The DOI matches its Crossref record; 40 of the 40 references it cites were found in a registry or an index.
Multicenter comparison of lung and oral microbiomes of HIV-infected and HIV-uninfected individuals.
Open accessAbstract
RATIONALE: Improved understanding of the lung microbiome in HIV-infected individuals could lead to better strategies for diagnosis, therapy, and prophylaxis of HIV-associated pneumonias. Differences in the oral and lung microbiomes in HIV-infected and HIV-uninfected individuals are not well defined. Whether highly active antiretroviral therapy influences these microbiomes is unclear. OBJECTIVES: We determined whether oral and lung microbiomes differed in clinically healthy groups of HIV-infected and HIV-uninfected subjects. METHODS: Participating sites in the Lung HIV Microbiome Project contributed bacterial 16S rRNA sequencing data from oral washes and bronchoalveolar lavages (BALs) obtained from HIV-uninfected individuals (n = 86), HIV-infected individuals who were treatment naive (n = 18), and HIV-infected individuals receiving antiretroviral therapy (n = 38). MEASUREMENTS AND MAIN RESULTS: Microbial populations differed in the oral washes among the subject groups (Streptococcus, Actinomyces, Rothia, and Atopobium), but there were no individual taxa that differed among the BALs. Comparison of oral washes and BALs demonstrated similar patterns from HIV-uninfected individuals and HIV-infected individuals receiving antiretroviral therapy, with multiple taxa differing in abundance. The pattern observed from HIV-infected individuals who were treatment naive differed from the other two groups, with differences limited to Veillonella, Rothia, and Granulicatella. CD4 cell counts did not influence the oral or BAL microbiome in these relatively healthy, HIV-infected subjects. CONCLUSIONS: The overall similarity of the microbiomes in participants with and without HIV infection was unexpected, because HIV-infected individuals with relatively preserved CD4 cell counts are at higher risk for lower respiratory tract infections, indicating impaired local immune function.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“The dominant genera of healthy lungs include Streptococcus, Fusobacterium, Pseudomonas, Veillonella, Prevotella, and Capnocytophaga (Beck et al., 2015; Dickson and Huffnagle, 2015; Wypych et al., 2019; Shen et al., 2020), colonizing the oral cavity as well.”
From Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection (2020) · cites this paper as Beck et al., 2015
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 19,549
Self-citationA new method for non-parametric multivariate analysis of variance
Anderson, M. J. (2001) · Austral Ecology · doi:10.1111/j.1442-9993.2001.01070.pp.x · Cited by 13,828
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
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies
Schloss, P. D., Gevers, D., & Westcott, S. L. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027310 · Cited by 2,112
Self-citationDisordered Microbial Communities in Asthmatic Airways
Hilty, M., Burke, C. M., Pedro, H., Cárdenas, P., Bush, A., Bossley, C. J., Davies, J. C., Ervine, A., Poulter, L. W., Pachter, L. S., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008578 · Cited by 1,874
The oral microbiome in health and disease
Wade, W. G. (2013) · Pharmacological Research · doi:10.1016/j.phrs.2012.11.006 · Cited by 1,347
Topographical Continuity of Bacterial Populations in the Healthy Human Respiratory Tract
Charlson, E. S., Bittinger, K., Haas, A. R., Fitzgerald, A. S., Frank, I., Yadav, A., Bushman, F. D., & Collman, R. G. (2011) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201104-0655oc · Cited by 1,144
Self-citationAnalysis of the lung microbiome in the “healthy” smoker and in COPD.
