Dr Lydia Bach
- Research Assistant (Institute of Biodiversity Animal Health & Comparative Medicine)
Only about half of the approximately 60 trillion cells found within our bodies are of human origin, the rest comprise bacterial cells known as the microbiome. Even within a single site in the human body, the microbiota is characterised by a vast richness of phylogenetic types, performing important functions such as resisting pathogen invasion or supporting the host’s immune system. Yet, we know startlingly little about the factors that determine the basic community ecology of these microbial communities, and how their ecology relates to the functions they perform and the health benefits they bestow on us.
Communities are a fundamental study unit in ecology, with a rich ecological theory underpinning the processes that regulate species richness and abundance in space and time. Concepts from community ecology, such as assembly and coexistence theory, have guided the management and conservation of real communities, allowing us, for example, to determine factors that influence past and current distribution of vegetation at both regional and global scales and, importantly, enabling prediction of how these communities will change in the future.
While there have been significant advances in the past 30 years the bulk of this research has focussed on macroecological communities, ignoring microbial communities. Key concepts derived from macroecologial communities such as nested measures of diversity, the flow of energy and biomass, interactions between species, succession and invasibility, and alternative stable states can be expected to apply equally to microbial communities. However, microbial communities can be sampled faster and more comprehensively than macro-ecological systems, and the development of affordable next-generation sequencing has vastly accelerated the study of microbial communities generating data that provide an unbiased, compositional snapshot of the genes present in a microbial community. Despite this, much of the work on microbial communities has been largely observational, correlative, and temporally static, therefore lacking frameworks within which to understand community dynamics and generate future predictions. Consequently, there is a reciprocal missed opportunity: the study of microbial community ecology does not contribute to more general ecological theory, and the rich methodological machinery developed to study macroecological communities is not used to develop predictive microbial ecology.
Figure 3. Simulating the effect of a perturbation on the abundance of ten bacterial species, removing gram-negative species using, for example, antibiotics results in a shift in the bacterial community as a whole.
Key limitations in microbial ecology are the absence of a framework that links the structure of microbial communities to the functions and ‘health services’ they provide us with, and the capacity to use knowledge of this linkage to predict and mitigate the consequences of changes to these communities. I am aiming to address this knowledge gap by integrating the rich opportunities for generating data about microbial communities that modern sequencing technology provides with contemporary ecological theory and analytical approaches of proven utility when applied to macrobial communities.
2013-2017: Queen’s University Belfast PhD: Scaling biodiversity and ecosystem processes in intertidal areas:
Supervisors: Prof Mark Emmerson and Dr Nessa O’Connor
2008 – 2013: University of Glasgow BSc. (Hons) MSci. 1st class in Marine and Freshwater Biology
I am an ecologist with a broad range of research interests, in particular in the interaction of species in ecosystems and its implications. As such, my PhD focussed on spatial and temporal variation food web topology in intertidal areas and the relationships between biodiversity and ecosystem process measures, part of the larger CBESS project (link: https://synergy.st-andrews.ac.uk/cbess/).
Figure 1. Conceptual interrelationships between abundance, body mass and food web structure. Combining these ecological components can provide insight into the structure of food webs. Diagram derived from Emmerson (2011).
Figure 2. Food webs at Belfast Lough, Essex mudflats, Carlingford Lough, Morecambe Bay and Lough Foyle.
With the limitations of studying macroecological systems in mind, my interest moved towards microbial ecosystems and population dynamics, which is what I am currently working on with my supervisors Jan Lindstrom and Dan Haydon.
Benefitting from the development of next-generation sequencing, our knowledge of microbial communities has expanded enormously in the past decade. To achieve a more comprehensive understanding of microbiota, however, research requires going beyond species lists towards a community ecology framework. We are using network analysis to derive interaction strengths between species and subsequently stability properties of the communities. This approach will allow us to move from mere species inventories and abundance data to a stage where the essential characteristics of a community can be unravelled, whilst gaining understanding whether macroevolution occurs in our system.