Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake.

BACKGROUND: Short-chain fatty acids (SCFAs) derived from gut bacteria are associated with protective roles in diseases ranging from obesity to colorectal cancers. Intake of microbially accessible dietary fibers (prebiotics) lead to varying effects on SCFA production in human studies, and gut microbial responses to nutritional interventions vary by individual. It is therefore possible that prebiotic therapies will require customizing to individuals. RESULTS: Here, we explored prebiotic personalization by conducting a three-way crossover study of three prebiotic treatments in healthy adults. We found that within individuals, metabolic responses were correlated across the three prebiotics. Individual identity, rather than prebiotic choice, was also the major determinant of SCFA response. Across individuals, prebiotic response was inversely related to basal fecal SCFA concentration, which, in turn, was associated with habitual fiber intake. Experimental measures of gut microbial SCFA production for each participant also negatively correlated with fiber consumption, supporting a model in which individuals' gut microbiota are limited in their overall capacity to produce fecal SCFAs from fiber. CONCLUSIONS: Our findings support developing personalized prebiotic regimens that focus on selecting individuals who stand to benefit, and that such individuals are likely to be deficient in fiber intake. Video Abstract.

Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture.

Culture and screening of gut bacteria enable testing of microbial function and therapeutic potential. However, the diversity of human gut microbial communities (microbiota) impedes comprehensive experimental studies of individual bacterial taxa. Here, we combine advances in droplet microfluidics and high-throughput DNA sequencing to develop a platform for separating and assaying growth of microbiota members in picoliter droplets (MicDrop). MicDrop enabled us to cultivate 2.8 times more bacterial taxa than typical batch culture methods. We then used MicDrop to test whether individuals possess similar abundances of carbohydrate-degrading gut bacteria, using an approach which had previously not been possible due to throughput limitations of traditional bacterial culture techniques. Single MicDrop experiments allowed us to characterize carbohydrate utilization among dozens of gut bacterial taxa from distinct human stool samples. Our aggregate data across nine healthy stool donors revealed that all of the individuals harbored gut bacterial species capable of degrading common dietary polysaccharides. However, the levels of richness and abundance of polysaccharide-degrading species relative to monosaccharide-consuming taxa differed by up to 2.6-fold and 24.7-fold, respectively. Additionally, our unique dataset suggested that gut bacterial taxa may be broadly categorized by whether they can grow on single or multiple polysaccharides, and we found that this lifestyle trait is correlated with how broadly bacterial taxa can be found across individuals. This demonstration shows that it is feasible to measure the function of hundreds of bacterial taxa across multiple fecal samples from different people, which should in turn enable future efforts to design microbiota-directed therapies and yield new insights into microbiota ecology and evolution.IMPORTANCE Bacterial culture and assay are components of basic microbiological research, drug development, and diagnostic screening. However, community diversity can make it challenging to comprehensively perform experiments involving individual microbiota members. Here, we present a new microfluidic culture platform that makes it feasible to measure the growth and function of microbiota constituents in a single set of experiments. As a proof of concept, we demonstrate how the platform can be used to measure how hundreds of gut bacterial taxa drawn from different people metabolize dietary carbohydrates. Going forward, we expect this microfluidic technique to be adaptable to a range of other microbial assay needs.

Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut.

How host and microbial factors combine to structure gut microbial communities remains incompletely understood. Redox potential is an important environmental feature affected by both host and microbial actions. We assessed how antibiotics, which can impact host and microbial function, change redox state and how this contributes to post-antibiotic succession. We showed gut redox potential increased within hours of an antibiotic dose in mice. Host and microbial functioning changed under treatment, but shifts in redox potentials could be attributed specifically to bacterial suppression in a host-free ex vivo human gut microbiota model. Redox dynamics were linked to blooms of the bacterial family Enterobacteriaceae. Ecological succession to pre-treatment composition was associated with recovery of gut redox, but also required dispersal from unaffected gut communities. As bacterial competition for electron acceptors can be a key ecological factor structuring gut communities, these results support the potential for manipulating gut microbiota through managing bacterial respiration.

Improving the permeability of lyophilized collagen-hydroxyapatite scaffolds for cell-based bone regeneration with a gelatin porogen.

