Introduction {#S1}
============

Microbes that inhabit in both gut and lung live in a mutualistic manner with the host. They benefit from a stable nutrient-rich microenvironment and also exert important functions such as fermentation of dietary components. Increasing evidence indicates the critical role of constitutive sensing of microbes and their metabolites to maintain the homeostasis of the immune system ([@B11]). In the microbial communities of gut, Bacteroidetes and Firmicutes are predominant while Bacteroidetes, Firmicutes, and Proteobacteria predominate in the lung. At the phylum level, the predominant microbial communities are similar in gut and lung ([@B75]). However, in terms of species level, they are significantly different. As the largest and most diverse community of the mammalian microbiome, there are about 10^14^ bacteria colonize in the intestinal tract, which have been studied most extensively ([@B44]). Emerging evidence has revealed that dysbiosis of gut microbiota is associated with various local and distant chronic diseases. A balanced microbial community in the gut is of great importance in immune function and health ([@B76]). The gut microbiota has been shown to affect pulmonary immunity through a vital cross-talk between gut microbiota and the lungs, which is referred to as gut--lung axis ([@B56]). This axis allows for the passage of endotoxins, microbial metabolites, cytokines, and hormones into the bloodstream connecting the gut niche with that one of the lung. Notably, the gut--lung axis is bidirectional, as shown in [Figure 1](#F1){ref-type="fig"}. When the inflammation occurring in the lung, the lung-gut axis can induce changes in the blood and gut microbiota ([@B25]).

![The cross-talk between gut and lung.](fmicb-11-00301-g001){#F1}

An emerging area of intense interest is the role of gut--lung axis in the pathogenesis of lung diseases ([@B11]). Increasing studies indicated that alterations in the gut microbial species and metabolites have been linked to changes in immune responses and inflammation as well as the disease development in the lungs. For example, the risk of developing allergic airway disease increased due to antibiotic-caused changes in the gut microbiota in early life, facilitating our understanding of the links between exposure to microbiota and airway allergy ([@B83]; [@B95]). The mechanisms by which the gut microbiota influences on the immune responses and inflammation in the lungs, and vice versa, are being extensively studied. The involvement of regulatory T cell subsets ([@B85]; [@B63]; [@B72]) and Toll-like receptors (TLRs) ([@B84]; [@B116]), inflammation cytokines and mediators ([@B98]), surfactant protein D ([@B24]) and several other factors have been proposed as the underlying mechanisms, but many details unknown. Nevertheless, novel therapeutic strategies that target manipulation of gut microbiome by anti-biotics, probiotics, prebiotics, natural products, or diets have been attempted in various lung diseases by clinical and laboratory studies. In present article, we summarize the emerging role of gut--lung axis in a variety of common lung diseases, review the therapeutic strategies targeting manipulation of gut microbiome. We aim to update the information and evidence of this hot field, highlighting gaps in our knowledge and the potential for treatment of lung diseases via gut--lung axis.

The Pathogenic Role of Gut Microbiota in Common Lung Diseases {#S2}
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Asthma {#S2.SS1}
------

Asthma is a common chronic respiratory diseases, which affects people of all ages but usually begins in childhood. It is a complex disease having multiple phenotypes with different pathophysiological and clinical characteristics ([@B35]; [@B13]). Since immunity has been recognized to play a vital role in the pathogenesis of asthma, such as the involvement of regulatory T cell subsets and TLRs, a link between gut microbes and allergy was hypothesized. This hypothesis was gradually verified via the finding of increased asthma risk due to antibiotic exposure in the first year of life ([@B77]; [@B103]). The immune alterations driven by microbial indicate that microbial exposures would affect the risk of asthma ([@B52]). In a study, it was found that 1-year-old children born to asthmatic mothers with an immature microbial composition had higher risk of asthma at age 5 years. This finding suggested that deficiency of microbial stimulation at the beginning of life might induce the inherited asthma risk, and sufficient maturation of the gut microbiome in this period may be beneficial to prevent ([@B104]). Low total diversity of the gut microbiota of infant during the first month of life was associated with asthma development in children at 7 years old ([@B1]). The diversity of the gut microbial in early life may avoid airway inflammation in asthma via mediating the balance of Th1/Th2 ([@B90]).

Then emerging evidence shows that maturation patterns of the gut microbiome affect the asthma risk for children. In a study, bacterial DNA isolated from the stool samples from 92 children diagnosed with asthma and 88 healthy children were detected. *Akkermansia muciniphila* and *Faecalibacterium prausnitzii* were found to be decreased in asthma group compared to healthy group. Both bacterial species may suppress inflammation via modulating secreted metabolites, such as increased IL-10 and decreased IL-12 ([@B22]). The levels of inflammatory factors including C-reactive protein (CRP), tumor necrosis factor-alpha (TNF-α), and interleukin-6 (IL-6) in peripheral serum of children with asthma were significantly higher than those in the controls. In particular, CRP was correlated positively with the total load of intestinal bacteria and gastrointestinal symptom rating scale (GSRS) scores, indicating that with the increased levels of inflammatory factors in peripheral serum, the likelihood of gut dysbiosis and gastrointestinal incommensurate symptoms will rises in children with asthma ([@B121]). In addition to the altered constituent of gut microbiota, the change of related metabolites has also been noted. A significant reduction of the total content of the fatty acids and the absolute concentrations of the specific acids including acetate, butyrate and propionate, as well as the content of isoacids in the feces from patients with bronchial was observed compared to normal controls ([@B49]). The gut microbiota patterns in adults with diagnosed asthma have also been studied. In a pilot study, significant relationships between gut microbiota composition, aeroallergen sensitization and lung function in asthmatic and non-asthmatic adults were observed ([@B6]).

