July 19, 2017

Today’s digest is a long one! There is high diversity of studies, with a high abundance of gut microbiome studies, a few publications on fecal transplant, and some very interesting early life/pregnancy/mother-infant science.  A normal serving of animal studies, of course a nice colony of environmental microbial studies, and a study reporting the presence of bacteria in Alzheimer’s post-mortem brains.

Events and jobs

Postdoctoral research fellow in translational microbiome research – Department of Microbiology, Tumor and Cell Biology (MTC) at Karolinska Institutet

General microbiome

Commensal bacteria modulate the tumor microenvironment – Theofilos Poutahidis – Cancer Letters

[Review]  The human microbiome – Hubert E. Blum – Advances in Medical Sciences

Microbiome and Metabolome Data Integration Provides Insight Into Health and Disease – Michael Shaffer – Translational Research

Metabolic potential and taxonomic assessment of bacterial community of an environment to chronic industrial discharge – Neelam Devpura – International Biodeterioration & Biodegradation

Impact of the Microbiota on Bacterial Infections during Cancer Treatment – Jessica Galloway-Peña – Trends in Microbiology

Pregnancy and early life

** The Bacterial Ecosystem of Mother’s Milk and Infant’s Mouth and Gut – Elana Biagi – Frontiers in Microbiology | Evolutionary and Genomic Microbiology

* What’s Normal? Immune Profiling of Human Milk from Healthy Women Living in Different Geographical and Socioeconomic Settings – Lorena Ruiz – Frontiers in Immunology | Nutritional Immunology

Microbiome Associated with Severe Caries in Canadian First Nations Children – M. Agnello – Journal of Dental Research

* Bacterial communities found in placental tissues are associated with severe chorioamnionitis and adverse birth outcomes – Ronan M. Doyle – PLoS One

Human oral microbiome

Characterization of Oral Microbiota in Removable Dental Prosthesis Users: Influence of Arterial Hypertension – Leila Maria Marchi-Alves – BioMed Research International

Human vaginal microbiome

The association between ethnicity and vaginal microbiota composition in Amsterdam, the Netherlands – Hanneke Borgdorff – PLoS One

Human nearly-sterile sites

** 16S rRNA Next Generation Sequencing Analysis Shows Bacteria in Alzheimer’s Post-Mortem Brain – David C. Emery – Frontiers in Aging Neuroscience

Human gut microbiome

The Gut Microbiota of Healthy Chilean Subjects Reveals a High Abundance of the Phylum Verrucomicrobia – Sayaka Fujio-Vejar – Frontiers in Microbiology | Microbial Symbioses

*[Review] Significance of Microbiota in Obesity and Metabolic Diseases and the Modulatory Potential by Medicinal Plant and Food Ingredients – Hoda M. Eid – Frontiers in Pharmacology | Ethnopharmacology

MOLECULAR CHARACTERIZATION OF FECAL MICROBIOTA OF HEALTHY CHINESE TOBACCO SMOKER SUBJECTS IN SHAANXI PROVINCE, XI’AN CHINA – Ishaq HM – Journal of Ayub Medical College

The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study – Hemmings, Sian M.J – Psychosomatic Medicine

The Impact of Gut Microbiota on Gender-Specific Differences in Immunity – Floris Fransen – Frontiers in Immunology | Nutritional Immunology

Involvement of gut microbiota in the association between gastrointestinal motility and 5‑HT expression/M2 macrophage abundance in the gastrointestinal tract – Mo Yang – Molecular Medicine Reports

Correspondence: Fecal Microbiota Transplant from a Rational Stool Donor Improves Hepatic Encephalopathy: A Randomized Clinical Trial – Benjamin H Mullish – Hepatology

Going to the Bank: Fecal Microbiota Transplantation in Pediatrics – Elaine Barfield – Clinical Pediatrics

INTERRELATIONSHIPS BETWEEN GUT MICROBIOTA AND HOST: Paradigms, Role in Neurodegenerative Diseases and Future Prospects – Villarraso JC – CNS & Neurological Disorders Drug Targets

