March 3, 2017

Events and jobs
Postdoctoral Teaching and Learning Fellow in Microbiome Data Analysis – Department of Microbiology and Immunology (MICB) – University of British Columbia

Commercial Support Manager, Probiotics for Human Health & Microbiome – Hørsholm, Denmark – Chr. Hansen

Position in experimental biochemistry including microbiology – University of Warsaw

Microbiology Laboratory Technician – Milwaukee, WI – Aerotek

Human vaginal microbiome
Specific vaginal lactobacilli suppress the inflammation induced by lipopolysaccharide stimulation through downregulation of toll-like receptor 4 expression in human embryonic intestinal epithelial cells – Keisuke Tobita – Bioscience of Microbiota, Food and Health

Human gut microbiome
Editorial: The gut microbiota and psychiatric illness – Glenda MacQueen – Journal of Psychiatry and Neurosciece

Animal experiments
Understanding the mechanisms of zinc bacitracin and avilamycin on animal production: linking gut microbiota and growth performance in chickens – Eduardo Crisol-Martínez – Applied Microbiology and Biotechnology

Transition of the intestinal microbiota of dogs with age – Hiroaki Masuoka – Bioscience of Microbiota, Food and Health

Faecal microbiota transplantation protects against radiation-induced toxicity – Ming Cui – EMBO Molecular Medicine

Animal microbiome
Comparative analysis of gut microbiota of mosquito communities in central Illinois – Ephantus J. Muturi – PLoS Neglected Tropical Diseases

Plant, root, and soil microbiome
Community Structure, Species Variation, and Potential Functions of Rhizosphere-Associated Bacteria of Different Winter Wheat (Triticum aestivum) Cultivars – Aaron K Mahoney – Frontiers in Plant Science

Water and extremophile microbiome
Microbial community assembly and evolution in subseafloor sediment – Piotr Starnawski – PNAS

Phylogenetic Diversity and Anti-MRSA Activity of Halotolerant Actinobacteria from sediments in Great Salt Plains, Oklahoma – Ahmed H Gad – bioRxiv

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

Food microbiology
Boswellia serrata resin extract alleviates azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced colon tumorigenesis – YC Chou – Molecular Nutrition Food Research

A series of review articles on the FODMAP diet has been published in the most recent issue of the Journal of Gastroenterology and Hepatology
Review: Use of the low-FODMAP diet in inflammatory bowel disease – Peter R Gibson – Journal of Gastroenterology and Hepatology
Review: How to institute the low-FODMAP diet – Jacqueline S Barrett – Journal of Gastroenterology and Hepatology
Review: When the low FODMAP diet does not work – Emma P Halmos – Journal of Gastroenterology and Hepatology
Review: Nutritional, microbiological and psychosocial implications of the low FODMAP diet – Heidi Maria Staudacher – Journal of Gastroenterology and Hepatology

The spxB gene as a target to identify Lactobacillus casei group species in cheese – Maria Luisa Savo Sardaro – Food Microbiology

Bioinformatics
GMPR: A novel normalization method for microbiome sequencing data – Jun Chen – bioRxiv

Cohesion: A method for quantifying the connectivity of microbial communities – Cristina Herren – bioRxiv

Techniques
Microbial population dynamics in continuous anaerobic digester systems during start up, stable conditions and recovery after starvation – Nadieh de Jonge – Bioresource Technology

Microbes in the news
How Bacteria Interfere with Insect Reproduction – Ruth Williams – The Scientist
This references two important papers on Wolbachia:
A Wolbachia deubiquitylating enzyme induces cytoplasmic incompatibility – John F Beckmann – Nature Microbiology
Prophage WO genes recapitulate and enhance Wolbachia-induced cytoplasmic incompatibility – Daniel P LePage – Nature

Synopsis: Racing Bacteria – Katherine Wright – APS Physics

Meet green bacteria, airport’s eco-friendly toilet cleaners – Times of India

Assessing Host-Microbiota Relationships – Richard A Stein – Genetic Engineering and Biotechnology News

Bacteria from the ancient city of Troy – Caitlin Pepperell – Microbe Post

Gut bacteria determines the beneficial impacts of soy food on heart health – David Templeton – Pittsburgh Post-Gazette

Microbes on the market
Vaginal Microbiota May Affect Tenofovir Applied Intravaginally – John Schieszer – Infectious Disease Advisor

The Human Microbiome: Advancing New Frontiers in a Rapidly Emerging Market – PR Newswire – Yahoo Finance

New research data published in Frontiers in Microbiology confirm the microbiome’s potential to impact plant health – PR Newswire – Yahoo Finance

Microbiome Therapeutics Market Growth, Forecast and Value Chain 2017-2027 – Future Market Insights – OpenPR

Random Science
Editorial: Microbiome yarns: microbiomology of curly and straight hair – Kenneth Timmis – Microbial Biotechnology

March 1, 2017

Posted on March 1, 2017 by Anitha Isaiah

Today’s digest features interesting reviews on the tole of gut microbiota in chronic kidney disease, and biotoxicity of soils from Mars. Impact of altered gut microbiota on bone strength in mice. Enjoy!

Events and jobs

Technical Service Representative (Microbiology) – ThermoFisher Scientific – Lenexa, Kansas

General microbiome

Review: Microbe social skill: the cell-to-cell communication between microorganisms – Xi Zhao – Science Bulletin

Review: Creating new business, economic growth and regional prosperity through microbiome-based products in the agriculture industry – Brajesh K. Singh – Microbial Biotechnology

Review: The link between inflammation, bugs, the intestine and the brain in alcohol dependence – S Leclercq – Translational Psychiatry

Editorial: The human microbiome: an emerging tool in forensics – Jarrad T. Hampton-Marcell – Microbial Biotechnology

Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome – Ohad Manor – Cell Host and Microbe

Pregnancy and early life

Review: Transfer of maternal psychosocial stress to the fetus – Florian Rakers – Neuroscience & Biobehavioral Reviews

Vaginal microbiome

Survival of vaginal microorganisms in three commercially available transport systems – Allison L. DeMarco – Anaerobe

Human skin microbiome

Review: Towards personalized modification of microbial imbalances – J.E.E. Totté – British Journal of Dermatology

Human gut microbiome

Review: Meta-analysis of the human gut microbiome from urbanized and pre-agricultural populations – Leonardo Mancabelli – Environmental Microbiology

