Category Archives: Human reproductive or urinary

August 17, 2017

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After two days of holidays on Microbiome Digest, today our blog is a bit longer with many papers in the part of water, soil and gut microbiome. Moreover, check new tools which can be used to deal with microbiome data (MicrobiomeDB and MetaMeta) and some interesting news about microbes in the “Microbes in the news” section. Enjoy the summer (in the lab or on the beach) while reading what is new in microbial world.

Events and jobs

Quality Control Manager, Microbiology, Technical Operations, Marlborough, Massachusetts, US

Assistant/Associate Professor – Microbiology and Immunology (Job ID #83258), Chicago, US

General microbiome

A macroecological theory of microbial biodiversity – William R. Shoemaker – Nature Ecology & Evolution

Community structure follows simple assembly rules in microbial microcosms – Jonathan Friedman – Nature Ecology & Evolution

Solagigasbacteria: Lone genomic giants among the uncultured bacterial phyla – Eric Becraft – bioRxiv

Review: Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life – Anja Spang – Science

Temperature-Dependent Alkyl Glycerol Ether Lipid Composition of Mesophilic and Thermophilic Sulfate-Reducing Bacteria – Arnauld Vinçon-Laugier – Frontiers in Microbiology

Advances in the analysis of “less-conventional” human body fluids: an overview of the ce- and hplc-ms applications in the years 2015–2017 – Monica Di Venere – Electrophoresis

Pregnancy and early life

Comparison of commercially-available preservatives for maintaining the integrity of bacterial DNA in human milk – Kimberly A.Lackey – Journal of Microbiological Methods

Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants – Danping Zhu – Scientific Reports

Multi-site human microbiome

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid –  Philipp Kirstahler – bioRxiv

Oral microbiome

Oral microbial community assembly under the influence of periodontitis – Hongju Chen – PLOS One

Subgingival Microbiome of Gingivitis in Chinese Undergraduates – Ke Deng – Chinese Journal of Dental Research

Human skin microbiome

Review: What is new in the pathophysiology of acne, an overview – B. Dréno – Journal of the European Academy of Dermatology and Venerology

The Role of the Skin and Gut Microbiome in Psoriatic Disease – Di Yan – Current Dermatology Reports

Human vaginal microbiome

The Vaginal Microbiome and its Potential to Impact Efficacy of HIV Pre-exposure Prophylaxis for Women –  Jennifer Velloza – Current HIV/AIDS Reports

The urinary microbiota of men and women and its changes in women during bacterial vaginosis and antibiotic treatment – Cornelia Gottschick – Microbiome

 

Human gut microbiome

Interactions between species introduce spurious associations in microbiome studies – Rajita Menon – bioRxiv

Bacteriophages in the gastrointestinal tract and their implications – Marzanna Łusiak-Szelachowska- Gut Pathogens

Analysis of intestinal microbial communities of cerebral infarction and ischemia patients based on high throughput sequencing technology and glucose and lipid metabolism –  Wenzhen Ji – Molecular Medicine Reports

Brain-gut-microbiota axis and mental health – Timothy G. Dinan – Psychosomatic Medicine

Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells – Mei San Tang – Inflamatory Bowel Diseases

Gut microbiome response to short-term dietary interventions in reactive hypoglycemia subjects – Sara Quercia –  Diabetes Metabolism Research and Reviews

The Impact of Western Diet and Nutrients on the Microbiota and Immune Response at Mucosal Interfaces – Donjete Statovci –  Frontiers in Immunology

Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects – Elena Buelow – Microbiome

Future prospect of faecal microbiota transplantation as a potential therapy in asthma – Y Kang  – Allergologia et Immunopathologia

Evidence of the Immune Relevance of Prevotella copri, a Gut Microbe, in Patients With Rheumatoid Arthritis – Annalisa Pianta – Arthritis & Rheumatology

Bacteriophages in the gastrointestinal tract and their implications – Marzanna Łusiak-Szelachowska – Gut Pathogens

The impact of age and gut microbiota on Th17 and Tfh cells in K/BxN autoimmune arthritis – Fei Teng – Arthritis Research & Therapy

Amoxapine Demonstrates Incomplete Inhibition of β-Glucuronidase Activity from Human Gut Microbiota – Wei Yang –  SLAS Discovery

Animal experiments 

Role of intestinal microbiome in American ginseng-mediated colon cancer protection in high fat diet-fed AOM/DSS mice –  C.-Z. Wang –  Clinical and Translational Oncology

The influence of the gut microbiota composition on Campylobacter jejuni colonization in chickens – Zifeng Han – Infection and Immunity

Animal microbiome 

Microbiota of little penguins and short-tailed shearwaters during development – Meagan L. Dewar – PLOS One

Transition of the intestinal microbiota of cats with age – Hiroaki Masuoka – PLOS One

Brief Communication: Climate warming reduces gut microbiota diversity in a vertebrate ectotherm – Elvire Bestion – Nature Ecology & Evolution

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

Comparison of the microbial population in rabbits and guinea pigs by next generation sequencing – Edward J. Crowley – PLOS One

Effects of contaminants of emerging concern on Megaselia scalaris (Lowe, Diptera: Phoridae) and its microbial community – Marcus J. Pennington – Scientific Reports

Plant, root, and soil microbiome

Influence of heavy metals on rhizosphere microbial communities of Siam weed (Chromolaena odorata (L.)) using a 16S rRNA gene amplicon sequencing approach – Thanyaporn Ruangdech – Agriculture and Natural Resources

Soil microbial community composition is correlated to soil carbon processing along a boreal wetland formation gradient – Eric J. Chapman – European Journal of Soil Biology

Bacteria from the rhizosphere and tissues of As-hyperaccumulator Pteris vittata and their role in arsenic transformation – Yong-HeHan – Chemosphere

Soil Characteristics Overwhelm Cultivar Effects on the Structure and Assembly of Root-Associated Microbiomes of Modern Maize – LinChen – Pedosphere

Comparative Transcriptomics of Bacillus mycoides Strains in Response to Potato-Root Exudates Reveals Different Genetic Adaptation of Endophytic and Soil Isolates – Yanglei Yi – Frontiers in Microbiology

Soil features in rookeries of Antarctic penguins reveal sea to land biotransport of chemical pollutants – Anna C. Santamans – PLOS One

Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism – Elias Broman – Microbiome

Effects of Short-Term Set-Aside Management Practices on Soil Microorganism and Enzyme Activity in China – Guangyu Li – International Journal of Environmental Research and Public Health

Microbial volatile compounds alter the soil microbial community – Jun Yuan –  Environmental Science and Pollution Research

Metagenomes from deep Baltic Sea sediments reveal how past and present environmental conditions determine microbial community composition – Ian P.G. Marshall – Marine Genomics

A More Comprehensive Community of Ammonia-Oxidizing Archaea (AOA) Revealed by Genomic DNA and RNA Analyses of amoA Gene in Subtropical Acidic Forest Soils – Ruo-Nan Wu – Microbial Ecology

Biophysical processes supporting the diversity of microbial life in soil – Robin Tecon – FEMS Microbiology Reviews

Water and extremophile microbiome 

Effect of short-term, diel changes in environmental conditions on active microbial communities in a salt marsh pond – Patrick J. Kearns – Aquatic Microbial Ecology

Linking Phylogenetic Identity and Biogeochemical Function of Uncultivated Marine Microbes with Novel Mass Spectrometry Techniques –  Samuel Bryson – Thesis, Oregon State University

Effects of alkali types on waste activated sludge (WAS) fermentation and microbial communities – Xiaoling Li – Chemosphere

Cyanobacterial Allelochemicals But Not Cyanobacterial Cells Markedly Reduce Microbial Community Diversity – Filipa Dias – Frontiers in Microbiology

Marinobacter aquaticus sp. nov., a moderately halophilic bacterium from a solar saltern –  María José León –  International Journal of Systematic and Evolutionary

Exploring the microbial diversity in Jordanian hot springs by comparative metagenomic analysis – Emad I. Hussein – Microbiology Open

Development of the first gene expression system for Salinicoccus strains with potential application in bioremediation of hypersaline wastewaters – Dahe Zhao – Applied Microbiology and Biotechnology

Bacterial biomes and potential human pathogens in irrigation water and leafy greens from different production systems described using pyrosequencing – M Jongman – Journal of Applied Microbiology

Report: Metabolic Flexibility Underpins Growth Capabilities of the Fastest Growing Alga – Haim Treves – Current Biology

The effects of morphology and neighbouring seaweeds on macroalgal microbiota – Thesis, The University of British Columbia

Relationships between and formation dynamics of the microbiota of consumers, producers, and the environment in an abalone aquatic system – Jing-Zhe Jiang – PLOS One

Vertical gradients in species richness and community composition across the twilight zone in the North Pacific Subtropical Gyre – Stephanie A. Sommer – Molecular Ecology

Metagenomic Insights into The Diversity and Functions of Microbial Assemblages in Tasik Kenyir Ecosystem – Mohd Ezhar Mohd Noor –  bioRxiv

The organizing effects of elevated CO2 on competition among estuarine primary producers – Craig S. Young – Scientific Reports

Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics – Kari M. Finstad – Frontiers in Microbiology

Draft Genome Sequence of Thiohalobacter thiocyanaticus Strain FOKN1, a Neutrophilic Halophile Capable of Thiocyanate Degradation – Mamoru Oshiki – Genome Announcements

Environmental drivers of a microbial genomic transition zone in the ocean’s interior – Daniel R. Mende – Nature Microbiology

Early photosynthetic eukaryotes inhabited low-salinity habitats – Patricia Sánchez-Baracaldo – PNAS

Microbial dynamics in petroleum oilfields and their relationship with physiological properties of petroleum oil reservoirs – Sunita J.Varjani – Bioresource Technology

Probiotics / prebiotics

Label-free quantitative proteomic analysis of Lactobacillus fermentum NCDC 400 during bile salt exposure – Gurjeet Kaur – Journal of Proteomics

Timely Use of Probiotics in Hospitalized Adults Prevents Clostridium difficile Infection: A Systematic Review With Meta-Regression Analysis – Nicole T. Shen – Gastroenterology

Phages and viruses

Phage in urban wastewater have the potential to disseminate antibiotic resistance – Gayathri Upeksha Gunathilaka – International Journal of Antimicrobial Agents

Bioinformatics

MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments – Francislon Silva de Oliveira – bioRxiv

MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling – Vitor C. Piro – Microbiome

A bioarchitectonic approach to the modular engineering of metabolism – Cheryl A. Kerfeld – Philosophical Transactions of the Royal Society B

Techniques

Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems – Joanne B. Emerson – Microbiome

A Note: A simple methodology to collect culturable bacteria from feces of Anopheles darlingi (Diptera: Culicidae) – Andrelisse Arruda – Journal of Microbiological Methods

Biotechnology

Predicting Microbial Fuel Cell Biofilm Communities and Bioreactor Performance using Artificial Neural Networks – Keaton Larson – Environmental Science & Technology

Microbial communities as biosensors for monitoring urban environments – Fangqiong Ling – Microbial Biotechnology

Perspectives for microbial community composition in anaerobic digestion: from abundance and activity to connectivity – Jo De Vrieze – Environmental Microbiology

Review: Purification and reuse of non-point source wastewater via Myriophyllum-based integrative biotechnology: A review – Liu F – Bioresource Technology

Improvements in algal lipid production: a systems biology and gene editing approach –  Avik Banerjee – Critical Reviews in Biotechnology

Microbes in the news 

Scientists Make Food From Bacteria, Water, Electricity, and a Whole Lot of Patience

Are you lonesome tonight? Why we, like Elvis, turn to food for comfort

Scientists See Bacteria Responding Electrically to Physical Stimuli for the First Time

Killing bacteria by hacking plastics with silver and electricity

Human Gut Microbes May Help Suppress MS, New Research Suggests 

Unexpected Microbial Life in Glacial Clay Could Offer Antibiotic Solutions

 

 

 

August 10, 2017

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Human urinary microbiome

The microbiome in urogenital schistosomiasis and induced bladder pathologies – Adewale S. Adebayo – PLoS Negl Trop Dis

Human gut microbiome

A 3-dimensional mathematical model of microbial proliferation that generates the characteristic cumulative relative abundance distributions in gut microbiomes – Lena Takayasu – PLoS ONE

Plant, root, and soil microbiome

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence – Yun Kit Yeoh – Nature Communications

