January 13, 2018

100+ alerts, meaning great papers in every category. Enjoy!

General microbiome
ReviewSphingolipids in host-microbial interactions – Stacey L Heaver – Current Opinion In Microbiology

EditorialThe Human Microbiome – Emily P Balskus – ACS Infectious Diseases

ReviewEmergent Heterogeneous Micro-environments in Biofilms:Substratum Surface Heterogeneity and Bacterial Adhesion Force-sensing – Yijin Ren – Fems Microbiology Reviews

Pregnancy and early life
Maturation of the gut microbiome and risk of asthma in childhood – Jakob Stokholm – Nature Communications

Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses – Thomas H A Ederveen – Microbiome

Fetal and early life antibiotics exposure and very early onset inflammatory bowel disease: a population-based study – Anne K Örtqvist – Gut

Review: Early Microbes Modify Immune System Development and Metabolic Homeostasis-The “Restaurant” Hypothesis Revisited – Michael J Nash – Frontiers In Endocrinology

Human respiratory microbiome
Genomics of Corynebacterium striatum, an emerging multi-drug resistant pathogen of immunocompromised patients – Kathleen Nudel – Clinical Microbiology And Infection

Human skin microbiome
Transcriptomic profiling of interacting nasal staphylococci species reveals global changes in gene and non-coding RNA expression – Grith M M Hermansen – Fems Microbiology Letters

Human oral microbiome
Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer – Richard B Hayes – JAMA Oncology

Composition of salivary microbiota in elderly subjects – Taiji Ogawa – Scientific Reports

Human gut microbiome
CX3CR1+ mononuclear phagocytes control immunity to intestinal fungi – Irina Leonardi – Science (New York, N.Y.)

Antagonism toward the intestinal microbiota and its effect on Vibrio cholerae virulence. – Wenjing Zhao – Science (New York, N.Y.)

Evaluation of bloodstream infections, Clostridium difficile infections, and gut microbiota in pediatric oncology patients – Bryan T. Nycz – PLoS One

Antibiotic Treatments for Clostridium difficile Infection Are Associated with Distinct Bacterial and Fungal Community Structures – Regina Lamendella – mSphere

Alterations of the gut microbiota in Hashimoto’s thyroiditis patients – Fuya Zhao – Thyroid : Official Journal Of The American Thyroid Association

Structural insights into a family 39 glycoside hydrolase from the gut symbiont Bacteroides cellulosilyticus WH2 – Ahmad Ali-Ahmad – Journal Of Structural Biology

Review: Gut Microbiota Dysbiosis Drives and Implies Novel Therapeutic Strategies for Diabetes Mellitus and Related Metabolic Diseases – Xuan Li – Frontiers In Immunology

ReviewPathogens, microbiome and the host: emergence of the ecological Koch’s postulates – Pascale Vonaesch – FEMS Microbiology Reviews

ReviewBiochemistry of Complex Glycan Depolymerisation by the Human Gut Microbiota – Didier Ndeh – FEMS Microbiology Reviews

Review: Segmented filamentous bacteria, Th17 inducers and helpers in a hostile world – Pamela Schnupf – Current Opinion In Microbiology

Microbial Ecology
Simulation of Escherichia coli Dynamics in Biofilms and Submerged Colonies with an Individual-Based Model Including Metabolic Network Information – Ignace L M M Tack – Frontiers In Microbiology

Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems – Elham Ehsani – Scientific Reports

Pan-genome analysis of the genus Finegoldia identifies two distinct clades, strain-specific heterogeneity, and putative virulence factors – Holger Brüggemann – Scientific Reports

Specifying the Harsh Conditions of Life: Resource Competition and Predation in the 1970s – Alita R. Burmeister – The American Naturalist

Animal experiments
Maternal metabolic, immune, and microbial systems in late pregnancy vary with malnutrition in mice – Kristin L Connor – Biology of Reproduction

Fecal Microbiota Transplantation, Commensal Escherichia coli and Lactobacillus johnsonii Strains Differentially Restore Intestinal and Systemic Adaptive Immune Cell Populations Following Broad-spectrum Antibiotic Treatment – Ira Ekmekciu – Frontiers In Microbiology

Impacts of feeding preweaned calves milk containing drug residues on the functional profile of the fecal microbiota – Richard Van Vleck Pereira – Scientific Reports

Gama-aminobutyric Acid Enriched Rice Bran Diet Attenuates Insulin Resistance and Balances Energy Expenditure via Modification of Gut Microbiota and SCFAs – Xu Si – Journal Of Agricultural And Food Chemistry

