Gut Microbiome in Critical Illness

 The Gut Microbiome in Critical Illness: Current Understanding and Therapeutic Implications

Abstract

The gut microbiome has emerged as a crucial factor in the pathophysiology and outcomes of critically ill patients. This review synthesizes recent evidence on gut dysbiosis during critical illness, its relationship with clinical outcomes, and emerging therapeutic approaches. We discuss mechanisms by which gut microbiome alterations influence systemic inflammation, immune dysfunction, and organ failure in critically ill patients. Current and potential future interventions targeting the gut microbiome are evaluated, including probiotics, fecal microbiota transplantation, and precision nutrition approaches. Understanding these complex interactions may lead to novel therapeutic strategies that improve outcomes in the intensive care unit.

Introduction

Critical illness is characterized by profound physiological stress that affects multiple organ systems, frequently resulting in organ dysfunction and failure. In recent years, the gut microbiome has been recognized as a key mediator in the pathophysiology of critical illness, leading to the concept of the "gut-organ axis" in critical care medicine.[1,2] This paradigm shift has been driven by advances in sequencing technologies and bioinformatics that allow comprehensive characterization of the gut microbiota.

The human gut harbors approximately 100 trillion microorganisms, collectively termed the gut microbiota, with a genetic repertoire (microbiome) that vastly exceeds the human genome.[3] Under normal conditions, the gut microbiota maintains a symbiotic relationship with the host, contributing to nutrient metabolism, immune system development, and protection against pathogens.[4] However, critical illness dramatically alters this ecosystem, with potentially profound consequences for patient outcomes.

This review aims to provide intensivists and critical care trainees with a comprehensive overview of the current understanding of gut microbiome alterations in critical illness, their clinical implications, and emerging therapeutic approaches. We also highlight key research gaps and future directions in this rapidly evolving field.

 

Gut Microbiome Alterations in Critical Illness

 Characterization of Dysbiosis

Critical illness induces rapid and profound alterations in the gut microbiome, collectively referred to as dysbiosis. Studies using 16S rRNA gene sequencing and metagenomic approaches have demonstrated consistent patterns of dysbiosis across various critical illness states, including sepsis, acute respiratory distress syndrome (ARDS), and major trauma.[5-7]

Key features of critical illness-associated dysbiosis include:

1. Reduced diversity: Critical illness consistently leads to reduced alpha diversity (within-sample diversity), a finding associated with worse clinical outcomes.[8,9]

2. Loss of commensal anaerobes: Beneficial commensal bacteria, particularly obligate anaerobes such as Faecalibacterium, Ruminococcus, and Blautia species, are rapidly depleted during critical illness.[10,11]

3. Expansion of pathobionts: Concomitant with the loss of commensals, there is often an overgrowth of potentially pathogenic bacteria, including Enterococcus, Staphylococcus, and Proteobacteria such as Escherichia coli and Klebsiella species.[12,13]

4. Functional alterations: Beyond taxonomic changes, critical illness alters the functional capacity of the gut microbiome, with reduced capacity for short-chain fatty acid production and increased virulence factor expression.[14,15]

 Drivers of Dysbiosis in Critical Illness

Multiple factors contribute to gut microbiome alterations in critically ill patients:

1. Antibiotics: Broad-spectrum antibiotics, commonly administered in critical care, are powerful drivers of dysbiosis, with effects that may persist long after discontinuation.[16,17]

2. Altered nutrition: Enteral and parenteral nutrition practices, as well as periods of fasting, significantly impact gut microbial communities.[18,19]

3. Vasoactive medications: Vasopressors used in shock states affect gut perfusion and may contribute to dysbiosis through altered local oxygen delivery.[20]

4. Altered gut motility: Critical illness is associated with gut dysmotility, which can promote bacterial overgrowth and translocation.[21]

5. Inflammation and stress response: The host inflammatory response and hypothalamic-pituitary-adrenal axis activation during critical illness directly affect gut microbiota composition and function.[22,23]

 Clinical Implications of Gut Dysbiosis

 Impact on Organ Dysfunction

The concept of gut-organ crosstalk has gained recognition as a crucial mechanism in the pathophysiology of multi-organ dysfunction syndrome (MODS). Several pathways have been identified:

1. Gut-Lung Axis: Gut dysbiosis influences pulmonary outcomes through multiple mechanisms. Translocation of bacterial products and metabolites can exacerbate lung inflammation and injury.[24,25] Shimizu et al. demonstrated that gut-derived bacterial products detected in mesenteric lymph nodes were associated with increased inflammatory cytokines in the lungs and worse ARDS outcomes.[26]

2. Gut-Brain Axis: Emerging evidence suggests that gut dysbiosis contributes to delirium and long-term cognitive impairment in critically ill patients. Gut-derived metabolites influence blood-brain barrier integrity and neuroinflammation.[27,28]

3. Gut-Kidney Axis: Dysbiotic gut microbiota contribute to acute kidney injury through increased production of uremic toxins and translocation of inflammatory mediators.[29,30]

4. Gut-Liver Axis: Alterations in the enterohepatic circulation and bacterial translocation during critical illness influence liver function and may exacerbate hepatic injury.[31,32]

 Impact on Immune Function

The gut microbiome plays a central role in regulating host immune responses, particularly relevant in critical illness:

1. Immunosuppression: Prolonged critical illness often leads to immunosuppression, partially mediated by alterations in gut microbiota. Loss of commensal bacteria reduces stimulation of Treg cells and alters the Th17/Treg balance.[33,34]

2. Trained immunity: Commensal-derived signals contribute to trained immunity, which may be disrupted during critical illness-associated dysbiosis.[35]

3. Barrier function: Healthy gut microbiota support epithelial barrier integrity through production of short-chain fatty acids and other metabolites. Dysbiosis compromises this function, potentially facilitating bacterial translocation.[36,37]

 Prognostic Significance

Several studies have demonstrated associations between gut microbiome alterations and clinical outcomes:

1. Mortality: Specific dysbiosis patterns, particularly domination by Enterococcus or certain Proteobacteria, correlate with increased mortality in critically ill patients.[38,39]

2. Secondary infections: Loss of microbiome diversity predisposes to secondary infections, including ventilator-associated pneumonia and Clostridioides difficile infection.[40,41]

3. ICU length of stay: Persistent gut dysbiosis is associated with prolonged ICU stays and delayed recovery from critical illness.[42]

 Therapeutic Approaches Targeting the Gut Microbiome

 Selective Decontamination Strategies

Selective digestive decontamination (SDD) and selective oropharyngeal decontamination (SOD) aim to reduce colonization by potentially pathogenic bacteria while preserving anaerobic commensals:

1. Conventional SDD/SOD: Traditional protocols combining non-absorbable antibiotics have shown mortality benefits in some contexts but raise concerns about antimicrobial resistance.[43,44]

2. Refined approaches: Newer, more targeted decontamination strategies aim to selectively reduce pathobionts while minimizing collateral damage to beneficial commensals.[45]

 Probiotic Interventions

Administration of live beneficial microorganisms has shown promise in critical care:

1. Clinical evidence: Meta-analyses indicate that probiotics may reduce ventilator-associated pneumonia and Clostridioides difficile infection in critically ill patients.[46,47] However, results remain heterogeneous across studies.

2. Specific strains: Lactobacillus rhamnosus GG, Saccharomyces boulardii, and specific Bifidobacterium strains have demonstrated beneficial effects in critical illness, though optimal strains, dosing, and timing require further investigation.[48,49]

3. Safety considerations: While generally safe, concerns exist regarding probiotic translocation and potential bacteremia, particularly in immunocompromised patients with compromised gut barrier function.[50]

Fecal Microbiota Transplantation

Fecal microbiota transplantation (FMT) represents a more comprehensive approach to restore gut microbiome function:

1. Emerging applications in critical care: Initial case series and small studies suggest potential benefits of FMT in critically ill patients with severe dysbiosis or recurrent C. difficile infection.[51,52]

2. Administration routes: FMT can be delivered via nasogastric tube, enema, or colonoscopy in critical care settings, with route selection based on patient factors and institutional protocols.[53]

3. Safety and standardization: Challenges include donor screening, standardization of preparations, and monitoring for adverse events in vulnerable critically ill populations.[54]

