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Antimicrobial resistance and the microbiome

Microbiome, Environmental Microbiome and Animal Microbiome are coming together to launch a special series inviting authors to submit their research pertaining to antimicrobial resistance (AMR) and the microbiome.

© Image by Arek Socha from Pixabay

The emergence and spread of AMR can only be described as a catastrophic problem for human and animal health. It is projected that there would be more deaths due to AMR than cancer by 2050.

During the last decade a large number of studies have reported the emergence and spread of antimicrobial resistance genes (ARG) and defined in detail how these are mobilized between pathogens and also within communities of bacteria. The impact of antibiotics on microbiomes particularly those of humans and animals is a cause for concern and can alter physiology quite dramatically. In addition the spread of ARG to these microbiomes has been reported and occurs on a global scale clearly indicated in studies of sewage and waste water treatment plants. Further spread may occur under selective conditions in the presence of antibiotics in sewage and other biocides such as detergents both of which could cause significant changes in diversity. We need to understand the impacts of ingression of ARG into microbiomes and consider the wider issue of AMR spread into the environment.

The importance of human microbiomes is indisputable now as many new aspects of their roles have emerged in the past few years and continue to build a complex picture of metabolic interactions with their hosts. Similarly, animal and plant microbiomes studies have provided an exciting view into the potential benefits of healthy, diverse and stable microbiomes for sustainable agriculture. Understanding the persistence and spread of ARG in agricultural and other food production systems such as aquaculture will be critical for food safety and production. We are just beginning to reveal the importance of microbial assemblages in the environment for both bioremediation and biodegradation in addition to the vital roles played in nutrient cycles. Antimicrobial agents can have impact on all these activities in addition to spreading new gene combinations due to the rapid mobilization of ARGs due to the highly selective effects of antibiotic therapy. Whilst some antibiotics are natural products others are xenobiotics and remain and persist in the environment and mobile ARG will spread as a result of selection. Most naturally occurring resistance genes are chromosomal and further work is needed to investigate these impacts.

Microbiomes may work syntrophically to degrade recalcitrant compounds and recent research has demonstrated the emergence of antibiotic biodegraders within the environment and these bacteria may provide the answer to reduce the persistence of antibiotics and their detrimental effects in nature. By understanding the natural role of antibiotics produced in nature we may find the clues to avoiding the arms race of ever increasing resistance in the face of novel drugs, streptomycin production gene clusters are still found in soil streptomycetes and were dated thought to have emerged several million years ago yet they are still apparently useful in nature today. Further research will inform new ways to administer antibiotics, new types of drugs and new ways to combat resistance.

Submission: You can submit to any one of the participating journals, as they are all part of the Microbiome journal family. The Editors will indicate to you during the peer review process if they think your manuscript would be a better fit for one of the other microbiome journals. Each manuscript will undergo peer review as normal in the appropriate journal and be included in this series upon publication.

Deadline for submissions: 31st December 2022

Submit to Animal Microbiome.

Submit to Environmental Microbiome.

Submit to Microbiome.

  1. Intramammary (IMM) ceftiofur treatment is commonly used in dairy farms to prevent mastitis, though its impact on the cattle gut microbiome and selection of antibiotic-resistant bacteria has not been elucidated...

    Authors: Karla A. Vasco, Samantha Carbonell, Rebekah E. Sloup, Bailey Bowcutt, Rita R. Colwell, Karlis Graubics, Ronald Erskine, Bo Norby, Pamela L. Ruegg, Lixin Zhang and Shannon D. Manning
    Citation: Animal Microbiome 2023 5:56
  2. Companion animals can contribute to the physical and mental health of people and often live in very close association with their owners. However, the antibiotic resistome carried by companion animals and the i...

    Authors: Yiwen Yang, Xinwen Hu, Shuang Cai, Nan Hu, Yilin Yuan, Yinbao Wu, Yan Wang, Jiandui Mi and Xindi Liao
    Citation: Microbiome 2023 11:235
  3. Early life plays a vital role in the development of the gut microbiome and subsequent health. While many factors that shape the gut microbiome have been described, including delivery mode, breastfeeding, and a...

    Authors: Molly Mills, Seungjun Lee, Barbara A. Piperata, Rebecca Garabed, Boseung Choi and Jiyoung Lee
    Citation: Microbiome 2023 11:207
  4. The COVID-19 pandemic has highlighted the extent to which the public transportation environment, such as in subways, may be important for the transmission of potential pathogenic microbes among humans, with th...

    Authors: Maria D’Accolti, Irene Soffritti, Francesca Bini, Eleonora Mazziga, Carolina Cason, Manola Comar, Antonella Volta, Matteo Bisi, Daniele Fumagalli, Sante Mazzacane and Elisabetta Caselli
    Citation: Microbiome 2023 11:64
  5. With the escalating risk of antimicrobial resistance (AMR), there are limited analytical options available that can comprehensively assess the burden of AMR carried by clinical/environmental samples. Food can ...

    Authors: Julie A. Shay, Laura S. E. Haniford, Ashley Cooper, Catherine D. Carrillo, Burton W. Blais and Calvin Ho-Fung Lau
    Citation: Environmental Microbiome 2023 18:25
  6. Many deep-sea invertebrates largely depend on chemoautotrophic symbionts for energy and nutrition, and some of them have reduced functional digestive tracts. By contrast, deep-sea mussels have a complete diges...

    Authors: Yao Xiao, Hao Wang, Yi Lan, Cheng Zhong, Guoyong Yan, Zhimeng Xu, Guangyuan Lu, Jiawei Chen, Tong Wei, Wai Chuen Wong, Yick Hang Kwan and Pei-Yuan Qian
    Citation: Animal Microbiome 2023 5:17
  7. Bacterial communities in humans, animals, and the external environment maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs are well-characterized and thus established ...

    Authors: Juan Salvador Inda-Díaz, David Lund, Marcos Parras-Moltó, Anna Johnning, Johan Bengtsson-Palme and Erik Kristiansson
    Citation: Microbiome 2023 11:44
  8. The plasmid-mediated resistance gene mcr-1 confers colistin resistance in Escherichia coli and paves the way for the evolution to pan-drug resistance. We investigated the impact of mcr-1 in gut colonization in th...

    Authors: Guillaume Dalmasso, Racha Beyrouthy, Sandrine Brugiroux, Etienne Ruppé, Laurent Guillouard, Virginie Bonnin, Pierre Saint-Sardos, Amine Ghozlane, Vincent Gaumet, Nicolas Barnich, Julien Delmas and Richard Bonnet
    Citation: Microbiome 2023 11:12

    The Correction to this article has been published in Microbiome 2023 11:23

  9. Understanding the natural microbiome and resistome of wildlife from remote places is necessary to monitor the human footprint on the environment including antimicrobial use (AU). Marine iguanas are endemic spe...

    Authors: Karla Vasco, Nataly Guevara, Juan Mosquera, Sonia Zapata and Lixin Zhang
    Citation: Animal Microbiome 2022 4:65
  10. The microbial community composition of urban environments is primarily determined by human activity. The use of metagenomics to explore how microbial communities are shaped in a city provides a novel input tha...

    Authors: Cecilia Salazar, Matias Giménez, Nadia Riera, Andrés Parada, Josefina Puig, Antonio Galiana, Fabio Grill, Mariela Vieytes, Christopher E. Mason, Verónica Antelo, Bruno D’Alessandro, Jimena Risso and Gregorio Iraola
    Citation: Microbiome 2022 10:208
  11. Metagenomic data can be used to profile high-importance genes within microbiomes. However, current metagenomic workflows produce data that suffer from low sensitivity and an inability to accurately reconstruct...

    Authors: Ilya B. Slizovskiy, Marco Oliva, Jonathen K. Settle, Lidiya V. Zyskina, Mattia Prosperi, Christina Boucher and Noelle R. Noyes
    Citation: Microbiome 2022 10:185
  12. Mammalian intestinal microbiomes are necessary for antagonizing systemic viral infections. However, very few studies have identified whether poultry commensal bacteria play a crucial role in protecting against...

    Authors: Hai-chang Yin, Zhen-dong Liu, Wei-wei Zhang, Qing-zhu Yang, Tian-fei Yu and Xin-jie Jiang
    Citation: Microbiome 2022 10:162
  13. 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
  14. Horizontal gene transfer (HGT) plays a critical role in the spread of antibiotic resistance and the evolutionary shaping of bacterial communities. Conjugation is the most well characterized pathway for the spr...

    Authors: Yue Wang, Zhigang Yu, Pengbo Ding, Ji Lu, Uli Klümper, Aimee K. Murray, William H. Gaze and Jianhua Guo
    Citation: Microbiome 2022 10:124
  15. Antibiotics and antibiotic resistance genes (ARGs) used in intensive animal farming threaten human health worldwide; however, the common resistome, ARG mobility, and ARG host composition in different animal ma...

    Authors: Tianlei Qiu, Linhe Huo, Yajie Guo, Min Gao, Guoliang Wang, Dong Hu, Cheng Li, Zhanwu Wang, Guiming Liu and Xuming Wang
    Citation: Environmental Microbiome 2022 17:42
  16. Antimicrobials are used in food-producing animals for purposes of preventing, controlling, and/or treating infections. In swine, a major driver of antimicrobial use is porcine reproductive and respiratory synd...

    Authors: Tara N. Gaire, Carissa Odland, Bingzhou Zhang, Tui Ray, Enrique Doster, Joel Nerem, Scott Dee, Peter Davies and Noelle Noyes
    Citation: Microbiome 2022 10:118
  17. Antibiotic resistome has been found to strongly interact with the core microbiota in the human gut, yet little is known about how antibiotic resistance genes (ARGs) correlate with certain microbes in large riv...

    Authors: Jiawen Wang, Rui Pan, Peiyan Dong, Shufeng Liu, Qian Chen, Alistair G. L. Borthwick, Liyu Sun, Nan Xu and Jinren Ni
    Citation: Microbiome 2022 10:111
  18. 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
  19. The spread of antibiotic resistance genes (ARGs) has been of global concern as one of the greatest environmental threats. The gut microbiome of animals has been found to be a large reservoir of ARGs, which is ...

    Authors: Huihui Sun, Xiaohuan Mu, Kexun Zhang, Haoyu Lang, Qinzhi Su, Xingan Li, Xin Zhou, Xue Zhang and Hao Zheng
    Citation: Microbiome 2022 10:69
  20. Hadal zone of the deep-sea trenches accommodates microbial life under extreme energy limitations and environmental conditions, such as low temperature, high pressure, and low organic matter down to 11,000 m be...

    Authors: Liuqing He, Xinyu Huang, Guoqing Zhang, Ling Yuan, Enhui Shen, Lu Zhang, Xiao-Hua Zhang, Tong Zhang, Liang Tao and Feng Ju
    Citation: Environmental Microbiome 2022 17:19
  21. 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
  22. Antimicrobial resistance (AMR) has been regarded as a major threat to global health. Pigs are considered an important source of antimicrobial resistance genes (ARGs). However, there is still a lack of large-sc...

    Authors: Yunyan Zhou, Hao Fu, Hui Yang, Jinyuan Wu, Zhe Chen, Hui Jiang, Min Liu, Qin Liu, Lusheng Huang, Jun Gao and Congying Chen
    Citation: Microbiome 2022 10:39
  23. Our interconnected world and the ability of bacteria to quickly swap antibiotic resistance genes (ARGs) make it particularly important to establish the epidemiological links of multidrug resistance (MDR) trans...

    Authors: You Che, Xiaoqing Xu, Yu Yang, Karel Břinda, William Hanage, Chao Yang and Tong Zhang
    Citation: Microbiome 2022 10:16
  24. Wastewater treatment plants are an essential part of maintaining the health and safety of the general public. However, they are also an anthropogenic source of antibiotic resistance genes. In this study, we ch...

    Authors: Paul Jankowski, Jaydon Gan, Tri Le, Michaela McKennitt, Audrey Garcia, Kadir Yanaç, Qiuyan Yuan and Miguel Uyaguari-Diaz
    Citation: Environmental Microbiome 2022 17:3
  25. Understanding environmental microbiomes and antibiotic resistance (AR) is hindered by over reliance on relative abundance data from next-generation sequencing. Relative data limits our ability to quantify chan...

    Authors: Amelie Ott, Marcos Quintela-Baluja, Andrew M. Zealand, Greg O’Donnell, Mohd Ridza Mohd Haniffah and David W. Graham
    Citation: Environmental Microbiome 2021 16:21
  26. Antimicrobial resistance is a serious concern. Although the widespread use of antimicrobials in livestock has exacerbated the emergence and dissemination of antimicrobial resistance genes (ARG) in farm environ...

    Authors: Dipti W. Pitta, Nagaraju Indugu, John D. Toth, Joseph S. Bender, Linda D. Baker, Meagan L. Hennessy, Bonnie Vecchiarelli, Helen Aceto and Zhengxia Dou
    Citation: Environmental Microbiome 2020 15:21
  27. The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more susta...

    Authors: Oscar Mencía-Ares, Raúl Cabrera-Rubio, José Francisco Cobo-Díaz, Avelino Álvarez-Ordóñez, Manuel Gómez-García, Héctor Puente, Paul D. Cotter, Fiona Crispie, Ana Carvajal, Pedro Rubio and Héctor Argüello
    Citation: Microbiome 2020 8:164
  28. It has been estimated that at least 3% of the USA population consumes unpasteurized (raw) milk from animal sources, and the demand to legalize raw milk sales continues to increase. However, consumption of raw ...

    Authors: Jinxin Liu, Yuanting Zhu, Michele Jay-Russell, Danielle G. Lemay and David A. Mills
    Citation: Microbiome 2020 8:99
  29. Antibiotic resistance developed by bacteria is a significant threat to global health. Antibiotic resistance genes (ARGs) spread across different bacterial populations through multiple dissemination routes, inc...

    Authors: Kira Moon, Jeong Ho Jeon, Ilnam Kang, Kwang Seung Park, Kihyun Lee, Chang-Jun Cha, Sang Hee Lee and Jang-Cheon Cho
    Citation: Microbiome 2020 8:75
  30. New antibiotic resistance determinants are generally discovered too late, long after they have irreversibly emerged in pathogens and spread widely. Early discovery of resistance genes, before or soon after the...

    Authors: Maria-Elisabeth Böhm, Mohammad Razavi, Nachiket P. Marathe, Carl-Fredrik Flach and D. G. Joakim Larsson
    Citation: Microbiome 2020 8:41
  31. Antibiotic-resistant pathogens pose high risks to human and animal health worldwide. In recent years, the role of gut microbiota as a reservoir of antibiotic resistance genes (ARGs) in humans and animals has b...

    Authors: Jian Cao, Yongfei Hu, Fei Liu, Yanan Wang, Yuhai Bi, Na Lv, Jing Li, Baoli Zhu and George F. Gao
    Citation: Microbiome 2020 8:26
  32. The impact of human activities on the environmental resistome has been documented in many studies, but there remains the controversial question of whether the increased antibiotic resistance observed in anthro...

    Authors: Kihyun Lee, Dae-Wi Kim, Do-Hoon Lee, Yong-Seok Kim, Ji-Hye Bu, Ju-Hee Cha, Cung Nawl Thawng, Eun-Mi Hwang, Hoon Je Seong, Woo Jun Sul, Elizabeth M. H. Wellington, Christopher Quince and Chang-Jun Cha
    Citation: Microbiome 2020 8:2
  33. Yamuna, a major tributary of Ganga, which flows through the national capital region of Delhi, is among the major polluted rivers in India. The accumulation of various effluents, toxic chemicals, heavy metals, ...

