Pulmonary-intestinal cross-talk in mucosal inflammatory disease

Acute ischemic colitis complicating an exacerbation of chronic obstructive pulmonary disease: A case report of gut-lung crosstalk

Acute ischemic colitis is a pathology as frequent as it is serious and requires urgent management. It's often occurring in a context of particular thromboembolic or hypovolemic risk, but certain clinical situations are not commonly known to provide mesenteric ischemia. Herein, we report the case of a 47-year-old man who presented with a severe acute colitis occurring in the course of acute exacerbation of a chronic obstructive pulmonary diseases with maintained stability of hemodynamic state. The diagnosis of acute ischemic colitis complicating an exacerbation of chronic obstructive pulmonary diseases was made. A clinical and biological improvement quickly marked the patient's condition after the management of the respiratory problem.

Gut microbiota, inflammatory proteins and COVID-19: a Mendelian randomisation study

Background

The human gut microbiota has been identified as a potentially important factor influencing the development of COVID-19. It is believed that the disease primarily affects the organism through inflammatory pathways. With the aim of improving early diagnosis and targeted therapy, it is crucial to identify the specific gut microbiota associated with COVID-19 and to gain a deeper understanding of the underlying processes. The present study sought to investigate the potential causal relationship between the gut microbiota and COVID-19, and to determine the extent to which inflammatory proteins act as mediators in this relationship.

Methods

Bidirectional mendelian randomization (MR) and Two-step mediated MR analyses were applied to examine causative associations among 196 gut microbiota, 91 inflammatory proteins and COVID-19. The main analytical method used in the MR was the random effects inverse variance weighted (IVW) method. This was complemented by the Bayesian weighted Mendelian randomization (BWMR) method, which was utilized to test the hypothesis of MR. In order for the results to be deemed reliable, statistical significance was required for both methods. Validation was then carried out using an external dataset, and further meta-analyses were conducted to authenticate that the association was reliable.

Results

Results of our research indicated that seven gut microbiota were actively associated to the COVID-19 risk. Five inflammatory proteins were associated with COVID-19 risk, of which three were positively and two were negatively identified with COVID-19. Further validation was carried out using sensitivity analyses. Mediated MR results revealed that CCL2 was a possible mediator of causality of family Bifidobacteriaceae and order Bifidobacteriales with COVID-19, mediating at a ratio of 12.73%.

Conclusion

Suggesting a genetic causation between specific gut microbiota and COVID-19, our present research emphasizes the underlying mediating role of CCL2, an inflammatory factor, and contributes to a deeper understanding of the mechanism of action underlying COVID-19.

Inflammatory bowel disease and allergic diseases: A Mendelian randomization study

BACKGROUND

Inflammatory bowel disease (IBD) and allergic diseases possess similar genetic backgrounds and pathogenesis. Observational studies have shown a correlation, but the exact direction of cause and effect remains unclear. The aim of this Mendelian randomization (MR) study is to assess bidirectional causality between inflammatory bowel disease and allergic diseases.

METHOD

We comprehensively analyzed the causal relationship between inflammatory bowel disease (IBD), Crohn's disease (CD), ulcerative colitis (UC) and allergic disease (asthma, Hay fever, and eczema) as a whole, allergic conjunctivitis (AC), atopic dermatitis (AD), allergic asthma (AAS), and allergic rhinitis (AR) by performing a bidirectional Mendelian randomization study using summary-level data from genome-wide association studies. The analysis results mainly came from the random-effects model of inverse variance weighted (IVW-RE). In addition, multivariate Mendelian randomization (MVMR) analysis was conducted to adjust the effect of body mass index (BMI) on the instrumental variables.

RESULTS

The IVW-RE method revealed that IBD genetically increased the risk of allergic disease as a whole (OR = 1.03, 95% CI = 1.01-1.04, fdr.p = .015), AC (OR = 1.04, 95% CI = 1.01-1.06, fdr.p = .011), and AD (OR = 1.06, 95% CI = 1.02-1.09, fdr.p = .004). Subgroup analysis further confirmed that CD increased the risk of allergic disease as a whole (OR = 1.02, 95% CI = 1.00-1.03, fdr.p = .031), AC (OR = 1.03, 95% CI = 1.01-1.05, fdr.p = .012), AD (OR = 1.06, 95% CI = 1.02-1.09, fdr.p = 2E-05), AAS (OR = 1.05, 95% CI = 1.02-1.08, fdr.p = .002) and AR (OR = 1.03, 95% CI = 1.00-1.07, fdr.p = .025), UC increased the risk of AAS (OR = 1.02, 95% CI = 0.98-1.07, fdr.p = .038). MVMR results showed that after taking BMI as secondary exposure, the causal effects of IBD on AC, IBD on AD, CD on allergic disease as a whole, CD on AC, CD on AD, CD on AAS, and CD on AR were still statistically significant. No significant association was observed in the reverse MR analysis.

CONCLUSION

This Mendelian randomized study demonstrated that IBD is a risk factor for allergic diseases, which is largely attributed to its subtype CD increasing the risk of AC, AD, ASS, and AR. Further investigations are needed to explore the causal relationship between allergic diseases and IBD.

Bufei Huoxue capsule attenuates COPD-related inflammation and regulates intestinal microflora, metabolites

Background: Bufei Huoxue capsule (BFHX) is widely used for the clinical treatment of chronic obstructive pulmonary disease (COPD) in China. Objectives: The aim of this study is to explore the effects on COPD and the underlying mechanism of BFHX. The process and methods: In this study, we established a COPD mouse model through cigarette smoke (CS) exposure in combination with lipopolysaccharide (LPS) intratracheal instillation. Subsequently, BFHX was orally administrated to COPD mice, and their pulmonary function, lung pathology, and lung inflammation, including bronchoalveolar lavage fluid (BALF) cell count and classification and cytokines, were analyzed. In addition, the anti-oxidative stress ability of BFHX was detected by Western blotting, and the bacterial diversity, abundance, and fecal microbiome were examined using 16S rRNA sequencing technology. Outcome: BFHX was shown to improve pulmonary function, suppress lung inflammation, decrease emphysema, and increase anti-oxidative stress, whereas 16S rRNA sequencing indicated that BFHX can dynamically regulate the diversity, composition, and distribution of the intestinal flora microbiome and regulate the lysine degradation and phenylalanine metabolism of COPD mice. These results highlight another treatment option for COPD and provide insights into the mechanism of BFHX.

First Exploration of the Altered Microbial Gut-Lung Axis in the Pathogenesis of Human Refractory Chronic Cough

PURPOSE

Cough represents a natural mechanism that plays an important defensive role in the respiratory tract, but in some conditions, it may become persistent, nonproductive, and harmful. In general, refractory chronic cough (RCC) occurs in about 20% of individuals; hence, we aimed to assess the presence of altered gut-lung communication in RCC patients through a compositional and functional characterization of both gut (GM) and oral microbiota (OM).

METHODS

16S rRNA sequencing was used to characterize both GM and OM composition of RCC patients and healthy controls (HC). PICRUST2 assessed functional changes in microbial communities while gas chromatography was used to evaluate fecal short-chain fatty acid levels and serum-free fatty acid (FFA) abundances.

RESULTS

In comparison with HC, RCC patients reported increased saliva alpha-diversity and statistically significant beta-diversity in both GM and OM. Also, a, respectively, significant increased or reduced Firmicutes/Bacteroidota ratio in stool and saliva samples of RCC patients has been shown, in addition to a modification of the abundances of several taxa in both GM and OM. Moreover, a potential fecal over-expression of lipopolysaccharide biosynthesis and lipoic acid metabolism pathways and several differences in serum FFA levels have been reported in RCC patients than in HC.

CONCLUSION

Since differences in both GM and OM of RCC patients have been documented, these findings could provide new information about RCC pathogenesis and also pave the way for the development of novel nutritional or pharmacological interventions for the management of RCC through the restoration of eubiotic gut-lung communication.

Exploring the relationship between intestinal microbiota and immune checkpoint inhibitors in the treatment of non-small cell lung cancer: insights from the "lung and large intestine stand in exterior-interior relationship" theory

Objective

This study is aim to discern the Traditional Chinese Medicine (TCM) syndrome classifications relevant to immunotherapy sensitive in non-small cell lung cancer (NSCLC) patients, and to delineate intestinal microbiota biomarkers and impact that wield influence over the efficacy of NSCLC immunotherapy, grounded in the TCM theory of "lung and large intestine stand in exterior-interior relationship."

