Round-up from the Nature Conference: Environmental Microbial Biofilms and Human Microbiomes: Drivers of Future Sustainability

A summary of the interactive panel discussions featured throughout the meeting

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The Nature Conference: Environmental Microbial Biofilms and Human Microbiomes: Drivers of Future Sustainability held in Singapore this week provided great insights into the scope of research focusing on biofilms and microbiomes around the globe.

One of the prominent threads throughout the meeting was the integration of multiple disciplines in researching various systems. The consideration of microbial systems in the conceptual framework of eukaryote ecology, coupled with a well-integrated multidisciplinary approach is providing the depth of insight needed for solid translational outcomes.

The theme of sustainability was loosely woven throughout the presentations and discussions, and at times seemed a little abstracted from many of the high-resolution studies presented. However, from a birds-eye view, and considering the content presented during the meeting as a whole, the links to sustainability are not too tenuous. The microbial world is at the heart of every ecosystem on the planet, and over the past century we have, often unknowingly, disrupted the systems that sustain us.

For example, by attempting to control the relatively few deleterious (to humans) microbes that cause disease we have disrupted the balance of co-evolved microbiomes that have sustained us, and the planet, for millennia. As this meeting has aptly demonstrated, we are now in a position to give the microbial world the recognition it warrants, and the more deeply we understand the microbes that permeate our world, the more benefits we can derive for sustainable environmental health and human wellbeing.

Each of the theme-based sessions featured in the conference was followed by an open floor discussion, lead by a panel of presenters, leading to some interesting dialogue and, sometimes, alternative perspectives. This feature of the program allowed the audience and speakers to engage in broader conceptual discussions and find commonalities in often disparate systems as well as the unifying approaches for studying these systems.

Theme 1: Environmental Biofilms - Fundamentals From Microbial Models to Complex Communities

Much of the discussion revolved around the technology and methodological tools required to resolve different scales, community structure and ecosystem service, to progress the field. Researchers were urged to push back from adopting a purely genomics approach, and apply alternative methods that provide insights into diversity and functioning. These included combining methods to impart greater meaning on the data attained and allow insight into the workings of the broader system, which could then be validated in hypothesis-based investigations.

The possibility of addressing complex systems with models was deemed feasible if considered in a robust conceptual framework. Models provide insight into what to manipulate in more complex, natural systems. Further, deciding and achieving the optima resolution of data will facilitate modelling accuracy. In a reiterative process, modelling can be used to predict an outcome, and thus help to design experiments that serve to validate and refine the model.

The construct of a ‘perfect microbiome’ to achieve and maintain a healthy, balanced system was discussed, along with how to create such an entity. Debate revolved around whether such a system could exist, given the constant state of flux natural communities experience, how to define ‘optimal’, and how to artificially construct such a system in engineered settings.

The ability to defining the equilibrium/stability points of a system was questioned, along with the desirability of creating such a system. A constructed/manipulated system should allow for ecologically relevant levels of perturbation. A community that is too robust is in danger of collapse, as it needs to have a degree of flexibility to withstand the constant flux of environmental variables.

A desire was expressed to build synthetic communities that are simple enough to construct and monitor, but complex enough to account for natural fluctuations/phenomena. Thus, the very big gap between simple and complex experimental communities needs to be bridged. Possible ways of achieving this in biofilm community studies using constructed communities could be to remove core species from consortia and test the effects, or to gradually build up the community over time, and subject it to a range of stresses/perturbations and/or interactions with higher organisms. Although this might be feasible for engineered communities in industry, the question of ecological relevance remains, however, for studying natural communities.

The argument for defining microbial ecosystem components operationally using ecotypes was presented, given that non-random mutations arise predictably in response to stress, and adding horizontal gene transfer to the mix, it is difficult to define what a strain is. Suggestions included categorising systems based on a dynamic core genome, or conceptualised guilds.

The dialogue concluded with an entreaty to undertake experiments that are “out of the box”, associated with high risk and potentially low pay-off, as any positive returns that result will be disproportionally valuable.

Theme 2: Molecular Microbial Ecology to Macro Ecology and Environmental Engineering

The discussion furthered concepts covered in the Theme 1, asking how we can link what happens at a microbial scale to larger systems with regards to resilience and persistence.

A microbiome is often defined by the physics and chemistry of the surroundings, and we need to extend our view of what a microbiome is to include its environment. Ensuring the ecological relevance of the tools used to study biofilms in vivo was emphasised. Experimental artefacts associated with artificial environments can confound results, for example, growing biofilms on charge-neutral surfaces such as glass. Thus, a ‘one-size-fits-all’ approach was deemed inappropriate.

The merger of life sciences disciplines such as botany and zoology achieved much in furthering our understanding of ecosystems. A similar merger with microbiology has not yet eventuated, but needs to be promoted. One mechanism for changing the mindsets of emerging researchers is to incorporate a structured integrated approach into formal education, to equip the next generation with the tools and framework to adopt a multidisciplinary focus.

Similarly, biology is often neglected in the education of chemists and physicists and our educational approaches need to incorporate all sciences to ensure we are producing well-rounded scientists capable of interdisciplinary research. Current education practices are also encouraging young people to delve too deeply and narrowly too quickly, which can be counterproductive in the longer term. To transform the field we need to ensure researchers are allowed to spend time diversifying, and are thereby capable of taking a broad approach.

The discussion concluded with delineating between ‘open’ and ‘closed’ systems when studying microbiomes. For example, bioreactors are relatively closed systems compared to open oceans. This has implications for concepts such as resilience and sustainability and different types of models are needed to cover the spectrum of interactions inherent in each system. The application of biogeography theory was suggested as relevant here.

Theme 3: Human Microbiome New Dimensions in Medical Microbiology

Theme three covered a diverse array of health and disease examples. The introduction of ‘omics technologies and bioinformatics has enabled a shift of focus from predominantly one-to-one, to one-to-many interactions. We have moved from investigating host-single pathogen relationships to scrutinising host-microbiome dynamics, which also include interactions within the microbiome itself.

Ongoing exploration of the concept of homeostasis, for the most part, remains descriptive/correlative, and there is a need to incorporate experimental components to address issues of causation.

This forum presented a strong focus on the gut microbiome, but the contribution to human health of other microbiomes such as those associated with the skin and lung should not be neglected.

A challenge remains in disentangling the study of local microbiomes to the massive systemic effect the gut microbiome has on its host. Using faecal samples as representative of the gut microbiome can also be problematic as, although indicative of microbial community structure/function in general, they do not reflect the specific habitats and environments that exist along the passage of the gut. The question of how far we could go to develop different tools to sample specific regions was raised, with suggestions including the development of remotely operated capsules capable of sampling at defined regions.

The utility of faecal sampling to indicated dysfunction/disease was mooted, as it serves as a window for associational studies and is not intended to be mechanistic. The sampling sites of gut microbes were highly dependent upon the scientific question being asked. If, for example, a researcher was interested in mucosal disease, then would be more appropriate to sample lumen-associated microbiome directly. However, if detecting metabolites, then faecal material could reflect activity, in much the same way as blood or urine samples current do.

Theme 4: Interrelation of Environmental and Human Sustainability

At the conclusion of the meeting presentations, the scope of the task of using microbe to drive sustainability was brought to bear. There was recognition that the frontier was immense and the prospect of translating microbial biofilm and microbiome research into sustainable options was daunting. Breaking this immense task into smaller components was suggested to provide a starting point, which could progress from the ‘boots on the ground’ level.

Focusing on the UN development goals (see post from day 1) would provide a platform to narrow the focus. Achieving sustainability would only come to fruition if the collective knowledge of the field was harnessed, to predict and control microbial consortia. However, the fact that microbial communities were very complex systems that varied from case to case was highlighted.

How an organism interacts with its environment has broad consequences. From the perspective of human health, increased hygiene and antibiotic use has impacted on immune system functioning, and consequently, the holobiont as a hole. Similarly, for environments, we have seen that larger scale impacts such as global warming have repercussions for holobionts such as macro algae. As we lose holobionts we lose diversity. The question remains, how can we use microbiomes to address or intervene in the process?

Much of the research on biofilms and microbiomes to date has relied on molecular data to qualitatively describe microbial communities and their interactions with the environment/higher organisms. However, management decisions are based on data and we therefore need to be quantitative in our approach. Better management of resources using microbiomes or more simplified techniques were suggested. We need to decide what is the minimal amount of knowledge required to go forward, and it was suggested that the high resolution of some studies might be redundant for ensuring resource management. Microbial ecology is very much data driven, but there remains a need to digest the data and develop a sense of the resolution needed for understanding different systems.

The discussion concluded by commenting that, as we are in the early stages of the argument, it was timely to consider the directions taken and how we can conduct our research to contribute to building sustainability.

Twitter: #EHMicrobiomes2017

Sharon Longford

Communications Manager, SCELSE