Clinically, weight loss and night sweats have the most relevant association with active Tuberculosis (TB), with an odds ratio of 4.47 and 3.29, respectively [30]. However, common symptoms include cough, fever, anorexia, and chest pain [31], all common to many respiratory illnesses, and thus cannot be used for TB diagnostics. This is why TB diagnosis must be confirmed by culture and molecular diagnostic tests [4]. Although a persistent cough is not a definite diagnosis, it is one of the most common symptoms of advanced pulmonary ATB. As the disease progresses, increased inflammation is followed by tissue necrosis that can progress into the tubercular caverns, which are regions with a high bacillary load. The inflammation of the lung parenchyma close to the pleura can cause pleuritic pain [32]. Dyspnoea can be a significant clinical component after a substantial amount of the lung is destroyed or there is a significant pleural effusion [30]. Physical examination of the chest in pulmonary TB is unrevealing [33]. However, the changes are more pronounced in the upper lobes because MTBC is strictly aerobic, and these areas are more ventilated, leading to greater growth of the bacilli [34].

Extrapulmonary Tuberculosis (EPTB) refers to any bacteriologically confirmed case of TB involving organs other than the lungs, e.g., pleura, lymph nodes, abdomen, genitourinary tract, skin, joints, bones, or meninges [35]. It represents 16% of all tuberculosis cases. Its development depends on age, presence, or absence of underlying disease, the MTB strain, immune status, and ethnic background, and, possibly, the microbiome [5,36]. About 10–50% of EPTB patients have associated pulmonary TB [37].

Without treatment, TB is a life-threatening disease. Studies in patients with pulmonary TB, and positive smear microscopy, prior to the advent of anti-TB drugs, were followed up for five years: 50–60% died; 20–25% were cured spontaneously; and 10–25% continued with symptoms of TB [38].

The objective of any TB therapy is, first, to reduce the number of actively growing bacilli in the patient, thereby decreasing the severity of the disease, and halting transmission of MTB; second, to eradicate populations of persisting bacilli to achieve a long-lasting cure and prevent relapse, and third to prevent the acquisition of drug resistance during therapy [39].

The treatment of ATB relies on multidrug regimens. In the case of drug-susceptible TB (DS-TB), the treatment includes six months of four first-line anti-TB drugs: isoniazid (H), rifampicin (R), ethambutol (E), and pyrazinamide (Z) [40]. This treatment is divided into two phases: an intensive or bactericidal phase with the four drugs H, R, E, Z, administered for two months, with the objective of reducing the bacillary load and the transmission, as well as avoiding the selection of resistant strains associated with these four drugs. The second, or sterilization, phase includes R and H administered for four months, this phase aims to continue with the sterilization of the tissue, including intracellular bacilli, prevent relapses, and therefore have a cure [39]. This regimen has proven to be very successful, with an 85% success rate, and has been widely adopted worldwide for decades [5]. Currently, it is possible to shorten the treatment from six to four months with a scheme with similar efficacy and safety, that includes Rifapentine (P), Moxifloxacin (Mfx), H, and Z [41].

Antibiotic resistance is a great concern for all infectious diseases, including TB. Drug-resistant TB (DR-TB) has increased from 30,000 cases in 2009 to 157,903 in 2020 worldwide [5,42]. There are several types of DR-TB: Rifampicin-Resistant (RR), bacteria resistant to Rifampicin; Multidrug-Resistant TB (MDR-TB), those resistant to at least isoniazid and rifampicin; Pre-Extreme Drug-Resistant (Pre-XDR) are MDR, as well as to any fluoroquinolone; and XDR-TB are strains that fulfill the definition of Pre-XDR for at least one drug of the WHO’s Group A list [43] (see below).

The treatment of DR-TB (MDR, Pre-XDR, XDR) can be either with standardized regimens recommended by WHO or individualized plans that are tailored to the pattern of resistance and the patient’s particular characteristics, in which specific drugs can be modified according to the pattern of resistance [44]. Anti-tubercular drugs have been classified based on efficacy into Group A: Levofloxacin (Lfx), Moxifloxacin (Mfx), Bedaquiline (Bdq) and Linezolid (Lzd); Group B: Clofazimine (CFZ), Cycloserine (Cs) or Terizidone (Trd); and Group C: Ethambutol (E), Delamanid (Dlm), Pyrazinamide (Z), Imipenem-cilastatin (Imp-Cln) or Meropenem (Mpm), Amikacin (Am) or Streptomycin (S), Ethionamide (Eto) or Prothionamide (Pto) or P-aminosalicylic acid (PAS) [45]. On the other hand, treatment of LTBI has several options: these include six to nine months of daily H or one month of daily Rifapentine plus Isoniazid and four months of daily Rifampicin, just to mention the more common options [25,46].