Spatiotemporal Variation and Networks in the Mycobiome of the Wheat Canopy – Rumakanta Sapkota – Frontiers in Plant Science

Water and extremophile microbiome

Active microorganisms thrive among extremely diverse communities in cloud water – Pierre Amato – PLoS ONE

Seasonal Analysis of Microbial Communities in Precipitation in the Greater Tokyo Area, Japan – Satoshi Hiraoka – Frontiers in Microbiology

Built environment

The US National Mall Microbiome: A Census of Rhizosphere Bacteria Inhabiting Landscape Turf – Jo Anne Crouch – Crop Science

Microbes in the news

For Healthy Skin, Just Add…Bacteria? – Adam Hurly – GQ

Microbes on the market

Reality vs. hype: A macro look at the microbiome market – Juliet Preston – MedCityNews

Science, publishing, and career

Prof claims victory over ‘#manel’ at microbiome conference – Dan Jackson – Campus Reform

August 9, 2017

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Events and jobs

ASM Journals Fellowship – American Society for Microbiology

General microbiome

A mechanistic Individual-based Model of microbial communities – Pahala Gedara Jayathilake – PLoS ONE

Human vaginal microbiome

Group B Streptococcus and the vaginal microbiota – Geoffrey H Rosen – The Journal of Infectious Diseases

Animal experiments

The microbial metabolite desaminotyrosine protects from influenza through type I interferon – Ashley L. Steed – Science

Development of Inflammatory Bowel Disease is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice – Thomas Sharpton – bioRxiv

Plant, root, and soil microbiome

Microbial Communities as Ecological Indicators of Ecosystem Recovery Following Chemical Pollution – Stéphane Pesce – Microbial Ecotoxicology

Assessment of rhizosphere processes for removing water-borne macrolide antibiotics in constructed wetlands – Yiping Tai – Plant and Soil

Poor-Soil Rhizosphere Enriched with Different Microbial Activities Influence the Availability of Base Elements – Faten Dhaw – Open Journal of Ecology

Water and extremophile microbiome

Impacts of leachates from livestock carcass burial and manure heap sites on groundwater geochemistry and microbial community structure – Man Jae Kwon – PLoS ONE

Built environment

Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity – Emma Ransom-Jones – mSphere

Probiotics / prebiotics

Utilization of Pyrosequencing to Monitor the Microbiome Dynamics of Probiotic Treated Poultry (Gallus gallus domesticus) during Downstream Poultry Processing – Vamsy Priya Guttala – Agricultural Sciences

Lactobacillus casei CCFM419 attenuates type 2 diabetes via a gut microbiota dependent mechanism – Gang Wang – Food & Function

Bioinformatics

Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information – Albert Barberán – mSphere

Techniques

Isolation of bacteriophages from air using vacuum filtration technique: An improved and novel method – Bhagyashree Magare – Journal of Applied Microbiology

Microbes in the news

Exploring the Equine Microbiome – Stacey Oke – The Horse

Study: Kitchen sponges carry more bacteria than a toilet – Darren Sweeney – Fox8 Cleveland

July 6, 2017

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The microbiota of spotted hyenas, a review of potential interactions between olfactory sensation and the microbiome-gut-brain axis, phylogenetic analysis of host-microbe symbioses to examine the evolution of dependence over time.

General microbiome

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia – Sami Ben Said – Frontiers in Microbiology

The evolution of host-symbiont dependence – Roberta M Fisher – Nature Communications

Review: The microbiota revolution: Excitement and caution – Maria Rescigno – European Journal of Immunology

Review: The Microbiome and Blood Pressure: Can Microbes Regulate Our Blood Pressure? – Souhaila Al Khodor – Frontiers in Pediatrics

Human oral microbiome

Suppression of αvβ6 Integrin Expression by Polymicrobial Oral Biofilms in Gingival Epithelial Cells – Jiarui Bi – Scientific Reports

Proteomic shifts in multi-species oral biofilms caused by Anaeroglobus geminatus – Kai Bao – Scientific Reports

Human vaginal microbiome

Quantifying the human vaginal community state types (CSTs) with the species specificity index – Zhanshan Ma – PeerJ

Animal experiments

Effects of iron supplementation on growth, gut microbiota, metabolomics and cognitive development of rat pups – Erica E Alexeev – PLOS ONE

Review: Disruptive physiology: olfaction and the microbiome-gut-brain axis – John Bienenstock – Biological Reviews Cambridge Philosophical Society

Effects of melanin from Sepiella Maindroni ink (MSMI) on the intestinal Microbiome of mice – Hui Dong – BMC Microbiology

Animal microbiome

The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition – Emanuel Heitlinger – Frontiers in Cellular and Infection Microbiology

Plant, root, and soil microbiome

Perspective: The deep, hot biosphere: Twenty-five years of retrospection – Daniel R Colman – PNAS

Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus “Hitchhiker” from the Soybean Rhizosphere – Gabriel L Lozano – Genome Announcements

Warmer winters increase the rhizosphere carbon flow to mycorrhizal fungi more than to other microorganisms in a temperate grassland – Johanna Birgander – Global Change Biology

Negative plant-phyllosphere feedbacks in native Asteraceae hosts – a novel extension of the plant-soil feedback framework – Briana K Whitaker – Ecology Letters

Water and extremophile microbiome

Size and composition of subseafloor microbial community in the Benguela upwelling area examined from intact membrane lipid and DNA analysis – Thomas W Evans – Organic Geochemistry

FurukawaMarine microbes as a valuable resource for brand new industrial biocatalysts – Azadeh Beygmoradi – Biocatalysts and Agricultural Biotechnology

Antagonistic Interactions and Biofilm Forming Capabilities Among Bacterial Strains Isolated from the Egg Surfaces of Lake Sturgeon (Acipenser fulvescens) – M Fujimoto – Microbial Ecology

Probiotics/prebiotics

Effects of the probiotic Bifidobacterium animalis subsp. lactis on the non-surgical treatment of periodontitis. A histomorphometric, microtomographic and immunohistochemical study in rats – Milla S T Ricoldi – PLOS ONE

Phages and viruses

Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics – Mohammad Moniruzzaman – Nature Communications

