Microbiome digest, September 18, 2014

It’s an exciting day at MicrobiomeDigest, with an Ig Nobel Prize awarded to the baby poop sausages paper, the Breaking Bad of gut microbiota, the microbiome of salami, and how bacteria can help in agriculture. Here we go:

Respiratory microbiome

Persistence of livestock-associated antibiotic-resistant Staphylococcus aureus among industrial hog operation workers in North Carolina over 14 days – Maya Nadimpalli – Occupational & Environmental Medicine (see also below)

“Nasal carriage of livestock-associated S. aureus, multidrug-resistant S. aureus and methicillin-resistant S. aureus can persist among industrial hog operation workers over a 14-day period, which included up to 96 h away from work.”

Human gut microbiome

Breaking Bad – the two sides of gut microbiota in portal hypertension – Gautam Mehta and Rajeshwar P Mookerjee – Liver International

“In this issue of Liver International, Rincon and colleagues bring these threads together by exploring the effects of modulating gut flora on portal hypertension in the context of decompensated cirrhosis.”

Pregnancy and birth

Winners of the 2014 Ig Nobel Prize in Nutrition – ABC News

2014 IgNobel Prize in Nutrition: “Raquel Rubio, Anna Jofra, Belen Martin, Teresa Aymerich and Margarita Garriga, for their study of using infant fecal bacteria as potential probiotic starter cultures for fermented sausages.”

Plant microbiome

Why Tiny Microbes Mean Big Things for Farming – Peter Andrey Smith – National Geographic

“The soil-dwelling bacteria that we walk on every day are working their way into technologies that could help feed the world.”

Plant interactions with other organisms: molecules, ecology and evolution – Amy T. Austin and Carlos L. Ballaré – New Phytologist

“There are still many open questions regarding how plant interactions with other organisms are shaped by evolutionary forces over time. “

Food microbiology

Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rRNA amplicons – Justyna Połka – Food Microbiology

“Salame Piacentino PDO was analysed by HTS (Illumina) of 16S rRNA amplicons.”

Techniques

1-day bowel preparation with polyethylene glycol 3350 is as effective and safe as a 3-day preparation for colonoscopy in children – Serge A Sorser – BMC Research Notes

“There were no differences between the groups in efficacy of bowel preparation based on colonoscopic grading or the safety of the preparation.”

Viruses and phages

Metagenomic Analysis of Double-stranded DNA viruses in Healthy Adults – Kristine M. Wylie – BMC Biology

“We analyzed eukaryotic double-stranded DNA (dsDNA) viruses, together with dsDNA replicative intermediates of single-stranded DNA viruses, in metagenomic sequence data generated by the HMP. “

see also: Your own personal virome – Biome – BioMedCentral

“If life gives you lemons, you make lemonade. And if your bacterial DNA datasets give you viral DNA contaminants, you use them to study the virome. “

Bioinformatics

Estimating overannotation across prokaryotic genomes using BLAST+, UBLAST, LAST and BLAT – Gabriel Moreno-Hagelsieb and Brigitte Hudy-Yuffa – BMC Research Notes

“Despite faster programs miss sequence matches otherwise found by NCBI?s BLAST, the overannotation estimates are very similar and thus these programs can be used with confidence for this task.”

Antibiotic and resistance

Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae – Sean Conlan – Science Translational Medicine

“we performed comprehensive surveillance and genomic sequencing of carbapenem-resistant Enterobacteriaceae in the National Institutes of Health (NIH) Clinical Center patient population and hospital environment. “

U.S. Lays Out Strategy to Combat Crisis of Antibiotic Resistance – Sabrina Tavernise – NY Times

“The Obama administration on Thursday announced measures to tackle the growing threat of antibiotic resistance”

Factory-Farm Workers Found to Carry High Levels of Antibiotic-Resistant Bacteria – Willy Blackmore – TakePart (see also above)

“While only one worker was found to be carrying MRSA after nostril swabs were tested, 86 percent carried staph bacteria associated with livestock—far higher than the general population. “

Microbes in the News

Microbirth: The Extra Question Every Expectant Mother Needs To Ask – Toni Harman – Huffington Post

“The doctor or midwife looks at the expectant mother blankly. “I’m sorry. I have never heard of the microbiome. And I’ve never heard of Microbirth.”

Science, publishing, and career

Rhubarb pie and science – Sandy Becker – Science Working Life

“When I am asked how I became a developmental biologist, I say, “Jim hired me for my rhubarb pie and my Phi Beta Kappa key, and the rest is history.””

Can Post-Publication Peer-Reviews Increase Research Transparency? – Liz Allen – Berkeley Bitts

“When Peer Review is done in the open by named individuals, we believe it should be more constructive and issues will surface more quickly.”

 

Bik’s Picks

Winners of the 2014 Ig Nobel Awards – ABC News

“The 2014 Ig Nobel winners, awarded Thursday at Harvard University by the Annals of Improbable Research magazine”

Europeans drawn from three ancient ‘tribes’ – Paul Rincon – BBC News

“The modern European gene pool was formed when three ancient populations mixed within the last 7,000 years, Nature journal reports.”

Bowl Half Empty: Dogs Can Be Pessimists – Richard Farrell – Discovery

“New PhD research out of the University of Sydney by Dr. Melissa Starling, from the school’s Faculty of Veterinary Science, sought to find out if dogs had underlying personalities that tended toward either optimism of pessimism.”

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