**4. Microbiome-oriented therapy: how to keep balance?**

In sepsis, disturbances of physiological parameters caused directly by patient's conditions and multiple treatment-induced factors might have powerful impact on the gut microbiome. Finding a therapy aimed at restoring the balance between "beneficial" and "harmful" microorganisms is highly relevant. At present, there are several possible approaches (**Table 1**):


The undoubtful effectiveness of probiotics for correction of functional disorders of the gastrointestinal tract has been widely accepted. A randomized placebo-controlled study on 4556 healthy newborns in India proved that oral probiotics *Lactobacillus plantarum* combined with fructo-oligosaccharides during the first postnatal week helped reduce sepsis incidence during the first 60 days of life [21]. A randomized, double-blind, placebo-controlled, experimental study of changes in the microbiome and intestinal barrier in early sepsis showed that probiotic intervention successfully modulates the microbiome and is therefore a promising tool for early intervention in sepsis [22]. At the same time, there are no recommendations for the use of probiotics in ICU yet. Present studies differ due to the diseases in patients, the microorganism strains used, and the prescribed dosage of probiotics. There is no consensus concerning the beginning and duration of treatment. As for today, the largest study of efficacy of probiotics and symbiotics in ICU patients was carried out by Manzanares et al. The sample of over 2700 patients demonstrated that the use of probiotics for microbiota recovery reduced incidence of infectious complications (specifically, ventilation-associated pneumonias); it was possible to reduce the use of antibiotics without increasing mortality or length of stay in ICU [23].

In another study, the use of symbiotics as an adjuvant therapy in surgical patients reduced incidence of such postoperative complications as wound infection [24]. One of the reasons for doubts concerning expediency of applying probiotics in ICU is intestinal barrier failure in critically ill patients. The translocation of bacteria to systemic blood flow and lymph is known to promote a complex chain of events leading to multiple organ failure [34]. On this


and simulate experimental changes in the internal environment of a person that occur with a radical "restructuring" of the microbiome in seriously ill patients. This approach opens new prospects for an objective monitoring of diseases, carrying out an assessment of the integral metabolic profile on common metabolites (particularly aromatic) within a given time, and

In sepsis, disturbances of physiological parameters caused directly by patient's conditions and multiple treatment-induced factors might have powerful impact on the gut microbiome. Finding a therapy aimed at restoring the balance between "beneficial" and "harmful" microorganisms is highly relevant. At present, there are several possible approaches (**Table 1**):

• Increase the "beneficial" microorganisms using pro-, pre-, and/or metabiotics.

• Improve the composition by transplantation of fecal microbiota transplantation (FMT).

• Suppress "harmful" microorganisms, and create favorable conditions for recovery of one's own "beneficial" microorganisms using selective antibacterial drugs (similar selective

The undoubtful effectiveness of probiotics for correction of functional disorders of the gastrointestinal tract has been widely accepted. A randomized placebo-controlled study on 4556 healthy newborns in India proved that oral probiotics *Lactobacillus plantarum* combined with fructo-oligosaccharides during the first postnatal week helped reduce sepsis incidence during the first 60 days of life [21]. A randomized, double-blind, placebo-controlled, experimental study of changes in the microbiome and intestinal barrier in early sepsis showed that probiotic intervention successfully modulates the microbiome and is therefore a promising tool for early intervention in sepsis [22]. At the same time, there are no recommendations for the use of probiotics in ICU yet. Present studies differ due to the diseases in patients, the microorganism strains used, and the prescribed dosage of probiotics. There is no consensus concerning the beginning and duration of treatment. As for today, the largest study of efficacy of probiotics and symbiotics in ICU patients was carried out by Manzanares et al. The sample of over 2700 patients demonstrated that the use of probiotics for microbiota recovery reduced incidence of infectious complications (specifically, ventilation-associated pneumonias); it was possible to reduce the use of antibiotics without increasing mortality or length of stay in ICU [23].

In another study, the use of symbiotics as an adjuvant therapy in surgical patients reduced incidence of such postoperative complications as wound infection [24]. One of the reasons for doubts concerning expediency of applying probiotics in ICU is intestinal barrier failure in critically ill patients. The translocation of bacteria to systemic blood flow and lymph is known to promote a complex chain of events leading to multiple organ failure [34]. On this

• Use a combination of probiotics and prebiotics known as symbiotics.

digestive decontamination).

30 Infectious Process and Sepsis

will provide new targets for therapeutic effects in the future.

**4. Microbiome-oriented therapy: how to keep balance?**


study with lethal combination of proteolytic enzymes of pancreas and high level of lactic acid caused by bacterial fermentation of carbohydrates as a key factor related to intake of probiotics. Nevertheless, authors suggest that a probiotic therapy may not be counterindicated for the prevention of secondary infections associated with acute pancreatitis, provided that future clinical studies start probiotic therapy early as possible and prevent bacterial overgrowth not only of patient's own intestinal flora but also the dose of probiotic bacteria [38]. An alternative to probiotics, "smart" direction, is infusion of liquid filtrate of feces from healthy fecal microbiota transplantation. The potential advantage of this method is enlargement of microbial biodiversity and the presence of biologically active substances and metabolites, which might assist a longer effect of microbiota recovery [39]. This procedure has been successfully used for treating the severe infection caused by *Clostridium difficile* in more than 1000 patients [26]. The recent meta-analysis (n = 284) has shown that FMT is significantly more effective in the treatment of such patients compared to the control group in spite of heterogeneity of groups due to the study sites (Europe vs. North America) and method of administration [27]. However, the current experience of FMT application in ICU is limited just to a few patients described only in sporadic publications [28]. The limited quantity of data, absence of objective criteria for efficacy evaluation, and insufficient knowledge of microbiota composition dynamics and its metabolic activity preclude wide application of this method in such vulnerable group of patients. The FDA does not currently approve of any use of fecal transplants. Two patients contracted severe infections, and one of them died, from fecal transplants that contained drug-resistant bacteria [29]. Putting it in another way, given the knowledge and risks, the use of FMT in critically ill patients can be compared to the first blood

Microbiota-Oriented Diagnostics and Therapy in Sepsis: Utopia or Necessity?

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33

We assume that the main efforts in fighting infection should be directed to decrease microbial metabolic activity. Considering that the intestine is the main reservoir of bacteria and therefore the main source of bacterial metabolites, it seems appropriate to correct the activity of intestinal microbiota in patient with infection. Enteral correction of the metabolic activity of

Selective digestive decontamination (SDD) is often considered a prophylactic mode of antibiotic therapy allowing targeted prevention of bowel colonization by "pathogenic" microorganisms. The effect is achieved thanks to the selective impact on potentially pathogenic aerobic and facultative aerobic bacteria by means of enteral administration of antibacterial drugs that do not suppress anaerobic microorganisms, thus creating conditions for recovery of microbiota balance and assisting its functioning even in the unfavorable environment in ICU. Currently, numerous clinical studies and meta-analyses have shown that SDD helps prevent hospital infection in ICU and reduce mortality [30]. Wide implementation of SDD was restricted, inter alia, because of fears of increasing resistance of nosocomial microorganisms to antibiotics [31]; however, convincing data have been obtained confirming the absence of resistant bacterial growth at the background of selective decolonization. A number of major investigations are currently underway, and their authors are expected to give shortly new clinical recommendations concerning the use of this method in ICU [32]. The pronounced clinical effect may be associated with a change in the profile of microbial metabolites, which

intestinal microbiota contributes to the improvement of the patients' state [33].

transfusion before the opening of the ABO system [19].

requires additional research.

**Table 1.** Generalized data on the possible current use of microbiome therapy.

basis, the use of live bioculture drugs (probiotics) in critically ill patients looks far from harmless and even dangerous. Possible, a NGS-based approach for the detection of bacteremia in patients with sepsis, which has shown promising results, will be a key step in the clinical use of NGS in this indication [35]. In randomized double-blind placebo-controlled independent study on severe acute pancreatitis patients (n = 298)—Probiotics in Pancreatitis Trial (PROPATRIA)—1 group (n = 153), for prophylaxis of suppurative complications received a biomedicine containing 4 species of lactic bacterial (*L. acidophilus*, *L. casei*, *L. salivarius*, *L. lactis*) and 2 species of bifid bacteria (*B. bifidum*, *B. lactis*) in a dose of 1010 daily, while the control group (n = 145) received placebo. The results disappointed the researches: in the group of patients who received probiotics, more severe course of the disease was recorded, necrotizing pancreatitis developed more frequently, secondary bacteremia and other infectious complications occurred, multiple organ failure developed reliably more frequently, and mortality was higher (р = 0.01). The authors of the study were unable to provide convincing explanations but expressed their doubts concerning reasonability for use of probiotics in critically ill patients [25].