Methods

The study cohort consisted of patients with advanced NSCLC who received treatment at the Oncology Department of Chengdu Fifth People's Hospital. These patients were categorized into distinct TCM syndrome types and subsequently administered immune checkpoint inhibitors (ICIs), specifically PD-1 inhibitors. Stool specimens were collected from patients both prior to and following treatment. To scrutinize the differences in microbial gene sequences and species of the intestinal microbiota, 16S rRNA amplicon sequencing technology was employed. Additionally, peripheral blood samples were collected, and the analysis encompassed the assessment of T lymphocyte subsets and myeloid suppressor cell subsets via flow cytometry. Subsequently, alterations in the immune microenvironment pre- and post-treatment were thoroughly analyzed.

Results

The predominant clinical manifestations of advanced NSCLC patients encompassed spleen-lung Qi deficiency syndrome and Qi-Yin deficiency syndrome. Notably, the latter exhibited enhanced responsiveness to ICIs with a discernible amelioration of the immune microenvironment. Following ICIs treatment, significant variations in microbial abundance were identified among the three strains: Clostridia, Lachnospiraceae, and Lachnospirales, with a mutual dependency relationship. In the subset of patients manifesting positive PD-L1 expression and enduring therapeutic benefits, the study recorded marked increases in the ratios of CD3+%, CD4+%, and CD4+/CD8+ within the T lymphocyte subsets. Conversely, reductions were observed in the ratios of CD8%, Treg/CD4+, M-MDSC/MDSC, and G-MDSC/MDSC.

Conclusion

The strains Clostridia, Lachnospiraceae, and Lachnospirales emerge as potential biomarkers denoting the composition of the intestinal microbiota in the NSCLC therapy. The immunotherapy efficacy of ICIs markedly accentuates in patients displaying durable treatment benefits and those expressing positive PD-L1.

The causal relationship between gut microbiota and COVID-19: A two-sample Mendelian randomization analysis

Recent studies have shown that gut microbiota is associated with coronavirus disease 2019 (COVID-19). However, the causal impact of the gut microbiota on COVID-19 remains unclear. We performed a bidirectional Mendelian randomization. The summary statistics on the gut microbiota from the MiBioGen consortium. Summary statistics for COVID-19 were obtained from the 6th round of the COVID-19 Host Genetics Initiative genome-wide association study meta-analysis. Inverse variance weighting was used as the main method to test the causal relationship between gut microbiota and COVID-19. Reverse Mendelian randomization analysis was performed. Mendelian randomization analysis showed that Intestinimas.id.2062 was associated with an increased risk of severe COVID-19. Bifidobacterium.id.436, LachnospiraceaeUCG010.id.11330, RikenellaceaeRC9gutgroup.id.11191 increase the risk of hospitalized COVID-19. RuminococcaceaeUCG014.id.11371 shows the positive protection on hospitalized COVID-19. There is no causal relationship between gut microbiota and infection with COVID-19. According to the results of reverse Mendelian randomization analysis, no significant causal effect of COVID-19 on gut microbiota was found. The study found that gut microbiota with COVID-19 has a causal relationship. This study provides a basis for the theory of the gut-lung axis. Further randomized controlled trials are needed to clarify the protective effect of probiotics against COVID-19 and the specific protective mechanisms. This study has important implications for gut microbiota as a nondrug intervention for COVID-19.

Lung Involvement in Patients with Ulcerative Colitis: Relationship between Exhaled Nitric Oxide and Lung Function

Ulcerative colitis (UC) is characterized by immune system dysregulation with frequent extraintestinal manifestations, including airway involvement. A reduction in CO diffusing capacity and functional alterations in small airways have been described. An extended analysis of fractional exhaled nitric oxide (FeNO) may distinguish the sites of production, and the presence of small airway inflammation may be a useful, non-invasive marker for patient follow-up. The aim of our study was to compare the PFTs as well as FeNO and CANO values of UC patients with different clinical disease activities and healthy subjects to reveal lung function abnormalities and the presence of subclinical airway inflammation. We enrolled 42 adult outpatients at different clinical activity stages of UC (39 ± 13 years) and a healthy control group of 41 subjects (29 ± 3 years). C-reactive protein (CRP) and FeNO values at different flows (50,100, and 200 mL/s) were collected. All patients performed pulmonary function tests (PFTs) with static volumes and diffusing capacity (DLCO). FeNO and CANO values were significantly increased in UC patients when compared with controls (p = 0.0008 and p < 0.0001, respectively) and were proportional to disease activity (FeNO class 3: 28.1 ppb vs. classes 1-2: 7.7 ppb; CANO values class 3: 8.6 ppb vs. classes 1-2: 2.7 ppb (p < 0.0001)). TLC and DLCO were significantly reduced in severe (Mayo 3) UC patients (p = 0.010 and p = 0.003, respectively). The results of this study show significant lung functional abnormalities in UC patients and suggest the presence of airway inflammation directly correlated with disease activity, suggesting the need for an integrated approach in routine assessment.

Radiation-induced multi-organ injury

PURPOSE

Natural history studies have been informative in dissecting radiation injury, isolating its effects, and compartmentalizing injury based on the extent of exposure and the elapsed time post-irradiation. Although radiation injury models are useful for investigating the mechanism of action in isolated subsyndromes and development of medical countermeasures (MCMs), it is clear that ionizing radiation exposure leads to multi-organ injury (MOI).

METHODS

The Radiation and Nuclear Countermeasures Program within the National Institute of Allergy and Infectious Diseases partnered with the Biomedical Advanced Research and Development Authority to convene a virtual two-day meeting titled 'Radiation-Induced Multi-Organ Injury' on June 7-8, 2022. Invited subject matter experts presented their research findings in MOI, including study of mechanisms and possible MCMs to address complex radiation-induced injuries.

RESULTS

This workshop report summarizes key information from each presentation and discussion by the speakers and audience participants.

CONCLUSIONS

Understanding the mechanisms that lead to radiation-induced MOI is critical to advancing candidate MCMs that could mitigate the injury and reduce associated morbidity and mortality. The observation that some of these mechanisms associated with MOI include systemic injuries, such as inflammation and vascular damage, suggests that MCMs that address systemic pathways could be effective against multiple organ systems.

Gut microbiota dysbiosis-related susceptibility to nontuberculous mycobacterial lung disease

The role of gut microbiota in host defense against nontuberculous mycobacterial lung disease (NTM-LD) was poorly understood. Here, we showed significant gut microbiota dysbiosis in patients with NTM-LD. Reduced abundance of Prevotella copri was significantly associated with NTM-LD and its disease severity. Compromised TLR2 activation activity in feces and plasma in the NTM-LD patients was highlighted. In the antibiotics-treated mice as a study model, gut microbiota dysbiosis with reduction of TLR2 activation activity in feces, sera, and lung tissue occurred. Transcriptomic analysis demonstrated immunocompromised in lung which were closely associated with increased NTM-LD susceptibility. Oral administration of P. copri or its capsular polysaccharides enhanced TLR2 signaling, restored immune response, and ameliorated NTM-LD susceptibility. Our data highlighted the association of gut microbiota dysbiosis, systematically compromised immunity and NTM-LD development. TLR2 activation by P. copri or its capsular polysaccharides might help prevent NTM-LD.

Fuzhengjiedu formula exerts protective effect against LPS-induced acute lung injury via gut-lung axis

BACKGROUND

Acute lung injury (ALI) is distinguished by rapid and severe respiratory distress and prolonged hypoxemia. A traditional Chinese medicine (TCM), known as the Fuzhengjiedu formula (FZJDF), has been shown to have anti-inflammatory benefits in both clinical and experimental studies. The precise underlying processes, nevertheless, are yet unclear.

PURPOSE

This study sought to enlighten the protective mechanism of FZJDF in ALI through the standpoint of the gut-lung crosstalk.

METHODS

The impact of FZJDF on lipopolysaccharide (LPS)-induced ALI murine model were investigated, and the lung injury score, serum interleukin-1β (IL-1β), and tumor necrosis factor-α (TNF-α) expression were measured to confirm its anti-inflammatory effects. Additionally, gut microbiota analysis and serum and fecal samples metabolomics were performed using metagenomic sequencing and high-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry, respectively.

RESULTS

FZJDF significantly induced histopathological changes caused by LPS-induced ALI as well as downregulated the serum concentration of IL-1β and TNF-α. Furthermore, FZJDF had an effect in gut microbiota disturbances, and linear discriminant effect size analysis identified signal transduction, cell motility, and amino acid metabolism as the potential mechanisms of action in the FZJDF-treated group. Several metabolites in the LPS and FZJDF groups were distinguished by untargeted metabolomic analysis. Correlations were observed between the relative abundance of microbiota and metabolic products. Comprehensive network analysis revealed connections among lung damage, gut microbes, and metabolites. The expression of glycine, serine, glutamate, cysteine, and methionine in the lung and colon tissues was dysregulated in LPS-induced ALI, and FZJDF reversed these trends.

CONCLUSION

This study revealed that FZJDF considerably protected against LPS-induced ALI in mice by regulating amino acid metabolism via the gut-microbiota-lung axis and offered thorough and in-depth knowledge of the multi-system linkages of systemic illnesses.

