Endophytes in Miscanthus seeds, the microbes of Blood Pond Hell, microbes in indoor dust, and Dada2 sample inference from Illumina data.
General microbiome
Moonshot or mania? – Sally Adee looks behind the hype – New Scientist
Human gut microbiome
Research Highlight: Microbiota trigger inflammation – Ellen F. Carney – Nature Reviews Nephrology
Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies – Emmanouil Angelakis – Scientific Reports
Microbiome of HIV-infected people – Grégory Dubourg – Microbial Pathogenesis
Review: The microbiota and immune response during Clostridium difficile infection – Erica L. Buonomo – Anaerobe
Animal experiments
Snapshot on a Pilot Metagenomic Study for the Appraisal of Gut Microbial Diversity in Mice, Cat, and Man – Coline Plé – Gastroenterology Research and Practice
Plant, root, and soil microbiome
The microbiomes and metagenomes of forest biochars – Genevieve L. Noyce – Scientific Reports
Endophytic bacteria in Miscanthus seed: implications for germination, vertical inheritance of endophytes, plant evolution and breeding – Naomi Cope-Selby – GCB Bioenergy
Impact of Faba Bean-Seed Rhizobial Inoculation on Microbial Activity in the Rhizosphere Soil during Growing Season – Anna Siczek – Int J Mol Sci
Evaluation of Strategies to Separate Root-Associated Microbial Communities: A Crucial Choice in Rhizobiome Research – Tim Richter-Heitmann – Frontiers in Microbiology
Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time – Ngoc-Lan Nguyen – PLOS ONE
Water and extremophile microbiome
Estimating planktonic diversity through spatial dominance patterns in a model ocean – Alice Soccodato – Marine Genomics
Microbial community profiling of the Chinoike Jigoku (“Blood Pond Hell”) hot spring in Beppu, Japan: isolation and characterization of Fe(III)-reducing Sulfolobus sp. strain GA1 – Yusei Masakia – Research in Microbiology
Near-Bottom Hypoxia Impacts Dynamics of Bacterioplankton Assemblage throughout Water Column of the Gulf of Finland (Baltic Sea) – Peeter Laas – PLOS ONE
Fungal communities in sediments of subtropical Chinese seas as estimated by DNA metabarcoding – Wei Li – Scientific Reports
Built environment microbiology
Characterization of the bacterial and fungal microbiome in indoor dust and outdoor air samples: a pilot study – Blake Hanson – Environmental Science: Processes & Impact
Microbiome Profiling of Drinking Water in Relation to Incidence of Inflammatory Bowel Disease – Jessica D Forbes – Canadian Journal of Microbiology
Infection microbiology
The scanning electron microscope in microbiology and diagnosis of infectious disease – Christine G. Golding – Scientific Reports
Bioinformatics
DADA2: High-resolution sample inference from Illumina amplicon data – Benjamin J Callahan – Nature Methods (OA by author)
MetaTrans: an open-source pipeline for metatranscriptomics – Xavier Martinez – Scientific Reports
An Introduction to Programming for Bioscientists: A Python-based Primer – Berk Ekmekci – Arxiv / PLOS
An Optimized Graph-Based Metagenomic Gene Classification Approach: Metagenomic Gene Analysis – Md Sarwar Kamal – Classification and Clustering in Biomedical Signal Processing
Complex heatmaps reveal patterns and correlations in multidimensional genomic data – Zuguang Gu – Bioinformatics
Unsupervised random forest: a tutorial with case studies – Nelson Lee Afanador – Journal of Chemometrics
Metagenomics
Review: The bright side of microbial dark matter: lessons learned from the uncultivated majority – Lindsey Solden – Current Opinion in Microbiology
Metabolomics
Review: Metabolomics of fecal samples: a practical consideration – Silke Matysik – Trends in Food Science & Technology
Viruses and phages
Targeted virus detection in next-generation sequencing data using an automated e-probe based approach – Marike Visser – Virology
Identification of diverse mycoviruses through metatranscriptomics characterization of the viromes of five major fungal plant pathogens – Shin-Yi Lee Marzano – Journal of Virology
Viruses and bacteria in Th2 biased allergic airway disease – Feng Lan – Allergy
More microbiology
Biofilms: Microbial Shelters Against Antibiotics – Skander Hathroubi – Microbial Drug Resistance
Microbes in the news
Building An Antibiotic To Kill Bad Microbes While Sparing Good Ones – Madeline K. Sofia – NPR
A rallying call for microbiome science national data management – A National Microbiome Data Center is essential for enabling exploration of all the environmental genomic data – EurekAlert
Could Gut Microbiome Be the Holy Grail for Diabetes Treatment? – An Expert Weighs In at International Endocrinology Congress – Business Wire
Painful pooping may stop panda sex. A gut-wrenching tummy ache can throw cold water on pandas’ love life. Amy Middleton reports. – Amy Middleton – Cosmos Magazine
Microbiome Digest - Bik's Picks 