Faecal microbiota transplant: a novel biological approach to extensively drug-resistant organism-related non-relapse mortality – Innes AJ – Bone Marrow Transplantation

* Gut microbiota is critical for the induction of chemotherapy-induced pain – Shiqian Shen – Nature Neuroscience

Relationships between Gastrointestinal Microbiota and Blood Group Antigens – Anuhya Gampa – Physiological Genomics

[Masters Thesis] Evaluating the Effectiveness of Select Bacteria Against Clostridium difficile – Choquette, Kelsey Rose – Iowa State University, ProQuest Dissertations Publishing

* Potential and active functions in the gut microbiota of a healthy human cohort – Alessandro Tanca – Microbiome

[Letter to Editor] The necessity of gut microbiome characterization in diseases prevention and therapy – Sama Rezasoltani – Gastroenterology and Hepatology from Bed to Bench

[Review Article] The Intricate Interaction between Enteric Microbiota and Brain: Principles and Clinical Implications – Giovanni Gherardi – Journal of Digestive Diseases and Hepatology

Gut microbiota dysbiosis associated with glucose metabolism disorders and the metabolic syndrome in older adults – K Lippert – Beneficial Microbes

Animal experiments

Western Diet–Induced Dysbiosis in Farnesoid X Receptor Knockout Mice Causes Persistent Hepatic Inflammation after Antibiotic Treatment – Prasant K – The American Journal of Pathology

Grape pomace improves performance, antioxidant status, fecal microbiota and meat quality of piglets – I. Kafantaris – Animal

Animal microbiome

Microorganisms of the Intestinal Microbiota of Oncorhynchus Mykiss Produce Antagonistic Substances Against Bacteria Contaminating Food and Causing Disease in Humans – Lobos O – Italian Journal of Food Safety

Population-Specific Responses to Interspecific Competition in the Gut Microbiota of Two Atlantic Salmon (Salmo salar) Populations – Xiaoping He – Microbial Ecology

Habitat and indigenous gut microbes contribute to the plasticity of gut microbiome in oriental river prawn during rapid environmental change – Cheng-Yu Chen – PLoS One

Vertically and horizontally transmitted microbial symbionts shape the gut microbiota ontogenesis of a skin-mucus feeding discus fish progeny – François-Étienne Sylvain – Scientific Reports

Microbiome overview in swine lungs – Franciele Maboni Siqueira – PLoS One

Plant, root, and soil microbiome

Integrated metagenomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops – Zhaojin Chen – Ecotoxicology and Environmental Safety

Dynamics of Soil Bacterial Communities Over a Vegetation Season Relate to Both Soil Nutrient Status and Plant Growth Phenology – Davide Francioli – Microbial Ecology

Microbial Populations of Stony Meteorites: Substrate Controls on First Colonizers – Alastair W. Tait – Frontiers in Microbiology | Extreme Microbiology

Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil – Mengting M. Yuan – Global Change Biology

[PrePrint] Conditionally rare taxa contribute but do not account for prokaryotic community changes in soils – Rachel Kaminsky – bioRxiv

Water and extremophile microbiome 

Performance and bacterial community structure of a 10-years old constructed mangrove wetland – Tingting Tian – Marine Pollution Bulletin

A comparative study revealed first insights into the diversity and metabolisms of the microbial communities in the sediments of Pacmanus and Desmos hydrothermal fields – Hai-liang Wang – PLoS One

Microbial Composition and Diversity Patterns in Deep Hyperthermal Aquifers from the Western Plain of Romania – Cecilia M. Chiriac – Microbiology of Aquatic Systems

Built environment

Pilot study to determine if microbial contamination levels in hospital washrooms are associated with hand drying method – Mark H. Wilcox – Journal of Hospital Infection

Probiotics / prebiotics

Arachidonic acid sex-dependently affects obesity through linking gut microbiota-driven inflammation to hypothalamus-adipose-liver axis – Pan Zhuang – BBA

Functional Characterization of Novel Faecalibacterium prausnitzii Strains Isolated from Healthy Volunteers: A Step Forward in the Use of F. prausnitzii as a Next-Generation Probiotic – Rebeca Martin – Frontiers in Microbiology | Food Microbiology

