Somewhere between March 8 and March 9, 2016

Human symbionts inject to persist, diet and exercise in mice, a 17-year long experiment, and using peanut butter as a vehicle to deliver probiotics in developing countries.

Human skin microbiome

Proteobacteria from the human skin microbiota: Species-level diversity and hypotheses – C. Cosseau – One Health

Human respiratory microbiome

Clinical metagenomics for the management of hospital- and healthcare-acquired pneumonia –  Etienne Ruppé – Future Microbiology

Human gut microbiome

Analysis of Gut Microbiota in Coronary Artery Disease Patients: a Possible Link between Gut Microbiota and Coronary Artery Disease – Takuo Emoto – Journal of Atherosclerosis and Thrombosis

PhD Thesis: Indigenous Australians have a distinctive gut microbial profile compared to Caucasian controls and patients with inflammatory bowel disease – Iyngkaran, Guruparan – Melbourne Medical School

Review: Changes in the Intestinal Microbiome and Alcoholic- and Non-alcoholic Liver Diseases—Causes or Effects? – Naga S. Betrapally – Gastroenterology

Review: Microbiome alterations in HIV infection a review – B Williams – Cellular Microbiology

Review: Extensive Intestinal Resection Triggers Behavioral Adaptation, Intestinal Remodeling and Microbiota Transition in Short Bowel Syndrome – Camille Mayeur – MDPI Microorganisms

Microbiome models

Human symbionts inject and neutralize antibacterial toxins to persist in the gut – Aaron G. Wexler – PNAS

The Effect of Diet and Exercise on Intestinal Integrity and Microbial Diversity in Mice – Sara C. Campbell – PLOS ONE

Chronic Psychological Stress Disrupted the Composition of the Murine Colonic Microbiota and Accelerated a Murine Model of Inflammatory Bowel Disease – Yohei Watanabe – PLOS ONE

Flavanol-Enriched Cocoa Powder Alters the Intestinal Microbiota, Tissue and Fluid Metabolite Profiles, and Intestinal Gene Expression in Pigs – Saebyeol Jang – The Journal of Nutrition

Deletion of the Toll-Like Receptor 5 Gene Per Se Does Not Determine the Gut Microbiome Profile That Induces Metabolic Syndrome: Environment Drumpfs Genotype
Wei Zhang – PLOS ONE

Animal microbiome

The microbiome of coral surface mucus has a key role in mediating holobiont health and survival upon disturbance – Bettina Glasl – ISME Journal

Repeated replacement of an intrabacterial symbiont in the tripartite nested mealybug symbiosis – Filip Husnik – BioRxiv

No access for me, but I assume this is in birds: Microbial shifts associated with necrotic enteritis – Gunther Antonissen – Avian Pathology

Plant, root, and soil microbiome
Orchids: Differences in mycorrhizal communities between Epipactis palustris, E. helleborine and its presumed sister species E. neerlandica – Hans Jacquemyn – Annals of Botany

Soil Respiration and Bacterial Structure and Function after 17 Years of a Reciprocal Soil Transplant Experiment – Ben Bond-Lamberty – PLOS ONE

Evaluation of a diagnostic microarray for the detection of major bacterial pathogens of potato from tuber samples – Y. Degefu – EPPO Bulletin

Shifts in symbiotic associations in plants capable of forming multiple root symbioses across a long-term soil chronosequence – Felipe E. Albornoz – Ecology and Evolution

Bacterial diversity and community along the succession of biological soil crusts in the Gurbantunggut Desert, Northern China – Bingchang Zhang – Journal of Basic Microbiology

Variation of Bacterial Community Diversity in Rhizosphere Soil of Sole-Cropped versus Intercropped Wheat Field after Harvest – Zhenping Yang – PLOS ONE

Characterization of bacterial communities in lithobionts and soil niches from Victoria Valley, Antarctica – Marc W. Van Goethem – FEMS Microbiology Ecology

Bacterial indicator taxa in soils under different long-term agricultural management – N.G. Jiménez-Bueno – Journal of Applied Microbiology