The mechanism by which gut microbiota influence the initiation and development of asthma, however, remains largely unknown. The microbes, bile salts and other immune stimuli from the digestive tract might play a vital role in mucosal immunity of the respiratory system ([@B7]). The epithelial mucosa and dendritic cells as well as antimicrobial peptides secreted by immune cells are major effectors in the response to environmental agents in the airway lumen ([@B27]). The epithelium controls the local respiratory immune activities that are also mediated by thymic stromal lymphopoietin, IL-25 and IL-33, which might lead to a Th2 type inflammation, thus facilitating the development of asthma ([@B34]). The gut microbiome contributes to the generation of Tregs, making the lung more susceptible to oral allergens ([@B88]). Tregs generated in the periphery, known as induced Tregs (iTreg), are predominantly stimulated in the mesenteric lamina propria Peyer's patches, and lymph nodes of the small and large intestines ([@B53]). Increasing evidence suggested that gut microbiome has an important role in coordinating both the innate and adaptive immunity that is involved in the development of asthma, whereas the underlying molecular mechanisms are needed to be further identified ([Figure 2](#F2){ref-type="fig"}).

![The potential role of gut--lung axis in asthma.](fmicb-11-00301-g002){#F2}

Chronic Obstructive Pulmonary Disease (COPD) {#S2.SS2}
--------------------------------------------

Chronic obstructive pulmonary disease (COPD) is a prevalent chronic inflammatory lung disease that causes obstructed airflow resulting from chronic aeropollutant exposure, primarily from smoking ([@B91]). Increasing evidence indicated that gut-liver-lung axis plays a vital role in the pathogenesis of COPD ([@B118]). The liver is a key organ to orchestrate innate immunity and participates actively in innate immune responses in other sites including gut and lung through generation of inflammatory cytokines and mediators ([@B48]; [@B51]). The elevated systemic inflammatory mediators due to overactive innate immune responsiveness, such as C-reactive protein (CRP) and IL-6, directly contributes to both morbidity and mortality in COPD. IL-6 activates the innate immune response to maintain the systematic inflammation as part of the normal immune in response to smoking or bacterial invasion exposure. In response to elevated serum IL-6, acute-phase proteins such as CRP is generated within the liver ([@B48]). Liver might amplify innate immune responsiveness in respiratory system when exposes to bacteria or smoking through facilitating alveolar macrophage release of IL-6 and acute-phase proteins.

Then, growing evidence suggested that gut is linked to the lungs and liver via dietary factors ([@B61]). Epidemiological studies found that a diet containing rich fiber was associated with decreased risk of COPD and better lung function ([@B54]; [@B111]). Fiber is the remaining substance in food that cannot be digested by the body, acting as a source of nutrition for most of the beneficial bacteria in the intestine. Its major physiology function is enhancing the activity of beneficial bacteria in the gut and maintaining intestinal health ([@B60]). Thus, gut and resident microbiota may play an essential role in the pathogenesis underlying COPD. The mechanism underlying the protective effect of high-fiber diets on COPD might be associated with modulation of innate immunity and systemic inflammation, epithelial integrity from microbial invasion, and stimulating beneficial bacteria to generate small chain fatty acids (SCFAs) ([@B54]; [@B111]; [@B87]; [@B16]; [@B73]). Among subjects with smoking exposure, lung function was improved via increased intake of dietary fiber, further supporting the vital role of gut-liver-lung axis in COPD ([Figure 3](#F3){ref-type="fig"}).

![The gut-liver-lung axis in COPD.](fmicb-11-00301-g003){#F3}

The change of gut microbiome and function of intestinal mucosal barrier was observed in COPD by experimental and clinical studies. In contrast to control subjects, the gut microbiota in COPD patients is characterized by the presence of representatives of the Pro-teobacteria, such as *Enterobacter cloacae*, *Citrobacter*, *Eggerthella*, *Pseudomonas*, *Anaerococcus*, *Proteus*, *Clostridium difficile*, and *Salmonella* ([@B14]). In a COPD rat model exposure to cigarette smoke for 6 months, structural and dysfunctional changes in the intestinal mucosal barrier were observed, associating with the aggravated intestinal inflammatory responses ([@B117]). Additionally, COPD has a high associated risk for cardiovascular disease and death due to an infectious cause. The gut, microflora-dependent metabolite trimethylamine-*N*-oxide (TMAO), as a dietary-associated risk factor for incident cardiovascular events ([@B107]), has been demonstrated to be predictive for adverse clinical outcomes in patients with COPD regardless type of exacerbation. Significantly higher median admission TMAO levels was observed in patients with shorter lifetime compared with survivors. Increased levels of circulating TMAO were associated with long-term all-cause mortality in exacerbated COPD patients. Nutritional interventions targeting reduction of TMAO levels might be strategies for the management of COPD and related cardiovascular disease ([@B86]).

Respiratory Infections {#S2.SS3}
----------------------

The pulmonary microbial community and gut microbiota have been observed to be considerably changed in a variety of respiratory disorders caused by a wide range of airborne pathogens ([@B25]). It is believed, these commensal bacteria affect the process of the airway infectious diseases via local or distal immune modulation. The use of probiotics, which has beneficial effects on the resistance of pathogens and activation of host immunity, shows promising effect in respiratory disorders ([@B2]). Although whether microbial dysbiosis is a cause or a consequence of respiratory infectious disease remains unclear, gut microbiota, as the most diverse community of the mammalian microbiome, has been demonstrated to show a vital impact on host immune response in both sites ([@B89]; [@B78]). The role of gut--lung axis in airway infectious diseases such as caused by tuberculosis bacillus, virus, fungi and other bacteria was focused in present review.