In our opinion, the use of live microbial cultures of lactic acid bacteria might have aggravated metabolic disturbances and led to adverse consequences in initially severe patients, in particular, because of excessive production of PhLA and p-HPhLA which are typical metabolites of bifido- and lactic bacteria [36, 37]. A group of authors who used probiotics with positive effect in short bowel syndrome patients have reached similar conclusions, namely, the importance of metabolic status evaluation. The colleagues associated high mortality in PROPATRIA study with lethal combination of proteolytic enzymes of pancreas and high level of lactic acid caused by bacterial fermentation of carbohydrates as a key factor related to intake of probiotics. Nevertheless, authors suggest that a probiotic therapy may not be counterindicated for the prevention of secondary infections associated with acute pancreatitis, provided that future clinical studies start probiotic therapy early as possible and prevent bacterial overgrowth not only of patient's own intestinal flora but also the dose of probiotic bacteria [38].

An alternative to probiotics, "smart" direction, is infusion of liquid filtrate of feces from healthy fecal microbiota transplantation. The potential advantage of this method is enlargement of microbial biodiversity and the presence of biologically active substances and metabolites, which might assist a longer effect of microbiota recovery [39]. This procedure has been successfully used for treating the severe infection caused by *Clostridium difficile* in more than 1000 patients [26]. The recent meta-analysis (n = 284) has shown that FMT is significantly more effective in the treatment of such patients compared to the control group in spite of heterogeneity of groups due to the study sites (Europe vs. North America) and method of administration [27]. However, the current experience of FMT application in ICU is limited just to a few patients described only in sporadic publications [28]. The limited quantity of data, absence of objective criteria for efficacy evaluation, and insufficient knowledge of microbiota composition dynamics and its metabolic activity preclude wide application of this method in such vulnerable group of patients. The FDA does not currently approve of any use of fecal transplants. Two patients contracted severe infections, and one of them died, from fecal transplants that contained drug-resistant bacteria [29]. Putting it in another way, given the knowledge and risks, the use of FMT in critically ill patients can be compared to the first blood transfusion before the opening of the ABO system [19].

We assume that the main efforts in fighting infection should be directed to decrease microbial metabolic activity. Considering that the intestine is the main reservoir of bacteria and therefore the main source of bacterial metabolites, it seems appropriate to correct the activity of intestinal microbiota in patient with infection. Enteral correction of the metabolic activity of intestinal microbiota contributes to the improvement of the patients' state [33].

basis, the use of live bioculture drugs (probiotics) in critically ill patients looks far from harmless and even dangerous. Possible, a NGS-based approach for the detection of bacteremia in patients with sepsis, which has shown promising results, will be a key step in the clinical use of NGS in this indication [35]. In randomized double-blind placebo-controlled independent study on severe acute pancreatitis patients (n = 298)—Probiotics in Pancreatitis Trial (PROPATRIA)—1 group (n = 153), for prophylaxis of suppurative complications received a biomedicine containing 4 species of lactic bacterial (*L. acidophilus*, *L. casei*, *L. salivarius*, *L. lactis*) and 2 species of bifid bacteria (*B. bifidum*, *B. lactis*) in a dose of 1010 daily, while the control group (n = 145) received placebo. The results disappointed the researches: in the group of patients who received probiotics, more severe course of the disease was recorded, necrotizing pancreatitis developed more frequently, secondary bacteremia and other infectious complications occurred, multiple organ failure developed reliably more frequently, and mortality was higher (р = 0.01). The authors of the study were unable to provide convincing explanations but expressed their doubts concerning reasonability for use of probiotics in

**Study Population Type of intervention Results**

10 ICU patients SDD The limited risks for

Enteral correction of the metabolic activity of the gut microbiota

SDD Favorable effect on

SDD SDD reduces ventilator-

mortality, with a direct evidence odds ratio of 0.73 (95% confidence interval 0.64 to 0.84)

antibiotic resistance SDD related

associated pneumonia (odds ratio (OR) = 0.28; 95% confidence interval (CI) = 0.20–0.38) and mortality (OR = 0.73; CI = 0.64–0.84)

The downward trend of mortality by 11%

Meta-analysis of 29 articles that enrolled patients in general intensive care units

Meta-analysis of 37 trials (involving more than 7000 patients)

56 patients with pneumonia or abdominal infection

Antimicrobial therapy under the control of the metabolic activity of the gut microbiota

**Table 1.** Generalized data on the possible current use of microbiome therapy.

In our opinion, the use of live microbial cultures of lactic acid bacteria might have aggravated metabolic disturbances and led to adverse consequences in initially severe patients, in particular, because of excessive production of PhLA and p-HPhLA which are typical metabolites of bifido- and lactic bacteria [36, 37]. A group of authors who used probiotics with positive effect in short bowel syndrome patients have reached similar conclusions, namely, the importance of metabolic status evaluation. The colleagues associated high mortality in PROPATRIA

critically ill patients [25].