In sum, all TB treatment involves long multidrug regimens that undoubtedly will have profound effects on the microbiome and the host’s overall wellbeing.

Although dysbiosis has been reported to have negative health effects [93], and was associated with the pathogenesis of various diseases: gastrointestinal diseases, obesity, diabetes, allergies, asthma, colorectal cancer, etc. [13,94], its influence on MTB infection in the lungs is still a subject of study [95].

As discussed above, MTB infection can have a spectrum of clinical manifestations, ranging from clearance of the bacillus to active establishment of the infection. What determines these outcomes is poorly understood, but has been primarily associated with host factors, such as the immune system response [96] and, more recently, the microbiome [9,97,98].

Although some authors have reported differences in the microbiota between healthy individuals and patients with active TB [99,100,101,102], the primary pulmonary response to MTB colonization is very difficult to assess directly on humans, which is why the use of animal models has been employed. These models have provided valuable information, increasing our knowledge of the disease.

Studies on aerosolized MTB-infected mice, showed a rapid loss (6 days) of intestinal microbial diversity followed by a gradual recovery of beta-diversity, probably because of crosstalk between the microbiome and the host immune system during TB infection [103]. However, similar studies observed slower (12 weeks) and less evident alterations in the intestinal microbiota of mice after the infection with MTB, probably due to differences in the MTB strain used (CDC1551 vs. H37Rv) and/or genetic factors between the animal models (Balb/c vs. C57BL/6 mice) [104].

Parallel studies using murine models of gastrointestinal dysbiosis induced by broad-spectrum antibiotics prior to MTB inoculation, show increased bacilli colonization and dissemination (liver and spleen). This dysbiosis was associated with a reduction in the number of mucosal-associated invariant T cells (MAIT), less expression of IL-17A, IFN-γ, and TNF-α (associated with protection against TB) and increased regulatory T cells (associated with susceptibility to TB); additionally more and larger pulmonary granulomas were observed in these mice, suggesting that antibiotic-induced dysbiosis increases the spread of the disease [9,97]. Furthermore, the restoration of the microbiome through fecal transplant reversed these effects: it increased the number of MAIT cells, the expression of IFN-γ and TNF-α (produced by MAIT cells Th1), and reduced the regulatory T cells, supporting a key role for the microbiome in the colonization of the lungs, the response to MTB, and the severity of the infection in mice [9,97].

Taken together, these findings demonstrate that microbial communities are essential for the modulation of host immunity and that changes in the microbiome, even at distal sites, can determine TB outcomes and prognosis. However, the precise role of dysbiosis in the balance between health and disease is just beginning to be understood.

As mentioned earlier, the immune system controls the infection of approximately 90% of people exposed to MTB; these individuals either completely clear the bacilli or remain asymptomatic throughout their lives as LTBI [80]. In LTBI, the immune response restrains MTB within granulomas, where the bacteria may persist, but not spread. It is possible that the lung microbiome is involved in the formation and dynamics of the granuloma, probably through the stimulation of the Th1 response through IL-17, and it is a dysbiotic state that influences the progression of the disease [105]. The influence of the microbiome on the host’s adaptive immune response has been reported in other respiratory infections such as influenza, where an intact gut, and/or nasal microbiome is necessary to induce Th1 cytotoxic T lymphocytes (CTL) and IgA responses during viral infection [19].

The role of the GI or LRT microbiome in TB progression is not yet fully understood. However, Perry et al. [106] reported that patients with LTBI and H. pylori infection, (one of the most prevalent pathogenic gastric bacteria in the world) had a better Th-1 cytokine response (INF-γ, IL2, TNF-α, CXCL-10) to TB antigens, compared to LTBI individuals with no H. pylori infection. In addition, non-human primates exposed to TB as well as individuals with LTBI are less likely to develop active TB when they have a prior H. pylori co-infection. This suggests that H. pylori infection generates a pro-inflammatory state that enhances the host’s innate immune response against MTB and other infectious diseases. Conversely, MTB inoculation after natural colonization of the intestine of mice by H. hepaticus, in combination with an intestinal dysbiosis characterized by a greater abundance of Bacteroidaceae and reduction of Clostridiales, Ruminococcaceae, Lachnospiraceae, and Prevotellaceae, cause an overstimulation of the innate immune response and excessive inflammation (increased pro-inflammatory cytokines) that increased the susceptibility to MTB, and severe lung damage [107].

