GNPS - Gut microbes cultured with 2-aminophenol and DCA
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Exploris 240
ORGANISM(S): Coprococcus (ncbitaxon:33042) Akkermansia (ncbitaxon:239934)
SUBMITTER: 
Pieter C. Dorrestein
PROVIDER: MSV000098171 | GNPS | Thu Jun 12 11:10:00 BST 2025
REPOSITORIES: GNPS
Similar Datasets
Project description:Gut bacteria were cultured with Asn-UDCA, asparagine, and UDCA acquired on Orbitrap Exploris 240 with chromatographic separation on a Phenomenex polar C18 column (Kinetex 2.6 um, 100 x 2.1 mm). Reversed-phase, ESI positive.
2025-02-19 | MSV000097155 | GNPS
Project description:Gut microbes were cultured with bile acids and drugs. Data was acquired on Orbitrap Exploris 240 with chromatographic separation on a Phenomenex polar C18 column (Kinetex 2.6 um, 100 x 2.1 mm). Reversed-phase, ESI positive.
2025-03-08 | MSV000097269 | GNPS
Project description:Gut microbiota plays a significant role in shaping gut and systematic immune and huge strain- and species- dependent differences exit. Using in-vitro MLN co-culture models, we want to initially uncover these differences. MLN cells were isolated from C57BL/6 mice and co-cultured with bacterial cells with or without anti-CD3 and anti-CD28 antibodies for three days. After that, IL-10 in cell supernatant was measured and RNA was extracted using Trizol reagent. RNA-seq was performed on Illumina Hiseq X ten. Raw sequenced data were filtered by fastp and clean data were mapped to reference genome (Mus_musculus, GRCm39). Data processing adopted featurecounts in subread, abundance_estimates_to_matirx.pl in Trinity, DEseq and ClusterProfiler. We found that all bacterial species activated the innate immunity response. However, only Akkermansia muciniphila and Clostridium butyricum had cognate T cell antigen and activated adaptive immunity responses even without stimulus.
2022-11-21 | GSE189176 | GEO
Project description:Skin microbes were cultured with drugs. Data was acquired on Orbitrap Exploris 240 with chromatographic separation on a Phenomenex polar C18 column (Kinetex 2.6 um, 100 x 2.1 mm). Reversed-phase, ESI positive.
2025-05-13 | MSV000097877 | GNPS
Project description:Gut-brain connections monitor the intestinal tissue and its microbial and dietary content1, regulating both intestinal physiological functions such as nutrient absorption and motility2,3, and brain–wired feeding behaviour2. It is therefore plausible that circuits exist to detect gut microbes and relay this information to central nervous system (CNS) areas that, in turn, regulate gut physiology4. We characterized the influence of the microbiota on enteric–associated neurons (EAN) by combining gnotobiotic mouse models with transcriptomics, circuit–tracing methods, and functional manipulation. We found that the gut microbiome modulates gut–extrinsic sympathetic neurons; while microbiota depletion led to increased cFos expression, colonization of germ-free mice with short-chain fatty acid–producing bacteria suppressed cFos expression in the gut sympathetic ganglia. Chemogenetic manipulations, translational profiling, and anterograde tracing identified a subset of distal intestine-projecting vagal neurons positioned to play an afferent role in microbiota–mediated modulation of gut sympathetic neurons. Retrograde polysynaptic neuronal tracing from the intestinal wall identified brainstem sensory nuclei activated during microbial depletion, as well as efferent sympathetic premotor glutamatergic neurons that regulate gastrointestinal transit. These results reveal microbiota–dependent control of gut extrinsic sympathetic activation through a gut-brain circuit.
2020-03-20 | GSE145986 | GEO
Project description:In this study we performed MeRIP-Seq to study N6-methyl adenosine (m6A) and and N6,2′ -O-dimethyladenosine (m6Am) modification of mRNA. We investigated the effect of the microbiota on the transcriptome and epitranscriptomic modifications in murine liver and cecum. We compared m6A/m modification profiles in cecum of conventionally raised (CONV) and germ-free (GF) mice. We additionally included GF mice colonised with the flora of CONV mice for four weeks (ex-GF), for which show that they exhibit similar patterns of the most abundant genera of gut bacteria as CONV mice. We added mice treated with several antibiotics to deplete the gut flora (abx)and vancomycin treated mice in which the genera Akkermansia, Escherichia/Shigella and Lactobacillus were enriched. Furthermore, we included GF mice colonised with the commensal bacterium Akkermansia muciniphila (Am), Lactobacillus plantarum (Lp) and Escherichia coli Nissle (Ec) and analysed their m6A/m modification profiles. In addition, we analysed changes in m6A/m- modified liver RNA for CONV, GF, and Am, Lp and Ec mice.
2020-02-12 | E-MTAB-6560 | biostudies-arrayexpress
Project description:The gut microbiome can impact brain health and is altered in Parkinson’s disease (PD) patients. The vermiform appendix is a lymphoid tissue implicated in the storage and regulation of the gut microbiome. Here, we investigate changes in the functional microbiome in the appendix of PD patients relative to controls by metatranscriptomic analysis. In the PD appendix, we find microbial dysbiosis affecting lipid metabolism, particularly an upregulation of bacteria responsible for secondary bile acid synthesis. Likewise, proteomic and transcript analysis in the PD gut corroborates a disruption in cholesterol homeostasis and lipid catabolism. Bile acid analysis in the PD appendix reveals an increase in the microbially-derived, toxic secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA). Synucleinopathy in mice induces similar microbiome alterations to those of PD patients and heightens microbial changes to gut inflammation. As observed in PD, the mouse model of synucleinopathy has elevated DCA and LCA. Raised levels of DCA and LCA can lead to liver injury, and an analysis of blood markers of liver dysfunction shows evidence of biliary abnormalities in PD patients, including elevated alkaline phosphatase and bilirubin. Increased bilirubin levels are also evident before PD diagnosis, in individuals at-risk of developing PD. In sum, microbially-derived toxic bile acids are heightened in PD and biliary changes may even precede the onset of overt motor symptoms.
2021-08-01 | GSE156647 | GEO
Project description:The gut microbiome can impact brain health and is altered in Parkinson’s disease (PD) patients. The vermiform appendix is a lymphoid tissue implicated in the storage and regulation of the gut microbiome. Here, we investigate changes in the functional microbiome in the appendix of PD patients relative to controls by metatranscriptomic analysis. In the PD appendix, we find microbial dysbiosis affecting lipid metabolism, particularly an upregulation of bacteria responsible for secondary bile acid synthesis. Likewise, proteomic and transcript analysis in the PD gut corroborates a disruption in cholesterol homeostasis and lipid catabolism. Bile acid analysis in the PD appendix reveals an increase in the microbially-derived, toxic secondary bile acids deoxycholic acid (DCA) and lithocholic acid (LCA). Synucleinopathy in mice induces similar microbiome alterations to those of PD patients and heightens microbial changes to gut inflammation. As observed in PD, the mouse model of synucleinopathy has elevated DCA and LCA. Raised levels of DCA and LCA can lead to liver injury, and an analysis of blood markers of liver dysfunction shows evidence of biliary abnormalities in PD patients, including elevated alkaline phosphatase and bilirubin. Increased bilirubin levels are also evident before PD diagnosis, in individuals at-risk of developing PD. In sum, microbially-derived toxic bile acids are heightened in PD and biliary changes may even precede the onset of overt motor symptoms.
2021-01-28 | PXD020988 | Pride
Project description:The human gut includes plasma cells (PCs) expressing immunoglobulin A1 (IgA1) or IgA2, two structurally distinct IgA subclasses with elusive regulation, function and reactivity. We show here that intestinal IgA1+ and IgA2+ PCs co-emerged early in life, comparably accumulated somatic mutations, and were enriched within short-lived CD19+ and long-lived CD19− PC subsets, respectively. IgA2+ PCs were often clonally related to IgA1+ PCs and a subset of them presumably emerged from IgA1+ precursors. Of note, secretory IgA1 (SIgA1) and SIgA2 dually coated a large fraction of mucus-embedded bacteria, including Akkermansia muciniphila. Disruption of homeostasis by inflammatory bowel disease (IBD) increased newly formed and actively proliferating IgA1+ plasmablasts, depleted long-lived IgA2+ PCs, and increased SIgA1+SIgA2+ gut microbiota. Such increase featured enhanced IgA1 reactivity to pathobionts, including Escherichia coli, combined with depletion of beneficial Akkermansia muciniphila. Thus, gut IgA1 and IgA2 emerge from clonally related PCs and show unique changes of both frequency and reactivity in IBD.
2024-10-17 | GSE268929 | GEO
Project description:The understanding of the effects of compounds on the gut microbiome is limited and in particular we don’t know whether structurally similar compounds have similar or distinct effects on the gut microbiome. Here we selected berberine (BBR), an isoquinoline quaternary alkaloid, and sixteen structural analogues, and evaluated their effects on in vitro cultured individual gut microbiomes. The responses of the individual microbiomes were evaluated by metaproteomic profiles and by assessing butyrate production. BBR and eight analogues led to changes in proteins involved in microbial defense and stress responses, and enrichment of proteins from Verrumicrobia, Proteobacteria and Bacteroides phyla. It also led to a decrease in proteins from the Firmicutes phylum and its Clostridiales order which correlated to decrease proteins involved in the butyrate production pathway and butyrate concentration. Three of the compounds, Sanguinarine, Chelerythrine and Ethoxysanguinarine activated bacterial protective mechanisms, enriched Proteobacteria, increased opacity proteins and markedly reduced butyrate production. Dihydroberberine had a similar function to BBR in enriching the Akkermansia genus. In addition, it showed less overall adverse impacts on the functionality of the gut microbiome, including a better maintenance of the butyrate level. Our study shows that ex vivo microbiome assay can assess differential regulating effects of compounds with subtle differences and reveals that compound analogues can have distinct effects on the microbiome.
2020-07-21 | PXD015934 | Pride