The Respiratory Microbiome in Paediatric Chronic Wet Cough: What Is Known and Future Directions

Chronic wet cough for longer than 4 weeks is a hallmark of chronic suppurative lung diseases (CSLD), including protracted bacterial bronchitis (PBB), and bronchiectasis in children. Severe lower respiratory infection early in life is a major risk factor of PBB and paediatric bronchiectasis. In these conditions, failure to clear an underlying endobronchial infection is hypothesised to drive ongoing inflammation and progressive tissue damage that culminates in irreversible bronchiectasis. Historically, the microbiology of paediatric chronic wet cough has been defined by culture-based studies focused on the detection and eradication of specific bacterial pathogens. Various 'omics technologies now allow for a more nuanced investigation of respiratory pathobiology and are enabling development of endotype-based models of care. Recent years have seen substantial advances in defining respiratory endotypes among adults with CSLD; however, less is understood about diseases affecting children. In this review, we explore the current understanding of the airway microbiome among children with chronic wet cough related to the PBB-bronchiectasis diagnostic continuum. We explore concepts emerging from the gut-lung axis and multi-omic studies that are expected to influence PBB and bronchiectasis endotyping efforts. We also consider how our evolving understanding of the airway microbiome is translating to new approaches in chronic wet cough diagnostics and treatments.

Genetic and observational associations of lung function with gastrointestinal tract diseases: pleiotropic and mendelian randomization analysis

BACKGROUND

The two-way communications along the gut-lung axis influence the immune function in both gut and lung. However, the shared genetic characteristics of lung function with gastrointestinal tract (GIT) diseases remain to be investigated.

METHODS

We first investigated the genetic correlations between three lung function traits and four GIT diseases. Second, we illustrated the genetic overlap by genome-wide pleiotropic analysis (PLACO) and further pinpointed the relevant tissue and cell types by partitioning heritability. Furthermore, we proposed pleiotropic genes as potential drug targets by drug database mining. Finally, we evaluated the causal relationships by epidemiologic observational study and Mendelian randomization (MR) analysis.

RESULTS

We found lung function and GIT diseases were genetically correlated. We identified 258 pleiotropic loci, which were enriched in gut- and lung-specific regions marked by H3K4me1. Among these, 16 pleiotropic genes were targets of drugs, such as tofacitinib and baricitinib targeting TYK2 for the treatment of ulcer colitis and COVID-19, respectively. We identified a missense variant in TYK2, exhibiting a shared causal effect on FEV1/FVC and inflammatory bowel disease (rs12720356, PPLACO=1.38 × 10- 8). These findings suggested TYK2 as a promising drug target. Although the epidemiologic observational study suggested the protective role of lung function in the development of GIT diseases, no causalities were found by MR analysis.

CONCLUSIONS

Our study suggested the shared genetic characteristics between lung function and GIT diseases. The pleiotropic variants could exert their effects by modulating gene expression marked by histone modifications. Finally, we highlighted the potential of pleiotropic analyses in drug repurposing.

Water extract of Pingchuan formula ameliorated murine asthma through modulating metabolites and gut microbiota

BACKGROUND

Pingchuan formula is a traditional Chinese herbal prescription for asthma, but its components and underlying mechanisms remain unclear. Here, we evaluated its anti-asthmatic actvity and regulatory effects on the gut microbiota in mice based on the traditional Chinese medicine Zang-Fu theory, which proposed the exterior-interior relationship between the lung and the large intestine.

METHODS

Mouse model withovalbumin (OVA)-induced asthma was used to assess the protective effect of the water extract of Pingchuan formula (PC). The chemical compounds of PC and mouse serum metabolites were identified by Ultraperformance liquid chromatography-Q Exactive HF-X spectrometry. Gut microbiota was evaluated by 16 S rRNA gene sequencing. The gut microbiota was depleted with a broad-spectrum antibiotic mixture (Abx) to explore whether it plays a role in the protective effects of PC.

RESULTS

PC mainly contains phenols, flavonoids, alkaloids, carboxylic acids, and their derivatives. PC attenuated OVA-induced asthma in mice by alleviating inflammatory infiltration, indicated by decreased levels of IL-18, IL-6, IL-4, and Eotaxin in lung tissues. PC treatment altered the serum metabolites and affected the pyrimidine pathway. In addition, our results showed that acacetin and abscisic acid were the key serum metabolites PC treatment changed the composition of gut microbiota by increasing the relative abundance of Clostridia_UCG_014 and Akkermansia while decreasing Blautia, Barnesiella, and Clostridium_Ⅲ at the genus level. Importantly, the Abx treatment partly abolished the anti-asthmatic effect of PC.

CONCLUSION

We demonstrated that PC could alleviate OVA-induced asthma in mice and protect against inflammatory infiltration in lungs via modulating the serum metabolites and gut microbiota, thereby providing a new reference for the therapeutic effect of PC.

TLR7 promotes smoke-induced experimental lung damage through the activity of mast cell tryptase

Toll-like receptor 7 (TLR7) is known for eliciting immunity against single-stranded RNA viruses, and is increased in both human and cigarette smoke (CS)-induced, experimental chronic obstructive pulmonary disease (COPD). Here we show that the severity of CS-induced emphysema and COPD is reduced in TLR7-deficient mice, while inhalation of imiquimod, a TLR7-agonist, induces emphysema without CS exposure. This imiquimod-induced emphysema is reduced in mice deficient in mast cell protease-6, or when wild-type mice are treated with the mast cell stabilizer, cromolyn. Furthermore, therapeutic treatment with anti-TLR7 monoclonal antibody suppresses CS-induced emphysema, experimental COPD and accumulation of pulmonary mast cells in mice. Lastly, TLR7 mRNA is increased in pre-existing datasets from patients with COPD, while TLR7+ mast cells are increased in COPD lungs and associated with severity of COPD. Our results thus support roles for TLR7 in mediating emphysema and COPD through mast cell activity, and may implicate TLR7 as a potential therapeutic target.

Lactobacillus rhamnosus Modulates Lung Inflammation and Mitigates Gut Dysbiosis in a Murine Model of Asthma-COPD Overlap Syndrome

The asthma-COPD overlap syndrome (ACOS) presents lung inflammation similar to both asthma and chronic obstructive pulmonary disease (COPD). Due to the immune response between the lung and gut, it is possible that ACOS individuals present gut dysbiosis. Due to therapeutic limitations in ACOS, Lactobacillus rhamnosus (Lr) have received attention once Lr has been effective in asthma and COPD. However, there is no data about the Lr effect on both lung inflammation and gut dysbiosis in ACOS. Thus, our study investigated the Lr effect on lung inflammation, bronchoconstriction, airway remodeling, and gut dysbiosis in the murine ACOS model. Treated mice with Lr were exposed to HDM and cigarette smoke to induce ACOS. Sixty days after ACOS induction, mice were euthanized. Lung inflammation was evaluated in leukocytes in bronchoalveolar lavage fluid (BALF), airway remodeling, cytokine secretion, and transcription factor expression in the lung. The gut microbiota was assayed by 16S mRNA sequencing from a fecal sample. Leukocyte population, bronchial hyperreactivity, pro-inflammatory cytokines, and airway remodeling were attenuated in Lr-treated ACOS mice. Likewise, IL-4, IL-5, and IL-13, STAT6 and GATA3, as well as IL-17, IL-21, IL-22, STAT3, and RORɣt were reduced after Lr. In addition, IL-2, IL-12, IFN-γ, STAT1, and T-bet as well as IL-10, TGF-β, STAT5, and Foxp3 were restored after the Lr. Firmicutes was reduced, while Deferribacteres was increased after Lr. Likewise, Lr decreased Staphylococcus and increased Mucispirillum in ACOS mice. Lr improves fecal bacterial β-diversity. Our findings show for the first time the Lr effect on lung inflammation and gut dysbiosis in murine ACOS.

Explore the changes of intestinal flora in patients with coronavirus disease 2019 based on bioinformatics

Background

Studies have revealed that there were significant changes in intestinal flora composition in patients with coronavirus disease 2019 (COVID-19) compared to non-COVID-19 patients, regardless of whether they were treated with medication. Therefore, a comprehensive study of the intestinal flora of COVID-19 patients is needed to further understand the mechanisms of COVID-19 development.

Methods

In total, 20 healthy samples and 20 COVID-19 samples were collected in this study. Firstly, alpha diversity and beta diversity were analyzed to assess whether there were difference in species richness and diversity as well as species composition between COVID-19 and control groups. The observed features index, Evenness index, PD index, and Shannon index were utilized to measure alpha diversity. The principal coordinates analysis (PCoA) and non-metric multidimensional scaling (NMDS) were performed to analyzed beta diversity. Linear discriminant analysis Effect Size (LEfSe) was utilized to analyze the variability in the abundance of bacterial taxa from different classification levels. The random forest (RF), Least absolute shrinkage and selection operator (LASSO), and univariate logistic regression were utilized to identify key Amplicon Sequence Variant (ASVs). Finally, the relevant networks of bacterial taxa were created in COVID-19 and control groups, separately.

Results

There were more species in the control group than in COVID-19 group. The observed features index, Shannon index, and Evenness index in the control groups were markedly higher than in the COVID-19 group. Therefore, there were marked variations in bacterial taxa composition between the COVID-19 and control groups. The nine bacterial taxa were significantly more abundant in the COVID-19 group, such as g-Streptococcus, f-Streptococcaceae, o-Lactobacillales, c-Bacilli and so on. In the control group, 26 bacterial taxa were significantly more abundant, such as c-Clostrjdia, o-Oscillospirales, f-Ruminococcaceae, etc. The 5 key ASVs were obtained through taking the intersection of the characteristic ASVs obtained by the three algorithms, namely ASV6, ASV53, ASV92, ASV96, and ASV105, which had diagnostic value for COVID-19. The relevance network in the control group was more complex compared to the COVID-19 group.

Conclusion

Our findings provide five key ASVs for diagnosis of COVID-19, providing a scientific reference for further studies of COVID-19.

Lung Involvement in Inflammatory Bowel Diseases: Shared Pathways and Unwanted Connections

Inflammatory bowel diseases (IBDs) are chronic, relapsing inflammatory disorders of the gastrointestinal tract, frequently associated with extraintestinal manifestations (EIMs) that can severely affect IBD patients' quality of life, sometimes even becoming life-threatening. Respiratory diseases have always been considered a rare and subsequently neglected extraintestinal manifestations of IBD. However, increasing evidence has demonstrated that respiratory involvement is frequent in IBD patients, even in the absence of respiratory symptoms. Airway inflammation is the most common milieu of IBD-related involvement, with bronchiectasis being the most common manifestation. Furthermore, significant differences in prevalence and types of involvement are present between Crohn's disease and ulcerative colitis. The same embryological origin of respiratory and gastrointestinal tissue, in addition to exposure to common antigens and cytokine networks, may all play a potential role in the respiratory involvement. Furthermore, other causes such as drug-related toxicity and infections must always be considered. This article aims at reviewing the current evidence on the association between IBD and respiratory diseases. The purpose is to raise awareness of respiratory manifestation among IBD specialists and emphasize the need for identifying respiratory diseases in early stages to promptly treat these conditions, avoid worsening morbidity, and prevent lung damage.

Gut microecological regulation on bronchiolitis and asthma in children: A review

INTRODUCTION

Asthma and bronchiolitis in children are considered common clinical problems associated with gut microbiota. However, the exact relationship between gut microbiota and the above-mentioned diseases remains unclear. Here, we discussed recent advances in understanding the potential mechanism underlying immune regulation of gut microbiota on asthma and bronchiolitis in children as well as the role of the gut-lung axis.

METHODS

We retrieved and assessed all relevant original articles related to gut microbiota, airway inflammation-induced wheezing in children, and gut-lung axis studies from databases that have been published so far, including PubMed/MEDLINE, Scopus, Google Scholar, China National Knowledge Infrastructure (CNKI) and the Wanfang Database.

RESULTS

The infant period is critical for the development of gut microbiota, which can be influenced by gestational age, delivery mode, antibiotic exposure and feeding mode. The gut microbiota in children with asthma and bronchiolitis is significantly distinct from those in healthy subjects. Gut microbiota dysbiosis is implicated in asthma and bronchiolitis in children. The presence of intestinal disturbances in lung diseases highlights the importance of the gut-lung axis.

CONCLUSION

Gut microbiota dysbiosis potentially increases the risk of asthma and bronchiolitis in children. Moreover, a deeper understanding of the gut-lung axis with regard to the gut microbiota of children with respiratory diseases could contribute to clinical practice for pulmonary diseases.

Favipiravir Protects Enterocytes From Cell Death After Inflammatory Storm

Over the past years, inflammatory bowel disease (IBD) treatment has become more targeted, anticipating the use of immune-modifying therapies at an earlier stage. During the treatment process prevention and management of viral infections hold significant importance. The protective role of favipiravir on enterocytes which are affected by inflammation is still unknown. We aim to analyze the effects of favipiravir on enterocytes after an inflammatory condition. We conducted a 2,5-diphenyl-2H-tetrazolium bromide (MTT) assay to assess the cytotoxicity of favipiravir on intestinal epithelioid cells (IEC-6). To mimic the inflammation model in cell culture conditions, we exposed IEC-6 cells to tumor necrosis factor-α (TNF-α) and interferon-γ (IFN-γ). The cells were categorized into four groups: control, inflammation model, application of favipiravir before inflammation (prophylactic), and application of favipiravir after inflammation (treatment). We assessed the presence and distribution of caspase 1, caspase 3, interleukin 6 (IL6), interleukin 8 (IL8), mixed lineage kinase domain-like protein (MLKL), receptor-interacting protein kinase 1 (RIPK1), and TNF-α using indirect immunoperoxidase staining. TNF-α and IL8 levels were analyzed with enzyme-linked immunosorbent assay (ELISA) in a culture medium. Caspase 1 was observed to be strong (+++) in the treatment group and weak (+) in the prophylactic group compared to the inflammation group. Caspase 3 was weak (+) in the inflammation group, and it was strong (+++) in the prophylactic and treatment group, the increase in the treatment group was significant. Therefore administering favipiravir before inducing inflammation appears to control the inflammatory caspase pathway in intestinal enterocytes, protecting them from inflammatory responses, while the caspase 3-dependent apoptotic pathway may not be active in enterocytes during inflammation. IL6 and IL8 were negative (-) in control, IL6 was weak (+) in inflammation and favipiravir treated groups; IL8 increased significantly in favipiravir groups compared to control and inflammation groups. Consequently, favipiravir may trigger IL6 release, initiating the inflammatory pathway and potentially enhancing IL8 interactions with other cytokines. TNF-α immunoreactivity was strong (+++) in the inflammation group, while it was moderate (++) in favipiravir-administered groups. MLKL immunoreactivity was strong (+++) in all groups, RIPK1 was weak (+) in control, strong (+++) in the inflammation and treatment group, moderate (++) in the prophylactic group, and the increase in inflammation and treatment group was significant compared to control. Our findings suggest that in the treatment group, necroptosis was triggered by increased MLKL and RIPK1, key players in inflammation and cell death. After immunocytochemical evaluation, our findings suggest that, after the onset of inflammation, favipiravir may play a role in cell death by increasing necroptosis rather than apoptosis.

Unravelling the gut-lung axis: insights into microbiome interactions and Traditional Indian Medicine's perspective on optimal health

The microbiome of the human gut is a complex assemblage of microorganisms that are in a symbiotic relationship with one another and profoundly influence every aspect of human health. According to converging evidence, the human gut is a nodal point for the physiological performance matrixes of the vital organs on several axes (i.e. gut-brain, gut-lung, etc). As a result of COVID-19, the importance of gut-lung dysbiosis (balance or imbalance) has been realised. In view of this, it is of utmost importance to develop a comprehensive understanding of the microbiome, as well as its dysbiosis. In this review, we provide an overview of the gut-lung axial microbiome and its importance in maintaining optimal health. Human populations have successfully adapted to geophysical conditions through traditional dietary practices from around the world. In this context, a section has been devoted to the traditional Indian system of medicine and its theories and practices regarding the maintenance of optimally customized gut health.

Imbalance of gut microbiota is involved in the development of chronic obstructive pulmonary disease: A review

Chronic obstructive pulmonary disease (COPD) is a common chronic disease characterized by chronic airway inflammation and remodeling, which seriously endangers human health. Recent developments in genomics and metabolomics have revealed the roles of the gut microbiota and its metabolites in COPD. Dysbiosis of the gut microbiota directly increases gut permeability, thereby promoting the translocation of pathological bacteria. The gut microbiota and associated metabolites may influence the development and progression of COPD by modulating immunity and inflammation. Furthermore, the systemic hypoxia and oxidative stress that occur in COPD may also be involved in intestinal dysfunction. The cross-talk between the gut and lungs is known as the gut-lung axis; however, an overview of its mechanism is lacking. This review highlights the critical and complex interplay of gut microbiota and immune responses in the gut-lung axis, further explores possible links between the gut and lungs, and summarizes new interventions through diet, probiotics, vitamins, and fecal microbiota transplantation, which are critical to COPD.

Metagenomic assessment of gut microbial communities and risk of severe COVID-19

BACKGROUND

The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure.

METHODS

We profiled 127 hospitalized patients with COVID-19 (n = 79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites.

RESULTS

Forty-eight species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or "long COVID," suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with classifying whether stool was obtained from patients with severe vs. moderate COVID-19, a finding that was externally validated in an independent cohort. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease.

