Eric J. Alm
A5091119492- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Clostridium difficile and Clostridium perfringens research
- Microbial Community Ecology and Physiology
- Diet and metabolism studies
- SARS-CoV-2 detection and testing
- SARS-CoV-2 and COVID-19 Research
- Bacteriophages and microbial interactions
- Metabolomics and Mass Spectrometry Studies
- Bacterial Genetics and Biotechnology
- Gastrointestinal motility and disorders
- Probiotics and Fermented Foods
- RNA and protein synthesis mechanisms
- Microscopic Colitis
- Evolution and Genetic Dynamics
- COVID-19 Clinical Research Studies
- Microbial Fuel Cells and Bioremediation
- Vibrio bacteria research studies
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Nutrition, Genetics, and Disease
- Epigenetics and DNA Methylation
- Biosensors and Analytical Detection
- Wastewater Treatment and Nitrogen Removal
- Food Security and Health in Diverse Populations
Massachusetts Institute of Technology
2016-2025
Broad Institute
2015-2024
Singapore-MIT Alliance for Research and Technology
2020-2024
Lawrence Berkeley National Laboratory
2002-2024
Harvard University
2008-2024
Center for Environmental Health
2024
Singapore-HUJ Alliance for Research and Enterprise
2020-2023
Washington University in St. Louis
2023
IIT@MIT
2010-2022
Moscow Institute of Thermal Technology
2013-2020
Studies of the human microbiome have revealed that even healthy individuals differ remarkably in microbes occupy habitats such as gut, skin and vagina. Much this diversity remains unexplained, although diet, environment, host genetics early microbial exposure all been implicated. Accordingly, to characterize ecology human-associated communities, Human Microbiome Project has analysed largest cohort set distinct, clinically relevant body so far. We found abundance each habitat's signature vary...
A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in health disease. The National Institutes Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting broad range quality-controlled resources data including standardized methods for creating, processing interpreting distinct types high-throughput available scientific community. Here...
High-throughput sequencing based techniques, such as 16S rRNA gene profiling, have the potential to elucidate complex inner workings of natural microbial communities - be they from world's oceans or human gut. A key step in exploring data is identification dependencies between members these communities, which commonly achieved by correlation analysis. However, it has been known since days Karl Pearson that analysis type generated techniques (referred compositional data) can produce...
Disturbance to human microbiota may underlie several pathologies. Yet, we lack a comprehensive understanding of how lifestyle affects the dynamics human-associated microbial communities.Here, link over 10,000 longitudinal measurements wellness and action daily gut salivary two individuals course one year. These time series show overall communities be stable for months. However, rare events in each subjects’ life rapidly broadly impacted dynamics. Travel from developed developing world...
Wastewater surveillance represents a complementary approach to clinical measure the presence and prevalence of emerging infectious diseases like novel coronavirus SARS-CoV-2. This innovative data source can improve precision epidemiological modeling understand penetrance SARS-CoV-2 in specific vulnerable communities. Here, we tested wastewater collected at major urban treatment facility Massachusetts detected RNA from N gene significant titers (57 303 copies per ml sewage) period 18 25 March...
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question whether advantageous mutations lead to selection of clonal genomes or, as in sexual eukaryotes, sweep through populations their own. Here, we show that two recently diverged ocean has occurred akin a mechanism: few genome regions have swept subpopulations habitat-specific manner, accompanied by gradual separation gene pools...
Recurrent hepatic encephalopathy (HE) is a leading cause of readmission despite standard care (SOC) associated with microbial dysbiosis. Fecal microbiota transplantation (FMT) may improve dysbiosis; however, it has not been studied in HE. We aimed to define whether FMT using rationally derived stool donor safe recurrent HE compared SOC alone. An open-label, randomized clinical trial 5-month follow-up outpatient men cirrhosis on was conducted 1:1 randomization. FMT-randomized patients...
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
DNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South African gold mine was sequenced and assembled into single, complete genome. This bacterium, Candidatus Desulforudis audaxviator, composes >99.9% of the microorganisms inhabiting fluid phase this particular fracture. Its genome indicates motile, sporulating, sulfate-reducing, chemoautotrophic thermophile that can fix its own nitrogen carbon by using machinery shared with archaea. audaxviator is capable an...
Abstract Antibiotic resistance genes (ARGs) are widespread among bacteria. However, not all ARGs pose serious threats to public health, highlighting the importance of identifying those that high-risk. Here, we developed an ‘omics-based’ framework evaluate ARG risk considering human-associated-enrichment, gene mobility, and host pathogenicity. Our classifies human-associated, mobile (3.6% ARGs) as highest risk, which further differentiate ‘current threats’ (Rank I; 3%) - already present...
Identifying ecologically differentiated populations within complex microbial communities remains challenging, yet is critical for interpreting the evolution and ecology of microbes in wild. Here we describe spatial temporal resource partitioning among Vibrionaceae strains coexisting coastal bacterioplankton. A quantitative model (AdaptML) establishes evolutionary history ecological differentiation, thus revealing specific seasons life-styles (combinations free-living, particle, or...
Differences in gut microbiota composition and function were observed between patients with inflammatory bowel disease or irritable syndrome.
Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea fungi thousands expression microarrays from diverse organisms ranging model such as Escherichia coli Saccharomyces cerevisiae to environmental microbes Desulfovibrio vulgaris Shewanella oneidensis. To assist in annotating genes reconstructing their evolutionary history, browser...
Abstract Whether mammal–microbiome interactions are persistent and specific over evolutionary time is controversial. Here we show that host phylogeny major dietary shifts have affected the distribution of different gut bacterial lineages did so on vastly phylogenetic resolutions. Diet mostly influences acquisition ancient large microbial lineages. Conversely, correlation with seen among more recently diverged lineages, consistent processes operating at similar timescales to evolution....
Fecal microbiota transplant is increasingly used to treat recurrent or relapsing Clostridium difficile infection. In this randomized controlled study, using a frozen inoculum from unrelated donors was safe and effective, whether administered by nasogastric tube colonoscopy. Background. Recurrent infection (CDI) with poor response standard antimicrobial therapy growing medical concern. We aimed investigate the outcomes of fecal (FMT) for CDI suspension donors, comparing colonoscopic (NGT)...