Category Archives: Water microbiome

December 9, 2015

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Student activity about the microbiome that uses pasta, nutritional supplementation in Malawian infants, fungi and drywall, and microbial aerosols from soiled hospital linens.

General microbiome

Cool student activity: Modeling the Dynamic Digestive System Microbiome – Anne M. Estes – Journal of Microbiology & Biology Education

Pregnancy and birth

Persistent microbial dysbiosis in preterm premature rupture of membranes from onset until delivery – Elizabeth A. Baldwin – PeerJ

No effect of supplementation: Gut microbiota in Malawian infants in a nutritional supplementation trial – Yin Bun Cheung – Tropical Medicine & International Health

Human vaginal microbiome

Bacterial vaginosis and inflammatory response showed association with severity of cervical neoplasia in HPV-positive women – Juçara Maria de Castro-Sobrinho – Diagnostic Cytopathology

Human gut microbiome

Review: Gut Microbiota Modulation and Mucosal Immunity: Focus on Rifaximin – Loris R. Lopetuso – Mini-Reviews in Medicinal Chemistry

Animal microbiome

The effects of omeprazole therapy on bacterial colonization of the pharynx in healthy dogs – Lauren A. Sullivan – Journal of Veterinary Emergency and Critical Care

Water microbiome

Spatial Patterns in Biofilm Diversity across Hierarchical Levels of River-Floodplain Landscapes – Marc Peipoch – PLOS ONE

 

Built environment microbiome

Moisture parameters and fungal communities associated with gypsum drywall in buildings – Sandra Dedesko – Microbiome

A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses – Thomas Weinmaier – Microbiome

Microbial aerosol liberation from soiled textiles isolated during routine residuals handling in a modern health care setting – Alina Handorean – Microbiome

Phages and viruses

Better together: bacteriophage combinations significantly reduce Clostridium difficile growth in vitro and proliferation in vivo – Janet Y. Nale – Antimicrobial Agents and Chemotherapy

Infection and transplantation

A genetic modifier of the gut microbiome influences the risk of GVHD and bacteremia following HSCT – Ahmad Rayes – Biology of Blood and Marrow Transplantation

World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data Synthesis – Martyn D. Kirk – PLOS Medicine

Functional foods

A novel consortium of Lactobacillus rhamnosus and Streptococcus thermophilus for increased access to functional fermented foods – Remco Kort – Microbial Cell Factories

Changes in the Milk Metabolome of the Giant Panda (Ailuropoda melanoleuca) with Time after Birth – Three Phases in Early Lactation and Progressive Individual Differences – Tong Zhang – PLOS ONE

Bioinformatics and metagenomics

Small Sample Kernel Association Tests for Human Genetic and Microbiome Association Studies – Jun Chen – Genetic Epidemiology

Microbes in the news

Questions About the Science Of Beer – Matt Shipman – NC State University News

Guest Post – Stadium Seat Bacteria – PeerJ – David Coil

How microbes in your gut today hold clues to tomorrow’s medicines: For the second episode of “Science Happens,” we hung out with Pamela Silver, a scientist who wants to hack the microbiome – Carl Zimmer – STAT news

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December 8, 2015

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The CF microbiome, microbes attaching to glycoproteins in sweat, gut bacteria make cockroach poop smell attractive for other cockroaches, mycobiome of South African Cabernet vines, and seasonality of Japanese cherry orchard soil fungi.

General microbiome

Perspective: Behavioral Microbiomics: A Multi-Dimensional Approach to Microbial Influence on Behavior – Adam C.-N. Wong – Frontiers in Microbiology

Research highlight: Microbiota-based nutrition plans – Cláudio Nunes-Alves – Nature Reviews Microbiology

Pregnancy and birth

Maternal risk factors for abnormal vaginal flora during pregnancy – Cecilia Tibaldi – International Journal of Gynecology & Obstetrics

Human respiratory microbiome

MiniReview: The cystic fibrosis microbiome in an ecological perspective and its impact in antibiotic therapy – Andreia P. Magalhães – Applied Microbiology and Biotechnology

Human oral microbiome

Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China – Xingdong Chen – PLOS ONE

Human skin microbiome

Sweating the small stuff: Glycoproteins in human sweat and their unexplored potential for microbial adhesion – Robyn A Peterson – Glycobiology

Human gut microbiome

Gut microbiota manipulation with prebiotics in patients with non-alcoholic fatty liver disease: a randomized controlled trial protocol – BMC Gastroenterology

Review: Current roles of specific bacteria in the pathogenesis of inflammatory
bowel disease – Lucy McMullen – Microbiology

Animal and bioreactor models

Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease – M Llopis – Gut

Development of a Laboratory Model of a Phototroph-Heterotroph Mixed-Species Biofilm at the Stone/Air Interface – Federica Villa – Frontiers in Microbiology

Animal microbiome

Gut bacteria mediate aggregation in the German cockroach – Ayako Wada-Katsumata – PNAS

The deep-sea glass sponge Lophophysema eversa harbors potential symbionts responsible for the nutrient conversions of carbon, nitrogen and sulfur – Ren-Mao Tian – Environmental Microbiology

Plant, root, and soil microbiome

The Anti-Phytophthora Effect of Selected Potato-Associated Pseudomonas Strains: From the Laboratory to the Field – Anouk Guyer – Frontiers in Microbiology

Defoliation reduces soil biota – and modifies stimulating effects of elevated CO2 – Marie Dam – Ecology and Evolution

Sequence-based Analysis of the Vitis vinifera L. cv Cabernet Sauvignon Grape Must Mycobiome in Three South African Vineyards Employing Distinct Agronomic Systems – Mathabatha E. Setati – