{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T01:23:31Z","timestamp":1793669011391,"version":"4.5.1"},"reference-count":43,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T00:00:00Z","timestamp":1766966400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T00:00:00Z","timestamp":1766966400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1R35GM156920-01"],"award-info":[{"award-number":["1R35GM156920-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008984","name":"International Anesthesia Research Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008984","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Med"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Gut microbial dysbiosis is common in the intensive care unit and certain derangements, like expansion of\n                      <jats:italic>Enterobacteriaceae<\/jats:italic>\n                      and other potential pathogens (pathobionts), are associated with increased morbidity. In other populations, dysbiosis is improved by enteral nutrition supplemented with prebiotic short-chain fructooligosaccharides (scFOS-EN). The impact of scFOS-EN on the microbiota in critical illness is unknown and difficult to predict in a dysbiotic environment. Thus, we conducted a pilot randomized control trial (RCT) in critically ill trauma patients to evaluate the effects of scFOS-EN versus a fiber-free enteral formula (NF-EN) on gut microbial dynamics.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>In this single-center, prospective, double-blind RCT, mechanically ventilated trauma ICU patients received scFOS-EN or a similar fiber-free formula (NF-EN). Microbial communities in longitudinally collected stool samples were characterized using 16S rRNA gene sequencing. We used linear mixed-effects models to assess microbial dynamics in the 10-day study period after scFOS-EN or NF-EN initiation, as well as a time-informed dimensionality reduction method to identify patient-specific temporal responses and clinical correlates and network approaches for microbe:microbe interactions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      A total of 57 stool samples were analyzed from 17 patients (7 NF-EN, 10 scFOS-EN). All participants had profound baseline dysbiosis and received broad-spectrum antibiotics. Compared to NF-EN, scFOS-EN was associated with an accelerated loss of\n                      <jats:italic>Bifidobacterium<\/jats:italic>\n                      (\u2212\u20090.6%\/day\n                      <jats:italic>p<\/jats:italic>\n                      \u2009=\u2009.026) and Firmicutes (3.5%\/day,\n                      <jats:italic>p<\/jats:italic>\n                      \u2009&lt;\u2009.001) and greater increases in several\n                      <jats:italic>Bacteroidaceae<\/jats:italic>\n                      members, with expansion of pathobiont\n                      <jats:italic>Enterobacteriaceae<\/jats:italic>\n                      (0.3%\/day,\n                      <jats:italic>p<\/jats:italic>\n                      \u2009=\u2009.003) unique to scFOS-EN participants. Detrimental microbial responses to scFOS-EN, including high\n                      <jats:italic>Enterobacteriaceae<\/jats:italic>\n                      burden, were dictated by pre-existing and ongoing antibiotic exposure and associated with enhanced microbial competition.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>In the dysbiotic gut of critically ill trauma patients, the effect of scFOS-EN is context-dependent. Prior exposure to anaerobic antibiotics appears to modify the microbial response from beneficial to detrimental. These findings challenge a universal approach to prebiotic therapy and underscore the need for personalized nutritional strategies in the ICU.