CONCLUSIONS

Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to expand upon these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention.

New drug target identification in Vibrio vulnificus by subtractive genome analysis and their inhibitors through molecular docking and molecular dynamics simulations

Vibrio vulnificus is a rod shape, Gram-negative bacterium that causes sepsis (with a greater than 50% mortality rate), necrotizing fasciitis, gastroenteritis, skin, and soft tissue infection, wound infection, peritonitis, meningitis, pneumonia, keratitis, and arthritis. Based on pathogenicity V. vulnificus is categorized into three biotypes. Type 1 and type 3 cause diseases in humans while biotype 2 causes diseases in eel and fish. Due to indiscriminate use of antibiotics V. vulnificus has developed resistance to many antibiotics so curing is dramatically a challenge. V. vulnificus is resistant to cefazolin, streptomycin, tetracycline, aztreonam, tobramycin, cefepime, and gentamycin. Subtractive genome analysis is the most effective method for drug target identification. The method is based on the subtraction of homologous proteins from both pathogen and host. By this process set of proteins present only in the pathogen and perform essential functions in the pathogen can be identified. The entire proteome of Vibrio vulnificus strain ATCC 27562 was reduced step by step to a single protein predicted as the drug target. AlphaFold2 is one of the applications of deep learning algorithms in biomedicine and is correctly considered the game changer in the field of structural biology. Accuracy and speed are the major strength of AlphaFold2. In the PDB database, the crystal structure of the predicted drug target was not present, therefore the Colab notebook was used to predict the 3D structure by the AlphaFold2, and subsequently, the predicted model was validated. Potent inhibitors against the new target were predicted by virtual screening and molecular docking study. The most stable compound ZINC01318774 tightly attaches to the binding pocket of bisphosphoglycerate-independent phosphoglycerate mutase. The time-dependent molecular dynamics simulation revealed compound ZINC01318774 was superior as compared to the standard drug tetracycline in terms of stability. The availability of V. vulnificus strain ATCC 27562 has allowed in silico identification of drug target which will provide a base for the discovery of specific therapeutic targets against Vibrio vulnificus.

Gut microbiota crosstalk mechanisms are key in pulmonary hypertension: The involvement of melatonin is instrumental too

The microbiota refers to a plethora of microorganisms with a gene pool of approximately three million, which inhabits the human gastrointestinal tract or gut. The latter, not only promotes the transport of nutrients, ions, and fluids from the lumen to the internal environment but is linked with the development of diseases including coronary artery disease, heart failure, and lung diseases. The exact mechanism of how the microbiota achieves crosstalk between itself and distant organs/tissues is not clear, but factors released to other organs may play a role, like inflammatory and genetic factors, and now we highlight melatonin as a novel mediator of the gut-lung crosstalk. Melatonin is present in high concentrations in the gut and the lung and has recently been linked to the pathogenesis of pulmonary hypertension (PH). In this comprehensive review of the literature, we suggest that melatonin is an important link between the gut microbiota and the development of PH (where suppressed melatonin-crosstalk between the gut and lungs could promote the development of PH). More studies are needed to investigate the link between the gut microbiota, melatonin and PH. Studies could also investigate whether microbiota genes play a role in the epigenetic aspects of PH. This is relevant because, for example, dysbiosis (caused by epigenetic factors) could reduce melatonin signaling between the gut and lungs, reduce subcellular melatonin concentrations in the gut/lungs, or reduce melatonin serum levels secondary to epigenetic factors. This area of research is largely unexplored and further studies are warranted.

Experimental allergic airway inflammation impacts gut homeostasis in mice

Background

/Aims: Epidemiological data show that there is an important relationship between respiratory and intestinal diseases. To improve our understanding on the interconnectedness between the lung and intestinal mucosa and the overlap between respiratory and intestinal diseases, our aim was to investigate the influence of ovalbumin (OVA)-induced allergic airway inflammation on gut homeostasis.

Methods

A/J mice were sensitized and challenged with OVA. The animals were euthanized 24 h after the last challenge, lung inflammation was determined by evaluating cells in Bronchoalveolar lavage fluid, serum anti-OVA IgG titers and colon morphology, inflammation and integrity of the intestinal mucosa were investigated. IL-4 and IL-13 levels and myeloperoxidase activity were determined in the colon samples. The expression of genes involved in inflammation and mucin production at the gut mucosa was also evaluated.

Results

OVA challenge resulted not only in lung inflammation but also in macroscopic alterations in the gut such as colon shortening, increased myeloperoxidase activity and loss of integrity in the colonic mucosal. Neutral mucin intensity was lower in the OVA group, which was followed by down-regulation of transcription of ATOH1 and up-regulation of TJP1 and MUC2. In addition, the OVA group had higher levels of IL-13 and IL-4 in the colon. Ova-specific IgG1 and OVA-specific IgG2a titers were higher in the serum of the OVA group than in controls.

Conclusions

Our data using the OVA experimental model suggested that challenges in the respiratory system may result not only in allergic airway inflammation but also in the loss of gut homeostasis.

The Role of Hemophilus influenzae Infection and Its Relationship With Colorectal Cancer

Background

Hemophilus influenzae is a gram-negative coccobacillus. Non-typeable H. influenzae infection is a significant cause of disease that activates the inflammatory pathway involving the nucleotide-binding domain, leucine-rich-containing family, pyrin domain-containing-3 (NLRP3) inflammasome. A gain-of-function mutation in NLRP3 results in cryopyrin-associated periodic syndromes characterized by inflammatory conditions in the lungs, skin, joints, and eyes but not in the gut. This leads to homeostasis of the gut microbiota, which reduces inflammation and may have protective effect against colorectal cancer (CRC). This study aimed to evaluate the correlation between H. influenzae infection and the incidence of CRC.

Methods

A retrospective study was conducted from 2010 to 2019 using a HIPAA-compliant national database. ICD-10, ICD-9, CPT, and National Drug Codes were used to identify patients with or without a history of H. influenzae infection. Standard statistical methods were used to analyze the outcomes.

Results

The query was analyzed and matched, resulting in 13,610 patients in both groups. The incidence of CRC was 167 and 446 in the H. influenzae and control groups, respectively. The difference was statistically significant with P < 2.2 ×10^-16 and an odds ratio of 0.41 (95% confidence interval: 0.36 - 0.47). Additionally, the groups were further evaluated and matched by treatment, which resulted in a statistically significant decrease in CRC incidence in the H. influenzae group.

Conclusion

This study showed a statistically significant correlation between H. influenzae and the reduced incidence of CRC. This reduction in CRC in patients with a history of H. influenzae infection suggests a potential link to the NLRP3 inflammasome, which should be further studied.

The gut-lung axis: Mendelian randomization identifies a causal association between inflammatory bowel disease and interstitial lung disease

BACKGROUND

Previous studies have suggested the association between interstitial lung disease (ILD) and inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC).

OBJECTIVES

To examine the potential bidirectional causal relationship between IBD and ILD using the Mendelian randomization (MR) method.

METHODS

We obtained the data from the genome-wide association studies (GWASs) in European individuals for IBD (25,042 cases and 34,915 controls) and ILD (21,806 cases and 196,986 controls) from the IEU GWAS database. We screened for instrumental variables based on the three assumptions of MR. The two-sample bidirectional MR analysis was performed using the inverse-variance weighted method and multiple sensitivity analyses.

RESULTS

Genetic liability to IBD was significantly associated with an increased ILD risk (odds ratio (OR) = 1.20, 95% confidence interval (CI) = 1.17-1.24, p = 3.67E-33). When considering the IBD subtypes, ILD risk was associated with genetic liability to both CD (OR = 1.14, 95% CI = 1.10-1.17, p = 1.91E-17) and UC (OR = 1.16, 95% CI = 1.12-1.21, p = 3.51E-13). There was weak evidence for the effect of genetic liability to ILD on IBD (OR = 1.32, 95% CI = 0.99-1.76, p = 0.062), CD (OR = 1.25, 95% CI = 1.00-1.55, p = 0.046), and UC (OR = 1.47, 95%CI = 1.01-2.14, p = 0.046).

CONCLUSION

The results indicate a strong causal effect of IBD (including CD and UC) on ILD.

Differences in gut metagenomes between dairy workers and community controls: a cross-sectional study

Background

As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens as they undergo evolution prior to a spillover event. In light of this, we are interested in characterizing the microbiome and resistome of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases.

Results

Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of the human gut microbiome of 10 dairy farm workers and 6 community controls, supplementing these samples with additional publicly available gut metagenomes. We observed greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes in dairy workers' metagenomes, and lower average gene diversity. We also found evidence of commensal organism association with plasmid-mediated tetracycline resistance genes in both dairy workers and community controls (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii). However, we did not find significant differences in the prevalence of resistance genes or virulence factors overall, nor differences in the taxonomic composition of dairy worker and community control metagenomes.

Conclusions

This study presents the first metagenomics analysis of United States dairy workers, providing insights into potential risks of exposure to antibiotics and pathogens in animal farming environments. Previous metagenomic studies of livestock workers in China and Europe have reported increased abundance and carriage of antibiotic resistance genes in livestock workers. While our investigation found no strong evidence for differences in the abundance or carriage of antibiotic resistance genes and virulence factors between dairy worker and community control gut metagenomes, we did observe patterns in the abundance of tetracycline resistance genes and the prevalence of cephamycin resistance genes that is consistent with previous work.

Global Research Trends on the Link Between the Microbiome and COPD: A Bibliometric Analysis

Background

The pathogenesis of chronic obstructive pulmonary disease (COPD) has been studied in relation to the microbiome, providing space for more targeted interventions and new treatments. Numerous papers on the COPD microbiome have been reported in the last 10 years, yet few publications have used bibliometric methods to evaluate this area.

Methods

We searched the Web of Science Core Collection for all original research articles in the field of COPD microbiome from January 2011 to August 2022 and used CiteSpace for visual analysis.

Results

A total of 505 relevant publications were obtained, and the number of global publications in this field is steadily increasing every year, with China and the USA occupying the first two spots in international publications. Imperial College London and the University of Leicester produced the most publications. Brightling C from the UK was the most prolific writer, while Huang Y and Sze M from the USA were first and second among the authors cited. The American Journal of Respiratory and Critical Care Medicine had the highest frequency of citations. The top 10 institutions, cited authors and journals are mostly from the UK and the US. In the ranking of citations, the first article was a paper published by Sze M on changes in the lung tissue's microbiota in COPD patients. The keywords "exacerbation", "gut microbiota", "lung microbiome", "airway microbiome", "bacterial colonization", and "inflammation" were identified as cutting-edge research projects for 2011-2022.

Conclusion

Based on the visualization results, in the future, we can use the gut-lung axis as the starting point to explore the immunoinflammatory mechanism of COPD, and study how to predict the effects of different treatments of COPD by identifying the microbiota, and how to achieve the optimal enrichment of beneficial bacteria and the optimal consumption of harmful bacteria to improve COPD.

Association of lung-intestinal microecology and lung cancer therapy

In recent years, the incidence of lung cancer is increasing. Lung cancer has become one of the most malignant tumors with the highest incidence in the world, which seriously affects people's health. The most important cause of death of lung cancer is metastasis. Therefore, it is crucial to understand the mechanism of lung cancer progression and metastasis. This review article discusses the physiological functions, pathological states and disorders of the lung and intestine based on the concepts of traditional Chinese medicine (TCM), and analyzes the etiology and mechanisms of lung cancer formation from the perspective of TCM. From the theory of "the exterior and interior of the lung and gastrointestinal tract", the theory of "the lung-intestinal axis" and the progression and metastasis of lung cancer, we proposed e "lung-gut co-treatment" therapy for lung cancer. This study provides ideas for studying the mechanism of lung cancer and the comprehensive alternative treatment for lung cancer patients.

Editorial of Special Issue "Human Pathogenic Fungi: Host-Pathogen Interactions and Virulence"

Most individuals harbour several species of yeast of the genus Candida, which are considered true symbionts of the human gut microbiota [...].

Association of gut microbiota with COVID-19 susceptibility and severity: A two-sample Mendelian randomization study

Evidence supports the observational associations of gut microbiota with the risk of COVID-19; however, it is unclear whether these associations reflect a causal relationship. This study investigated the association of gut microbiota with COVID-19 susceptibility and severity. Data were obtained from a large-scale gut microbiota data set (n = 18 340) and the COVID-19 Host Genetics Initiative (n = 2 942 817). Causal effects were estimated with inverse variance weighted (IVW), MR-Egger, and weighted median, and sensitivity analyses were implemented with Cochran's Q test, MR-Egger intercept test, MR-PRESSO, leave-one-out analysis, and funnel plots. For COVID-19 susceptibility, IVW estimates suggested that Gammaproteobacteria (odds ratio [OR] = 0.94, 95% confidence interval [CI], 0.89-0.99, p = 0.0295] and Streptococcaceae (OR = 0.95, 95% CI, 0.92-1.00, p = 0.0287) had a reduced risk, while Negativicutes (OR = 1.05, 95% CI, 1.01-1.10, p = 0.0302), Selenomonadales (OR = 1.05, 95% CI, 1.01-1.10, p = 0.0302), Bacteroides (OR = 1.06, 95% CI, 1.01-1.12, p = 0.0283), and Bacteroidaceae (OR = 1.06, 95% CI, 1.01-1.12, p = 0.0283) were associated with an increased risk (all p < 0.05, nominally significant). For COVID-19 severity, Subdoligranulum (OR = 0.80, 95% CI, 0.69-0.92, p = 0.0018), Cyanobacteria (OR = 0.85, 95% CI, 0.76-0.96, p = 0.0062), Lactobacillales (OR = 0.87, 95% CI, 0.76-0.98, p = 0.0260), Christensenellaceae (OR = 0.87, 95% CI, 0.77-0.99, p = 0.0384), Tyzzerella3 (OR = 0.89, 95% CI, 0.81-0.97, p = 0.0070), and RuminococcaceaeUCG011 (OR = 0.91, 95% CI, 0.83-0.99, p = 0.0247) exhibited negative correlations, while RikenellaceaeRC9 (OR = 1.09, 95% CI, 1.01-1.17, p = 0.0277), LachnospiraceaeUCG008 (OR = 1.12, 95% CI, 1.00-1.26, p = 0.0432), and MollicutesRF9 (OR = 1.14, 95% CI, 1.01-1.29, p = 0.0354) exhibited positive correlations (all p < 0.05, nominally significant). Sensitivity analyses validated the robustness of the above associations. These findings suggest that gut microbiota might influence the susceptibility and severity of COVID-19 in a causal way, thus providing novel insights into the gut microbiota-mediated development mechanism of COVID-19.

Crosstalk between the lung microbiome and lung cancer

The human microbiome is a complex ecosystem that mediates interaction between the human host and the environment. All of the human body is colonized by microorganisms. The lung as an organ used to be considered sterile. Recently, however, there has been a growing number of reports with evidence that the lungs are also in a state of carrying bacteria. The pulmonary microbiome is associated with many lung diseases and is increasingly reported in current studies. These include; chronic obstructive pulmonary disease (COPD), asthma, acute chronic respiratory infections, and cancers. These lung diseases are associated with reduced diversity and dysbiosis. It directly or indirectly affects the occurrence and development of lung cancer. Very few microbes directly cause cancer, while many are complicit in cancer growth, usually working through the host's immune system. This review focuses on the correlation between lung microbiota and lung cancer, and investigates the mechanism of action of lung microorganisms on lung cancer, which will provide new and reliable treatments and diagnosis of lung cancer in the future.

Changes in upper airways microbiota in ventilator-associated pneumonia

BACKGROUND

The role of upper airways microbiota and its association with ventilator-associated pneumonia (VAP) development in mechanically ventilated (MV) patients is unclear. Taking advantage of data collected in a prospective study aimed to assess the composition and over-time variation of upper airway microbiota in patients MV for non-pulmonary reasons, we describe upper airway microbiota characteristics among VAP and NO-VAP patients.

METHODS

Exploratory analysis of data collected in a prospective observational study on patients intubated for non-pulmonary conditions. Microbiota analysis (trough 16S-rRNA gene profiling) was performed on endotracheal aspirates (at intubation, T0, and after 72 h, T3) of patients with VAP (cases cohort) and a subgroup of NO-VAP patients (control cohort, matched according to total intubation time).

RESULTS

Samples from 13 VAP patients and 22 NO-VAP matched controls were analyzed. At intubation (T0), patients with VAP revealed a significantly lower microbial complexity of the microbiota of the upper airways compared to NO-VAP controls (alpha diversity index of 84 ± 37 and 160 ± 102, in VAP and NO_VAP group, respectively, p-value < 0.012). Furthermore, an overall decrease in microbial diversity was observed in both groups at T3 as compared to T0. At T3, a loss of some genera (Prevotella 7, Fusobacterium, Neisseria, Escherichia-Shigella and Haemophilus) was found in VAP patients. In contrast, eight genera belonging to the Bacteroidetes, Firmicutes and Fusobacteria phyla was predominant in this group. However, it is unclear whether VAP caused dysbiosis or dysbiosis caused VAP.

CONCLUSIONS

In a small sample size of intubated patients, microbial diversity at intubation was less in patients with VAP compared to patients without VAP.

Gut microbiota and synbiotic foods: Unveiling the relationship in COVID-19 perspective

The Coronavirus disease 2019 (COVID-19) has spread across the globe and is causing widespread disaster. The impact of gut microbiota on lung disease has been widely documented. Diet, environment, and genetics all play a role in shaping the gut microbiota, which can influence the immune system. Improving the gut microbiota profile through customized diet, nutrition, and supplementation has been shown to boost immunity, which could be one of the preventative methods for reducing the impact of various diseases. Poor nutritional status is frequently linked to inflammation and oxidative stress, both of which can affect the immune system. This review emphasizes the necessity of maintaining an adequate level of important nutrients to effectively minimize inflammation and oxidative stress, moreover to strengthen the immune system during the COVID-19 severity. Furthermore, the purpose of this review is to present information and viewpoints on the use of probiotics, prebiotics, and synbiotics as adjuvants for microbiota modification and its effects on COVID-19 prevention and treatment.

Omega-3 polyunsaturated fatty acids ameliorate PM2.5 exposure induced lung injury in mice through remodeling the gut microbiota and modulating the lung metabolism

Short-term or long-term exposure to fine particulate matter (PM2.5) is related to increased incidences of respiratory diseases. This study aimed to investigate the influences of omega-3 polyunsaturated fatty acids (ω-3 PUFAs) supplementation on oxidative stress, inflammation, lung metabolic profile, and gut microbiota in PM2.5-induced lung injury mice. Mice were divided into four groups (n = 15, per group): two unsupplemented groups, control group and PM2.5 group, and two supplemented groups with ω-3 PUFAs, ω-3 PUFAs group, and ω-3 PUFAs + PM2.5 group. Mice in the supplemented groups were placed on an ω-3 PUFAs-enriched diet (ω-3 PUFAs, 21 g/kg). During the 5th to 6th week of dietary supplementation, mice were exposed to PM2.5 by intra-tracheal instillation. ω-3 PUFAs ameliorate lung histopathological injury, reduce inflammatory responses and oxidative stress, affect lung metabolite profile, and modulate gut microbiota in PM2.5-induced lung injury mice. Thus, supplementary ω-3 PUFAs showed effectiveness in attenuation of PM2.5-induced lung injury, indicating that the interventions exhibited preventive and therapeutic potential.

Decoding the bidirectional relationship between gut microbiota and COVID-19

From late 2019, whole world has been facing COVID-19 pandemic which is caused by SARS-CoV-2 virus. This virus primarily attacks the respiratory tract and enter host cell by binding with angiotensin 2 converting enzyme receptors present on alveoli of the lungs. Despite its binding in the lungs, many patients have reported gastrointestinal symptoms and indeed, RNA of the virus have been found in faecal sample of patients. This observation gave a clue of the involvement of gut-lung axis in this disease development and progression. From several studies reported in past two years, intestinal microbiome has shown to have bidirectional link with lungs i.e., gut dysbiosis increases the tendency of infection with COVID-19 and coronavirus can also cause perturbations in intestinal microbial composition. Thus, in this review we have tried to figure out the mechanisms by which disturbances in the gut composition can increase the susceptibility to COVID-19. Understanding these mechanisms can play a crucial role in decreasing the disease outcomes by manipulating the gut microbiome using prebiotics, probiotics, or combination of two. Even, faecal microbiota transplantation can also show better results, but intensive clinical trials need to be done first.

Gut Microbiota and Metabolome Changes in Three Pulmonary Hypertension Rat Models

Dysbiosis of the gut microbiota and metabolites is found in both pulmonary hypertension patients and pulmonary hypertension rodent models. However, the exact changes in gut microbiota during the development of pulmonary hypertension is unclear. The function of the gut microbiota is also ambiguous. Here, this study showed that the gut microbiota was disrupted in rats with hypoxia (Hyp)-, hypoxia/Sugen5416 (HySu)-, and monocrotaline (MCT)-induced pulmonary hypertension. The gut microbiota is dynamically changed during the development of Hyp-, HySu-, and MCT-induced rat pulmonary hypertension. The variation in the α diversity of the gut microbiota in Hyp-induced pulmonary hypertension rats was similar to that in rats with MCT-induced pulmonary hypertension and different from that in rats with HySu-induced pulmonary hypertension. In addition, six plasma biomarkers, His, Ala, Ser, ADMA, 2-hydroxybutyric acid, and cystathionine, were identified in Hyp-induced pulmonary hypertension rats. Furthermore, a disease-associated network connecting Streptococcus with Hyp-induced pulmonary hypertension-associated metabolites was described here, including trimethylamine N-oxide, Asp, Asn, Lys, His, Ser, Pro, and Ile.

The direct correlation between microbiota and SARS-CoV-2 infectious disease

The human microbiota is the good part of the human organism and is a collection of symbiotic microorganisms which aid in human physiological functions. Diseases that can be generated by an altered microbiota are continuously being studied, but it is quite evident how a damaged microbiota is involved in chronic inflammatory diseases, psychiatric diseases, and some bacterial or viral infections. However, the role of the microbiota in the host immune response to bacterial and viral infections is still not entirely understood. Metabolites or components which are produced by the microbiota are useful in mediating microbiota-host interactions, thus influencing the host's immune capacity. Recent evidence shows that the microbiota is evidently altered in patients with viral infections such as post-acute COVID-19 syndrome (PACS). In this review, the associations between microbiota and COVID-19 infection are highlighted in terms of biological and clinical significance by emphasizing the mechanisms through which metabolites produced by the microbiota modulate immune responses to COVID-19 infection.

Gut microbiota and COVID-19: A systematic review

Background and Aims

Alteration in humans' gut microbiota was reported in patients infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The gut and upper respiratory tract (URT) microbiota harbor a dynamic and complex population of microorganisms and have strong interaction with host immune system homeostasis. However, our knowledge about microbiota and its association with SARS-CoV-2 is still limited. We aimed to systematically review the effects of gut microbiota on the SARS-CoV-2 infection and its severity and the impact that SARS-CoV-2 could have on the gut microbiota.

Methods

We searched the keywords in the online databases of Web of Science, Scopus, PubMed, and Cochrane on December 31, 2021. After duplicate removal, we performed the screening process in two stages; title/abstract and then full-text screening. The data of the eligible studies were extracted into a pre-designed word table. This study adhered to the PRISMA checklist and Newcastle-Ottawa Scale Bias Assessment tool.

Results

Sixty-three publications were included in this review. Our study shows that among COVID-19 patients, particularly moderate to severe cases, the gut and lung microbiota was different compared to healthy individuals. In addition, the severity, and viral load of COVID-19 disease would probably also be influenced by the gut, and lung microbiota's composition.

Conclusion

Our study concludes that there was a significant difference in the composition of the URT, and gut microbiota in COVID-19 patients compared to the general healthy individuals, with an increase in opportunistic pathogens. Further, research is needed to investigate the probable bidirectional association of COVID-19 and human microbiome.

Combined analysis of gut microbiome and serum metabolomics reveals novel biomarkers in patients with early-stage non-small cell lung cancer

Non-small cell lung cancer (NSCLC) is the predominant form of lung cancer and is one of the most fatal cancers worldwide. Recently, the International Association for the Study of Lung Cancer (IASLC) proposed a novel grading system based on the predominant and high-grade histological patterns for invasive pulmonary adenocarcinoma (IPA). To improve outcomes for NSCLC patients, we combined serum metabolomics and fecal microbiology to screen biomarkers in patients with early-stage NSCLC and identified characteristic microbial profiles in patients with different grades of IPA. 26 genera and 123 metabolites were significantly altered in the early-stage NSCLC patients. Agathobacter, Blautia, Clostridium, and Muribaculacea were more abundant in the early-stage NSCLC patients compared with healthy controls. For the different grades of IPA, the characteristic microorganisms are as follows: Blautia and Marinobacter in IPA grade type 1; Dorea in IPA grade type 2; and Agathobacter in IPA grade type 3. In the metabolome results, the early-stage NSCLC group mainly included higher levels of sphingolipids (D-erythro-sphingosine 1-phosphate, palmitoyl sphingomyelin), fatty acyl (Avocadyne 1-acetate, 12(S)-HETE, 20-Carboxy-Leukotriene B4, Thromboxane B3, 6-Keto-prostaglandin f1alpha, Sebacic acid, Tetradecanedioic acid) and glycerophospholipids (LPC 20:2, LPC 18:0, LPC 18:4, LPE 20:2, LPC 20:1, LPC 16:1, LPC 20:0, LPA 18:2, LPC 17:1, LPC 17:2, LPC 19:0). Dysregulation of pathways, such as sphingolipid metabolism and sphingolipid signaling pathway may become an emerging therapeutic strategy for early-NSCLC. Correlation analysis showed that gut microbiota and serum metabolic profiles were closely related, while Muribaculacea and Clostridium were the core genera. These findings provide new biomarkers for the diagnosis of early-stage NSCLC and the precise grading assessment of prognostic-related IPAs, which are of clinical importance and warrant further investigation of the underlying molecular mechanisms.

Airway microbiome-immune crosstalk in chronic obstructive pulmonary disease

Chronic Obstructive Pulmonary Disease (COPD) has significantly contributed to global mortality, with three million deaths reported annually. This impact is expected to increase over the next 40 years, with approximately 5 million people predicted to succumb to COPD-related deaths annually. Immune mechanisms driving disease progression have not been fully elucidated. Airway microbiota have been implicated. However, it is still unclear how changes in the airway microbiome drive persistent immune activation and consequent lung damage. Mechanisms mediating microbiome-immune crosstalk in the airways remain unclear. In this review, we examine how dysbiosis mediates airway inflammation in COPD. We give a detailed account of how airway commensal bacteria interact with the mucosal innate and adaptive immune system to regulate immune responses in healthy or diseased airways. Immune-phenotyping airway microbiota could advance COPD immunotherapeutics and identify key open questions that future research must address to further such translation.

Association between microbiota and immune response to Sars-CoV-2 infection

In recent times, the key role of the human microbiota in the body's response to infectious diseases has been increasingly demonstrated. The human microbiota is the set of symbiotic microorganisms which coexist with the human organism without harming it. However, diseases related to the microbiota occur and are being studied, and numerous publications suggest that altered microbiota composition is implicated in psychiatric diseases, chronic inflammatory diseases, and some viral infections. On the other hand, the role of the human microbiota in the host immune response to viral infections is not entirely clear. Metabolites or components produced by the microbiota are the main mediators of microbiota-host interactions that influence host immunity. It has been shown that in patients with COVID-19 and post-acute COVID-19 syndrome (PACS), the microbiota is significantly altered. In this brief review, we examine the associations between the role of the microbiota in response to COVID-19 infection in terms of molecular biology and clinical relevance. We finally discuss the mechanisms by which metabolites produced by the microbiota modulate host immune responses to SARS-CoV-2 infection.

Wine-processed radix scutellariae alleviates ARDS by regulating tryptophan metabolism through gut microbiota

Acute respiratory distress syndrome (ARDS) is an acute and diffuse pulmonary inflammation, characterized by severe hypoxic respiratory failure caused by inflammatory tissue damage, which is a common cause of respiratory failure. Currently, there is no treatment available that can prevent or reverse the devastating effects caused by these conditions. The purpose of this study was to determine the effects of WRS on gut microbiota and the potential effect of gut microbiota on the treatment of lung disease by using a staphylococcal enterotoxin B (SEB)-induced ARDS model. The results showed that WRS could significantly reduce the pathological damage to lung and colon tissues and improve the lung and intestinal functions of ARDS mice. WRS was able to improve the level of cytokines in serum and lung tissue. Additionally, WRS could reverse the gut microbiota dysbiosis caused by SEB in ARDS mice. WRS increases the production of short-chain fatty acids (SCFAs) in the gut. This increase in SCFAs may lead to increased migration of SCFAs to the lungs and activation of free fatty acid receptors (FFAR) three and FFAR2 in lung epithelial cells, alleviating the symptoms of ARDS. Interestingly, WRS improves the faecal metabolite profiles in SEB-induced ARDS mice via tryptophan metabolism. On the basis of the component-target-metabolism strategy, baicalin, oroxylin A-7-O-glucuronide and skullcapflavon II were identified as the potential bioactive markers in WRS for the treatment of ARDS. Our study showed that WRS could ameliorate SEB-induced ARDS by regulating the structure of gut microbiota, increasing the production of SCFAs and modifying the faecal metabolite profiles through the lung-gut axis, and providing alternative treatment strategies for lung disease.

Probiotic Bifidobacterium longum subsp. longum Protects against Cigarette Smoke-Induced Inflammation in Mice

Bifidobacterium are prominent gut commensals that produce the short-chain fatty acid (SCFA) acetate, and they are often used as probiotics. Connections between the gut and the lung, termed the gut-lung axis, are regulated by the microbiome. The gut-lung axis is increasingly implicated in cigarette smoke-induced diseases, and cigarette smoke exposure has been associated with depletion of Bifidobacterium species. In this study, we assessed the impact of acetate-producing Bifidobacterium longum subsp. longum (WT) and a mutant strain with an impaired acetate production capacity (MUT) on cigarette smoke-induced inflammation. The mice were treated with WT or MUT B. longum subsp. longum and exposed to cigarette smoke for 8 weeks before assessments of lung inflammation, lung tissue gene expression and cecal SCFAs were performed. Both strains of B. longum subsp. longum reduced lung inflammation, inflammatory cytokine expression and adhesion factor expression and alleviated cigarette smoke-induced depletion in caecum butyrate. Thus, the probiotic administration of B. longum subsp. longum, irrespective of its acetate-producing capacity, alleviated cigarette smoke-induced inflammation and the depletion of cecal butyrate levels.

A High-Fiber Diet or Dietary Supplementation of Acetate Attenuate Hyperoxia-Induced Acute Lung Injury

A high fiber diet (HFD) and dietary supplementation with acetate have been reported to have beneficial effects in a variety of diseases. We investigated the effects of a HFD and acetate supplementation on the gut microbiota and hyperoxia-induced acute lung injury (HALI) in mice. Mice were fed a control diet, HFD, or acetate supplementation for three weeks, and their gut microbiome composition, lung tissues, and bronchoalveolar lavage fluid (BALF) were examined after exposure to ambient air or hyperoxia. Both the HFD and acetate supplementation modified the gut microbiota community and increased the proportion of acetate-producing bacteria in mice exposed to hyperoxia. The HFD and acetate supplementation also increased the abundance of Bacteroides acidifaciens and reduced gut dysbiosis according to the ratio of Firmicutes to Bacteroidetes. Compared with hyperoxia-exposed mice fed a control diet, both the HFD and acetate supplementation significantly increased the survival time while reducing the severity of pulmonary edema and the concentrations of protein and inflammatory mediators in BALF. Moreover, the HFD and acetate supplementation reduced the production of free radicals, attenuated NF-κB signaling activation, and decreased apoptosis in the lung tissues. Overall, this study indicates that a HFD or acetate supplementation reduces the severity of HALI through alterations in the gut microbiota to exert anti-inflammatory effects.

Incidence, Characteristics, Clinical Course, and Risk Factors of Ulcerative Colitis-related Lung Diseases

BACKGROUND

Ulcerative colitis (UC) is a chronic GI inflammatory disorder involving various extraintestinal organs, including the lungs. Although UC-related lung diseases (UC-LDs) have been widely recognized, much remains unclear.

RESEARCH QUESTION

What are the incidence, characteristics, clinical course, and risk factors of UC-LD?

STUDY DESIGN AND METHODS

This study retrospectively identified and classified UC-LDs by reviewing the medical records of consecutive patients with UC. The incidence, characteristics, and clinical course of each UC-LD type were investigated, and the clinical characteristics of patients with and without each UC-LD type were compared.

RESULTS

Among 563 patients with UC, 28 (5.0%) developed UC-LD during a mean follow-up period of 77 months. A majority of them displayed airway disease (AD) (n = 13 [2.3%]) or organizing pneumonia (OP) (n = 10 [1.8%]); there were six cases of interstitial pneumonias other than OP (IP) (0.8%) and one of pleuritis (0.2%). All 13 patients with AD responded favorably to inhaled or systemic corticosteroids, although five experienced frequent exacerbations. Older age and a history of colectomy were identified as the risk factors for developing AD. Nine of the 10 cases of OP were possibly due to drug-induced pathogenesis. Only one case showed recurrence, and all cases of OP exhibited a favorable clinical course with discontinuation of the suspicious drug and/or initiation of corticosteroid. The clinical course of IP depended on the existence of fibrosis, and IP with fibrosis was associated with gradual deterioration. Older age was associated with the development of IP.

INTERPRETATION

A nonnegligible number of patients with UC may develop UC-LD. AD, OP, and IP without fibrosis show good prognosis following steroid therapy along with the specific management for each UC-LD type, whereas IP with fibrosis shows gradual deterioration with poor prognosis. Our results provide cues to establish better management of UC-LDs.

Gut microbiome and anti-viral immunity in COVID-19

SARS-CoV-2 mainly affects the respiratory system, but the gastrointestinal tract is also a target. Prolonged gut disorders, in COVID-19 patients, were correlated with decreased richness and diversity of the gut microbiota, immune deregulation and delayed viral clearance. Although there are no definitive conclusions, ample evidence would suggest that the gut microbiome composition and function play a role in COVID-19 progression. Microbiome modulation strategies for population stratification and management of COVID-19 infection are under investigation, representing an area of interest in the ongoing pandemic. In this review, we present the existing data related to the interaction between gut microbes and the host's immune response to SARS-CoV-2 and discuss the implications for current disease management and readiness to face future pandemics.