A very late Saturday digest, after a fun day at the pool and dinner with family. Germ-free jewel wasps, tooth extraction in horses, dormancy in lakes, subways and urban biomes.
Pregnancy and birth
Review: Fetal, neonatal, and infant microbiome: Perturbations and subsequent effects on brain development and behavior – Rochellys Diaz Heijtz – Seminars in Fetal and Neonatal Medicine
Determination of Bifidobacterium and Lactobacillus in breast milk of healthy women by digital PCR – L. Qian – Beneficial Microbes
Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants – Tali Raveh-Sadka – The ISME Journal
Human gut microbiome
Capturing One of the Human Gut Microbiome’s Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data – Patricio Jeraldo – Frontiers in Microbiology
Identification, recovery, and refinement of hitherto undescribed population-level genomes from the human gastrointestinal tract – Cedric C. Laczny – Frontiers in Microbiology
Cryptic functional variation in the human gut microbiome – Patrick H Bradley – bioRxiv Preprint
Review: The gut microbiome in human immunodeficiency virus infection – Gili Zilberman-Schapira – BMC Medicine
Review: The Gut Microbiome and Obesity – George Kunnackal John – Current Oncology Reports
Animal experiments
An optimized approach to germ-free rearing in the jewel wasp Nasonia – J. Dylan Shropshire – PeerJ Preprints
Bacteraemia before, during and after tooth extraction in horses in the absence of antimicrobial administration – I. Kern – Equine Veterinary Journal
Effects of Diets Supplemented with Ensiled Mulberry Leaves and Sun-Dried Mulberry Fruit Pomace on the Ruminal Bacterial and Archaeal Community Composition of Finishing Steers – Yuhong Niu – PLOS ONE
Uncovering the composition of microbial community structure and metagenomics among three gut locations in pigs with distinct fatness – Hui Yang – Scientific Reports
Animal microbiome
Gut microbial communities associated with the molting stages of the giant freshwater prawn Macrobrachium rosenbergii – Eleni Mente
DGGE: A comparison of microbial profiles of different regions of the equine hindgut –
K. Fliegerova – Livestock Science
Diversity and composition of cultivable gut bacteria in an endemic island bird and its mainland sister species – Elisa Lobato – Symbiosis
Bacterial Community Diversity Harboured by Interacting Species – Mikaël Bili – PLOS ONE
Plant, root, and soil microbiome
Structure of Fungal Communities in Sub-Irrigated Agricultural Soil from Cerrado Floodplains – Elainy Cristina A. M. Oliveira – Diversity
Phylogenetic and multivariate analyses to determine the effect of agricultural land-use intensification and soil physico-chemical properties on N-cycling microbial communities in drained Mediterranean peaty soils – Valentina Ciccolini – Biology and Fertility of Soils
The impact of pasture systems on soil microbial biomass and community-level physiological profiles – Francisco Marques Cardozo Junior – Land Degradation & Development
Effect of Heavy Metals Pollution on Soil Microbial Diversity and Bermudagrass Genetic Variation – Yan Xie – Frontiers in Plant Science
Isolation, identification and oenological characterization of non-Saccharomyces yeasts in a Mediterranean island – G. Polizzotto – Letters in Applied Microbiology
Water and extremophile microbiome
Diversity and distribution of cultured endolichenic fungi in the Ny-Ålesund Region, Svalbard (High Arctic) – Tao Zhang – Extremophiles
Bacterial dormancy is more prevalent in freshwater than hypersaline lakes – Zachary T. Aanderud – Frontiers in Microbiology
Changes in the water quality and bacterial community composition of an alkaline and saline oxbow lake used for temporary reservoir of geothermal waters – Andrea K. Borsodi – Environmental Science and Pollution Research
Responses of aquatic bacteria to terrestrial runoff: effects on community structure and key taxonomic groups – Huong T. Le – Frontiers in Microbiology
Metagenomics accelerates species discovery and unravel great biodiversity of benthic invertebrates in marine sediments in Campos basin, Brazil – Milena Marcela D P Schettini – PeerJ Preprint
Built environment microbiome
Microbial communities in dairy processing environment floor-drains are dominated by product-associated bacteria and yeasts – Kerstin Schön – Food Control
The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report – The MetaSUB International Consortium – Microbiome
Bioinformatics and metagenomics
The Pepsi Challenge, Metagenomics style? COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge – Yang Young Lu – Bioinformatics
Microbial Ecology
A stable genetic polymorphism underpinning microbial syntrophy – Tobias Großkopf – The ISME Journal
Microbes in the news
Two Stanford microbiology and immunology professors elected to National Academy of Sciences – Stanford Medicine
Crowds of crows spread C. jejuni: Are humans vulnerable? – EurekAlert
Antimicrobial Kills E. Coli Within 30 Seconds – Greg Watry – RD Magazine
Just a short Microbiome Digest in between funeral ceremonies today. But today also brought good news: Microbiome Digest / Bik’s Picks received the “Microbiome Pioneer Award” today at 
Microbiome Digest - Bik's Picks 