Proteomics in biofilms at different temperatures, neonatal immune metabolic network, co-occurrence, something wonky with Unifrac, and microbiome in the news.
Metabolomics and proteomics
Turning up the heat on biofilms – Christina Tobin Kåhrström – Nature Reviews Microbiology
“This study used tandem mass tag (TMT)-based proteomics to measure protein expression in acid mine drainage biofilms at 40 °C, 43 °C and 46 °C. “
Identification of a human neonatal immune-metabolic network associated with bacterial infection – Claire L. Smith – Nature Communications
“Here, a system-level investigation of neonatal systemic responses to infection shows a surprisingly strong but unbalanced homeostatic immune response; developing an elevated set-point of myeloid regulatory signalling and sugar-lipid metabolism with concomitant inhibition of lymphoid responses. “
Secondary metabolite gene expression and interplay of bacterial functions in a tropical freshwater cyanobacterial bloom – Kevin Penn – ISME Journal
“To characterize microbial activities in a cyanoHAB, transcripts from a eutrophic freshwater reservoir in Singapore were sequenced for six samples collected over one day-night period.”
Microbial Ecology
Demonstrating microbial co-occurrence pattern analyses within and between ecosystems
Ryan J. Williams – Frontiers in Microbiology
“To demonstrate our co-occurrence analysis approach, we gathered publicly available 16S rRNA amplicon datasets to compare and contrast microbial co-occurrence at different taxonomic levels across different ecosystems. “
Fluvial network organization imprints on microbial co-occurrence networks – Stefanie Widder – PNAS USA
“We combined co-occurrence analyses of biofilms based on next-generation sequencing with a probabilistic hydrological model, and showed how fragementation of microbial co-occurrence networks change across stream networks. “
Bioinformatics
Equivalent input produces different output in the UniFrac significance test – Jeffrey R Long – BMC Bioinformatics
“UniFrac produces different outputs for these equivalent forms of the same input tree.”
More microbes
PNAS has an upcoming 100th Anniversary Special Feature on Vaccines. Here is the introduction: Vaccines: Science, health, longevity, and wealth – Rino Rappuoli – PNAS
“The special issue of the centenary of PNAS provides an opportunity to review the his- tory of vaccines, the most exciting features of vaccine science, and to contemplate the future. “
Microbes in the news
Gut Check: Exploring your Microbiome – University of Colorado Boulder course
“Join us on a guided tour of the human gut and its microscopic inhabitants. “
* The ‘Whoville’ in Your Gut: Your Microbiome – Raphael Kellman – Everyday Health
“Just as Horton’s neighbors could not “see” the tiny residents of Whoville, most of us are unaware of the microscopic world within us. “
Your Gut Bacteria Want You to Eat a Cupcake – Julie Beck – The Atlantic
“But a recent review published in BioEssays suggests that these bacteria might be a little too big for their britches, bossing their hosts around and demanding certain kinds of foods. “
* Diversify Your Microbiome by Rock Climbing Indoors – Embriette Hyde – MicroBEnet
“Though I don’t feel as though the findings in the study are earth shattering, they do illustrate an important point-the built environments that we inhabit each and every day-whether they are our houses, workplaces, or gyms-are perfect places for sharing microbes of all sorts-both environmental and human-associated. “
Sea Smells By The Sea Shore – Benjamin Wolfe – PopSci.com
“A microbiologist explores the distinctive odors of a day at the beach”
Bik’s Picks
Effect of soccer shoe upper on ball behaviour in curve kicks – Hideyuki Ishii – Nature Scientific Reports
“In this study, by using a finite element simulation, we investigated the factors that affect ball behaviour immediately after impact in a curve kick. Five experienced male university soccer players performed one curve kick. “‘
Illegal killing for ivory drives global decline in African elephants – George Wittemyer – PNAS USA
“…to our knowledge we provide the first detailed assessment of African elephant illegal killing rates at population, regional, and continental scales. “
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Microbiome Digest - Bik's Picks 