Anaerobic bacterial fermentation products increase tuberculosis risk in antiretroviral-drug-treated HIV patients.

QIIME allows analysis of high-throughput community sequencing data

Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887

Cutadapt removes adapter sequences from high-throughput sequencing reads

Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889

Metagenomic biomarker discovery and explanation

Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W. S., & Huttenhower, C. (2011) · Genome Biology · doi:10.1186/gb-2011-12-6-r60 · Cited by 16,192

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2676 · Cited by 9,116

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S. M., Betley, J., Fraser, L., Bauer, M., et al. (2012) · The ISME Journal · doi:10.1038/ismej.2012.8 · Cited by 8,839

UniFrac: a New Phylogenetic Method for Comparing Microbial Communities

Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

McDonald, D. T., Price, M. N., Goodrich, J. K., Nawrocki, E. P., DeSantis, T. Z., Probst, A. J., Andersen, G. L., Knight, R. D., & Hugenholtz, P. (2011) · The ISME Journal · doi:10.1038/ismej.2011.139 · Cited by 5,144

Quality control and preprocessing of metagenomic datasets

Schmieder, R., & Edwards, R. A. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr026 · Cited by 5,119

STAMP: statistical analysis of taxonomic and functional profiles

Parks, D. H., Tyson, G. W., Hugenholtz, P., & Beiko, R. G. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu494 · Cited by 4,246

Gut Microbiota Metabolism of Dietary Fiber Influences Allergic Airway Disease and Hematopoiesis

Trompette, A., Gollwitzer, E. S., Yadava, K., Sichelstiel, A. K., Sprenger, N., Ngom-Bru, C., Blanchard, C., Junt, T., Nicod, L. P., Harris, N. L., et al. (2014) · Nature Medicine · doi:10.1038/nm.3444 · Cited by 2,862

Microbiota in health and diseases

Hou, K., Wu, Z.-X., Chen, X.-Y., Wang, J.-Q., Zhang, D., Xiao, C., Zhu, D., Koya, J. B., Wei, L., Li, J., et al. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-00974-4 · Cited by 3,171

The dynamic lung microbiome in health and disease

Natalini, J. G., Singh, S., & Segal, L. N. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00821-x · Cited by 546

Functional effects of the microbiota in chronic respiratory disease

Budden, K. F., Shukla, S. D., Rehman, S. F., Bowerman, K. L., Keely, S., Hugenholtz, P., Armstrong-James, D. P. H., Adcock, I. M., Chotirmall, S. H., Chung, K. F., et al. (2019) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(18)30510-1 · Cited by 453

The role of the lung microbiota and the gut–lung axis in respiratory infectious diseases

Dumas, A., Bernard, L., Poquet, Y., Lugo-Villarino, G., & Neyrolles, O. (2018) · Cellular Microbiology · doi:10.1111/cmi.12966 · Cited by 444

Lung microbiome: new insights into the pathogenesis of respiratory diseases

Li, R., Li, J., & Zhou, X. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01722-y · Cited by 483

Lower Airway Dysbiosis Affects Lung Cancer Progression

Tsay, J.-C. J., Wu, B. G., Sulaiman, I., Gershner, K., Schluger, R., Li, Y., Yie, T.-A., Meyn, P., Olsen, E., Perez, L., et al. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-20-0263 · Cited by 322

Intratumoural microbiota: a new frontier in cancer development and therapy

Cao, Y., Xia, H., Tan, X., Shi, C., Ma, Y., Meng, D., Zhou, M., Lv, Z., Wang, S., & Jin, Y. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01693-0 · Cited by 269

Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection

Bao, L., Zhang, C., Dong, J., Zhao, L., Li, Y., & Sun, J. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01840 · Cited by 207

Antibiotic treatment for Tuberculosis induces a profound dysbiosis of the microbiome that persists long after therapy is completed

Wipperman, M. F., Fitzgerald, D. W., Juste, M. A. J., Taur, Y., Namasivayam, S., Sher, A., Bean, J. M., Bucci, V., & Glickman, M. S. (2017) · Scientific Reports · doi:10.1038/s41598-017-10346-6 · Cited by 213