*Review: Gut microbiota in chronic kidney disease – Secundino Cigarran Guldris – Nefrología (English Edition)

Review: The clinical value of breath hydrogen testing – Chu K Yao – Journal of Gastroenterology and Hepatology

Commentary: Atopic dermatitis and gut microbiota – M. Lindberg – British Journal of Dermatology

Animal experiments

SYN-004 (ribaxamase), an Oral Beta-Lactamase, Mitigates Antibiotic-Mediated Dysbiosis in a Porcine Gut Microbiome Model – Sheila Connelly – Journal of Applied Microbiology

*Alterations to the Gut Microbiome Impair Bone Strength and Tissue Material Properties – Jason D Guss – Journal of Bone and Mineral Research

Plant, root, and soil microbiome

*Biotoxicity of Mars Soils: 2. Survival of Bacillus subtilis and Enterococcus faecalis in Aqueous Extracts Derived from Six Mars Analog Soils – Andrew C. Schuerger – Icarus

Food microbiology

Polyphenolic extracts of cherry (Prunus cerasus L.) and blackcurrant (Ribes nigrum L.) leaves as natural preservatives in meat products – Agnieszka Nowak – Food Microbiology

Probiotics / prebiotics

Effects of synbiotic supplementation on growth performance, carcass characteristics, meat quality and muscular antioxidant capacity and mineral contents in broilers – Yefei Cheng – Journal of the Science of Food and Agriculture

GH11 xylanase increases prebiotic oligosaccharides from wheat bran favouring butyrate-producing bacteria in vitro – Jonas Laukkonen Ravn – Animal Feed Science and Technology

Effects of Bacillus subtilis strains and the prebiotic Previda® on growth, immune parameters and susceptibility to Aeromonas hydrophila infection in Nile tilapia, Oreochromis niloticus – Samuel Addo – Aquaculture Research

Enhancing growth and resistance to Vibrio alginolyticus disease in catarina scallop (Argopecten ventricosus) with Bacillus and Lactobacillus probiotic strains during early development – Fernando Abasolo-Pacheco – Aquaculture Research

The association of a probiotic with a prebiotic (Flortec, Bracco) to improve the quality/quantity of spermatozoa in infertile patients with idiopathic oligoasthenoteratospermia: a pilot study – C. Maretti – Andrology

In vitro fermentation of oat β-glucan and hydrolysates by fecal microbiota and selected probiotic strains – Dong Ji-lin – Journal of the Science of Food and Agriculture

Microbes in the news

WHO: These 12 bacteria pose greatest risk to human health

A Bizarre Bacteria Could Be the Key to Controlling Mosquitoes

Flesh-eating bugs lurking on ATMs and killer bacteria found on phones

Microbes on the market

Proof-of-Concept Study Published in Clinical Microbiology and Infection Reports the Benefit of PathoQuest NGS-Based Metagenomics Test to Identify Clinically-Relevant Pathogens in Immunocompromised Patients Suspected of Infection

Anitha’s non-microbiology picks

Glass Microbiology at the At-Bristol Science Centre

Mysterious ‘Cosmic’ Jellyfish Spotted in Remote Ocean Depths

Unity Biotechnology: Investment In A Long And Healthy Life Becoming Possible

February 28, 2017

Posted on February 28, 2017 by Alyaa Mohamed

Events and jobs

Postdoctoral Fellow/Microbiology – University of Tennessee Health Science Center – Memphis, TN

QC Microbiology Analyst – Leidos – FREDERICK, MD US

General microbiome

Preprint: Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes – Kevin R. Theis – bioRxiv

Preprint: Genome-wide phenotypic analysis of growth, cell morphogenesis and cell cycle events in Escherichia coli – Manuel Campos – bioRxiv

Preprint: Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing E. coli – Nicole Stoesser – bioRxiv

Preprint: How to name and classify your phage: an informal guide – Evelien M Adriaenssens – bioRxiv

Pregnancy and early life

Antibiotic treatment at delivery shapes the initial oral microbiome in neonates – Luisa F. Gomez-Arango – Scientific reports

Multi-site human microbiome

A randomised clinical study to determine the effect of a toothpaste containing enzymes and proteins on plaque oral microbiome ecology – S. E. Adams – Scientific reports

Human skin microbiome

Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis – Teruaki Nakatsuji – Science translational medicine

Human vaginal microbiome

Bacterial species colonizing the vagina of healthy women are not associated with race – May A. Beamer – Anaerobes in the microbiome

Human gut microbiome

Combined Signature of the Fecal Microbiome and Metabolome in Patients with Gout – Tiejuan Shao – Frontiers in microbiology

Review: Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies – Sudarshan A. Shetty – FEMS-Microbiology reviews

The microbiome and systemic lupus erythematosus – Nurit Katz-Agranov – Immunologic Research

Animal microbiome

Unexplored Archaeal Diversity in the Great Ape Gut Microbiome – Kasie Raymann – mSphere

Plant, root, and soil microbiome

Plant Growth Promoting Bacteria Associated with Langsdorffia hypogaea-Rhizosphere-Host Biological Interface: A Neglected Model of Bacterial Prospection – Érica B. Felestrino – Frontiers in microbiology

Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees – Bram Beckers – Microbiome

Plant cultivars imprint the rhizosphere bacterial community composition and association networks – Yuji Jiang – Soil Biology and Biochemistry

Retention and survival of E. coli in stormwater biofilters: Role of vegetation, rhizosphere microorganisms and antimicrobial filter media – G.I. Chandrasena – Ecological Engineering

Nitrogen addition shifts the microbial community in the rhizosphere of Pinus tabuliformis in Northwestern China – Fenglian Lv – PLoS ONE

Investigation of the fungal community structures of imported wheat using high-throughput sequencing technology – Shi Y – PLoS ONE

Players over the Surface: Unraveling the Role of Exopolysaccharides in Zinc Biosorption by Fluorescent Pseudomonas Strain Psd – Anamika Upadhyay – Frontiers in Microbiology
Potential microbial contamination during sampling of permafrost soil assessed by tracers – Toke Bang-Andreasen – Scientific reports

Water and extremophile microbiome

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

Ubiquitous and persistent Proteobacteria and other Gram-negative bacteria in drinking water – Ivone Vaz-Moreira – Science of The Total Environment

