A5025670930- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Bacteriophages and microbial interactions
- Clostridium difficile and Clostridium perfringens research
- Viral gastroenteritis research and epidemiology
- Engineering and Environmental Studies
- Toxin Mechanisms and Immunotoxins
- CRISPR and Genetic Engineering
- Animal Disease Management and Epidemiology
- Ichthyology and Marine Biology
- Coal and Coke Industries Research
- Identification and Quantification in Food
- Biochemical Analysis and Sensing Techniques
- Genetics, Bioinformatics, and Biomedical Research
- Transgenic Plants and Applications
- Respiratory viral infections research
- Scientific Computing and Data Management
- Vibrio bacteria research studies
- Arctic and Russian Policy Studies
- Biomedical and Engineering Education
- Distributed and Parallel Computing Systems
- Plant Virus Research Studies
San Diego State University
2017-2020
The approximately 1011 viruses and microbial cells per gram of fecal matter (dry weight) in the large intestine are important to human health. responses three common gut bacteria species, one opportunistic pathogen, 117 commonly consumed foods, chemical additives, plant extracts were tested. Many compounds, including Stevia rebaudiana bee propolis extracts, exhibited species-specific growth inhibition by prophage induction. Overall, these results show that various foods may change abundances...
Diversity-generating retroelements (DGRs) are genetic cassettes that selectively mutate target genes to produce hypervariable proteins. First characterized in Bordetella bacteriophage BPP-1, the DGR creates a phage tail fiber enables host tropism switching. Subsequent surveys for DGRs conclude majority identified date bacterial or archaeal origin. This work examines and genomes novel phage-encoded DGRs. survey discovered 92 were only found phages exhibiting temperate lifestyle. The of as...
The Sequence Read Archive (SRA), the world's largest database of sequences, hosts approximately 10 petabases (1016 bp) sequence data and is growing at alarming rate TB per day. Yet this rich trove inaccessible to most researchers: searching through SRA requires large storage computing facilities that are beyond capacity laboratories. Enabling scientists analyze existing will provide insight into ecology, medicine, industrial applications. In project we specifically focus on metagenomic...
The common thresher shark (Alopias vulpinus) is an important fisheries species in the northeastern Pacific Ocean along California, USA and Mexico; yet genetic understanding of this incomplete. Using IonTorrent PGM generated metagenomic libraries constructed from skin surface, we recovered complete mitogenome shark. length was 16,712 basepairs consisted 22 tRNA, two rRNA, 13 protein coding sequences, a replication origin control region, similar to other Alopias spp. median coverage across 21...
Microbiomes are vast communities of microbes and viruses that populate all natural ecosystems. Viruses have been considered the most variable component microbiomes, as supported by virome surveys examples high genomic mosaicism. However, recent evidence suggests human gut is remarkably stable compared to other environments. Here we investigate origin, evolution, epidemiology crAssphage, a widespread virus. Through global collaboratory, obtained DNA sequences crAssphage from over one-third...
A wealth of viral data sits untapped in publicly available metagenomic sets when it might be extracted to create a usable index for the virological research community. We hypothesized that work this complexity and scale could done hackathon setting. Ten teams comprised over 40 participants from six countries, assembled crowd-sourced set analysis processing pipelines complex biological three-day event on San Diego State University campus starting 9 January 2019. Prior hackathon, 141,676...
Many commensal bacteria antagonize each other or their host by producing syringe-like secretion systems called contractile injection (CIS). Members of the Bacteroidales family have been shown to produce only one type CIS-a contact-dependent 6 system that mediates bacterium-bacterium interactions. Here, we show a second distinct cluster genes from human microbiome may encode yet-uncharacterized term (BIS). We found BIS are present in gut microbiomes 99% individuals United States and Europe...
ABSTRACT An imbalance of normal bacterial groups such as Bacteroidales within the human gut is correlated with diseases like obesity. A current grand challenge in microbiome field to identify factors produced by bacteria that cause these observed health and disease correlations. While identifying a injection system could provide missing explanation for why correlates host health, no factor has been identified date. The lack knowledge about significant barrier improving therapies fecal...