Microbiome digest, October 24, 2014

Microbiome of placentas, infant respiratory microbiome, metabolomics, mutipartite genomes, microbes in the news, and some weekend picks.
Human microbiome general

Microbiome/microbiota and allergies – Yuzaburo Inoue, Naoki Shimojo – Seminars in Immunopathology

“In this review, we summarize the recent findings regarding the importance of the microbiome/microbiota in the development of allergic diseases and also the results of interventional studies using probiotics or prebiotics to prevent allergies.”

Pregnancy and birth

Term and preterm labour are associated with distinct microbial community structures in placental membranes which are independent of mode of delivery – Ronan M. Doyle – Placenta

“In this study, 16S rDNA pyrosequencing was used to identify bacteria in placental membranes. Caesarean sections and vaginal deliveries at term were found to harbour common genera”

Early Respiratory Microbiota Composition Determines Bacterial Succession Patterns and Respiratory Health in Children – Giske Biesbroek – Am J Respir Crit Care Med.

“Upper respiratory microbiota profiles of 60 healthy children at the ages of 1.5, 6, 12 and 24 months were characterized by 16S-based pyrosequencing”

From the “old NEC” to the “new NECs” – Melania Puddu – Journal of Pediatric and Neonatal Individualized Medicine

“This review describes in detail the new NECs especially those which affect preterm infants: contagion or lymphocytosis associated, transfusion associated and cow’s milk allergy associated.”


The effects of variable sample biomass on comparative metagenomics – Meghan Chafee – Environmental Microbiology

“We investigated the interacting effects of DNA input and library amplification by PCR on comparative metagenomic analysis using dilutions of a single complex template from an Arabidopsis-associated microbial community.”


The nexus of syntrophy-associated microbiota in anaerobic digestion revealed by long-term enrichment and community survey – Takashi Narihiro – Environmental Microbiology

“16S pyrotag analysis revealed core populations of known syntrophs (six clades) and methanogens (nine clades) associated with acid degradation, and evidence for substrate- and/or inoculum-dependent specificity in syntrophic partnerships.”

In Vitro Fermentation of Lactulose by Human Gut Bacteria – Bingyong Mao – Journal of Agricultural and Food Chemistry

“This study aimed to identify lactulose-metabolizing bacteria in the human gut, using in-silico and traditional culture methods. “

Epigenomic regulation of host–microbiota interactions – Theresa Alenghat, David Artis – Trends in Immunology

“We review recent advances in understanding the interplay between the microbiota and mammalian epigenomic pathways, and highlight emerging findings that implicate a central role for histone deacetylases (HDACs) in orchestrating host–microbiota interactions.”

More microbiology

Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction – George C. diCenzo – PLOS Genetics

“To gain insight into the role and evolutionary history of these replicons, we have ‘reversed evolution’ by constructing a S. meliloti strain consisting solely of the chromosome and lacking the pSymB chromid and pSymA megaplasmid.”

Microbes in the news

How An Antibiotic Gene Jumped All Over The Tree of Life – Ed Yong – National Geographic

“Metcalf showed that it has also jumped from bacteria into every other major branch of life. It’s in animals, plants, fungi, archaea, and even some viruses.”

Research investigates bacteria on banknotes – Harper Adams University

“This study investigates how easy it is for bacteria and pathogens to survive on currency and whether the material the notes are made of, has an effect on the transfer.”

How millennials will save us all – Jennifer Block – Quartz

“Millennials get a bad rap for loading up on debt, mooching off their parents, and hiding behind technology. But there’s one problem that they may be particularly suited to tackling: our shrinking microbiome.“

Bik’s Picks

World’s Most Asked Questions: How Much Water Should I Drink a Day? – SciShow – Youtube

“People ask Google everything under the sun. One of the most commonly searched questions in the world is “How much water should I drink a day?” SciShow has the answer!”

Ten Simple Rules for Writing a PLOS Ten Simple Rules Article – Harriet Dashnow – PLOS Computational Biology

“This search left us wanting, until we discovered the PLOS Ten Simple Rules collection. We have found them to be a series of concise articles that capture the professional zeitgeist of being a scientist in an approachable manner.”

Satire: Ambitious New High-Speed Rail Plan Will Fly Americans To Japan To Use Their Trains – The Onion

“The transit system that the U.S. has needed for so long is now just a 7,000-mile plane journey to Tokyo’s Narita International Airport and a brief passage through Japanese customs away,” Obama continued.”