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  1. Tropical members of the sponge genus Ircinia possess highly complex microbiomes that perform a broad spectrum of chemical processes that influence host fitness. Despite the pervasive role of microbiomes in Ircini...

    Authors: Joseph B. Kelly, David E. Carlson, Jun Siong Low and Robert W. Thacker
    Citation: Microbiome 2022 10:164
    Content type: Research Published on:

    The Correction to this article has been published in Microbiome 2022 10:182

  3. Mammalian intestinal microbiomes are necessary for antagonizing systemic viral infections. However, very few studies have identified whether poultry commensal bacteria play a crucial role in protecting against...

    Authors: Hai-chang Yin, Zhen-dong Liu, Wei-wei Zhang, Qing-zhu Yang, Tian-fei Yu and Xin-jie Jiang
    Citation: Microbiome 2022 10:162
    Content type: Research Published on:

  4. Microbial symbioses in marine invertebrates are commonplace. However, characterizations of invertebrate microbiomes are vastly outnumbered by those of vertebrates. Protists and fungi run the gamut of symbiosis...

    Authors: Corey C. Holt, Vittorio Boscaro, Niels W. L. Van Steenkiste, Maria Herranz, Varsha Mathur, Nicholas A. T. Irwin, Gracy Buckholtz, Brian S. Leander and Patrick J. Keeling
    Citation: Microbiome 2022 10:161
    Content type: Research Published on:

  5. Although the lack of estrogen receptor β (ERβ) is a risk factor for the development of inflammatory bowel disease (IBD) and psychiatric disorders, the underlying cellular and molecular mechanisms are not fully...

    Authors: Yuanyuan Ma, Tianyao Liu, Xin Li, Anqi Kong, Rui Xiao, Ruxin Xie, Junwei Gao, Zhongke Wang, Yun Cai, Jiao Zou, Ling Yang, Lian Wang, Jinghui Zhao, Haiwei Xu, Warner Margaret, Xingshun Xu…
    Citation: Microbiome 2022 10:160
    Content type: Research Published on:

  6. Tooth decay is one of the most prevalent diseases worldwide, and efficient tooth brushing with a fluoride-containing dentifrice is considered fundamental to caries prevention. Fluoride-containing dentifrices h...

    Authors: Miguel Carda-Diéguez, Rebecca Moazzez and Alex Mira
    Citation: Microbiome 2022 10:159
    Content type: Research Published on:

  7. The intestinal microbiota fundamentally guides the development of a normal intestinal physiology, the education, and functioning of the mucosal immune system. The Citrobacter rodentium-carrier model in germ-free ...

    Authors: Rossana Romero, Agnieszka Zarzycka, Mathieu Preussner, Florence Fischer, Torsten Hain, Jan-Paul Herrmann, Katrin Roth, Corinna U. Keber, Kushal Suryamohan, Hartmann Raifer, Maik Luu, Hanna Leister, Wilhelm Bertrams, Matthias Klein, Hosam Shams-Eldin, Ralf Jacob…
    Citation: Microbiome 2022 10:158
    Content type: Research Published on:

  8. DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in c...

    Authors: Hoon Je Seong, Simon Roux, Chung Yeon Hwang and Woo Jun Sul
    Citation: Microbiome 2022 10:157
    Content type: Research Published on:

  9. Many insects house symbiotic intracellular bacteria (endosymbionts) that provide them with essential nutrients, thus promoting the usage of nutrient-poor habitats. Endosymbiont seclusion within host specialize...

    Authors: Mariana Galvão Ferrarini, Elisa Dell’Aglio, Agnès Vallier, Séverine Balmand, Carole Vincent-Monégat, Sandrine Hughes, Benjamin Gillet, Nicolas Parisot, Anna Zaidman-Rémy, Cristina Vieira, Abdelaziz Heddi and Rita Rebollo
    Citation: Microbiome 2022 10:156
    Content type: Research Published on:

  10. The large intestine is a colonization site of beneficial microbes complementing the nutrition of cattle but also of zoonotic and animal pathogens. Here, we present the first global gene catalog of cattle fecal...

    Authors: S. Teseo, S. Otani, C. Brinch, S. Leroy, P. Ruiz, M. Desvaux, E. Forano, F. M. Aarestrup and P. Sapountzis
    Citation: Microbiome 2022 10:155
    Content type: Research Published on:

  11. Complex interactions between the gut microbiome and immune cells in infancy are thought to be part of the pathogenesis for the marked rise in pediatric allergic diseases, particularly food allergies. Food prot...

