SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Gut microbial signature in lung cancer patients highlights specific taxa as predictors for durable clinical benefit

Stool samples for microbial 16S amplicon sequencing and clinical data were collected from 75 lung cancer patients (50 of which were treated with checkpoint inhibitors) and 31 age-matched healthy volunteers. We compared using multivariate analyses cancer patients to healthy controls, and within lung cancer we compared patients with DCB to those without DCB.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
study the alteration in gut and lung microbiome of asthma mice after fecal microbiota transplant

we extract 16s rRNA form fecal and lung sample of mice. Those mice were receipted fecal microbiota from healthy donors and asthmatics.

Biome: root:Host-associated:Mammals
Colonization of Stenotrophomonas and its associated microbiome between paired primary colorectal cancers and their lung metastatic tumors

Our work highlights the great potential of S. maltophilia and its associated microbiome as biomarkers in pathogenesis and prognosis of CRC lung metastases.

Biome: root:Host-associated:Human
Whole Exome Sequencing of Non-alpha-fetoprotein Elevated Lung Hepatoid Adenocarcinoma

Hepatoid adenocarcinoma (HAC) is an exceptional rare malignant tumor with prominent Hepatic-like characteristics in organs or tissue outside the liver. Most reported HAC of the lung (HAL) cases have varying degrees of serum alpha-fetoprotein (AFP) level and exhibit a similar origin and clonal evolution process to hepatocellular carcinoma. We report a case of HAL without elevating AFP level, moreover performed whole-exome sequencing (WES) and bioinformatics analyses after surgical resection. Our results showed mutations in two driver genes, NLRP3 and PBX1, and we identified HNRNPR, TP73, CFAP57, COL11A1, RUSC1, SLC6A9, DISC1, NBPF26, OR10K1 as potential driver mutation genes in HAL. In addition, 76 genes were differentially expressed in HAL tumor tissue versus normal tissue.

Biome: root:Host-associated:Mammals:Respiratory system
Lung transplant microbiome

16S rRNA amplicon sequencing of lung transplant bronchoalveolar lavage samples

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Metabolome and microbiome multi-omics integration from a murine model of bronchopulmonary dysplasia

This study uses a neonatal mouse model of bronchopulmonary dysplasia (BPD) to examine the impact on the lung metabolome and microbiome. Lipopolysaccharide and hyperoxia were used as a double-hit approach to trigger lung inflammation and model BPD within the first two weeks of life. The study examines the impact of each exposure separately as well as their interaction, ultimately identifying putative metabolomic and microbiome-based biomarkers of stressors that can cause BPD. These data were then linked to a published transcriptome. Associations identified in this study have implications for the potential use of these biomarkers in clinical application and basic science research.

Biome: root:Host-associated:Mammals:Respiratory system:Pulmonary system
BALF microbial diversity of bronchiectasis patients

This study intends to explore the correlation between the diversity of bronchoalveolar lavage fluid flora, metabolites and neutrophil inflammation in patients with bronchiectasis.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Black tea alleviates particulate matter-induced lung injury via the gut-lung axis in mice

Exposure to particulate matters (PMs) induces lung injury and gut microbiota disruption in mice. While daily intake of black tea or its fractions, including ethanol-soluble fraction (ES) and ethanol precipitate fraction (EP), can provide pre-protection against the PM-induced lung injury. Furthermore, the gut microbiota differentially reshaped by tea infusion (TI) and its fractions directly alleviate the injury induced by PMs, indicating gut microbiota mediates the protective effects of black tea and its fractions. Here, we performed gut microbiota 16sRNA sequencing on mice from each treatment groups.

Biome: root:Host-associated:Mammals:Digestive system
Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in advanced non-small cell lung cancer patients.

Aside from PD-L1 expression, biomarkers of response to immune checkpoint inhibitors (ICI) in non-small cell lung cancer (NSCLC) are needed. In a previous retrospective analysis, we documented that fecal Akkermansia muciniphila (Akk) associated with clinical benefit of ICI in NSCLC and kidney cancer patients. In the current study, we performed shotgun metagenomics-based microbiome profiling in a large cohort of advanced NSCLC patients (n=338) treated with first or second line ICI, to prospectively validate the predictive value of fecal Akk. Baseline stool Akk was associated with increased objective response rates and overall survival in multivariate analyses, independent of PD-L1 expression, antibiotics and performance status. Intestinal Akk was accompanied by a richer commensalism, including Eubacterium hallii and Bifidobacterium adolescentis, and a more inflamed tumor microenvironment in a subset of patients. However, antibiotic use (20% of cases) coincided with a relative dominance of Akk above 4.8% accompanied with the genus Clostridium, both associated with resistance to ICI. Our study shows significant differences in relative abundance of Akk that may represent potential biomarkers to refine patient stratification in future studies.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
BreathDx - Diversity and composition of the lung microbiome in patients with suspected ventilator-associated pneumonia

