January 21, 2018

A light reading for Sunday!
Events and jobs

Professor (Chairperson), Department of Microbiology and Immunology (MIC) – The Uniformed Services University of the Health Sciences – Bethesda, Maryland

Postdoc in Intestinal Microbiology and Ecology – The National Food Institute (DTU Food) – Denmark

SCIENCE INQUIRY LECTURE: “FLYING” BACTERIA AS POTENTIAL RAINMAKERS – APRIL 18, 2018; 7:00PM – 8:30PM – HAGER AUDITORIUM, Montana 

General microbiome

Review: Bacterial RNA Biology on a Genome Scale – Jens Hör  – Molecular Cell

Multi-site human microbiome

Epigenetics, microbiota, and intraocular inflammation: New paradigms of immune regulation in the eye – Xiaofeng Wen – Progress in Retinal and Eye Research

Human skin microbiome

The role of fatty acids and their endocannabinoid-like derivatives in the molecular regulation of appetite – Renger F. Witkamp – Molecular Aspects of Medicine

Non-classical Immunity Controls Microbiota Impact on Skin Immunity and Tissue Repair – Jonathan L. Linehan – Cell

Propionibacterium acnes Strains Differentially Regulate the Fate of Th17 Responses in the Skin – Emmanuel Contassot – Journal of Investigative Dermatology

Human gut microbiome

P038 FECAL MICROBIOTA TRANSPLANT (FMT) FOR IMMUNO-CHECKPOINT INHIBITOR-INDUCED COLITIS (ICI-C) IN A 50 YEAR OLD FEMALE WITH BLADDER CANCER – Yinghong Wang – Gastroenterology

P110 STEROID-RESISTANCE AND STEROID-DEPENDENCE IN INFLAMMATORY BOWEL DISEASE CAN BE LINKED WITH GUT MICROBIOTA COMPOSITION CHANGES – Natalia Danilova – Gastroenterology

P069 LOW FAT DIET IMPROVES QUALITY OF LIFE AND CHANGES THE MICROBIOME IN A CATERED, CROSS-OVER DESIGN INTERVENTION OF UC PATIENTS WITH QUIESCENT DISEASE: RESULTS OF A PILOT STUDY – Matthew C. Phillips  – Gastroenterology

Animal experiments 

The family Coriobacteriaceae is a potential contributor to the beneficial effects of Roux-en-Y gastric bypass on type 2 diabetes – Haijun Liu – Surgery for Obesity and Related Diseases

P039 FECAL MIRNAS SHAPE THE INTESTINAL MICROBIOTA – Emilie Viennois – Gastroenterology

P125 TLR4 ACTIVATION UPREGULATES EXPRESSION OF OXIDATIVE ENZYMES: IMPLICATIONS FOR INTESTINAL TUMORIGENESIS AND LUMINAL MICROBIOTA – Juan F. Burgueno – Gastroenterology

Effect of live yeast supplementation on gastric ecosystem in horses fed a high-starch diet – Samy Julliand – Livestock Science

The symbiont Lactobacillus plantarum causes intestinal pathogenesis in adult Drosophila. – David Fast – bioRxiv

Plant, root and soil microbiome

Distinct responses of soil bacterial and fungal communities to changes in fertilization regime and crop rotation – Chao Ai – Geoderma

Microbial degradation of poly(ε-caprolactone) in a coastal environment – Miwa Suzuki – Polymer Degradation and Stability

Shifts in prokaryotic communities under forest and grassland within a tropical mosaic landscape – Sergio E. Morales – Applied Soil Ecology

Food microbiology

Polyphasic identification of Penicillia and Aspergilli isolated from Italian grana cheese – Simone Decontardi – Food Microbiology

Phages and viruses

Bacteriophages as modulator for the human gut microbiota: Release from dairy food systems and survival in a dynamic human gastrointestinal model – Meike Samtlebe – LWT

Techniques

Metagenomic analysis uncovers strong relationship between periodontal pathogens and vascular dysfunction in American Indian population – Prathik K Vijay Kumar – bioRxiv

P168 WHERE WILL FECAL MICROBIOTA TRANSPLANTATION FIT IN THE TREATMENT ALGORITHMS FOR CROHN’S DISEASE AND ULCERATIVE COLITIS: A SYNTHESIS OF COMPLETED, ONGOING AND FUTURE TRIALS – Yiran Song – Gastroenterology

Microbes in the news

The Prehistoric Bacteria That Helped Create Our Cells Billions of Years Ago – Mental Floss

IIT Delhi develops a novel platform to test drug sensitivity in bacteria – The Hindu

Scientists Unlock Key Information About the World’s Soil Microbes – Yale Environment 360

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January 20, 2018

Our Saturday digest has microbes associated with oesophageal region; sore throat; aphids, stingless bees; common carps, Italian cheeses and many more!

General microbiome

Bipartite network analysis of gene sharings in the microbial world – Eduardo Corel –

FEMS Microbiology Ecology

Is the impact of starvation on the gut microbiota specific or unspecific to anorexia nervosa? A narrative review based on a systematic literature search – Isabelle Mack – Current Neuropharmacology

Pregnancy and early life

Association between sn-2 fatty acid profiles of breast milk and development of the infant intestinal microbiome – Teimin Jiang – Food and Function

Multi-site human microbiome

The microbiology and treatment of human mastitis. – A Angelopoulou – Medical Microbiology and Immunology

Human respiratory microbiome

Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children – Marianne S. Muhlebach – PLoS Pathogens

Analysis of the tonsillar microbiome in young adults with sore throat reveals a high relative abundance of Fusobacterium necrophorum with low diversity – T. Preskott Atkinson – PLoS One

Human gut microbiome

Diet Affects Gut Microbiota and Modulates Hospitalization Risk Differentially In an International Cirrhosis Cohort – JS Bajaj – Hepatology

Emerging Insights into the Esophageal Microbiome – M May – Current Treatment Options in Gastroenterology

Analysis of gut microbiota diversity and auxiliary diagnosis as a biomarker in patients with schizophrenia: A cross-sectional study –  Y Shen – Schizophrenia Research

Animal experiments 

Colonization of the cervicovaginal space with Gardnerella vaginalis leads to local inflammation and cervical remodeling in pregnant mice – Luz-Jeannette Sierra – PLoS One

Kudingcha and Fuzhuan Brick Tea Prevent Obesity and Modulate Gut Microbiota in High-Fat Diet Fed Mice – Guijie Chen – Molecular Nutrition & Food Research

Sequential BMP7/TGF-β1 signaling and microbiota instruct mucosal Langerhans cell differentiation. – Tal Capucha – Journal of Experimental Medicine

A host-pathogen interaction screen identifies ada2 as a mediator of Candida glabrata defences against reactive oxygen species – I Kounatidis – bioRxiv

Animal microbiome 

A large-scale field study of bacterial communities in cereal aphid populations across Morocco – Samir Fakhour – FEMS Microbiology Ecology

Common cuckoos (Cuculus canorus) affect the bacterial diversity of the eggshells of their great reed warbler (Acrocephalus arundinaceus) hosts  – Nikoletta Geltsch – PLoS One

Stingless Bee Larvae Require Fungal Steroid to Pupate. – Camila R. Paludo – Scientific Reports

Plant, root and soil microbiome

Succession of microbial communities and changes of incremental oil in a post-polymer flooded reservoir with nutrient stimulation – Peike Gao – Applied Microbiology and Biotechnology

Draft Genome Sequence of Bacillus subtilis 2C-9B, a Strain with Biocontrol Potential against Chili Pepper Root Pathogens and Tolerance to Pb and Zn – Claudia Y. Muñoz-Moreno – Genome Announcements

Biotic elicitation of ginsenoside metabolism of mutant adventitious root culture in Panax ginseng – Kim-Cuong Le – Applied Microbiology and Biotechnology

Streptomyces AcH 505 triggers production of a salicylic acid analogue in the fungal pathogen Heterobasidion abietinum that enhances infection of Norway spruce seedlings – Nadine Keilhofer – Antonie van Leeuwenhoek

Seed Endophyte Microbiome of Crotalaria pumila Unpeeled: Identification of Plant-Beneficial Methylobacteria – AS Sánchez-López – International Journal of Molecular Sciences

Extreme rainfall affects assembly of the root-associated fungal community – CJ Barnes – The New Phytologist

Abrupt burial imparts persistent changes to the bacterial diversity of turbidite-associated sediment profiles. – BK Harrison – Geobiology

Review: Fungal-Mediated Solid Waste Management: A Review –  A Jain – Mycoremediation and Environmental Sustainability

The PEG-responding desiccome of the alder microsymbiont Frankia alni – K Ghedira – Scientific Reports

Composition of pelagic microbial communities in Mediterranean coastal aquatic ecosystems under extreme drought conditions – N Àvila –  Estuarine, Coastal and Shelf Science

Water microbiome and extremophile 

What color should glacier algae be? – Roman J dial – FEMS Microbiology Ecology

Microbial Community Structure of Sea Spray Aerosols at Three California Beaches – Katherine Graham – FEMS Microbiology Ecology

The early conversion of deep-sea wood falls into chemosynthetic hotspots revealed by in situ monitoring – Dimitri Kalenitchenko – Scientific Reports

Microbial communities and their predicted metabolic functions in a desiccating acid salt lake – Elena Zaikova – Extremophiles

Protein adaptations in extremophiles: An insight into extremophilic connection of mycobacterial proteome – A Kumar – Seminars in Cell & Developmental Biology

Built environment 

Composition and role of the attached and planktonic microbial communities in mesophilic and thermophilic xylose-fed microbial fuel cells – Paolo Dessi – RSC Advances

Food microbiology

Development and implementation of multilocus sequence typing to study the diversity of the yeast Kluyveromyces marxianus in Italian cheeses – Fabrizia Tittarelli – Microbial Genomics

Application of molecular tools to elucidate the microbiota of seafood – Paloma Almeida Rodrigues – Journal of Applied Microbiology

Review: Recent Past, Present, and Future of the Food Microbiome – Francesca De Filippis – Annual Review of Food Science and Technology

Extracellular Enzyme Composition and Functional Characteristics of Aspergillus niger An-76 Induced by Food Processing Byproducts and Based on Integrated Functional-omics – L Liu – Journal of Agricultural and Food Chemistry

Changes in microbial communities and quality attributes of white muscle and dark muscle from common carp (Cyprinus carpio) during chilled and freeze-chilled storage – Q Li – Food Microbiology

Phages and viruses

Comparative transcriptomics reveals a conserved Bacterial Adaptive Phage Response (BAPR) to viral predation – BG Blasdel – bioRxiv

Single-cell transcriptional dynamics of flavivirus infection – F Zanini – bioRxiv

Techniques

A distance-based approach for testing the mediation effect of the human microbiome – J Zhang – Bioinformatics

ReprDB and panDB: minimalist databases with maximal microbial representation – W Zhou – Microbiome

Diverse spatial organization of photosynthetic membranes among purple nonsulfur bacteria – B LaSarre – bioRxiv

Microbes in the news 

WEBINAR REVIEW: IMMUNO-ONCOLOGY AND THE MICROBIOME – Taconic

Scientists Peek Inside The ‘Black Box’ Of Soil Microbes To Learn Their Secrets – npr

Broadways Nursing Home: Legionella bacteria found in plumbing – BBC

Agros refuses Troodos water after coliform bacteria found – Cyprus Mail Online

Strange Weather Triggered Bacteria That Killed 200,000 Endangered Antelope – npr

Bacterial biofilm cellulose found to differ from plant cellulose – Phys.org

This is what happens to your gut when you go on a juice cleanse – Well and Good

New Course in Virus Hunting – SDSU NewsCenter

January 19, 2018

Today’s digest features a review on gut microbial glycerol metabolism as a source of Acrolein, and an interesting article on the impact of climate cooling on ecosystem community structure and function in alpine soils. Happy reading!

 

Careers and Events

Research Fellow – National University of Singapore

Postdoctoral Fellow – Boston Children’s Hospital, Harvard Medical School

Scientific Officer/Senior Scientific Officer – The Cancer Research UK Beatson Institute

Staff Clinician – National Institutes of Health (NIH) National Heart, Blood and Lung Institute (NHLBI)

Human respiratory microbiome

Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children – Marianne S. Muhlebach – Plos Pathogens

Human skin microbiome

Association of Disease Severity With Skin Microbiome and Filaggrin Gene Mutations in Adult Atopic Dermatitis – Maja-Lisa Clausen – JAMA Dermatology

Human gut microbiome

Review : Genetic and microbiome influence on lipid metabolism and dyslipidemia – Maria Matey Hernandez – Physiological Genomics

Review : Bile acids in glucose metabolism in health and disease – Hagit Shapiro – Journal of Experimental Microbiology

*Review: Gut Microbial Glycerol Metabolism as an Endogenous Acrolein Source – Jianbo Zhang – mBio

Review: How does ‘metabolic surgery’ work its magic? New evidence for gut microbiota – Peck Bailey C.E – Current Opinion in Endocrinology, Diabetes and Obesity

Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease – Gavin M. Douglas – Microbiome

Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease – Ahmed Moustafa – Clinical and translational gastroenterology

Animal experiments

Flaxseed-enriched diets change milk concentration of the antimicrobial danofloxacin in sheep – Jon Andoni Otero – BMC Veterinary Research

Colonization of the cervicovaginal space with Gardnerella vaginalis leads to local inflammation and cervical remodeling in pregnant mice – Luz-Jeannette Sierra – Plos One

Kudingcha and Fuzhuan Brick Tea Prevent Obesity and Modulate Gut Microbiota in High-Fat Diet Fed Mice – Guijie Chen – Molecular Nutrition and Food Research

Plant, root, and soil microbiome

*Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling – Linwei Wu – ISME Journal

Cultivable fungi present in Antarctic soils: taxonomy, phylogeny, diversity, and bioprospecting of antiparasitic and herbicidal metabolites – Eldon C. Q. Gomes – Extremophiles

Clearcutting alters decomposition processes and initiates complex restructuring of fungal communities in soil and tree roots – Petr Kohout – The ISME Journal

A large-scale field study of bacterial communities in cereal aphid populations across Morocco – Samir Fakhour – FEMS Microbiology Ecology

Microbial Mitigation-Exacerbation Continuum: A novel framework for microbiome effects on hosts in the face of stress – Aaron S. David – Ecology

Water and extremophile microbiome

Brief Report: Effects of grazing, phosphorus and light on the growth rates of major bacterioplankton taxa in the coastal NW Mediterranean – Olga Sánchez – Environmental Microbiology Reports

Development of a mediated whole cell-based electrochemical biosensor for joint toxicity assessment of multi-pollutants using a mixed microbial consortium – Guanyue Gao – Analytica Chimica Acta

The acute effects of erythromycin and oxytetracycline on enhanced biological phosphorus removal system: shift in bacterial community structure – Zhetai Hu – Environmental Science and Pollution Research

Probiotics / prebiotics

Valorization of Brewer’s spent grain to prebiotic oligosaccharide: production, xylanase catalyzed hydrolysis, in-vitro evaluation with probiotic strains and in a batch human fecal fermentation model – Mursalin Sajib – Journal of Biotechnology

In vitro fermentation of gum acacia – impact on the faecal microbiota – Sehad Alarifi -International Journal of Food Sciences and Nutrition

A bioluminescent test system reveals valuable antioxidant properties of lactobacillus strains from human microbiota – Maria Marsova – World Journal of Microbiology and Biotechnology

Yeasts / Fungi

Review: Sequence-based classification and identification of Fungi – David Hibbett – Mycologia

Phages and viruses

Detection of bovine Deltapapillomavirus DNA in peripheral blood of healthy sheep (Ovis aries) – S. Roperto – Transboundary and Emerging Diseases

Metagenomics

In-depth resistome analysis by targeted metagenomics – Val F. Lanza – Microbiome

Metabolomics

Qualitative metabolomics profiling of serum and bile from dogs with gallbladder mucocele formation – Jody L. Gookin – Plos One

Bioinformatics

A distance-based approach for testing the mediation effect of the human microbiome -Jie Zhang – Bioinformatics

Anitha’s non-microbiology picks

NASA test proves pulsars can function as a celestial GPS

The dark side of light: how artificial lighting is harming the natural world

Ultrathin 2-D metals get their own periodic table

January 18, 2018

Today’s digest has quite a few reviews in “Human Gut Microbiome” section and quite interesting news: what killed Aztecs, the womb might not be sterile, while surfers might be spreading antibiotic-resistant bacteria. Check as well an interesting blog post on “How can academia kick its addiction to the impact factor?” and news about “Dimensions” – new science search engine. Dimensions not only indexes papers and their citations, but also – uniquely among scholarly databases – connects publications to their related grants, funding agencies, patents and clinical trials.

 

 

General microbiome

Conserved collateral susceptibility networks in diverse clinical strains of Escherichia coli – Nicole L Podnecky – bioRxiv

Interactions between species introduce spurious associations in microbiome studies – Rajita Menon – PLOS Computational Biology

Antimicrobial resistant Klebsiella pneumoniae carriage and infection in specialized geriatric care wards linked to acquisition in the referring hospital – Claire L Gorrie – Clinical Infectious Diseases

Microbiological and molecular characterization of thermophilic Streptomycesvariabilis with antimicrobial activity – Ramy Fikry – Journal of Basic and Environmental Sciences

Population level evidence for seasonality of the human microbiome – Christina Korownyk – Chronobiology International

Metagenomic analysis of microbial communities yields insight into impacts of nanoparticle design –  Jacob W. Metch – Nature Nanotechnology

Microbial Competition of Rhodotorula mucilaginosa UANL-001L and E. coli increase biosynthesis of Non-Toxic Exopolysaccharide with Applications as a Wide-Spectrum Antimicrobial – Augusto Vazquez-Rodriguez – Scientific Reports

Pregnancy and early life

Perturbations of the gut microbiome genes in infants with atopic dermatitis according to feeding type – Min-Jung Lee – Journal of Allergy and Clinical Immunology

Overweight and obesity status in pregnant women are related to intestinal microbiota and serum metabolic and inflammatory profiles – Noora Houttu – Clinical Nutrition

Human respiratory microbiome

Give me a sample of air and I will tell which species are found from your region – molecular identification of fungi from airborne spore samples – Nerea Abrego – Molecular Ecology Resources

Fungi stabilize connectivity in the lung and skin microbial ecosystems – Laura Tipton – BMC Microbiome

Oral microbiome

Microbiome associated with denture malodour – S Yitzhaki – Journal of Breath Research

High-resolution microbiome profiling uncovers Fusobacterium nucleatum, Lactobacillus gasseri/johnsonii, and Lactobacillus vaginalis associated to oral and oropharyngeal cancer in saliva from HPV positive and HPV negative patients treated with surgery and chemo-radiation – Rafael Guerrero-Preston – Oncotarget

Location-Specific Oral Microbiome Possesses Features Associated With CKD – Jianzhong Hu – Kidney International Reports

Oral microbiota reduce wound healing capacity of epithelial monolayers, irrespective of the presence of 5-fluorouracil – Eline Vanlancker – Experimental Biology and Medicine

An experimental study for rapid detection and quantification of endodontic microbiota following photo-activated disinfection via new multiplex real-time PCR assay – Maryam Pourhajibagher – Photodiagnosis and Photodynamic Therapy

Review: Genome analysis and clinical implications of the bacterial communities in early biofilm formation on dental implants restored with titanium or zirconia abutments –  Flávia Correa Raffaini – Biofueling

Human skin microbiome

Association of Disease Severity With Skin Microbiome and Filaggrin Gene Mutations in Adult Atopic Dermatitis – Maja-Lisa Clausen – JAMA Dermatology

Human nearly-sterile sites

The Microbiome and Neurologic Disease: Past and Future of a 2-Way Interaction – Javier Ochoa-Repáraz – Neurotherapeutics

Human gut microbiome

Mini Review: Beneficial actions of microbiota-derived tryptophan metabolites – J. J. Galligan – Neurogastroenterology & Motility

Review: Gut microbiome influences on anastomotic leak and recurrence rates following colorectal cancer surgery – S. Gaines – BJS

Review: Microbiota Signaling Pathways that Influence Neurologic Disease – Laura M. Cox – Neurotherapeutics

Review: How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota – Grégory Dubourg – Expert Review of Proteomics

Concise Review: Gut microbiota and probiotics: novel immune system modulators in myasthenia gravis? – Elena Rinaldi – Annals of the New York Academy of Science

Research Highlights: Gut microbiota: Targeting of specific microbial species mitigates colitis – Hugh Thomas – Nature Reviews Gastroenterology and Hepatology

Research Highlights: Gut microbiota: Filling up on fibre for a healthy gut – Katrina Ray – Nature Reviews Gastroenterology and Hepatology

Stachyose Improves Inflammation Through Modulating Gut Microbiota of High-Fat Diet / Streptozotocin Induced Type 2 Diabetes in Rats – Guimei Liu – Molecular Nutrition & Food Research

Analysis of fecal microbiota in patients with functional constipation undergoing treatment with synbiotics – Lin Sheng Huang – European Journal of Clinical Microbiology & Infectious Diseases

The microbiota metabolite indole inhibits Salmonella virulence: Involvement of the PhoPQ two-component system – Nandita Kohli – PLOS

Metatranscriptome of human faecal microbial communities in a cohort of adult men – Galeb S. Abu-Ali – Nature Microbiology

Early-life gut microbial colonization shapes Th1/Th2 balance in asthma model in BALB/c mice – Li-Juan Qian –

Animal experiments

Impact of Trans-Fats on Heat-Shock Protein Expression and the Gut Microbiota Profile of Mice – Gessika Cristina Borges Castro Carvalho – Journal of Food Science

Animal microbiome 

The impact of depuration on mussel hepatopancreas bacteriome composition and predicted metagenome – J. A. Rubiolo – Antonie van Leeuwenhoek

The Sarda Sheep Host Fecal Proteome – Antonio Palomba – Proteomics

Interactions Between Parasites and the Bacterial Microbiota of Chickens – Rüdiger Hauck – Avian Diseases

Plant, root, and soil microbiome

Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming – Kyle Hartman – BMS Microbiome

Saving seed microbiomes – Gabriele Berg – The ISME

Rice Crop Growth and Rhizospheric Microbial Dynamics in Heavy Metals Contaminated Inceptisol – Manoj Shrivastava – Water Quality Management

Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming – Kyle Hartman – BMC Microbiome

Water and extremophile microbiome

Diverse spatial organization of photosynthetic membranes among purple nonsulfur bacteria – Breah LaSarre – bioRxiv

Homologous recombination and transposon propagation shapes the population structure of an organism from the deep subsurface with minimal metabolism – Alexander J Probst – bioRxiv

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate – Michael Winslow Henson -bioRxiv

Data Descriptor: The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans – Benjamin J. Tully – Scientific Data

Survey of sulfur-oxidizing bacterial community in the Pearl River water using soxB, sqr, and dsrA as molecular biomarkers – Jianfei Luo – 3 Biotech

Cultivable fungi present in Antarctic soils: taxonomy, phylogeny, diversity, and bioprospecting of antiparasitic and herbicidal metabolites – Eldon C. Q. Gomes – Extremophiles

Taxonomical Resolution and Distribution of Bacterioplankton Along the Vertical Gradient Reveals Pronounced Spatiotemporal Patterns in Contrasted Temperate Freshwater Lakes – J. Keshri – Microbial Ecology

Coral physiology and microbiome dynamics under combined warming and ocean acidification – Andréa G. Grottoli – PLOS

Crenothrix are major methane consumers in stratified lakes – Kirsten Oswald – The ISME

 

Food microbiology

Review: Modern perspectives on the health benefits of kefir in next generation sequencing era: improvement of the host gut microbiota – Dong-Hyeon Kim –  Critical Reviews in Food Science and Nutrition

Probiotics / prebiotics

Lactobacillus acidophilus Improves Intestinal Inflammation in an Acute Colitis Mouse Model by Regulation of Th17 and Treg Cell Balance and Fibrosis Development – Park Jin-Sil – Journal of Medicinal Food

Phages and viruses

Interferons: Reprogramming the Metabolic Network against Viral Infection – Kavita Raniga  – Viruses

Bioinformatics

FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data – Saima Sultana Tithi – PeerJ

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data – Jie Ren – BMC Microbiome

Techniques

In-depth resistome analysis by targeted metagenomics – Val F. Lanza – BMC Microbiome

Microbes in the news

500 years later, scientists discover what probably killed the Aztecs

Could baby’s first bacteria take root before birth?

Robotic baby helps researchers understand how biological dust develops immunity in crawling babies

Surfers May Be Spreading Antibiotic-Resistant Bacteria From Swallowing Poop-Laced Water

Microbes and Art

Artist Hunter Cole Presents Exhibit Featuring Photos of Bacteria That Create Their Own Light

Science, publishing, and career 

Science search engine links papers to grants and patents

How can academia kick its addiction to the impact factor?

 

January 17, 2018

In today’s digest, a review of the skin microbiome and a brilliant article on role of microbes in plant speciation. Lastly, the microbiome of the ever impressive water bear.

General Microbiome

Editorial: Special Issue on ‘Microbe-host interactions’.Hammerschmidt S. FEBS Letters.

Review: The stress concept in gastroenterology: from Selye to today.Elsenbruch S. F1000 Research

Review:Role of human microbiome and selected bacterial infections in the pathogenesis of rheumatoid arthritis. Roszyk E. Reumatologia

Gut Microbiome

Review: Non-digestible carbohydrates in infant formula as substitution for human milk oligosaccharide functions: Effects on microbiota and gut maturation.Akkerman R. Critical Reviews in Food Science and Nutrition

Review: Diet, Gut Microbiota, and Colorectal Cancer Prevention: A Review of Potential Mechanisms and Promising Targets for Future Research.Song M. Current Colorectal Cancer Reports

Skin Microbiome

Review: The human skin microbiome. Byrd AL. Nature Reviews Microbiology

Anal Microbiome

Is there a link between aging and microbiome diversity in exceptional mammalian longevity? Hughes GM. PeerJ

Plant, Soil, and Water Microbiome

Out of sight, but no longer out of mind – towards an increased recognition of the role of soil microbes in plant speciation.Geml J. New Phytologist.

Investigating the Microbial Degradation Potential in Oil Sands Fluid Fine Tailings Using Gamma Irradiation: A Metagenomic Perspective.VanMensel D. Microbial Ecology

Animan Experiments and Microbiome

The Microbial Community of Tardigrades: Environmental Influence and Species Specificity of Microbiome Structure and Composition.Vecchi M, Newton ILG, Cesari M. Microbial Ecology

Peracetic acid disinfection kinetics for combined sewer overflows: indicator organisms, antibiotic resistance genes, and microbial community.Eramo A. Environmental Science: Water Research and Technology

Protocol

Oral Microbiome Characterization in Murine Models. Abusleme L. Bio-protocol

Microbes in the NEWS

Can Probiotics Improve the Gut Flora and Reduce Complications after Surgery?

-Medical News Bulletin

 

January 16, 2018

Today, a set of interesting papers about the stability of human microbiome, ancient genomes from XVI Century Salmonella strains, a nice review about human skin microbiome, antimicrobial resistance genes in the International Space Station and more!

 

Human Microbiome

Stability of the human faecal microbiome in a cohort of adult men – Raaj S. Mehta – Nature Microbiology

Non-digestible carbohydrates in infant formula as substitution for human milk oligosaccharide functions: Effects on microbiota and gut maturation – Renate Akkerman – Critical Reviews in Food Science and Nutrition

Review: The human skin microbiome – Allyson L. Byrd – Nature Reviews Microbiology

The Relationship between Habitual Dietary Intake and Gut Microbiota in Young Japanese Women – Takahiro Seura – Journal of Nutritional Science and Vitaminology

Oral microbiota of periodontal health and disease and their changes after nonsurgical periodontal therapy – Casey Chen – The ISME Journal

Cigarette smoking is associated with an altered vaginal tract metabolomic profile – T. M. Nelson – Scientific Reports

Review: Infectious Agents and Inflammation: The Role of Microbiota in Autoimmune Arthritis – Andrea Picchianti-Diamanti – Frontiers in Microbiology

Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study – Edda Russo – Frontiers in Microbiology

 

Animal Microbiome

Fosfomycin residues in colostrum: Impact on morpho-physiology and microbiology of suckling piglets – M.B. Fernández Paggi – Journal Of Veterinary Pharmacology And Therapeutics

The Microbial Community of Tardigrades: Environmental Influence and Species Specificity of Microbiome Structure and Composition – Matteo Vecchi – Microbial Ecology

Oral Microbiome Characterization in Murine Models – Loreto Abusleme – Bio-Protocol

Corallivory and the microbial debacle in two branching scleractinians – Yvan Bettarel – The ISME Journal

The Inner Workings of the Outer Surface: Skin and Gill Microbiota as Indicators of Changing Gut Health in Yellowtail Kingfish – Thibault P. R. A. Legrand – Frontiers in Microbiology

 

Built Microbiome

Detection of antimicrobial resistance genes associated with the International Space Station environmental surfaces – C. Urbaniak – Scientific Reports

 

Plant and Environmental Microbiome

The stage of soil development modulates rhizosphere effect along a High Arctic desert chronosequence – Francesca Mapelli – The ISME Journal

Perspective: Saving seed microbiomes – Gabriele Berg – The ISME Journal

Preprint: Microbial biogeography of 1,000 geothermal springs in New Zealand – Jean F Power – Biorxiv

 

Pathogen Research

Effect of outpatient antibiotics for urinary tract infections on antimicrobial resistance among commensal Enterobacteriaceae: a multinational prospective cohort study – Andrew J. Stewardson – Clinical microbiology and infection

Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico – Åshild J. Vågene – Nature Ecology & Evolution

Bovine Lactoferrin and Lactoferrin-Derived Peptides Inhibit the Growth of Vibrio cholerae and Other Vibrio species – Erika Acosta-Smith – Frontiers in Microbiology

 

General Microbiome

The stress concept in gastroenterology: from Selye to today – Sigrid Elsenbruch – F1000Reseach

Review: Deoxynivalenol, gut microbiota and immunotoxicity: A potential approach? – Yuxiao Liao – Food and Chemical Toxicology

Research Highlight: Anti-PD1 in the wonder-gut-land – Marie Vetizou – Cell Research

 

Other

The deep-subsurface sulfate reducer Desulfotomaculum kuznetsovii employs two methanol-degrading pathways – Diana Z. Sousa – Nature Communications

Preprint: Conserved mass peaks in MALDI-TOF mass spectra of bacterial species – Wenfa Ng – PeerJ

January 15, 2018

Today’s digest is full of great papers, including new methods of detection and quantificaion of HGT in anoxic conditions, and a brilliant paper on root-rhizosphere interactome.

General Microbiome

Impact of the start-up process on the microbial communities in biocathodes for electrosynthesis. Mateos, R. Bioelectrochemistry.

Gut Microbiome

Dietary Factors Modulate Colonic Tumorigenesis Through the Interaction of Gut Microbiota and Host Chloride Channels. Zhang Y. Molecular Nutrition Food Research

Metagenomic and metabolomic analyses unveil dysbiosis of gut microbiota in chronic heart failure patients. Cui, X. Scientific Reports

Nasal Microbiome

An insight into intestinal mucosal microbiota disruption after stroke.Stanley,D. Scientific Reports

Influence of pig farming on the human’s nasal microbiota: The key role of the airborne microbial communities. Kraemer, JG. Applied and Environmental Microbiology

Fecal Microbiome

Letters to Editor: Sucrase-isomaltase 15Phe IBS risk variant in relation to dietary carbohydrates and faecal microbiota composition. Thingholm L. Gut

Plant, Soil, and Water Microbiome

Soil contamination alters the willow root and rhizosphere metatranscriptome and the root-rhizosphere interactome. Yergeau, E. The ISME Journal

Indoor Microbiome

Microbiomes in Dishwashers: Analysis of the microbial diversity and putative opportunistic pathogens in dishwasher biofilm communities.Raghupathi, PK. Applied and Environmental Microbiology

Resitome

Characteristics of ARG-carrying plasmidome in the cultivable microbial community from wastewater treatment system under high oxytetracycline concentration. Shi, Y. Applied Microbioloby and Biotechnology

Animan Experiments and Microbiome

Characterizing the bacterial microbiota in different gastrointestinal tract segments of the Bactrian camel. He, J. Scientific Reports

Effect of atorvastatin on the gut microbiota of high fat diet-induced hypercholesterolemic rats. Khan, TJ. Scientific Reports

Protocol/Techniques

Fluorescence recovery allows the implementation of a fluorescence reporter gene platform applicable for the detection and quantification of horizontal gene transfer in anoxic environments. Pinilla, R. Applied and Environmental Microbiology

Microbiome Jobs

Part-Time Microbiology Laboratory Technician

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