Influenza Virus Affects Intestinal Microbiota and Secondary Salmonella Infection in the Gut through Type I Interferons

A core gut microbiome in obese and lean twins

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The gut microbiota shapes intestinal immune responses during health and disease

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Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

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Interferon-stimulated genes: A complex web of host defenses

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Type I interferons in infectious disease

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Interleukin (IL)-22 and IL-17 are coexpressed by Th17 cells and cooperatively enhance expression of antimicrobial peptides

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Inducible Foxp3 + regulatory T-cell development by a commensal bacterium of the intestinal microbiota

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An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis

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Influenza A H1N1 Induced Disturbance of the Respiratory and Fecal Microbiome of German Landrace Pigs – a Multi-Omics Characterization

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The Influence of the Gut Microbiota on Host Health: A Focus on the Gut–Lung Axis and Therapeutic Approaches

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Co‐ and polymicrobial infections in the gut mucosa: The host–microbiota–pathogen perspective

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SARS-CoV-2-Induced Gut Microbiome Dysbiosis: Implications for Colorectal Cancer

Howell, M., Green, R. J., McGill, A. R., Dutta, R., Mohapatra, S., & Mohapatra, S. S. (2021) · Cancers · doi:10.3390/cancers13112676 · Cited by 35

Mild and Severe SARS-CoV-2 Infection Induces Respiratory and Intestinal Microbiome Changes in the K18-hACE2 Transgenic Mouse Model

Seibert, B., Cáceres, C. J., Garcia, S. C., Carnaccini, S., Geiger, G., Rajão, D. S., Ottesen, E. A., & Perez, D. R. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.00536-21 · Cited by 33

Moderately pathogenic maternal influenza A virus infection disrupts placental integrity but spares the fetal brain

Antonson, A. M., Kenney, A. D., Chen, H. J., Corps, K. N., Yount, J. S., & Gur, T. (2021) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2021.05.004 · Cited by 33

Influenza A virus during pregnancy disrupts maternal intestinal immunity and fetal cortical development in a dose- and time-dependent manner

Otero, A. M., Connolly, M. G., Gonzalez-Ricon, R., Wang, S. S., Allen, J. M., & Antonson, A. M. (2024) · Molecular Psychiatry · doi:10.1038/s41380-024-02648-9 · Cited by 33

Bacterial Gut Microbiota and Infections During Early Childhood

George, S., Aguilera, X., Gallardo, P., Farfán, M. J., Lucero, Y., Torres, J. P., Vidal, R. M., & O’Ryan, M. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.793050 · Cited by 32

Interactions between commensal bacteria and viral infection: insights for viral disease control in farmed animals

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Inhibiting virus replication and excessive inflammatory response: Mechanism of combined prescription of Ma-Xing-Shi-Gan decoction and Xiao-Chai-Hu decoction against influenza virus

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Associations of faecal microbiota with influenza-like illness in participants aged 60 years or older: an observational study

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Type 1 Interferon in the Human Intestine—A Co-ordinator of the Immune Response to the Microbiota

Giles, E. M., & Stagg, A. J. (2017) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000001078 · Cited by 30

Potential probiotics for regulation of the gut-lung axis to prevent or alleviate influenza in vulnerable populations

Wang, Y.-H., Limaye, A., Liu, J., & Wu, T.-N. (2022) · Journal of Traditional and Complementary Medicine · doi:10.1016/j.jtcme.2022.08.004 · Cited by 30

Influence of Novel Highly Pathogenic Avian Influenza A (H5N1) Virus Infection on Migrating Whooper Swans Fecal Microbiota

Zhao, N., Wang, S., Li, H., Liu, S., Li, M., Luo, J., Su, W., & He, H. (2018) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2018.00046 · Cited by 28

The gut microbiome: a missing link in understanding the gastrointestinal manifestations of COVID-19?Preprint

Brooks, E. F., & Bhatt, A. S. (2021) · Molecular Case Studies · doi:10.1101/mcs.a006031 · Cited by 29

Porcine deltacoronavirus infection alters bacterial communities in the colon and feces of neonatal piglets

Li, H., Li, B., Liang, Q., Jin, X., Tang, L., Ding, Q., Wang, Z., & Wei, Z. (2020) · MicrobiologyOpen · doi:10.1002/mbo3.1036 · Cited by 27

Profiling of Intestinal Microbiota in Patients Infected with Respiratory Influenza A and B Viruses

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Roles of the gut microbiota in severe SARS-CoV-2 infection