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. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016384 · Cited by 973 · cited 2×
“Although sampling during surgery can approach a gold standard (9, 10), this methodology is BAL Negative”
MethodResultSelf-citationNeutral theory in community ecology and the hypothesis of functional equivalence
Hubbell, S. P. (2005) · Functional Ecology · doi:10.1111/j.0269-8463.2005.00965.x · Cited by 898
Dynamics and associations of microbial community types across the human body
Ding, T., & Schloss, P. D. (2014) · Nature · doi:10.1038/nature13178 · Cited by 885
Self-citation
Cited by
Sorted by citations
Stress and stability: applying the Anna Karenina principle to animal microbiomes
Zaneveld, J. R., McMinds, R., & Vega Thurber, R. (2017) · Nature Microbiology · doi:10.1038/nmicrobiol.2017.121 · Cited by 977
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
Accounting for reciprocal host–microbiome interactions in experimental science
Stappenbeck, T. S., & Virgin, H. W. (2016) · Nature · doi:10.1038/nature18285 · Cited by 272
Yildiz, S., Mazel-Sanchez, B., Kandasamy, M., Manicassamy, B., & Schmolke, M. (2018) · Microbiome · doi:10.1186/s40168-017-0386-z · Cited by 264
Airway microbiota across age and disease spectrum in cystic fibrosis
Zemanick, E. T., Wagner, B. D., Robertson, C. E., Ahrens, R. C., Chmiel, J. F., Clancy, J. P., Gibson, R. L., Harris, W. T., Kurland, G., Laguna, T. A., et al. (2017) · European Respiratory Journal · doi:10.1183/13993003.00832-2017 · Cited by 241
Fungal-Bacterial Interactions in Health and Disease
Krüger, W., Vielreicher, S., Kapitan, M., Jacobsen, I. D., & Niemiec, M. J. (2019) · Pathogens · doi:10.3390/pathogens8020070 · Cited by 234
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
Methods in Lung Microbiome Research
Carney, S. M., Clemente, J. C., Cox, M. J., Dickson, R. P., Huang, Y. J., Kitsios, G. D., Kloepfer, K. M., Leung, J. M., LeVan, T. D., Molyneaux, P. L., et al. (2019) · American Journal of Respiratory Cell and Molecular Biology · doi:10.1165/rcmb.2019-0273tr · Cited by 201
Koch, C. D., Gladwin, M. T., Freeman, B. A., Lundberg, J. O., Weitzberg, E., & Morris, A. (2017) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2016.12.015 · Cited by 186
Self-citationPathogenesis 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
Self-citationMuhlebach, M. S., Zorn, B., Esther, C. R., Hatch, J., Murray, C. P. J., Turkovic, L., Ranganathan, S., Boucher, R. C., Stick, S. M., & Wolfgang, M. C. (2018) · PLoS Pathogens · doi:10.1371/journal.ppat.1006798 · Cited by 170
Bacterial-Host Interactions: Physiology and Pathophysiology of Respiratory Infection
Håkansson, A., Orihuela, C. J., & Bogaert, D. (2018) · Physiological Reviews · doi:10.1152/physrev.00040.2016 · Cited by 129
Lung cancer in persons with HIV
Sigel, K. M., Makinson, A., & Thaler, J. (2016) · Current Opinion in HIV and AIDS · doi:10.1097/coh.0000000000000326 · Cited by 113
Abbas, A. A., Diamond, J. M., Chehoud, C., Chang, B., Kotzin, J. J., Young, J. C., Imai, I., Haas, A. R., Cantu, E., Lederer, D. J., et al. (2017) · American Journal of Transplantation · doi:10.1111/ajt.14076 · Cited by 112
Self-citationEffect of Advanced HIV Infection on the Respiratory Microbiome
Twigg, H. L., Knox, K. S., Zhou, J. J., Crothers, K. A., Nelson, D. E., Toh, E. C., Day, R. B., Lin, H., Gao, X., Dong, Q., et al. (2016) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201509-1875oc · Cited by 98
Self-citationHuman encroachment into wildlife gut microbiomes
Fackelmann, G., Gillingham, M. A. F., Schmid, J., Heni, A. C., Wilhelm, K., Schwensow, N., & Sommer, S. (2021) · Communications Biology · doi:10.1038/s42003-021-02315-7 · Cited by 88
