Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza
Open accessAbstract
The upper respiratory tract microbiome has an important role in respiratory health. Influenza A is a common viral infection that challenges that health, and a well-recognized sequela is bacterial pneumonia. Given this connection, we sought to characterize the upper respiratory tract microbiota of individuals suffering from the pandemic H1N1 influenza A outbreak of 2009 and determine if microbiome profiles could be correlated with patient characteristics. We determined the microbial profiles of 65 samples from H1N1 patients by cpn60 universal target amplification and sequencing. Profiles were examined at the phylum and nearest neighbor "species" levels using the characteristics of patient gender, age, originating health authority, sample type and designation (STAT/non-STAT). At the phylum level, Actinobacteria-, Firmicutes- and Proteobacteria-dominated microbiomes were observed, with none of the patient characteristics showing significant profile composition differences. At the nearest neighbor "species" level, the upper respiratory tract microbiomes were composed of 13-20 "species" and showed a trend towards increasing diversity with patient age. Interestingly, at an individual level, most patients had one to three organisms dominant in their microbiota. A limited number of discrete microbiome profiles were observed, shared among influenza patients regardless of patient status variables. To assess the validity of analyses derived from sequence read abundance, several bacterial species were quantified by quantitative PCR and compared to the abundance of cpn60 sequence read counts obtained in the study. A strong positive correlation between read abundance and absolute bacterial quantification was observed. This study represents the first examination of the upper respiratory tract microbiome using a target other than the 16S rRNA gene and to our knowledge, the first thorough examination of this microbiome during a viral infection.
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Another study of patients with 2009 pandemic H1N1 influenza infection revealed that the predominant phyla of the upper respiratory tract (nasal and nasopharyngeal samples) in patients harboring pandemic H1N1 were Actinobacteria, Firmicutes, and Proteobacteria although normal controls were not included.
“Another study of patients with 2009 pandemic H1N1 influenza infection revealed that the predominant phyla of the upper respiratory tract (nasal and nasopharyngeal samples) in patients harboring pandemic H1N1 were Actinobacteria, Firmicutes, and Proteobacteria although normal controls were not included;”
From Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. (2018) · cites this paper as [109]
These studies demonstrated that there was considerable inter-subject variability, highlighting the need for longitudinal studies to decipher changes following viral infection.
“However, these studies demonstrated that there was considerable inter-subject variability, highlighting the need for longitudinal studies to decipher changes following viral infection.”
From Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. (2018) · cites this paper as [109]
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Cites
R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,706 · see citing works
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 · see citing works
vegan: Community Ecology Package
Oksanen, J., Simpson, G. L., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O’Hara, R. B., Sólymos, P., Stevens, M. H. H., Szöcs, E., et al. (2001) · doi:10.32614/cran.package.vegan · Cited by 27,099 · see citing works
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 20,966 · see citing works
Alberts, B., Johnson, A., Lewis, J. H., Morgan, D. O., RAFF, M. C., Roberts, K. J., & Walter, P. (2017) · W.W. Norton eBooks · doi:10.1201/9781315735368 · Cited by 7,937 · see citing works
Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction
Ye, J., Coulouris, G., Zaretskaya, I., Cutcutache, I., Rozen, S., & Madden, T. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-134 · Cited by 6,138 · see citing works
Topographical and Temporal Diversity of the Human Skin Microbiome
Grice, E. A., Kong, H. H., Conlan, S., Deming, C. B., Davis, J., Young, A. C., Program, N. C. S., Bouffard, G. G., Blakesley, R. W., Murray, P. R., et al. (2009) · Science · doi:10.1126/science.1171700 · Cited by 2,953 · see citing works
Morens, D. M., Taubenberger, J. K., & Fauci, A. S. (2008) · The Journal of Infectious Diseases · doi:10.1086/591708 · Cited by 1,625 · cited 2× · see citing works
“mortality associated with influenza [3], and Streptococcus”
BackgroundBellerophon: a program to detect chimeric sequences in multiple sequence alignments
Huber, T., Faulkner, G. J., & Hugenholtz, P. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth226 · Cited by 1,532 · see citing works
Bias in template-to-product ratios in multitemplate PCR
Polz, M. F., & Cavanaugh, C. M. (1998) · Applied and Environmental Microbiology · doi:10.1128/aem.64.10.3724-3730.1998 · Cited by 1,484 · see citing works
UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context
Lozupone, C., Hamady, M., & Knight, R. D. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-371 · Cited by 1,454 · see citing works
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 · see citing works
Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78
Martinez, D. A., Larrondo, L. F., Putnam, N. H., Gelpke, M. D. S., Huang, K. H., Chapman, J., Helfenbein, K. G., Ramaiya, P., Detter, J. C., Larimer, F. W., et al. (2004) · Nature Biotechnology · doi:10.1038/nbt967 · Cited by 933 · see citing works
Carvalho, M. D. G. S., Tondella, M. L., McCaustland, K., Weidlich, L., McGee, L., Mayer, L. W., Steigerwalt, A., Whaley, M., Facklam, R. R., Fields, B., et al. (2007) · Journal of Clinical Microbiology · doi:10.1128/jcm.02498-06 · Cited by 588 · see citing works
Quantifying microbial communities with 454 pyrosequencing: does read abundance count?
