The International Scientific Association for Probiotics and Prebiotics defines probiotics as “live microorganisms that, when given in sufficient amounts, have a beneficial effect on the health of the host” [73]. They protect the intestinal barrier, attenuate pathogen overgrowth, decrease bacterial translocation, reduce serum pro-inflammatory cytokine concentrations while increasing the serum anti-inflammatory cytokine concentrations, and induce host immunomodulation to prevent infection [74,75,76,77]. In addition, probiotics also act through pharmacokinetics. For example, gut Actinobacterium Eggerthella lenta could affect the pharmacokinetic of digoxin and reduce its toxicity in treating congestive heart failure [78]. Moreover, the probiotic E. coli strain Nissle 1917 influences the pharmacokinetics of the antiarrhythmic amiodarone and increases drug absorption [79].

Several probiotics play a role in adult intensive care [80]. Probiotic therapy significantly reduces the incidence of diarrhea, acquired infections, and VAP in critically ill patients [24,26,81]. In sepsis-induced, severe ALI, Akkermansia muciniphila (A. muciniphila) was significantly negatively correlated with TNF-α, IL-1β and IL-6, suggesting that Gut A. muciniphila plays an important role in ALI and that supplementation with A. muciniphila may be a possible therapy for ALI [82]. In addition, the combination of probiotics Bifidobacterium longum, Lactobacillus bulgaricus and Streptococcus thermophilus was more effective as an adjuvant therapy for severe and critically ill patients with COVID-19, shortening the nucleic acid conversion time, and reducing the inflammatory index such as procalcitonin and C-reactive protein [83]. Another probiotic, L. reuteri., can reduce lung inflammation and mortality of ARDS [30]. In uremic dialysis patients, oral administration of Lactobacillus acidophilus led to a decrease in serum dimethylamine, a potential uremic toxin [84]. The administration of probiotics (e.g., Bifidobacterium bifidum, Bifidobacterium catenulatum, Bifidobacterium longum, Lactobacillus plantarum) can also significantly reduce serum proinflammatory endotoxin, decrease cytokine levels, and improve life quality [85]. A double-blind clinical study has shown that the probiotics Lactobacillus rhamnosus GG or a combination application of probiotics (including streptococcus thermophiles, lactobacillus acidophilus, lactobacillus delbrueckii ssp. bulgaricus, lactobacillus paracasei, lactobacillus plantarum, Bifidobacterium longum, Bifidobacterium infantis, and Bifidobacterium breve) has beneficial effects on heart failure caused by adverse cardiac remodeling after myocardial infarction (MI). These probiotics play roles through decreasing the levels of intestinal metabolite trimethylamine N-oxide (TMAO) [34,86].

Prebiotics are substrates that can be selectively utilized by host microbes to maintain gut homeostasis and improve health outcomes. Dietary fiber (DF) is a powerful beneficial prebiotic that promotes the production of SCFAs [87].

Several prospective cohort studies have found that the use of DF in critically ill patients is effective in enhancing intestinal barrier function, reducing the systemic inflammatory response, modulating gut microbiota: increasing the abundance of the SCFAs-producing bacteria, and decreasing the level of potentially pathogenic microbiota [35]. The use of DF also improves the clinical outcomes, shortening hospital days, and reducing morbidity and mortality in critically ill patients [35]. Researchers have also found that prebiotics may ameliorate the prognosis of COVID-19 by offering anti-inflammatory nutrition, improving malnutrition, and enhancing immunity through the gut–lung microbial axis [36,37,88]. More importantly, DF-fermented SCFAs increase the production of CD103DCs, promote the differentiation of activated CD8T cells to effector cells with a memory phenotype, and improve the outcomes of anti-PD-1 immune checkpoint inhibitor therapy in patients with melanoma [89,90]. Similarly, the SCFAs produced by DF provide energy to the gut microbiota and promote the amino acids to reach the colon for absorption into the body rather than fermenting into uremic solutes [38].

In addition, flavonoid is an important class of natural products widely found in fruits which belongs to a class of plant secondary metabolites [91]. Clinical trials have demonstrated that flavonoids can upregulate the abundance of probiotics, such as Bifidobaterium and Lactobacillus, while downregulating the abundance of some pathogenic bacteria such as Staphylococcus aureus and Clostridium histolyticum [92,93]. Moreover, flavonoids can also promote the production of SCFAs [94].

Synbiotics are mixtures of probiotics and prebiotics that exert beneficial effects on the host in two main ways: enhancing the viability of probiotic microorganisms and providing specific health effects [95,96]. Probiotics stimulated by prebiotics could regulate the metabolic activity of the gut, maintain the intestinal biostructure, and promote the growth and multiplication of probiotics and its resistance to reactive oxygen species and bile salts/acids [97]. In addition, synbiotic agents modulate the innate and adaptive immune systems to reduce systemic inflammation and promote extraintestinal organ function [71,97]. Synbiotics lead to lower concentrations of adverse metabolites which results in significantly increased SCFAs levels, which may contribute to a positive effect on the host health [95].