### Tuberculosis {#S2.SS3.SSS1}

The weakening in immune health status is related with tuberculosis infection ([@B106]). Gut microbiome, which is implicated in the modulation of host immunity and metabolism, has been intensively studied in patients with tuberculosis ([@B71]; [@B74]; [@B45]). In patients with active tuberculosis, significantly enriched butyrate and propionate-producing bacteria like *Roseburia*, *Faecalibacterium*, *Phascolarctobacterium*, and *Eubacterium* were observed compared to those healthy household controls. In a recent study, it was found that the gut microbiota of patients with active tuberculosis were mostly featured by the striking decrease of short-chain fatty acids (SCFAs)-producing bacteria as well as associated metabolic pathways ([@B96]). This discrepancy might result from the difference of ethnics, body mass index, disease status and some other parameters of selected patients from different studies. Further study with large sample size is needed. A classification model based on the abundance of three species, *Haemophilus parainfluenzae, Roseburia inulinivorans*, and *Roseburia hominis*, performed well for discriminating between healthy and diseased patients, as assessed by the receiving operational curve (ROC) analysis, achieved the area under the ROC (AUC) of 84.6%, and a 95% confidence interval (CI) of 0.651--0.956. Additionally, the healthy and diseased states can be distinguished by SNPs in the species of *B. vulgatus*. The decreased biosynthesis of amino acids and vitamins in favor of augmented metabolism of butyrate and propionate was found in active tuberculosis patients by functional analysis. In addition to altered gut microbiota, intestinal lesions in many active tuberculosis patients were also detected by using small bowel capsule endoscopy ([@B96]). The differences of gut microbiota in new tuberculosis patients, and recurrent tuberculosis patients were also characterized. Proteobacteria and *Actinobacteria* were significantly enriched whereas Bacteroidetes, having various beneficial commensal bacteria, was reduced in the gut of patients with recurrent tuberculosis compared to healthy controls. The genus *Prevotella* and *Lachnospira* were significantly decreased in both the new and recurrent tuberculosis patient groups compared with the healthy subjects ([@B71]). The variation of gut microbiota during the course of treatment was also investigated in subjects with tuberculosis. A rapid and significant change in the community structure was observed after anti-tuberculosis treatment. The relative abundance of members of phylum Firmicutes and genus *Clostridiales* reduced significantly, whereas genus *Bacteroides*, including *Bacteroides fragilis* and *Bacteroides OTU230*, was increased. OTU2972 and OTU8 from family Erysipelotrichaceae of the phylum Firmicutes showed a significant increase in 1 week after the beginning of treatment, while the other members of this family reduced ([@B46]). After treatment of anti-tuberculosis drugs for a month, significant alteration in metagenome gene pool was observed, suggesting the recovery in functional ability ([@B74]). In another study, it was found that the commensal bacterium Helicobacter pylori may protect lung from tuberculosis disease, while H. hepaticus may increase susceptibility to *Mycobacterium tuberculosis* infection ([@B106]). Thus, these findings from pilot studies indicate that microbial dysbiosis may contribute to pathophysiology of lung tuberculosis infection and the beneficial role of the intestinal microbiota against lung infections throws light on promising therapeutic and immunization strategies.

In a recent study, the mechanism underlying the interaction of intestinal microbiota and lung in immune response to *Mycobacterium tuberculosis* infection has been explored ([@B80]). It was found that gut dysbiosis induced by antibiotics reduced the lung macrophage inducible C-type lectin (mincle) expression with a concomitant increase in *Mycobacterium tuberculosis* survival. Furthermore, antibiotics elevated the population of regulatory T cells (Tregs) while reduced the effector and memory T cell population in the lungs. Mice receiving antibiotics showed low mincle expression on lung dendritic cells. These impaired dendritic cells caused decreased ability to activate naïve CD4 T cells, resulting in *Mycobacterium tuberculosis* survival. Administration of trehalose-6,6-dibehenate, a mincle ligand, could enhance the function of lung dendritic cells and T cell response. Therefore, gut microbial components, serving as ligand for a variety of pattern recognition receptors on immune cells, orchestrate host immunity involved in *Mycobacterium tuberculosis* infection ([@B80]).

### Viral and Fungal Infections {#S2.SS3.SSS2}

The effects of alteration in intestinal microbiota on respiratory viral infections have been studied in recent years ([@B8]; [@B42]; [@B67]). In a study, C57BL6 mice were treated with streptomycin before or during infection with murine paramyxoviral virus type 1, Sendai virus (SeV) ([@B36]). A significant reduction in intestinal microbial diversity without impact on lung microbiota was observed after the administration of streptomycin. Reduction in diversity in the gastrointestinal tract was followed by greatly increased mortality to respiratory viral infection. This increase in mortality to respiratory viral infection was associated with a defected immune response characterized by increased lung IFN-γ, IL-6 and CCL2, and decreased count of Tregs in lung and intestinal. Neutralization of IFN- γor adoptive transfer of Tregs significantly reduced increased mortality ([@B36]). In another study using murine models of influenza virus and respiratory syncytial virus ([@B92]), significantly altered gut microbiota diversity, with a decrease in Firmicutes phyla abundance and an increase in Bacteroidetes was observed in mice infected with influenza virus or RSV. Viral lung infections also caused an increase in colonic Muc5ac levels and fecal lipocalin-2, indicating low-grade inflammation in gut ([@B37]). In patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HCT), respiratory viral infections are occurring frequently, which could further progress to lower respiratory tract infection. Higher population of butyrate-producing bacteria in intestinal microbiota contributes to the risk of lower respiratory tract infection following viral infection in patients with allo-HCT ([@B40]).

The diversity of the gut microbiota was significantly changed by lung infection with *Pneumocystis murina* (*P. murina*). In mice without CD4 + T cell infected with *P. murina* showed gut microbial community that was significantly distinct from normal mice with *P. murina* infection, indicating that lacking of CD4 + T cells may alter the gut microbiota as well in *Pneumocystis* pneumonia. Furthermore, the functional potential for carbohydrate, energy, and xenobiotic metabolism, as well as signal transduction pathways of intestinal microbiota was altered in the setting of *Pneumocystis* pneumonia ([@B97]). In the setting of pulmonary fungal infection, it was found that anti-TNFα treatment promoted the migration of dendritic cells from the gut to the lung that enhanced Tregs, facilitating susceptibility to pulmonary *Histoplasma capsulatum* infection ([@B109]). Together, gut microbiota regulate immune responses at distant mucosal sites and is able to affect mortality in response to viral lung and fungal infection ([@B36]).

### *Staphylococcus aureus* Pneumonia {#S2.SS3.SSS3}

Streptococcus pneumoniae is a common pathogen responsible for great morbidity and mortality worldwide ([@B43]). The protective role of gut microbiota during pneumococcal pneumonia has been revealed several years ago ([@B100]). It could improve primary alveolar macrophage function. In particular, it was found that segmented filamentous bacteria (SFB) contributes to resistance against *Staphylococcus aureus* (*S. aureus*) in immunocompromised host. In Rag(−/−) C57BL/6 mice with adaptive immune deficiency, SFB affected lung protection by mediating innate immunity. A significant decrease in lung neutrophils in the resolution phase of *S. aureus* infection, along with decreased expression of CD47 that impedes phagocytosis of apoptotic cells, was demonstrated in SFB-colonized Rag(−/−) mice. SFB stimulated inflammatory neutrophils to shift toward pro-resolution neutrophils via down-regulating CD47. Thus, in immunocompromised hosts, gut commensal SFB may offer much-needed defense partly through promoting neutrophil resolution in Pneumococcal pneumonia ([@B29]). In normal C57BL/6 mice, SFB stimulates the induction of pulmonary type 17 immunity and resistance to *S. aureus* pneumonia ([@B33]).

The mechanism by which gut microbiota protect lung from *S. aureus* infection has been explored recently. Gut microbiota disruption caused by antibiotics decreases pulmonary resistance to *S. aureus* resulting from impaired Toll-like receptor 4 (TLR4) function ([@B116]). Mast cells are involved in regulation of lung-gut axis during *S. aureus* pneumonia. After *S. aureus* infection, decreased lung inflammation, reduced level of cathelicidin-related antimicrobial peptide (CRAMP), higher bacterial lung load and intestinal flora dysbiosis were found in mast cells-deficient mice compared with wild-type mice. Adoptive transfer of mast cells from bone marrow into the lung successfully rebuilt the host defense against *S. aureus* and led to recovery of intestinal dysfunction induced by *S. aureus* pneumonia. Additionally, treatment of exogenous CRAMP also significantly improved the host immunity to against bacterial in the lungs of mice without mast cells ([@B69]).

In the setting of *S. aureus* pneumonia-induced sepsis, the mechanism by which intestinal injury is caused has been intensively studied. A microRNA that has been identified in various cancers, miR-182-5p, contributes to intestinal injury via targeting surfactant protein D (SP-D). Moreover, SP-D was reduced significantly in pneumonia mice models. It binds with the bacterial pathogens and eradicate the pathogens and apoptotic bodies, playing vital role in the regulation of immune responses ([@B24]). In another study, it was demonstrated that SP-A and SP-D diminished severity of *S. aureus* pneumonia and gut mucosal injury. The potential mechanism underlying their protection are attributed to enhanced pulmonary clearance of *S. aureus*, decreased expressions of caspase-3 and Bax/Bcl-2 as well as reduced activation of the NF-κB signaling pathway in gut during pneumonia ([@B23]).

Cystic Fibrosis {#S2.SS4}
---------------

Cystic fibrosis is a genetic disease that affects mostly the lungs and digestive system ([@B39]). Increasing evidence shows a link between gastrointestinal microbiota and progression of lung disease in cystic fibrosis ([@B99]; [@B65]; [@B81]; [@B94]; [@B12]; [@B32]) ([Figure 4](#F4){ref-type="fig"}). In infants with cystic fibrosis, alpha diversity was not increased over the first year of life as expected in control cohort, while the beta diversity of these two cohorts was significantly different, associating with airway exacerbations ([@B3]). Compared with controls, levels of *Bacteroides*, a bacterial genus related with immune modulation, were decreased over the first year of life. *Bacteroides* species supernatants could reduce the generation of IL-8 from intestinal cell lines, indicating the alteration in the gut microbiota influences the inflammation in cystic fibrosis ([@B3]). During this critical window of immune programing, interventions targeting to establish a healthy state of gastrointestinal microbiota in infants with cystic fibrosis may be beneficial for lifelong health ([@B3]).

![The changes of gstrointestinal microbiota in cystic fibrosis patients at different ages.](fmicb-11-00301-g004){#F4}

A significant decrease in the richness and diversity of gut bacteria of cystic fibrosis children in age from 0.87 to 17 years was detected. Strategy to correct the reduction of bacterial diversity and maintain bacterial physiological function should be performed no later than early childhood ([@B81]). In children with cystic fibrosis, reduced abundances of *Bacteroides*, Firmicutes, *Faecalibacterium prausnitzii, Bifidobacterium adolescentis* and *Eubacterium rectale*, along with increased *Streptococcus*, *Staphylococcus*, *Veillonella dispar, Clostridium difficile, Pseudomonas aeruginosa*, and *Escherichia coli* were observed, showing similarities as Crohn's disease ([@B18]; [@B28]). In particular, the increase of Streptococcus in children with intestinal inflammation seems to be specific to cystic fibrosis, suggesting the involvement of gut--lung axis in its pathogenesis ([@B28]). Furthermore, the intestinal inflammation in patients with cystic fibrosis might be related to alterations of the composition of the gut microbiota ([@B18]). It has been demonstrated that the gut microbiota pattern is caused by cystic fibrosis transmembrane conductance regulator (CFTR) function impairment ([@B19]; [@B113]). The interaction of cystic fibrosis host--gut microbiota provides new insights to the treatments or interventions to enhance intestinal function and nutritional status of children suffering from cystic fibrosis.

In stable adults with cystic fibrosis, the altered intestinal microbiota functionality has also been demonstrated ([@B26]; [@B47]; [@B32]; [@B112]). Significantly decreased Bacteroidetes and increased Firmicutes were observed in cystic fibrosis adults ([@B12]; [@B32]). By fecal proteomics study, it was demonstrated that the abundances of *Ruminococcus gnavus*, Enterobacteriaceae, and *Clostridia* species was increased while butyrate reducers *Faecalibacterium prausnitzii* was decreased in patients with cystic fibrosis ([@B20]). Pathway abundances and gene families involved in unsaturated fatty acid biosynthesis and pathway of xenobiotic metabolism were higher in cystic fibrosis adults compared to that of healthy controls ([@B32]). Furthermore, remarkable differences in the metabolites from gut microbiota also occurred between cystic fibrosis patient and healthy controls ([@B32]).

Lung Cancer {#S2.SS5}
-----------

Lung cancer is one of the deadliest malignancies with the fastest growing morbidity and mortality worldwide. The role of gut microbiome in various cancers have been reported by numerous studies ([@B30]). In patients with cancer, the composition of the gut microbiota often develops significantly different from that of normal controls. In the setting of lung cancer, previous studies mainly focus on the impact of lung microbes, which have direct contact with the lung tissues. Until recently, the relationship between gut microbiome and lung cancer has been explored. It was found that the increased levels of *Enterococcus* sp. and decreased levels of *Bifidobacterium* sp. and *Actinobacteria* sp. are associated with lung cancer. Furthermore, the impairment of the normal function of the gut microbiome impacts on the progression of lung cancer ([@B123]). In another study, lower levels of *Dialister, Enterobacter, Escherichia--Shigella, Fecalibacterium*, and *Kluyvera* but higher levels of *Veillonella*, *Bacteroides*, and Fusobacterium compared to that of the controls were found ([@B120]). The correlations between the relative abundance of the above-mentioned bacterial genera and systemic inflammation-related markers including platelet-to-lymphocyte ratio (PLR), neutrophil-to-lymphocyte ratio (NLR), prognostic nutritional index ([@B31]), and lymphocyte-to-monocyte ratio (LMR) were analyzed. The results showed that *Enterobacter* and *Escherichia--Shigella*, were correlated positively with serum NLR level, while *Dialister* was negatively correlated with contents of PLR and NLR in the serum. Moreover, *Dialister* was also correlated with serum levels of CTLA-4 and IL-12 ([@B120]).

Gut microbiota variation is correlated with the risk of immune-related diarrhea in lung cancer patients after the treatment of anti-programed cell death protein-1 (anti-PD-1) antibodies. *Phascolarctobacterium*, as well as *Bacteroides* and *Parabacteroides* were more abundant whereas *Veillonella* was lower in patients without diarrhea ([@B70]). Given the vital role of gut microbiota in shaping immune responses, the influence of antibiotics on the efficacy of immunotherapy in patients with lung cancer was studied by a retrospective analysis. Although there is a certain trend showing the negative influence of antibiotic use, no statistical significance was observed between survival and prior antibiotic use in non-small cell lung cancer patients treated with nivolumab ([@B41]).

Manipulation of Gut Microbiota in the Treatment of Common Lung Diseases {#S3}
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Given the role of gut microbiota, whether manipulation of gut microbiota represents a promising therapeutic strategy for lung diseases has been validated by increasing clinical and experimental studies. Interventions including anti-biotics, probiotics, prebiotics, and natural products or diets that target manipulation of gut microbiota were attempted in subjects with lung diseases ([Table 1](#T1){ref-type="table"}). Major attempts have been made in patients with cystic fibrosis or lung cancers. In this section, we discussed and reviewed herbal plants targeting manipulation of gut microbiota via regulating inflammation and immune-response, acting as probiotics and prebiotics, supplementing micronutrients and exerting cytotoxic effects on cancer cells in the treatment of common lung disease.

###### 

Interventions targeting manipulation of gut microbiota in lung diseases.