Proton Pump Inhibitors Increase the Susceptibility of Mice to Oral Infection with Enteropathogenic Bacteria – Eiichiro Yasutomi – Digestive Diseases And Sciences

Rhubarb supplementation promotes intestinal mucosal innate immune homeostasis through modulating intestinal epithelial microbiota in goat kids – Jinzhen Jiao – Journal Of Agricultural And Food Chemistry

Impact of dietary induced precocious gut maturation on cecal microbiota and its relation to the blood-brain barrier during the postnatal period in rats – N Marungruang – Neurogastroenterology And Motility : The Official Journal Of The European Gastrointestinal Motility Society

Exercise Prevents Enhanced Postoperative Neuroinflammation and Cognitive Decline and Rectifies the Gut Microbiome in a Rat Model of Metabolic Syndrome – Xiaomei Feng – Frontiers In Immunology

Rifampicin treatment of Blattella germanica evidences a fecal transmission route of their gut microbiota – Tania Rosas – Fems Microbiology Ecology

Gut Flora-Dependent Metabolite Trimethylamine-N-oxide Accelerates Endothelial Cell Senescence and Vascular Aging through Oxidative Stress – Yilang Ke – Free Radical Biology & Medicine

Nanocomposite of Half-Fin Anchovy Hydrolysates/Zinc Oxide Nanoparticles Exhibits Actual Non-Toxicity and Regulates Intestinal Microbiota, Short-Chain Fatty Acids Production and Oxidative Status in Mice – Ru Song – Marine Drugs

Animal microbiome
Is there a link between aging and microbiome diversity in exceptional mammalian longevity? – Graham M. Hughes – PeerJ (Specifically, bats or Myotis myotis)

Gut Microbes Egested during Bites of Infected Sand Flies Augment Severity of Leishmaniasis via Inflammasome-Derived IL-1β – Ranadhir Dey – Cell Host & Microbe

The Sarda Sheep Host Fecal Proteome – Antonio Palomba – Proteomics

Host Specificity for Bacterial, Archaeal and Fungal Communities Determined for High- and Low-Microbial Abundance Sponge Species in Two Genera – Maryam Chaib De Mares – Frontiers In Microbiology (from December 2017)

Comparative Metagenomics of Cellulose- and Poplar Hydrolysate-Degrading Microcosms from Gut Microflora of the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus) after Long-Term Enrichment. – Mabel T Wong – Frontiers In Microbiology (from December 2017)

Regular Wounding in a Natural System: Bacteria Associated With Reproductive Organs of Bedbugs and Their Quorum Sensing Abilities – Oliver Otti – Frontiers In Immunology

Plant, root, and soil microbiome
Forest conversion induces seasonal variation in microbial β-diversity – Shengen Liu – Environmental Microbiology

Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere – Hector Urbina – Fungal Biology

Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils – Peng Liu – Chemosphere

Intra-species variation in a widely distributed tree species regulates the responses of soil microbiome to different temperature regimes – Cui-Jing Zhang – Environmental Microbiology Reports

Positive diversity-functioning relationships in model communities of methanotrophic bacteria – Elvira Schnyder – Ecology

Plant Phylogeny and Life History Shape Rhizosphere Bacterial Microbiome of Summer Annuals in an Agricultural Field – Bryan D. Emmett – Frontiers in Microbiology (from December 2017)

Soil microbial communities and enzyme activities in sea-buckthorn (Hippophae rhamnoides) plantation at different ages – Miao Yang – Plos One

The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics – Mohammad Bahram – Environmental Microbiology Reports

Ecological mechanisms underlying soil bacterial responses to rainfall along a steep natural precipitation gradient – Bonnie Waring – FEMS Microbiology Ecology

ReviewCurrent Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils – Ruth Gómez Expósito – Frontiers in Microbiology (from December 2017)

Water and extremophile microbiome
Microbially mediated aluminosilicate formation in acidic anaerobic environments: A cell-scale chemical perspective – J. Sánchez-España – GeoBiology

Responses of Periphyton to Fe2O3 Nanoparticles: A Physiological and Ecological Basis for Defending Nanotoxicity – Jun Tang – Environmental Science & Technology

Variations in bacterial and archaeal communities along depth profiles of Alaskan soil cores – Binu Mani Tripathi – Scientific Reports