We evaluated how the lung microbiome differs between patients suspected of VAP with positive and negative bronchoalveolar lavage fluid (BALF) cultures and if its composition can be used to exclude the presence of pathogens that drive the use of broad spectrum antibiotics.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Oral microbes contribute to the majority of lung microbiota and indicate lung health

16S rRNA gene sequencing for 99 bronchoalveolar lavage fluid 87 oropharyngeal swabs 86 nasal swabs and 81 saliva

Biome: root:Host-associated:Human:Respiratory system:Nasopharyngeal
Lung microbiome in non-small cell lung cancer

We measured the microbiome in lung tumor and normal lung tissue from stage II NSCLC patients, to examine associations of the lung microbiome with lung cancer recurrence.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Characterization of the microbiota in the lower respiratory tract of Influenza A patients

In order to detect dysbiosis and co-infections we characterized the microbial communities in the lower respiratory tract of patients with severe Influenza A.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Association of bacterial community types, functional microbial processes, and lung disease in cystic fibrosis airways

We analyzed the bacterial communities of sputum samples from persons with cystic fibrosis by sequencing bacterial 16S rRNA gene amplicons. Community types (pulmotypes) were identified using a Dirichlet multinomial mixture model, and correlations were determined between pulmotypes and patient clinical status. Pulmotype-specific metabolic activity profiles suggested that pulmotype microbiota drive distinct community functions.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
lung metagenome Raw sequence reads

To detect changes of lung microbiota in healthy and disease states

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Gastroesophageal reflux disease is associated with differences in the allograft microbiome, microbial density and inflammation in lung transplantation.

Rationale: Gastroesophageal reflux disease (GERD) may affect lung allograft inflammation and function through its effects on allograft microbial community composition in lung transplant recipients.Objectives: Our objective was to compare the allograft microbiota in lung transplant recipients with or without clinically diagnosed GERD in the first post-transplant year, and assess associations between GERD, allograft microbiota, inflammation and acute and chronic lung allograft dysfunction (ALAD/CLAD).Methods: 268 bronchoalveolar lavage samples were collected from 75 lung transplant recipients at a single transplant centre every 3 months post-transplant for 1 year. Ten transplant recipients from a separate transplant centre provided samples pre/post-anti-reflux Nissen fundoplication surgery. Microbial community composition and density were measured using 16S rRNA gene sequencing and qPCR, respectively and inflammatory markers and bile acids were quantified.Measurements and Main Results: We observed three community composition profiles (labelled community state types, CSTs 1-3). Transplant recipients with GERD were more likely to have CST1, characterized by high bacterial density and relative abundance of the oropharyngeal colonizing genera Prevotella and Veillonella. GERD was associated with more frequent transition to CST1. CST1 was associated with lower per-bacteria inflammatory cytokine levels than the pathogen-dominated CST3. Time-dependant models revealed associations between CST3 and development of ALAD/CLAD. Nissen fundoplication decreased bacterial load and pro-inflammatory cytokines.Conclusion: GERD was associated with a high density, Prevotella/Veillonella dominated CST1. CST3, but not CST1 or GERD, was associated with inflammation and early development of ALAD/CLAD. Nissen fundoplication was associated with decreases in microbial density in BALF samples, especially the CST1-specific genus, Prevotella.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
bacterial community diversity

bacterial composition in pulmonary tuberculosis

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
The airway microbiota of non-small-cell lung cancer patients and its relationship to tumor stage and EGFR gene mutation

The airway microbiota and its association with clinical parameters of lung cancer remained largely unknown. This study identified associations between sputum microbiota and clinical stage, intrathoracic metastasis, lymph node metastasis and EGFR mutation. Our study provided potential bacterial markers linked with various important clinical parameters and called for larger and deeper studies for further investigation of the nature of airway microbiota alteration and lung cancer development and progression.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
lung metagenome Raw sequence reads

Vitamin D3 pretreatment changed lung microbiota composition

Biome: root:Host-associated:Mammals:Respiratory system
Airway microbiomes from Portuguese patients with chronic lung disorders

We characterized the microbiome of bronchoalveolar lavage samples from individuals with and without cancer using 16S rRNA high-throughput sequencing

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
The role of respiratory microbiome in early bactericidal activity of anti-tuberculosis therapy and treatment outcome