Marine-Derived Biocatalysts: Importance, Accessing, and Application in Aromatic Pollutant Bioremediation – Efstratios Nikolaivits – Frontiers in microbiology

Marine Actinobacteria as a source of compounds for phytopathogen control: An integrative metabolic-profiling / bioactivity and taxonomical approach – Luz A. Betancur – PLoS ONE

Archaeal and bacterial communities in deep-sea hydrogenetic ferromanganese crusts on old seamounts of the northwestern Pacific – Shota Nitahara – PLoS ONE

A Proteomic Perspective on the Bacterial Adaptation to Cold: Integrating OMICs Data of the Psychrotrophic Bacterium Exiguobacterium antarcticum B7 – Rafael A. Baraúna – Proteomes

Beneficial Microorganisms for Corals (BMC): proposed mechanisms for coral health and resilience – Raquel Peixoto – Frontiers in microbiology

Science, publishing, and career

Preprint: Preprinting Microbiology – Patrick D. Schloss – bioRxiv

February 27, 2017

Posted on February 27, 2017 by cgarrettwilson

The ‘horseshoe effect’ in analyzing microbial niches; fecal microbiota transplantation (FMT) in immunocompromised individuals; effects of long-term ceftriaxone sodium administration on gut microbiota diversity; DNA extraction bias in soil microbial community analysis; and a multistrain probiotic clinical trial in NAFLD.

Events and jobs

Postdoctoral Fellow in Microbiology – University of Tennessee Health Science Center, Memphis, TN

QC Microbiology Analyst – Leidos – Frederick, MD

General microbiome
Uncovering the Horseshoe Effect in Microbial Analyses – James T. Morton – mSystems

Pregnancy and early life
Microbiome, autoimmunity, allergy, and helminth infection: The importance of the pregnancy period – Xian Chen – American Journal of Reproductive Immunology

Implications of intrapartum azithromycin on neonatal microbiota – Jenny Mei – The Lancet Infectious Diseases

Human respiratory microbiome
Restoring CFTR Function Reduces Airway Bacteria and Inflammation in People With Cystic Fibrosis and Chronic Lung Infections – Katherine B. Hisert – American Journal of Respiratory and Critical Care Medicine

Microbiome of the Lung in Patient with Idiopathic Pneumonia Syndrome (IPS) after HCT – Sachiko Seo – Biology of Blood and Marrow Transplantation

Oral and nasal microbiota in Parkinson’s disease – Pedro A.B. Pereira – Parkinsonism & Related Disorders

Human skin microbiome
N-acetylcysteine inhibits growth, adhesion and biofilm formation of Gram-positive skin pathogens – Daria Eroshenko – Microbial Pathogenesis

Human vaginal microbiome
Olegusella massiliensis gen. nov., sp. nov., strain KHD7T, a new bacterial genus isolated from the female genital tract of a patient with bacterial vaginosis – Khoudia Diop – Anaerobe

Bacterial species colonizing the vagina of healthy women are not associated with race – May A. Beamer – Anaerobe

The influence of sexual activity on the vaginal microbiota and Gardnerella vaginalis clade diversity in young women – Vodstrcil LA – PLoS One

Human gut microbiome
Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients – Eli Moss – bioRxiv

Long-term use of ceftriaxone sodium induced changes in gut microbiota and immune system – Yanjie Guo – Scientific Reports

Two dynamic regimes in the human gut microbiome – Sean M. Gibbons – PLoS Computational Biology

Review: The gut microbiome in human neurological disease: A review – Helen Tremlett – Annals of Neurology

The Effects of Moderate Whole Grain Consumption on Fasting Glucose and Lipids, Gastrointestinal Symptoms, and Microbiota – Danielle N. Cooper – Nutrients

Gut microbial profile is altered in primary biliary cholangitis and partially restored after UDCA therapy – Ruqi Tang – Gut

Randomised clinical trial: faecal microbiota transplantation for recurrent Clostridum difficile infection – fresh, or frozen, or lyophilised microbiota from a small pool of healthy donors delivered by colonoscopy – Z. D. Jiang – Alimentary Pharmacology and Therapeutics

Gut microbiota and systemic inflammation changes after bread consumption: The ingredients and the processing influence – Maykel Arias – Journal of Functional Foods

Review: Gut microbiome-based medical methodologies for early-stage disease prevention – Jing-Zhang Wong – Microbial Pathogenesis

The dual role of short fatty acid chains in the pathogenesis of autoimmune disease models – Mizuno M – PLoS One

Giardia duodenalis induces dysbiosis of human intestinal microbiota biofilms – Jennifer K. Beatty – International Journal for Parasitology

Animal experiments
Apple Polysaccharide inhibits microbial dysbiosis and chronic inflammation and modulates gut permeability in HFD-fed rats – Sheng Wang – International Journal of Biological Macromolecules

Animal microbiome
Metatranscriptomic profiling reveals linkages between the active rumen microbiome and feed efficiency in beef cattle – Fuyong Li – Applied and Environmental Microbiology

Plant, root, and soil microbiome
Review: Genomic dissection of host–microbe and microbe–microbe interactions for advanced plant breeding – Samuel Kroll – Current Opinion in Plant Biology

Differential sharing and distinct co-occurrence networks among spatially close bacterial microbiota of bark, mosses and lichens‬‬ – Ines Aline Aschenbrenner – Molecular Ecology

The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis – Sylwia Zielińska – Microbiology Open

High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils – Adrienne B. Narrowe – Environmental Microbiology

A comprehensive phylogenetic analysis of copper transporting P1B ATPases from bacteria of the Rhizobiales order uncovers multiplicity, diversity and novel taxonomic subtypes – Ciro Cubillas – Microbiology Open

Host-parasite-bacteria triangle: the microbiome of the parasitic weed Phelipanche aegyptiaca and tomato-Solanum lycopersicum (Mill.) as a host – Lilach Iasur Kruh – Frontiers in Plant Science

Diversity of root-associated fungi of Vaccinium mandarinorum along a human disturbance gradient in subtropical forests, China – Yanhua Zhang – Journal of Plant Ecology

Loss of soil microbial diversity may increase insecticide uptake by crop – Min Zhang – Agriculture, Ecosystems & Environment