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Trial registration<\/jats:title>\n                    <jats:p>The trial was prospectively registered at ClinicalTrials.gov (Identifier: NCT03153397; first posted May 15, 2017) prior to participant enrollment and approved by the Duke Health Institutional Review Board (IRB Pro00081414).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12916-025-04511-2","type":"journal-article","created":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T17:12:26Z","timestamp":1767028346000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Impact of fiber-containing enteral nutrition on microbial community dynamics in critically ill trauma patients: a pilot-randomized trial"],"prefix":"10.1186","volume":"23","author":[{"given":"Mara A.","family":"Serbanescu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary C.","family":"Wright","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamed","family":"Elebasy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pixu","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason W.","family":"Arnold","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Krista L.","family":"Haines","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James R.","family":"White","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neeraj K.","family":"Surana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul E.","family":"Wischmeyer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,12,29]]},"reference":[{"key":"4511_CR1","doi-asserted-by":"publisher","unstructured":"Nicole A, Cho Kathryn, Strayer Breenna, Dobson Braedon, McDonald. Pathogenesis and therapeutic opportunities of gut microbiome dysbiosis in critical illness Gut Microbes. 2024;16(1). https:\/\/doi.org\/10.1080\/19490976.2024.2351478.","DOI":"10.1080\/19490976.2024.2351478"},{"issue":"8","key":"4511_CR2","doi-asserted-by":"publisher","first-page":"1203","DOI":"10.1007\/s00134-018-5268-8","volume":"44","author":"DE Freedberg","year":"2018","unstructured":"Freedberg DE, Zhou MJ, Cohen ME, Annavajhala MK, Khan S, Moscoso DI, et al. Pathogen colonization of the gastrointestinal microbiome at intensive care unit admission and risk for subsequent death or infection. Intensive Care Med. 2018;44(8):1203\u201311.","journal-title":"Intensive Care Med"},{"issue":"1","key":"4511_CR3","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1186\/s13099-023-00567-8","volume":"15","author":"TJ Salameh","year":"2023","unstructured":"Salameh TJ, Roth K, Schultz L, Ma Z, Bonavia AS, Broach JR, et al. Gut microbiome dynamics and associations with mortality in critically ill patients. Gut Pathog. 2023;15(1):66.","journal-title":"Gut Pathog"},{"issue":"4","key":"4511_CR4","doi-asserted-by":"publisher","first-page":"1017","DOI":"10.1038\/s41591-023-02243-5","volume":"29","author":"J Schlechte","year":"2023","unstructured":"Schlechte J, Zucoloto AZ, Yu I-l, Doig CJ, Dunbar MJ, McCoy KD, et al. Dysbiosis of a microbiota\u2013immune metasystem in critical illness is associated with nosocomial infections. Nat Med. 2023;29(4):1017\u201327.","journal-title":"Nat Med"},{"issue":"15","key":"4511_CR5","doi-asserted-by":"publisher","first-page":"1478","DOI":"10.1001\/jama.2020.2717","volume":"323","author":"JL Vincent","year":"2020","unstructured":"Vincent JL, Sakr Y, Singer M, Martin-Loeches I, Machado FR, Marshall JC, et al. Prevalence and outcomes of infection among patients in intensive care units in 2017. JAMA. 2020;323(15):1478\u201387.","journal-title":"JAMA"},{"key":"4511_CR6","doi-asserted-by":"crossref","unstructured":"Valdes AM, Walter J, Segal E, Spector TD. Role of the gut microbiota in nutrition and health. BMJ. 2018;361:k2179.","DOI":"10.1136\/bmj.k2179"},{"issue":"5","key":"4511_CR7","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1016\/j.cmet.2014.07.003","volume":"20","author":"ED Sonnenburg","year":"2014","unstructured":"Sonnenburg ED, Sonnenburg JL. Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metab. 