Journal: Frontiers in Cellular and Infection Microbiology

Article Title: How to Count Our Microbes? The Effect of Different Quantitative Microbiome Profiling Approaches

doi: 10.3389/fcimb.2020.00403

Figure Lengend Snippet: Microbiome profile comparisons. Genus-level fecal microbial composition of both replicates of all 16 healthy study subjects ( n = 32 samples) based upon (A) relative microbiome profiling (RMP), (B) quantitative microbiome profiling (QMP, cells per gram feces), (C) QMP after PMAxx-treatment of fecal samples (QMP-PMA, cells per gram feces), and (D) QMP using qPCR for quantification of bacterial load (QMP-qPCR, cells per gram feces).

Article Snippet: We used the Gut Microbiome Whole cell Mix (ATCC® MSA-2006 TM ) containing an even mixture of whole bacterial cells (12 different species) in order to assess whether cell-based or molecular-based quantification was more accurate.

Techniques:

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: How to Count Our Microbes? The Effect of Different Quantitative Microbiome Profiling Approaches

doi: 10.3389/fcimb.2020.00403

Figure Lengend Snippet: Within method dissimilarity of sample replicates and between methods dissimilarity of samples. Fecal microbial community structure variation based upon Bray–Curtis (BC) dissimilarity between samples and sample replicates. (A) Principal coordinates analysis of the study cohort based upon BC dissimilarity. Each segment connects the two replicates of the same sample as profiled by QMP (blue), QMP-PMA (green), and QMP-qPCR (red), (B) Box-plot of BC distance between sample replicates for all quantitative profiling methods (within-method variability) and BC distance in microbial community structure from the same sample profiled with different quantitative methods (between-method variability). The significance was checked pairwise using the Wilcoxon test and then adjusted for multiple comparisons using the FDR correction. The significance coding is indicated as *** p < 0.005, ** p < 0.01, * p < 0.05 and N.S. for p ≥ 0.05. For clarity only significance of the comparisons between within QMP-method dissimilarity and all other within- and between-method dissimilarities are indicated (all FDR-corrected p -values are presented in ).

Article Snippet: We used the Gut Microbiome Whole cell Mix (ATCC® MSA-2006 TM ) containing an even mixture of whole bacterial cells (12 different species) in order to assess whether cell-based or molecular-based quantification was more accurate.

Techniques:

Journal: Frontiers in Microbiology

Article Title: High-throughput screening of the effects of 90 xenobiotics on the simplified human gut microbiota model (SIHUMIx): a metaproteomic and metabolomic study

doi: 10.3389/fmicb.2024.1349367

Figure Lengend Snippet: Experimental overview of the screening of 90 xenobiotics with the simplified model of human microbiota (SIHUMIx). The community was inoculated in bioreactors until steady-state. Then, SIHUMIx were cultured in 96-deep-well plates at 37°C under anaerobic conditions for 24 h exposed to the individual xenobiotics. Pellets and supernatants were collected for metaproteomic and metabolomic analysis, respectively.

Article Snippet: In this experiment, the extended simplified human intestinal microbiota (SIHUMIx) ( ) was utilized, which comprised a total of eight species: Anaerostipes caccae (DSMZ 14662), Bacteroides thetaiotaomicron (DSMZ 2079), Bifidobacterium longum (NCC 2705), Blautia producta (DSMZ 2950), Clostridium butyricum (DSMZ 10702), Erysipelatoclostridium ramosum (DSMZ 1402), Escherichia coli K-12 (MG1655), and Lactobacillus plantarum (DSMZ 20174).

Techniques: Cell Culture

Journal: Frontiers in Microbiology

Article Title: High-throughput screening of the effects of 90 xenobiotics on the simplified human gut microbiota model (SIHUMIx): a metaproteomic and metabolomic study

doi: 10.3389/fmicb.2024.1349367

Figure Lengend Snippet: Impact of plant protection products, food additives, and dyes on the composition of SIHUMIx. The species abundance was measured by metaproteomics and is displayed as log 2 FC for (A) 14 plant protection products and (B) 17 food additives and dyes which affected at least the abundance of one species compared to the control. Statistically significant effects ( P adj < 0.05) are highlighted by asterisks.

Article Snippet: In this experiment, the extended simplified human intestinal microbiota (SIHUMIx) ( ) was utilized, which comprised a total of eight species: Anaerostipes caccae (DSMZ 14662), Bacteroides thetaiotaomicron (DSMZ 2079), Bifidobacterium longum (NCC 2705), Blautia producta (DSMZ 2950), Clostridium butyricum (DSMZ 10702), Erysipelatoclostridium ramosum (DSMZ 1402), Escherichia coli K-12 (MG1655), and Lactobacillus plantarum (DSMZ 20174).

Techniques: Metaproteomics, Control

Journal: Frontiers in Microbiology

Article Title: High-throughput screening of the effects of 90 xenobiotics on the simplified human gut microbiota model (SIHUMIx): a metaproteomic and metabolomic study

doi: 10.3389/fmicb.2024.1349367

Figure Lengend Snippet: Impact of xenobiotics on SCFA concentration. Log 2 FC of the 8 detected SCFAs following 24 h of exposure of SIHUMIx to (A) plant protection products and (B) food additives and dyes. Statistically significant effects ( P adj < 0.05) are indicated by asterisks.

Article Snippet: In this experiment, the extended simplified human intestinal microbiota (SIHUMIx) ( ) was utilized, which comprised a total of eight species: Anaerostipes caccae (DSMZ 14662), Bacteroides thetaiotaomicron (DSMZ 2079), Bifidobacterium longum (NCC 2705), Blautia producta (DSMZ 2950), Clostridium butyricum (DSMZ 10702), Erysipelatoclostridium ramosum (DSMZ 1402), Escherichia coli K-12 (MG1655), and Lactobacillus plantarum (DSMZ 20174).

Techniques: Concentration Assay

Journal: Frontiers in Microbiology

Article Title: High-throughput screening of the effects of 90 xenobiotics on the simplified human gut microbiota model (SIHUMIx): a metaproteomic and metabolomic study

doi: 10.3389/fmicb.2024.1349367

Figure Lengend Snippet: Impact of xenobiotics on SIHUMIx pathways and their relationship with SCFA production. Effects of (A) ethoxyquin and (B) acid orange 7 exposure on SIHUMIx significantly (1) affected pathways and their association with changes in (2) short-chain fatty acid (SCFA) concentrations. Following exposure to the plant protection product, we observed a reduction in energy pathways, notably the metabolism of pyruvate, a key precursor for SCFAs. Acid orange 7, on the other hand, led to a decline in butyrate metabolism, resulting in a significant decrease in butyrate concentration levels in the supernatant. Statistically significant effects ( P adj < 0.05) are indicated by asterisks.

Article Snippet: In this experiment, the extended simplified human intestinal microbiota (SIHUMIx) ( ) was utilized, which comprised a total of eight species: Anaerostipes caccae (DSMZ 14662), Bacteroides thetaiotaomicron (DSMZ 2079), Bifidobacterium longum (NCC 2705), Blautia producta (DSMZ 2950), Clostridium butyricum (DSMZ 10702), Erysipelatoclostridium ramosum (DSMZ 1402), Escherichia coli K-12 (MG1655), and Lactobacillus plantarum (DSMZ 20174).

Techniques: Concentration Assay

Journal: Frontiers in Microbiology

Article Title: High-throughput screening of the effects of 90 xenobiotics on the simplified human gut microbiota model (SIHUMIx): a metaproteomic and metabolomic study

doi: 10.3389/fmicb.2024.1349367

Figure Lengend Snippet: Pearson’s correlation values between relative species abundance and affected pathways. Values for the relative abundance of SIHUMIx species and pathways lower than −0.6 and higher than 0.6 and P adj < 0.05 after exposure to (A) plant protection products and (B) food additives and dyes.

Article Snippet: In this experiment, the extended simplified human intestinal microbiota (SIHUMIx) ( ) was utilized, which comprised a total of eight species: Anaerostipes caccae (DSMZ 14662), Bacteroides thetaiotaomicron (DSMZ 2079), Bifidobacterium longum (NCC 2705), Blautia producta (DSMZ 2950), Clostridium butyricum (DSMZ 10702), Erysipelatoclostridium ramosum (DSMZ 1402), Escherichia coli K-12 (MG1655), and Lactobacillus plantarum (DSMZ 20174).

Techniques:

Journal: Frontiers in Immunology

Article Title: Safety and efficacy of fecal microbiota transplantation for autoimmune diseases and autoinflammatory diseases: A systematic review and meta-analysis

doi: 10.3389/fimmu.2022.944387

Figure Lengend Snippet: The characteristics of the included studies.

Article Snippet: Systemic sclerosis , Fretheim et al. (2020) ( ) , NCT03444220 , Norway , 5 , 5 , Commercially available anaerobic cultivated human intestinal microbiota (ACHIM) transplant to upper gastrointestinal tract , ACHIM bacteria medium transplant to upper gastrointestinal tract , Clinical symptoms, modified Rodnan Skin Score (mRSS), new-onset digital ulcers, forced vital capacity (FVC), diffusing capacity of the lungs for carbon monoxide (DLCO), CRP, ESR, fecal microbiota changes, adverse events , 58.0 ± 5.6 , 66.0 ± 1.5 , 16 weeks , ACHIM is produced by ACHIM AB biotherapeutics (556939-7788), Sweden. It is a standardized human fecal microbiota composition. The microbiota originates from feces donated back in 1995, by a single healthy feces donor.

Techniques: Control, Clinical Proteomics, Bacteria, Modification, Produced, Saline