A5044247683- Oral microbiology and periodontitis research
- Salivary Gland Disorders and Functions
- Gut microbiota and health
- Probiotics and Fermented Foods
- Oral Health Pathology and Treatment
- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Streptococcal Infections and Treatments
- Infective Endocarditis Diagnosis and Management
- Indigenous Studies and Ecology
- Otolaryngology and Infectious Diseases
- Aquatic Ecosystems and Phytoplankton Dynamics
- Microbial infections and disease research
- Environmental DNA in Biodiversity Studies
- Advanced Chemical Sensor Technologies
- Protist diversity and phylogeny
- Bacteriophages and microbial interactions
- Cervical Cancer and HPV Research
- Biocrusts and Microbial Ecology
- Advanced Image Fusion Techniques
- HIV/AIDS oral health manifestations
- Bayesian Methods and Mixture Models
- Cephalopods and Marine Biology
- Coastal wetland ecosystem dynamics
- Algal biology and biofuel production
Marine Biological Laboratory
2014-2024
American Dental Association
2024
Harvard University Press
2022
Texas A&M University
2014
Woods Hole Oceanographic Institution
2014
Harvard University
1998-2004
Significance The physiology and ecology of complex microbial communities are strongly dependent on the immediate surroundings each microbe, including identity neighboring microbes; however, information micron-scale organization microbiomes is largely lacking. Using sequencing data combined with spectral fluorescence imaging, we have discovered a multigenus, highly organized consortium in human dental plaque. spatial structure reveals unanticipated interactions provides framework for...
Significance We demonstrate, to our knowledge for the first time, that bacterial biofilms are associated with colorectal cancers, one of leading malignancies in United States and abroad. Colon biofilms, dense communities bacteria encased a likely complex matrix contact colon epithelial cells, nearly universal on right tumors. Most remarkably, biofilm presence correlates tissue invasion changes biology enhanced cellular proliferation, basic feature oncogenic transformation occurring even...
Microbes in nature frequently function as members of complex multitaxon communities, but the structural organization these communities at micrometer level is poorly understood because limitations labeling and imaging technology. We report here a combinatorial strategy coupled with spectral image acquisition analysis that greatly expands number fluorescent signatures distinguishable single image. As an proof principle, we first demonstrated visualization Escherichia coli labeled by...
The Human Microbiome Project provided a census of bacterial populations in healthy individuals, but an understanding the biomedical significance this has been hindered by limited taxonomic resolution. A high-resolution method termed oligotyping overcomes limitation evaluating individual nucleotide positions using Shannon entropy to identify most information-rich positions, which then define oligotypes. We have applied comprehensively analyze oral microbiome. Using 16S rRNA gene sequence data...
Significance Spatial structure is postulated to have a powerful influence on establishing and sustaining the signaling metabolic exchanges that define relationships among members of gut microbiota host. However, information about community spatial limited. Simultaneous imaging components 15-member model human bacterial over range scales in gnotobiotic mice revealed colon better conceptualized as an incompletely mixed bioreactor, rather than having sharply stratified luminal mucosal...
Abstract Introduction Microbial residents of the human oral cavity have long been a major focus microbiology due to their influence on host health and intriguing patterns site specificity amidst lack dispersal limitation. However, determinants niche partitioning in this habitat are yet be fully understood, especially among taxa that belong recently discovered branches microbial life. Results Here, we assemble metagenomes from tongue dental plaque samples multiple individuals reconstruct 790...
A fundamental question in microbial ecology is how microbes are spatially organized with respect to each other and their host. test bed for examining this the tongue dorsum, which harbors a complex important community. Here, we use multiplexed fluorescence spectral imaging investigate organization of microbiome at micron hundred-micron scales. We design oligonucleotide probes taxa both abundant prevalent, as determined by sequence analysis. Imaging reveals highly structured spatial...