Bioinformatics

* Abundance estimation and differential testing on strain level in metagenomics data – Martina Fischer – Bioinformatics

Techniques

Development and Use of a Real-Time Quantitative PCR Method for Detecting and Quantifying Equol-Producing Bacteria in Human Faecal Samples and Slurry Cultures – Lucía Vázquez – Frontiers in Microbiology | Food Microbiology

Next-generation Sequencing of the DNA Virome from Fecal Samples – Monaco CL – Bio-protocol

Synthetic multispecies microbial communities reveals shifts in secondary metabolism and facilitates cryptic natural product discovery – Yutong Shi – Environmental Microbiology

Whole-genome sequencing of eukaryotes: From sequencing of DNA fragments to a genome assembly – K. S. Zadesenets – Russian Journal of Genetics

Microbes on the market

Microbiome Sequencing Services Market: trends, analysis, Overview, forecast up to 2021

Ed’s non-microbiology picks

Heavy metal accumulation by Saccharomyces cerevisiae cells armed with metal binding hexapeptides targeted to the inner face of the plasma membrane – Lavinia Liliana Ruta –Applied Microbiology and Biotechnology

Fracking can contaminate rivers and lakes with radioactive material, study finds

Subacute normobaric oxygen and hyperbaric oxygen therapy in drowning, reversal of brain volume loss: a case report – Paul G Harch – Medical Gas Research

No Effect of Commercial Cognitive Training on Neural Activity During Decision-Making – Joseph W. Kable – Journal of Neuroscience

Health Insurance Expansion and Incidence of Out‐of‐Hospital Cardiac Arrest: A Pilot Study in a US Metropolitan Community – Eric C. Stecker – Journal of the American Heart Association

July 14, 2017

Events and jobs

Postdoc, Lieberman Lab

General microbiome

Assembly of Microbial Communities in Replicate Nutrient-Cycling Model Ecosystems Follows Divergent Trajectories, Leading to Alternate Stable States – Eulyn Pagaling – Environmental Microbiology

Human respiratory microbiome

Influence of lung CT changes in chronic obstructive pulmonary disease (COPD) on the human lung microbiome – Marion Engel – PLOS ONE

Human gut microbiome

Gut bacterial peptides with autoimmunity potential as environmental trigger for late onset complex diseases: In–silico study – Sapna Negi – PLOS ONE

Impact of environmental microbiota on human microbiota of workers in academic mouse research facilities: An observational study – Peggy S. Lai – PLOS ONE

Reduced Mass and Diversity of the Colonic Microbiome in Patients with Multiple Sclerosis and Their Improvement with Ketogenic Diet – Alexander Swidsinski – Frontiers in Microbiology

Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls – Christopher J. Stewart – Microbiome

Other Human microbiome

The oral bacterial microbiome of occlusal surfaces in children and its association with diet and caries – Apoena Aguiar Ribeiro – PLOS ONE

The oral fungal mycobiome: characteristics and relation to periodontitis in a pilot study – Brandilyn A. Peters – BMC Microbiology

Animal experiments

Three distinct pneumotypes characterize the microbiome of the lung in BALB/cJ mice – Julia Scheiermann – PLOS ONE

Assessment of gut microbiota populations in lean and obese Zucker rats – Reza Hakkak – PLOS ONE

Preparing the Gut with Antibiotics Enhances Gut Microbiota Reprogramming Efficiency by Promoting Xenomicrobiota Colonization – Shou K. Ji – Frontiers in Microbiology

Animal microbiome

On the core bacterial flora of Ixodes persulcatus (Taiga tick) – Shuo Sui – PLOS ONE

Skin microbiota in frogs from the Brazilian Atlantic Forest: Species, forest type, and potential against pathogens – Ananda Brito de Assis – PLOS ONE

Brackish habitat dictates cultivable Actinobacterial diversity from marine sponges – Gregory A. Ellis – PLOS ONE

