Human microbiome, July 29

Papillomaviruses in human skin, gastric mucosa in cancer patients, breast milk metabolome, microbiome of a human family, and more.

Skin microbiome

Deep sequencing extends the diversity of human papillomaviruses in human skin
Davit Bzhalava – Nature Scientific Reports

“This deeper sequencing without prior PCR of a pool of 142 whole genome amplified skin lesions identified 23 known HPV types, 3 novel putative HPV types and 4 non-HPV viruses.”

Gastric microbiome

Differences in Gastric Mucosal Microbiota Profiling in Patients with Chronic Gastritis, Intestinal Metaplasia, and Gastric Cancer Using Pyrosequencing Methods – Chang Soo Eun – Helicobacter

“Gastric mucosal biopsy samples were collected from 31 patients during endoscopy. After the extraction of genomic DNA, variable region V5 of the 16S rRNA gene was amplified. PCR products were sequenced using 454 high-throughput sequencer. “

Pregnancy and Birth

Breast milk metabolome characterization in a single phase extraction, multiplatform analytical approach – Alma Villaseñor – Analytical Chemistry

“We conducted this single-phase extraction procedure on a representative pool of BM, and characterized the metabolic composition using LC-QTOF-MS and GC-Q-MS for polar and lipidic metabolites. “

Effects of Bifidobacterial Supplementation to Pregnant Women and Infants in the
Prevention of Allergy Development in Infants and on Fecal Microbiota [PDF]- Tadao Enomoto – Allergology International

“Effects of Bifidobacterial Supplementation to Pregnant Women and Infants in the Prevention of Allergy Development in Infants and on Fecal Microbiota”

Gut microbiome
The dynamics of a family’s gut microbiota reveal variations on a theme – Patrick D Schloss – Microbiome

“Here we study a chronosequence of the gut microbiota found in eight individuals from a family consisting of two parents and six children ranging in age from two months to ten years old.”

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression – Charles K. Fisher – PLOS ONE

“Here we introduce an approach, Learning Interactions from MIcrobial Time Series (LIMITS), that overcomes these obstacles. LIMITS uses sparse linear regression with boostrap aggregation to infer a discrete-time Lotka-Volterra model for microbial dynamics. “

Antivirulence Activity of the Human Gut Metabolome – L. Caetano M. Antunes – mBio

“We found that a secreted molecule produced by clostridia acts as a strong repressor of Salmonella virulence, obliterating expression of the Salmonella pathogenicity island 1 as well as host cell invasion.”

 Metagenomic Identification of a Novel Salt Tolerance Gene from the Human Gut Microbiome Which Encodes a Membrane Protein with Homology to a brp/blh-Family β-Carotene 15,15′-Monooxygenase – Eamonn P. Culligan – PLOS ONE

“Herein, we report the identification and characterisation of a novel stress tolerance gene from the human gut metagenome. The locus, assigned brpA, encodes a membrane protein with homology to a brp/blh-family β-carotene monooxygenase. “

Review: Archaea and the human gut: New beginning of an old story [DOC]- Gaci N – World Journal of Gastroenterology

“Here we provide an updated census of the archaeal diversity associated to human GIT and their possible role in the gut physiology and health.”

 

Animal models of human microbiome and disease

Maternal high protein or prebiotic fiber diets affect maternal milk composition and gut microbiota in rat dams and their offspring – Megan C. Hallam – Obesity

“Fecal microbiota was analyzed in dams at parturition and 2 weeks post-partum and in offspring at 5 and 22 weeks along with cecal digesta at termination.”

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Microbiome and general biology, June 20

It was a quiet day on the microbiome research front, so there will only be one post today. But, with vampire bats, Bacillus anthracis, and fish-eating spiders, it’s a good one!

Pregnancy and Birth

Screen Shot 2014-06-20 at 10.08.36 PMStudy Finds Certain Birth Defects are more Common in Hispanics – Cheri Cheng

“”One of the things that caught our eye was, while Hispanics represent 17 percent of the population, 24 percent of premature babies are Hispanic,” said Dr. Edward McCabe, senior vice president and chief medical officer of the March of Dimes, a nonprofit organization.”

Animal models of human microbiota

BacillusColonic Immune Suppression, Barrier Dysfunction, and Dysbiosis by Gastrointestinal Bacillus anthracis Infection – Yaíma L. Lightfoot – PLOS ONE

“Herein, we investigated the pathogenesis of GI anthrax in animals orally infected with toxigenic non-encapsulated B. anthracis Sterne strain (pXO1+ pXO2−) spores that resulted in rapid animal death.”

Screen Shot 2014-06-20 at 9.53.32 PMBiology Students Study Stomach Bacteria – Pengxeu Thao – University of Minnesota Morris

Wyckoff and her students are spending the summer studyingHelicobacter pylori (H. pylori), a Gram-negative bacterium found in the human stomach.”

Amphibian microbiome

AmphibCool Temperatures Reduce Antifungal Activity of Symbiotic Bacteria of Threatened Amphibians – Implications for Disease Management and Patterns of Decline – Joshua H. Daskin – PLOS ONE

“We characterized, at a range of temperatures approximating natural seasonal variation, the anti-Bd activity of bacterial symbionts from the skins of three species of rainforest tree frogs (Litoria nannotis, Litoria rheocola, and Litoria serrata)”

Plant microbiology

Screen Shot 2014-06-20 at 10.09.21 PMScientists look to bacteria to protect crop yields in the face of climate change – Jennifer Huizen – E&E Publishing

“If proved effective, this technology would decrease the amount of key nutrients like nitrogen and, most notably, water needed by the plant, while increasing the yield,” said Lin Myat, a postdoctoral fellow of molecular biology and genetics at Cornell “

belongs to

Screen Shot 2014-06-20 at 10.06.07 PMβ-Carboxysomal proteins assemble into highly organized structures in Nicotiana chloroplasts – Myat T. Lin – The Plant Journal

“We demonstrate that a foreign protein can be targeted with a 17-amino-acid CcmN peptide to the shell proteins inside chloroplasts. Our experiments establish the feasibility of introducing carboxysomes into chloroplasts for the potential compartmentalization of Rubisco or other proteins.”

Food microbiology

Screen Shot 2014-06-20 at 10.23.17 PMHaley Oliver: Master of Meat – Jef Akst – The Scientist

“In her own lab at Purdue University, Oliver studies the spread of Listeria in other foods, such as melons, and investigates sanitation strategies that may limit contamination and increase food shelf life. “

Infection and host response

InflammationInflammation: Gone with Translation – Carola G. Vinuesa, Thomas Preiss – PLOS Genetics

“Over the last few years, a number of studies have investigated global gene activation induced by pathogen-derived stimuli to gain insights into the modes of induction of the inflammatory mediators and regulators.”

Dengue

Screen Shot 2014-06-20 at 9.18.31 PMThe Need for More Research and Public Health Interventions on Dengue Fever in Burkina Faso – Valéry Ridde – PLOS Neglected Tropical Diseases

“…our aim in this article is to draw attention to the need for rapid deployment of research and interventions on dengue fever in Burkina Faso, because it appears to have been overlooked, with the focus being, instead, on malaria.”

Dengue NKTInvariant NKT Cell Response to Dengue Virus Infection in Human
Ponpan Matangkasombut – PLOS Neglected Tropical Diseases

“iNKT cells activation were analyzed by the expression of CD69 by flow cytometry. Their cytokine production was then analyzed after α-GalCer stimulation”

General microbiology

Screen Shot 2014-06-20 at 9.19.15 PMVampire Bats and Rabies: Toward an Ecological Solution to a Public Health Problem – Benjamin Stoner-Duncan – PLOS Neglected Tropical Diseases

“In the first half of 2011, 21 school-age children and two adults died of rabies transmitted by the common vampire bat (Desmodus rotundus) in and around the small rural village of Yupicusa in the Peruvian Amazon”

VectorCrossing the Interspecies Barrier: Opening the Door to Zoonotic Pathogens – Christian Gortazar – PLOS Pathogens

“The species barriers separating nonhuman animal species from humans represent a major hurdle for effective exposure to, infection by, and subsequent spread of zoonotic pathogens among humans”

Screen Shot 2014-06-20 at 9.35.19 PMHuman sweat can reduce bacteria fighting capabilities – ZeeNews

“A new research has revealed that human sweat can diminish bacteria-fighting qualities of brass objects like door knobs and taps within an hour of contact.”

 

Dr. Bik’s Picks

Screen Shot 2014-06-20 at 10.11.49 PMFish Predation by Semi-Aquatic Spiders: A Global Pattern – Martin Nyffeler – PLOS ONE

“More than 80 incidences of fish predation by semi-aquatic spiders – observed at the fringes of shallow freshwater streams, rivers, lakes, ponds, swamps, and fens – are reviewed.”

Screen Shot 2014-06-20 at 10.15.09 PMUS sets up honey bee loss task force – BBC News

“In the plan announced on Friday, Mr Obama directed the EPA and the agriculture department to lead a government-wide task force to develop a strategy within six months to fight bee and other pollinator declines.“

Screen Shot 2014-06-20 at 10.17.07 PMStrict diet suspends development, doubles lifespan of worms – Science Daily

“Researchers at Duke University found that taking food away from C. elegans triggers a state of arrested development: while the organism continues to wriggle about, foraging for food, its cells and organs are suspended in an ageless, quiescent state. “

Screen Shot 2014-06-20 at 10.26.39 PMFinding thoughts in speech: How human brain processes thoughts during natural communication – Science Daily

“The novelty of the authors’ approach is that the participants were not instructed to think and talk about a given topic in an experimental setting. “

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