Liu, Y., Kuang, D., Li, D., Yang, J., Yan, J., Xia, Y., Zhang, F., & Cao, H. (2022) · Cytokine & Growth Factor Reviews · doi:10.1016/j.cytogfr.2022.01.007 · Cited by 30

Description of a Newly Isolated Blautia faecis Strain and Its Benefit in Mouse Models of Post-Influenza Secondary Enteric and Pulmonary Infections

Verstraeten, S., Sencio, V., Raise, A., Huillet, E., Layec, S., Deruyter, L., Heumel, S., Auger, S., Robert, V., Langella, P., et al. (2022) · Nutrients · doi:10.3390/nu14071478 · Cited by 26

Transcriptome and 16S rRNA analysis revealed the response of largemouth bass (Micropterus salmoides) to Rhabdovirus infection

Fei, H., Yi, S. F., Zhang, H. M., Cheng, Y., Zhang, Y. Q., Yu, X., Qian, S. C., Huang, M., & Yang, S. F. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.973422 · Cited by 26

Oral probiotic extracellular vesicle therapy mitigates Influenza A Virus infection via blunting IL-17 signaling

Zhou, H., Huang, W., Li, J., Chen, P., Shen, L., Huang, W., Mai, K., Zou, H., Shi, X., Weng, Y., et al. (2024) · Bioactive Materials · doi:10.1016/j.bioactmat.2024.11.016 · Cited by 26

Alteration of the gut microbiota’s composition and metabolic output correlates with COVID-19-like severity in obese NASH hamsters

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Modulation of Gut Microbiota, Short-Chain Fatty Acid Production, and Inflammatory Cytokine Expression in the Cecum of Porcine Deltacoronavirus-Infected Chicks

Li, H., Zhang, H., Zhao, F., Wang, S., Wang, Z., & Wei, Z. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00897 · Cited by 23

Alteration of Intestinal Flora Stimulates Pulmonary microRNAs to Interfere with Host Antiviral Immunity in Influenza

Pang, P., Yu, B., Shi, Y., Deng, L., Xu, H., Wu, S., & Chen, X. (2018) · Molecules · doi:10.3390/molecules23123151 · Cited by 24

Maternal infection and antibiotic use in pregnancy and the risk of childhood obesity in offspring: a birth cohort study

Li, D., Chen, H., Ferber, J. R., & Odouli, R. (2019) · International Journal of Obesity · doi:10.1038/s41366-019-0501-2 · Cited by 24

CD8 T cells drive anorexia, dysbiosis, and blooms of a commensal with immunosuppressive potential after viral infection

Labarta-Bajo, L., Gramalla-Schmitz, A., Gerner, R. R., Kazane, K. R., Humphrey, G., Schwartz, T., Sanders, K., Swafford, A. D.-E., Knight, R. D., Raffatellu, M., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2003656117 · Cited by 26

Freeze-Thaw Pretreatment Can Improve Efficiency of Bacterial DNA Extraction From Meconium

Xin, Y., Xie, J., Nan, B., Tang, C. Y., Xiao, Y., Wu, Q., Lin, Y., Zhang, X., & Shen, H. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.753688 · Cited by 21

Ménage à trois: Virus, Host, and Microbiota in Experimental Infection Models

Mazel‐Sanchez, B., Yildiz, S., & Schmolke, M. (2019) · Trends in Microbiology · doi:10.1016/j.tim.2018.12.004 · Cited by 25

Chronic SARS-CoV-2, a Cause of Post-acute COVID-19 Sequelae (Long-COVID)?

O’Donnell, J. S., & Chappell, K. J. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.724654 · Cited by 24

The Aftermath of Surviving Acute Radiation Hematopoietic Syndrome and its Mitigation

Micewicz, E. D., Iwamoto, K. S., Ratikan, J. A., Nguyen, C., Xie, M. W., Cheng, G., Boxx, G. M., Deriu, E., Damoiseaux, R. D., Whitelegge, J. P., et al. (2019) · Radiation Research · doi:10.1667/rr15231.1 · Cited by 25

Lipocalin 2 modulates dendritic cell activity and shapes immunity to influenza in a microbiome dependent manner

Watzenboeck, M. L., Drobits, B., Zahalka, S., Gorki, A.-D., Farhat, A., Quattrone, F., Hladik, A., Lakovits, K., Richard, G. M., Lederer, T., et al. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009487 · Cited by 22

A recombinant glucocorticoid‐induced leucine zipper protein ameliorates symptoms of dextran sulfate sodium‐induced colitis by improving intestinal permeability

