Same same, but different – a comparative genomics story

Posted on September 11, 2024   by Dr. Hung Nguyen

Dr. Hung Nguyen takes us behind the scenes of their latest publication 'Genomic investigations of diverse corbiculate bee gut-associated Gilliamella reveal conserved pathways for energy metabolism, with diverse and variable energy sources' published in Access Microbiology.

Hi there! My name is Hung Nguyen, and I am the founder and primary investigator of my independent research organization - Project Genomes to Functional, Ecological, and Evolutionary Characterizations (G2FEEC). I started the organization after completing my PhD in 2022 and dedicated it to uncovering the treasure trove that is the vast amount of genomic data available.

Corbiculate bees are important pollinators in agriculture and the wild (their name references the corbiculae, i.e. pollen baskets). Their microbiota often comprises a few highly conserved phylotypes, especially among honeybees and bumblebees. These symbionts are crucial in mediating host health, including the degradation of consumed plant matter and derivatives, and antagonistic roles against bee pathogens. Among these phylotypes is Gilliamella, which often dominates the host ileum. Much research has been done on this genus in vivo and in vitro, but in silico studies have been lacking. For many years, this has meant it was unclear if differential features were characterized. Sometimes, it was not even possible to identify if a certain characteristic may be present or absent. This was particularly true for energy metabolism, whereby it was unclear what was the cause of the differential patterns of fermentation, and if Gilliamella may even be capable of respiration.

Yet energy metabolism is crucial to understanding an organism’s physiology. It determines everything from growth and reproduction rates to what environments an organism can inhabit. In total, I analysed 95 high-quality Gilliamella genomes, the results of which answered many preexisting questions and comprised several new discoveries.

First and foremost were the questions surrounding the ability to respire and how it may vary across taxa. Crucially, and as suspected, I uncovered that Gilliamella is not genetically capable of fully aerobic respiration, which has important implications for their activity outside the host environment. At the same time, I identified the conserved capability for effective respiration under microoxic conditions, exactly that of their host ileum environment, and very likely explains why they are so often able to dominate the bee gut microbial community they are a part of. This is a highly important discovery, as it also led to the discovery that all Gilliamella should be capable of ubiquinone biosynthesis, despite lacking ubiC, which was once thought to be vital in the biosynthesis pathway. As the various omics fields continued to develop, we continuously found exceptions to what were once considered ‘rules,’ and this discovery is no different. It is exciting to consider how future studies will uncover just how Gilliamella replaces the function of UbiC, whether with a different enzyme or via an entirely unknown mechanism.

Fermentation pathways were also highly conserved across the genomes examined, which is a very important finding as that meant previous differential patterns of fermentation identified were phenotypic, not genotypic. This has significant implications for both past and future studies. It is evidence that despite apparently identical growth conditions, there were still unaccounted factors in prior laboratory experiments, factors that should continue to be investigated or at least considered in future studies.

Beyond being conserved, the core energy metabolism pathways are also highly ‘robust,’ often comprising many alternate pathways allowing for the interconversion of diverse substrates. A very exciting discovery was that such robust core energy metabolism pathways could also be found in the genomes of sister genera to the Gilliamella from the same order, comprising members isolated from animal guts. This may mean such conserved energy metabolism features are pre-adaptations not only to the bee gut environment but also to that of other animals!

Despite the conserveness observed, the specific energy sources that can be utilized were highly variable across species and sometimes strains. I found that the robustness of the core energy metabolism pathways may itself be driving this metabolism flexibility. Due to the multiple alternate conversion pathways present, it would have only taken the acquisition of a few additional genes to confer the ability for a strain to uptake and digest new types of sugars. It was known that the diversity of energy sources likely reflects adaptations to specific host species and/or environments, but now we also know why and how such adaptations could arise.

All in all, we are no longer in the dark about the genomic underpinnings of Gilliamella energy metabolism. It is very exciting to see how future research will build on my discoveries here, both to confirm my findings and to better design experiments in the future, now that we know what Gilliamella should and should not be capable of when it comes to energy metabolism.

Fun fact – despite the clear importance of this genus of bacteria, it was entirely by chance that they would be the focus of my research. In the beginning, I just randomly picked a high-quality genome, and it happened to be that of an undescribed Gilliamella species. Characterizing this species in depth has, and continues to be, my main project. Characterizing the energy metabolism of the entire genus was, in fact, just a spin-off of the main project, which I deemed necessary when I realized it would lead to material and meaningful contributions to the field. To me, laboratory and computational research go hand-in-hand, and when the chance arose to answer the many questions posed by laboratory investigations, it was not an opportunity I could pass. I am excited that my research can fuel future laboratory research. I hope I can keep the cycle going as both sides of research continue to complement each other to greatly further our knowledge of the fascinating biology of life.

Remarkably, my research was entirely self-funded, with minimal expenditure required. Much of the analysis utilized publicly available, free tools and databases: the Department of Energy Systems Biology Knowledgebase (KBase), GTDB, the Integrated Microbial Genomes & Microbiomes (IMG/M) database and web service, MEGAX, NCBI. I spent very little setting up my organization and website, and only paid for interactive Tree of Life (iTOL), LucidChart, and MetaCyc subscriptions. I want to highlight that all of these expenditures were optional. The key message? If you, like me, want to carry out self-funded, independent research… maybe it is possible! Consider your options. Perhaps it is truly out of reach, and so it is what it is. Or perhaps… with all the available public resources out there, you can do your own independent research too!