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  1. Microorganisms have intimate functional relationships with invertebrate and vertebrate taxa, with the potential to drastically impact health outcomes. Perturbations that affect microbial communities residing o...

    Authors: Denita M. Weeks, Matthew J. Parris and Shawn P. Brown

    Citation: Animal Microbiome 2020 2:35

    Content type: Research Article

    Published on:

  2. The small intestine, while serving as the main absorption organ, also possesses a unique bacterial environment and holds the critical function of conversion of primary bile acids. Bile acids are, in turn, able...

    Authors: Jianan Liu, Fang Liu, Wentao Cai, Cunling Jia, Ying Bai, Yanghua He, Weiyun Zhu, Robert W. Li and Jiuzhou Song

    Citation: Animal Microbiome 2020 2:33

    Content type: Research Article

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  3. Little is known about maturation of calves’ gut microbiome in veal farms, in which animals are confined under intensive-farming conditions and the administration of collective antibiotic treatment in feed is c...

    Authors: Méril Massot, Marisa Haenni, Thu Thuy Nguyen, Jean-Yves Madec, France Mentré and Erick Denamur

    Citation: Animal Microbiome 2020 2:32

    Content type: Research Article

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  4. The dam is considered an important source of microbes for the calf; consequently, the development of calf microbiota may vary with farming system due to differences between the contact the calf has with the da...

    Authors: Matthew Barden, Peter Richards-Rios, Erika Ganda, Luca Lenzi, Richard Eccles, Joseph Neary, Joanne Oultram and Georgios Oikonomou

    Citation: Animal Microbiome 2020 2:31

    Content type: Research Article

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  5. Gut microbiota plays important roles in host animal metabolism, homeostasis and environmental adaptation. However, the interplay between the gut microbiome and urochordate ascidian, the most closet relative of...

    Authors: Jiankai Wei, Hongwei Gao, Yang Yang, Haiming Liu, Haiyan Yu, Zigui Chen and Bo Dong

    Citation: Animal Microbiome 2020 2:30

    Content type: Research Article

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  6. Commonly known as sun-coral, Tubastraea tagusensis is an azooxanthellate scleractinian coral that successfully invaded the Southwestern Atlantic causing significant seascape changes. Today it is reported to over ...

    Authors: Aline Aparecida Zanotti, Gustavo Bueno Gregoracci, Katia Cristina Cruz Capel and Marcelo Visentini Kitahara

    Citation: Animal Microbiome 2020 2:29

    Content type: Research Article

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  7. Laying hens with access to outdoor ranges are exposed to additional environmental factors and microorganisms, including potential pathogens. Differences in composition of the cloacal microbial community betwee...

    Authors: Janneke Schreuder, Francisca C. Velkers, Ruth J. Bouwstra, Nancy Beerens, J. Arjan Stegeman, Willem F. de Boer, P. van Hooft, Armin R. W. Elbers, Alex Bossers and Stephanie D. Jurburg

    Citation: Animal Microbiome 2020 2:28

    Content type: Research Article

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  8. The skin microbiome of marine fish is thought to come from bacteria in the surrounding water during the larval stages, although it is not clear how different water conditions affect the microbial communities i...

    Authors: Emily T. Dodd, Melissa L. Pierce, Jonathan S. F. Lee and Rachel S. Poretsky

    Citation: Animal Microbiome 2020 2:27

    Content type: Research Article

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  9. The use of antibiotics in aquaculture is a common infection treatment and is increasing in some sectors and jurisdictions. While antibiotic treatment can negatively shift gut bacterial communities, recovery an...

    Authors: Thibault P. R. A. Legrand, Sarah R. Catalano, Melissa L. Wos-Oxley, James W. Wynne, Laura S. Weyrich and Andrew P. A. Oxley

    Citation: Animal Microbiome 2020 2:26

    Content type: Research Article

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  10. The hamadryas baboon (Papio hamadryas) is a highly social primate that lives in complex multilevel societies exhibiting a wide range of group behaviors akin to humans. In contrast to the widely studied human micr...

    Authors: Xuanji Li, Urvish Trivedi, Asker Daniel Brejnrod, Gisle Vestergaard, Martin Steen Mortensen, Mads Frost Bertelsen and Søren Johannes Sørensen

    Citation: Animal Microbiome 2020 2:25

    Content type: Research Article

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  11. Stereotyped sunning behaviour in birds has been hypothesized to inhibit keratin-degrading bacteria but there is little evidence that solar irradiation affects community assembly and abundance of plumage microb...

