Millions of individuals acquire a latent or active TB infection annually without obvious immune deficiency, indicating the existence of previously unidentified risk factors (Namasivayam et al., 2018). Alterations in the gut-lung axis is hypothesized to be a contributing factor in Mtb infection pathogenesis and its clinical presentation (Comberiati et al., 2021). Early GF models initially suggested no difference in Mtb tissue load between GF and conventional mice (Suter and Kirsanow, 1962; Huempfner and Deuschle, 1966), however recent developments in the understanding of gut microbiome-mediated immunomodulation has renewed interest in the area. Human immunodeficiency virus (HIV) infection, malnutrition, diabetes, alcohol, smoking and air pollution which are important risk factors for TB have all also been shown to cause changes in the gut microbiome (Naidoo et al., 2019). These factors and others can cause gut dysbiosis (Figure 1), resulting in alterations in the microbiota’s biosynthetic pathways, changes in the lung microbiome and downstream immunomodulatory effects (Shah et al., 2021). This results in reduced resistance to colonization by external pathogens, escape of a contained pathogen or loss of benign lung commensals, leading to lung disease (Naidoo et al., 2019).

C3HeB/FeJ mice fed with a high fat diet showed proinflammatory responses that increased the risk for developing active TB and impaired the immune protection from BCG vaccination in obese mice (Arias et al., 2019). The authors hypothesized that this was due to a reduction in the Firmicutes/Bacteroidetes phyla ratio and decreased Porphyromonadaceae family abundance in the gut microbiota (Arias et al., 2019). Additionally, increases in the genera associated with dysbiosis such as Alistipes, Parasuterella, Mucispirillum, and Akkermansia were observed (Arias et al., 2019). However, an increased Firmicutes/Bacteroidetes ratio was found in a murine model of type 2 diabetes (T2D) generated through the administration of an energy dense diet (Sathkumara et al., 2021). The study also suggested that these changes in the gut microbiome may increase susceptibility to TB through alterations in SCFA metabolism (Sathkumara et al., 2021). Additionally, rhesus macaque monkeys that developed severe disease from Mtb infection had distinct intestinal microbiota compared to those with less severe disease (Namasivayam et al., 2019). In particular, animals with more severe disease had enriched Lachonospiraceae and Clostridiaceae and depleted Streptococcaceae bacterial families (Namasivayam et al., 2019). These findings, support the importance of factors that impact gut dysbiosis due to crosstalk on the gut-lung axis and implications for TB pathogenesis and susceptibility.

Aerosol Mtb infection in mice can lead to rapid changes in intestinal bacterial composition, particularly in the orders Closteridiales and Bacteroidetales (Winglee et al., 2014). A low dose Mtb aerosol challenge caused rapid intestinal dysbiosis and loss of diversity in both diabetic and nondiabetic mice in a murine model of T2D (Sathkumara et al., 2021). A similar study of Mtb infection in a murine model found similar trends but these were not significant over the duration of the study (Namasivayam et al., 2017). Patients with a Mtb respiratory infection have been shown to have reduced gut microbiome diversity compared to healthy controls, evidencing the role of the gut-lung axis in susceptibility to TB (Hu et al., 2019; Comberiati et al., 2021). Pulmonary Mtb infection was also shown to decrease the α diversity of the gut microbiome, particularly through alterations in the populations of the genus Bacteroides in recent human studies (Hu et al., 2019; Wang Y. et al., 2022; Wang S. et al., 2022). One cross-sectional study contradicted these results by finding no significant alterations in gut microbiota in latent TB patients, but the same patients were not sampled before and after infection (Wipperman et al., 2017; Naidoo et al., 2019).

Gut bacteria from the phylum Bacteroidetes, which include many beneficial commensals, were also found to be reduced in patients with recurrent TB (Table 1; Luo et al., 2017). Species from the genera Lachnospira and Roseburia (phylum Firmicutes) were also depleted in TB patients, with possible negative ramifications for the production of SCFAs and their consequent downstream regulatory effects (Luo et al., 2017). Species from the more pathogenic phyla Actinobacteria and Proteobacteria including Escherichia coli were increased in recurrent TB patients’ feces samples, consistent with previous studies analyzing sputum (Luo et al., 2017). Both the genera Prevotella and Lachnospira were shown to inversely correlate with recurrent TB, positively correlate with peripheral CD4⁺ cell counts in new cases and decrease in both new and recurrent TB patient groups (Luo et al., 2017). However, in a HIV⁺ positive population on anti-retroviral treatment with high TB incidence, increased oral anaerobes including species of the genus Prevotella, were associated with higher levels of pulmonary SCFA that positively correlated with risk of developing active TB (Segal et al., 2017).

