Towards a more comprehensive concept for prebiotics, Nat Rev Gastroenterol Hepatol, vol.12, pp.303-310, 2015. ,
Influence of functional food components on gut health, Crit Rev Food Sci Nutr, vol.59, pp.1927-1936, 2019. ,
Expert consensus document: the International Scientific Association for Probiotics and Prebiotic (ISAPP) consensus statement on the definition and scope of prebiotics, Nat Rev Gastroenterol Hepatol, vol.14, pp.491-502, 2017. ,
Immune-stimulating and gut healthpromoting properties of short-chain fructo-oligosaccharides, Nutr Rev, vol.60, pp.326-334, 2002. ,
Recent trends in the microbial production, analysis and application of fructooligosaccharides, Trends Food Sci Technol, vol.16, pp.442-457, 2005. ,
Non-digestible carbohydrates in infant formula as substitution for human milk oligosaccharide functions: effects on microbiota and gut maturation, Crit Rev Food Sci Nutr, vol.9, pp.1486-1497, 2019. ,
, Inulin market by application (food & beverage, dietary supplements, pharmaceuticals) is expected to reach USD 2.35 billion by 2020, 2015.
, Fructooligosaccharides (FOS) market worth $3.52 billion By 2024, 2016.
The gut microbiota at the intersection of diet and human health, Science, vol.362, pp.776-780, 2018. ,
Dietary fructooligosaccharides affect intestinal barrier function in healthy men, J Nutr, vol.136, pp.70-74, 2006. ,
Short-chain fatty acids in control of body weight and insulin sensitivity, Nat Rev Endocrinol, vol.11, pp.577-591, 2015. ,
,
A dietary intervention with functional foods reduces metabolic endotoxaemia and attenuates biochemical abnormalities by modifying faecal microbiota in people with type 2 diabetes, Diabetes Metab, vol.45, pp.122-131, 2019. ,
In vitro fermentation of fructooligosaccharides with human gut bacteria, Food Funct, vol.6, pp.947-954, 2015. ,
Reclassification of Eubacterium formicigenerans Holdeman and Moore 1974 as Dorea formicigenerans gen. nov., comb. nov., and description of Dorea longicatena sp. nov. isolated from human, Int J Syst Evol Microbiol, vol.52, pp.423-428, 2002. ,
Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome, Gastroenterology, vol.141, pp.1792-1801, 2011. ,
Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome, Gastroenterology, vol.141, pp.1782-1791, 2011. ,
We are what our bacteria eat: the role of bacteria in personalizing nutrition therapy in gastrointestinal conditions, J Gastroenterol Hepatol, vol.32, pp.352-357, 2017. ,
Fiberutilizing capacity varies in Prevotella-versus Bacteroides-dominated gut microbiota, Sci Rep, vol.7, 2017. ,
Short-chain fructo-oligosaccharides modulate intestinal microbiota and metabolic parameters of humanized gnotobiotic diet induced obesity mice, PLoS One, vol.8, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01190544
Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria, PLoS One, vol.8, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01189721
The extra-intestinal avian pathogenic Escherichia coli strain BEN2908 invades avian and human epithelial cells and survives intracellularly, Vet Microbiol, vol.147, pp.435-439, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-01129535
A genomic island of an extraintestinal pathogenic Escherichia coli strain enables the metabolism of fructooligosaccharides, which improves intestinal colonization, J Bacteriol, vol.191, pp.388-393, 2008. ,
The carbohydrate-active enzymes database (CAZy) in 2013, Nucleic Acids Res, vol.42, pp.490-495, 2014. ,
Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis, Nat Rev Microbiol, vol.6, pp.121-131, 2008. ,
How glycan metabolism shapes the human gut microbiota, Nat Rev Microbiol, vol.10, pp.323-335, 2012. ,
The Sus operon: a model system for starch uptake by the human gut Bacteroidetes, Cell Mol Life Sci, vol.73, pp.2603-2617, 2016. ,
Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-01204274