Bone tissue engineering using biomaterial scaffolds and culture-expanded osteoprogenitor cells has been demonstrated in several studies; however, it is not yet a clinical reality. One challenge is the optimal design of scaffolds for cell delivery and the identification of scaffold parameters that can delineate success and failure in vivo. Motivated by a previous experiment in which a batch of lyophilized collagen-hydroxyapatite (HA) scaffolds displayed modest bone formation in vivo, despite having large pores and high porosity, we began to investigate the effect of scaffold permeability on bone formation. Herein, we fabricated scaffolds with a permeability of 2.17 ± 1.63 × 10-9 m4 /(N s) and fourfold higher using a sacrificial gelatin porogen. Scaffolds were seeded with mouse bone marrow stromal cells carrying a fluorescent reporter for osteoblast differentiation and implanted into critical-size calvarial defects in immunodeficient mice. The porogen scaffold group containing a 1:1 ratio of solids to beads was significantly more radiopaque than the scaffold group without the bead porogen 3 weeks after implantation. Quantitative histomorphometry uncovered the same trend between the 1:1 group and scaffolds without porogen found in the radiographic data; however, this was not statistically significant here. Taken together, the X-ray and histology suggest that the 1:1 ratio of porogen to scaffold solids, resulting in a fourfold increase in permeability, may enhance bone formation when compared to scaffolds without porogen. Scaffold permeability can be a useful quality control measure before implantation and this practice should improve the consistency and efficacy of cell-based bone tissue engineering. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 104B: 1580-1590, 2016.

Bone tissue engineering with a collagen-hydroxyapatite scaffold and culture expanded bone marrow stromal cells.

Osteoprogenitor cells combined with supportive biomaterials represent a promising approach to advance the standard of care for bone grafting procedures. However, this approach faces challenges, including inconsistent bone formation, cell survival in the implant, and appropriate biomaterial degradation. We have developed a collagen-hydroxyapatite (HA) scaffold that supports consistent osteogenesis by donor-derived osteoprogenitors, and is more easily degraded than a pure ceramic scaffold. Herein, the material properties are characterized as well as cell attachment, viability, and progenitor distribution in vitro. Furthermore, we examined the biological performance in vivo in a critical-size mouse calvarial defect. To aid in the evaluation of the in-house collagen-HA scaffold, the in vivo performance was compared with a commercial collagen-HA scaffold (Healos(®) , Depuy). The in-house collagen-HA scaffold supported consistent bone formation by predominantly donor-derived osteoblasts, nearly completely filling a 3.5 mm calvarial defect with bone in all samples (n = 5) after 3 weeks of implantation. In terms of bone formation and donor cell retention at 3 weeks postimplantation, no statistical difference was found between the in-house and commercial scaffold following quantitative histomorphometry. The collagen-HA scaffold presented here is an open and well-defined platform that supports robust bone formation and should facilitate the further development of collagen-hydroxyapatite biomaterials for bone tissue engineering.

Effects of cell-attachment and extracellular matrix on bone formation in vivo in collagen-hydroxyapatite scaffolds.

Cell-based tissue engineering can be used to replace missing or damaged bone, but the optimal methods for delivering therapeutic cells to a bony defect have not yet been established. Using transgenic reporter cells as a donor source, two different collagen-hydroxyapatite (HA) scaffolds, and a critical-size calvarial defect model, we investigated the effect of a cell-attachment period prior to implantation, with or without an extracellular matrix-based seeding suspension, on cell engraftment and osteogenesis. When quantitatively compared, the in-house scaffold implanted immediately had a higher mean radiopacity than in-house scaffolds incubated overnight. Both scaffold types implanted immediately had significantly higher area fractions of donor cells, while the in-house collagen-HA scaffolds implanted immediately had higher area fractions of the mineralization label compared with groups incubated overnight. When the cell loading was compared in vitro for each delivery method using the in-house scaffold, immediate loading led to higher numbers of delivered cells. Immediate loading may be preferable in order to ensure robust bone formation in vivo. The use of a secondary ECM carrier improved the distribution of donor cells only when a pre-attachment period was applied. These results have improved our understanding of cell delivery to bony defects in the context of in vivo outcomes.

Visualizing osteogenesis in vivo within a cell-scaffold construct for bone tissue engineering using two-photon microscopy.

Tissue-engineering therapies have shown early success in the clinic, however, the cell-biomaterial interactions that result in successful outcomes are not yet well understood and are difficult to observe. Here we describe a method for visualizing bone formation within a tissue-engineered construct in vivo, at a single-cell resolution, and in situ in three dimensions using two-photon microscopy. First, two-photon microscopy and histological perspectives were spatially linked using fluorescent reporters for cells in the skeletal lineage. In the process, the tissue microenvironment that precedes a repair-focused study was described. The distribution and organization of type I collagen in the calvarial microenvironment was also described using its second harmonic signal. Second, this platform was used to observe in vivo, for the first time, host cells, donor cells, scaffold, and new bone formation within cell-seeded constructs in a bone defect. We examined constructs during bone repair 4 and 6 weeks after implantation. New bone formed on scaffolds, primarily by donor cells. Host cells formed a new periosteal layer that covered the implant. Scaffold resorption appeared to be site specific, where areas near the top were removed and deeper areas were completely embedded in new mineral. Visualizing the in vivo progression of the cell and scaffold microenvironment will contribute to our understanding of tissue-engineered regeneration and should lead to the development of more streamlined and therapeutically powerful approaches.