    Authors: Victoria M. Martin, Yamini V. Virkud, Ehud Dahan, Hannah L. Seay, Dvir Itzkovits, Hera Vlamakis, Ramnik Xavier, Wayne G. Shreffler, Qian Yuan and Moran Yassour
    Citation: Microbiome 2022 10:154
    Content type: Research Published on:

  12. Infectious diseases have caused huge economic loss and food security issues in fish aquaculture. Current management and breeding strategies heavily rely on the knowledge of regulative mechanisms underlying dis...

    Authors: Qian Zhou, Xue Zhu, Yangzhen Li, Pengshuo Yang, Shengpeng Wang, Kang Ning and Songlin Chen
    Citation: Microbiome 2022 10:153
    Content type: Research Published on:

  13. Pneumococcal carriage has often been studied from a serotype perspective; however, little is known about the strain-specific carriage and inter-strain interactions. Here, we examined the strain-level carriage ...

    Authors: Oluwaseun Rume-Abiola Oyewole, Philipp Latzin, Silvio D. Brugger and Markus Hilty
    Citation: Microbiome 2022 10:152
    Content type: Research Published on:

  14. The role of bacterial symbionts that populate octocorals (Cnidaria, Octocorallia) is still poorly understood. To shed light on their metabolic capacities, we examined 66 high-quality metagenome-assembled genom...

    Authors: Tina Keller-Costa, Lydia Kozma, Sandra G. Silva, Rodolfo Toscan, Jorge Gonçalves, Asunción Lago-Lestón, Nikos C. Kyrpides, Ulisses Nunes da Rocha and Rodrigo Costa
    Citation: Microbiome 2022 10:151
    Content type: Research Published on:

  15. Controlling excess biomass accumulation and clogging is important for maintaining the performance of gas biofilters and reducing energy consumption. Interruption of bacterial communication (quorum quenching) c...

    Authors: Yong-Chao Wang, Yu-Ting Lin, Can Wang, Zhen Tong, Xu-Rui Hu, Ya-Hui Lv, Guan-Yu Jiang, Meng-Fei Han, Ji-Guang Deng, Hsing-Cheng Hsi and Chung-Hak Lee
    Citation: Microbiome 2022 10:150
    Content type: Research Published on:

  16. The pathogenesis of inflammatory bowel diseases (IBD) is multifactorial, and diagnostic and treatment strategies for IBD remain to be developed. RhoB regulates multiple cell functions; however, its role in col...

    Authors: Jianming Yang, Geng Pei, Xuan Sun, Yawen Xiao, Chunhui Miao, Lu Zhou, Bangmao Wang, Liu Yang, Mingyu Yu, Zhi-Song Zhang, Evan T. Keller, Zhi Yao and Quan Wang
    Citation: Microbiome 2022 10:149
    Content type: Research Published on:

  17. In nature, microbial communities undergo changes in composition that threaten their resiliency. Here, we interrogated sourdough, a natural cereal-fermenting metacommunity, as a dynamic ecosystem in which playe...

    Authors: Francesco Maria Calabrese, Hana Ameur, Olga Nikoloudaki, Giuseppe Celano, Mirco Vacca, Wilson JFLemos Junior, Caterina Manzari, Fabienne Vertè, Raffaella Di Cagno, Graziano Pesole, Maria De Angelis and Marco Gobbetti
    Citation: Microbiome 2022 10:148
    Content type: Research Published on:

  18. The human gut is home to a largely underexplored microbiome component, the archaeome. Little is known of the impact of geography, urbanization, ethnicity, and diet on the gut archaeome in association with host...

    Authors: Xiaowu Bai, Yang Sun, Yue Li, Maojuan Li, Zhirui Cao, Ziyu Huang, Feng Zhang, Ping Yan, Lan Wang, Juan Luo, Jing Wu, Dejun Fan, Hongxia Chen, Min Zhi, Ping Lan, Zhong Zeng…
    Citation: Microbiome 2022 10:147
    Content type: Research Published on:

  19. Enteric methane emissions from dairy cows are an environmental problem as well as a gross feed energy loss to the animal. Methane is generated in the rumen by methanogenic archaea from hydrogen (H2) + carbon diox...

