Next Article in Journal
Modeling of Environmental Pollution Due to the Fashion Industry Using Fractional Programming
Previous Article in Journal
Satellite Characterization of Methane Point Sources by Offshore Oil and Gas PlatForms
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Proceeding Paper

The Knowns and Unknowns of Chemically Induced Lower Respiratory Tract Microbiota Dysbiosis and Lung Disease †

Wells Utembe
1,* and
Arox Wadson Kamng’ona
Toxicology and Biochemistry Department, National Institute for Occupational Health (NIOH), National Health Laboratory Services (NHLS), Johannesburg 2000, South Africa
School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre Campus, Mahatma Gandhi Road, Blantyre 312224, Malawi
Author to whom correspondence should be addressed.
Presented at the 6th International Electronic Conference on Atmospheric Sciences, 15–30 October 2023; Available online:
Environ. Sci. Proc. 2023, 27(1), 21;
Published: 27 November 2023
(This article belongs to the Proceedings of The 6th International Electronic Conference on Atmospheric Sciences)


Exposure to chemicals in many occupational and environmental settings has the capacity to significantly disturb the commensal microbiota that symbiotically reside in humans. However, much more is known about gut microbiota (GM) than lung microbiota (LM) due to the challenges of collecting LM samples. The advent of culture-independent methodologies has revealed the complex and dynamic community of microbes harbored by the respiratory tract. It is now being recognized that LM can directly impact immunity in a manner that can result in disease. Significant differences in community composition and diversity have been shown between the LM of diseased lungs and those of healthy subjects. Studies have linked LM dysbiosis with human diseases such as idiopathic pulmonary fibrosis, lung inflammation, chronic obstructive pulmonary disease (COPD), asthma, and lung cancer. However, it is not known whether LM dysbiosis initiates/promotes disease pathogenesis or is merely a biomarker of disease. Many chronic lung diseases often occur together with chronic GIT diseases in what is termed as the gut–lung axis. The LM also affects the CNS, in the bidirectional lung–brain axis, through a number of potential mechanisms that include the direct translocation of micro-organisms. Chemically induced LM dysbiosis appears to play a significant part in human diseases as has been shown to arise due to air pollution, cigarette smoking, and the use of chemical antibiotics.

1. Introduction

Some human diseases and disorders have been linked to the disturbance/dysbiosis of approximately 100 trillion bacteria, fungi, viruses, and other microbes that inhabit the human body [1]. In this regard, the human body can be viewed as an ecosystem of distinct habitats of a large diversity and huge numbers of colonizing microbes, with each habitat supporting a discrete collection of microorganisms that interact with each other and with the host. The host–microbiota symbiotic equilibrium is very sensitive to a number of factors, including changes in the concentration of exogenous and endogenous chemicals [2].
For a long time, the lungs were thought to be sterile and free of microbes [3], an assertion that has recently been disproved, following the advent of culture-independent approaches such as next-generation sequencing. The presence or absence of specific microbes in the respiratory tract can have significant effects on the health and well-being of human hosts. For example, the Hygiene Hypothesis suggests that a broad range of microbial exposures contribute to the incidence of allergenic reactions and asthma, both positively and negatively [4]. According to this hypothesis, recurrent microbial exposures initiate T-helper 1 (Th1) response rather than a Th2-mediated immune response that is associated with high levels of interleukin-4 (IL-4) and IL-5 and eosinophilia [5]. The hypothesis is used to explain the higher prevalence of asthma in urban populations than in rural populations [6]. The Epithelial Barrier Hypothesis also links disrupted epithelia, through bacterial leakage and dysbiosis, with inflammatory diseases such as asthma [5].
The respiratory tract harbors a collection of microbiota that are distinct from those that inhabit the gastrointestinal (GI) tract [7]. Consequently, LM dysbiosis is linked to individual disease conditions that are likely to be different from those that result from GM dysbiosis. Moreover, there have been links between the respiratory system and other systems such as the GI tract, in what has been termed as the Gut-lung axis. This study explores the knowns and unknowns of chemically-induced LM dysbiosis and disease, especially regarding the nature of microbes that inhabit the respiratory tract, the methods used to analyze LM dysbiosis together with their challenges and recent advances, and the diseases linked to LM dysbiosis, along with evidence and the purported mechanisms.

2. Respiratory Tract Microbiota and Methodological Issues and Challenges in Its Determination

Because of many limitations such as low culturable bacterial burdens in the lung, contamination during sampling, and challenges in culturing fastidious bacteria, culture-dependent methods could not reveal lung microbial populations. However, the exponential increase in sequencing technology and bioinformatics analysis has resulted in great insights into lung microbiome in a manner that could not be revealed using culture-dependent methods. Studies using quantitative PCR for 16S ribosomal RNA (rRNA) genes have shown a diverse microbiome often of taxa that are represented in the oral cavity; although, lower bacterial burdens have been detected in the lower airways compared to those in the upper airways [3]. Furthermore, the composition of the upper respiratory tract microbiota in healthy individuals differs significantly from that of the lower respiratory tract. In the lungs of healthy individuals, the predominant phyla are Bacteroidetes and Firmicutes, whereas Firmicutes, Proteobacteria, and Bacteroidetes dominate in the oropharynx [8].

3. Lung Microbiota Dysbiosis and Human Diseases

The structure and diversity of LM vary in different populations (healthy and different diseased individuals), which could play a role in respiratory diseases through a number of mechanisms. in one of the mechanisms, microbiota shape the mucosal immune system, as shown by defective immunity in germ-free mice [9]. However, in the respiratory tract, little is known about the impact of microbiota on immune cell development and maturation [3]. Nevertheless, children that are exposed to a wide range of microbial exposures, such as those that exist on traditional farms, seem to be protected from childhood asthma and atopy. Indeed, Ege and Mayer [6] reported of lower prevalences of asthma and atopy in children who lived on farms and who were exposed to a greater variety of environmental microorganisms compared to children from non-farming environments. The diversity of microbial exposure was inversely related to the risk of asthma. for example, exposure to fungal taxon eurotium species, and a variety of bacterial species, including Listeria monocytogenes, bacillus species, corynebacterium species, and others, were inversely related to the risk of asthma. Similarly, Birzele and Depner [10] reported that farming environments were associated with higher bacterial diversity in mattress dust samples as determined by the richness and Shannon index, which were in turn inversely associated with asthma.
While the healthy lung is characterized by a prevalence of bacteria belonging to the phyla Bacteroidetes, Actinobacteria, and Firmicutes, asthma (in both young people and adults) as well as other viral respiratory infections are associated with abundances of Proteobacteria with the genera Hemophilus and Moraxella [7]. Furthermore, many studies have shown that LM dysbiosis can result in a variety of chronic lung disorders such as COPD [11,12], asthma [13], bronchopulmonary dysplasia (BPD) [14,15], and cystic fibrosis [16]. However, questions remain on the extent to which chemicall- induced LM dysbiosis can cause or stimulate asthma. In this regard, Li and Sun [17] reported of significant differences in pulmonary function and oropharyngeal microbiota in regions of high, medium, and low air pollution.
Cigarette smoking also significantly affects the composition of LM. In this regard, Zhang and Chen [18] observed higher microbial diversity in mice exposed to cigarette smoke, while Enterobacter, Acidimicrobiales_norank, and Caulobacteraceae_ were significantly more abundant in the control group. Most importantly, denser inflammation and congestion were observed in the lungs of the exposed mice compared to the non-exposed mice. In humans, however, conflicting results have been reported about the effect of smoking on LM. For example, while Turek and Cox [19] associated smoking with diversity loss, loss of abundance, profound alterations to network structure, and the expansion of Streptococcus spp., Morris and Beck [20] reported similarities between the LM of smokers and non-smokers.
Associations have also been made between the use of chemical antibiotics and asthma. Asthma has been reported to be significantly more likely to develop in children who receive antibiotics in their first year of life, with the risk of asthma being highest in children receiving more than four courses of antibiotics [21]. Between 2000 and 2014, Patrick and Sbihi [22] observed a reduction in asthma incidence associated with decreasing antibiotic use in infancy, whereas in the prospective arm of the study, asthma incidence increased by 24% with each 10% increase in antibiotic prescribing.

3.1. The Gut–Lung Axis

Many chronic lung diseases often occur together with chronic GIT diseases. For example, patients with COPD are two to three times more likely to be diagnosed with inflammatory bowel disease (IBD) [23], while individuals with COPD typically have increased intestinal permeability [24]. Indeed, a number of lung diseases can be influenced by changes in the GI microenvironment, and vice versa, through mechanisms that are still not very clear. A number of mechanisms have been postulated: The absorption of signals from the endothelium by epithelial cells and immune cells form a local cytokine microenvironment that leads to changes in distal immune responses. Secondly, short-chain fatty acids (SCFAs) derived from gut bacteria are reported to have inhibitory effects on pro-inflammatory responses in the lungs [25]. Therefore, GM dysbiosis will have effects on the lungs, and GM dysbiosis early in life has been linked with an enhanced risk of asthma development later in life [7].

3.2. The Lung–Brain Axis

The dysbiosis of LM is not only linked to diseases in the lungs and GIT, but also diseases in remote parts of the body such as the brain (the central nervous system, CNS). The LM affects the CNS, in the bidirectional interaction known as the lung–brain axis, through a number of potential mechanisms that include the direct translocation of micro-organisms, effects of lung microbes on systemic immunity, nerve, HPA axis, as well as metabolic changes [26]. The lungs and brain interact through specific signaling pathways or triggered inflammatory factors, largely involving the vagus nerve and the hypothalamic–pituitary–adrenal axis [27]. Furthermore, Hosang and Canals [28] showed a link between LM and brain autoimmunity in rats, where LM dysbiosis significantly affected the susceptibility of rats to developing CNS autoimmune disease. Links between LM and other CNS diseases such as Parkinson’s disease, Alzheimer’s disease, intracerebral hemorrhage, and glioma are yet to be established. Moreover, Azzoni and Marsland [29] raised a number of questions regarding the role of LM in CNS diseases, including if changes in LM can explain the roles of smoking and respiratory infections in multiple sclerosis, why more patients with chronic lung diseases do not present with neurological disorders, and if LM-derived products can influence CNS.
It is indeed pertinent to know if chemical exposure can induce adverse effects on the CNS via LM-mediated mechanisms. In that regard, the intratracheal administration of neomycin was reported to shift the composition of LM to a higher abundance of lipopolysaccharide (LPS)-producing bacteria, which can cross the blood–brain barrier to result in the amelioration of autoimmune encephalomyelitis (EAE) [29].

4. Summary and Conclusions

The advent of culture-independent methodologies has revealed the complex and dynamic community of microbes harbored by the respiratory tract. LM dysbiosis has been linked with human diseases such idiopathic pulmonary fibrosis, lung inflammation, COPD, asthma, and lung cancer. Moreover, many chronic lung diseases often occur together with chronic GIT diseases, in what is termed as the gut–lung axis. The LM also affects the CNS, in the bidirectional lung–brain axis, through a number of potential mechanisms that can include the direct translocation of micro-organisms. Chemically-induced LM dysbiosis plays a significant part in human diseases as has been shown to be caused by air pollution, cigarette smoking, and the use of chemical antibiotics.

Author Contributions

Conceptualization, W.U. and A.W.K.; writing—original draft preparation, W.U. and A.W.K.; writing—review and editing, W.U. and A.W.K. All authors have read and agreed to the published version of the manuscript.


This research received no external funding.

Institutional Review Board Statement

Not applicable as the study does not involve human or animal subjects.

Informed Consent Statement

Not applicable.

Data Availability Statement

There is no additional data linked to this manuscript.

Conflicts of Interest

The authors declare no conflict of interest.


  1. Sender, R.; Fuchs, S.; Milo, R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 2016, 14, e1002533. [Google Scholar] [CrossRef]
  2. Dumas, A.; Bernard, L.; Poquet, Y.; Lugo-Villarino, G.; Neyrolles, O. The role of the lung microbiota and the gut-lung axis in respiratory infectious diseases. Cell. Microbiol. 2018, 20, e12966. [Google Scholar] [CrossRef]
  3. Segal, L.N.; Blaser, M.J. A brave new world: The lung microbiota in an era of change. Ann. Am. Thorac. Soc. 2014, 11 (Suppl. S1), S21–S27. [Google Scholar] [CrossRef]
  4. Liu, A.H. Hygiene theory and allergy and asthma prevention. Paediatr. Perinat. Epidemiol. 2007, 21, 2–7. [Google Scholar] [CrossRef]
  5. Kiykim, A.; Ogulur, I.; Yazici, D.; Cokugras, H.; Akdis, M.; Akdis, C.A. Epithelial Barrier Hypothesis and Its Comparison with the Hygiene Hypothesis. Turk. Arch. Pediatr. 2023, 58, 122–128. [Google Scholar] [CrossRef]
  6. Ege, M.J.; Mayer, M.; Normand, A.-C.; Genuneit, J.; Cookson, W.O.; Braun-Fahrländer, C.; Heederik, D.; Piarroux, R.; von Mutius, E. Exposure to environmental microorganisms and childhood asthma. N. Engl. J. Med. 2011, 364, 701–709. [Google Scholar] [CrossRef]
  7. Hufnagl, K.; Pali-Schöll, I.; Roth-Walter, F.; Jensen-Jarolim, E. Dysbiosis of the gut and lung microbiome has a role in asthma. Semin. Immunopathol. 2020, 42, 75–93. [Google Scholar] [CrossRef]
  8. Dang, A.T.; Marsland, B.J. Microbes, metabolites, and the gut–lung axis. Mucosal Immunol. 2019, 12, 843–850. [Google Scholar] [CrossRef]
  9. Chung, H.; Pamp, S.J.; Hill, J.A.; Surana, N.K.; Edelman, S.M.; Troy, E.B.; Reading, N.C.; Villablanca, E.J.; Wang, S.; Mora, J.R.; et al. Gut Immune Maturation Depends on Colonization with a Host-Specific Microbiota. Cell 2012, 149, 1578–1593. [Google Scholar] [CrossRef] [PubMed]
  10. Birzele, L.T.; Depner, M.; Ege, M.J.; Engel, M.; Kublik, S.; Bernau, C.; Loss, G.J.; Genuneit, J.; Horak, E.; Schloter, M.; et al. Environmental and mucosal microbiota and their role in childhood asthma. Allergy 2017, 72, 109–119. [Google Scholar] [CrossRef] [PubMed]
  11. Erb-Downward, J.R.; Thompson, D.L.; Han, M.K.; Freeman, C.M.; McCloskey, L.; Schmidt, L.A.; Young, V.B.; Toews, G.B.; Curtis, J.L.; Sundaram, B.; et al. Analysis of the Lung Microbiome in the “Healthy” Smoker and in COPD. PLoS ONE 2011, 6, e16384. [Google Scholar] [CrossRef]
  12. Sze, M.A.; Dimitriu, P.A.; Hayashi, S.; Elliott, W.M.; McDonough, J.E.; Gosselink, J.V.; Cooper, J.; Sin, D.D.; Mohn, W.W.; Hogg, J.C. The lung tissue microbiome in chronic obstructive pulmonary disease. Am. J. Respir. Crit. Care Med. 2012, 185, 1073–1080. [Google Scholar] [CrossRef]
  13. Hilty, M.; Burke, C.; Pedro, H.; Cardenas, P.; Bush, A.; Bossley, C.; Davies, J.; Ervine, A.; Poulter, L.; Pachter, L.; et al. Disordered microbial communities in asthmatic airways. PLoS ONE 2010, 5, e8578. [Google Scholar] [CrossRef]
  14. Yuksel, N.; Gelmez, B.; Yildiz-Pekoz, A. Lung Microbiota: Its Relationship to Respiratory System Diseases and Approaches for Lung-Targeted Probiotic Bacteria Delivery. Mol. Pharm. 2023, 20, 3320–3337. [Google Scholar] [CrossRef]
  15. Lal, C.V.; Ambalavanan, N.; Gaggar, A.; Morrow, C. Inhaled Respiratory Probiotics for Lung Diseases of Infancy, Childhood and Adulthood. U.S. Patent 11,141,443, 12 October 2021. [Google Scholar]
  16. Zhao, J.; Schloss, P.D.; Kalikin, L.M.; Carmody, L.A.; Foster, B.K.; Petrosino, J.F.; Cavalcoli, J.D.; VanDevanter, D.R.; Murray, S.; Li, J.Z.; et al. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc. Natl. Acad. Sci. USA 2012, 109, 5809–5814. [Google Scholar] [CrossRef]