Occurrence of Bacillus thuringensis Bacteriophages in the Egyptian Arid Soil – Amel S M Abo-Senna – International Journal of Virology and Molecular Biology

Bioinformatics

A conceptual framework for quality assessment and management of biodiversity data – Allan Koch Veiga – PLOS ONE

Techniques

SParticle, an algorithm for the analysis of filamentous microorganisms in submerged cultures – Joost Willemse – bioRxiv

Mapping-based all-RNA-information sequencing analysis (ARIseq) pipeline simultaneously revealed taxonomic composition, gene expression, and their correlation in an acidic stream ecosystem – Arisa Tsuboi – bioRxiv

More microbes

Review: Metabolic engineering pathways for rare sugars biosynthesis, physiological functionalities, and applications – A review – Muhammad Bilal – Critical Reviews in Food Science and Nutrition

Microbes in the news

Microbes aren’t the enemy, they’re a big part of who we are – Amy Loughman – Medical Xpress

What Cheese Can Tell Us About Antibiotic Resistance – Jason Tetro – Huffington Post Canada

Cases of recurrent Clostridium difficile infection are soaring – Medical Xpress

Helium ions reveal how viruses attack bacteria – ScienceDaily

June 28, 2017

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Human vaginal microbiome

Vaginal seeding or vaginal microbial transfer from the mother to the cesarean born neonate: a commentary regarding clinical management – Thor Haahr – BJOG

Human gut microbiome

*Review: The resilience of the intestinal microbiota influences health and disease – Felix Sommer – Nature Reviews Microbiology

Other human microbiome

Urinary catheter-associated microbiota change in accordance with treatment and infection status – Laetitia Bossa – PLOS ONE

Dynamics of the Oral Microbiota as a Tool to Estimate Time Since Death – Joe Adserias Garriga – Molecular Oral Microbiology

Animal experiments

Tuftsin-Phosphorylcholine maintains normal gut microbiota in collagen induced arthritic mice – Hila Ben-Amram – Frontiers in Microbiology

Animal microbiome

The Diet and Gut Microbial Communities of Two Closely Related Combtooth Blennies, Chasmodes saburrae and Scartella cristata – Peter J. Hundt – Copeia

Variation in the microbiome of the urogenital tract of koalas (Phascolarctos cinereus) with and without “wet bottom” – Alistair R. Legione – bioRxiv

Plant, root, and soil microbiome

Dominant Groups of Potentially Active Bacteria Shared by Barley Seeds become Less Abundant in Root Associated Microbiome – Luhua Yang – Frontiers in Plant Science

Understanding the variation of microbial community in heavy metals contaminated soil using high throughput sequencing – Honghong Guo – Ecotoxicology and Environmental Safety

Root Hair Mutations Displace the Barley Rhizosphere Microbiota – Senga Robertson-Albertyn – Frontiers in Plant Science

*Review: Below-ground connections underlying above-ground food production: a framework for optimising ecological connections in the rhizosphere – Franciska T. de Vries – Journal of Ecology

Rhizosphere microorganisms affected by soil solarization and cover cropping in Capsicum annuum and Phaseolus lunatus agroecosystems – Nancy Kokalis-Burelle – Applied Soil Ecology

Bacterial community dynamics in the rhizosphere of a long-lived, leguminous shrub across a 40-year age sequence – Xiaofan Na – Journal of Soils and Sediments

Microbial populations of stony meteorites: Substrate controls on first colonisers – Alastair W. Tait – Frontiers in Microbiology

Water and extremophile microbiome

Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage – Wenkai Teng – Minerals

Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer – Donald Pan – Frontiers in Microbiology

Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat – Jackson Z Lee – bioRxiv

Bioinformatics

Mixed Effect Dirichlet-Tree Multinomial for Longitudinal Microbiome Data and Weight Prediction – Yunfan Tang – arXiv

Segal’s Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project – James B. Pettengill – PeerJ

Techniques

Assembly and Tracking of Microbial Community Development within a Microwell Array Platform – Andrea C. Timm – JOVE

May 21, 2017

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Events and jobs

FULLY FUNDED POSTDOCTORAL FELLOW POSITION TO STUDY MICROBIOME-BEHAVIOR INTERACTIONS: PORTUGAL

General microbiome

Bioinorganic antimicrobial strategies in the resistance era – Regiel-Futyra et al, Coordination Chemistry Reviews

Biofilm microenvironment induces a widespread adaptive amino-acid fermentation pathway conferring strong fitness advantage in Escherichia coli – Letoffe et al, PLoS Genetics

A bloodstream infection by Ruminococcus gnavus in a patient with a gall bladder perforation – Kim et al, Anerobe

Microbial community compositional analysis for membrane bioreactor treating antibiotics containing wastewater – Zhu et al, Chemical Engineering Journal

Thermophilic Moorella thermoautotrophica-immobilized cathode enhanced microbial electrosynthesis of acetate and formate from CO2 – Yu et al, Bioelectrochemistry

Arumberiamorph structure in modern microbial mats: implications for Ediacaran palaeobiology – Kolesnikov et al, Bulletin de la Société Géologique de France

Succession in the petroleum reservoir microbiome through an oil field production lifecycle – Vigneron et al, ISME

Human respiratory microbiome

Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307 – Long et al, Mbio

Human oral microbiome

Pro-resolving mediators in the regulation of periodontal disease – Van Dyke, Molecular Aspects of Medicine

A structure-derived snap-trap mechanism of a multispecific serpin from the dysbiotic human oral microbiome – Goulas et al, Journal of Biological Chemistry

Human gut microbiome

Is frozen fecal microbiota transplantation as effective as fresh fecal microbiota transplantation in patients with recurrent or refractory clostridium difficile infection: a meta-analysis? – Tang et al, Diagnostic Microbiology and Infectious Disease

Weight-loss interventions and gut microbiota changes in overweight and obese patients: a systematic review – Seganfredo et al, Obesity Reviews

 

Dysbiosis of Gut Microbiome and Its Impact on Epigenetic Regulation – Lee et al, Journal of Clinical Epigenetics

Hypoxia and Inactivity Related Physiological Changes (Constipation, Inflammation) Are Not Reflected at the Level of Gut Metabolites and Butyrate Producing Microbial Community: The PlanHab Study – Sket et al, Frontiers in Physiology

