Human microbiome, June 10

Today we’ll cover the lung microbiome, salivary gland function, NEC, and sequencing of cosmid clones.
Oral microbiome

AutophagyAutophagy Correlates with Maintenance of Salivary Gland Function Following Radiation – Maria Morgan-Bathke – Nature Scientific Reports

“Thus, autophagy appears to play a beneficial role in salivary glands following radiation”

UbiquitousUbiquitous Sialometabolism Present among Oral Fusobacteria – Saori Yoneda – PLOS ONE

“Using microarray analysis, we examined the transcriptional response of F. nucleatum subspecies nucleatum to whole blood in order to identify some of the genetic responses that might occur during the transition from health to disease.”

NYU and UCSF researchers develop a framework for monitoring oral cancer – ScienceCodex

“”We know that other cancers, including gallbladder, colon, lung and prostate, have been associated with particular bacterial infections, so we hypothesized that shifts in the composition of the normal oral cavity microbiome could be promoters or causes of oral cancer,” said Dr. Albertson.”

Respiratory microbiome

Screen Shot 2014-06-10 at 9.32.19 PMBreathing Life into Lung Microbiome Research – Rina Shaikh-Lesko – The Scientist

“Although it’s far less populated than the mouth community that helps feed it, researchers increasingly appreciate the role of the lung microbiome in respiratory health.”

Impact off extImpact of Experimental Human Pneumococcal Carriage on Nasopharyngeal Bacterial Densities in Healthy Adults – Joshua R. Shak – PLOS ONE

“To better understand how these bacteria change in relation to pneumococcal colonization, we used species-specific quantitative PCR to examine bacterial densities in 52 subjects 7 days before, and 2, 7, and 14 days after controlled inoculation of healthy human adults with S. pneumoniae serotype 6B.”

Pregnancy and Birth

BrainModerate and Late Preterm Birth: Effect on Brain Size and Maturation at Term-Equivalent Age – Jennifer M. Walsh – Radiology

“MLPT birth is associated with smaller brain size, less-developed myelination of the posterior limb of the internal capsule, and more immature gyral folding than those associated with full-term birth. “

Preemie Research Highlights Concerns With Human Experimentation – Frederick Reese – Mintpress

“Parents weren’t fully aware of the risks associated with a medical research trial they allowed their babies to participate in.”

Screen Shot 2014-06-10 at 9.30.20 PMSmall Intestinal Intraepithelial TCRγδ+ T Lymphocytes Are Present in the Premature Intestine but Selectively Reduced in Surgical Necrotizing Enterocolitis – Jörn-Hendrik Weitkamp – PLOS ONE

“In human preterm infants, the proportion of IEL was reduced by 66% in 11 NEC ileum resections compared to 30 non-NEC controls (p<0.001). While γδ IEL dominated over conventional αβ IEL early in gestation in mice and in humans, γδ IEL were preferential decreased in the ileum of surgical NEC patients compared to non-NEC controls (50% reduction, p<0.05).”

Antibiotics and microbiome

Synthetic Biologics and Enterome Bioscience Collaborate on Microbiome Research to Support Synthetic Biologics’ C. difficile Program – MarketWatch

“Synthetic Biologics, Inc. (nyse mkt:SYN), a developer of novel anti-infective biologic and drug candidates targeting specific pathogens that cause serious infections and diseases, and Enterome Bioscience SA, a pioneer in the development of innovative disease management solutions based on a deep understanding of the gut microbiome, today announced that they have entered into an agreement to conduct metagenomic research on the effects of beta-lactam antibiotics on the gastrointestinal microflora (microbiome) of human patients”

Animal models of human disease

Screen Shot 2014-06-10 at 9.38.10 PMSaccharomyces boulardii Administration Changes Gut Microbiota and Reduces Hepatic Steatosis, Low-Grade Inflammation, and Fat Mass in Obese and Type 2 Diabetic db/db Mice – Amandine Everard – mBio

“Here we found that type 2 diabetic and obese mice (db/db) treated with Saccharomyces boulardii exhibited reduced body weight, fat mass, hepatic steatosis, and inflammatory tone. “

Metagenomics and sequencing

Evaluation of a pooledEvaluation of a Pooled Strategy for High-Throughput Sequencing of Cosmid Clones from Metagenomic Libraries – Kathy N. Lam – PLOS ONE

“We investigated a hybrid Sanger/Illumina pooled sequencing strategy that omits barcoding altogether, and we evaluated this strategy by comparing the pooled sequencing results to reference sequence data obtained from traditional barcode-based sequencing of the same set of clones. “


Human microbiome digest, June 4, 2014

Today’s featured paper describes the gut microbiota of malnourished Bangladeshi children and was published in Nature. But we also cover oral cancer and babies’ dummies (pacifiers).

Gut microbiome

Screen Shot 2014-06-05 at 12.35.59 AMPersistent gut microbiota immaturity in malnourished Bangladeshi children – Sathish Subramanian – Nature

“ In the current study, bacterial species whose proportional representation define a healthy gut microbiota as it assembles during the first two postnatal years were identified by applying a machine-learning-based approach to 16S ribosomal RNA data sets generated from monthly faecal samples obtained from birth onwards in a cohort of children living in an urban slum of Dhaka, Bangladesh, who exhibited consistently healthy growth. “

Screen Shot 2014-06-05 at 12.37.44 AMAnd an accompanying News And Views: Population health: Immaturity in the gut microbial community – Elizabeth K. Costello- Nature

“Undernourished children fall behind not only on growth, but also on maturation of their intestinal bacterial communities, according to a study comparing acutely malnourished and healthy Bangladeshi children.”

Screen Shot 2014-06-05 at 12.36.53 AMThe Scientist also writes about the Subramanian paper: How Malnutrition Affects the Microbiome – Rina Shaikh-Lesko – The Scientist

“The gut bacterial communities of severely malnourished children appear to be less developed than those of healthy children, a study on Bangladeshi infants and toddlers finds.”

Oral microbiome

Screen Shot 2014-06-05 at 12.34.59 AMChanges in Abundance of Oral Microbiota Associated with Oral Cancer – Brian L. Schmidt – PLOS ONE

“To investigate changes in the microbiome associated with oral cancers, we profiled cancers and anatomically matched contralateral normal tissue from the same patient by sequencing 16S rDNA hypervariable region amplicons. “

The strange micro-biome that is your mouth – Paul Kulpinski – Mountain Waves Healing Arts

“In this post I will report on my most recent self-experiment. Some of this experiment was intentional, and some of it was non-intentional – with regards to my oral hygiene at least.”

Pregnancy and birth

Screen Shot 2014-06-05 at 12.43.20 AMMothers should suck their babies’ dummies, scientists say – Sarah Knapton – The Telegraph

“Children whose mother’s sucked their dummies to clean them were a third less likely to develop asthma and eczema, Prof Graham Rook, told the Cheltenham Science Festival. “If the parents pick up the dummy right away and sterilises it or replace it with a new clean one, that child has a considerably greater chance of having eczema and asthma,” he said.”

Influence of interpregnancy interval on birth timing – EA DeFranco – BJOG: An International Journal of Obstetrics & Gynaecology

“While short IPI is a known risk factor for preterm birth, our data show that inadequate birth spacing is associated with decreased gestational age for all births.”

Health of Hispanic Moms and Babies a Growing Concern, New Report Says – Hola Arkansas

“March of Dimes Global Ambassador Thalia Urges Hispanic Women To Be Informed About Pregnancy and Baby Health”


General microbiome
Pharmacomicrobiomics: The Impact of Human Microbiome Variations on Systems Pharmacology and Personalized Therapeutics – A summary of key findings and applications from the Human Microbiome Project. – Marwa ElRakaiby – Omics Journal

In this review article, we summarize the key findings and applications of the HMP that may impact pharmacology and personalized therapeutics.