A case–control study of pulmonary TB in pediatric patients also found significant gut dysbiosis in comparison to healthy controls with enriched Prevotellaceae and Enterococcaceae, but decreased beneficial Oscillospiraceae and Bifidobacteriaceae bacterial families (Table 1; Li et al., 2019). The authors speculated that the increased populations of Prevotella may induce a proinflammatory cytokine production that worsens TB, though this remains to be mechanistically confirmed (Li et al., 2019). Faecalibacterium ruminococcaceae and Faecalibacterium prausnitzii species depletion (part of the Oscillospiraceae family) may have negative effects through reduced immunomodulatory SCFAs while reductions in the bacterial family Bifidobacteriacae have been associated with many other respiratory diseases (Li et al., 2019).

A study examining gut microbiome alterations in TB patients through 16S rRNA gene and whole-genome shotgun sequencing also found significant depletion of Provetalla and increased Bacteroides intestinal bacterial genera (Table 1; Maji et al., 2018). Considerable increases in butyrate and propionate producing intestinal bacteria in Faecalibacterium, Roseburia, Eubacterium and Phascolarctobacterium genera were detected among TB patients (Maji et al., 2018). Pre-treatment TB patients also showed increased butyrate-producing anaerobic species from the bacterial families Lachnospiraceae and Erysipelotrichaeceae in stool samples compared to healthy controls (Table 1; Naidoo et al., 2021). Butyrate inhibits IFNγ and IL-17A, strongly reducing Th17 proliferation and causing a detrimental dysregulation of the immune response against Mtb (Lachmandas et al., 2016; Segal et al., 2017; Naidoo et al., 2021). Additionally, through induction of immunosuppressive Tregs in the gut and consequent IL-10 release, butyrate may suppress critical pro-inflammatory T cell responses in TB patients facilitating immune evasion and chronic infection (Figure 1; Maji et al., 2018). Furthermore, this study showed a positive correlation between species from the Lachnospiraceae and Erysipelotrichaceae family and interferon regulation, inflammasome activation, cell death signaling and antibacterial activity in TB patients (Naidoo et al., 2021).

In contrast, a small cohort study found that healthy controls have higher levels of SCFA producing bacteria in their gut microbiota, such as the butyrate-producing Roseburia, Coprococcus and Eubacterium genera, compared to TB patients (Table 1; Hu et al., 2019). TB patients had altered activity of microbiome metabolic pathways through decreased production of precursor metabolites and energy, decreased degradation/utilization/assimilation capacities and increased vitamin synthesis (Hu et al., 2019). The study authors found that active TB patients had a unique microbiota signature through strain level single nucleotide polymorphisms and species patterns that differentiates them from healthy controls (Hu et al., 2019).

Colonization by Helicobacter spp. has diverse effects on the pathogenesis of TB. Murine models of Helicobacter hepaticus show increased inflammation, severe lung pathology, increased Mtb burden and worsened mortality and morbidity after aerosol challenge (Arnold et al., 2015; Majlessi et al., 2017). This is postulated to result from increased IL-10 (Cervantes and Hong, 2017), which suppresses macrophage activation and DC function in the early immune response to Mtb (Redford et al., 2011). Helicobacter pylori in contrast may induce a protective immunomodulatory response that reduces the TB risk in humans (Perry et al., 2010). Individuals with H. pylori infections were found to have heightened IFNγ and Th1-like responses to Mtb antigens (Figure 1), more likely to maintain latency and less likely to develop active disease (Perry et al., 2010, 2013). However, these results contradict the results of three studies which found no association between Mtb and H. pylori (Sanaka et al., 1998; Tsang et al., 1998; Torres et al., 2003), and three studies that found that H. pylori increased the incidence of Mtb infections (Mitchell et al., 1992; Woeltje et al., 1997; Philippou et al., 2003). H. pylori may worsen TB through its ability to increase Treg populations, interfere with DC maturation and prevent T lymphocyte maturation (Bustamante-Rengifo et al., 2021). However, the exact relationship between H. pylori and Mtb remains to be fully elucidated through larger studies with appropriate controls.