Is there a potential role of fecal microbiota transplantation in the treatment of inflammatory bowel disease? – Eun, Intestinal Research

Diet and contaminants: driving the rise to obesity epidemics? – Di Ciaula and Portincasa, Current Medical Chemistry

How to: Establish and run a stool bank – Terveer et al, Clinical Microbiology and Infection

Animal experiments

Transforming growth factor β: a master regulator of the gut microbiota and immune cell interactions – Bauche and Marie, Clinical and Translational Immunology

Aloin, a Component of the Aloe Vera Plant Leaf, Induces Pathological Changes and Modulates the Composition of Microbiota in the Large Intestine of F344/N Male Rats – Boudraeu et al, Toxicology Science

Diabetes-associated microbiota in fa/fa rats is modified by Roux-en-Y gastric bypass – Arora et al, ISME

Absorption and degradation of sulfated polysaccharide from pacific abalone in in vitro and in vivo models – Ai et al, Journal of Functional Foods

Dietary ZnO nanoparticles alters intestinal microbiota and inflammation response in weaned piglets – Xia et al, Oncotarget

Dietary delta-tocotrienol favors abundance and diversity of beneficial microbiomes in obese male mice – Shen et al, FASEB

Bile acid binding resin prevents fat accumulation through intestinal microbiota in high-fat diet-induced obesity in mice – Kusumoto et al, Metabolism

In vitro ability of mastitis causing pathogens to form biofilms – Schonborn et al, Journal of Dairy Research

Dysbiosis of Intestinal Microbiota and Decreased Antimicrobial Peptide Level in Paneth Cells during Hypertriglyceridemia-Related Acute Necrotizing Pancreatitis in Rats – Huang et al, Frontiers in Microbiology

Effects of replacing Leymus chinensis with whole-crop wheat hay on Holstein bull apparent digestibility, plasma parameters, rumen fermentation, and microbiota – Niu et al, Scientific Reports

Physiological responses of insects to microbial fermentation products: insights from the interactions between Drosophila and acetic acid – Kim et al, Journal of Insect Physiology

Animal microbiome

Molecular detection by analysis of the 16S rRNA gene of fecal coliform bacteria from the two Korean Apodemus species (Apodemus agrarius and A. peninsulae) – Rahman et al, Genetics and Molecular Research

Detection and genetic characterization of Pasteurella multocida from alpaca (Vicugna pacos) pneumonia cases – Rimac et al, Tropical Animal Health and Production

Plant, root, and soil microbiome

Soil depth and crop determinants of bacterial communities under ten biofuel cropping systems – Zhang et al, Soil Biology and Biochemistry

Ground cover and slope exposure effects on micro- and mesobiota in forest soils – Gomez-Brandon et al, Ecological Indicators

Root chemical traits and their roles in belowground biotic interactions – Tsunoda and van Dam, Pedobiologia

Proteomics analysis of Fusarium proliferatum under various initial pH during fumonisin production – Li et al, Journal of Proteomics

Culturable bacterial diversity from the chestnut (Castanea sativa Mill.) phyllosphere and antagonism against the fungi causing the chestnut blight and ink diseases – Valverde et al, AIMS Microbiology

Water and extremophile microbiome

The removal of nitrogen compounds from farming wastewater – The effect of different carbon substrates and different microbial activators – Mankiewicz-Boczek et al, Ecological Engineering

How do physicochemical properties influence the toxicity of silver nanoparticles on freshwater decomposers of plant litter in streams? – Batista et al, Ecotoxicology and Environmental Safety

The heterogeneity of composition and assembly processes of the microbial community between different nutrient loading lake zones in Taihu Lake – Zhao et al, Applied Microbiology and Biotechnology

Towards a sustainable biobased industry – Highlighting the impact of extremophiles – Kruger et al, New Biotechnology

Distribution and genetic diversity of microbial populations in the pilot-scale biofilter for simultaneous removal of ammonia, iron and manganese from real groundwater – Cheng et al, Chemosphere

Pilot plant demonstration of stable and efficient high rate biological nutrient removal with low dissolved oxygen conditions – Keene et al, Water Research

Study on The Removal of Hexavalent Chromium from Contaminated Groundwater using Emulsified Vegetable Oil – Wen et al, Process Safety and Environmental Protection

A Novel Roseosiphophage Isolated from the Oligotrophic South China Sea – Yang et al, Viruses

Oxidative Stickland reactions in an obligate aerobic organism — amino acid catabolism in the Crenarchaeon Sulfolobus solfataricus – Stark et al, FEBS

Microbial Diversity in Extreme Marine Habitats and Their Biomolecules – Poli et al, Microorganisms

Methanogenic community was stable in two contrasting freshwater marshes exposed to elevated atmospheric CO2 – Lin et al, Frontiers in Microbiology

Plant-microbial interactions in agriculture and the use of farming systems to improve diversity and productivity – Ishaq, AIMS Microbiology

Effect of arbuscular mycorrhizal fungi on survival and growth of micropropagated Comanthera mucugensis spp. mucugensis (Eriocaulaceae) – Pereira et al, African Journal of Agricultural Research

Native communities of arbuscular mycorrhizal fungi associated with Capsicum annuum L. respond to soil properties and agronomic management under field conditions – Carballar-Hernandez et al, Agriculture, Ecosystems & Environment

Food microbiology

Microbial cell-free extracts affect the biochemical characteristics and sensorial quality of sourdough bread – Cavallo et al, Food Chemistry

Analysis of the microbiota of refrigerated chopped parsley after treatments with a coating containing enterocin AS-48 or by high-hydrostatic pressure – Burgos et al, Food Research International

Microorganisms Found in MPR and Packaged Produce and Their Detection Methods – Acar and Soyer, Minimally Processed Refridgerated Fruits and Vegetables, Food Engineering Series

Applications of Kluyveromyces marxianus in Biotechnology – Varela et al, Yeast Diversity in Human Welfare

Mucin- and carbohydrate-stimulated adhesion and subproteome changes of the probiotic bacterium Lactobacillus acidophilus NCFM – Celebioglu et al, Journal of Proteomics

Techniques

Metaproteomics-guided selection of targeted enzymes for bioprospecting of mixed microbial communities – Speda et al, Biotechnology Biofuels

Microbes in the news

Probiotics are popular, but some questions remain – Reading Eagle

May 5, 2017

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A PLoS One paper, with Dr. Bik as one of the co-authors, to characterize human gut microbiome and compare certain taxa against healthy profiles, the relationship between diet, circadian rhythm and gut microbiome, and much more.

Events

Webinar: Interactions between the Mycobiome and Bacteriome: Impact on Health and Disease – Zymo Research

The Real Impact of Rodent Diet on Microbiome and Gut Health Research Webinar Q&A – Taconic

Jobs

PhD position in microbiology – Uppsala Universitet

Microbiology Technician – Pharmaceutical Industry – Runcorn

QC Microbiology/Environmental Control Associate – Yoh’s client – Phoenix

Human multi-site microbiome

Preprint: Microbial Metagenome Of Urinary Tract Infection – Ahmed Moustafa – bioRxiv

Human skin microbiome

Inhibition of fracture healing in the presence of contamination by Staphylococcus aureus: Effects of growth state and immune response – Krystle A. Blanchette et al. – Journal of Orthopaedic Research

Human gut microbiome

Conditional postnatal deletion of the neonatal murine hepatic circadian gene, Npas2, alters the gut microbiome following restricted feeding – Derek S. O’Neil et al. – American Journal of Obstetrics and Gynecology

Press: Study: Alterations to circadian clock change the body’s response to diet – Amy Wallace – UPI

16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome – Daniel E. Almonacid and Laurens Kraal et al. (including our Elisabeth Bik) – PLoS One

Press: uBiome Publishes Peer-Reviewed Scientific Paper in PLOS ONE on First Version of Technology for Gut Health Screening Test – PRWeb

Commentary: The microbiota: an underestimated actor in radiation-induced lesions? – Harry Sokol and Timon Erik Adolph – Gut

Animal microbiome

Bacterial microbiota in small brown planthopper populations with different rice viruses – Shuo Li et al. – Journal of Basic Microbiology

Plant, root and soil microbiome

Small mammal activity alters plant community composition and microbial activity in an old-field ecosystem – Leigh C. Moorhead et al. – Ecosphere

Edaphic Conditions, Aboveground Carbon Stocks and Plant Diversity on Nickel Mine Tailings Dump Vegetated with Senegalia polyacantha (Willd.) Seigler & Ebinger – Edeth Mukaro et al. – Land Degradation & Development

Water and extremophile microbiome

Preprint: 290 Metagenome-assembled Genomes from the Mediterranean Sea: a resource for marine microbiology – Benjamin J Tully et al. – bioRxiv

Technology

Development of a multiplex real-time PCR assay for phylogenetic analysis of Uropathogenic Escherichia coli – Mojtaba Hasanpour and Akram Najafi – Journal of Microbiological Methods

New issue of the Journal of Microbiological Methods

Microbes in the news

Zika fight: Bacteria-laden mosquitoes unleashed in Florida to combat virus – Phil Keating – Fox News

Drought-quenching bacteria the future of farming? – Taylor Hartman – Daily Sun

Officials warn swimmers to avoid bacteria-laden parts of Lake Lanier – Ellen Eldridge – The Atlanta Journal-Constitution

Pathogenic bacteria train their defence in lakes and oceans – Phys.org

Cross-sector collaboration needed in fight against antimicrobial resistance – Sara Wyant – Agri-Pulse

Microbes on the market

Taconic Biosciences Expands Microbiome Portfolio – P&T Community

Careers

Microbiology Career Profiles – Market Specialist at Pacific Biosciences with Melissa Smith, PhD – ASM

April 26, 2017

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A series of commentary on the effects of microbiota on vaccines, a fascinating news release about a phage therapy against multi-drug resistant bacterial infection, and can our gut microbes tell us what to eat?

General microbiology

Evaluation of serotypes 5 and 8 capsular polysaccharides in protection against Staphylococcus aureus in murine models of infection – Brian L. Cheng – Human Vaccines & Immunotherapeutics

Do the Microbiota Influence Vaccines and Protective Immunity to Pathogens? If So, Is There Potential for Efficacious Microbiota-Based Vaccines? – Dan R Littman – Cold Spring Harbor Perspectives in Biology

Do the Microbiota Influence Vaccines and Protective Immunity to Pathogens? Engaging Our Endogenous Adjuvants – Nicholas Collins1 and Yasmine Belkaid – Cold Spring Harbor Perspectives in Biology

Do the Microbiota Influence Vaccines and Protective Immunity to Pathogens? Issues of Sovereignty, Federalism, and Points-Testing in the Prokaryotic and Eukaryotic Spaces of the Host-Microbial Superorganism – Andrew J. Macpherson – Cold Spring Harbor Perspectives in Biology

Web alert: Microbial therapeutics – Microbial Biotechnology

Human multi-site microbiome

The urinary microbiome and its contribution to lower urinary tract symptoms; ICI-RS 2015 – Marcus J. Drake – Neurourology and Urodynamics

Human gut microbiome

Doctoral Dissertation: The Effects of the Gut Microbiota on the Host Chromatin Landscape – Nicholas Paul Semenkovich – University of Washington, St. Louis

Tissue adaptation: Implications for gut immunity and tolerance – Ana M.C. Faria – Journal of Experimental Medicine

Animal experiments

Doctoral Dissertation, Mouse: The impact of malnutrition on host-microbe interactions in the intestine – Eric Brown – University of British Columbia

Mouse: Deciphering the mechanism of Huang-Lian-Jie-Du-Decoction on the treatment of sepsis by formula decomposition and metabolomics: enhancement of cholinergic pathways and inhibition of HMGB-1/TLR4/NF-κB signaling – Dingqiao Xu – Pharmacological Research

Dysbiosis of intestinal microbiota and decrease in paneth cell antimicrobial peptide level during acute necrotizing pancreatitis in rats – Jing Chen – PLoS One

Commensal bacteria and essential amino acids control food choice behavior and reproduction – Ricardo Leitão-Gonçalves – PLoS Biology

Press: How Gut Bacteria Tell Their Hosts What to Eat – Knvul Sheikh – Scientific American

Press: Are Gut Bacteria Driving Your Cravings? – Shayla Love – Vice

Maternal obese-type gut microbiota differentially impact cognition, anxiety and compulsive behavior in male and female offspring in mice – Annadora J. Bruce-Keller – PLoS One

Animal microbiome

Discovery of tauroursodeoxycholic acid biotransformation enzymes from the gut microbiome of black bears using metagenomics – Can Song – Scientific Reports

Diversity and functions of the sheep faecal microbiota: a multi-omic characterization – Alessandro Tanca – Microbial Biotechnology

New issue of Microbial Biotechnology is available online.