The presence of aggressive ants is associated with insect visits to coffee flowers and floral microbe communities – Rachel L. Vannette – Basic and Applied Ecology

Metagenomic assessment of methane production-oxidation and nitrogen metabolism of long term manured systems in lowland rice paddy – P. Bhattacharyya – Science of the Total Environment

The Introduction of Woody Plants For Freshwater Wetland Restoration Alters The Archaeal Community Structure in Soil – Xiao-Yan Liu – Land Degradation & Development

A distinctive root-inhabiting denitrifying community with high N2O/(N2O+N2) product ratio – Chao Ai – Soil Biology and Biochemistry

Plant cultivars imprint the rhizosphere bacterial community composition and association networks – Yuji Jiang – Soil Biology and Biochemistry

Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees – Bram Beckers – Microbiome

Water and extremophile microbiome
Development of a prototype 16S rRNA gene-based microarray for monitoring planktonic actinobacteria in shrimp ponds – Jingjing Wang – International Aquatic Research

Serpentinization-influenced groundwater harbors extremely low diversity microbial communities adapted to high pH – Katrina I. Twing – Frontiers in Microbiology

Cold adaptation of the Antarctic haloarchaea Halohasta litchfieldiae and Halorubrum lacusprofundi – Timothy J. Williams – Environmental Microbiology

Diversity of crude oil-degrading bacteria and alkane hydroxylase (alkB) genes from the Qinghai-Tibet Plateau – Haozhi Long – Environmental Monitoring and Assessment

Ubiquitous and persistent Proteobacteria and other Gram-negative bacteria in drinking water – Ivone Vaz-Moreira – Science of the Total Environment

Acidicapsa ferrireducens sp. nov., Acidicapsa acidiphila sp. nov., and Granulicella acidiphila sp. nov.: novel acidobacteria isolated from metal-rich acidic waters – Carmen Falagán – Extremophiles

Synthetic extreme environments: overlooked sources of potential biotechnologically relevant microorganisms – Timothy Sibanda – Microbial Biotechnology

Acinetobacter halotolerans sp. nov., a novel halotolerant, alkalitolerant, and hydrocarbon degrading bacterium, isolated from soil – Ram Hari Dahal – Arhives of Microbiology

Physiological and comparative genomic analysis of Acidithiobacillus ferrivorans PQ33 provides psychrotolerant fitness evidence for oxidation at low temperature – Robert Ccorahua-Santo – Research in Microbiology

Genome-resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings – Sumayah F. Rahman – Microbiology Open

Food microbiology
Nondairy beverage produced by controlled fermentation with potential probiotic starter cultures of lactic acid bacteria and yeast – Ana Luiza Freire – International Journal of Food Microbiology

Probiotics / prebiotics
Targeting the Microbiota-Gut-Brain Axis: Prebiotics Have Anxiolytic and Antidepressant-like Effects and Reverse the Impact of Chronic Stress in Mice – Aurelijus Burokas – Biological Psychiatry

Review: Clinical effects of probiotics in cystic fibrosis patients: A systematic review – Stephanie Van Biervliet – Clinical Nutrition ESPEN

Effects of Multistrain Probiotic Supplementation on Glycemic and Inflammatory Indices in Patients with Nonalcoholic Fatty Liver Disease: A Double-Blind Randomized Clinical Trial – Abbaszadeh Sepideh – Journal of the American College of Nutrition

Microbes in the news
Glass Microbiology at the At-Bristol Science Centre – Culture Calling

Bacteria And Babies: A Scientific Debate – Part One – American Council on Science and Health

Reference: Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns – Maria G. Dominguez-Bello – PNAS

February 25, 2017

Posted on February 25, 2017 by barnettburns

Insight into the role of gut microbiome lipid metabolites in central nervous system diseases. A role of invasive plants in altering the soil microbiome. Evidence that microbiome alterations in Crohn’s disease are not genetically based.

Events and jobs

Research Scientist – Department of Microbiology – University of Illinois at Urbana-Champaign, USA

Part-Time Microbiology Instructor – Foothill-De Anza Community College District, California, USA

First Stage Researcher with background in environmental microbiology – Faculty of Biology, University of Warsaw, Poland

General microbiome

Altered antibiotic tolerance in anaerobic digesters acclimated to triclosan or triclocarban – Daniel E. Carey – Chemosphere

Antimicrobial Resistance and Molecular Characterization of Extended-Spectrum β-Lactamases and Other Escherichia coli Isolated from Food of Animal Origin and Human Intestinal Isolates – Krizman M – Journal of Food Protection

Human oral microbiome

Prospective, randomised, controlled study evaluating early modification of oral microbiota following admission to the intensive care unit and oral hygiene with chlorhexidine – Felipe Francisco Tuon – Journal of Global Antimicrobial Resistance

The potential effect of oral microbiota in the prediction of mucositis during radiotherapy for nasopharyngeal carcinoma -Xiao-Xia Zhu – EBioMedicine

Human urinary microbiome

*Special Issue Preface: Preface to the human microbiome in urologic health and disease – Daniel A. Shoskes – Annals of Translational Medicine

*Review: The mycobiome of the human urinary tract: potential roles for fungi in urology – A. Lenore Ackerman – Annals of Translational Medicine

Human vaginal microbiome

Longitudinal analysis of vaginal microbiota in women with recurrent vulvovaginal candidiasis – Ma X – Journal of Southern Medical University (Nan Fang Yi Ke Da Xue Xue Bao)

Human gut microbiome

The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred – Umer Zeeshan Ijaz – PLOS

Randomised clinical trial: faecal microbiota transplantation for recurrent Clostridum difficile infection – fresh, or frozen, or lyophilised microbiota from a small pool of healthy donors delivered by colonoscopy – Z.D Jiang – Alimentary Pharmacology and Therapeutics

Gut-brain axis: Role of lipids in the regulation of inflammation, pain and CNS diseases – Russo R – Current Medicinal Chemistry

What roles do colon stem cells and gap junctions play in the left and right location of origin of colorectal cancers? – James E. Trosko – Journal of Cell Communication and Signaling

Contributions of the Interaction between Dietary Protein and Gut Microbiota to Intestinal Health – Ma N – Current Protein and Peptide Science

*Review: Dietary Fiber Gap and Host Gut Microbiota – Han M – Protein Peptide Letters

