Today’s digest is about the shortcomings of the midstream urine test for urinary tract infection, contacts between phages and bacterial hosts, and contamination in marker-gene and metagenomic sequencing. There is a very interesting podcast on “Seeing double” in scientific papers. Happy reading/listening!

Urinary microbiome

Cross-over data supporting long-term antibiotic treatment in patients with painful lower urinary tract symptoms, pyuria and negative urinalysis – Sheela Swamy – International Urogynecology Journal

*Reassessment of routine midstream culture in diagnosis of urinary tract infection – Sanchutha Sathiananthamoorthya – Journal of Clinical Microbiology

Gut microbiome

Drivers of human gut microbial community assembly: Coadaptation, determinism and stochasticity – Kaitlyn Oliphan – BioRxiv

Animal experiments

*Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay – Martial Marbouty – Science Advances

Antidepressant treatment modulates the gut microbiome and metabolome during pregnancy and lactation in rats with a depressive-like phenotype – Anouschka S Ramsteijn – BioRxiv

General Anesthesia Alters the Diversity and Composition of the Intestinal Microbiota in Mice – Mara A. Serbanescu – Anesthesia & Analgesia

Water microbiome

Bacterial community activity and dynamics in the biofilm of an experimental hybrid wetland system treating greywater – Marika Truu – Environmental Science and Pollution Research

Plant/root/soil microbiome

Introducing THOR, a model microbiome for genetic dissection of community behavior – Gabriel L. Lozano – BioRxiv

Bacterial analogs of plant piperidine alkaloids mediate microbial interactions in a rhizosphere model system – Gabriel L. Lozano – BioRxiv

Bioinformatics

*Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data – Nicole M. Davis – Microbiome

Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences – Kirill Kryukov – BioRxiv

Podcast

*Seeing double [Elisabeth Bik speaks about the problematic images in scientific papers, the state of microbiome research, and making the jump from academia to industry] – Dan Quintana and James Heathers – Everything Hertz.