A double-blinded controlled clinical trial demonstrates that a combination of antibiotic intervention led to a significant reduction in pharyngeal aspiration in critically ill patients and an increased level of patient consciousness [98]. In addition, for hospital-acquired infections in critically ill patients, synbiotics may be a safer and more effective way to reduce endotoxin and inflammatory markers in serum and the complications of sepsis [76,81]. Studies have shown that prophylactic synbiotics (e.g., Bifidobacterium breve strain Yakult combined with Lactobacillus casei strain Shiorta, and galactooligosaccharides) increases the number of probiotics (e.g., Bifidobacterium, Lactobacillus) in fecal bacteria and intestinal SCFA levels, especially acetate. These may modulate the gut microbiota and environment, and have preventive effects on the incidence of enterocolitis and VAP in sepsis patients [25]. Moreover, synbiotics are used to maintain a stable intestinal microbiota after SIRS and major surgery including high-risk hepatectomy, colorectal resection surgery, Roux-en-Y gastric bypass (RYGB), and sepsis-associated encephalitis (SAE) [40,99]. Synbiotics could also reduce the incidence of diseases such as VAP and healthcare-associated pneumonia, and shorten ICU length of stay [100,101]. In the late stage of intestinal disorders, supplementation with synbiotics can accelerate the recovery of the microbiota, thus preventing the development of sepsis and the onset and progression of critical diseases such as ARDS to some extent [44]. Synbiotics intake has been demonstrated to reduce plasma levels of uremic toxin and may exert nephroprotective effects [84].

Based on the above literature, the different scenarios in which FMT, SDD, probiotics, prebiotics, and synbiotics act directly by regulating the gut microbiota were summarized in Table 2.

Transfer of sterile filtrates from donor feces, rather than fecal microbiota, has been shown to be sufficient to restore normal bowel habits and eliminate symptoms [106]. Therefore, researchers speculate that gut metabolites may contribute to critical illness and dysbiosis. There is observational data that correlates critical illness, dysbiosis, and altered gut metabolites, including SCFAs, flavonoids, indole derivations, amines, bile acids, etc. [107]. In this section, several microbiota-derived metabolites and proteins therapies will be summarized.

Typically, undigested DF, as well as proteins and peptides, can be fermented by gut bacteria in the cecum and colon. The main products of these fermentative reactions are SCFAs, consisting of groups of fatty acids with less than six carbons. SCFAs include formic acid (C1), acetic acid (C2), propionic acid (C3), butyric acid (C4), and valeric acid (C5). The major SCFAs in the gut are C2, C3, and C4, accounting for more than 95% of all SCFAs [108]. SCFAs are key mediators in the regulation of myocardial tissue repair by gut microbiota [20]. Decreased microbiota abundance has been shown to alter immune cell responses to infectious damage, usually resulting in a pro-inflammatory phenotype [109], which further aggravates disease progression. Normal levels of SCFAs support the activity of innate lymphocytes, T cells, and B cells in the gut, thereby improving immune tolerance in the gut, strengthening the gut immune barrier, and enhancing its ability to clear pathogens [14,110]. Furthermore, a large proportion of gut-derived SCFAs are transported out of the gut to affect other organs through the gut–lung axis, gut–brain axis, gut–liver axis, gut–kidney axis, gut–bone axis, gut–skin axis, gut–fat axis, gut–heart axis, and so on [111,112,113,114,115,116]. Available studies have shown that gut microbiota dysbiosis and a lack of SCAFs are significantly associated with the severity of COVID-19 [45]. Therefore, maintaining healthy gut microbiota and normal levels of SCFAs contribute to critical illness prevention and prognosis. However, little is known about their therapeutic mechanism in critically ill patients, except for mouse models, so verifying the therapeutic mechanism of SCFAs in clinical trials may be a possible direction in subsequent research.

Previous work on mouse models has shown that butyrate, a specific type of SCFAs readily produced from fiber-rich diets through microbial fermentation, is critical for the maintenance of intestinal homeostasis [117]. 

In a mouse model of sepsis-associated encephalitis, butyrate is a major metabolite of intestinal microbiota and may have a neuroprotective effect in the process of sepsis through the GPR109A/Nrf2/HO-1 pathway [118].

Butyrate acid promotes the proliferation and differentiation of intestinal epithelial cells (IECs) and the synthesis of intestinal epithelial tight junction protein, such as the increased expression of Zo-1 and Occludin, reduces cell apoptosis, and inhibits intestinal permeability, resulting in enhanced intestinal mucosa mechanical barrier function [119,120]. In addition, butyrate acid enhances the intestinal mucosal immune barrier. It can maintain immune homeostasis by restoring the IRF3 signaling pathway [50]. Moreover, butyrate acid promotes the production of anti-microbial peptides (AMPs) [121]. AMPs are small molecular peptides produced by IECs with broad-spectrum antimicrobial activities, such as butyrate acid which promotes RegIIIγ and β-defensins in a GPR43-dependent manner, which play important roles in limiting bacteria and manipulating species composition [122,123]. Furthermore, butyrate acid strengthens the intestinal biological barrier function. Elevated levels of butyrate acid lowers colonic PH and inhibits the growth and colonization of pathogenic bacteria [124]. It also prevents bacterial translocation across the intestinal barrier by promoting the antimicrobial activity of intestinal macrophages [125].

