Citation: Microbiome 2020 8:149

    Content type: Research

    Published on:

  31. An amendment to this paper has been published and can be accessed via the original article.

    Authors: Oskar Modin, Raquel Liébana, Soroush Saheb-Alam, Britt-Marie Wilén, Carolina Suarez, Malte Hermansson and Frank Persson

    Citation: Microbiome 2020 8:148

    Content type: Correction

    Published on:

    The original article was published in Microbiome 2020 8:132

  32. Imbalances in the gut microbial community (dysbiosis) of vertebrates have been associated with several gastrointestinal and autoimmune diseases. However, it is unclear which taxa are associated with gut dysbio...

    Authors: Elin Videvall, Se Jin Song, Hanna M. Bensch, Maria Strandh, Anel Engelbrecht, Naomi Serfontein, Olof Hellgren, Adriaan Olivier, Schalk Cloete, Rob Knight and Charlie K. Cornwallis

    Citation: Microbiome 2020 8:147

    Content type: Research

    Published on:

  33. Kissing bugs (Triatominae) are blood-feeding insects best known as the vectors of Trypanosoma cruzi, the causative agent of Chagas’ disease. Considering the high epidemiological relevance of these vectors, their ...

    Authors: Joel J. Brown, Sonia M. Rodríguez-Ruano, Anbu Poosakkannu, Giampiero Batani, Justin O. Schmidt, Walter Roachell, Jan Zima Jr, Václav Hypša and Eva Nováková

    Citation: Microbiome 2020 8:146

    Content type: Research

    Published on:

  34. Interest in the interplay between host genetics and the gut microbiome in complex human diseases is increasing, with prior evidence mainly being derived from animal models. In addition, the shared and distinct...

    Authors: Fengzhe Xu, Yuanqing Fu, Ting-yu Sun, Zengliang Jiang, Zelei Miao, Menglei Shuai, Wanglong Gou, Chu-wen Ling, Jian Yang, Jun Wang, Yu-ming Chen and Ju-Sheng Zheng

    Citation: Microbiome 2020 8:145

    Content type: Research

    Published on:

  35. Viruses directly affect the most important biological processes in the ocean via their regulation of prokaryotic and eukaryotic populations. Marine sponges form stable symbiotic partnerships with a wide divers...

    Authors: Cecília Pascelli, Patrick W. Laffy, Emmanuelle Botté, Marija Kupresanin, Thomas Rattei, Miguel Lurgi, Timothy Ravasi and Nicole S. Webster

    Citation: Microbiome 2020 8:144

    Content type: Research

    Published on:

  36. “Western” style dietary patterns are characterized by a high proportion of highly processed foods rich in fat and low in fiber. This diet pattern is associated with a myriad of metabolic dysfunctions, includin...

    Authors: Hongli Shi, Yinghua Yu, Danhong Lin, Peng Zheng, Peng Zhang, Minmin Hu, Qiao Wang, Wei Pan, Xiaoying Yang, Tao Hu, Qianqian Li, Renxian Tang, Feng Zhou, Kuiyang Zheng and Xu-Feng Huang

    Citation: Microbiome 2020 8:143

    Content type: Research

    Published on:

  37. The soil mycobiome is composed of a complex and diverse fungal community, which includes functionally diverse species ranging from plant pathogens to mutualists. Among the latter are arbuscular mycorrhizal fun...

    Authors: Yuji Jiang, Lu Luan, Kaijie Hu, Manqiang Liu, Ziyun Chen, Stefan Geisen, Xiaoyun Chen, Huixin Li, Qinsong Xu, Michael Bonkowski and Bo Sun

    Citation: Microbiome 2020 8:142

    Content type: Research

    Published on:

  38. Despite the importance of the mucosal interface between microbiota and the host in gut homeostasis, little is known about the mechanisms of bacterial gut colonization, involving foraging for glycans produced b...

    Authors: Alexandra S. Tauzin, Mariana Rangel Pereira, Liisa D. Van Vliet, Pierre-Yves Colin, Elisabeth Laville, Jeremy Esque, Sandrine Laguerre, Bernard Henrissat, Nicolas Terrapon, Vincent Lombard, Marion Leclerc, Joël Doré, Florian Hollfelder and Gabrielle Potocki-Veronese

    Citation: Microbiome 2020 8:141

    Content type: Research

    Published on:

  39. The gut-brain axis and the intestinal microbiota are emerging as key players in health and disease. Shifts in intestinal microbiota composition affect a variety of systems; however, evidence of their direct im...

    Authors: Alfonsina D’Amato, Lorenzo Di Cesare Mannelli, Elena Lucarini, Angela L. Man, Gwenaelle Le Gall, Jacopo J. V. Branca, Carla Ghelardini, Amedeo Amedei, Eugenio Bertelli, Mari Regoli, Alessandra Pacini, Giulia Luciani, Pasquale Gallina, Annalisa Altera, Arjan Narbad, Massimo Gulisano…

    Citation: Microbiome 2020 8:140

    Content type: Research

    Published on:

  40. Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. L...

    Authors: Shawn P. Brown, Michael A. Grillo, Justin C. Podowski and Katy D. Heath

    Citation: Microbiome 2020 8:139

    Content type: Research

    Published on:

    The Correction to this article has been published in Microbiome 2021 9:105

  41. Undernutrition is a prevalent and spontaneous condition in animal production which always affects microbiota-host interaction in gastrointestinal tract. However, how undernutrition affects crosstalk homeostasi...

    Authors: Yanfeng Xue, Limei Lin, Fan Hu, Weiyun Zhu and Shengyong Mao

    Citation: Microbiome 2020 8:138

    Content type: Research

    Published on:

  42. Plant diseases caused by fungal pathogen result in a substantial economic impact on the global food and fruit industry. Application of organic fertilizers supplemented with biocontrol microorganisms (i.e. bioorga...

    Authors: Chengyuan Tao, Rong Li, Wu Xiong, Zongzhuan Shen, Shanshan Liu, Beibei Wang, Yunze Ruan, Stefan Geisen, Qirong Shen and George A. Kowalchuk

    Citation: Microbiome 2020 8:137

    Content type: Research

    Published on:

  43. Gonadal steroid hormones have been suggested as the underlying mechanism responsible for the sexual dimorphism observed in metabolic diseases. Animal studies have also evidenced a causal role of the gut microb...

    Authors: Jordi Mayneris-Perxachs, María Arnoriaga-Rodríguez, Diego Luque-Córdoba, Feliciano Priego-Capote, Vicente Pérez-Brocal, Andrés Moya, Aurelijus Burokas, Rafael Maldonado and José-Manuel Fernández-Real

    Citation: Microbiome 2020 8:136

    Content type: Research

    Published on:

  44. Shark Bay, Australia, harbours one of the most extensive and diverse systems of living microbial mats that are proposed to be analogs of some of the earliest ecosystems on Earth. These ecosystems have been sho...

    Authors: Hon Lun Wong, Fraser I. MacLeod, Richard Allen White III, Pieter T. Visscher and Brendan P. Burns

    Citation: Microbiome 2020 8:135

    Content type: Research

    Published on:

Annual Journal Metrics