Microbiome

January 28, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Multiple Enzymes and Beads for Longer Metagenomic Reads

Joshua Quick from the University of Birmingham in the UK has developed several Nanopore protocols and tools. Tonight I watched Quick present at London Calling 2019 on “The ‘Three Peaks Challenge’ and developing extraction methods suitable for long-read, ultra-deep stool metagenomics on the PromethION. Quick spoke about how they are studying fecal microbiome transplants for […]

January 21, 2024
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Characterizing Active Blueberry Microbiomes

Seda Mirzoyan from Rutgers University presented at the Nanopore Community Meeting 2019 on “Using SIP and MinION sequencing to uncover active microbial communities in blueberry farm and forest soil systems.” Mirzoyan characterized active communities by using SIP and the MinION system. They spoke about the United States being the largest blueberry producer, with over fourteen […]

December 26, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Swab to Sequence in Space

Sarah Castro-Wallace from NASA spoke at the Nanopore Community Meeting in Houston. The title of their session is “2043: A Minion Space Odyssey.” Castro-Wallace helped the audience think about a Martian habitat and using Nanopore devices to monitor crew health, planetary protection (“forward and back contamination”), and microbial surveillance. Importantly, Castro-Wallace wanted us to consider […]

December 21, 2023
By Carlos C. Goller
Metagenomics, Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Fieldwork to Study Mangrome Microbial Diversity

Felipe Baez Aguirre from the University of the Andes in Colombia presented a session entitled “On-site nanopore sequencing reveals microbial diversity of a Colombian Pacific Coast mangrove soils” at the Nanopore Community Meeting in Houston. Baez Aguirre spoke about the location of the studies. They had limited access to electricity in the Bahia Malaga. The […]

October 12, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Ten Applications of Nanopore Technologies in Thailand

Thidathip Wongsurawat from the Siriraj Long-read Lab in the Mahidol University in Thailand, presented at the Nanopore Community Meeting in Singapore on “Ten case studies on the recent applications of nanopore sequencing in Thailand.” Number ten was nCNV-seq: Nanopore-based multiple copy number variation analyses. They developed the open access bioinformatics tool. Wongsurawat also spoke about […]

August 26, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares, Why

The ONT Mobile Suitcase Lab

Ahmed Abd El Wahed from Leipzig University in Germany talked at London Calling 2023 about “Pathogen and species identification using a mobile suitcase laboratory.” I have been thinking about this for a while and just today received an email from Bento Lab. El Wahed recorded the talk outside and next to the mobile suitcase lab. […]

April 23, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing, Softwares

Fecal Samples for Epigenetic Age Estimations

Continuing with epigenetics, tonight I watched the London Calling 2022 session by Eveliina Hanski from the University of Oxford in the UK. The title of the session is “From laboratory to the wild: a non-invasive, MinION-based method for determining the epigenetic age of mice.” Hanski is a final year graduate student and is interested in […]

April 20, 2023
By Carlos C. Goller
Oxford Nanopore Technologies, Reflections, sequencing

Green Seaweed Microbiomes

Luna van der Loos from Ghent University in Belgium presented at the London Calling 2022 conference on “Salinity structures the microbiome of the green seaweed Ulva.” van der Loos noted that they are fairly common and rely on their bacterial partners. This interaction is key but highly variable. van der Loos hypothesized that the interaction […]

December 27, 2022
By Carlos C. Goller
Academic Development, Books, Constructivism, DBER and SoTL, Delftia, Discussions, Diversity, Information Literacy, Instructor Behaviors, Pedagogy, Reflections, Service Learning, UDL, Why

Swabs and Microbes in the Second Grade Classroom

The JMBE Live session I watched tonight was entitled “Microscopic Communities: Interdisciplinary Exploration of Microbes in the Classroom” and presented by Dr. Jennifer Surtees and Dr. Sandra K. Small from the University of Buffalo. They are both part of the Genome, Environment and Microbiome (GEM) program that aims to integrate research, education, and engagement. GEM […]

October 13, 2022
By Carlos C. Goller
Academic Development, Constructivism, Course Design, Discussions, Information Literacy, Pedagogy, Reflections, Student groups

You never shower alone!

Stephanie Mathews from Campbell University presented at ASMCUE 2022 on two case studies they created as part of HITS! Yay! The session was entitled “Showerhead Microbiome and Antibiotic Resistance Case Studies for 200-level Microbiology Courses.” The case studies focused on high-throughput approaches and fundamental microbiology concepts. The hook for the first case study was… a […]