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Gut Microbiome and Animal Health

A cross-journal collection exploring the microbial contribution to animal health

The gut microbiome is closely associated with the health and performance of animals, which receives wide attention from researchers. Studies using meta-omics approaches could help researchers to further understand the functions and roles of animal-associated microbiome. This cross-journal collection welcomes research and review papers in all aspects including but not limited to:

1) Structure and function of gut microbiota and its interplay with the host

2) Nutritional manipulation and animal health

3) Microbiome-driven adaption to the environment of domestic and non-domestic animals

4) Application potential of gut microbiome and the mechanism

5) Microbial cultures and their function in the complex eco-system

6) Development and application of bioinformatic tools

Submissions are welcomed to Microbiome, Journal of Animal Science and Biotechnology, and Animal Microbiome. Each manuscript will be peer-reviewed using the journals' usual peer review process and may be suggested to transfer to another journal to ensure it is placed in the most appropriate journal within this collection. Upon publication, all papers will be included in this collection.

Please find each journal's peer review policies as follows:
Animal Microbiome, Microbiome, Journal of Animal Science and Biotechnology.

This collection will be open for submissions until 30th June 2023.


  1. Yellow mealworm larvae (YML; Tenebrio molitor) are considered as a valuable insect species for animal feed due to their high nutritional values and ability to grow under different substrates and rearing condition...

    Authors: Linggawastu Syahrulawal, Magnhild Oust Torske, Rumakanta Sapkota, Geir Næss and Prabhat Khanal
    Citation: Journal of Animal Science and Biotechnology 2023 14:146
    Content type: Review Published on:

  2. Many studies have investigated how nanoplastics (NPs) exposure mediates nerve and intestinal toxicity through a dysregulated brain-gut axis interaction, but there are few studies aimed at alleviating those eff...

    Authors: Miaomiao Teng, Yunxia Li, Xiaoli Zhao, Jason C. White, Lihui Zhao, Jiaqi Sun, Wentao Zhu and Fengchang Wu
    Citation: Microbiome 2023 11:266
    Content type: Research Published on:

  3. Liver abscesses (LAs) are one of the most common and important problems faced by the beef industry. The most efficacious method for the prevention of LAs in North America is through dietary inclusion of low do...

    Authors: Lee J. Pinnell, J. Daniel Young, Tyler W. Thompson, Cory A. Wolfe, Tony C. Bryant, Mahesh N. Nair, John T. Richeson and Paul S. Morley
    Citation: Animal Microbiome 2023 5:58
    Content type: Research Published on:

  4. Minimizing mortality losses due to multiple stress and obtaining maximum performance are the production goals for newly received cattle. In recent years, vaccination and metaphylaxis treatment significantly de...

    Authors: Yanjiao Li, Kang Mao, Yitian Zang, Guwei Lu, Qinghua Qiu, Kehui Ouyang, Xianghui Zhao, Xiaozhen Song, Lanjiao Xu, Huan Liang and Mingren Qu
    Citation: Microbiome 2023 11:238
    Content type: Research Published on:

  5. Modern dairy diets have shifted from being forage-based to grain and energy dense. However, feeding high-starch diets can lead to a metabolic disturbance that is linked to dysregulation of the gastrointestinal...

    Authors: Yuchao Zhao, Shiqiang Yu, Huiying Zhao, Liuxue Li, Yuqin Li, Ming Liu and Linshu Jiang
    Citation: Microbiome 2023 11:236
    Content type: Research Published on:

  6. Shrimp cultured in a biofloc system (BFS) have a lower disease incidence than those farmed in a water exchange system (WES). Although a number of studies have reported that the gut bacterial community induced ...

    Authors: Haipeng Guo, Xuezhi Fu, Jikun He, Ruoyu Wang, Mengchen Yan, Jing Wang, Pengsheng Dong, Lei Huang and Demin Zhang
    Citation: Microbiome 2023 11:230
    Content type: Research Published on:

  7. Pet cats frequently have diarrhea in their daily life. Bacillus has a protective role that has crucial beneficial functions on intestinal homeostasis. The aim of this research was to investigate the effects of th...

    Authors: Fei Wang, Xiaoying Mei, Qi Wang, Pengwei Zhao, Yuanhao Zhou, Li Tang, Baikui Wang, Shujie Xu, Xiang Li, Qian Jin, Yingping Xiao and Weifen Li
    Citation: Animal Microbiome 2023 5:49
    Content type: Research Published on:

  8. To improve our understanding of host and intestinal microbiome interaction, this research investigated the effects of a high-level zinc oxide in the diet as model intervention on the intestinal microbiome and ...

    Authors: Dirkjan Schokker, Soumya K. Kar, Els Willems, Alex Bossers, Ruud A. Dekker and Alfons J. M. Jansman
    Citation: Journal of Animal Science and Biotechnology 2023 14:122
    Content type: Research Published on:

  9. The gut microbiota is modulated by a combination of diet, host genetics, and sex effects. The magnitude of these effects and interactions among them is important to understanding inter-individual variability i...

    Authors: Anna C. Salvador, M. Nazmul Huda, Danny Arends, Ahmed M. Elsaadi, C. Anthony Gacasan, Gudrun A. Brockmann, William Valdar, Brian J. Bennett and David W. Threadgill
    Citation: Microbiome 2023 11:220
    Content type: Research Published on:

  10. The dog is the most popular companion animal and is a valuable large animal model for several human diseases. Canine immune-mediated hematological diseases, including immune-mediated hemolytic anemia (IMHA) an...

    Authors: P.-Y. Liu, D. Xia, K. McGonigle, A. B. Carroll, J. Chiango, H. Scavello, R. Martins, S. Mehta, E. Krespan, E. Lunde, D. LeVine, C. L. Fellman, R. Goggs, D. P. Beiting and O. A. Garden
    Citation: Animal Microbiome 2023 5:46
    Content type: Research Published on:

  12. The existence of the gut microbiota produces an “individual drug reaction.” As members of the intestinal microbiota, probiotics, although they have prebiotic functions, may accelerate the degradation of drugs,...

    Authors: Siyuan Shen, Jun Wang, Chenchen Ma, Yanni Chen, Hao Ding and Jiachao Zhang
    Citation: Microbiome 2023 11:209
    Content type: Research Published on:

  13. Cryptosporidium parvum is the main cause of calf scour worldwide. With limited therapeutic options and research compared to other Apicomplexa, it is important to understand the parasites’ biology and interactions...

    Authors: M. F. Hares, B. E. Griffiths, F. Johnson, C. Nelson, S. Haldenby, C. J. Stewart, J. S. Duncan, G. Oikonomou and J. L. Coombes
    Citation: Animal Microbiome 2023 5:43
    Content type: Research Published on:

  14. Improving feed efficiency is the most important goal for modern animal production. The regulatory mechanisms of controlling feed efficiency traits are extremely complex and include the functions related to hos...

    Authors: Zhengxiao He, Ranran Liu, Mengjie Wang, Qiao Wang, Jumei Zheng, Jiqiang Ding, Jie Wen, Alan G. Fahey and Guiping Zhao
    Citation: Microbiome 2023 11:198
    Content type: Research Published on:

  15. Bioconversion using insects is a promising strategy to convert organic waste (catering leftovers, harvest waste, food processing byproducts, etc.) into biomass that can be used for multiple applications, turne...

    Authors: Maurielle Eke, Kévin Tougeron, Alisa Hamidovic, Leonard S. Ngamo Tinkeu, Thierry Hance and François Renoz
    Citation: Animal Microbiome 2023 5:40
    Content type: Review Published on:

  16. Heritable rumen microbiota is an important modulator of ruminant growth performance. However, no information exists to date on host genetics-rumen microbiota interactions and their association with phenotype i...

    Authors: Weimin Wang, Yukun Zhang, Xiaoxue Zhang, Chong Li, Lvfeng Yuan, Deyin Zhang, Yuan Zhao, Xiaolong Li, Jiangbo Cheng, Changchun Lin, Liming Zhao, Jianghui Wang, Dan Xu, Xiangpeng Yue, Wanhong Li, Xiuxiu Wen…
    Citation: Microbiome 2023 11:197
    Content type: Research Published on:

  17. Some microbiota compositions are associated with negative outcomes, including among others, obesity, allergies, and the failure to respond to treatment. Microbiota manipulation or supplementation can restore a...

    Authors: Oshrit Shtossel, Sondra Turjeman, Alona Riumin, Michael R. Goldberg, Arnon Elizur, Yarin Bekor, Hadar Mor, Omry Koren and Yoram Louzoun
    Citation: Microbiome 2023 11:181
    Content type: Research Published on:

  18. The fungal component of the human gut microbiome, also known as the mycobiome, plays a vital role in intestinal ecology and human health. However, the overall structure of the gut mycobiome as well as the inte...

    Authors: Senying Lai, Yan Yan, Yanni Pu, Shuchun Lin, Jian-Ge Qiu, Bing-Hua Jiang, Marisa Isabell Keller, Mingyu Wang, Peer Bork, Wei-Hua Chen, Yan Zheng and Xing-Ming Zhao
    Citation: Microbiome 2023 11:179
    Content type: Research Published on:

  19. Despite the long-established importance of zebrafish (Danio rerio) as a model organism and their increasing use in microbiome-targeted studies, relatively little is known about how husbandry practices involving d...

    Authors: Michael J. Sieler Jr., Colleen E. Al-Samarrie, Kristin D. Kasschau, Zoltan M. Varga, Michael L. Kent and Thomas J. Sharpton
    Citation: Animal Microbiome 2023 5:38
    Content type: Research Published on:

  20. Ginkgo biloba extract (GBE) is evidenced to be effective in the prevention and alleviation of metabolic disorders, including obesity, diabetes and fatty liver disease. However, the role of GBE in alleviating fatt...

    Authors: Xinyue Yang, Depeng Li, Meihong Zhang, Yuqing Feng, Xiaolu Jin, Dan Liu, Yuming Guo and Yongfei Hu
    Citation: Journal of Animal Science and Biotechnology 2023 14:97
    Content type: Research Published on:

  21. The inclusion of alternative ingredients in poultry feed is foreseen to impact poultry gut microbiota. New feeding strategies (probiotics/prebiotics) must be adopted to allow sustainable productions. Therefore...

    Authors: Ilario Ferrocino, Ilaria Biasato, Sihem Dabbou, Elena Colombino, Kalliopi Rantsiou, Simone Squara, Marta Gariglio, Maria Teresa Capucchio, Laura Gasco, Chiara Emilia Cordero, Erica Liberto, Achille Schiavone and Luca Cocolin
    Citation: Animal Microbiome 2023 5:36
    Content type: Research Published on:

  22. Antibiotics are widely used for prophylactic therapy and for improving the growth performance of chicken. The problem of bacterial drug resistance caused by antibiotic abuse has previously attracted extensive ...

    Authors: Xianghui Liang, Zhipeng Zhang, Hai Wang, Xingbang Lu, Wen Li, Haoran Lu, Ayan Roy, Xuejuan Shen, David M. Irwin and Yongyi Shen
    Citation: Microbiome 2023 11:163
    Content type: Research Published on:

  23. For more than a century, the Koch’s postulates have been the golden rule for determining the causative agents in diseases. However, in cases of multiple pathogens-one disease, in which different pathogens can ...

    Authors: Dongwei Hou, Taixin Lian, Guangyu Guo, Han Gong, Chengcheng Wu, Peiyun Han, Shaoping Weng and Jianguo He
    Citation: Microbiome 2023 11:155
    Content type: Research Published on:

  24. Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome researc...

    Authors: Brandi Feehan, Qinghong Ran, Victoria Dorman, Kourtney Rumback, Sophia Pogranichniy, Kaitlyn Ward, Robert Goodband, Megan C. Niederwerder and Sonny T. M. Lee
    Citation: Animal Microbiome 2023 5:35
    Content type: Research Published on:

  25. Artificial rearing system, commonly used in prolific sheep breeds, is associated to increased mortality and morbidity rates before weaning, which might be linked to perturbations in digestive tract maturation,...

    Authors: Lysiane Dunière, Philippe Ruiz, Yacine Lebbaoui, Laurie Guillot, Mickael Bernard, Evelyne Forano and Frédérique Chaucheyras-Durand
    Citation: Animal Microbiome 2023 5:34
    Content type: Research Published on:

  26. The development of a sustainable business model with social acceptance, makes necessary to develop new strategies to guarantee the growth, health, and well-being of farmed animals. Debaryomyces hansenii is a yeas...

    Authors: Ignasi Sanahuja, Alberto Ruiz, Joana P. Firmino, Felipe E. Reyes-López, Juan B. Ortiz-Delgado, Eva Vallejos-Vidal, Lluis Tort, Dariel Tovar-Ramírez, Isabel M. Cerezo, Miguel A. Moriñigo, Carmen Sarasquete and Enric Gisbert
    Citation: Journal of Animal Science and Biotechnology 2023 14:90
    Content type: Research Published on:

  27. Soybean (Glycine max) meal is one of the important protein sources for fish, but the non-starch polysaccharides (NSP) in soybean meal impair the intestinal barrier function. Here we aimed to investigate whether ...

    Authors: Tong Wang, Nannan Zhou, Junyi He, Zhenzhen Hao, Chentao Zhou, Yidi Du, Zhenyu Du, Xiaoyun Su and Meiling Zhang
    Citation: Journal of Animal Science and Biotechnology 2023 14:86
    Content type: Research Published on:

  28. Cold regions have long autumn and winter seasons and low ambient temperatures. When pigs are unable to adjust to the cold, oxidative damage and inflammation may develop. However, the differences between cold a...

    Authors: Teng Teng, Guodong Sun, Hongwei Ding, Xin Song, Guangdong Bai, Baoming Shi and Tingting Shang
    Citation: Journal of Animal Science and Biotechnology 2023 14:84
    Content type: Research Published on:

  29. Alginate oligosaccharide (AOS) holds great potential as a novel feed supplement in farm animals. However, the effects of AOS on chicken health and the underlying mechanisms are not fully understood. This study...

    Authors: A La Teng Zhu La, Yuqing Feng, Die Hu, Yimei Feng, Xiaolu Jin, Dan Liu, Yuming Guo, Gong Cheng and Yongfei Hu
    Citation: Journal of Animal Science and Biotechnology 2023 14:96
    Content type: Research Published on:

  30. Intestinal inflammation has become a threatening concern in chicken production worldwide and is closely associated with Th17/Treg cell imbalance. Several studies described that gut microbiota is significantly ...

    Authors: Ziyu Ma, Muhammad Akhtar, Hong Pan, Qiyao Liu, Yan Chen, Xinxin Zhou, Yingting You, Deshi Shi and Huazhen Liu
    Citation: Microbiome 2023 11:137
    Content type: Research Published on:

  31. Pathogen infections seriously affect host health, and the use of antibiotics increases the risk of the emergence of drug-resistant bacteria and also increases environmental and health safety risks. Probiotics ...

    Authors: Xiaozhou Qi, Yong Zhang, Yilin Zhang, Fei Luo, Kaige Song, Gaoxue Wang and Fei Ling
    Citation: Microbiome 2023 11:135
    Content type: Research Published on:

  32. The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disr...

    Authors: Ikaia Leleiwi, Josué Rodriguez-Ramos, Michael Shaffer, Anice Sabag-Daigle, Katherine Kokkinias, Rory M. Flynn, Rebecca A. Daly, Linnea F. M. Kop, Lindsey M. Solden, Brian M. M. Ahmer, Mikayla A. Borton and Kelly C. Wrighton
    Citation: Microbiome 2023 11:114
    Content type: Research Published on:

  33. Some insects can degrade both natural and synthetic plastic polymers, their host and gut microbes play crucial roles in this process. However, there is still a scientific gap in understanding how the insect ad...

    Authors: Tursunay Mamtimin, Huawen Han, Aman Khan, Pengya Feng, Qing Zhang, Xiaobiao Ma, Yitian Fang, Pu Liu, Saurabh Kulshrestha, Toshiro Shigaki and Xiangkai Li
    Citation: Microbiome 2023 11:98
    Content type: Research Published on:

  34. The Western dietary pattern, characterized by high consumption of fats and sugars, has been strongly associated with an increased risk of developing Crohn’s disease (CD). However, the potential impact of mater...

    Authors: Chongyang Huang, Huishi Tan, Mengyao Song, Ke Liu, Hongbin Liu, Jun Wang, Yanqiang Shi, Fengyi Hou, Qian Zhou, Ruo Huang, Binghai Shen, Xinlong Lin, Xiaoming Qin and Fachao Zhi
    Citation: Microbiome 2023 11:96
    Content type: Research Published on:

  35. Accumulating evidence from human trials and rodent studies has indicated that modulation of gut microbiota affects host physiological homeostasis and behavioral characteristics. Similarly, alterations in gut m...

    Authors: Yuechi Fu, Jiaying Hu, Marisa A. Erasmus, Huanmin Zhang, Timothy A. Johnson and Hengwei Cheng
    Citation: Journal of Animal Science and Biotechnology 2023 14:66
    Content type: Research Published on:

  36. To understand mechanisms of adaptation and plasticity of pollinators and other insects a better understanding of diversity and function of their key symbionts is required. Commensalibacter is a genus of acetic ac...

    Authors: Juliana Botero, Atena Sadat Sombolestani, Margo Cnockaert, Charlotte Peeters, Wim Borremans, Luc De Vuyst, Nicolas J. Vereecken, Denis Michez, Guy Smagghe, German Bonilla-Rosso, Philipp Engel and Peter Vandamme
    Citation: Animal Microbiome 2023 5:25
    Content type: Research Published on:

  37. Human encroachment into nature and the accompanying environmental changes are a big concern for wildlife biodiversity and health. While changes on the macroecological scale, i.e. species community and abundanc...

    Authors: Alexander Christoph Heni, Gloria Fackelmann, Georg Eibner, Swetlana Kreinert, Julian Schmid, Nina Isabell Schwensow, Jonas Wiegand, Kerstin Wilhelm and Simone Sommer
    Citation: Animal Microbiome 2023 5:22
    Content type: Research Published on:

  38. Crohn’s disease (CD) is associated with changes in the microbiota, and murine models of CD-like ileo-colonic inflammation depend on the presence of microbial triggers. Increased abundance of unknown Clostridia...

    Authors: Amira Metwaly, Jelena Jovic, Nadine Waldschmitt, Sevana Khaloian, Helena Heimes, Deborah Häcker, Mohamed Ahmed, Nassim Hammoudi, Lionel Le Bourhis, Aida Mayorgas, Kolja Siebert, Marijana Basic, Tobias Schwerd, Matthieu Allez, Julian Panes, Azucena Salas…
    Citation: Microbiome 2023 11:66
    Content type: Research Published on:

  40. Bacterial vaginosis (BV) is a disease caused by vaginal microbiota dysbiosis. Here, we propose the use of synthetic bacterial consortia transplantation (SBCT) for the treatment of Gardnerella vaginalis-induced BV...

    Authors: Yunxia Li, Wei Zhu, Yan Jiang, Duncan James Lessing and Weihua Chu
    Citation: Microbiome 2023 11:54
    Content type: Brief Report Published on:

  41. Pectin is a heteropolysaccharide that acts as an intestinal immunomodulator, promoting intestinal development and regulating intestinal flora in the gut. However, the relevant mechanisms remain obscure. In thi...

    Authors: Guoqi Dang, Xiaobin Wen, Ruqing Zhong, Weida Wu, Shanlong Tang, Chong Li, Bao Yi, Liang Chen, Hongfu Zhang and Martine Schroyen
    Citation: Journal of Animal Science and Biotechnology 2023 14:38
    Content type: Research Published on:

  42. Postpartum dairy cows experiencing excessive lipolysis are prone to severe immunosuppression. Despite the extensive understanding of the gut microbial regulation of host immunity and metabolism, its role durin...

    Authors: Fengfei Gu, Senlin Zhu, Yifan Tang, Xiaohan Liu, Minghui Jia, Nilusha Malmuthuge, Teresa G. Valencak, Joseph W. McFadden, Jian-Xin Liu and Hui-Zeng Sun
    Citation: Microbiome 2023 11:40
    Content type: Research Published on:

  43. Prebiotic feed additives aim to improve gut health by influencing the microbiota and the gut barrier. Most studies on feed additives concentrate on one or two (monodisciplinary) outcome parameters, such as imm...

    Authors: Adrià López Nadal, Jos Boekhorst, Carolien Lute, Frank van den Berg, Michelle A. Schorn, Tommy Bergen Eriksen, David Peggs, Charles McGurk, Detmer Sipkema, Michiel Kleerebezem, Geert F. Wiegertjes and Sylvia Brugman
    Citation: Animal Microbiome 2023 5:15
    Content type: Research Published on:

  44. Wild boar has experienced several evolutionary trajectories from which domestic (under artificial selection) and the feral pig (under natural selection) originated. Strong adaptation deeply affects feral popul...

    Authors: Simona Petrelli, Maria Buglione, Eleonora Rivieccio, Ezio Ricca, Loredana Baccigalupi, Giovanni Scala and Domenico Fulgione
    Citation: Animal Microbiome 2023 5:14
    Content type: Research Published on:

  45. Dairy cattle (Bos taurus), especially Holstein cows, which are the highest-producing dairy animals and are widely bred to provide milk products to humans, rely critically on their associated gastrointestinal trac...

    Authors: Limei Lin, Zheng Lai, Jiyou Zhang, Weiyun Zhu and Shengyong Mao
    Citation: Microbiome 2023 11:10
    Content type: Research Published on:

  46. As a domesticated species vital to humans, horses are raised worldwide as a source of mechanical energy for sports, leisure, food production, and transportation. The gut microbiota plays an important role in t...

    Authors: Cunyuan Li, Xiaoyue Li, Rongjun Guo, Wei Ni, Kaiping Liu, Zhuang Liu, Jihong Dai, Yueren Xu, Shamshidin Abduriyim, Zhuangyuan Wu, Yaqi Zeng, Bingbing Lei, Yunfeng Zhang, Yue Wang, Weibin Zeng, Qiang Zhang…
    Citation: Microbiome 2023 11:7
    Content type: Research Published on:

  47. Rice-fish symbiosis, as an ecological and green aquaculture model, is an effective measure to relieve the environmental stress from intensive aquaculture. Compared with traditional aquaculture, the altered rea...

    Authors: Erlong Wang, Ya Zhou, Yue Liang, Fei Ling, Xiaoshu Xue, Xianlin He, Xuliang Zhai, Yang Xue, Chunlong Zhou, Guo Tang and Gaoxue Wang
    Citation: Microbiome 2022 10:231
    Content type: Research Published on:

  48. 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
    Content type: Research Published on:

  49. Vascular calcification is a major cause of the high morbidity and mortality of cardiovascular diseases and is closely associated with the intestinal microbiota. Short-chain fatty acids (SCFAs) are derived from...

    Authors: Jianlong Yan, Yanbin Pan, Wenming Shao, Caiping Wang, Rongning Wang, Yaqiong He, Min Zhang, Yongshun Wang, Tangzhiming Li, Zhefeng Wang, Wenxing Liu, Zhenmin Wang, Xin Sun and Shaohong Dong
    Citation: Microbiome 2022 10:195
    Content type: Research Published on: