May 24, 2017

Human Microbiome

Non-pylori Helicobacters (NHPHs) induce shifts in gastric microbiota in Helicobacter pylori-infected patients – Peng et al. – Frontiers in Microbiology

Association between body mass index and Firmicutes/Bacteroidetes ratio in an adult Ukrainian population – Koliada et al. – BMC Microbiology

The effect of heritability and host genetics on the gut microbiota and metabolic syndrome – Young Lim et al. – Gut (BMJ)

Fungal microbiota dysbiosis in IBD – Sokol et al. – Gut (BMJ)

A tale of two risks: smoking, diabetes and the subgingival microbiome – Ganesan et al. – The ISME Journal

Animal Microbiome

The Structural and Functional Capacity of Ruminal and Cecal Microbiota in Growing Cattle Was Unaffected by Dietary Supplementation of Linseed Oil and Nitrate  – Popova et al. – Frontiers in Microbiology

Probiotics – Prebiotics

Gut Bacteria Missing in Severe Acute Malnutrition, Can We Identify Potential Probiotics by Culturomics? – Tidjani Alou et al – Frontiers in Microbiology

Detection and Physicochemical Characterization of Membrane Vesicles (MVs) of Lactobacillus reuteri DSM 17938 –  Grande et al. – Frontiers in Microbiology

Review: Resistant Starch Regulates Gut Microbiota: Structure, Biochemistry and Cell Signalling – Yang et al. – Cellular Physiology and Biochemistry

Food Microbiology

A Functional Metagenomic Analysis of Tetracycline Resistance in Cheese Bacteria – Flórez et al. – Frontiers in Microbiology

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria – Bonham et al. – BioRxiv

Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access – Taboada et al. – Frontiers in Microbiology

In vitro assessment of Pediococcus acidilactici Kp10 for its potential use in the food industry – Abbasiliasi et al. – BMC Microbiology

Pathogen Research

In-depth Profiling of MvfR-Regulated Small Molecules in Pseudomonas aeruginosa after Quorum Sensing Inhibitor Treatment – Allegretta et al. – Frontiers in Microbiology

Metabolic anticipation in Mycobacterium tuberculosis – Eoh et al. – Nature Microbiology

Predicting Drug Resistance Evolution: Antimicrobial Peptides Vs. Antibiotics – Yi et al. – BioRxiv

Environmental Microbiology

Undocumented Potential For Primary Productivity In A Globally-Distributed Bacterial Photoautotroph – Graham et al. – BioRxiv

Epibionts dominate metabolic functional potential of Trichodesmium colonies from the oligotrophic ocean – Frischkorn et al. – The ISME Journal

Bioinformatics

BSocial: Deciphering Social Behaviors within Mixed Microbial Populations – Purswani et al. – Frontiers in Microbiology

A Phylogenetic Method To Perform Genome-Wide Association Studies In Microbes That Accounts For Population Structure And Recombination – Collins and Didelot – BioRxiv

Association Mapping From Sequencing Reads Using K-mers – Rahman et al. – BioRxiv

MATAM: Reconstruction Of Phylogenetic Marker Genes From Short Sequencing Reads In Metagenomes – Pericard et al. – BioRxiv

Other

Perspective: Our path to better science in less time using open data science tools – Stewart Lowndes et al. – Nature Ecology & Evolution

Teaching genetics prior to teaching evolution improves evolution understanding but not acceptance –  Mead et al. – PLoS Biology

Review: Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure – Siliakus et al. – Extremophiles

May 19, 2017

Microbiome research

Exploring a possible link between the intestinal microbiota and feed efficiency in pigs

Ursula M. McCormack et al., Applied and Environmental Microbiology

Modulation of the Gut Microbiota by Krill Oil in Mice Fed a High-Sugar High-Fat Diet

Chenyang Lu et al., Frontiers in Microbiology

Opinion: Gut microbiome as a clinical tool in gastrointestinal disease management: are we there yet?

Eamonn M. M. Quigley, Nature Reviews Gastroenterology & Hepatology (Online since March 30, 2017; however this has not been pointed out here before)

 

Pathogen microbiology

Mini review: The Role of Ribonucleases and sRNAs in the Virulence of Foodborne Pathogens

Rute G. Matos et al., Frontiers in Microbiology

Pathogenic Characteristics of Staphylococcus aureus Endovascular Infection Isolates from Different Clonal Complexes

Dafne Pérez-Montarelo et al., Frontiers in Microbiology

Pseudomonas aeruginosa Exolysin promotes bacterial growth in lungs, alveolar damage and bacterial dissemination

Stéphanie Bouillot et al., Scientific Reports (Nature)

Intrinsic Toxin-Derived Peptides Destabilize and Inactivate Clostridium difficile TcdB

Jason L. Larabee et al., mBio

 

Probiotics – Prebiotics

Vaginal Lactobacillus Inhibits HIV-1 Replication in Human Tissues Ex Vivo

Rogers A. Ñahui Palomino et al., Frontiers in Microbiology

Assessing the Risk of Probiotic Dietary Supplements in the Context of Antibiotic Resistance

Min Zheng et al., Frontiers in Microbiology

Review: Lactic Acid Bacteria and Bifidobacteria with Potential to Design Natural Biofunctional Health-Promoting Dairy Foods

Daniel M. Linares et al., Frontiers in Microbiology

In silico Prediction, in vitro Antibacterial Spectrum, and Physicochemical Properties of a Putative Bacteriocin Produced by Lactobacillus rhamnosus Strain L156.4

Letícia de C. Oliveira et al., Frontiers in Microbiology

Health benefit of vegetable/fruit juice-based diet: Role of microbiome

Susanne M. Henning et al., Scientific Reports (Nature)

Characterization of bile salt hydrolase from Lactobacillus gasseri FR4 and demonstration of its substrate specificity and inhibitory mechanism using molecular docking analysis

Rizwana Parveen Rani et al., Frontiers in Microbiology

Lactobacillus johnsonii ameliorates intestinal, extra-intestinal and systemic pro-inflammatory immune responses following murine Campylobacter jejuni infection

Stefan Bereswill et al., Scientific Reports (Nature)

News and Views: Paediatrics: Are human milk oligosaccharides the magic bullet for necrotizing enterocolitis?

Michael S. Caplan, Nature Reviews Gastroenterology & Hepatology

Assessing the Challenges in the Application of Potential Probiotic Lactic Acid Bacteria in the Large-Scale Fermentation of Spanish-Style Table Olives

Francisco Rodríguez-Gómez et al., Frontiers in Microbiology

 

Antimicrobials

A broad-spectrum bactericidal lipopeptide with anti-biofilm properties

Ohad Meir et al., Scientific Reports (Nature)

The anticancer peptide TAT-RasGAP317-326 exerts broad antimicrobial activity

Mathieu Heulot et al., Frontiers in Microbiology

 

Genomics

Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655

Sang Woo Seo et al., Scientific Reports (Nature)

High-Definition Electronic Genome Maps From Single Molecule Data

John S. Oliver et al., BioRxiv

Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations

Ben Pascoe et al., PeerJ (not peer reviewed)

Feature: Mining microbes: Creating genomic tools to fight disease

Amber Dance, Science

 

Microbiology – Other

Variation in soil microbial community structure associated with different legume species is greater than that associated with different grass species

Yang Zhou et al.,  Frontiers in Microbiology

Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development

Stephanie Turner et al., Frontiers in Microbiology

Autotrophic and heterotrophic acquisition of carbon and nitrogen by a mixotrophic chrysophyte established through stable isotope analysis

Ramon Terrado et al., The ISME Journal

Hypothesis & Theory: The hyperarid core of the Atacama Desert, an extremely dry and carbon deprived habitat of potential interest for the field of carbon science

Armando Azua-Bustos et al., Frontiers in Microbiology

 

non-Microbiology picks

Divergent prebiotic synthesis of pyrimidine and 8-oxo-purine ribonucleotides

Shaun Stairs et al., Nature Communications

Virus origin could relate to the act of prey among primitive life forms

Eslam Abbas, PeerJ (not peer reviewed)

Beyond the protein-only hypothesis: A novel mineral-lipid hypothesis in prion and protein-misfolding disease

Kavitha Reddy, PeerJ (not peer reviewed)

Feature: Introducing ORCID

John Bohannon and Kirk Doran, Science

 

May 17, 2017

Today’s digest includes a few studies of the interactions between microbes (and synergy in metabolism and other processes), a filling of human gut microbiology, and interesting insights into probiotics both in animals and humans.  Also, check out my post later in the day reviewing microbiome related talks at BioData World West 2017 (late April)

Events and jobs

Scientist – Microbiomics – ZymoResearch

PhD in microbiology – Université Catholique de Louvain (UCL)

Microbiology Laboratory Technologist – Yukon Hospital Corporation – Whitehorse, YT

General microbiome

Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communities – Margaret F Romine – The ISME Journal

Identification of the potentiating mutations and synergistic epistasis that enabled the evolution of inter-species cooperation – Sarah M. Douglas – PLOS ONE

Pregnancy and early life

PrePrint – Gut dysbiosis following C-section instigates higher colonisation of toxigenic Clostridium perfringens in infants – Nagpal R – Benef Microbes

The influence of dietary immunomodulatory factors on development of food allergy in children – Sardecka I – Postepy Dermatol Alergol.

 

Human oral microbiome

The microbiome of site-specific dental plaque of children with different caries status – Richards VP – Infection and Immunity

Human gut microbiome

Healthy gut microbiota can resolve undernutrition – Emmanuel Hermann – HBSN

The Gut Microbiota and Autism Spectrum Disorders – Qinrui Li – Frontiers in Cellular Neuroscience

The ecological community of commensal, symbiotic, and pathogenic gastrointestinal microorganisms – an appraisal – Haque SZ – Dovepress

Comparative Effectiveness of Faecal Microbiota Transplant by Route of Administration – Nathan D. Gundacker – The Journal of Hospital Infection

Fecal microbiota transplantation in recurrent Clostridium difficile infection in a patient with concomitant inflammatory bowel disease – Gravito-Soares M – Rev Esp Enferm Dig

Alterations in intestinal microbiota relate to intestinal failure-associated liver disease and central line infections – Panliang Wang – Journal of Pediatric Surgery

* The Gastric Microbiome and Its Influence on Gastric Carcinogenesis: Current Knowledge and Ongoing Research – Chao Zhang – Hematology/Oncology Clinics of North America

Insights into the role of the intestinal microbiota in colon cancer – Oke S – Therapeutic Advances in Gastroenterology

Gut microbiota changes as a risk factor for obesity – Kvit KB – Wiad Lek.

Animal experiments 

Drosophila melanogaster as a High-Throughput Model for Host–Microbiota Interactions – Mark Trinder – Frontiers in Microbiology

Dietary Chitosan Supplementation Increases Microbial Diversity and Attenuates the Severity of Citrobacter rodentium Infection in Mice – Guiping Guan – Mediators of Inflammation

Changes in the intestinal bacterial community, short-chain fatty acid profile, and intestinal development of preweaned Holstein calves. 2. Effects of gastrointestinal site and age – J.J. Castro – Journal of Dairy Science

The microbiome regulates amygdala-dependent fear recall – Hoban AE – Molecular Psychiatry

Animal microbiome

The malleable gut microbiome of juvenile rainbow trout (Oncorhynchus mykiss): Diet-dependent shifts of bacterial community structures – Stéphanie Céline Michl – PLOS ONE

The influence of a probiotic supplementation on memory in quail suggests a role of gut microbiota on cognitive abilities in birds – Severine Parois – Behavioural Brain Research

Gut microbial communities of American pikas (Ochotona princeps): evidence for phylosymbiosis and adaptations to novel diets – Kevin D. Kohl – Journal of Animal Ecology

This Gut Ain’t Big Enough for Both of Us. Or Is It? Helminth-Microbiota Interactions in Veterinary Species – Peachey LE – Trends in Parasitology

Convergence of gut microbiotas in the adaptive radiations of African cichlid fishes – Baldo L – ISME

Plant, root, and soil microbiome

Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire – Sang-Hoon Lee – The ISME Journal

Prokaryotic Communities at Different Depths between Soils with and without Tomato Bacterial Wilt but Pathogen-Present in a Single Greenhouse – Chol Gyu Lee – Microbes and Environments

Water and extremophile microbiome

Annual community patterns are driven by seasonal switching between closely related marine bacteria – Christopher S Ward – The ISME Journal

A bacterial community-based index to assess the ecological status of estuarine and coastal environments – Eva Aylagas – Marine Pollution Bulletin

The impact of wastewater treatment effluent on microbial biomasses and diversities in coastal sediment microcosms of Hangzhou Bay – Yile Tao – Marine Pollution Bulletin

The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats – Johanne Aubé – Marine Pollution Bulletin

Changes in microbial community during hydrogen and methane production in two-stage thermophilic anaerobic co-digestion process from biowaste – S. Zahedi – Waste Management

Comparative analysis of microbial diversity in two hot springs of Bakreshwar, West Bengal, India – Chaudhuri B – Genomics Data

Built environment (subways, indoor surfaces)

Characterizing bacterial communities in paper production-troublemakers revealed – Zumsteg A – MicrobiologyOpen

 

Probiotics / prebiotics

Dairy Propionibacteria: Versatile Probiotics – Rabah H – Microorganisms

Contribution of anthocyanin-rich foods in obesity control through gut microbiota interactions – Jamar G – BioFactors

Positive Effect of Probiotics on Constipation in Children: A Systematic Review and Meta-Analysis of Six Randomized Controlled Trials – Huang R – Frontiers in Cellular and Infection Microbiology

Mechanisms of Action of Probiotics and the Gastrointestinal Microbiota on Gut Motility and Constipation – Dimidi E – Advances in Nutrition

Bioinformatics

PrePrint – MetaMeta: Integrating Metagenome Analysis Tools To Improve Taxonomic Profiling – Vitor C. Piro – bioRxiv

Using null models to infer microbial co-occurrence networks – Nora Connor – PLOS ONE

Techniques

Characterization of microbial mixtures by mass spectrometry – Sandrin TR – Mass Spectrometry Reviews

Microbes in the news 

Cork scientists link gut bacteria to anxiety disorders

New tick bacteria in Australia being investigated as possible cause of Lyme disease-type illness

Optical nanofiber ‘hears’ bacteria swim, cancer cells move

Microbes on the market 

BiomX raises $24 million to boost bacteria based drugs

 

Ed’s non-microbiology picks

Breakthrough in delirium research ‘solves 2,500-year-old mystery’

Novel tissue-engineered islet transplant achieves insulin independence in type 1 diabetes – Bioengineering of an Intraabdominal Endocrine Pancreas -David A. Baidal – New England Journal of Medicine

High levels of exercise linked to nine years of less aging (at the cellular level)

Migratory birds bumped off schedule as climate change shifts spring

PrePrint – Using Social Network Analysis to Better Understand Compulsive Exercise Behavior among a Sample of Sorority Members –  Megan S. Patterson – Human Kinetics

Edible insects could play key role in cutting harmful emissions – EurkAlert!

May 11, 2017

Gram-negative gut bacteria and Toll-like receptor 4 linked to stimulation of cerebral cavernous malformations, suppression of a single gene by the microbiota promotes T cell survival in mice, quorum sensing negatively regulates toxin production in insect-associated bacteria and may facilitate stable colonization.

General microbiome

Lactobacillus plantarum producing a Chlamydia trachomatis antigen induces a specific IgA response after mucosal booster immunization – Katarzyna Kuczkowska – PLoS ONE

Human oral microbiome

The dental calculus metabolome in modern and historic samples – Irina M Velsko – bioRxiv

Insights of the dental calculi microbiome of pre-Columbian inhabitants from Puerto Rico – Tasha M Santiago-Rodriguez – PeerJ

Arginine Improves pH Homeostasis via Metabolism and Microbiome Modulation – M Angelo – Journal of Dental Research

Human gut microbiome

Faecal Microbiota Transplantation for Inflammatory Bowel Disease: A Systematic Review and Meta-analysis – Sudarshan Paramsothy – Journal of Crohn’s and Colitis

Significantly higher faecal counts of the yeasts candida and saccharomyces identified in people with coeliac disease – Joanna Harnett – Gut Pathogens

Research Highlight: Tooling up for microbiota research – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology

Review: The gut microbiota: a key factor in the therapeutic effects of (poly)phenols – Juan Carlos Espín – Biochemical Pharmacology

Animal experiments

* Endothelial TLR4 and the microbiome drive cerebral cavernous malformations – Alan T Tang – Nature

* Microbiota promotes systemic T-cell survival through suppression of an apoptotic factor – Raymond Soto – PNAS

Bifidobacterium adolescentis IM38 ameliorates high-fat diet-induced colitis in mice by inhibiting NF-κB activation and lipopolysaccharide production by gut microbiota – Su-Min Lim – Nutrition Research

Tyrosine kinase inhibitors of Ripk2 attenuate bacterial cell wall-mediated lipolysis, inflammation and dysglycemia – Brittany M Duggan – Scientific Reports

Total fecal microbiota transplantation alleviates high-fat diet-induced steatohepatitis in mice via beneficial regulation of gut microbiota – Da Zhou – Scientific Reports

Animal microbiome

* Quorum Sensing Attenuates Virulence in Sodalis praecaptivus – Shinichiro Enomoto – Cell Host & Microbe

The digestive and defensive basis of carcass utilization by the burying beetle and its microbiota – Heiko Vogel – Nature Communications

Plant, root, and soil microbiome

Antibacterial producing actinomycetes from Extra Andean Patagonia – M S Vela Gurovic – Journal of Arid Environments

High-throughput sequencing reveals bacterial community composition in the rhizosphere of the invasive plant Flaveria bidentis – Z Song – Weed Research

Microbiomes associated with infective stages of root-knot and lesion nematodes in soil – Ahmed Elhady – PLoS ONE

Review: Plant-insect-pathogen interactions: a naturally complex ménage à trois – Flávia P Franco – Current Opinion in Microbiology

Review: CuO and ZnO Nanoparticles Modify Interkingdom Cell Signaling Processes Relevant to Crop Production: A Review – Anne Anderson – Journal of Agricultural and Food Chemistry

The phosphotransferase system gene ptsi in Bacillus cereus regulates expression of soda2 and contributes to colonization of wheat roots – Tantan Gao – Research in Microbiology

Water and extremophile microbiome

Review: Microbial processes driving coral reef organic carbon flow – Cynthia B Silveira – FEMS Microbiology Reviews

Diversity of biocrust-forming cyanobacteria in a semiarid gypsiferous site from Central Spain – Concha Cano-Díaz – bioRxiv

Probiotics/prebiotics

Probiotic Bifidobacterium longum NCC3001 Reduces Depression Scores and Alters Brain Activity: a Pilot Study in Patients With Irritable Bowel Syndrome – Maria Ines Pinto-Sanchez – Gastroenterology

Bioinformatics

dbOTU3: A new implementation of distribution-based OTU calling – Scott W Olesen – PLoS ONE

MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads – Thomas Nordahl Petersen – PLoS ONE

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes – Sheng-Yong Niu – Briefings on Bioinformatics

Techniques

Review: Imaging mass spectrometry for metabolites: technical progress, multimodal imaging, and biological interactions – Ying-Ning Ho – WIREs Systems Biology and Medicine

Live-Cell Nanoscopy in Antiadhesion Therapy – Joan A Geoghegan – Trends in Microbiology

Low concentration DNA extraction and recovery using a silica solid phase – Constantinos Katevatis – PLoS ONE

More microbes

When more is less: Emergent suppressive interactions in three-drug combinations – Casey Beppler – BMC Microbiology

Effects of stochasticity and division of labor in toxin production on two-strain bacterial competition in Escherichia coli – Benedikt von Bronk – PLoS Biology

Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker’s yeast – Ali R Awan – Nature Communications

Microbes in the news

Cosmetics: The next microbiome frontier – Marc S Reisch – Chemical and Engineering News

A defence mechanism that can trap and kill TB bacteria – Science Daily

Is IBS All In Your Mind? New Study Hints at Close Ties Between the Brain and the Gut – Jessica Wapner – Newsweek

Bacteria art

Scientists ‘paint’ with bacteria, create microbial masterpieces – Tom Ensey – wistv.com

May 9, 2017

Today’s digest is full of exciting papers that look at how climate change is influencing the gut microbiome of lizards, biogeography of bacteria along the Amazon river, lastly how going to the gym might be bad for you.

Human gut microbiome

Preprint : The Landscape Of Type VI Secretion Across Human Gut Microbiomes Reveals Its Role In Community Composition. Verster A. bioRxiv

Ocean, river, and stream microbiome

Disentangling multi‐scale environmental effects on stream microbial communities. Jyrkänkallio‐Mikkola J. Journal of Biogeography

Bacterial biogeography across the Amazon river-ocean continuum  Doherty M. Frontiers in Microbiology

Spatial variation of microbial communities in sediments along the environmental gradients from Xiaoqing River to Laizhou Bay.   Yu SX.  Marine Pollution Bulletin

The impact of long-term water level draw-down on microbial biomass: A comparative study from two peatland sites with different nutrient status Mpamah PA. European Journal of Soil Biology

The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the Candidate Superphylum Parcubacteria (OD1). León‐Zayas. Environmental Microbiology

Plant, soil, and air microbiome

Postmortem microbial communities in burial soil layers of skeletonized humans. Thomas TB. Journal of Forensic and Legal Medicine

Metagenomic Analysis of Bacterial Communities in the Rhizosphere of Leguminous Crops and Trees. Ahrenhoerster C. The FASEB Journal

Animal gut microbiome

Can fecal samples be used to inform about microbial communities of the equine hindgut? Reed KJ. Journal of Equine Veterinary Science

Normal variation and changes over time in the equine intestinal microbiome Martin EJ. Journal of Equine Veterinary Science

Climate warming reduces gut microbiota diversity in a vertebrate ectotherm. Bestion E. Nature:Ecology and Evolution

Effect of dietary supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) on caecum microbioma and productive performance in broiler chickens De Cesare A. PLoS One

Biotechnology 

Editorial Petroleum Microbial Biotechnology: Challenges and Prospects Ismail WA.Frontiers in Microbiology

Antibiotic 

Networks of exchanging antibiotic resistance between environmental, commensal, and pathogenic microbes Dantas G- The FASEB Journal

Extreme environment 

Decoupling of microbial carbon, nitrogen, and phosphorus cycling in response to extreme temperature events Mooshammer M. Science Advances

Faecal microbiome 

pH-Mediated Microbial and Metabolic Interactions in Fecal Enrichment Cultures Ilhan ZE. mSpehere

Anemia During Infancy Affects the Fecal Microbiome and Fecal and Serum Metabolomes McClorry S. The FASEB Journal

Microbes in the news

Southern California beaches get bacteria warnings after rain

Monterey County Herald

The Amount Of Bacteria On Gym Equipment Will Make Sure You Never Forget To Wipe Down The Elliptical Again

Bustle


 

April 27, 2017

An exploration of fish as an alternative to mice for models of host-microbe interactions, a review on what we can learn from Bacteroides about the gut micriobiome, a news story on successful phage therapy for a multi drug resistant infection.

