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Title: Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness

Journal Article · · mBio (Online)
 [1];  [2];  [3];  [3];  [1];  [1];  [1];  [3];  [4];  [1];  [1]
  1. Univ. of Chicago, Chicago, Illinois, (United States)
  2. Argonne National Lab. (ANL), Argonne, IL (United States); Baylor College of Medicine, Houston, TX (United States)
  3. Michigan State Univ., East Lansing, Michigan, (United States)
  4. Univ. of Chicago, Chicago, Illinois, (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
+ Show Author Affiliations

We analyzed the 16S rRNA amplicon composition in fecal samples of selected patients during their prolonged stay in an intensive care unit (ICU) and observed the emergence of ultra-low-diversity communities (1 to 4 bacterial taxa) in 30% of the patients. Bacteria associated with the genera Enterococcus and Staphylococcus and the family Enterobacteriaceae comprised the majority of these communities. The composition of cultured species from stool samples correlated to the 16S rRNA analysis and additionally revealed the emergence of Candida albicans and Candida glabrata in ~75% of cases. Four of 14 ICU patients harbored 2-member pathogen communities consisting of one Candida taxon and one bacterial taxon. Bacterial members displayed a high degree of resistance to multiple antibiotics. The virulence potential of the 2-member communities was examined in C. elegans during nutrient deprivation and exposure to opioids in order to mimic local conditions in the gut during critical illness. Under conditions of nutrient deprivation, the bacterial members attenuated the virulence of fungal members, leading to a “commensal lifestyle.” However, exposure to opioids led to a breakdown in this commensalism in 2 of the ultra-low-diversity communities. Application of a novel antivirulence agent (phosphate-polyethylene glycol [Pi-PEG]) that creates local phosphate abundance prevented opioid-induced virulence among these pathogen communities, thus rescuing the commensal lifestyle. To conclude, the gut microflora in critically ill patients can consist of ultra-low-diversity communities of multidrug-resistant pathogenic microbes. Local environmental conditions in gut may direct pathogen communities to adapt to either a commensal style or a pathogenic style.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH); Argonne National Laboratory; USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22), Materials Sciences and Engineering Division
Grant/Contract Number:
AC02-06CH11357
OSTI ID:
1214650
Alternate ID(s):
OSTI ID: 1392642
Journal Information:
mBio (Online), Vol. 5, Issue 5; ISSN 2150-7511
Publisher:
American Society for MicrobiologyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 197 works
Citation information provided by
Web of Science

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Critically ill patients demonstrate large interpersonal variation in intestinal microbiota dysregulation: a pilot study journal November 2016
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Fecal microbiota transplantation in the ICU: perspectives on future implementations journal May 2019
Medium chain unsaturated fatty acid ethyl esters inhibit persister formation of Escherichia coli via antitoxin HipB journal August 2018
Metagenomic Analysis Reveals Dynamic Changes of Whole Gut Microbiota in the Acute Phase of Intensive Care Unit Patients journal December 2015
Morphine Promotes Colonization of Anastomotic Tissues with Collagenase - Producing Enterococcus faecalis and Causes Leak journal August 2016
Pseudomonas aeruginosa Colonization in the Intensive Care Unit: Prevalence, Risk Factors, and Clinical Outcomes journal February 2016
Enrichment of the lung microbiome with gut bacteria in sepsis and the acute respiratory distress syndrome journal July 2016
The gut microbiota and gastrointestinal surgery journal October 2016
Antibiotic treatment for Tuberculosis induces a profound dysbiosis of the microbiome that persists long after therapy is completed journal September 2017
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Remodeling gut microbiota by Streptococcus thermophilus 19 attenuates inflammation in septic mice posted_content January 2020
Systematic gene overexpression in Candida albicans identifies a regulator of early adaptation to the mammalian gut journal August 2018
Consensus and contentious statements on the use of probiotics in clinical practice: A south east Asian gastro-neuro motility association working team report: Consensus contentious probiotic clinical use journal June 2018
Mycobacterium tuberculosis , antimicrobials, immunity, and lung–gut microbiota crosstalk: current updates and emerging advances journal January 2020
Collagen degradation and MMP9 activation by Enterococcus faecalis contribute to intestinal anastomotic leak journal May 2015
What Is a Host? Incorporating the Microbiota into the Damage-Response Framework: TABLE 1 journal November 2014
Plasmid Dynamics in KPC-Positive Klebsiella pneumoniae during Long-Term Patient Colonization journal June 2016
Mice Fed an Obesogenic Western Diet, Administered Antibiotics, and Subjected to a Sterile Surgical Procedure Develop Lethal Septicemia with Multidrug-Resistant Pathobionts journal July 2019
Extreme Dysbiosis of the Microbiome in Critical Illness journal August 2016
Rectal and Naris Swabs: Practical and Informative Samples for Analyzing the Microbiota of Critically Ill Patients journal June 2018
Hospitalization Type and Subsequent Severe Sepsis journal September 2015
Gut microbiome patterns correlate with higher postoperative complication rates after pancreatic surgery journal February 2019
Serum indoxyl sulfate is associated with mortality in hospital-acquired acute kidney injury: a prospective cohort study journal February 2019
Microbial dysbiosis and mortality during mechanical ventilation: a prospective observational study journal December 2018
The emerging role of the microbiota in the ICU journal March 2018
Dysbiosis of the intestinal microbiota in neurocritically ill patients and the risk for death journal May 2019
Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients journal February 2017
Disruption of the microbiota across multiple body sites in critically ill children journal December 2016
Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects journal August 2017
Gut integrity in critical illness journal March 2019
Manipulation of the microbiome in critical illness—probiotics as a preventive measure against ventilator-associated pneumonia journal July 2019
Sepsis therapies: learning from 30 years of failure of translational research to propose new leads journal March 2020
Spinal cord injury and the human microbiome: beyond the brain–gut axis journal March 2019
Therapeutic Potential of the Gut Microbiota in the Prevention and Treatment of Sepsis journal September 2018
Microbiota-Immune Interaction in the Pathogenesis of Gut-Derived Infection journal August 2019
A Review of Traumatic Brain Injury and the Gut Microbiome: Insights into Novel Mechanisms of Secondary Brain Injury and Promising Targets for Neuroprotection journal June 2018
Metagenome Analysis as a Tool to Study Bacterial Infection Associated with Acute Surgical Abdomen journal October 2018
A Systematic Review, Meta-Analysis, and Meta-Regression Evaluating the Efficacy and Mechanisms of Action of Probiotics and Synbiotics in the Prevention of Surgical Site Infections and Surgery-Related Complications journal December 2018
The Importance of the Microbiome in Critically Ill Patients: Role of Nutrition journal December 2019
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The Emerging Role of the Microbiota in the ICU book January 2018
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TGF ‐β1 improves mucosal IgA dysfunction and dysbiosis following intestinal ischaemia–reperfusion in mice journal January 2016
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