Dietary fiber and butyrate production by human gut communities

Fiber consumption is a potential way to enhance butyrate production by gut microbiota, which supports gut health. However, variations in fiber type and individual responses limit reliable increases in butyrate production. Gut microbial communities engage in complex interactions, making it difficult to predict changes in butyrate production in response to fiber.

In collaboration with the lab of Federico Rey, our research team used high-throughput experimentation, Machine Learning Models, gnotobiotic mice, and metatranscriptomics to identify interactions that impact butyrate production in response to fiber, and the contribution of the mammalian host. 

We found that the interaction between Bacteroides caccae and Bifidobacteria reduced the production of butyrate in human clinical trials. We were able to recapitulate this result in gnotobiotic mice. Further analysis showed that regulation of inulin and mucin utilization enzymes, and biotin transport changed in response to conditions that suppressed butyrate production, and we were able to recreate this effect in defined communities grown in vitro. 

Overall, our findings suggest that factors like fiber type, biotin levels, and interactions between different gut bacteria play a key role in shaping butyrate production in the human gut. 

Dietary fiber affects the growth of gut bacteria, but less was known about how different types of fiber shape the interactions between these microbes. Using defined communities of human gut microbiota and data-driven ecological and mechanistic models, our research team explored how fibers with different levels of chemical complexity, as well as non-polymerized sugars, influence the composition, and interspecies interactions within communities, as well as community responses to disruptions. 

We found that increasing the chemical complexity of different types of fiber decreases the relative proportion of fiber utilizing species and increases positive interspecies interactions within the community. Ecological and mechanistic models suggest this is due to increased competition for simple carbohydrates. Additionally, more complex carbohydrates help make microbial communities less sensitive to changes in initial species abundance during community assembly and better able to resist invasion by new species. 

Overall, our findings suggest that the chemical complexity of carbohydrates affects community ecology in predictable ways, and this knowledge is important in designing dietary or bacterial treatments to improve community stability. 

Read the full publication. 

Soil-dwelling fungi are known for their remarkable metabolic versatility, including their ability to degrade complex organic compounds that are toxic to humans. While much is understood about how certain bacteria degrade environmental pollutants, the mechanisms employed by fungi are poorly understood. Among the various harmful substances present in the environment, benzo[a]pyrene (BaP), a polycyclic aromatic hydrocarbon (PAH), is a persistent carcinogen commonly found in polluted soils, sediments, and air. Understanding the mechanisms that enable fungi to degrade such toxic compounds is crucial for both environmental toxicology and the development of bioremediation strategies.

In this study, we explore the ability of several Aspergillus species, common soil fungi, to metabolize BaP. Through a combination of transcriptomic and metabolic analyses, we demonstrate that Aspergillus nidulans can utilize BaP as a growth substrate, triggering cellular and metabolic responses related to energy production. Central to this process is the bapA gene, which encodes a cytochrome P450 monooxygenase necessary for BaP degradation. Furthermore, we uncover the role of fungal NF-κB-type velvet regulators, specifically VeA and VelB, in controlling the expression of bapA under nutrient-limited conditions. 

This study not only advances our understanding of fungal BaP metabolism but also opens new avenues for the development of enhanced bioremediation strategies to address environmental contamination by toxic pollutants. 

See the full publication for more information.