The human gut is an ecosystem comprising trillions of microbes interacting with the host. The composition of the microbiota and their interactions play roles in different biological processes and in the development of human diseases. Close relationships between dietary modifications, microbiota composition and health status have been established. This review focuses on prebiotics, or compounds which selectively encourage the growth of beneficial bacteria, their mechanisms of action and benefits to human hosts. We also review advances in synthesis technology for human milk oligosaccharides, part of one of the most well-characterized prebiotic–probiotic relationships. Current and future research in this area points to greater use of prebiotics as tools to manipulate the microbial and metabolic diversity of the gut for the benefit of human health.

The enteric pathogen Clostridioides difficile (Cd) is responsible for a toxin-mediated infection that causes more than 200,000 recorded hospitalizations and 13,000 deaths in the United States every year1. However, Cd can colonize the gut in the absence of disease symptoms. Prevalence of asymptomatic colonization by toxigenic Cd in healthy populations is high; asymptomatic carriers are at increased risk of infection compared to noncolonized individuals and may be a reservoir for transmission of Cd infection2,3. Elucidating the molecular mechanisms by which Cd persists in the absence of disease is necessary for understanding pathogenesis and developing refined therapeutic strategies. Here, we show with gut microbiome metatranscriptomic analysis that mice recalcitrant to Cd infection and inflammation exhibit increased community-wide expression of arginine and ornithine metabolic pathways. To query Cd metabolism specifically, we leverage RNA sequencing in gnotobiotic mice infected with two wild-type strains (630 and R20291) and isogenic toxin-deficient mutants of these strains to differentiate inflammation-dependent versus -independent transcriptional states. A single operon encoding oxidative ornithine degradation is consistently upregulated across non-toxigenic Cd strains. Combining untargeted and targeted metabolomics with bacterial and host genetics, we demonstrate that both diet- and host-derived sources of ornithine provide a competitive advantage to Cd, suggesting a mechanism for Cd persistence within a non-inflammatory, healthy gut.

Dental erosion is a growing health problem linked to the exceptional increase in the consumption of soft drinks, fruit juices, and sport drinks in many countries including Bangladesh. Dental erosion is the chemical dissolution of the dental hard tissues by acids without the involvement of microorganisms. Hydrogen ions (H + ) from acidic solutions can replace the calcium ions (Ca 2+ ) of the enamel, consequently breaking the crystal structure of the enamel and initiating dental erosion. Erosive tooth wear can lead to severe impairment of esthetics along with loss of hardness and functionality. Sources of the erosive acidic challenges can be intrinsic (i.e., gastroesophaegal reflux disease) and/or extrinsic (i.e., exposure from acidic foods and beverages). Continuous intake of drinks or food with pH lower than the critical erosive pH of enamel (5.2-5.5) and root dentin (~6.7) are considered to be responsible for dental erosion. Drinks with low pH and high titratable acidity (TA) have more potential to dissolved enamel and root dentin; on the other hand, drinks with low degree of saturation can stimulate leaching of minerals. In Bangladesh, there is limited scientific information available to assess the potential of dental erosion of the commercially available beverages and drinking water. This research aims to characterize the dental erosion potential of soft drinks, energy drinks, fruit juices, and bottled drinking water available in Bangladesh by determining their pH, TA, calcium (Ca 2+ ), and phosphate (PO 4 3− ). The degrees of saturation of the selected samples were calculated from the experimental results of pH, calcium, and phosphate levels. Soft drinks were found to have high erosion potential followed by energy drinks, fruit juices, and bottled drinking water. Most of the beverages locally available were found highly acidic. Phosphate levels were high in black cola drinks. Total TA was highest for the energy drinks, and moderate for soft drinks and fruit juices. Fruit juices contained high level of calcium compared with other beverages. The degree of saturation was moderate for fruit juices, and very low for few of the soft drinks and most of the bottled drinking waters. This study will be useful as a reference line for the health professionals and regulatory authorities for quality control of the beverages and bottled drinking water available in the local market. ARTICLE HISTORY

Human milk oligosaccharides (HMOs) are important prebiotic complex carbohydrates with demonstrated beneficial effects on the microbiota of neonates. However, optimization of their biotechnological synthesis is limited by the relatively low throughput of monosaccharide and linkage analysis. To enable high-throughput screening of HMO structures, we constructed a whole-cell biosensor that uses heterologous expression of glycosidases to generate linkage-specific, quantitative fluorescent readout for a range of HMOs at detection limits down to 20 μM in approximately 6 hr. We also demonstrate the use of this system for orthogonal control of growth rate or protein expression of particular strains in mixed populations. This work enables rapid non-chromatographic linkage analysis and lays the groundwork for the application of directed evolution to biosynthesis of complex carbohydrates as well as the prebiotic manipulation of population dynamics in natural and engineered microbial communities.

Industrialization has transformed the gut microbiota, reducing the prevalence ofPrevotellarelative toBacteroides. Here, we isolateBacteroidesandPrevotellastrains from the microbiota of Hadza hunter-gatherers of Tanzania, a population with high levels ofPrevotella. We demonstrate that plant-derived microbiota-accessible carbohydrates (MACs) are required for persistence ofPrevotella copribut notBacteroides thetaiotaomicron in vivo. Differences in carbohydrate metabolism gene content, expression, and in vitro growth reveal that HadzaPrevotellastrains specialize in degrading plant carbohydrates, while HadzaBacteroidesisolates use both plant and host-derived carbohydrates, a difference mirrored inBacteroidesfrom non-Hadza populations. When competing directly,P. coprirequires plant-derived MACs to maintain colonization in the presence ofB. thetaiotaomicron, as a no MAC diet eliminatesP. copricolonization.Prevotella'sreliance on plant-derived MACs andBacteroides'ability to use host mucus carbohydrates could explain the reduced prevalence ofPrevotellain populations consuming a low-MAC, industrialized diet.

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The human microbiome has been inextricably linked to multiple facets of human physiology. From an engineering standpoint, the ability to precisely control the composition and activity of the microbiome holds great promise for furthering our understanding of disease etiology and for new avenues of therapeutic and diagnostic agents. While the field of microbiome research is still in its infancy, growing engineering efforts are emerging to enable new studies in the microbiome and to rapidly translate these findings to microbiome-based interventions. At the 3rd International Conference on Microbiome Engineering, leading experts in the field presented state-ofthe-art work in microbiome engineering, discussing probiotics, prebiotics, engineered microbes, microbially derived biomolecules, and bacteriophage.

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