2014;20(5):779\u201386.","journal-title":"Cell Metab"},{"key":"4511_CR8","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1186\/s12915-015-0224-3","volume":"14","author":"WS Chung","year":"2016","unstructured":"Chung WS, Walker AW, Louis P, Parkhill J, Vermeiren J, Bosscher D, et al. Modulation of the human gut microbiota by dietary fibres occurs at the species level. BMC Biol. 2016;14:3.","journal-title":"BMC Biol"},{"issue":"8","key":"4511_CR9","doi-asserted-by":"publisher","first-page":"1896","DOI":"10.1093\/jn\/135.8.1896","volume":"135","author":"K Whelan","year":"2005","unstructured":"Whelan K, Judd PA, Preedy VR, Simmering R, Jann A, Taylor MA. Fructooligosaccharides and fiber partially prevent the alterations in fecal microbiota and short-chain fatty acid concentrations caused by standard enteral formula in healthy humans. J Nutr. 2005;135(8):1896\u2013902.","journal-title":"J Nutr"},{"key":"4511_CR10","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/1475-2891-5-8","volume":"5","author":"Y Bouhnik","year":"2006","unstructured":"Bouhnik Y, Raskine L, Simoneau G, Paineau D, Bornet F. The capacity of short-chain fructo-oligosaccharides to stimulate faecal bifidobacteria: a dose-response relationship study in healthy humans. Nutr J. 2006;5:8.","journal-title":"Nutr J"},{"key":"4511_CR11","doi-asserted-by":"crossref","unstructured":"Azpiroz F, Dubray C, Bernalier-Donadille A, Cardot JM, Accarino A, Serra J, et al. Effects of scFOS on the composition of fecal microbiota and anxiety in patients with irritable bowel syndrome: a randomized, double blind, placebo controlled study. Neurogastroenterol Motil. 2017;29:e12911.","DOI":"10.1111\/nmo.12911"},{"key":"4511_CR12","doi-asserted-by":"crossref","unstructured":"Cantu-Jungles TM, Hamaker BR. New view on dietary fiber selection for predictable shifts in gut microbiota. MBio. 2020;11(1).","DOI":"10.1128\/mBio.02179-19"},{"issue":"1","key":"4511_CR13","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1111\/1574-6941.12186","volume":"87","author":"KP Scott","year":"2014","unstructured":"Scott KP, Martin JC, Duncan SH, Flint HJ. Prebiotic stimulation of human colonic butyrate-producing bacteria and bifidobacteria, in vitro. FEMS Microbiol Ecol. 2014;87(1):30\u201340.","journal-title":"FEMS Microbiol Ecol"},{"issue":"1","key":"4511_CR14","doi-asserted-by":"publisher","first-page":"6860","DOI":"10.1038\/s41467-021-27191-x","volume":"12","author":"KE Huus","year":"2021","unstructured":"Huus KE, Hoang TT, Creus-Cuadros A, Cirstea M, Vogt SL, Knuff-Janzen K, et al. Cross-feeding between intestinal pathobionts promotes their overgrowth during undernutrition. Nat Commun. 2021;12(1):6860.","journal-title":"Nat Commun"},{"issue":"4","key":"4511_CR15","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2025.101240","volume":"16","author":"A Aranda-Diaz","year":"2025","unstructured":"Aranda-Diaz A, Willis L, Nguyen TH, Ho PY, Vila J, Thomsen T, et al. Assembly of stool-derived bacterial communities follows \u201cearly-bird\u201d resource utilization dynamics. Cell Syst. 2025;16(4):101240.","journal-title":"Cell Syst"},{"key":"4511_CR16","doi-asserted-by":"crossref","unstructured":"Haak BW, Argelaguet R, Kinsella CM, Kullberg RFJ, Lankelma JM, Deijs M, et al. Integrative transkingdom analysis of the gut microbiome in antibiotic perturbation and critical illness. mSystems. 