Good morning from New Jersey! Lots of papers to share today, particularly regarding animal microbiota and new bioinformatics tools.
General microbiome
Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer, Alice Tzeng et al., Genome Medicine
Pregnancy and early life
The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition, Xuanji Li et al., Cell Host & Microbe
Multi-site human microbiome
Review: Microbiome-immune interactions in tuberculosis, Giorgia Mori et al., PLOS Pathogens
Human gut microbiome
Dynamic Changes in Microbiome Composition Following Mare’s Milk Intake for Prevention of Collateral Antibiotic Effect, Almagul Kushugulova et al., Frontiers in Cellular and Infection Microbiology
Review: The aging gut microbiome and its impact on host immunity, Bosco and Noti, Genes & Immunity
Animal experiments
Ingestion of Bifidobacterium longum changes miRNA levels in the brains of mice, DeVries and Horstman et al., PLOS ONE
Heat-inactivated Lactobacillus plantarum nF1 promotes intestinal health in Loperamide-induced constipation rats, Seon-Ah Park et al., PLOS ONE
The pregnane X receptor drives sexually dimorphic hepatic changes in lipid and xenobiotic metabolism in response to gut microbiota in mice, Sharon Ann Barretto et al., Microbiome
One dog’s waste is another dog’s wealth: A pilot study of fecal microbiota transplantation in dogs with acute hemorrhagic diarrhea syndrome, Arnon Gal et al., PLOS ONE
Animal microbiome
Diversity and functional landscapes in the microbiota of animals in the wild, Levin, Raab, Pinto, and Rothschild et al., Science
Microbiome reduction and endosymbiont gain from a switch in sea urchin life history, Tyler J. Carrier et al., PNAS
Diet and gut microbiome enterotype are associated at the population level in African buffalo, Claire E. Couch et al., Nature Communications
Coral microbiome changes over the day–night cycle, Alicia M. Caughman et al., Coral Reefs
An investigation of conventional microbial culture for the Naja atra bite wound, and the comparison between culture-based 16S Sanger sequencing and 16S metagenomics of the snake oropharyngeal bacterial microbiota, Mao and Chuang et al., PLOS Neglected Tropical Diseases
Plant, root, and soil microbiome
Preprint: Genome-centric analyses of seasonal phyllosphere microbiome activities in perennial crops, Adina Howe et al., bioRxiv
Influence of Plant Host and Organ, Management Strategy, and Spore Traits on Microbiome Composition, Kristi Gdanetz et al., Phytobiomes Journal
Built environment
Categorisation of culturable bioaerosols in a fruit juice manufacturing facility, Shirleen M. Theisinger et al., PLOS ONE
Bioinformatics
Preprint: Deconstructing taxa x taxa x environment interactions in the microbiota: A theoretical examination, Senay Yitbarek et al., bioRxiv
Preprint: Extended taxonomic profiling of diverse environments with mOTUs 2.6, Hans-Joachim Ruscheweyh et al., bioRxiv
Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome, Donovan H. Parks et al., Frontiers in Microbiology
Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC, Bruce Parrello et al., PLOS ONE