Structural Modulation of Gut Microbiota during Alleviation of Antibiotic-Associated Diarrhea with Herbal Formula – Weijie Lv – International Journal of Biological Macromolecules

Association of diverse bacterial communities in human bile samples with biliary tract disorders: a survey using culture and polymerase chain reaction-denaturing gradient gel electrophoresis methods – E. Tajeddin – European Journal of Clinical Microbiology & Infectious Disease

Immunomodulatory Effects of Lactobacillus plantarumLp62 on Intestinal Epithelial and Mononuclear Cells – Thalis Ferreira dos Santos – BioMed Research International

How to modulate gut microbiota: diet, pre-probiotics or antibiotics? – Ponziani FR – Minerva Gastroenterologica E Dietologica

* Review: AISF position paper on nonalcoholic fatty liver disease (NAFLD): Updates and future directions – Italian Association for the Study of the Liver (AISF), Lonardo A – Digestive and Liver Disease

Clostridium difficile infection in acute flares of inflammatory bowel disease: A prospective study -Harry Sokol – Digestive and Liver Disease

Plant, root, and soil microbiome

Response of rhizosphere soil microbial to Deyeuxia angustifolia encroaching in two different vegetation communities in alpine tundra – Lin Li – Scientific Reports

Influence of phylogenetic conservatism and trait convergence on the interactions between fungal root endophytes and plants – Sevda Haghi Kia – The ISME Journal

Comparative fibre-degrading capacity in foals at immediate and late post-weaning periods – C. Faubladier – Cambridge Core

The effect of the source of microorganisms on adaptation of hydrolytic consortia dedicated to anaerobic digestion of maize silage – Krzysztof Poszytek – Anaerobe

Water and extremophile microbiome

Diversity of crude oil-degrading bacteria and alkane hydroxylase (alkB) genes from the Qinghai-Tibet Plateau – Haozhi Long – Environmental Monitoring and Assessment

Direct single-cell biomass estimates for marine bacteria via Archimedes’ principle – Nathan Cermak – The ISME Journal

Evidence for a role of viruses in the thermal sensitivity of coral photosymbionts – Rachel Ashley Levin – The ISME Journal

Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton – Ryan W Paerl – The ISME Journal

Elevated temperature increases carbon and nitrogen fluxes between phytoplankton and heterotrophic bacteria through physical attachment – Nestor Arandia-Gorostidi – The ISME Journal

Warming and nutrient enrichment in combination increase stochasticity and beta diversity of bacterioplankton assemblages across freshwater mesocosms – Lijuan Ren – The ISME Journal

Integration of Metagenomic and Stable Carbon Isotope Evidence Reveals the Extent and Mechanisms of Carbon Dioxide Fixation in High-Temperature Microbial Communities – Ryan de Montmollin Jennings – Frontiers in Microbiology

Seasonal Variation in Abundance and Diversity of Bacterial Methanotrophs in Five Temperate Lakes – Md Sainur Samad – Frontiers in Microbiology

Predominance of Viable Spore-Forming Piezophilic Bacteria in High-Pressure Enrichment Cultures from ~1.5 to 2.4 km-Deep Coal-Bearing Sediments below the Ocean Floor – Jiasong Fang – Frontiers in Microbiology

Metagenomics and resistome

Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection – Li-Guan Li – The ISME

Metabolomics

Assessment of the bimodality in the distribution of bacterial genome sizes – Hyun S Gweon – The ISME Journal

Genome of ‘Ca. Desulfovibrio trichonymphae’, an H₂-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut – Hirokazu Kuwahara – The ISME Journal

A family of interaction-adjusted indices of community similarity – Thomas Sebastian Benedikt Schmidt – The ISME Journal

Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates – Po-Hsiang Wang – The ISME Journal

Phylogenetic relationships among Staphylococcus aureus isolated from clinical samples in Mashhad, Iran – Farzad Khadem – Journal of Infection and Public Health

Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk-disease complex – Abraham Morales-Cruz – Molecular Plant Pathology

More microbes

Redox potential as a master variable controlling pathways of metal reduction by Geobacter sulfurreducens – Caleb E Levar – The ISME Journal

Coupled molecular and isotopic evidence for denitrifier controls over terrestrial nitrogen availability – Erin F E Lennon – The ISME Journal

Enhanced microbial electrosynthesis by using defined co-cultures – Jörg S Deutzmann – The ISME Journal

Temperature is a key factor in Micromonas–virus interactions – David Demory – The ISME Journal

Evolutionary convergence in experimental Pseudomonas populations – Peter A Lind – The ISME Journal

Microbes in the news

Are There Health Benefits To Exposing Our Immune Systems To Bacteria? – Forbes
Nutrition: Trust your gut instincts — whole grains are good for you – Los Angeles Daily News

There could be a surprising link between how people respond to a new cancer treatment and their microbiome – Lydia Ramsey – Business Insider

February 24, 2017

Posted on February 24, 2017 by anjacobson

Bioassay-guided metabolomics reveal new polyketide macrolactams from termite-associated actinomycete, the microbiota affects host antibody repertoire, artist makes agar molds of her face and grows bacteria on them, the fecal microbiota of Old World vultures.

Events and jobs

“Research Instructor – Microbiology & Immunology” at the Medical University of South Carolina

General microbiome

Review: Carcinogenesis and therapeutics: the microbiota perspective – Matthew C. B. Tsilimigras – Nature Microbiology

Pregnancy and early life

Review: Microbiome, autoimmunity, allergy, and helminth infection: The importance of the pregnancy period – Xian Chen – American Journal of Reproductive Immunology

Impact of microbial invasion of amniotic cavity and the type of microorganisms on short-term neonatal outcome in women with preterm labor and intact membranes – Teresa Cobo – Acta Obstetricia et Gynecologica Scandinavica

Human oral microbiome

Betel nut chewing, oral premalignant lesions, and the oral microbiome – Brenda Y. Hernandez – PLOS One

Human gut microbiome

Review: Gut Microbiota: A Potential Regulator of Neurodevelopment – Paola Tognini – Frontiers in Cellular Neuroscience

New evidences on the altered gut microbiota in autism spectrum disorders – Francesco Strati – Microbiome

Massilioclostridium coli gen. nov., sp. nov., a new member of the Clostridiaceae family isolated from the left colon of a 27-year-old woman – C. I. Lo – New Microbes and New Infections

Impact of humic acids on the colonic microbiome in healthy volunteers – Alexander Swidsinski – World Journal of Gastroenterology

Animal experiments

* IgD class switching is initiated by microbiota and limited to mucosa-associated lymphoid tissue in mice – Jin Huk Choi – PNAS

Editorial: Microbiome-dependent recombination shapes the host antibody repertoire – Alexandra A. Mushegian – Science Signaling

An Intestinal Farnesoid X Receptor-Ceramide Signaling Axis Modulates Hepatic Gluconeogenesis in Mice – Cen Xie – Diabetes

Editorial: Targeting the Gut Microbiota–FXR Signaling Axis for Glycemic Control: Does a Dietary Supplement Work Magic? – Show-Ling Shyng – Diabetes

Effects of xylanase supplementation on growth performance, nutrient digestibility, blood parameters, fecal microbiota, fecal score and fecal noxious gas emission of weaning pigs fed corn-soybean meal-based diet – Ruixia Lan – Animal Science Journal

Animal microbiome

Assessment of Ruminal Bacterial and Archaeal Community Structure in Yak (Bos grunniens) – Zhenming Zhou – Frontiers in Microbiology

Changes in Metabolically Active Bacterial Community during Rumen Development, and Their Alteration by Rhubarb Root Powder Revealed by 16S rRNA Amplicon Sequencing – Zuo Wang – Frontiers in Microbiology

Metataxonomics reveal vultures as a reservoir for Clostridium perfringens – Xiangli Meng – Emerging Microbes and Infections

The fecal microbiome of dogs with exocrine pancreatic insufficiency – Anitha Isaiah – Anaerobe

Plant, root, and soil microbiome

Host-parasite-bacteria triangle: the microbiome of the parasitic weed Phelipanche aegyptiaca and tomato-Solanum lycopersicum (Mill.) as a host – Lilach Iasur Kruh – Frontiers in Plant Science

Diversity of root-associated fungi of Vaccinium mandarinorum along a human disturbance gradient in subtropical forests, China – Yanhua Zhang – Journal of Plant Ecology

Effects of long-term heavy metals contamination on soil microbial characteristics in calcareous agricultural lands (Saiss plain, North Morocco) – A. Kouchou – Journal of Materials and Environmental Sciences

Global transcriptional response to salt shock of the plant microsymbiont Mesorhizobium loti MAFF303099 – Marta Laranjo – Research in Microbiology

Novosphingobium pokkalii sp nov, a novel rhizosphere-associated bacterium with plant beneficial properties isolated from saline-tolerant pokkali rice – Ramya Krishnan – Research in Microbiology

Assembly patterns of soil-dwelling lichens after glacier retreat in the European Alps – Juri Nascimbene – Journal of Biogeography

Soil classification predicts differences in prokaryotic communities across a range of geographically distant soils once pH is accounted for – Rachel Kaminsky – bioRxiv

Water and extremophile microbiome

Different types of diatom-derived extracellular polymeric substances drive changes in heterotrophic bacterial communities from intertidal sediments – Julio Bohorquez – Frontiers in Microbiology

Broadcast Spawning Coral Mussismilia hispida Can Vertically Transfer its Associated Bacterial Core – Deborah C. A. Leite – Frontiers in Microbiology

Built environment

Microbial diversity of a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment: integration of 16S rRNA gene amplicon and shotgun metagenomic sequencing – Tiago Palladino Delforno – MicrobiologyOpen

Metabolomics

* Macrotermycins A−D, Glycosylated Macrolactams from a Termite- Associated Amycolatopsis sp. M39 – Christine Beemelmanns – Organic Letters

compMS2Miner: an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets – William Matthew Bell Edmands – Analytical Chemistry

More microbes

Indole production provides limited benefit to Escherichia coli during co-culture with Enterococcus faecalis – Shelly L. Pringle – Archives of Microbiology

Microbes in the news

* Art Grows on You – Lara Medlam – Nouse

Beware! Are bacteria raising your oxidative stress? – Purna Kashyap – Science Translational Medicine

Microbes on the market

Finch Therapeutics Announces Strategic Collaboration with OpenBiome to Develop Microbiome Therapies for FDA Approval – Business Wire

February 23, 2017

Posted on February 23, 2017 by Anitha Isaiah

Today’s selection includes an interesting review on how bacteria keep their time. Long term ceftriaxon sodium usage alters gut microbiota and immune system. Clostridium perfringens toxin genes in the gut microbiota of autistic children. Taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic. Enjoy!

General microbiome

Distinct signatures of dental plaque metabolic byproducts dictated by periodontal inflammatory status. – Akito Sakanaka – Scientific Reports

*Review: Timing the day: what makes bacterial clocks tick? – Carl Hirschie Johnson – Nature Reviews Microbiology

Human urinary microbiome

Review: The female urinary microbiota, urinary health and common urinary disorders. – Linda Brubaker – Annals of Translational Medicine

Review: Questions and challenges associated with studying the microbiome of the urinary tract – Yige Bao – Annals of Translational Medicine

Review: The association between bacteria and urinary stones. – Andrew L. Schwaderer – Annals of Translational Medicine

Human nearly-sterile sites

The Conserved Phylogeny of Blood Microbiome – Malay Bhattacharyya – Molecular Phylogenetics and Evolution

Human gut microbiome

Review: The gut microbiome in human neurological disease: A review. – Helen Tremlett – Annals of Neurology

Review: Gut microbiome-based medical methodologies for early-stage disease prevention – Jing-Zhang Wang – Microbial Pathogenesis

Review: Gut microbiome and chronic prostatitis/chronic pelvic pain syndrome. – Hans C. Arora – Annals of Translational Medicine

*Long-term use of ceftriaxone sodium induced changes in gut microbiota and immune system. – Yanjie Guo – Scientific Reports

Note Elies Bik: This study was not performed in humans but in a horrible rat model that can only be qualified as torture. This does not test for depression but for extreme stress. Should not have performed. Proceed with extreme caution. Variations in gut microbiota and fecal metabolic phenotype associated with depression by 16S rRNA gene sequencing and LC/MS-based metabolomics. – Meng Yu – Journal of Pharmaceutical and Biomedical Analysis

Specific inulin-type fructan fibers protect against autoimmune diabetes by modulating gut immunity, barrier function and microbiota homeostasis. – Kang Chen – Molecular Nutrition and Food Research

Gut microbiota and oxalate homeostasis. – Marguerite Hatch – Annals of Translational Medicine

Tryptophan: A gut microbiota-derived metabolites regulating inflammation. – Lucie Etienne-Mesmin – World Journal of Gastrointestestinal Pharmacology

*Detection of Clostridium perfringens toxin genes in the gut microbiota of autistic children. – Sydney M. Finegold – Anaerobe

Animal experiments

Butyrate restores HFD induced adaptations in brain function and metabolism in mid-adult obese mice – Ilse A. C. Arnoldussen – International Journal of Obesity

Toxin-positive Clostridium difficile latently infect mouse colonies and protect against highly pathogenic C. difficile. – Lucie Etienne-Mesmin – Gut

Animal microbiome

Individual Signatures Define Canine Skin Microbiota Composition and Variability. – Anna Cuscó – Frontiers in Veterinary Science

Plant, root, and soil microbiome

Differential sharing and distinct co-occurrence networks among spatially close bacterial microbiota of bark, mosses and lichens‬‬. – Ines Aline Aschenbrenner – Molecular Ecology

Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change. – Lin Li – Ecology and Evolution

Water and extremophile microbiome

*Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic. – Etienne Yergeau – Scientific Reports

High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils. – Adrienne Narrowe – Environmental Microbiology

Food microbiology

Enhanced Control of Listeria monocytogenes by Enterococcus faecium KE82, a Multiple Enterocin–Producing Strain, in Different Milk Environments. – Elpinki Vandera – Journal of food protection

Probiotics / prebiotics

Review: Probiotics for prevention of urinary stones. – John C. Lieske – Annals of Translational Medicine

Review: Review of the mechanisms of probiotic actions in the prevention of colorectal cancer. – Sandra A. dos Reis – Nutrition Research

Phages and viruses

The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses – Lisa Zeigler Allen – mSystems

Microbes in the news

The Future Of Skin Care: Lotions That Feed Our Microbiome

Collapse of Aztec society linked to catastrophic salmonella outbreak

Smart’ bacteria remodel their genes to infect our intestines

Smallest CRISPR So Far Comes from Food Poisoning Bacteria

Anitha’s non-microbiology picks

An epigenetics gold rush: new controls for gene expression

Scientists discover 7 ‘Earthlike’ planets orbiting a nearby star

February 22, 2017

Posted on February 22, 2017 by xinhuang7

Here’s your daily routine. Autoregressive and non-autoregressive regimes in the human gut microbiome. The interaction between diet, microbiota and personalized nutrition. More topics to think about: reproducibility in the microbiome studies, intellectual property in the microbiome industry, and heavy rain brings fatal bugs to northern Californian dogs.

Events and jobs

The 3rd Annual Translational Microbiome Conference – April 11-13, 2017 – Boston, MA

Microbiology Laboratory Technician – ALS Life Sciences – Ireland

Field Sales Manager, Microbiology, Molecular Biology, Chemistry – Cromwell and Clark – UK

General microbiology

Vancomycin displays time-dependent eradication of mature Staphylococcus aureus biofilms – Virginia Post – Journal of Orthopaedic Research

Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment – James E. Gomez – eLife

Press: Genetic mutations that drive antibiotic resistance in bacteria – Science Daily

Global Proteomic Analyses of Macrophage Response to Mycobacterium tuberculosis Infection – Valerie Poirier – BioRxiv

Human gut microbiome

*Two dynamic regimes in the human gut microbiome – Sean M. Gibbons – PLoS Computational Biology

Human intestinal microbiota: Role in development and functioning of the nervous system – O. V. Averina and V. N. Danilenko – Microbiology

Editorial: How can the gut microbiota affect immune recovery in HIV-infected individuals? – Sergio Serrano-Villar – Future Microbiology

Review: The Influence of the Microbiome on Early-Life Severe Viral Lower Respiratory Infections and Asthma—Food for Thought? – Jason P. Lynch – Frontiers in Immunology

Review: “We are what our bacteria eat”: The role of bacteria in personalizing nutrition therapy in gastrointestinal conditions – Ruth Harvie – Journal of Gastroenterology and Hepatology

The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred – Umer Zeeshan Ijaz – PLoS One

Animal experiments

Not peer reviewed: Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructooligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing – Jose F Garcia-Mazcorro – PeerJ

Mouse: The influence of rosuvastatin upon the gastrointestinal microbiota and host gene expression profiles – James A. Nolan – American Journal of Physiology – Gastrointestinal and Liver Physiology

High-cholesterol diet does not alter gut microbiota composition in mice – Lidiya G. Dimova – Nutrition & Metabolism

The effect of gut microbiome on tolerance to morphine mediated antinociception in mice – Minho Kang – Scientific Reports

Mouse: Ambient Ultrafine Particle Ingestion Alters Gut Microbiota in Association with Increased Atherogenic Lipid Metabolites – Rongsong Li – Scientific Reports

Editorial: Sources of variation: Animal microbiota – Alexandra A. Mushegian – Science Signaling

The effects of amoxicillin treatment of newborn piglets on the prevalence of hernias and abscesses, growth and ampicillin resistance of intestinal coliform bacteria in weaned pigs – Jinhyeon Yun – PLoS One

Animal microbiome

Culture-independent genomics of a novel chlamydial pathogen of fish provides new insight into host-specific adaptations utilised by these intracellular bacteria – Alyce Taylor-Brown – Environmental Microbiology

Corals: Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach – Edward G Smith – The ISME Journal

Prevalence of AmpC- and Extended-Spectrum β-Lactamase-Harbouring Enterobacteriaceae in Faecal Flora of a Healthy Domestic Canine Population – D. A. Mathys – Zoonoses and Public Health

Different antibiotic growth promoters induce specific changes in the cecal microbiota membership of broiler chicken – Marcio C. Costa – PLoS One

Plant, root and soil microbiome

A Plant Bacterial Pathogen Manipulates Its Insect Vector’s Energy Metabolism – Nabil Killiny – Applied and Environmental Microbiology

Effective control of root-knot nematode disease with Pseudomonad rhizobacteria filtrate – Ishwar Prakash Sharma and A.K. Sharma – Rhizosphere

