Non-invasive VOCs detection to monitor the gut microbiota metabolism in-vitro

Eckburg, P. B. et al. Diversity of the human intestinal microbial flora. Science 308, 1635–1638 (2005).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Consortium, T. H. M. P. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012).Article 
ADS 

Google Scholar 
Pérez-Burillo, S. et al. An in vitro batch fermentation protocol for studying the contribution of food to gut microbiota composition and functionality. Nat. Protoc. 16, 3186–3209 (2021).Article 
PubMed 

Google Scholar 
Liu, Y. et al. Clostridium sporogenes uses reductive stickland metabolism in the gut to generate ATP and produce circulating metabolites. Nat. Microbiol. 7, 695–706 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Qiao, S. et al. Gut parabacteroides merdae protects against cardiovascular damage by enhancing branched-chain amino acid catabolism. Nat. Metab. 4, 1271–1286 (2022).Article 
CAS 
PubMed 

Google Scholar 
Van de Wiele, T., Van den Abbeele, P., Ossieur, W., Possemiers, S. & Marzorati, M. The simulator of the human intestinal microbial ecosystem (shime®). The Impact of Food Bioactives on Health: in vitro and ex vivo models 305–317 (2015).De Paepe, K., Verspreet, J., Courtin, C. M. & Van de Wiele, T. Microbial succession during wheat bran fermentation and colonisation by human faecal microbiota as a result of niche diversification. ISME J. 14, 584–596 (2020).Article 
PubMed 

Google Scholar 
Faust, K., Lahti, L., Gonze, D., De Vos, W. M. & Raes, J. Metagenomics meets time series analysis: Unraveling microbial community dynamics. Curr. Opin. Microbiol. 25, 56–66 (2015).Article 
PubMed 

Google Scholar 
Meredith, L. K. & Tfaily, M. M. Capturing the microbial volatilome: An oft overlooked ‘ome’. Trends Microbiol. 30, 622–631 (2022).Article 
CAS 
PubMed 

Google Scholar 
Weisskopf, L., Schulz, S. & Garbeva, P. Microbial volatile organic compounds in intra-kingdom and inter-kingdom interactions. Nat. Rev. Microbiol. 19, 391–404 (2021).Article 
CAS 
PubMed 

Google Scholar 
Kai, M. et al. Bacterial volatiles and their action potential. Appl. Microbiol. Biotechnol. 81, 1001–1012 (2009).Article 
CAS 
PubMed 

Google Scholar 
Audrain, B., Farag, M. A., Ryu, C.-M. & Ghigo, J.-M. Role of bacterial volatile compounds in bacterial biology. FEMS Microbiol. Rev. 39, 222–233 (2015).Article 
CAS 
PubMed 

Google Scholar 
Schulz-Bohm, K., Martín-Sánchez, L. & Garbeva, P. Microbial volatiles: Small molecules with an important role in intra-and inter-kingdom interactions. Front. Microbiol. 8, 2484 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Topping, D. L. & Clifton, P. M. Short-chain fatty acids and human colonic function: Roles of resistant starch and nonstarch polysaccharides. Physiol. Rev. 81, 1031–1064 (2001).Article 
CAS 
PubMed 

Google Scholar 
Ma, Y., Liu, X. & Wang, J. Small molecules in the big picture of gut microbiome-host cross-talk. EBioMedicine 81, 104085 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Yuille, S., Reichardt, N., Panda, S., Dunbar, H. & Mulder, I. E. Human gut bacteria as potent class i histone deacetylase inhibitors in vitro through production of butyric acid and valeric acid. PLoS ONE 13, e0201073 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Wu, M. et al. Associations between disordered gut microbiota and changes of neurotransmitters and short-chain fatty acids in depressed mice. Transl. Psychiatry 10, 350 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Saresella, M. et al. Alterations in circulating fatty acid are associated with gut microbiota dysbiosis and inflammation in multiple sclerosis. Front. Immunol. 11, 1390 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Amann, A. et al. The human volatilome: Volatile organic compounds (VOCs) in exhaled breath, skin emanations, urine, feces and saliva. J. Breath Res. 8, 034001 (2014).Article 
ADS 
CAS 
PubMed 

Google Scholar 
Raman, M. et al. Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease. Clin. Gastroenterol. Hepatol. 11, 868–875 (2013).Article 
CAS 
PubMed 

Google Scholar 
Shanahan, F., van Sinderen, D., O’Toole, P. W. & Stanton, C. Feeding the microbiota: Transducer of nutrient signals for the host. Gut 66, 1709–1717 (2017).Article 
CAS 
PubMed 

Google Scholar 
Silva, Y. P., Bernardi, A. & Frozza, R. L. The role of short-chain fatty acids from gut microbiota in gut-brain communication. Front. Endocrinol. 11, 25 (2020).Article 

Google Scholar 
Huang, Z., Boekhorst, J., Fogliano, V., Capuano, E. & Wells, J. M. Distinct effects of fiber and colon segment on microbiota-derived indoles and short-chain fatty acids. Food Chem. 398, 133801 (2023).Article 
CAS 
PubMed 

Google Scholar 
Vitali, B. et al. An in vitro evaluation of the effect of probiotics and prebiotics on the metabolic profile of human microbiota. Anaerobe 18, 386–391 (2012).Article 
CAS 
PubMed 

Google Scholar 
Defois, C. et al. Food chemicals disrupt human gut microbiota activity and impact intestinal homeostasis as revealed by in vitro systems. Sci. Rep. 8, 11006 (2018).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Cárdenas-Castro, A. P. et al. In vitro gastrointestinal digestion and colonic fermentation of tomato (Solanum lycopersicum L.) and husk tomato (Physalis ixocarpa Brot.): Phenolic compounds released and bioconverted by gut microbiota. Food Chemistry 360, 130051 (2021).Article 
PubMed 

