Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome

The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In this study, gnotobiotic mice were colonized with an artificial microbiota comprising 12 sequenced human gut bacterial species and fed oscillating diets of disparate composition. Rapid, reproducible, and reversible changes in the structure of this assemblage were observed. Time-series microbial RNA-Seq analyses revealed staggered functional responses to diet shifts throughout the assemblage that were heavily focused on carbohydrate and amino acid metabolism. High-resolution shotgun metaproteomics confirmed many of these responses at a protein level. One member, Bacteroides cellulosilyticus WH2, proved exceptionally fit regardless of diet. Its genome encoded more carbohydrate active enzymes than any previously sequenced member of the Bacteroidetes. Transcriptional profiling indicated that B. cellulosilyticus WH2 is an adaptive forager that tailors its versatile carbohydrate utilization strategy to available dietary polysaccharides, with a strong emphasis on plant-derived xylans abundant in dietary staples like cereal grains. Two highly expressed, diet-specific polysaccharide utilization loci (PULs) in B. cellulosilyticus WH2 were identified, one with characteristics of xylan utilization systems. Introduction of a B. cellulosilyticus WH2 library comprising >90,000 isogenic transposon mutants into gnotobiotic mice, along with the other artificial community members, confirmed that these loci represent critical diet-specific fitness determinants. Carbohydrates that trigger dramatic increases in expression of these two loci and many of the organism's 111 other predicted PULs were identified by RNA-Seq during in vitro growth on 31 distinct carbohydrate substrates, allowing us to better interpret in vivo RNA-Seq and proteomics data. These results offer insight into how gut microbes adapt to dietary perturbations at both a community level and from the perspective of a well-adapted symbiont with exceptional saccharolytic capabilities, and illustrate the value of artificial communities

Long-term culture captures injury-repair cycles of colonic stem cells

The colonic epithelium can undergo multiple rounds of damage and repair, often in response to excessive inflammation. The responsive stem cell that mediates this process is unclear, in part because of a lack of in vitro models that recapitulate key epithelial changes that occur in vivo during damage and repair. Here, we identify a Hop

Genome-wide association study of Arabidopsis thaliana leaf microbial community

communit

Islet primary cilia motility controls insulin secretion

Primary cilia are specialized cell-surface organelles that mediate sensory perception and, in contrast to motile cilia and flagella, are thought to lack motility function. Here, we show that primary cilia in human and mouse pancreatic islets exhibit movement that is required for glucose-dependent insulin secretion. Islet primary cilia contain motor proteins conserved from those found in classic motile cilia, and their three-dimensional motion is dynein-driven and dependent on adenosine 5\u27-triphosphate and glucose metabolism. Inhibition of cilia motion blocks beta cell calcium influx and insulin secretion. Human beta cells have enriched ciliary gene expression, and motile cilia genes are altered in type 2 diabetes. Our findings redefine primary cilia as dynamic structures having both sensory and motile function and establish that pancreatic islet cilia movement plays a regulatory role in insulin secretion

Microbial community dynamics and stability during an ammonia-induced shift to syntrophic acetate oxidation

Anaerobic digesters rely on the diversity and distribution of parallel metabolic pathways mediated by complex syntrophic microbial communities to maintain robust and optimal performance. Using mesophilic swine waste digesters, we experimented with increased ammonia loading to induce a shift from aceticlastic methanogenesis to an alternative acetate-consuming pathway of syntrophic acetate oxidation. In comparison with control digesters, we observed shifts in bacterial 16S rRNA gene content and in functional gene repertoires over the course of the digesters' 3-year operating period. During the first year, under identical startup conditions, all bioreactors mirrored each other closely in terms of bacterial phylotype content, phylogenetic structure, and evenness. When we perturbed the digesters by increasing the ammonia concentration or temperature, the distribution of bacterial phylotypes became more uneven, followed by a return to more even communities once syntrophic acetate oxidation had allowed the experimental bioreactors to regain stable operation. The emergence of syntrophic acetate oxidation coincided with a partial shift from aceticlastic to hydrogenotrophic methanogens. Our 16S rRNA gene analysis also revealed that acetate-fed enrichment experiments resulted in communities that did not represent the bioreactor community. Analysis of shotgun sequencing of community DNA suggests that syntrophic acetate oxidation was carried out by a heterogeneous community rather than by a specific keystone population with representatives of enriched cultures with this metabolic capacity

