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Jack A. Gilbert
University of California, San Diego
MicrobiomeMetagenomicsEcologyGeneticsBiology
514Publications
67H-index
20.2kCitations
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Publications 442
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#1Alexander Zaborin (U of C: University of Chicago)H-Index: 15
#2Beatriz Penalver Bernabe (UIC: University of Illinois at Chicago)
Last. John C. Alverdy (U of C: University of Chicago)H-Index: 51
view all 9 authors...
ABSTRACT The cecum is a unique region in the mammalian intestinal tract in which the microbiome is localized to two compartments, the lumen and the crypts. The microbiome within crypts is particularly important as it is in direct contact with lining epithelial cells including stem cells. Here, we analyzed the microbiome in cecum of mice using multiple techniques including metagenomics. The lumen microbiome comprised Firmicutes and Bacteroidetes whereas the crypts were dominated by Proteobacteria...
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#1Bin Ma (ZJU: Zhejiang University)H-Index: 16
#2Yiling Wang (ZJU: Zhejiang University)
Last. Cesar Cardona (U of C: University of Chicago)H-Index: 10
view all 12 authors...
Microbial interactions shape the structure and function of microbial communities; microbial co-occurrence networks in specific environments have been widely developed to explore these complex systems, but their interconnection pattern across microbiomes in various environments at the global scale remains unexplored. Here, we have inferred an Earth microbial co-occurrence network from a communal catalog with 23,595 samples and 12,646 exact sequence variants from 14 environments in the Earth Micro...
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#1Jarrad T. Hampton-Marcell (UIC: University of Illinois at Chicago)H-Index: 12
#2Peter E. Larsen (Argonne National Laboratory)H-Index: 18
Last. George Duncan (NSU: Nova Southeastern University)H-Index: 12
view all 12 authors...
Abstract When mapped to the environments we interact with on a daily basis, the 36 million microbial cells per hour that humans emit leave a trail of evidence that can be leveraged for forensic analysis. We employed 16S rRNA amplicon sequencing to map unique microbial sequence variants between human skin and building surfaces in three experimental conditions: over time during controlled and uncontrolled incidental interactions with a door handle, and during multiple mock burglaries in ten real r...
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#1Sean P. Polster (U of C: University of Chicago)H-Index: 6
#2Anukriti Sharma (UCSD: University of California, San Diego)H-Index: 9
Last. Dongdong Zhang (U of C: University of Chicago)H-Index: 2
view all 26 authors...
Cavernous angiomas (CA) are common vascular anomalies causing brain hemorrhage. Based on mouse studies, roles of gram-negative bacteria and altered intestinal homeostasis have been implicated in CA pathogenesis, and pilot study had suggested potential microbiome differences between non-CA and CA individuals based on 16S rRNA gene sequencing. We here assess microbiome differences in a larger cohort of human subjects with and without CA, and among subjects with different clinical features, and con...
1 CitationsSource
#1Jeremiah J. Minich (UCSD: University of California, San Diego)H-Index: 5
#2Farhana Ali (UCSD: University of California, San Diego)H-Index: 1
Last. Rob Knight (UCSD: University of California, San Diego)H-Index: 150
view all 12 authors...
To control the growing COVID-19 pandemic, increased testing and containment is essential, yet clinical-grade sampling supplies are expensive and rapidly being depleted. We demonstrate the feasibility of using alternative consumer-grade swabs stored in 95% ethanol rather than viral transport media to detect SARS-CoV-2 from ten hospitalized persons and hospital rooms.
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#1Sangman M. Kim (U of C: University of Chicago)H-Index: 5
#2Jennifer R. DeFazio (U of C: University of Chicago)
Last. Katharine G. Harris (U of C: University of Chicago)H-Index: 2
view all 25 authors...
Death due to sepsis remains a persistent threat to critically ill patients confined to the intensive care unit and is characterized by colonization with multi-drug-resistant healthcare-associated pathogens. Here we report that sepsis in mice caused by a defined four-member pathogen community isolated from a patient with lethal sepsis is associated with the systemic suppression of key elements of the host transcriptome required for pathogen clearance and decreased butyrate expression. More specif...
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#1Samira Shojaee (MCV: VCU Medical Center)H-Index: 2
#1Samira Shojaee (MCV: VCU Medical Center)H-Index: 5
Last. Najib M. Rahman (University of Oxford)H-Index: 29
view all 6 authors...
INTRODUCTION: There is ongoing research into the development of novel molecular markers that may complement fluid cytology malignant pleural effusion (MPE) diagnosis. In this exploratory pilot study, we hypothesized that there are distinct differences in the pleural fluid microbiome profile of malignant and non-malignant pleural diseases. METHOD: From a prospectively enrolled pleural fluid biorepository, samples of MPE were included. Non-MPE effusion were included as comparators. 16S rRNA gene V...
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#1Beatriz Penalver Bernabe (UIC: University of Illinois at Chicago)
#2Shannon Dowty (UIC: University of Illinois at Chicago)
Last. Jack A. Gilbert (UCSD: University of California, San Diego)H-Index: 67
view all 9 authors...
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#1Sanjiv Hyoju (U of C: University of Chicago)H-Index: 5
#2C. Adriaansens (U of C: University of Chicago)H-Index: 1
Last. John C. Alverdy (U of C: University of Chicago)H-Index: 51
view all 14 authors...
BACKGROUND: Both obesity and the presence of collagenolytic bacterial strains (Enterococcus faecalis) can increase the risk of anastomotic leak. The aim of this study was to determine whether mice chronically fed a high-fat Western-type diet (WD) develop anastomotic leak in association with altered microbiota, and whether this can be mitigated by a short course of standard chow diet (SD; low fat/high fibre) before surgery. METHODS: Male C57BL/6 mice were assigned to either SD or an obesogenic WD...
2 CitationsSource
#1Beatriz Peñalver Bernabé (UCSD: University of California, San Diego)H-Index: 9
#2Hannah S. Rackers (UNC: University of North Carolina at Chapel Hill)H-Index: 1
Last. Jack A. Gilbert (UCSD: University of California, San Diego)H-Index: 67
view all 11 authors...
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