Jonathan A. Eisen
A5059066311- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Obsessive-Compulsive Spectrum Disorders
- Gut microbiota and health
- Protist diversity and phylogeny
- Bacteriophages and microbial interactions
- Probiotics and Fermented Foods
- Body Image and Dysmorphia Studies
- Eating Disorders and Behaviors
- Plant Pathogens and Fungal Diseases
- Genetics, Bioinformatics, and Biomedical Research
- Autism Spectrum Disorder Research
- Microbial Metabolism and Applications
- Insect symbiosis and bacterial influences
- Methane Hydrates and Related Phenomena
- Marine and coastal plant biology
- Legume Nitrogen Fixing Symbiosis
- Oral microbiology and periodontitis research
- RNA and protein synthesis mechanisms
- Microbial Natural Products and Biosynthesis
- Metal Extraction and Bioleaching
- Environmental DNA in Biodiversity Studies
- Coral and Marine Ecosystems Studies
- Marine Biology and Ecology Research
- Bacterial Identification and Susceptibility Testing
University of California, Davis
2016-2025
McLean Hospital
2019-2025
Harvard University
1992-2024
University of California Davis Medical Center
2015-2024
Massachusetts General Hospital
2021-2023
University of California System
2022
McGovern Institute for Brain Research
2021
Massachusetts Institute of Technology
2021
University of Oregon
2015-2020
Universidade Federal do Rio de Janeiro
2020
We have applied "whole-genome shotgun sequencing" to microbial populations collected en masse on tangential flow and impact filters from seawater samples the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs nonredundant sequence was generated, annotated, analyzed elucidate gene content, diversity, relative abundance organisms within these environmental samples. These data are estimated derive at least 1800 genomic species based relatedness, including 148 previously unknown...
Significance Land plants continuously contact beneficial, commensal, and pathogenic microbes in soil via their roots. There is limited knowledge as to how the totality of root-associated (i.e., microbiome) shaped by various factors or its pattern acquisition root. Using rice a model, we show that there exist three different root niches hosting microbial communities eubacteria methanogenic archaea. These are affected geographical location, source, host genotype, cultivation practice. Dynamics...
Genome sequencing enhances our understanding of the biological world by providing blueprints for evolutionary and functional diversity that shapes biosphere. However, microbial genomes are currently available limited phylogenetic breadth, owing to historical inability cultivate most microorganisms in laboratory. We apply single-cell genomics target sequence 201 uncultivated archaeal bacterial cells from nine diverse habitats belonging 29 major mostly uncharted branches tree life, so-called...
The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here metagenomic study marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part Sorcerer II Global Ocean Sampling expedition. These samples, collected across several-thousand km transect from North Atlantic through Panama Canal ending South Pacific yielded an extensive dataset consisting 7.7 million...
We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of Minimum Information about Any (x) Sequence (MIxS). The a Single Amplified Genome (MISAG) Metagenome-Assembled (MIMAG), including, but not limited to, assembly quality, estimates completeness contamination. These can be used in combination with other GSC checklists, including (MIGS), Metagenomic (MIMS), Marker Gene (MIMARKS). Community-wide...
Here we determine the complete genomic sequence of Gram negative, γ-Proteobacterium Vibrio cholerae El Tor N16961 to be 4,033,460 base pairs (bp). The genome consists two circular chromosomes 2,961,146 bp and 1,072,314 that together encode 3,885 open reading frames. vast majority recognizable genes for essential cell functions (such as DNA replication, transcription, translation cell-wall biosynthesis) pathogenicity (for example, toxins, surface antigens adhesins) are located on large...
The 2,160,837–base pair genome sequence of an isolate Streptococcus pneumoniae , a Gram-positive pathogen that causes pneumonia, bacteremia, meningitis, and otitis media, contains 2236 predicted coding regions; these, 1440 (64%) were assigned biological role. Approximately 5% the is composed insertion sequences may contribute to rearrangements through uptake foreign DNA. Extracellular enzyme systems for metabolism polysaccharides hexosamines provide substantial source carbon nitrogen S. also...
Summary Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as biosafety host for the cloning of foreign genes. The also considerable potential biotechnological applications. Sequence analysis 6.18 Mb genome strain KT2440 reveals diverse transport and metabolic systems. Although there high level conservation with pathogenic Pseudomonad aeruginosa (85% predicted coding regions are shared), key virulence factors including exotoxin A type III...
The 2,272,351-base pair genome of Neisseria meningitidis strain MC58 (serogroup B), a causative agent meningitis and septicemia, contains 2158 predicted coding regions, 1158 (53.7%) which were assigned biological role. Three major islands horizontal DNA transfer identified; two these contain genes encoding proteins involved in pathogenicity, the third island sequences only for hypothetical proteins. Insights into commensal virulence behavior N. can be gleaned from genome, structural pilus...