Amend, A. S., Seifert, K. A., & Bruns, T. D. (2010) · Molecular Ecology · doi:10.1111/j.1365-294x.2010.04898.x · Cited by 516 · see citing works
The 2009 A (H1N1) influenza virus pandemic: A review
Girard, M. P., Tam, J. S., Assossou, O. M., & Kiény, M. P. (2010) · Vaccine · doi:10.1016/j.vaccine.2010.05.031 · Cited by 489 · see citing works
Systematic artifacts in metagenomes from complex microbial communities
Gomez‐Alvarez, V., Teal, T. K., & Schmidt, T. M. (2009) · The ISME Journal · doi:10.1038/ismej.2009.72 · Cited by 467 · see citing works
Lee, D. H., Zo, Y.-G., & Kim, S. J. (1996) · Applied and Environmental Microbiology · doi:10.1128/aem.62.9.3112-3120.1996 · Cited by 439 · see citing works
Xu, J., Saunders, C. W., Hu, P., Grant, R. A., Boekhout, T., Kuramae, E. E., Kronstad, J. W., DeAngelis, Y. M., Reeder, N. L., Johnstone, K. R., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706756104 · Cited by 431 · see citing works
The Human Nasal Microbiota and Staphylococcus aureus Carriage
Frank, D. N., Feazel, L. M., Bessesen, M. T., Price, C. S., Janoff, E. N., & Pace, N. R. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010598 · Cited by 422 · see citing works
Comparative analyses of the bacterial microbiota of the human nostril and oropharynx
Lemon, K. P., Klepac-Ceraj, V., Schiffer, H. K., Brodie, E. L., Lynch, S. V., & Kolter, R. (2010) · mBio · doi:10.1128/mbio.00129-10 · Cited by 322 · see citing works
The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites
Ursell, L. K., Clemente, J. C., Rideout, J. R., Gevers, D., Caporaso, J. G., & Knight, R. D. (2012) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2012.03.010 · Cited by 310 · see citing works
Streptococcus pneumoniae coinfection is correlated with the severity of H1N1 pandemic influenza
Palacios, G., Hornig, M., Cisterna, D., Savji, N., Bussetti, A. V., Kapoor, V., Hui, J., Tokarz, R., Briese, T., Baumeister, E., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0008540 · Cited by 275 · see citing works
Nakamura, S., Yang, C.-S., Sakon, N., Ueda, M., Tougan, T., Yamashita, A., Goto, N., Takahashi, K., Yasunaga, T., Ikuta, K., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004219 · Cited by 267 · see citing works
Marcet‐Houben, M., Ballester, A., de la Fuente, B., Harries, E., Marcos, J. F., González-Candelas, L., & Gabaldón, T. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-646 · Cited by 250 · see citing works
cpnDB: A Chaperonin Sequence DatabasePreprint
Hill, J. E., Penny, S. L., Crowell, K. G., Goh, S. H., & Hemmingsen, S. M. (2004) · Genome Research · doi:10.1101/gr.2649204 · Cited by 225 · see citing works
Self-citationBiesbroek, G., Sanders, E. A. M., Roeselers, G., Wang, X., Caspers, M. P. M., Trzciński, K., Bogaert, D., & Keijser, B. J. F. (2012) · PLoS ONE · doi:10.1371/journal.pone.0032942 · Cited by 196 · see citing works
A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America
Greninger, A. L., Chen, E. C., Sittler, T., Scheinerman, A., Roubinian, N., Yu, G., Kim, E., Pillai, D. R., Guyard, C., Mazzulli, T., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013381 · Cited by 193 · see citing works
Self-citationLinks, M. G., Dumonceaux, T., Hemmingsen, S. M., & Hill, J. E. (2012) · PLoS ONE · doi:10.1371/journal.pone.0049755 · Cited by 158 · see citing works
Self-citationSchellenberg, J. J., Links, M. G., Hill, J. E., Dumonceaux, T., Peters, G. A., Tyler, S. D., Ball, T. B., Severini, A., & Plummer, F. A. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01640-08 · Cited by 106 · see citing works
Self-citationMolecular Definition of Vaginal Microbiota in East African Commercial Sex Workers
Schellenberg, J. J., Links, M. G., Hill, J. E., Dumonceaux, T., Kimani, J., Jaoko, W. G., Wachihi, C., Mungai, J. N., Peters, G. A., Tyler, S. D., et al. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.02943-10 · Cited by 77 · see citing works
Self-citationHill, J. E., Town, J. R., & Hemmingsen, S. M. (2005) · Environmental Microbiology · doi:10.1111/j.1462-2920.2005.00944.x · Cited by 77 · see citing works
Self-citationChaban, B. L., Links, M. G., & Hill, J. E. (2011) · Microbial Ecology · doi:10.1007/s00248-011-9931-7 · Cited by 42 · see citing works
Self-citationHill, J. E., Fernando, W. M. U., Zello, G. A., Tyler, R. T., Dahl, W. J., & Kessel, A. G. V. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.01510-09 · Cited by 39 · see citing works
Self-citationSchellenberg, J. J., Links, M. G., Hill, J. E., Hemmingsen, S. M., Peters, G. A., & Dumonceaux, T. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-089-8_10 · Cited by 27 · see citing works
Self-citationA region of mitochondrial division in the epithelium of the small intestine of the rat
Jeynes, B., & Altmann, G. G. (1975) · The Anatomical Record · doi:10.1002/ar.1091820303 · Cited by 25 · see citing works
Martinez, D., Larrondo, L. F., Putnam, N., et al. (2004) · Nature Biotechnology · doi:10.1038/nbt0704-899b · Cited by 2 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [2]Director-General Who (2011) Report of the review committee on the functioning of the international health regulations (2005) in relation to pandemic (H1N1) 2009. Sixty-fourth World Health Assembly: World Health Organization. 49-50 p
Cited by
Sorted by citations
Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia.
Hanada, S., Pirzadeh, M., Carver, K. Y., & Deng, J. C. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.02640 · Cited by 495 · see citing works
Characterization of the vaginal microbiota of healthy Canadian women through the menstrual cycle
Chaban, B. L., Links, M. G., Jayaprakash, T. P., Wagner, E. C., Bourque, D. K., Zoe, L., Albert, A., van Schalkwyk, J., Reid, G., Hemmingsen, S. M., et al. (2014) · Microbiome · doi:10.1186/2049-2618-2-23 · Cited by 274 · see citing works
Self-citationDysbiosis of upper respiratory tract microbiota in elderly pneumonia patients
de Steenhuijsen Piters, W. A. A., Huijskens, E. G. W., Wyllie, A. L., Biesbroek, G., van den Bergh, M. R., Veenhoven, R. H., Wang, X., Trzciński, K., Bonten, M. J., Rossen, J. W. A., et al. (2016) · The ISME Journal · doi:10.1038/ismej.2015.99 · Cited by 235 · see citing works
Increased richness and diversity of the vaginal microbiota and spontaneous preterm birth
Freitas, A. C., Bocking, A. D., Hill, J. E., & Money, D. (2018) · Microbiome · doi:10.1186/s40168-018-0502-8 · Cited by 199 · see citing works
Self-citationFreitas, A. C., Chaban, B. L., Bocking, A. D., Rocco, M., Yang, S., Hill, J. E., Money, D., Hemmingsen, S. M., Reid, G., Dumonceaux, T., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-07790-9 · Cited by 198 · see citing works
Self-citationAlbert, A., Chaban, B. L., Wagner, E. C., Schellenberg, J. J., Links, M. G., van Schalkwyk, J., Reid, G., Hemmingsen, S. M., Hill, J. E., & Money, D. (2015) · PLoS ONE · doi:10.1371/journal.pone.0135620 · Cited by 109 · see citing works
Self-citationKaul, D., Rathnasinghe, R., Marcela Ferrés, G., Tan, G. S., Barrera, A., Pickett, B. E., Methé, B. A., Das, S. R., O, I. B., Halpin, R., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16429-9 · Cited by 105 · see citing works
Plasmodium berghei ANKA causes intestinal malaria associated with dysbiosis
Taniguchi, T., Miyauchi, E., Nakamura, S., Hirai, M., Suzue, K., Imai, T., Nomura, T., Handa, T., Okada, H., Shimokawa, C., et al. (2015) · Scientific Reports · doi:10.1038/srep15699 · Cited by 95 · see citing works
Within-host dynamics shape antibiotic resistance in commensal bacteria
Davies, N. G., Flasche, S., Jit, M., & Atkins, K. E. (2019) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0786-x · Cited by 87 · see citing works
Assessment of Fungal Diversity in the Environment using Metagenomics:a Decade in Review
Cuadros-Orellana, S. (2013) · Fungal Genomics & Biology · doi:10.4172/2165-8056.1000110 · Cited by 84 · see citing works
Tarabichi, Y., Li, K., Hu, S., Nguyen, C., Wang, X., Elashoff, D., Saira, K., Frank, B., Bihan, M., Ghedin, E., et al. (2015) · Microbiome · doi:10.1186/s40168-015-0133-2 · Cited by 77 · see citing works
Lee, J., Kim, S., Lee, M., Kim, B., Song, W., Park, H., Cho, S., Hong, S., Chang, Y., & Kim, B. (2018) · Allergy · doi:10.1111/all.13608 · Cited by 75 · see citing works
Langevin, S., Pichon, M., Smith, E., Morrison, J., Bent, Z., Green, R., Barker, K., Solberg, O., Gillet, Y., Javouhey, E., et al. (2017) · Journal of General Virology · doi:10.1099/jgv.0.000920 · Cited by 64 · see citing works
Wen, Z., Xie, G., Zhou, Q., Qiu, C., Li, J., Hu, Q., Dai, W., Li, D., Zheng, Y., & Wen, F. (2018) · BioMed Research International · doi:10.1155/2018/6362716 · Cited by 63 · see citing works
Lehtinen, M. J., Hibberd, A. A., Männikkö, S., Yeung, N., Kauko, T., Forssten, S. D., Lehtoranta, L., Lahtinen, S. J., Stahl, B., Lyra, A., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-29793-w · Cited by 60 · see citing works
Correlation between Nasal Microbiome Composition and Remote Purulent Skin and Soft Tissue Infections
Johnson, R. C., Ellis, M. W., Lanier, J. B., Schlett, C. D., Cui, T., & Merrell, D. S. (2014) · Infection and Immunity · doi:10.1128/iai.02664-14 · Cited by 56 · see citing works
Ganz, H. H., Doroud, L., Firl, A. J., Hird, S. M., Eisen, J. A., & Boyce, W. M. (2017) · mSystems · doi:10.1128/msystems.00188-16 · Cited by 55 · see citing works
Ding, T., Song, T., Zhou, B., Geber, A. B., Ma, Y., Zhang, L., Volk, M., Kapadia, S. N., Jenkins, S. G., Salvatore, M., et al. (2019) · mBio · doi:10.1128/mbio.01296-19 · Cited by 52 · see citing works
The Effect of Influenza Virus on the Human Oropharyngeal Microbiome
Ramos‐Sevillano, E., Wade, W. G., Mann, A., Gilbert, A., Lambkin‐Williams, R., Killingley, B., Nguyen‐Van‐Tam, J. S., & Tang, C. M. (2018) · Clinical Infectious Diseases · doi:10.1093/cid/ciy821 · Cited by 48 · see citing works
Dual and mutual interaction between microbiota and viral infections: a possible treat for COVID-19
Baghbani, T., Nikzad, H., Azadbakht, J., Izadpanah, F., & Kashani, H. H. (2020) · Microbial Cell Factories · doi:10.1186/s12934-020-01483-1 · Cited by 44 · see citing works
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 · see citing works
Severe viral respiratory infections: are bugs bugging?
Vissers, M., de Groot, R., & Ferwerda, G. (2013) · Mucosal Immunology · doi:10.1038/mi.2013.93 · Cited by 37 · see citing works
The Unexpected Impact of Vaccines on Secondary Bacterial Infections Following Influenza
Smith, A. M., & Huber, V. C. (2017) · Viral Immunology · doi:10.1089/vim.2017.0138 · Cited by 36 · see citing works
Port d’Entrée for Respiratory Infections – Does the Influenza A Virus Pave the Way for Bacteria?
Siemens, N., Oehmcke-Hecht, S., Mettenleiter, T. C., Kreikemeyer, B., Valentin‐Weigand, P., & Hammerschmidt, S. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.02602 · Cited by 34 · see citing works
Sommerstein, R., Merz, T. M., Berger, S., Kraemer, J. G., Marschall, J., & Hilty, M. (2019) · Antimicrobial Resistance and Infection Control · doi:10.1186/s13756-019-0530-6 · Cited by 32 · see citing works
Host factors facilitating SARS‐CoV‐2 virus infection and replication in the lungs
Boutin, S., Hildebrand, D., Boulant, S., Kreuter, M., Rüter, J., Pallerla, S. R., Velavan, T. P., & Nurjadi, D. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03889-5 · Cited by 32 · see citing works
The personal touch: strategies toward personalized vaccines and predicting immune responses to them
Kennedy, R. B., Ovsyannikova, I. G., Lambert, N. D., Haralambieva, I. H., & Poland, G. A. (2014) · Expert Review of Vaccines · doi:10.1586/14760584.2014.905744 · Cited by 27 · see citing works
Dietl, B., Henares, D., Boix-Palop, L., Muñoz‐Almagro, C., Garau, J., & Calbo, E. (2021) · Frontiers in Medicine · doi:10.3389/fmed.2021.650271 · Cited by 25 · see citing works
Santos, S. J. D., Pakzad, Z., Elwood, C. N., Albert, A., Gantt, S. M., Manges, A. R., Dumonceaux, T., Maan, E. J., Hill, J. E., Money, D., et al. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.00067-21 · Cited by 23 · see citing works
Self-citationAljabr, W. A., Alruwaili, M., Penrice-Randal, R., Alrezaihi, A. F., Harrison, A., Ryan, Y., Bentley, E. G., Jones, B., Alhatlani, B. Y., AlShahrani, D. A., et al. (2021) · mSphere · doi:10.1128/msphere.00219-21 · Cited by 23 · see citing works
THE HUMAN MICROBIOTA: THE ROLE OF MICROBIAL COMMUNITIES IN HEALTH AND DISEASE
Botero, L. E., Delgado-Serrano, L., Hernández, M. L. C., Portillo, P. D., & Eder, M. M. Z. (2015) · Acta Biológica Colombiana · doi:10.15446/abc.v21n1.49761 · Cited by 19 · see citing works
Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling
Vancuren, S. J., Santos, S. J. D., Hill, J. E., & the Maternal Microbiome Legacy Project Team (2020) · PLoS ONE · doi:10.1371/journal.pone.0235682 · Cited by 18 · see citing works
Self-citationThe human microbiota: a new direction in the investigation of thoracic diseases.
Hui, A. W. H., Lau, H.-W., Chan, T. H.-T., & Tsui, S. K. (2013) · Europe PMC (PubMed Central) · doi:10.3978/j.issn.2072-1439.2013.07.41 · Cited by 18 · see citing works
Johnson, L. A., Chaban, B. L., Harding, J. C. S., & Hill, J. E. (2015) · BMC Research Notes · doi:10.1186/s13104-015-1170-4 · Cited by 17 · see citing works
Self-citationTief, F., Hoppe, C., Seeber, L., Obermeier, P., Chen, X., Karsch, K., Muehlhans, S., Adamou, E., Conrad, T., Béresniak, A., et al. (2015) · Antiviral Therapy · doi:10.3851/imp3034 · Cited by 17 · see citing works
Shetty, S. A., van Beek, J., Bijvank, E., Groot, J. A., Kuiling, S., Bosch, T., van Baarle, D., & Fuentes, S. (2022) · Scientific Reports · doi:10.1038/s41598-022-05618-9 · Cited by 16 · see citing works
Hernández‐Terán, A., Vega-Sánchez, Á. E., Mejía-Nepomuceno, F., Serna-Muñoz, R., Rodríguez‐Llamazares, S., Salido-Guadarrama, I., Romero-Espinoza, J. A., Guadarrama-Pérez, C., Sandoval-Gutiérrez, J. L., Campos, F., et al. (2023) · Virology Journal · doi:10.1186/s12985-023-01979-3 · Cited by 15 · see citing works
Seibert, B., Cáceres, C. J., Carnaccini, S., Garcia, S. C., Gay, L. C., Ortiz, L., Geiger, G., Rajão, D. S., Ottesen, E. A., & Perez, D. R. (2022) · PLoS Pathogens · doi:10.1371/journal.ppat.1010734 · Cited by 14 · see citing works
Hu, Y., Zhang, Y., Ren, X., Liu, Y., Xiao, Y., Li, L., Yang, F., Su, H., Liu, F., Liu, H., et al. (2016) · Journal of Clinical Virology · doi:10.1016/j.jcv.2015.12.013 · Cited by 14 · see citing works
Li, Y., Ding, J., Xiao, Y., Xu, B., He, W., Yang, Y., Yang, L., Su, M.-Q., Hao, X., & Ma, Y. (2017) · Frontiers in Laboratory Medicine · doi:10.1016/j.flm.2017.02.005 · Cited by 13 · see citing works
Influence of obesity on the response to influenza infection and vaccination
Karlsson, E. A., Milner, J. J., Green, W. D., Rebeles, J., Schultz‐Cherry, S., & Beck, M. A. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-813553-2.00010-5 · Cited by 13 · see citing works
Katyal, I., Chaban, B. L., & Hill, J. E. (2015) · Microbial Ecology · doi:10.1007/s00248-015-0708-2 · Cited by 11 · see citing works
Self-citationValeris-Chacin, R. J., Sponheim, A., Fano, E., Isaacson, R. E., Singer, R. S., Nerem, J., Leite, F., & Pieters, M. (2021) · Microorganisms · doi:10.3390/microorganisms9020252 · Cited by 11 · see citing works
Rapid and accurate taxonomic classification of cpn60 amplicon sequence variants
Ren, Q., & Hill, J. E. (2023) · ISME Communications · doi:10.1038/s43705-023-00283-z · Cited by 10 · see citing works
Self-citationLinking the westernised oropharyngeal microbiome to the immune response in Chinese immigrants
Guo, J., Zhang, X., Saiganesh, A., Peacock, C. S., Chen, S., Dykes, G. A., Hales, B. J., Souëf, P. N. L., & Zhang, G. (2020) · Allergy Asthma and Clinical Immunology · doi:10.1186/s13223-020-00465-7 · Cited by 10 · see citing works
cpn60 metagenomic amplicon library preparation for the Illumina Miseq platformPreprint
Fernando, C., & Hill, J. E. (2021) · Research Square · doi:10.21203/rs.3.pex-1438/v1 · Cited by 10 · see citing works
Self-citationEffects of 10-valent pneumococcal conjugate (PCV10) vaccination on the nasopharyngeal microbiome
Salgado, V. R., Fukutani, K. F., Fukutani, E. R., Lima, J. V., Rossi, E. A., Barral, A. M. P., de Oliveira, C. I., Nascimento-Carvalho, C. M., Weyenbergh, J. V., & Queiroz, A. T. L. (2019) · Vaccine · doi:10.1016/j.vaccine.2019.11.079 · Cited by 8 · see citing works
Porto, B. N., & Moraes, T. J. (2021) · Expert Review of Respiratory Medicine · doi:10.1080/17476348.2021.1893168 · Cited by 6 · see citing works
Dietl, B., Henares, D., Cuchí, E., Blanco-Fuertes, M., Rajadell, M., Brotons, P., Lluansí, A., Boix-Palop, L., Calbo, E., & Muñoz‐Almagro, C. (2025) · Journal of Infection · doi:10.1016/j.jinf.2025.106589 · Cited by 5 · see citing works
TROKHYMCHUK, A., Waldner, C., Gow, S., Chaban, B. L., & Hill, J. E. (2014) · Journal of Food Protection · doi:10.4315/0362-028x.jfp-13-331 · Cited by 5 · see citing works
Self-citationSchellenberg, J. J., Oh, A. Y., & Hill, J. E. (2017) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2017.03.003 · Cited by 5 · see citing works
Self-citationBacterial Microbiota Analysis Present in the Nose and Pharynx of a Mexican Young Population
Rodríguez-Vicente, A. K., Bustos‐Martínez, J., Reyes‐Duarte, D., & Sáinz‐Espuñes, T. (2016) · International Journal of Current Microbiology and Applied Sciences · doi:10.20546/ijcmas.2016.506.026 · Cited by 4 · see citing works
Comparing sputum microbiota characteristics between severe and critically ill influenza patients
Gu, Z., Zhang, Y., Zhao, X., Liu, T., Sheng, S., Song, R., & Jin, R. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1297946 · Cited by 3 · see citing works
Domínguez-Sánchez, C., Álvarez-Martínez, R., Gendron, D., & Acevedo‐Whitehouse, K. A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.29.522252 · Cited by 3 · see citing works
The pediatric nasal microbiome and its role in chronic ENT disorders: a narrative review
Sirbu, A. E., Pîrcălăbioru, G. G., Deaconu, D. M., Andronic, O., & Gheorghe, D. C. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1699707 · Cited by 2 · see citing works
Wiemken, T. L., Jala, V. R., Kelley, R. R., Peyrani, P., Mattingly, W. A., Arnold, F. W., Cabral, P. W., Cavallazzi, R., Haribabu, B., & Ramírez, J. A. (2015) · Pneumonia · doi:10.15172/pneu.2015.6/682 · Cited by 2 · see citing works
Microbiome in Influenza-A Virus Infection
Awati, S. S., Singh, S. K., Raizaday, A., Kumar, P., Singh, Y. P., Shaikh, M. A. J., & Gupta, G. (2022) · Springer eBooks · doi:10.1007/978-981-16-8957-4_16 · Cited by 2 · see citing works
cpn60 metagenomic amplicon library preparation for the Illumina Miseq platformPreprint
Fernando, C., & Hill, J. E. (2023) · Research Square · doi:10.21203/rs.3.pex-1438/v2 · Cited by 2 · see citing works
Self-citationViruses and the lung microbiome
Flight, W. G., Turkington, C. J. R., & Clokie, M. R. J. (2019) · European Respiratory Society eBooks · doi:10.1183/2312508x.10016018 · Cited by 1 · see citing works
Analysis of bronchoalveolar lavage fluid metatranscriptomes among patients with COVID-19 disease
Jochum, M. D., Lee, M., Curry, K. D., Zaksas, V., Vitalis, E., Treangen, T. J., Aagaard, K. M., & Ternus, K. L. (2022) · Scientific Reports · doi:10.1038/s41598-022-25463-0 · Cited by 1 · see citing works
Bacterial levels in Saskatchewan retail ground beef
Trokhymchuk, A. (2013) · University Library - University of Saskatchewan (University of Saskatchewan)
Upper respiratory tract microbiota in health and disease – a minireview
Chwiejczak, E., & Kosikowska, U. (2018) · Current Issues in Pharmacy and Medical Sciences · doi:10.1515/cipms-2018-0035
