Simultaneous measurement of plasma concentrations and 13C-enrichment of short-chain fatty acids, lactic acid and ketone bodies by gas chromatography coupled to mass spectrometry

Moreau, Noëlle M.; Goupry, Stéphane M.; Antignac, Jean‐Philippe; Monteau, Fabrice; Bizec, Bruno Le; Champ, Martine; Martin, Lucile; Dumon, H.

doi:10.1016/s1570-0232(02)00827-9

Cited by 123 publications

(102 citation statements)

References 31 publications

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“…The extraction and GC-MS measurement of shortchain fatty acids was based on a protocol from Moreau et al 71 (Supplementary Note 8 and Supplementary Table 20). Extracellular polar metabolites from the supernatant samples and external concentration curves for each compound of interest were extracted applying a liquid-liquid extraction (Methanol/Water).…”

Section: Methodsmentioning

confidence: 99%

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

et al. 2016

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1 r e s o u r c eChanges in the composition of the human gut microbiota have been associated with the development of chronic diseases including type 2 diabetes, obesity, and colorectal cancer 1 . Gut bacterial functions, such as synthesis of amino acids and vitamins 2 , breakdown of indigestible plant polysaccharides 3 , and production of metabolites involved in energy metabolism 4 , have been linked to human health. The use of 'omics approaches to study human microbiome communities has led to the generation of enormous data sets whose interpretations require systems biology tools to shed light on the functional capacity of gut microbiomes and their interactions with the human host 5 .In order to infer the metabolic repertoire of a gut metagenome data set, researchers usually map sequenced genes or organisms onto metabolic networks derived from the Kyoto Encyclopedia of Genes and Genomes (KEGG) 6 , and functional annotations from KEGG ontologies 7 . However, this approach cannot identify the contribution of each bacterial species to the metabolic repertoire of the whole gut microbiome, nor can it infer the effects of different gut microbial communities on host metabolism.A technique that can bridge this gap is constraint-based reconstruction and analysis (COBRA) 8 using genome-scale metabolic reconstructions (GENREs) of individual human gut microbes. GENREs are assembled using the genome sequence and experimental information 9 . These reconstructions form the basis for the development of condition-specific metabolic models whose functions are simulated and validated by comparison with experimental results. The models can be used to investigate genotype-phenotype relationships 10 , microbe-microbe interactions 11 , and host-microbe interactions 11 . Numerous tools can be used to automatically generate draft GENREs but such models contain errors 12 and are incomplete.Manual curation of draft reconstructions is time consuming because it involves an extensive literature review and experimental validation of metabolic functions 9 .To provide an extensive resource of GENREs for human gut microbes, we developed a comparative metabolic reconstruction method that enables any refinement to one metabolic reconstruction to be propagated to others. This accelerates reconstruction and improves model quality. We generated AGORA, which includes 773 gut microbes, comprising 205 genera and 605 species. All reconstructions were based on literature-derived experimental data and comparative genomics. The metabolic predictions of two AGORA reconstructions and their derived metabolic models were validated against experimental data. RESULTS Metabolic reconstruction pipelineWe devised a comparative metabolic reconstruction method (Fig. 1a,c), which is analogous to the comparative microbial genome annotation approach 13 that has enabled accelerated annotation by propagation of refinements to one genome to others. First, we downloaded draft GENREs using Model SEED 14 and KBase (US Department of Energy Systems Biology Knowledgebase, http:/...

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Section: Methodsmentioning

confidence: 99%

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

et al. 2016

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“…The SCFA analysis performed on the mice plasma was a modification of the protocol described elsewhere (27). Because of the minute amount of sample (11-80 mg was analyzed, whereas the referenced method used 400 l of plasma), the entire sample was transferred into a 2-ml vial and the weight recorded.…”

Section: Methodsmentioning

confidence: 99%

Beneficial Metabolic Effects of a Probiotic via Butyrate-induced GLP-1 Hormone Secretion

Yadav

Lee

Lloyd³

et al. 2013

Journal of Biological Chemistry

590

404

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Background:The prescription of probiotics as obesity and diabetes therapy is limited because of insufficient efficacy data and lack of understanding of their mechanism of action. Results: The probiotic VSL#3 prevents obesity and diabetes in mice via induction of butyrate and GLP-1. Conclusion: Probiotics modulate the gut flora to elicit beneficial metabolic effects. Significance: Administration of probiotics represents a viable treatment option for obesity and diabetes.

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“…SCFAs in mouse serum and cecal samples were assayed by using a modification of the method of Moreau et al (35). For analysis of sera, mice were fasted for 4 h; blood was collected by retro-orbital phlebotomy into serum separation tubes (Becton Dickinson) and spun; and the super- per experiment; two independent experiments; mean Ϯ SEM plotted).…”

Section: Rna Isolation and Genechip Analysismentioning

confidence: 99%

A humanized gnotobiotic mouse model of host–archaeal–bacterial mutualism

Samuel

Gordon²

2006

Proc. Natl. Acad. Sci. U.S.A.

583

491

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Our colons harbor trillions of microbes including a prominent archaeon, Methanobrevibacter smithii. To examine the contributions of Archaea to digestive health, we colonized germ-free mice with Bacteroides thetaiotaomicron, an adaptive bacterial forager of the polysaccharides that we consume, with or without M. smithii or the sulfate-reducing bacterium Desulfovibrio piger. Wholegenome transcriptional profiling of B. thetaiotaomicron, combined with mass spectrometry, revealed that, unlike D. piger, M. smithii directs B. thetaiotaomicron to focus on fermentation of dietary fructans to acetate, whereas B. thetaiotaomicron-derived formate is used by M. smithii for methanogenesis. B. thetaiotaomicron-M. smithii cocolonization produces a significant increase in host adiposity compared with monoassociated, or B. thetaiotaomicron-D. piger biassociated, animals. These findings demonstrate a link between this archaeon, prioritized bacterial utilization of polysaccharides commonly encountered in our modern diets, and host energy balance. adiposity ͉ energy homeostasis ͉ gut microbial ecology ͉ polysaccharide metabolism ͉ Methanobrevibacter smithii T he role of Archaea in human health remains unclear (1). One site where their influence may be profound is the gut. Hydrogen-consuming methanogenic archaeons are present in the intestinal tracts of many invertebrate and vertebrate species (2-4). Our adult intestine contains 10 trillion to 100 trillion microbial cells and is dominated by members of just two divisions of Bacteria, the Bacteroidetes and the Firmicutes (5). Archaea, the only known producers of methane, are present at high levels in 50-85% of humans (6-8). Concordance rates for methane production are equivalent for both monozygotic and dizygotic twins, underscoring the importance of family environment (mothers) in acquisition of methanogens (9). The most comprehensive enumeration of the adult human colonic microbiota reported to date (5) found a single predominant archaeal species, Methanobrevibacter smithii. This Euryarchaeote can comprise up to 10% of all anaerobes in the colons of healthy adults, while Methanosphaera stadtmanae and Crenarchaeotes can be minor members (10, 11).One manifestation of the mutualism between humans and their distal gut microbiota is that the latter extracts energy that would be lost from otherwise indigestible dietary polysaccharides (fiber). Fermentation of dietary fiber is accomplished by syntrophic interactions between microbes linked in a metabolic food web and is a major energy-producing pathway for members of the Bacteroidetes and the Firmicutes. These primary bacterial fermentors generate short-chain fatty acids (SCFAs), principally acetate, propionate, and butyrate, as well as other organic acids (e.g., formate) and gases [e.g., hydrogen (H 2 ) and carbon dioxide (CO 2 )]. Accumulation of H 2 inhibits bacterial NADH dehydrogenases, thereby reducing the yield of ATP. Studies in man-made bioreactors have shown that removal of H 2 by means of archaeal methanogenesis improves ferment...

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Simultaneous measurement of plasma concentrations and 13C-enrichment of short-chain fatty acids, lactic acid and ketone bodies by gas chromatography coupled to mass spectrometry

Cited by 123 publications

References 31 publications

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

Beneficial Metabolic Effects of a Probiotic via Butyrate-induced GLP-1 Hormone Secretion

A humanized gnotobiotic mouse model of host–archaeal–bacterial mutualism

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