April 12, 2016, part 1

Too many alerts to go through after taking one day off, so here is part one. An updated tree of life, acute appendicitis, rhizosphere of a living fossil plant, Antarctic surface snow, and effects of Superstorm Sandy on creek water.

Jobs and events

Senior Scientist with significant track record in microbiome research – The National Institute for Biological Standards and Control, South Mimms, UK

General microbiome

A new view of the tree of life – Laura A. Hug – Nature Microbiology

Pregnancy and birth

The Gestational Vaginal Microbiome and Spontaneous Preterm Birth among Nulliparous African American Women – Deborah B. Nelson – American Journal of Perinatology

Early colonization of functional groups of microbes in the infant gut – Van T. Pham – Environmental Microbiology

The gut resistome is highly dynamic during the first months of life – Christian JH von Wintersdorff – Future Medicine

Human skin microbiome

Review: Skin Biomes – N. Fyhrquist – Current Allergy and Asthma Reports

Human respiratory microbiome

Review: Next Generation Sequencing and the Microbiome of Chronic Rhinosinusitis – A Primer for Clinicians and Review of Current Research, Its Limitations, and Future Directions – Jake Jervis Bardy – Ann Otol Rhinol Laryngol

Human oral microbiome

The salivary microbiome for differentiating individuals: proof of principle – Sarah L. Leake – Microbes and Infection

Concordance of HOMIM and HOMINGS technologies in the microbiome analysis of clinical samples – Jean-Luc C. Mougeot – Journal of Oral Microbiology

Human gut microbiome

There are no Enterotypes: Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle – Anastassia Gorvitovskaia – Microbiome

Experiment with n=1: Understanding the Impact of Omega-3 Rich Diet on the Gut Microbiota – Blanca S. Noriega – Case Reports in Medicine

First Occurrence of Severe Extraintestinal Manifestations of Crohn’s Disease Following Faecal Microbiota Transplantation – Niels Teich – Journal of Crohn’s and Colitis

Acute appendicitis in children is associated with a local expansion of Fusobacteria – Matthew B. Rogers – Clinical Infectious Diseases

Hypothesis: Gut Microbiota Diversity and Human Diseases: Should We Reintroduce Key Predators in Our Ecosystem? – Alexis Mosca – Frontiers in Microbiology

Not endorsing, because highly controversial and not well founded: Bread and Other Edible Agents of Mental Disease – Paola Bressan and Peter Kramer – Frontiers in Human Neuroscience

Review: The human gut microbiome in health: establishment and resilience of microbiota over a lifetime – Kacy Greenhalgh – Environmental Microbiology

Review: Cytotoxicity of Nanoparticles Contained in Food on Intestinal Cells and the Gut Microbiota – Esther E. Fröhlich – MDPI International Journal of Molecular Sciences

Review: The Role of the Gut Microbiota in Childhood Obesity – Pihl Andreas Friis – Childhood Obesity

Animal models

Gnotobiotic Rodents: An In Vivo Model for the Study of Microbe–Microbe Interactions – Rebeca Martín – Frontiers in Microbiology

Depletion of Cultivatable Gut Microbiota by Broad-Spectrum Antibiotic Pretreatment Worsens Outcome After Murine Stroke – Katarzyna Winek – Stroke

Plant, root, and soil microbiome

Common mycorrhizal networks and their effect on the bargaining power of the fungal partner in the arbuscular mycorrhizal symbiosis – Heike Bückinga – Communicative & Integrative Biology

Rhizosphere Microbiomes of European + Seagrasses Are Selected by the Plant, But Are Not Species Specific – Catarina Cúcio – Frontiers in Microbiology

Specific Microbial Communities Associate with the Rhizosphere of Welwitschia mirabilis, a Living Fossil – Angel Valverde – PLOS ONE

Impact of alien pines on local arbuscular mycorrhizal fungal communities – evidence from two continents – Antonio Gazol – FEMS Microbiology Ecology

Differences in stability of seed-associated microbial assemblages in response to invasion by phytopathogenic microorganisms – Samir Rezki – PeerJ

Using Ancient Traits to Convert Soil Health into Crop Yield: Impact of Selection on Maize Root and Rhizosphere Function – Jennifer E. Schmidt – Frontiers in Plant Science

Partitioning of Functional and Taxonomic Diversity in Surface-Associated Microbial Communities – Alexandra J. Roth-Schulze – Environmental Microbiology

Temporal dynamics of sediment bacterial communities in monospecific stands of Juncus maritimus and Spartina maritima – Daniel F R Cleary – Plant Biology

Thorough high-throughput sequencing analyses unravels huge diversities of soil parasitic protists – Stefan Geisen – Environmental Microbiology

Water and extremophile microbiome

Temporal and Spatial Dynamics of Archaeal Communities in Two Freshwater Lakes at Different Trophic Status – Yuyin Yang – Frontiers in Microbiology

Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow – Anna Lopatina – Frontiers in Microbiology

Partitioning of Functional and Taxonomic Diversity in Surface-Associated Microbial Communities – Alexandra J. Roth-Schulze – Environmental Microbiology

Impact of an intense water column mixing (0-1500m) on prokaryotic diversity and activities during an open-ocean convection event in the NW Mediterranean Sea – T. Severin – Environmental Microbiology

Aquatic bacterial community is restructured by hydric dynamics associated with Superstorm Sandy – Nikea Ulrich – Applied and Environmental Microbiology

Metagenomic analysis of lacustrine viral diversity along a latitudinal transect of the Antarctic Peninsula – Daniel Aguirre de Cárcer – FEMS Microbiology Ecology

Response of bacterial communities from California coastal waters to alginate particles and an alginolytic Alteromonas macleodii strain – Maximilian Mitulla – Environmental Microbiology

Waste and pollution microbiology

Partitioning of Viruses in Wastewater Systems and Potential for Aerosolization – Mari Titcombe Lee – Environmental Science & Technology Letters

Seasonality of antibiotic prescriptions for outpatients and resistance genes in sewers and wastewater treatment plant outflow – Serena Caucci – FEMS Microbiology Ecology

Spatial and temporal variability of bacterial communities within a combined sewer system – Henriette Stokbro Jensen – MicrobiologyOpen

Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters – Rasmus Hansen Kirkegaard – The ISME Journal


Not endorsing: Motif-Based Text Mining of Microbial Metagenome Redundancy Profiling Data for Disease Classification – Yin Wang – BioMed Research International

More microbiology

Host-Derived Sialic Acids Are an Important Nutrient Source Required for Optimal Bacterial Fitness In Vivo – Nathan D. McDonald – mBio

Review: Network-based metabolic analysis and microbial community modeling – Cesar Cardona – Current Opinion in Microbiology

Review: DNA-sensing inflammasomes: regulation of bacterial host defense and the gut microbiota – Si Ming Man – Pathogens and Disease

Microbes in the news

Most of the Tree of Life is a Complete Mystery. We know certain branches exist, but we have never seen the organisms that perch there – Ed Yong – The Atlantic

Wealth of unsuspected new microbes expands tree of life – Science Daily

Can more fiber restore microbiome diversity? – Science Daily

Science, publishing, and career

Research Funding: the Case for a Modified Lottery – Ferric C. Fang and Arturo Casadevall – mBio


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