Effects of Kluyveromyces marxianus supplementation on immune responses, intestinal structure and microbiota in broiler chickens – Weiwei Wang – PLOS ONE

Dominance-function relationships in the amphibian skin microbiome – Jenifer B. Walke – Environmental Microbiology

Microbial community sequencing analysis of the calf eye microbiota and relationship to infectious bovine keratoconjunctivitis – J.N.Cullen – Veterinary Microbiology

Bacterial community composition in Adélie (Pygoscelis adeliae) and Chinstrap (Pygoscelis antarctica) Penguin stomach contents from Signy Island, South Orkney Islands – W. C. Yew – Polar Biology

Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows – Ilma Tapio – PLOS ONE

Honeybee (Apis mellifera)-associated bacterial community affected by American foulbrood: detection of Paenibacillus larvae via microbiome analysis – Tomas Erban – Scientific Reports

Plant, root, and soil microbiome

Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium – Arthur Prudêncio de Araujo Pereira – PLOS ONE

Maize Phyllosphere Microbial Community Niche Development Across Stages of Host Leaf Growth – Heather C. Manching – bioRxiv

Major phylum-level differences between porefluid and host rock bacterial communities in the terrestrial deep subsurface – Lily Momper – Environmental Microbiology Reports

Patterns of soil bacterial richness and composition tied to plant richness, soil nitrogen, and soil acidity in alpine tundra – Xia Yuan – Arctic, Antarctic, and Alpine Research

Water and extremophile microbiome

Unravelling riverine microbial communities under wastewater treatment plant effluent discharge in large urban areas – Yang Huo – Applied Microbiology and Biotechnology

Phages and viruses

Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans – Felipe H. Coutinho – Nature Communications

Science, publishing, and career

Jonathan Eisen named Faculty Director of the UC Davis Microbiome Initiative

July 2, 2017

Events and jobs

Post-doc in High-Throughput Metagenomics – University of Cambridge

Microbes in the news

Before you head out to the beach this weekend, check bacteria levels – ABC News

Oil-Munching Bacteria Helped Clean Up the Deepwater Horizon Oil Spill –  Cynthia Wallentine, Invisiverse

Bacteria Hysteria

Here’s What the Gross Bacteria on Your Expired Makeup Really Looks Like – Erin Reimel, Glamour Magazine

June 25, 2017

Lots of interesting pre-prints in this post that might be worth following! Also a blog post on some cool science art with kombucha, as well as a lot of articles on rhizosphere-microbe interactions.

Events and jobs

Research Opportunities in Molecular Microbiology – Washington University in St. Louis

PhD scholarship in Metagenomics analysis and systems biology – Danmarks Tekniske Universitet

General microbiome

Microbiome yarns: microbial forensics for auditing provenance in global food chains – Timmis et al. – Microbial Biotechnology

Adjuncts and alternatives in the time of antibiotic resistance and in-feed antibiotic bans – Brüssow – Microbial Biotechnology

Human gut microbiome

Bacteria facilitate viral co-infection of mammalian cells and promote genetic recombination – Erickson et al. – bioRXiv

Chemical transformation of xenobiotics by the human gut microbiota – Koppel et al. – Science

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer – Purcell et al. – bioRXiv

Animal microbiome

Whole genome sequencing-based detection of antimicrobial resistance and virulence in non-typhoidal Salmonella enterica isolated from wildlife – Thomas et al. – bioRXiv

 

Plant, root, and soil microbiome

Antagonism between two root-associated beneficial Pseudomonas strains does not affect plant growth promotion and induced resistance against a leaf-chewing herbivore – Pangesti et al. – FEMS Microbiology Ecology

Bioelectrochemical approach for control of methane emission from wetlands – Liu et al. – Bioresource Technology

The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks – Duke et al. – BMC Genomics

Delftia rhizosphaerae sp. nov. isolated from the rhizosphere of Cistus ladanifer – Carro et al. – International Journal of Systematic and Evolutionary Microbiology

Synthesis and Secretion of Isoflavones by Field-Grown Soybean – Sugiyama et al. – Plant Cell Physiology

The Variation in the Rhizosphere Microbiome of Cotton with Soil Type, Genotype and Developmental Stage – Qiao et al. – Scientific Reports

Complete Genome Sequence of Bacillus paralicheniformis MDJK30, a Plant Growth -Promoting Rhizobacterium with Antifungal Activity – Wang et al. – Genome Anouncements

Extensive Overlap of Tropical Rainforest Bacterial Endophytes between Soil, Plant Parts, and Plant Species – Haruna et al. – Microbial Ecology

Phytoavailability of Cr in Silene vulgaris: The role of soil, plant genotype and bacterial rhizobiome – García-Gonzalez et al. – Ecotoxicology and Environmental Safety

Water and extremophile microbiome

Sulfolobus islandicus meta-populations in Yellowstone National Park hot springs – Campbell et al. – Environmental Microbiology

Bottled aqua incognita: Microbiota assembly and dissolved organic matter diversity in natural mineral waters – Lesaulnier et al. – bioRXiv

Techniques

Rapid whole genome amplification and sequencing of low cell numbers in a bacteraemia model – Anscombe et al. – bioRXiv

Microbes in the news

Do Probiotics Really Work? – Ferris Jabr – Scientific American

Fungi and bacteria team up in dental plaque – Evans – LabRoots

Scientists spy on the secret inner life of bacteria – Saey – Science News

Biofilms: The eradication has begun – McGill University Health Centre – Science Daily

Bacteria and Mental Health: Gut Bacteria Linked to Bipolar Disorder – Villamil – Medical News Bulletin

The Kombucha Craze Steps into Art and the Science of the Microbiome – Fernández – Labiotech

Microbes on the market

Global Microbiome Drugs Industry Market Research Report 2017 – Medgadget

June 21, 201

Today’s Microbiome Digest has quite a few articles from water environment. Both articles I would like to highlight are with cyanobacteria as stars. The first one from Anne D. Jungblut reports on Antarctic cynobacteria diversity, while the second one reveals the new freshwater cyanobacterial genome. One more thing to highlight come from news. Exxon Mobil Corps and Sintetic Genomics Inc have announced a new breakthrough with genetically modified algae which was able to convert 40% of CO2 to lipids, up from the previous 15%. Algae are still far away from being able to run the process at commercial scale and replace fossil fuels, but we love algae! Enjoy this summer reading.

Events and jobs

Microbiome Research Scientist (BS or MS or PhD) – St. John of God Foundation for Research and Teaching, Barcelona, Spain

Quality Associate Specialist – Merck, Durham, NC, US

Microbiology Manager OR Microbiology Laboratory Manager Opening, Madison, WI, US
General microbiome

A null model for microbial diversification – Timothy J. Straub – PNAS

Pregnancy and early life

Association between breast milk bacterial communities and establishment and development of the infant gut microbiome – JAMA Pediatrics
Human skin microbiome

Topical antimicrobial treatments can elicit shifts to resident skin bacterial communities and reduce colonization by competitors – Adam J. SanMiguel – Antimicrobial Agents and Chemotherapy
Human gut microbiome

Liver transplant modulates gut microbial dysbiosis and cognitive function in cirrhosis – Jasmohan S. Bajaj – Liver Transplatation

How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans – Alan Cartmell – PNAS

Microbiome restoration diet improves digestion, cognition and physical and emotional wellbeing – Kate Lawrence – PLOS
Animal microbiome 

The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish – Keaton Stagaman – The ISME Journal
Plant, root, and soil microbiome

Biofilm formation enables free-living nitrogen-fixing rhizobacteria to fix nitrogen under aerobic conditions – Di Wang – The ISME Journal

Novel antibiotic resistance determinants from agricultural soil exposed to antibiotics widely used in human medicine and animal farming – Calvin Ho-Fung Lau – Applied and Environmental Microbiology
Water and extremophile microbiome 

Animal-like prostaglandins in marine microalgae – Valeria Di Dato – The ISME Journal

Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents – Dimitri V Meier – The ISME Journal

