SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Horizontal transmission of gut microbiota in lung fibrosis

We determine the impact of gut microbiota in pre-clinical models of pulmonary fibrosis in different sub-strains of C57BL/6 experimental mice derived from vendors (C57BL/6J and C57BL/6Cr). We use germ free models, fecal microbiota transplantation and cohousing approaches to transmit gut microbiota and investigate causality.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
Cystic fibrosis lung microbiome.

Species isolated from sputum samples collected from cystic fibrosis lungs. Raw sequence reads, assembly.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Lower respiratory tract microbiome composition and community interactions in smokers

Lung microbiome study conducted on active, former, and non-smokers

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Lung Microbiota in Lung Transplant Recipients at CLAD Onset

The goal of this project was to determine the relationship between lung microbiota, clinical outcomes, and treatment response among lung transplant recipients with chronic rejection. Bacterial communities in acellular bronchoalveolar lavage fluid collected near the time of chronic lung allograft dysfunction (CLAD) diagnosis were characterized using 16S rRNA gene amplicon sequencing using the Illumina MiSeq platform

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Microbiome Raw sequence reads

Metagenomic Analysis of Lung Microbiome in Pulmonary Tuberculosis - a pilot study

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Lung microbiome dysbiosis in  lower airway in progression of lung cancer.

The difference in lung microbiota between LC patients and patients with non-lung cancer was detected by 16S ribosomal DNA gene sequencing, with the purpose of exploring the interaction between lung microbiota and lung cancer.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Influence of targeted therapy on the composition of the lung microbiome of patients with cystic fibrosis

Approved targeted drugs have different effects on the rate of recovery of the lung microbiome of patients with cystic fibrosis

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Lung mycobiome Raw sequence reads

Fungal Internal Transcribed Spacer (ITS2) from Broncho-alveolar lavage samples (BAL) and environental samples were was sequenced

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Taxonomic signatures of Cystic Fibrosis airway microbiota

In order to gain insight into the underlying causes of severe lung disease and identify potential determinants of ecological and clinical changes in lung function, we compared the airway microbiota composition and diversity of CF patients with a substantial decline in lung function (SD) with that of patients with stable lung function (S).

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
The bronchial epithelial cell bacterial microbiome and host response in patients infected with human immunodeficiency virus

Here we describe the HIV bacterial microbiome and investigate using gene expression the pathways that these bacterial communities may be interacting with.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Human_sputum_16S Raw sequence reads

The microbial samples were taken from sputum of 21 hospitalized patients with pneunomia, DNA was purified and the 16S rRNA DNA was amplified and sequenced

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Neutrophilic Proteolysis in the Cystic Fibrosis Lung Favors a Pathogenic Microbiome

Studies of the cystic fibrosis (CF) lung microbiome have consistently shown lung disease progression is associated with decreased microbial diversity due to the dominance of opportunistic pathogens, but it remains unknown how this phenomenon is reflected in the metabolites and chemical environment of lung secretions. We investigated the microbial and metabolomic composition of CF sputum samples to determine the molecular relationships between disease severity, lung function decline and microbial infections.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Experimental sepsis and the lung microbiome at extended timepoints

Here we assess for changes in the lung microbiome at 5 days, 14 days and 8 weeks after experimental sepsis in mice

Biome: root:Mixed
Human microbiome Targeted Locus (Loci)

We examined the respiratory and intestinal microbiota development in infants with CF from birth to 21 months. Gut and lung microbiome in CF in infancy. PI Juliette Madan

Biome: root:Host-associated:Human
Experimental sepsis and the lung microbiome at 24 hours

Here we assess for changes in the lung microbiome 24 hours after experimental sepsis in mice