    Authors: Gary R. Graves, Kenan O. Matterson, Christopher M. Milensky, Brian K. Schmidt, Michael J. V. O’Mahoney and Sergei V. Drovetski

    Citation: Animal Microbiome 2020 2:24

    Content type: Research Article

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  12. The development and maturation of rumen microbiota across the lifetime of grazing yaks remain unexplored due to the varied lifestyles and feed types of yaks as well as the challenges of obtaining samples. In a...

    Authors: Wei Guo, Mi Zhou, Tao Ma, Sisi Bi, Weiwei Wang, Ying Zhang, Xiaodan Huang, Le Luo Guan and Ruijun Long

    Citation: Animal Microbiome 2020 2:23

    Content type: Research Article

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  13. Ruminant gastrointestinal tract homeostasis deploys interactive microbiome–host metabolic communication and signaling axes to underpin the fitness of the host. After this stable niche is destroyed by environme...

    Authors: Limei Lin, Yue Wang, Lei Xu, Junhua Liu, Weiyun Zhu and Shengyong Mao

    Citation: Animal Microbiome 2020 2:22

    Content type: Research Article

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  14. The relevance of the host microbiota to host ecology and evolution is well acknowledged. However, the effect of the microbial environment on host immune function and host microbiota dynamics is understudied in...

    Authors: H. Pieter J. van Veelen, Joana Falcão Salles, Kevin D. Matson, Marco van der Velde and B. Irene Tieleman

    Citation: Animal Microbiome 2020 2:21

    Content type: Research Article

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  15. Pupfishes frequently enter paradoxical anaerobism in response to endogenously produced or exogenously supplied ethanol in a dose-dependent manner. To decipher the role of the gut microbiota in ethanol-associat...

    Authors: Shrikant S. Bhute, Brisa Escobedo, Mina Haider, Yididya Mekonen, Dafhney Ferrer, Stanley D. Hillyard, Ariel D. Friel, Frank van Breukelen and Brian P. Hedlund

    Citation: Animal Microbiome 2020 2:20

    Content type: Research Article

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  16. The pig gut microbiome harbors thousands of species of archaea, bacteria, viruses and eukaryotes such as protists and fungi. However, since the majority of published studies have been focused on prokaryotes, l...

    Authors: Yuliaxis Ramayo-Caldas, Francesc Prenafeta-Boldú, Laura M. Zingaretti, Olga Gonzalez-Rodriguez, Antoni Dalmau, Raquel Quintanilla and Maria Ballester

    Citation: Animal Microbiome 2020 2:18

    Content type: Research Article

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  17. The microbiota plays a critical role in host homeostasis and has been shown to be a major driving force in host evolution. However, our understanding of these important relationships is hampered by a lack of d...

    Authors: Titus Franciscus Scheelings, Robert J. Moore, Thi Thu Hao Van, Marcel Klaassen and Richard D. Reina

    Citation: Animal Microbiome 2020 2:17

    Content type: Research Article

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  18. The gut microbiome harbors trillions of bacteria that play a major role in dietary nutrient extraction and host metabolism. Metabolic diseases such as obesity and diabetes are associated with shifts in microbi...

    Authors: Dimitrios N. Sidiropoulos, Gabriel A. Al-Ghalith, Robin R. Shields-Cutler, Tonya L. Ward, Abigail J. Johnson, Pajau Vangay, Dan Knights, Purna C. Kashyap, Yibo Xian, Amanda E. Ramer-Tait and Jonathan B. Clayton

    Citation: Animal Microbiome 2020 2:16

    Content type: Research Article

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  19. The microorganisms populating the gastro-intestinal tract of vertebrates, collectively known as “microbiota”, play an essential role in digestion and are important in regulating the immune response. Whereas th...

    Authors: Bruno C. M. Oliveira, Maureen Murray, Florina Tseng and Giovanni Widmer

    Citation: Animal Microbiome 2020 2:15

    Content type: Research Article

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  20. Increasing evidence suggests a causal relationship between the gut microbiome and psychiatric illnesses. In particular, autism spectrum disorder is associated with gastrointestinal symptoms and alterations in ...

