Human metabolome variation along the upper intestinal tract

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · see citing works

DADA2: High–resolution sample inference from Illumina amplicon data

Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods · doi:10.1038/nmeth.3869 · Cited by 35,698 · see citing works

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1219 · Cited by 33,055 · see citing works

U1 snRNP regulates cancer cell migration and invasion in vitro

Oh, J.-M., Venters, C. C., Di, C., Pinto, A. M., Wan, L., Younis, I., Cai, Z., Arai, C., So, B. R., Duan, J., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-13993-7 · Cited by 7,157 · see citing works

Identifying Small Molecules via High Resolution Mass Spectrometry: Communicating Confidence

Schymanski, E. L., Jeon, J., Gulde, R., Fenner, K., Ruff, M., Singer, H. P., & Hollender, J. (2014) · Environmental Science & Technology · doi:10.1021/es5002105 · Cited by 4,519 · see citing works

Bile salt biotransformations by human intestinal bacteria

Ridlon, J. M., Kang, D.-J., & Hylemon, P. B. (2006) · Journal of Lipid Research · doi:10.1194/jlr.r500013-jlr200 · Cited by 2,829 · see citing works

Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics

Matyash, V., Liebisch, G., Kurzchalia, T. V., Shevchenko, A., & Schwudke, D. (2008) · Journal of Lipid Research · doi:10.1194/jlr.d700041-jlr200 · Cited by 2,615 · see citing works

Journal of the science of food and agriculture

(1962) · Journal of the Science of Food and Agriculture · doi:10.1002/jsfa.2740131302 · Cited by 2,424 · see citing works

Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health

Ríos-Covián, D., Ruas‐Madiedo, P., Margollés, A., Gueimonde, M., Reyes‐Gavilán, C. G. D. L., & Salazar, N. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00185 · Cited by 2,215 · see citing works

Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses

Thévenot, E., Roux, A., Xu, Y., Ezan, É., & Junot, C. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00354 · Cited by 1,760 · see citing works

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

Djoumbou-Feunang, Y., Eisner, R., Knox, C., Chepelev, L. L., Hastings, J., Owen, G., Fahy, E., Steinbeck, C., Subramanian, S., Bolton, E., et al. (2016) · Journal of Cheminformatics · doi:10.1186/s13321-016-0174-y · Cited by 1,543 · see citing works

The gastrointestinal mucus system in health and disease

Johansson, M. E. V., Sjövall, H., & Hansson, G. C. (2013) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2013.35 · Cited by 1,438 · see citing works

Measurement of gastrointestinal pH profiles in normal ambulant human subjects

Evans, D. F., Pye, G., Bramley, R., Clark, A. G., Dyson, T. J., & Hardcastle, J. D. (1988) · Gut · doi:10.1136/gut.29.8.1035 · Cited by 1,240 · see citing works

Food microstructure affects the bioavailability of several nutrients.

Parada, J., & Aguilera, J. (2007) · Journal of Food Science · doi:10.1111/j.1750-3841.2007.00274.x · Cited by 1,010 · see citing works

Metabolomics by Gas Chromatography–Mass Spectrometry: Combined Targeted and Untargeted Profiling

Fiehn, O. (2016) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb3004s114 · Cited by 917 · see citing works

Double-check: validation of diagnostic statistics for PLS-DA models in metabolomics studies

Szymańska, E., Saccenti, E., Smilde, A. K., & Westerhuis, J. A. (2011) · Metabolomics · doi:10.1007/s11306-011-0330-3 · Cited by 913 · see citing works

A lipidome atlas in MS-DIAL 4

Tsugawa, H., Ikeda, K., Takahashi, M., Satoh, A., Mori, Y., Uchino, H., Okahashi, N., Yamada, Y., Tada, I., Bonini, P., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0531-2 · Cited by 895 · see citing works

Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content

Rothwell, J. A., Pérez‐Jiménez, J., Neveu, V., Medina‐Remón, A., M'hiri, N., Garcia-Lobato, P., Manach, C., Knox, C., Eisner, R., Wishart, D. S., et al. (2013) · Database · doi:10.1093/database/bat070 · Cited by 884 · see citing works

Discovery of a Class of Endogenous Mammalian Lipids with Anti-Diabetic and Anti-inflammatory Effects

Yore, M. M., Syed, I., Moraes‐Vieira, P. M., Zhang, T., Herman, M. A., Homan, E. A., Patel, R. T., Lee, J., Chen, S., Peroni, O. D., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.035 · Cited by 845 · see citing works

Dietary flavonoid and isoflavone glycosides are hydrolysed by the lactase site of lactase phlorizin hydrolase

Day, A. J., Cañada, F. J., Diaz, J. C., Kroon, P. A., McLAUCHLAN, R. W., Faulds, C. B., Plumb, G. W., Morgan, M. R. A., & Williamson, G. (2000) · FEBS Letters · doi:10.1016/s0014-5793(00)01211-4 · Cited by 821 · see citing works

Global chemical effects of the microbiome include new bile-acid conjugations

Quinn, R. A., Melnik, A. V., Vrbanac, A., Fu, T., Patras, K. A., Christy, M. P., Bodai, Z., Belda-Ferre, P., Tripathi, A., Chung, L. K., et al. (2020) · Nature · doi:10.1038/s41586-020-2047-9 · Cited by 579 · see citing works

Carnitine and Acylcarnitines

Reuter, S. E., & Evans, A. M. (2012) · Clinical Pharmacokinetics · doi:10.1007/bf03261931 · Cited by 496 · see citing works

Profiling the human intestinal environment under physiological conditions

Shalon, D., Culver, R. N., Grembi, J. A., Folz, J., Treit, P. V., Shi, H., Rosenberger, F. A., Dethlefsen, L., Meng, X., Yaffe, E., et al. (2023) · Nature · doi:10.1038/s41586-023-05989-7 · Cited by 484 · see citing works

High-confidence structural annotation of metabolites absent from spectral libraries

Hoffmann, M. A., Nothias, L.-F., Ludwig, M., Fleischauer, M., Gentry, E. C., Witting, M., Dorrestein, P. C., Dührkop, K., & Böcker, S. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-01045-9 · Cited by 388 · see citing works

The effect of antibiotics on the composition of the intestinal microbiota—a systematic review

Zimmermann, P., & Curtis, N. (2019) · Journal of Infection · doi:10.1016/j.jinf.2019.10.008 · Cited by 383 · see citing works

The absolute bioavailability of caffeine in man

Blanchard, J., & Sawers, S. J. A. (1983) · European Journal of Clinical Pharmacology · doi:10.1007/bf00613933 · Cited by 378 · see citing works

A review on the food digestion in the digestive tract and the used in vitro models

Şensoy, İ. (2021) · Current Research in Food Science · doi:10.1016/j.crfs.2021.04.004 · Cited by 362 · see citing works

Normalization method for metabolomics data using optimal selection of multiple internal standards

Sysi‐Aho, M., Katajamaa, M., Yetukuri, L., & Orešič, M. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-93 · Cited by 358 · see citing works

Chemical Similarity Enrichment Analysis (ChemRICH) as alternative to biochemical pathway mapping for metabolomic datasets

Barupal, D. K., & Fiehn, O. (2017) · Scientific Reports · doi:10.1038/s41598-017-15231-w · Cited by 339 · see citing works

Growth and activities of sulphate-reducing bacteria in gut contents of healthy subjects and patients with ulcerative colitis

Gibson, G. R., Cummings, J. H., & Macfarlane, G. T. (1991) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1991.tb04799.x · Cited by 301 · see citing works

Metabolomics in nutritional epidemiology: identifying metabolites associated with diet and quantifying their potential to uncover diet-disease relations in populations

Guertin, K. A., Moore, S. C., Sampson, J. N., Huang, W., Xiao, Q., Stolzenberg‐Solomon, R. Z., Sinha, R. R., & Cross, A. J. (2014) · American Journal of Clinical Nutrition · doi:10.3945/ajcn.113.078758 · Cited by 282 · see citing works

The human saliva metabolome

Dame, Z. T., Aziat, F., Mandal, R., Krishnamurthy, R., Bouatra, S., Borzouie, S., Guo, A. C., Sajed, T., Deng, L., Lin, H., et al. (2015) · Metabolomics · doi:10.1007/s11306-015-0840-5 · Cited by 275 · see citing works

Metabolic profiling strategy for discovery of nutritional biomarkers: proline betaine as a marker of citrus consumption

Heinzmann, S. S., Brown, I. J., Chan, Q., Bictash, M., Dumas, M.-E., Kochhar, S., Stamler, J., Holmes, E., Elliott, P., & Nicholson, J. K. (2010) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.2010.29672 · Cited by 271 · see citing works

Mind the gap—deficits in our knowledge of aspects impacting the bioavailability of phytochemicals and their metabolites—a position paper focusing on carotenoids and polyphenols

Bohn, T., McDougall, G. J., Alegrı́a, A., Alminger, M., Arrigoni, E., Aura, A., Brito, C., Cilla, A., El, S. N., Karakaya, S., et al. (2015) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201400745 · Cited by 266 · see citing works

Bilirubin in the Liver–Gut Signaling Axis

Hamoud, A.-R. A., Weaver, L., Stec, D. E., & Hinds, T. D. (2018) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2018.01.002 · Cited by 256 · see citing works

Fruit quality and bioactive compounds relevant to human health of sweet cherry (Prunus avium L.) cultivars grown in Italy

Ballistreri, G., Continella, A., Gentile, A., Amenta, M., Fabroni, S., & Rapisarda, P. (2012) · Food Chemistry · doi:10.1016/j.foodchem.2012.11.024 · Cited by 253 · see citing works

Bilirubin Chemistry and Metabolism; Harmful and Protective Aspects

Vı́tek, L., & Ostrow, J. D. (2009) · Current Pharmaceutical Design · doi:10.2174/138161209789058237 · Cited by 252 · see citing works

Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics

Bonini, P., Kind, T., Tsugawa, H., Barupal, D. K., & Fiehn, O. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.9b05765 · Cited by 251 · see citing works

The relationship between phenolic compounds from diet and microbiota: impact on human health

Valdés, L., Cuervo, A. J. V., Salazar, N., Ruas‐Madiedo, P., Gueimonde, M., & González, S. (2015) · Food & Function · doi:10.1039/c5fo00322a · Cited by 236 · see citing works

Physiology of bile secretion

Esteller, A. (2008) · World Journal of Gastroenterology · doi:10.3748/wjg.14.5641 · Cited by 235 · see citing works

Malnutrition is associated with increased mortality in older adults regardless of the cause of death

Söderström, L., Rosenblad, A., Adolfsson, E. T., & Bergkvist, L. (2017) · British Journal Of Nutrition · doi:10.1017/s0007114517000435 · Cited by 235 · see citing works

Dynamic balancing of intestinal short-chain fatty acids: The crucial role of bacterial metabolism

Xu, Y., Zhu, Y., Li, X., & Sun, B. (2020) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2020.02.026 · Cited by 234 · see citing works

Fatty acid omega‐oxidation as a rescue pathway for fatty acid oxidation disorders in humans

Wanders, R. J. A., Komen, J. C., & Kemp, S. (2010) · FEBS Journal · doi:10.1111/j.1742-4658.2010.07947.x · Cited by 221 · see citing works

The influence of flaxseed and lignans on colon carcinogenesis and β-glucuronidase activity

Jenab, M., & Thompson, L. U. (1996) · Carcinogenesis · doi:10.1093/carcin/17.6.1343 · Cited by 213 · see citing works

Enzymatic ω-Oxidation

McKenna, E. J., & Coon, M. J. (1970) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)62932-1 · Cited by 207 · see citing works

Caffeine metabolism by human hepatic cytochromes p450: Contributions of 1A2, 2E1 and 3A isoforms

Tassaneeyakul, W., Birkett, D. J., McManus, M. E., Tassaneeyakul, W., Veronese, M. E., Andersson, T., Tukey, R. H., & Miners, J. O. (1994) · Biochemical Pharmacology · doi:10.1016/0006-2952(94)90304-2 · Cited by 198 · see citing works

Normalizing and Integrating Metabolomics Data

Livera, A. M. D., Dias, D. A., Souza, D. P. D., Rupasinghe, T., Pyke, J. S., Tull, D., Roessner, U., McConville, M. J., & Speed, T. P. (2012) · Analytical Chemistry · doi:10.1021/ac302748b · Cited by 194 · see citing works

Ileal recovery of starch from whole diets containing resistant starch measured in vitro and fermentation of ileal effluent

Silvester, K. R., Englyst, H., & Cummings, J. (1995) · American Journal of Clinical Nutrition · doi:10.1093/ajcn/62.2.403 · Cited by 181 · see citing works

The volatile compound BinBase mass spectral database

Skogerson, K., Wohlgemuth, G., Barupal, D. K., & Fiehn, O. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-321 · Cited by 181 · see citing works

Dominant Bacterial Phyla from the Human Gut Show Widespread Ability To Transform and Conjugate Bile Acids

Lucas, L. N., Barrett, K., Kerby, R. L., Zhang, Q., Cattaneo, L. E., Stevenson, D., Rey, F. E., & Amador-Noguez, D. (2021) · mSystems · doi:10.1128/msystems.00805-21 · Cited by 168 · see citing works

Omega-Hydroxyceramides are Required for Corneocyte Lipid Envelope (CLE) Formation and Normal Epidermal Permeability Barrier Function

Behne, M. J., Uchida, Y., Seki, T., de Montellano, P. R. O., Elias, P. M., & Holleran, W. M. (2000) · Journal of Investigative Dermatology · doi:10.1046/j.1523-1747.2000.00846.x · Cited by 163 · see citing works

Proanthocyanidin metabolites associated with dietary fibre from in vitro colonic fermentation and proanthocyanidin metabolites in human plasma

Saura-Calixto, F. D., Pérez‐Jiménez, J., Touriño, S., Serrano, J. C. E., Fuguet, E., Torres, J. L., & Goñi, I. (2010) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.200900276 · Cited by 156 · see citing works

Identification and Characterization of the CYP52 Family of Candida tropicalis ATCC 20336, Important for the Conversion of Fatty Acids and Alkanes to α,ω-Dicarboxylic Acids

Craft, D. L., Madduri, K. M., Mark, E., & Wilson, C. R. (2003) · Applied and Environmental Microbiology · doi:10.1128/aem.69.10.5983-5991.2003 · Cited by 152 · see citing works

Upper Gastrointestinal Involvement of Crohn’s Disease: A Prospective Study on the Role of Upper Endoscopy in the Diagnostic Work-Up

Annunziata, M. L., Caviglia, R., Papparella, L. G., & Cicala, M. (2012) · Digestive Diseases and Sciences · doi:10.1007/s10620-012-2072-0 · Cited by 147 · see citing works

Sulfonolipids as novel metabolite markers of Alistipes and Odoribacter affected by high-fat diets

Walker, A., Pfitzner, B., Harir, M., Schaubeck, M., Ćalasan, J., Heinzmann, S. S., Turaev, D., Rattei, T., Endesfelder, D., zu Castell, W., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-10369-z · Cited by 128 · see citing works

The Relative Bioavailability of Enterolignans in Humans Is Enhanced by Milling and Crushing of Flaxseed

Kuijsten, A., Arts, I. C. W., Veer, P. V., & Hollman, P. C. H. (2005) · Journal of Nutrition · doi:10.1093/jn/135.12.2812 · Cited by 119 · see citing works

A review of pharmacological and pharmacokinetic properties of stachydrine

Cheng, F., Zhou, Y., Wang, M., Guo, C., Cao, Z., Zhang, R., & Peng, C. Y. (2020) · Pharmacological Research · doi:10.1016/j.phrs.2020.104755 · Cited by 116 · see citing works

Genetic characterization of caffeine degradation by bacteria and its potential applications

Summers, R. M., Mohanty, S. K., Gopishetty, S. R., & Subramanian, M. V. (2015) · Microbial Biotechnology · doi:10.1111/1751-7915.12262 · Cited by 102 · see citing works

The biological significance of ω-oxidation of fatty acids

Miura, Y. (2013) · Proceedings of the Japan Academy Series B · doi:10.2183/pjab.89.370 · Cited by 102 · see citing works

Digestive fate of polyphenols: updated view of the influence of chemical structure and the presence of cell wall material

Nagar, E. E., Okun, Z., & Shpigelman, A. (2019) · Current Opinion in Food Science · doi:10.1016/j.cofs.2019.10.009 · Cited by 99 · see citing works

Gut microbial and metabolomic profiles after fecal microbiota transplantation in pediatric ulcerative colitis patients

Nusbaum, D. J., Sun, F., Ren, J., Zhu, Z., Ramsy, N., Pervolarakis, N., Kunde, S. S., England, W., Gao, B., Fiehn, O., et al. (2018) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiy133 · Cited by 86 · see citing works

Blood kinetics of ethyl glucuronide and ethyl sulphate in heavy drinkers during alcohol detoxification

Høiseth, G., Morini, L., Polettini, A. E., Christophersen, A. S., & Mørland, J. G. (2009) · Forensic Science International · doi:10.1016/j.forsciint.2009.03.017 · Cited by 83 · see citing works

l-Amino acid oxidases from microbial sources: types, properties, functions, and applications

Hossain, G. S., Li, J., Shin, H., Du, G., Liu, L., & Chen, J. (2013) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-013-5444-2 · Cited by 81 · see citing works

Analysis of Fatty Acid Esters of Hydroxyl Fatty Acid in Selected Plant Food

Liberati-Čizmek, A.-M., Biluš, M., Brkić, A. L., Barić, I. C., Bakula, M., Hozić, A., & Cindrić, M. (2019) · Plant Foods for Human Nutrition · doi:10.1007/s11130-019-00728-8 · Cited by 73 · see citing works

The American journal of digestive diseases 1934?1977

Farrar, J. T. (1979) · Digestive Diseases and Sciences · doi:10.1007/bf01297227 · Cited by 73 · see citing works

Physiology, biochemistry and possible applications of microbial caffeine degradation

Gummadi, S. N., Bhavya, B., & Ashok, N. (2011) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-011-3737-x · Cited by 71 · see citing works

Effect of Carrot (Daucus carota) Microstructure on Carotene Bioaccessibility in the Upper Gastrointestinal Tract. 2. In Vivo Digestions

Tydeman, E. A., Parker, M. L., Faulks, R. M., Cross, K. L., Fillery‐Travis, A., Gidley, M. J., Rich, G. T., & Waldron, K. W. (2010) · Journal of Agricultural and Food Chemistry · doi:10.1021/jf1010353 · Cited by 70 · see citing works

Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn’s disease

Zhang, X., Ning, Z., Mayne, J., Yang, Y., Deeke, S. A., Walker, K., Farnsworth, C. L., Stokes, M. P., Couture, J., Mack, D. R., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17916-9 · Cited by 69 · see citing works

Elucidation of Gut Microbiota-Associated Lipids Using LC-MS/MS and 16S rRNA Sequence Analyses

Yasuda, S., Okahashi, N., Tsugawa, H., Ogata, Y., Ikeda, K., Suda, W., Arai, H., Hattori, M., & Arita, M. (2020) · iScience · doi:10.1016/j.isci.2020.101841 · Cited by 69 · see citing works

Alkaline sphingomyelinases and ceramidases of the gastrointestinal tract

Nilsson, Å., & Duan, R. (1999) · Chemistry and Physics of Lipids · doi:10.1016/s0009-3084(99)00078-x · Cited by 66 · see citing works

Comparative analysis of the chemical and biochemical synthesis of keto acids

Luo, Z., Yu, S., Zeng, W., & Zhou, J. (2021) · Biotechnology Advances · doi:10.1016/j.biotechadv.2021.107706 · Cited by 64 · see citing works

Towards Standardization of Data Normalization Strategies to Improve Urinary Metabolomics Studies by GC×GC-TOFMS

Nam, S. L., de la Mata, A. P., Dias, R. P., & Harynuk, J. J. (2020) · Metabolites · doi:10.3390/metabo10090376 · Cited by 61 · see citing works

Betaines in Fruits of Citrus Genus Plants

Servillo, L., Giovane, A., Balestrieri, M. L., Bata-Csere, A., Cautela, D., & Castaldo, D. (2011) · Journal of Agricultural and Food Chemistry · doi:10.1021/jf2014815 · Cited by 59 · see citing works

Enzymatic Oxidation of Vanillin, Isovanillin and Protocatechuic Aldehyde with Freshly Prepared Guinea Pig Liver Slices

Panoutsopoulos, G. I., & Beedham, C. (2005) · Cellular Physiology and Biochemistry · doi:10.1159/000083641 · Cited by 59 · see citing works

Identification of bilirubin reduction products formed by Clostridium perfringens isolated from human neonatal fecal flora

Vı́tek, L., Majer, F., Lucie Muchova, A., Zelenka, J., Jirásková, A., Branny, P., Malina, J., & Ubik, K. (2006) · Journal of Chromatography B · doi:10.1016/j.jchromb.2006.01.032 · Cited by 59 · see citing works

Metabolite Damage and Metabolite Damage Control in Plants

Hanson, A. D., Henry, C. S., Fiehn, O., & de Crécy‐Lagard, V. (2015) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-043015-111648 · Cited by 58 · see citing works

Peach Fruit: Metabolic Comparative Analysis of Two Varieties with Different Resistances to Insect Attacks by NMR Spectroscopy

Capitani, D., Sobolev, A. P., Tomassini, A., Sciubba, F., Salvador, F. R. D., Mannina, L., & Delfini, M. (2012) · Journal of Agricultural and Food Chemistry · doi:10.1021/jf303248z · Cited by 56 · see citing works

A Comprehensive Plasma Metabolomics Dataset for a Cohort of Mouse Knockouts within the International Mouse Phenotyping Consortium

Barupal, D. K., Zhang, Y., Shen, T., Fan, S., Roberts, B. S., Fitzgerald, P., Wancewicz, B., Valdiviez, L., Wohlgemuth, G., Byram, G., et al. (2019) · Metabolites · doi:10.3390/metabo9050101 · Cited by 56 · see citing works

Ethanol and its non-oxidative metabolites profoundly inhibit CFTR function in pancreatic epithelial cells which is prevented by ATP supplementation

Judák, L., Hegyi, P. J., Rakonczay, Z., Maléth, J., Gray, M. A., & Venglovecz, V. (2013) · Pflügers Archiv - European Journal of Physiology · doi:10.1007/s00424-013-1333-x · Cited by 53 · see citing works

Identification of short‐chain fatty acid esters of hydroxy fatty acids (SFAHFAs) in a murine model by nontargeted analysis using ultra‐high‐performance liquid chromatography/linear ion trap quadrupole‐Orbitrap mass spectrometry

Gowda, S. G. B., Liang, C., Gowda, D., Hou, F., Kawakami, K., Fukiya, S., Yokota, A., Chiba, H., & Hui, S. (2020) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.8831 · Cited by 52 · see citing works

Influence of Antibiotics on the Faecal Excretion of Bile Pigments in Healthy Subjects

Saxerholt, H., Carlstedt‐Duke, B., Høverstad, T., Lingaas, E., Norin, K. E., Steinbakk, M., & Midtvedt, T. (1986) · Scandinavian Journal of Gastroenterology · doi:10.3109/00365528608996410 · Cited by 48 · see citing works

Using untargeted metabolomics for detecting exposome compounds

Bloszies, C. S., & Fiehn, O. (2018) · Current Opinion in Toxicology · doi:10.1016/j.cotox.2018.03.002 · Cited by 42 · see citing works

Choline Uptake in Human Intestinal Caco-2 Cells Is Carrier-Mediated

Kamath, A. V., Darling, I. M., & Morris, M. E. (2003) · Journal of Nutrition · doi:10.1093/jn/133.8.2607 · Cited by 40 · see citing works

Branched Fatty Acyl Esters of Hydroxyl Fatty Acids (FAHFAs), Appealing Beneficial Endogenous Fat against Obesity and Type‐2 Diabetes

Balas, L., Feillet‐Coudray, C., & Durand, T. (2018) · Chemistry - A European Journal · doi:10.1002/chem.201800853 · Cited by 38 · see citing works

Identification and Biosynthesis of Pro-Inflammatory Sulfonolipids from an Opportunistic Pathogen Chryseobacterium gleum

Hou, L., Tian, H., Wang, L., Ferris, Z. E., Wang, J., Cai, M., Older, E. A., Raja, M. R. K., Xue, D., Sun, W., et al. (2022) · ACS Chemical Biology · doi:10.1021/acschembio.2c00141 · Cited by 36 · see citing works

Plasma Methionine Levels in Normal Adult Subjects after Oral Loading with L-Methionine and N-Acetyl-L-Methionine

Stegink, L. D., Filer, L. J., & Baker, G. L. (1980) · Journal of Nutrition · doi:10.1093/jn/110.1.42 · Cited by 35 · see citing works

Effects of Ca2+ on catalytic activity and conformation of trypsin and α-chymotrypsin in aqueous ethanol

Kotormán, M., Laczkó, I., Szabó, A., & Simon, L. M. (2003) · Biochemical and Biophysical Research Communications · doi:10.1016/s0006-291x(03)00534-5 · Cited by 35 · see citing works

Chronic Alcohol-Induced Alterations in the Pancreatic Secretory Control Mechanisms

Deng, X., Wood, P. G., Eagon, P. K., & Whitcomb, D. C. (2004) · Digestive Diseases and Sciences · doi:10.1023/b:ddas.0000030093.25897.61 · Cited by 35 · see citing works

Metabolome of Pancreatic Juice Delineates Distinct Clinical Profiles of Pancreatic Cancer and Reveals a Link between Glucose Metabolism and PD-1+ Cells

Cortese, N., Capretti, G. L., Barbagallo, M., Rigamonti, A., Takis, P. G., Castino, G. F., Vignali, D., Maggi, G., Gavazzi, F., Ridolfi, C., et al. (2020) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-19-0403 · Cited by 35 · see citing works

Upper Gastrointestinal Tract Involvement in Inflammatory Bowel Diseases: Histologic Clues and Pitfalls

Kovari, B. P., & Pai, R. K. (2021) · Advances in Anatomic Pathology · doi:10.1097/pap.0000000000000311 · Cited by 31 · see citing works

Inhibitory effects of sulfobacin B on DNA polymerase and inflammation

Mizushina (2010) · International Journal of Molecular Medicine · doi:10.3892/ijmm_00000522 · Cited by 28 · see citing works

Uptake of L-carnitine by a human intestinal epithelial cell line, Caco- 2

McCloud, E., Ma, T., Grant, K., Mathis, R., & Said, H. (1996) · Gastroenterology · doi:10.1016/s0016-5085(96)70015-x · Cited by 26 · see citing works

Metabolism, distribution, seminal excretion and pharmacokinetics of caffeine in the rabbit.

Beach, C. A., Mays, D. C., Sterman, B., & Gerber, N. (1985) · Journal of Pharmacology and Experimental Therapeutics · doi:10.1016/s0022-3565(25)21134-x · Cited by 21 · see citing works

Optimization of the 16S rRNA sequencing analysis pipeline for studying in vitro communities of gut commensals

Celis, A. I., Aranda-Díaz, A., Culver, R. N., Xue, K. S., Relman, D. A., Shi, H., & Huang, K. C. (2022) · iScience · doi:10.1016/j.isci.2022.103907 · Cited by 21 · see citing works

Salvage of the 5-deoxyribose byproduct of radical SAM enzymes

Beaudoin, G. A. W., Li, Q., Folz, J. S., Fiehn, O., Goodsell, J. L., Angerhofer, A., Bruner, S. D., & Hanson, A. D. (2018) · Nature Communications · doi:10.1038/s41467-018-05589-4 · Cited by 20 · see citing works

Absorption of enterally administered N-acetyl-l-glutamine versus glutamine in pigs

Arnaud, A., Ramı́rez, M., Baxter, J. H., & Angulo, A. J. (2004) · Clinical Nutrition · doi:10.1016/j.clnu.2004.04.004 · Cited by 17 · see citing works

Metabolomics analysis of time-series human small intestine lumen samples collected in vivo

Folz, J. S., Shalon, D., & Fiehn, O. (2021) · Food & Function · doi:10.1039/d1fo01574e · Cited by 17 · see citing works

Malnutrition and gastrointestinal disease

Kastin, D. A., & Buchman, A. L. (2002) · Current Opinion in Gastroenterology · doi:10.1097/00001574-200203000-00012 · Cited by 8 · see citing works

Microbiota–gut–brain axis and its therapeutic applications in neurodegenerative diseases

Loh, J. S., Mak, W. Q., Tan, L. K. S., Ng, C. X., Chan, H. H., Yeow, S. H., Foo, J. B., Ong, Y. S., How, C. W., & Khaw, K. Y. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01743-1 · Cited by 1,193 · see citing works

Profiling the human intestinal environment under physiological conditions

Shalon, D., Culver, R. N., Grembi, J. A., Folz, J., Treit, P. V., Shi, H., Rosenberger, F. A., Dethlefsen, L., Meng, X., Yaffe, E., et al. (2023) · Nature · doi:10.1038/s41586-023-05989-7 · Cited by 484 · see citing works

A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation

Ma, Z., Zuo, T., Frey, N., & Rangrez, A. Y. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01946-6 · Cited by 297 · see citing works

The changing metabolic landscape of bile acids – keys to metabolism and immune regulation

Mohanty, I., Allaband, C., Mannochio-Russo, H., Abiead, Y. E., Hagey, L. R., Knight, R. D., & Dorrestein, P. C. (2024) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-024-00914-3 · Cited by 227 · see citing works

Lachnospiraceae -derived butyrate mediates protection of high fermentable fiber against placental inflammation in gestational diabetes mellitus

Huang, S., Chen, J., Cui, Z., Ma, K., Wu, D., Luo, J., Li, F., Xiong, W., Rao, S., Xiang, Q., et al. (2023) · Science Advances · doi:10.1126/sciadv.adi7337 · Cited by 185 · see citing works

Gut physiology and environment explain variations in human gut microbiome composition and metabolism

Procházková, N., Laursen, M. F., Barbera, G. L., Tsekitsidi, E., Jørgensen, M. S., Rasmussen, M. A., Raes, J., Licht, T. R., Dragsted, L. O., & Roager, H. M. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01856-x · Cited by 174 · see citing works

How bile acids and the microbiota interact to shape host immunity

Lee, M. H., Nuccio, S.-P., Mohanty, I., Hagey, L. R., Dorrestein, P. C., Chu, H., & Raffatellu, M. (2024) · Nature Reviews Immunology · doi:10.1038/s41577-024-01057-x · Cited by 143 · see citing works

Small intestine vs. colon ecology and physiology: Why it matters in probiotic administration

Jensen, B. A. H., Heyndrickx, M., Jonkers, D. M. A. E., Mackie, A. R., Millet, S., Naghibi, M., Pærregaard, S. I., Pot, B., Saulnier, D. M. A., Sina, C., et al. (2023) · Cell Reports Medicine · doi:10.1016/j.xcrm.2023.101190 · Cited by 135 · see citing works

microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data

Zuffa, S., Schmid, R., Bauermeister, A., Gomes, P. W. P., Caraballo‐Rodríguez, A. M., Abiead, Y. E., Aron, A. T., Gentry, E. C., Zemlin, J., Meehan, M. J., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-023-01575-9 · Cited by 125 · see citing works

Untargeted faecal metabolomics for the discovery of biomarkers and treatment targets for inflammatory bowel diseases

Vila, A. V., Zhang, J., Liu, M., Faber, K. N., & Weersma, R. K. (2024) · Gut · doi:10.1136/gutjnl-2023-329969 · Cited by 109 · see citing works

Microbial transformation of dietary xenobiotics shapes gut microbiome composition

Culp, E. J., Nelson, N. T., Verdegaal, A. A., & Goodman, A. L. (2024) · Cell · doi:10.1016/j.cell.2024.08.038 · Cited by 104 · see citing works

Small intestinal microbiota: from taxonomic composition to metabolism

Yersin, S., & Vonaesch, P. (2024) · Trends in Microbiology · doi:10.1016/j.tim.2024.02.013 · Cited by 100 · see citing works

The central role of the gut microbiota in the pathophysiology and management of type 2 diabetes

Baars, D. P., Fondevila, M. F., Meijnikman, A. S., & Nieuwdorp, M. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.07.017 · Cited by 102 · see citing works

Intestinal pH: a major driver of human gut microbiota composition and metabolism

Brinck, J. E., Sinha, A. K., Laursen, M. F., Dragsted, L. O., Raes, J., Vazquez-Uribe, R., Walter, J., Roager, H. M., & Licht, T. R. (2025) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-025-01092-6 · Cited by 100 · see citing works

Gut microbiota development across the lifespan: Disease links and health‐promoting interventions

Schoultz, I., Claesson, M. J., Domínguez-Bello, M. G., Hållenius, F. F., Konturek, P. C., Korpela, K., Laursen, M. F., Penders, J., Roager, H. M., Vatanen, T., et al. (2025) · Journal of Internal Medicine · doi:10.1111/joim.20089 · Cited by 93 · see citing works

Distribution of gut microbiota across intestinal segments and their impact on human physiological and pathological processes

Yang, K., Li, G., Li, Q., Wang, W., Zhao, X. X., Shao, N., Qiu, H., Liu, J., Xu, L., & Zhao, J. (2025) · Cell & Bioscience · doi:10.1186/s13578-025-01385-y · Cited by 88 · see citing works

Digesting the complex metabolic effects of diet on the host and microbiome

Carmody, R. N., Varady, K. A., & Turnbaugh, P. J. (2024) · Cell · doi:10.1016/j.cell.2024.06.032 · Cited by 71 · see citing works

Beyond butyrate: microbial fiber metabolism supporting colonic epithelial homeostasis

Fagundes, R. R., Belt, S. C., Bakker, B. M., Dijkstra, G. D. H., Harmsen, H. J. M., & Faber, K. N. (2023) · Trends in Microbiology · doi:10.1016/j.tim.2023.07.014 · Cited by 70 · see citing works

Select microbial metabolites in the small intestinal lumen regulate vagal activity via receptor-mediated signaling

Jameson, K. G., Kazmi, S. A., Ohara, T. E., Son, C., Yu, K. B., Mazdeyasnan, D., Leshan, E., Vuong, H. E., Paramo, J., Lopez-Romero, A., et al. (2024) · iScience · doi:10.1016/j.isci.2024.111699 · Cited by 79 · see citing works

A lipidome landscape of aging in mice

Tsugawa, H., Ishihara, T., Ogasa, K., Iwanami, S., Hori, A., Takahashi, M., Yamada, Y., Satoh‐Takayama, N., Ohno, H., Minoda, A., et al. (2024) · Nature Aging · doi:10.1038/s43587-024-00610-6 · Cited by 60 · see citing works

Microbiome mismatches from microbiota transplants lead to persistent off-target metabolic and immunomodulatory effects

DeLeon, O., Mocanu, M., Tan, A., Sidebottom, A. M., Koval, J., Ceccato, H. D., Kralicek, S. E., Colgan, J. J., George, M. M. S., Lake, J., et al. (2025) · Cell · doi:10.1016/j.cell.2025.05.014 · Cited by 62 · see citing works

Precision nutrition for cardiometabolic diseases

Guasch‐Ferré, M., Wittenbecher, C., Palmnäs, M. S. A., Ben-Yacov, O., Blaak, E. E., Dahm, C. C., Fall, T., Heitmann, B. L., Licht, T. R., Löf, M., et al. (2025) · Nature Medicine · doi:10.1038/s41591-025-03669-9 · Cited by 53 · see citing works

Biosynthetic enzyme analysis identifies a protective role for TLR4-acting gut microbial sulfonolipids in inflammatory bowel disease

Older, E. A., Zhang, J., Ferris, Z. E., Xue, D., Zhong, Z., Mitchell, M. K., Madden, M., Wang, Y., Chen, H., Nagarkatti, P. S., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-53670-y · Cited by 45 · see citing works

Microbiota and kidney disease: the road ahead

Bloom, P. P., Garrett, W. S., Penniston, K. L., Winkler, M. K. H., Hazen, S. L., Agudelo, J., Suryavanshi, M. V., Babiker, A., Dodd, D., Fischbach, M. A., et al. (2025) · Nature Reviews Nephrology · doi:10.1038/s41581-025-00988-5 · Cited by 44 · see citing works

Lab-on-chip technologies for exploring the gut–immune axis in metabolic disease

Wheeler, A., Stoeger, V., & Owens, R. M. (2024) · Lab on a Chip · doi:10.1039/d3lc00877k · Cited by 30 · see citing works

Cold exposure, gut microbiota and health implications: A narrative review

Zhou, E., Zhang, L., He, L., Xiao, Y., Zhang, K., & Luo, B. (2024) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2024.170060 · Cited by 33 · see citing works

Oral tryptophan activates duodenal aryl hydrocarbon receptor in healthy subjects: a crossover randomized controlled trial

Rueda, G. H., Calo, N. C., Borojevic, R., Nardelli, A., Pinto-Sánchez, M. I., Constante, M., Libertucci, J., Mohan, V., Langella, P., Loonen, L. M. P., et al. (2024) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00306.2023 · Cited by 30 · see citing works

Exploring the mechanism of intestinal bacterial translocation after severe acute pancreatitis: the role of Toll-like receptor 5

Zhang, C., Chen, S., Wang, Z., Zhang, J., Yu, W., Wang, Y., Si, W., Zhang, Y., Zhang, Y., & Liang, T. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2489768 · Cited by 28 · see citing works

Gut microbiota and tuberculosis

Liu, Y., Yang, L., Meskini, M., Goel, A., Opperman, M., Shyamal, S. S., Manaithiya, A., Xiao, M., Ni, R., An, Y., et al. (2025) · iMeta · doi:10.1002/imt2.70054 · Cited by 30 · see citing works

Upper small intestine microbiome in obesity and related metabolic disorders: A new field of investigation

Steinbach, E., Masi, D., Ribeiro, A., Serradas, P., Roy, T. L., & Clément, K. (2023) · Metabolism · doi:10.1016/j.metabol.2023.155712 · Cited by 30 · see citing works

Liquid chromatography–mass spectrometry–based metabolomics approaches for foodomics research

Čajka, T. (2024) · Current Opinion in Food Science · doi:10.1016/j.cofs.2024.101201 · Cited by 31 · see citing works

Soft autonomous ingestible device for sampling the small-intestinal microbiome

Del‐Rio‐Ruiz, R., da Silva, D. R. R., Suresh, H., Creasey, H., Asci, C., Santos, D. M. D., Sharma, A., Widmer, G., & Sonkusale, S. (2024) · Device · doi:10.1016/j.device.2024.100406 · Cited by 24 · see citing works

Microbially conjugated bile salts found in human bile activate the bile salt receptors TGR5 and FXR

Ay, Ü., Leníček, M., Haider, R. S., Claßen, A., van Eijk, H. M. H., Koelfat, K. V. K., van der Kroft, G., Neumann, U. P., Hoffmann, C., Bolm, C., et al. (2024) · Hepatology Communications · doi:10.1097/hc9.0000000000000383 · Cited by 22 · see citing works

The measurement, regulation and biological activity of FAHFAs

Tan, D., & Saghatelian, A. (2025) · Nature Chemical Biology · doi:10.1038/s41589-024-01827-7 · Cited by 22 · see citing works

Personalized prediction of glycemic responses to food in women with diet-treated gestational diabetes: the role of the gut microbiota

Popova, P., Isakov, A. O., Rusanova, A. N., Sitkin, S. I., Anopova, A. D., Vasukova, E. A., Tkachuk, A., Nemikina, I. S., Stepanova, E. A., Eriskovskaya, A. I., et al. (2025) · npj Biofilms and Microbiomes · doi:10.1038/s41522-025-00650-9 · Cited by 22 · see citing works

Ingestible Sensor Based on Fluorescent Gold Nanoparticles and Molecularly Imprinted Polymers on Thread for Localized Quantification of Escherichia Coli in the Gastrointestinal Tract

Khachornsakkul, K., Del‐Rio‐Ruiz, R., Zeng, W., Santos, D. M. D., da Silva, D. R. R., Widmer, G., & Sonkusale, S. (2024) · Advanced Functional Materials · doi:10.1002/adfm.202408056 · Cited by 21 · see citing works

LibGen: Generating High Quality Spectral Libraries of Natural Products for EAD-, UVPD-, and HCD-High Resolution Mass Spectrometers

Kong, F., Keshet, U., Shen, T., Rodríguez, E. P., & Fiehn, O. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.3c02263 · Cited by 20 · see citing works

Gut phages and their interactions with bacterial and mammalian hosts

Godsil, M., Ritz, N. L., Venkatesh, S., & Meeske, A. J. (2025) · Journal of Bacteriology · doi:10.1128/jb.00428-24 · Cited by 19 · see citing works

The fermented cabbage metabolome and its protection against cytokine-induced intestinal barrier disruption of Caco-2 monolayers

Wei, L., & Marco, M. L. (2025) · Applied and Environmental Microbiology · doi:10.1128/aem.02234-24 · Cited by 20 · see citing works

Adaptive and metabolic convergence in rhizosphere and gut microbiomes

Ilyaskina, D., Altveş, S., Dong, L., Bouwmeester, H. J., & Aidy, S. E. (2025) · Microbiome · doi:10.1186/s40168-025-02179-7 · Cited by 19 · see citing works

Pharmacomicrobiomics

Gronich, N., Geva‐Zatorsky, N., Herren, R., Kelly, L., Cohen, Z., Zhou, H., Chen, Y. H., Shah, K., Robinson‐Catala, T. A., Frisby, G., et al. (2025) · Clinical Pharmacology & Therapeutics · doi:10.1002/cpt.70066 · Cited by 22 · see citing works

Microbial-Transferred Metabolites and Improvement of Biological Activities of Green Tea Catechins by Human Gut Microbiota

Su, Y., Hu, K., Li, D., Guo, H., Sun, L., & Xie, Z. (2024) · Foods · doi:10.3390/foods13050792 · Cited by 19 · see citing works

Changes in Bacterial Gut Composition in Parkinson’s Disease and Their Metabolic Contribution to Disease Development: A Gut Community Reconstruction Approach

Forero-Rodríguez, J., Zimmermann, J., Taubenheim, J., Rodríguez, N. A., Caicedo, J. D., Best, L., Mendieta, C. V., López-Castiblanco, J. A., Gómez-Muñoz, L. A., Gonzalez-Santos, J., et al. (2024) · Microorganisms · doi:10.3390/microorganisms12020325 · Cited by 17 · see citing works

Chemotherapy-driven intestinal dysbiosis and indole-3-propionic acid rewire myelopoiesis to promote a metastasis-refractory state

Bersier, L., Lorenzo‐Martín, L. F., Chiang, Y.-H., Durot, S., Czauderna, A., Yarahmadov, T., Wyss, T., Roçi, I., Kim, J., Zamboni, N., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-67169-7 · Cited by 15 · see citing works

Closing the Knowledge Gap of Post-Acquisition Sample Normalization in Untargeted Metabolomics

Low, B., Wang, Y., Zhao, T., Yu, H., & Huan, T. (2024) · ACS Measurement Science Au · doi:10.1021/acsmeasuresciau.4c00047 · Cited by 14 · see citing works

MassCube improves accuracy for metabolomics data processing from raw files to phenotype classifiers

Yu, H., Ding, J., Shen, T., Liu, M., Li, Y., & Fiehn, O. (2025) · Nature Communications · doi:10.1038/s41467-025-60640-5 · Cited by 15 · see citing works

Physiologically based kinetic (PBK) modeling as a new approach methodology (NAM) for predicting systemic levels of gut microbial metabolites

Stevanoska, M., Folz, J. S., Beekmann, K., & Aichinger, G. (2024) · Toxicology Letters · doi:10.1016/j.toxlet.2024.04.013 · Cited by 13 · see citing works

Untargeted metabolomics unravels distinct gut microbial metabolites derived from plant-based and animal-origin proteins using in vitro modeling

Izquierdo-Sandoval, D., Duan, X., Fryganas, C., Portolés, T., Sancho, J. V., & Rubert, J. (2024) · Food Chemistry · doi:10.1016/j.foodchem.2024.140161 · Cited by 13 · see citing works

Clinical Microbiome Analysis by Mass Spectrometry–Based Metaproteomics

Zhang, X., Ning, Z., Mayne, J., & Figeys, D. (2025) · Annual Review of Analytical Chemistry · doi:10.1146/annurev-anchem-071124-113819 · Cited by 13 · see citing works

Vagal interoception of microbial metabolites from the small intestinal lumenPreprint

Jameson, K. G., Kazmi, S. A., Son, C., Mazdeyasnan, D., Leshan, E., Vuong, H. E., Paramo, J., Lopez-Romero, A., Yang, L., Schweizer, F. E., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.18.572257 · Cited by 13 · see citing works

Portal bile acid composition and microbiota along the murine intestinal tract exhibit sex differences in physiology

Reichardt, F., Lucas, L. N., Okyere, L., Choi, J., Amador‐Noguez, D., Gaulke, C. A., & Anakk, S. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2540483 · Cited by 12 · see citing works

Synthesis and quantification of short-chain fatty acid esters of hydroxy fatty acids in rat intestinal contents and fecal samples by LC-MS/MS

Gowda, S. G. B., Hou, F., Gowda, D., Chiba, H., Kawakami, K., Fukiya, S., Yokota, A., & Hui, S. (2023) · Analytica Chimica Acta · doi:10.1016/j.aca.2023.342145 · Cited by 12 · see citing works

Data-Independent Acquisition Coupled with Electron-Activated Dissociation for In-Depth Structure Elucidation of the Fatty Acid Ester of Hydroxy Fatty Acids

Kurizaki, Y., Matsuzawa, Y., Takahashi, M., Takeda, H., Hasegawa, M., Arita, M., Miyamoto, J., & Tsugawa, H. (2025) · Analytical Chemistry · doi:10.1021/acs.analchem.4c06736 · Cited by 12 · see citing works

Engineering strategies for producing medium-long chain dicarboxylic acids in oleaginous yeasts

Wang, X., Sun, M.-L., Lin, L., Ledesma‐Amaro, R., Wang, K., & Ji, X.-J. (2025) · Bioresource Technology · doi:10.1016/j.biortech.2025.132593 · Cited by 12 · see citing works

Perspective: Challenges and Future Directions in Clinical Research with Nuts and Berries

Zuelch, M. L., Radtke, M. D., Holt, R. R., Basu, A., Burton‐Freeman, B. M., Ferruzzi, M. G., Li, Z., Shay, N. F., Shukitt‐Hale, B., Keen, C. L., et al. (2023) · Advances in Nutrition · doi:10.1016/j.advnut.2023.07.010 · Cited by 13 · see citing works

L. rhamnosus CNCM I-3690 survival, adaptation, and small bowel microbiome impact in human

Zaccaria, E., Klaassen, T., Alleleyn, A. M. E., Boekhorst, J., Chervaux, C., Smokvina, T., Troost, F. J., & Kleerebezem, M. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2244720 · Cited by 11 · see citing works

GelMA as scaffold material for epithelial cells to emulate the small intestinal microenvironment

Roegiers, I. H., Gheysens, T., Minsart, M., Clercq, P. D., Vanbeversluys, K., Rać, N., Stroka, G., de Croock, J., de Wiele, T. V., Dubruel, P., et al. (2025) · Scientific Reports · doi:10.1038/s41598-024-81533-5 · Cited by 11 · see citing works

Noninvasive sampling of the small intestinal chyme for microbiome, metabolome and antimicrobial resistance genes in dogs, a proof of concept

Menard, J. M., Bagheri, S., Menon, S., Yu, Y. T., & Goodman, L. B. (2023) · Animal Microbiome · doi:10.1186/s42523-023-00286-0 · Cited by 12 · see citing works

Hydrogel-based experimental models of the gastrointestinal tract

Sieders, M., Candry, P., & Aidy, S. E. (2025) · Microbiome · doi:10.1186/s40168-025-02208-5 · Cited by 10 · see citing works

Untargeted and semi-targeted metabolomics approach for profiling small intestinal and fecal metabolome using high-resolution mass spectrometry

Tronel, A., Roger‐Margueritat, M., Plazy, C., Cunin, V., Mohanty, I., Dorrestein, P. C., Soranzo, T., & Gouëllec, A. L. (2025) · Metabolomics · doi:10.1007/s11306-025-02288-2 · Cited by 9 · see citing works

Effects of refrigeration and freezing on milk fat globule membrane lipids in stored breast milk: Insights from non-targeted lipidomics

Wang, S., Wang, P., Ma, X., Qiao, F., Zhang, Z., Li, J., Yi, H., Souza, C. D., Zhang, L., & Lin, K. (2024) · Food Chemistry · doi:10.1016/j.foodchem.2024.142478 · Cited by 9 · see citing works

Exploring gut microbiota's influence on cognitive health and neurodegenerative disorders: mechanistic insights and therapeutic approaches

Bhadoriya, P., Jatley, A., Singh, A., Mehrotra, R., Jain, M., Mohammed, A., Hamzah, Z., & Bukke, S. P. N. (2025) · Discover Immunity. · doi:10.1007/s44368-025-00010-x · Cited by 9 · see citing works

Chemical exchange saturation transfer MRI-trackable peptide hydrogel for drug release monitoring and targeted therapy in inflammatory bowel disease

Li, F., Zhao, R., Ding, W., Yang, J., Wen, Q., Dou, W., Chen, L., Zhang, J., Qiu, B., Bulte, J. W. M., et al. (2025) · Cell Biomaterials · doi:10.1016/j.celbio.2025.100098 · Cited by 9 · see citing works

Crosstalk between the microbiota and intestinal dendritic cells in IBD

Letz, P., Huber, S., & Velásquez, L. N. (2025) · Seminars in Immunopathology · doi:10.1007/s00281-025-01062-9 · Cited by 9 · see citing works

A lipidomics roadmap: from basic research to societal challenges

Fedorova, M., Bendt, A. K., Bertrand‐Michel, J., Fiehn, O., Godzień, J., Goracci, L., Gruber, F., Guan, X. L., Han, X., Holčapek, M., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-73797-4 · Cited by 10 · see citing works

Differences in the Stool Metabolome between Vegans and Omnivores: Analyzing the NIST Stool Reference Material

Cumeras, R., Shen, T., Valdiviez, L., Tippins, Z., Haffner, B. D., & Fiehn, O. (2023) · Metabolites · doi:10.3390/metabo13080921 · Cited by 9 · see citing works

Investigating regional-specific gut microbial distribution: an uncharted territory in disease therapeutics

Kuang, J., Zheng, X., & Jia, W. P. (2024) · Protein & Cell · doi:10.1093/procel/pwae058 · Cited by 9 · see citing works

Quantifying compositional variability in microbial communities with FAVA

Morrison, M. L., Xue, K. S., & Rosenberg, N. A. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2413211122 · Cited by 8 · see citing works

Offline Two-Dimensional Liquid Chromatography–Mass Spectrometry for Deep Annotation of the Fecal Metabolome Following Fecal Microbiota Transplantation

Anderson, B. G., Raskind, A. B., Hissong, R., Dougherty, M., McGill, S., Gulati, A., Theriot, C. M., Kennedy, R. T., & Evans, C. R. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00022 · Cited by 9 · see citing works

Gastrointestinal digestion of yerba mate, rosemary and green tea extracts and their subsequent colonic fermentation by human, pig or rat inocula

Corrêa, V. G., Garcia, J. A. A., Días, M. I., Pereira, C., Mandim, F., Barros, L., Ferreira, I. C. F. R., Peralta, R. M., & Bracht, A. (2024) · Food Research International · doi:10.1016/j.foodres.2024.114918 · Cited by 8 · see citing works

Fuel stores and time of day account for variation in serum metabolomes of passerine migrants stopping over

Zimin, S. V., Zimin, A., Shochat, E., Brotman, Y., & Ovadia, O. (2024) · Journal of Avian Biology · doi:10.1111/jav.03311 · Cited by 7 · see citing works

How nutrient starvation impacts the gut microbiome

Estrela, S., Long, J. Z., & Huang, K. C. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02139-9 · Cited by 7 · see citing works

A global survey of taxa-metabolic associations across mouse microbiome communities.

Yilmaz, B., Baertschi, I., Meier, K., Gac, C. L., Jordi, S., Black, C., Li, J.-Q., Lindholm, A., König, B., Sauer, U., et al. (2025) · Cell Host and Microbe · doi:10.1016/j.chom.2025.10.010 · Cited by 7 · see citing works

Exploring the human small intestinal luminal microbiome via a newly developed ingestible sampling device

Tronel, A., Roger‐Margueritat, M., Plazy, C., Biennier, S., Craspay, A., Mohanty, I., Cools-Portier, S., Laiola, M., Roeselers, G., Mathieu, N., et al. (2025) · ISME Communications · doi:10.1093/ismeco/ycaf224 · Cited by 9 · see citing works

Microbiome-produced nicotinic acid controls colon regional identity and injury susceptibility

Rispal, J., Garcia, J. R., Palikuqi, B., Vegesna, M., Vaka, D., Kang, S., Trentesaux, C., Du, J., Realini, N. R., Vega, P. N., et al. (2026) · Cell · doi:10.1016/j.cell.2026.02.007 · Cited by 7 · see citing works

Identification and Characterization of Multiple Paneth Cell Types in the Mouse Small Intestine

Timmermans, S., Wallaeys, C., García-González, N., Pollaris, L., Saeys, Y., & Libert, C. (2024) · Cells · doi:10.3390/cells13171435 · Cited by 7 · see citing works

A non-invasive tool to collect small intestine content in post weaning pigs: validation study

Viñado, I. G., Correa, F., Trevisi, P., Bee, G., & Ollagnier, C. (2024) · Scientific Reports · doi:10.1038/s41598-024-59950-3 · Cited by 7 · see citing works

Intra- and inter-individual variation of the human lipidome

Anh, N. H., Beyene, H. B., Mocciaro, G., Hahnefeld, L., Lamichhane, S., Fabritius, M., Avela, H. F., Wang, Y., Dickens, A. M., Gurke, R., et al. (2025) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2025.118368 · Cited by 7 · see citing works

Recent advancements in plant metabolomics: trends, tools, and techniques

Bharat, J. S., Kumar, N., Kumar, A., & Jaitak, V. (2025) · Plant Biotechnology Reports · doi:10.1007/s11816-025-01021-8 · Cited by 6 · see citing works

Fecal metabolomics in Crohn’s disease reveal N-Acetylglutamine as a Th17/Treg modulator

Han, M., Dong, X., Zhao, R., Hu, X., Li, D., Yan, X., Liu, Y., Du, Q., & Li, M. (2025) · Molecular Immunology · doi:10.1016/j.molimm.2025.11.012 · Cited by 6 · see citing works

Colon or semicolon: gut sampling microdevices for omics insights

Nagpal, S., & Srivastava, S. K. (2024) · npj Biofilms and Microbiomes · doi:10.1038/s41522-024-00536-2 · Cited by 6 · see citing works

Microbiome-driven alterations in metabolic pathways and impaired cognition in aged female TgF344-AD rats

Hernandez, A. R., Parker, E. S., Babar, M., Banerjee, A., Ding, S., Simley, A. L., & Buford, T. W. (2024) · Aging Brain · doi:10.1016/j.nbas.2024.100119 · Cited by 5 · see citing works

Novel Insights into the Physiology of Nutrient Sensing and Gut-Brain Communication in Surgical and Experimental Obesity Therapy

Frick, L. D., Hankir, M. K., Borner, T., Malagola, E., File, B., & Gerö, D. (2023) · Obesity Surgery · doi:10.1007/s11695-023-06739-4 · Cited by 5 · see citing works

A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics DataPreprint

Zuffa, S., Schmid, R., Bauermeister, A., Gomes, P. W. P., Caraballo‐Rodríguez, A. M., Abiead, Y. E., Aron, A. T., Gentry, E. C., Zemlin, J., Meehan, M. J., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.20.549584 · Cited by 5 · see citing works

Gut environmental factors explain variations in the gut microbiome composition and metabolism within and between healthy adultsPreprint

Procházková, N., Laursen, M. F., Barbera, G. L., Tsekitsidi, E., Jørgensen, M. S., Rasmussen, M. A., Raes, J., Licht, T. R., Dragsted, L. O., & Roager, H. M. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.01.23.574598 · Cited by 5 · see citing works

MS/MS Mass Spectrometry Filtering Tree for Bile Acid Isomer AnnotationPreprint

Mohanty, I., Xing, S., Castillo, V., Agongo, J., Patan, A., Abiead, Y. E., Mannochio-Russo, H., Zuffa, S., Zemlin, J., Tronel, A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.04.641505 · Cited by 5 · see citing works

Role of microbiota in pain: From bench to bedside

Ren, H., Cao, B., Xu, Q., Zhao, R., Li, H., & Wei, B. (2025) · iMetaOmics. · doi:10.1002/imo2.58 · Cited by 6 · see citing works

A Multiomics Framework to Unlock the Relationships between Wine, Food, and Gut Health

Abrieux, A., Barboza, M., Hirahatake, K. M., Jacobs, H., Schmitz, H. H., Adams, S. H., & Siegel, J. B. (2025) · Advances in Nutrition · doi:10.1016/j.advnut.2025.100468 · Cited by 5 · see citing works

Passive intestinal microbiome sampling using an ingestible device with tortuous lattices

Mohammed, H. A., Usmani, S., Bhushan, B. M., Ahmad, A. R., Al‐Ketan, O., Shibl, A. A., Boitet, M., Dev, D., Naser, H., Jha, A. R., et al. (2025) · Device · doi:10.1016/j.device.2025.100904 · Cited by 4 · see citing works

Microbial metabolites at the front line: Orchestrating gastrointestinal and systemic barrier immunity across the lifespan

Koren, O., Collado, M. C., Chassaing, B., Silverman, M. A., & Konnikova, L. (2026) · Cell Reports · doi:10.1016/j.celrep.2026.117556 · Cited by 5 · see citing works

A multi-omic trip through the human gut

Quinn, R. A., Christian Martin, H., & Guzior, D. V. (2023) · Nature Metabolism · doi:10.1038/s42255-023-00773-3 · Cited by 4 · see citing works

Decoupled Nutrient Status: a framework to disentangle host from microbial responses to diets that vary in digestibility

Venable, E. M., & Carmody, R. N. (2024) · Frontiers in Food Science and Technology · doi:10.3389/frfst.2024.1469470 · Cited by 4 · see citing works

Gut dysbiosis narrative in psoriasis: matched-pair approach identifies only subtle shifts correlated with elevated fecal calprotectin

Yunusbayev, B., Bogdanova, A. A., Nadyrchenko, N., Danilov, L. G., Bogdanov, V. P., Sergeev, G., Altinbaev, R., Bilalov, F. S., & Yunusbaeva, M. M. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.01382-24 · Cited by 4 · see citing works

Spatiotemporal coordination between local flux and systemic homeostasis in the small intestine

Zhang, J., Zhang, S., Du, L., Zhao, Y., & Wang, D. (2025) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2025.07.009 · Cited by 3 · see citing works

Prebiotic Administration to Chronic Kidney Disease Patients Modifies Their Fecal Microbiome and Host Metabolism

Raj, D. S., Gao, B., Sohn, M. B., Brydges, C. R., Srivastava, A., Rabb, H., Cheung, A. K., Fiehn, O., Kendrick, C. A., Gassman, J., et al. (2025) · Journal of Renal Nutrition · doi:10.1053/j.jrn.2025.10.015 · Cited by 3 · see citing works

The role of the gut non-bacterial microbiome (virome, mycobiome, archaeome) and its impact on obesity

Chue, K. M., Wong, S. H., Zuo, T., & Ali, Y. (2025) · Molecular Metabolism · doi:10.1016/j.molmet.2025.102289 · Cited by 3 · see citing works

Restriction of IgA secretion in gut plasma cells is driven by a tissue-specific glycolytic program

Zoccoli-Rodriguez, V., Iwaniec, J., & Wilmore, J. R. (2025) · The Journal of Immunology · doi:10.1093/jimmun/vkaf310 · Cited by 3 · see citing works

MS/MS Mass Spectrometry Filtering Tree for Bile Acid Regio- and Stereoisomer Annotation

Mohanty, I., Xing, S., Castillo, V., Agongo, J., Patan, A., Abiead, Y. E., Mannochio-Russo, H., Zuffa, S., Zemlin, J., Tronel, A., et al. (2026) · Analytical Chemistry · doi:10.1021/acs.analchem.5c05677 · Cited by 10 · see citing works

Ingestible active capsule for gastrointestinal microbiome sampling

Shahadha, M. H., Voigt, A., Gruner, D., Marschner, U., Floch, M. L., Hampe, J., Brauer, F., Schostek, S., Luniak, M., Bock, K., et al. (2026) · Biomedical Microdevices · doi:10.1007/s10544-026-00802-4 · Cited by 3 · see citing works

Enzymatic Acrolein Production System and Its Impact on Human Cells

Hurley, K. A., Folz, J. S., Zgraggen, J., Cruz, T. N., Diedrich, S., & Sturla, S. J. (2024) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.4c00119 · Cited by 3 · see citing works

A sampling pill to swallow

Fyfe, I. (2023) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-023-00804-0

Exploring the human small intestinal luminal microbiome via a newly developed ingestible sampling device

Tronel, A., Roger‐Margueritat, M., Plazy, C., Biennier, S., Craspay, A., Mohanty, I., Cools-Portier, S., Laiola, M., Roeselers, G., Mathieu, N., et al. (2025) · ISME Communications · doi:10.1093/ismeco/ycaf224 · Cited by 9 · see citing works

Profiling the human luminal small intestinal microbiome using a novel ingestible medical devicePreprint

Tronel, A., Roger‐Margueritat, M., Plazy, C., Biennier, S., Craspay, A., Mohanty, I., Cools-Portier, S., Laiola, M., Roeselers, G., Mathieu, N., et al. (2025) · medRxiv · doi:10.1101/2025.04.18.25326056 · Cited by 1 · see citing works

Profiling of the human intestinal microbiome and bile acids under physiologic conditions using an ingestible sampling devicePreprint

Shalon, D., Culver, R. N., Grembi, J. A., Folz, J. S., Treit, P. V., Dethlefsen, L., Meng, X., Yaffe, E., Spencer, S. P., Shi, H., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.19.476920 · Cited by 8 · see citing works

Dietary Modulation of The Human Small Intestine Metabolome and MicrobiomePreprint

Fernandes, N. J., Cai, M., Warren, F. J., Duncan, A., Harris, H. C., Contreras, J. I. S., Sidorczuk, K., Bernal, A., Castillo, A., Petropoulou, K., et al. (2025) · medRxiv · doi:10.1101/2025.11.25.25340785