Our Work

***Selected publications – growing everyday


Microcystis Toxin-Mediated Tumor Promotion and Toxicity Lead to Shifts in Mouse Gut Microbiome. Link

Distinctive gut microbiota of honey bees assessed using deep sampling from individual worker bees. Link

Nitrogen recycling and nutritional provisioning by Blattabacterium, the cockroach endosymbiont. Link

Gut microbiota in wild and captive Guizhou snub‐nosed monkeys, Rhinopithecus brelichi. Link


A Pathovar of Xanthomonas oryzae Infecting Wild Grasses Provides Insight Into the Evolution of Pathogenicity in Rice Agroecosystems. Link


Water security and gut microbiome in rural Nicaraguan children. Link

Amish (Rural) vs. non-Amish (Urban) Infant Fecal Microbiotas Are Highly Diverse and Their Transplantation Lead to Differences in Mucosal Immune Maturation in a Humanized Germfree Piglet Model. Link

Indoor microbial communities: Influence on asthma severity in atopic and nonatopic children. Link

Clostridioides difficile uses amino acids associated with gut microbial dysbiosis in a subset of patients with diarrhea. Link


Tile drainage and land use contribute to harmful algal bloom and microbiota shift in inland water. Link

Urban stormwater microbiome and antibiotic resistance profile. Link

Microbiome and resistome of drinking water treatment residuals that are used for agricultural application. Link

Microbiome and antibiotic resistance in integrated fish farm water. Link

Community Genomics Among Stratified Microbial Assemblages in the Ocean’s Interior. Link

Quantitative evaluation of bioaerosols in different particle size fractions in dust collected on the International Space Station (ISS). Link

Genome-centric view of carbon processing in thawing permafrost. Link

Methane dynamics regulated by microbial community response to permafrost thaw. Link

Host-linked soil viral ecology along a permafrost thaw gradient. Link

Expanding Tara Oceans protocols for underway, ecosystemic sampling of the ocean-atmosphere interface during Tara Pacific expedition. Link

The Tara Pacific expedition—A pan-ecosystemic approach of the “-omics” complexity of coral reef holobionts across the Pacific Ocean. Link

Oil Biodegradation and Oil-Degrading Microbial Populations in Marsh Sediments Impacted by Oil from the Deepwater Horizon Well Blowout. Link

Global forensic geolocation with deep neural networks. Link

Genome-centric view of carbon processing in thawing permafrost. Link

Morphology and quantification of fungal growth in residential dust and carpets. Link

Engineered Systems

Fighting Fire with Fire: Phage Potential for the Treatment of E. coli O157 Infection. Link

Community Resources and Tools

The ISOGENIE project

iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. Link