    Authors: Supritha Dugyala, Travis S. Ptacek, Jeremy M. Simon, Yuhui Li and Flavio Fröhlich

    Citation: Animal Microbiome 2020 2:14

    Content type: Research Article

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  21. Dietary yeast inclusions in a pig diet may drive changes both in gut bacterial composition and bacterial functional profile. This study investigated the effect of Cyberlindnera jadinii as a protein to replace 40%...

    Authors: Stanislav Iakhno, Özgün C. O. Umu, Ingrid M. Håkenåsen, Caroline P. Åkesson, Liv T. Mydland, Charles McL. Press, Henning Sørum and Margareth Øverland

    Citation: Animal Microbiome 2020 2:13

    Content type: Research Article

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  22. The impact of the microbiota on host fitness has so far mainly been demonstrated for the bacterial microbiome. We know much less about host-associated protist and viral communities, largely due to technical is...

    Authors: S. Dupont, A. Lokmer, E. Corre, J.-C. Auguet, B. Petton, E. Toulza, C. Montagnani, G. Tanguy, D. Pecqueur, C. Salmeron, L. Guillou, C. Desnues, B. La Scola, J. Bou Khalil, J. de Lorgeril, G. Mitta…

    Citation: Animal Microbiome 2020 2:12

    Content type: Research Article

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  23. Within complex microbial ecosystems, microbe-microbe interrelationships play crucial roles in determining functional properties such as metabolic potential, stability and colonization resistance. In dairy cows...

    Authors: Hooman Derakhshani, Jan C. Plaizier, Jeroen De Buck, Herman W. Barkema and Ehsan Khafipour

    Citation: Animal Microbiome 2020 2:11

    Content type: Research Article

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  24. Coral reefs have sustained damage of increasing scale and frequency due to climate change, thereby intensifying the need to elucidate corals’ biological characteristics, including their thermal tolerance and m...

    Authors: Leon Michael Hartman, Madeleine Josephine Henriette van Oppen and Linda Louise Blackall

    Citation: Animal Microbiome 2020 2:10

    Content type: Research Article

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  25. Comprehensive studies of wild bird microbiomes are often limited by difficulties of sample acquisition. However, widely used non-invasive cloacal swab methods and under-explored museum specimens preserved in a...

    Authors: Kasun H. Bodawatta, Katerina Puzejova, Katerina Sam, Michael Poulsen and Knud A. Jønsson

    Citation: Animal Microbiome 2020 2:9

    Content type: Research Article

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  26. Compared to horses and ponies, donkeys have increased degradation of dietary fiber. The longer total mean retention time of feed in the donkey gut has been proposed to be the basis of this, because of the incr...

    Authors: J. E. Edwards, A. Schennink, F. Burden, S. Long, D. A. van Doorn, W. F. Pellikaan, J. Dijkstra, E. Saccenti and H. Smidt

    Citation: Animal Microbiome 2020 2:8

    Content type: Research Article

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  27. Next-generation sequencing has opened new avenues for studying metabolic capabilities of bacteria that cannot be cultured. Here, we provide a metagenomic description of chemoautotrophic gammaproteobacterial sy...

    Authors: Bonita McCuaig, Lourdes Peña-Castillo and Suzanne C. Dufour

    Citation: Animal Microbiome 2020 2:7

    Content type: Research Article

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  28. Equine gut microbiology studies to date have primarily focused on horses and ponies, which represent only one of the eight extant equine species. This is despite asses and mules comprising almost half of the w...

    Authors: J. E. Edwards, S. A. Shetty, P. van den Berg, F. Burden, D. A. van Doorn, W. F. Pellikaan, J. Dijkstra and H. Smidt

    Citation: Animal Microbiome 2020 2:6

    Content type: Research Article

    Published on:

  29. Coral-associated microbial communities are sensitive to multiple environmental and biotic stressors that can lead to dysbiosis and mortality. Although the processes contributing to these microbial shifts remai...

    Authors: Leïla Ezzat, Thomas Lamy, Rebecca L. Maher, Katrina S. Munsterman, Kaitlyn M. Landfield, Emily R. Schmeltzer, Cody S. Clements, Rebecca L. Vega Thurber and Deron E. Burkepile

    Citation: Animal Microbiome 2020 2:5

    Content type: Research Article

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  30. As one of the most densely populated microbial communities on Earth, the gut microbiota serves as an important reservoir of antibiotic resistance genes (ARGs), referred to as the gut resistome. Here, we invest...

