A5069073018- Gut microbiota and health
- Plant and animal studies
- Insect and Arachnid Ecology and Behavior
- Insect symbiosis and bacterial influences
- Insect and Pesticide Research
- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Clostridium difficile and Clostridium perfringens research
- Probiotics and Fermented Foods
- Insect-Plant Interactions and Control
- Metabolomics and Mass Spectrometry Studies
- Epigenetics and DNA Methylation
- Nutritional Studies and Diet
- Diet and metabolism studies
- Food Security and Health in Diverse Populations
- Marine Biology and Ecology Research
- Molecular Biology Techniques and Applications
- Forest Insect Ecology and Management
- Insect behavior and control techniques
- Botany and Plant Ecology Studies
- Colorectal Cancer Screening and Detection
- Plant Parasitism and Resistance
- Microbial Natural Products and Biosynthesis
- Helicobacter pylori-related gastroenterology studies
- Research on scale insects
Cornell University
2019-2025
University of California, San Diego
2016-2025
University of Wisconsin–Extension
2024
University of Vermont
2024
Harvard University
2009-2021
Beijing Normal University
2021
George Washington University
2021
State Key Laboratory of Earth Surface Processes and Resource Ecology
2021
Drexel University
2021
La Jolla Bioengineering Institute
2020
Abstract Microbial genomes are available at an ever-increasing pace, as cultivation and sequencing become cheaper obtaining metagenome-assembled (MAGs) becomes more effective. Phylogenetic placement methods to contextualize hundreds of thousands must thus be efficiently scalable sensitive from closely related strains divergent phyla. We present PhyloPhlAn 3.0, accurate, rapid, easy-to-use method for large-scale microbial genome characterization phylogenetic analysis multiple levels...
The immune system responds vigorously to microbial infection while permitting lifelong colonization by the microbiome. Mechanisms that facilitate establishment and stability of gut microbiota remain poorly described. We found a regulatory in prominent human commensal Bacteroides fragilis modulates its surface architecture invite binding immunoglobulin A (IgA) mice. Specific recognition facilitated bacterial adherence cultured intestinal epithelial cells intimate association with mucosal...
Abstract Whether mammal–microbiome interactions are persistent and specific over evolutionary time is controversial. Here we show that host phylogeny major dietary shifts have affected the distribution of different gut bacterial lineages did so on vastly phylogenetic resolutions. Diet mostly influences acquisition ancient large microbial lineages. Conversely, correlation with seen among more recently diverged lineages, consistent processes operating at similar timescales to evolution....
Recent studies increasingly note the effect of captivity or built environment on microbiome humans and other animals. As symbiotic microbes are essential to many aspects biology (e.g., digestive immune functions), it is important understand how lifestyle differences can impact microbiome, and, consequently, health hosts. Animals living in experience a range changes that may influence gut bacteria, such as diet changes, treatments, reduced contact with individuals, species variable...
Massively parallel DNA sequencing offers many benefits, but major inhibitory cost factors include: (1) start-up (i.e., purchasing initial reagents and equipment); (2) buy-in getting the smallest possible amount of data from a run); (3) sample preparation. Reducing preparation costs is commonly addressed, are rarely addressed. We present dual-indexing systems to address all three these issues. By breaking library construction process into universal, re-usable, combinatorial components, we...
In this comprehensive survey of microbiomes >900 species, including 315 mammals and 491 birds, we find a striking convergence the birds animals that fly. nonflying mammals, diet short-term evolutionary relatedness drive microbiome, many microbial species are specific to particular kind mammal, but flying break pattern with microbes shared across different little correlation either or hosts. This finding suggests adaptation flight breaks long-held relationships between hosts their microbes.
Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution individual genes. Here we build a reference phylogeny 10,575 evenly-sampled bacterial and archaeal genomes, based on comprehensive set 381 markers, using multiple strategies. Our trees indicate remarkably closer proximity between Archaea Bacteria than previous estimates that were limited to fewer "core" genes, such as ribosomal proteins. The...
Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the taxa that differentiate these can be challenging. These issues stem compositional nature of 16S rRNA gene data (or, more generally, taxon or functional data); changes relative abundance one influence apparent abundances others. Here we acknowledge inferring properties...
Abstract Correlation between gut microbiota and host phylogeny could reflect codiversification over shared evolutionary history or a selective environment that is more similar in related hosts. These alternatives imply substantial differences the relationship symbiont, but can they be distinguished based on patterns community data themselves? We explored of phylogenetic correlation distribution bacteria among species turtle ants (genus C ephalotes ), which dense microbial community. used 16...
Shotgun sequencing of microbial communities provides in-depth knowledge the microbiome by cataloging bacterial, fungal, and viral gene content within a sample, providing an advantage over amplicon approaches that assess taxonomy but not function are taxonomically limited. However, mammalian DNA can dominate host-derived samples, obscuring changes in populations because few sequence reads from component. We developed optimized novel method for enriching human oral samples compared its...
Abstract Mammals host gut microbiomes of immense physiological consequence, but the determinants diversity in these communities remain poorly understood. Diet appears to be dominant factor, phylogeny also seems an important, if unpredictable, correlate. Here we show that baleen whales, which prey on animals (fish and crustaceans), harbor unique with surprising parallels functional capacity higher level taxonomy those terrestrial herbivores. These similarities likely reflect a shared role for...
Microbial sequences inferred as belonging to one sample may not have originated from that sample. Such contamination arise laboratory or reagent sources physical exchange between samples. This study seeks rigorously assess the behavior of this often-neglected between-sample contamination. Using unique bacteria, each assigned a particular well in plate, we frequency at which source appear other wells. We evaluate effects different DNA extraction methods performed two laboratories using...
Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure function microbial communities multiple habitats on a planetary scale. Here we present multi-omics analysis diverse set 880 community samples collected for Earth Microbiome Project. We include amplicon (16S, 18S, ITS) shotgun metagenomic sequence data, untargeted metabolomics data (liquid chromatography-tandem mass spectrometry gas chromatography...
Abstract The collection of fecal material and developments in sequencing technologies have enabled standardised non-invasive gut microbiome profiling. Microbiome composition from several large cohorts been cross-sectionally linked to various lifestyle factors diseases. In spite these advances, prospective associations between health remained uncharacterised due the lack sufficiently representative population with comprehensive follow-up data. Here, we analyse long-term association variation...
Invasive species are increasingly prevalent in marine ecosystems worldwide. Although many studies have examined the ecological effects of invasives, little is known about physiological mechanisms that might contribute to invasive success. The mussel Mytilus galloprovincialis, a native Mediterranean Sea, successful invader on central and southern coasts California, where it has largely displaced congener, trossulus. It been previously shown thermal responses several traits may underlie...
Limpets of the genus Lottia occupy a broad vertical distribution on wave-exposed rocky shores, range that encompasses gradients in frequency and severity thermal desiccation stress brought by aerial emersion. Using western blot analysis levels heat-shock protein 70 (Hsp70), we examined responses four congeners: scabra L. austrodigitalis, which occur high-intertidal zone, pelta scutum, are restricted to low- mid-intertidal zones. Our results suggest distinct strategies Hsp70 expression...