A5045059192- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Cystic Fibrosis Research Advances
- Probiotics and Fermented Foods
- Bacteriophages and microbial interactions
- Clostridium difficile and Clostridium perfringens research
- Bacterial biofilms and quorum sensing
- Tracheal and airway disorders
- Microbial Community Ecology and Physiology
- RNA and protein synthesis mechanisms
- Neonatal Respiratory Health Research
- Respiratory Support and Mechanisms
- Pediatric health and respiratory diseases
- Pancreatitis Pathology and Treatment
- Bacterial Identification and Susceptibility Testing
- Respiratory viral infections research
- Air Quality and Health Impacts
- Pancreatic and Hepatic Oncology Research
- RNA modifications and cancer
- Antibiotic Resistance in Bacteria
Broad Institute
2022-2025
Massachusetts General Hospital
2024-2025
Harvard University
2024-2025
German Center for Lung Research
2021-2023
Medizinische Hochschule Hannover
2020-2023
Persistent colonization and outgrowth of potentially pathogenic organisms in the intestine can result from long-term antibiotic use or inflammatory conditions, may perpetuate dysregulated immunity tissue damage
Shotgun metagenome sequencing of respiratory secretions with spike-in controls for normalization demonstrated that 1 year high-efficient CFTR modulation elexacaftor/tezacaftor/ivacaftor extensively reduced the bacterial load. Longer observation periods will be necessary to resolve whether partial reversion basic defect is achieved ELX/TEZ/IVA sufficient in long run render CF lungs robust against recolonization common opportunistic pathogens.
The microbial metagenome in cystic fibrosis (CF) airways was investigated by whole-genome shotgun sequencing of total DNA isolated from nasal lavage samples, oropharyngeal swabs, and induced sputum samples collected 65 individuals with CF aged 7 to 50 years. Each patient harbored a personalized unique load composition, the exception being monocultures most common pathogens Staphylococcus aureus Pseudomonas aeruginosa patients advanced lung disease. sampling upper uncovered fungus Malassezia...
Objective This study aims to validate the existence of a microbiome within intraductal papillary mucinous neoplasm (IPMN) that can be differentiated from taxonomically diverse DNA background next-generation sequencing procedures. Design We generated 16S rRNA amplicon data analyse 338 cyst fluid samples 190 patients and 19 negative controls, latter collected directly sterile syringes in operating room. A subset (n=20) blanks (n=5) were spiked with known concentrations bacterial cells alien...
Genome-wide gene expression of bacteria is commonly studied by high-throughput sequencing size-selected cDNA fragment libraries reverse-transcribed RNA preparations. However, the depletion rRNAs, enzymatic reverse transcription, and fragmentation, size selection, amplification during library preparation lead to inevitable losses information about initial composition pool.
Abstract The metagenome development of the human respiratory tract was investigated by shotgun metagenomic sequencing cough swabs from healthy children and with cystic fibrosis (CF) between 3 weeks 6 years age. A microbial community signature associated increased absolute abundances in terms bacterial–human cell ratios core rare species across all age groups, a higher diversity tightly interconnected co-occurrence network, which individual members were found close proximity to each other...
The default removal of low-abundance (rare) taxa from microbial community analyses may lead to an incomplete picture the taxonomic and functional potential within human habitat. Publicly available shotgun metagenomics data healthy children with cystic fibrosis (CF) were reanalysed study development rare species biosphere, which was here defined by either 15th, 25th or 35th abundance percentile. We found that contained age-independent network abundant (core) both entities being essential in...
In shotgun metagenomic sequencing applications, low signal-to-noise ratios may complicate species-level differentiation of genetically similar core species and impede high-confidence detection rare species. However, can take pivotal roles in their habitats should hence be studied as one entity to gain insights into the total potential microbial communities terms taxonomy functionality. Here, we offer a solution towards increased specificity, decreased false discovery omission rates complex...
Abstract Background Shotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome of fungal, viral, archaeal bacterial taxonomy, particularly with regard to visualization read mapping location, normalization options, growth dynamics functional gene repertoires. Current classification tools use non-standard output formats, or do not fully show information on location. As reference datasets are perfect, portrayal is critical judging results effectively....
Preterm birth is accompanied with many complications and requires severe therapeutic regimens at the neonatal intensive care unit. The influence of above-mentioned factors on premature-born infants' respiratory metagenome or more generally its maturation unknown. We therefore applied shotgun sequencing oropharyngeal swabs to analyze airway development 24 preterm infants from one week postpartum 15 months age. Beta diversity analysis revealed a distinct clustering microbial communities...
<title>Abstract</title> <bold>Persistent colonization and outgrowth of pathogenic organisms in the intestine may occur due to long-term antibiotic usage or inflammatory conditions, which perpetuate dysregulated immunity tissue damage</bold><sup><bold>1,2</bold></sup><bold>. Gram-negative </bold><italic><bold>Enterobacteriaceae</bold></italic><bold> gut pathobionts are particularly recalcitrant conventional treatment</bold><sup><bold>3,4</bold></sup><bold>, though an emerging body evidence...
Plasticity of Pseudomonas aeruginosa chromosomes is mainly driven by an extended accessory genome that shaped insertion and deletion events. Further modification the composition can be induced chromosomal inversion events which lead to relocation genes in affected genomic DNA segments, modify otherwise highly conserved core synteny could even alter location replication terminus. Although first sequenced strain, PAO1, displayed such a large inversion, knowledge on recombination P. population...
Summary The updated Wobble Hypothesis reasonably explains why some 40 tRNA species are sufficient to decode the 61 amino acid codons of Universal Genetic Code. However, we still have no clue eubacteria lack isoacceptors with ANN anticodons, whereas eukaryotes universally eight GNN only one which is also absent in bacteria. Direct sequencing could resolve patterns nucleoside modification that had been driving divergent evolution prokaryotes and eukaryotes, but this task will require...
Abstract Background Shotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome of fungal, viral, archaeal bacterial taxonomy, particularly with regard to visualization read mapping location, normalization options, growth dynamics functional gene repertoires. Current classification tools use non-standard output formats, or do not fully show information on location. As reference datasets are perfect, portrayal is critical judging results effectively....