Microbiome digest, September 24, 2014

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Today we will learn how to feed shit to flies, the gut microbes of Mexican monkeys, and soil microbes and climate change.

Human microbiome general

Microbes Central to Human Reproduction – Gregor Reid – American Journal of Reproductive Immunology

“A meeting of the International Scientific Association for Probiotics and Prebiotics held in Aberdeen, Scotland (June 2014), presented new views and challenged established concepts on the role of microbes in reproduction and health of the mother and infant. “

Mammal microbiome

The role of gut microbes in satisfying the nutritional demands of adult and juvenile wild, black howler monkeys (Alouatta pigra) – Katherine R. Amato – American Journal of Physical Anthropology

“..we examined differences in activity budget, diet, and the gut microbial community among adult male .., adult female .., and juvenile .. wild black howler monkeys (Alouatta pigra) across a ten-month period in Palenque National Park, Mexico “

Soil microbiome

Incorporating Soil Microbes in Climate Change Models – Joe Turner – The Scientist

“Without a solid understanding of how the soil microbiome contributes to atmospheric carbon, researchers are struggling to determine whether dirt-dwelling bacteria could impact—and be impacted by—climate change.”

Metabolomics

Metabolomic profiles and childhood obesity – Wei Perng – Obesity

“Principal components analysis was used to consolidate 345 metabolites into 18 factors and identified two that differed between obese .. and lean children “

Microbes in the news

A beginners guide to feeding shit to flies – Edan Foley – Frontiers blog

“The title pretty much sums this one up”

Meet my Microbiome – An Introduction to the bacterial zoo hidden in my colon – Edan Foley – Frontiers blog

“As detailed in the previous blog post, I fed a solution of my feces to axenic flies this summer.“

Giving Chickens Bacteria … To Keep Them Antibiotic-Free – Dan Charles – NPR The Salt

“Poultry companies are turning to probiotics as an alternative to antibiotics, which have become increasingly controversial.”

 Three Girls Won The Google Science Fair With A Bacteria-Based Plan To Solve The Food Crisis – Jessica Orwig – Business Insider

“Three young girls won the Google science fair on September 22 with their innovative way to feed the world: treat plants with bacteria to help farmers grow more food, faster”

Honeybees healing bacteria: The antimicrobial properties of honey – Jeremiah Yarmie – The Manitoban

“A research group from Lund University in Sweden has been investigating bacteria found in the honey-producing stomach of bees. “

Science and publishing

The Top Eleven Ways to Tell that a Journal is Fake – Shaili Jain – PLOS Blogs

“If you have ever published a scholarly paper, your email inbox is probably peppered with invitations to submit papers to new journals with plausible-sounding names. “

Women in Science

When words fail: women, science, and women-in-science – Jacquelyn Gill – The Contemplative Mammoth

“I don’t want to write about women in science today. I want to write about glaciers, or passenger pigeons, or the way the tilt of the earth is making the squirrels outside my window stash acorns”

Gender balance among University Research Fellows – Paul Nurse – UK Royal Society

“It was a great day for the 43 scientists who were awarded grants but I, like many Fellows, was personally very disappointed to see that only two of them were women.”

Bik’s Picks

Fossil Dolphin Otekaikea marplesi (Latest Oligocene, New Zealand) Expands the Morphological and Taxonomic Diversity of Oligocene Cetaceans – Yoshihiro Tanaka – PLOS ONE

“The New Zealand fossil dolphin “Prosqualodon” marplesi (latest Oligocene, ≥23.9 Ma) is here identified as a crown odontocete that represents a new genus, Otekaikea”

Review: The design and function of birds’ nests – Mark C. Mainwaring – Ecology and Evolution

“the design of birds’ nests is far more sophisticated than previously realized and that nests are multifunctional structures that have important fitness consequences for the builder/s.”

False memories could be a side-effect of human ability to learn rules – Science Daily

“New research suggests that individuals who are particularly good at learning rules and classifying objects by common properties are also particularly prone to false memory illusions.”

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Microbiome Digest, August 29, 2014

@MicrobiomDigest will be enjoying vacation for the next two weeks, so I won’t be able to post as much as usual. I might occasionally have some time and internet access at the same time, and post something, but don’t rely on this blog during that time for your daily Microbiome fix. But I will be back! Enjoy this last (short) one for now:
Human oral microbiome

Bacterial community composition of chronic periodontitis and novel oral sampling sites for detecting disease indicators – Vaia Galimanas – Microbiome

Human gut microbiome

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease – Noah W Palm – Cell

Modulation of immune development and function by intestinal microbiota – Agnieszka M. Kabat – Trends in Immunology

 

Worms, bacteria, and micronutrients: an elegant model of our diet – Lutfu Safak Yilmaz, Albertha J.M. Walhout – Trends in Genetics

 

Mammal microbiome

Spatial heterogeneity of gut microbiota reveals multiple bacterial communities with distinct characteristics (in flying squirrels) – Hsiao-Pei Lu – Scientific Reports

Social influences on the gut microbiome of developing monkeys – W.Z. Amaral – Brain, Behavior, and Immunity

 

Do Rumen Bacteroidetes Utilize an Alternative Mechanism for Cellulose Degradation? – AE Naas – mBio

 

Characterization of the Fecal Microbiota of Pigs before and after Inoculation with “Brachyspira hampsonii” – Matheus O. Costa – PLOS ONE

 

Sponges and corals

The versatile nature of coral-associated viruses – Bettarel Yvan – Environmental Microbiology

Onset and establishment of diazotrophs and other bacterial associates in the early life history stages of the coral Acropora millepora – Kimberley A. Lema – Molecular Ecology

Rocks and Water Microbiome

Microbial Colonization of Bare Rocks: Laboratory Biofilm Enhances Mineral Weathering – F. Seiffert – Procedia Earth and Planetary Science

Microbial diversity and biogeochemical cycling in soda lakes – Dimitry Y. Sorokin – Extremophiles

Food microbiome

Switzerland Puts Secret Bacteria In Cheese To Catch Knockoffs – Sarah Zhang – Gizmodo

Bioinformatics

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data – Yuan Zhang – PLOS Computational Biology

Metabolomics

Taking your breath away: metabolomics breathes life in to personalized medicine
Nicholas J.W. Rattray – Trends in Biotechnology

Phages and Viruses

Identifying and analyzing bacteriophages in human fecal samples: what could we discover? – Maite Muniesa1 & Juan Jofre – Future Medicine

Microbes in the news

Hotel rooms aren’t yucky – you colonize them with your own personal bacteria within hours — Rachel Feltman – Washington Post

A touching story: The ancient conversation between plants, fungi and bacteria – David Tenenbaum – News UW Madison

Bik’s Picks

The universal ‘anger face’: Each element makes you look physically stronger and more formidable – Science Daily

Zombie Bacteria Invasion? Nothing To Worry About – Science 2.0

Report: Ice Bucket Challenge Causing Ecological Mayhem in California – The Allium (Satire)

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