Eric J. Alm
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View article: Host transcriptional responses to gut microbiome variation arising from urbanism
Host transcriptional responses to gut microbiome variation arising from urbanism Open
Gut microbiomes of urban communities are compositionally different from their rural counterparts, and are associated with immune dysregulation and gastrointestinal disease. However, it is unknown whether these compositional differences imp…
View article: Convergent genomic responses of human gut bacteria to variations in industrialization
Convergent genomic responses of human gut bacteria to variations in industrialization Open
Summary To what extent gut bacteria respond to the distinct ecological pressures imposed by human lifestyle remains unclear. Here, we investigate how genomic adaptation in gut bacteria differ between industrialized and non-industrialized h…
View article: Industrialization drives convergent microbial and physiological shifts in the human metaorganism
Industrialization drives convergent microbial and physiological shifts in the human metaorganism Open
Summary Understanding how host lifestyle and industrialization shape the human gut microbiome and intestinal physiology requires multimodal analyses across diverse global host contexts. Here, we generate multivariate data from the Global M…
View article: Sparse autoencoders uncover biologically interpretable features in protein language model representations
Sparse autoencoders uncover biologically interpretable features in protein language model representations Open
Foundation models in biology—particularly protein language models (PLMs)—have enabled ground-breaking predictions in protein structure, function, and beyond. However, the “black-box” nature of these representations limits transparency and …
View article: An integrated framework for early detection and transmissibility assessment of emerging variants in wastewater
An integrated framework for early detection and transmissibility assessment of emerging variants in wastewater Open
Tracking the emergence of new SARS-CoV-2 variants is important for a comprehensive understanding of the pandemic's progression. However, it remains challenging due to the low variant prevalence in the early stage of an outbreak. Here, we p…
View article: CRISPR-Cas spacer acquisition is a rare event in human gut microbiome
CRISPR-Cas spacer acquisition is a rare event in human gut microbiome Open
Host-parasite relationships drive the evolution of both parties. In microbe-phage dynamics, CRISPR functions as an adaptive defense mechanism, updating immunity via spacer acquisition. Here, we investigated these interactions within the hu…
View article: Modest functional diversity decline and pronounced composition shifts of microbial communities in a uranium-contaminated aquifer
Modest functional diversity decline and pronounced composition shifts of microbial communities in a uranium-contaminated aquifer Open
Background Microbial taxonomic diversity declines with increased environmental stress. Yet, few studies have explored whether phylogenetic and functional diversities track taxonomic diversity along the stress gradient. Here, we investigate…
View article: Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA): Molecular and Computational Technologies for Environmental Microbiology (Final Scientific/Technical Report)
Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA): Molecular and Computational Technologies for Environmental Microbiology (Final Scientific/Technical Report) Open
The ENIGMA science focus area (SFA) is a multi-disciplinary, multi-institutional research effort focused on addressing foundational knowledge gaps in environmental microbial communities by studying groundwater and sediment microbiomes in t…
View article: Phosphorothioate DNA modification by BREX Type 4 systems in the human gut microbiome
Phosphorothioate DNA modification by BREX Type 4 systems in the human gut microbiome Open
Among dozens of microbial DNA modifications regulating gene expression and host defense, phosphorothioation (PT) is the only known backbone modification, with sulfur inserted at a non-bridging oxygen by dnd and ssp gene families. Here we e…
View article: Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome
Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome Open
Background Epigenetic regulation of gene expression and host defense is well established in microbial communities, with dozens of DNA modifications comprising the epigenomes of prokaryotes and bacteriophage. Phosphorothioation (PT) of DNA,…
View article: Longitudinal Microbiome Changes in Children Exposed to Proton Pump Inhibitors
Longitudinal Microbiome Changes in Children Exposed to Proton Pump Inhibitors Open
INTRODUCTION: Proton pump inhibitor (PPI) use has been associated with an increased risk of gastrointestinal and upper respiratory infections in children. There are limited longitudinal data on the effect of PPI in children. The goal of th…
View article: An immune-competent human gut microphysiological system enables inflammation-modulation by Faecalibacterium prausnitzii
An immune-competent human gut microphysiological system enables inflammation-modulation by Faecalibacterium prausnitzii Open
Crosstalk of microbes with human gut epithelia and immune cells is crucial for gut health. However, there is no existing system for a long-term co-culture of human innate immune cells with epithelium and oxygen-intolerant commensal microbe…
View article: Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia
Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia Open
Increasing levels of industrialization have been associated with changes in gut microbiome structure and loss of features thought to be crucial for maintaining gut ecological balance. The stability of gut microbial communities over time wi…
View article: Structured community transitions explain the switching capacity of microbial systems
Structured community transitions explain the switching capacity of microbial systems Open
Microbial systems appear to exhibit a relatively high switching capacity of moving back and forth among few dominant communities (taxon memberships). While this switching behavior has been mainly attributed to random environmental factors,…
View article: Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics
Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics Open
Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable suc…
View article: DOP69 Longitudinal gut microbiome dynamics in relation to disease flares in Inflammatory Bowel Disease, pilot data from the IBD-Tracker study
DOP69 Longitudinal gut microbiome dynamics in relation to disease flares in Inflammatory Bowel Disease, pilot data from the IBD-Tracker study Open
Background The pathogenetic mechanisms that lead to IBD flares are unknown and the absence of reliable predictive biomarkers results in a therapeutic approach focused on treating active flares rather than prevention. While IBD is known to …
View article: An immune-competent human gut microphysiological system enables inflammation-modulation of Faecalibacterium prausnitzii
An immune-competent human gut microphysiological system enables inflammation-modulation of Faecalibacterium prausnitzii Open
Crosstalk of microbes with human gut epithelia and immune cells is crucial for gut health. However, there is no existing system for a long-term co-culture of human innate immune cells with epithelium and oxygen-intolerant commensal microbe…
View article: Lectin-Seq: A method to profile lectin-microbe interactions in native communities
Lectin-Seq: A method to profile lectin-microbe interactions in native communities Open
Soluble human lectins are critical components of innate immunity. Genetic models suggest that lectins influence host-resident microbiota, but their specificity for commensal and mutualist species is understudied. Elucidating lectins’ roles…
View article: Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia
Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia Open
Background Increasing levels of industrialization have been associated with changes in gut microbiome structure and loss of features thought to be crucial for maintaining gut ecological balance. The stability of gut microbial communities o…
View article: Supplemental Figure 3 from Dietary Microbes Modulate Transgenerational Cancer Risk
Supplemental Figure 3 from Dietary Microbes Modulate Transgenerational Cancer Risk Open
L. reuteri dietary enrichment protects the F1 progeny of NWD-fed mothers from transgenerational cancer. Pulmonary adenocarcinoma, hepatocellular carcinoma and mesenteric lymph node lymphoma in the children of mothers consuming NWD are show…
View article: Supplemental Figure 3 from Dietary Microbes Modulate Transgenerational Cancer Risk
Supplemental Figure 3 from Dietary Microbes Modulate Transgenerational Cancer Risk Open
L. reuteri dietary enrichment protects the F1 progeny of NWD-fed mothers from transgenerational cancer. Pulmonary adenocarcinoma, hepatocellular carcinoma and mesenteric lymph node lymphoma in the children of mothers consuming NWD are show…