Human oral microbiome

The human oral microbiome is shaped by shared environment rather than genetics: evidence from a large family of closely-related individuals – Liam Shaw – bioRxiv

Human gut microbiome

* Review: An insider’s perspective: Bacteroides as a window into the microbiome – Aaron G Wexler – Nature Microbiology

Gut Microbiota: Small Molecules Modulate Host Cellular Functions – Jacob M. Luber – Current Biology

Fecal microbial characterization of hospitalized patients with suspected infectious diarrhea shows significant dysbiosis – Tzipi Braun – Scientific Reports

Animal experiments

Supplemental feeding of a gut microbial metabolite of linoleic acid, 10-hydroxy-cis-12-octadecenoic acid, alleviates spontaneous atopic dermatitis and modulates intestinal microbiota in NC/nga mice – Hiroko Kaikiri – International Journal of Food Sciences and Nutrition

Microbiota-activated CD103+ DCs stemming from microbiota adaptation specifically drive γδT17 proliferation and activation – Chris Flemming – Microbiome

Radiation induces proinflammatory dysbiosis: transmission of inflammatory susceptibility by host cytokine induction – Shiran Gerassy-Vainberg – Gut

Animal microbiome

Tick-Pathogen Interactions and Vector Competence: Identification of Molecular Drivers for Tick-Borne Diseases – José de la Fuente – Frontiers in Cellular and Infection Microbiology

Plant, root, and soil microbiome

Review: Managing the plant microbiome for biocontrol fungi: examples from Hypocreales – Ryan M Kepler – Current Opinion in Microbiology

Occurrence of perchlorate in groundwater, paired farmland soil, lettuce, and rhizosphere soil from Chengdu, China – Yulu Tang – Environmental Science: Processes & Impact

Water and extremophile microbiome

The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential interactions – Michael D Lee – The ISME Journal

Bringing methanotrophy in rivers out of the shadows – Felicity Shelley – Limnology and Oceanography

Rainfall increases the abundance of antibiotic resistance genes within a riverine microbial community – Andrea Di Cesare – Environmental Pollution

Impact of selectively enriched microbial communities on long-term fermentative biohydrogen production – R Kanniah Goud – Bioresource Technology

Probiotics/prebiotics

Perspective: Next-generation probiotics: the spectrum from probiotics to live biotherapeutics – Paul W O’Toole – Nature Microbiology

Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructo-oligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing – Jose F Garcia-Mazcorro – PeerJ

Bioinformatics

Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments – Arghya Mukherjee – Scientific Reports

Techniques

Faecal volatile organic compounds analysis using field asymmetric ion mobility spectrometry: non-invasive diagnostics in paediatric inflammatory bowel disease – Nora van Gaal – Journal of Breath Research

Teleosts as Model Organisms to Understand Host-Microbe Interactions – Emily A Lescak – Journal of Bacteriology

Synthetic and analytical strategies for the quantification of phenyl-γ-valerolactone conjugated metabolites in human urine – Nicoletta Brindani – Molecular Nutrition & Food Research

More microbes

Species ecological similarity modulates the importance of colonization history for adaptive radiation – Jiaqi Tan – International Journal of Organic Evolution

Interaction of Bacterial Membrane Vesicles with Specific Species and Their Potential for Delivery to Target Cells – Yosuke Tashiro – Frontiers in Microbiology

Microbes in the news

Phage Therapy Saves Patient from Drug-Resistant Microbes – Genetic Engineering & Biotechnology News

Chronic fatigue syndrome linked to imbalanced microbiome – EurekAlert

Komodo Dragon Blood Could Become Tool in Fight Against Bacteria – Elizabeth Pratt – Healthline