Electrochemiluminescent Detection of Metal Cations Using a Ruthenium(II) Bipyridyl Complex Containing a Crown Ether Moiety

The effects of metal ions on the electrochemiluminescence (ECL) properties of (bpy)2Ru(AZA-bpy) (bpy = 2,2‘-bipyridine; AZA-bpy = 4-(N-aza-18-crown-6-methyl-2,2‘-bipyridine) have been investigated. The electrochemistry, photophysics and ECL of Ru(bpy)32+ in the presence of Pb2+, Hg2+, Cu2+, and K+ are reported. The anodic oxidation of Ru(bpy)32+ produces ECL in the presence of tri-n-propylamine (TPrA) in 50:50 (v/v) CH3CN:H2O solution. Increases in ECL efficiency (photons generated per redox event) up to 20-fold that depend on both the concentration and nature of the metal ion have been observed, making this an interesting system for electrochemiluminescence metal ion sensing

Multicolored Electrogenerated Chemiluminescence from Ortho-Metalated Iridium(III) Systems

The electrogenerated chemilumescence (ECL) of F(Ir)pic (bis(3,5-difluoro-2-(2-pyridyl)phenyl-(2-carboxypyridyl))iridium III) and (btp)2Ir(acac) (bis[2,(2‘-benzothienyl)-pyridinato-N,C3‘](acetlyacetonate)Ir(III) has been investigated in acetonitrile (MeCN), mixed MeCN/H2O (50:50, v/v), and aqueous solutions using the oxidative reductive coreactant tri-n-propylamine. ECL was also studied in the presence of the nonionic surfactant Triton X-100 (poly-(ethylene glycol) tert-octylphenyl ether). F(Ir)pic is a blue emitter (λECL ∼ 470 nm), and (btp)2Ir(acac) emits in the red (λECL ∼ 600 nm). The ECL spectrum of each compound is identical to its photoluminescence spectrum, indicating the same metal-to-ligand (MLCT) excited states. The ECL emission spectrum of F(Ir)pic can be distinguished from Ru(bpy)32+ when both are present in the same solution, raising the possibility of using these compounds for detection of multiple analytes in the same solution. ECL intensity increased in the presence of surfactant up to 6-fold for F(Ir)pic and up to 20-fold for (btp)2Ir(acac). Oxidative current also increased for both compounds. These data support the theory of surfactant adsorption at the electrode surface, leading to greater concentrations of TPrA and Ir species near the electrode surface and higher ECL intensities

Electrochemiluminescence of Tris(8-hydroxyquinoline-5-sulfonic acid)aluminum(III) in Aqueous Solution

The electrochemiluminescence (ECL) of tris(8-hydroxyquinoline-5-sulfonic acid)aluminum(III) in aqueous solution is reported. ECL is generated by complexing aluminum ions with the chelating agent 8-hydroxyquinoline-5-sulfonic acid (HQS) to form Al(HQS)3, followed by oxidation in the presence of tri-n-propylamine (TPrA). The ECL intensity peaks a potential corresponding to oxidation of both TPrA and Al(HQS)3, and the ECL emission spectrum (λmax = 499 nm) matches the photoluminescence emission spectrum, indicating that the emission is from a Al(HQS)3* excited state. ECL efficiencies (φecl, photons generated per redox event) of 0.002 using Ru(bpy)32+ (φecl = 1) as relative standard. Conditions for ECL emission were optimized and used to generate a calibration curve that was linear over the 7 × 10-6−4 × 10-4 M (5−281 mg/L (ppm)) range with a theoretical limit of detection of 1 ppm. The ECL of several metal ions other than aluminum with HQS and effects on Al(HQS)3 ECL were also examined