Pathogenesis of HIV-Related Lung Disease: Immunity, Infection, and Inflammation

Cribbs, S. K., Crothers, K. A., & Morris, A. (2019) · Physiological Reviews · doi:10.1152/physrev.00039.2018 · Cited by 175

Short Chain Fatty Acids: Fundamental mediators of the gut-lung axis and their involvement in pulmonary diseases

Ashique, S., Rubis, G. D., Sirohi, E., Mishra, N., Rihan, M., Garg, A., Reyes, R.-J., Manandhar, B., Bhatt, S., Jha, N. K., et al. (2022) · Chemico-Biological Interactions · doi:10.1016/j.cbi.2022.110231 · Cited by 179

Effects of metabolites derived from gut microbiota and hosts on pathogens

Li, Z., Quan, G., Jiang, X., Yang, Y., Ding, X., Zhang, D., Wang, X., Hardwidge, P. R., Ren, W., & Zhu, G. (2018) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2018.00314 · Cited by 157

The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients

Hu, Y., Feng, Y., Wu, J., Liu, F., Zhang, Z., Hao, Y., Liang, S., Li, B., Li, J., Lv, N., et al. (2019) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2019.00090 · Cited by 154

The gut–airway microbiome axis in health and respiratory diseases

Özçam, M., & Lynch, S. V. (2024) · Nature Reviews Microbiology · doi:10.1038/s41579-024-01048-8 · Cited by 164

The microbiome and tuberculosis: state of the art, potential applications, and defining the clinical research agenda

Naidoo, C., Nyawo, G. R., Wu, B. G., Walzl, G., Warren, R. M., Segal, L. N., & Theron, G. (2019) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(18)30501-0 · Cited by 144

Short-Chain Fatty Acids as a Potential Treatment for Infections: a Closer Look at the Lungs

Machado, M. G., Sencio, V., & Trottein, F. (2021) · Infection and Immunity · doi:10.1128/iai.00188-21 · Cited by 115

The Microbiome and Tuberculosis: Early Evidence for Cross Talk

Namasivayam, S., Sher, A., Glickman, M. S., & Wipperman, M. F. (2018) · mBio · doi:10.1128/mbio.01420-18 · Cited by 97

The Lung Microbiome and Its Role in Pneumonia

Wu, B. G., & Segal, L. N. (2018) · Clinics in Chest Medicine · doi:10.1016/j.ccm.2018.07.003 · Cited by 92

New Players in Immunity to Tuberculosis: The Host Microbiome, Lung Epithelium, and Innate Immune Cells

Gupta, N., Kumar, R. K., & Agrawal, B. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.00709 · Cited by 91

Nutritional immunity: the impact of metals on lung immune cells and the airway microbiome during chronic respiratory disease

Healy, C. M., Muñoz‐Wolf, N., Strydom, J., Faherty, L., Williams, N. C., Kenny, S., Donnelly, S. C., & Cloonan, S. M. (2021) · Respiratory Research · doi:10.1186/s12931-021-01722-y · Cited by 90

The microbiome: an integral player in immune homeostasis and inflammation in the respiratory tract

Perdijk, O., Azzoni, R., & Marsland, B. J. (2023) · Physiological Reviews · doi:10.1152/physrev.00020.2023 · Cited by 94

Microbiota and lung cancer

Goto, T. (2022) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2022.07.006 · Cited by 86

Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism

Sulaiman, I., Wu, B. G., Li, Y., Tsay, J.-C. J., Sauthoff, M., Scott, A. S., Ji, K., Koralov, S. B., Weiden, M. D., Clemente, J. C., et al. (2021) · European Respiratory Journal · doi:10.1183/13993003.03434-2020 · Cited by 83

Mycobacterium tuberculosis, antimicrobials, immunity, and lung–gut microbiota crosstalk: current updates and emerging advances

Sekyere, J. O., Maningi, N. E., & Fourie, P. B. (2020) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.14300 · Cited by 74

Short-chain fatty acid acetate triggers antiviral response mediated by RIG-I in cells from infants with respiratory syncytial virus bronchiolitis

Antunes, K. H., Stein, R. T., Franceschina, C. M., da Silva, E. F., de Freitas, D. N., Silveira, J. S., Mocellin, M., Leitão, L. A. D. A., Fachi, J. L., Pral, L. P., et al. (2022) · EBioMedicine · doi:10.1016/j.ebiom.2022.103891 · Cited by 75

Microbiome-immune interactions in tuberculosis

Mori, G., Morrison, M., & Blumenthal, A. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009377 · Cited by 80

The role of microbiota in respiratory health and diseases, particularly in tuberculosis

Shah, T., Shah, Z., Baloch, Z., & Cui, X. (2021) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2021.112108 · Cited by 73

Microbiota and Immunity during Respiratory Infections: Lung and Gut Affair

Marrella, V., Nicchiotti, F., & Cassani, B. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25074051 · Cited by 72

Microbiota and Tuberculosis: A Potential Role of Probiotics, and Postbiotics

Liu, Y., Wang, J., & Wu, C. (2021) · Frontiers in Nutrition · doi:10.3389/fnut.2021.626254 · Cited by 60

Lung microbiota predict invasive pulmonary aspergillosis and its outcome in immunocompromised patients

Hérivaux, A., Willis, J. R., Mercier, T., Lagrou, K., Gonçalves, S. M., Gonçales, R. A., Maertens, J. A., Carvalho, A., Gabaldón, T., & Cunha, C. (2021) · Thorax · doi:10.1136/thoraxjnl-2020-216179 · Cited by 63

Metagenomic analysis of the lung microbiome in pulmonary tuberculosis - a pilot study

Hu, Y., Cheng, M., Liu, B., Dong, J., Sun, L., Yang, J., Yang, F., Chen, X., & Jin, Q. (2020) · Emerging Microbes & Infections · doi:10.1080/22221751.2020.1783188 · Cited by 57

Anaerobe-enriched gut microbiota predicts pro-inflammatory responses in pulmonary tuberculosis

Naidoo, C., Nyawo, G. R., Sulaiman, I., Wu, B. G., Turner, C. T., Bu, K., Palmer, Z., Li, Y., Reeve, B. W. P., Moodley, S., et al. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103374 · Cited by 50

The Human Microbiota, Infectious Disease, and Global Health: Challenges and Opportunities

Waldman, A. J., & Balskus, E. P. (2017) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.7b00232 · Cited by 54

The Role of Gut and Lung Microbiota in Susceptibility to Tuberculosis

Comberiati, P., Cicco, M. D., Paravati, F., Pelosi, U., Gangi, A. D., Arasi, S., Barni, S., Caimmi, D. P., Mastrorilli, C., Licari, A., et al. (2021) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph182212220 · Cited by 54

Systemic proinflammation after Mycobacterium tuberculosis infection was correlated to the gut microbiome in HIV‐uninfected humans

Huang, S., Yang, Y., Chou, K., Fung, C., Wang, F., & Su, W. (2019) · European Journal of Clinical Investigation · doi:10.1111/eci.13068 · Cited by 47

Microbiota in cancer: current understandings and future perspectives

Yao, Y., Zhu, Y., Chen, K., Chen, J., Li, Y., Li, D., & Wei, P. (2026) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-025-02335-3 · Cited by 56

Dietary Fibers: Effects, Underlying Mechanisms and Possible Role in Allergic Asthma Management

Verstegen, R. E. M., Kostadinova, A. I., Merenciana, Z., Garssen, J., Folkerts, G., Hendriks, R. W., & Willemsen, L. E. M. (2021) · Nutrients · doi:10.3390/nu13114153 · Cited by 42

The internationalization of human microbiome research

Porras, A. M., & Brito, I. (2019) · Current Opinion in Microbiology · doi:10.1016/j.mib.2019.09.012 · Cited by 41

Gut microbiome and metabolites: The potential key roles in pulmonary fibrosis

Wu, Y., Li, Y., Luo, Y., Zhou, Y., Ji, W., Chen, L., Liang, X., Wu, T., Tan, C., & Liu, Y. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.943791 · Cited by 42

Butyrate Prevents TGF-β1-Induced Alveolar Myofibroblast Differentiation and Modulates Energy Metabolism