  17. Li, X.; Sun, Y.; An, Y.; Wang, R.; Lin, H.; Liu, M.; Li, S.; Ma, M.; Xiao, C. Air pollution during the winter period and respiratory tract microbial imbalance in a healthy young population in Northeastern China. Environ. Pollut. 2019, 246, 972–979. [Google Scholar] [CrossRef]
  18. Zhang, R.; Chen, L.; Cao, L.; Li, K.-J.; Huang, Y.; Luan, X.-Q.; Li, G. Effects of smoking on the lower respiratory tract microbiome in mice. Respir. Res. 2018, 19, 253. [Google Scholar] [CrossRef]
  19. Turek, E.M.; Cox, M.J.; Hunter, M.; Hui, J.; James, P.; Willis-Owen, S.A.; Cuthbertson, L.; James, A.; Musk, A.; Moffatt, M.F.; et al. Airway microbial communities, smoking and asthma in a general population sample. eBioMedicine 2021, 71, 103538. [Google Scholar] [CrossRef]
  20. Morris, A.; Beck, J.M.; Schloss, P.D.; Campbell, T.B.; Crothers, K.; Curtis, J.L.; Flores, S.C.; Fontenot, A.P.; Ghedin, E.; Huang, L.; et al. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am. J. Respir. Crit. Care Med. 2013, 187, 1067–1075. [Google Scholar] [CrossRef] [PubMed]
  21. Kozyrskyj, A.L.; Ernst, P.; Becker, A.B. Increased risk of childhood asthma from antibiotic use in early life. Chest 2007, 131, 1753–1759. [Google Scholar] [CrossRef] [PubMed]
  22. Patrick, D.M.; Sbihi, H.; Dai, D.L.; Al Mamun, A.; Rasali, D.; Rose, C.; Marra, F.; Boutin, R.C.; Petersen, C.; Stiemsma, L.T.; et al. Decreasing antibiotic use, the gut microbiota, and asthma incidence in children: Evidence from population-based and prospective cohort studies. Lancet Respir. Med. 2020, 8, 1094–1105. [Google Scholar] [CrossRef]
  23. Keely, S.; Talley, N.J.; Hansbro, P.M. Pulmonary-intestinal cross-talk in mucosal inflammatory disease. Mucosal Immunol. 2012, 5, 7–18. [Google Scholar] [CrossRef]
  24. Rutten, E.P.; Lenaerts, K.; Buurman, W.A.; Wouters, E.F. Disturbed intestinal integrity in patients with COPD: Effects of activities of daily living. Chest 2014, 145, 245–252. [Google Scholar] [CrossRef]
  25. Barcik, W.; Boutin, R.C.T.; Sokolowska, M.; Finlay, B.B. The role of lung and gut microbiota in the pathology of asthma. Immunity 2020, 52, 241–255. [Google Scholar] [CrossRef]
  26. Bell, J.S.; Spencer, J.I.; Yates, R.L.; Yee, S.A.; Jacobs, B.M.; DeLuca, G.C. Invited Review: From nose to gut—The role of the microbiome in neurological disease. Neuropathol. Appl. Neurobiol. 2019, 45, 195–215. [Google Scholar] [CrossRef]
  27. Chen, J.; Li, T.; Ye, C.; Zhong, J.; Huang, J.-D.; Ke, Y.; Sun, H. The Lung Microbiome: A New Frontier for Lung and Brain Disease. Int. J. Mol. Sci. 2023, 24, 2170. [Google Scholar] [CrossRef]
  28. Hosang, L.; Canals, R.C.; van der Flier, F.J.; Hollensteiner, J.; Daniel, R.; Flügel, A.; Odoardi, F. The lung microbiome regulates brain autoimmunity. Nature 2022, 603, 138–144. [Google Scholar] [CrossRef] [PubMed]
  29. Azzoni, R.; Marsland, B.J. The lung-brain axis: A new frontier in host-microbe interactions. Immunity 2022, 55, 589–591. [Google Scholar] [CrossRef] [PubMed]
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Utembe, W.; Kamng’ona, A.W. The Knowns and Unknowns of Chemically Induced Lower Respiratory Tract Microbiota Dysbiosis and Lung Disease. Environ. Sci. Proc. 2023, 27, 21.

AMA Style

Utembe W, Kamng’ona AW. The Knowns and Unknowns of Chemically Induced Lower Respiratory Tract Microbiota Dysbiosis and Lung Disease. Environmental Sciences Proceedings. 2023; 27(1):21.

Chicago/Turabian Style

Utembe, Wells, and Arox Wadson Kamng’ona. 2023. "The Knowns and Unknowns of Chemically Induced Lower Respiratory Tract Microbiota Dysbiosis and Lung Disease" Environmental Sciences Proceedings 27, no. 1: 21.

Article Metrics

Back to TopTop