The role of respiratory microbiome in earlybactericidal activity of anti-tuberculosis therapyand treatment outcome

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Magnetic activated cell-sorting identifies a unique lung microbiome community associated with disease states

Studies of lung microbiome taxonomy often reveal few differences between health and disease, but microbial host response may be different between members of similar communities in health and disease. We adapted magnetic-activated cell sorting to examine populations of immunoglobulin-bound lung bacteria, determine differences in the normal lung microbiome, and distinguish the lung microbiome in HIV as a representative disease. Using bronchoalveolar lavage from 42 people living with HIV and 22 HIV-uninfected individuals, we found that while bacteria in raw BAL samples did not differ by HIV status, the immunoglobulin G-bound lung microbiome differed by disease state and was associated with an inflammatory response.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Study of gut microbial diversity in lung cancer

Exploring the relationship between gut microbial diversity and the development of lung cancer using 16s rRNA technology

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Monocarboxylate transporter 2 (MCT2) in murine model of lung cancer: a multi-omic analysis

These 16S rRNA amplicon sequencing data were generated using fecal DNA from tamoxifen-induced MCT2 conditional knockout mice, in the presence or absence of tamoxifen

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Modulation of the pulmonary innate immune response does not change lung microbiota in healthy mice

A study determining whether modulating of murine lung immunity via inhaled TLR agonists changes lung microbiota.

Biome: root:Host-associated:Mammals:Respiratory system
Fungi sequencing of sputum

The respiratory microbiome of lung cancer patients is different from healthy people. Finding the characteristics of microorganisms is conducive to exploring new directions for the assist in distinguishing different histological types of lung cancer.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Bacterial sequencing of sputum

The respiratory microbiome of lung cancer patients is different from healthy people. Finding the characteristics of microorganisms is conducive to exploring new directions for the assist in distinguishing different histological types of lung cancer.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
TLR5 lung microbiome and fibrosis

Raw 16S sequencing data from TLR5 fibrosis experiments

Biome: root:Host-associated:Mammals:Respiratory system
Analysis of gut, stool and lung microbiota in CF mice

Evaluation of the response of the lung and gut microbiota in wildtype and CF mice in the naive status and after Pseudomonas aeruginosa chronicinfection

Biome: root:Host-associated:Mammals
Characterize and compare the composition of the pulmonary bacterioma in women exposed to risk factors for chronic lung diseases

The present investigation aimed to characterize and compare the composition of the pulmonary bacterioma in women exposed to risk factors for chronic lung diseases (tobacco smoking and exposure to smoke from biomass-burning) but without lung function affectation.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
bacterial community diversity

the bacterial community diversity in Mycobacteria tuberculosis infected lung tissues

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Human airway Targeted Locus (Loci)

Human airway specimen microbiome analysis from patients with Cystic Fibrosis

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Community dynamics and the lower airway microbiota in stable chronic obstructive pulmonary disease, smokers and healthy non-smokers

Lower airway microbiota from stable chronic obstructive pulmonary disease, smokers and healthy non-smokers

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Human BAL Targeted Locus (Loci)

Microbiome study of the lower airways in patients with cystic fibrosis and controls

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
EMG produced TPA metagenomics assembly of PRJNA552294 data set (Subgingival metagenome of aggressive periodontitis).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA552294, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque.

Biome: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
Gut microbiome and randomized housing of TLR deficient mice

Data on gut micorbiota from TLR deficeint and wild type mice who are housed randomly to study the impact of hosuing on the gut microbiome in these mice

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Lung microbiota are altered by cage and enviroment

Study was used

Biome: root:Host-associated:Mammals:Respiratory system
lung microbiota of patients S.aureus infection and COVID-19


Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Sequencing of microbial diversity in feces and lungs of diabetic mice


Biome: root:Host-associated:Mammals
Correlations between the patient microbiome with response and development of immune mediated adverse effects to immunotherapy in lung cancer

Immune checkpoint inhibitors comprise a rapidly burgeoning treatment modality in multiple cancers, but outcomes to treatment, including tumor regression/response and immune-mediated adverse events, are highly variable for as yet unclear reasons. Our project seeks to identify any associations tying fecal, oral and respiratory microbiomes to immunotherapy treatment response and toxicities in lung cancer, as well as each other.

Biome: root:Host-associated:Human
Lung microbiota associations with clinical features of COPD in the SPIROMICS cohort

In this study, one of the largest bronchoscopy-based evaluations of the lung microbiome (N=181) in a multicenter COPD cohort, significant relationships between characteristics of the lung bacterial community, profiled from bronchoalveolar lavage samples, and clinical and biological features of disease were observed. These included markers of lung function impairment, symptom burden and inflammatory/immune biomarkers. In this cohort enriched in subjects with mild to moderate COPD and ever-smokers at risk for the disease, the findings suggest lung microbiota-host interactions during earlier stages of COPD that may contribute to disease pathogenesis.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Lung bacterial microbiome of critical COVID-19

The study was aimed to characterize the lower respiratory tract microbiome of COVID-19 critically ill patients and investigate the microbiome diversity in comparison to COVID-19-negative patients. We performed a microbiome analysis on bronchoalveolar lavage (BAL) samples collected between April and May 2020 from 24 COVID-19 critically ill subjects and 24 patients with non-COVID-19 pneumonia.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Lung microbiome of chronic obstructive pulmonary disease patients in Tshwane, South Africa

This study compared variations in the lung microbiome (using next-generation sequencing and the IS-Pro method) and virome (using next-generation sequencing) in COPD patients during stable and exacerbated states of disease

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
Bronchiectasis lung microbiome

Sputum lung microbiome from patients diagnosed with bronchiectasis.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
EcoCF- Pediatric CF lung microbiomes

This project (EcoCF) is a longitudinal study of the microbiome of pediatric cystic fibrosis patients being cared for at Columbia University between February 2010 and June 2014. The samples, which were collected as part of routine care, are bronchoalveolar lavage, expectorated sputum, and oropharyngeal swabs.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Gut microbiome is associated with exercise tolerance of resected early-stage lung cancer patients

Evaluation of the associations between gut microbiota and outcomes in lung cancer patients who underwent lung resection surgery

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Gut and lung microbiota in RSV-infected mice and streptomycin-treatment mice

Investigate alteration of gut and lung microbiota by RSV infection and streptomycin treatment.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
CF Sputum Microbiome Profiles Associated with Lung Function

CF Sputum Profiles (N=77). Referenced in the manuscript "Microbiome data enhances predictive models of lung function in people with cystic fibrosis" by CYZhao et al.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
NEOSTAR Study: Non-small cell lung cancer treated with nivolumab or nivolumab plus ipilimumab

Phase 2 randomized study of neoadjuvant nivolumab or nivolumab plus ipilimumab followed by surgery in patients with resectable NSCLC using major pathologic response as primary endpoint (NCT03158129)

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Three clinically distinct chronic pediatric airway infections share a common core microbiota

We used bacterial 16S rRNA gene pyrosequencing and ecological statistical tools to compare the core respiratory microbiota from three cohorts of children with clinically distinct airway diseases: Protracted bacterial bronchitis, non-CF bronchiectasis, and CF. The subject groups also differed in age, geography, antibiotic and steroid use, culture results, and lung function. We found that the core respiratory microbiota of all three cohorts were strikingly similar, arguing against airway disease-specific microbiota initiating chronic infection.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Microbial alteration of lower respiratory tract from critically ill patients with community-acquired pneumonia

Pneumonia is the most common infectious disease that causes significant morbidity and mortality in intensive care unit (ICU) and its mortality rate varies from 24% to 50%. Early identification of the pathogens to administrate adequate antibiotics is the most important factor in decreasing the mortality in pneumonia. In this study, we aim to investigate the microbial alteration of bronchoalveolar lavage (BAL) samples using 16S rRNA metagenomics sequencing in respiratory failure patients due to severe pneumonia in ICU.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
human lung metagenome Raw sequence reads

The aim of the study was to evaluate the bacterial microbiome composition and to determine associations between the observed microbial diversity and biological and clinical characteristics in sputum samples collected from patients with bronchiectasis, recruited in stable state.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Sputum
lung metagenome Raw sequence reads

Under eubiotic conditions commensal microbes are known to provide a natural competitive shield against invading bacterial pathogens in the densely colonized intestinal tract, on the skin or on the vaginal mucosa. A comparable function of commensal bacteria in the respiratory tract was so far not described. Here, we evaluate the role of respiratory microbiota in Pneumococcus colonization of the lung in a mouse model.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Airway host-microbiome interplay associated with chronic obstructive pulmonary disease

Airway host-microbiome interactions in chronic obstructive pulmonary disease

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
Microbiome of human lungs with aspergillosis infection

Microbiome samples were taken from the lungs of individuals from Portugal with and without aspergillosis infection. Samples were sequenced by 16S rRNA metabarcoding and statistical analyses were performed to determine the effects and correlations of the microbiome with aspergillosis infection and a number of other relevant variables, such as cytokine levels.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung