Metagenomics provides quantitative measurements for microbial species over time. To obtain a global overview of an experiment and to explore the full potential of a given dataset, intuitive and interactive visualization tools are needed. Therefore, we established BioSankey to visualize microbial species in microbiome studies over time as a Sankey diagram. These diagrams are embedded into a project-specific webpage which depends only on JavaScript and Google API to allow searches of interesting species without requiring a web server or connection to a database. BioSankey is a valuable tool to visualize different data elements from single or dual RNA-seq datasets and additionally enables a straightforward exchange of results among collaboration partners.
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http://dx.doi.org/10.1515/jib-2017-0063 | DOI Listing |
Sci Data
January 2025
Centre for Ecosystem Science, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
Antarctica, Earth's least understood and most remote continent, is threatened by human disturbances and climate-related changes, underscoring the imperative for biodiversity inventories to inform conservation. Antarctic ecosystems support unique species and genetic diversity, deliver essential ecosystem services and contribute to planetary stability. We present Antarctica's first comprehensive ecosystem classification and map of ice-free lands, which host most of the continent's biodiversity.
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January 2025
Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel.
Active matter, from motile bacteria to animals, can exhibit striking collective and coherent behavior. Despite significant advances in understanding the behavior of homogeneous systems, little is known about the self-organization and dynamics of heterogeneous active matter, such as complex and diverse bacterial communities. Under oxygen gradients, many bacterial species swim towards air-liquid interfaces in auto-organized, directional bioconvective flows, whose spatial scales exceed the cell size by orders of magnitude.
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January 2025
Teagasc Food Research Centre, Fermoy, Co. Cork, Ireland.
Rapid advancements in long-read sequencing have facilitated species-level microbial profiling through full-length 16S rRNA sequencing (~ 1500 bp), and more notably, by the newer 16S-ITS-23S ribosomal RNA operon (RRN) sequencing (~ 4500 bp). RRN sequencing is emerging as a superior method for species resolution, exceeding the capabilities of short-read and full-length 16S rRNA sequencing. However, being in its early stages of development, RRN sequencing has several underexplored or understudied elements, highlighting the need for a critical and thorough examination of its methodologies.
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January 2025
Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston Salem, NC, USA.
Microbial species must compete for space and nutrients to persist in the gastrointestinal (GI) tract, and our understanding of the complex pathobiont-microbiota interactions is far from complete. Klebsiella pneumoniae, a problematic, often drug-resistant nosocomial pathogen, can colonize the GI tract asymptomatically, serving as an infection reservoir. To provide insight on how K.
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January 2025
WIL@NUS Corporate Laboratory, National University of Singapore, Centre for Translational Medicine, Singapore, Singapore.
Healthy dietary patterns rich in legumes can improve metabolic health, although their additional benefits in conjunction with calorie restriction have not been well-established. We investigated effects of a calorie-restricted, legume-enriched, multicomponent intervention diet compared with a calorie-restricted control diet in 127 Chinese prediabetes participants, living in Singapore. The study was a 16-week, single-blind, parallel-design, randomized controlled trial (n = 63 intervention group (IG), n = 64 control group (CG); mean ± SD age 62.
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