, Genome Res, vol.20, pp.1605-1612
PULDB: the expanded database of polysaccharide utilization loci, Nucleic Acids Res, vol.46, pp.677-683, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02094620
Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic, Firmicutes. Microb Genom, vol.2, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01604326
Genetic mechanisms of prebiotic oligosaccharide metabolism in probiotic microbes, Annu Rev Food Sci Technol, vol.6, pp.137-156, 2015. ,
Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations, Cell, vol.141, pp.1241-1252, 2010. ,
Genetic variation of the SusC/SusD homologs from a polysaccharide utilization locus underlies divergent fructan specificities and functional adaptation in Bacteroides thetaiotaomicron strains, vol.3, pp.185-203, 2018. ,
Crossfeeding amongst probiotic bacterial strains on prebiotic inulin involving the extracellular exo-inulinase of Lactobacillus paracasei strain W20, Appl Environ Microbiol, vol.84, pp.1539-1557, 2018. ,
Trends in inulinase production-a review, Crit Rev Biotechnol, vol.29, pp.67-77, 2009. ,
Functional and comparative genomic analyses of an operon involved in fructooligosaccharide utilization by Lactobacillus acidophilus, Proc Natl Acad Sci U S A, vol.100, pp.8957-8962, 2003. ,
The ABC transporter encoded at the pneumococcal fructooligosaccharide utilization locus determines the ability to utilize long-and short-chain fructooligosaccharides, J Bacteriol, vol.195, pp.1031-1041, 2013. ,
Metabolism of fructooligosaccharides in Lactobacillus plantarum ST-III via differential gene transcription and alteration of cell membrane fluidity, Appl Environ Microbiol, vol.81, pp.7697-7707, 2015. ,
Polysaccharide degradation by the intestinal microbiota and its influence on human health and disease, J Mol Biol, vol.428, pp.3230-3252, 2016. ,
Polysaccharide utilization loci: fueling microbial communities, J Bacteriol, vol.199, pp.860-876, 2017. ,
Humans as holobionts: implications for prevention and therapy, vol.6, p.81, 2018. ,
The bacterial phosphoenolpyruvate:carbohydrate phosphotransferase system: regulation by protein phosphorylation and phosphorylation-dependent protein-protein interactions, Microbiol Mol Biol Rev, vol.78, pp.231-256, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01204432
The chitin disaccharide, N,N=-diacetylchitobiose, is catabolized by Escherichia coli and is transported/phosphorylated by the phosphoenolpyruvate: glycose phosphotransferase system, J Biol Chem, vol.275, pp.33084-33090, 2000. ,
The complete phosphotransferase system in Escherichia coli, J Mol Microbiol Biotechnol, vol.3, pp.329-346, 2001. ,
Genome sequencing of Clostridium butyricum DKU-01, isolated from infant feces, Gut Pathog, vol.7, 2015. ,
Identification of prebiotic fructooligosaccharide metabolism in Lactobacillus plantarum WCFS1 through microarrays, Appl Environ Microbiol, vol.73, pp.1753-1765, 2007. ,
An integrated catalog of reference genes in the human gut microbiome, Nat Biotechnol, vol.32, pp.834-841, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01195478
Pull in and push out: mechanisms of horizontal gene transfer in bacteria, Front Microbiol, vol.9, 2018. ,
Bread consumption in the UK: what are the main attitudinal factors affecting current intake and its place in a healthy diet, Nutr Bull, vol.37, pp.368-379, 2012. ,
Energy flows and greenhouses gases of EU (European Union) national breads using an LCA (life cycle assessment) approach, J Clean Prod, vol.140, pp.455-469, 2017. ,
Food consumption patterns and nutrition transition in South-East Asia, Public Health Nutr, vol.16, pp.1637-1643, 2013. ,
White rice consumption and risk of type 2 diabetes: meta-analysis and systematic review, BMJ, vol.344, p.1454, 2012. ,