Microbiological and Geochemical Survey of CO2-Dominated Mofette and Mineral Waters of the Cheb Basin, Czech Republic – Patryk Krauze – Frontiers In Microbiology

In Situ Field Sequencing and Life Detection in Remote (79°26’N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities – J Goordial – Frontiers In Microbiology (from December 2017)

Built environment
Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro) in Okinawa Island, Japan – Taha Soliman – Frontiers In Microbiology

Microbial Contamination on Touch Surfaces in Sick- and Well-Child Waiting Rooms in Pediatric Outpatient Facilities – Irina Gudakova – The Pediatric Infectious Disease Journal

Biostimulation and bioaugmentation of native microbial community accelerated bioremediation of oil refinery sludge – Ajoy Roy – Bioresource Technology

Temporal variation in bacterial and methanogenic communities of three full-scale anaerobic digesters treating swine wastewater – Gyuseong Han – Environmental Science And Pollution Research International

Microbial community of a gasworks aquifer and identification of nitrate-reducing Azoarcus and Georgfuchsia as key players in BTEX degradation – Martin Sperfeld – Water Research

Review: Microbiome analysis and -omics studies of microbial denitrification processes in wastewater treatment: recent advances – Lili Miao – Science China. Life Sciences

Food microbiology
Absorption and Metabolism of Phenolics from Digests of Polyphenol-Rich Potato Extracts Using the Caco-2/HepG2 Co-Culture System – Shima Sadeghi Ekbatan – Foods (Basel, Switzerland)

Effects of polysaccharides from purple sweet potatoes on immune response and gut microbiota composition in normal and cyclophosphamide treated mice – Chao Tang – Food & Function

A Combined LC-MS Metabolomics- and 16S rRNA Sequencing Platform to Assess Interactions between Herbal Medicinal Products and Human Gut Bacteria in Vitro: a Pilot Study on Willow Bark Extract – Eva-Maria Pferschy-Wenzig – Frontiers In Pharmacology

Review: Inflammatory Bowel Diseases and Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols: An Overview – Sandra Maria Barbalho – Journal Of Medicinal Food

Probiotics / prebiotics / antibiotics
The antimicrobial peptide SAAP-148 combats drug-resistant bacteria and biofilms – Anna de Breij – Science Translational Medicine

Low amounts of dietary fibre increase in vitro production of short-chain fatty acids without changing human colonic microbiota structure – Daisuke Sasaki – Scientific Reports

Single Cell Observations Show Persister Cells Wake Based on Ribosome Content – Jun-Seob Kim – bioRxiv

Evidence for PMAT- and OCT-like biogenic amine transporters in a probiotic strain of Lactobacillus: Implications for interkingdom communication within the microbiota-gut-brain axis. – Mark Lyte – Plos One

Phages and viruses
Metagenomic Virome Analysis of Culex Mosquitoes from Kenya and China. – Evans Atoni – Viruses

Virus Dynamics Are Influenced by Season, Tides and Advective Transport in Intertidal, Permeable Sediments – Verona Vandieken – Frontiers In Microbiology

Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis – Soner Yildiz – Microbiome

Genome Announcements
Draft Genome Sequence of Megamonas funiformis Strain Marseille-P3344, Isolated from a Human Fecal Microbiota. – Mossaab Maaloum – Genome Announcements

Draft Genome Sequences of Bifidobacterium Strains N4G05 and N5G01, Isolated from the Human Vaginal Microbiome. – Aline C Freitas – Genome Announcements

Lactomassilus timonensis,’ a new anaerobic bacterial species isolated from the milk of a healthy African mother – A H Togo – New Microbes And New Infections

Microbes in the news
AGA enrolls 1st patient into largest planned fecal microbiota transplantation study – Eric Oliver – GI & Endoscopy

Will This Swallowable Sensor Replace Colonoscopies? – Bob Curley – HealthLine

**A Patient’s Journey: Taming the Glucose Monster – Howard Wolinsky – MedPage Today**

Microbes on the market
CoreBiome Bolsters Its Board of Directors with the Addition of Daniel Pomp, Ph.D. – BusinessWire

Curetis and MGI Advance Strategic Partnership in NGS-Based Molecular Microbiology – BioSpace

Science, publishing, and career
“Available upon request”: not good enough for microbiome data! – Morgan G I Langille – Microbiome

Tiffany’s non-microbiology picks
Chemists go green to make better blue jeans – Nature
I did not know demin was so dirty until I heard about Everlane’ new jeans – and now there are new method to make them!

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