Researchers move closer to preventing frost damage in vineyards by managing bacteria on the vines – Greg Northcutt – Western FarmPress

Underwater volcano eruptions allow new bacteria to take over seafloor – Lisa-Ann Lee – New Atlas

Microbes on the market

Taconic Biosciences Expands Microbiome Product and Service Platform – GlobeNewswire

Bacteria and art

This Art Exhibition Is Made From Bacteria, Live Insects And Human Sweat – Ryan F Mandelbaum – Gizmodo Australia

Art Made with CRISPR Aims to Raise Awareness of Antibiotic Resistance – Clara Rodríguez Fernández – Labiotech.eu

Amy’s non-microbiology picks

Microscopy: A larger palette for biological imaging – Charles H Camp Jr – Nature

April 24, 2017

General Microbiome

Review: Ecology of the Oral Microbiome: Beyond Bacteria – Jonathon L. Baker – Trends in Microbiology

Dietary High Zinc Oxide Modulates the Microbiome of Ileum and Colon in Weaned Piglets – Ting Yu – Frontiers in Microbiology

Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut environments –  Matthew L Jenior – BioRxiv

Review: Strategies to promote abundance of Akkermansia muciniphila, an emerging probiotics in the gut, evidence from dietary intervention studies – Kequan Zhou – Journal of Functional Foods

Protective effects of milk fermented by Lactobacillus plantarum B7 from Brazilian artisanal cheese on a Salmonella enterica serovar Typhimurium infection in BALB/c mice – Journal of Functional Foods

 

Pathogens

Molecular Demonstration of a Pneumocystis Outbreak in Stem Cell Transplant Patients: Evidence for Transmission in the Daycare Center – Frontiers in Microbiology

A New Rabbit-skin Model to Evaluate Protective Efficacy of Tuberculosis Vaccines – Xun Liu – Frontiers in Microbiology

Molecular epidemiology and antibiotic resistance profiles of methicillin-resistant Staphylococcus aureus strains in a tertiary hospital in China – Haishen Kong – Frontiers in Microbiology

 

Environmental Microbiology

Microbial community assembly differs by mineral type in the rhizosphere – Thea Whitman – BioRxiv

Interaction between DAPG and HCN producing Pseudomonas brassicacearum LBUM300 and Clavibacter michiganensis subsp. michiganensis in the rhizosphere of tomato – Applied Environmental Microbiology

Nitrogen-Fixing Populations Of Planctomycetes And Proteobacteria Are Abundant In The Surface Ocean – Tom O. Delmont – BioRxiv

Bacterial communities in boreal forest mushrooms are shaped both by soil parameters and host identity – Mari Pent – Frontiers in Microbiology

 

Genomics

Isoprenoid Pyrophosphate-Dependent Transcriptional Regulation of Carotenogenesis in Corynebacterium glutamicum – Nadja A. Henke – Frontiers in Microbiology

Whole genome sequencing of 7 strains of Staphylococcus lugdunensis allows identification of mobile genetic elements – Xavier Argemi – Genome Biology and Evolution

Pooled CRISPR interference screens enable high-throughput functional genomics study and elucidate new rules for guide RNA library design in Escherichia coli – Tianmin Wang – BioRxiv

 

Evolution

Tunneling through time: Horizontal gene transfer constrains the timing of methanogen evolution –  Joanna M. Wolfe – BioRxiv

 

Bioinformatics

AliTV-interactive visualization of whole genome comparisons – Markus J. Ankenbrand – PeerJ (not peer-reviewed)

TaxaSE: Exploiting evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotation – Ali Z Ijaz – PeerJ (not peer-reviewed)

 

Other

Preprinting Microbiology – Patrick D Schloss – BioRxiv

 

Non – Microbiology picks

News: Scientists across the world take to the streets to demand freedom from political interference – The Telegraph (via Yahoo News)

Human umbilical cord plasma proteins revitalize hippocampal function in aged mice – Joseph M. Castellano –  Nature