Identification of dimethylamine monooxygenase in marine bacteria reveals a metabolic bottleneck in the methylated amine degradation pathway – Ian Lidbury – The ISME Journal

DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments – Anders Lanzén – PLOS

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters – David M Needham – The ISME Journal

Integrated metabolism in sponge–microbe symbiosis revealed by genome-centered metatranscriptomics – Lucas Moitinho-Silva – The ISME Journal

Spontaneous mutations of a model heterotrophic marine bacterium – Ying Sun – The ISME Journal

Plastid thylakoid architecture optimizes photosynthesis in diatoms – Serena Flori –  Nature Communications

Evolutionary radiation of lanthipeptides in marine cyanobacteria – Andres Cubillos-Ruiz –  PNAS

Using Captain Scott’s Discovery specimens to unlock the past: has Antarctic cyanobacterial diversity changed over the last 100 years? Anne D. Jungblut – Proceedings of the Royal Society B

Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs – Pedro J. Cabello-Yeves – Frontiers in Microbiology

Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment – Yu Wang – Frontiers in Microbiology

Atribacteria from the Subseafloor Sedimentary Biosphere Disperse to the Hydrosphere through Submarine Mud Volcanoes – Tatsuhiko Hoshino – Frontiers in Microbiology
Phages and viruses

Effect of acute predation with bacteriophage on intermicrobial aggression by Pseudomonas aeruginosa – Patrick R. Secor
Bioinformatics

The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data – Gerben Menschaert –

Microbes in the news 

Zombie bacteria and viruses in melting permafrost are waking up  

ExxonMobil and Synthetic Genomics Report Breakthrough in Algae Biofuel Research

Gut microbiome changes linked to numerous biomarkers of type 2 diabetes 

Funky tasting beer? Biofilms may be to blame, MSU researchers say

Bacteria in Your Coughs And Sneezes Can Stay Alive in The Air For Up to 45 Minutes

Microbes on the market

This Company Uses the Human Microbiome to Discover New Disease Mechanisms

June 17, 2017

Today: A few job searches, a lot of microbes in the news (as we all ponder our bread choices), and some articles about microbes in the wild.

Events and jobs

Assistant Professor-Microbiology (Tenure-Track) – The College of New Jersey

Microbiology Technician – Matchtech, England

Microbiology Analyst – Stericycle, Massachusetts

Animal microbiome

Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux’s sifakas (Propithecus verreauxi) – Springer et al, Ecology and Evolution

Water and extremophile microbiome

Undocumented Potential For Primary Productivity In A Globally-Distributed Bacterial Photoautotroph – Graham et al, bioRxiv (pre-print)

Microbes in the news

White or Whole Wheat Bread Study May Shed Light on Diet Failure – Patrick Keeffe, HealthLine

Gene transfer keeps bacteria fit – University of Basel, Phys.org

In dying, blood-starved heart, bacteria injections offer cellular life support – Beth Mole, Ars Technica

New antibiotic effective against drug-resistant bacteria – Rutgers University, Science Daily

June 16, 2017

Gut microbiome focus: Differences in the gut microbiome between children and adults can mediate the metabolism of arsenic possibly leading to differences in exposure risk, the gut microbiome’s ability to protect against salmonella infection is dependent on the IFNy producing bacteria, the microbiome of insoluble fibre is characterized, and a new in vitro technique to interrogate intestinal transport of microbiota and antigens. Plus an overview of the world data centre for microorganisms, and MicroScope for microbial genome annotation. 

  • Events and jobs

Microbiology Technologist OR Microbiology Medical Technologist – Orlando Florida  

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  • General microbiome

Conference: Current concepts in chronic inflammatory diseases: Interactions between microbes, cellular metabolism, and inflammation – Holger Garn – Allergy and Clinical Immunology

  • Human oral microbiome

Characterisation of Roseomonas mucosa isolated from the root canal of an infected tooth – Nina Diesendorf – BMC Research Notes

  • Human gut microbiome

* Interindividual variability of soil arsenic metabolism by human gut microbiota using SHIME model – Naiyi Yin – Chemosphere

