Recognition of extremophilic archaeal viruses by eukaryotic cells, special issue about the holobiont concept, sleep deprivation, respiratory viruses in infants. So many new papers that I had to spend another couple of hours on the digest today!

General microbiome and ecology

* Themed issue with papers about the holobiont and endosymbionts: Biological Individuality – Biology & Philosphophy

Review: Making a microbiome: the many determinants of host-associated microbial community composition – Karen L Adair – Current Opinion in Microbiology

Pregnancy and early life

* Interactions of Respiratory Viruses and the Nasal Microbiota during the First Year of Life in Healthy Infants – Insa Korten – mSphere

Does vaginal delivery mitigate or strengthen the intergenerational association of overweight and obesity? Findings from the boston birth cohort – N T Mueller – International Journal of Obesity

The oral cavities of healthy infants harbor high proportions of Streptococcus salivarius strains with phenotypic and genotypic resistance to multiple classes of antibiotics – Thaís H. Palma – Journal of Medical Microbiology

Human respiratory microbiome

Bacterial community collapse: A meta-analysis of the sinonasal microbiota in chronic rhinosinusitis – Brett Wagner Mackenzie – Environmental Microbiology

Review: Viral-Bacterial interactions in the respiratory tract – Carla Bellinghausen – Journal of General Virology

Human skin microbiome

Dysbiotic Bacterial and Fungal Communities Not Restricted to Clinically Affected Skin Sites in Dandruff – Renan C. Soares – Frontiers in Cellular and Infection Microbiology

Gene Function Analysis in the Ubiquitous Human Commensal and Pathogen Malassezia Genus – Giuseppe Ianiri – mBio

Review: Microbial biofilms and the human skin microbiome – Michael Brandwein – NPJ Biofilms and Microbiomes

Human gut microbiome

Clostridium difficile carriage in adult cystic fibrosis (CF); implications for patients with CF and the potential for transmission of nosocomial infection – D.G. Burke – Journal of Cystic Fibrosis

* Gut microbiota and glucometabolic alterations in response to recurrent partial sleep deprivation in normal-weight young individuals – Christian Benedict – Molecular Metabolism

Community-Metabolome Correlations of Gut Microbiota from Child-Turcotte-Pugh of A and B Patients – Xiao Wei – Frontiers in Microbiology

Review: Role of gut microbiota in atherosclerosis – Annika Lindskog Jonsson- Nature Reviews Cardiology

Review: The role of diet on gut microbiota composition – S. Bibbò – European Review for Medical and Pharmacological Sciences

Review: Gut barrier structure, mucosal immunity and intestinal microbiota in the pathogenesis and treatment of HIV infection – Camilla Tincati – AIDS Research and Therapy

Review: Microbiome and metabolic disease: revisiting the bacterial phylum Bacteroidetes – Elizabeth L. Johnson – Journal of Molecular Medicine

Review: Gut Homeostasis, Microbial Dysbiosis, and Opioids – Fuyuan Wang – Toxicologic Pathology

Animal and in vitro experiments

Sensitive and Simplified Detection of Antibiotic Influence on the Dynamic and Versatile Changes of Fecal Short-Chain Fatty Acids – Xiaoya Zhao – PLOS ONE

* Recognition of extremophilic archaeal viruses by eukaryotic cells: a promising nanoplatform from the third domain of life – Kristine Buch Uldahl – Scientific Reports

Unconjugated Bile Acids Influence Expression of Circadian Genes: A Potential Mechanism for Microbe-Host Crosstalk – Kalaimathi Govindarajan – PLOS ONE

Viral Metagenomic Analysis Displays the Co-Infection Situation in Healthy and PMWS Affected Pigs – Anne-Lie Blomström – PLOS ONE

Intraluminal Flagellin Differentially Contributes to Gut Dysbiosis and Systemic Inflammation following Burn Injury – Logan Grimes – PLOS ONE

Early-Life Sugar Consumption Affects the Rat Microbiome Independently of Obesity –
Emily E Noble – Journal of Nutrition

Obese Mice Fed a Diet Supplemented with Enzyme-Treated Wheat Bran Display Marked Shifts in the Liver Metabolome Concurrent with Altered Gut Bacteria – Dorothy A Kieffer – Journal of Nutrition

Dietary fat and gut microbiota interactions determine diet-induced obesity in mice – Raphaela Kübeck – Molecular Metabolism

Animal microbiome

Deconstructing the Bat Skin Microbiome: Influences of the Host and the Environment –
Christine V. Avena – Frontiers in Microbiology

Plant, root, and soil microbiome

A temporal assessment of nematode community structure and diversity in the rhizosphere of cisgenic Phytophthora infestans-resistant potatoes – Vilma Ortiz – BMC Ecology

Diversity of Bacillus-like bacterial community in the sediments of the Bamenwan mangrove wetland in Hainan, China – Min Liu – Canadian Journal of Microbiology

Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach – Véronique Gourmelon – PLOS ONE

Plants, microorganisms, and soil temperatures contribute to a decrease in methane fluxes on a drained Arctic floodplain – Min Jung Kwon – Global Change Biology

Comparative Investigation of Bacterial, Fungal, and Archaeal Community Structures in Soils in a Typical Oilfield in Jianghan, China – Zhi-Feng Zhou – Archives of Environmental Contamination and Toxicology

Method: Assessing Bacterial and Fungal Diversity in the Plant Endosphere – Bernd Wemheuer – Methods in Molecular Biology: Metagenomics

Water microbiome

Method: Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a cDNA as Universal Template for Marker Gene Studies – Dominik Schneider – Methods in Molecular Biology: Metagenomics

Method: Construction and Screening of Marine Metagenomic Large Insert Libraries – Nancy Weiland-Bräuer – Methods in Molecular Biology: Metagenomics

Food microbiology

Microbiological Quality and Variability of Natural Microbiota in Croatian Cheese Maturing in Lambskin Sacks – Jadranka Frece – Food Technology and Biotechnology

Bioinformatics and metagenomics

MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing – Hardik I. Parikh – BMC Bioinformatics

Microbes in the news

Podcast (17 min) – Tracking the Daily Rhythms of the Microbiome – Science Friday

ASM delivers “Gift of Knowledge” to Ethiopia with Microbiology Mentoring Program – ASM

Science, publishing, and career
How Trump Could Wage a War on Scientific Expertise. The mechanics of stripping empiricism out of America’s regulatory systems – Ed Yong – The Atlantic