March 18, 2015

Human skin microbiome

Book (hopefully also covering women’s skin): The Epidermis of Man: Co-existing with Commensals – Eds. Peter J Heidt et al.

Human oral microbiome

Salivary Microbiota Associated with Immunoglobulin A Nephropathy – Maria Piccolo – Microbial Ecology

Human gut microbiome

ReviewGut bacteria in children with autism spectrum disorders: challenges and promise of studying how a complex community influences a complex disease – Rosa Krajmalnik-Brown – Microbial Ecology in Health and Disease

Microbiome of pregnancy and birth

The Perinatal Microbiome and Pregnancy: Moving Beyond the Vaginal Microbiome –
Prince AL – CSH Perspect Med (only NCBI link available as of now)

Association between breastfeeding and intelligence, educational attainment, and income at 30 years of age: a prospective birth cohort study from Brazil – Cesar G Victora – The Lancet

Review: Individualized medicine and the microbiome of the reproductive tract – Andrea G. Braundmeier – Frontiers in Physiology

Animal and other models

The Quorum Sensing Peptides PhrG, CSP and EDF Promote Angiogenesis and Invasion of Breast Cancer Cells In Vitro – Bart De Spiegeleer – PLOS ONE

Registered report of a replication study: Intestinal inflammation targets cancer-inducing activity of the microbiota – Kate Eaton – eLIFE

Ablation of Tumor Necrosis Factor Is Associated with Decreased Inflammation and Alterations of the Microbiota in a Mouse Model of Inflammatory Bowel Disease – Yava L. Jones-Hall – PLOS ONE

Phytase Modulates Ileal Microbiota and Enhances Growth Performance of the Broiler Chickens – Anna Ptak – PLOS ONE

Intestinal Microbiota Succession and Immunomodulatory Consequences after Introduction of Lactobacillus reuteri I5007 in Neonatal Piglets – Chengli Hou – PLOS ONE

Animal microbiome

MonkeysMetagenomic analysis of the Rhinopithecus bieti fecal microbiome reveals a broad diversity of bacterial and glycoside hydrolase profiles related to lignocellulose degradation – Bo Xu – BMC Genomics

FrogsComposition of symbiotic bacteria predicts survival in Panamanian golden frogs infected with a lethal fungus – Matthew H. Becker – Proceedings of the Royal Society B

CowsAltered Microbiomes in Bovine Digital Dermatitis Lesions, and the Gut as a Pathogen Reservoir – Martin Zinicola – PLOS ONE

Culture based, horses: Occurrence of bacteria and polymorphonuclear leucocytes (PMNLs) in foetal compartments at parturition; relationships with foal and mare health in the peripartum period- E. Hemberg – Theriogenology

BeesVariation in Honey Bee Gut Microbial Diversity Affected by Ontogenetic Stage, Age and Geographic Location – Zuzana Hroncova – PLOS ONE

Bees: Deep Sequencing and Ecological Characterization of Gut Microbial Communities of Diverse Bumble Bee Species – Haw Chuan Lim – PLOS ONE

Sponges: Molecular investigation of the microbial community associated with the fire sponge, Tedania ignis, in Bermuda – Nicholas J Jouett – PeerJ

Millipedes: Microbial dynamics in food, intestine and fecal pellets of two endemic pill-millipedes (Arthrosphaera: Sphaerotheriida) of the Western Ghats [PDF] – C.N. Ambarish and K.R. Sridhar – Journal of Agricultural Technology

Mosquitoes: RNA shotgun metagenomic sequencing of northern California (USA) mosquitoes uncovers viruses, bacteria, and fungi – James Angus Chandler – Frontiers in Microbiology

Soil and plant root microbiome

Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench) – Mapula Kgomotso Annah Maropola – Journal of Microbiological Methods

Rhizosphere microbial community manipulated by 2 years of consecutive biofertilizer application associated with banana Fusarium wilt disease suppression – Zongzhuan Shen – Biology and Fertility of Soils

The Effect of Phylogenetically Different Bacteria on the Fitness of Pseudomonas fluorescens in Sand Microcosms – Olaf Tyc – PLOS ONE

Organic amendments in avocado crops induce suppressiveness and influence the composition and activity of soil microbial communities – Nuria Bonilla – Applied and Environmental Microbiology

Water microbiome

The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China – Lemian Liu – The ISME Journal

Marine Fungi from Deep Subseafloor Sediments: Species richness and Adaptation -Vanessa Rédou – Applied and Environmental Microbiology

Microbial Methane Potential for the South Sumatra Basin Coal: Formation Water Screening and Coal Substrate Bioavailability – Rita Susilawati – Energy Procedia

Site history and edaphic features override the influence of plant species on microbial communities in restored tidal freshwater wetlands – Christine E. Prasse – Applied and Environmental Microbiology

Spatial variability of microbial assemblages associated with a dominant habitat-forming seaweed – Alexandra H. Campbell – Frontiers in Microbiology

Bioreactor microbiome

Dissecting microbial community structure and methane-producing pathways of a full-scale anaerobic reactor digesting activated sludge from wastewater treatment by metagenomic sequencing – Jianhua Guo – Microbial Cell Factories

Anaerobic codigestion of pretreated wheat straw with cattle manure and analysis of the microbial community – Zilin Song – Bioresource Technology

Analysis of Microbial Communities in the Oil Reservoir Subjected to CO2-Flooding by Using Functional Genes as Molecular Biomarkers for Microbial CO2 Sequestration – Jin-Feng Liu – Frontiers in Microbiology

Bacterial and archaeal guilds associated with electrogenesis and methanogenesis in paddy field soil – Bo Lin – Geoderma

Food microbiology

Comparing natural and selected starter cultures in meat and cheese fermentations – Daniela Bassi – Current Opinion in Food Science

Phages and viruses

PerspectiveThe Next Epidemic — Lessons from Ebola – Bill Gates – The New England Journal of Medicine

Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages – Simon Roux – Frontiers in Microbiology

Isolation of Phages for Phage Therapy: A Comparison of Spot Tests and Efficiency of Plating Analyses for Determination of Host Range and Efficacy – Mohammadali Khan Mirzaei – PLOS ONE

Evaluation of a Viral Microarray Based on Simultaneous Extraction and Amplification of Viral Nucleotide Acid for Detecting Human Herpesviruses and Enteroviruses – Yi Liu – PLOS ONE

Review: Origins and evolution of viruses of eukaryotes: The ultimate modularity – Eugene V. Koonin – Virology

Metagenomics and bioinformatics

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures – Tracey Allen K. Freitas – Nucleic Acid Research

k-mer analysisCrossing the streams: a framework for streaming analysis of short DNA sequencing reads – Qingpeng Zhang – PeerJ

Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum – Keith H. Turner – PNAS USA

Hypothesis: Systems modeling approaches for microbial community studies: From metagenomics to inference of the community structure – Mark Hanemaaijer – Frontiers in Microbiology


Review: Role of Resistant Starch in Improving Gut Health, Adiposity, and Insulin Resistance – Michael J Keenan – Advances in Nutrition

Microbial Degradation of Whole-Grain Complex Carbohydrates and Impact on Short-Chain Fatty Acids and Health – Knud Erik Bach Knudsen – Advances in Nutrition

Microbes in the news

Pet Peeves on 16S rRNA gene sequencing – Noah Fierer – Fierer lab

Can Probiotic Bacteria Save An Endangered Frog? – Ed Yong – National Geographic

New paper examines social effects on the gut microbiome of wild baboons – William G. Gilroy – Notre Dame News

Breast-Feeding Boosts Chances Of Success, Study In Brazil Finds – Rob Stein – NPR

Breast-Feeding May Have Benefits Decades Later – Nicholas Bakalar – New York Times

Lab creates bioinformatics tool for metagenome analysis –

Could Man’s Best Friend Be Man’s Best Medicine? – Alexis Blue – University of Arizona

Dog germs may be good for you – Bradley J. Fikes – UT San Diego

The vaginal microbiome changes during and after pregnancy – American Microbiome Institute

Can the bacteria in your bowels increase your cancer risk? – Amy Yurkanin –

Your microbiome: groundbreaking research about our gut bacteria shows it could be the key to health – Jacqui Gibbons – High 50 Health

From human gut to the smartphone, new health monitoring – Tim Sandle – Digital Journal

Parasite turns shrimp into voracious cannibals – Chris Bunting – University of Leeds

Gut Bacteria, ASD, and Probiotics: Exploring the Relationship – Elizabeth Gough-Gordon – EMPR

New Molecular Tool Assesses Vaginal Microbiome Health, Diagnosis Infections-Fast – ASM

Technology helps unlock secrets of rare bacteria –

Stanford researchers unravel secrets of shape-shifting bacteria – Tom Abate and Chris Cesare – Stanford News

VideoAlexander Fleming – Inventor of Penicillin – Scientiflix

Bik’s Picks

Ultrasoundings: monitoring a pregnant dolphin – Bill Van Bonn – Shedd Aquarium

Why are there so many freaking beetles? Science may finally have the answer. – Rachel Feltman – Washington Post

The myopia boom: Short-sightedness is reaching epidemic proportions. Some scientists think they have found a reason why – Elie Dolgin – Nature


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