Breast cancer development and progression involve both germline and somatic mutations. High-throughput genotyping and next-generation sequencing technologies have enabled discovery of genetic risk variants and acquired somatic mutations driving the disease. However, the possible oncogenic interactions between germline genetic risk variants and somatic mutations in triple-negative breast cancer (TNBC) and non-triple-negative breast cancer (non-TNBC) have not been characterized. Here, we delineated the possible oncogenic interactions between genes containing germline and somatic mutations in TNBC and non-TNBC and investigated whether there are differences in gene expression and mutation burden between the two types of breast cancer.  We addressed this problem by integrating germline mutation information from genome-wide association studies with somatic mutation information from next-generation sequencing using gene expression data as the intermediated phenotype. We performed network and pathway analyses to discover molecular networks and signalling pathways enriched for germline and somatic mutations.  The investigation revealed signatures of differentially expressed and differentially somatic mutated genes between TNBC and non-TNBC. Network and pathway analyses revealed functionally related genes interacting in gene regulatory networks and multiple signalling pathways enriched for germline and somatic mutations for each type of breast cancer. Among the signalling pathways discovered included the DNA repair and Androgen and ATM signalling pathways for TNBC and the DNA damage response, molecular mechanisms of cancer, and ATM and GP6 signalling pathways for non-TNBC.  The results show that integrative genomics is a powerful approach for delineating oncogenic interactions between genes containing germline and genes containing somatic mutations in TNBC and non-TNBC and establishes putative functional bridges between genetic and somatic alterations and the pathways they control in the two types of breast cancer. Breast cancer is the second most diagnosed malignancy and the second leading cause of cancer-related deaths among women in the US . In 2018Breast cancer development is driven by acquired driver somatic mutations; however, germline genetic variants play a role in tumorigenesis by partaking in critical biological and cellular processes. For decades, germline mutations, contained within the heritable genome, and somatic mutations, acquired de novo by breast cancer cells, have been considered as separate research endeavours, and each has unique clinical applications and implications for patient care. A critical challenge faced by clinicians and patients is the identification of patients at high risk of developing aggressive disease that could guide the application of precision medicine and precision prevention in TNBC and non-TNBC. Achieving that goal requires understanding the germline somatic mutation interaction landscape and discovery of molecular markers driving each disease and distinguishing the two types of breast cancer.Advances in microarray technology have enabled molecular classification of TNBC and non-TNBC , 14. At The recent surge of next-generation sequencing of the cancer genomes has opened new options in clinical oncology, from discovery of driver mutations to implementation of precision medicine , 28. ComThe objective of this study was to delineate germline and somatic mutation interaction landscape in TNBC and non-TNBC and to determine whether there are differences in gene expression and somatic mutation burden between the two types of breast cancer. We focus on the two types of breast cancer. Our working hypotheses were that (1) genomic alterations in genes containing germline and somatic variations could lead to measurable changes associating genetic predisposition with tumorigenesis and distinguishing TNBC from non-TNBC and (2) integrative analysis combining germline and somatic mutation information at the gene level will uncover molecular networks and signalling pathways through which germline and somatic variations interact and cooperate to drive TNBC and non-TNBC. We addressed these hypotheses using an integrative genomic approach that integrates germline variation information from GWAS with somatic mutation information from next-generation sequencing on TNBC and non-TNBC from TCGA, using gene expression data from TCGA as the intermediate phenotype. Our modelling approach focuses on the genes, gene regulatory networks, and signalling pathways rather than on individual mutations. This robust approach was designed to establish the potential causal association between genetic predisposition and tumorigenesis and to provide valuable insights about the broader biological context in which germline and somatic mutations interact and cooperate to drive TNBC and non-TNBC. It is worth noting that the two subtypes of breast cancer have many subtypes which we did not consider here, a weakness that we readily acknowledge as it is beyond the scope of this investigation. As pointed out earlier in this section, our focus on TNBC and non-TNBC was motivated by evidence from both clinical and epidemiological studies showing that TNBC has poorer outcomes and poorer survival rates when compared to non-TNBC –12.Advances in high-throughput genotyping and next-generation sequencing technologies enabled discovery and creation of comprehensive catalogues of germline and somatic mutations. These discoveries have increased our understanding of the genetic susceptibility landscape and the molecular taxonomy of breast cancer. However, analyses of germline and somatic mutations have historically been considered as separate endeavours in breast cancer research. With the availability of germline, somatic, and gene expression variation data and powerful bioinformatics tools, we are now well-positioned to understand the causal association between genetic susceptibility and tumorigenesis through integrative analysis. Here, we integrated data on germline, somatic, and gene expression variation to delineate the germline-somatic mutation interaction landscape in TNBC and non-TNBC. The overall study design and execution strategy used in this study is presented in P value as well as original published GWAS reports from which the information was derived. A complete list of genes and germline variants along with original sources of published GWAS reports from which germline mutations were derived is presented in Supplementary Table We used population-level GWAS discoveries, specifically single-nucleotide polymorphisms (SNPs) (herein referred to as germline mutations) and genes associated with an increased risk of developing breast cancer from a comprehensive catalogue that we have developed and published , 21 and https://gdc.cancer.gov/ [N = 883 non-TNBC samples and N = 99 TNBC samples used in this study. Samples without clinical or mutation information (N = 126) were not included in the analysis as they could not be ascertained for mutation status and/or correctly assigned to either type of breast cancer. The data was further processed and checked for quality. We performed noise reduction by filtering or removing rows with missing data as determined by the number of reads, such that each row had at least ≥30% data points. Data filtering was performed using counts per million (CPM) filter (>0.5) implemented in the R Package [M values (TMM) normalization method and log transformed the data using the Voom module in the LIMMA package implemented in R [Somatic mutation and gene expression along with clinical information were obtained from TCGA via the Genomics Data Commons (GDC) using the data transfer tool cer.gov/ . Somatic Package . Followited in R . ProcessThe data processing and analysis steps are shown in the project design and execution workflow presented in P values and FDR. Significantly differentially expressed genes in each type and between the two types of breast cancer were grouped as either mutated or not mutated. Somatic mutated genes were further assessed for the number of mutation events per gene within each type and in both types of breast cancer to discover differentially mutated genes between TNBC and non-TNBC. A gene was considered highly mutated if the number of mutation events was ≥3. A gene was considered differentially mutated if it was only mutated in one type of breast cancer. Significantly differentially expressed genes without mutations were grouped into four groups, genes significantly associated with TNBC, genes significantly associated with non-TNBC, genes significantly associated with both diseases, and genes distinguishing the two diseases.The genes were ranked on To discover significantly differentially expressed and differentially somatic mutated genes distinguishing TNBC from non-TNBC, we compared gene expression levels and number of mutation events per gene between the two types of breast cancer. Genes associated with both types of breast cancer were not included in this analysis to avoid confounding of the results. Differentially somatic mutated genes were identified by counting the number of mutation events per gene in each type of breast cancer. If the gene had somatic mutations in only one type of breast cancer, it was considered differentially mutated. To identify genes containing germline and somatic mutations, we evaluated all the 754 genes containing germline mutations for the presence of somatic mutations and their association with each type of breast cancer measured by their expression. Germline mutated genes significantly associated with each type of breast cancer were further evaluated for differences in their expression levels and somatic mutations between the two types of breast cancer.Z score and P values , respectively; indicating the level of significance for correctly assigning the mutated genes to the network, functional category, and pathways. Significance of molecular functions and the canonical pathways was tested by the Fisher exact test as implemented in IPA. To ensure the reliability of the predicted networks, we used the trim module implemented in IPA to filter out networks with ≤3 connections and genes without any connections.We used the Core Analysis and pathways build modules implemented in the Ingenuity Pathway Analysis (IPA) software platform, QIAGEN Inc., USA , to modeFor the first assay, we used the Prosigna (PAM50), a 50-gene signature that has gained prominence in clinical applications as a prognostic gene signature in breast cancer –17. The For the second assay, we used the MammaPrint, a clinically validated assay consisting of 70 genes developed by Agendia Corporation , 19. MamTo test whether the genes containing germline and somatic mutations discovered in this investigation have clinical utility and to validate them as potential clinically actionable biomarkers, we evaluated them against two clinically validated assays as described below:We chose the two assays because both the PAM50 and MammaPrint were developed using gene expression, which is also used in this investigation as the intermediate phenotype. For these validation analyses, we used several approaches: First, we investigated whether the genes containing both germline and somatic mutations are present in the PAM50 and the MammaPrint assays. Second, we evaluated the genes in these assays against highly somatic mutated genes significantly associated with each disease to eliminate the bias imposed by the limited number of genes containing germline mutations. Third, we investigated whether the genes containing germline