Sunit Jain
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View article: Gut microbial composition modulates food-specific CD4 <sup>+</sup> T cells in food allergy
Gut microbial composition modulates food-specific CD4 <sup>+</sup> T cells in food allergy Open
The growing food allergy epidemic is thought to be related to changing environmental factors, particularly changes in the gut microbiome. While prior work has demonstrated that food allergy can be modulated by gut microbes, little is known…
View article: High-resolution lineage tracking of within-host evolution and strain transmission in a human gut symbiont across ecological scales
High-resolution lineage tracking of within-host evolution and strain transmission in a human gut symbiont across ecological scales Open
Summary Gut bacteria rapidly evolve in vivo , but their long-term success requires dispersal across hosts. Here, we quantify this interplay by tracking >50,000 genomically barcoded lineages of the prevalent commensal Bacteroides thetaiotao…
View article: Discovery and engineering of the antibody response against a prominent skin commensal
Discovery and engineering of the antibody response against a prominent skin commensal Open
The ubiquitous skin colonist Staphylococcus epidermidis elicits a CD8 + T cell response pre-emptively, in the absence of an infection 1 . However, the scope and purpose of this anti-commensal immune program are not well defined, limiting o…
View article: Randomly barcoded transposon mutant libraries for gut commensals I: Strategies for efficient library construction
Randomly barcoded transposon mutant libraries for gut commensals I: Strategies for efficient library construction Open
Randomly barcoded transposon mutant libraries are powerful tools for studying gene function and organization, assessing gene essentiality and pathways, discovering potential therapeutic targets, and understanding the physiology of gut bact…
View article: Design, construction, and in vivo augmentation of a complex gut microbiome
Design, construction, and in vivo augmentation of a complex gut microbiome Open
Please cite: 10.1016/j.cell.2022.08.003 Cheng AG, Ho PY, Aranda-Díaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, D…
View article: Design, construction, and in vivo augmentation of a complex gut microbiome
Design, construction, and in vivo augmentation of a complex gut microbiome Open
Please cite: 10.1016/j.cell.2022.08.003 Cheng AG, Ho PY, Aranda-Díaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, D…
View article: Design, construction, and in vivo augmentation of a complex gut microbiome
Design, construction, and in vivo augmentation of a complex gut microbiome Open
Please cite: 10.1016/j.cell.2022.08.003 Cheng AG, Ho PY, Aranda-Díaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, D…
View article: Robust variation in infant gut microbiome assembly across a spectrum of lifestyles
Robust variation in infant gut microbiome assembly across a spectrum of lifestyles Open
Infant microbiome assembly has been intensely studied in infants from industrialized nations, but little is known about this process in nonindustrialized populations. We deeply sequenced infant stool samples from the Hadza hunter-gatherers…
View article: Mapping the T cell repertoire to a complex gut bacterial community
Mapping the T cell repertoire to a complex gut bacterial community Open
Certain bacterial strains from the microbiome induce a potent, antigen-specific T cell response 1–5 . However, the specificity of microbiome-induced T cells has not been explored at the strain level across the gut community. Here, we colon…
View article: Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles
Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles Open
Infant microbiome assembly is intensely studied in infants from industrialized nations, but little is known about this process in populations living non-industrialized lifestyles. In this study we deeply sequenced infant stool samples from…
View article: Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes
Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes Open
Summary The gut microbiome is a key modulator of immune and metabolic health. Human microbiome data is biased towards industrialized populations, providing limited understanding of the distinct and diverse non-industrialized microbiomes. H…
View article: Omics-Inferred Partitioning and Expression of Diverse Biogeochemical Functions in a Low-O <sub>2</sub> Cyanobacterial Mat Community
Omics-Inferred Partitioning and Expression of Diverse Biogeochemical Functions in a Low-O <sub>2</sub> Cyanobacterial Mat Community Open
Cyanobacterial mats are dense communities of microorganisms that contain photosynthetic cyanobacteria along with a host of other bacterial species that play important yet still poorly understood roles in this ecosystem. Although such cyano…
View article: Plant Breeding Integrated with Genomic-Enabled Prediction
Plant Breeding Integrated with Genomic-Enabled Prediction Open
Plant breeding programs have used conventional breeding methods, such as hybridization, induced mutations, and other methods to manipulate the plant genome within the species' natural genetic boundaries to improve crop varieties. However, …
View article: Systematic dissection of a complex gut bacterial community
Systematic dissection of a complex gut bacterial community Open
Efforts to model the gut microbiome have yielded important insights into the mechanisms of interspecies interactions, the impact of priority effects on ecosystem dynamics, and the role of diet and nutrient availability in determining commu…
View article: <i>In vivo</i> augmentation of a complex gut bacterial community
<i>In vivo</i> augmentation of a complex gut bacterial community Open
Efforts to model the human gut microbiome in mice have led to important insights into the mechanisms of host-microbe interactions. However, the model communities studied to date have been defined or complex but not both, limiting their uti…
View article: Airborne Bacteria in Earth's Lower Stratosphere Resemble Taxa Detected in the Troposphere: Results From a New NASA Aircraft Bioaerosol Collector (ABC)
Airborne Bacteria in Earth's Lower Stratosphere Resemble Taxa Detected in the Troposphere: Results From a New NASA Aircraft Bioaerosol Collector (ABC) Open
Airborne microorganisms in the upper troposphere and lower stratosphere remain elusive due to a lack of reliable sample collection systems. To address this problem, we designed, installed, and flight-validated a novel Aircraft Bioaerosol C…
View article: Elucidating the impact of microbial community biodiversity on pharmaceutical biotransformation during wastewater treatment
Elucidating the impact of microbial community biodiversity on pharmaceutical biotransformation during wastewater treatment Open
Summary In addition to removing organics and other nutrients, the microorganisms in wastewater treatment plants ( WWTP s) biotransform many pharmaceuticals present in wastewater. The objective of this study was to examine the relationship …
View article: Are Oligotypes Meaningful Ecological and Phylogenetic Units? A Case Study of Microcystis in Freshwater Lakes
Are Oligotypes Meaningful Ecological and Phylogenetic Units? A Case Study of Microcystis in Freshwater Lakes Open
Oligotyping is a computational method used to increase the resolution of marker gene microbiome studies. Although oligotyping can distinguish highly similar sequence variants, the resulting units are not necessarily phylogenetically and ec…
View article: Genomic and Transcriptomic Resolution of Organic Matter Utilization Among Deep-Sea Bacteria in Guaymas Basin Hydrothermal Plumes
Genomic and Transcriptomic Resolution of Organic Matter Utilization Among Deep-Sea Bacteria in Guaymas Basin Hydrothermal Plumes Open
Microbial chemosynthesis within deep-sea hydrothermal vent plumes is a regionally important source of organic carbon to the deep ocean. Although chemolithoautotrophs within hydrothermal plumes have attracted much attention, a gap remains i…
View article: Unraveling the Physiological Roles of the Cyanobacterium Geitlerinema sp. BBD and Other Black Band Disease Community Members through Genomic Analysis of a Mixed Culture
Unraveling the Physiological Roles of the Cyanobacterium Geitlerinema sp. BBD and Other Black Band Disease Community Members through Genomic Analysis of a Mixed Culture Open
Black band disease (BBD) is a cyanobacterial-dominated polymicrobial mat that propagates on and migrates across coral surfaces, necrotizing coral tissue. Culture-based laboratory studies have investigated cyanobacteria and heterotrophic ba…
View article: Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity
Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity Open
The genus Thiomargarita includes the world's largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus, a genomics approach, applied to a single Candidatus Thio…