The ecology of microbiome research (in the new journal Nature Microbiology), gut microbiome of infants, dentition status and teeth microbes, human impact on corals, metagenomics, CRISPRs, rainforest and desert soils, and tropical oceans.
General microbiome
An assessment of US microbiome research – Elizabeth Stulberg – Nature Microbiology
Microbiome: Ecology of stable gut communities – Luke McNally – Nature Microbiology
Pregnancy and birth microbiome
Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants – Juliette C. Madan – JAMA Pediatrics
Human oral microbiome
Supragingival Microbial Profiles of Permanent and Deciduous Teeth in Children with Mixed Dentition – Weihua Shi – PLOS ONE
Human gut microbiome
Human Gut Bacteria Are Sensitive to Melatonin and Express Endogenous Circadian Rhythmicity – Jiffin K. Paulose – PLOS ONE
A New High-Throughput Approach to Genotype Ancient Human Gastrointestinal Parasites – Nathalie M. L. Côté – PLOS ONE
Intestinal Microbiota in Patients with Spinal Cord Injury – Bilgi Gungor – PLOS ONE
Editorial: A Potential Role for Host- Microbe Dysbiosis in Enteropathy Associated with HIV Infection – Michael D. George – Primary & Acquired Immunodeficiency Research
Review: The obese gut microbiome across the epidemiologic transition – Lara R. Dugas – Emerging Themes in Epidemiology
Animal microbiome
Obligate bacterial mutualists evolving from environmental bacteria in natural insect populations – Takahiro Hosokawa – Nature Microbiology
The Microbiome of Ehrlichia-Infected and Uninfected Lone Star Ticks (Amblyomma americanum) – R. T. Trout Fryxell – PLOS ONE
Coral microbial community dynamics in response to anthropogenic impacts near a major city in the central Red Sea – Maren Ziegler – Marine Pollution Bulletin
Application of Faecalibacterium 16S rDNA genetic marker for accurate identification of duck faeces – Da Sun – Environmental Science and Pollution Research
Review: Understanding the canine intestinal microbiota and its modification by pro-, pre- and synbiotics – what is the evidence? – Silke Schmitz – Veterinary Medicine and Science
Plant, root, and soil microbiome
Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest – Julia Elidia Lima-Perim – PLOS ONE
Corky root severity, root knot nematode galling and microbial communities in soil, rhizosphere and rhizoplane in organic and conventional greenhouse compartments –
Ariena H.C. van Bruggen – Applied Soil Ecology
Metacommunity analysis of amoeboid protists in grassland soils – Anna Maria Fiore-Donno – Scientific Reports
Microbial communities of buried soils of the Tsaritsyn Defense Line (1718–1720) – T. S. Demkina – Soil Biology
Perspective: Exploring rhizospheric interactions for agricultural sustainability: The need of integrative research on multi-trophic interactions – Rama Kant Dubey – Journal of Cleaner Production
Water microbiome
Genetic Diversity Affects the Daily Transcriptional Oscillations of Marine Microbial Populations – Irina N. Shilova – PLOS ONE
Low diversity of planktonic bacteria in the tropical ocean – Mathias Milici – Scientific Reports
Out of thin air: Microbial utilization of atmospheric gaseous organics in the surface ocean – Jesus M. Arrieta – Frontiers in Microbiology
Elevated nutrients change bacterial community composition and connectivity: high throughput sequencing of young marine biofilms – Jasmin C. Lawes – Biofouling
Waste microbiology
Dynamics of bacterial populations during bench-scale bioremediation of oily seawater and desert soil bioaugmented with coastal microbial mats – Nidaa Ali – Microbial Biotechnology
Sequential Changes of Microbial Community Composition During Biological Wastewater Treatment in Single Unit Waste Stabilization System – Subhasis Sarkar – Waste and Biomass Valorization
Diversity and interactions of microbial functional genes under differing environmental conditions: insights from a membrane bioreactor and an oxidation ditch – Yu Xia – Scientific Reports
Food microbiology
Investigation of chocolate produced from four different Brazilian varieties of cocoa (Theobroma cacao L.) inoculated with Saccharomyces cerevisiae – Aline Galvão Tavares Menezesa – Food Research International
Microbial diversity and metabolite composition of Belgian red-brown acidic ales – Isabel Snauwaert – International Journal of Food Microbiology
Metagenomics, CRISPRs, viruses, and bioinformatics
Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls – Tatiana C. Mangericao – BMC Systems Biology
Identification of physical interactions between genomic regions by enChIP-Seq – Toshitsugu Fujita – BioRxiv
Metaviromics of Namib Desert Salt Pans: A Novel Lineage of Haloarchaeal Salterproviruses and a Rich Source of ssDNA Viruses – Evelien M. Adriaenssens – MDPI Viruses
A novel semi-supervised algorithm for the taxonomic assignment of metagenomic reads – Vinh Van Le – BMC Bioinformatics
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations – Matthew L Bendall – The ISME Journal
Techniques in microbiology
The 6th International Conference on Analysis of Microbial Cells at the Single Cell Level, Retz, Austria, 19-22 July, 2015 – Nina Bydlinski – New Biotechnology
Microbes in the news
Microbe Cells Don’t Outnumber Your Own – Marissa Fessenden – Smithsonian
Getting to know the vagina: Microbiomes and our health – Daniel Vosberg – McGillDaily
Acidification affects the ability of bacteria to clean our oceans – Phys.org
Science, publishing, and career
Do prestigious science journals attract bad science? – Julia Belluz – Vox
Female professors are woefully outnumbered at med schools nationwide – Melissa Bailey – STAT News
[hr]
Microbiome Digest - Bik's Picks 