Today’s digest is chock-full of human gut studies related to disease, soil/plant and water/environmental studies, quite a lot of research on animal microbiomes and symbiotic microbes, as well as some discussion of techniques to improve various metagenomic applications.
Events and jobs
Scientist – Microbiology Development – BD (Becton, Dickinson and Company)
Microbiology Technical Manager – UKAS – W.Midlands
Multi-site human microbiome
Integration of microbiome and epigenome to decipher the pathogenesis of autoimmune diseases – Beidi Chen – Journal of Autoimmunity
Human respiratory microbiome
Integrating the microbiota of the respiratory tract with the unified airway model – Alissa S. Hanshew – Respiratory Medicine
The role of acute and chronic respiratory colonization and infections in the pathogenesis of COPD – Janice M. Leung – Respirology
Human nearly-sterile sites (blood, organs, brain)
* The blood DNA virome in 8,000 humans – Ahmed Moustafa – PLOS Pathogens
Human gut microbiome
Role of External and Environmental Factors in Drug Resistance Emergence: Gut Microbiota – Daniel Ryan – Drug Resistance in Bacteria, Fungi, Malaria, and Cancer
* Changes in intestinal microbiota composition and metabolism coincide with increased intestinal permeability in young adults under prolonged physiologic stress – J. Philip Karl – American Journal of Physiology-Gastrointestinal and Liver Physiology
Robust Microbiota-Based Diagnostics for Inflammatory Bowel Disease – A. Eck – Journal of Clinical Microbiology
Tackling the Antibiotic Resistance: The “Gut” Feeling – Richa Misra – Drug Resistance in Bacteria, Fungi, Malaria, and Cancer
Book Chapter – Human Gut Microbiota and Obesity During Development – Tomás Cerdó – Adiposity – Omics and Molecular Understanding
Fecal microbiota transplantation – methods of treatment of recurrent Clostridium difficile infections and other diseases – Juszczuk K – Postepy Hig Med Dosw (Online)
Gut Colonization by Methanogenic Archaea Is Associated with Organic Dairy Consumption in Children – van de Pol JA – Frontiers in Microbiology
Gut Microbiome in Chronic Kidney Disease – R. G. Armani – Current Hypertension Reports
Sex-dependent effects on gut microbiota regulate hepatic carcinogenic outcomes – Guoxiang Xie – Scientific Reports
Gut microbiome analysis of type 2 diabetic patients from the Chinese minority ethnic groups the Uygurs and Kazaks – Ye Wang – PLOS ONE
Animal experiments
Stressor exposure has prolonged effects on colonic microbial community structure in Citrobacter rodentium-challenged mice – Jeffrey D. Galley – Scientific Reports
Engineered Resistant-Starch (ERS) Diet Shapes Colon Microbiota Profile in Parallel with the Retardation of Tumor Growth in In Vitro and In Vivo Pancreatic Cancer Models – Concetta Panebianco – Nutrients
Alcohol-related changes in the intestinal microbiome influence neutrophil infiltration, inflammation and steatosis in early alcoholic hepatitis in mice – Patrick P. Lowe – PLOS ONE
Altered gut microbiome in a mouse model of Gulf War Illness causes neuroinflammation and intestinal injury via leaky gut and TLR4 activation – Firas Alhasson – PLOS ONE
Olive oil bioactives protect pigs against experimentally-induced chronic inflammation independently of alterations in gut microbiota – Martin Liehr – PLOS ONE
Animal microbiome
Mosquito Microbiome Dynamics, a Background for Prevalence and Seasonality of West Nile Virus – Eva Novakova – Frontiers in Microbiology
The nasopharyngeal microbiota of beef cattle before and after transport to a feedlot – Devin B. Holman – BMC Microbiology
Fungal diversity and community structure in gut, mound and surrounding soil of fungus-cultivating termites – Huxley Mae Makonde – African Journal of Microbiology Research
Integrated metabolism in sponge–microbe symbiosis revealed by genome-centered metatranscriptomics – Lucas Moitinho-Silva – The ISME Journal (Microbial Ecology)
Inferring Microbial Interactions in the Gut of the Hong Kong Whipping Frog (Polypedates megacephalus) and a Validation Using Probiotics – Francis C. Weng – Frontiers in Microbiology
Plant, root, and soil microbiome
Mineral Ecology: Surface Specific Colonization and Geochemical Drivers of Biofilm Accumulation, Composition, and Phylogeny – Aaron A. Jones – Frontiers in Microbiology
Defining the core citrus leaf- and root-associated microbiota: Factors associated with community structure and implications for managing Huanglongbing (Citrus greening) disease – Ryan A. Blaustein – American Society for Microbiology
The preservation of microbial DNA in archived soils of various genetic types – Ekaterina A. Ivanova – PLOS ONE
Unknown risks to soil biodiversity from commercial fungal inoculants – Miranda M. Hart – Nature Ecology and Evolution
Genetic and functional diversity of ubiquitous DNA viruses in selected Chinese agricultural soils – Li-Li Han – Scientific Reports
Relationship of microbial communities and suppressiveness of Trichoderma fortified composts for pepper seedlings infected by Phytophthora nicotianae – Margarita Ros – PLOS ONE
Metagenomic analyses of bacterial endophytes associated with the phyllosphere of a Bt maize cultivar and its isogenic parental line from South Africa – Ramadimetja A – World Journal of Microbiology and Biotechnology
Water and extremophile microbiome
* Characterization of culturable bacteria isolated from hot springs for plant growth promoting traits and effect on tomato (Lycopersicon esculentum) seedling – Kinjal Samir Patel – Comptes Rendus Biologies
* Microbial indicators as a diagnostic tool for assessing water quality and climate stress in coral reef ecosystems – Bettina Glasl – Marine Biology
Pre-print – Response Of Microbial Community Function To Fluctuating Geochemical Conditions Within A Legacy Radioactive Waste Trench Environment – Xabier Vázquez-Campos – bioRxiv
* Patterns of variation in diversity of the Mississippi river microbiome over 1,300 kilometers – Jason T. Payne – PLOS ONE
Food microbiology
Monitoring of the bacterial communities of bamboo shoots (Dendrocalamus latiflorus) during pickling process – Xuejuan Xia – International Journal of Food Science + Technology
Bioinformatics
Preprint – MIMIX: a Bayesian Mixed-Effects Model for Microbiome Data from Designed Experiments – Neal S. Grantham – arXiv
Techniques
Integrated Methodology to Characterize Microbial Populations and Functions across Small Spatial Scales in an Oil Production Facility – Christopher R. Marks – Routledge
Next-Generation Sequencing Combined with Specific PCR Assays To Determine the Bacterial 16S rRNA Gene Profiles of Middle Ear Fluid Collected from Children with Acute Otitis Media – Saara Sillanpää – American Society for Microbiology Journals
Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding – Matthieu Leray – PeerJ
Novel 16S rDNA primers revealed the diversity and habitats-related community structure of sphingomonads in 10 different niches – Yili Huang – Antonie van Leeuwenhoek
Assessment of REPLI-g Multiple Displacement Whole Genome Amplification (WGA) Techniques for Metagenomic Applications – Ahsanuddin S – Journal of Biomolecular Techniques
Improvement of identification methods for honeybee specific Lactic Acid Bacteria; future approaches – Sepideh Lamei – PLOS ONE
Microbes in the news
Bacteria, deadwood and climate change—forest floor as carbon sink
Basic microbiology research study unexpectedly uncovers practical findings for growers
Bacteria That Cause Human Diseases Found in Orca Blowholes
Bacteria Hysteria
Keep Your Phone Bacteria Free with PhoneSoap
Science, publishing, and career
Behar, Finberg and Luzuriaga elected fellows of American Academy of Microbiology
Ed’s non-microbiology picks
Spinach Leaf Transformed Into Beating Human Heart Tissue
Low Socioeconomic Status Affects Life Expectancy More Than Obesity
Caesarean sections and for-profit status of hospitals: systematic review and meta-analysis – Ilir Hoxha – BMJ Open
Work organization and mental health problems in PhD students – Katia Levecque – Research Policy
Influence of Anthropogenic Climate Change on Planetary Wave Resonance and Extreme Weather Events – Michael E. Mann – Scientific Reports
Microbiome Digest - Bik's Picks 