March 15, 2015

Microbiome of pregnancy and birth

The vaginal microbiome during pregnancy and the postpartum period in a European population – David A. MacIntyre – Scientific Reports

Probiotic potential of Enterococcus faecalis strains isolated from meconium – Ahmed Khassaf Al Atyaa – Frontiers in Microbiology

Review: The human neonatal gut microbiome: a brief review – Emily C. Gritz and Vineet Bhandari – Frontiers in Pediatrics

Human gut microbiome

Gut microbiome of the Hadza hunter-gatherers – Stephanie L. Schnorr – Nature Communications

Gut microbiome variations during hematopoietic stem cell transplant in severe combined immunodeficiency – Jonathan P. Lane – Journal of Allergy and Clinical Immunology

Despite the title, this is 16S rRNA gene-based analysis: Metagenomic analysis of the impact of nitrofurantoin treatment on the human faecal microbiota – Jascha Vervoort – Journal of Antimicrobial Chemotherapy

Literature review: Mast Cell Activation Disease and Microbiotic Interactions – Lawrence B. Afrin, Alexander Khoruts- Clinical Therapeutics

Review: Autoimmune host–microbiota interactions at barrier sites and beyond – William E. Ruff, Martin A. Kriegel – Trends in Molecular Medicine

Review: Microbiota Regulation of the Mammalian Gut–Brain Axis – Aurelijus Buroka – Advances in Applied Microbiology

Review: IBD and the Gut Microbiota—from Bench to Personalized Medicine – Emanuelle Bellaguarda, Eugene B. Chang – Current Gastroenterology Reports

Review: Mutualistic presence of normal Flora in Human Intestine: A review – Karishma Kabir Nipa- Journal of Bio-Science

Animal models

Monosodium L-Glutamate and Dietary Fat Differently Modify the Composition of the Intestinal Microbiota in Growing Pigs – Feng Z-M – Obesity Facts

Altered profile of gut microbiota after subchronic exposure to neochamaejasmin A in rats – Lifeng Yan – Environmental Toxicology and Pharmacology

Effects of mulberry (Morus alba L.) leaf polysaccharides on growth performance, diarrhea, blood parameters, and gut microbiota of early-weanling pigs – Xiangjie Zhao – Livestock Science

Effect of grinding or pelleting high grain maize- or barley-based concentrates on rumen environment and microbiota of beef cattle – A. Gimeno – Animal Feed Science and Technology

Animal microbiome

Earthworms: Taxonomic and functional annotation of gut bacterial communities of Eisenia foetida and Perionyx excavatus – Arjun Singh – Microbiological Research

Plant microbiome

Diversity and community ecology of forest epiphyte testate amoebae from European Russia – Richard J. Payne – European Journal of Protistology

Soil and plant root microbiome

Effects of single-root-grafting, double-root-grafting and compost application on microbial properties of rhizosphere soils in Chinese protected cucumber (Cucumis sativus L.) production systems – Yinan Gao – Scientia Horticulturae

Response of belowground communities to short-term phosphorus addition in a phosphorus-limited woodland – Uffe N. Nielsen – Plant and Soil

Composition of soil microbiome along elevation gradients in southwestern highlands of Saudi Arabia – Muhammad Yasir – BMC Microbiology

Illumina MiSeq sequencing investigation on the contrasting soil bacterial community structures in different iron mining areas – Chen Hong – Environmental Science and Pollution Research

Geomicrobiology of Iron Layers in the Sediment of Lake Superior – M. Dittrich – Aquatic Geochemistry

Water and ice microbiome

Microbial abundance in surface ice on the Greenland Ice Sheet – Marek Stibal – Frontiers in Microbiology

Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing – Chia Sing Chan – Frontiers in Microbiology

Review: New perspectives in benthic deep-sea microbial ecology – Cinzia Corinaldesi – Frontiers in Marine Science

Bioreactor microbiome

The microbial community of a passive biochemical reactor treating arsenic, zinc, and sulfate-rich seepage – Susan Anne Baldwin – Frontiers in Bioengineering and Biotechnology

Food microbiology

Process-driven bacterial community dynamics are key to cured meat colour formation by coagulase-negative staphylococci via nitrate reductase or nitric oxide synthase activities – María Sánchez Mainar, Frédéric Leroy – International Journal of Food Microbiology

Metagenomics and Bioinformatics

Modelling Computational Resources for Next Generation Sequencing Bioinformatics Analysis of 16S rRNA Samples – Matthew J. Wade – ArXiv

Accurate multiplexing and filtering for high-throughput amplicon-sequencing – Philippe Esling – Nucleic Acids Research

Transmission and Microevolution of USA300 MRSA in U.S. Households: Evidence from Whole-Genome Sequencing – Md Tauqeer Alam – mBio

Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population – Jessica Labonté – Frontiers in Microbiology

ISMapper: Identifying insertion sequences in bacterial genomes from short read sequence data – Jane Hawkey – BioRXiv

Perspective: Wiretapping into microbial interactions by single cell genomics – Ramunas Stepanauskas – Frontiers in Microbiology

Perspective: Bridging the knowledge gap: from microbiome composition to function – Jeremiah J Faith – Molecular Systems Biology

Metabolomics and Transcriptomics

Clostridium difficile heterogeneously impacts intestinal community architecture but drives stable metabolome responses – David Rojo – ISME Journal

Study of the diversity and short-chain fatty acids production by the bacterial community in overweight and obese Mexican children – S. Murugesan – European Journal of Clinical Microbiology & Infectious Diseases

Genomic Analysis of Xylose Metabolism in Members of the Deinoccocus-Thermus Phylum from Thermophilic Biomass-Deconstructing Bacterial Consortia – Yu-Wei Wu – BioEnergy Research

Proteomics as the final step in the functional metagenomics study of antimicrobial resistance – Fiona Fouhy – Frontiers in Microbiology

Fish: Proteomic profile of the skin mucus of farmed gilthead seabream (Sparus aurata) – Juan Jurado – Journal of Proteomics

Transcriptomic analysis of three Veillonella spp. present in carious dentine and in the saliva of caries-free individuals – Thuy Do – Frontiers in Cellular and Infection Microbiology

The transcriptional response of microbial communities in thawing Alaskan permafrost soils – M J. Coolen and William D. Orsi – Frontiers in Microbiology

Review: Mucin glycan foraging in the human gut microbiome – Louise Tailford – Frontiers in Genetics

More microbial science

Untangling the origin of viruses and their impact on cellular evolution – Arshan Nasir – Annals of the New York Academy of Sciences

The Great Escape: Pathogen Versus Host – Eric Kong, Mary Ann Jabra-Rizk – PLOS Pathogens

A fantastic voyage for sliding bacteria – Joshua D. Shrout – Trends in Microbiology

CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity – Roger A. Garrett – Life

Etiology of Pericarditis in a prospective cohort of 1162 cases – Frédérique Gouriet – The American Journal of Medicine

Microbes in the news

Overselling the microbiome award: Dr. Raphael Kellman at MindBodyGreen – Jonathan Eisen – The Tree of Life
belongs to:
Why The Microbiome Is Your Key To Glowing Skin & Healthy Weight – Dr. Raphael Kellman – MindBodyGreen

The Era of the Microbiome – SXSW Session on Monday March 16

Mind Altering Microbes: How your gut microbiome may influence your mood – Jill Carnahan

CDC: Misuse of garments may have led to release of bacteria at Tulane lab – Debra Goldschmidt and Ed Payne – CNN

The dawn of the cyborg bacteria is here – Robert Boos – PRI

Famous Microbiologists – Paul Ehrlich – Today we honor Paul Ehrlich who was born on March 14 in 1912 – LumiByte

Science and art – microbial edition

Bacterial Paintings? New Art Uses Tiny Life Forms – Tia Ghose – LiveScience

How microbes inspire art (Video) – BBC

Fungi on Tea – Microbe World

Louis Pasteur T-shirt – The Strange company

Bik’s Picks

Five research papers that revolutionised health – Deborah Cohen – BBC News Health

Folic acid plus blood pressure drug lowers stroke risk: study – Daily Mail

Man Credits Hot Chili Sauce Challenge for Brain Cancer Diagnosis – Youth Health Magazine

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