The bacterial and archaeal genomes that have been sequenced to date were chosen for sequencing based mainly on their physiology, which is fine but has resulted in a distinct phylogenetic bias. An alternative approach taken the Genomic Encyclopedia of Bacteria Archaea (GEBA) project, advocates choosing organism's position, with aim filling gaps along branches tree life. value this demonstrated by pilot study genome sequences 56 culturable species selected maximize coverage. Analysis provides...
The complete genome sequence of the radiation-resistant bacterium Deinococcus radiodurans R1 is composed two chromosomes (2,648,638 and 412,348 base pairs), a megaplasmid (177,466 small plasmid (45,704 yielding total 3,284,156 pairs. Multiple components distributed on that contribute to ability D. survive under conditions starvation, oxidative stress, high amounts DNA damage were identified. represents an organism in which all systems for repair, export, desiccation starvation recovery,...
OBJECTIVE: The authors sought to observe the long-term clinical course of anxiety disorders over 12 years and examine influence comorbid psychiatric on recovery from or recurrence panic disorder, generalized social phobia. METHOD: Data were drawn Harvard/Brown Anxiety Disorders Research Program, a prospective, naturalistic, longitudinal, multicenter study adults with current past history disorders. Probabilities calculated by using standard survival analysis methods. Proportional hazards...
Recent theories of obsessive-compulsive disorder (OCD) emphasize the importance cognitive contents (beliefs and appraisals) processes in etiology maintenance OCD. In order to evaluate these assess mechanisms treatment-related change, it is necessary develop measures relevant processes. Several scales have been developed, although many are unpublished there a great deal overlap among measures. The purpose present article describe progress an international group investigators who commenced...
The complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical isolate, revealed that more than quarter the consists probable mobile or foreign DNA. One predicted elements is previously unknown vanB vancomycin-resistance conjugative transposon. Three plasmids were identified, including two pheromone-sensing plasmids, one encoding undescribed pheromone inhibitor. apparent propensity for incorporation probably contributed to rapid acquisition and dissemination drug...
Metagenomics projects based on shotgun sequencing of populations micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a comprehensive dataset consisting sequences from available databases together 6.12 million predicted an assembly 7.7 Global Ocean Sampling (GOS) sequences. The GOS covers nearly all known prokaryotic A total 3,995 medium- and large-sized clusters only are identified, out which 1,700 have no detectable homology...
The complete sequence of the 1,267,782 bp genome Wolbachia pipientis wMel, an obligate intracellular bacteria Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety invertebrate species, great interest due to their diverse interactions with different hosts, range from many forms reproductive parasitism mutualistic symbioses. Analysis wMel genome, particular phylogenomic comparisons other bacteria, revealed insights into biology and evolution general. For...
Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities, conferred in part by multicomponent, branched electron transport systems. Here we report the sequencing S. genome, which consists a 4,969,803–base pair circular chromosome with 4,758 predicted protein-encoding open reading frames (CDS) and 161,613–base plasmid 173 CDSs. We identified first lambda-like phage, providing potential tool further genome engineering....
The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists a circular chromosome, linear and two plasmids. Extensive orthology nucleotide colinearity between genomes A. symbiont Sinorhizobium meliloti suggest recent evolutionary divergence. Their similarities include metabolic, transport, regulatory systems that promote survival in highly competitive rhizosphere; differences are apparent their structure virulence gene complement. Availability sequence will...
The cyanobacterial phylum encompasses oxygenic photosynthetic prokaryotes of a great breadth morphologies and ecologies; they play key roles in global carbon nitrogen cycles. chloroplasts all eukaryotes can trace their ancestry to cyanobacteria. Cyanobacteria also attract considerable interest as platforms for "green" biotechnology biofuels. To explore the molecular basis different phenotypes biochemical capabilities, we sequenced genomes 54 phylogenetically phenotypically diverse strains....
The genome sequences of Chlamydia trachomatis mouse pneumonitis (MoPn) strain Nigg (1 069 412 nt) and pneumoniae AR39 229 853 were determined using a random shotgun strategy. MoPn exhibited general conservation gene order content with the previously sequenced C.trachomatis serovar D. Differences between strains focused on an ~50 kb 'plasticity zone' near termination origins. In this region contained three copies novel encoding >3000 amino acid toxin homologous to predicted from Escherichia...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline soma functions that are embodied by distinct nuclei within single cell. germline-like micronucleus (MIC) its genome held in reserve sexual reproduction. soma-like macronucleus (MAC), which possesses processed from of the MIC, center gene expression does not directly contribute DNA to progeny. We report here shotgun sequencing, assembly, analysis...