Water and extremophile microbiome

Delta-proteobacterial SAR324 group in hydrothermal plumes on the South Mid-Atlantic Ridge – Huiluo Cao – Scientific Reports

Nutrient treatments alter microbial mat colonization in two glacial meltwater streams from the McMurdo Dry Valleys, Antarctica – Tyler J. Kohler – FEMS Microbiology Ecology

Bioreactor microbiology

Gut microbiota-involved mechanisms in enhancing systemic exposure of ginsenosides by coexisting polysaccharides in ginseng decoction – Shan-Shan Zhou – Scientific Reports

Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis
Gang Luo – Biotechnology for Biofuels

Waste and pollution microbiology

Temporal dynamics of biotic and abiotic drivers of litter decomposition – Pablo García-Palacios – Ecology Letters

Microbial Community Structures in Petroleum Contaminated Soils at an Oil Field, Hebei, China – Yizhi Sheng – CLEAN – Soil, Air, Water

Effect of microbial community structure on organic removal and biofouling in membrane adsorption bioreactor used in seawater pretreatment – Sanghyun Jeong – Chemical Engineering Journal

Performance assessment and microbial diversity of two pilot scale multi-stage sub-surface flow constructed wetland systems – Journal of Environmental Sciences – A.O. Babatunde

Functional foods and food microbiology

For applications in developing countries: Influence of probiotics, included in peanut butter, on the fate of selected Salmonella and Listeria strains under simulated gastrointestinal conditions – Y.A.K. Klu – Journal of Applied Microbiology

Bioinformatics and metagenomics

Read networks and k-laminar graphs – Finn Volkel – ArXiv

CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment – Jeongsu Oh – PLOS ONE

Protocol: Using QIIME to Evaluate the Microbial Communities Within Hydrocarbon Environments – Luke K. Ursell – Springer Protocols Handbooks

Regression Analysis for Microbiome Compositional Data – Pixu Shi – ArXiv

bioOTU: An Improved Method for Simultaneous Taxonomic Assignments and Operational Taxonomic Units Clustering of 16s rRNA Gene Sequences – Chen Shi-Yi – Journal of Computational Biology


Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies – James L. O’Donnell – PLOS ONE

More microbiology

Alice’s living croquet theory – Didier Raoult – International Journal of Antimicrobial Agents

Genomic approaches for understanding dengue: insights from the virus, vector, and host – Shuzhen Sim – Genome Biology

Microbes and infection

Multiplex detection and identification of viral, bacterial, and protozoan pathogens in human blood and plasma using a high-density resequencing pathogen microarray platform – Moussa Kourout – Transfusion

Local Action with Global Impact: Highly Similar Infection Patterns of Human Viruses and Bacteriophages – Rachelle Mariano – mSystems

Microbes in the news

Cutting Board Companions – Katherine Dahlhausen – MicroBEnet @PhDKD

Standard practice of giving premature babies antibiotics needs to be rethought, argues new study – Jessica Firger – Newsweek

Bacterial brawls mark life in the gut’s microbiome – Bill Hathaway –

How your microbiome can put you at the scene of the crime – Kai Kupferschmidt – Science

Soy protein may diversify gut microbiota more than dairy protein: Study – Stephen Daniells – Nutraingredients
Sleep Deprivation Caused By Jet Lag And Shift Work Could Be Treated Through Your Gut Microbiome – Cayla Dengate – Huffington Post

U-M Students Analyze Their Own Biological Samples to Study How Microbes Affect Human Health – Infection Control Today

#1 is outdated but rest ok: 10 things you need to know about your gut – Naomi Mead – Netdoctor

The Dannon Company Announces Fourth-Annual Winner of Yogurt and Probiotics Fellowship Grant: Micah Eimerbrink – BusinessWire

Science, publishing, and career

Insights into the PeerJ Preprint: “Gender bias in open source” – PeerJ Blog

Bik’s Picks

I Speak Whale: Vast assembly of vocal marine mammals from diverse species on fish spawning ground – Delin Wang – Nature


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