  Intervention                                                                        Study type                                                         Effects and outcomes                                                                                                                                                                                                                                                                         Underlying mechanisms                                                                                                                                                                       References
  ----------------------------------------------------------------------------------- ------------------------------------------------------------------ -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ------------
  Multispecies probiotic                                                              Randomized, placebo-controlled, double-blind study COPD patients   Showed a modest effect on the bacterial subgroups but no effect on occurrence of diarrhea-like bowel movements and the composition of the dominant fecal microbiota                                                                                                                          Resulted from an existing imbalance of the microbiota                                                                                                                                       [@B59]
  *Lactobacillus rhamnosus* GG                                                        Mice model with *Pseudomonas aeruginosa* pneumonia                 Reduced inflammation and maintained intestinal barrier homeostasis                                                                                                                                                                                                                           Enhancing gut mucin expression/barrier formation, reducing apoptosis, and improving cell proliferation                                                                                      [@B57]
  Flavonoid                                                                           Clinical study, adult patients with cystic fibrosis                Associated with gut microbita variations, such as correlating with the genus Actinomyces and family Actinomycetaceae (Actinobacteria)                                                                                                                                                        With potential consequences for metabolism, immune function, and inflammation                                                                                                               [@B66]
  Vitamin D                                                                           Clinical and laboratory study, cystic fibrosis                     Developed a healthy gut microbiota, maintained the integrity of the gut mucosal barrier, allowed beneficial bacteria to outcompete opportunistic pathogens                                                                                                                                   Enhancing intercellular junctions, reducing pro-inflammatory cytokines such as IL-8, inhibiting apoptosis of intestinal epithelial cells                                                    [@B55]
  Micronutrient such as vitamin C, vitamin E, niacin, beta-carotene, and riboflavin   Clinical study, adults with cystic fibrosis                        Correlated negatively with *Bacteroides*; positively correlated with Firmicutes                                                                                                                                                                                                              Not yet clarified                                                                                                                                                                           [@B64]
  Streptomycin                                                                        A cystic fibrosis mouse model                                      Altered the intestinal microbiome, pulmonary T cell profile and airway hyperresponsiveness                                                                                                                                                                                                   By reducing the intestinal bacterial overgrowth in Cftr(tm1UNC) mice and by affecting *Lactobacillus* levels                                                                                [@B5]
  A *Lactobacillus reuteri* probiotic preparation                                     A double blind prospective study                                   Improvement in the gastrointestinal health and decrease of the calprotectin levels                                                                                                                                                                                                           Reduction in gamma-proteobacterial populations                                                                                                                                              [@B21]
  Diet therapies                                                                      Clinical study, patients with cystic fibrosis                      Improving symptom associated with chronic systemic inflammation                                                                                                                                                                                                                                                                                                                                                                                                                          [@B65]
  *Lactobacillus* GG                                                                  A Randomized Clinical Trial, children with cystic fibrosis         Reduced microbial richness and intestinal inflammation                                                                                                                                                                                                                                       Partially restored intestinal microbiota                                                                                                                                                    [@B10]
  Probiotics                                                                          A Randomized Controlled Trial, patients with cystic fibrosis       Reduced number of pulmonary exacerbations and improving quality of life                                                                                                                                                                                                                      Immunomodulatory and anti-inflammatory                                                                                                                                                      [@B50]
  Pentaherbs formula                                                                  Allergic Asthma, ovalbumin-induced allergic asthma mice model      Reduce airway hyperresponsiveness, airway wall remodeling and goblet cells hyperplasia, suppressed pulmonary eosinophilia and asthma-related cytokines IL-4 and IL-33, altered the microbial community structure and the short chain fatty acids content in the gut of the asthmatic mice.   Suppressing various immune effector cells                                                                                                                                                   [@B108]
  *Bifidobacterium longum* BB536                                                      Randomized, double-blind, parallel and placebo-controlled study    Potential protective effects                                                                                                                                                                                                                                                                 Higher abundance of the genus *Faecalibacterium* associating with anti-inflammatory and immuno-modulatory properties                                                                        [@B62]
  Recuperating Lung Decoction                                                         Rats with Allergic Bronchial Asthma                                Increased *Lactobacillus* and *Bifidobacterium* spp.                                                                                                                                                                                                                                                                                                                                                                                                                                     [@B58]
  Diet enriched with acidic oligosaccharides                                          Mice with pulmonary *Pseudomonas aeruginosa* infection             Led to increased bacterial clearance after P. aeruginosa infections, limited the number and severity of pulmonary exacerbations                                                                                                                                                              Stimulating the growth of species involved in immunity development, such as *Sutturella wadsworthia*, and *Bifidobacterium* species, increased the generation of butyrate and propionate.   [@B9]
  *Enterococcus faecium κ*-50 and *Saccharomyces cerevisiae* 14*κ*                    Lewis lung carcinoma, mice                                         Inhibited metastasis                                                                                                                                                                                                                                                                                                                                                                                                                                                                     [@B105]
  *Bifidobacterium infantis*-mediated sFlt-1 gene transferring system                 Lung cancer, C57BL/6 mice                                          Inhibition of the tumor growth and prolonged survival time                                                                                                                                                                                                                                                                                                                                                                                                                               [@B122]
  *Bifidobacterium infantis*-mediated soluble kinase insert domain receptor           Lung cancer, C57BL/6 mice                                          Tumor growth Inhibition and prolonged survival time                                                                                                                                                                                                                                          Increasing the necrosis rate of the tumor                                                                                                                                                   [@B68]
  Commensal microbiota                                                                Lewis lung carcinoma and B16F10 lung metastases, C57BL/6 mice      Microbiota modifications                                                                                                                                                                                                                                                                     γδT17 immune cell-dependent mechanism                                                                                                                                                       [@B15]
  *L. acidophilus*                                                                    Lung cancer, C57BL/6 mice                                          Increased anti-tumor effect of cisplatin and survival rates                                                                                                                                                                                                                                                                                                                                                                                                                              [@B38]
  *Lactococcus lactis* NK34                                                           Lung cancer cells, *in vitro*                                      Cytotoxic effect                                                                                                                                                                                                                                                                                                                                                                                                                                                                         [@B79]
  *Lactococcus lactis* KC24                                                           Lung cancer cells, *in vitro*                                      Strong cytotoxic effect                                                                                                                                                                                                                                                                                                                                                                                                                                                                  [@B102]
  *Bacteroides fragilis*                                                              Non-small cell lung carcinoma, mice                                Anti-tumor effect                                                                                                                                                                                                                                                                            Immunostimulatory effects of CTLA-4 blockade                                                                                                                                                [@B114]
  *Fermented milk by L. casei CRL 431*                                                Lung metastasis, BALB/c mice                                       Reduced tumor growth and lung metastasis                                                                                                                                                                                                                                                     Decreasing macrophages infiltration and increasing CD4 + CD8 + lymphocytes                                                                                                                  [@B4]
  Kefir (a probiotic-containing fermented milk product)                               Lung metastasis, BALB/c mice                                       A reduction in metastasis to lung                                                                                                                                                                                                                                                            increasing T helper cells and cytotoxic T cells                                                                                                                                             [@B124]
  *Enterococcus hirae* and *Barnesiella intestinihominis*                             Advanced lung, mice                                                Increased cyclophosphamide-anticancer effects                                                                                                                                                                                                                                                Promoting the infiltration of IFN-γ-producing γδT cells in cancer lesions                                                                                                                   [@B17]

Regulating Inflammation and Immune-Response {#S3.SS1}
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Herbal plants, which show regulation effect on gut microbiota, have also been used in asthma. Pentaherbs formula, comprising five traditional Chinese herbal medicines *Moutan Cortex*, *Phellodendri Cortex*, *Menthae Herba*, *Atractylodis Rhizoma*, and *Lonicerae Flos*, shows anti-inflammatory and anti-allergic potential via suppressing a variety of immune effector cells. In ovalbumin-induced allergic asthma mice model, it decreased airway hyperresponsiveness, airway wall remodeling and goblet cells hyperplasia, inhibited pulmonary eosinophilia and asthma-related cytokines IL-4 and IL-33. Notably, it altered the gut microbial community structure and metabolites such as short chain fatty acids level of asthmatic mice. Herbal medicines can alleviate symptoms of allergic asthma via impacting on gut microbiota and related metabolites ([@B108]).

