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  1. The mammalian gut harbors very complex and diverse microbiota that play an important role in intestinal homeostasis and host health. Exposure to radiation results in dysbiosis of the gut microbiota leading to ...

    Authors: Amrita K. Cheema, Yaoxiang Li, Jatinder Singh, Ryan Johnson, Michael Girgis, Stephen Y. Wise, Oluseyi O. Fatanmi, Michael D. Kaytor and Vijay K. Singh
    Citation: Animal Microbiome 2021 3:71
  2. Equine grass sickness (EGS) is a multiple systems neuropathy of grazing horses of unknown aetiology. An apparently identical disease occurs in cats, dogs, rabbits, hares, sheep, alpacas and llamas. Many of the...

    Authors: Bruce C. McGorum, Zihao Chen, Laura Glendinning, Hyun S. Gweon, Luanne Hunt, Alasdair Ivens, John A. Keen, R. Scott Pirie, Joanne Taylor, Toby Wilkinson and Gerry McLachlan
    Citation: Animal Microbiome 2021 3:70
  3. Interactions between microorganisms associated with metazoan hosts are emerging as key features of symbiotic systems. Little is known about the role of such interactions on the maintenance of host-microorganis...

    Authors: Robin Guilhot, Antoine Rombaut, Anne Xuéreb, Kate Howell and Simon Fellous
    Citation: Animal Microbiome 2021 3:68
  4. Changes in wild animal gut microbiotas may influence host health and fitness. While many studies have shown correlations between gut microbiota structure and external factors, few studies demonstrate causal li...

    Authors: Melissa R. Ingala, Lauren Albert, Alyssa Addesso, Mackenzie J. Watkins and Sarah A. Knutie
    Citation: Animal Microbiome 2021 3:67
  5. A major focus of research on the gut microbiota of poultry has been to define signatures of a healthy gut and identify microbiota components that correlate with feed conversion. However, there is a high variat...

    Authors: Yugal Raj Bindari, Robert J. Moore, Thi Thu Hao Van, Stephen W. Walkden-Brown and Priscilla F. Gerber
    Citation: Animal Microbiome 2021 3:66
  6. Antibiotics alter the diversity, structure, and dynamics of host-associated microbial consortia, including via development of antibiotic resistance; however, patterns of recovery from microbial imbalances and ...

    Authors: Sally L. Bornbusch, Rachel L. Harris, Nicholas M. Grebe, Kimberly Roche, Kristin Dimac-Stohl and Christine M. Drea
    Citation: Animal Microbiome 2021 3:65
  7. A commensal microbiota regulates and is in turn regulated by viruses during host infection which can influence virus infectivity. In this study, analysis of colon microbiota population changes following a low ...

    Authors: Klaudia Chrzastek, Joy Leng, Mohammad Khalid Zakaria, Dagmara Bialy, Roberto La Ragione and Holly Shelton
    Citation: Animal Microbiome 2021 3:64
  8. Rumen microorganisms carry antimicrobial resistance genes which pose a threaten to animals and humans in a One Health context. In order to tackle the emergence of antimicrobial resistance it is vital to unders...

    Authors: Adrián López-Catalina, Raquel Atxaerandio, Aser García-Rodríguez, Idoia Goiri, Mónica Gutierrez-Rivas, José Antonio Jiménez‐Montero and Oscar González-Recio
    Citation: Animal Microbiome 2021 3:63
  9. The bovine upper respiratory tract (URT) microbiome includes opportunistic pathogens that cause respiratory disease and stress associated with maternal separation and transportation contributes to the severity...

    Authors: Nilusha Malmuthuge, Angela Howell, Natasa Arsic, Tracy Prysliak, Jose Perez-Casal and Philip Griebel
    Citation: Animal Microbiome 2021 3:62
  10. Elasmobranchs (sharks, skates and rays) are of broad ecological, economic, and societal value. These globally important fishes are experiencing sharp population declines as a result of human activity in the oc...

    Authors: Cameron T. Perry, Zoe A. Pratte, Ana Clavere-Graciette, Kim B. Ritchie, Robert E. Hueter, Alisa L. Newton, G. Christopher Fischer, Elizabeth A. Dinsdale, Michael P. Doane, Krystan A. Wilkinson, Kim Bassos-Hull, Kady Lyons, Alistair D. M. Dove, Lisa A. Hoopes and Frank J. Stewart
    Citation: Animal Microbiome 2021 3:61
  11. Microbial communities of wild animals are being increasingly investigated to provide information about the hosts’ biology and promote conservation. Loggerhead sea turtles (Caretta caretta) are a keystone species ...

    Authors: Klara Filek, Adriana Trotta, Romana Gračan, Antonio Di Bello, Marialaura Corrente and Sunčica Bosak
    Citation: Animal Microbiome 2021 3:59
  12. The porcine gastrointestinal microbiota has been linked to both host health and performance. Most pig gut microbiota studies target faecal material, which is not representative of microbiota dynamics in other ...

    Authors: Jolinda Pollock, Laura Glendinning, Lesley A. Smith, Hamna Mohsin, David L. Gally, Michael R. Hutchings and Jos G. M. Houdijk
    Citation: Animal Microbiome 2021 3:58
  13. The role of the microbiome in livestock production has been highlighted in recent research. Currently, little is known about the microbiome's impact across different systems of production in swine, particularl...

    Authors: Christian Maltecca, Rob Dunn, Yuqing He, Nathan P. McNulty, Constantino Schillebeeckx, Clint Schwab, Caleb Shull, Justin Fix and Francesco Tiezzi
    Citation: Animal Microbiome 2021 3:57
  14. Thirteen-lined ground squirrels (Ictidomys tridecemlineatus) are obligate hibernators and are only active 4–5 months annually. During this period, squirrels rapidly acquire fat for use during hibernation. We inve...

    Authors: Kirsten Grond, Courtney C. Kurtz, Jasmine Hatton, Michelle M. Sonsalla and Khrystyne N. Duddleston
    Citation: Animal Microbiome 2021 3:56
  15. Zebrafish used in research settings are often housed in recirculating aquaculture systems (RAS) which rely on the system microbiome, typically enriched in a biofiltration substrate, to remove the harmful ammon...

    Authors: Aaron C. Ericsson, Susheel B. Busi, Daniel J. Davis, Henda Nabli, David C. Eckhoff, Rebecca A. Dorfmeyer, Giedre Turner, Payton S. Oswalt, Marcus J. Crim and Elizabeth C. Bryda
    Citation: Animal Microbiome 2021 3:55
  16. Health surveillance of murine colonies employed for scientific purposes aim at detecting unwanted infection that can affect the well-being of animals and personnel, and potentially undermine scientific results...

    Authors: Ferdinando Scavizzi, Cristian Bassi, Laura Lupini, Paola Guerriero, Marcello Raspa and Silvia Sabbioni
    Citation: Animal Microbiome 2021 3:53
  17. Conventional pig housing and management conditions are associated with gastrointestinal pathophysiology and disease susceptibility in early life. Developing new strategies to reduce both therapeutic and prophy...

    Authors: Caifang Wen, Ingrid van Dixhoorn, Dirkjan Schokker, Henri Woelders, Norbert Stockhofe-Zurwieden, Johanna M. J. Rebel and Hauke Smidt
    Citation: Animal Microbiome 2021 3:52
  18. Papillomaviruses are small nonenveloped, circular double-stranded DNA viruses that belong to the Papillomaviridae family. To date, 29 Bos taurus papillomavirus (BPV) types have been described. Studies involving m...

    Authors: Jéssica Tatiane Sauthier, Cíntia Daudt, Flavio Roberto Chaves da Silva, Christian Diniz Beduschi Travassos Alves, Fabiana Quoos Mayer, Ronaldo Michel Bianchi, David Driemeier, Rodrigo Silva Araujo Streit, Charley Christian Staats, Cláudio Wageck Canal and Matheus Nunes Weber
    Citation: Animal Microbiome 2021 3:51
  19. The chicken gut microbiota passes through different stages of maturation; therefore, strengthening it with well characterised probiotics increases its resilience required for optimum gut health and wellbeing. ...

    Authors: Samiullah Khan and Kapil K. Chousalkar
    Citation: Animal Microbiome 2021 3:50
  20. Farmed fish food with reduced fish-derived products are gaining growing interest due to the ecological impact of fish-derived protein utilization and the necessity to increase aquaculture sustainability. Altho...

    Authors: David Pérez-Pascual, Ana Elena Pérez-Cobas, Dimitri Rigaudeau, Tatiana Rochat, Jean-François Bernardet, Sandrine Skiba-Cassy, Yann Marchand, Eric Duchaud and Jean-Marc Ghigo
    Citation: Animal Microbiome 2021 3:47
  21. Dietary fibers are widely considered to be beneficial to health as they produce nutrients through gut microbial fermentation while facilitating weight management and boosting gut health. To date, the gene expr...

    Authors: Jie Xu, Rongying Xu, Menglan Jia, Yong Su and Weiyun Zhu
    Citation: Animal Microbiome 2021 3:45
  22. Antimicrobial resistance poses super challenges in both human health and livestock production. Rumen microbiota is a large reservoir of antibiotic resistance genes (ARGs), which show significant varations in d...

    Authors: Hui-Zeng Sun, Ke-Lan Peng, Ming-Yuan Xue and Jian-Xin Liu
    Citation: Animal Microbiome 2021 3:44
  23. Beneficial microbes can be vertically transmitted from mother to offspring in many organisms. In oviparous animals, bacterial transfer to eggs may improve egg success by inhibiting fungal attachment and infect...

    Authors: M. E. Bunker, G. Elliott, H. Heyer-Gray, M. O. Martin, A. E. Arnold and S. L. Weiss
    Citation: Animal Microbiome 2021 3:43
  24. Dietary content and environmental factors can shape the gut microbiota, and consequently, the way the gut microbiota metabolizes fats, carbohydrates, and proteins, affecting overall health of the host. We eval...

    Authors: Lina María Martínez-López, Amy Pepper, Rachel Pilla, Andrew P. Woodward, Jan S. Suchodolski and Caroline Mansfield
    Citation: Animal Microbiome 2021 3:42
  25. Undesirable microbial infiltration into the female bovine reproductive tracts, for example during calving or mating, is likely to disturb the commensal microflora. Persistent establishment and overgrowth of ce...

    Authors: Chian Teng Ong, Conny Turni, Patrick J. Blackall, Gry Boe-Hansen, Ben J. Hayes and Ala E. Tabor
    Citation: Animal Microbiome 2021 3:41
  26. Captive animals, compared to their wild counterparts, generally harbor imbalanced gut microbiota owing, in part, to their altered diets. This imbalance is particularly striking for folivores that fundamentally...

    Authors: Lydia K. Greene, Marina B. Blanco, Elodi Rambeloson, Karlis Graubics, Brian Fanelli, Rita R. Colwell and Christine M. Drea
    Citation: Animal Microbiome 2021 3:39
  27. Oral diseases are common in dogs, with microbiota playing a prominent role in the disease process. Oral cavity habitats harbor unique microbiota populations that have relevance to health and disease. Despite t...

    Authors: Patrícia M. Oba, Meredith Q. Carroll, Celeste Alexander, Helen Valentine, Amy J. Somrak, Stephanie C. J. Keating, Adrianna M. Sage and Kelly S. Swanson
    Citation: Animal Microbiome 2021 3:38

    The Correction to this article has been published in Animal Microbiome 2021 3:40

  28. For more than 30 years, the tetracycline on/off system of inducible gene expression has been leveraged to study disease mechanisms across many research areas, especially that of metabolism and neuroscience. Th...

    Authors: Elizabeth M. Hill, Christopher D. Howard, Tracy L. Bale and Eldin Jašarević
    Citation: Animal Microbiome 2021 3:37
  29. Probiotics have been demonstrated to ameliorate clinical signs of gastrointestinal diseases in dogs in various studies. However, the effect of probiotics in a healthy population, as well as factors contributin...

    Authors: Jirayu Tanprasertsuk, Aashish R. Jha, Justin Shmalberg, Roshonda B. Jones, LeeAnn M. Perry, Heather Maughan and Ryan W. Honaker
    Citation: Animal Microbiome 2021 3:36
  30. Tenacibaculum maritimum is a fish pathogen known for causing serious damage to a broad range of wild and farmed marine fish populations worldwide. The recently sequenced genome of T. maritimum strain NCIMB 2154T ...

    Authors: J. Le Luyer, Q. Schull, P. Auffret, P. Lopez, M. Crusot, C. Belliard, C. Basset, Q. Carradec, J. Poulain, S. Planes and D. Saulnier
    Citation: Animal Microbiome 2021 3:35
  31. The gut microbiota is critical for host function. Among mammals, host phylogenetic relatedness and diet are strong drivers of gut microbiota structure, but one factor may be more influential than the other. He...

    Authors: Connie A. Rojas, Santiago Ramírez-Barahona, Kay E. Holekamp and Kevin R. Theis
    Citation: Animal Microbiome 2021 3:33
  32. Volatile fatty acids (VFA) generated from ruminal fermentation by microorganisms provide up to 75% of total metabolizable energy in ruminants. Ruminal pH is an important factor affecting the profile and produc...

    Authors: Meng M. Li, Robin R. White, Le Luo Guan, Laura Harthan and Mark D. Hanigan
    Citation: Animal Microbiome 2021 3:32
  33. The rumen bacterial communities are changing dynamically throughout the first year of calf’s life including the weaning period as a critical event. Rumen microbiome analysis is often limited to invasive rumen ...

    Authors: Nida Amin, Sarah Schwarzkopf, Asako Kinoshita, Johanna Tröscher-Mußotter, Sven Dänicke, Amélia Camarinha-Silva, Korinna Huber, Jana Frahm and Jana Seifert
    Citation: Animal Microbiome 2021 3:31
  34. Infectious diseases cause significant production losses in aquaculture every year. Since the gut microbiota plays an essential role in regulating the host immune system, health and physiology, altered gut micr...

    Authors: Davide Bozzi, Jacob A. Rasmussen, Christian Carøe, Harald Sveier, Kristian Nordøy, M. Thomas P. Gilbert and Morten T. Limborg
    Citation: Animal Microbiome 2021 3:30
  35. The cotton rat (genus Sigmodon) is an essential small animal model for the study of human infectious disease and viral therapeutic development. However, the impact of the host microbiome on infection outcomes has...

    Authors: Britton A. Strickland, Mira C. Patel, Meghan H. Shilts, Helen H. Boone, Arash Kamali, Wei Zhang, Daniel Stylos, Marina S. Boukhvalova, Christian Rosas-Salazar, Shibu Yooseph, Seesandra V. Rajagopala, Jorge C. G. Blanco and Suman R. Das
    Citation: Animal Microbiome 2021 3:29
  36. The knowledge about blood circulating microbiome and its functional relevance in healthy individuals remains limited. An assessment of changes in the circulating microbiome was performed by sequencing peripher...

    Authors: Ainize Peña-Cearra, Alejandro Belanche, Monika Gonzalez-Lopez, José Luis Lavín, Miguel Ángel Pascual-Itoiz, Elisabeth Jiménez, Héctor Rodríguez, Ana Mª. Aransay, Juan Anguita, David R. Yáñez-Ruiz and Leticia Abecia
    Citation: Animal Microbiome 2021 3:28
  37. The nutrition of calves from birth until weaning is predominantly from liquid (milk or milk-based) feeds. Liquid feed allowances are often restricted during artificial rearing to accelerate the development of ...

    Authors: Sandeep Kumar, M. Ajmal Khan, Emma Beijer, Jinxin Liu, Katherine K. Lowe, Wayne Young, David A. Mills and Christina D. Moon
    Citation: Animal Microbiome 2021 3:27
  38. The microbiomes of foundation (habitat-forming) species such as corals and sponges underpin the biodiversity, productivity, and stability of ecosystems. Consumers shape communities of foundation species throug...

    Authors: Carsten G. B. Grupstra, Kristen M. Rabbitt, Lauren I. Howe-Kerr and Adrienne M. S. Correa
    Citation: Animal Microbiome 2021 3:25
  39. Little is known about the complex interactions between the diet, the gut microbiota, and enteropathogens. Here, the impact of two specific diets on the composition of the mouse gut microbiota and on the transc...

    Authors: Nicoletta Prax, Stefanie Wagner, Jakob Schardt, Klaus Neuhaus, Thomas Clavel and Thilo M. Fuchs
    Citation: Animal Microbiome 2021 3:24
  40. Diet acidification, dietary calcium (Ca) level, and phytase supplementation are known influences on the microbial community in the digestive tract and on phosphorus (P) utilization of broiler chickens. Effects of...

    Authors: Jochen Krieg, Daniel Borda-Molina, Wolfgang Siegert, Vera Sommerfeld, Yung Ping Chi, Hamid Reza Taheri, Dieter Feuerstein, Amélia Camarinha-Silva and Markus Rodehutscord
    Citation: Animal Microbiome 2021 3:23
  41. Clinical intervention during bacterial infections in farm animals such as pigs commonly includes the use of antimicrobials. With the rise of antimicrobial resistance and the attempts to reduce the use of antib...

    Authors: Adrian Muwonge, Anbu K. Karuppannan and Tanja Opriessnig
    Citation: Animal Microbiome 2021 3:22
  42. The environment exerts a strong influence on the fish external microbiota, with lower diversity and increased abundances of opportunistic bacterial groups characterizing cultured fish compared to their wild co...

    Authors: Andrea M. Tarnecki, Noah J. Levi, Matthew Resley and Kevan Main
    Citation: Animal Microbiome 2021 3:21

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