Extreme Dysbiosis of the Microbiome in Critical Illness

ABSTRACT Critical illness is hypothesized to associate with loss of “health-promoting” commensal microbes and overgrowth of pathogenic bacteria (dysbiosis). This dysbiosis is believed to increase susceptibility to nosocomial infections, sepsis, and organ failure. A trial with prospective monitoring...

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Autores principales:	Daniel McDonald, Gail Ackermann, Ludmila Khailova, Christine Baird, Daren Heyland, Rosemary Kozar, Margot Lemieux, Karrie Derenski, Judy King, Christine Vis-Kampen, Rob Knight, Paul E. Wischmeyer
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2016
Materias:	16S RNA critical care fecal organisms human microbial source tracking Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/76312f269bba46118c1dfb47667e3557
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spelling	oai:doaj.org-article:76312f269bba46118c1dfb47667e35572021-11-15T15:21:15ZExtreme Dysbiosis of the Microbiome in Critical Illness10.1128/mSphere.00199-162379-5042https://doaj.org/article/76312f269bba46118c1dfb47667e35572016-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00199-16https://doaj.org/toc/2379-5042ABSTRACT Critical illness is hypothesized to associate with loss of “health-promoting” commensal microbes and overgrowth of pathogenic bacteria (dysbiosis). This dysbiosis is believed to increase susceptibility to nosocomial infections, sepsis, and organ failure. A trial with prospective monitoring of the intensive care unit (ICU) patient microbiome using culture-independent techniques to confirm and characterize this dysbiosis is thus urgently needed. Characterizing ICU patient microbiome changes may provide first steps toward the development of diagnostic and therapeutic interventions using microbiome signatures. To characterize the ICU patient microbiome, we collected fecal, oral, and skin samples from 115 mixed ICU patients across four centers in the United States and Canada. Samples were collected at two time points: within 48 h of ICU admission, and at ICU discharge or on ICU day 10. Sample collection and processing were performed according to Earth Microbiome Project protocols. We applied SourceTracker to assess the source composition of ICU patient samples by using Qiita, including samples from the American Gut Project (AGP), mammalian corpse decomposition samples, childhood (Global Gut study), and house surfaces. Our results demonstrate that critical illness leads to significant and rapid dysbiosis. Many taxons significantly depleted from ICU patients versus AGP healthy controls are key “health-promoting” organisms, and overgrowth of known pathogens was frequent. Source compositions of ICU patient samples are largely uncharacteristic of the expected community type. Between time points and within a patient, the source composition changed dramatically. Our initial results show great promise for microbiome signatures as diagnostic markers and guides to therapeutic interventions in the ICU to repopulate the normal, “health-promoting” microbiome and thereby improve patient outcomes. IMPORTANCE Critical illness may be associated with the loss of normal, “health promoting” bacteria, allowing overgrowth of disease-promoting pathogenic bacteria (dysbiosis), which, in turn, makes patients susceptible to hospital-acquired infections, sepsis, and organ failure. This has significant world health implications, because sepsis is becoming a leading cause of death worldwide, and hospital-acquired infections contribute to significant illness and increased costs. Thus, a trial that monitors the ICU patient microbiome to confirm and characterize this hypothesis is urgently needed. Our study analyzed the microbiomes of 115 critically ill subjects and demonstrated rapid dysbiosis from unexpected environmental sources after ICU admission. These data may provide the first steps toward defining targeted therapies that correct potentially “illness-promoting” dysbiosis with probiotics or with targeted, multimicrobe synthetic “stool pills” that restore a healthy microbiome in the ICU setting to improve patient outcomes. Podcast: A podcast concerning this article is available.Daniel McDonaldGail AckermannLudmila KhailovaChristine BairdDaren HeylandRosemary KozarMargot LemieuxKarrie DerenskiJudy KingChristine Vis-KampenRob KnightPaul E. WischmeyerAmerican Society for Microbiologyarticle16S RNAcritical carefecal organismshumanmicrobial source trackingMicrobiologyQR1-502ENmSphere, Vol 1, Iss 4 (2016)
institution	DOAJ
collection	DOAJ