As a histone deacetylase inhibitor, it affects the gene expression profile of intestinal epithelial cells and immune cells through histone deacetylases [126,127,128]. It can alter the gene expression profile of immune cells such as Treg cells, intestinal macrophages, and bone marrow-derived macrophages through G protein-coupled receptors (GPCR), affecting their response to microbial stimulation [125,129]. Butyrate acid can relieve inflammation and clinical symptoms in critically ill patients by activating Treg cells [130]. In addition to directly affecting the function of the intestine itself, butyrate acid can also affect the organs via the gut–lung axis and gut–brain axis. Studies have shown that the GPCR overlap with each other in extraintestinal or intestinal organs [131]. For example, GPR109A viewed as GPCR common to both lung and intestine can be activated by butyrate [108]. Butyrate acid affects the intestinal epithelial barrier function and immune function regulation through GPR109A, with similar effects on lung tissue (Table 3). Intraperitoneal injection of sodium butyrate acid can decrease the expression of hypermobility protein 1 (HP-1), pro-inflammatory cytokines such as tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6), and inhibit the activation of the NF-κB signaling pathway in an ALI/ARDS mouse model [60,132].

丙酸盐主要由拟杆菌属产生，在肝脏和肠道中用作糖异生底物，为机体提供能量[124]。丙酸是一种抗炎细胞因子，其在血清中的水平可预测危重症患者的严重程度和预后，并可能作为脓毒症等危重疾病的细胞因子调节标志物[144]。

醋酸盐主要来源于肠道微生物，是肠道菌群中的厌氧菌释放到肠腔内的代谢产物，然后被IEC吸收并分布到外周毛细血管[145]。近年来，在小鼠中的研究发现，醋酸盐抑制肺泡-毛细血管屏障的通透性，减少肺水肿，抑制氧化应激，抑制炎性细胞募集和炎症介质产生，调节MAPK通路激活;从而改善ALI和ARDS[146]。乙酸盐水平升高可能通过抑制内毒素和增加claudin来防止IEC易位，从而降低脓毒症的发生率[25,71,147]。

研究人员发现，与食物一起摄入的类黄酮通过肠道进入循环系统，发挥其有益作用[148]。通常，类黄酮作为代谢物被吸收，肠道菌群参与这种代谢[149,150]。类黄酮代谢产物可以通过抑制各种病原体的生长和增加有益属来塑造肠道菌群;这些可以减少内毒素，维持肠道免疫稳态，促进营养吸收[151,152]。黄酮类代谢物具有抗炎作用，在局部和全身免疫中发挥作用。在小鼠模型中，类黄酮代谢物可以通过减少肠粘膜炎症和维持肠道紧密连接屏障和结构来改善肠道屏障功能[46,153,154]。此外，类黄酮代谢物通过抑制内皮活化、NLRP3 炎症小体、toll样受体（TLR）或含溴结构域蛋白4（BRD4）以及激活核因子红系衍生的2相关因子2（Nrf2）来调节炎症介质，从而在包括SARS-CoV-2感染在内的危重疾病中恢复细胞因子风暴[47].DAT是一种类黄酮代谢产物，已被证明可以治疗小鼠的上呼吸道感染，并保护小鼠免受细菌内毒素诱导的感染性休克[155,156]。因此，研究人员提出，当危重患者和宿主感染病毒和致死细菌感染时，肠道微生物代谢产生的类黄酮代谢产物起着重要作用。

除了短链脂肪酸和类黄酮代谢物外，其他微生物群衍生的代谢物和蛋白质在维持肠粘膜平衡和治疗危重疾病方面也起着关键作用。吲哚-3-丙酸（IPA）可以调节正常小鼠的肠道菌群，增加一些益生菌（如阿克曼西科、双歧杆菌科）的水平，增强粘液屏障，并通过增加粘蛋白和杯状细胞分泌产物来减弱LPS诱导的脓毒症炎症因子[157]。对脓毒症小鼠模型的研究表明，IPA的抗炎活性可能与双歧杆菌科丰度增加和肠杆菌科扩张抑制有关，有助于降低脓毒症的死亡率[158]。在脓毒症患者血清中观察到芳香族微生物代谢物（aromatic microbial metabolites， AMM），如苯乳酸和4-羟基苯乳酸，其水平远高于正常水平[159]。一项前瞻性观察性初步研究发现，高水平AMM与危重症患者的严重程度和死亡率相关，可能成为改善危重症预后的一个可能方向[160]。研究发现，心力衰竭患者的TMAO比对照组高，这表明TMAO是心力衰竭发展的一种新的危险因素，可导致心脏肥大和心脏纤维化[161]。β-内酰胺酶主要由超广谱β内酰胺肠杆菌科产生，已被证明可以降低空肠抗生素浓度，防止抗生素到达结肠，从而减轻抗生素对肠道菌群紊乱的影响[162,163]。