For the Saturday digest the theses on making pipelines of microbial communities available and microbes of butterflies; plus the whole section of animal microbiome would be my choice for reading.

General microbiome

Thesis: Making Pipelines and Large Processing Microbial Community Studies Available to Any User, Any Time, Any Place – JAN Molina – ProQuest

Multi-site human microbiome

Social networks, cooperative breeding, and the human milk microbiome – CL Meehan  – American Journal of Human Biology

Human gut microbiome

Fecal Microbiota Composition Drives Immune Activation in HIV-infected Individuals – CP Neff – EBioMedicine

Animal microbiome 

Thesis: Evolution of Microbial Communities and Chemosensory Genes in Passion-Vine Butterflies – B van Schooten – ProQuest

Microbial community and diversity in the feces of Sichuan takin (Budorcas taxicolor tibetana) as revealed by Illumina Miseq sequencing and quantitative real-time PCR – H Zhu – AMB Express

Comparison of the fecal microbiota of domestic commercial meat, laboratory, companion, and shelter rabbits (Oryctolagus cuniculi) – J Kylie – BMC Veterinary Research

Plant, root, and soil microbiome

Diversity of Bacillus-like bacterial community in the rhizospheric and non-rhizospheric soil of halophytes (Salsola stocksii and Atriplex amnicola) and characterization of osmoregulatory genes in halophilic Bacilli – S Mukhtar – Canadian Journal of Microbiology

Contrasting beneficial and pathogenic microbial communities across consecutive cropping fields of greenhouse strawberry – Y Huang – Applied Microbiology and Biotechnology

Reanalysis of microbiomes in soils affected by apple replant disease (ARD): Old foes and novel suspects lead to the proposal of extended model of disease development – L Nicola – Applied Soil Ecology

Root–Microbe Interactions: Understanding and Exploitation of Microbiome – A Sharma – Root Biology

Biodegradation of pyraclostrobin by two microbial communities from Hawaiian soils and metabolic mechanism – X Chen – Journal of Hazardous Materials

Water and extremophile microbiome 

Prokaryotic and eukaryotic community structure affected by the presence of an acid mine drainage from an abandoned gold mine – JO Bonilla – Extremophiles

Techniques

Neutral models of short-term microbiome dynamics with host subpopulation structure and migration limitation – Q Zeng – Microbiome

DNA microarray-based assessment of virulence potential of Shiga toxin gene-carrying Escherichia coli O104:H7 isolated from feedlot cattle feces – PB Shridhar – PLoS One

Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay – MS Reza – Gene