Microbiome Digest, October 23, 2014

Not much microbiome news today – which was good because I got time to watch the solar eclipse and a huge solar storm at the same time.  Enjoy the read!

Animal models of microbiome research

Lyn Deficiency Leads to Increased Microbiota-Dependent Intestinal Inflammation and Susceptibility to Enteric Pathogens – Morgan E. Roberts – Journal of Immunology

“Lyn2/2 mice exhibited profound cecal inflammation, bacterial dissemination, and morbidity following S. Typhimurium challenge and greater colonic inflammation throughout the course of C. rodentium infection.”

Rock microbiome

* Halophilic Archaea Cultivated from Surface Sterilized Middle-Late Eocene Rock Salt Are Polyploid – Salla T. Jaakkola – PLOS ONE

“We used real-time PCR to show that our isolates are polyploid, with genome copy numbers of 11–14 genomes per cell in exponential growth phase.”

More Microbiology

Zooming in to see the bigger picture: Microfluidic and nanofabrication tools to study bacteria – Felix J. H. Hol, Cees Dekker – Science

“Here, we review the new scientific insights gained by using a diverse set of nanofabrication and microfluidic techniques to study individual bacteria and multispecies communities.”

Review: Theory and Empiricism in Virulence Evolution – James J. Bull, Adam S. Lauring – PLOS Pathogens

“Our purpose here is to offer a brief introduction to virulence theory, explain some of its strengths and weaknesses, and suggest how theory might be united with empiric data”


Comparing the new 16S rRNA V4 and ITS primers to the old primers-RESULTS! – Embriette Hyde – MicroBEnet

“The Knight lab has been working hard testing new primers for 16S rRNA amplicon production and its time to share our progress.”

Microbes in the News

As permafrost soils thaw, soil microbes amplify global climate change – Science Daily

“Now, research by an international team of scientists from the U.S., Sweden and Australia, led by University of Arizona scientists, shows that a single species of microbe, discovered only very recently, is an unexpected key player in climate change.”

* The Scientist: Prof. Esther Angert Studies Extreme Bacteria – Siddesh Ramesh – Cornell Sun

“While the majority of bacteria cannot be seen without a microscope, there exists a group of bacterial species that is visible to the naked eye. Known as Epulopiscium, they are “an extreme on the spectrum of diversity of bacterial life in existence,” according to Prof. Esther Angert, microbiology.”

Bik’s Picks

Flare Alert: Monster Sunspot Turns Toward Earth – Ian O’Neill – Discovery

“Amateur astronomers have been wowed by a vast sunspot that has rotated to face Earth, the largest since this solar cycle began in 2008, and solar observatories (on the ground and orbiting Earth) are closely monitoring the region.“

Watch cell division with new, remarkable resolution: Nobel winner Betzig strikes again – Tech Times

“Just weeks after sharing the Nobel Prize in chemistry for his work involving high-resolution microscopes, a U.S. researcher has again stunned the scientific world with a new technique that peers deeply into living cells.

Ancient Europeans do not drink milk according to new study – BetaWired

“Almost everyone drinks milk today but a new study shows that ancient Europeans were not milk lovers back in the old days. According to a DNA analysis result, ancient Europeans are lactose intolerant.”


Human microbiome, June 27

How to grow the “Most Wanted” gut bacteria in microfluidic chips, effect of Vitamin D on gut microbiota, and probiotics for your skin.

Human gut microbiome

Screen Shot 2014-06-27 at 10.10.29 PMGene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project’s Most Wanted taxa – Liang Ma – PNAS

“We developed a microfluidics-based, genetically targeted approach to address these challenges. This approach corrects sampling bias from differential bacterial growth kinetics, enables the use of growth stimulants available only in small quantities, and allows targeted isolation and cultivation of a previously uncultured microbe from the human cecum that belongs to the high-priority group of the Human Microbiome Project’s “Most Wanted” list.”

From the ICE/ENDO meeting: Vitamin D May Improve Metabolic Health of African American Men – Lara C. Pullen – Medscape.com

“Vitamin-D supplementation not only improved insulin sensitivity but also shifted the microbiome from a prediabetes spectrum to a healthy signature. “

Exploring the Microbiome – Chris Anderson – Genetic Engineering & Biotechnology News

““These cover a broad range of options including complex approaches like fecal transplants that could include early uncharacterized strains of bacteria and other microorganisms, all the way to reductionist approaches,” noted Bernat Olle, a partner in the venture capital firm Puretech Ventures, who moderated a panel “Microbiome modulators: Opportunities and Challenges to Creating a New Drug Class” Thursday at BIO 2014.”

Human skin microbiome

LiveScienceProbiotics Hold Promise for 4 Skin Conditions – Cari Nierenberg – Live Science

“Bowe said probiotics — whether they are eaten as foods, taken as supplements or spread topically — are not a stand-alone treatment for skin problems, but could be used by patients in combination with their current treatment.”