* Inter-individual differences determine the outcome of wheat bran colonization by the human gut microbiome – Kim De Paepe – Environmental Microbiology

Review: Microbiota Therapy for Clostridium difficile and Antibiotic Resistant Enteric Infections – Brittany Lewis – Annual Review of Microbiology

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  • Animal experiments

* Enhancement of IFNγ Production by Distinct Commensals Ameliorates Salmonella-Induced Disease – Sophie Thiemann – Cell Host and Microbe

Efficacy of antibiotic treatment of implant-associated Staphylococcus aureus infections with moxifloxacin, flucloxacillin, rifampin, and combination therapy: an animal study – Felix Greimel – Drug Design, Development and Therapy

The scales of the zebrafish: host–microbiota interactions from proteins to populations – Adam Burns – Current Opinion in Microbiology

IL-17 Receptor A Maintains and Protects the Skin Barrier To Prevent Allergic Skin Inflammation – Achilleas Floudas – The Journal of Immunology

Irf4-dependent CD103+CD11b+ dendritic cells and the intestinal microbiome regulate monocyte and macrophage activation and intestinal peristalsis in postoperative ileus – Judith-Mira Pohl – Gut

  • Animal microbiome

Effect of three lactobacilli with strain-specific activities on the growth performance, faecal microbiota and ileum mucosa proteomics of piglets – Yating Su – Journal of Animal Science and Biotechnology

  • Plant, root, and soil microbiome

Characterization of the regulation of a plant polysaccharide utilization operon and its role in biofilm formation in Bacillus subtilis – Cameron Habib – PLOSone

Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function – Sebastian Flues – Environmental Microbiology

Green alder (Alnus viridis) encroachment shapes microbial communities in subalpine soils and impacts its bacterial or fungal symbionts differently – G Schwob – Environmental Microbiology

The role of organic acids on microbial deterioration in the Radix pseudostellariae rhizosphere under continuous monoculture regimes – Hongmiao Wu – Scientific Reports

Specificity traits consistent with legume-rhizobia coevolution displayed by Ensifer meliloti rhizosphere colonization – María Eugenia Salas – Environmental Microbiology

  • Water and extremophile microbiome

Cascading influence of inorganic nitrogen sources on DOM production, composition, lability and microbial community structure in the open ocean – SJ Goldberg – Environmental Microbiology

Functional diversity and redundancy across fish gut, sediment, and water bacterial communities – Arthur Escalas – Environmental Microbiology

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  • Phages and viruses

Preprint: Bacteria defend against phages through type IV pilus glycosylation – Hanjeong Harvey- bioRxiv

  • Techniques

Dissecting the human microbiome with single-cell genomics – Andrew Tolonen – Genome Medicine

* A human intestinal M-cell-like model for investigating particle, antigen and microorganism translocation – Ana Beloqui – Nature Protocols

  • Metagenomics

* World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide – Linhuan Wu – Nucleic Acids Research

* MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes – David Vallenet – Nucleic Acids Research

Bacteriocin Gene-Trait matching across the complete Lactobacillus Pan-genome – Fergus Collins – Scientific Reports

Screening and characterization of a novel thermostable lipase with detergent-additive potential from the metagenomic library of a mangrove soil – Leli Tang – Gene

  • Microbial Physiology

Preprint: Phenotypic consequences of RNA polymerase dysregulation in Escherichia coli – Paramita Sarkar – bioRxiv

Preprint: Campylobacter jejuni transcriptome changes during loss of culturability in water – Christina Bronowski – bioRxiv

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  • Microbes in the news

You Are What You Eat, And What You Eat Is Millions of MicrobesKyle Frischkorn – Smithsonian.com

John Bartlett’s Take on Critical Infectious Disease Topics: Part 3 – John Bartlett – Medscape

Placental Microbiome – Sally Robertson – Life Sciences News

Light-activated bacteria protect rats from heart attacks – Michael Price – Science

These light-eating bacteria could one day help us survive heart attacks – Alessandra Potenza – The Verge

Scientists image molecular machinery never before seen in bacteria – Brooke Hays – UPI