    Authors: Younjung Kim, Marcus H. Y. Leung, Wendy Kwok, Guillaume Fournié, Jun Li, Patrick K. H. Lee and Dirk U. Pfeiffer

    Citation: Animal Microbiome 2020 2:4

    Content type: Research Article

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  31. One of the greatest impediments to global small ruminant production is infection with the gastrointestinal parasite, Haemonchus contortus. In recent years there has been considerable interest in the gut microbiot...

    Authors: Md. Abdullah Al Mamun, Mark Sandeman, Phil Rayment, Phillip Brook-Carter, Emily Scholes, Naga Kasinadhuni, David Piedrafita and Andrew R. Greenhill

    Citation: Animal Microbiome 2020 2:3

    Content type: Research Article

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  32. In pig production systems, weaning is a crucial period characterized by nutritional, environmental, and social stresses. Piglets transition from a milk-based diet to a solid, more complex plant-based diet, and...

    Authors: Francesca Romana Massacci, Mustapha Berri, Gaetan Lemonnier, Elodie Guettier, Fany Blanc, Deborah Jardet, Marie Noelle Rossignol, Marie-José Mercat, Joël Doré, Patricia Lepage, Claire Rogel-Gaillard and Jordi Estellé

    Citation: Animal Microbiome 2020 2:2

    Content type: Research Article

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  33. Scrub typhus, caused by a bacterial pathogen (Orientia spp.), is a potentially life-threatening febrile illness widely distributed in the Asia-Pacific region and is emerging elsewhere. The infection is transmitte...

    Authors: Kittipong Chaisiri, A. Christina Gill, Alexandr A. Stekolnikov, Soawapak Hinjoy, John W. McGarry, Alistair C. Darby, Serge Morand and Benjamin L. Makepeace

    Citation: Animal Microbiome 2019 1:18

    Content type: Research article

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  34. Dietary intake is known to be a driver of microbial community dynamics in ruminants. Beef cattle go through a finishing phase that typically includes very high concentrate ratios in their feed, with consequent...

    Authors: Timothy J. Snelling, Marc D. Auffret, Carol-Anne Duthie, Robert D. Stewart, Mick Watson, Richard J. Dewhurst, Rainer Roehe and Alan W. Walker

    Citation: Animal Microbiome 2019 1:16

    Content type: Research article

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  35. Digestive processes in the rumen lead to the release of methyl-compounds, mainly methanol and methylamines, which are used by methyltrophic methanogens to form methane, an important agricultural greenhouse gas...

    Authors: William J. Kelly, Sinead C. Leahy, Janine Kamke, Priya Soni, Satoshi Koike, Roderick Mackie, Rekha Seshadri, Gregory M. Cook, Sergio E. Morales, Chris Greening and Graeme T. Attwood

    Citation: Animal Microbiome 2019 1:15

    Content type: Research article

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  36. Understanding the complex interactions of microbial communities including bacteria, archaea, parasites, viruses and fungi of the gastrointestinal tract (GIT) associated with states of either health or disease ...

    Authors: Anne Kauter, Lennard Epping, Torsten Semmler, Esther-Maria Antao, Dania Kannapin, Sabita D. Stoeckle, Heidrun Gehlen, Antina Lübke-Becker, Sebastian Günther, Lothar H. Wieler and Birgit Walther

    Citation: Animal Microbiome 2019 1:14

    Content type: Review

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  37. Elucidating the interplay between hosts and their microbiomes in ecological adaptation has become a central theme in evolutionary biology. A textbook example of microbiome-mediated adaptation is the adaptation...

    Authors: Lena Waidele, Judith Korb, Christian R. Voolstra, Franck Dedeine and Fabian Staubach

    Citation: Animal Microbiome 2019 1:13

    Content type: Research article

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  38. Clostridium perfringens is a key pathogen in poultry-associated necrotic enteritis (NE). To date there are limited Whole Genome Sequencing based studies describing broiler-associated C. perfringens in healthy and...

    Authors: Raymond Kiu, Joseph Brown, Harley Bedwell, Charlotte Leclaire, Shabhonam Caim, Derek Pickard, Gordon Dougan, Ronald A. Dixon and Lindsay J. Hall

    Citation: Animal Microbiome 2019 1:12

    Content type: Research article

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  39. Captivity presents extreme lifestyle changes relative to the wild, and evidence of microbiome dysbiosis in captive animals is growing. The gut microbiome plays a crucial role in host health. Whilst captive bre...

