Critically ill patients demonstrate large interpersonal variation in intestinal microbiota dysregulation: a pilot study

Abstract

Purpose: The intestinal microbiota has emerged as a virtual organ with essential functions in human physiology. Antibiotic-induced disruption of the microbiota in critically ill patients may have a negative influence on key energy resources and immunity. We set out to characterize the fecal microbiota composition in critically ill patients both with and without sepsis and to explore the use of microbiota-derived markers for clinical outcome measurements in this setting.

Methods: In this prospective observational cohort study we analyzed the fecal microbiota of 34 patients admitted to the intensive care unit. Fifteen healthy subjects served as controls. The fecal microbiota was phylogenetically characterized by 16S rRNA gene sequencing, and associations with clinical outcome parameters were evaluated.

Results: A marked shift in fecal bacterial composition was seen in all septic and non-septic critically ill patients compared with controls, with extreme interindividual differences. In 13 of the 34 patients, a single bacterial genus made up >50% of the gut microbiota; in 4 patients this was even >75%. A significant decrease in bacterial diversity was observed in half of the patients. No associations were found between microbiota diversity, Firmicutes/Bacteroidetes ratio, or Gram-positive/Gram-negative ratio and outcome measurements such as complications and survival.

Conclusions: We observed highly heterogeneous patterns of intestinal microbiota in both septic and non-septic critically ill patients. Nevertheless, some general patterns were observed, including disappearance of bacterial genera with important functions in host metabolism. More detailed knowledge of the short- and long-term health consequences of these major shifts in intestinal bacterial communities is needed.

Keywords: Antibiotics; Critically ill; Gut microbiota; Intensive care unit; Sepsis.

Fig. 1

High interindividual diversity in fecal microbiota composition at the phylum level in both septic and non-septic critically ill patients. A single fecal sample was collected from septic and non-septic intensive care unit (ICU) patients and healthy subjects. Total bacterial 16S rDNA was isolated and sequenced to investigate the bacterial composition of these samples. Each bar represents the microbiota composition of one individual patient (patient number indicated at bottom of each bar) at the phylum level, which is the highest bacterial taxonomic rank. Data are presented as the percentage of total 16S rDNA reads in each sample; colors indicate different phyla. Patients are grouped according to their main diagnosis. Table shows which classes of antibiotics each patient received during their stay in the intensive care unit prior to fecal sampling. Topical P/T/A Topical application of polymyxin E, tobramycin, and amphotericin B. None of the healthy subjects had received antibiotics for at least 12 months prior to fecal sampling

Fig. 2

High interindividual diversity in septic critically ill patients with sepsis. a Pearson correlations were calculated to investigate the level of similarity in microbiota composition between patients with a critical illness of different origin (sepsis originating from lung, abdomen, urinary tract, or other location and non-septic critical illness). Patient groups are indicated by colors. Healthy individuals are depicted as additional control group. Data are presented as mean ± standard deviation. *p < 0.05, **p < 0.001 vs. healthy controls; p = 0.0005 for all septic patients vs. healthy controls. b A canonical correspondence analysis to deduce the major driving forces (Axis 1, Axis 2) in the variability within the microbial data of all ICU patients, thereby indicating whether samples are alike (in close proximity to each other) or not (increased distance). The variance is indicated as percentages. Symbols/colors represent patient groups as indicated (see a)

Fig. 3

Decreased intestinal microbiota diversity in critically ill patients is not associated with survival in an exploratory setting. a Microbiota diversity, presented as the Shannon index, was calculated from 15 healthy subjects, as well as from all 34 critically ill patients. Data are presented as dot plot with the mean (solid horizontal line). ****p < 0.0001. b Shannon diversity from all 34 patient samples plotted against the number of different antibiotic classes (categorized as in Fig. 1) that a patient had received prior to fecal sampling. c Based on the range in diversity in healthy subjects, the patient cohort was split into two groups: Shannon index <4 (normal diversity) and Shannon index >4 (high diversity), for which a 90-day Kaplan–Meier survival plot is shown. Numbers below the curve Patients at risk per group

Fig. 4

Firmicutes/Bacteroidetes ratio (F/B-ratio) and Gram-positive/Gram-negative bacteria ratio are not associated with short- and long-term survival in an exploratory setting. a The F/B-ratio was calculated from healthy subjects (dotted horizontal lines range of F/B-ratio in healthy subjects) and from all 34 critically ill patients. and plotted against survival at 4 time points. b Survival data were collected at four time points: during ICU stay (ICU) and at 30 and 90 days and 1 year (d30, d90, 1y, respectively). c The ratio of total Gram-positive/Gram-negative bacteria was calculated from healthy subjects (dotted horizontal lines range of ratio of Gram-positive/Gram-negative bacteria in health subjects. d Survival data collected at same time points as for b. b, d Data are presented as box-and-whisker plots, with median (horizontal line in box), interquartile range (ends of box), and range (whiskers). Black boxes Healthy subjects, white boxes surviving ICU patients, gray boxes non-surviving ICU patients