    Authors: Dipti W. Pitta, Nagaraju Indugu, Audino Melgar, Alexander Hristov, Krishna Challa, Bonnie Vecchiarelli, Meagan Hennessy, Kapil Narayan, Stephane Duval, Maik Kindermann and Nicola Walker
    Citation: Microbiome 2022 10:146
    Content type: Research Published on:

  20. The human mouth is a natural laboratory for studying how bacterial communities differ across habitats. Different bacteria colonize different surfaces in the mouth—teeth, tongue dorsum, and keratinized and non-...

    Authors: Viviana Morillo-Lopez, Alexandra Sjaarda, Imon Islam, Gary G. Borisy and Jessica L. Mark Welch
    Citation: Microbiome 2022 10:145
    Content type: Research Published on:

  21. Authors: Xingyu Ma, Tengxu Wang, Zhou Shi, Nona R. Chiariello, Kathryn Docherty, Christopher B. Field, Jessica Gutknecht, Qun Gao, Yunfu Gu, Xue Guo, Bruce A. Hungate, Jiesi Lei, Audrey Niboyet, Xavier Le Roux, Mengting Yuan, Tong Yuan…
    Citation: Microbiome 2022 10:144
    Content type: Correction Published on:

    The original article was published in Microbiome 2022 10:112

  24. Women with a cervicovaginal microbiota dominated by Lactobacillus spp. are at reduced risk of acquiring sexually transmitted infections including HIV, but the biological mechanisms involved remain poorly defined....

    Authors: David Jose Delgado-Diaz, Brianna Jesaveluk, Joshua A. Hayward, David Tyssen, Arghavan Alisoltani, Matthys Potgieter, Liam Bell, Elizabeth Ross, Arash Iranzadeh, Imane Allali, Smritee Dabee, Shaun Barnabas, Hoyam Gamieldien, Jonathan M. Blackburn, Nicola Mulder, Steven B. Smith…
    Citation: Microbiome 2022 10:141
    Content type: Research Published on:

  25. Symbiotic gut microbes have a rich genomic and metabolic pool and are closely related to hosts’ health. Traditional sequencing profiling masks the genomic and phenotypic diversity among strains from the same s...

    Authors: Yujie Meng, Shuang Li, Chong Zhang and Hao Zheng
    Citation: Microbiome 2022 10:140
    Content type: Research Published on:

  26. Post-weaning diarrhea in piglets reduces growth performance and increases mortality, thereby causing serious economic losses. The intestinal epithelial cells and microbiota reciprocally regulate each other in ...

    Authors: Bing Xia, Ruqing Zhong, Weida Wu, Chengzeng Luo, Qingshi Meng, Qingtao Gao, Yong Zhao, Liang Chen, Sheng Zhang, Xin Zhao and Hongfu Zhang
    Citation: Microbiome 2022 10:139
    Content type: Research Published on:

  27. Plant floral nectars contain natural sugars such as fructose, which are a primary energy resource for adult mosquitoes. Despite the importance of carbohydrates for mosquito metabolism, a limited knowledge is a...

    Authors: Morgane Guégan, Edwige Martin, Van Tran Van, Benjamin Fel, Anne-Emmanuelle Hay, Laurent Simon, Noémie Butin, Floriant Bellvert, Feth el Zahar Haichar and Claire Valiente Moro
    Citation: Microbiome 2022 10:138
    Content type: Research Published on:

  28. Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity m...

    Authors: Vincent Somerville, Thibault Schowing, Hélène Chabas, Remo S. Schmidt, Ueli von Ah, Rémy Bruggmann and Philipp Engel
    Citation: Microbiome 2022 10:137
    Content type: Research Published on:

  29. Probiotic use in preterm infants can mitigate the impact of antibiotic exposure and reduce rates of certain illnesses; however, the benefit on the gut resistome, the collection of antibiotic resistance genes, ...

    Authors: Allison K. Guitor, Efrah I. Yousuf, Amogelang R. Raphenya, Eileen K. Hutton, Katherine M. Morrison, Andrew G. McArthur, Gerard D. Wright and Jennifer C. Stearns
    Citation: Microbiome 2022 10:136
    Content type: Research Published on:

  30. Succinate is produced by both human cells and by gut bacteria and couples metabolism to inflammation as an extracellular signaling transducer. Circulating succinate is elevated in patients with obesity and typ...

    Authors: Isabel Huber-Ruano, Enrique Calvo, Jordi Mayneris-Perxachs, M-Mar Rodríguez-Peña, Victòria Ceperuelo-Mallafré, Lídia Cedó, Catalina Núñez-Roa, Joan Miro-Blanch, María Arnoriaga-Rodríguez, Aurélie Balvay, Claire Maudet, Pablo García-Roves, Oscar Yanes, Sylvie Rabot, Ghjuvan Micaelu Grimaud, Annachiara De Prisco…
    Citation: Microbiome 2022 10:135
    Content type: Research Published on:

  31. Antimicrobial resistance (AMR) has a detrimental impact on human health on Earth and it is equally concerning in other environments such as space habitat due to microgravity, radiation and confinement, especia...

    Authors: Pedro Madrigal, Nitin K. Singh, Jason M. Wood, Elena Gaudioso, Félix Hernández-del-Olmo, Christopher E. Mason, Kasthuri Venkateswaran and Afshin Beheshti
    Citation: Microbiome 2022 10:134
    Content type: Research Published on:

  32. Crohn’s disease (CD), an inflammatory bowel disease (IBD) subtype, results from pathologic interactions between host cells and its resident gut microbes. CD manifests in both isolated disease locations (ileum ...

    Authors: Carlos G. Gonzalez, Robert H. Mills, Qiyun Zhu, Consuelo Sauceda, Rob Knight, Parambir S. Dulai and David J. Gonzalez
    Citation: Microbiome 2022 10:133
    Content type: Research Published on:

  33. Small molecule metabolites produced by the microbiome are known to be neuroactive and are capable of directly impacting the brain and central nervous system, yet there is little data on the contribution of the...

    Authors: Victoria Rea, Ian Bell, Taylor Ball and Terence Van Raay
    Citation: Microbiome 2022 10:132
    Content type: Research Published on:

  34. Top-soil microbiomes make a vital contribution to the Earth’s ecology and harbor an extraordinarily high biodiversity. They are also key players in many ecosystem services, particularly in arid regions of the ...

    Authors: DA Cowan, PH Lebre, CER Amon, RW Becker, HI Boga, A Boulangé, TL Chiyaka, T Coetzee, PC de Jager, O Dikinya, F Eckardt, M Greve, MA Harris, DW Hopkins, HB Houngnandan, P Houngnandan…
    Citation: Microbiome 2022 10:131
    Content type: Research Published on:

  36. The increasing prevalence of resistance against the last-resort antibiotic colistin is a significant threat to global public health. Here, we discovered a novel colistin resistance mechanism via enzymatic inac...

    Authors: Do-Hoon Lee, Ju-Hee Cha, Dae-Wi Kim, Kihyun Lee, Yong-Seok Kim, Hyo-Young Oh, You-Hee Cho and Chang-Jun Cha
    Citation: Microbiome 2022 10:129
    Content type: Research Published on:

  37. As important producers using photosynthesis on Earth, cyanobacteria contribute to the oxygenation of atmosphere and the primary production of biosphere. However, due to the eutrophication of urban waterbodies ...

    Authors: Kang Du, Feng Yang, Jun-Tao Zhang, Rong-Cheng Yu, Ziqing Deng, Wei-Fang Li, Yuxing Chen, Qiong Li and Cong-Zhao Zhou
    Citation: Microbiome 2022 10:128
    Content type: Research Published on:

  38. The emergence of antimicrobial resistance is a major threat to global health and has placed pressure on the livestock industry to eliminate the use of antibiotic growth promotants (AGPs) as feed additives. To ...

    Authors: Angela Zou, Kerry Nadeau, Xuejian Xiong, Pauline W. Wang, Julia K. Copeland, Jee Yeon Lee, James St. Pierre, Maxine Ty, Billy Taj, John H. Brumell, David S. Guttman, Shayan Sharif, Doug Korver and John Parkinson
    Citation: Microbiome 2022 10:127
    Content type: Research Published on:

  39. Microorganisms in the seafloor use a wide range of metabolic processes, which are coupled to the presence of functional genes within their genomes. Aquatic environments are heterogenous and often characterized...

    Authors: Elias Broman, Dandan Izabel-Shen, Alejandro Rodríguez-Gijón, Stefano Bonaglia, Sarahi L. Garcia and Francisco J. A. Nascimento
    Citation: Microbiome 2022 10:126
    Content type: Research Published on:

  40. The viral community has the potential to influence the structure of the microbiome and thus the yield of the anaerobic digestion process. However, the virome composition in anaerobic digestion is still under-i...