 Precision Nutrition Approaches

Tailoring nutritional support to promote beneficial microbiota represents a promising strategy:

1. Prebiotic supplementation: Non-digestible fibers and oligosaccharides can selectively promote growth of beneficial bacteria, with preliminary evidence suggesting improved gut barrier function in critical illness.[55,56]

2. Synbiotics: Combinations of probiotics and prebiotics have shown synergistic effects in small critical care studies, warranting larger trials.[57]

3. Specialized nutrition formulations: Enteral formulas enriched with specific fibers, polyphenols, and omega-3 fatty acids may help maintain microbiome diversity during critical illness.[58,59]

 Emerging Microbiome-Based Therapies

Novel approaches currently under investigation include:

1. Postbiotics: Cell-free supernatants, bacterial lysates, or purified bacterial components that provide benefits without live bacteria may offer advantages in terms of safety and stability.[60]

2. Engineered microbiota: Genetically modified bacterial strains designed to produce anti-inflammatory compounds or compete with pathobionts represent an emerging frontier.[61]

3. Bacteriophage therapy: Targeted bacteriophages may selectively reduce pathobionts while sparing beneficial commensals, potentially addressing antibiotic resistance concerns.[62]

 Practical Considerations for Critical Care Clinicians

Microbiome-Conscious Antibiotic Stewardship

Intensivists can minimize microbiome disruption through:

1. Narrowing antibiotic spectrum when possible, based on culture results and clinical response.

2. Limiting duration of antibiotic therapy to the minimum necessary period.

3. Considering antibiotic rotation strategies to reduce selective pressure.

4. Implementing antimicrobial stewardship programs with microbiome preservation as an explicit goal.[63,64]

 Nutrition Optimization

Evidence-based approaches include:

1. Early enteral nutrition when feasible to maintain gut barrier function and microbiome diversity.

2. Including fiber in enteral nutrition when tolerated, preferably a mix of soluble and insoluble fibers.

3. Avoiding unnecessary fasting for procedures when possible.

4. Considering trophic feeding during periods when full enteral nutrition is not possible.[65,66]

 Microbiome Monitoring in Critical Care

While not yet standard practice, emerging technologies may enable:

1. Point-of-care testing for gut dysbiosis to guide therapeutic interventions.

2. Serial monitoring to track microbiome restoration during recovery.

3. Integration of microbiome data with clinical decision support systems.[67,68]

Future Directions and Research Gaps

Methodological Considerations

Advancing the field requires:

1. Standardized protocols for sample collection and processing in critically ill patients.

2. Integration of multi-omic approaches (metagenomics, metabolomics, proteomics) for comprehensive microbiome assessment.

3. Development of clinically relevant endpoints for microbiome intervention trials.[69,70]

Key Research Questions

Critical areas for future investigation include:

1. Determining causality versus association between specific microbiome alterations and clinical outcomes.

2. Identifying patient subpopulations most likely to benefit from microbiome-targeted interventions.

3. Establishing optimal timing, dosing, and duration of microbiome-based therapies.

4. Developing predictive models incorporating microbiome data to guide personalized critical care.[71,72]

 Translation to Clinical Practice

Moving from research to implementation requires:

1. Large, well-designed multicenter trials with clinically relevant endpoints.

2. Cost-effectiveness analyses of microbiome-based interventions.

3. Development of practical guidelines for microbiome management in the ICU.

4. Education of critical care clinicians on microbiome science and its clinical applications.[73,74]

Conclusion

The gut microbiome represents a dynamic and modifiable factor in the complex pathophysiology of critical illness. Growing evidence supports its role in influencing inflammation, immunity, and organ dysfunction in critically ill patients. While microbiome-targeted interventions show promise, challenges remain in translating this knowledge into effective clinical strategies. Future research focusing on mechanistic understanding, intervention optimization, and implementation science will be essential to realize the full potential of microbiome-based approaches in critical care medicine.

References

1. Dickson RP. The microbiome and critical illness. Lancet Respir Med. 2016;4(1):59-72.

2. Kitsios GD, Morowitz MJ, Dickson RP, et al. Dysbiosis in the intensive care unit: Microbiome science coming to the bedside. J Crit Care. 2017;38:84-91.

3. Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 2016;14(8):e1002533.

4. Belkaid Y, Hand TW. Role of the microbiota in immunity and inflammation. Cell. 2014;157(1):121-141.

5. McDonald D, Ackermann G, Khailova L, et al. Extreme dysbiosis of the microbiome in critical illness. mSphere. 2016;1(4):e00199-16.

6. 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(1):59-68.

7. 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(5):e01361-14.

8. 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(6):1628-1634.

9. Yeh A, Rogers MB, Firek B, et al. Dysbiosis across multiple body sites in critically ill adult surgical patients. Shock. 2016;46(6):649-654.

10. Livanos AE, Snider EJ, Whittier S, et al. Rapid gastrointestinal loss of Clostridial clusters IV and XIVa in the ICU associates with an expansion of gut pathogens. PLoS One. 2018;13(8):e0200322.

11. Byndloss MX, Litvak Y, Bäumler AJ. Microbiota-nourishing immunity and its relevance for ulcerative colitis. Inflamm Bowel Dis. 2019;25(5):811-815.

12. Freedberg DE, Zhou MJ, Cohen ME, 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):1203-1211.

13. Haak BW, Wiersinga WJ. The role of the gut microbiota in sepsis. Lancet Gastroenterol Hepatol. 2017;2(2):135-143.

14. Agudelo-Ochoa GM, Valdés-Duque BE, Giraldo-Giraldo NA, et al. Gut microbiota in critically ill patients with systemic inflammatory response syndrome. Nutrition. 2020;78:110783.

15. Feng Y, Ralls MW, Xiao W, et al. Loss of enteral nutrition in a mouse model results in intestinal epithelial barrier dysfunction. Ann N Y Acad Sci. 2012;1258:71-77.

16. Taur Y, Xavier JB, Lipuma L, et al. Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clin Infect Dis. 2012;55(7):905-914.

17. Jernberg C, Löfmark S, Edlund C, et al. Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J. 2007;1(1):56-66.

18. Ralls MW, Miyasaka E, Teitelbaum DH. Intestinal microbial diversity and perioperative complications. JPEN J Parenter Enteral Nutr. 2014;38(3):392-399.

19. Yeh A, Rogers MB, Firek B, et al. Dysbiosis across multiple body sites in critically ill adult surgical patients. Shock. 2016;46(6):649-654.

20. Alverdy JC, Krezalek MA. Collapse of the microbiome, emergence of the pathobiome, and the immunopathology of sepsis. Crit Care Med. 2017;45(2):337-347.

21. 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(8):2361-2365.

22. Bailey MT, Coe CL. Maternal separation disrupts the integrity of the intestinal microflora in infant rhesus monkeys. Dev Psychobiol. 1999;35(2):146-155.

23. Karl JP, Margolis LM, Madslien EH, et al. Changes in intestinal microbiota composition and metabolism coincide with increased intestinal permeability in young adults under prolonged physiological stress. Am J Physiol Gastrointest Liver Physiol. 2017;312(6):G559-G571.

24. 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(10):16113.

25. Panzer AR, Lynch SV, Langelier C, et al. Lung microbiota is related to smoking status and to development of acute respiratory distress syndrome in critically ill trauma patients. Am J Respir Crit Care Med. 2018;197(5):621-631.

26. 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(4):1171-1177.

27. Maes M, Kubera M, Leunis JC, et al. Increased IgA and IgM responses against gut commensals in chronic depression: further evidence for increased bacterial translocation or leaky gut. J Affect Disord. 2012;141(1):55-62.

28. Shen Y, Xu J, Li Z, et al. Analysis of gut microbiota diversity and auxiliary diagnosis as a biomarker in patients with schizophrenia: a cross-sectional study. Schizophr Res. 2018;197:470-477.

29. Yang J, Lim SY, Ko YS, et al. Intestinal barrier disruption and dysregulated mucosal immunity contribute to kidney fibrosis in chronic kidney disease. Nephrol Dial Transplant. 2019;34(3):419-428.