Lung inflammation and disease: A perspective on microbial homeostasis and metabolism
Méndez, R., Banerjee, S., Bhattacharya, S. K., & Banerjee, S. (2018) · IUBMB Life · doi:10.1002/iub.1969 · Cited by 86
Microbiome alterations in HIV infection a review
Williams, B., LANDAY, A. L., & Presti, R. M. (2016) · Cellular Microbiology · doi:10.1111/cmi.12588 · Cited by 80
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
Self-citationLim, W. S. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-801238-3.11636-8 · Cited by 70
Impact of long-term antiretroviral therapy on gut and oral microbiotas in HIV-1-infected patients
Imahashi, M., Ode, H., Kobayashi, A., Nemoto, M., Matsuda, M., Hashiba, C., Hamano, A., Nakata, Y., Mori, M., Seko, K., et al. (2021) · Scientific Reports · doi:10.1038/s41598-020-80247-8 · Cited by 74
Merenstein, C., Bushman, F. D., & Collman, R. G. (2022) · Microbiome · doi:10.1186/s40168-022-01342-8 · Cited by 66
Self-citationAirflow limitation in people living with HIV and matched uninfected controls
Ronit, A., Lundgren, J. D., Afzal, S., Benfield, T., Roen, A. O., Mocroft, A., Gerstoft, J., Nordestgaard, B. G., Vestbo, J., & Nielsen, S. D. (2018) · Thorax · doi:10.1136/thoraxjnl-2017-211079 · Cited by 67
Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function
Yang, L., Dunlap, D. G., Qin, S., Fitch, A. C., Li, K., Koch, C. D., Nouraie, M. S., DeSensi, R., Ho, K. S., Martinson, J. J., et al. (2019) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201905-1016oc · Cited by 59
Self-citationAllometry and Ecology of the Bilaterian Gut Microbiome
Sherrill-Mix, S. A., McCormick, K., Lauder, A. P., Bailey, A., Zimmerman, L., Li, Y., Django, J.-B. N., Bertolani, P., Colin, C., Hart, J. A. L., et al. (2018) · mBio · doi:10.1128/mbio.00319-18 · Cited by 61
Self-citationLung Microbiota and Its Impact on the Mucosal Immune Phenotype
Wu, B. G., & Segal, L. N. (2017) · Microbiology Spectrum · doi:10.1128/microbiolspec.bad-0005-2016 · Cited by 56
Presti, R. M., Handley, S. A., Droit, L., Ghannoum, M. A., Jacobson, M. Z., Shiboski, C. H., Webster-Cyriaque, J. Y., Brown, T., Yin, M. T., & Overton, E. T. (2018) · AIDS · doi:10.1097/qad.0000000000001811 · Cited by 58
Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection
Morris, A., Paulson, J. N., Talukder, H., Tipton, L., Kling, H. M., Cui, L., Fitch, A. C., Pop, M., Norris, K. A., & Ghedin, E. (2016) · Microbiome · doi:10.1186/s40168-016-0183-0 · Cited by 50
Self-citationHuman diseases, immunity and the oral microbiota—Insights gained from metagenomic studies
Idris, A., Hasnain, S. Z., Huat, L. Z., & Koh, D. S. Q. (2016) · Oral Science International · doi:10.1016/s1348-8643(16)30024-6 · Cited by 51
Konstantinidis, I., Crothers, K. A., Kunisaki, K. M., Drummond, M., Benfield, T., Zar, H. J., Huang, L., & Morris, A. (2023) · Nature Reviews Disease Primers · doi:10.1038/s41572-023-00450-5 · Cited by 52
Self-citationMukherjee, P. K., Chandra, J., Retuerto, M., Tatsuoka, C. M., Ghannoum, M. A., & McComsey, G. A. (2018) · PLoS ONE · doi:10.1371/journal.pone.0200285 · Cited by 48
Protected sampling is preferable in bronchoscopic studies of the airway microbiome
Grønseth, R., Drengenes, C., Wiker, H. G., Tangedal, S., Xue, Y., Husebø, G. R., Svanes, Ø., Lehmann, S., Aardal, M. E., Hoang, T., et al. (2017) · ERJ Open Research · doi:10.1183/23120541.00019-2017 · Cited by 48
Bidirectional transfer of Anelloviridae lineages between graft and host during lung transplantation
Abbas, A. A., Young, J. C., Clarke, E., Diamond, J. M., Imai, I., Haas, A. R., Cantu, E., Lederer, D. J., Meyer, K. C., Milewski, R. K., et al. (2018) · American Journal of Transplantation · doi:10.1111/ajt.15116 · Cited by 48
