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  1. Short-chain fatty acids (SCFAs) produced by the gut microbiota have beneficial anti-inflammatory and gut homeostasis effects and prevent type 1 diabetes (T1D) in mice. Reduced SCFA production indicates a loss ...

    Authors: Kirstine J. Bell, Sonia Saad, Bree J. Tillett, Helen M. McGuire, Sara Bordbar, Yu Anne Yap, Long T. Nguyen, Marc R. Wilkins, Susan Corley, Shannon Brodie, Sussan Duong, Courtney J. Wright, Stephen Twigg, Barbara Fazekas de St Groth, Leonard C. Harrison, Charles R. Mackay…
    Citation: Microbiome 2022 10:9
  2. Deep-sea hydrothermal vents represent unique ecosystems that redefine our understanding of the limits of life. They are widely distributed in deep oceans and typically form along mid-ocean ridges. To date, the...

    Authors: Jie Pan, Wei Xu, Zhichao Zhou, Zongze Shao, Chunming Dong, Lirui Liu, Zhuhua Luo and Meng Li
    Citation: Microbiome 2022 10:8

    The Correction to this article has been published in Microbiome 2022 10:40

  3. Coronal sulcus (CS) anaerobe abundance and IL-8 levels are linked to HIV acquisition, and are dramatically reduced after penile circumcision (PC). The distal urethra may be the site of some HIV acquisition bef...

    Authors: Ronald M. Galiwango, Daniel E. Park, Sanja Huibner, Abigail Onos, Maliha Aziz, Kelsey Roach, Aggrey Anok, James Nnamutete, Yahaya Isabirye, John Bosco Wasswa, Deo Male, Godfrey Kigozi, Aaron A. R. Tobian, Jessica L. Prodger, Cindy M. Liu and Rupert Kaul
    Citation: Microbiome 2022 10:7
  4. The lack of a definition of urinary microbiome health convolutes diagnosis of urinary tract infections (UTIs), especially when non-traditional uropathogens or paucity of bacteria are recovered from symptomatic...

    Authors: Boahemaa Adu-Oppong, Robert Thänert, Meghan A. Wallace, Carey-Ann D. Burnham and Gautam Dantas
    Citation: Microbiome 2022 10:6
  5. Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface eco...

    Authors: Kaela K. Amundson, Mikayla A. Borton, Rebecca A. Daly, David W. Hoyt, Allison Wong, Elizabeth Eder, Joseph Moore, Kenneth Wunch, Kelly C. Wrighton and Michael J. Wilkins
    Citation: Microbiome 2022 10:5

    The Correction to this article has been published in Microbiome 2022 10:30

  6. Metal corrosion in seawater has been extensively studied in surface and shallow waters. However, infrastructure is increasingly being installed in deep-sea environments, where extremes of temperature, salinity...

    Authors: Pauliina Rajala, Dong-Qiang Cheng, Scott A. Rice and Federico M. Lauro
    Citation: Microbiome 2022 10:4
  7. Host tp53 mutations are frequently found during the early stages of colitis-associated colorectal cancer (CAC), but whether such mutations induce gut microbiota dysbiosis and chronic intestinal inflammation that ...

    Authors: Jae-Geun Lee, Soohyun Lee, Juhee Jeon, Hyun Gi Kong, Hyun-Ju Cho, Jong-Hwan Kim, Seon-Young Kim, Myung Jin Oh, Daum Lee, Nari Seo, Ki Hun Park, Kweon Yu, Hyun Joo An, Choong-Min Ryu and Jeong-Soo Lee
    Citation: Microbiome 2022 10:3
  8. In ecology, population density is a key feature of community analysis. Yet in studies of the gut microbiome, bacterial density is rarely reported. Studies of hospitalized patients commonly use rectal swabs for...

    Authors: Rishi Chanderraj, Christopher A. Brown, Kevin Hinkle, Nicole Falkowski, Robert J. Woods and Robert P. Dickson
    Citation: Microbiome 2022 10:2
  9. Previous evidence indicates associations between the female reproductive tract microbiome composition and reproductive outcome in infertile patients undergoing assisted reproduction. We aimed to determine whet...

    Authors: Inmaculada Moreno, Iolanda Garcia-Grau, David Perez-Villaroya, Marta Gonzalez-Monfort, Mustafa Bahçeci, Marcelo J. Barrionuevo, Sagiri Taguchi, Elena Puente, Michael Dimattina, Mei Wei Lim, Georgina Meneghini, Mira Aubuchon, Mark Leondires, Alexandra Izquierdo, Martina Perez-Olgiati, Alejandro Chavez…
    Citation: Microbiome 2022 10:1
  10. 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
  11. Through connecting genomic and metabolic information, metaproteomics is an essential approach for understanding how microbiomes function in space and time. The international metaproteomics community is delight...

    Authors: Tim Van Den Bossche, Magnus Ø. Arntzen, Dörte Becher, Dirk Benndorf, Vincent G. H. Eijsink, Céline Henry, Pratik D. Jagtap, Nico Jehmlich, Catherine Juste, Benoit J. Kunath, Bart Mesuere, Thilo Muth, Phillip B. Pope, Jana Seifert, Alessandro Tanca, Sergio Uzzau…
    Citation: Microbiome 2021 9:243
  12. 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

  13. 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

  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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

  21. 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

  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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

  42. 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
  43. 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

  44. 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

  45. 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

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