Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems

Metabolic exchange mediates interactions among microbes, helping explain diversity in microbial communities. As these interactions often involve a fitness cost, it is unclear how stable cooperation can emerge. Here we use genome-scale metabolic models to investigate whether the release of “costless” metabolites (i.e. those that cause no fitness cost to the producer), can be a prominent driver of intermicrobial interactions. By performing over 2 million pairwise growth simulations of 24 species in a combinatorial assortment of environments, we identify a large space of metabolites that can be secreted without cost, thus generating ample cross-feeding opportunities. In addition to providing an atlas of putative interactions, we show that anoxic conditions can promote mutualisms by providing more opportunities for exchange of costless metabolites, resulting in an overrepresentation of stable ecological network motifs. These results may help identify interaction patterns in natural communities and inform the design of synthetic microbial consortia.We thank Dr. Niels Klitgord for pioneering ideas that inspired launch of this work. We are also grateful to David Bernstein, Joshua E. Goldford, Meghan Thommes, Demetrius DiMucci, and all members of the Segre Lab for helpful discussions. A.R.P. is supported by a National Academies of Sciences, Engineering, and Medicine Ford Foundation Predoctoral Fellowship and a Howard Hughes Medical Institute Gilliam Fellowship. This work was supported by funding from the Defense Advanced Research Projects Agency (purchase request no. HR0011515303, contract no. HR0011-15-C-0091), the U.S. Department of Energy (grants DE-SC0004962 and DE-SC0012627), the NIH (grants 5R01DE024468, R01GM121950, and Sub_P30DK036836_P&F), the National Science Foundation (grants 1457695 and NSFOCE-BSF 1635070), MURI Grant W911NF-12-1-0390, the Human Frontiers Science Program (grant RGP0020/2016), and the Boston University Inter-disciplinary Biomedical Research Office. (National Academies of Sciences, Engineering, and Medicine Ford Foundation Predoctoral Fellowship; Howard Hughes Medical Institute Gilliam Fellowship; HR0011515303 - Defense Advanced Research Projects Agency; HR0011-15-C-0091 - Defense Advanced Research Projects Agency; DE-SC0004962 - U.S. Department of Energy; DE-SC0012627 - U.S. Department of Energy; 5R01DE024468 - NIH; R01GM121950 - NIH; Sub_P30DK036836_PF - NIH; 1457695 - National Science Foundation; NSFOCE-BSF 1635070 - National Science Foundation; W911NF-12-1-0390 - MURI Grant; RGP0020/2016 - Human Frontiers Science Program; Boston University Inter-disciplinary Biomedical Research Office)Published versio

Contextualizing context for synthetic biology--identifying causes of failure of synthetic biological systems.

Despite the efforts that bioengineers have exerted in designing and constructing biological processes that function according to a predetermined set of rules, their operation remains fundamentally circumstantial. The contextual situation in which molecules and single-celled or multi-cellular organisms find themselves shapes the way they interact, respond to the environment and process external information. Since the birth of the field, synthetic biologists have had to grapple with contextual issues, particularly when the molecular and genetic devices inexplicably fail to function as designed when tested in vivo. In this review, we set out to identify and classify the sources of the unexpected divergences between design and actual function of synthetic systems and analyze possible methodologies aimed at controlling, if not preventing, unwanted contextual issues

Metabolic evolution and the self-organization of ecosystems

Metabolism mediates the flow of matter and energy through the biosphere. We examined how metabolic evolution shapes ecosystems by reconstructing it in the globally abundant oceanic phytoplankter Prochlorococcus To understand what drove observed evolutionary patterns, we interpreted them in the context of its population dynamics, growth rate, and light adaptation, and the size and macromolecular and elemental composition of cells. This multilevel view suggests that, over the course of evolution, there was a steady increase in Prochlorococcus' metabolic rate and excretion of organic carbon. We derived a mathematical framework that suggests these adaptations lower the minimal subsistence nutrient concentration of cells, which results in a drawdown of nutrients in oceanic surface waters. This, in turn, increases total ecosystem biomass and promotes the coevolution of all cells in the ecosystem. Additional reconstructions suggest that Prochlorococcus and the dominant cooccurring heterotrophic bacterium SAR11 form a coevolved mutualism that maximizes their collective metabolic rate by recycling organic carbon through complementary excretion and uptake pathways. Moreover, the metabolic codependencies of Prochlorococcus and SAR11 are highly similar to those of chloroplasts and mitochondria within plant cells. These observations lead us to propose a general theory relating metabolic evolution to the self-amplification and self-organization of the biosphere. We discuss the implications of this framework for the evolution of Earth's biogeochemical cycles and the rise of atmospheric oxygen.Simons Foundation (Grant SCOPE 329108)Gordon and Betty Moore Foundation (Grant 3778)Gordon and Betty Moore Foundation (Grant 495.01

Pathogenesis and environmental maintenance of Mycobacterium ulcerans, The

2014 Summer.Buruli Ulcer Disease (BUD) is a severe, neglected tropical disease of the skin caused by the acid-fast bacillus Mycobacterium ulcerans. The disease is characterized by necrosis of subcutaneous adipose tissue, and healing with contracture and/or intense scarring of the skin. Little is known about the host response to M. ulcerans from transmission and infection, through the course of disease and resolution. Understanding the host-pathogen interaction is key to development of treatment programs for this neglected disease. In this dissertation, a systems biology approach was used to evaluate a laboratory mouse model of M. ulcerans infection and an analysis of the capability of Anopheles gambiae mosquitoes to maintain and transmit the bacterium is described following the introduction and literature review (Chapters 1 and 2). In Chapter 4, the histology and immune responses in a mouse model that mimics human M. ulcerans infection is described, providing insight into the host response during active infection with M. ulcerans. Specifically, non-toxigenic, virulent M. ulcerans was inoculated into the mouse footpad, and the resulting progression of infection and immune response was characterized in both a wild-type C57BL/6 mouse and an immunodeficient Rag1tm1Mom (Rag-/-) mutant mouse strain. Assessment of the bacterial burden in the mouse as a correlate of the infectious process was documented and demonstrated a persistent or latent feature of infection. Additionally, a mechanism of host immunosuppression was described in immunocompetent animals, in the absence of the toxin mycolatone, highlighting the need for better understanding of virulence determinants employed by the bacilli during infection. Chapter 5 reports an expansion of the mouse model to investigate the transmission of M. ulcerans by a mosquito vector. After exposure to M. ulcerans, larval A. gambiae mosquitoes experienced significant developmental delay, resulting in reduced survival and stunted growth. Adult A. gambiae demonstrated bacterial contamination of their external mouthparts with live M. ulcerans bacteria. The contamination pattern of adult mosquitoes implicates these insects in the mechanical transmission of M. ulcerans. The mouse model from chapter 4 was used to evaluate mosquito borne transmission of the bacillus. Infected mosquitoes were allowed to take a blood meal from mice. The subsequent immune response of the mice was measured for sero-reactivity against M. ulcerans. In addition, larval mosquitoes were documented to readily consume water-borne M. ulcerans, consistent with their feeding mechanism. Thus, larval mosquitoes represent a reservoir or point of environmental maintenance of the pathogen. Chapter 6 details the initiation of a study to investigate the metabolic effects of the exposure of adult mosquitoes to virulent M. ulcerans. The developmental delay and subsequent stunted growth of adult mosquitoes after exposure to M. ulcerans was analyzed through the mass spectrometric investigation of small molecules of metabolism in an attempt to elucidate the biological effects of exposure. In summary (Chapter 7), the availability of a well-defined animal model for BUD provides a valuable tool, which can be used to investigate the specialized pathogenic features of this emerging infection and explore novel disease interventions

The compositional and evolutionary logic of metabolism

Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which layers of that system emerged. Metabolism also serves as the foundation in other hierarchies, at least up to cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, suggests metabolism as a source of causation or constraint on many forms of organization in the biosphere. We identify as modules widely reused subsets of chemicals, reactions, or functions, each with a conserved internal structure. At the small molecule substrate level, module boundaries are generally associated with the most complex reaction mechanisms and the most conserved enzymes. Cofactors form a structurally and functionally distinctive control layer over the small-molecule substrate. Complex cofactors are often used at module boundaries of the substrate level, while simpler ones participate in widely used reactions. Cofactor functions thus act as "keys" that incorporate classes of organic reactions within biochemistry. The same modules that organize the compositional diversity of metabolism are argued to have governed long-term evolution. Early evolution of core metabolism, especially carbon-fixation, appears to have required few innovations among a small number of conserved modules, to produce adaptations to simple biogeochemical changes of environment. We demonstrate these features of metabolism at several levels of hierarchy, beginning with the small-molecule substrate and network architecture, continuing with cofactors and key conserved reactions, and culminating in the aggregation of multiple diverse physical and biochemical processes in cells.Comment: 56 pages, 28 figure