Hello from the Sonoran Desert! It is a lovely morning here in Tucson, Az. I am excited to send my first contribution to Microbiome Digest! There is a lot of diversity in today’s digest, but if microbes thriving in all kinds of strange, extreme conditions are your area of interest, you’ll be interested in the book compiling the latest studies on extremophiles. Each chapter focuses on a particular environment, ranging from deserts to deep-sea hydrothermal vents, and explores the mechanisms allowing microbes to survive these incredible conditions.
If like me, you are a computational biology enthusiast and a machine learning addict, you should enjoy reading the last entry, a short perspective paper examining how machine learning algorithms can help predict antibiotic resistance!
Have a great Sunday!
General microbiology
Preprint: Interspecies interactions in bacterial colonies are determined by physiological traits and the environment – Booth – BioRxiv
Human gut and mouth microbiome
Bacterial colonization reprograms the neonatal gut metabolome – Bittinger – Nature microbiology
Salivary Factors that Maintain the Normal Oral Commensal Microflora – Carpenter – Journal of dental research
Preprint: Metagenomic Next-Generation Sequencing of Rectal Swabs for the Surveillance of Antimicrobial Resistant Organisms on the Illumina Miseq and Oxford MinION Platforms – Yee – bioRxiv
Animal microbiome
Preprint: Mortality of native and invasive ladybirds co-infected by ectoparasitic and entomopathogenic fungi – Haelewaters – bioRxiv
Built environment
Preprint: The Microbes Found in the Honey of New York City Beehives – Weiss – BioRxiv
Correlation between autochthonous microbial communities and key odorants during the fermentation of red pepper (Capsicum annuum L.) – Xu – Food Microbiology
Water and extremophile microbiome
Book: Microbial Versatility in Varied Environments: Microbes in Sensitive Environments – collective – Springer Nature
The seasonal variation of microbial communities in drinking water sources in Shanghai – Guo – Journal of Cleaner Production
Plant, root and soil microbiome
LDPE microplastics significantly alter the temporal turnover of soil microbial communities – Wang – Science of the total environment
High abundance of Ralstonia solanacearum changed tomato rhizosphere microbiome and metabolome – Wen – BMC Plant Biology
Phages and viruses
Preprint : First evidence of virus-like particles in the bacterial symbionts of Bryozoa – Vishnyakov – BioRxiv
Microbial community development on model particles in the deep sulfidic waters of the Black Sea – Suominen – Environmental microbiology
The stepwise assembly of the neonatal virome is modulated by breastfeeding – Liang – Nature
Bioinformatics
Preprint: Bayesian classification, anomaly detection, and survival analysis using network inputs with application to the microbiome – Josephs – arXiv
Techniques
Preprint: Expanding the diversity of bacterioplankton isolates and modeling isolation efficacy with large scale dilution-to-extinction cultivation – Henson – bioRxiv
Catalyzing rapid discovery of gold-precipitating bacterial lineages with university students – Riley – PeerJ
COVID-19 and career
Science-ing from home – Powell – Nature
My non-microbiology pick
Perspective: Lean, mean, learning machines – Wheeler – Nature review microbiology
Microbiome Digest - Bik's Picks 