24 Result(s)

Article

Cabozantinib and nivolumab with or without live bacterial supplementation in metastatic renal cell carcinoma: a randomized phase 1 trial

Supplementation with CBM588, a bifidogenic live bacterial product, has been associated with improved clinical outcomes in persons with metastatic renal cell carcinoma (mRCC) receiving nivolumab and ipilimumab....

Hedyeh Ebrahimi, Nazli Dizman, Luis Meza, Jasnoor Malhotra, **aochen Li… in Nature Medicine (2024)

Article

Environmental and structural factors associated with bacterial diversity in household dust across the Arizona-Sonora border

We previously reported that asthma prevalence was higher in the United States (US) compared to Mexico (MX) (25.8% vs. 8.4%). This investigation assessed differences in microbial dust composition in relation to...

Lauren D. Benton, Nicolas Lopez-Galvez, Chloe Herman… in Scientific Reports (2024)

Article

Oligofructose improves small intestinal lipid-sensing mechanisms via alterations to the small intestinal microbiota

Upper small intestinal dietary lipids activate a gut-brain axis regulating energy homeostasis. The prebiotic, oligofructose (OFS) improves body weight and adiposity during metabolic dysregulation but the exact...

Savanna N. Weninger, Chloe Herman, Rachel K. Meyer, Eve T. Beauchemin… in Microbiome (2023)

Article

Leptospira in river and soil in a highly endemic area of Ecuador

Leptospira are shed into the environment via urine of infected animals. Rivers are thought to be an important risk factor for transmission to humans, though much is unknown about the types of environment or chara...

Erin Miller, Veronica Barragan, Jorge Chiriboga, Chad Weddell… in BMC Microbiology (2021)

Article

Species abundance information improves sequence taxonomy classification accuracy

Popular naive Bayes taxonomic classifiers for amplicon sequences assume that all species in the reference database are equally likely to be observed. We demonstrate that classification accuracy degrades linear...

Benjamin D. Kaehler, Nicholas A. Bokulich, Daniel McDonald… in Nature Communications (2019)

Article

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Evan Bolyen, Jai Ram Rideout, Matthew R. Dillon… in Nature Biotechnology (2019)

Article

Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota

Many studies have reported abnormal gut microbiota in individuals with Autism Spectrum Disorders (ASD), suggesting a link between gut microbiome and autism-like behaviors. Modifying the gut microbiome is a pot...

Dae-Wook Kang, James B. Adams, Devon M. Coleman, Elena L. Pollard… in Scientific Reports (2019)

Article

Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16–17, 2017

The National Cancer Institute (NCI) sponsored a 2-day workshop, “Next Steps in Studying the Human Microbiome and Health in Prospective Studies,” in Bethesda, Maryland, May 16–17, 2017. The workshop brought tog...

Rashmi Sinha, Habibul Ahsan, Martin Blaser, J. Gregory Caporaso… in Microbiome (2018)

Article

Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018

The Mid-Atlantic Microbiome Meet-up (M³) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M³ held its f...

Jacquelyn S. Meisel, Daniel J. Nasko, Brian Brubach, Victoria Cepeda-Espinoza… in Microbiome (2018)

Article

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

Taxonomic classification of marker-gene sequences is an important step in microbiome analysis.

Nicholas A. Bokulich, Benjamin D. Kaehler, Jai Ram Rideout, Matthew Dillon… in Microbiome (2018)

Article

Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study

Autism spectrum disorders (ASD) are complex neurobiological disorders that impair social interactions and communication and lead to restricted, repetitive, and stereotyped patterns of behavior, interests, and ...

Dae-Wook Kang, James B. Adams, Ann C. Gregory, Thomas Borody, Lauren Chittick… in Microbiome (2017)

Article

Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets

Bioinformatics software often requires human-generated tabular text files as input and has specific requirements for how those data are formatted. Users frequently manage these data in spreadsheet programs, wh...

Jai Ram Rideout, John H. Chase, Evan Bolyen, Gail Ackermann… in GigaScience (2016)

Article

ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses

Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fung...

Jennifer Fouquier, Jai Ram Rideout, Evan Bolyen, John Chase, Arron Shiffer… in Microbiome (2016)

Article

Erratum to: Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity

Yan He, J. Gregory Caporaso, **ao-Tao Jiang, Hua-Fang Sheng, Susan M. Huse… in Microbiome (2015)

Article

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity

The operational taxonomic unit (OTU) is widely used in microbial ecology. Reproducibility in microbial ecology research depends on the reliability of OTU-based 16S ribosomal subunit RNA (rRNA) analyses.

Yan He, J Gregory Caporaso, **ao-Tao Jiang, Hua-Fang Sheng, Susan M Huse… in Microbiome (2015)

Article

Temporal variability is a personalized feature of the human microbiome

It is now apparent that the complex microbial communities found on and in the human body vary across individuals. What has largely been missing from previous studies is an understanding of how these communitie...

Gilberto E Flores, J Gregory Caporaso, Jessica B Henley, Jai Ram Rideout… in Genome Biology (2014)

Article

Individual diet has sex-dependent effects on vertebrate gut microbiota

Vertebrates harbour diverse communities of symbiotic gut microbes. Host diet is known to alter microbiota composition, implying that dietary treatments might alleviate diseases arising from altered microbial c...

Daniel I. Bolnick, Lisa K. Snowberg, Philipp E. Hirsch… in Nature Communications (2014)

Article

From molecules to dynamic biological communities

Microbial ecology is flourishing, and in the process, is making contributions to how the ecology and biology of large organisms is understood. Ongoing advances in sequencing technology and computational method...

Daniel McDonald, Yoshiki Vázquez-Baeza, William A. Walters… in Biology & Philosophy (2013)

Article

Meeting Report: Fungal ITS Workshop (October 2012)

This report summarizes a meeting held in Boulder, CO USA (19–20 October 2012) on fungal community analyses using ultra-high-throughput sequencing of the internal transcribed spacer (ITS) region of the nuclear ...

Scott T. Bates, Steven Ahrendt, Holly M. Bik… in Standards in Genomic Sciences (2013)

Article

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

We present the Biological Observation Matrix (BIOM, pronounced “biome”) format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated sample and observati...

Daniel McDonald, Jose C Clemente, Justin Kuczynski, Jai Ram Rideout… in GigaScience (2012)