Receptor uptake arrays for vitamin B₁₂, siderophores, and glycans shape bacterial communities

Abstract

Molecular variants of vitamin B12, siderophores, and glycans occur. To take up variant forms, bacteria may express an array of receptors. The gut microbe Bacteroides thetaiotaomicron has three different receptors to take up variants of vitamin B12 and 88 receptors to take up various glycans. The design of receptor arrays reflects key processes that shape cellular evolution. Competition may focus each species on a subset of the available nutrient diversity. Some gut bacteria can take up only a narrow range of carbohydrates, whereas species such as B. thetaiotaomicron can digest many different complex glycans. Comparison of different nutrients, habitats, and genomes provides opportunity to test hypotheses about the breadth of receptor arrays. Another important process concerns fluctuations in nutrient availability. Such fluctuations enhance the value of cellular sensors, which gain information about environmental availability and adjust receptor deployment. Bacteria often adjust receptor expression in response to fluctuations of particular carbohydrate food sources. Some species may adjust expression of uptake receptors for specific siderophores. How do cells use sensor information to control the response to fluctuations? This question about regulatory wiring relates to problems that arise in control theory and artificial intelligence. Control theory clarifies how to analyze environmental fluctuations in relation to the design of sensors and response systems. Recent advances in deep learning studies of artificial intelligence focus on the architecture of regulatory wiring and the ways in which complex control networks represent and classify environmental states. I emphasize the similar design problems that arise in cellular evolution, control theory, and artificial intelligence. I connect those broad conceptual aspects to many testable hypotheses for bacterial uptake of vitamin B12, siderophores, and glycans.

Functional Roles of B‐Vitamins in the Gut and Gut Microbiome

“…Cobalamin transport systems have been reviewed in detail elsewhere. [137][138][139][140] However, cobalamin represents only a small portion (1.4%) of the total amount in human feces. [141] Therefore, it is doubtful whether colonic-derived cobalamin has a role in nutrition of the host.…”

Gut microbiota-derived cholic acid mediates neonatal brain immaturity and white matter injury under chronic hypoxia

“…Previous reports have proposed that B. thetaiotaomicron and P. distasonis possess the ability to convert primary bile acids into secondary bile acids through bile salt hydrolase 40 and 7α-dehydrogenase. 18 , 41 Notably, we observed a reduction in the activity of 7α-dehydrogenase associated with the decrease of B. thetaiotaomicron and P. distasonis under chronic hypoxia ( Figure 6 ). Analogous findings have been reported in various disease models, including Parkinson’s disease, multiple sclerosis, and metabolic syndrome.…”

“…To simulate the chronic hypoxic state of CCHD, a neonatal chronic hypoxic rat model was utilized to study the role of the gut microbiome during brain development. 18 In this model, the hypoxia group exhibited disordered and enlarged ventricle size ( Figure S1 A), as well as enlarged caeca with increased weights and dark-colored cecal contents in both normoxic and hypoxic rats ( Figure S1 B).…”

“…B. thetaiotaomicron and P. distasonis were cultured anaerobically in MRS broth at 37°C in a 90% N 2 , 5% CO 2 , and 5% H 2 environment, as previously described. 18 , 21 After culture, the medium was centrifuged to obtain the bacteria and then resuspended in PBS. The bacterial liquid was frozen at −80 。 C until use.…”

Development of Gallium(III) as an Antimicrobial Drug Targeting Pathophysiologic Iron Metabolism of Human Pathogens

“…Once the sidero/hemophores have become saturated with iron/heme, they bind to specialized surface receptors unique to each sidero/hemophore . Once bound siderophores use them to bypass porins and the lipid bilayer and enter the periplasm .…”