language	EN
topic	16S RNA critical care fecal organisms human microbial source tracking Microbiology QR1-502
spellingShingle	16S RNA critical care fecal organisms human microbial source tracking Microbiology QR1-502 Daniel McDonald Gail Ackermann Ludmila Khailova Christine Baird Daren Heyland Rosemary Kozar Margot Lemieux Karrie Derenski Judy King Christine Vis-Kampen Rob Knight Paul E. Wischmeyer Extreme Dysbiosis of the Microbiome in Critical Illness
description	ABSTRACT Critical illness is hypothesized to associate with loss of “health-promoting” commensal microbes and overgrowth of pathogenic bacteria (dysbiosis). This dysbiosis is believed to increase susceptibility to nosocomial infections, sepsis, and organ failure. A trial with prospective monitoring of the intensive care unit (ICU) patient microbiome using culture-independent techniques to confirm and characterize this dysbiosis is thus urgently needed. Characterizing ICU patient microbiome changes may provide first steps toward the development of diagnostic and therapeutic interventions using microbiome signatures. To characterize the ICU patient microbiome, we collected fecal, oral, and skin samples from 115 mixed ICU patients across four centers in the United States and Canada. Samples were collected at two time points: within 48 h of ICU admission, and at ICU discharge or on ICU day 10. Sample collection and processing were performed according to Earth Microbiome Project protocols. We applied SourceTracker to assess the source composition of ICU patient samples by using Qiita, including samples from the American Gut Project (AGP), mammalian corpse decomposition samples, childhood (Global Gut study), and house surfaces. Our results demonstrate that critical illness leads to significant and rapid dysbiosis. Many taxons significantly depleted from ICU patients versus AGP healthy controls are key “health-promoting” organisms, and overgrowth of known pathogens was frequent. Source compositions of ICU patient samples are largely uncharacteristic of the expected community type. Between time points and within a patient, the source composition changed dramatically. Our initial results show great promise for microbiome signatures as diagnostic markers and guides to therapeutic interventions in the ICU to repopulate the normal, “health-promoting” microbiome and thereby improve patient outcomes. IMPORTANCE Critical illness may be associated with the loss of normal, “health promoting” bacteria, allowing overgrowth of disease-promoting pathogenic bacteria (dysbiosis), which, in turn, makes patients susceptible to hospital-acquired infections, sepsis, and organ failure. This has significant world health implications, because sepsis is becoming a leading cause of death worldwide, and hospital-acquired infections contribute to significant illness and increased costs. Thus, a trial that monitors the ICU patient microbiome to confirm and characterize this hypothesis is urgently needed. Our study analyzed the microbiomes of 115 critically ill subjects and demonstrated rapid dysbiosis from unexpected environmental sources after ICU admission. These data may provide the first steps toward defining targeted therapies that correct potentially “illness-promoting” dysbiosis with probiotics or with targeted, multimicrobe synthetic “stool pills” that restore a healthy microbiome in the ICU setting to improve patient outcomes. Podcast: A podcast concerning this article is available.
format	article
author	Daniel McDonald Gail Ackermann Ludmila Khailova Christine Baird Daren Heyland Rosemary Kozar Margot Lemieux Karrie Derenski Judy King Christine Vis-Kampen Rob Knight Paul E. Wischmeyer
author_facet	Daniel McDonald Gail Ackermann Ludmila Khailova Christine Baird Daren Heyland Rosemary Kozar Margot Lemieux Karrie Derenski Judy King Christine Vis-Kampen Rob Knight Paul E. Wischmeyer
author_sort	Daniel McDonald
title	Extreme Dysbiosis of the Microbiome in Critical Illness
title_short	Extreme Dysbiosis of the Microbiome in Critical Illness
title_full	Extreme Dysbiosis of the Microbiome in Critical Illness
title_fullStr	Extreme Dysbiosis of the Microbiome in Critical Illness
title_full_unstemmed	Extreme Dysbiosis of the Microbiome in Critical Illness
title_sort	extreme dysbiosis of the microbiome in critical illness
publisher	American Society for Microbiology
publishDate	2016
url	https://doaj.org/article/76312f269bba46118c1dfb47667e3557
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Extreme Dysbiosis of the Microbiome in Critical Illness

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