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  1. Cats are strict carnivores but possess a complex gastrointestinal (GI) microbial community that actively ferments dietary substrates that are not digested and reach the colon. The GI microbiota responses to di...

    Authors: Anne H. Lee, Aashish R. Jha, Sungho Do, Elisa Scarsella, Justin Shmalberg, Amy Schauwecker, Andrew J. Steelman, Ryan W. Honaker and Kelly S. Swanson
    Citation: Animal Microbiome 2022 4:61
  2. Probiotics have been reported to exhibit positive effects on host health, including improved intestinal barrier function, preventing pathogenic infection, and promoting nutrient digestion efficiency. These int...

    Authors: Woong Ji Lee, Sangdon Ryu, An Na Kang, Minho Song, Minhye Shin, Sangnam Oh and Younghoon Kim
    Citation: Animal Microbiome 2022 4:60
  3. Staphylococcus aureus is a common cause of clinical mastitis (CM) in dairy cattle. Optimizing the bovine mammary gland microbiota to resist S. aureus colonization is a growing area of research. However, the detai...

    Authors: Soyoun Park, Dongyun Jung, Ianina Altshuler, Daryna Kruban, Simon Dufour and Jennifer Ronholm
    Citation: Animal Microbiome 2022 4:59
  4. Prebiotics are known to have a positive impact on fish health and growth rate, and β-glucans are among the most used prebiotics on the market. In this study, rainbow trout (Oncorhynchus mykiss) were treated with ...

    Authors: Simon Menanteau-Ledouble, Jakob Skov, Mie Bech Lukassen, Ulrike Rolle-Kampczyk, Sven-Bastiaan Haange, Inger Dalsgaard, Martin von Bergen and Jeppe Lund Nielsen
    Citation: Animal Microbiome 2022 4:58
  5. Microbiome analysis is quickly moving towards high-throughput methods such as metagenomic sequencing. Accurate taxonomic classification of metagenomic data relies on reference sequence databases, and their ass...

    Authors: Rebecca H. Smith, Laura Glendinning, Alan W. Walker and Mick Watson
    Citation: Animal Microbiome 2022 4:57
  6. The critically endangered kākāpō is a flightless, nocturnal parrot endemic to Aotearoa New Zealand. Recent efforts to describe the gastrointestinal microbial community of this threatened herbivore revealed a l...

    Authors: Annie G. West, Andrew Digby, Gavin Lear and Michael W. Taylor
    Citation: Animal Microbiome 2022 4:55
  7. Changes in the gut microbial composition is an important response to cope with the seasonal fluctuations in the environment such as food availability. We examined the bacterial gut microbiome of the wild nonhu...

    Authors: Akiko Sawada, Takashi Hayakawa, Yosuke Kurihara, Wanyi Lee and Goro Hanya
    Citation: Animal Microbiome 2022 4:54
  8. Rapidly spreading parasitic infections like amoebic gill disease (AGD) are increasingly problematic for Atlantic salmon reared in aquaculture facilities and potentially pose a risk to wild fish species in surr...

    Authors: Patrick Schaal, Bachar Cheaib, Joshka Kaufmann, Karl Phillips, Liz Ryder, Phil McGinnity and Martin Llewellyn
    Citation: Animal Microbiome 2022 4:53
  9. Broilers are among the most common and dense poultry production systems, where antimicrobials have been used extensively to promote animal health and performance. The continuous usage of antimicrobials has con...

    Authors: Ingrid Cárdenas-Rey, Teresita d. J. Bello Gonzalez, Jeanet van der Goot, Daniela Ceccarelli, Gerwin Bouwhuis, Danielle Schillemans, Stephanie D. Jurburg, Kees T. Veldman, J. Arjan G. M. de Visser and Michael S. M. Brouwer
    Citation: Animal Microbiome 2022 4:51
  10. Bovine respiratory disease (BRD) is caused by interactions among host, environment, and pathogens. One standard method for antemortem pathogen identification in cattle with BRD is deep-guarded nasopharyngeal s...

