Accès ouvert
2026
article
OpenAlex
Ioannis Ntekas, Lena Takayasu, David W. McKellar, Benjamin Grodner et autres
Intermicrobial and host-microbial interactions are critical for the functioning of the gut microbiome, but few tools are available to measure these interactions in situ. Here we report a method for broad spatial sampling of microbiome-host interactions in the gut at high resolution …
us
(code pays fourni par la source)
Accès ouvert
2025
article
OpenAlex
Joshua P. Jones, Karla Yvonne García-Martínez, Yi-Yuan Lee, Rahul R. Nath et autres
Macrophages serve as sentinels at the intestinal surface, responding to organismal cues to drive proinflammatory or tolerogenic responses. To date, studies of combinations of these cues do not fully capture the heterogeneity of macrophage responses. To address this gap, we performed multiplexed …
us
(code pays fourni par la source)
Accès ouvert
2024
preprint
OpenAlex
Ioannis Ntekas, Lena Takayasu, David W. McKellar, Benjamin Grodner et autres
ABSTRACT Inter-microbial and host–microbial interactions are thought to be critical for the functioning of the gut microbiome, but few tools are available to measure these interactions. Here, we report a method for unbiased spatial sampling of microbiome-host interactions in the gut at …
us
(code pays fourni par la source)
Accès ouvert
2024
preprint
OpenAlex
Benjamin Grodner, David T. Wu, Sumin Hahm, Lena Takayasu et autres
Microbiome dysbiosis has largely been defined using compositional analysis of metagenomic sequencing data; however, differences in the spatial arrangement of bacteria between healthy and diseased microbiomes remain largely unexplored. In this study, we measured the spatial arrangement of bacteria in dental implant …
us
(code pays fourni par la source)
Accès ouvert
2024
article
OpenAlex
Benjamin Grodner, Hao Shi, Owen Farchione, Albert C. Vill et autres
The exchange of mobile genetic elements (MGEs) facilitates the spread of functional traits including antimicrobial resistance within bacterial communities. Tools to spatially map MGEs and identify their bacterial hosts in complex microbial communities are currently lacking, limiting our understanding of this process. …
us
(code pays fourni par la source)
Accès ouvert
2023
preprint
OpenAlex
Benjamin Grodner, Hao Shi, Owen Farchione, Albert C. Vill et autres
The frequent exchange of mobile genetic elements (MGEs) between bacteria accelerates the spread of functional traits, including antimicrobial resistance, within the human microbiome. Yet, progress in understanding these intricate processes has been hindered by the lack of tools to map the spatial …
us
(code pays fourni par la source)
Accès ouvert
2023
dataset
OpenAlex
Benjamin Grodner, Hao Shi, Owen Farchione, Albert C. Vill et autres
We used Escherichia coli transformed with pJKR-H-tetR plasmids encoding an inducible GFP gene as a model system to assess and optimize MGE-FISH on a confocal microscope. We designed FISH probes for the non-coding strand of the GFP gene, used non-transformed E. coli …
us
(code pays fourni par la source)
Accès ouvert
2023
dataset
OpenAlex
Benjamin Grodner, Hao Shi, Owen Farchione, Albert C. Vill et autres
We stained for the GFP gene in samples that contained mixtures of plaque and GFP-transformed E. coli. We mapped mefE, an AMR gene located on a plasmid and encoding an antibiotic efflux pump, in the plaque metagenomic data of volunteer A but …
us
(code pays fourni par la source)
Accès ouvert
2023
dataset
OpenAlex
Benjamin Grodner, Hao Shi, Owen Farchione, Albert C. Vill et autres
We staged infections at four multiplicities of infection (MOI 0, 0.01, 0.1, and 1), and took snapshots every ten minutes over a 40-minute period. We designed FISH probes targeting the non-coding strand of the gp34 gene, which encodes a tail fiber protein …
us
(code pays fourni par la source)
Accès ouvert
2023
dataset
OpenAlex
Benjamin Grodner, Hao Shi, Owen Farchione, Albert C. Vill et autres
We used rRNA FISH to stain five common oral genera, Veillonella, Streptococcus, Corynebacterium, Lautropia, and Neisseria, each with a different fluorophore, and we used MGE-FISH to stain the termL gene of an active prophage with a sixth fluorophore. We chose a target …
us
(code pays fourni par la source)
Accès ouvert
2023
dataset
OpenAlex
Benjamin Grodner, Hao Shi, Owen Farchione, Albert C. Vill et autres
We used rRNA FISH to stain five common oral genera, Veillonella, Streptococcus, Corynebacterium, Lautropia, and Neisseria, each with a different fluorophore, and we used MGE-FISH to stain the termL gene of an active prophage with a sixth fluorophore. We chose a target …
us
(code pays fourni par la source)
Accès ouvert
2023
dataset
OpenAlex
Benjamin Grodner, Hao Shi, Owen Farchione, Albert C. Vill et autres
We staged infections at four multiplicities of infection (MOI 0, 0.01, 0.1, and 1), and took snapshots every ten minutes over a 40-minute period. We designed FISH probes targeting the non-coding strand of the gp34 gene, which encodes a tail fiber protein …
us
(code pays fourni par la source)