Comment

As microbiome science expands, academic centres scramble to fill many needs, from service provider to industry liaison. A newly created network aims to share strategies and accelerate knowledge transfer, and invites others to join the efforts.

Innovations in teaching STEM subjects can help build critical science literacy and address global economic needs. Virology teachers and researchers are actively developing and integrating innovative educational materials for students, creating engaging teaching programs and improving information platforms for the general public.

Looking back at how Zika virus emergence was handled during and after the 2015–2016 outbreak will be important for assessing how well multiple relevant stakeholders were integrated to mount a response, and can provide the groundwork to better cope with emerging infections in the future.

A noticeable part of the microbiome literature, especially that working with low-biomass samples, is plagued by reagent contamination. Here we describe visual, statistical, methodical and ecological techniques to facilitate recognition of signals that represent contamination.

Pandemic influenza remains the single greatest threat to global heath security. Efforts to increase our preparedness, by improving predictions of viral emergence, spread and disease severity, by targeting reduced transmission and improved vaccination and by mitigating health impacts in low- and middle-income countries, should receive renewed urgency.

Faecal microbiota richness is considered a hallmark of gut health and stability. However, in healthy hosts, richness would primarily reflect the stage of ecosystem development through the gut, rather than community resilience. This Comment discusses the need to rethink microbiome biomarkers in the context of gut ecology.

Antimicrobial resistance is one of the great challenges for twenty-first century healthcare. While new therapeutics are undoubtedly required, there are major challenges in rapidly identifying resistant infections and tailoring therapy accordingly; and in how we deploy antimicrobials with suppression of resistance in mind.

The 2017 Nobel Prize in Chemistry was awarded to Jacques Dubochet, Richard Henderson and Joachim Frank for the development of cryo-electron microscopy, a technique for high-resolution structural determination of biomolecules in solution that has provided unprecedented insight into the biology of microorganisms.

In many countries, the success of misinformation, alternative facts or fake news is promoting a climate of science denial, where false claims such as vaccination causing autism can spread. Learning lessons from behavioural studies can help advocate for vaccination in the face of vaccine refusers and deniers.

CRISPR–Cas is an adaptive immune system found in Bacteria and Archaea that confers sequence-specific protection against invasion by foreign nucleic acids. CRISPR–Cas is also a powerful tool for microbiology education and has been an inspiring model for our students for the past three years.

Many species of Archaea, Bacteria and eukaryotes are polyploid in natural populations. The mixture of species with unknown but widely varying ploidy levels compromises marker-gene-based analyses of community structures, population dynamics and microbiomes.

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.