    Authors: William B. Crosby, Lee J. Pinnell, John T. Richeson, Cory Wolfe, Jake Castle, John Dustin Loy, Sheryl P. Gow, Keun Seok Seo, Sarah F. Capik, Amelia R. Woolums and Paul S. Morley
    Citation: Animal Microbiome 2022 4:49
  11. Parasitic infections disturb gut microbial communities beyond their natural range of variation, possibly leading to dysbiosis. Yet it remains underappreciated that most infections are accompanied by one or mor...

    Authors: Dominik W. Schmid, Gloria Fackelmann, Wasimuddin, Jacques Rakotondranary, Yedidya R. Ratovonamana, B. Karina Montero, Jörg U. Ganzhorn and Simone Sommer
    Citation: Animal Microbiome 2022 4:48
  12. Caves are special natural laboratories for most biota and the cave communities are unique. Establishing population in cave is accompanied with modifications in adaptability for most animals. To date, little is...

    Authors: Xin Gong, Ting-Wen Chen, Lili Zhang, Václav Pižl, Karel Tajovský and Miloslav Devetter
    Citation: Animal Microbiome 2022 4:47
  13. Diet has a large influence on gut microbiota diversity and function. Although previous studies have investigated the effect of dietary interventions on the gut microbiome, longitudinal changes in the gut micro...

    Authors: Ching-Yen Lin, Aashish R. Jha, Patrícia M. Oba, Sofia M. Yotis, Justin Shmalberg, Ryan W. Honaker and Kelly S. Swanson
    Citation: Animal Microbiome 2022 4:46
  14. Microbiomes are essential to a host’s physiology and health. Despite the overall importance of microbiomes to animal health, they remain understudied in wildlife. Microbiomes function as physical barriers to i...

    Authors: Andrew W. Bartlow, S. Kane Moser, Jeremy E. Ellis, Charles D. Hathcock and Jeanne M. Fair
    Citation: Animal Microbiome 2022 4:45
  15. In a diverse microbial world immune function of animals is essential. Diverse microbial environments may contribute to extensive variation in immunological phenotypes of vertebrates, among and within species a...

    Authors: H. Pieter J. van Veelen, Joana Falcão Salles, Kevin D. Matson, G. Sander van Doorn, Marco van der Velde and B. Irene Tieleman
    Citation: Animal Microbiome 2022 4:44
  16. Mastitis pathogenesis involves a wide range of opportunistic and apparently resident microorganims including bacteria, viruses and archaea. In dairy animals, microbes reside in the host, interact with environm...

    Authors: M. Nazmul Hoque, M. Shaminur Rahman, Tofazzal Islam, Munawar Sultana, Keith A. Crandall and M. Anwar Hossain
    Citation: Animal Microbiome 2022 4:43
  17. The welfare of farmed fish is influenced by numerous environmental and management factors. Fish skin is an important site for immunity and a major route by which infections are acquired. The objective of this ...

    Authors: Ashraf Al-Ashhab, Rivka Alexander-Shani, Yosef Avrahami, Roberto Ehrlich, Rosa Ines Strem, Shiri Meshner, Noam Shental and Galit Sharon
    Citation: Animal Microbiome 2022 4:42
  18. Diet is a key driver of equine hindgut microbial community structure and composition. The aim of this study was to characterize shifts in the fecal microbiota of grazing horses during transitions between forag...

    Authors: Jennifer R. Weinert-Nelson, Amy S. Biddle and Carey A. Williams
    Citation: Animal Microbiome 2022 4:41
  19. Host microbiomes may differ under the same environmental conditions and these differences may influence susceptibility to infection. Amphibians are ideal for comparing microbiomes in the context of disease def...

    Authors: Renato A. Martins, Sasha E. Greenspan, Daniel Medina, Shannon Buttimer, Vanessa M. Marshall, Wesley J. Neely, Samantha Siomko, Mariana L. Lyra, Célio F. B. Haddad, Vinícius São-Pedro and C. Guilherme Becker
    Citation: Animal Microbiome 2022 4:40
  20. The use of rumen microbial community (RMC) profiles to predict methane emissions has driven interest in ruminal DNA preservation and extraction protocols that can be processed cheaply while also maintaining or...