In a randomized double-blind prospective trial, the supplementation of probiotic reduced upper respiratory infection rate by stimulating immune response ([@B119]). A probiotic *Bifidobacterium longum* 5(1A) was demonstrated to protect mice against lung infection caused by Klebsiella pneumonia. It induced faster resolution of inflammation by increased production of IL-10, decreased lung injury with significant decrease of bacterial burden. The underlying mechanism is partly attributed to activation of the TLRs adapter protein Mal ([@B115]). In a randomized clinical trial, a galacto-oligosaccharide/polidextrose enriched formula protected infants who were born to atopic parents from respiratory infections. It increased the colonization of the protective bacteria including *Bifidobacteria* and *Clostridium* cluster I ([@B93]).

Acting as Probiotics and Prebiotics {#S3.SS2}
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Probiotics, as immunomodulatory and anti-inflammatory substances, are useful nutritional supplements on improving quality of life and decreasing number of pulmonary exacerbations in patients with cystic fibrosis ([@B50]). *Bifidobacterium longum* BB536, a multifunctional probiotic, has been shown to relieve upper respiratory diseases with intestinal microbiota modulating properties by a randomized double-blind study of Malaysian pre-school children aged 2--6 years old ([@B62]). The abundance of the genus *Faecalibacterium* associating with anti-inflammation and immuno-modulation was significantly increased by the BB536 treatment compared to the placebo group. As concluded by a systematic review, some randomized clinical trials suggested that the probiotic supplementation is beneficial for management of pulmonary exacerbation and intestinal inflammation in cystic fibrosis patients, however the evidence is limited and high quality of study is needed ([@B82]).

In a randomized, placebo-controlled, double-blind study, a multispecies probiotic or placebo was treated to COPD patients who received antibiotics for respiratory tract infection ([@B59]). The multispecies probiotic showed a modest effect on the bacterial subgroups whereas it affected neither the occurrence of diarrhea-like bowel movements nor the composition of the dominant fecal microbiota ([@B59]). The non-effective of probiotic might resulted from an existing imbalance of the microbiota ([@B59]). Another herbal formula, recuperating lung decoction, increase the level of intestinal lactic acid-producing bacteria *Lactobacillus* and *Bifidobacterium* spp. in asthma model rats ([@B58]). *Lactobacillus* play a vital role in cystic fibrosis as a beneficial flora. In a Randomized Clinical Trial of children with cystic fibrosis, *Lactobacillus rhamnosus* GG partially restored intestinal microbiota, leading to reduced microbial richness and intestinal inflammation ([@B10]). The administration of *Lactobacillus rhamnosus* GG via oral improved gut permeability and modulated inflammatory response and homeostasis of spleen and colon in FVB/N mice with *Pseudomonas aeruginosa* pneumonia. The mechanism underlying its protection is enhancing gut mucin expression, improving cell proliferation and reducing the pro-inflammatory cytokine expression ([@B57]). A *Lactobacillus reuteri* probiotic preparation was demonstrated to improve gastrointestinal health and decrease the calprotectin levels due to the reduction of gamma-proteobacterial populations by a double blind prospective study of cystic fibrosis patients ([@B21]). In a cystic fibrosis mouse model, antibiotic streptomycin treatment affected the intestinal microbiome, pulmonary lymphocyte profile and airway hyperresponsiveness. It reduced the overgrowth of intestinal bacterial in Cftr mice and principally altered *Lactobacillus* levels ([@B5]).

Probiotics on elevating efficacy of anti-tumor medicines has been demonstrated. For example, *L. acidophilus* increased anti-tumor effect of cisplatin and increased survival rates of C57BL/6 mice with lung cancer ([@B38]). In another study, *Enterococcus hirae* and *Barnesiella intestinihominis* increased cyclophosphamide-anticancer effects in mice with advanced lung cancer through promoting the infiltration of IFN-γ-producing γδT cells in cancer lesions ([@B17]).

Several probiotics exert effect on suppressing metastasis to lung via immune modulation. A probiotic-containing fermented milk product showed significant cytotoxic on 4T1 breast tumor cells and reduced metastasis to lung by increasing T helper cells and cytotoxic T cells ([@B124]). In another research, the treatment of fermented milk by *L. casei* CRL 431 on BALB/c mice with breast cancer led to the suppression of tumor growth with decreased extravasation of tumor cells and tumor vascularity, as well as lung metastasis. The mechanism was attributed to altered immune response such as increasing CD4 + and CD8 + lymphocytes and decreasing infiltrated macrophages ([@B4]). *Enterococcus faecium κ*50 and *Saccharomyces cerevisiae* 14*κ* inhibited metastasis in mice with Lewis lung carcinoma ([@B105]). In melanoma lung metastasis, commensal microbiota transplantation reduced the number of metastatic lung foci through a γδT17 immune cell-dependent mechanism ([@B15]).

