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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. Methane is an end product of microbial fermentation in the human gastrointestinal tract. This gas is solely produced by an archaeal subpopulation of the human microbiome. Increased methane production has been ...

    Authors: Christina Kumpitsch, Florian Ph. S. Fischmeister, Alexander Mahnert, Sonja Lackner, Marilena Wilding, Corina Sturm, Anna Springer, Tobias Madl, Sandra Holasek, Christoph Högenauer, Ivan A. Berg, Veronika Schoepf and Christine Moissl-Eichinger
    Citation: Microbiome 2021 9:193
  12. Flavonoids are important plant secondary metabolites (PSMs) that have been widely used for their health-promoting effects. However, little is known about overall flavonoid metabolism and the interactive effect...

    Authors: Le Wang, Guangping Huang, Rong Hou, Dunwu Qi, Qi Wu, Yonggang Nie, Zhenqiang Zuo, Rui Ma, Wenliang Zhou, Yingjie Ma, Yibo Hu, Zhisong Yang, Li Yan and Fuwen Wei
    Citation: Microbiome 2021 9:192
  13. Biosurfactants are naturally derived products that play a similar role to synthetic dispersants in oil spill response but are easily biodegradable and less toxic. Using a combination of analytical chemistry, 1...

    Authors: Christina N. Nikolova, Umer Zeeshan Ijaz, Clayton Magill, Sara Kleindienst, Samantha B. Joye and Tony Gutierrez
    Citation: Microbiome 2021 9:191
  14. Coastal aquatic ecosystems include chemically distinct, but highly interconnected environments. Across a freshwater-to-marine transect, aquatic communities are exposed to large variations in salinity and nutri...

    Authors: Hwee Sze Tee, David Waite, Gavin Lear and Kim Marie Handley
    Citation: Microbiome 2021 9:190
  15. Increasing our knowledge of soil biodiversity is fundamental to forecast changes in ecosystem functions under global change scenarios. All multicellular organisms are now known to be holobionts, containing lar...

    Authors: Dong Zhu, Manuel Delgado-Baquerizo, Jing Ding, Michael R. Gillings and Yong-Guan Zhu
    Citation: Microbiome 2021 9:189
  16. Non-alcoholic liver disease (NAFLD) is the hepatic manifestation of metabolic syndrome, and it can progress to non-alcoholic steatohepatitis (NASH). Alterations in the gut microbiome have been implicated in th...

    Authors: Ryo Aoki, Masayoshi Onuki, Koya Hattori, Masato Ito, Takahiro Yamada, Kohei Kamikado, Yun-Gi Kim, Nobuhiro Nakamoto, Ikuo Kimura, Julie M. Clarke, Takanori Kanai and Koji Hase
    Citation: Microbiome 2021 9:188
  17. The plant microbiome is an integral part of the host and increasingly recognized as playing fundamental roles in plant growth and health. Increasing evidence indicates that plant rhizosphere recruits beneficia...

    Authors: Min Gao, Chao Xiong, Cheng Gao, Clement K. M. Tsui, Meng-Meng Wang, Xin Zhou, Ai-Min Zhang and Lei Cai
    Citation: Microbiome 2021 9:187
  18. Studies on the inhibition of inflammation by infection with helminth parasites have, until recently, overlooked a key determinant of health: the gut microbiota. Infection with helminths evokes changes in the c...

    Authors: Adam Shute, Blanca E. Callejas, ShuHua Li, Arthur Wang, Timothy S. Jayme, Christina Ohland, Ian A. Lewis, Brian T. Layden, André G. Buret and Derek M. McKay
    Citation: Microbiome 2021 9:186
  19. Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) have been suggested to prevent the development of metabolic disorders. However, their individual role in treating hyperglycemia and the mechanism of a...

    Authors: Pan Zhuang, Haoyu Li, Wei Jia, Qiyang Shou, Ya’er Zhu, Lei Mao, Wenqiao Wang, Fei Wu, Xiaoqian Chen, Xuzhi Wan, Yuqi Wu, Xiaohui Liu, Yin Li, Fanghuan Zhu, Lilin He, Jingnan Chen…
    Citation: Microbiome 2021 9:185
  20. Alteration of the gut microbiota may contribute to the development of inflammatory bowel disease (IBD). Epigallocatechin-3-gallate (EGCG), a major bioactive constituent of green tea, is known to be beneficial ...

    Authors: Zhenhua Wu, Shimeng Huang, Tiantian Li, Na Li, Dandan Han, Bing Zhang, Zhenjiang Zech Xu, Shiyi Zhang, Jiaman Pang, Shilan Wang, Guolong Zhang, Jiangchao Zhao and Junjun Wang
    Citation: Microbiome 2021 9:184
  21. P-glycoprotein (P-gp) plays a critical role in protection of the intestinal epithelia by mediating efflux of drugs/xenobiotics from the intestinal mucosa into the gut lumen. Recent studies bring to light that ...

    Authors: Sage E. Foley, Christine Tuohy, Merran Dunford, Michael J. Grey, Heidi De Luca, Caitlin Cawley, Rose L. Szabady, Ana Maldonado-Contreras, Jean Marie Houghton, Doyle V. Ward, Randall J. Mrsny and Beth A. McCormick
    Citation: Microbiome 2021 9:183
  22. Deep-sea animals in hydrothermal vents often form endosymbioses with chemosynthetic bacteria. Endosymbionts serve essential biochemical and ecological functions, but the prokaryotic viruses (phages) that deter...

    Authors: Kun Zhou, Ying Xu, Rui Zhang and Pei-Yuan Qian
    Citation: Microbiome 2021 9:182
  23. Identification of bacterial taxa associated with diseases, exposures, and other variables of interest offers a more comprehensive understanding of the role of microbes in many conditions. However, despite cons...

    Authors: Wodan Ling, Ni Zhao, Anna M. Plantinga, Lenore J. Launer, Anthony A. Fodor, Katie A. Meyer and Michael C. Wu
    Citation: Microbiome 2021 9:181
  24. Probiotics have been used to regulate the gut microbiota and physiology in various contexts, but their precise mechanisms of action remain unclear.

    Authors: Yue Xiao, Chao Yang, Leilei Yu, Fengwei Tian, Yarong Wu, Jianxin Zhao, Hao Zhang, Ruifu Yang, Wei Chen, Colin Hill, Yujun Cui and Qixiao Zhai
    Citation: Microbiome 2021 9:180
  25. The aquaculture sector now accounts for almost 50% of all fish for human consumption and is anticipated to provide 62% by 2030. Innovative strategies are being sought to improve fish feeds and feed additives t...

    Authors: Raminta Kazlauskaite, Bachar Cheaib, Chloe Heys, Umer Zeeshan Ijaz, Stephanie Connelly, William Sloan, Julie Russel, Laura Rubio, John Sweetman, Alex Kitts, Philip McGinnity, Philip Lyons and Martin Llewellyn
    Citation: Microbiome 2021 9:179
  26. Therapeutic and growth-promoting antibiotics are frequently used in broiler production. Indirect evidence indicates that these practices are linked to the proliferation of antimicrobial resistance (AMR), the s...

    Authors: Chhedi Lal Gupta, Shlomo E. Blum, Karuppasamy Kattusamy, Tali Daniel, Shelly Druyan, Roni Shapira, Oleg Krifucks, Yong-Guan Zhu, Xin-Yuan Zhou, Jian-Qiang Su and Eddie Cytryn
    Citation: Microbiome 2021 9:178
  27. The microbiota in the cecum of laying hens is crucial for host digestion, metabolism, and odor gas production. The results of recent studies have suggested that host microRNAs (miRNAs) can regulate gene expres...

    Authors: Si-Cheng Xing, Chun-Bo Huang, Rui-Ting Wu, Yi-Wen Yang, Jing-Yuan Chen, Jian-Dui Mi, Yin-Bao Wu, Yan Wang and Xin-Di Liao
    Citation: Microbiome 2021 9:177
  28. An Escherichia coli (E. coli) pathotype with invasive properties, first reported by Darfeuille-Michaud and termed adherent-invasive E. coli (AIEC), was shown to be prevalent in up to half the individuals with Cro...

    Authors: Grégoire Chevalier, Arnaud Laveissière, Guillaume Desachy, Nicolas Barnich, Adeline Sivignon, Marc Maresca, Cendrine Nicoletti, Eric Di Pasquale, Margarita Martinez-Medina, Kenneth William Simpson, Vijay Yajnik, Harry Sokol, Jonathan Plassais, Francesco Strozzi, Alessandra Cervino, Rachel Morra…
    Citation: Microbiome 2021 9:176
  29. Excessive fat accumulation of pigs is undesirable, as it severely affects economic returns in the modern pig industry. Studies in humans and mice have examined the role of the gut microbiome in host energy met...

    Authors: Congying Chen, Shaoming Fang, Hong Wei, Maozhang He, Hao Fu, Xinwei Xiong, Yunyan Zhou, Jinyuan Wu, Jun Gao, Hui Yang and Lusheng Huang
    Citation: Microbiome 2021 9:175
  30. The catabolic activity of the microbiota contributes to health by aiding in nutrition, immune education, and niche protection against pathogens. However, the nutrients consumed by common taxa within the gut mi...

    Authors: Connor R. Tiffany, Jee-Yon Lee, Andrew W. L. Rogers, Erin E. Olsan, Pavel Morales, Franziska Faber and Andreas J. Bäumler
    Citation: Microbiome 2021 9:174
  31. The determination of taxon-specific composition of microbiomes by combining high-throughput sequencing of ribosomal genes with phyloinformatic analyses has become routine in microbiology and allied sciences. S...

    Authors: Luis Gonzalez-de-Salceda and Ferran Garcia-Pichel
    Citation: Microbiome 2021 9:173
  32. Oceanic microbiomes play a pivotal role in the global carbon cycle and are central to the transformation and recycling of carbon and energy in the ocean’s interior. SAR324 is a ubiquitous but poorly understood...

    Authors: Dominique Boeuf, John M. Eppley, Daniel R. Mende, Rex R. Malmstrom, Tanja Woyke and Edward F. DeLong
    Citation: Microbiome 2021 9:172
  33. Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how host development impacts the assembly, functions and microbial interactions of crop mi...

    Authors: Chao Xiong, Brajesh K. Singh, Ji-Zheng He, Yan-Lai Han, Pei-Pei Li, Li-Hua Wan, Guo-Zhong Meng, Si-Yi Liu, Jun-Tao Wang, Chuan-Fa Wu, An-Hui Ge and Li-Mei Zhang
    Citation: Microbiome 2021 9:171
  34. Bogs are unique ecosystems inhabited by distinctive, coevolved assemblages of organisms, which play a global role for carbon storage, climate stability, water quality and biodiversity. To understand ecology an...

    Authors: Wisnu Adi Wicaksono, Tomislav Cernava, Christian Berg and Gabriele Berg
    Citation: Microbiome 2021 9:170
  35. Humans spend the bulk of their time in indoor environments. This space is shared with an indoor ecosystem of microorganisms, which are in continuous exchange with the human inhabitants. In the particular case ...

    Authors: Tilman E. Klassert, Rasmus Leistner, Cristina Zubiria-Barrera, Magdalena Stock, Mercedes López, Robert Neubert, Dominik Driesch, Petra Gastmeier and Hortense Slevogt
    Citation: Microbiome 2021 9:169
  36. Authors: Sharon A. Huws, Joan E. Edwards, Wanchang Lin, Francesco Rubino, Mark Alston, David Swarbreck, Shabhonam Caim, Pauline Rees Stevens, Justin Pachebat, Mi-Young Won, Linda B. Oyama, Christopher J. Creevey and Alison H. Kingston-Smith
    Citation: Microbiome 2021 9:168

    The original article was published in Microbiome 2021 9:143

  37. The gut microbiome changes in response to a range of environmental conditions, life events and disease states. Pregnancy is a natural life event that involves major physiological adaptation yet studies of the ...

    Authors: Alexandra J. Roth-Schulze, Megan A. S. Penno, Katrina M. Ngui, Helena Oakey, Esther Bandala-Sanchez, Alannah D. Smith, Theo R. Allnutt, Rebecca L. Thomson, Peter J. Vuillermin, Maria E. Craig, William D. Rawlinson, Elizabeth A. Davis, Mark Harris, Georgia Soldatos, Peter G. Colman, John M. Wentworth…
    Citation: Microbiome 2021 9:167
  38. Our understanding of the gut microbiota of animals is largely based on studies of mammals. To better understand the evolutionary basis of symbiotic relationships between animal hosts and indigenous microbes, i...

    Authors: Pil Soo Kim, Na-Ri Shin, Jae-Bong Lee, Min-Soo Kim, Tae Woong Whon, Dong-Wook Hyun, Ji-Hyun Yun, Mi-Ja Jung, Joon Yong Kim and Jin-Woo Bae
    Citation: Microbiome 2021 9:166
  39. A major bottleneck in the use of metagenome sequencing for human gut microbiome studies has been the lack of a comprehensive genome collection to be used as a reference database. Several recent efforts have be...

    Authors: Pranvera Hiseni, Knut Rudi, Robert C. Wilson, Finn Terje Hegge and Lars Snipen
    Citation: Microbiome 2021 9:165
  40. Authors: Hong Zheng, Pengtao Xu, Qiaoying Jiang, Qingqing Xu, Yafei Zheng, Junjie Yan, Hui Ji, Jie Ning, Xi Zhang, Chen Li, Limin Zhang, Yuping Li, Xiaokun Li, Weihong Song and Hongchang Gao
    Citation: Microbiome 2021 9:164

    The original article was published in Microbiome 2021 9:145

  41. Cervicovaginal bacterial communities composed of diverse anaerobes with low Lactobacillus abundance are associated with poor reproductive outcomes such as preterm birth, infertility, cervicitis, and risk of sexua...

    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 9:163

    The Correction to this article has been published in Microbiome 2021 9:206

  42. Feelings of hunger and satiety are the key determinants for maintaining the life of humans and animals. Disturbed appetite control may disrupt the metabolic health of the host and cause various metabolic disor...

    Authors: Hui Han, Bao Yi, Ruqing Zhong, Mengyu Wang, Shunfen Zhang, Jie Ma, Yulong Yin, Jie Yin, Liang Chen and Hongfu Zhang
    Citation: Microbiome 2021 9:162
  43. A foodborne pathogen, Vibrio vulnificus, encounters normal microflora inhabiting the gut environments prior to causing fatal septicemia or gastroenteritis and should overcome the barriers derived from the gut com...

    Authors: Jeong-A Kim, Bo-Ram Jang, Yu-Ra Kim, You-Chul Jung, Kun-Soo Kim and Kyu-Ho Lee
    Citation: Microbiome 2021 9:161
  44. Glacier ice archives information, including microbiology, that helps reveal paleoclimate histories and predict future climate change. Though glacier-ice microbes are studied using culture or amplicon approache...

    Authors: Zhi-Ping Zhong, Funing Tian, Simon Roux, M. Consuelo Gazitúa, Natalie E. Solonenko, Yueh-Fen Li, Mary E. Davis, James L. Van Etten, Ellen Mosley-Thompson, Virginia I. Rich, Matthew B. Sullivan and Lonnie G. Thompson
    Citation: Microbiome 2021 9:160
  45. Authors: Mateus B. Casaro, Andrew M. Thomas, Eduardo Mendes, Claudio Fukumori, Willian R. Ribeiro, Fernando A. Oliveira, Amanda R. Crisma, Gilson M. Murata, Bruna Bizzarro, Anderson Sá-Nunes, Joao C. Setubal, Marcia P. A. Mayer, Flaviano S. Martins, Angélica T. Vieira, Ana T. F. B. Antiorio, Wothan Tavares-de-Lima…
    Citation: Microbiome 2021 9:159

    The original article was published in Microbiome 2021 9:134

  46. This study focuses on the processes occurring during the acidogenic step of anaerobic digestion, especially resulting from nutritional interactions between dark fermentation (DF) bacteria and lactic acid bacte...

    Authors: Anna Detman, Daniel Laubitz, Aleksandra Chojnacka, Pawel R. Kiela, Agnieszka Salamon, Albert Barberán, Yongjian Chen, Fei Yang, Mieczysław K. Błaszczyk and Anna Sikora
    Citation: Microbiome 2021 9:158
  47. Autism spectrum disorders (ASD) are associated with dysregulation of the microbiota-gut-brain axis, changes in microbiota composition as well as in the fecal, serum, and urine levels of microbial metabolites. ...

    Authors: Patricia Bermudez-Martin, Jérôme A. J. Becker, Nicolas Caramello, Sebastian P. Fernandez, Renan Costa-Campos, Juliette Canaguier, Susana Barbosa, Laura Martinez-Gili, Antonis Myridakis, Marc-Emmanuel Dumas, Aurélia Bruneau, Claire Cherbuy, Philippe Langella, Jacques Callebert, Jean-Marie Launay, Joëlle Chabry…
    Citation: Microbiome 2021 9:157
  48. Manufacturing and resource industries are the key drivers for economic growth with a huge environmental cost (e.g. discharge of industrial effluents and post-mining substrates). Pollutants from waste streams, ...

    Authors: Obulisamy Parthiba Karthikeyan, Thomas J. Smith, Shamsudeen Umar Dandare, Kamaludeen Sara Parwin, Heetasmin Singh, Hui Xin Loh, Mark R Cunningham, Paul Nicholas Williams, Tim Nichol, Avudainayagam Subramanian, Kumarasamy Ramasamy and Deepak Kumaresan
    Citation: Microbiome 2021 9:156

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