Other studies, working with a non-human primate model and a combination of 16S rRNA and metagenomics, found an enrichment of the families Lachnospiraceae and Clostridiaceae, even before infection, in the gut microbiome of monkeys that developed severe TB. The prevalence of these bacteria continued after MTB infection with an added reduction of Streptococcaceae, Bacteroidales RF16, and Clostridiales vadin B660 [14]. Furthermore, studies in West Africa where both M. africanum (MAF) and MTB are endemic, showed that patients with TB due to MAF had lower alpha diversity, increased Enterobacteriaceae in the GI tract, and higher expression of inflammatory genes prior to antibiotic treatment, when compared to the MTB patients and healthy controls. In addition, the MAF patients had a reduction in Actinobacteria and Verrucomicrobia when compared to the MTB patients. The authors speculate that in this region, where an individual can encounter both bacilli, which bacteria (MTB or MAF) will establish an infection is determined by the host’s immune system and its microbiome [108]. This further supports the hypothesis that the gastrointestinal microbiome modulates the susceptibility and development of TB.

On the other hand, studies on the LRT microbiome of TB patients have shown variable results when compared to healthy individuals, perhaps due to differences in samples (BAL vs. sputum), populations analyzed, experimental design, and the definition of healthy. However, several authors have reported an increased microbial diversity in the lower respiratory tract of ATB patients [100,101,102,109,110]. Other studies have shown increased diversity in DR-TB vs. DS-TB patients [102,111].

This increased microbial diversity during ATB may be due to tissue damage reduction of lung commensal bacterial and a higher susceptibility to opportunistic microorganisms such as members of the Leptotrichia, Granulicatella, Campylobacter, Delfitia or Kingella genus; or pathogens such as Klebsiella, Pseudomonas and Acinetobacter, which have been associated with other respiratory tract pathologies [109,111], and may contribute to additional damage and aggravated symptoms. In fact, epidemiological studies have shown a correlation between opportunistic infections and increased risk of DR-TB development [112], probably due to an indiscriminate use of antibiotics.

Thus, in addition to multiple risk factors (diabetes, malnutrition, co-infections, parasites, etc.) [113], there is clear evidence that supports the crosstalk between the microbiome and the immune system in the establishment of MTB infection, and between microbiome dysbiosis and progression of MTB infection.

As aforementioned, the standard treatment for drug-susceptible TB requires the use of broad-spectrum and specific antibiotics (H, R, Z, and E) against mycobacteria for at least six months, causing intestinal dysbiosis that persists in patients for more than a year after finishing the treatment [104]. In fact, rifampicin, a broad-spectrum bactericide, causes the greatest alterations in the microbiome [114].

As mentioned previously, there is an increase in the incidence of antibiotic-resistant TB (DR-TB) [5], whose treatment can be up to 20 months and involves the use of combinations of antibiotics that induce intestinal dysbiosis during and for up to eight years after treatment [93]. Fecal transplantation and the use of probiotics have been proposed for the restoration of microbiome eubiosis after DR-TB treatment to reduce the development of comorbidities and poor outcomes [93].

Oral administration of Lactobacillus rhamnosus NK210 and Bifidobacterium longum NK219 partially help to restore the populations of Firmicutes, Bacteroidetes, Proteobacteria, and Verrucomicrobia in a murine model of gut dysbiosis caused by the use of ampicillin, and during a state of LPS-induced systemic inflammation. In both cases, the administration of NK210 and NK219 decreased the expression of IFN-γ, TNF-α, Tbet; it increased the expression of IL-10 and Foxp3 (both involved in the reduction of the inflammatory response), improving gut dysbiosis and decreasing inflammation [115]. However, the inoculation of a single microorganism was not enough to restore the normal microbial community or prevent recurrent infections in patients with other diseases, such as intractable bacterial vaginosis, but a microbiome transplant from healthy donors was effective in improving symptoms and the laboratory features of the disease [116].

Lung damage, reduced pulmonary function, and proinflammatory lung microenvironment in post-TB patients make them more susceptible to develop recurrent respiratory infections by bacteria (P. aeruginosa, H. influenzae, M. catarrhalis, and S. aureus) and fungi (A. fumigatus, A. niger and A. flavus) [111,117].

Furthermore, approximately 6% of patients who complete the standard treatment for drug-susceptible TB, relapse [118]. The persistent dysbiosis of the lung microbiome of TB patients has been associated with treatment failure and relapse [80,119]. Relapsing patients show differences in alpha diversity with an increase in the phyla Proteobacteria and Actinobacteria (rich in pathogenic species) and a reduction in Bacteroidetes (mainly beneficial commensal organisms) in the gut microbiome [80]. Notably, a higher Pseudomonas/Mycobacterium and lower Treponema/Mycobacterium ratio in the lung microbiome may be a risk factor associated with relapse [119].

These data suggest that maintaining microbiome eubiosis could be beneficial for TB recovery, as well as to avoid relapse [80]. However, more studies are needed to establish the connection between the microbiome and poor TB outcome [120].