Kozhakhmetov, S., Aitenov, Y., Рамазанова, Б. А., Koloskova, Y., Burkutbayeva, T. N., Yeraliyeva, L. T., Mustafina, K., Beglarova, G., Yergazina, M., & Kushugulova, A. R. (2021) · Biodiversitas Journal of Biological Diversity · doi:10.13057/biodiv/d221142
Virome in the context of health and pathology of the human respiratory system
Стома, И. О. (2023) · Health and Ecology Issues · doi:10.51523/2708-6011.2022-19-4-01
Ihongbe, J. C., Adeyemo, S. O. A., Enitan, S. S., Dada, M. O., Ofem, O. G., Joseph, E. E., Okorochi, C. M., & Ogbonna, N. I. (2023) · Trends in Infection and Global Health · doi:10.24815/tigh.v2i2.29972
Hernández‐Terán, A., Vega-Sánchez, Á. E., Mejía-Nepomuceno, F., Serna-Muñoz, R., Rodríguez‐Llamazares, S., Salido-Guadarrama, I., Romero-Espinoza, J. A., Guadarrama-Pérez, C., Sandoval-Gutierrez, J. L., Campos, F., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26565519
Guo, J., Zhang, X., Saiganesh, A., Peacock, C. S., Chen, S., Dykes, G. A., Hales, B. J., Souëf, P. N. L., & Zhang, G. (2020) · Figshare · doi:10.6084/m9.figshare.12720031
Guo, J., Zhang, X., Saiganesh, A., Peacock, C. S., Chen, S., Dykes, G. A., Hales, B. J., Souëf, P. N. L., & Zhang, G. (2020) · Figshare · doi:10.6084/m9.figshare.12720028
Sedaghat-Rostami, E., Yang, L., Vats, A., Paudyal, B., Briggs, E., Carr, B. V., Freimanis, G., Ruedas‐Torres, I., Downing, T., Rollier, C. S., et al. (2026) · Communications Biology · doi:10.1038/s42003-026-10400-y
- Authors
- Chaban, B., Albert, A., Links, M. G., Gardy, J., Tang, P., & Hill, J. E.
- Affiliations
- University of Saskatchewan (CA)
- Women's Health Research Institute (CA)
- Agriculture and Agri-Food Canada (CA)
- BC Centre for Disease Control (CA)
- University of British Columbia (CA)
- Corresponding author
- Chaban, Bonnie
- Albert, Arianne
- Links, Matthew G.
- Gardy, Jennifer
- Tang, Patrick
- Hill, Janet E.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2013-07-02
- Volume
- 8
- Issue
- 7
- Pages
- e69559
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3699515
- OpenAlex
- W2026338038
- Cited by
- 69
- References
- 36
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 1 · 2023: 6 · 2022: 5 · 2021: 8 · 2020: 6 · 2019: 5 · 2018: 9 · 2017: 7 · 2016: 2 · 2015: 10 · 2014: 4 · 2013: 4
- FWCI
- 4.86
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Genome British Columbia
- Provincial Health Services Authority
- British Columbia Centre for Disease Control
- Canadian Institutes of Health Research
- Topics
- Health Sciences › Medicine › Epidemiology › Influenza Virus Research Studies
- Life Sciences › Immunology and Microbiology › Microbiology › Microbial infections and disease research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- upper respiratory tract microbiome, cpn60 gene, bacterial diversity, bacterial species composition, bacterial pneumonia
- MeSH terms
- Adolescent, Adult, Aged, Aged, 80 and over, Bacteria, British Columbia, Child, Child, Preschool, Female, Fungi, Humans, Infant, Infant, Newborn, Influenza, Human, Male, Middle Aged, Phylogeny, Respiratory System, RNA, Ribosomal, 16S, RNA, Viral, Reverse Transcriptase Polymerase Chain Reaction, Influenza A Virus, H1N1 Subtype, Young Adult, Pandemics, Microbiota
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