A personal perspective on microbiome research, phenotypic heterogeneity in microorganisms, ruling out viruses as causes for necrotizing enterocolitis, and Robert Edgar’s USEARCH.
Job openings
Philipps-Universität Marburg and the Max-Planck Institute for Terrestrial Microbiology are looking for 2 postdocs (one experimentalist and one bioinformatician)
General microbiome
Personal perspective: From cell biology to the microbiome: An intentional infinite loop – Wendy S. Garrett – Journal of Cell Biology
Microbiome of pregnancy and birth
Cytomegalovirus and other common enteric viruses are not commonly associated with Necrotizing Enterocolitis – Thomas Skeath – Acta Paediatrica
Viremia during pregnancy and risk of childhood leukemia and lymphomas in the offspring: Nested case-control study – Davit Bzhalava – International Journal of Cancer
Human oral microbiome
The Oral Bacterial Communities of Children with Well-Controlled HIV Infection and without HIV Infection – Brittany E. Goldberg – PLOS ONE
Human respiratory microbiome
Sputum Bacterial and Fungal Dynamics during Exacerbations of Severe COPD – Jin Su – PLOS ONE
Human gut microbiome
Chemotherapy-driven dysbiosis in the intestinal microbiome – E. Montassier – Alimentary Pharmacology & Therapeutics
Animal models of microbiome research
Perilipin-2 Modulates Lipid Absorption and Microbiome Responses in the Mouse Intestine – Daniel N. Frank – PLOS ONE
Animal microbiome
NGS metabarcoding proves successful for quantitative assessment of symbiont abundance: the case of feather mites on birds – J. Diaz-Real
Genetic Structure and Antimicrobial Resistance of Escherichia coli and Cryptic Clades in Birds with Diverse Human Associations – Michaela D. J. Blyton – Applied and Environmental Microbiology
Coral transplantation triggers shift in microbiome and promotion of coral disease associated potential pathogens – Jordan M. Casey – Scientific Reports
Plant, root, and soil microbiome
Metabarcoding Analysis of Fungal Diversity in the Phyllosphere and Carposphere of Olive (Olea europaea) – Ahmed Abdelfattah – PLOS ONE
High carbon use efficiency in soil microbial communities is related to balanced growth, not storage compound synthesis – Paul Dijkstra – Soil Biology and Biochemistry
Earthworms modify microbial community structure and accelerate maize stover decomposition during vermicomposting – Yuxiang Chen – Environmental Science and Pollution Research
Water microbiome
Microbial Communities Associated with Zones of Elevated Magnetic Susceptibility in Hydrocarbon-contaminated Sediments – Carol L. Beaver – Geomicrobiology Journal
Bacterial diversity differences along an epigenic cave stream reveal evidence of community dynamics, succession, and stability – Kathleen Brannen-Donnelly – Frontiers in Microbiology
Firmicutes is an Important Component of Microbial Communities in Water-Injected and Pristine Oil Reservoirs; Western Siberia, Russia – Yulia Frank – Geomicrobiology Journal
Functional interactions among filamentous Epsilonproteobacteria and Bacteroidetes in a deep-sea hydrothermal vent biofilm – Runar Stokke – Environmental Microbiology
Temporal Study of the Microbial Diversity of the North Arm of Great Salt Lake, Utah, U.S. – Swati Almeida-Dalmet – Microorganisms
Diversity of the Sediment Microbial Community in the Aha Watershed (Southwest China) in Response to Acid Mine Drainage Pollution Gradients – Weimin Sun – Applied and Environmental Microbiology
Microbial Transport, Retention, and Inactivation in Streams: A Combined Experimental and Stochastic Modeling Approach – Jennifer D. Drummond – Environmental Science & Technology
Extremophile microbiome
Ribosomal tag pyrosequencing of DNA and RNA reveals ‘rare’ taxa with high protein synthesis potential in the sediment of a hypersaline lake in Western Australia – Pascal Weigold – Geomicrobiology Journal
Microbial Diversity in Engineered Haloalkaline Environments Shaped by Shared Geochemical Drivers Observed in Natural Analogues – Talitha C. Santini – Applied and Environmental Microbiology
Built environment microbiome
A New Perspective on Microbiome and Resource Management in Wastewater Systems – Veera Gnaneswar Gude – Biotechnology & Biomaterials
Microbial Ecology
A functional perspective on phenotypic heterogeneity in microorganisms – Martin Ackermann – Nature Reviews Microbiology
Bioinformatics and statistics
USEARCH: Error filtering, pair assembly, and error correction for next-generation sequencing reads – Robert C. Edgar – Bioinformatics
Assessment and Selection of Competing Models for Zero-Inflated Microbiome Data – Lizhen Xu – PLOS ONE
Metabolomics and metatranscriptomics
Functional metabolomics: from biomarker discovery to metabolome reprogramming – Bo Peng – Protein & Cell
Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation – Michael Reck – BMC Genomics
Hydrodynamic chronoamperometry for probing kinetics of anaerobic microbial metabolism – case study of Faecalibacterium prausnitzii – Antonin Prévoteau – Scientific Reports
Techniques
A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes – Craig W. Herbold – Frontiers in Microbiology
This paper is not novel at all: An improved method for bacterial identification through 16S rDNA sequencing using double set of primers: a case study – Amanat Ali – Pak. J. Agri. Sci.,
Microbes in the news
How Bacteria Make This Underground, Awe-Inspiring Cave Shine Gold – Michele Lent Hirsch – Smithsonian
Bacteria in a bottle? AOBiome offers ways to stay clean without traditional soap – Nidhi Subbaraman – The Boston Globe
uBiome to Award Grant of up to $100k for Groundbreaking Microbiome Research – PR Web
Bik’s Picks
NASA Releases Time-Lapse Video Of Mars Rover Opportunity’s Journey: 11 Years In Just 8 Minutes – Jim Algar – Tech Times
Self-Driving ‘Robocabs’ Could Help Curb Global Warming – Wendy Koch – National Geographic
‘Vampires’ keep doctors in the dark for fear of stereotyping: study – Reuters
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Microbiome Digest - Bik's Picks 