Updated status of the microbial census, bacteria in the nasopharynx, deodorant and armpit microbiome, lichen microbiome, fungi on decomposing forest materials, and metagenomics cover the amplicon gaps. So many papers I had to do a second installment today!
Events and jobs
Microbiology and bioinformatics positions at Whole Biome in San Francisco. Wearing hoodies encouraged.
General microbiome
The status of the microbial census: an update – Patrick D Schloss – BioRxiv
Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes – Kevin R Theis – BioRxiv
Human oral microbiome
Interactions between Streptococcus oralis, Actinomyces oris, and Candida albicans in the development of multispecies oral microbial biofilms on salivary pellicle – Indira M.G. Cavalcanti – Molecular Oral Microbiology
Human respiratory microbiome
Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure – Wouter A. A. de Steenhuijsen Piters – mBio
Human skin microbiome
The effect of habitual and experimental antiperspirant and deodorant product use on the armpit microbiome – Julie Urban – PeerJ
Skin microbiome surveys are strongly influenced by experimental design – Jacquelyn S. Meisel – Journal of Investigative Dermatology
Unique features of a global human ectoparasite identified through sequencing of the bed bug genome – Joshua B. Benoit – Nature Communications
Human vaginal microbiome
Hormonal Contraceptive Effects on the Vaginal Milieu: Microbiota and Immunity – Jessica Tarleton – Current Obstetrics and Gynecology Reports
Human gut microbiome
Sex differences in the gut microbiome–brain axis across the lifespan – Eldin Jašarević – Philosophical Transactions of the Royal Society B
Very poor English and presentation, does not look peer reviewed: Preliminary analysis showed country-specific gut resistome based on 1267 feces samples – Zhenyu Yang – Gene
Confusing study design and interpretations: Gut Microbiota Linked to Sexual Preference and HIV Infection – Marc Noguera-Julian – EBioMedicine
Sequence-based methods for detecting and evaluating the human gut mycobiome – M.J. Suhr – Letters in Applied Microbiology
Review: Microbiota and arthritis: correlations or cause? – Bravo-Blas, Alberto – Current Opinion in Rheumatology
Perspective: Gut microbiota in 2015: Prevotella in the gut: choose carefully – Ruth E. Ley – Nature Reviews Gastroenterology & Hepatology
Editorial: PPIs alter gut microbiota composition – Nature Reviews Gastroenterology & Hepatology
Review: Samples and techniques highlighting the links between obesity and microbiota –
Emmanouil Angelakis – Microbial Pathogenesis
Animal models of microbiome
Bidirectional interactions between indomethacin and the murine intestinal microbiota – Xue Liang – eLife
Mixed feelings about this study that killed turtles to look at effect of probiotics on their shells: Dietary Probiotics Affect Gastrointestinal Microbiota, Histological Structure and Shell Mineralization in Turtles – Mateusz Rawski – PLOS ONE
Animal microbiome
The Role of the Microbial Environment in Drosophila Post-Embryonic Development –
Maura Strigini – Developmental & Comparative Immunology
Plant, root, and soil microbiome
Review about lichen bacterial microbiome: Understanding microbial multi-species symbioses – Ines A. Aschenbrenner – Frontiers in Microbiology
Dead fungal mycelium in forest soil represents a decomposition hotspot and a habitat for a specific microbial community – Vendula Brabcová – New Phytologist
Litter decomposition, residue chemistry and microbial community structure under two subtropical forest plantations: A reciprocal litter transplant study –
Zongming He – Applied Soil Ecology
Disentangling nematode-bacteria interactions using a modular soil model system and biochemical markers – Michael Ackermann – Nematology
Using native trees and cacti to improve soil potential nitrogen fixation during long-term restoration of arid lands – Nguyen E. Lopez-Lozano – Plant and Soil
Warming and nitrogen deposition are interactive in shaping surface soil microbial communities near the alpine timberline zone on the eastern Qinghai–Tibet Plateau, southwestern China – Qinli Xiong – Applied Soil Ecology
Short-term effects of mechanical drainage on fungal and bacterial community structure in a managed grassland soil – B.J. Fay – Applied Soil Ecology
Water and extremophile microbiome
Microbial Communities in Methane- and Short Chain Alkane-Rich Hydrothermal Sediments of Guaymas Basin – Frederick Dowell – Frontiers in Microbiology
Bioreactor and crude oil microbiology
Illumina MiSeq sequencing reveals the key microorganisms involved in partial nitritation followed by simultaneous sludge fermentation, denitrification and anammox process – Bo Wang – Bioresource Technology
Microbial communities of light crude from Nigeria and potential for in situ biodegradation, souring, and corrosion – Okoro Chuma Conlette – Petroleum Science and Technology
Built environment microbiome
Rhinitis, Ocular, Throat and Dermal Symptoms, Headache and Tiredness among Students in Schools from Johor Bahru, Malaysia: Associations with Fungal DNA and Mycotoxins in Classroom Dust – Dan Norbäck – PLOS ONE
Bioinformatics and metagenomics
Metagenomics uncovers gaps in amplicon-based detection of microbial diversity – Emiley A. Eloe-Fadrosh – Nature Microbiology
Development of an Analysis Pipeline Characterizing Multiple Hypervariable Regions of 16S rRNA Using Mock Samples – Jennifer J. Barb – PLOS ONE
Optimization of alignment-based methods for taxonomic binning of metagenomics reads – Magali Jaillard – Bioinformatics
Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes – John A Lees – BioRxiv
Proteomics
Review: Recent development of mass spectrometry and proteomics applications in identification and typing of bacteria – Keding Cheng – Proteomics – Clinical Applications
Microbes in the news
Study shows maternal diet alters the breast milk microbiome and microbial gene content – EurekAlert
Deodorant And Antiperspirant Alter The Skin Microbiome, But Researchers Can’t Be Sure Of Long-Term Effects – Stephanie Castillo – Medical Daily
Beard bacteria could lead to new antibiotics – Matthew Stock – Reuters
Science, publishing, and career
“Those who can, publish. Those who can’t, blog.” Jingmai O’Connor – Current Biology
Chill out about Jingmai O’Connor’s criticism of bloggers – Jeremy Fox – Dynamic Ecology
Paul Knoepfler: Stem cell scientist finds his ‘niche’ in blogging – Karen Weintraub – STAT News
How to (not) write a microbiome grant, part I
How to (not) write a microbiome grant, part II. A deeper dive on preliminary data – David Baltrus – My Chrobial Romance
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