February 2, 2017

Did you ever wonder about vitamin B12 role in microbiome organization and function? using a chemical probe mimic of vitamin B12, the authors reveal a light- and B12-dependent DNA regulator and predict that organismal interdependencies for B12 may be critical to microbiome stability and overall function.  On the extremophiles front, a study provides an analysis of the genomic content of the most abundant bacterial inhabitants of the salt-secreting desert tree Tamarix aphylla.  An interesting paper reinforced linkages between the colonization of the foodborne pathogen E. coli O157:H7 in cattle and the nature of the microbial community inhabiting the digestive tract of super-shedders. And as for future generations, if you want to get your kids or students excited about microbiology, try an interactive tool created by Stanford bioengineers: the 3D printed microscope powered by your smartphone.

Events: The second San Francisco Bay Area Microbiome meetup

The successful event was hosted at the Illumina Accelerator. Starting with networking and a welcome note from George Roche (the organizing team), the evening continued with a panel discussion and concluded with tours of the Accelerator.  The panel discussion was moderated by Amanda Chasin (Illumina Accelerator) and focused on tools and techniques for microbiome analysis.  The participants,  Nick Conley (EpiBiome), David Hanzel (Naked Biome), Alberto Acedo Bécares (Biome Makers) and Elisabeth Bik (uBiome and The Microbiome Digest) shared the main tools they are using to foster innovation. Their diverse answers included automation (EpiBiome), WGS of a variety of microorganisms (Naked Biome), cloud computing and improving 16S quantification (Biome makers), 16S and metagenomic sequencing (uBiome). The panel agreed that while standardized methods are very important and would benefit academia and industry, it will not be easy to streamline protocols across the board.   The last issue discussed was how to balance new with old technologies and was concluded by David Hanzel sharing his vision about the importance of new technologies to reveal exciting discoveries.  Join the LinkedIn group and stay tuned for the next meetup that will be focused on nutrition.


The panel participants, 2nd SF  Microbiome meetup


Group Leaders/Research Professors in Microbiology, VIB life sciences institute , the University of Leuven

General microbiome

Polysaccharide Utilization Loci: Fuelling microbial communities -JM Grondin – Journal of Bacteriology

Elucidation of roles for vitamin B12 in regulation of folate, ubiquinone, and methionine metabolism  – Romine MF – PNAS

Human vaginal microbiome

Lactobacillus crispatus Modulates Vaginal Epithelial Cell Innate Response to Candida albicans  -Niu XX – Chin Med Journal

Human gut microbiome

Review: Gut Microbiota in Obesity and Undernutrition – NC de Clercq – Advances in Nutrition

Review: Roseburia spp.: a marker of health? – Z Tamanai-Shacoori -Future medicine

Pacaella massiliensis gen. nov., sp. nov., a new bacterial species isolated from the human gut – S. Ndongo – New Microbes and New Infections

Bacterial short-chain fatty acid metabolites modulate the inflammatory response against infectious bacteria – RO Corrêa – Cellular Microbiology

Animal experiments

Changes in bacterial community composition of Escherichia coli O157:H7 super-shedder cattle occur in the lower intestine – R.  Zaheer -PLoS One

Animal microbiome

Bacterial microbiota in harbor seals (PHOCA VITULINA) from the north sea of Schleswig-Holstein, Germany, around the time of Morbillivirus and influenza epidemics – Siebert U – Journal of Wildlife Diseases

Phytotoxic, Antifungal and Immunosuppressive Metabolites from Aspergillus terreus QT122 Isolated from the Gut of Dragonfly -YH Lu -Current Microbiology

Plant, root, and soil microbiome

Archaea and bacteria mediate the effects of native species root loss on fungi during plant invasion  -SD Mamet – The ISME Journal

Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments – X Xiao – Molecular Ecology

Production and characterization of a novel antifungal chitinase identified by functional screening of a suppressive-soil metagenome – F Berini F – Microbial Cell Factories

Low abundant soil bacteria can be metabolically versatile and fast growing -V Kurm – Ecology

Water and extremophile microbiome

Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree – Finkel OM – Applied and Environmental Microbiology

Probiotics / prebiotics

Lactobacillus acidophilus INMIA 9602 Er-2 strain 317/402 probiotic regulates growth of commensal Escherichia coli in gut microbiota of familial Mediterranean fever disease subjects – AZ Pepoyan – Lett Appl Microbiol.

Review: Impact of Dietary Fibers on Nutrient Management and Detoxification Organs: Gut, Liver, and Kidneys -Kieffer DA – Advances in Nutrition

Microbes in the news

Get your kids or classroom excited about microbiology with the 3D printed microscope powered by your smartphone: microscope developed by Stanford bioengineer creates interactive tool for microbiology

Evolution of fast and efficient antibiotic-resistant bacterial genomes – C Reding-Roman – Nature Ecology & Evolution

Nature knows best: employing whole microbial strategies to tackle antibiotic resistant pathogens – J Tyson – Environmental Microbiology Reports



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