Abstract Plastic marine debris (PMD) affects spatial scales of life from microbes to whales. However, understanding interactions between plastic and in the “Plastisphere”—the thin layer on surface PMD—has been technology‐limited. Research into microbe–microbe microbe–substrate requires knowledge community phylogenetic composition but also tools visualize distributions intact microbial biofilm communities. We developed a CLASI‐FISH (combinatorial labelling spectral imaging – fluorescence situ...
Dental plaque is a bacterial biofilm composed of characteristic set organisms. Relatively little information from cultivation-independent, high-throughput analyses has been published on the temporal dynamics dental microbiome. We used Minimum Entropy Decomposition, an theory-based approach similar to oligotyping that provides single-nucleotide resolution, analyze previously time series data and investigate microbiome at various analytic taxonomic levels. At both genus 97% Operational...
Abstract Background Elucidating the spatial structure of host-associated microbial communities is essential for understanding taxon-taxon interactions within microbiota and between host. Macroalgae are colonized by complex communities, suggesting intimate symbioses that likely play key roles in both macroalgal bacterial biology, yet little known about organization microbes associated with macroalgae. Canopy-forming kelp ecologically significant, fixing teragrams carbon per year coastal...
Abstract Human microbiome composition is closely tied to health, but how the host manages its microbial inhabitants remains unclear. One important, understudied, factor natural environment: mucus, which contains gel-forming glycoproteins (mucins) that display hundreds of glycan structures with potential regulatory function. Leveraging a tractable culture-based system study mucins influence oral communities, we found mucin glycans enable coexistence diverse microbes, while resisting...
Rotifers of class Bdelloidea have evolved for millions years apparently without sexual reproduction. We sequenced 45- to 70-kb regions surrounding the four copies hsp82 gene bdelloid rotifer Philodina roseola, each which is on a separate chromosome. The comprise two colinear gene-rich pairs with content, order, and orientation conserved within pair. Only minority genes are common both pairs, also in same but separated by segments present only one or other pattern consistent degenerate...
Abstract Background The increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. human oral microbiome with its diverse habitats abundant, relatively well-characterized inhabitants presents an opportunity investigate bacterial population structures at ecosystem scale. Results Here, we employ a metapangenomic approach that combines public Human Microbiome Project (HMP) study diversity...
The human mouth is a natural laboratory for studying how bacterial communities differ across habitats. Different bacteria colonize different surfaces in the mouth-teeth, tongue dorsum, and keratinized non-keratinized epithelia-despite short physical distance between these habitats their connection through saliva. We sought to determine whether more tightly defined microhabitats might have sets of resident bacteria. A microhabitat may be characterized, example, as space adjacent particular...
Arabidopsis thaliana KORRIGAN1 (KOR1) is an integral membrane endo-β1,4-glucanase in the trans-Golgi network and plasma that essential for cellulose biosynthesis. The extracellular domain of KOR1 contains eight N-glycosylation sites, N1 to N8, which only N3 N7 are highly conserved. Genetic evidence indicated cellular defects attachment maturation these N-glycans affect function vivo, whereas manner by modulate remained obscure. Site-directed mutagenesis analysis green fluorescent protein...
Understanding the microbial ecology of mouth is fundamental for understanding human physiology. In this study, metapangenomics demonstrated that different Veillonella species have clear ecological preferences in oral cavity healthy humans, validating site specialist hypothesis.
ABSTRACT The human oral microbiome is a diverse ecosystem in which bacterial species have evolved to occupy specific niches within the cavity. Neisseriaceae family, includes genera Neisseria , Eikenella Kingella and Simonsiella plays significant role both commensal pathogenic relationships. In this study, we investigate distribution functional adaptations of across habitats, focusing on their site tropisms ecological roles. We employed metapangenomic approach curated set reference genomes...
DNA sequencing has shown individual bdelloid rotifer genomes to contain two or more diverged copies of every gene examined and revealed no closely similar copies. These other findings are consistent with long-term asexual evolution bdelloids. It is not entirely ruled out, however, that consist previously undetected pairs sequences so as be identical over the regions sequenced, might result if bdelloids were highly inbred sexual diploids polyploids. Here, we employ fluorescent in situ...