How can we define “optimal microbiota?”: a comparative review of structure and functions of microbiota of animals, fish, and plants in agriculture

Ikeda-Ohtsubo, Wakako, Brugman, Sylvia, Warden, Craig H., Rebel, Johanna M. J., Folkerts, Gert, Pieterse, Corné M. J.·2018·Frontiers in Nutrition

Cites (260)

Items 201–262 of 262

  1. Microbial small molecules – weapons of plant subversion
    Ioannis A. Stringlis, Hao Zhang, Corné M. J. Pieterse, Melvin D. Bolton, Ronnie de Jonge · 2018 · Natural Product Reports
  2. Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima—ancestor of all beet crops—and modern sugar beets
    Christin Zachow, Henry Müller, Ralf Tilcher, Gabriele Berg · 2014 · Frontiers in Microbiology
  3. O 2 -Sensing and O 2 -dependent gene regulation in facultatively anaerobic bacteria
    Gottfried Unden, S. Becker, Johannes Bongaerts, G. Holighaus, Jan Schirawski, Stephan Six · 1995 · Archives of Microbiology
  4. Mechanism of gastric mucosal damage induced by ammonia
    Masahiko Tsujii, Sunao Kawano, Shingo Tsuji, Hideyuki Fusamoto, Takenobu Kamada, Nobuhiro Sato · 1992 · Gastroenterology
  5. Molecular characterization of the cloacal microbiota of wild and captive parrots
    Panagiotis G. Xenoulis, Patricia L. Gray, Donald J. Brightsmith, Blake Palculict, Sharman M. Hoppes, Jörg M. Steiner, Ian R. Tizard, Jan S. Suchodolski · 2010 · Veterinary Microbiology
  6. Inhibitory effects of H2 on growth of Clostridium cellobioparum
    Kyungmi Chung · 1976 · Applied and Environmental Microbiology
  7. A Comparative Review on Microbiota Manipulation: Lessons From Fish, Plants, Livestock, and Human Research
    Sylvia Brugman, Wakako Ikeda‐Ohtsubo, Saskia Braber, Gert Folkerts, Corné M. J. Pieterse, Peter A. H. M. Bakker · 2018 · Frontiers in Nutrition
  8. Molecular Players Involved in the Interaction Between Beneficial Bacteria and the Immune System
    Arancha Hevia, Susana Delgado, Borja Sánchez, Abelardo Margollés · 2015 · Frontiers in Microbiology
  9. Autoinducer-2-Based Chemical Communication in Bacteria: Complexities of Interspecies Signaling
    Michael J. Federle · 2009 · Contributions to microbiology
  10. Effects of arabinoxylan-oligosaccharides (AXOS) on juvenile Siberian sturgeon (Acipenser baerii) performance, immune responses and gastrointestinal microbial community
    Zahra Geraylou, Caroline Souffreau, Eugene Rurangwa, Sofie D’hondt, Lien Callewaert, Christophe M. Courtin, Jan A. Delcour, Johan G. Buyse, F. Ollevier · 2012 · Fish & Shellfish Immunology
  11. Transit time of epithelial cells in the small intestines of germfree mice and ex-germfree mice associated with indigenous microorganisms
    Savage, D C, Siegel, J E, Snellen, J E, Whitt, D D · 1981 · Applied and Environmental Microbiology
  12. Quorum sensing signal molecules (acylated homoserine lactones) in Gram-negative fish pathogenic bacteria
    JB Bruhn, Inger Dalsgaard, Kristian Fog Nielsen, Christiane Buchholtz, JL Larsen, Lone Gram · 2005 · Diseases of Aquatic Organisms
  13. Unveiling bifidobacterial biogeography across the mammalian branch of the tree of life
    Christian Milani, Marta Mangifesta, Leonardo Mancabelli, Gabriele Andrea Lugli, Kieran James, Sabrina Duranti, Francesca Turroni, Chiara Ferrario, Maria Cristina Ossiprandi, Douwe van Sinderen et al. · 2017 · The ISME Journal
  14. Differences in Microbiota Membership along the Gastrointestinal Tract of Piglets and Their Differential Alterations Following an Early-Life Antibiotic Intervention
    Chunlong Mu, Yuxiang Yang, Yong Su, Erwin G. Zoetendal, Weiyun Zhu · 2017 · Frontiers in Microbiology
  15. Modify the Histone to Win the Battle: Chromatin Dynamics in Plant–Pathogen Interactions
    Juan S. Ramirez-Prado, Sophie J. M. Piquerez, Abdelhafid Bendahmane, Heribert Hirt A, Cécile Raynaud, Moussa Benhamed · 2018 · Frontiers in Plant Science
  16. Composition and diversity of mucosa‐associated microbiota along the entire length of the pig gastrointestinal tract; dietary influences
    Jennifer Kelly, Kristian Daly, Andrew W. Moran, Sheila Ryan, D. Bravo, Soraya P. Shirazi‐Beechey · 2016 · Environmental Microbiology
  17. Understanding the mechanisms of zinc bacitracin and avilamycin on animal production: linking gut microbiota and growth performance in chickens
    Eduardo Crisol‐Martínez, Dragana Stanley, Mark S. Geier, Robert Hughes, Robert J. Moore · 2017 · Applied Microbiology and Biotechnology
  18. Culture-independent exploration of the teat apex microbiota of dairy cows reveals a wide bacterial species diversity
    Gorik Braem, Sarne De Vliegher, Bert Verbist, Marc Heyndrickx, Frédéric Leroy, Luc De Vuyst · 2011 · Veterinary Microbiology
  19. Phyllosphere Microbiota Composition and Microbial Community Transplantation on Lettuce Plants Grown Indoors
    THOMAS RHYS WILLIAMS, Maria L. Marco · 2014 · mBio
  20. Bacterial endophyte communities of three agricultural important grass species differ in their response towards management regimes
    Franziska Wemheuer, Kristin Kaiser, Petr Karlovský, Rolf Daniel, Stefan Vidal, Bernd Wemheuer · 2017 · Scientific Reports
  21. Beneficial actions of microbiota‐derived tryptophan metabolites
    Galligan, J. J. · 2018 · Neurogastroenterology & Motility
  22. Influence of Pig Farming on the Human Nasal Microbiota: Key Role of Airborne Microbial Communities
    Julia G. Kraemer, Alban Ramette, Suzanne Aebi, Anne Oppliger, Markus Hilty · 2018 · Applied and Environmental Microbiology
  23. The Hologenome Concept: Human, Animal and Plant Microbiota
    EUGENE B. ROSENBERG, Ilana Zilber‐Rosenberg · 2013 · Springer eBooks
  24. Protists are an integral part of the Arabidopsis thaliana microbiome
    Melanie Sapp, Sebastian Ploch, Anna Maria Fiore‐Donno, Michael Bonkowski, Laura E. Rose · 2017 · Environmental Microbiology
  25. Fermentation of dietary carbohydrates to short-chain fatty acids by gut microbes and its influence on intestinal morphology of a detritivorous teleost tilapia (Oreochromis niloticus)
    Minoru Kihara, Takashi Sakata · 1997 · Comparative Biochemistry and Physiology Part A Physiology
  26. Deciphering microbial landscapes of fish eggs to mitigate emerging diseases
    Yiying Liu, Irene de Bruijn, Allison L H Jack, Keith Drynan, Albert Hendrik van den Berg, Even Thoen, José Vladimir Sandoval-Sierra, Ida Skaar, Pieter van West, Javier Diéguez‐Uribeondo et al. · 2014 · The ISME Journal
  27. Seasonal dynamics of bacterial and archaeal methanogenic communities in flooded rice fields and effect of drainage
    Björn Breidenbach, Ralf Conrad · 2015 · Frontiers in Microbiology
  28. Metabolic regulation by lactate
    Mauro Sola‐Penna · 2008 · IUBMB Life
  29. Exploring the microbial diversity of the distal intestinal lumen and mucosa of farmed rainbow troutOncorhynchus mykiss(Walbaum) using next generation sequencing (NGS)
    Philip P Lyons, James F Turnbull, Karl A. Dawson, Margaret Crumlish · 2015 · Aquaculture Research
  30. Repeated inoculation of cattle rumen with bison rumen contents alters the rumen microbiome and improves nitrogen digestibility in cattle
    Gabriel O Ribeiro, Daniela Batista Oss, Zhixiong He, Robert J. Gruninger, Chijioke O. Elekwachi, Robert J. Forster, Wenzhu Z Yang, Karen Ann Beauchemin, Tim Angus McAllister · 2017 · Scientific Reports
  31. Housing Systems Influence Gut Microbiota Composition of Sows but Not of Their Piglets
    Tereza Kubasová, Lenka Dávidová‐Geržová, Élodie Merlot, Matej Medvecký, Ondřej Polanský, Delphine Gardan‐Salmon, Hélène Quesnel, Ivan Rychlı́k · 2017 · PLoS ONE
  32. Short-Chain Fatty Acids Induce Colonic Mucosal Injury in Rats with Various Postnatal Ages
    Suhas M. Nafday, Wei Chen, Luying Peng, Mark W. Babyatsky, Ian R. Holzman, Jing Lin · 2004 · Pediatric Research
  33. Development of Culture Medium for the Isolation of Flavobacterium and Chryseobacterium from Rhizosphere Soil
    Tomoki Nishioka, Mohsen Mohamed Elsharkawy, Haruhisa Suga, Koji Kageyama, Mitsuro Hyakumachi, Masafumi Shimizu · 2016 · Microbes and Environments
  34. Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high‐throughput parallel pyrosequencing
    Jakub Kreisinger, Dagmar Čížková, Jaroslav Vohánka, Jaroslav Piálek · 2014 · Molecular Ecology
  35. Diversity and activity of cellulolytic bacteria, isolated from the gut contents of grass carp (Ctenopharyngodon idellus) (Valenciennes) fed on Sudan grass (Sorghum sudanense) or artificial feedstuffs
    Huan Li, Shangong Wu, Stephan J. Wirth, Yaotong Hao, Weiwei Wang, Hong Zou, Wenxiang Li, Guitang Wang · 2014 · Aquaculture Research
  36. Unraveling uncultivable pesticide degraders via stable isotope probing (SIP)
    Bo Jiang, Naifu Jin, Yi Xing, Yuping Su, Dayi Zhang · 2018 · Critical Reviews in Biotechnology
  37. Are There Acyl-Homoserine Lactones within Mammalian Intestines?
    Matthew C. Swearingen, Anice Sabag-Daigle, Brian M. M. Ahmer · 2012 · Journal of Bacteriology
  38. Ingestion of Milk Containing Very Low Concentration of Antimicrobials: Longitudinal Effect on Fecal Microbiota Composition in Preweaned Calves
    Richard Van Vleck Pereira, Svetlana Ferreira Lima, Julie D. Siler, Carla Foditsch, Lorin D. Warnick, Rodrigo Carvalho Bicalho · 2016 · PLoS ONE
  39. Comparison of the Luminal and Mucosa-Associated Microbiota in the Colon of Pigs with and without Swine Dysentery
    Eric Ryan Burrough, Bailey L. Arruda, Paul Joseph Plummer · 2017 · Frontiers in Veterinary Science
  40. The role of organic acids on microbial deterioration in the Radix pseudostellariae rhizosphere under continuous monoculture regimes
    Hongmiao Wu, Linkun Wu, Quan Zhu, Juanying Wang, Xianjin Qin, Jiahui Xu, Lufei Kong, Jun Chen, Sheng Lin, Muhammad Umar Khan et al. · 2017 · Scientific Reports
  41. Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota
    Gregorio Iraola, Samuel C. Forster, Nitin Kumar, Philippe Lehours, Sadjia Békal, Francisco Javier García-Peña, Fernando Alberto Paolicchi, Claudia Morsella, Helmut Hotzel, Po‐Ren Hsueh et al. · 2017 · Nature Communications
  42. Diversity in Endophyte Populations Reveals Functional and Taxonomic Diversity between Wild and Domesticated Grapevines
    Andrea Campisano, Michael Pancher, Gerardo Puopolo, Antonio Puddu, Sebastián López-Fernández, Barbara Biagini, Sohail Yousaf, Ilaria Pertot · 2014 · American Journal of Enology and Viticulture
  43. Altered Cell Wall Plasticity Can Restrict Plant Growth under Ammonium Nutrition
    Anna Podgórska, Maria Burian, Katarzyna B. Gieczewska, Monika Ostaszewska-Bugajska, Jacek Żebrowski, Danuta Solecka, Bożena Szal · 2017 · Frontiers in Plant Science
  44. Effect of succinate on phosphate solubilization in nitrogen fixing bacteria harbouring chick pea and their effect on plant growth
    Bhagya Iyer, Mahendrapalsingh Rajput, Shalini Rajkumar · 2017 · Microbiological Research
  45. Succinate accumulation in pig large intestine during antibiotic-associated diarrhea and the constitution of succinate-producing flora.
    Takamitsu Tsukahara, Kazunari Ushida · 2002 · The Journal of General and Applied Microbiology
  46. Organic Acid Profiles in Feces of Pigs with Pathogenic or Non-Pathogenic Diarrhea.
    Takamitsu Tsukahara, Kazunari Ushida · 2001 · Journal of Veterinary Medical Science
  47. Nitrate reduction, nitrous oxide formation, and anaerobic ammonia oxidation to nitrite in the gut of soil-feeding termites (Cubitermes and Ophiotermes spp.).
    D. Ngugi, A. Brune · 2012 · Environmental Microbiology
  48. Microbiota of Atlantic cod (Gadus morhua L.) rearing systems at pre- and posthatch stages and the effect of different treatments
    Hélène L. Lauzon, Sigríður Guðmundsdóttir, Sólveig K. Pétursdóttir, Eyjólfur Reynisson, Agnar Steinarsson, Matthías Oddgeirsson, Rannveig Björnsdóttir, B K Gudmundsdóttir · 2010 · Journal of Applied Microbiology
  49. The General Composition of the Faecal Virome of Pigs Depends on Age, but Not on Feeding with a Probiotic Bacterium
    Jana Sachsenröder, Sven Olaf Twardziok, Matthias Scheuch, Reimar Johne · 2014 · PLoS ONE
  50. Nitrogen fixation and nifH diversity in human gut microbiota
    Katsura Igai, Manabu Itakura, Suguru Nishijima, Hirohito Tsurumaru, Wataru Suda, Takumi Tsutaya, Eriko Tomitsuka, Kiyoshi Tadokoro, Jun Baba, Shingo Odani et al. · 2016 · Scientific Reports
  51. Oxygen-Inducible Conversion of Lactate to Acetate in Heterofermentative Lactobacillus brevis ATCC 367
    Tingting Guo, Li Zhang, Yongping Xin, Zhenshang Xu, Huiying He, Jian Kong · 2017 · Applied and Environmental Microbiology
  52. Domestication and cereal feeding developed domestic pig-type intestinal microbiota in animals of suidae
    Kazunari Ushida, Sayaka Tsuchida, Yoshitoshi Ogura, Atsushi Toyoda, Fumito Maruyama · 2015 · Animal Science Journal
  53. Evf, a Virulence Factor Produced by the Drosophila Pathogen Erwinia carotovora, Is an S-Palmitoylated Protein with a New Fold That Binds to Lipid Vesicles
    Sophie Quevillon‐Chéruel, Nicolas Leulliot, Carlos Horacio Acosta‐Muñiz, Michel Vincent, Jacques Gallay, Manuela Argentini, David Cornu, Frédéric Boccard, Bruno Lemaître, Herman VAN TILBEURGH · 2008 · Journal of Biological Chemistry
  54. Comparison of the Rhizosphere Bacterial Communities of Zigongdongdou Soybean and a High-Methionine Transgenic Line of This Cultivar
    jingang liang, Shi Sun, Jun Ji, Haiying Wu, Fang Meng, Mingrong Zhang, Xiaobo Zheng, Cunxiang Wu, Zhengguang Zhang · 2014 · PLoS ONE
  55. Alterations in Ileal Mucosa Bacteria Related to Diet Complexity and Growth Performance in Young Pigs
    Crystal Lynette Levesque, Seema Hooda, Kelly Scott Swanson, Kees de Lange · 2014 · PLoS ONE
  56. O 2 -Sensing and O 2 -dependent gene regulation in facultatively anaerobic bacteria
    Gottfried Unden, S. Becker, Johannes Bongaerts · 1995 · Archives of Microbiology
  57. Physiological Concentration of Exogenous Lactate Reduces Antimycin A Triggered Oxidative Stress in Intestinal Epithelial Cell Line IPEC-1 and IPEC-J2 In Vitro
    Stefan Kahlert, Sami Junnikkala, Lydia Renner, Ulla Hynönen, Roland Hartig, Constanze Nossol, Anikó Barta-Böszörményi, Sven Dänicke, Wolfgang-Bernhard Souffrant, Airi Palva et al. · 2016 · PLoS ONE
  58. Lack of Evidence That Selenium-Yeast Improves Chicken Health and Modulates the Caecal Microbiota in the Context of Colonization by Campylobacter jejuni
    Alexandre Thibodeau, Ann Letellier, Étienne Yergeau, Guillaume Larivière-Gauthier, Philippe Fravalo · 2017 · Frontiers in Microbiology
  59. Ammonia blockade of intestinal epithelial K+ conductance
    Bruce J. Hrnjez, Jaekyung Cecilia Song, Madhu Prasad, Julio M. Mayol, Jeffrey B. Matthews · 1999 · American Journal of Physiology-Gastrointestinal and Liver Physiology
  60. Characterization of the bacterial community associated with early-developmental stages of grass carp (Ctenopharyngodon idella)
    Weiwei Wang, Shan-Gong Wu, Yingzhen Zheng, Yingyin Cheng, Wenxiang Li, Hong Zou, Guitang Wang · 2014 · Aquaculture Research
  61. Variations in the Post-weaning Human Gut Metagenome Profile As Result of Bifidobacterium Acquisition in the Western Microbiome
    Matteo Soverini, Simone Rampelli, Silvia Turroni, Stephanie L. Schnorr, Sara Quercia, Andrea Castagnetti, Elena Biagi, Patrizia Brigidi, Marco Candela · 2016 · Frontiers in Microbiology
  62. Pathogens as Symbionts
    EUGENE B. ROSENBERG, Ilana Zilber‐Rosenberg · 2013 · Springer eBooks