Lee, H. Y., Nam, S., Kim, M. J., Kim, S. J., Back, S. H., & Yoo, H. J. (2021) · Metabolites · doi:10.3390/metabo11050258 · Cited by 39

Modulation of innate immunity in airway epithelium for host-directed therapy

Myszor, I. T., & Gudmundsson, G. H. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1197908 · Cited by 36

GV-971 prevents severe acute pancreatitis by remodeling the microbiota-metabolic-immune axis

Chen, X., Chen, X., Ding, Y. P., Zhang, N., Fu, W., Wu, M., Ge, F., Wang, J., Li, X., Geng, M., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-52398-z · Cited by 33

Alterations in the Gut Microbiome of Individuals With Tuberculosis of Different Disease States

Wang, Y., Deng, Y., Liu, N., Chen, Y., Jiang, Y., Teng, Z., Ma, Z., Chang, Y., & Xiang, Y. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.836987 · Cited by 32

Gut microbiota in HIV–pneumonia patients is related to peripheral CD4 counts, lung microbiota, and in vitro macrophage dysfunction

Shenoy, M. K., Fadrosh, D. W., Lin, D. L., Worodria, W. O., Byanyima, P., Musisi, E., Kaswabuli, S., Zawedde, J., Sanyu, I., Chang, E. G., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0651-4 · Cited by 30

Pathogen Metagenomics Reveals Distinct Lung Microbiota Signatures Between Bacteriologically Confirmed and Negative Tuberculosis Patients

Ding, L., Liu, Y., Wu, X., Wu, M., Luo, X., Ouyang, H., Xia, J., Liu, X., & Ding, T. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.708827 · Cited by 29

Gut microbiota and tuberculosis

Liu, Y., Yang, L., Meskini, M., Goel, A., Opperman, M., Shyamal, S. S., Manaithiya, A., Xiao, M., Ni, R., An, Y., et al. (2025) · iMeta · doi:10.1002/imt2.70054 · Cited by 36

The implication of Mycobacterium tuberculosis-mediated metabolism of targeted xenobiotics

Singh, V., Dziwornu, G. A., & Chibale, K. (2023) · Nature Reviews Chemistry · doi:10.1038/s41570-023-00472-3 · Cited by 27

The human microbiota in pulmonary tuberculosis: Not so innocent bystanders

Tarashi, S., Badi, S. A., Moshiri, A., Nasehi, M., Fateh, A., Vaziri, F., & Siadat, S. D. (2018) · Tuberculosis · doi:10.1016/j.tube.2018.10.010 · Cited by 26

The Sputum Microbiome in Pulmonary Tuberculosis and Its Association With Disease Manifestations: A Cross-Sectional Study

Ticlla, M., Hella, J., Hiza, H. C., Sasamalo, M., Mhimbira, F., Rutaihwa, L. K., Droz, S., Schaller, S., Reither, K., Hilty, M., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.633396 · Cited by 28

HIV, Cancer, and the Microbiota: Common Pathways Influencing Different Diseases

Herrera, S., Martínez‐Sanz, J., & Villar, S. S. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.01466 · Cited by 25

Cystic fibrosis airway microbiota associated with outcomes of nontuberculous mycobacterial infection

Caverly, L. J., Zimbric, M., Azar, M., Opron, K., & LiPuma, J. J. (2021) · ERJ Open Research · doi:10.1183/23120541.00578-2020 · Cited by 23

Symbiotic microbial communities in various locations of the lung cancer respiratory tract along with potential host immunological processes affected

Cheng, J., Zhou, L., & Wang, H. (2024) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2024.1296295 · Cited by 24

Effects of second-line anti-tuberculosis drugs on the intestinal microbiota of patients with rifampicin-resistant tuberculosis

Wu, C., Yi, H., Hu, Y., Luo, D., Tang, Z., Wen, X., Zhang, Y., Tang, M., Zhang, L., Wu, S., et al. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1127916 · Cited by 22

Friends and foes of tuberculosis: modulation of protective immunity

Brighenti, S., & Joosten, S. A. (2018) · Journal of Internal Medicine · doi:10.1111/joim.12778 · Cited by 20

