March 10, 2018

Many interesting perspectives from a recent mSystems issue, along with plenty of plant/soil articles!

Events and jobs
Group Leader R&D | (Microbiology/Biomarkers), 8685 – Stratacuity: Proven Scientific Placement  Company – Boston, Massachusetts

General microbiome
Preprint: Biogeography & environmental conditions shape bacteriophage-bacteria networks across the human microbiome – Geoffrey D. Hannigan – bioRxiv

Preprint/Review: Host genetics and microbiome associations from the lens of genome wide association studies – Omer Weissbrod – PeerJ

ReviewStudying microbial functionality within the gut ecosystem by systems biology – Bastian Hornung – BMC Genes and Nutrition

PerspectiveMaking Millennial Medicine More Meta – Peter J. Turnbaugh – MSystems

Perspective: Spatial Analyses of Specialized Metabolites: The Key to Studying Function in Hosts – Melissa M. Galey – MSystems

Pregnancy and early life
Development of the Human Mycobiome over the First Month of Life and across Body Sites – Tonya L. Ward – mSystems

The potential of gut microbiota and fecal volatile organic compounds analysis as early diagnostic biomarker for necrotizing enterocolitis and sepsis in preterm infants – Daniel Johannes Cornelis Berkhout – Expert Review of Gastroenterology & Hepatology

Review: Factors Affecting the Immunity to Respiratory Syncytial Virus: From Epigenetics to Microbiome. – Wendy Fonseca – Frontiers In Immunology

Human respiratory microbiome
The Nasal Microbiome in Asthma. – Mina Fazlollahi – The Journal Of Allergy And Clinical Immunology

Human oral microbiome
Review: Metatranscriptome of the Oral Microbiome in Health and Disease. – J Solbiati – Journal Of Dental Research

Human vaginal microbiome
The effect of vaginal microbial communities on colonization by Staphylococcus aureus with the gene for toxic shock syndrome toxin 1 (TSST-1): a case control study – Jacob D Pierson – Pathogens and Disease

Human gut microbiome
Preprint: Gut microbiota density influences host physiology and is shaped by host and microbial factors – Eduardo Contijoch – bioRxiv

ReviewGender Differences in the Gut Microbiome and How These Affect Cardiovascular Diseases – Adriana Cabal – Gender Differences in the Pathogenesis and Management of Heart Disease

Microbial ecology
Perspective: A Microbial Perspective on the Grand Challenges in Comparative Animal Physiology – Kevin D. Kohl – mSystems

Animal experiments
Rapid environmental effects on gut nematode susceptibility in rewilded mice. – Jacqueline M Leung – Plos Biology

Calcineurin B in CD4+ T Cells Prevents Autoimmune Colitis by Negatively Regulating the JAK/STAT Pathway – Andrea Mencarelli – Frontiers In Immunology

Green tea extract and black tea extract differentially influence cecal levels of short-chain fatty acids in rats – Tomonori Unno – Food Science and Nutrition

Animal microbiome
Detailed ecological associations of triatomines revealed by metabarcoding and next-generation sequencing: implications for triatomine behavior and Trypanosoma cruzi transmission cycles. – Eric Dumonteil – Scientific Reports

Comparative Metagenomic Profiling of Viromes Associated with Four Common Mosquito Species in China – Han Xia – Virologica Sinica

Preprint: Two novel strains of Torulaspora delbrueckii isolated from the honey bee microbiome and their use in honey fermentation – Joseph P. Barry – bioRxiv

16S rRNA metagenomic analysis of the symbiotic community structures of bacteria in foregut, midgut, and hindgut of the wood-feeding termite Bulbitermes sp. – Yue Ming Chew – Symbiosis

Plant, root, and soil microbiome
Towards a Natural History of Soil Bacterial Communities – Jennifer B.H. Martiny – Trends in Microbiology

Soil pH mediates the balance between stochastic and deterministic assembly of bacteria. – Binu M Tripathi – The Isme Journal

Composition of bacterial community in enrichment cultures of shale by-products from Irati Formation, Brazil – Kelly Campos Guerra Pinheiro de Goes – Brazilian Journal of Microbiology

Large Blooms of Bacillales (Firmicutes) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity – Ulas Karaoz – mBio

Long-term irrigation affects the dynamics and activity of the wheat rhizosphere microbiome – Dmitri Mavrodi – Frontiers in Plant Science

Specialized core bacteria associate with plants adapted to adverse environment with high calcium contents. – Fei Li – Plos One

Diversity of the Bacterial Microbiome in the Roots of Four Saccharum Species: S. spontaneum, S. robustum, S. barberi, and S. officinarum – Meng Dong – Frontiers In Microbiology

Long-Term Harvest Residue Retention Could Decrease Soil Bacterial Diversities Probably Due to Favouring Oligotrophic Lineages – Yaling Zhang – Microbial Ecology

Trichoderma-Inoculated Miscanthus Straw Can Replace Peat in Strawberry Cultivation, with Beneficial Effects on Disease Control – Jane Debode – Frontiers In Plant Science

Heterologous Expression of Secreted Bacterial BPP and HAP Phytases in Plants Stimulates – Lia R Valeeva – Frontiers In Plant Science

PerspectiveMetabolomics and Agriculture: What Can Be Done? – Rodolpho Martin do Prado – MSystems

PerspectiveComputational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology – Marnix H. Medema – mSystems

Soil Inoculation with Bacillus spp. Modifies Root Endophytic Bacterial Diversity, Evenness, and Community Composition in a Context-Specific Manner – Kiran R. Gadhave – Microbial Ecology

BookAdvances in Soil Microbiology: Recent Trends and Future Prospects – Tapan Kumar Adhya:
Many chapters may be of interest, including:

Water and extremophile microbiome
Persistent nitrogen limitation of stream biofilm communities along climate gradients in the arctic. – Maria Myrstener – Global Change Biology

Biodiversity of biological soil crusts from the Polar Regions revealed by metabarcoding – Rippin Martin – FEMS Microbiology Ecology

Archaeal community compositions in tilapia pond systems and their influencing factors – Limin Fan – World Journal of Microbiology and Biotechnology

Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics. – Rafael R C Cuadrat – Frontiers In Microbiology

Abundance and observations of thermophilic microbial and viral communities in submarine and terrestrial hot fluid systems of the French Southern and Antarctic Lands – Kaarle J. Parikka – Polar Biology

An Assessment of Sub-Meter Scale Spatial Variability of Arcellinida (Testate Lobose Amoebae) Assemblages in a Temperate Lake: Implications for Limnological Studies – Riley E. Steele – Microbial Ecology

Built environment
The classroom microbiome and asthma morbidity in children attending three inner-city schools. – Peggy S Lai – The Journal Of Allergy And Clinical Immunology

Decomposition of lignocellulose and readily degradable carbohydrates during sewage sludge biodrying, insights of the potential role of microorganisms from a metagenomic analysis – Lu Cai – Chemosphere

Illumina MiSeq Sequencing reveals microbial community in HA process for dyeing wastewater treatment fed with different co-substrates – Xuehui Xie – Chemosphere

Food microbiology
An Ultrahigh-Performance Liquid Chromatography-Time-of-Flight Mass Spectrometry Metabolomic Approach to Studying the Impact of Moderate Red-Wine Consumption on Urinary Metabolome – Adelaida Esteban-Fernández – Journal of Proteome Research

Probiotics / prebiotics / antibiotics
Fate of antibiotic and metal resistance genes during two-phase anaerobic digestion of residue sludge revealed by metagenomic approach. – V Richarte – Environmental Science And Pollution Research International

Intra-species Genomic and Physiological Variability Impact Stress Resistance in Strains of Probiotic Potential. – Jason W Arnold – Frontiers In Microbiology

Phages and viruses
Deciphering the Human Virome with Single-Virus Genomics and Metagenomics – Maria José de la Cruz Peña – Viruses

Urinary Virome perturbations in kidney transplantation – Neil Mercer – Frontiers in Microbiology

Preprint: Anti-CRISPR phages cooperate to overcome CRISPR-Cas immunity – Mariann Landsberger – bioRxiv

Preprint: Bacteriophage cooperation suppresses CRISPR-Cas3 and Cas9 immunity – Adair L Borges – bioRxiv

Bioinformatics
From Whole-Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool – Simone Rampelli – Viral Metagenomics

Techniques
Multiplexed chemostat system for quantification of biodiversity and ecosystem functioning in anaerobic digestion. – Diane Plouchart – Plos One

ReviewElectrochemical Probes of Microbial Community Behavior – Hunter J. Sismaet – Annual Review of Analytical Chemistry

Antibiotic-Responsive Bioart: Exploring DIYbio as a Design Studio Practice – Stacey Kuznetsov – ACM

Microbes in the news
Four stories of antibacterial breakthroughs – Natasha Gilbert – Nature

How baby’s first microbes could be crucial to future health – Sarah DeWeerdt – Nature

Hacking a Cow’s Gut Bacteria Could Make More Meat, Less Pollution – Chelsea Gohd – Futurism

High-Fiber Diet Shifts Gut Microbes, Lowering Blood Sugar in Diabetics – Ashley Yeager – The Scientist

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