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Murine lung microbiota

Commensal bacteria control the micro-ecology of metazoan epithelial surfaces with pivotal effect on tissue homeostasis and host defense. In contrast to the upper respiratory tract, the lower respiratory tract of healthy individuals is largely considered free of microorganisms. To understand airway micro-ecology we studied microbiota of sterilely excised lungs from mice of different origin including outbred wild mice caught in the natural environment or kept under non-specific-pathogen-free (SPF) conditions as well as inbred mice maintained in non-SPF, SPF or germ-free (GF) facilities. High-throughput pyrosequencing revealed that Betaproteobacteria and Ralstonia sp. represent the major constituents of murine lung microbiota. Non-cultivatable Betaproteobacteria were also identified by 16S rRNA gene cloning analysis in all but GF mice. Additionally, Pasteurellaceae, Enterobacteria and Firmicutes were isolated from the lungs of non-SPF, but not from SPF mouse lungs. Bacterial communities were detectable by FISH at alveolar epithelia without induction of inflammation. The overall composition across samples was similar at the phylum and family level, although significant differences with respect to the origin of the mice were observed at the community level. In addition, changing from a SPF to non-SPF environment was associated with increased species richness. Notably, higher bacterial colonization correlated with more and smaller sized alveolae in those mice. Our data indicate a common microbial composition in murine lungs, which is diversified through different environmental conditions and whose richness affects lung architecture. Identification of the microbiota of murine lungs will pave the path to study their influence on pulmonary immunity to infection and allergens using mouse models.

Biome: root:Host-associated:Mammals:Respiratory system
Gut and Lung Microbiomes in AIDS with or without PCP

This study tried to explore the pathogenesis of Pneumocystis Pneumonia(PCP) in AIDS patients from the microbiome perspectives, so as to provide better strategies for the diagnosis, treatment and prevention of PCP.

Biome: root:Host-associated:Human
features of multi-site microtiota in patients with Crohn's disease

features of microtiota in oral cavity, sputum and ileum in patients with Crohn's disease

Biome: root:Host-associated:Human
COVID-19 Cadaver Microbiome (Dr. Gulnaz Javan et al.)

Study performed by Dr. Gulnaz Javan et al. Data obtained from these studies facilitated the defining of microbiome signatures in COVID-19 decedents that could be identified as taxonomic biomarkers effective for predicting the occurrence, the co-infections involved in its dysbiosis, and the evolution of the virus.

Biome: root:Host-associated:Human
lung microbiota

lung microbiota of juvenile mouse

Biome: root:Host-associated:Mammals:Respiratory system
Mouse lung metagenome Raw sequence reads

Intervention of Mahuang Fuzi Xixin decoction on lung microbiota in AR mice

Biome: root:Host-associated:Mammals:Respiratory system
Meta-omics profiling of the gut-lung axis illuminates metabolic networks and host-microbial interactions associated with elevated lung elastance in a murine model of obese asthma

We evaluated nitro-oleic acid as a host- and microbial-targeted treatment intervention for obesity-associated asthma. Allergic airway disease was induced using house dust mite and cholera toxin adjuvant in C57BL6/J mice with diet-induced obesity to model obesity-associated asthma. Mice were treated with either glycerol trioleate vehicle (n = 11) or 9,10-nitro-oleic acid (n = 11) via gavage, followed by allergen challenge 3 hours later. Controls included a mock sensitization group (n = 12) that only received adjuvant during sensitization and a group of naive obese mice (n = 7). Lung function was measured by flexiVent following a week of nitro-oleic acid treatment and allergen challenge. 16S rRNA gene (from DNA, taxa presence) and 16S rRNA (from RNA, taxa activity) sequencing were performed on stool samples collected from mice on the day of lung function measurement. Stool RNA and DNA were isolated using ZymoBIOMICS DNA/RNA Miniprep kit, and cDNA was synthesized with the SuperScript IV VILO kit. 16S rRNA amplicons were run on Illumina MiSeq. Targeting both the host and gut microbiota, NO2-OA attenuated airway inflammation, improved lung elastance, and modified the gut microbiome

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Microbial communities of neonates from allergic mothers

16S rRNA sequencing was performed on lung microbiota from mouse pups born to allergic mothers and control.

