February 22, 2017

Here’s your daily routine. Autoregressive and non-autoregressive regimes in the human gut microbiome. The interaction between diet, microbiota and personalized nutrition. More topics to think about: reproducibility in the microbiome studies, intellectual property in the microbiome industry, and heavy rain brings fatal bugs to northern Californian dogs.

Events and jobs

The 3rd Annual Translational Microbiome Conference – April 11-13, 2017 – Boston, MA

Microbiology Laboratory Technician – ALS Life Sciences – Ireland

Field Sales Manager, Microbiology, Molecular Biology, Chemistry – Cromwell and Clark – UK

General microbiology

Vancomycin displays time-dependent eradication of mature Staphylococcus aureus biofilms – Virginia Post – Journal of Orthopaedic Research

Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment – James E. Gomez – eLife

Press: Genetic mutations that drive antibiotic resistance in bacteria – Science Daily

Global Proteomic Analyses of Macrophage Response to Mycobacterium tuberculosis Infection – Valerie Poirier – BioRxiv

Human gut microbiome

*Two dynamic regimes in the human gut microbiome – Sean M. Gibbons – PLoS Computational Biology

Human intestinal microbiota: Role in development and functioning of the nervous system – O. V. Averina and V. N. Danilenko – Microbiology

Editorial: How can the gut microbiota affect immune recovery in HIV-infected individuals? – Sergio Serrano-Villar – Future Microbiology

Review: The Influence of the Microbiome on Early-Life Severe Viral Lower Respiratory Infections and Asthma—Food for Thought? – Jason P. Lynch – Frontiers in Immunology

Randomised clinical trial: faecal microbiota transplantation for recurrent Clostridum difficile infection – fresh, or frozen, or lyophilised microbiota from a small pool of healthy donors delivered by colonoscopy – Z. D. Jiang – Alimentary Pharmacology and Therapeutics

Review: “We are what our bacteria eat”: The role of bacteria in personalizing nutrition therapy in gastrointestinal conditions – Ruth Harvie – Journal of Gastroenterology and Hepatology

The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred – Umer Zeeshan Ijaz – PLoS One

Animal experiments

Not peer reviewed: Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructooligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing – Jose F Garcia-Mazcorro – PeerJ

Mouse: The influence of rosuvastatin upon the gastrointestinal microbiota and host gene expression profiles – James A. Nolan – American Journal of Physiology – Gastrointestinal and Liver Physiology

High-cholesterol diet does not alter gut microbiota composition in mice – Lidiya G. Dimova – Nutrition & Metabolism

The effect of gut microbiome on tolerance to morphine mediated antinociception in mice – Minho Kang – Scientific Reports

Mouse: Ambient Ultrafine Particle Ingestion Alters Gut Microbiota in Association with Increased Atherogenic Lipid Metabolites – Rongsong Li – Scientific Reports

Editorial: Sources of variation: Animal microbiota – Alexandra A. Mushegian – Science Signaling

The effects of amoxicillin treatment of newborn piglets on the prevalence of hernias and abscesses, growth and ampicillin resistance of intestinal coliform bacteria in weaned pigs – Jinhyeon Yun – PLoS One

Animal microbiome

Culture-independent genomics of a novel chlamydial pathogen of fish provides new insight into host-specific adaptations utilised by these intracellular bacteria – Alyce Taylor-Brown – Environmental Microbiology

Corals: Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach – Edward G Smith – The ISME Journal

Prevalence of AmpC- and Extended-Spectrum β-Lactamase-Harbouring Enterobacteriaceae in Faecal Flora of a Healthy Domestic Canine Population – D. A. Mathys – Zoonoses and Public Health

Different antibiotic growth promoters induce specific changes in the cecal microbiota membership of broiler chicken – Marcio C. Costa – PLoS One

Plant, root and soil microbiome

A Plant Bacterial Pathogen Manipulates Its Insect Vector’s Energy Metabolism – Nabil Killiny – Applied and Environmental Microbiology

Effective control of root-knot nematode disease with Pseudomonad rhizobacteria filtrate – Ishwar Prakash Sharma and A.K. Sharma – Rhizosphere

Biodiversity of aerobic methylobacteria associated with the phyllosphere of the southern Moscow region – E. N. Kaparullina – Microbiology

Epiphytic microorganisms degrading aromatic hydrocarbons from the phyllosphere of urban woody plants – O. I. Sazonova – Microbiology

Book chapter: Improving Soil Fertility and Soil Functioning in Cover Cropped Agroecosystems with Symbiotic Microbes – Yang Zhou – Agro-Environmental Sustainability

Book chapter: Role of Phosphate-Solubilising Microorganisms in Sustainable Agricultural Development – Rajesh Kumar and Beenu Shastri – Agro-Environmental Sustainability

Influence of rhinoceros beetle (Trypoxylus dichotomus septentrionalis) larvae and temperature on the soil bacterial community composition under laboratory conditions – Jinu Eo – Soil Biology and Biochemistry

Water and extremophile microbiome

Deep sequencing analysis of bacterial community structure of Soldhar hot spring, India – A. Sharma – Microbiology

Microbial community compositions in different functional zones of Carrousel oxidation ditch system for domestic wastewater treatment – Dong Xu – AMB Express

Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens – Jessica Chopyk – Microbiome

The interaction between the proliferating macroalga Asparagopsis taxiformis and the coral Astroides calycularis induces changes in microbiome and metabolomic fingerprints – Stéphane Greff – Scientific Reports


MetaGaAP: A Novel Pipeline to Estimate Community Composition and Abundance from Non-Model Sequence Data – Christopher Noune and Caroline Hauxwell – Biology


DNA Barcoding for Fractured Reservoir Analysis – An Initial Investigation – Yuran Zhang – PROCEEDINGS, 42nd Workshop on Geothermal Reservoir Engineering

Novel approaches for the taxonomic and metabolic characterization of lactobacilli: Integration of 16S rRNA gene sequencing with MALDI-TOF MS and 1H-NMR – Claudio Foschi – PLoS One

Microbes in space

The Effect of High-Dose Ionizing Radiation on the Isolated Photobiont of the Astrobiological Model Lichen Circinaria gyrosa – Joachim Meeßen – Astrobiology

Phages and viruses

Non-classical phase diagram for virus bacterial coevolution mediated by clustered regularly interspaced short palindromic repeats – Pu Han and Michael W. Deem – Journal of the Royal Society Interface

Microbes in the news

Probiotics: IP Perspectives on the Microbiome – Jing Liu and Daniel Yarbrough – JDSupra

Targeting Gut Bacteria May Be The Key To Preventing Alzheimer’s – Carolyn Gregoire – The Huffington Post

Space Bacteria Draws Focus of Researchers – Robert Lee Hotz – Wall Street Journal (subscription required)

Irish experts key to battling bacteria – Niall Murray – Irish Examiner

Heavy Rains Bring Dog-Killing Bacteria to Northern California – Tex Dwokin – Care2

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