Murine models have consistently demonstrated that antibiotics can cause dramatic alterations in the gut microbiome,(Khan et al., 2016; Namasivayam et al., 2017; Dumas et al., 2018) potentially contributing to TB pathogenesis and affecting treatment efficacy. A mouse model of dysbiosis induced by the administration of wide-spectrum antibiotics showed increased colonization of the lungs by Mtb and reduced mucosal associated invariant T (MAIT) cells during the first week of infection (Dumas et al., 2018). Inoculation with a gavage of microbiota from non-treated mice reversed these changes and regenerated the MAIT cell population (Dumas et al., 2018). Another study of antibiotic therapy in a murine model of TB also demonstrated significant alterations in the microbiome (Khan et al., 2016). The antibiotic regimen was chosen to specifically not change Mtb viability but solely cause gut dysbiosis (Khan et al., 2016). Mice on the antibiotic therapy had higher Mtb burden both in the lungs and extra-pulmonary sites (Khan et al., 2016). This likely resulted from the suppression of Th1 immunity and enhancement of Tregs due to the alterations in gut microbiota (Khan et al., 2016). Furthermore, fecal transplants were effective to rebuild the gut microbiota, improve Th1 immunity, inhibit Treg populations and reduce Mtb burden (Khan et al., 2016). Similarly, treatment of mice with widely used anti-TB drugs isoniazid and pyrazinamide prior to Mtb infection resulted in significant gut dysbiosis and increased Mtb burden (Khan et al., 2019). This was associated with impaired AM metabolism and defective bactericidal activity and was reversible with fecal transplantation form untreated animals (Khan et al., 2019). These antibiotics are associated with more selective alterations in the gut microbiome including decreases in the Closteridia genera,(Khan et al., 2019) associated with Treg induction (Atarashi et al., 2013).

The use of broad-spectrum antibiotics on Mtb infected mice showed that the antibiotics caused significant gut dysbiosis that resulted in the deregulation of approximately 7,592 long noncoding RNA (lncRNA) sequences (Yang et al., 2022). One especially depleted highly conserved lncRNA, temporarily named lncRNA-CGB (commensal gut bacteria associated lncRNA), was especially downregulated in both mouse models and humans with active TB, correlating with poor outcomes in Mtb infections (Yang et al., 2022). Both murine lncRNA-CGB Genomic knock-out (KO) models and a human lncRNA-CGB knockdown CD3⁺ T cell model showed impaired ability to control Mtb replication and infections (Yang et al., 2022). B. fragilis, typically depleted in Mtb infections, was found to be a key up-regulator of lnRNA-CGB in mouse models and patients with active TB (Yang et al., 2022) LncRNA-CGB was found to epigenetically regulate IFNγ through interaction with enhancer of zeste homolog 2 (EZH2) (Yang et al., 2022). These findings provide a direct link between microbiota and the immune protection against TB conferred through the gut-lung axis.

A recent study also indicated that parenteral BCG vaccination in murine models causes time-dependent development of gut dysbiosis associated with increased production of butyrate (Jeyanathan et al., 2022). Additionally, BCG induces mild self-limiting, time-dependent intestinal inflammation causing significantly increased intestinal permeability, enabling the leakage of luminal molecules such as butyrate through the epithelium (Jeyanathan et al., 2022). Naïve mice treated with antibiotics and then transplanted with microbiota from BCG-immunized hosts were found to have alveolar macrophages (AM) with elevated MHC II, IL-6, and TNF production at base line and upon stimulation (Jeyanathan et al., 2022). These results indicate that a component of the protection conferred by BCG vaccination occurs through modulation of the lung-gut axis (Jeyanathan et al., 2022).

