Here are my search alerts and strategies that I use to create these daily posts. Updated April 2016. To read more about Microbiome Digest, click here.

PubMed alerts

• ‘phyllosphere OR rhizosphere’ (1-5 articles every day)
• ‘microbiome OR microbiota OR (microbial communities)’ (10-100 articles every day)

Google Alerts

• archaea
• bacteria
• biofilm
• host response
• metagenome
• metagenomics
• microbiology
• microbiome
• microbiota
• mothur
• phage
• phyloseq
• preterm birth
• qiime

Google Scholar Alerts

• preterm birth microbiome
• microbiome pyrosequencing
• microbial communities
• metagenome assembly
• metabolomics microbiome
• host response sepsis “16S”
• Glyphosate microbiome
• extremophiles
• extremophile
• dolphin microbiota
• dolphin microbiome
• chromosome conformation capture
• arsenic microbiota
• arsenic microbiome

Journal eTOC Alerts

• ASM journals (mBio, IaI, JCM, mSystems, etc)
• bioRxiv
• BMC Microbiology
• DNA Research
• eLIFE
• Environmental Science & Technology
• Environmental Science & Technology Letters
• Frontiers in Microbiology
• Genome Biology
• Genome Medicine
• Gut
• ISME Journal
• Journal of Applied Microbiology
• Journal of Infectious Diseases
• Letters in Applied Microbiology
• Marine Mammal Science
• Molecular Microbiology
• Nature journals (Nature, Nature Communications, Scientific Reports, Reviews Microbiology)
• PeerJ
• PLOS journals (PLOS Pathogens, NTD, Genetics, Computational Biology)
• PNAS
• Science
• The Lancet

Publisher Alerts

Search terms usually something like: (“microbial communities” in All Fields OR “bacterial communities” in All Fields OR microbiome in All Fields OR microbiota in All Fields)

• ACS Publications
• BioMedCentral
• HighWire Press
• Science Direct
• Wiley Online Library

Other Alerts

• MicroBE.net
• MicrobePost
• Retraction Watch
• Stanford Daily
• STAT News
• The Scientist
• The Tree of Life