Project description:This study investigated how gut-derived bacterial supplementation influences the honey bee gut microbiota, metabolism, and proteome under three experimental settings: (i) controlled laboratory conditions (C versus B), (ii) semi-controlled laboratory conditions with or without social interaction with older nestmates (COB versus BOB), and (iii) field conditions (CON versus TRT). A bacterial mixture containing Lactobacillus helsingborgensis, L. apis, Bifidobacterium choladohabitans, and B. polysaccharolyticum was administered. Gut samples were collected after 10 days and analyzed for microbiome (16s rRNA sequencing), metabolome (1H NMR), and proteome profiles (LFQ-proteomics, laboratory experiment only). Proteomic profiling revealed distinct group-specific host responses. Control bees (C and COB) upregulated ribosomal proteins linked to protein synthesis and cellular stress. Supplemented bees in group B showed strong induction of major royal jelly proteins (MRJP1 and MRJP5), associated with neural modulation and colony behavior. In BOB, elevated expression of mitochondrial enzymes suggested improved energy metabolism in the presence of social context. Bacterial supplementation induces reproducible, condition-dependent changes across microbiota, metabolic, and proteomic layers. These findings provide mechanistic insight into how microbial interventions reshape gut function and support honey bee health under realistic environmental conditions.
Project description:The response of the model cyanobacterium Synechocystis sp. PCC6803 towards light and carbon limitation was systematically probed. To this end, Synechocystis sp. PCC6803 was cultivated in a photo-bioreactor driven in turbidostat-mode. The turbidostat is a continuous cultivation that enabled cells to adapt to a constant environment, leading to a stable and 'optimal' proteome for the respective condition. The major dataset in this project consisted of 5 different 'concentrations' for light and CO2. Changes in the proteome were determined using using liquid chromatography/mass spectrometry and it was found that carbon and light limitation induced gradual but broad responses in gene expression. With decreasing substrate concentration (increasing limitation) a decrease in growth rate and a gradually more severe response in the proteome was visible.
Project description:Olfactory systems are one of the most conserved and ancient sensory systems in vertebrates. The vertebrate olfactory epithelium is colonized by complex communities of commensal microorganisms, but their impact on olfactory epithelial development and function remains unknown. Using germ-free mouse model, we aim to understand the transcriptional responses that colonization with a microbiota induces in olfactory organs. This study was aimed to understand the changes in gene expression in the nose of Germ Free (GF) mice compared to conventionalized (ConvD) mice. This experiment is related to E-MTAB-5045 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5045)
Project description:We performed scRNA-seq analysis on sympathetic ganglia, including the superior cervical ganglion (SCG), stellate ganglion (SG), and coeliac–superior mesenteric ganglion (CG-SMG). Comparative analysis of the transcriptomic profiling revealed molecularly distinct cell subtypes. We then performed scRNA-seq analysis in SCG and CG-SMG under control and stressed conditions (cold and microbiota-depletion). These analyses show that sympathetic ganglia undergo dynamic remodeling under stress, with distinct stressors driving ganglion-specific plasticity directly coupled to altered neuronal function.
Project description:The human gut microbiota is a complex microbial community with critical functions for the host, including the transformation of various chemicals. While effects on microorganisms has been evaluated using single-species models, their functional effects within more complex microbial communities remain unclear. In this study, we investigated the response of a simplified human gut microbiota model (SIHUMIx) cultivated in an in vitro bioreactor system in combination with 96 deep-well plates after exposure to 90 different xenobiotics, comprising 54 plant protection products and 36 food additives and dyes, at environmentally relevant concentrations. We employed metaproteomics and metabolomics to evaluate changes in bacterial abundances, the production of Short Chain Fatty Acids (SCFAs), and the regulation of metabolic pathways. Our findings unveiled significant changes induced by 23 out of 54 plant protection products and 28 out of 36 food additives across all three categories assessed. Notable highlights include azoxystrobin, fluoroxypyr, and ethoxyquin causing a substantial reduction (log2FC <-0.5) in the concentrations of the primary SCFAs: acetate, butyrate, and propionate. Several food additives had significant effects on the relative abundances of bacterial species; for example, acid orange 7 and saccharin led to a 75% decrease in Clostridium butyricum, with saccharin causing an additional 2.5-fold increase in E. coli compared to the control. Furthermore, both groups exhibited up- and down-regulation of various pathways, including those related to the metabolism of amino acids such as histidine, valine, leucine, and isoleucine, as well as bacterial secretion systems and energy pathways like starch, sucrose, butanoate, and pyruvate metabolism. This research introduces an efficient in vitro technique that enables high-throughput screening of the structure and function of a simplified and well-defined human gut microbiota model against 90 chemicals using metaproteomics and metabolomics. We believe this approach will be instrumental in characterizing chemical-microbiota interactions especially important for regulatory chemical risk assessments.
Project description:We have pioneered human pluripotent stem cell (hPSC) manufacturing in stirred suspension bioreactors. Cell therapies require large numbers of quality-controlled hPSCs yet technologies are limited in their ability to efficiently grow and scale clinically-viable hPSCs. We report here that naive hPSCs exhibit superior growth in suspension bioreactors compared to their primed counterpart. Naive hPSCs exhibited a shorter lag phase, and grew into more uniform, homogenous aggregates. Compared to static culture, gene expression analyses revealed that the bioreactor environment promoted the upregulation of naïve- and downregulation of primed-associated transcripts in both primed and naive hPSCs. Bioreactor-cultured naive hPSCs similarly showed more hypomethylated DNA and less primed hPSC-associated surface protein marker compared to statically-cultured naive hPSCs. Gene expression, epigenetic, and cell surface protein marker analyses all suggest that the bioreactor environment promotes the transition from primed-to-naive pluripotent state. Our research shows that reprogramming conventional hPSCs to the naive pluripotent state enhances hPSC manufacturing.
Project description:Human saliva microbiota is phylogenetically divergent among host individuals yet their roles in health and disease are poorly appreciated. We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults. Saliva microbiota in the pilot population featured a vast diversity of functional genes. No significant distinction in gene number or diversity indices was observed between healthy and caries-active microbiota. However, co-presence network analysis of functional genes revealed that caries-active microbiota was more divergent in non-core genes than healthy microbiota, despite both groups exhibited a similar degree of conservation at their respective core genes. Furthermore, functional gene structure of saliva microbiota could potentially distinguish caries-active patients from healthy hosts. Microbial functions such as Diaminopimelate epimerase, Prephenate dehydrogenase, Pyruvate-formate lyase and N-acetylmuramoyl-L-alanine amidase were significantly linked to caries. Therefore, saliva microbiota carried disease-associated functional signatures, which could be potentially exploited for caries diagnosis. The DMFT INDEX (Decayed, Missing, Filled [DMF] teeth index used in dental epidemiology) values are provided for each sample We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults.
Project description:This study applies proteomic stable isotope probing (proteomic SIP) to profile microbial protein synthesis during anaerobic incubation with 100% U ¹³C glucose. Cecal microbiota were cultured in deoxygenated M9 medium supplemented with 0.3 g L⁻¹ sodium thioglycolate, with U ¹³C glucose. Following incubation, microbial proteins were extracted, digested, and analyzed by nanoLC–MS/MS in DDA mode. Peptides (1 µg) were separated on an XSelect CSH C18 column over a 90 min gradient and acquired on an Orbitrap Fusion Tribrid. MS1 scans were collected at 120,000 resolution (m/z 375–1500); HCD MS2 scans at 30,000 resolution with a 5 m/z isolation window, 10 ppm isolation tolerance, and 20 s dynamic exclusion. Charge state specific NCE settings were used, and precursors with charge <+2, >+7, or unknown were excluded. The dataset enables evaluation of ¹³C glucose incorporation and supports metaproteomic characterization of active cecal taxa under anaerobic conditions.