    Authors: Parul Mittal, Vishnu Prasoodanan PK, Darshan B. Dhakan, Sanjiv Kumar and Vineet K. Sharma
    Citation: Environmental Microbiome 2019 14:5
  34. The interconnectivities of built and natural environments can serve as conduits for the proliferation and dissemination of antibiotic resistance genes (ARGs). Several studies have compared the broad spectrum o...

    Authors: Suraj Gupta, Gustavo Arango-Argoty, Liqing Zhang, Amy Pruden and Peter Vikesland
    Citation: Microbiome 2019 7:123
  35. Hospital wastewaters contain fecal material from a large number of individuals, of which many are undergoing antibiotic therapy. It is, thus, plausible that hospital wastewaters could provide opportunities to ...

    Authors: Nachiket P. Marathe, Fanny Berglund, Mohammad Razavi, Chandan Pal, Johannes Dröge, Sharvari Samant, Erik Kristiansson and D. G. Joakim Larsson
    Citation: Microbiome 2019 7:97
  36. Direct and indirect selection pressures imposed by antibiotics and co-selective agents and horizontal gene transfer are fundamental drivers of the evolution and spread of antibiotic resistance. Therefore, effe...

    Authors: G. A. Arango-Argoty, D. Dai, A. Pruden, P. Vikesland, L. S. Heath and L. Zhang
    Citation: Microbiome 2019 7:88
  37. Beef cattle in North America frequently receive an antibiotic injection after feedlot placement to control and manage bovine respiratory disease. The potential collateral effect of these antibiotics on the bov...

    Authors: Devin B. Holman, Wenzhu Yang and Trevor W. Alexander
    Citation: Microbiome 2019 7:86
  38. Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing...

    Authors: Frédéric Raymond, Maurice Boissinot, Amin Ahmed Ouameur, Maxime Déraspe, Pier-Luc Plante, Sewagnouin Rogia Kpanou, Ève Bérubé, Ann Huletsky, Paul H. Roy, Marc Ouellette, Michel G. Bergeron and Jacques Corbeil
    Citation: Microbiome 2019 7:56
  39. Environmental and commensal bacteria maintain a diverse and largely unknown collection of antibiotic resistance genes (ARGs) that, over time, may be mobilized and transferred to pathogens. Metagenomics enables...

    Authors: Fanny Berglund, Tobias Österlund, Fredrik Boulund, Nachiket P. Marathe, D. G. Joakim Larsson and Erik Kristiansson
    Citation: Microbiome 2019 7:52
  40. Microbial communities present in environmental waters constitute a reservoir for antibiotic-resistant pathogens that impact human health. For this reason, a diverse variety of water environments are being anal...

    Authors: Pablo Fresia, Verónica Antelo, Cecilia Salazar, Matías Giménez, Bruno D’Alessandro, Ebrahim Afshinnekoo, Christopher Mason, Gastón H. Gonnet and Gregorio Iraola
    Citation: Microbiome 2019 7:35
  41. Aquaculture is on the rise worldwide, and the use of antibiotics is fostering higher production intensity. However, recent findings suggest that the use of antibiotics comes at the price of increased antibioti...

    Authors: Johan S. Sáenz, Tamires Valim Marques, Rafael Simões Coelho Barone, José Eurico Possebon Cyrino, Susanne Kublik, Joseph Nesme, Michael Schloter, Susanne Rath and Gisle Vestergaard
    Citation: Microbiome 2019 7:24
  42. The International Space Station (ISS) is an ideal test bed for studying the effects of microbial persistence and succession on a closed system during long space flight. Culture-based analyses, targeted gene-ba...

    Authors: Nitin Kumar Singh, Jason M. Wood, Fathi Karouia and Kasthuri Venkateswaran
    Citation: Microbiome 2018 6:204

    The Correction to this article has been published in Microbiome 2018 6:214