2021;6(2):e01148\u201320.","DOI":"10.1128\/msystems.01148-20"},{"issue":"2","key":"4511_CR17","first-page":"169","volume":"27","author":"PE Wischmeyer","year":"2021","unstructured":"Wischmeyer PE. Overcoming challenges to enteral nutrition delivery in critical care. Curr Opin Crit Care. 2021;27(2):169\u201376.","journal-title":"Curr Opin Crit Care"},{"issue":"2","key":"4511_CR18","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1177\/0148607115621863","volume":"40","author":"SA McClave","year":"2016","unstructured":"McClave SA, Taylor BE, Martindale RG, Warren MM, Johnson DR, Braunschweig C, et al. Guidelines for the provision and assessment of nutrition support therapy in the adult critically ill patient: Society of Critical Care Medicine (SCCM) and American Society for Parenteral and Enteral Nutrition (A.S.P.E.N.). JPEN J Parenter Enteral Nutr. 2016;40(2):159\u2013211.","journal-title":"JPEN J Parenter Enteral Nutr"},{"issue":"9","key":"4511_CR19","doi-asserted-by":"publisher","first-page":"1671","DOI":"10.1016\/j.clnu.2023.07.011","volume":"42","author":"P Singer","year":"2023","unstructured":"Singer P, Blaser AR, Berger MM, Calder PC, Casaer M, Hiesmayr M, et al. ESPEN practical and partially revised guideline: clinical nutrition in the intensive care unit. Clin Nutr. 2023;42(9):1671\u201389.","journal-title":"Clin Nutr"},{"issue":"6","key":"4511_CR20","doi-asserted-by":"publisher","first-page":"138","DOI":"10.4291\/wjgp.v2.i6.138","volume":"2","author":"SJ O\u2019Keefe","year":"2011","unstructured":"O\u2019Keefe SJ, Ou J, Delany JP, Curry S, Zoetendal E, Gaskins HR, et al. Effect of fiber supplementation on the microbiota in critically ill patients. World J Gastrointest Pathophysiol. 2011;2(6):138\u201345.","journal-title":"World J Gastrointest Pathophysiol"},{"issue":"3","key":"4511_CR21","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1002\/jpen.1682","volume":"44","author":"Y Fu","year":"2020","unstructured":"Fu Y, Moscoso DI, Porter J, Krishnareddy S, Abrams JA, Seres D, et al. Relationship between dietary fiber intake and short-chain fatty acid-producing bacteria during critical illness: a prospective cohort study. JPEN J Parenter Enteral Nutr. 2020;44(3):463\u201371.","journal-title":"JPEN J Parenter Enteral Nutr"},{"issue":"6","key":"4511_CR22","volume":"2","author":"DE Freedberg","year":"2020","unstructured":"Freedberg DE, Messina M, Lynch E, Tess M, Miracle E, Chong DH, et al. Impact of fiber-based enteral nutrition on the gut microbiome of ICU patients receiving broad-spectrum antibiotics: a randomized pilot trial. Crit Care Explor. 2020;2(6):e0135.","journal-title":"Crit Care Explor"},{"issue":"6","key":"4511_CR23","doi-asserted-by":"publisher","first-page":"966","DOI":"10.1016\/j.clnu.2013.11.008","volume":"33","author":"HA Majid","year":"2014","unstructured":"Majid HA, Cole J, Emery PW, Whelan K. Additional oligofructose\/inulin does not increase faecal bifidobacteria in critically ill patients receiving enteral nutrition: a randomised controlled trial. Clin Nutr. 2014;33(6):966\u201372.","journal-title":"Clin Nutr"},{"issue":"8","key":"4511_CR24","doi-asserted-by":"publisher","first-page":"1621","DOI":"10.1038\/ismej.2012.8","volume":"6","author":"JG Caporaso","year":"2012","unstructured":"Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6(8):1621\u20134.","journal-title":"ISME J"},{"key":"4511_CR25","doi-asserted-by":"crossref","unstructured":"Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, et al. Improved bacterial 16S rRNA gene (V4 and V4\u20135) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems. 2015;1(1):e00009\u201315.","DOI":"10.1128\/mSystems.00009-15"},{"issue":"7","key":"4511_CR26","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","volume":"13","author":"BJ Callahan","year":"2016","unstructured":"Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581\u20133.","journal-title":"Nat Methods"},{"key":"4511_CR27","doi-asserted-by":"crossref","unstructured":"Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(Database issue):D590\u20136.","DOI":"10.1093\/nar\/gks1219"},{"key":"4511_CR28","doi-asserted-by":"crossref","unstructured":"Kodikara S, Ellul S, Le Cao KA. Statistical challenges in longitudinal microbiome data analysis. Brief Bioinform. 