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Microbiology conferences can be powerful places to build collaborations and exchange scientific thought, but for queer and transgender (trans) scientists they can also become sources of alienation and isolation. Many conference organizers would like to create welcoming and inclusive events but feel ill-equipped to make this vision a reality, and a historical lack of representation of queer and trans folks in microbiology means we rarely occupy these key leadership roles ourselves. Looking more broadly, queer and trans scientists are systematically marginalized across scientific fields, leading to disparities in career outcomes, professional networks, and opportunities, as well as loss of unique scientific perspectives at all levels. For queer and trans folks with multiple, intersecting, marginalized identities, these barriers often become even more severe. Here, we provide concrete, practical advice to help conference organizers in the microbial sciences design inclusive, safe, and welcoming conferences, where queer and trans microbiologists can flourish.

Microbial communities are ubiquitous and play crucial roles in many natural processes. Despite their importance for the environment, industry and human health, there are still many aspects of microbial community dynamics that we do not understand quantitatively. Recent experiments have shown that the structure and composition of microbial communities are intertwined with the metabolism of the species that inhabit them, suggesting that properties at the intracellular level such as the allocation of cellular proteomic resources must be taken into account when describing microbial communities with a population dynamics approach. In this work, we reconsider one of the theoretical frameworks most commonly used to model population dynamics in competitive ecosystems, MacArthur’s consumer-resource model, in light of experimental evidence showing how proteome allocation affects microbial growth. This new framework allows us to describe community dynamics at an intermediate level of complexity between classical consumer-resource models and biochemical models of microbial metabolism, accounting for temporally-varying proteome allocation subject to constraints on growth and protein synthesis in the presence of multiple resources, while preserving analytical insight into the dynamics of the system. We first show with a simple experiment that proteome allocation needs to be accounted for to properly understand the dynamics of even the simplest microbial community, i.e. two bacterial strains competing for one common resource. Then, we study our consumer-proteome-resource model analytically and numerically to determine the conditions that allow multiple species to coexist in systems with arbitrary numbers of species and resources.

[This corrects the article DOI: 10.1371/journal.pcbi.1007896.].

Microbial communities are ubiquitous and play crucial roles in many natural processes. Despite their importance for the environment, industry and human health, there are still many aspects of microbial community dynamics that we do not understand quantitatively. Recent experiments have shown that the metabolism of species in a community is intertwined with its composition, suggesting that properties at the intracellular level such as the allocation of cellular proteomic resources must be taken into account when describing microbial communities with a population dynamics approach. In this work we reconsider one of the theoretical frameworks most commonly used to model population dynamics in competitive ecosystems, MacArthur’s consumer-resource model, in light of experimental evidence showing how pro-teome allocation affects microbial growth. This new framework allows us to describe community dynamics at an intermediate level of complexity between classical consumer-resource models and biochemical models of microbial metabolism, accounting for temporally-varying proteome allocation subject to constraints on growth and protein synthesis in the presence of multiple resources, while preserving analytical insight into the dynamics of the system. We first show experimentally that proteome allocation needs to be accounted for to properly understand the dynamics of even the simplest microbial community, i.e. two bacterial strains competing for one common resource. We then study the model analytically and numerically to determine the conditions that allow multiple species to coexist in systems with arbitrary numbers of species and resources.

Bacteria are able to adapt to different environments by changing their “metabolic strategies”, i.e. the ways in which they uptake available resources from the environment. For example, in a celebrated experiment Jacques Monod showed that bacteria cultured in media containing two different sugars consume them sequentially, resulting in bi-phasic growth curves called “diauxic shifts”. From the theoretical point of view, microbial communities are commonly described using MacArthur’s consumer-resource model, which describes the population dynamics of species competing for a given set of resources. In this model, however, metabolic strategies are treated as constant parameters. Here, we introduce adaptive metabolic strategies in the framework of consumer-resource models, allowing the strategies to evolve to maximize each species’ relative fitness. By doing so, we are able to describe quantitatively, and without invoking any specific molecular mechanisms for the metabolism of the microbial species, growth curves of the baker’s yeastSaccharomyces cerevisiaemeasured in a controlled experimental set-up, with galactose as the primary carbon source. We also show that metabolic adaptation enables the community to self-organize, allowing species to coexist even in the presence of few resources, and to respond optimally to a time-dependent environment. A connection between the Competitive Exclusion Principle and the metabolic theory of ecology is also discussed.