Biome: root:Host-associated:Mammals:Respiratory system
Distinct community structures of the fungal microbiome and respiratory health in adults with cystic fibrosis

The early description of cystic fibrosis (CF) was marked by malnutrition and lung infections. The diagnosis and treatment of infection has transformed disease prognosis to a median predicted survival over 50 years. Yet, chronic infections continue to significantly impact morbidity and mortality in CF. Over time, the microbial epidemiology has changed, with a rise of filamentous fungi and yeast recovered by culture from the CF respiratory tract. The pressures of cumulative and chronic exposure to antibiotics in the course of CF likely contributes to the observed changes in fungal detection.Conventional culture-based detection methods are the primary modality to identify microorganisms in CF sputum. However, the adoption of DNA sequence-based analyses has greatly expanded our understanding of bacterial diversity in CF. Unbiased 16S rRNA gene sequencing of CF respiratory samples have yielded insight into age-specific bacterial diversity and resiliency of the bacterial community during pulmonary exacerbations. However, mycologic profiling of the CF airway has remained limited. Our study aimed to molecularly define the fungal composition and community structure in CF sputa and evaluate their associations with clinical characteristics and outcomes.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
The lung microbiota in nontuberculous mycobacterial pulmonary disease

To compare the bacterial microbiome of disease-invaded lesions and non-invaded lung tissue from NTM-PD patients.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Clinical Trial of a Probiotic and Herbal Supplement for Lung and Gut Health

Microbiome data for clinical trial of probiotic and herbal blend in healthy and asthma patients

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
Homo sapiens Raw sequence reads

Lung microbiota in SARS-CoV-2 infected patients

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Dynamic changes of intestinal flora and metabolic function in patients with postoperative pneumonia after lung cancer surgery

This study aims to investigate the dynamic changes and metabolic function of intestinal flora in patients with lung cancer and postoperative pneumonia (POP), and to provide new ideas and targets for the prevention and treatment of POP.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Microbiome analysis of the gut-lung axis in bronchiectasis (mouse model)

This submission contains data related to targeted 16S (bacteriome) and ITS (mycobiome) data from the mouse gut microbiome assessed in a controlled P. aeruginosa intratracheal infection model are also present, including 6 samples per arm, across 4 arms, from P. aeruginosa infected and P. aeruginosa uninfect mice in the presence or absence of orally administered Imipenem consisting of (24 samples). Sequence data from relevant pre-post antibiotic treatment and background contamination controls are also present.

Biome: root:Host-associated:Mammals
Lung microbiota in mice underwent intestinal ischemia/reperfusion injury (Singly housing)

To provide the data of the lung microbiota after intestinal ischemia/reperfusion injury under singly housing condition

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
lung cancer manifested as radiological ground-glass opacity Raw sequence reads

Using 16S rRNA gene sequencing to identify significant differences in the lower respiratory tract and lung microbiome between GGO and the non-malignant control group through the BALF and lung tissues

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Microbial Dysregulation of the Lung-Gut axis in high-risk bronchiectasis

Analysis of lung and gut microbiome profiles in bronchiectasis

Biome: root:Host-associated:Human
Intestinal microbiota-derived propionic acid protects zinc  oxide nanoparticles-induced lung injury

BACKGROUND: Inhalation zinc oxide fumes results in the development of the clinical syndrome known as metal fume fever, the severe cases of which may develop to diffuse alveolar damage. However, the link between inhaled zinc oxide at nano-size (zinc oxide nanoparticles, ZnONPs)-induced acute lung injury (ALI) and intestinal microbiota remains largely unknown.OBJECTIVE: To investigate the role and mechanism of intestinal microbiota and its metabolites short chain fatty acids (SCFAs) in the pathology of ZnONPs-induced ALI and the therapeutic potential of modulating intestinal microbiota in ZnONPs-induced ALI.METHODS: Intratracheal instillation of ZnONPs was used to establish a ALI mice model; antibiotic cocktail treatment (ABX) and fecal microbiota transplantation (FMT) were used to modulate intestinal microbiota; 16S rRNA sequencing and LC-MS/MS were applied to evaluate the change of intestinal microbiota and SCFAs.RESULTS: Intratracheal instillation of ZnONPs caused macrophage-mediated ALI in mice. ABX-mediated depletion of intestinal microbiota aggravated ZnONPs-induced ALI; in contrast, FMT-mediated restoration of intestinal microbiota exerted opposite effects; ZnONPs inhalation resulted in the perturbation of intestinal flora and consequently the decrease of SCFAs (especial acetate acid or propionate acid) in the plasma; supplementation of sodium propionate, but not sodium acetate, remarkably ameliorated ZnONPs-induced ALI; GPR43 was the major receptor of propionate acid in RAW 264.7 macrophage cell lines.CONCLUSION: We illuminates a novel gut-lung axis mechanism that intestinal microbiota and its-derived metabolite propionate acid plays protective role against ZnONPs-induced ALI through repressing macrophage-mediated inflammation and oxidative stress via GPR43 receptor. FMT and supplementation of propionate acid are potential remedy strategies.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
An optimized approach for processing of frozen lung and lavage samples for microbiome studies