Microbiota-Dependent Regulation of Antimicrobial Immunity in the Lung

Maschirow, L., Suttorp, N., & Opitz, B. (2019) · American Journal of Respiratory Cell and Molecular Biology · doi:10.1165/rcmb.2019-0101tr · Cited by 24

Gut microbiota and tuberculosis infection: interaction and therapeutic potential

Chai, Y., Li, M., Deng, X., Ma, C., Zhou, N., Chen, Y., Yao, Y., Li, K. C., Gong, W., & Lei, H. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2531201 · Cited by 25

The Lung Microbiome in COPD and Lung Cancer: Exploring the Potential of Metal-Based Drugs

O’Shaughnessy, M., Sheils, O. M., & Baird, A. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241512296 · Cited by 22

Non-immune cell components in tumor microenvironment influencing lung cancer Immunotherapy

Zhang, J., Liu, S., Chen, X., Xu, X., & Xu, F. (2023) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2023.115336 · Cited by 21

Regulatory functions and mechanisms of human microbiota in infectious diseases

Fang, Y., Lei, Z., Zhang, L., Liu, C. H., & Chai, Q. (2024) · hLife · doi:10.1016/j.hlife.2024.03.004 · Cited by 20

Perspectives in lung microbiome research

Sulaiman, I., Schuster, S., & Segal, L. N. (2020) · Current Opinion in Microbiology · doi:10.1016/j.mib.2020.06.001 · Cited by 19

Impact of the gut-lung axis on tuberculosis susceptibility and progression

Enjeti, A., Sathkumara, H. D., & Kupz, A. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1209932 · Cited by 17

Gut microbiota: a crucial player in the combat against tuberculosis

Jie, L., Chen, D., Yan, Y., Pi, J., Xu, J.-F., Chen, L., & Zheng, B. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1442095 · Cited by 16

Host microbiome in tuberculosis: disease, treatment, and immunity perspectives

Pant, A., Das, B., & Arimbasseri, G. A. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1236348 · Cited by 18

The uncharted territory of host-pathogen interaction in tuberculosis

Ghoshal, A., Verma, A., Bhaskar, A., & Dwivedi, V. P. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1339467 · Cited by 18

Short-Chain Fatty Acids Promote Mycobacterium avium subsp. hominissuis Growth in Nutrient-Limited Environments and Influence Susceptibility to Antibiotics

Silva, C. A. M., Rojony, R., Bermudez, L. E., & Danelishvili, L. (2020) · Pathogens · doi:10.3390/pathogens9090700 · Cited by 17

Role of the lung microbiome in HIV pathogenesis

Shenoy, M. K., & Lynch, S. V. (2017) · Current Opinion in HIV and AIDS · doi:10.1097/coh.0000000000000427 · Cited by 13

The functional consequences of the microbiome in HIV

Villar, S. S., Moreno, S., & Ferrer, M. (2017) · Current Opinion in HIV and AIDS · doi:10.1097/coh.0000000000000430 · Cited by 14

Longitudinal Lower Airway Microbial Signatures of Acute Cellular Rejection in Lung Transplantation

Natalini, J. G., Wong, K. K., Nelson, N. C., Wu, B. G., Rudym, D., Lesko, M. B., Qayum, S., Lewis, T. C., Wong, A., Chang, S. H., et al. (2024) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.202309-1551oc · Cited by 13

Bacteria and fungi of the lung: allies or enemies?

Garaci, E., Pariano, M., Nunzi, E., Costantini, C., Bellet, M. M., Antognelli, C., Russo, M. A., & Romani, L. R. (2024) · Frontiers in Pharmacology · doi:10.3389/fphar.2024.1497173 · Cited by 12

Characteristics of the lung microbiota in lower respiratory tract infections with and without history of pneumonia

Hong, L., Chen, Y., & Ye, L. (2021) · Bioengineered · doi:10.1080/21655979.2021.1997563 · Cited by 12

Strategic use of nanomaterials as double-edged therapeutics to control carcinogenesis via regulation of dysbiosis and bacterial infection: current status and future prospects

Verma, M., Randhawa, S., Bathla, M., Teji, N., & Acharya, A. (2025) · Journal of Materials Chemistry B · doi:10.1039/d4tb02409e · Cited by 13

