A5078915248- SARS-CoV-2 and COVID-19 Research
- Viral gastroenteritis research and epidemiology
- Gut microbiota and health
- Clostridium difficile and Clostridium perfringens research
- Probiotics and Fermented Foods
- SARS-CoV-2 detection and testing
- Inflammasome and immune disorders
- Streptococcal Infections and Treatments
- Mycobacterium research and diagnosis
- Bacteriophages and microbial interactions
- Immune Response and Inflammation
The University of Texas Southwestern Medical Center
2020-2024
Bead-beating within a DNA extraction protocol is critical for complete microbial cell lysis and accurate assessment of the abundance composition microbiome. While impact bead-beating on recovery OTUs at phylum class level have been studied, its influence species-level microbiome not clear. Recent advances in sequencing technology has allowed resolution using full length 16S rRNA gene instead smaller amplicons that only capture few hypervariable regions gene. We sequenced v3-v4 region as well...
High viral transmission in the COVID-19 pandemic has enabled SARS-CoV-2 to acquire new mutations that may impact genome sequencing methods. The ARTIC.v3 primer pool amplifies short amplicons a multiplex-PCR reaction is one of most widely used methods for genome. We observed some genomic intervals are poorly captured with ARTIC primers. To improve coverage and variant detection across these intervals, we designed long amplicon primers evaluated performance (ARTIC) plus (MRL) approach....
Abstract DNA extraction methods play an important role in the acquisition of accurate and reproducible 16S sequencing data microbiome studies. In this study, we assessed impact bead-beating intensity during on recovery mouse human stool. We observed a higher yield, better integrity, Shannon’s entropy Simpson’s index samples beaten for 4 9 minutes as compared to unbeaten samples. showed that bead beating has statistically-significant (p<0.05) many clinically relevant microbes live gut,...
<title>Abstract</title> Background. Young children have frequent viral/bacterial infections and antibiotic exposures. Whether these events promote translocation of bacterial factors from oral cavity into the bloodstream remains poorly studied. Method. We performed 16S sequencing immune profiling blood in 210 healthy 1–2-year age range. Observed DNA signatures were analyzed context host cytokine antibody responses. Results. About 12% toddlers showed a signature related to commensals...
Abstract High viral transmission in the COVID-19 pandemic has enabled SARS-CoV-2 to acquire new mutations that impact genome sequencing methods. The ARTIC.v3 primer pool amplifies short amplicons a multiplex-PCR reaction is one of most widely used methods for genome. We observed some genomic intervals are poorly captured with ARTIC primers. To improve coverage and variant detection across these intervals, we designed long amplicon primers evaluated performance (ARTIC) plus (MRL) approach....