BALB/c mice bronchoalveolar lavage fluid (BALF) and lung tissue samples were collected to test different forms of sample pre-treatment and extraction methods to improve DNA yield and optimize library preparation (V4 16S rRNA) of frozen low microbial biomass samples.

Biome: root:Host-associated:Mammals:Respiratory system:Pulmonary system
Microbial diversity in the lung and gut microbiome of Plasmodium infected mice

16S rRNA amplicon sequencing study of the lung and gut microbiome of two mouse strains (C57BL/6J and DBA2), when infected or not with different strains of Plasmodium that lead to different pathologies, particularly with and without lung pathology.

Biome: root:Host-associated:Mammals
Lung fungal microbiome of critical COVID-19 patients

The study was aimed to characterize the lower respiratory tract mycobiome of COVID-19 critically ill patients and investigate the fungal microbiome diversity in comparison to COVID-19-negative patients. We performed ITS rRNA gene profiling, with the Illumina MiSeq platform to analyse the fungal microbiome in bronchoalveolar lavage (BAL) samples collected from COVID-19 critically ill subjects and patients with non-COVID-19 pneumonia

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Pathogensis of Obstruction/Emphysema and the Microbiome in HIV Targeted Locus (Loci)

Microbial flora of the respiratory tract in persons with and without HIV. The flora is expected to play a role in HIV-associated Chronic obstructive pulmonary disease (COPD). We sampled the respiratory tract including oral washes (OW), induced sputum (IS), and bronchoalveolar lavages (BAL). We examined the relationship between microbial flora and smoking, HIV infection status, and COPD.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system
Lung microbiome dynamics in chronic obstructive pulmonary disease exacerbations

Increasing evidence suggests that the lung microbiome plays an important role in chronic obstructive pulmonary disease (COPD) severity. However, the dynamics of the lung microbiome during COPD exacerbations and its potential role in disease aetiology remains poorly understood. We completed a longitudinal 16S ribosomal RNA survey of the lung microbiome on 476 sputum samples collected from 87 subjects with COPD at four visits defined as stable state, exacerbation, two weeks post therapy and six weeks recovery. Our analysis revealed a dynamic lung microbiota where changes appeared to be associated with exacerbation events and indicative of specific exacerbation phenotypes. Antibiotic and steroid treatments appear to have differential effects on the lung microbiome. We depict a microbial interaction network for the lung microbiome and suggest that perturbation of a few bacterial operational taxonomic units, in particular Haemophilus spp, could greatly impact the overall microbial community structure. Furthermore, several serum and sputum biomarkers, in particular sputum interleukin-8 (IL-8), appear to be highly correlated with the structure and diversity of the microbiome. Our study furthers our understanding of lung microbiome dynamics in COPD patients and highlights its potential as a biomarker, and possibly a target, for future respiratory therapeutics.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Dendrobium nobile protects against ovalbumin-induced allergic rhinitis by regulating intestinal flora and suppressing inflammation in the lungs

This project aims to elucidate the effects of intestinal flora dysbiosis on allergic rhinitis and the mechanism by which Shihu extract restores intestinal flora balance to improve allergic rhinitis.

