New paper: Genome content predicts the metabolic preferences of bacteria

Bacteria grow in communities of many co-occurring species in , e.g., in your gut, in soil, or in the ocean. A fundamental process in these communities (more specifically, communities of heterotrophic bacteria, i.e., bacteria that utilize organic carbon sources) is that bacteria take up substrates (basically, food) like sugars and amino acids from the environment and turn them into biomass or convert them into something else they then excrete. For this new paper, what we wanted to know was: which substrates can different bacteria use (we were focused on substrates they can use as a carbon source)? Can we identify patterns of substrate utilization, e.g., are similar compounds consumed by similar bacteria? Can we predict these patterns by looking at which genes different bacteria encode? Our work touches on several important questions in microbiology, from microbial ecology (how do microbial communities work?) to biochemistry (how does the structure of metabolic pathways shape substrate utilization patterns?) to genomics & evolution (how are capabilities of substrate utilization encoded in the genome, and how did evolution shape these genomic patterns?).

High-throughput growth characterization workflow used in this project

By analyzing the growth of 182 different strains of marine bacteria on 135 different potential carbon sources, we found that we can describe the substrate preferences of our bacteria to a first approximation in terms of their preference for sugars (e.g., glucose or polysaccharides like starch) relative to acids (e.g., amino acids or organic acids which are important intermediate during the chemical conversion of substrates into biomass). This preference is encoded in the genomes of bacteria, which tells us about the evolution of these preferences, but also makes the preferences predictable from genomes.

Analysis of growth phenotypes shows that the main discriminatory characteristic between species is the degree to which they prefer sugars or acids.

Our work reveals a way to simplify how we think about the metabolic capabilities of bacteria: we can describe a given heterotrophic bacterium by its degree of specialization along the axis of sugar to acid specialists. This is very useful because it allows us to describe communities of bacteria in a simple way (e.g., by their collective degree of specialization). More fundamentally, our work also shows how the evolution of bacterial genomes is structured by biochemical constraints which drives bacteria to specialize along this axis of sugar to acid specialists. Since the metabolic preferences are encoded in genomes, we can estimate the metabolic capabilities of species that we have not (yet) cultured, but for which we have genomic information (e.g., by sequencing entire communities and piecing together the genomes of the constituent species, a process called metagenomics). This allows us to begin to understand the metabolic processes in many microbial communities in the environment in a simplified manner.

Through evolution, species may be selected to specialize in either glycolysis or gluconeogenesis. This saves them from having to switch directions often as environmental conditions change (which is expensive), but this reduces their metabolic adaptability, which may be bad in fluctuating environments.

Out now: Genome content predicts the carbon catabolic preferences of heterotrophic bacteria

State of the union of the lab at the Hortus Botanicus

A custom of our lab is to start the academic year with a state-of-the-union day at the Hortus Botanicus of Amsterdam.

During this day, the PIs give an research overview of the last year, an outlook on the coming year, current duties, and their long-term research vision in the presence of the research (support) staff and all the researchers working on funded projects (PhDs and postdocs).

Bas gave an overview of the Holomicrobiome “groeifonds” project proposal that he is involved in, as an organising member. This is a 240 million euro project that aims to link Dutch microbiome research and company demands: to together drive innovations that will improve the quality of our soils, water, crops and human health by improved methods and technologies. The outlook is that this should give an input to the Dutch economy in an environmentally friendly and sustainable manner. The proposal needs to be reshaped in the coming months, resubmitted, and reevaluated by an independent committee on behalf of the Dutch government for approval (or rejection). Exciting times!

Matti chaired a session on the reconsideration of the logo of our lab, which now has effectively turned this into competition between groups of colleagues. Let’s see what they come up with!