    Authors: Juliana C. C. Budel, Melanie K. Hess, Timothy P. Bilton, Hannah Henry, Ken G. Dodds, Peter H. Janssen, John C. McEwan and Suzanne J. Rowe
    Citation: Animal Microbiome 2022 4:39
  21. The resistome describes the array of antibiotic resistant genes (ARGs) present within a microbial community. Recent research has documented the resistome in the rumen of ruminants and revealed that the type an...

    Authors: Tao Ma, Rahat Zaheer, Tim A. McAllister, Wei Guo, Fuyong Li, Yan Tu, Qiyu Diao and Le Luo Guan
    Citation: Animal Microbiome 2022 4:38
  22. Biological invasion is one of the main components of global changes in aquatic ecosystems. Unraveling how establishment in novel environments affects key biological features of animals is a key step towards un...

    Authors: Arthur Escalas, Jean-Christophe Auguet, Amandine Avouac, Jonathan Belmaker, Thanos Dailianis, Moshe Kiflawi, Renanel Pickholtz, Grigorios Skouradakis and Sébastien Villéger
    Citation: Animal Microbiome 2022 4:37
  23. Multidrug resistance in companion animals poses significant risks to animal and human health. Prolonged antimicrobial drug (AMD) treatment in animals is a potential source of selection pressure for antimicrobi...

    Authors: Julie Menard, Robert Goggs, Patrick Mitchell, Yufan Yang, Sarah Robbins, Rebecca J. Franklin-Guild, Anil J. Thachil, Craig Altier, Renee Anderson, Gregory G. Putzel, Holly McQueary and Laura B. Goodman
    Citation: Animal Microbiome 2022 4:36
  24. The major greenhouse gas from ruminants is enteric methane (CH4) which in 2010, was estimated at 2.1 Gt of CO2 equivalent, accounting for 4.3% of global anthropogenic greenhouse gas emissions. There are extensive...

    Authors: Robert J. Gruninger, Xiu Min Zhang, Megan L. Smith, Limin Kung Jr., Diwakar Vyas, Sean M. McGinn, Maik Kindermann, Min Wang, Zhi Liang Tan and Karen A. Beauchemin
    Citation: Animal Microbiome 2022 4:35
  25. Animal-associated microbiomes can be influenced by both host and environmental factors. Comparing wild animals to those in zoos or aquariums can help disentangle the effects of host versus environmental factor...

    Authors: Ana G. Clavere-Graciette, Mary E. McWhirt, Lisa A. Hoopes, Kim Bassos-Hull, Krystan A. Wilkinson, Frank J. Stewart and Zoe A. Pratte
    Citation: Animal Microbiome 2022 4:34
  26. Gut microorganisms aid in the digestion of food by providing exogenous metabolic pathways to break down organic compounds. An integration of longitudinal microbial and chemical data is necessary to illuminate ...

    Authors: Wesley J. Sparagon, Emily C. Gentry, Jeremiah J. Minich, Lisa Vollbrecht, Lieve M. L. Laurens, Eric E. Allen, Neil A. Sims, Pieter C. Dorrestein, Linda Wegley Kelly and Craig E. Nelson
    Citation: Animal Microbiome 2022 4:33
  27. The term holobiont is widely accepted to describe animal hosts and their associated microorganisms. The genomes of all that the holobiont encompasses, are termed the hologenome and it has been proposed as a un...

    Authors: Andrea Unzueta-Martínez, Elliot Scanes, Laura M. Parker, Pauline M. Ross, Wayne O’Connor and Jennifer L. Bowen
    Citation: Animal Microbiome 2022 4:32
  28. Despite well-known effects of diet on gut microbiota diversity, relatively little is known about how maternal diet quality shapes the longitudinal maturation of gut microbiota in offspring. To investigate, we ...

    Authors: Kyoko Hasebe, Michael D. Kendig, Nadeem O. Kaakoush, Aynaz Tajaddini, R. Frederick Westbrook and Margaret J. Morris
    Citation: Animal Microbiome 2022 4:31
  29. Invertebrates are a very attractive subject for studying host-microbe interactions because of their simple gut microbial community and host diversity. Studying the composition of invertebrate gut microbiota an...

    Authors: Woorim Kang, Pil Soo Kim, Euon Jung Tak, Hojun Sung, Na-Ri Shin, Dong-Wook Hyun, Tae Woong Whon, Hyun Sik Kim, June-Young Lee, Ji-Hyun Yun, Mi-Ja Jung and Jin-Woo Bae
    Citation: Animal Microbiome 2022 4:30
  30. Inter-population variation in host-associated microbiota reflects differences in the hosts’ environments, but this characterization is typically based on studies comparing few populations. The diversity of nat...

    Authors: Sally L. Bornbusch, Lydia K. Greene, Sylvia Rahobilalaina, Samantha Calkins, Ryan S. Rothman, Tara A. Clarke, Marni LaFleur and Christine M. Drea
    Citation: Animal Microbiome 2022 4:29
  31. Heat stress (HS) has negative effects on poultry productivity, health and welfare resulting in economic losses. Broiler chickens are particularly susceptible to HS due to their high metabolic rate and rapid gr...

    Authors: Nima K. Emami, Lori L. Schreier, Elizabeth Greene, Travis Tabler, Sara K. Orlowski, Nicholas B. Anthony, Monika Proszkowiec-Weglarz and Sami Dridi
    Citation: Animal Microbiome 2022 4:28
  32. Animal-associated microbial communities appear to be key factors in host physiology, ecology, evolution and its interactions with the surrounding environment. Teleost fish have received relatively little atten...

    Authors: Mathilde Scheifler, Sophie Sanchez-Brosseau, Elodie Magnanou and Yves Desdevises
    Citation: Animal Microbiome 2022 4:27
  33. In recent years, the number of studies concerning microbiota of the intramammary environment has increased rapidly due to the development of high-throughput sequencing technologies that allow mapping of microb...

    Authors: Anja Ruud Winther, Judith A. Narvhus, Marit Smistad, Vinicius da Silva Duarte, Alberto Bombelli and Davide Porcellato
    Citation: Animal Microbiome 2022 4:26
  34. Backgrounding (BKG), the stage between weaning and finishing, significantly impacts feedlot performance in beef cattle; however, the contributions of the rumen microbiome to this growth stage remain unexplored...

    Authors: Bobwealth O. Omontese, Ashok K. Sharma, Samuel Davison, Emily Jacobson, Alfredo DiConstanzo, Megan J. Webb and Andres Gomez
    Citation: Animal Microbiome 2022 4:25
  35. Bats are important long-distance dispersers of many tropical plants, yet, by consuming fruits, they may disperse not only the plant’s seeds, but also the mycobiota within those fruits. We characterized the cul...

    Authors: Priscila Chaverri and Gloriana Chaverri
    Citation: Animal Microbiome 2022 4:24
  36. Helminth parasitism is a world-wide problem in livestock industries, with major impacts on health, welfare and productivity. The role of the gut microbiota in host-helminth interactions in ruminants has been e...

    Authors: Erwin A. Paz, Eng Guan Chua, Shamshad Ul Hassan, Johan C. Greeff, Dieter G. Palmer, Shimin Liu, Binit Lamichhane, Néstor Sepúlveda, Junhua Liu, Chin Yen Tay and Graeme B. Martin
    Citation: Animal Microbiome 2022 4:23
  37. Molecular hydrogen (H2) and formate (HCOO) are metabolic end products of many primary fermenters in the mammalian gut. Both play a vital role in fermentation where they are electron sinks for individual microbes...

    Authors: William J. Kelly, Roderick I. Mackie, Graeme T. Attwood, Peter H. Janssen, Tim A. McAllister and Sinead C. Leahy
    Citation: Animal Microbiome 2022 4:22
  38. The potential to distribute bacteria resistant to antimicrobial drugs in the meat supply is a public health concern. Market cows make up a fifth of the U.S. beef produced but little is known about the entire p...

    Authors: Margaret D. Weinroth, Kevin M. Thomas, Enrique Doster, Amit Vikram, John W. Schmidt, Terrance M. Arthur, Tommy L. Wheeler, Jennifer K. Parker, Ayanna S. Hanes, Najla Alekoza, Cory Wolfe, Jessica L. Metcalf, Paul S. Morley and Keith E. Belk
    Citation: Animal Microbiome 2022 4:21
  39. Mucosal surfaces of fish provide cardinal defense against environmental pathogens and toxins, yet these external mucosae are also responsible for maintaining and regulating beneficial microbiota. To better our...

    Authors: Jacob W. Bledsoe, Michael R. Pietrak, Gary S. Burr, Brian C. Peterson and Brian C. Small
    Citation: Animal Microbiome 2022 4:20
  40. Rumen microbial composition and functions have vital roles in feed digestion and fermentation and are linked to feed efficiency in cattle. This study selected Holstein cows, which are high in both milk protein...

    Authors: Yunyi Xie, Huizeng Sun, Mingyuan Xue and Jianxin Liu
    Citation: Animal Microbiome 2022 4:19
  41. Bovine mastitis is one of the most economically important diseases affecting dairy cows. The choice of bedding material has been identified as an important risk factor contributing to the development of mastit...

    Authors: Tui Ray, Tara Nath Gaire, Christopher J. Dean, Sam Rowe, Sandra M. Godden and Noelle R. Noyes
    Citation: Animal Microbiome 2022 4:18
  42. Sharks play essential roles in ocean food webs and human culture, but also face population declines worldwide due to human activity. The relationship between sharks and the microbes on and in the shark body is...

    Authors: Zoe A. Pratte, Cameron Perry, Alistair D. M. Dove, Lisa A. Hoopes, Kim B. Ritchie, Robert E. Hueter, Chris Fischer, Alisa L. Newton and Frank J. Stewart
    Citation: Animal Microbiome 2022 4:17
  43. Similar to many other animals, the honey bee Apis mellifera relies on a beneficial gut microbiota for regulation of immune homeostasis. Honey bees exposed to agrochemicals, such as the herbicide glyphosate or ant...

    Authors: Erick V. S. Motta, J. Elijah Powell and Nancy A. Moran
    Citation: Animal Microbiome 2022 4:16
  44. Bovine respiratory disease (BRD) is an ongoing health and economic challenge in the dairy and beef cattle industries. Multiple risk factors make an animal susceptible to BRD. The presence of Mannheimia haemolytic...

    Authors: Ruth Eunice Centeno-Martinez, Natalie Glidden, Suraj Mohan, Josiah Levi Davidson, Esteban Fernández-Juricic, Jacquelyn P. Boerman, Jon Schoonmaker, Deepti Pillai, Jennifer Koziol, Aaron Ault, Mohit S. Verma and Timothy A. Johnson
    Citation: Animal Microbiome 2022 4:15
  45. Eukaryotic microbes can modulate mammalian host health and disease states, yet the molecular contribution of gut fungi remains nascent. We previously showed that mice exclusively colonised with fungi displayed...

    Authors: Veronika Kuchařová Pettersen, Antoine Dufour and Marie-Claire Arrieta
    Citation: Animal Microbiome 2022 4:14
  46. The koala (Phascolarctos cinereus), an iconic yet endangered specialised folivore experiencing widespread decline across Australia, is the focus of many conservation programs. Whilst animal translocation and prog...

    Authors: B. L. Littleford-Colquhoun, L. S. Weyrich, K. Hohwieler, R. Cristescu and C. H. Frère
    Citation: Animal Microbiome 2022 4:12

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