E. J. Alm

Phosphorothioate DNA modification by BREX Type 4 systems in the human gut microbiome

The paper identifies new phosphorothioate DNA modification systems in the human gut microbiome using genomic and mass spectrometric analysis.

Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome

The paper characterizes phosphorothioate (PT) modifications in the human gut microbiome using metagenomics and mass spectrometry, revealing temporal dynamics and species-specific patterns.

Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia

This study examines gut microbiome temporal dynamics in non-industrialized Amazonian populations, finding greater variability and frequent bacterial replacements compared to industrialized groups.

Lectin-Seq: a method to profile lectin-microbe interactions in native communities

Lectin-Seq profiles lectin-microbe interactions in human fecal microbiota, revealing distinct binding preferences for MBL and hItln1.

Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance

The paper identifies 41 viral clusters in groundwater plasmidomes, links them to bacterial hosts, and detects novel phage genera and host-specific genes.

Sustained ability of a natural microbial community to remove nitrate from groundwater

This study demonstrates that a natural microbial community can sustain nitrate removal from groundwater even after prolonged absence of an electron donor.

Anatomy promotes neutral coexistence of strains in the human skin microbiome

The paper investigates how host anatomy influences strain coexistence in the human skin microbiome, finding that pores limit competition by maintaining single-strain dominance.

Culturing of "Unculturable" Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria from Groundwater

This study shows that complex natural organic carbon sources better enrich diverse subsurface bacteria than simple organic sources.

Microbe-seq: high-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

Microbe-seq enables strain-resolved genome reconstruction from complex microbial communities, revealing intra-phylum horizontal gene transfer and bacteriophage-bacterial associations in the human gut.

Antigen-specific induction of CD4+CD8αα+ intraepithelial T lymphocytes byBacteroidetes species

This study identifies Bacteroidetes species that induce CD4+CD8αα+ intraepithelial T lymphocytes, which provide protective immunity against colitis.

Industrialization is associated with elevated rates of horizontal gene transfer in the human microbiome

The paper shows that horizontal gene transfer in the human microbiome is more common within the same host and is linked to industrialization and lifestyle factors.

Choosing Your Battles: Which Resistance Genes Warrant Global Action?

This paper develops a framework to prioritize antibiotic resistance genes (ARGs) based on risk factors and identifies high-risk ARGs for global action.

Dynamic colonization of microbes and their functions after fecal microbiota transplantation for inflammatory bowel disease

This study profiles microbial colonization and immune function transfer after fecal microbiota transplantation in IBD, revealing dynamic competition and immune interactions that influence clinical outcomes.

Multi-site sampling and risk prioritization reveals the public health relevance of antibiotic resistance genes found in wastewater environments

This study assesses the public health risk of antibiotic resistance genes in wastewater by combining metagenomic analysis with risk prioritization across multiple countries.

Transmission of human-associated microbiota along family and social networks

The paper examines bacterial transmission in gut and oral microbiomes of a closed cohort in Fiji, finding weak but significant transmission within households and between spouses using strain-level data.

Capturing the Diversity of Subsurface Microbiota - Choice of Carbon Source for Microcosm Enrichment and Isolation of Groundwater Bacteria

This study evaluates different carbon sources for enriching groundwater bacteria, finding that natural complex carbon sources enhance biodiversity compared to simple organic carbon sources.

Interactions in self-assembled microbial communities saturate with diversity

The paper shows that community function in microbial communities saturates with diversity, with no net change in function beyond 20 taxa.

Adaptive evolution within the gut microbiome of individual people

This study tracks genetic adaptation of B. fragilis in individual human gut microbiomes over time, revealing persistent evolutionary dynamics and niche differentiation within a single host.

Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota

The paper identifies variation in endospore and stress-resistant bacterial states across individuals and over time, showing their role in cross-host dissemination and response to dietary fatty acids.

Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in public receptors

This study tracks T cell receptor beta diversity in healthy individuals over a year, finding persistent receptors linked to antigen exposure history and stable repertoire features.

Meta Analysis Of Microbiome Studies Identifies Shared And Disease-Specific Patterns

The paper performs a meta-analysis of microbiome studies to identify shared and disease-specific patterns, finding common core microbes associated with multiple diseases.