2022;23(4):bbac273.23.","DOI":"10.1093\/bib\/bbac273"},{"issue":"1","key":"4511_CR29","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1186\/s13059-024-03453-x","volume":"25","author":"P Shi","year":"2024","unstructured":"Shi P, Martino C, Han R, Janssen S, Buck G, Serrano M, et al. TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies. Genome Biol. 2024;25(1):317.","journal-title":"Genome Biol"},{"issue":"6","key":"4511_CR30","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0259756","volume":"17","author":"N Favila","year":"2022","unstructured":"Favila N, Madrigal-Trejo D, Legorreta D, Sanchez-Perez J, Espinosa-Asuar L, Eguiarte LE, et al. Micnet toolbox: visualizing and unraveling a microbial network. PLoS ONE. 2022;17(6):e0259756.","journal-title":"PLoS ONE"},{"issue":"9","key":"4511_CR31","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002687","volume":"8","author":"J Friedman","year":"2012","unstructured":"Friedman J, Alm EJ. Inferring correlation networks from genomic survey data. PLoS Comput Biol. 2012;8(9):e1002687.","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"4511_CR32","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1007\/s00134-016-4613-z","volume":"43","author":"JM Lankelma","year":"2017","unstructured":"Lankelma JM, van Vught LA, Belzer C, Schultz MJ, van der Poll T, de Vos WM, et al. Critically ill patients demonstrate large interpersonal variation in intestinal microbiota dysregulation: a pilot study. Intensive Care Med. 2017;43(1):59\u201368.","journal-title":"Intensive Care Med"},{"key":"4511_CR33","doi-asserted-by":"crossref","unstructured":"Wang Z, Tauzin AS, Laville E, Tedesco P, Letisse F, Terrapon N, et al. Harvesting of prebiotic fructooligosaccharides by nonbeneficial human gut bacteria. mSphere. 2020;5(1):e00771\u201319.","DOI":"10.1128\/mSphere.00771-19"},{"issue":"1","key":"4511_CR34","doi-asserted-by":"publisher","first-page":"388","DOI":"10.1128\/JB.01052-08","volume":"191","author":"C Schouler","year":"2009","unstructured":"Schouler C, Taki A, Chouikha I, Moulin-Schouleur M, Gilot P. A genomic island of an extraintestinal pathogenic Escherichia coli strain enables the metabolism of fructooligosaccharides, which improves intestinal colonization. J Bacteriol. 2009;191(1):388\u201393.","journal-title":"J Bacteriol"},{"key":"4511_CR35","doi-asserted-by":"crossref","unstructured":"McDonald D, Ackermann G, Khailova L, Baird C, Heyland D, Kozar R, et al. Extreme dysbiosis of the microbiome in critical illness. mSphere. 2016;1(4):e00199\u201316.","DOI":"10.1128\/mSphere.00199-16"},{"issue":"1","key":"4511_CR36","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ijmm.2010.04.021","volume":"301","author":"C Le Bouguenec","year":"2011","unstructured":"Le Bouguenec C, Schouler C. Sugar metabolism, an additional virulence factor in enterobacteria. Int J Med Microbiol. 2011;301(1):1\u20136.","journal-title":"Int J Med Microbiol"},{"key":"4511_CR37","doi-asserted-by":"crossref","unstructured":"Hecht AL, Harling LC, Friedman ES, Tanes C, Lee J, Firrman J, et al. Dietary carbohydrates regulate intestinal colonization and dissemination of Klebsiella pneumoniae. J Clin Invest. 2024;134(9):e174726.","DOI":"10.1172\/JCI174726"},{"issue":"1","key":"4511_CR38","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1016\/j.cell.2019.08.011","volume":"179","author":"ML Patnode","year":"2019","unstructured":"Patnode ML, Beller ZW, Han ND, Cheng J, Peters SL, Terrapon N, et al. Interspecies competition impacts targeted manipulation of human gut bacteria by fiber-derived glycans. Cell. 2019;179(1):59-73 e13.","journal-title":"Cell"},{"issue":"1","key":"4511_CR39","doi-asserted-by":"publisher","first-page":"1993598","DOI":"10.1080\/19490976.2021.1993598","volume":"13","author":"A Marfil-Sanchez","year":"2021","unstructured":"Marfil-Sanchez A, Zhang L, Alonso-Pernas P, Mirhakkak M, Mueller M, Seelbinder B, et al. An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness. Gut Microbes. 2021;13(1):1993598.","journal-title":"Gut Microbes"},{"issue":"1","key":"4511_CR40","doi-asserted-by":"publisher","first-page":"5094","DOI":"10.1038\/s41467-023-40872-z","volume":"14","author":"AYG Yip","year":"2023","unstructured":"Yip AYG, King OG, Omelchenko O, Kurkimat S, Horrocks V, Mostyn P, et al. Antibiotics promote intestinal growth of carbapenem-resistant Enterobacteriaceae by enriching nutrients and depleting microbial metabolites. Nat Commun. 2023;14(1):5094.","journal-title":"Nat Commun"},{"issue":"1","key":"4511_CR41","doi-asserted-by":"publisher","DOI":"10.1186\/s40635-018-0185-2","volume":"6","author":"C Venturini","year":"2018","unstructured":"Venturini C, Ginn AN, Wilson BE, Tsafnat G, Paulsen I, Partridge SR, et al. Ecological effects of cefepime use during antibiotic cycling on the Gram-negative enteric flora of ICU patients. Intensive Care Med Exp. 2018;6(1):19.","journal-title":"Intensive Care Med Exp"},{"key":"4511_CR42","doi-asserted-by":"crossref","unstructured":"Chanderraj R, Baker JM, Kay SG, Brown CA, Hinkle KJ, Fergle DJ, et al. In critically ill patients, anti-anaerobic antibiotics increase risk of adverse clinical outcomes. Eur Respir J. 2023;61(2):2200910.","DOI":"10.1183\/13993003.00910-2022"},{"key":"4511_CR43","unstructured":"Impact of Fiber-Containing Enteral Nutrition Pilot RCT Sequencing Data. Bethesda, MD, USA: NCBI Sequence Read Archive (SRA); 2025. Available from: https:\/\/identifiers.org\/ncbi\/bioproject:PRJNA1358002"}],"container-title":["BMC Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12916-025-04511-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12916-025-04511-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12916-025-04511-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T17:12:29Z","timestamp":1767028349000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12916-025-04511-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,29]]},"references-count":43,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["4511"],"URL":"https:\/\/doi.org\/10.1186\/s12916-025-04511-2","relation":{},"ISSN":["1741-7015"],"issn-type":[{"value":"1741-7015","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,29]]},"assertion":[{"value":"17 February 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 November 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 December 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Completion of this study was approved by the Duke University institutional review board (IRB Pro00081414) following review and approval of study protocols and informed consent forms. As patients included in this study lacked capacity, written informed consent was sought at time of inclusion from the patient\u2019s legally authorized representative. For patients that regained capacity, deferred written consent was obtained.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"Dr. Wischmeyer reports receiving investigator-initiated grant funding related to research on nutrition in critical illness from National Institutes of Health, Department of Defense, Canadian Institutes of Health Research, Abbott, Baxter, and the Fresenius Kabi Deutschland GmbH. Dr. Wischmeyer has served as a consultant for Abbott, Fresenius, Baxter, Cardinal Health, and Nutricia. He has received unrestricted gift donation for nutrition research from Musclesound and DSM and received honoraria or travel expenses for CME lectures on improving nutrition care from Abbott, Baxter, Fresenius, Danone-Nutricia, DSM, and Nestle. Funding for this study was provided in part by an Investigator Initiated Grant to Dr. Wischmeyer from Abbott Nutrition Inc., who also provided the EN formulations used. Abbott Nutrition Inc. did not participate in any part of the study design, execution, analysis, interpretation of results and had no involvement in preparation of the manuscript.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"706"}}