Biodiversity of aerobic methylobacteria associated with the phyllosphere of the southern Moscow region – E. N. Kaparullina – Microbiology

Epiphytic microorganisms degrading aromatic hydrocarbons from the phyllosphere of urban woody plants – O. I. Sazonova – Microbiology

Book chapter: Improving Soil Fertility and Soil Functioning in Cover Cropped Agroecosystems with Symbiotic Microbes – Yang Zhou – Agro-Environmental Sustainability

Book chapter: Role of Phosphate-Solubilising Microorganisms in Sustainable Agricultural Development – Rajesh Kumar and Beenu Shastri – Agro-Environmental Sustainability

Influence of rhinoceros beetle (Trypoxylus dichotomus septentrionalis) larvae and temperature on the soil bacterial community composition under laboratory conditions – Jinu Eo – Soil Biology and Biochemistry

Water and extremophile microbiome

Deep sequencing analysis of bacterial community structure of Soldhar hot spring, India – A. Sharma – Microbiology

Microbial community compositions in different functional zones of Carrousel oxidation ditch system for domestic wastewater treatment – Dong Xu – AMB Express

Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens – Jessica Chopyk – Microbiome

The interaction between the proliferating macroalga Asparagopsis taxiformis and the coral Astroides calycularis induces changes in microbiome and metabolomic fingerprints – Stéphane Greff – Scientific Reports

Bioinformatics

MetaGaAP: A Novel Pipeline to Estimate Community Composition and Abundance from Non-Model Sequence Data – Christopher Noune and Caroline Hauxwell – Biology

Techniques

DNA Barcoding for Fractured Reservoir Analysis – An Initial Investigation – Yuran Zhang – PROCEEDINGS, 42nd Workshop on Geothermal Reservoir Engineering

Novel approaches for the taxonomic and metabolic characterization of lactobacilli: Integration of 16S rRNA gene sequencing with MALDI-TOF MS and 1H-NMR – Claudio Foschi – PLoS One

Microbes in space

The Effect of High-Dose Ionizing Radiation on the Isolated Photobiont of the Astrobiological Model Lichen Circinaria gyrosa – Joachim Meeßen – Astrobiology

Phages and viruses

Non-classical phase diagram for virus bacterial coevolution mediated by clustered regularly interspaced short palindromic repeats – Pu Han and Michael W. Deem – Journal of the Royal Society Interface

Microbes in the news

Probiotics: IP Perspectives on the Microbiome – Jing Liu and Daniel Yarbrough – JDSupra

Targeting Gut Bacteria May Be The Key To Preventing Alzheimer’s – Carolyn Gregoire – The Huffington Post

Space Bacteria Draws Focus of Researchers – Robert Lee Hotz – Wall Street Journal (subscription required)

Irish experts key to battling bacteria – Niall Murray – Irish Examiner

Heavy Rains Bring Dog-Killing Bacteria to Northern California – Tex Dwokin – Care2

February 21, 2017

Posted on February 21, 2017 by Tiff

Events and jobs
Microbiology Analyst Level II – DTS Food Laboratories – Brisbane, AU

Microbial Menagerie is profiling #ActualLivingScientists, especially microbiologists! Visit here for more information, or sign up here!

4th International Symposium on the Environmental Dimension of Antibiotic Resistance – Aug 13-17, 2017 in Lansing, MI

5th Molecular Microbiology Meeting & 4th Midlands Molecular Microbiology Meeting (M4) – Sept 13-14, 2017 in Birmingham, UK

General microbiome
Metagenomic DNA sequencing for the diagnosis of intraocular infections – Thuy Doan – bioRxiv

Human skin microbiome
Bacterial biofilm in chronic lesions of hidradenitis suppurativa – H.C. Ring – British Journal of Dermatology

Human gut microbiome
Review: Bile acid control of metabolism and inflammation in obesity, type 2 diabetes, dyslipidemia and NAFLD – Oscar Chavez-Talavera – Gastroenterology

Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients – Eli Moss – bioRxiv

Isolation and high-dimensional phenotyping of gastrointestinal immune cells – Bruna A. David – Imumunology
Not focused on microbes – but may be of use to those working with these cells!

Water and extremophile microbiome
Oxygenic and anoxygenic photosynthesis in a microbial mat from an anoxic and sulfidic spring – Dirk de Beer – Environmental Microbiology

A six thousand-year record of climate and land-use change from Mediterranean seagrass mats – Lourdes Lopez-Merino – Journal of Ecology
There is a hidden section on fungi.

High-Throughput Metabolic Network Analysis and Metatranscriptomics of a Cosmopolitan and Streamlined Freshwater Lineage – Joshua J Hamilton – bioRxiv

Are oceanic fronts ecotones? Seasonal changes along the Subtropical Front show fronts as bacterioplankton transition zones but not diversity hotspots – Sergio E Morales – bioRxiv

Built environment
Genome-resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings – Sumayah F. Rahman – MicrobiologyOpen

Comparative analysis of metagenomes of Italian top soil improvers – F. Gigiliucci – Environmental Research
This does not seem available yet, so PubMed is linked rather than the paper.

Food microbiology
Diversity analysis and quantification of lactic acid bacteria in traditionally fermented yaks’ milk products from Tibet – Yan Ren – Food Biotechnology

Phages and viruses
Review: Risk of waterborne virus spread – review of survival of relevant fish and crustacean viruses in the aquatic environment and implications for control measures – Birgit Oidtmann – Reviews in Aquaculture

Microbial interactions
Local interactions lead to spatially correlated gene expression levels in bacterial groups – Simon van Vliet – bioRxiv

Science, publishing, and career
Broad Institute prevails in heated dispute over CRISPR patents – Sharon Begley – STAT News, along with six takeaways.

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Microbiome Digest – Bik's Picks

A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

March 3, 2017

March 2, 2017

March 1, 2017

February 28, 2017

February 27, 2017

February 25, 2017

Events and jobs

General microbiome

Human oral microbiome

Human urinary microbiome

Human vaginal microbiome

Human gut microbiome

Multi-site human microbiome

Animal experiments

Animal microbiome

Water and extremophile microbiome

Metagenomics and resistome

Metabolomics

More microbes

Microbes in the news

February 24, 2017

February 23, 2017

February 22, 2017

February 21, 2017