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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.

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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 mobilised 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 mobilisation 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 collected into this series upon publication.

Deadline for submissions: 31st December 2019

  1. Content type: Research article

    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

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  2. Content type: Short report

    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

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  3. Content type: Software

    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

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  4. Content type: Research

    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

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  5. Content type: Research

    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

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  6. Content type: Software

    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

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  7. Content type: Research

    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

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  8. Content type: Research

    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

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  9. Content type: Research

    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

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