Biome: root:Host-associated:Birds:Digestive system:Fecal
lung microbiome of  children with pneumonia

To understand involvement of lung microbiome in pneumonia etiology, and distinct microbial correlation under pneumonia infected with different pathogens.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
A Multi-Center Study of the Lung Microbiome in Chronic Obstructive Pulmonary Disease

An international cohort study to determine whether respiratory micro biome differs by geography, smoke exposure type, and disease severity in COPD

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Impact of long-term azithromycin treatment on the respiratory microbiome in HIV-associated chronic lung disease

Obliterative bronchiolitis is a recently diagnosed chronic lung disease (CLD) detected in 30% of older children and adolescents living with HIV in Sub-Saharan Africa. Although there are no management guidelines, long-term azithromycin has been suggested as a treatment option due to its dual antimicrobial and immunomodulatory action and effectiveness in other CLDs such as cystic fibrosis, bronchiectasis and asthma. However, its effect on the respiratory bacterial community in this disease context remains unknown. Therefore, this study aims to investigate the impact of 48 weeks of once-weekly, weight-based dosing of azithromycin on the respiratory microbiome of children and adolescents with HIV-associated CLD in an individually randomised, placebo-controlled, double-blinded clinical trial in Zimbabwe and Malawi. We also assessed the persistence of the azithromycin effect on the respiratory microbiome six months post-intervention. Finally, we evaluated the differences in the respiratory microbiome of HIV-infected children with and without CLD. This study's findings extend our understanding of the pathogenesis of this novel CLD and the mechanisms underlying the effectiveness of azithromycin.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Lung microbiota in mice underwent intestinal ischemia/reperfusion injury

None

Biome: root:Host-associated:Mammals
Antibiotic-induced microbiome depletion ameliorates LPS-induced acute lung injury in mice.

In this research, treatment with ABX significantly attenuated LPS-induced lung injury of mice. Considering the key role of gut microbiota in immune system, it is likely that alternations in the gut microbiota by ABX may play a role in LPS-induced lung injury.

Biome: root:Host-associated:Mammals:Gastrointestinal tract
The microbiota of human lung of pulmonary tuberculosis

An in-depth understanding of the lung microbiota of tuberculosis (TB) could provide better strategies for the prophylaxis, diagnosis, and treatment of TB.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Propionic acid protects ZnONPs-induced lung injury

Inhalation zinc oxide fumes results in the development of the clinical syndrome known as metal fume fever, the severe cases of which may develop to diffuse alveolar damage. However, the link between inhaled zinc oxide at nano-size (zinc oxide nanoparticles, ZnONPs)-induced acute lung injury (ALI) and intestinal microbiota remains largely unknown.To investigate the role and mechanism of intestinal microbiota and its metabolites short chain fatty acids (SCFAs) in the pathology of ZnONPs-induced ALI and the therapeutic potential of modulating intestinal microbiota in ZnONPs-induced ALI.Intratracheal instillation of ZnONPs was used to establish a ALI mice model; antibiotic cocktail treatment (ABX) and fecal microbiota transplantation (FMT) were used to modulate intestinal microbiota; 16S rRNA sequencing and LC-MS/MS were applied to evaluate the change of intestinal microbiota and SCFAs.Intratracheal instillation of ZnONPs caused macrophage-mediated ALI in mice. ABX-mediated depletion of intestinal microbiota aggravated ZnONPs-induced ALI; in contrast, FMT-mediated restoration of intestinal microbiota exerted opposite effects; ZnONPs inhalation resulted in the perturbation of intestinal flora and consequently the decrease of SCFAs (especial acetate acid or propionate acid) in the plasma; supplementation of sodium propionate, but not sodium acetate, remarkably ameliorated ZnONPs-induced ALI; GPR43 was the major receptor of propionate acid in RAW 264.7 macrophage cell lines. We illuminates a novel gut-lung axis mechanism that intestinal microbiota and its-derived metabolite propionate acid plays protective role against ZnONPs-induced ALI through repressing macrophage-mediated inflammation and oxidative stress via GPR43 receptor. FMT and supplementation of propionate acid are potential remedy strategies

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal