Thanks for all the encouraging comments here and per email! This blog appears to fill an important niche in the coverage of scientific microbiome research, in a wide range of hosts and environmental sources, so I will continue writing this. But please spread the word – 100 viewers per day is nice, but more is better!
As one of the commenters suggested, I will try to mark Reviews as such, so they are easier to find (or skip).
Here we go with a new post. It’s Monday, so there is a lot to cover.
Human oral microbiome
Herpesvirus in the oral cavity of children with leukaemia and its impact on the oral bacterial community profile – Tacíria M Bezerra – Journal of Clinical Pathology
Bifidobacteria strains isolated from stools of iron deficient infants can efficiently sequester iron – Pamela Vazquez-Gutierrez – BMC Microbiology
Review: Tuning the Brain-Gut Axis in Health and Disease – Rainbo Hultman – Current Stem Cell Reports
Microbiome of pregnancy and birth
Clinical chorioamnionitis at term I: microbiology of the amniotic cavity using cultivation and molecular techniques – Roberto Romero – Journal of Perinatal Medicine
Review: Relationship between periodontal diseases and preterm birth: Recent epidemiological and biological data – Moneet Walia, Navdeep Saini – International Journal of Applied and Basic Medical Research
Review: Viral Infections During Pregnancy – Michelle Silasi – American Journal of Reproductive Immunology
Review: Stress and the Commensal Microbiota: Importance in parturition and infant neurodevelopment – Tamar L. Gur – Frontiers in Psychiatry
Animal models of microbiome research
Commensal microbiota influence systemic autoimmune responses – Jens T Van Praet – The EMBO Journal
Modulation of the Intestinal Microbiota Is Associated with Lower Plasma Cholesterol and Weight Gain in Hamsters Fed Chardonnay Grape Seed Flour – Hyunsook Kim – J. Agric. Food Chem
Dysbiotic bacteria translocate in progressive SIV infection – Z Klase – Mucosal Immunology
Animal microbiome
Comparison of the gut microbiomes of 12 bony fish and 3 shark species – Carrie E. Givens – Marine Ecology Progress Series
Genomes of the rice pest brown planthopper and its endosymbionts reveal complex complementary contributions for host adaptation – Jian Xue – Genome Biology
Review: Towards an integrated understanding of the consequences of fungus domestication on the fungus-growing termite gut microbiota – Michael Poulsen – Environmental Microbiology
Plant microbiome
Primary succession of Bistorta vivipara (L.) Delabre (Polygonaceae) root associated fungi mirrors plant succession in two glacial chronosequences – Marie Davey – Environmental Microbiology
Book: Beneficial Plant-Bacterial Interactions – Bernard R. Glick
Soil and sediment microbiome
Soil Bacterial Communities are Shaped by Temporal and Environmental Filtering: Evidence from a Long-Term Chronosequence – Zachary Freedman and Donald R. Zak – Environmental Microbiology
Abstract: Garlic mustard and its effects on soil microbial communities in a sandy pine forest in central Illinois – Alexander B Faulkner – Proceedings, 19th Central Hardwood Forest Conference; 2014 March
Bacterial community composition at anodes of microbial fuel cells for paddy soils: the effects of soil properties – Ning Wang – Journal of Soils and Sediments
Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine – Lur Epelde – FEMS Microbiology Ecology
Soil-Borne Microbiome: Linking Diversity to Function – Lucas W. Mendes – Microbial Ecology
Phytoextraction of nickel and rhizosphere microbial communities under mono- or multispecies hyperaccumulator plant cover in a serpentine soil – Marie Rue – Australian Journal of Botany
Methane-derived carbon flow through microbial communities in arctic lake sediments – Ruo He – Environmental Microbiology
Review: Potential applications of soil microbial ecology and next-generation sequencing in criminal investigations – Sheree J. Finley – Applied Soil Ecology
Water microbiome
Book (open access): Subseafloor Biosphere Linked to Hydrothermal Systems
Some chapters of interest:
– Intra-Field Variation of Prokaryotic Communities On and Below the Seafloor in the Back-Arc Hydrothermal System of the Southern Mariana Trough – Shingo Kato
– Microbial Cell Densities, Community Structures, and Growth in the Hydrothermal Plumes of Subduction Hydrothermal Systems – Michinari Sunamura, Katsunori Yanagawa
– Comparative Investigation of Microbial Communities Associated with Hydrothermal Activities in the Okinawa Trough – Ken Takai, Satoshi Nakagawa
– Quantification of Microbial Communities in Hydrothermal Vent Habitats of the Southern Mariana Trough and the Mid-Okinawa Trough – Katsunori Yanagawa
Microbiome of the built environment
Review: From commensalism to mutualism: integrating the microbial ecology, building science, and indoor air communities to advance research on the indoor microbiome – Brent Stephens – Indoor Air
Food microbiology
Diversity of Lactic Acid Bacteria Isolated from Brazilian Water Buffalo Mozzarella Cheese – Luana Faria Silva – Journal of Food Science
Metagenomics
Metagenome assembly through clustering of next-generation sequencing data using protein sequences – Mikang Sim, Jaebum Kim – Journal of Microbiological Methods
An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data – Xutao Deng – Nucleic Acids Research
Review: Tales from the crypt and coral reef: the successes and challenges of identifying new herpesviruses using metagenomics – Charlotte J. Houldcroft and Judith Breuer – Frontiers in Microbiology
Metabolomics, transcriptomics, and proteomics
Effects of high fructose and salt feeding on systematic metabonome probed via 1H NMR spectroscopy – Yongxia Yang – Magnetic Resonance in Chemistry
Also see above: Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine – Lur Epelde – FEMS Microbiology Ecology
Isolation and characterization of novel lipases/esterases from a bovine rumen metagenome – Florence Privé – Applied Microbiology and Biotechnology
Review: Proteomics of hosts and pathogens in cystic fibrosis – Karthik Shantharam Kamath – Proteomics – Clinical Applications
Bioinformatics
Book chapter: e-DNA Meta-Barcoding: From NGS Raw Data to Taxonomic Profiling – Fosso Bruno – RNA Bioinformatics / Methods in Molecular Biology
Book chapter: Deciphering Metatranscriptomic Data – Evguenia Kopylova – RNA Bioinformatics / Methods in Molecular Biology
Amplification and sequencing techniques
Quantitative evaluation of bias in PCR amplification and next-generation sequencing derived from metabarcoding samples – Marta Pawluczyk – Analytical and Bioanalytical Chemistry
Probiotics
Consecutive oral administration of Bifidobacterium longum MM-2 improves the defense system against influenza virus infection by enhancing natural killer cell activity in a murine model – Tomohiro Kawahara – Microbiology and Immunology
Microbes in the news
* One Scientist’s Race To Help Microbes Help You – Katherine Harmon Courage – NPR Shots
Researchers reveal link between the microbiome of young mice and later onset of autoimmune disease – News Medical
Podcast: Do Gut Bacteria Tell Us What To Eat? – Beth Anne Austein / The Food Guys – Montana Public Radio
The Fungus in Your Cheese Is Having Weird Sex – Rose Eveleth – Smithsonian.com
Disturbed gut microbiome linked to Parkinson’s disease – News Medical
#BacteriaHysteria
Honoring last week’s Law Enforcement Appreciation Day: Sheriff’s Office gets bacteria cleanse – Richard Goad – Cleveland Banner
Science, publishing, and career
7 Tips for Women at Science Conferences – Hilda Bastian – PLOS Blogs
Bik’s Picks
Do 80% of Americans not know there’s DNA in food? – Ben Lillie blog
Researchers Who Provided Key Evidence For Gluten Sensitivity Have Now Thoroughly Shown That It Doesn’t Exist – Jennifer Welsh – Business Insider
This whale might be old, but it does not look too happy (or it is swimming upside down?)
The Secret To Living 200 Years? Ask A Whale – Paul Rodgers – Forbes.com
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Microbiome Digest - Bik's Picks 