Phys .org: An open-source data platform for researchers studying archaea. “To foster scientific exchange and to advance discovery, biologists in the School of Arts & Sciences led by postdoc Stefan Schulze and professor Mecky Pohlschroder have launched the Archaeal Proteome Project (ArcPP), a web-based database to collect and make available datasets to further the work of all scientists interested in archaea, a domain of life composed of microorganisms that can dwell anywhere from deep-sea vents to the human gut.”
National Geographic: Key ingredient in coronavirus tests comes from Yellowstone’s lakes. “MICROBIOLOGIST THOMAS BROCK was tramping through Yellowstone in the 1960s when he stumbled upon a species of bacteria that would transform medical science. Brock was investigating the tiny life-forms that manage to eke out a living in the superheated waters of the park’s thermal pools. There, he and a student found golden mats of stringy growth in Yellowstone’s Mushroom Spring containing a microbe that produces unusual heat-resistant enzymes.”
EurekAlert: Microbiome search engine can increase efficiency in disease detection and diagnosis. “Big data makes big promises when it comes to providing insights into human behavior and health. The problem is how to harness the information it provides in an efficient manner. An international team of researchers has proposed a microbiome search-based method, via Microbiome Search Engine (MSE), to analyze the wealth of available health data to detect and diagnose human diseases.”
Chemistry World: Open access Atlas maps out microbial natural products. “A new open access database of microbial natural products has launched online. The Natural Products Atlas (NPAtlas) is free to use and contains more than 24,000 chemical structures. The tool is based on Fair data principles, making the information within it easier to search and use in secondary analysis.” I don’t put anything in RB unless I can get a basic understanding of what the resource is about. (I have skipped including items because I just didn’t get the underlying discipline or presentation.) In this case I had no idea what microbial natural products are, but I now understand better thanks to PubMed.
PR Newswire: Million Microbiome of Humans Project (MMHP) is launched, aiming to build the world’s largest human microbiome database (PRESS RELEASE). ” The ‘Million Microbiome of Humans Project’ (MMHP) was officially launched at the 14th International Conference on Genomics (ICG-14). Scientists from China, Sweden, Denmark, France, Latvia and other countries will cooperate in microbial metagenomic research, aiming to sequence and analyze one million microbial samples from intestines, mouth, skin, reproductive tract and other organs in the next three to five years to draw a microbiome map of the human body and build the world’s largest database of human microbiome.”
Phys .org: Powerful online tool will help researchers make new genomic discoveries. “By integrating data across thousands of microbial genomes, ‘AnnoTree’ provides a comprehensive framework for exploring the evolution of microbial genes and functions, and can be used to advance research across a wide range of industries including microbiology, biotechnology, industrial products, biofuels, and food science.”
EurekAlert: Mapping the ocean’s unseen heroes, one microbe at a time. “Invisible to the naked eye, the health and movement of marine microbes that drift as part of the plankton is difficult to picture even for scientists – let alone everyday citizens. This challenge, to visualise the range of conditions that drifting marine microbes encounter, brought a group of expert scientists and visual designers together on a path to create the online citizen science project Adrift. Adrift is a portal that connects the public with the lives of microscopic marine microbes as they are propelled around the globe by ocean currents, with temperature and nutrient availability changing along the way.”
Phys .org: Researchers use 3-D printing to push knowledge of microbial communities. “As enthusiasm grows for 3-D printing, hailed by hobbyists and high-tech industry as a new frontier in the creation of custom products, researchers at Montana State University are using the technology for another purpose: studying bacteria.”
Also new-to-me, from MEDIZIN ASPEKTE: Unlimited access to microbiological research data at BacDive. “The possibilities of using BacDive are continuously being expanded, currently scientists can use more than 600 data fields to search for microbiological information. The repertoire includes initial species descriptions and metabolic profiles as well as data on enzymatic activities and antibiotic resistance. In addition, BacDive offers 9,000 Analytical Profile Tests (API) for over 5,000 bacterial strains, the largest publicly available API data collection worldwide.”
EurekAlert: The web meets genomics: a DNA search engine for microbes . “The search engine, called Bitsliced Genomic Signature Index (BIGSI), fulfils a similar purpose to internet search engines, such as Google. The amount of sequenced microbial DNA is doubling every two years. Until now, there was no practical way to search this data. This type of search could prove extremely useful for understanding disease. Take, for example, an outbreak of food poisoning, where the cause is a Salmonella strain containing a drug-resistance plasmid (a ‘hitchhiking’ DNA element that can spread drug resistance across different bacterial species). For the first time, BIGSI allows researchers to easily spot if and when the plasmid has been seen before.”
Dentistry Today: More Than 80 Species Added to Oral Microbiome Database. “The list of bugs in your mouth keeps growing, as the Forsyth Institute has added more than 80 species to its online expanded Human Oral Microbiome Database (eHOMD). It now indexes 772 microbial species present in the aerodigestive tract (ADT), which includes the mouth, throat, nose, sinuses, and esophagus.? Eww. Pardon me, I need to go chug some Listerine.
Phys.org: New gene catalog of ocean microbiome reveals surprises . “Microbes dominate the planet, especially the ocean, and help support the entire marine food web. In a recent report published in Nature Microbiology, University of Hawai’i at Mānoa (UHM) oceanography professor Ed DeLong and his team report the largest single-site microbiome gene catalog constructed to date.”
Now available: a database of DNA viruses and retroviruses. “There are more microbes in, on, and around the planet than there are stars in the Milky Way. Microbes affect food production; air quality; natural breakdown of plants, trees and biomass; soil quality for agriculture; and much more. To work with these microbes, scientists need to learn more about how microbes and viruses interact. Viruses influence microbes’ abilities to work. Scientists at the U.S. Department of Energy (DOE) Joint Genome Institute built the largest publicly available database for viruses. This single effort increases the number of known viral genes by a factor of 16. Further, in a series of four articles published in Nucleic Acids Research, DOE Joint Genome Institute researchers report on the latest updates to several other publicly accessible databases and computational tools. These databases and tools will benefit the global community of microbial researchers.”
This showed up in my Google Alerts from Labiotech.eu,and I’m not sure if I’m impressed or squicked out: Microorganisms in the Library: Bringing Centuries-Old Books to Life . “Sarah Craske describes herself as a ‘British artist, without category.’ Her work, at the intersection of art and science, revolves around the development of her own discipline: Biological Hermeneutics. Hermeneutics refers to the interpretation of texts, a term commonly used regarding the bible or philosophy. Craske translates the concept to biology by exploring the role of books as ‘centers of microbial data and data transfer.'” I think I’m squicked first, then I get past that and am impressed.