30. Andersen K, Kesper MS, Marschner JA, et al. Intestinal dysbiosis, barrier dysfunction, and bacterial translocation account for CKD-related systemic inflammation. J Am Soc Nephrol. 2017;28(1):76-83.

31. Wiest R, Albillos A, Trauner M, et al. Targeting the gut-liver axis in liver disease. J Hepatol. 2017;67(5):1084-1103.

32. Albillos A, de Gottardi A, Rescigno M. The gut-liver axis in liver disease: pathophysiological basis for therapy. J Hepatol. 2020;72(3):558-577.

33. Schuijt TJ, Lankelma JM, Scicluna BP, et al. The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia. Gut. 2016;65(4):575-583.

34. Lamas B, Richard ML, Leducq V, et al. CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nat Med. 2016;22(6):598-605.

35. Netea MG, Joosten LA, Latz E, et al. Trained immunity: a program of innate immune memory in health and disease. Science. 2016;352(6284):aaf1098.

36. Feng Y, Huang Y, Wang Y, et al. Antibiotics induced intestinal tight junction barrier dysfunction is associated with microbiota dysbiosis, activated NLRP3 inflammasome and autophagy. PLoS One. 2019;14(6):e0218384.

37. Earley ZM, Akhtar S, Green SJ, et al. Burn injury alters the intestinal microbiome and increases gut permeability and bacterial translocation. PLoS One. 2015;10(7):e0129996.

38. Shimizu K, Ogura H, Goto M, et al. Altered gut flora and environment in patients with severe SIRS. J Trauma. 2006;60(1):126-133.

39. Taur Y, Jenq RR, Perales MA, et al. The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation. Blood. 2014;124(7):1174-1182.

40. Dickson RP, Schultz MJ, van der Poll T, et al. Lung microbiota predict clinical outcomes in critically ill patients. Am J Respir Crit Care Med. 2020;201(5):555-563.

41. Buffie CG, Pamer EG. Microbiota-mediated colonization resistance against intestinal pathogens. Nat Rev Immunol. 2013;13(11):790-801.

42. Lamarche D, Johnstone J, Zytaruk N, et al. Microbial dysbiosis and mortality during mechanical ventilation: a prospective observational study. Respir Res. 2018;19(1):245.

43. de Smet AM, Kluytmans JA, Cooper BS, et al. Decontamination of the digestive tract and oropharynx in ICU patients. N Engl J Med. 2009;360(1):20-31.

44. Daneman N, Sarwar S, Fowler RA, et al. Effect of selective decontamination on antimicrobial resistance in intensive care units: a systematic review and meta-analysis. Lancet Infect Dis. 2013;13(4):328-341.

45. Zaborin A, Defazio JR, Kade M, et al. Phosphate-containing polyethylene glycol polymers prevent lethal sepsis by multidrug-resistant pathogens. Antimicrob Agents Chemother. 2014;58(2):966-977.

46. Morrow LE, Kollef MH, Casale TB. Probiotic prophylaxis of ventilator-associated pneumonia: a blinded, randomized, controlled trial. Am J Respir Crit Care Med. 2010;182(8):1058-1064.

47. Su GL, Ko CW, Bercik P, et al. AGA clinical practice guidelines on the role of probiotics in the management of gastrointestinal disorders. Gastroenterology. 2020;159(2):697-705.

48. Zeng J, Wang CT, Zhang FS, et al. Effect of probiotics on the incidence of ventilator-associated pneumonia in critically ill patients: a randomized controlled multicenter trial. Intensive Care Med. 2016;42(6):1018-1028.

49. Manzanares W, Lemieux M, Langlois PL, et al. Probiotic and synbiotic therapy in critical illness: a systematic review and meta-analysis. Crit Care. 2016;20(1):262.

50. Yelin I, Flett KB, Merakou C, et al. Genomic and epidemiological evidence of bacterial transmission from probiotic capsule to blood in ICU patients. Nat Med. 2019;25(11):1728-1732.

51. McClave SA, Patel J, Bhutiani N. Should fecal microbial transplantation be used in the ICU? Curr Opin Crit Care. 2018;24(2):105-111.