An Army Marches on Its Stomach: Metabolic Intermediates as Antimicrobial Mediators in Mycobacterium tuberculosis Infection

Hackett, E. E., & Sheedy, F. J. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.00446 · Cited by 11

Emerging cellular and molecular interactions between the lung microbiota and lung diseases

Li, X., & Meng, X. (2021) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2021.1992345 · Cited by 11

The microbiota as a modulator of mucosal inflammation and HIV/HPV pathogenesis: From association to causation

Moreno, E., Ron, R., & Villar, S. S. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1072655 · Cited by 11

Does periodontitis influence the risk of COVID‐19? A scoping review

Ghosh, A., Joseph, B., & Anil, S. (2022) · Clinical and Experimental Dental Research · doi:10.1002/cre2.584 · Cited by 12

Airway microbiome signature accurately discriminates Mycobacterium tuberculosis infection status

Kayongo, A., Ntayi, M. L., Olweny, G., Kyalo, E., Ndawula, J. C., Ssengooba, W., Kigozi, E., Kalyesubula, R., Munana, R., Namaganda, J., et al. (2024) · iScience · doi:10.1016/j.isci.2024.110142 · Cited by 10

Microbiome-Mucosal Immunity Nexus: Driving Forces in Respiratory Disease Progression

Park, Y. C., Choi, S. Y., Cha, Y., Yoon, H. W., & Son, Y. M. (2024) · The Journal of Microbiology · doi:10.1007/s12275-024-00167-4 · Cited by 11

Full-length 16S rDNA sequencing based on Oxford Nanopore Technologies revealed the association between gut-pharyngeal microbiota and tuberculosis in cynomolgus macaques

Sawaswong, V., Chanchaem, P., Klomkliew, P., Rotcheewaphan, S., Meesawat, S., Kemthong, T., Kaewparuehaschai, M., Noradechanon, K., Ekatat, M., Kanitpun, R., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-53880-w · Cited by 8

Sulforaphane Inhibits Oxidative Stress and May Exert Anti-Pyroptotic Effects by Modulating NRF2/NLRP3 Signaling Pathway in Mycobacterium tuberculosis-Infected Macrophages

Chen, G., Shen, L., Hu, H., Feng, Y., Wen, D., Liu, Y., Zhai, H., Sun, W., Wang, M., Lei, X., et al. (2024) · Microorganisms · doi:10.3390/microorganisms12061191 · Cited by 9

PneumoniaCheck, a novel aerosol collection device, permits capture of airborne Mycobacterium tuberculosis and characterisation of the cough aeromicrobiome in people with tuberculosis

Chiyaka, T. L., Nyawo, G. R., Naidoo, C. C., Moodley, S., Clemente, J. C., Malherbe, S. T., Warren, R. M., Ku, D. N., Segal, L. N., & Theron, G. (2024) · Annals of Clinical Microbiology and Antimicrobials · doi:10.1186/s12941-024-00735-x · Cited by 8

Helper T cell bias following tuberculosis chemotherapy identifies opportunities for therapeutic vaccination to prevent relapse

Martinez-Martinez, Y. B., Huante, M. B., Chauhan, S., Naqvi, K. F., Bharaj, P., & Endsley, J. J. (2023) · npj Vaccines · doi:10.1038/s41541-023-00761-4 · Cited by 8

Non-tuberculous mycobacteria enhance the tryptophan-kynurenine pathway to induce immunosuppression and facilitate pulmonary colonization

Li, L., Shao, J., Tong, C., Gao, W., Pan, P., Chen, Q., Gao, C., Zhang, Y., Zhu, Y. J., & Chen, C. (2024) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2024.1455605 · Cited by 8

Exact variance component tests for longitudinal microbiome studies

Zhai, J., Knox, K. S., Twigg, H. L., Zhou, H., & Zhou, J. J. (2019) · Genetic Epidemiology · doi:10.1002/gepi.22185 · Cited by 8

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Wang, Y., Malmuthuge, N., Yao, J., & Guan, L. L. (2025) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00180-25 · Cited by 10

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Emadi, R., Saki, S., Yousefi, P., & Tabibzadeh, A. (2025) · Immunity Inflammation and Disease · doi:10.1002/iid3.70145 · Cited by 8

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Marimón, J. M. (2018) · Clinical Pulmonary Medicine · doi:10.1097/cpm.0000000000000268 · Cited by 7

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Liu, Y., Zhang, J., Leng, G., Hu, J., Wang, W., Deng, G., Ma, Y., & Sha, S. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1256866 · Cited by 6

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Baker, J. M., & Dickson, R. P. (2024) · Clinics in Chest Medicine · doi:10.1016/j.ccm.2024.10.006 · Cited by 6

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Moore, P. J., Hoffman, K., Ahmed, S., Fletcher, J. R., Wiggen, T. D., Lucas, S. K., Arif, S. J., Gilbertsen, A. J., Kent, L. A., Fiege, J. K., et al. (2025) · mBio · doi:10.1128/mbio.01338-24 · Cited by 5

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Nyawo, G. R., Naidoo, C. C., Wu, B. G., Sulaiman, I., Clemente, J. C., Li, Y., Minnies, S., Reeve, B. W. P., Moodley, S., Rautenbach, C., et al. (2022) · Thorax · doi:10.1136/thorax-2022-219103 · Cited by 6

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Moodley, S., Kroon, E. E., Naidoo, C. C., Nyawo, G. R., Wu, B. G., Naidoo, S., Chiyaka, T. L., Tshivhula, H., Singh, S., Li, Y., et al. (2024) · Microorganisms · doi:10.3390/microorganisms12061048 · Cited by 5

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Darawshy, F., Tsay, J.-C. J., Segal, L. N., & Pass, H. I. (2025) · Cancer Biomarkers · doi:10.1177/18758592251322045 · Cited by 5

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Luo, D., Shi, C.-Y., Wei, N.-S., Yang, B.-Y., Qin, K., Liu, G., Dong, B., Qin, Y.-X., Qin, X., Chen, S., et al. (2023) · Tuberculosis · doi:10.1016/j.tube.2023.102413 · Cited by 5

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Perumal, R., Somboro, A. M., Tulsi, J., Ngcapu, S., & Naidoo, K. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1643900 · Cited by 4

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Nyawo, G. R., Naidoo, C. C., Wu, B. G., Kwok, B., Clemente, J. C., Li, Y., Minnies, S., Reeve, B. W. P., Moodley, S., John, T.-J., et al. (2024) · Microbes and Infection · doi:10.1016/j.micinf.2024.105434 · Cited by 3

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Napier, E. G., Doratt, B. M., Cinco, I. R., Stuart, E. V., Geron, R. D., Davies, M. H., Malherbe, D. C., Kohama, S. G., Bermudez, L. E., Winthrop, K. L., et al. (2025) · Journal of Infection · doi:10.1016/j.jinf.2025.106626 · Cited by 3

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Yu, Y., Guo, Z., Luo, Z., Dian, Y., Yang, X., Chen, X., Zeng, F., & Deng, G. (2026) · Molecular Biomedicine · doi:10.1186/s43556-026-00473-w · Cited by 4

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Philips, J. A. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aan3781 · Cited by 1

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Sereti, I., Verburgh, M. L., Gifford, J., Lo, A., Boyd, A. C., Verheij, E., Verhoeven, A., Wit, F. W. N. M., van der Loeff, M. F. S., Giera, M. A., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113336 · Cited by 38

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Ruiz-Briseño, M. D. R., Ratkovich-González, S., Álvarez-Zavala, M., Magaña, A. V., González-Hernández, L. A., Ramos‐Solano, M., & Andrade-Villanueva, J. F. (2019) · Poster presentations · doi:10.1136/sextrans-2019-sti.331

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Devadiga, P., Batgire, J., Karandikar, K., Bhowmick, S., Birje, S., Kerkar, S. C., Nagar, V. S., Patil, D. P., Agrawal, S. R., Shastri, J. S., et al. (2026) · Gut Microbes · doi:10.1080/19490976.2026.2721739

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Wilkinson, K., Schneider-Luftman, D., Lai, R., Barrington, C., Jhilmeet, N., Lowe, D., Kelly, G., & Wilkinson, R. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2021.645446 · Cited by 7