Comment

Marine microorganisms inhabit diverse environments and interact over different spatial and temporal scales. To fully understand how these interactions shape genome structures, cellular responses, lifestyles, community ecology and biogeochemical cycles, integration of diverse approaches and data is essential.

Dysbiosis, an imbalance in the microbiota, has been a major organizing concept in microbiome science. Here, we discuss how the balance concept, a holdover from prescientific thought, is irrelevant to — and may even distract from — useful microbiome research.

The threat of antimicrobial resistance causing drug-resistant infections and the escalating health, social and economic consequences are now becoming visible at a global level. Here, we discuss the economic and political considerations for creating a truly global and effective response to antimicrobial resistance.

The global effect of human activities on Earth's microbiota has not yet been considered. Here, we identify potential trajectories of microbial change, and highlight knowledge gaps that need to be addressed to better understand how microbial communities across the globe will change in the future.

Whole genome sequencing is often used to determine the presence of known antimicrobial resistance genes and identify new resistance mechanisms. However, without phenotypic confirmation of resistance, caution needs to be taken in attributing relevance to any genes hitherto not shown to confer drug resistance.

Multi-omic techniques are often seen as the future of microbiome studies. We argue that recent strategies for simplifying complex omic-derived data will need to be combined with improved cultivation techniques to pave the way towards a more targeted approach for understanding microbial communities.

Microbiomes of native peoples could provide constituents to improve our health. Research must be conducted ethically and native peoples appropriately rewarded. However, sharing our medical practice risks spoiling these microbial oases and could lead to the same disease risks that we are trying to prevent.

There are no antibiotic candidates simply waiting to be brought to market. Overcoming the scientific barriers to innovation will require research and coordination beyond anything that exists in academia, industry or government. We discuss a plan to accelerate the discovery of antibiotics and their transition into the clinic.

Integration of multiple ‘omics’ technologies will allow researchers to gain a more complete picture of the constituents and functions of microbial communities and provide far richer information for predictive modelling of community phenotypes.

The intestinal microbiota and its interactions with host immunity have been intensely studied in many disease states. This knowledge could ultimately modify clinical management of allogeneic haematopoietic stem cell transplantation, which is accompanied by dramatic immunological and microbiota perturbations.

Faecal microbiota transplantation has proved efficacious for diseases such as recurrent Clostridium difficile infection via restoration of gut microbial ecology and bile acid content. However, despite its adoption by mainstream medicine, misuse of this technology in clinical or domestic settings warrants caution.

The apparent emergence of new and devastating Vibrio diseases in Latin America during significant El Niño events is striking. New microbiological, genomic and bioinformatic tools are providing us with evidence that El Niño may represent a long-distance corridor for waterborne diseases into the Americas from Asia.

Concern over Ebola becoming endemic in West Africa has appeared in the medical and lay media. Routes of transmission, rates of viral evolution, suitability of humans as hosts and rarity of spillover events make this very unlikely. Without evidence that endemic Ebola is likely, ending epidemics should remain the focus.

Widespread antibiotic resistance is a growing public health problem. Can we revive large-scale screening to keep the pipelines flowing or will we depend increasingly on biological and ecological insights?

Advances in culturing hepatitis C virus have given hope for a universal cell culture system amenable to primary isolate replication. However, low replication efficiency needs to be overcome. The development of fully susceptible yet immunocompetent in vivo models would aid research towards a prophylactic vaccine.