Gentili, M., Hidalgo‐Garcia, L., Vezza, T., Ricci, E., Migliorati, G., Rodríguez‐Nogales, A., Riccardi, C., Gálvez, J., & Ronchetti, S. (2021) · The FASEB Journal · doi:10.1096/fj.202100778rrrr · Cited by 22

Anti-influenza A virus activity of two Newtonia species and the isolated compound myricetin-3-o-rhamnoside

Motlhatlego, K. E., Mehrbod, P., Fotouhi, F., Abdalla, M. A., Eloff, J. N., & McGaw, L. J. (2021) · BMC Complementary Medicine and Therapies · doi:10.1186/s12906-021-03250-0 · Cited by 21

The Impact of SARS-CoV-2 on the Human Immune System and Microbiome

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Gut Feelings: How Microbes, Diet, and Host Immunity Shape Disease

Theis, B. F., Park, J. S., Kim, J. S., Zeydabadinejad, S., Vijay–Kumar, M., Yeoh, B. S., & Saha, P. (2025) · Biomedicines · doi:10.3390/biomedicines13061357 · Cited by 24

Lingering SARS-CoV-2 in Gastric and Gallbladder Tissues of Patients with Previous COVID-19 Infection Undergoing Bariatric Surgery

Hany, M., Zidan, A., Gaballa, M., Ibrahim, M., Agayby, A. S. S., Abouelnasr, A. A., Sheta, E., & Torensma, B. (2022) · Obesity Surgery · doi:10.1007/s11695-022-06338-9 · Cited by 20

The Clinical Impact of Cirrhosis on the Hospital Outcomes of Patients Admitted With Influenza Infection: Propensity Score Matched Analysis of 2011–2017 US Hospital Data

Lee, D. U., Fan, G. H., Hastie, D. J., Prakasam, V. N., Addonizio, E. A., Ahern, R. R., Seog, K. J., & Karagozian, R. (2021) · Journal of Clinical and Experimental Hepatology · doi:10.1016/j.jceh.2021.01.005 · Cited by 19

Mechanism of Jinzhen Oral Liquid against influenza-induced lung injury based on metabonomics and gut microbiome

Feng, J., Gao, X., Chen, X., Tong, X., Qian, M., Gao, H., Wang, J., Wang, S., Fei, C., Cao, L., et al. (2022) · Journal of Ethnopharmacology · doi:10.1016/j.jep.2022.115977 · Cited by 20

Effects of Intranasal Pseudorabies Virus AH02LA Infection on Microbial Community and Immune Status in the Ileum and Colon of Piglets

Zhang, C., Liu, Y., Chen, S., Qiao, Y., Zheng, Y., Xu, M., Wang, Z., Hou, J., Wang, J., & Fan, H. (2019) · Viruses · doi:10.3390/v11060518 · Cited by 19

Nonrespiratory sites of influenza‐associated disease: mechanisms and experimental systems for continued study

Froggatt, H. M., & Heaton, N. S. (2022) · FEBS Journal · doi:10.1111/febs.16363 · Cited by 20

Nitrate Is Crucial for the Proliferation of Gut Escherichia coli Caused by H9N2 AIV Infection and Effective Regulation by Chinese Herbal Medicine Ageratum-Liquid

Zhang, X., Zhao, Q., Wu, C., Xie, Z., Ci, X., Li, H., Lin, W., Zhang, H., & Xie, Q. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.555739 · Cited by 18

Microbial and Immune Regulation of the Gut-Lung Axis during Viral-Bacterial Coinfection

Lane, S., Hilliam, Y., & Bomberger, J. M. (2022) · Journal of Bacteriology · doi:10.1128/jb.00295-22 · Cited by 18

The gut microbiota contributes to the infection of bovine viral diarrhea virus in mice

Zhang, Z., Huang, J., Li, C., Zhao, Z., Cui, Y., Yuan, X., Wang, X., Liu, Y., Zhou, Y., & Zhu, Z. (2024) · Journal of Virology · doi:10.1128/jvi.02035-23 · Cited by 17

Human metapneumovirus respiratory infection affects both innate and adaptive intestinal immunity

Sepúlveda-Alfaro, J., Catalán, E. A., Vallejos, O. P., Ramos-Tapia, I., Madrid-Muñoz, C., Mendoza-León, M. J., Suazo, I. D., Rivera-Asín, E., Silva, P. H., Álvarez-Mardones, O., et al. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1330209 · Cited by 17

Gastrointestinal Microbiota Dysbiosis Associated with SARS-CoV-2 Infection in Colorectal Cancer: The Implication of Probiotics

Odun-Ayo, F., & Reddy, L. (2022) · Gastroenterology Insights · doi:10.3390/gastroent13010006 · Cited by 18

Porcine circovirus type 2 promotes Actinobacillus pleuropneumoniae survival during coinfection of porcine alveolar macrophages by inhibiting ROS production

Qi, W., Zhu, R., Bao, C., Xiao, J., Liu, B., Sun, M., Feng, X., Gu, J., Li, Y., & Lei, L. (2019) · Veterinary Microbiology · doi:10.1016/j.vetmic.2019.04.028 · Cited by 17

How to boost the immune defence prior to respiratory virus infections with the special focus on coronavirus infections

Jawhara, S. (2020) · Gut Pathogens · doi:10.1186/s13099-020-00385-2 · Cited by 18

Pathobiology and dysbiosis of the respiratory and intestinal microbiota in 14 months old Golden Syrian hamsters infected with SARS-CoV-2

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

Exploring the complexities of poultry respiratory microbiota: colonization, composition, and impact on health

Oladokun, S., & Sharif, S. (2024) · Animal Microbiome · doi:10.1186/s42523-024-00308-5 · Cited by 19

Progression and Trends in Virus from Influenza A to COVID-19: An Overview of Recent Studies

Daemi, H. B., Kulyar, M. F., He, X., Li, C., Karimpour, M., Sun, X., Zou, Z., & Jin, M. (2021) · Viruses · doi:10.3390/v13061145 · Cited by 17

Distinct Metagenomic Signatures in the SARS-CoV-2 Infection

Liu, Y., Zhang, H., Tang, X., Jiang, X., Yan, X., Liu, X., Gong, J., Mew, K., Sun, H., Chen, X., et al. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.706970 · Cited by 16

Virus and microbiota relationships in humans and other mammals: An evolutionary view

Lima, M. T., Andrade, A. C. D. S. P., Oliveira, G. P., Nicoli, J. R., Martins, F. S., Kroon, E. G., & Abrahão, J. S. (2019) · Human Microbiome Journal · doi:10.1016/j.humic.2018.11.001 · Cited by 16

Gut microbiome dysbiosis during COVID-19 is associated with increased risk for bacteremia and microbial translocationPreprint

Venzon, M., Bernard, L., Klein, J., Axelrad, J. E., Zhang, C., Hussey, G. A., Sullivan, A. P., Casanovas‐Massana, A., Noval, M. G., Valero-Jimenez, A. M., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.15.452246 · Cited by 15

The 16S rRNA Gene Sequencing of Gut Microbiota in Chickens Infected with Different Virulent Newcastle Disease Virus Strains

Tong, L., Wang, W., Ren, S., Wang, J., Wang, J., Qu, Y., Adam, F. E. A., Li, Z., & Gao, X. (2022) · Animals · doi:10.3390/ani12192558 · Cited by 14

Type I IFNs facilitate innate immune control of the opportunistic bacteria Burkholderia cenocepacia in the macrophage cytosol

Dorrington, M. G., Bradfield, C. J., Lack, J., Lin, B., Liang, J. J., Starr, T., Ernst, O., Gross, J. L., Sun, J., Miller, A. H., et al. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009395 · Cited by 14

Role of the gut microbiota in airway immunity and host defense against respiratory infections

Willers, M., & Viemann, D. (2021) · Biological Chemistry · doi:10.1515/hsz-2021-0281 · Cited by 15

Qin-Qiao-Xiao-Du formula alleviate influenza virus infectious pneumonia through regulation gut microbiota and metabolomics

Lian, B., He, S., Jiang, H., Guo, Y., Cui, X., Jiang, T., Su, R. J., Chen, Y., Zhao, C., Zhang, M., et al. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.1032127 · Cited by 14

Epstein Barr virus infection in tree shrews alters the composition of gut microbiota and metabolome profile

Xia, W., Liu, L., Shi, N., Zhang, C., Tang, A., & He, G. (2023) · Virology Journal · doi:10.1186/s12985-023-02147-3 · Cited by 13

Oral co-administration of Lactiplantibacillus plantarum 16 and Lacticaseibacillus rhamnosus P118 improves host defense against influenza A virus infection

Han, M., Lu, Q., Wang, D., Zhou, K., Jia, C., Teng, L., Hamuti, A., Peng, X., Hu, Y., Li, W., et al. (2024) · Journal of Virology · doi:10.1128/jvi.00950-24 · Cited by 16

The (digestive) path less traveled: influenza A virus and the gastrointestinal tract

Bullock, T. A., Pappas, C., Uyeki, T. M., Brock, N., Kieran, T. J., Olsen, S. J., Davis, C. T., Tumpey, T. M., Maines, T. R., & Belser, J. A. (2025) · mBio · doi:10.1128/mbio.01017-25 · Cited by 13

SARS-CoV-2-associated gut microbiome alteration; A new contributor to colorectal cancer pathogenesis

Mozaffari, S. A., Salehi, A., Mousavi, E., Zaman, B. A., Nassaj, A. E., Ebrahimzadeh, F., Nasiri, H., Valedkarimi, Z., Adili, A., Asemani, G., et al. (2022) · Pathology - Research and Practice · doi:10.1016/j.prp.2022.154131 · Cited by 13

Association of gut microbial dysbiosis with disease severity, response to therapy and disease outcomes in Indian patients with COVID-19

Talukdar, D., Bandopadhyay, P., Ray, Y., Paul, S. R., Sarif, J., D’Rozario, R., Lahiri, A., Das, S., Bhowmik, D., Chatterjee, S., et al. (2023) · Gut Pathogens · doi:10.1186/s13099-023-00546-z · Cited by 14

Pulmonary Aspergillus fumigatus infection in rats affects gastrointestinal homeostasis

Kulaš, J. B., Mirkov, I. I., Tucović, D., Zolotarevski, L. D., Glamočlija, J., Veljović, K., Tolinački, M., Golić, N., & Kataranovski, M. V. (2018) · Immunobiology · doi:10.1016/j.imbio.2018.10.001 · Cited by 13

The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites

Li, H., Li, H., Wang, J., Guo, L., Fan, H., Zheng, H., Yang, Z., Huang, X., Chu, M., Yang, F., et al. (2019) · Virology Journal · doi:10.1186/s12985-019-1211-z · Cited by 14

An Update on the Mutual Impact between SARS-CoV-2 Infection and Gut Microbiota

Li, S., Zhou, Y., Yan, D., & Wan, Y. (2022) · Viruses · doi:10.3390/v14081774 · Cited by 12

Gut microbial dysbiosis occurring during pulmonary fungal infection in rats is linked to inflammation and depends on healthy microbiota composition

Popović, D., Kulaš, J. B., Tucović, D., Aleksandrov, A. P., Malešević, A., Glamočlija, J., Brdarić, E., Bajić, S. S., Golić, N., Mirkov, I. I., et al. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.01990-23 · Cited by 12

Role of the intestinal microbiota in host defense against respiratory viral infections

Boncheva, I., Poudrier, J., & Falcone, E. L. (2024) · Current Opinion in Virology · doi:10.1016/j.coviro.2024.101410 · Cited by 13

Pediococcus pentosaceus MIANGUAN2 Alleviates Influenza Virus Infection by Modulating Gut Microbiota and Enhancing Short-Chain Fatty Acid Production

Chen, Y., Song, L., Chen, M., Huang, Y., Wang, Z., Ren, Z., & Xu, J. (2024) · Nutrients · doi:10.3390/nu16121923 · Cited by 12

Influenza and the gut microbiota: A hidden therapeutic link

Luo, C., Yang, Y., Jiang, C., Lv, A., Zuo, W., Ye, Y., & Ke, J. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e37661 · Cited by 13

Research progress on the mechanism of traditional Chinese medicine regulating intestinal microbiota to combat influenza a virus infection

Ma, L., Ji, L., Wang, T., Zhai, Z., Su, P., Zhang, Y., Wang, Y., Zhao, W., Wu, Z., Yu, H., et al. (2023) · Virology Journal · doi:10.1186/s12985-023-02228-3 · Cited by 13

Microbiota and Coronavirus Disease 2019. Which Came First, the Chicken or the Egg?

Marcialis, M. A., Bardanzellu, F., & Fanos, V. (2020) · Clinical Infectious Diseases · doi:10.1093/cid/ciaa965 · Cited by 11

Role and significance of virus–bacteria interactions in disease progression

Pokhrel, V., Kuntal, B. K., & Mande, S. S. (2024) · Journal of Applied Microbiology · doi:10.1093/jambio/lxae130 · Cited by 10

Influenza a virus subtype H9N2 infection induces respiratory microbiota dysbiosis in chickens via type-I interferon-mediated mechanisms

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Effects of melittin on laying performance and intestinal barrier function of quails

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