Savage DC. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol. 1977;31:107–133.
CAS
PubMed
Article
Google Scholar
Qin J, Li R, Raes J et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59–65.
CAS
PubMed
PubMed Central
Article
Google Scholar
Backhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science. 2005;307:1915–1920.
PubMed
Article
CAS
Google Scholar
Sommer F, Backhed F. The gut microbiota–masters of host development and physiology. Nat Rev Microbiol. 2013;11:227–238.
CAS
PubMed
Article
Google Scholar
Petersen C, Round JL. Defining dysbiosis and its influence on host immunity and disease. Cell Microbiol. 2014;16:1024–1033.
CAS
PubMed
PubMed Central
Article
Google Scholar
Thaiss CA, Zmora N, Levy M, Elinav E. The microbiome and innate immunity. Nature. 2016;535:65–74.
CAS
PubMed
Article
Google Scholar
Shimizu K, Ogura H, Hamasaki T et al. Altered gut flora are associated with septic complications and death in critically ill patients with systemic inflammatory response syndrome. Dig Dis Sci. 2011;56:1171–1177. https://doi.org/10.1007/s10620-010-1418-8
Article
PubMed
Google Scholar
Shimizu K, Ogura H, Asahara T et al. Gut microbiota and environment in patients with major burns—a preliminary report. Burns. 2015;41:e28-33.
PubMed
Article
Google Scholar
Yeh A, Rogers MB, Firek B, Neal MD, Zuckerbraun BS, Morowitz MJ. Dysbiosis across multiple body sites in critically ill adult surgical patients. Shock. 2016;46:649–654.
PubMed
Article
Google Scholar
Dickson RP, Singer BH, Newstead MW et al. Enrichment of the lung microbiome with gut bacteria in sepsis and the acute respiratory distress syndrome. Nat Microbiol. 2016;1:16113.
CAS
PubMed
PubMed Central
Article
Google Scholar
Tringe SG, Rubin EM. Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet. 2005;6:805–814.
CAS
PubMed
Article
Google Scholar
McDonald D, Ackermann G, Khailova L, et al. Extreme Dysbiosis of the Microbiome in Critical Illness. mSphere. 2016;1.
Lankelma JM, van Vught LA, Belzer C et al. Critically ill patients demonstrate large interpersonal variation in intestinal microbiota dysregulation: a pilot study. Intensive Care Med. 2017;43:59–68.
CAS
PubMed
Article
Google Scholar
Ojima M, Motooka D, Shimizu K et al. Metagenomic analysis reveals dynamic changes of whole gut microbiota in the acute phase of intensive care unit patients. Dig Dis Sci. 2016;61:1628–1634. https://doi.org/10.1007/s10620-015-4011-3
Article
PubMed
Google Scholar
Bolyen E, Rideout JR, Dillon MR et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:852–857.
CAS
PubMed
PubMed Central
Article
Google Scholar
Mikasa K, Aoki N, Aoki Y et al. JAID/jsc guidelines for the treatment of respiratory infectious diseases: the Japanese association for infectious diseases/Japanese society of chemotherapy—the JAID/JSC guide to clinical management of infectious disease/guideline-preparing committee respiratory infectious disease WG. J Infect Chemother. 2016;22:S1–S65.
PubMed
PubMed Central
Article
Google Scholar
Yoshimura J, Kinoshita T, Yamakawa K et al. Impact of Gram stain results on initial treatment selection in patients with ventilator-associated pneumonia: a retrospective analysis of two treatment algorithms. Crit Care. 2017;21:156.
PubMed
PubMed Central
Article
Google Scholar
Knaus WA, Draper EA, Wagner DP, Zimmerman JE. APACHE II: a severity of disease classification system. Crit Care Med. 1985;13:818–829.
CAS
PubMed
Article
Google Scholar
Vincent JL, Moreno R, Takala J et al. The SOFA (sepsis-related organ failure assessment) score to describe organ dysfunction/failure. On behalf of the working group on sepsis-related problems of the european society of intensive care medicine. Intensive Care Med. 1996;22:707–710.
CAS
PubMed
Article
Google Scholar
Knights D, Costello EK, Knight R. Supervised classification of human microbiota. FEMS Microbiol Rev. 2011;35:343–359.
CAS
PubMed
Article
Google Scholar
Lozupone CA, Hamady M, Kelley ST, Knight R. Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol. 2007;73:1576–1585.
CAS
PubMed
PubMed Central
Article
Google Scholar
Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature. 2006;444:1022–1023.
CAS
PubMed
Article
Google Scholar
Breiman L, Friedman JH, Olshen RA, Stone CJ. Classification and regression trees. New York: Chapman Hall CRC; 1984.
Google Scholar
Human Microbiome Project C. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–214.
Article
CAS
Google Scholar
Yamada T, Shimizu K, Ogura H et al. Rapid and sustained long-term decrease of fecal short-chain fatty acids in critically ill patients with systemic inflammatory response syndrome. JPEN J Parenter Enteral Nutr. 2015;39:569–577.