Google Scholar 
Majchrzak, T. et al. PTR-MS and GC-MS as complementary techniques for analysis of volatiles: A tutorial review. Anal. Chim. Acta 1035, 1–13 (2018).Article 
CAS 
PubMed 

Google Scholar 
Timm, C. M., Lloyd, E. P., Egan, A., Mariner, R. & Karig, D. Direct growth of bacteria in headspace vials allows for screening of volatiles by gas chromatography mass spectrometry. Front. Microbiol. 9, 491 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Kataoka, H., Lord, H. L. & Pawliszyn, J. Applications of solid-phase microextraction in food analysis. J. Chromatogr. A 880, 35–62 (2000).Article 
CAS 
PubMed 

Google Scholar 
Pawliszyn, J. Handbook of Solid Phase Microextraction (Elsevier, 2011).
Google Scholar 
Madssen, T. S., Giskeødegård, G. F., Smilde, A. K. & Westerhuis, J. A. Repeated measures ASCA+ for analysis of longitudinal intervention studies with multivariate outcome data. PLoS Comput. Biol. 17, e1009585 (2021).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kedia, G., Vázquez, J. A., Charalampopoulos, D. & Pandiella, S. S. In vitro fermentation of oat bran obtained by debranning with a mixed culture of human fecal bacteria. Curr. Microbiol. 58, 338–342 (2009).Article 
CAS 
PubMed 

Google Scholar 
Jarmund, A. H., Madssen, T. S. & Giskeødegård, G. F. ALASCA: An R package for longitudinal and cross-sectional analysis of multivariate data by ASCA-based methods. Front. Mol. Biosci. 9, 962431 (2022).Article 
PubMed 
PubMed Central 

Google Scholar 
Nakajima, H. et al. Inulin reduces visceral adipose tissue mass and improves glucose tolerance through altering gut metabolites. Nutr. Metab. 19, 1–10 (2022).Article 

Google Scholar 
Falony, G., Calmeyn, T., Leroy, F. & De Vuyst, L. Coculture fermentations of bifidobacterium species and bacteroides thetaiotaomicron reveal a mechanistic insight into the prebiotic effect of inulin-type fructans. Appl. Environ. Microbiol. 75, 2312–2319 (2009).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Procházková, N. et al. Effects of a wholegrain-rich diet on markers of colonic fermentation and bowel function and their associations with the gut microbiome: a randomised controlled cross-over trial. Front. Nutr. 10, 1187165 (2023).Article 
PubMed 
PubMed Central 

Google Scholar 
Straube, J., Gorse, A.-D., of Excellence Team, P. C., Huang, B. E. & Lê Cao, K.-A. A linear mixed model spline framework for analysing time course ‘omics’ data. PLoS ONE 10, e0134540 (2015).Scarborough, M. J., Lawson, C. E., Hamilton, J. J., Donohue, T. J. & Noguera, D. R. Metatranscriptomic and thermodynamic insights into medium-chain fatty acid production using an anaerobic microbiome. MSystems 3, e00221-18 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Englyst, H., Hay, S. & Macfarlane, G. Polysaccharide breakdown by mixed populations of human faecal bacteria. FEMS Microbiol. Ecol. 3, 163–171 (1987).Article 

Google Scholar 
Leitch, E. C. M., Walker, A. W., Duncan, S. H., Holtrop, G. & Flint, H. J. Selective colonization of insoluble substrates by human faecal bacteria. Environ. Microbiol. 9, 667–679 (2007).Article 
PubMed 

Google Scholar 
Knudsen, K. E. B., Jensen, B. B. & Hansen, I. Oat bran but not a \(\beta\)-glucan-enriched oat fraction enhances butyrate production in the large intestine of pigs. J. Nutr. 123, 1235–1247 (1993).Article 
CAS 
PubMed 

Google Scholar 
Dixon, E. et al. Solid-phase microextraction and the human fecal VOC metabolome. PLoS ONE 6, e18471 (2011).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Wang, R., Koutinas, A. A. & Campbell, G. M. Dry processing of oats-application of dry milling. J. Food Eng. 82, 559–567 (2007).Article 
CAS 

Google Scholar 
Koper, J. E. et al. Polyphenols and tryptophan metabolites activate the aryl hydrocarbon receptor in an in vitro model of colonic fermentation. Mol. Nutr. Food Res. 63, 1800722 (2019).Article 
PubMed 

Google Scholar 
Mathur, H. et al. Methods to mitigate Escherichia coli blooms in human ex vivo colon model experiments using the high throughput micro-matrix bioreactor fermentation system. MethodsX 11, 102393 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Amigo, J. M., Skov, T., Bro, R., Coello, J. & Maspoch, S. Solving GC-MS problems with parafac2. TrAC Trends Anal. Chem. 27, 714–725 (2008).Article 
CAS 

Google Scholar 
Johnsen, L. G., Skou, P. B., Khakimov, B. & Bro, R. Gas chromatography–mass spectrometry data processing made easy. J. Chromatogr. A 1503, 57–64 (2017).Article 
CAS 
PubMed 

Google Scholar 
Shen, V. K., Siderius, D. W., Krekelberg, W. P. & Hatch, H. W. Nist standard reference simulation website, nist standard reference database number 173. 20899 (National Institute of Standards and Technology, 2014).Waskom, M. L. Seaborn: Statistical data visualization. J. Open Source Softw. 6, 3021, https://doi.org/10.21105/joss.03021 (2021).

Hot Topics

Related Articles