{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T15:55:40Z","timestamp":1785426940134,"version":"3.56.0"},"reference-count":45,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T00:00:00Z","timestamp":1780963200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"Ministry of Science and ICT","doi-asserted-by":"publisher","award":["RS-2023-00219563"],"award-info":[{"award-number":["RS-2023-00219563"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"award":["RS-2023-00219563"],"award-info":[{"award-number":["RS-2023-00219563"]}],"id":[{"id":"https:\/\/ror.org\/01wpjm123","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003052","name":"Ministry of Trade, Industry and Energy","doi-asserted-by":"publisher","award":["P0027492"],"award-info":[{"award-number":["P0027492"]}],"id":[{"id":"10.13039\/501100003052","id-type":"DOI","asserted-by":"publisher"}]},{"award":["P0027492"],"award-info":[{"award-number":["P0027492"]}],"id":[{"id":"https:\/\/ror.org\/008nkqk13","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Soonchunhyang University Research Fund"},{"id":[{"id":"https:\/\/ror.org\/03qjsrb10","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Life"],"abstract":"<jats:p>With the growing interest in the microbiome, short-chain fatty acids (SCFAs) have emerged as key metabolites due to their critical roles in host physiology, including immune regulation, energy homeostasis, and inflammatory control. As a result, the accurate quantification of SCFAs in various biological samples has become increasingly important. However, reliable and standardized methods for measuring SCFAs across different sample types remain underdeveloped, highlighting the need for methodological refinement. To address this need, we optimized two analytical methods, headspace GC-MS and GC-MS\/MS, for SCFA quantification. These techniques were applied to a range of biological matrices, including pure microbial cultures, low-abundance animal liver, animal feces, and standardized simulated human fecal samples. The headspace GC-MS approach enables direct analysis with minimal sample preparation, thereby enhancing throughput and ease of use. In contrast, the GC-MS\/MS method, involving methanol extraction, alkaline treatment, and derivatization with MTBSTFA, offers superior sensitivity and precision, making it particularly suitable for small-volume and low-abundance samples. Together, these optimized protocols provide robust, sensitive platforms for profiling SCFAs across diverse biological matrices, facilitating a deeper understanding of microbiome\u2013host interactions and supporting future translational applications.<\/jats:p>","DOI":"10.3390\/life16060974","type":"journal-article","created":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T06:57:17Z","timestamp":1781161037000},"page":"974","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Development of Mass Spectrometry-Based SCFA Analysis Methods in Diverse Samples for Microbiome Research"],"prefix":"10.3390","volume":"16","author":[{"given":"Chaeeun","family":"Park","sequence":"first","affiliation":[{"name":"Department of Medical Science, Graduate School, Soonchunhyang University, 22, Soonchunhyang-Ro, Sinchang-Myeon, Asan-si 31538, Republic of Korea"},{"name":"K-Microbiome Institute, 813-26 Yisunsin-Daero, Asan-si 31462, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2000-5602","authenticated-orcid":false,"given":"Md Abdur","family":"Rahim","sequence":"additional","affiliation":[{"name":"K-Microbiome Institute, 813-26 Yisunsin-Daero, Asan-si 31462, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1180-0380","authenticated-orcid":false,"given":"Indrajeet","family":"Barman","sequence":"additional","affiliation":[{"name":"K-Microbiome Institute, 813-26 Yisunsin-Daero, Asan-si 31462, Republic of Korea"},{"name":"Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, 31, Suncheonhyang 6-Gil, Dongnam-Gu, Cheonan-Si 31151, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7299-1240","authenticated-orcid":false,"given":"Hanieh","family":"Tajdozian","sequence":"additional","affiliation":[{"name":"K-Microbiome Institute, 813-26 Yisunsin-Daero, Asan-si 31462, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9315-883X","authenticated-orcid":false,"given":"Youjin","family":"Yoon","sequence":"additional","affiliation":[{"name":"K-Microbiome Institute, 813-26 Yisunsin-Daero, Asan-si 31462, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7963-9776","authenticated-orcid":false,"given":"Sukyung","family":"Kim","sequence":"additional","affiliation":[{"name":"K-Microbiome Institute, 813-26 Yisunsin-Daero, Asan-si 31462, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mijung","family":"Kim","sequence":"additional","affiliation":[{"name":"K-Microbiome Institute, 813-26 Yisunsin-Daero, Asan-si 31462, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hoonhee","family":"Seo","sequence":"additional","affiliation":[{"name":"Department of Medical Science, Graduate School, Soonchunhyang University, 22, Soonchunhyang-Ro, Sinchang-Myeon, Asan-si 31538, Republic of Korea"},{"name":"K-Microbiome Institute, 813-26 Yisunsin-Daero, Asan-si 31462, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ho-Yeon","family":"Song","sequence":"additional","affiliation":[{"name":"K-Microbiome Institute, 813-26 Yisunsin-Daero, Asan-si 31462, Republic of Korea"},{"name":"Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, 31, Suncheonhyang 6-Gil, Dongnam-Gu, Cheonan-Si 31151, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.trsl.2012.10.007","article-title":"Short chain fatty acids and their receptors: New metabolic targets","volume":"161","author":"Layden","year":"2013","journal-title":"Transl. 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