CAS
PubMed
Article
Google Scholar
Hayakawa M, Asahara T, Henzan N et al. Dramatic changes of the gut flora immediately after severe and sudden insults. Dig Dis Sci. 2011;56:2361–2365. https://doi.org/10.1007/s10620-011-1649-3
CAS
Article
PubMed
Google Scholar
Shimizu K, Yamada T, Ogura H et al. Synbiotics modulate gut microbiota and reduce enteritis and ventilator-associated pneumonia in patients with sepsis: a randomized controlled trial. Crit Care. 2018;22:239.
PubMed
PubMed Central
Article
Google Scholar
Manzanares W, Lemieux M, Langlois PL, Wischmeyer PE. Probiotic and synbiotic therapy in critical illness: a cystamatic review and meta-analysis. Crit Care. 2016;19:262.
PubMed
Article
Google Scholar
Iapichino G, Callegari ML, Marzorati S et al. Impact of antibiotics on the gut microbiota of critically ill patients. J Med Microbiol. 2008;57:1007–1014.
CAS
PubMed
Article
Google Scholar
Zaborin A, Smith D, Garfield K, et al. Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness. mBio. 2014;5:e01361–14.
Ianiro G, Tilg H, Gasbarrini A. Antibiotics as deep modulators of gut microbiota: between good and evil. Gut. 2016;65:1906–1915.
CAS
PubMed
Article
Google Scholar
Hidalgo-Cantabrana C, Delgado S, Ruiz L, Ruas-Madiedo P, Sánchez B, Margolles A. Bifidobacteria and their health-promoting effects. Microbiol Spectr. 2017;5.
Wieërs G, Belkhir L, Enaud R et al. How probiotics affect the microbiota. Front Cell Infect Microbiol. 2019;9:454.
PubMed
Article
CAS
Google Scholar
Krajmalnik-Brown R, Ilhan ZE, Kang DW, DiBaise JK. Effects of gut microbes on nutrient absorption and energy regulation. Nutr Clin Pract. 2012;27:201–214.
PubMed
PubMed Central
Article
Google Scholar
Jia W, Xie G, Jia W. Bile acid-microbiota crosstalk in gastrointestinal inflammation and carcinogenesis. Nat Rev Gastroenterol Hepatol. 2018;15:111–128.
CAS
PubMed
Article
Google Scholar
Morrison DJ, Preston T. Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism. Gut Microbes. 2016;7:189–200.
PubMed
PubMed Central
Article
Google Scholar
Staley C, Weingarden AR, Khoruts A, Sadowsky MJ. Interaction of gut microbiota with bile acid metabolism and its influence on disease states. Appl Microbiol Biotechnol. 2017;101:47–64.
CAS
PubMed
Article
Google Scholar
Vital M, Karch A, Pieper DH. Colonic butyrate-producing communities in humans: an overview using omics data. mSystems.
Furusawa Y, Obata Y, Fukuda S et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature. 2013;504:446–450.
CAS
PubMed
Article
Google Scholar
Devaux CA, Million M, Raoult D. The butyrogenic and lactic bacteria of the gut microbiota determine the outcome of allogenic hematopoietic cell transplant. Front Microbiol. 2020;11:1642.
PubMed
PubMed Central
Article
Google Scholar
Lavelle A, Sokol H. Gut microbiota-derived metabolites as key actors in inflammatory bowel disease. Nat Rev Gastroenterol Hepatol. 2020;17:223–237.
PubMed
Article
Google Scholar
Shimizu K, Ogura H, Goto M et al. Altered gut flora and environment in patients with severe SIRS. J Trauma. 2006;60:126–133.
PubMed
Article
Google Scholar
Osuka A, Shimizu K, Ogura H et al. Prognostic impact of fecal pH in critically ill patients. Crit Care. 2012;16:R119.
PubMed
PubMed Central
Article
Google Scholar
Peled JU, Gomes ALC, Devlin SM et al. Microbiota as predictor of mortality in allogeneic hematopoietic-cell transplantation. New Engl J Med. 2020;382:822–834.
CAS
PubMed
Article
Google Scholar
Kusakabe S, Fukushima K, Maeda T et al. Pre- and post-serial metagenomic analysis of gut microbiota as a prognostic factor in patients undergoing haematopoietic stem cell transplantation. Br J Haematol. 2020;188:438–449.
CAS
PubMed
Article
Google Scholar
Xu R, Tan C, Zhu J, et al. Dysbiosis of the intestinal microbiota in neurocritically ill patients and the risk for death. Crit Care. 2019;23.
Gupta VK, Paul S, Dutta C. Geography, ethnicity or subsistence-specific variations in human microbiome composition and diversity. Front Microbiol. 2017;8:1162.
PubMed
PubMed Central
Article
Google Scholar
Chen L, Zhang YH, Huang T, Cai YD. Gene expression profiling gut microbiota in different races of humans. Sci Rep. 2016;6:23075.
CAS
PubMed
PubMed Central
Article
Google Scholar
Nishijima S, Suda W, Oshima K et al. The gut microbiome of healthy Japanese and its microbial and functional uniqueness. DNA Res. 2016;23:125–133.
CAS
PubMed
PubMed Central
Article
Google Scholar