    Authors: Rowena Chong, Catherine E. Grueber, Samantha Fox, Phil Wise, Vanessa R. Barrs, Carolyn J. Hogg and Katherine Belov

    Citation: Animal Microbiome 2019 1:8

    Content type: Research article

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  40. Sharks are in severe global decline due to human exploitation. The additional concern of emerging diseases for this ancient group of fish, however, remains poorly understood. While wild-caught and captive shar...

    Authors: Claudia Pogoreutz, Mauvis A. Gore, Gabriela Perna, Catriona Millar, Robert Nestler, Rupert F. Ormond, Christopher R. Clarke and Christian R. Voolstra

    Citation: Animal Microbiome 2019 1:9

    Content type: Research article

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  41. Growing evidence supports the role of gut microbiota in obesity and its related disorders including type 2 diabetes. Ob/ob mice, which are hyperphagic due to leptin deficiency, are commonly used models of obes...

    Authors: Alireza Kashani, Asker Daniel Brejnrod, Chunyu Jin, Timo Kern, Andreas Nygaard Madsen, Louise Aas Holm, Georg K. Gerber, Jens-Christian Holm, Torben Hansen, Birgitte Holst and Manimozhiyan Arumugam

    Citation: Animal Microbiome 2019 1:11

    Content type: Research article

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  42. The popularity of Galleria mellonella as invertebrate model is increasing rapidly, because it forms an attractive alternative to study bacterial, fungal and viral infections, toxin biology, and to screen antimicr...

    Authors: Camille Nina Allonsius, Wannes Van Beeck, Ilke De Boeck, Stijn Wittouck and Sarah Lebeer

    Citation: Animal Microbiome 2019 1:7

    Content type: Short report

    Published on:

  43. The intestinal microbiota is shaped by many interactions between microorganisms, host, diet, and the environment. Exposure to microorganisms present in the environment, and exchange of microorganisms between h...

    Authors: Jannigje G. Kers, Francisca C. Velkers, Egil A. J. Fischer, Gerben D. A. Hermes, David M. Lamot, J. Arjan Stegeman and Hauke Smidt

    Citation: Animal Microbiome 2019 1:10

    Content type: Research article

    Published on:

  44. Differences between individuals in their gastrointestinal microbiomes can lead to variation in their ability to persist on particular diets. Koalas are dietary specialists, feeding almost exclusively on Eucalyptu...

    Authors: Michaela D. J. Blyton, Rochelle M. Soo, Desley Whisson, Karen J. Marsh, Jack Pascoe, Mark Le Pla, William Foley, Philip Hugenholtz and Ben D. Moore

    Citation: Animal Microbiome 2019 1:6

    Content type: Research article

    Published on:

  45. There is good evidence for a substantial endogenous phytase activity originating from the epithelial tissue or the microbiota resident in the digestive tract of broiler chickens. However, ionophore coccidiosta...

    Authors: Susanne Künzel, Daniel Borda-Molina, Rebecca Kraft, Vera Sommerfeld, Imke Kühn, Amélia Camarinha-Silva and Markus Rodehutscord

    Citation: Animal Microbiome 2019 1:5

    Content type: Research article

    Published on:

  46. .

    Authors: Breanna Michell Roque, Charles Garrett Brooke, Joshua Ladau, Tamsen Polley, Lyndsey Jean Marsh, Negeen Najafi, Pramod Pandey, Latika Singh, Robert Kinley, Joan King Salwen, Emiley Eloe-Fadrosh, Ermias Kebreab and Matthias Hess

    Citation: Animal Microbiome 2019 1:4

    Content type: Correction

    Published on:

    The original article was published in Animal Microbiome 2019 1:3

  47. Recent studies using batch-fermentation suggest that the red macroalgae Asparagopsis taxiformis has the potential to reduce methane (CH4) production from beef cattle by up to ~ 99% when added to Rhodes grass hay;...

    Authors: Breanna Michell Roque, Charles Garrett Brooke, Joshua Ladau, Tamsen Polley, Lyndsey Jean Marsh, Negeen Najafi, Pramod Pandey, Latika Singh, Robert Kinley, Joan King Salwen, Emiley Eloe-Fadrosh, Ermias Kebreab and Matthias Hess

    Citation: Animal Microbiome 2019 1:3

    Content type: Research article

    Published on:

    The Correction to this article has been published in Animal Microbiome 2019 1:4

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