52. DeFilipp Z, Bloom PP, Torres Soto M, et al. Drug-resistant E. coli bacteremia transmitted by fecal microbiota transplant. N Engl J Med. 2019;381(21):2043-2050.

53. Lahtinen P, Mattila E, Anttila VJ, et al. Faecal microbiota transplantation in patients with Clostridium difficile and significant comorbidities as well as in patients with new indications: a case series. World J Gastroenterol. 2017;23(39):7174-7184.

54. Cammarota G, Ianiro G, Kelly CR, et al. International consensus conference on stool banking for faecal microbiota transplantation in clinical practice. Gut. 2019;68(12):2111-2121.

55. Klingensmith NJ, Coopersmith CM. The gut as the motor of multiple organ dysfunction in critical illness. Crit Care Clin. 2016;32(2):203-212.

56. Tuncay P, Arpali E, Kalayoglu M, et al. Use of standard enteral formula versus enteric formula with prebiotic content in nutrition therapy: a randomized controlled study among neuro-critical care patients. Clin Nutr ESPEN. 2018;25:26-36.

57. 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(1):239.

58. Rice TW. Enteral nutrition in the mechanically ventilated patient. Curr Opin Crit Care. 2012;18(2):206-211.

59. Mahmoodpoor A, Hamishehkar H, Asghari R, et al. Effect of a probiotic preparation on ventilator-associated pneumonia in critically ill patients admitted to the intensive care unit: a prospective double-blind randomized controlled trial. Nutr Clin Pract. 2019;34(1):156-162.

60. Tsilingiri K, Rescigno M. Postbiotics: what else? Benef Microbes. 2013;4(1):101-107.

61. Duan FF, Liu JH, March JC. Engineered commensal bacteria reprogram intestinal cells into glucose-responsive insulin-secreting cells for the treatment of diabetes. Diabetes. 2015;64(5):1794-1803.

62. Schooley RT, Biswas B, Gill JJ, et al. Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection. Antimicrob Agents Chemother. 2017;61(10):e00954-17.

63. McDonald LC, Gerding DN, Johnson S, et al. Clinical practice guidelines for Clostridium difficile infection in adults and children: 2017 update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA). Clin Infect Dis. 2018;66(7):987-994.

64. Rhodes A, Evans LE, Alhazzani W, et al. Surviving Sepsis Campaign: International Guidelines for Management of Sepsis and Septic Shock: 2016. Intensive Care Med. 2017;43(3):304-377.

65. McClave SA, Taylor BE, Martindale RG, 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):159-211.

66. Singer P, Blaser AR, Berger MM, et al. ESPEN guideline on clinical nutrition in the intensive care unit. Clin Nutr. 2019;38(1):48-79.

67. Rogers MB, Firek B, Shi M, et al. Disruption of the microbiota across multiple body sites in critically ill children. Microbiome. 2016;4(1):66.

68. Alverdy JC, Hyoju SK, Weigerinck M, et al. The gut microbiome and the mechanism of surgical infection. Br J Surg. 2017;104(2):e14-e23.

69. Johanson WG Jr, Pierce AK, Sanford JP. Changing pharyngeal bacterial flora of hospitalized patients. Emergence of gram-negative bacilli. N Engl J Med. 1969;281(21):1137-1140.

70. Dickson RP, Erb-Downward JR, Freeman CM, et al. Spatial variation in the healthy human lung microbiome and the adapted island model of lung biogeography. Ann Am Thorac Soc. 2015;12(6):821-830.

71. Haak BW, Prescott HC, Wiersinga WJ. Therapeutic potential of the gut microbiota in the prevention and treatment of sepsis. Front Immunol. 2018;9:2042.

72. Wischmeyer PE, McDonald D, Knight R. Role of the microbiome, probiotics, and 'dysbiosis therapy' in critical illness. Curr Opin Crit Care. 2016;22(4):347-353.

73. Gareau MG, Sherman PM, Walker WA. Probiotics and the gut microbiota in intestinal health and disease. Nat Rev Gastroenterol Hepatol. 2010;7(9):503-514.

74. Sertaridou E, Papaioannou V, Kolios G, et al. Gut failure in critical care: old school versus new school. Ann Gastroenterol. 2015;28(3):309-322.