Plant, root and soil microbiome

Microbial communities associated with plants: learning from nature to apply it in agriculture – Fernando Dini Andreote and Michele de Cássia Pereira e Silva- Current Opinion in Microbiology

Life in earth – the root microbiome to the rescue? – Tim H Mauchline, Jacob G Malone – Current Opinion in Microbiology

Unique rhizosphere micro-characteristics facilitate phytoextraction of multiple metals in soil by the hyperaccumulating plant Sedum alfredii – Dandi Hou – Environmental Science & Technology

Water and extremophile microbiome

Doctoral Dissertation: Microbial community variation in an Arctic shelf seafloor – Tan Thi Nguyen – The Arctic University of Norway

Diversity Analysis and Bioresource Characterization of Halophilic Bacteria Isolated from a South African Saltpan – Ramganesh Selvarajan – Molecules

Arsenic metabolism in high altitude modern stromatolites revealed by metagenomic analysis – Daniel Kurth – Scientific Reports

Probiotics

VSL#3 probiotic differently influences IEC-6 intestinal epithelial cell status and function – Benedetta Cinque – Journal of Cellular Physiology

Phages and viruses

Press Release: Novel phage therapy saves patient with multidrug-resistant bacterial infection – University of California, San Diego

Technology

Preprint: Assessing species biomass contributions in microbial communities via metaproteomics – Manuel Kleiner – bioRxiv

Microbes in the news

Are Probiotics the Answer to Acne? – Kristen Fischer – Healthline News

Are the microbes in our gut affecting how fast we age? – Vincent Maffei – OUPblog

Bacteria May be Reason Some Foods Cause Heart Disease, Stroke – Maggie Fox – NBC News

The Slow-Motion Bacteria Buried Deep in the Ocean’s Floor – Veronique Greenwood – The Atlantic

Bacteria from India’s hot springs could help contain oil spills – Dinesh C Sharma – Firstpost

Bacteria causing diarrhoea deaths in children resists key antibiotic – Syed Akbar – The Times of India

Fat rats, slow sperm, and unhealthy bacteria – Lee Evslin – The Garden Island

April 22, 2017

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General microbiome

The Microbiome – The Biochemist (full issue)

Human vaginal microbiome

*Review: What fertility specialists should know about the vaginal microbiome: a review – Juan Antonio García-Velascoa – Reproductive BioMedicine Online

Animal experiments

Microbiota-Induced Antibodies Are Essential for Host Inflammatory Responsiveness to Sterile and Infectious Stimuli – Daniel Cisalpino – Journal of Immunology

Host-Microbe Co-metabolism Dictates Cancer Drug Efficacy in C. elegans – Timothy A. Scott – Cell

Bacterial Metabolism Affects the C. elegans Response to Cancer Chemotherapeutics – Aurian P. García-González – Cell

Examining the role of the microbiome in the effectiveness of colorectal cancer treatment – Jim Fessenden – UMass Medical School Communications

Neonatal acquisition of Clostridia species protects against colonization by bacterial pathogens – Yun-Gi Kim – Science

Infant mice lack microbes that help fight intestinal infection – EurekAlert!

Effects of different oligosaccharides at various dosages on the composition of gut microbiota and short-chain fatty acids in mice with constipation – Linlin Wang –  Food & Function

Short Term High Fat Diet Induces Obesity-Enhancing Changes in Mouse Gut Microbiota That are Partially Reversed by Cessation of the High Fat Diet – Yue Shang – Lipids

Animal microbiome

Resilience of the prokaryotic microbial community of Acropora digitifera to elevated temperature – Andrian P. Gajigan – Microbiology Open

Characterization of the gut microbiota in the golden takin (Budorcas taxicolor bedfordi) – Jun Chen – AMB Express

*Opinion: Mammary microbiota of dairy ruminants: fact or fiction? – Pascal Rainard – Veterinary Research

Determination of the microbial community features of Haemaphysalis flava in different developmental stages by high-throughput sequencing – Deyong Duan – Journal of Basic Microbiology

Plant, root, and soil microbiome

A signature of tree health? Shifts in the microbiome and the ecological drivers of horse chestnut bleeding canker disease – Britt Koskella – New Phytologist

Soil aggregates as massively concurrent evolutionary incubators – Matthias C Rillig – ISME

Responses of soil nitrous oxide production and abundances and composition of associated microbial communities to nitrogen and water amendment – Qing Wang – Biology and Fertility of Soils

*Editorial: Signalling in the phytomicrobiome: Understanding and harnessing the plant holobiont – Donald L. Smith – Frontiers in Plant Science

Warming enhances old organic carbon decomposition through altering functional microbial communities – Lei Cheng – ISME

Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau – Kaoping Zhang – Frontiers in Microbiology

Long-term straw returning affects Nitrospira-like nitrite oxidizing bacterial community in a rapeseed-rice rotation soil – Xuesong Luo – Journal of Basic Microbiology

Water and extremophile microbiome

Attenuation and modification of the ballast water microbial community during voyages into the Canadian Arctic – Mattias L. Johansson – Diversity and Distributions

Prokaryote species richness is positively correlated with eukaryote abundance in wastewater treatment biofilms – Inga Leena Angell – Letters in Applied Microbiology

*Review: The life sulfuric: Microbial ecology of sulfur cycling in marine sediments – Kenneth Wasmund – Environmental Microbiology Reports

Microbial community function in the bleaching disease of the marine macroalgae Delisea pulchra – Enrique Zozaya-Valdés – Environmental Microbiology

Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds – Christian Wurzbacher – ISME

Built environment

Diversity changes of microbial communities into hospital surface environments – Rika Yano – Journal of Infection and Chemotherapy

Bioinformatics

A Robust Symmetric Nonnegative Matrix Factorization Framework for Clustering Multiple Heterogeneous Microbiome Data – Yuanyuan Ma – Preprints

Assessing the Impact of Assemblers on Virus Detection in a De Novo Metagenomic Analysis Pipeline – Daniel J. White – Journal of Computational Biology