Furthermore, *Bifidobacterium infantis*, a recombinant probiotic bacteria, has been proposed as a possible therapeutic agent against lung cancer. *Bifidobacterium infantis*-mediated sFlt-1 gene transferring system showed suppression on the tumor growth and longer survival time in C57BL/6 mice with lung cancer ([@B122]). *Bifidobacterium infantis*-mediated soluble kinase insert domain receptor inhibited the tumor growth via increasing the necrosis rate of the tumor ([@B68]). However, negative effect of microbial agents on cancer development has also been pointed out due to the potentially oncogenic toxins and metabolites by bacteria. Therefore, the combination of microbiome and its products and more conventional therapies represents novel approach for the treatment of lung cancers ([@B102]).

Supplementing Micronutrients to Regulate Gut Microbiota {#S3.SS3}
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Due to gut malabsorption, in cystic fibrosis patients, vitamin D deficiency frequently occurs ([@B101]). Given the vital role of vitamin D in mediating gut mucosal inflammation, vitamin D as a therapeutic approach for gut microbiota modification in cystic fibrosis has been attempted ([@B110]; [@B55]). Vitamin D can develop a healthy gut microbiota, maintain the integrity of the gut mucosal barrier, and allow beneficial bacteria to outcompete opportunistic pathogens ([@B55]). Enhancing intercellular junctions, reducing pro-inflammatory cytokines such as IL-8, and inhibiting apoptosis of intestinal epithelial cells might be involved in the action mechanism of vitamin D ([@B55]). Current evidence for the application of vitamin D in patients with cystic fibrosis is encouraging but sparse, and more sufficient evidence is expected.

Intakes of micronutrients such as vitamin C, vitamin E, niacin, beta-carotene, and riboflavin negatively correlated with the intestinal abundance of *Bacteroides* while intakes of beta-carotene and vitamin E correlated positively with Firmicutes in the setting of cystic fibrosis. Mechanism by which antioxidant vitamins influence gut microbiota still yet not being clarified ([@B64]). Intakes of some flavonoids may be associated with gut microbiota variations as demonstrated by a clinical study of adult with cystic fibrosis ([@B66]). For example, intake of gallocatechin positively correlated with the genus Actinomyces and family Actinomycetaceae while intake of gallocatechin negatively correlated with class Coriobacteriia. Its potential impact on metabolism, immune function, and inflammation are crucial in management of cystic fibrosis patients ([@B66]).

Diet enriched with 5% acidic oligosaccharides led to increased bacterial clearance after *P. aeruginosa* infections in mice, resulting in limited the number and severity of pulmonary exacerbations. It stimulated the growth of bacteria involved in immunity development, such as *Sutturella wadsworthia* and *Bifidobacterium* species, and also increased the generation of butyrate and propionate ([@B9]). Diet therapies such as probiotics and prebiotics have shown certain efficacy in improving symptom associated with chronic systemic inflammation in cystic fibrosis patients, while further study is needed to confirm this effect ([@B65]). Moreover the promise of other dietary strategies such as indigestible carbohydrate and modulating dietary fat to optimize nutritional status in in cystic fibrosis are also warranted ([@B65]).

Cytotoxic Effect on Lung Cancer Cells {#S3.SS4}
-------------------------------------

With the development of metagenomics, metatranscriptomics and culturomics platforms, increasing studies showed the promising role of probiotics in the prevention of lung cancer. The efficacies of probiotics in lung cancer cell lines, lung cancer-bearing mouse and patients with lung cancers have been studied. Two kinds of *Lactococcus lactis bacteria, L. lactis* NK34 and KC24 showed remarkable cytotoxic effect on lung cancer cells *in vitro* ([@B79]). In mice with non-small cell lung carcinoma, *Bacteroides fragilis* showed anti-tumor effect due to its immunostimulation of CTLA-4 blockade ([@B114]).

Conclusion and Perspectives {#S4}
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In chronic lung diseases and respiratory infections, alternations in the composition of the intestinal and airway microbiota are presented, commonly presenting as an outgrowth of Proteobacteria and Firmicutes. A vital cross-talk between these two compartments has been noted in the setting of lung diseases. This gut--lung axis allows for the passage of endotoxins, microbial metabolites, cytokines and hormones into the bloodstream connecting the gut niche with that one of the lung. Increasing studies indicated that alterations in the gut microbial species and metabolites have been linked to changes in immune responses and inflammation as well as the disease development in the lungs. However, mechanisms by which the lung impacts the intestinal environment have not yet fully identified. By recent increasing studies, it has been demonstrated that the gut microbiota has a critical role in mediating immune responses in distant sites, including the lung. Their metabolites such as SCFAs can reach other organs via the bloodstream to exert immune regulation and anti-inflammatory effects. The direct colonization of beneficial bacteria from the gut microbiota into the airways is another possibility. As a matter of fact, due to the complex cross-talk, the causality between lung diseases and gut microbiota is still under explored. Further mechanistic insight into the pathways and mediators are expected. Nevertheless, novel therapeutic strategies that target manipulation of gut microbiome by anti-biotics, probiotics, prebiotics, natural products or diets have been tried in various lung diseases by clinical and laboratory studies. These approaches showed encouraging results in most cases. They can restore the dysbiosis of microbiota and enhance the immune responses. The effects and mechanisms of these therapeutic approaches on the overall microbiome and lung disease progression need to be understood properly by future studies.

Author Contributions {#S5}
====================

DZ wrote the manuscript. SL revised the manuscript. NW, H-YT, and ZZ commented on the manuscript and discussed the manuscript. YF designed, revised, and finalized the manuscript.

Conflict of Interest {#conf1}
====================

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

**Funding.** The financial grant of this work has been sponsored by the Talent Upgrading Project form Construction of High-level Universities in Guangzhou city.

[^1]: Edited by: Jessy L. Labbé, Oak Ridge National Laboratory (DOE), United States

[^2]: Reviewed by: Valerio Iebba, Istituto Pasteur Italia, Italy; Teresa Zelante, University of Perugia, Italy

[^3]: This article was submitted to Systems Microbiology, a section of the journal Frontiers in Microbiology
