Cecilia Noecker
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View article: Microbiome Single Cell Atlases Generated with a Commercial Instrument
Microbiome Single Cell Atlases Generated with a Commercial Instrument Open
Single‐cell sequencing is useful for resolving complex systems into their composite cell types and computationally mining them for unique features that are masked in pooled sequencing. However, while commercial instruments have made single…
View article: Expansion of a bacterial operon during cancer treatment ameliorates fluoropyrimidine toxicity
Expansion of a bacterial operon during cancer treatment ameliorates fluoropyrimidine toxicity Open
Dose-limiting toxicities remain a major barrier to drug development and therapy, revealing the limited predictive power of human genetics. Here, we demonstrate the utility of a more comprehensive approach to studying drug toxicity through …
View article: Coordinated variation in the immune systems and microbiomes of healthy humans is linked to tonic interferon states
Coordinated variation in the immune systems and microbiomes of healthy humans is linked to tonic interferon states Open
Human immune systems are highly variable, with most variation attributable to non-genetic sources. The gut microbiome crucially shapes the immune system; however, its relationship with the baseline immune states of healthy humans remains i…
View article: Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity
Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity Open
Dose-limiting toxicities remain a major barrier to drug development and therapy, revealing the limited predictive power of human genetics. Herein, we demonstrate the utility of a more comprehensive approach to studying drug toxicity throug…
View article: Simvastatin induces human gut bacterial cell surface genes
Simvastatin induces human gut bacterial cell surface genes Open
Drugs intended to target mammalian cells can have broad off‐target effects on the human gut microbiota with potential downstream consequences for drug efficacy and side effect profiles. Yet, despite a rich literature on antibiotic resistan…
View article: Microbiome single cell atlases generated with a commercial instrument
Microbiome single cell atlases generated with a commercial instrument Open
Single cell sequencing is useful for resolving complex systems into their composite cell types and computationally mining them for unique features that are masked in pooled sequencing. However, while commercial instruments have made single…
View article: Main Manuscript for Microbiome single cell atlases generated with a benchtop instrument
Main Manuscript for Microbiome single cell atlases generated with a benchtop instrument Open
Single cell sequencing is useful for resolving complex systems into their composite cell types and computationally mining them for unique features that are masked in pooled sequencing. However, while commercial instruments have made single…
View article: Mild SARS-CoV-2 infection results in long-lasting microbiota instability
Mild SARS-CoV-2 infection results in long-lasting microbiota instability Open
Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of severe acute respiratory syndrome cor…
View article: Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta
Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta Open
Human gut bacteria perform diverse metabolic functions with consequences for host health. The prevalent and disease-linked Actinobacterium Eggerthella lenta performs several unusual chemical transformations, but it does not metabolize suga…
View article: Processed data to regenerate figures in Noecker et al, "Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta"
Processed data to regenerate figures in Noecker et al, "Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta" Open
This archive contains the processed source data for the publication by Noecker et al, "Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta" (2023, in review). Data tables un…
View article: Processed data to regenerate figures in Noecker et al, "Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta"
Processed data to regenerate figures in Noecker et al, "Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta" Open
This archive contains the processed source data for the publication by Noecker et al, "Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta" (2023, in review). Data tables un…
View article: Processed data to regenerate figures in Noecker et al, "Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta"
Processed data to regenerate figures in Noecker et al, "Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta" Open
This archive contains the processed source data for the publication by Noecker et al, "Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta" (2023, in review). Data tables un…
View article: Genetic manipulation of the human gut bacterium Eggerthella lenta reveals a widespread family of transcriptional regulators
Genetic manipulation of the human gut bacterium Eggerthella lenta reveals a widespread family of transcriptional regulators Open
View article: Mild SARS-CoV-2 infection results in long-lasting microbiota instability
Mild SARS-CoV-2 infection results in long-lasting microbiota instability Open
Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of SARS-CoV-2 infection that require hos…
View article: Systems biology illuminates alternative metabolic niches in the human gut microbiome
Systems biology illuminates alternative metabolic niches in the human gut microbiome Open
SUMMARY Human gut bacteria perform diverse metabolic functions with consequences for host health. The prevalent and disease-linked Actinobacterium Eggerthella lenta performs several unusual chemical transformations, but it does not metabol…
View article: MIMOSA2: a metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data
MIMOSA2: a metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data Open
Motivation Recent technological developments have facilitated an expansion of microbiome–metabolome studies, in which samples are assayed using both genomic and metabolomic technologies to characterize the abundances of microbial taxa and …
View article: The East Asian gut microbiome is distinct from colocalized White subjects and connected to metabolic health
The East Asian gut microbiome is distinct from colocalized White subjects and connected to metabolic health Open
East Asians (EAs) experience worse metabolic health outcomes compared to other ethnic groups at lower body mass indices; however, the potential role of the gut microbiota in contributing to these health disparities remains unknown. We cond…
View article: Author response: The East Asian gut microbiome is distinct from colocalized White subjects and connected to metabolic health
Author response: The East Asian gut microbiome is distinct from colocalized White subjects and connected to metabolic health Open
Article Figures and data Abstract eLife digest Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract East Asians (EAs) experience …
View article: MIMOSA2: A metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data
MIMOSA2: A metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data Open
Motivation Recent technological developments have facilitated an expansion of microbiome-metabolome studies, in which a set of microbiome samples are assayed using both genomic and metabolomic technologies to characterize the composition o…
View article: Differences in the gut microbiomes of distinct ethnicities within the same geographic area are linked to host metabolic health
Differences in the gut microbiomes of distinct ethnicities within the same geographic area are linked to host metabolic health Open
Background: The human gut microbiota exhibits marked variation around the world, which has been attributed to dietary intake and other environmental factors. However, the degree to which ethnicity-associated differences in gut microbial co…
View article: Dissecting the contribution of host genetics and the microbiome in complex behaviors
Dissecting the contribution of host genetics and the microbiome in complex behaviors Open
View article: Differences in the gut microbiomes of distinct ethnicities within the same geographic area are linked to host metabolic health
Differences in the gut microbiomes of distinct ethnicities within the same geographic area are linked to host metabolic health Open
Background The human gut microbiota exhibits marked variation around the world, which has been attributed to dietary intake and other environmental factors. However, the degree to which ethnicity-associated differences in gut microbial com…
View article: Patterns of salivary microbiota injury and oral mucositis in recipients of allogeneic hematopoietic stem cell transplantation
Patterns of salivary microbiota injury and oral mucositis in recipients of allogeneic hematopoietic stem cell transplantation Open
Oral mucositis (OM) is a common debilitating dose-limiting toxicity of cancer treatment, including hematopoietic stem cell transplantation (HSCT). We hypothesized that the oral microbiome is disturbed during allogeneic HSCT, partially acco…
View article: A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria
A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria Open
View article: Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies
Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies Open
Identifying the key microbial taxa responsible for metabolic differences between microbiomes is an important step toward understanding and manipulating microbiome metabolism. To achieve this goal, researchers commonly conduct microbiome-me…
View article: Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice
Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice Open
View article: Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies
Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies Open
Correlation-based analysis of paired microbiome-metabolome datasets is becoming a widespread research approach, aiming to comprehensively identify microbial drivers of metabolic variation. To date, however, the limitations of this approach…
View article: The Skin Microbiome of the Neotropical Frog Craugastor fitzingeri: Inferring Potential Bacterial-Host-Pathogen Interactions From Metagenomic Data
The Skin Microbiome of the Neotropical Frog Craugastor fitzingeri: Inferring Potential Bacterial-Host-Pathogen Interactions From Metagenomic Data Open
Skin symbiotic bacteria on amphibians can play a role in protecting their host against pathogens. Chytridiomycosis, the disease caused by Batrachochytrium dendrobatidis, Bd, has caused dramatic population declines and extinctions of…
View article: BURRITO: An Interactive Multi-Omic Tool for Visualizing Taxa–Function Relationships in Microbiome Data
BURRITO: An Interactive Multi-Omic Tool for Visualizing Taxa–Function Relationships in Microbiome Data Open
The abundance of both taxonomic groups and gene categories in microbiome samples can now be easily assayed via various sequencing technologies, and visualized using a variety of software tools. However, the assemblage of taxa in the microb…
View article: BURRITO: An interactive multi-omic tool for visualizing taxa-function relationships in microbiome data
BURRITO: An interactive multi-omic tool for visualizing taxa-function relationships in microbiome data Open
The abundance of both taxonomic groups and gene categories in microbiome samples can now be easily assayed via various sequencing technologies, and visualized using a variety of software tools. However, the assemblage of taxa in the microb…