Skip to main content

Articles

Page 3 of 26

  1. Plants in nature interact with other species, among which are mutualistic microorganisms that affect plant health. The co-existence of microbial symbionts with the host contributes to host fitness in a natural...

    Authors: Da-Ran Kim, Chang-Wook Jeon, Gyeongjun Cho, Linda S. Thomashow, David M. Weller, Man-Jeong Paik, Yong Bok Lee and Youn-Sig Kwak
    Citation: Microbiome 2021 9:244
  2. Authors: Anneliek M. ter Horst, Christian Santos-Medellín, Jackson W. Sorensen, Laura A. Zinke, Rachel M. Wilson, Eric R. Johnston, Gareth Trubl, Jennifer Pett-Ridge, Steven J. Blazewicz, Paul J. Hanson, Jeffrey P. Chanton, Christopher W. Schadt, Joel E. Kostka and Joanne B. Emerson
    Citation: Microbiome 2021 9:242

    The original article was published in Microbiome 2021 9:233

  3. The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We,...

    Authors: Imane Allali, Regina E. Abotsi, Lemese Ah. Tow, Lehana Thabane, Heather J. Zar, Nicola M. Mulder and Mark P. Nicol
    Citation: Microbiome 2021 9:241

    The Correction to this article has been published in Microbiome 2022 10:10

  4. The gut microbiota is associated with diverse age-related disorders. Several rejuvenation methods, such as probiotic administration and faecal microbiota transplantation, have been applied to alter the gut mic...

    Authors: Jongoh Shin, Jung-Ran Noh, Donghui Choe, Namil Lee, Yoseb Song, Suhyung Cho, Eun-Jung Kang, Min-Jeong Go, Seok Kyun Ha, Dong-Ho Chang, Jae-Hoon Kim, Yong-Hoon Kim, Kyoung-Shim Kim, Haiyoung Jung, Myung Hee Kim, Bong-Hyun Sung…
    Citation: Microbiome 2021 9:240
  5. Men who have sex with men (MSM) have been disproportionately affected by HIV-1 since the beginning of the AIDS pandemic, particularly in the USA and Europe. Compared to men who have sex with women (MSW), MSM h...

    Authors: Yue Chen, Huang Lin, Mariah Cole, Alison Morris, Jeremy Martinson, Heather Mckay, Matthew Mimiaga, Joseph Margolick, Adam Fitch, Barbara Methe, Vatsala Rangachar Srinivas, Shyamal Peddada and Charles R. Rinaldo
    Citation: Microbiome 2021 9:237
  6. The Spacecraft Assembly Facility (SAF) at the NASA’s Jet Propulsion Laboratory is the primary cleanroom facility used in the construction of some of the planetary protection (PP)-sensitive missions developed b...

    Authors: Ryan Hendrickson, Camilla Urbaniak, Jeremiah J. Minich, Heidi S. Aronson, Cameron Martino, Ramunas Stepanauskas, Rob Knight and Kasthuri Venkateswaran
    Citation: Microbiome 2021 9:238
  7. There is growing recognition that bidirectional signaling between the digestive tract and the brain contributes to irritable bowel syndrome (IBS). We recently showed in a large randomized controlled trial that...

    Authors: Jonathan P. Jacobs, Arpana Gupta, Ravi R. Bhatt, Jacob Brawer, Kan Gao, Kirsten Tillisch, Venu Lagishetty, Rebecca Firth, Gregory D. Gudleski, Benjamin M. Ellingson, Jennifer S. Labus, Bruce D. Naliboff, Jeffrey M. Lackner and Emeran A. Mayer
    Citation: Microbiome 2021 9:236
  8. Communication between the gut microbiota and the brain is primarily mediated via soluble microbe-derived metabolites, but the details of this pathway remain poorly defined. Methylamines produced by microbial m...

    Authors: Lesley Hoyles, Matthew G. Pontifex, Ildefonso Rodriguez-Ramiro, M. Areeb Anis-Alavi, Khadija S. Jelane, Tom Snelling, Egle Solito, Sonia Fonseca, Ana L. Carvalho, Simon R. Carding, Michael Müller, Robert C. Glen, David Vauzour and Simon McArthur
    Citation: Microbiome 2021 9:235
  9. The hyperarid core of the Atacama Desert is an extremely harsh environment thought to be colonized by only a few heterotrophic bacterial species. Current concepts for understanding this extreme ecosystem are m...

    Authors: Yunha Hwang, Dirk Schulze-Makuch, Felix L. Arens, Johan S. Saenz, Panagiotis S. Adam, Christof Sager, Till L. V. Bornemann, Weishu Zhao, Ying Zhang, Alessandro Airo, Michael Schloter and Alexander J. Probst
    Citation: Microbiome 2021 9:234
  10. Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for vir...

    Authors: Anneliek M. ter Horst, Christian Santos-Medellín, Jackson W. Sorensen, Laura A. Zinke, Rachel M. Wilson, Eric R. Johnston, Gareth Trubl, Jennifer Pett-Ridge, Steven J. Blazewicz, Paul J. Hanson, Jeffrey P. Chanton, Christopher W. Schadt, Joel E. Kostka and Joanne B. Emerson
    Citation: Microbiome 2021 9:233

    The Correction to this article has been published in Microbiome 2022 10:17

    The Correction to this article has been published in Microbiome 2021 9:242

  11. Ecological interactions among microorganisms are fundamental for ecosystem function, yet they are mostly unknown or poorly understood. High-throughput-omics can indicate microbial interactions through associat...

    Authors: Ina Maria Deutschmann, Gipsi Lima-Mendez, Anders K. Krabberød, Jeroen Raes, Sergio M. Vallina, Karoline Faust and Ramiro Logares
    Citation: Microbiome 2021 9:232

    The Correction to this article has been published in Microbiome 2021 9:245

  12. In Antarctica, summer sunlight enables phototrophic microorganisms to drive primary production, thereby “feeding” ecosystems to enable their persistence through the long, dark winter months. In Ace Lake, a str...

    Authors: Pratibha Panwar, Michelle A. Allen, Timothy J. Williams, Sabrina Haque, Sarah Brazendale, Alyce M. Hancock, David Paez-Espino and Ricardo Cavicchioli
    Citation: Microbiome 2021 9:231
  13. The microbiome affects the health of plants and animals, including humans, and has many biological, ecological, and evolutionary consequences. Microbiome studies typically rely on sequencing ribosomal 16S RNA ...

    Authors: Kevin Xu Zhong, Anna Cho, Christoph M. Deeg, Amy M. Chan and Curtis A. Suttle
    Citation: Microbiome 2021 9:230
  14. Carbohydrate-active enzymes (CAZymes) form the most widespread and structurally diverse set of enzymes involved in the breakdown, biosynthesis, or modification of lignocellulose that can be found in living org...

    Authors: André L. A. Neves, Jiangkun Yu, Yutaka Suzuki, Marisol Baez-Magana, Elena Arutyunova, Eóin O’Hara, Tim McAllister, Kim H. Ominski, M. Joanne Lemieux and Le Luo Guan
    Citation: Microbiome 2021 9:229
  15. Mesenteric adipose tissue (mAT) hyperplasia, known as creeping fat is a pathologic characteristic of Crohn’s disease (CD). The reserve of creeping fat in surgery is associated with poor prognosis of CD patient...

    Authors: Zhen He, Jinjie Wu, Junli Gong, Jia Ke, Tao Ding, Wenjing Zhao, Wai Ming Cheng, Zhanhao Luo, Qilang He, Wanyi Zeng, Jing Yu, Na Jiao, Yanmin Liu, Bin Zheng, Lei Dai, Min Zhi…
    Citation: Microbiome 2021 9:228
  16. Low dietary fiber intake has been shown to disturb the gut microbiome community, damage the mucus barrier, and promote pathogen susceptibility. However, little is known about the temporal response of the gut m...

    Authors: Zhenyu Wang, Yu Bai, Yu Pi, Walter J. J. Gerrits, Sonja de Vries, Lijun Shang, Shiyu Tao, Shiyi Zhang, Dandan Han, Zhengpeng Zhu and Junjun Wang
    Citation: Microbiome 2021 9:227
  17. Parkinson’s disease (PD) is a prevalent neurodegenerative disorder, displaying not only well-known motor deficits but also gastrointestinal dysfunctions. Consistently, it has been increasingly evident that gut...

    Authors: Zhe Zhao, Jingwen Ning, Xiu-qi Bao, Meiyu Shang, Jingwei Ma, Gen Li and Dan Zhang
    Citation: Microbiome 2021 9:226
  18. Honey bee gut microbiota transmitted via social interactions are beneficial to the host health. Although the microbial community is relatively stable, individual variations and high strain-level diversity have...

    Authors: Jiaqiang Wu, Haoyu Lang, Xiaohuan Mu, Zijing Zhang, Qinzhi Su, Xiaosong Hu and Hao Zheng
    Citation: Microbiome 2021 9:225
  19. Male fertility impaired by exogenous toxins is a serious worldwide issue threatening the health of the new-born and causing infertility. However, the metabolic connection between toxic exposures and testicular...

    Authors: Qi Zhao, Jian-Feng Huang, Yan Cheng, Man-Yun Dai, Wei-Feng Zhu, Xiu-Wei Yang, Frank J. Gonzalez and Fei Li
    Citation: Microbiome 2021 9:224
  20. Cognitive impairment, an increasing mental health issue, is a core feature of the aging brain and neurodegenerative diseases. Industrialized nations especially, have experienced a marked decrease in dietary fi...

    Authors: Hongli Shi, Xing Ge, Xi Ma, Mingxuan Zheng, Xiaoying Cui, Wei Pan, Peng Zheng, Xiaoying Yang, Peng Zhang, Minmin Hu, Tao Hu, Renxian Tang, Kuiyang Zheng, Xu-Feng Huang and Yinghua Yu
    Citation: Microbiome 2021 9:223
  21. Children spend considerable time in daycare centers in parts of the world and are exposed to the indoor micro- and mycobiomes of these facilities. The level of exposure to microorganisms varies within and betw...

    Authors: Eva Lena F. Estensmo, Luis Morgado, Sundy Maurice, Pedro M. Martin-Sanchez, Ingeborg B. Engh, Johan Mattsson, Håvard Kauserud and Inger Skrede
    Citation: Microbiome 2021 9:220
  22. Fructo-oligosaccharides (FOS), inulin, and galacto-oligosaccharides (GOS) are widely recognized prebiotics that profoundly affect the intestinal microbiota, including stimulation of bifidobacteria and lactobac...

    Authors: Jori Fuhren, Markus Schwalbe, Jos Boekhorst, Christiane Rösch, Henk A. Schols and Michiel Kleerebezem
    Citation: Microbiome 2021 9:218
  23. Plant health and growth are negatively affected by pathogen invasion; however, plants can dynamically modulate their rhizosphere microbiome and adapt to such biotic stresses. Although plant-recruited protectiv...

    Authors: Zhefei Li, Xiaoli Bai, Shuo Jiao, Yanmei Li, Peirong Li, Yan Yang, Hui Zhang and Gehong Wei
    Citation: Microbiome 2021 9:217
  24. Microbial acquisition and development of the gut microbiota impact the establishment of a healthy host-microbes symbiosis. Compared with other animals, the eusocial bumblebees and honeybees possess a simple, r...

    Authors: Qinzhi Su, Qinglin Wang, Xiaohuan Mu, Hao Chen, Yujie Meng, Xue Zhang, Li Zheng, Xiaosong Hu, Yifan Zhai and Hao Zheng
    Citation: Microbiome 2021 9:216
  25. The gut microbiome is altered in patients with inflammatory bowel disease, yet how these alterations contribute to intestinal inflammation is poorly understood. Murine models have demonstrated the importance o...

    Authors: Amy M. Tsou, Jeremy A. Goettel, Bin Bao, Amlan Biswas, Yu Hui Kang, Naresh S. Redhu, Kaiyue Peng, Gregory G. Putzel, Jeffrey Saltzman, Ryan Kelly, Jordan Gringauz, Jared Barends, Mai Hatazaki, Sandra M. Frei, Rohini Emani, Ying Huang…
    Citation: Microbiome 2021 9:215
  26. Upper gastrointestinal (GI) disorders and abdominal pain afflict between 12 and 30% of the worldwide population and research suggests these conditions are linked to the gut microbiome. Although large-intestine...

    Authors: Jacob T. Barlow, Gabriela Leite, Anna E. Romano, Rashin Sedighi, Christine Chang, Shreya Celly, Ali Rezaie, Ruchi Mathur, Mark Pimentel and Rustem F. Ismagilov
    Citation: Microbiome 2021 9:214
  27. Studies of the microbiomes on surfaces in built environment have largely focused on indoor spaces, while outdoor spaces have received far less attention. Piers are engineered infrastructures commonly found in ...

    Authors: Xinzhao Tong, Marcus H. Y. Leung, Zhiyong Shen, Justin Y. Y. Lee, Christopher E. Mason and Patrick K. H. Lee
    Citation: Microbiome 2021 9:213
  28. Nitrogen-fixing prokaryotes (diazotrophs) contribute substantially to nitrogen input in mangrove sediments, and their structure and nitrogen fixation rate (NFR) are significantly controlled by environmental co...

    Authors: Zhiwen Luo, Qiuping Zhong, Xingguo Han, Ruiwen Hu, Xingyu Liu, Wenjun Xu, Yongjie Wu, Weiming Huang, Zhengyuan Zhou, Wei Zhuang, Qingyun Yan, Zhili He and Cheng Wang
    Citation: Microbiome 2021 9:212
  29. The magnitude of microbiota perturbations after exposure to antibiotics varies among individuals. It has been suggested that the composition of pre-treatment microbiota underpins personalized responses to anti...

    Authors: Armin Rashidi, Maryam Ebadi, Tauseef Ur Rehman, Heba Elhusseini, Harika Nalluri, Thomas Kaiser, Shernan G. Holtan, Alexander Khoruts, Daniel J. Weisdorf and Christopher Staley
    Citation: Microbiome 2021 9:211
  30. The intestinal microbiota plays an important role in regulating gastrointestinal (GI) physiology in part through interactions with the enteric nervous system (ENS). Alterations in the gut microbiome frequently...

    Authors: Fernando A. Vicentini, Catherine M. Keenan, Laurie E. Wallace, Crystal Woods, Jean-Baptiste Cavin, Amanda R. Flockton, Wendy B. Macklin, Jaime Belkind-Gerson, Simon A. Hirota and Keith A. Sharkey
    Citation: Microbiome 2021 9:210
  31. Microbes can grow in indoor environments if moisture is available, and we need an improved understanding of how this growth contributes to emissions of microbial volatile organic compounds (mVOCs). The goal of...

    Authors: Sarah R. Haines, Emma C. Hall, Katarzyna Marciniak, Pawel K. Misztal, Allen H. Goldstein, Rachel I. Adams and Karen C. Dannemiller
    Citation: Microbiome 2021 9:209

    The Correction to this article has been published in Microbiome 2021 9:219

  32. Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling vi...

    Authors: Gareth Trubl, Jeffrey A. Kimbrel, Jose Liquet-Gonzalez, Erin E. Nuccio, Peter K. Weber, Jennifer Pett-Ridge, Janet K. Jansson, Mark P. Waldrop and Steven J. Blazewicz
    Citation: Microbiome 2021 9:208
  33. Dimethyl sulfide (DMS) is the dominant volatile organic sulfur in global oceans. The predominant source of oceanic DMS is the cleavage of dimethylsulfoniopropionate (DMSP), which can be produced by marine bact...

    Authors: Zhao-Jie Teng, Qi-Long Qin, Weipeng Zhang, Jian Li, Hui-Hui Fu, Peng Wang, Musheng Lan, Guangfu Luo, Jianfeng He, Andrew McMinn, Min Wang, Xiu-Lan Chen, Yu-Zhong Zhang, Yin Chen and Chun-Yang Li
    Citation: Microbiome 2021 9:207

    The Correction to this article has been published in Microbiome 2021 9:221

  34. Authors: Alexander Munoz, Matthew R. Hayward, Seth M. Bloom, Muntsa Rocafort, Sinaye Ngcapu, Nomfuneko A. Mafunda, Jiawu Xu, Nondumiso Xulu, Mary Dong, Krista L. Dong, Nasreen Ismail, Thumbi Ndung’u, Musie S. Ghebremichael and Douglas S. Kwon
    Citation: Microbiome 2021 9:206

    The original article was published in Microbiome 2021 9:163

  35. Long-read sequencing has shown its tremendous potential to address genome assembly challenges, e.g., achieving the first telomere-to-telomere assembly of a gapless human chromosome. However, many issues remain...

    Authors: Lei Liu, Yulin Wang, Yu Yang, Depeng Wang, Suk Hang Cheng, Chunmiao Zheng and Tong Zhang
    Citation: Microbiome 2021 9:205
  36. The microorganisms that inhabit food processing environments (FPE) can strongly influence the associated food quality and safety. In particular, the possibility that FPE may act as a reservoir of antibiotic-re...

    Authors: José F. Cobo-Díaz, Adrián Alvarez-Molina, Elena A. Alexa, Calum J. Walsh, Oscar Mencía-Ares, Paula Puente-Gómez, Eleni Likotrafiti, Paula Fernández-Gómez, Bernardo Prieto, Fiona Crispie, Lorena Ruiz, Montserrat González-Raurich, Mercedes López, Miguel Prieto, Paul Cotter and Avelino Alvarez-Ordóñez
    Citation: Microbiome 2021 9:204
  37. Obtaining high-quality (HQ) reference genomes from microbial communities is crucial for understanding the phylogeny and function of uncultured microbes in complex microbial ecosystems. Despite improvements in ...

    Authors: Koji Arikawa, Keigo Ide, Masato Kogawa, Tatsuya Saeki, Takuya Yoda, Taruho Endoh, Ayumi Matsuhashi, Haruko Takeyama and Masahito Hosokawa
    Citation: Microbiome 2021 9:202
  38. Although considered as holobionts, macroalgae and their surface microbiota share intimate interactions that are still poorly understood. Little is known on the effect of environmental parameters on the close r...

    Authors: Benoît Paix, Nicolas Layglon, Christophe Le Poupon, Sébastien D’Onofrio, Benjamin Misson, Cédric Garnier, Gérald Culioli and Jean-François Briand
    Citation: Microbiome 2021 9:201
  39. The development of suppressive soils is a promising strategy to protect plants against soil-borne diseases in a sustainable and viable manner. The use of crop rotation and the incorporation of plant residues i...

    Authors: Xianfu Yuan, Shan Hong, Wu Xiong, Waseem Raza, Zongzhuan Shen, Beibei Wang, Rong Li, Yunze Ruan, Qirong Shen and Francisco Dini-Andreote
    Citation: Microbiome 2021 9:200
  40. Microbial communities in both natural and applied settings reliably carry out myriads of functions, yet how stable these taxonomically diverse assemblages can be and what causes them to transition between stat...

    Authors: Yulin Wang, Jun Ye, Feng Ju, Lei Liu, Joel A. Boyd, Yu Deng, Donovan H. Parks, Xiaotao Jiang, Xiaole Yin, Ben J. Woodcroft, Gene W. Tyson, Philip Hugenholtz, Martin F. Polz and Tong Zhang
    Citation: Microbiome 2021 9:199
  41. Intestinal Peyer’s patches (PPs) form unique niches for bacteria-immune cell interactions that direct host immunity and shape the microbiome. Here we investigate how peroral administration of probiotic bacterium

    Authors: Hao-Yu Liu, Antoine Giraud, Cedric Seignez, David Ahl, Feilong Guo, John Sedin, Tomas Walden, Jee-Hwan Oh, Jan Peter van Pijkeren, Lena Holm, Stefan Roos, Stefan Bertilsson and Mia Phillipson
    Citation: Microbiome 2021 9:198
  42. Dental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are thus an important source of information regarding o...

    Authors: Lena Granehäll, Kun D. Huang, Adrian Tett, Paolo Manghi, Alice Paladin, Niall O’Sullivan, Omar Rota-Stabelli, Nicola Segata, Albert Zink and Frank Maixner
    Citation: Microbiome 2021 9:197
  43. The ubiquitous gut microbiotas acquired from the environment contribute to host health. The gut microbiotas of soil invertebrates are gradually assembled from the microecological region of the soil ecosystem w...

    Authors: Qi Zhang, Zhenyan Zhang, Tao Lu, Yitian Yu, Josep Penuelas, Yong-Guan Zhu and Haifeng Qian
    Citation: Microbiome 2021 9:196
  44. Soil and sediment microorganisms are highly phylogenetically diverse but are currently largely under-represented in public molecular databases. Their functional characterization by means of metaproteomics is u...

    Authors: Virginie Jouffret, Guylaine Miotello, Karen Culotta, Sophie Ayrault, Olivier Pible and Jean Armengaud
    Citation: Microbiome 2021 9:195
  45. Cyanobacteria from the genus Microcystis can form large mucilaginous colonies with attached heterotrophic bacteria—their microbiome. However, the nature of the relationship between Microcystis and its microbiome ...

    Authors: Olga M. Pérez-Carrascal, Nicolas Tromas, Yves Terrat, Elisa Moreno, Alessandra Giani, Laisa Corrêa Braga Marques, Nathalie Fortin and B. Jesse Shapiro
    Citation: Microbiome 2021 9:194

Annual Journal Metrics