Conventional anti-TB regimens of isoniazid-rifampicin-pyrazinamide-ethambutol (HRZE) induce significant long-term gut dysbiosis that persist well beyond treatment cessation both in companion murine and human studies (Namasivayam et al., 2017; Wipperman et al., 2017). Subjects showed increased populations of Erysipelayoclotridium, Prevotella and Fusobacterium, and decreased population of Blautia, Lactobacillus, Coprococcus, Bifidobacterium and Bacteroides genera compared to latent TB controls (Wipperman et al., 2017). Polysaccharides produced by Bacteroides have been demonstrated to induce IL-10 producing Treg cells in mice (Johnson et al., 2018; Erturk-Hasdemir et al., 2019). Similarly, some Lactobaccillus spp. also can increase Treg cell populations and contribute to immune tolerance (Ding et al., 2017), Coprococcus can modulate IL-1β, IFNγ, and other cytokines in response to fungal stimuli (Schirmer et al., 2016), and Bifidobacterium is capable of inducing intestinal Th17 cells in animal models (Tan et al., 2016). This supports the notion that gut dysbiosis drives changes in immune signaling that potentially contribute to the variable efficacy of HRZE treatment (Wipperman et al., 2017). Additionally, the persistence of gut dysbiosis beyond treatment cessation may increase the likelihood of reinfection or other infections in TB patients (Osei Sekyere et al., 2020).

Due to the adverse dysbiotic effects, expense and adherence challenge of conventional anti-TB therapy and growing evidence of the role of microbiota in TB, probiotics are now being explored as novel therapeutic avenue (Wipperman et al., 2017; Rahim et al., 2022). Probiotics have been previously shown to be effective in suppressing antibiotic resistant organisms which otherwise require more intensive and expensive treatments (Rahim et al., 2022). Lacticaseibacillus rhamnosus isolated from the vagina of healthy women, inhibited Mtb growth in culture medium and showed intracellular killing activity against drug sensitive and resistant strains of Mtb in a murine macrophage cell line without cytotoxicity (Rahim et al., 2022). A murine experiment involving the intragastric administration of Lactobacillus casei indicated a protective role for probiotics against the gut-based adverse reactions of isoniazid and rifampicin through modulation of SCFAs (Li Y. et al., 2022). This was consistent with a larger randomized open label dose–response clinical trial of Lactobacillus casei that found reduced anti-TB associated gastrointestinal adverse effects (Lin et al., 2020).

As evidence strongly supports that microbiome immunomodulation is primarily modulated through their secreted metabolites, the use of inactivated microbial cells or their components, termed as postbiotics, is also being investigated (Liu Y. et al., 2021). In a whole-cell screen of a fragment library, a recent study found that the gut microbial metabolite indole propionic acid (IPA) showed significant dose-dependent anti-tubercular in vitro potency comparable to first line antibiotics (Negatu et al., 2018). In vivo experiments confirmed the effect of IPA through 7-fold reductions in bacterial load in the spleen of Mtb-infected mice (Negatu et al., 2018). The antimycobacterial-specific activity in vitro of IPA has been shown to occur through mimicking the allosteric inhibitory effect of tryptophan (Trp) on anthranilate synthase TrpE as part of the physiological negative feedback loop on tryptophan synthesis (Kaufmann, 2018; Negatu et al., 2019). Thus, while evidence supports the beneficial role of probiotics and microbial metabolites in TB, it remains limited and should be explored through larger scale animal experiments.

The existence of the gut-lung axis has been consistently supported through recent literature. Gut microbiota have been shown to influence lung immunity through production of signaling molecules or SCFAs that modulate inflammatory responses in disease states. Significant evidence also supports a role for the gut-lung axis in TB pathogenesis and recent studies have demonstrated direct links between bacterial species and immunity against TB. However, evidence around the changes in microbiota composition in Mtb infection and its significance is contradictory and needs to be evaluated in more detail through large scale human studies. The use of antibiotics in TB therapy has been linked to significant gut dysbiosis which may be resolved through supplementation with probiotics. The limited research in the use of probiotics in TB is favorable to its use, but this hypothesis needs to be tested more thoroughly in animal and human studies. The strength of association between TB pathogenesis and microbiota alterations holds promise for the development of new therapeutics particularly through probiotic agents or purified bacterial compounds to be used against TB.

AE and AK conceived the manuscript. AE wrote the first draft. HS provided editorial and intellectual input and designed the Figure. All authors contributed to manuscript revision and approved the submitted version.

AE was supported by an Amuthan Medical Research Grant from James Cook University. AK was supported by an NHMRC Ideas (APP2001262) and Investigator Grant (APP2008715).

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.

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