Self-citationCadena, A. M., Ma, Y., Ding, T., Bryant, M., Maiello, P. A., Geber, A. B., Lin, P. L., Flynn, J. L., & Ghedin, E. (2018) · Microbiome · doi:10.1186/s40168-018-0560-y · Cited by 44
Self-citationAlterations in the oral microbiome in HIV infection: causes, effects and potential interventions
Li, S., Su, B., He, Q., Wu, H., & Zhang, T. (2021) · Chinese Medical Journal · doi:10.1097/cm9.0000000000001825 · Cited by 47
Acute Infections Caused by Tropheryma Whipplei
Lagier, J., Fenollar, F., & Raoult, D. (2017) · Future Microbiology · doi:10.2217/fmb-2017-0178 · Cited by 43
Development of a Stable Lung Microbiome in Healthy Neonatal Mice
Kostrić, M., Milger, K., Krauss‐Etschmann, S., Engel, M., Vestergaard, G., Schloter, M., & Schöler, A. (2017) · Microbial Ecology · doi:10.1007/s00248-017-1068-x · Cited by 45
Battaglini, D., Robba, C., Fedele, A., Trancă, S., Sukkar, S. G., Pilato, V. D., Bassetti, M., Giacobbe, D. R., Vena, A., Patroniti, N. A., et al. (2021) · Frontiers in Medicine · doi:10.3389/fmed.2021.671714 · Cited by 44
Significant effect of HIV/HAART on oral microbiota using multivariate analysis
Griffen, A. L., Thompson, Z. A., Beall, C. J., Lilly, E. A., Granada, C., Treas, K., Dubois, K. R., Hashmi, S. B., Mukherjee, C., Gilliland, A. E., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-55703-9 · Cited by 41
Ladva, C. N., Golan, R., Greenwald, R., Yu, T., Sarnat, S. E., Flanders, W. D., Uppal, K., Walker, D. I., Tran, V., Liang, D., et al. (2017) · Journal of Breath Research · doi:10.1088/1752-7163/aa863c · Cited by 41
Metagenomics: A New Way to Illustrate the Crosstalk between Infectious Diseases and Host Microbiome
Zhang, Y., Lun, C.-Y., & Tsui, S. K. (2015) · International Journal of Molecular Sciences · doi:10.3390/ijms161125957 · Cited by 38
Obstructive Lung Disease in HIV—Phenotypes and Pathogenesis
Singhvi, D., Bon, J. M., & Morris, A. (2019) · Current HIV/AIDS Reports · doi:10.1007/s11904-019-00456-3 · Cited by 38
Self-citationCurrent trends and new developments in HIV research and periodontal diseases
Ryder, M. I., Shiboski, C. H., Yao, T., & Moscicki, A. (2019) · Periodontology 2000 · doi:10.1111/prd.12321 · Cited by 37
Targeting the Pulmonary Microbiota to Fight against Respiratory Diseases
Li, Z., Li, Y., Sun, Q., Wei, J., Li, B., Qiu, Y., Liu, K., Shao, D., & Ma, Z. (2022) · Cells · doi:10.3390/cells11050916 · Cited by 38
Lai, R. P. J., Cortes, T., Marais, S., Rockwood, N., Burke, M. L., Garza-Garcı́a, A., Horswell, S. D., Sesay, A. K., O’Garra, A., Young, D. B., et al. (2021) · mBio · doi:10.1128/mbio.01766-21 · Cited by 37
Kastner, J., Hossain, R., & WHITE, C. S. (2019) · Seminars in Roentgenology · doi:10.1053/j.ro.2019.10.003 · Cited by 39
Yin, H., Yang, L., Peng, G., Yang, K., Mi, Y., Hu, X., Hao, X., Jiao, Y., Wang, X., & Wang, Y. (2021) · Cancer Biology and Medicine · doi:10.20892/j.issn.2095-3941.2020.0450 · Cited by 36
Lung microbiome in human immunodeficiency virus infection
Twigg, H. L., Weinstock, G. M., & Knox, K. S. (2016) · Translational research · doi:10.1016/j.trsl.2016.07.008 · Cited by 33
Self-citationMartino, C., Kellman, B. P., Sandoval, D. R., Clausen, T. M., Marotz, C. A., Song, S. J., Wandro, S., Zaramela, L. S., Benítez, R. A. S., Zhu, Q., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.17.238444 · Cited by 33
Mechanisms Underlying HIV-Associated Noninfectious Lung Disease
Presti, R. M., Flores, S. C., Palmer, B. E., Atkinson, J. J., Lesko, C. R., Lau, B. M., Fontenot, A. P., Roman, J., McDyer, J. F., & Twigg, H. L. (2017) · CHEST Journal · doi:10.1016/j.chest.2017.04.154 · Cited by 32
Self-citationImmune status, and not HIV infection or exposure, drives the development of the oral microbiota
Coker, M. O., Mongodin, E. F., El‐Kamary, S. S., Akhigbe, P., Obuekwe, O., Omoigberale, A. I., LANGENBERG, P. W., Enwonwu, C. O., Hittle, L. E., Blattner, W. A., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-67487-4 · Cited by 32
Drengenes, C., Eagan, T., Haaland, I., Wiker, H. G., & Nielsen, R. (2021) · BMC Genomics · doi:10.1186/s12864-020-07252-z · Cited by 35
Effect of HIV/HAART and Other Clinical Variables on the Oral Mycobiome Using Multivariate Analyses
Fidel, P. L., Thompson, Z. A., Lilly, E. A., Granada, C., Treas, K., Dubois, K. R., Cook, L. B., Hashmi, S. B., Lisko, D. J., Mukherjee, C., et al. (2021) · mBio · doi:10.1128/mbio.00294-21 · Cited by 31
Lung microbial-host interface through the lens of multi-omics
Singh, S., Natalini, J. G., & Segal, L. N. (2022) · Mucosal Immunology · doi:10.1038/s41385-022-00541-8 · Cited by 31
Alsayed, A. R., Abed, A. I., Khader, H. A., Al-Shdifat, L., Hasoun, L., Al‐Rshaidat, M. M. D., Alkhatib, M., & Zihlif, M. A. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24044086 · Cited by 32
The Oral Microbiome and Lung Diseases
Pu, C. Y., Seshadri, M., Manuballa, S., & Yendamuri, S. (2020) · Current Oral Health Reports · doi:10.1007/s40496-020-00259-1 · Cited by 30
Xie, Y., Sun, J. M., Hu, C., Ruan, B., & Zhu, B. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.794746 · Cited by 27
The palatine tonsil bacteriome, but not the mycobiome, is altered in HIV infection
Fukui, Y., Aoki, K., Ishii, Y., & Tateda, K. (2018) · BMC Microbiology · doi:10.1186/s12866-018-1274-9 · Cited by 27
Influence of the FIV Status and Chronic Gingivitis on Feline Oral Microbiota
Older, C. E., Gomes, M. D. O. S., Hoffmann, A. R., Policano, M. D., Reis, C. A. D. C., Carregaro, A. B., Ambrósio, C. E., & Lara, V. M. (2020) · Pathogens · doi:10.3390/pathogens9050383 · Cited by 27
Tavárez, Z. Q., Li, D., Croft, D. P., Gill, S. R., Ossip, D. J., & Rahman, I. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.589501 · Cited by 27
Presence of Tropheryma whipplei in Different Body Sites in a Cohort of Healthy Subjects
Qin, S., Clausen, E. S., Lucht, L. A., Michael, H., Beck, J. M., Curtis, J. L., Freeman, C. M., & Morris, A. (2016) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201601-0162le · Cited by 22
Self-citationSamuelson, D. R., Siggins, R. W., Ruan, S., Amedee, A. M., Sun, J., Zhu, Q. K., Marasco, W. A., Taylor, C. M., Luo, M., Welsh, D. A., et al. (2018) · Alcohol · doi:10.1016/j.alcohol.2018.08.012 · Cited by 25
The respiratory microbiome of HIV-infected individuals
Lawani, M. B., & Morris, A. (2016) · Expert Review of Anti-infective Therapy · doi:10.1080/14787210.2016.1206469 · Cited by 26
Self-citationTan, Y., Chen, Z., Zeng, Z., Wu, S., Liu, J., Zou, S., Wang, M., & Liang, K. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.00005-23 · Cited by 23
Impact of HIV infection on aging and immune status
Blanco, J. R., Negredo, E., Bernal, E., & Blanco, J. (2020) · Expert Review of Anti-infective Therapy · doi:10.1080/14787210.2021.1848546 · Cited by 22
Coker, M. O., Akhigbe, P., Osagie, E., Idemudia, N. L., Igedegbe, O., Chukwumah, N. M., Adebiyi, R., Mann, A. E., O’Connell, L. M., Obuekwe, O., et al. (2021) · BMC Oral Health · doi:10.1186/s12903-021-01944-y · Cited by 21
Decreased microbiome diversity in the HIV small airway epithelium
Xu, S., Tsai, A., Sze, M. A., Vucic, E. A., Shaipanich, T., Harris, M., Guillemi, S. A., Yang, J., Sinha, S., Nislow, C., et al. (2018) · Respiratory Research · doi:10.1186/s12931-018-0835-7 · Cited by 21
Maintaining lung health with longstanding HIV
Collini, P., & Morris, A. M. (2015) · Current Opinion in Infectious Diseases · doi:10.1097/qco.0000000000000221 · Cited by 19
Self-citationLi, J., Chang, S., Guo, H., Ji, Y., Jiang, H., Ruan, L., & Du, M. (2020) · Pathogens · doi:10.3390/pathogens9110960 · Cited by 19
Interplay between oral immunity in HIV and the microbiome
Fidel, P. L., Moyes, D. L., Samaranayake, L. P., & Hagensee, M. E. (2020) · Oral Diseases · doi:10.1111/odi.13515 · Cited by 18
Qin, S., Clausen, E. S., Nouraie, M. S., Kingsley, L., McMahon, D. K., Kleerup, E. C., Huang, L., Ghedin, E., Greenblatt, R. M., & Morris, A. M. (2018) · PLoS ONE · doi:10.1371/journal.pone.0205065 · Cited by 18
Self-citationKayongo, A., Bartolomaeus, T. U. P., Birkner, T., Markó, L., Löber, U., Kigozi, E., Atugonza, C., Munana, R., Mawanda, D., Sekibira, R., et al. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.02139-21 · Cited by 19
Chronic Lung Disease in HIV Patients
Santoro, A., Guaraldi, G., Besutti, G., Leung, J. M., Fabbri, L. M., & Neri, S. (2018) · Aids Reviews · doi:10.24875/aidsrev.18000002 · Cited by 16
The microbiota-related coinfections in COVID-19 patients: a real challenge
Mohapatra, R. K., Dhama, K., Mishra, S., Sarangi, A. K., Kandi, V., Tiwari, R., & Pintilie, L. (2021) · Beni-Suef University Journal of Basic and Applied Sciences · doi:10.1186/s43088-021-00134-7 · Cited by 16
Chang, S., Guo, H., Li, J., Ji, Y., Jiang, H., Ruan, L., & Du, M. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.781246 · Cited by 16
Gonçalves, L. S., Ferreira, D. D. C., Heng, N. C. K., Vidal, F., dos Santos, H. F., Zanicotti, D. G., Vasconcellos, M., Stambovsky, M., Lawley, B., Rubini, N. D. P. M., et al. (2019) · Journal Of Clinical Periodontology · doi:10.1111/jcpe.13176 · Cited by 15
Ryder, M. I., Yao, T., Russell, J. S., Moscicki, A., Shiboski, C. H., & Study, T. P. H. C. (2016) · Journal Of Clinical Periodontology · doi:10.1111/jcpe.12646 · Cited by 14
Microbiome Studies in Non-human Primates
Brenchley, J. M., & Ortiz, A. M. (2021) · Current HIV/AIDS Reports · doi:10.1007/s11904-021-00584-9 · Cited by 16
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
Self-citationOgunbayo, A. E., Mogotsi, M. T., Sondlane, H., Nkwadipo, K. R., Sabiu, S., & Nyaga, M. M. (2022) · Viruses · doi:10.3390/v14112516 · Cited by 14
Beall, C. J., Lilly, E. A., Granada, C., Treas, K., Dubois, K. R., Hashmi, S. B., Vázquez, J. A., Hagensee, M. E., Griffen, A. L., Leys, E. J., et al. (2023) · mBio · doi:10.1128/mbio.00409-23 · Cited by 13
COPD in People with HIV: Epidemiology, Pathogenesis, Management, and Prevention Strategies
Byanova, K. L., Abelman, R. A., North, C. M., Christenson, S. A., & Huang, L. (2023) · International Journal of COPD · doi:10.2147/copd.s388142 · Cited by 14
Self-citationVariance Component Selection With Applications to Microbiome Taxonomic Data
Zhai, J., Kim, J., Knox, K. S., Twigg, H. L., Zhou, H., & Zhou, J. J. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00509 · Cited by 11
Self-citationThe Lung Microbiome in HIV: Getting to the HAART of the Host–Microbe Interface
Segal, L. N., & Dickson, R. P. (2016) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201602-0280ed · Cited by 12
Changes in Conjunctival Microbiota Associated With HIV Infection and Antiretroviral Therapy
Liu, Q., Xu, Z.-Y., Wang, X., Huang, X., Zheng, W.-L., Li, M., Xiao, F., Ouyang, P.-W., Yang, X.-H., Cui, Y., et al. (2021) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.62.12.1 · Cited by 11
Peña, D. E. R., Santos, E. D. S., Bezerra, R. D. S., Nobre, Á. V. V., Pólvora, T. L. S., da Fonseca, B. A. L., Pozzetto, B., Lourenço, A. G., do Nascimento, C., & Motta, A. C. F. (2022) · Journal of Periodontology · doi:10.1002/jper.21-0466 · Cited by 11
Impact of HIV on the human gut microbiota: Challenges and perspectives
Dubourg, G. (2016) · Human Microbiome Journal · doi:10.1016/j.humic.2016.10.001 · Cited by 11
Meng, J., Tao, J., Abu, Y. F., Sussman, D. A., Girotra, M., Franceschi, D., & Roy, S. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.02472-22 · Cited by 10
Rofael, S., Brown, J., Pickett, E., Johnson, M. A., Hurst, J. R., Spratt, D. A., Lipman, M. C. I., & McHugh, T. D. (2020) · EClinicalMedicine · doi:10.1016/j.eclinm.2020.100427 · Cited by 12
Sze, M. A., Xu, S., Leung, J. M., Vucic, E. A., Shaipanich, T., Moghadam, A., Harris, M., Guillemi, S. A., Sinha, S., Nislow, C., et al. (2016) · BMC Pulmonary Medicine · doi:10.1186/s12890-016-0303-4 · Cited by 9
The respiratory tract microbial biogeography in alcohol use disorder
Samuelson, D. R., Burnham, E. L., Maffei, V. J., Vandivier, R. W., Blanchard, E., Shellito, J. E., Luo, M., Taylor, C. M., & Welsh, D. A. (2017) · American Journal of Physiology-Lung Cellular and Molecular Physiology · doi:10.1152/ajplung.00277.2017 · Cited by 10
Family‐based study reveals decreased abundance of sputum Granulicatella in asthmatics
Wang, L., Solá, D. D. Á., Mao, Y., Bielecki, P., Zhu, Y. L., Sun, Z., Shan, L., Flavell, R. A., Bazzy‐Asaad, A., & DeWan, A. T. (2018) · Allergy · doi:10.1111/all.13493 · Cited by 9
The lung microbiome in children with HIV-bronchiectasis: a cross-sectional pilot study
Masekela, R., Vosloo, S., Venter, S. N., de Beer, Z. W., & Green, R. J. (2018) · BMC Pulmonary Medicine · doi:10.1186/s12890-018-0632-6 · Cited by 8
A Summary of the Fifth Annual Virology Education HIV Microbiome Workshop
Sherrill-Mix, S. A., Connors, K. A., Aldrovandi, G. M., Brenchley, J. M., Boucher, C. A., Bushman, F. D., Collman, R. G., Dandekar, S., Klatt, N. R., Lagenaur, L. A., et al. (2020) · AIDS Research and Human Retroviruses · doi:10.1089/aid.2020.0121 · Cited by 6
Self-citationKuhn, L., Wang, T., Li, F., Strehlau, R., Tobin, N. H., Violari, A., Brooker, S., Patel, F., Liberty, A., Shiau, S., et al. (2023) · AIDS · doi:10.1097/qad.0000000000003599 · Cited by 6
The Microbiome and Pulmonary Immune Function
Baker, J. M., & Dickson, R. P. (2024) · Clinics in Chest Medicine · doi:10.1016/j.ccm.2024.10.006 · Cited by 6
Magnetic-activated cell sorting identifies a unique lung microbiome community
Dunlap, D. G., Yang, L., Qin, S., Li, K., Fitch, A. C., Huang, L., McVerry, B. J., Hand, T. W., Methé, B. A., & Morris, A. M. (2023) · Microbiome · doi:10.1186/s40168-022-01434-5 · Cited by 6
Self-citationLiu, F., Yang, X., OuYang, C., Zhaohui, H., Yang, C., & Yang, C. (2024) · Infection and Drug Resistance · doi:10.2147/idr.s451477 · Cited by 7
Motivation and response rates in bronchoscopy studies
Martinsen, E. M. H., Eagan, T., Leiten, E. O., Nordeide, E., Bakke, P. S., Lehmann, S., & Nielsen, R. (2019) · Multidisciplinary Respiratory Medicine · doi:10.1186/s40248-019-0178-3 · Cited by 6
Jude, M. S., Yang, C., Filho, F. S. L., Cordero, A. I. H., Yang, J., Shaipanich, T., Li, X., Lin, D. T. S., MacIsaac, J. L., Kobor, M. S., et al. (2023) · Respiratory Research · doi:10.1186/s12931-023-02431-4 · Cited by 5
Metadata
- Authors
- Beck, J. M., Schloss, P. D., Venkataraman, A., Twigg, H., Jablonski, K. A., Bushman, F. D., Campbell, T. B., Charlson, E. S., Collman, R. G., Crothers, K., Curtis, J. L., Drews, K. L., Flores, S. C., Fontenot, A. P., Foulkes, M. A., Frank, I., Ghedin, E., Huang, L., Lynch, S. V., Morris, A., Palmer, B. E., Schmidt, T. M., Sodergren, E., Weinstock, G. M., & Young, V. B.
