David Zeevi

David Zeevi
The Rockefeller University | Rockefeller · Center for Studies in Physics and Biology

PhD

About

26
Publications
24,615
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7,435
Citations

Publications

Publications (26)
Article
Animals in the wild are able to subsist on pathogen-infected and poisonous food and show immunity to various diseases. These may be due to their microbiota, yet we have a poor understanding of animal microbial diversity and function. We used metagenomics to analyze the gut microbiota of over 180 species in the wild, covering diverse classes, feedin...
Article
Full-text available
The serum metabolome contains a plethora of biomarkers and causative agents of various diseases, some of which are endogenously produced and some that have been taken up from the environment¹. The origins of specific compounds are known, including metabolites that are highly heritable2,3, or those that are influenced by the gut microbiome⁴, by life...
Article
Nutrient limitation drives competition for resources across organisms. However, much is unknown about how selective pressures resulting from nutrient limitation shape microbial coding sequences. Here, we study this “resource-driven selection” by using metagenomic and single-cell data of marine microbes, alongside environmental measurements. We show...
Preprint
Ocean microbes are responsible for about 50% of primary production on Earth, but selective forces governing their evolution are not well understood. We studied evolutionary conservation by examining single-nucleotide variants in the marine environment, and discovered strong purifying selection exerted across marine microbial genes. We show evidence...
Article
Full-text available
Differences in the presence of even a few genes between otherwise identical bacterial strains may result in critical phenotypic differences. Here we systematically identify microbial genomic structural variants (SVs) and find them to be prevalent in the human gut microbiome across phyla and to replicate in different cohorts. SVs are enriched for CR...
Article
Probiotics are widely prescribed for prevention of antibiotics-associated dysbiosis and related adverse effects. However, probiotic impact on post-antibiotic reconstitution of the gut mucosal host-microbiome niche remains elusive. We invasively examined the effects of multi-strain probiotics or autologous fecal microbiome transplantation (aFMT) on...
Article
Full-text available
Human gut microbiome composition is shaped by multiple factors but the relative contribution of host genetics remains elusive. Here we examine genotype and microbiome data from 1,046 healthy individuals with several distinct ancestral origins who share a relatively common environment, and demonstrate that the gut microbiome is not significantly ass...
Preprint
Human gut microbiome composition is shaped by multiple host intrinsic and extrinsic factors, but the relative contribution of host genetic compared to environmental factors remains elusive. Here, we genotyped a cohort of 696 healthy individuals from several distinct ancestral origins and a relatively common environment, and demonstrate that there i...
Article
Bread is consumed daily by billions of people, yet evidence regarding its clinical effects is contradicting. Here, we performed a randomized crossover trial of two 1-week-long dietary interventions comprising consumption of either traditionally made sourdough-leavened whole-grain bread or industrially made white bread. We found no significant diffe...
Article
Full-text available
A report on the first EMBO conference entitled "Next Gen Immunology-From Host Genome to the Microbiome: Immunity in the Genomic Era", held at the Weizmann Institute of Science, Israel, 14-16 February, 2016.
Article
The intestinal microbiota undergoes diurnal compositional and functional oscillations that affect metabolic homeostasis, but the mechanisms by which the rhythmic microbiota influences host circadian activity remain elusive. Using integrated multi-omics and imaging approaches, we demonstrate that the gut microbiota features oscillating biogeographic...
Article
The genomic revolution enabled the clinical inclusion of an immense body of person-specific information to an extent that is revolutionizing medicine and science. The gut microbiome, our "second genome," dynamically integrates signals from the host and its environment, impacting health and risk of disease. Herein, we summarize how individualized ch...
Article
Full-text available
Life on Earth is dictated by circadian changes in the environment, caused by the planet's rotation around its own axis. All forms of life have evolved clock systems to adapt their physiology to the daily variations in geophysical parameters. The intestinal microbiome serves as a signaling hub in the communication between the host and its environmen...
Article
Familial dysautonomia (FD) is a severe neurodegenerative genetic disorder restricted to the Ashkenazi Jewish population. The most common mutation in FD patients is a T-to-C transition at position 6 of intron 20 of the IKBKAP gene. This mutation causes aberrant skipping of exon 20 in a tissue-specific manner, leading to reduction of the IκB kinase c...
Article
Full-text available
Bacterial genes are commonly encoded in clusters, known as operons, which share transcriptional regulatory control and often encode functionally related proteins that take part in certain biological pathways. Operons that are coregulated are known to colocalize in the genome, suggesting that their spatial organization is under selection for efficie...
Data
Primers used for validation of microarray results. Primers forward and reverse used for validation by QPCR of 11 genes from the microarray analysis. (DOC)
Data
PS effect on IKAP mRNA levels in FDD cell line. FDD cells were treated with 0, 5, 10, 100, 200 and 300 µg/ml PS. RNA was extracted after 24 hr (A) and 48 hr (B). Left side: QPCR analysis of the level of exon 20 inclusion isoform (wt). Data were normalized to levels in untreated control cells. Right side: RT‐PCR analysis of the splicing of the endog...
Data
Complete Gene Ontology enrichment for up‐regulated genes. Continued from Table 1. GO analysis for up‐regulated genes revealed by microarray analysis following PS treatment of FDB cells. Enriched categories were identified using DAVID to cluster differentially genes into functional categories using GO identification terms. Significant GO enrichment...
Data
Genes up‐ and down‐regulated after PS treatment in FD cells. Gene expression microarray analysis was performed on cDNA samples from FDB cells treated with PS; data were compared to that from FDB cells treated with the solvent only. All 441 up‐regulated genes and 436 down‐regulated genes identified by significant analysis of microarray (SAM) are lis...
Article
Full-text available
Familial Dysautonomia (FD) is an autosomal recessive congenital neuropathy that results from abnormal development and progressive degeneration of the sensory and autonomic nervous system. The mutation observed in almost all FD patients is a point mutation at position 6 of intron 20 of the IKBKAP gene; this gene encodes the IκB kinase complex-associ...

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