Functional characterization of a gene locus from an uncultured gut Bacteroides conferring xylo-oligosaccharides utilization to Escherichia coli, Mol Microbiol, vol.102, pp.579-592, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01886420
Mechanistic diversity in ATP-binding cassette (ABC) transporters, Nat Struct Mol Biol, vol.23, pp.487-493, 2016. ,
Diversity in ABC transporters: type I, II and III importers, Crit Rev Biochem Mol Biol, vol.49, pp.426-437, 2014. ,
Further elucidation of galactose utilization in Lactococcus lactis MG1363, Front Microbiol, vol.9, p.1803, 2018. ,
Crystal structure of a phosphorylation-coupled saccharide transporter, Nature, vol.473, pp.50-54, 2011. ,
Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont, Cell Host Microbe, vol.4, pp.447-457, 2008. ,
Navigating the gut buffet: control of polysaccharide utilization in Bacteroides spp, Trends Microbiol, vol.25, pp.1005-1015, 2017. ,
Molecular dissection of xyloglucan recognition in a prominent human gut symbiont, vol.7, pp.2134-2149, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01886398
Structural basis for regulation and specificity of fructooligosaccharide import in Streptococcus pneumoniae, Structure, vol.25, pp.79-93, 2017. ,
Structure and function of the glucose PTS transporter from Escherichia coli, J Struct Biol, vol.176, pp.395-403, 2011. ,
The chitin catabolic cascade in the marine bacterium Vibrio furnissii, J Biol Chem, vol.271, pp.33409-33413, 1996. ,
Transport of sugars, Annu Rev Biochem, vol.84, pp.865-894, 2015. ,
Rates of ligand binding to periplasmic proteins involved in bacterial transport and chemotaxis, J Biol Chem, vol.258, pp.13665-13672, 1983. ,
Growth kinetics of Escherichia coli with galactose and several other sugars in carbon-limited chemostat culture, Can J Microbiol, vol.46, pp.72-80, 1999. ,
The growth of Escherichia coli in glucose-limited chemostat cultures: a reexamination of the kinetics, Biochim Biophys Acta, vol.1201, pp.424-436, 1994. ,
Sampling of intracellular metabolites for stationary and non-stationary 13 C metabolic flux analysis in Escherichia coli, Anal Biochem, vol.465, pp.38-49, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01268941
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Mol Syst Biol, vol.2, p.8, 2006. ,
TCDB: the Transporter Classification Database for membrane transport protein analyses and information, Nucleic Acids Res, vol.34, pp.181-186, 2006. ,
Topological predictions for integral membrane permeases of the phosphoenolpyruvate: sugar phosphotransferase system, J Mol Microbiol Biotechnol, vol.11, pp.345-360, 2006. ,
Identification of primary free radicals in trehalose dihydrate single crystals X-irradiated at 10 K, Phys Chem Chem Phys, vol.13, pp.11294-11302, 2011. ,
The Pfam protein families database in 2019, Nucleic Acids Res, vol.47, pp.427-432, 2019. ,
Genomes OnLine database (GOLD) v.7: updates and new features, Nucleic Acids Res, vol.47, pp.649-659, 2019. ,
Bacteroidetes use thousands of enzyme combinations to break down glycans, Nat Commun, vol.10, 2019. ,
Carbohydrate catabolic flexibility in the mammalian intestinal commensal Lactobacillus ruminis revealed by fermentation studies aligned to genome annotations, Microb Cell Fact, vol.10, 2011. ,
Global analysis of carbohydrate utilization by Lactobacillus acidophilus using cDNA microarrays, Proc Natl Acad Sci U S A, vol.103, pp.3816-3821, 2006. ,
Stoichiometry and substrate affinity of the mannitol transporter, enzymeII mtl , from Escherichia coli, Biophys J, vol.89, pp.201-210, 2005. ,
Cloning and sequencing of a cellobiose phosphotransferase system operon from Bacillus stearothermophilus XL-65-6 and functional expression in Escherichia coli, J Bacteriol, vol.175, pp.6441-6450, 1993. ,
Cloning of cellobiose phosphoenolpyruvate-dependent phosphotransferase genes: functional expression in recombinant, Appl Environ Microbiol, vol.63, pp.355-363, 1997. ,
Simultaneous consumption of cellobiose and xylose by Bacillus coagulans to circumvent glucose repression and identification of its cellobiose-assimilating operons, Biotechnol Biofuels, vol.11, issue.320, 2018. ,
Polysaccharide utilization loci of North Sea Flavobacteriia as basis for using SusC/D-protein expression for predicting major phytoplankton glycans, ISME J, vol.13, pp.76-91, 2019. ,
Use of photoswitchable fluorescent proteins for droplet-based microfluidic screening, J Microbiol Methods, vol.147, pp.59-65, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01849551
Structural basis for nutrient acquisition by dominant members of the human gut microbiota, Nature, vol.541, pp.407-411, 2017. ,
A classification of glycosyl hydrolases based on amino acid sequence similarities, Biochem J, vol.280, pp.309-316, 1991. ,
URL : https://hal.archives-ouvertes.fr/hal-00310263
Selected fructooligosaccharide composition of petfood ingredients, J Nutr, vol.128, pp.2803-2805, 1998. ,
Enzymatic determination of inulin and fructooligosaccharides in food, Eur Food Res Technol, vol.217, pp.530-534, 2003. ,
Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls, Sci Rep, vol.6, pp.28484-28410, 2016. ,
Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity, Proc Natl Acad Sci U S A, vol.111, pp.4485-4493, 2014. ,
Fungal microbiota dysbiosis in IBD, Gut, vol.66, pp.1039-1048, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01270909
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment, Genome Biol, vol.13, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00736429
Analysis of mucosal microbiota in inflammatory bowel disease using a custom phylogenetic microarray, Austin J Gastroenterol, vol.1, p.1020, 2014. ,
Structural robustness of the gut mucosal microbiota is associated with Crohn's disease remission after surgery, Gut, vol.65, pp.954-962, 2016. ,
Clinical, microbiological, and immunological effects of fructo-oligosaccharide in patients with Crohn's disease, Gut, vol.55, pp.348-355, 2006. ,
Randomised, double-blind, placebo-controlled trial of fructo-oligosaccharides in active Crohn's disease, Gut, vol.60, pp.923-929, 2011. ,
Prebiotic inulin-type fructans and galactooligosaccharides: definition, specificity, function, and application in gastrointestinal disorders, J Gastroenterol Hepatol, vol.32, pp.64-68, 2017. ,
Transcriptional pattern of Escherichia coli ihfB (himD) gene expression, Gene, vol.181, pp.468-472, 1996. ,
Analysis of relative gene expression data using real-time quantitative PCR and the 2 -??CT method, Methods, vol.25, pp.402-408, 2001. ,
Determination of carbon labeling distribution of intracellular metabolites from single fragment ions by ion chromatography tandem mass spectrometry, Anal Biochem, vol.360, pp.182-188, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-02183207
Methods for the bioinformatic identification of bacterial lipoproteins encoded in the genomes of Gram-positive bacteria, World J Microbiol Biotechnol, vol.24, pp.2377-2382, 2008. ,
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes, J Mol Biol, vol.305, pp.567-580, 2001. ,
CDD/SPARCLE: functional classification of proteins via subfamily domain architectures, Nucleic Acids Res, vol.45, pp.200-203, 2017. ,
Enzyme function initiative-enzyme similarity tool (EFI-EST): a web tool for generating protein sequence similarity networks, Biochim Biophys Acta, vol.1854, pp.1019-1037, 2015. ,
The Transporter Classification Database (TCDB): recent advances, Nucleic Acids Res, vol.44, pp.372-379, 2016. ,
Sucrose metabolism contributes to in vivo fitness of Streptococcus pneumoniae, Mol Microbiol, vol.66, pp.1-13, 2007. ,
Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res, vol.13, pp.2498-2504, 2003. ,
Basic local alignment search tool, J Mol Biol, vol.215, issue.05, pp.80360-80362, 1990. ,