    Authors: Alessandro Rossi, Maria Silvia Morlino, Maria Gaspari, Arianna Basile, Panagiotis Kougias, Laura Treu and Stefano Campanaro
    Citation: Microbiome 2022 10:125
    Content type: Research Published on:

  41. Horizontal gene transfer (HGT) plays a critical role in the spread of antibiotic resistance and the evolutionary shaping of bacterial communities. Conjugation is the most well characterized pathway for the spr...

    Authors: Yue Wang, Zhigang Yu, Pengbo Ding, Ji Lu, Uli Klümper, Aimee K. Murray, William H. Gaze and Jianhua Guo
    Citation: Microbiome 2022 10:124
    Content type: Research Published on:

  42. Effective standardisation of the microbiome field is essential to facilitate global translational research and increase the reproducibility of microbiome studies. In this study, we describe the development and...

    Authors: Chrysi Sergaki, Saba Anwar, Martin Fritzsche, Ryan Mate, Robert J. Francis, Kirsty MacLellan-Gibson, Alastair Logan and Gregory C. A. Amos
    Citation: Microbiome 2022 10:123
    Content type: Research Published on:

  43. Hyperglycaemia in pregnancy (HIP) is a common metabolic disorder that not only poses risks to maternal health but also associates with an increased risk of diabetes among offspring. Vertical transmission of mi...

    Authors: Cunxi Xue, Qinyuan Xie, Chenhong Zhang, Yimeng Hu, Xiaoting Song, Yifan Jia, Xiaoyang Shi, Yiqi Chen, Yalei Liu, Lingyun Zhao, Fenglian Huang and Huijuan Yuan
    Citation: Microbiome 2022 10:122
    Content type: Research Published on:

  44. With the rapid accumulation of microbiome-wide association studies, a great amount of microbiome data are available to study the microbiome’s role in human disease and advance the microbiome’s potential use fo...

    Authors: Chan Wang, Leopoldo N. Segal, Jiyuan Hu, Boyan Zhou, Richard B. Hayes, Jiyoung Ahn and Huilin Li
    Citation: Microbiome 2022 10:121
    Content type: Methodology Published on:

  45. Ixodes ricinus ticks vector pathogens that cause serious health concerns. Like in other arthropods, the microbiome may affect the tick’s biology, with consequences for pathogen transmission. Here, we explored th...

    Authors: Aleksandra I. Krawczyk, Lisa Röttjers, Manoj Fonville, Katshuisa Takumi, Willem Takken, Karoline Faust and Hein Sprong
    Citation: Microbiome 2022 10:120
    Content type: Research Published on:

  46. The cervicovaginal (CV) microbiome is highly associated with vaginal health and disease in both pregnant and nonpregnant individuals. An overabundance of Gardnerella vaginalis (G. vaginalis) in the CV space is co...

    Authors: Lauren Anton, Briana Ferguson, Elliot S. Friedman, Kristin D. Gerson, Amy G. Brown and Michal A. Elovitz
    Citation: Microbiome 2022 10:119
    Content type: Research Published on:

  47. Antimicrobials are used in food-producing animals for purposes of preventing, controlling, and/or treating infections. In swine, a major driver of antimicrobial use is porcine reproductive and respiratory synd...

    Authors: Tara N. Gaire, Carissa Odland, Bingzhou Zhang, Tui Ray, Enrique Doster, Joel Nerem, Scott Dee, Peter Davies and Noelle Noyes
    Citation: Microbiome 2022 10:118
    Content type: Research Published on:

  48. Carbon fixation through biological methanation has emerged as a promising technology to produce renewable energy in the context of the circular economy. The anaerobic digestion microbiome is the fundamental bi...

    Authors: Nicola De Bernardini, Arianna Basile, Guido Zampieri, Adam Kovalovszki, Beatrix De Diego Diaz, Elisabetta Offer, Nantharat Wongfaed, Irini Angelidaki, Panagiotis G. Kougias, Stefano Campanaro and Laura Treu
    Citation: Microbiome 2022 10:117
    Content type: Research Published on:

  50. Disease resistance phenotypes are associated with immune regulatory functions and immune tolerance and have implications for both the livestock industry and human health. Microbiota plays an essential role in ...

    Authors: Xuan Zhao, Lin Jiang, Xiuyu Fang, Zhiqiang Guo, Xiaoxu Wang, Baoming Shi and Qingwei Meng
    Citation: Microbiome 2022 10:115
    Content type: Research Published on:
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