December 16, 2017

Multiple articles on plant and soil microbiome, along with new BSCs (under “Water and extremophile microbiome) and some new computational methods! And a search for a microbiome core director from my thesis lab, please forward!

Events and jobs

Microbiome Core Director (Research Associate/Research Scientist) – Huttenhower Lab, Harvard T.H. Chan School of Public Health

Microbiology/Majors Biology Professor – College of the Sequoias Community College District in Visalia, CA

Pregnancy and early life
Modeling Metabolic Interactions in a Consortium of the Infant Gut Microbiome – Francisco Pinto – Frontiers in Microbiology

Faecal microbiota transplant in a child with very early onset inflammatory bowel disease – Carlos Sierra Salinas – Anales De Pediatria (Barcelona, Spain : 2003)

Multi-site human microbiome
Review: Gut microbial balance and liver transplantation: alteration, management, and prediction – Xinyao Tian – Frontiers of Medicine

Human respiratory microbiome
Atopobium and Fusobacterium as novel candidates for sarcoidosis-associated microbiota. – Alexandra Zimmermann – The European Respiratory Journal

Associations between infant fungal and bacterial dysbiosis and childhood atopic wheeze in a nonindustrialized setting – Marie-Claire Arrieta – The Journal Of Allergy And Clinical Immunology

Human vaginal microbiome
High rates of bacterial vaginosis and Chlamydia in a low-income, high-population-density community in Cape Town – Katie S. Lennard – South African Journal of Science and Technology

Human gut microbiome
Subspecies in the global human gut microbiome – Paul I Costea – Molecular Systems Biology

Investigation of bioaccessibility of Cu, Fe, Mn, and Zn in market vegetables in the colon using PBET combined with SHIME. – Naiyi Yin – Scientific Reports

Improving regulation of microbiota transplants – Diane Hoffmann – Science

The Human Gut Microbial Metabolome Modulates Fungal Growth via the TOR Signaling Pathway – Carlos García – MSphere

Review: Our Gut Microbiome: The Evolving Inner Self. – Parag Kundu – Cell

Review: The gut microbiota – an emerging risk factor for cardiovascular and cerebrovascular disease – Stefanie Ascher – European Journal of Immunology

Animal experiments
Microbial communities exhibit host-species distinguishability and phylosymbiosis along the length of the gastrointestinal tract – Kevin D. Kohl – Molecular Ecology

Bile acid is a significant host factor shaping the gut microbiome of diet-induced obese mice. – Xiaojiao Zheng – Bmc Biology

Rumen Bacteria Communities and Performances of Fattening Lambs with a Lower or Greater Subacute Ruminal Acidosis Risk – Fei Li – Frontiers in Microbiology: Systems Microbiology

Dietary Antioxidant Micronutrients Alter Mucosal Inflammatory Risk in a Murine Model of Genetic and Microbial Susceptibility  – JF Pierre – The Journal of Nutritional Biochemistry

Dietary stachyose altered the intestinal microbiota profile and improved the intestinal mucosal barrier function of juvenile turbot, Scophthalmus maximus L. – Pei Yang – Aquaculture

Diversity, in-vitro virulence traits and antifungal susceptibility pattern of gastrointestinal yeast flora of healthy poultry, Gallus gallus domesticus. – Supram Hosuru Subramanya – Bmc Microbiology

Animal microbiome
Dispersal limitation promotes the diversification of the mammalian gut microbiota – Andrew H. Moeller – PNAS

Plant, root, and soil microbiome
Multiple new cryptic pathogenic Phytophthora species from Fagaceae forests in Austria, Italy and Portugal – Thomas Jung – IMA Fungus

Soil characteristics determine the rhizobia in association with different species of Mimosa in central Brazil – Raquel de Castro Pires – Plant and Soil

Effects of organochlorine pesticides on plant growth-promoting traits of phosphate-solubilizing rhizobacterium, Paenibacillus sp. IITISM08 – Rupa Rani – Environmental Science and Pollution Research

Duration of continuous cropping with straw return affects the composition and structure of soil bacterial communities in cotton fields – Lei Yang – Canadian Journal of Microbiology

The greater roles of indigenous microorganisms in removing nitrobenzene from sediment compared with the exogenous Phragmites australis and strain JS45 – Xiangqun Chi – Frontiers of Environmental Science & Engineering

Seasonal Variations in Soil and Bacteriological Properties as Affected by Phytogenic Mounds (Nebkhas) of Halocnemum strobilaceum in Lake Manzala, Egypt – Heba K. Issa – Egyptian Journal of Botany

Investigating monsoon and post-monsoon variabilities of bacterioplankton communities in a mangrove ecosystem – Anwesha Ghosh – Environmental Science and Pollution Research

Invasion by Cordgrass Increases Microbial Diversity and Alters Community Composition in a Mangrove Nature Reserve – Min Liu – Frontiers in Microbiology

Effects of temperature, soil substrate, and microbial community on carbon mineralization across three climatically contrasting forest sites – Zuoxin Tang – Ecology and Evolution

Effects of biotic and abiotic factors on soil organic matter mineralization: Experiments and structural modeling analysis – Husen Qiu – European Journal of Soil Biology

Available forms of nutrients and heavy metals control the distribution of microbial phospholipid fatty acids in sediments of the Three Gorges Reservoir, China – Hongyan Sun – Environmental Science and Pollution Research

Temporal diversity dynamics of the arbuscular mycorrhizal fungi of Larrea tridentata (Sesse & Mocino ex DC) Coville in a semi-arid ecosystem – G Hernández-Zamudio – Revista Argentina de Microbiología (Article in Spanish)

Water and extremophile microbiome
Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality – Gregory C. A. Amos – PNAS

Molecular Mechanisms for Microbe Recognition and Defense by the Red Seaweed Laurencia dendroidea. – Louisi Souza de Oliveira – Msphere

Mycobiota of the disused ore mine of Marcinków in Śnieżnik Masiff (western Poland) – Wojciech Pusz – Journal of Mountain Science

Thermophilic bacterial communities inhabiting the microbial mats of “indifferent” and chalybeate (iron-rich) thermal springs: Diversity and biotechnological analysis. – Xue-Ping Wang – Microbiologyopen

Review: The Seagrass Holobiont and Its Microbiome – Kelly Ugarelli – Microorganisms

Built environment
PCR–DGGE Analysis on Microbial Community Structure of Rural Household Biogas Digesters in Qinghai Plateau – Rui Han – Current Microbiology

Deciphering the core fouling-causing microbiota in a membrane bioreactor: Low abundance but important roles – Shaoqing Zhang – ChemoSphere

Increasing tetracycline concentrations on the performance and communities of mixed microalgae-bacteria photo-bioreactors – Yanghui Xiong – Algal Research

Biostimulation of nutrient additions on indigenous microbial community at the stage of nitrogen limitations during composting – Huan Wang – Waste Management

Food microbiology
Mutually stimulating interactions between lactic acid bacteria and Saccharomyces cerevisiae in sourdough fermentation – S. Sieuwerts – LWT – Food Science and Technology

Review: The Mediterranean diet: metabolic and molecular mechanisms – Valeria Tosti – The Journals Of Gerontology. Series A, Biological Sciences And Medical Sciences

Probiotics / prebiotics/ antibiotics
Prebiotic Dietary Fiber and Gut Health: Comparing the in Vitro Fermentations of Beta-Glucan, Inulin and Xylooligosaccharide – Justin L Carlson – Nutrients

ReviewFinding the needle in the haystack: systematic identification of psychobiotics. – Aisling Bambury – British Journal Of Pharmacology

Comment: Narrowing the spectrum: the new frontier of precision antimicrobials – Alexandra E Paharik – Genome Medicine

A Dirichlet-Multinomial Bayes Classifier for Disease Diagnosis with Microbial Compositions. – Xiang Gao – Msphere

Amplicon sequencing of the 16S-ITS-23S rRNA operon with long-read technology for improved phylogenetic classification of uncultured prokaryotes – Joran Martijn – bioRxiv

Novel ITS1 Fungal Primers for Characterization of the Mycobiome. – Mykhaylo Usyk – Msphere

Microbes in the news
BIDMC Researchers Use Artificial Intelligence to Identify Bacteria Quickly and Accurately – Beth Israel Deaconess Medical Center

Magnetically Guided Bacteria Move Confidently Within Strong Currents, May Soon Deliver Drugs Inside Body – MedGadget

Is hand sanitizer bad for my microbiome? – Claire Maldarelli – Popular Science

Nanoparticles as a solution against antibiotic resistance? – Science Daily

Microbes on the market 
Light ‘Em Up: S&N’s Device Images Bacteria in Wounds – Nancy Crotti – MDDI

Contemplating Regulatory Frameworks for FMT – Cristi Rosa – Contagion Live

Vedanta Granted Four U.S. Patents for Therapeutics Based on Beneficial Gut Bacteria – Carolina Henriques – IBD News Today

Science, publishing, and career
What’s Responsible for the Retraction Boom? – Adam Marcus – Research Ethics in the Digital Age

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