and/or somatic mutations significantly associated with each disease are functionally related and interact with genes in the PAM50 and/or MammaPrint assays. The third approach was necessitated by the limited number of the genes in each assay. We reasoned that genes in these clinically validated assays may be regulated or may be regulating other genes which are altered in the germline, somatic, or both genomes.P values adjusted for multiple hypothesis testing. Comparison of gene expression levels between patients with TNBC and controls produced a signature of 22,968 significantly differentially expressed genes (P < 0.05), of which 5,502 genes contained somatic mutations and 17,466 genes had no somatic mutations. Comparison of gene expression levels between patients with non-TNBC and controls produced a signature of 19,463 significantly differentially expressed genes (P < 0.05), of which 11,399 genes contained somatic mutations and 8,064 genes were without somatic mutations. A complete list of somatic mutated genes significantly associated with TNBC and non-TNBC is presented in Supplementary Table We compared gene expression levels between TNBC and controls and between non-TNBC and controls to discover and characterize signatures of mutated and nonmutated genes associated with the two types of breast cancer. Genes were ranked and selected using estimates of P values derived from analysis of gene expression. A summary of the results showing the distribution of mutated and nonmutated genes significantly associated with each type and both types of breast cancer is presented in Venn diagrams in To discover gene signatures uniquely associated with each type of breast cancer and gene signatures associated with both types of breast cancer, we evaluated mutated and nonmutated genes using adjusted Among the somatic mutated genes , 1,489 gHaving discovered signatures of mutated and nonmutated genes associated with each type and/or both types of breast cancer, we performed additional analysis to investigate the differences in gene expression and mutation burden between TNBC and non-TNBC. For this analysis, we created and analysed a new data set of 8,875 genes, which was generated by combining the 1,489 genes containing somatic mutations significantly associated with TNBC only and the 7,386 genes containing somatic mutations significantly associated with non-TNBC only. Genes associated with both types of breast cancer were not included in this analysis to eliminate confounding of the results.The analysis revealed a signature of 6,887 significantly differentially expressed genes distinguishing TNBC from non-TNBC. The signature included 290 genes somatic mutated in TNBC, 4,957 genes somatic mutated in non-TNBC, and 1,640 genes somatic mutated in both types of breast cancer. A list of the top 30 highly significantly differentially expressed somatic mutated genes between TNBC and non-TNBC with high somatic mutation events per gene is presented in COPE, ENPP5, and RBM22 . The results of this evaluation are presented in ARID1B, BRCA1, ERBB4, ARHGAP5, EFR3B, AKAP9, ASH1L, ATM, BAHCC1, and HAST9 containing germline mutations reported to be directly associated with TNBC  that were highly significantly associated with TNBC. Likewise, for non-TNBC, we used the 243 genes containing both germline and somatic mutations uniquely associated with the disease and the 246 highly somatic mutated associated with the disease. The rationale for including highly somatic mutated genes without germline mutations was driven by the realization that GWAS discoveries explain only a small proportion of the phenotypic variation. Crucially, genetic variants from GWAS may not necessarily be causal but may be interacting and cooperating with highly somatic mutated oncogenes involved in the causal mechanisms through ATM signalling pathways, all of which have been implicated in TNBC [CD24, TCF20, PUF60, and RBBP4.The results showing molecular networks enriched for germline and somatic mutations in TNBC are presented in  in TNBC . The topBRCA1 in DNA damage response, molecular mechanisms of cancer, and ATM and GP6 signalling pathways. The top upstream regulators included ERBB2 and ITGB1.The results showing molecular networks enriched for germline and somatic mutations in non-TNBC are presented in Overall, there was overlap in molecular networks and signalling pathways discovered in TNBC and non-TNBC. For example, the signalling pathways involved in DNA repair and DNA damage were discovered in both types of breast cancer. Interestingly, in both TNBC and non-TNBC, genes containing germline mutations strongly associated with breast cancer were functionally related and interacting with highly somatic mutated genes in gene regulatory networks and signalling pathways. Taken together, the results of this investigation confirmed our hypothesis that in the context of breast cancer, TNBC and non-TNBC can be considered as emergent properties of molecular networks and signalling pathways influenced by both germline and somatic mutations. The investigation revealed that integrating germline with somatic mutation information holds promise for discovering the molecular mechanisms through which germline and somatic mutations interact and cooperate to drive TNBC and non-TNBC.in silico validation using the two clinically validated assays as described in Material and Methods using the Prosigna (PAM50) [To validate and investigate the potential clinical utility of the discovered germline-somatic mutated genes, we performed  (PAM50) –17 and t (PAM50) , 19. We MYC gene containing both germline and somatic mutations associated with TNBC. Evaluating the same assay on non-TNBC revealed four genes: ERBB2, ESR1, PHGDH, and TYMS containing both germline and somatic mutations significantly associated with that type of breast cancer. In addition, we discovered six genes: CCNE1, CEP55, EGFR, EXO1, FGFR4, and MAPT associated with both types of breast cancer. Further evaluation focusing on highly somatic mutated genes unique to TNBC revealed the genes CDC20, CXXC5, and MYC.Evaluation using PM50 revealed the CDC42BPA, EXT1, and PRC1 significantly associated with both types of breast cancer. Additionally, evaluation focusing on highly somatic mutated genes unique to non-TNBC revealed the genes BAG1, BIRC5, BLVRA, CCNB1, CDC6, ERBB2, ESR1, FOXA1, GPR160, GRB7, KIF2C, KRT5, MELK, MIA, NAT1, NDC80, PHGDH, PTTG1, RRM2, SFRP1, SLC39A6, TYMS, UBE2C, and UBE2T, confirming our hypothesis that somatic mutated genes have the promise to serve as potential clinically actionable molecular markers. Taken together, these results demonstrate that integrative analysis combining germline and somatic mutated information using gene expression as the intermediate phenotype is a powerful approach for delineating possible oncogenic interactions between germline and somatic mutations and correlating this information with clinically validated assays.Evaluation using MammaPrint did not reveal genes containing both germline and somatic mutations significantly associated with TNBC or non-TNBC. However, the analysis revealed 3 somatic mutated genes: We used an integrative genomic approach combining data on germline and somatic variation using gene expression data as the intermediate phenotype to delineate possible oncogenic interactions and cooperation between genes containing germline and somatic mutations in TNBC and non-TNBC and to investigate the difference in mutation burden between the two types of breast cancer. The investigation revealed that genes containing germline mutations also contain somatic mutations. The investigation also revealed differences in gene expression and mutation burden between TNBC and non-TNBC. Most notably, the investigation revealed multiple gene regulatory networks and signalling pathways enriched for germline and somatic mutations in each type of breast cancer. To our knowledge, this is the first study to comprehensively characterize the germline-somatic mutation interaction landscape in TNBC and non-TNBC. The link between germline and somatic mutations in breast cancer has been explored . RecentlThe discovery of highly significantly differentially somatic mutated gene signatures between TNBC and non-TNBC suggests that breast cancer may be amenable to mutation-based classification . These rThe discovery of functionally related genes containing both germline and somatic mutations is of particular interest. The clinical significance of this finding is that it provides a rational basis that breast cancer may be amenable to predictive modelling to identify patients at high risk of developing aggressive disease such as TNBC, a key step in the realization of precision prevention strategies. This discovery may also provide insights about how and when the cancer cells are likely to gain the propensity to acquire malignancy transformation into a lethal disease.The discovery of gene regulatory networks and signalling pathways enriched for germline and somatic mutations is highly significant. It suggests that breast cancer is an emergent property of molecular networks and signalling pathways enriched for germline and somatic mutations. The investigation further revealed that interaction and cooperation between germline and somatic mutations during tumorigenesis occurs through gene regulatory networks and signalling pathways. The clinical significance of these findings is that such signalling pathways could be used as therapeutic targets.The majority of the germline mutations discovered thus far through GWAS map to noncoding regions such as intronic regions with undefined functions and their causal relationship with the disease have not been characterized. This investigation demonstrates that integrating germline with somatic mutation information provides a rational basis for establishing causal relationship between germline mutations and tumorigenesis. This is important given the limited evidence showing that cancer susceptibility variants are preferential targets for somatic mutations  and the As noted earlier in this report, to date, genetic variants are being incorporated in risky prediction models such as polygenic risk scores , 26. TheIn this study, we used the PAM50 and MammaPrint clinically validated and FDA-approved prognostic assays –19 to vaThis study delineated the germline-somatic mutation interaction landscape in TNBC and non-TNBC. However, limitations must be acknowledged. Both GWAS and TCGA data sets lack diversity in ethnic population and clinical phenotype representation that would further inform these results. This limited progress must be balanced against the recognition that GWAS and TCGA studies have almost been exclusively focused on women of European ancestry. There is need for similar studies including women from underrepresented ethnic populations to ensure equitable use of genomic information to improve human health and eliminate health disparities . We did The investigation revealed oncogenic interactions and cooperation between genes containing germline and somatic mutations and showed that these complex arrays of interacting genetic factors occur through molecular networks and signalling pathways driving TNBC and non-TNBC. The investigation revealed differences in gene expression and somatic mutation burden between TNBC and non-TNBC. Further research is recommended to validate and ascertain the specificity of germline mutations to TNBC and non-TNBC in different ethnic populations including African American women to ensure equitable use of genomic information to improve human health.


Heme oxygenase (HO) enzymes catalyze heme into biliverdin, releasing carbon monoxide (CO) and iron into circulation. These byproducts of heme degradation can have potent cytoprotective effects in the face of stressors such as hypoxia and ischemia-reperfusion events. The potential for exogenous use of CO as a therapeutic agent has received increasing attention throughout the past few decades. Further, HO and CO are noted as putatively adaptive in diving mammals and certain high-altitude human populations that are frequently exposed to hypoxia and/or ischemia-reperfusion events, suggesting that HO and endogenous CO afford an evolutionary advantage for hypoxia tolerance and are critical in cell survival and injury avoidance. Our goal is to describe the importance of examining HO and CO in several systems, the physiological links, and the genetic factors that underlie variation in the HO/CO pathway. Finally, we emphasize the ways in which evolutionary perspectives may enhance our understanding of the HO/CO pathway in the context of diverse clinical settings. Hmox, which encodes the protein heme oxygenase (HO), the rate limiting enzyme responsible for the degradation of heme. HO catabolizes heme into biliverdin, which is subsequently converted to bilirubin by biliverdin reductase, releasing carbon monoxide (CO) and iron as byproducts. Paradoxically, CO was strictly considered a toxic pollutant. This notion stems from CO having a high affinity for the O2-binding site on hemoproteins. Therefore, elevated levels of CO can reduce O2 storage capacity and inhibit O2 transport, resulting in CO toxicity. However, recent studies have revealed the biological effects of the gas, leading to the acceptance of CO having therapeutic and cytoprotective effects in modulating inflammation, cell death, and proliferation  to cells  events have upregulated or modified the HO/CO pathway in a manner that could afford beneficial side effects . Here, wThe late August Krogh stated that, “for such a large number of problems there will be some animal of choice, or a few such animals, on which it can be most conveniently studied” . Model oSome deep-diving mammals are known to experience levels of hypoxemia during dives that resemble arterial oxygen saturations of humans breathing ambient air on the summit of Mount Everest . These d2-binding affinity of hemoglobin, impacting O2-delivery mechanics. Considering the low arterial pO2 values routinely experienced during breath-holds (<15–20 mmHg), it is possible that a higher hemoglobin-O2 affinity due to moderate COHb levels could preserve blood O2 stores, increasing O2 availability later in the dive . Considering hypoxia as a stressor that increases HO-1 activity  is associated with increased HMOX2 expression  degrade elevated heme released during tissue damage in part due to an increase in intracellular hemoproteins and (2) to generate bioactive products to further enhance cell and tissue recovery  and sustained hypoxemia (as seen in COPD or at high altitude; The concept that evolutionary mechanisms have optimized the biology and physiology of HO and CO is relevant in the context of hypoxia adaptation. Examples can be observed across species and under varying physiologic and pathophysiologic conditions ranging from diving mammals to individuals living at altitude, as well as physical exercise and in response to tissue injury. Increasing our understanding of the natural activity and regulation of the HO/CO pathway associated with injury avoidance and maintenance of cellular health will contribute valuable knowledge regarding the benefits of tissue-specific, moderate-level CO exposure.The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.The studies involving human participants were reviewed and approved by UCSD IRB #171772. The patients/participants provided their written informed consent to participate in this study.All authors contributed to the article and approved the submitted version.LO is a Scientific Advisor for Hillhurst Biopharmaceuticals. AM is funded by NHLBI. He reports income from Merck and Livanova related to medical education. ResMed provided a philanthropic donation to UC San Diego.The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Liver fibrosis is a chronic, highly prevalent disease that may progress to cirrhosis and substantially increases the risk for development of hepatocellular carcinoma (HCC). Fibrotic livers are characterized by an inflammatory microenvironment that is composed of various immunologically active cells, including liver-resident populations  and infiltrating leukocytes . While inflammatory injury drives both fibrogenesis and carcinogenesis, the tolerogenic microenvironment of the liver conveys immunosuppressive effects that encourage tumor growth. An insufficient crosstalk between dendritic cells (DCs), the professional antigen presenting cells, and T cells, the efficient anti-tumor effector cells, is one of the main mechanisms of HCC tumor tolerance. The meticulous analysis of patient samples and mouse models of fibrosis-HCC provided in-depth insights into molecular mechanisms of immune interactions in liver cancer. The therapeutic modulation of this multifaceted immunological response, e.g., by inhibiting immune checkpoint molecules, in situ vaccination, oncolytic viruses or combinations thereof, is a rapidly evolving field that holds the potential to improve the outcome of patients with HCC. This review aims to highlight the current understanding of DC–T cell interactions in fibrogenesis and hepatocarcinogenesis and to illustrate the potentials and pitfalls of therapeutic clinical translation. The liver is not only important for metabolism, detoxification and protein synthesis, but also contains many immune cells that control homeostasis and defense against pathogens. The immunological landscape of the liver is shaped by continuous exposure to non-self antigens from the portal venous blood that would ordinarily provoke an immediate immune response. An intense immunological interaction is facilitated by a slow blood flow in the liver sinusoids, their lining by specialized liver sinusoidal cells (LSECs) and a fenestrated endothelium that enables the contact to the underlying space of Disse, and thus, hepatocytes . A plethHepatic fibrosis and cirrhosis constitute a major source of morbidity and mortality worldwide, with viral hepatitis, alcohol-related liver disease (ALD) and nonalcoholic steatohepatitis (NASH) constituting the most common etiologies . FibrosiHepatocellular carcinoma (HCC) is the most common primary liver tumor and typically develops in the context of liver fibrosis or cirrhosis. The incidence of HCC in cirrhotic patients is between 2 and 7% per year, depending on the etiology of the chronic liver disease . GeneralThe last years have witnessed a rapid development of therapeutic strategies specifically targeting communication of APCs, T cells and tumor cells, justifying an intensified interest in the DC T cell axis. A such, the interaction of DCs, as the most potent APCs, can mediate a tolerogenic or immunogenic direction of the T cell response, while CD8+ T cells, once activated, constitute the most effective antitumor defense. Here, we will focus on the DC–T cell axis and describe other cellular compartments if they pertain to the general understanding of liver physiology or disease or if they influence the antigen-presenting axis. This review aims to give a comprehensive overview of the role of DC and T cell interaction in liver cirrhosis and hepatocarcinogenesis in the context of new therapeutic opportunities to overcome the immune tolerance of HCC and to improve patient outcomes.Since the first morphological report of a cutaneous DC type of unknown function by Langerhans in 1868 and the description of DCs by Steinman and Cohn in peripheral lymphoid organs in 1973, it has been recognized that DCs form an essential link between innate and adaptive immunity . As suchHuman DCs commonly express the major histocompatibility complex (MHC) molecule, human leukocyte antigen (HLA)-DR, cluster of differentiation (CD) 209 and integrin CD11c, which can also be found on subsets of macrophages, activated T cells, B cells and natural killer (NK) cells . There iIn 2013, Ibrahim et al. suggested a compelling classification of liver DCs based on DC lipid content and lipid metabolism. A DC population with high lipid concentrations (high-DC) that activated T cells, NK cells and NKT cells, exhibited a high MHC class II (MHCII) and toll-like receptor (TLR) expression accounted for approximately 75% of liver DCs, whereas a second DC population with low levels of lipids (low-DC) induced regulatory T cells, anergy to cancer and oral tolerance .The hepatic composition of lymphocytes differs from blood and other lymphoid organs. The liver contains a large number of “unconventional” lymphocytes, including innate and innate-like lymphocytes, mucosa-associated invariant T cells, γδ T cells, NK and NKT cells, alongside classical components of the adaptive immunity such as T- and B-cells . With reCirculating DCs, monocytes and other DC precursors migrate through the liver, exerting phagocytic activity and then move from the sinusoidal area through the hepatic lymph tracts to the locoregional lymph nodes . In the On the way to the lymph node DC mature, reflected by their expression of CCR7 and the loss of CCR1 and CCR5 . After aThe hepatic innate immune response is influenced by a chronic low-level exposure to endotoxins  from the portal blood. This leads to the desensibilization against LPS, the downregulation of responses to infective triggers and the secretion of interleukin (IL)-10 by Kupffer cells . A similLiver fibrosis constitutes the major complication of chronic liver disease that can ultimately progress to liver cirrhosis—a fibrotic remodeling with a distortion of the vasculature and the development of regenerative nodules. The major complications of cirrhosis include an impaired hepatic function and severe systemic effects such as portal hypertension, hepatic encephalopathy and disturbances of blood coagulation and an increased risk to develop HCC ,46. CharhighCD16− classical monocytes ..129].Immune checkpoint inhibitors were celebrated as the “breakthrough of the year” in 2013 by Science magazine and in 2018, JP Allison and T. Honjo were jointly awarded the Nobel Prize in Physiology or Medicine for their discovery of negative immune regulation inhibition for cancer therapy ,131. AntIn HCC, response rates of 15–20%  to NSeveral predictors of the response to the checkpoint blockade have been suggested, such as a high expression of PD-L1, high tumor baseline expression of immune-related genes, lymphocyte tumor infiltration, mismatch repair-deficiency and IFN-γ signaling ,137,138.Large-scale gene expression profiling revealed that about 27% of HCCs exhibit elevated markers of an inflammatory response, such as a high infiltration of immune cells, respective PD-1 and PD-L1 expression and enhanced cytolytic activity or IFN-γ signaling. This HCC group with an inflammatory response, in turn, was divided into subgroups based on the TME with about 65% belonging to an active immune response subtype with an activated adaptive T cell response and about 35% exhibiting an exhausted immune response, characterized by the presence of immunosuppressive signals like TGF-β and M2-type macrophages. The first group had a significantly better OS. Particularly the active immune response group thus resembled the immunological landscape of melanomas amenable to checkpoint inhibition therapy . HoweverWhile a subset of patients—for which predictive biomarkers in HCC have to yet be clinically implemented and tested—shows an impressive response to checkpoint blockade, it is clear that a large group of HCC patients derives little benefit from checkpoint inhibition because of primary resistance . PossiblArguing that poor tumor immunogenicity and defective DC maturation result in an impaired priming of cytotoxic CD8+ T cells, the ex vivo exposure of DCs to tumor antigens with concomitant stimulatory signals has been proposed to trigger an antitumor response. Most studies on ex vivo DC vaccines employ a similar procedure: first, mononuclear cells are isolated from peripheral blood and transferred into cell culture. Then, DCs are stimulated with activating cytokines such as granulocyte-macrophage colony-stimulating factor (GM-CSF), IL-4 and TNF-α and the exposure to a specific antigen is induced, usually by incubation with either tumor lysates or TAAs, but methods of cell fusion or tumor-associated RNA or DNA transfection have also been described ,145. SubAlternative stimulation techniques of the DC–T cell axis are emerging, such as the intratumoral injection of allogeneic moDCs previously stimulated with proinflammatory factors . Due to The realization that poorly immunogenic tumors do not respond sufficiently to checkpoint inhibition prompted the approach of inducing an endogenous antitumor response before the checkpoint blockade. As such, studies conducted in poorly immunogenic melanoma more than two decades ago showed that, while the tumors did not respond to anti-CTLA4, a combination with a GM-CSF-transduced cellular vaccine induced a tumor response . CombinaOncolytic viruses selectively infect and lyse tumor cells, triggering an immunological response to TAA. GM-CSF production from infected tumor cells has been suggested as an additional immunostimulatory mechanism ,152. Ini4 models considered most similar to the human disease [A possible explanation for the discrepancy between initially encouraging results in mouse models and early human trials and the negative results in subsequent human studies may lie in the pitfalls of the translation from mice models to humans. As such, murine fibrosis/HCC models, which constitute the foundation of basic immunological science, usually cannot reflect the full spectrum of human HCC etiologies and pathophysiology, with CCL disease . Further disease .The combination of different immune checkpoint inhibiting agents has been suggested early in the experience with checkpoint inhibition of melanoma, but long-term follow-up data are not yet available for most tumor entities . The fouIn 2019, several studies have shown that the two most prominent checkpoint inhibitors, anti-CTLA4 and anti-PD-1/PD-L1 convey distinctly different effects: CTLA-4 inhibition relieves constraints on CD4+ T cell phenotypes and allows for the differentiation of inducible costimulator (ICOS)+ CD4 Th1 cells , while aIdentifying the role of DC–T cell interactions in liver cirrhosis and carcinogenesis may not only help to unravel the mechanisms of fibrogenesis, but also provide essential clues towards the therapy of chronic hepatic diseases and HCC. Hepatocellular carcinoma arises against the background of a highly deregulated immune milieu with constitutive inflammatory signaling, activation of usually quiescent cell types and an antitumor response that is impaired by T cell exhaustion and by the physiologically tolerogenic direction of hepatic immune responses.After several decades of a futile search for an efficient systemic HCC therapy, the last decade has witnessed the clinical incorporation of new agents into the clinical practice at a breathtaking pace. DCs and T cells form an immunologic backbone of tumor defense that is amenable to therapeutic targeting by the checkpoint blockade and DC vaccines. The forward and reverse translation between clinical experience and basic research enabled the advancement of additive or complimentary approaches in this field. At the same time, careful consideration of observations from animal models is necessary to gauge the efficacy of these strategies on humans to avoid the aforementioned pitfalls of translation. An improvement of our understanding of the role of DCs and T cells in HCC holds promise to optimize patient selection for existing treatments through biomarker-embedded approaches, to develop new strategies to overcome tumor tolerance and to improve the overall outcomes of patients with HCC.


In the context of the Sustainable Development Goals and the shifting global burden of disease, this systematic review analyses the evidence from rigorously evaluated programmes that seek to transform the gendered social norms undermining the health and wellbeing of children, adolescents, and young adults. The aim of this study was threefold: to describe the landscape of gender-transformative programmes that attempt to influence health-related outcomes; to identify mechanisms through which successful programmes work; and to highlight where gaps might exist in implementation and evaluation.We systematically reviewed rigorous evaluations published between Jan 1, 2000, and Nov 1, 2018 of programmes that sought to decrease gender inequalities and transform restrictive gender norms to improve the health and wellbeing of 0–24 year olds. We included rigorously evaluated health programmes that met the Interagency Gender Working Group definition of gender-transformative programming, regardless of where in the world they were implemented and what area of health they focused on.Among 22 993 articles identified by our search, 61 evaluations of 59 programmes met review criteria. Programmes were concentrated in sub-Saharan Africa (25 [42%]), south Asia (13 [22%]), and North America (13 [22%]) and mainly measured health indicators related to reproductive health (29 [48%]), violence (26 [43%]), or HIV (18 [30%]). Programmes most frequently focused on improving the individual power of the beneficiaries, rather than working on broader systems of inequality. 45 (74%) of the evaluations measured significant improvements in health-related and gender-related indicators; however, only ten (16%) showed evidence of, or potential for, broader norm change. These ten programmes worked with sectors beyond health, included multiple stakeholders, implemented diversified strategies, and fostered critical awareness and participation among affected community members.This review can accelerate efforts to improve global health by leading to more strategic investment in programmes that promote gender equality and target restrictive gender norms among young people. Such programmes can lead to a lifetime of improved health and wellbeing by challenging not only attitudes and behaviours related to gender at an early age, but also the gendered systems that surround them.Bill & Melinda Gates Foundation. The health consequences of gender inequality have the greatest effect on women and girls, but restrictive gender norms harm health and limit life choices for all.Depending on their gender, children, adolescents, and young adults are valued differently within society and face divergent expectations, leading to potentially harmful customs, such as child marriage for girls and risky forms of labour for boys.Evidence before this studyThis analysis builds on and brings together two previous streams of research. The first stream is comprised of systematic reviews of the evidence for the effect of gender-transformative interventions on sexual and reproductive health, HIV, and violence outcomes in low-income and middle-income countries; the second stream identifies individual, interpersonal, and community-level predictors of gender norms among young adolescents. In the context of meeting the Sustainable Development Goals and responding to the shifting global burden of disease, this systematic review highlights what is being done programmatically to address the influence of gender inequality and restrictive gender norms on child and adolescent health.Added value of this studyThis systematic review builds on existing literature reviews by searching for and including evaluations of any type of programme, in any geographical location, that intentionally addressed gender norms and power imbalances  to benefit 0–24 year olds, and rigorously measured potential changes in health-related outcomes. We found that three-quarters of all programmes that met our study criteria significantly impacted both gender-related and health-related variables simultaneously. The highest quality programmes shared several characteristics, which suggest that they have potential to powerfully affect both gender equality and health. These programmes worked with sectors beyond health to create change; included the participation of multiple stakeholders; implemented diversified strategies; and fostered critical awareness and participation among affected community members, encouraging them to become active agents in shaping their own health.Implications of all the available evidenceOur research highlights gaps in implementation of gender-transformative activities, including the types of activities being implemented and the underlying norms and health outcomes that interventions have focused on. The shift in the global burden of disease among young people calls for a sharper focus on how to shift the gender-related norms that contribute to poor mental health, infectious disease, substance use, injury, and chronic disease. Our focus on children, adolescents, and young adults highlights the global opportunity to address gendered constraints on health and wellbeing at an early age to ensure young people benefit from the effects for their lifetime.Lancet Series on Gender Norms and Health.Given the importance of this age group, this systematic review aims to supplement the We did a systematic review of the peer-reviewed literature and a comprehensive review of the grey literature following PRISMA guidelines  to identWe reviewed evaluations published in English, French, Spanish, or Portuguese between Jan 1, 2000, and Nov 1, 2018, that used quantitative, qualitative, or mixed methods to infer a high level of causality. To optimise the quality of studies included in the review, we adapted a protocol used by the Overseas Development InstituteWe ran our search terms  in ScopuTwo researchers independently coded and categorised key programmatic material, using the software programme EPPI-Reviewer ; differeThe funder of the study had no role in study design, data collection, data analysis, data interpretation, or writing of the report. The corresponding author had full access to all the data in the study and had final responsibility for the decision to submit for publication.Our search of peer-reviewed literature identified 22 993 articles, from which further screening identified 36 evaluations of 34 distinct programmes meeting our inclusion criteria. Our internet search retrieved 173 potential evaluations, among which we identified 25 distinct programme evaluations that met the same inclusion criteria used for the peer-reviewed articles. Altogether, we reviewed 61 evaluations of 59 programmes .Figure 133 (54%) of the 61 evaluations that met our screening criteria used exclusively quantitative approaches, 27 (44%) used mixed methods, and one used only qualitative methods . 28 47%, and the55 (90%) of the 61 evaluations measured outcomes related to family planning or sexual and reproductive health (29 [48%]), physical, sexual, or emotional violence (26 [43%]), and HIV (18 [30%]). Programme evaluations also measured outcomes related to nutrition (seven [12%] of 61); maternal and child health (five [8%]); water, sanitation, and hygiene (five [8%]); mental health (four [7%]); substance use (four [7%]); and infectious disease (one [2%]). 25 (41%) of the programme evaluations measured two or more areas of health at once; 14 (56%) of these 25 evaluations were in sub-Saharan Africa .50 (82%) of 61 evaluations measured outcomes among children and adolescents aged 10–14 years (44 [72%]) or 15–19 years (48 [79%]) as either targeted participants or beneficiaries of the programme. 33 (54%) of the 61 studies included community members, caretakers, parents, or teachers to enhance programme outcomes, and five (8%) focused on outcomes among children below the age of 10 years. Six (10%) evaluations were of programmes that targeted young adults aged 20–24 years and aimed to improve sexual and reproductive health outcomes, including HIV.More than half of the programmes (33 [56%] of 59) engaged men or boys through activities to improve interpersonal skills, shift notions of masculinity, decrease violence, and redefine roles and responsibilities within the household. 11 (33%) of these 33 programmes focused on males as the primary beneficiary population and were designed to improve health among males specifically; the other 23 (67%) programmes implemented activities to primarily benefit females.A few programmes addressed intersectionality across ethnicity, socioeconomic status, or other social categories. Eight (14%) of 59 programmes focused primarily on gender inequality among one or more of their country's minority ethnic populations and 12 (20%) worked with subpopulations living in relative poverty. Other targeted social groups included those affected by conflict, married and unmarried girls, married men, newly married couples, orphans, out-of-school girls and boys, and university students. No programme exclusively targeted gender minorities or LGBTQ populations.Activities also often focused on engaging communities or building social support systems (53 [90%] of 59). For example, programmes included community events such as theatre and drama productions (11 [19%]) and local health fairs (one [2%]); and facilitated social integration through life skills training (17 [29%]), community and civic engagement (11 [19%]), mentorship or peer support (ten [17%]), and sports (five [9%]). Activities such as role-playing allowed participants to build communication skills and rethink norms related to the right to express opinions and negotiate choices (33 [56%]).14 programmes (24%), all in sub-Saharan Africa (nine) and south Asia (five), addressed the problems that women and girls often face in not having access to and control over resources. These programmes aimed to enhance the economic stability of these women and girls by building their financial literacy and providing access to savings programmes, loans, stipends, incentives, and vocational livelihood training. 28 programmes (47%) in sub-Saharan Africa (14), south Asia (11), and the Middle East (three) provided safe spaces for participants to explore sensitive topics or to safely socialise and build social networks. In North America, three programmes implementing these activities focused on violence prevention; in Latin America, one programme provided a safe space for boys to discuss issues like violence, relationships, and family. Two programmes explicitly mentioned involving religious leaders as allies, and all programmes implemented activities within or through secular spaces.Rather than focusing on systemic inequity, programmes most frequently implemented activities meant to improve the power and influence that beneficiaries have over their own lives. More than half of the evaluations (34 [56%] of 61) assessed changes in the agency of participants, measuring indicators related to self-confidence, self-efficacy, freedom of movement, and age at marriage.Almost three-quarters (45 [74%]) of the evaluations showed significant improvements in indicators of health and measures related to gender inequality, of which 32 (71%) were evaluations of programmes that targeted people aged 10–19 years as their primary beneficiary population. 31 (69%) of these 45 studies showed changes in knowledge about health topics such as sexually transmitted infections, contraception, and body satisfaction; 38 (84%) showed changes in health behaviours, such as substance abuse, breastfeeding practices, and exercise; and four (9%) showed significant improvements in the use of health services. Only 13 (21%), however, actually measured health outcomes—rather than knowledge, attitudes, or behaviour related to health—and found significant decreases in the incidence of unwanted or unintended pregnancy (five [8%]), HIV (3 [5%]), female genital mutilation or cutting , stunting (two [3%]), child morbidity (one [2%]), and violence (five [8%]) or anxiety (one [2%]).Regardless of their indicators of health, these 45 evaluations were of programmes that relied on activities mainly targeting mechanisms that enforce gender norms and are related to agency (27 [60%]), social and intrafamilial support (23 [51%]), and attitudes towards restrictive gender norms (28 [62%]), including gender norms related to violence, FGMC, and early marriage. Almost two-thirds of these 45 programmes were implemented for 12–24 months (11 [24%]) or more (17 [38%]). Programmes that were implemented for shorter periods, yet still produced significant outcomes, mainly measured changes in health knowledge or behaviours related to condom use, risky sex, or perpetration of violence.These 45 programmes were primarily implemented in the community (27 [60%]), as part of a school curriculum (13 [29%]), or as part of after-school programmes (14 [31%]). One (2%) incorporated activities in a prison, and one (2%) was implemented within a health-care setting. Regardless of their setting, these programmes used diverse methods to disseminate information and challenge the long-held beliefs of participants, including role play, dialogue and discussion, peer-to-peer activities, circulation of print materials, audiovisual media , and digital media. Although the diversity of the programmes made it impossible to compare effective combinations of approaches, 20 (44%) implemented three or more of these activities to accomplish their goals.Among the 45 programmes that brought about significant changes in their measured outcomes related to health and gender, 14 (31%) implemented activities that engaged girls and boys in the same activity at the same time. This approach enabled participants to engage with members of another sex in a safe, structured setting to explore, discuss, and reframe gender roles, assumptions, and decision making. However, in settings with restrictive gender norms and little informal contact between women and men, introducing topics in segregated groups is important.Only ten (17%) of all 59 programmes showed evidence of, or potential for, broad change in gender norms ; table. This systematic review assessed rigorously evaluated programmes that sought to transform gender relations to promote equality and achieve health and wellbeing among people aged 0–24 years, living in any part of the world. These gender-transformative programmes exemplify the Sustainable Development Goal principle of investing in areas that spark or catalyse diffusion of change.Although this systematic review shows the potential contributions that gender-transformative programming can have on gender equality and health, our analysis found several gaps in current programme design, implementation, and evaluation. The same limitation applied to downstream health outcomes, which are often driven by external forces as well as internal decisions and power. For example, evaluations of programmes that attempted to improve attitudes to violence (21 [34%] of 61) found significant improvement 81% of the time, and evaluations of programmes that attempted to improve behaviours related to violence (18 [30%]) found significant improvement 72% of the time. However, only five (38%) of the 13 programmes that measured participants' experience of violence showed significant improvement. Thus, societal and structural elements of restrictive gender norms often overpower efforts to improve a single aspect of individual or even interpersonal power, making health outcomes difficult to change without a more holistic, systems approach.The programmes in our review were also potentially limited by their narrow health focus. Most programme evaluations (55 [90%] of 61) were designed to measure only outcomes related to HIV, sexual and reproductive health, or violence, which is problematic given the growing evidence that gender norms influence many different health areas.Programmes were also limited by their poor inclusivity of activities and beneficiary participation. Programmes succeeded at producing significant changes in indicators related to gender or health when the implemented activities facilitated joint reflection and allyship among girls and boys or women and men. Yet, even the high-quality programmes identified in our review often emphasised the empowerment of girls and women to the comparative neglect of masculinity and restrictive gender norms that affect sexual orientation and gender identity and expression. Furthermore, very few gender-transformative programmes were working to improve health among gender-diverse people.Our research also highlights the need to understand gender in the context of intersectionality—the overlapping effects of different aspects of status and identity—which can magnify the influence of gender inequalities and restrictive gender norms on health. Although programmes in our review often focused on disadvantaged subpopulations, fewer than 10% explored the specific contributions of race and ethnicity, religion, or geographic location. Furthermore, only one programme primarily targeted a population of children younger than 10 years,In addition to design and implementation gaps in the programmes themselves, we identified opportunities for improving the evaluation of such programmes. Given that they appear to work upstream from several positive outcomes, programmes that seek to transform norms have the potential to improve health and wellbeing across many areas of health and for long periods across the life course. Yet, little is known about the full effect of these programmes, because the majority of the 61 evaluations in our review measured outcomes related to one area of health (36 [59%]) and evaluated outcomes during implementation or within 6 months of programme completion (36 [59%]). Only four (7%)—all of which produced significant, sustainable change—evaluated the outcomes more than 3 years after programme completion. Furthermore, very few evaluations triangulated their measures by collecting data on the same outcome from multiple sources. Given the social nature of gender norms, understanding and measuring effects beyond the individual is important. As programmes increasingly address gender inequality and restrictive gender norms to improve health and other aspects of wellbeing, innovative and comprehensive ways of measuring norm change are needed.We could have missed programmes that might be considered gender transformative but did not indicate as such in the title or abstract or their evaluation. Moreover, we might have missed strong programmes that improve health through gender-transformative work but did not measure health-related outcomes. For example, programmes that aimed to end child marriage were excluded unless they measured an associated health outcome. Our systematic review was also restricted to methods suitable for examining causal effect. The hierarchy of evidence developed for clinical interventions might not be ideally suited for complex social interventions because it does not fully account for complexity and non-linear causality. We might thus have excluded effective programmes that were small or did not otherwise meet our evaluation criteria. Moreover, the evidence available might be biased because financial donors have preferences in the health areas, geographies, interventions, and research methods that they fund. Additionally, we were able to analyse only what was measured and reported in the evaluation publications. The disparate indicators and measurement and analysis techniques used in the different studies made it impossible to compare magnitude of change or generate summative statistics.Future research could build on this study by focusing more explicitly on evaluations that use rigorous qualitative methods to further unpack specific mechanisms of change. An important programmatic and research challenge is to conceptualise and address gender inequalities and restrictive gender norms that affect gender minorities or LGBTQ populations. What are the attitudes and behaviours of the majority population that create the conditions of stigma and exclusion for people who depart from the norm? How can gender-transformative programmes address such issues?An initial aspiration of this study was to assess the contributions of gender-transformative programmes to reducing the causes of morbidity and mortality that contribute most heavily to the global burden of disease. Although we found a continued focus on HIV, sexual and reproductive health, and violence, as the global burden of disease shifts so does the opportunity to implement gender-transformative programmes in other areas of health and development. Indeed, programmes that decrease gender inequality and transform restrictive gender norms are arguably key to achieving the Sustainable Development Goals.14


Bacteria that colonize the human gastrointestinal tract are essential for good health. The gut microbiota has a critical role in pulmonary immunity and host’s defense against viral respiratory infections. The gut microbiota’s composition and function can be profoundly affected in many disease settings, including acute infections, and these changes can aggravate the severity of the disease. Here, we discuss mechanisms by which the gut microbiota arms the lung to control viral respiratory infections. We summarize the impact of viral respiratory infections on the gut microbiota and discuss the potential mechanisms leading to alterations of gut microbiota’s composition and functions. We also discuss the effects of gut microbial imbalance on disease outcomes, including gastrointestinal disorders and secondary bacterial infections. Lastly, we discuss the potential role of the lung–gut axis in coronavirus disease 2019. Experimental and clinical evidences demonstrate that the gut microbiota has a crucial role in the maintenance of human health.2 Tightly regulated microbiota-host interplay influences the development, instruction, and priming of the immune system.6 Recent research studies have shown that this interplay has a major role in the control of infection.7 The mechanism by which the gut microbiota regulates immune responses depends on microbial-associated molecular patterns, microbial metabolites, and the microbes’ interactions with progenitor cells and mature immune cells.10The gastrointestinal tract hosts a complex, highly diverse microbial ecosystem (mostly obligate anaerobic bacteria) that is commonly referred to as the gut microbiota. Collectively, intestinal bacteria constitute a genome of more than 3 million genes—150 times larger than the human genome.11 Changes in intestinal bacterial communities can influence disease outcomes even in distant organs (including the lungs), as demonstrated by transfer experiments with dysbiotic microbiota.11 Here, we summarize mechanisms through which the gut microbiota remotely promotes pulmonary defense against viral infection. We review the effects of acute viral respiratory infections on the gut microbiota, discuss the potential mechanisms of gut dysbiosis and debate the impact of altered gut microbiota on secondary disease outcomes. The potential importance of the gut–lung axis in the outcome of coronavirus disease-19 (COVID-19) is discussed in the light of this knowledge.Many factors can alter the diversity and composition of the gut microbiota, leading to dysbiosis. This includes dietary patterns and stress inducers, such as broad-spectrum antibiotics and cancer drugs. Disease situations—such as infections and chronic inflammatory or metabolic disorders—can also lead to dysbiosis.7 Accordingly, alterations of the microbiota notably induced by antibiotics, which eradicate more or less completely intestinal bacteria or specific species, increase susceptibility to enteric infections like Salmonella and enteroaggregative Escherichia coli.11 This beneficial effect of the gut microbiota in immunity is not limited to the gut compartment but also extends to systemic compartments and distant organs such as the lungs.13 Mice lacking microbiota  or those orally treated with antibiotics  have impaired responses to systemic and respiratory infections.25 In the setting of viral respiratory infections caused by, for example, influenza A virus (IAV) and respiratory syncytial virus (RSV), the profound disturbance of the gut microbiota’s ecology by antibiotic therapy weakens the host’s innate and adaptive defenses.26 Mechanisms through which the gut microbiota arms the lung to control viral respiratory infection are numerous. These points will not be extensively reviewed in the present review but some examples will be provided . Briefly, several studies have highlighted the impact of the gut microbiota on the lung’s production of type I interferons (IFNs),31 which are well known to control viral infections including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19.34 In this setting, microbial metabolites such as desaminotyrosine (derived from flavonoid and amino acid metabolism) and short chain fatty acids  have been shown to be critical.18 For example, it was shown that desaminotyrosine, produced by an obligate clostridial anaerobe  from the digestion of plant flavonoids, could diffuse into blood, reach the lungs and prime the (innate) immune system to protect from influenza infection.18 Desaminotyrosine promoted the synthesis of IFN-stimulated genes in lungs and pulmonary phagocytes were critical in this mechanism. In this setting, desaminotyrosine augmented type I IFN signaling by IFN amplification via IFN-α/β receptor and signal transducer and activator of transcription 1.18 For SCFAs, a myriad of commensals, including members of the Lachnospiraceae family, are able to ferment dietary fibers. For example, it was shown that acetate could diffuse into blood and activate the G protein coupled receptor (GPR) 43  expressed by stromal cells. This activating pathway improved type I IFN responses and increased IFN-stimulated gene expression.15 The mechanism through which GPR43 promoted type I IFN-mediated protection from influenza infection needs to be elucidated. Along with microbial metabolites, microbial membrane components derived from intact gut microbiota, including Toll-like receptor (TLR) ligands, also play a critical part in host defense against viral respiratory infections. Indeed, local and distal inoculation of Poly (I:C) (TLR3 agonist) or peptidoglycan (TLR2 agonist) rescued the immune impairment in the antibiotic-treated mice.17 It is noteworthy that in addition to these distal signals emanating from the gut microbiota, local microbes from the upper airway also regulate lower airway immunity and play a part in pulmonary defense against viral infections. The mechanisms have been described and/or reviewed elsewhere29 and will not be discussed in this review. The gut microbiota not only affects the innate immune response but also boosts CD8+ T-cell effector function—a process that is also involved in viral (influenza) clearance.31 As described above, altering the gut microbiota with antibiotics increased the severity of viral respiratory infections such as influenza. On the contrary, stimulating the microbiome with a high-fiber diet had the opposite effect.31 In the case of influenza, a high-fiber (fermentable inulin) diet conveyed protection through two distinct pathways. Fermentation of dietary fiber resulted in altered bone marrow hematopoiesis, leading to accumulation of alternatively activated macrophages in the lung of IAV-infected mice.31 These macrophages produced less chemokine (C-X-C motif) ligand 1, thus lowering early neutrophil infiltration into the airways. This pathway profoundly reduced exaggerated pulmonary inflammation and damage. The diet also boosted CD8+ T-cell metabolism and enhanced the effector functions of CD8+ T cells, effectively enhancing viral clearance. The GPR41  was required for the protective effect, and oral administration of SCFAs (butyrate) was sufficient to confer protection.31 Similar protective effects have been observed during RSV infection.15 A high-fiber (fermentable pectin) diet protected against RSV infection by modulating type I IFN response in lung epithelial cells and by increasing expression of interferon-stimulated genes in the lung. The GPR43 was required for the protective effect, and oral administration of acetate was sufficient to confer protection.15The role of the gut microbiota in resistance to colonization to enteric pathogens is well established.18 More recently, a study based on the comparison of susceptible and resistant animals demonstrated that colonization by Bifidobacterium genus  is strongly associated with the survival of influenza-infected mice.35 It is likely that in a near future, other commensal members will be identified and will serve as novel biomarkers to predict the severity and mortality of patients experiencing severe viral respiratory infections.The nature of gut commensal bacteria that exert antiviral effect in the lungs is still elusive. As discussed above, members of clostridial anaerobes (desaminotyrosine) and SCFA producers are important in the priming of the pulmonary innate immune system.Hence, at steady state, resident bacteria from the gut microbiota can naturally and remotely buttress the lungs to combat viral respiratory infections. It has yet to be determined whether the gut microbiota is also involved in the early control (innate immunity) and late control (adaptive immunity) of infections by coronaviruses like SARS-CoV-2. The effect of gut microbiota depletion (by means of antibiotics) on the outcome of SARS-CoV-2 infection awaits further studies.37 In these situations, it is possible that the dysfunctional gut microbiota distally influences pulmonary defenses against respiratory viruses. Fecal microbiota transplantation experiments  will be necessary to demonstrate this.Regarding the role of the gut microbiota in lung’s defenses against respiratory viruses, it is plausible that any alteration in the microbiota composition and function can alter the beneficial cross-talk between the gut and the lungs Fig. . Among fThe “gut–lung axis” is bidirectional and pulmonary diseases (including infections) can influence the composition of the gut microbiota. Over the last few years, many researchers have used animal models of lung infections to analyse the effects of respiratory viruses (mostly IAV and RSV) on the gut microbiota. The impact of viral respiratory infections on the lung’s own microbiota is out of the scope of the present review.38 Influenza can also cause devastating pandemics; the 1918 and 2009 pandemics killed 50 million people and 250,000–500,000 additional people, respectively.41 Influenza infections can lead to mild to severe pneumonia, acute respiratory distress syndrome (ARDS), clinically defined as acute respiratory failure, and multi-organ dysfunction.42 Despite the apparent absence of virus in the gut, some patients nevertheless present gastroenteritis-like symptoms such as abdominal pain, nausea, vomiting, and diarrhea.43 This suggests that the lung–gut axis is potentially important during influenza infection. Several research groups have studied the nature of microbial changes in the context of IAV infection in the mouse, mostly by 16S rRNA sequencing.49 Several IAV subtypes  and sites, including the small intestine, cecum, and colon, have been studied. The data are convergent, i.e., alteration of the gut microbiota’s composition peaks at days 7–9 post infection. No virus was detected in the gut, and no change in the gut microbiota’s composition was observed after inoculation of an attenuated virus.46 The latter finding suggested that the change in the gut microbiota was specifically driven by a live viral infection and that the signal was not directly due to local replication. Alteration of the gut microbiota’s composition was transient and, although differences were still present, the composition globally returned to its initial state by 14 days post infection.49 The bacterial load and alpha diversity, as assessed by the number of operational taxonomic units, were not strongly impacted by IAV infection.49 At the phylum level, few changes were observed. Infections by the H1N1 subtype of IAV led to a decrease in the Bacteroidetes/Firmicutes ratio; this was mainly due to an increase in the S24-7  and Porphyromonadaceae families46 (Table S24-7 family.49 An increase in Verrucomicrobia (mainly composed by the Akkermansia genus) was also observed during infection by H3N2 and H1N1 subtypes.47 These bacteria are known to degrade the intestinal mucus layer—as does Ruminococcus, numbers of which also increased during an IAV infection. A decrease in Actinobacteria (mainly due to reduction in Bifidobacteriaceae genus) has also been observed after IAV infection.47 Broader changes have been observed at lower taxonomic levels. Briefly, most studies found an increase in Gammaproteobacteria  and, less frequently, a decrease in the Lactobacillus genius (the Bacilli class)49 , Ruminococcaceae, and Mogibacteriacecea families and the Coprococcus, Roseburia, Defluvittalea, Dorea, Ruminococcus, and Gemmiger genera were relatively more abundant during infection.47 Furthermore, IAV infection in mice was associated with a drop in the proportion of segmented filamentous bacteria (Clostridiaceae family).48 This bacterium interacts closely with the intestinal epithelium and is important in host resistance against enteric pathogens like Citrobacter rodentium.50 Taken as a whole, the data from murine models of influenza indicated that infection promotes the emergence of potentially detrimental bacterial species, such as members of Gammaproteobacteria and mucus-degrading bacteria. Conversely, infection appears to blunt the growth of health-promoting bacteria such as Lactobacilli, Bifidobacteria, and segmented filamentous bacteria.48 Interestingly, a recent study showed that the nature of the gut microbiota alteration due to IAV (H7N9) infection is different in mice that survived infection relative to mice that succumbed to infection.35 In particular, Bifidobacterium pseudolongum and Bifidobacterium animalis levels were significantly elevated in surviving mice when compared to mice which died. It was suggested that Bifidobacterium mediates the anti-influenza effect via several specific metabolic molecules including valine and coenzyme A.35Influenza infections are responsible for significant morbidity and mortality, with 3–5 million severe cases and 290,000–650,000 deaths each year worldwide.51 A decrease in diversity and the overgrowth of Escherichia coli and Enterococcus faecium were observed. Eubacterium, Ruminococcus, Bifidobacterium, and Roseburia were all less abundant in infected patients. In a cohort of 24 influenza A (H1N1) patients, Gu et al. reported a decrease in the relative abundance of Actinobacteria, Erysipelotrichea, Clostridia and beneficial butyrate producers (Lachnospiraceae and Ruminococcaceae families).52 On the other hand, opportunistic pathogens such as Shigella and Escherichia species developed. Studies of the impact of influenza infection on the gut microbiota in large human cohorts are now warranted.Surprisingly, few studies have analysed the nature of gut microbiota alteration during viral respiratory infections in the human setting. Quin and colleagues analysed samples from 40 patients infected with H9N2 avian virus.47 The concentrations of acetate, propionate, and butyrate were all lower than in mock-infected controls. Infection with IAV also resulted in a shift in glycolipid metabolism. Interestingly, IAV infection altered the synthesis of alpha-galactosylceramides53 which are known ligands for invariant natural killer T cells and play an important role in the immune system in rodents and humans.54 It is not clear whether these metabolic changes influence gut homeostasis and function. However, one can speculate that reduced alpha-galactosylceramide availability may interfere with the immune regulatory functions of intestinal invariant natural killer T cells.55 Along with ligands for (invariant) natural killer T cells, it is also possible that the synthesis of ligands for mucosal-associated invariant T (MAIT) cells could also be altered during a viral respiratory infection. Indeed, bacterial commensals, including species belonging to Bacteroidetes and Proteobacteria phyla, as well as pathogenic bacteria, can produce vitamin B2 and vitamin B9 metabolites, known to act as agonists or antagonists for MAIT cells. Regarding the key role of MAIT cells in mucosal immunity,58 altered synthesis of MAIT cell ligands during viral respiratory infections might have important consequences on disease outcomes, a hypothesis that needs to be investigated.Gut microbiota’s metabolites are important in health. Whether or not change in the gut microbiota composition during IAV infection alters the gut’s metabolic output has been recently addressed. In the mouse system, infection with IAV led to changes in the gut  metabolome, with a significant drop in the production of SCFAs.59 This pathogen is also a significant cause of respiratory illness in older adults. As observed with IAV infection, RSV induces seasonal outbreaks and causes up to 118,000 deaths each year worldwide.60 In a mouse model, RSV resulted in significant alterations in gut microbiota diversity  at day 7 post infection, with an increase in Bacteroidetes and a decrease in Firmicutes.46 This increase in the Bacteroidetes phylum was mainly due to the rise in the Bacteroidaceae and S24-7 family, whereas the decreased abundance of Firmicutes was related to attenuation of both Lachnospiraceae and Lactobacillaceae families. The impact of RSV infection on the gut microbiota’s metabolic activity has rarely been addressed. In one study, RSV infection predominantly increased the metabolism of lipids, including sphingolipids, polyunsaturated fatty acids, and the SCFA valerate.61RSV is the most common cause of bronchiolitis and pneumonia in children under the age of 2 years. It accounts for over 80% of pediatric lower respiratory tract infections.62 Specific antivirals or approved vaccines against SARS-CoV and Middle East respiratory syndrome coronavirus are not yet available. In late 2019, a new infectious respiratory disease emerged in Wuhan, China.64 This disease  rapidly spread through China and many other countries worldwide.64Coronaviruses continuously circulate in human populations and generally cause mild respiratory diseases, including the common cold. In contrast, SARS-CoV and the Middle East respiratory syndrome coronavirus—both of which are zoonotic in origin—can cause severe respiratory diseases and have a high mortality rate.69 Recent studies have reported the impact of a SARS-CoV-2 infection on the gut microbiota in humans.73 Briefly, SARS-CoV-2 infection lowered the abundance of butyrate producers such as several genera from the Ruminococcaceae and Lachnospiraceae (Roseburia) families.71 A significantly higher relative abundance of opportunistic bacterial pathogens including Streptococcus (class Bacilli), Rothia, and Actinomyces was also observed. Another recent study revealed, by RNA shotgun metagenomics sequencing, the presence of opportunistic bacterial pathogens including Collinsella aerofaciens and Morganella morganii as well as Streptococcus infantis (an abundant colonizer in the upper respiratory tract) in fecal samples of patients with COVID-19 who had high SARS-CoV-2 infectivity.73 In contrast, SCFAs and tryptophan producers were enriched in the fecal samples with signature of low-to-none SARS-CoV-2 infectivity. Of interest, the feces with high SARS-CoV-2 infectivity had a higher microbiome functional capacity for nucleotide de novo biosynthesis, amino acid biosynthesis and glycolysis.73 Of note, overgrowth of opportunistic fungal pathogens (Aspergillus and Candida spps) was also described in COVID-19 patients.72 It is interesting to notice that in the Gu’s study, similarities and also differences between influenza (H1N1) and SARS-CoV-2 patients were described.52 The discovery of core gut microbial features—and related metabolites—may serve as potential diagnostic markers.Surprisingly, few studies have addressed the impact of coronavirus infection on the gut microbiota and most of them focused on chicken and pig models .74 In parallel, large human cohorts and more relevant animal models  are needed. These approaches will be instrumental in determining the potential clinical relevance of the findings. Along the same line, a better understanding of the overall impact of acute viral respiratory infection on the gut microbiota’ metabolic output is urgently needed. Research in this area is in its infancy in the context of viral respiratory infections. Metabolomics studies might provide a more detailed understanding of consequences of gut microbiota changes on disease outcomes and might also lead to the discovery of biomarkers of disease severity. Genome-scale metabolic modeling will also be instrumental to estimate the metabolic capabilities of gut microbiota. Correlation analyses between changes in gut microbiota composition, microbial metabolites, proinflammatory cytokine levels and disease severity will be very informative. This approach may serve as a preventive/treatment target for intervention especially among patients who are highly susceptible to viral respiratory infections.Animal models and clinical data clearly show that acute viral respiratory infections lead to a transient disruption of the balanced gut microbial ecosystem, with less salutary bacteria and more pathogenic bacteria. However, a more comprehensive description must be obtained. Further research should include metagenomics analyses such as shotgun metagenomic sequencing. The later approach offers the possibility to analyse potential changes in the composition of fungi, viruses and parasites and to evaluate major changes in the microbial metabolic pathways.76 This weight loss is mainly due to a loss of appetite (inappetence).78 Reductions in food and calorie intakes are known to perturb the gut microbiota.79 The results of pair-feeding experiments have clearly indicated that a rapid fall in food intake mimics the changes in the gut microbiota observed during infection  although differences  were also observed.61 Consistently with the decrease in fiber intake, pair-fed mice had lower SCFA concentrations.47 Among them, butyrate fuels colonic epithelial cells and favors epithelial oxygen consumption, thus allowing oxygen deprivation in the intestinal lumen. The drop of SCFAs due to reduced food (fiber) intake is likely to alter epithelial cell metabolism. One of the main explanation for inappetence during viral infection is the overproduction of inflammatory cytokines, including tumor necrosis factor alpha.80 The neutralization of this cytokine during an RSV infection reduced the weight loss and partly attenuated the perturbation of the gut microbiota.61 Along the same line, depleting cytokine-producing CD8+ T cells during an RSV infection reduced inappetence and reversed changes in the gut microbiota.61 Type I and II IFNs are essential components of the host antiviral response - notably during influenza.81 These cytokines potently disturbed the gut microbiota.48 Relative to wild type mice, mice deficient in type I IFN receptor presented reduced blooming of Proteobacteria (Escherichia genus) and, conversely, an elevated proportion of segmented filamentous bacteria.45 Along the same line, depletion of IFN-γ during an IAV infection restored changes in segmented filamentous bacteria (reduced in IFN-γ-competent mice), the Lactobacillus genus (reduced), and Enterobacteriaceae (augmented).48 Hence, inflammatory cytokines and loss of appetite can drive gut dysbiosis during viral respiratory infections, at least in the mouse system. Other mechanisms might also be implicated. Intestinal inflammation, due for instance to infiltrated CD4+ T cells or systemic IFN release,48 is known to alter the metabolism of epithelial cells—resulting in the accumulation of a novel set of nutrients, for which the microbes that inhabit the intestinal lumen compete. Along with increased oxygen availability (see below), this phenomenon appears to explain the shift from obligate anaerobes to facultative anaerobes such as Proteobacteria Enterobacteriaceae.86 Hypoxia is a major clinical symptom during the acute phase of respiratory viral infection, including in COVID-19 patients.87 It also associates with chronic intestinal injury. Regarding the role of oxygen in intestinal homeostasis, including microbiota composition and function,88 disruption of the oxygen gradient for instance due to SCFA availability, might play a part in gut dysbiosis and gastrointestinal disorders during respiratory viral infections. Defective intestinal  immune functions during respiratory viral infections  may also participate in dysbiosis.There are several causes of gut microbiota changes during acute viral respiratory infections; these may include the release of inflammatory cytokines and reduced food intake Fig. . In the 92 Around half of COVID-19 patients have SARS-CoV-2 RNAs in the stools—even when it is no longer found in the respiratory tract.92 Importantly, infectious viruses were detected in fecal samples of COVID-19 patients suggesting that the digestive tract might be a site of viral replication and activity.94 In line, several recent studies using human small intestinal organoids have shown that SARS-CoV-2 replicates in enterocytes.96 Hence, local viral replication is likely to disturb the local ecosystem leading to changes in the gut microbiota composition and functions. Moreover, binding of the viral spike protein to the cell surface receptor angiotensin-converting enzyme II (ACE2) results in downregulated expression of the latter.97 With regard to the critical role of ACE2 in the maintenance of the gut’s microbial ecology ,98 it is likely that the lack of available ACE2 during a SARS-CoV-2 infection has a critical role in dysbiosis.In contrast to the situation with IAV and RSV, viral RNA is detected in the gut during coronavirus infection, including SARS-CoV-2 infection.35 Whether this protective effect extends to other IAV subtypes and to other respiratory viruses is still unknown and worth of future studies. Hence, alteration of the gut microbiota composition and functional activities due to respiratory viral infections might lead to beneficial effects. However, as developed below, dysbiosis due to an acute respiratory viral infection also leads to detrimental effects and participates in the outcomes of infection.Fecal transfer experiments indicated that a gut microbiota collected from mice that have survived influenza (H7N9) infection can transfer protection in recipient (naive) mice challenged with IAV.8 This critical role depends mostly on microbiota’s metabolites. During homeostasis, the gut exerts a relatively anti-inflammatory immune state.99 Perturbations of the gut microbiota contribute to several gut diseases, such as inflammatory bowel disease, irritable bowel syndrome, coeliac disease, and colorectal cancer.101 Based on these observations, researchers have investigated the possible negative impact of the gut dysbiosis observed during viral respiratory infections on gut homeostasis and functions.The gut microbiota is critical in the maintenance of epithelial integrity and in the development of regulatory T cells.103 Mice infected with IAV presented intestinal injuries, including a reduction in the length of the colon (a marker of inflammation), elimination of the mucosal layer in the small intestine, and mild diarrhea.49 In parallel, enhanced mRNA expression of inflammatory cytokines and IFN-stimulated genes was observed.48 One important feature of the gut is its barrier function; under healthy conditions, this prevents the excessive diffusion of microbial components. Many diseases are associated with disruption of the barrier function and thus lead to bacterial translocation, systemic inflammation, and shock. The impact of IAV on the gut’s barrier property has not been characterized in details104 and merits investigation. In the case of RSV, no histological evidence of significant inflammation of the colon was observed in a mouse model, other than an elevated feces level of lipocalin-2, a marker of gut inflammation.46As stated above, viral respiratory infections, including IAV, RSV, and coronavirus infections, can induce gastroenteritis-like symptoms, such as abdominal pain, nausea, vomiting, and diarrhea.Enterobacteriaceae) reduced intestinal inflammation.48 Moreover, fecal transfer experiments indicated that the IAV-experienced microbiota triggered the local accumulation of T helper 17 cells, which subsequently cause gut inflammation.48 Along with Enterobacteriaceae, it is also likely that mucus-degrading bacteria (such as Ruminococcus and Akkermansia) are important factors in the maintenance and/or amplification of gut inflammation. Indeed, these bacteria are known to erode the colonic mucosa and favor interactions between luminal bacteria and the intestinal epithelium; in turn, this leads to inflammation and the impairment of barrier function.106One can question whether in the context of viral respiratory infection, the altered microbiota initiates gut inflammation, or whether inflammation induces dysbiosis. This is a “chicken and egg” situation. As stated above, inflammation might influence the composition of the gut microbiota. On the other hand, the dysbiotic microbiota might directly initiate and sustain gut disorders. Indeed, antibiotic treatment during an IAV infection , metabolism and immune homeostasis remain to be analysed in details. Altered gut function following viral respiratory infections might have both immediate and long-term consequences for health. For example, the gut barrier is vital for the maintenance of homeostasis, and any perturbation can lead to the systemic dissemination of bacterial components and thus harmful health outcomes.108 Dysbiosis can increase the risk of developing an enteric bacterial infection.110 Experiments in animal models showed that IAV enhances susceptibility to secondary enteric infection by Salmonella enterica serovar Thyphimurium.49 This enhancement was due, at least in part, to type I IFNs and the associated reduction in antimicrobial peptide and inflammatory cytokine release.45 Reduction in the gut microbiota’s diversity is also likely to be involved in secondary enteric infection;49 for instance (in the mouse system), the proportion of segmented filamentous bacteria (known to be important in T helper 17-mediated immune responses) fell during IAV infection.50 In parallel, a fall in the proportion of SCFA producers47 might be important in secondary enteric infections. These fatty acids are known to control the equilibrium of the gut microbiota and to prevent the development of enteric pathogens like Enterococcus faecalis and Salmonella enterica serovar Thyphimurium.112 It remains to be seen whether oral supplementation of SCFAs during IAV infection can lower secondary enteric infection.The gut microbiota is vital in the local control of pathogenic infections through direct microbial antagonism and stimulation of the host’s effector responses .Streptococcus pneumoniae, Staphylococcus aureus, and Haemophilus influenzae. This complication primarily affects children and older adults114 and contributes to the excess morbidity and mortality observed during epidemics and pandemics.42 Experiments in animal models have demonstrated that the enhanced susceptibility is due in part to an impairment of the antibacterial innate immune response  affected the bactericidal activity of alveolar macrophages. In the context of dual influenza and pneumococcal infections, acetate supplementation lowered bacterial loads, reduced lung disease, and enhanced survival rate. Hence, changes in gut microbiota (and ablated SCFA production) during influenza is associated with bacterial superinfection. Further research in this field might help to define predictive markers  and/or to develop therapeutic approaches against bacterial superinfections, for instance by harnessing the power of the gut microbiota via prebiotics and/or probiotics. Of note, along with the gut microbiota, it is also likely that changes in microbial composition and function in the respiratory tract, that associate with acute viral respiratory infections , are important in bacterial superinfection. This local dysbiosis may alter the dynamics of inter-microbial interactions, thereby enhancing the proliferation of potentially pathogenic bacterial species. Changes of local microbial metabolic output might also lower pulmonary defense against secondary bacterial infection. Collectively, gut dysbiosis during viral respiratory infections (at least influenza) impacts on bacterial superinfection in lungs. Whether microbial changes affect other disease outcomes during viral respiratory infections such as ARDS, sepsis and multiple organ dysfunction is still an open question.A healthy gut microbiota has a beneficial, physiological role in pulmonary immunity,ion Fig. .47 In me119 The available evidence suggests that SARS-CoV-2 infection alters the gut barrier, leading to the systemic spread of bacteria, endotoxins, and microbial metabolites.121 This might affect the host’s response to COVID-19 infection and might contribute to multisystem dysfunction, septic shock, and the systemic inflammatory storm that occurs in the second phase of the SARS-CoV-2 infection and which is in part responsible for the disease’s mortality. Gut disorders during SARS-CoV-2 infection might also participate in concomitant or secondary bacterial infections, which develop in severely ill COVID-19 patients.124 Gastrointestinal disorders in patients with COVID-19 are associated with a more aggressive clinical course, including ARDS, liver injury, a higher body temperature, and shock.118 The nature of the intestinal disorders, particularly the microbiota’s function and the gut’s barrier property, must be urgently investigated, with a view to developing targeted therapies. Risk factors for COVID-19  may be of particular importance.125 Indeed, obesity and diabetes are known to be associated with disturbances of the intestinal microbiota and an impairment of the gut’s barrier function.37 When combined with the virus’s effect on gut homeostasis, these chronic impairments might amplify the severity of COVID-19.The conseqences of the gut dysbiosis on COVID-19 progression and severity has yet to be fully characterized. COVID-19 patients with gastrointestinal symptoms have overall more severe/critical diseases indicating the importance of the lung–gut axis in this setting.The gut microbiota is vital in the lung’s defenses against respiratory infections, as exemplified by the cases of IAV and RSV infections. It remains to be seen whether this is also the case for other dangerous respiratory viruses, such as SARS-CoV-2. The use of relevant animal models should rapidly generate important information for the design of interventional strategies that can reinforce the lungs against viral pathogens. These strategies might include the use of SCFA-producing probiotics and prebiotics, such as fiber-rich diets. These procedures might reinforce the gut microbiota’s ability to preventively arm the immune system and also protect the microbiota against the perturbations associated with viral infections. Alteration of the gut microbiota not only participates in intestinal disorders but also favors systemic damage and bacterial superinfections. Research in this area may lead to preventive and therapeutic approaches to better fight against viral respiratory infections.