Techniques

Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut – Bentley Lim – Cell

‘Genetic scalpel’ can manipulate the microbiome, Yale study shows – Bill Hathaway – Yale News

What is broad-range 16S rDNA PCR? – Amani Patel – Microbiology and Infectious Disease

Microbes in the news

Microbiome: The Body’s Great Conductor –  Conan Milner – Epoch Times

Our Gut Microbes Have Circadian Rhythms, Too — And They Might Own Us – Jesslyn Shields – HowStuffWorks

The Bacteria That Can Help Find Land Mines – Daniel Akst – The Wall Street Journal

Science, publishing, and career

Grant Addresses Computational Challenges in Microbiome Research – Jacobs School of Medicine and Biomedical Science

April 19, 2017

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Exciting papers with locoregional effects of microbiota in a mouse model of colon carcinogenesis, maternal high fat diet detrimentally alterring epigenetic and gut microbiome pathways leading to fatty liver disease in mice.

Events and jobs

ASM Microbe 2017 : New Orleans

QC Microbiology Product Testing Associate – Experis : Irvine, CA
General microbiome

Review: Applying the design-build-test paradigm in microbiome engineering – Hoang Long Pham – Current Opinion in Biotechnology

Cohort Profile: African Collaborative Center for Microbiome and Genomics Research’s (ACCME) Human Papillomavirus (HPV) and Cervical Cancer Study – Sally N. Adebamowo – International Journal of Epidemiology

Review: Cultured microbes represent a substantial fraction of the human and mouse gut microbiota – Ilias Lagkouvardos – Gut Microbes

Human skin microbiome

A distinct cutaneous microbiota pofile in autoimmune bullous disease patients – Mor Miodovnika – Experimental Dermatology

Human gut microbiome

Review : A psychology of the human brain–gut–microbiome axis – Andrew P. Allen – Social and Personality Psychology Compass

Multivariate modelling of faecal bacterial profiles of patients with IBS predicts responsiveness to a diet low in FODMAPs – Sean M P Bennet – Gut

Animal microbiome

Temporal changes in cutaneous bacterial communities of terrestrial- and aquatic- phase newts (Amphibia) – Joana Sabino-Pinto – Environmental Microbiology

The low diverse gastric microbiome of the jellyfish Cotylorhiza tuberculata is dominated by four novel taxa – Tomeu Viver – Environmental Microbiology

Studying the effect of administration route and treatment dose on the selection of enrofloxacin resistance in commensal Escherichia coli in broilers – Ilias Chantziaras -Journal of Antimicrobial Chemotherapy

The skin microbiome of the Common thresher shark (Alopias vulpinus) has low taxonomic and potential metabolic β-diversity – Michael P. Doane – Environmental Microbiology Reports

Animal experiments

Intestinal, extra-intestinal and systemic sequelae of Toxoplasma gondii induced acute ileitis in mice harboring a human gut microbiota – Eliane von Klitzing – PLOS ONE

Effects of the inclusion of a Bacillus direct-fed microbial on performance parameters, bone quality, recovered gut microflora, and intestinal morphology in broilers consuming a grower diet containing corn distillers dried grains with solubles – J. D. Latorre – Poultry Science

Effect of high-fat diet and growth stage on the diversity and composition of intestinal microbiota in healthy bovine livestock – Shengyin Jiao – Journal of the Science of Food and Agriculture

*Locoregional effects of microbiota in a preclinical model of colon carcinogenesis – Sarah Tomkovich – Cancer Research

Selection of Cholesterol-Lowering Lactic Acid Bacteria and its Effects on Rats Fed with High-Cholesterol Diet – Yufang Liu – Current Microbiology

*Enhanced offspring predisposition to steatohepatitis with maternal high-fat diet is associated with epigenetic and microbiome alterations – Umesh D. Wankhade – PLOS ONE

Plant, root, and soil microbiome

Archaea and bacteria mediate the effects of native species root loss on fungi during plant invasion – Steven D Mamet- The ISME Journal

An acid-tolerant ammonia-oxidizing γ-proteobacterium from soil – Masahito Hayatsu – The ISME Journal

Investigation of Arsenotrophic Microbiome in Arsenic-Affected Bangladesh Groundwater – Munawar Sultana – Groundwater

Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses – Patricia Moya – Plos ONE

Tuber indicum shapes the microbial communities of ectomycorhizosphere soil and ectomycorrhizae of an indigenous tree (Pinus armandii) – Qiang Li – Plos ONE

The ‘known’ genetic potential for microbial communities to degrade organic phosphorus is reduced in low-pH soils – Ian D. E. A. Lidbury – Microbiology Open

Shifting microbial communities sustain multiyear iron reduction and methanogenesis in ferruginous sediment incubations – M. S. Bray – Gebiology

Water and extremophile microbiome

Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats – Dimitry Y Sorokin – The ISME Journal

Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system – Laura A Sauder – The ISME Journal

Minireview: Microbial ecology of mountain glacier ecosystems: Biodiversity, ecological connections, and implications of a warming climate – Scott Hotaling – Environmental Microbiology

Probiotics / prebiotics
Colonic gas homeostasis: Mechanisms of adaptation following HOST-G904 galactooligosaccharide use in humans – M. Mego – Neurogastroenterology and Motility

Techniques

Stochastically reduced communities—Microfluidic compartments as model and investigation tool for soil microorganism growth in structured spaces – Jialan Cao – Engineering in Life Sciences

Protocol : Metagenomics and CAZyme Discovery – Benoit J. Kunath – Protein-Carbohydrate Interactions : Methods in Molecular Biology

The resident microflora of voided midstream urine of healthy controls: standard versus expanded urine culture protocols – L. Coorevits – European Journal of Clinical Microbiology & Infectious Diseases

Microbes in the news

Study finds amoeba ‘grazing,’ killing bacteria usually protected by film

How Bacteria-Laden Beetle Poop Is Killing American Squash and Melons

Glowing bacteria detect buried landmines

Science, publishing, and career

Saturday, Science Advocates Prepare for a Long March

Anitha’s non-microbiology picks

Research unlocks molecular key to animal evolution and disease

Cumulative culture can emerge from collective intelligence in animal groups – Takao Sasaki – Nature Communications