- Affiliations
- VA Eastern Colorado Health Care System (US)
- University of Michigan (US)
- Indiana University Indianapolis (US)
- George Washington University (US)
- Department of Microbiology and
- University of Colorado Denver (US)
- University of Pennsylvania (US)
- University of Washington (US)
- Department of Computational and Systems Biology and
- University of California, San Francisco (US)
- University of Pittsburgh (US)
- The Jackson Laboratory for Genomic Medicine (US)
- Corresponding author
- Beck, James M.
- ORCID
- Schloss, Patrick D.
- Venkataraman, Arvind
- Twigg, Homer
- Bushman, Frederic D.
- Campbell, Thomas B.
- Collman, Ronald G.
- Crothers, Kristina
- Curtis, Jeffrey L.
- Drews, Kimberly L.
- Fontenot, Andrew P.
- Frank, Ian
- Ghedin, Elodie
- Huang, Laurence
- Lynch, Susan V.
- Morris, Alison
- Palmer, Brent E.
- Schmidt, Thomas M.
- Sodergren, Erica
- Weinstock, George M.
- Young, Vincent B.
- Venue
- American Journal of Respiratory and Critical Care Medicine
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-12-01
- Volume
- 192
- Issue
- 11
- Pages
- 1335-1344
- ISSN
- 1073-449X (ISSN-L)
- 1535-4970
- PMC
- PMC4731698
- OpenAlex
- W1793747226
- Cited by
- 150
- References
- 40
- Citations by year
- 2026: 5 · 2025: 6 · 2024: 12 · 2023: 11 · 2022: 12 · 2021: 24 · 2020: 14 · 2019: 15 · 2018: 21 · 2017: 13 · 2016: 15 · 2015: 2
- FWCI
- 18.23
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- American Journal of Respiratory and Critical Care Medicine (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
- Funders
- U.S. Public Health Service (U01HL98961, R01HG005975, U01HL098960, U01HL098958, U01HL098957, R01HL090342, U01HL098996, U01HL098962, U01HL098964)
- National Institutes of Health
- Human Microbiome Project (R0100417746, T32 HL007749)
- University of Pittsburgh Clinical and Translational Science Institute (UL1 RR024153, UL1 TR000005)
- University of California San Francisco Clinical and Translational Science Institute (UL1 TR000004)
- University of Colorado
- Clinical and Translational Science Institute (UL1 TR001082)
- Topics
- Health Sciences › Dentistry › General Dentistry › HIV/AIDS oral health manifestations
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- HIV infection, lung microbiome, oral microbiota, HIV-associated pneumonia, antiretroviral therapy, bronchoalveolar lavage, oral wash, bacterial diversity, CD4 count, Streptococcus, Veillonella, Rothia, Granulicatella, Actinomyces, Atopobium, lower respiratory tract infection
- MeSH terms
- Adult, Bronchoalveolar Lavage Fluid, Female, Humans, Lung, Male, Middle Aged, Mouth, Prospective Studies, Cohort Studies, HIV Infections, Antiretroviral Therapy, Highly Active, Microbiota
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