SDD

☺ Price et al.

32 Infectious Process and Sepsis

☺ Buelow et al.

☺ Webster et al.

☺ Beloborodova

[30]

[31]

[32]

and Sarshor [33]

> Selective digestive decontamination (SDD) is often considered a prophylactic mode of antibiotic therapy allowing targeted prevention of bowel colonization by "pathogenic" microorganisms. The effect is achieved thanks to the selective impact on potentially pathogenic aerobic and facultative aerobic bacteria by means of enteral administration of antibacterial drugs that do not suppress anaerobic microorganisms, thus creating conditions for recovery of microbiota balance and assisting its functioning even in the unfavorable environment in ICU. Currently, numerous clinical studies and meta-analyses have shown that SDD helps prevent hospital infection in ICU and reduce mortality [30]. Wide implementation of SDD was restricted, inter alia, because of fears of increasing resistance of nosocomial microorganisms to antibiotics [31]; however, convincing data have been obtained confirming the absence of resistant bacterial growth at the background of selective decolonization. A number of major investigations are currently underway, and their authors are expected to give shortly new clinical recommendations concerning the use of this method in ICU [32]. The pronounced clinical effect may be associated with a change in the profile of microbial metabolites, which requires additional research.

underestimation earned it a name of "forgotten organ." In the past decades, the number of studies of microbiota in various diseases, including sepsis, has increased drastically and is likely to keep rising. Now it is clear that the "forgotten organ" is a reservoir of pathogens and possibly of genes associated with antibiotic resistance, as well as a marker of disease severity and outcome. Therapy aimed at restoring microbiota equilibrium rather than blindly prescribing broad-spectrum antibiotics may be the best choice. Understanding the metabolic language of microorganisms will serve as a catalyst for the development of new strategies, which will be especially important in the era of antibiotic resistance. New, culturally independent technologies allowing a fast accurate and comprehensive assessment of microbiome will be adapted in the coming years for practical use and wide application. Characterization of changes in ICU patient's microbiome will enable advancement in the development of diagnostic and therapeutic interventions based on changes

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35

We used gas chromatography-mass spectrometry (GC-MS) method to quantify metabolites in human serum from septic patients and healthy volunteers. For taxonomic identification of samples, Ion 16S Metagenomics Kits, Ion Reporter metagenomic workflow solution, and Ion Torrent sequencing systems were used. Clinical and laboratory data and APACHE II and SOFA scores in patients were matched. Data were compared by Mann-Whitney U test;

not only in the microbiota's composition but also in its metabolic profile as well.

p-values less than 0.05 were considered significant.

Ekaterina Chernevskaya\* and Natalia Beloborodova\*

\*Address all correspondence to: kate.chernevskaya@gmail.com

Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology,

ICU. Critical Care. 2018;**22**(1):78. DOI: 10.1186/s13054-018-1999-8

[1] Wolff NS, Hugenholtz F, Wiersinga WJ. The emerging role of the microbiota in the

[2] Haak BW, Wiersinga WJ. The role of the gut microbiota in sepsis. The Lancet Gastroenterology and Hepatology. 2017;**2**:135-143. DOI: 10.1016/S2468-1253(16)30119-4

[3] Beloborodova NV, Grechko AV, Olenin AY. Metabolomic discovery of microbiota dysfunction as the cause of pathology. IntechOpen. [Online First] 26 June 2019. DOI:

**6. Methods**

**Author details**

Moscow, Russia

**References**

and nvbeloborodova@yandex.ru

**Figure 4.** Factors affecting the metabolism of microbiota in ICU [41].

As shown above, the "harmful/beneficial" gut bacteria disbalance is frequently associated with nosocomial pathogens and adverse outcome. The influence of negative factors related to changed internal environment of the macroorganism, and rather aggressive therapy leads to a drastic change in the species diversity of microbiota [40] and, as a consequence, a disturbance of functional activity of microbial community and a development of the maximal disorders that may cause irreversible breakdowns of homeostasis and host body death. A "vicious circle" is created: disturbance of gut microbiome function in critically ill patients leads to overproduction of certain microbial metabolites, which, in turn, have pathological impact on macroorganism's organs and systems (**Figure 4**).

Two potential points of effect in sepsis treatment can be identified as:

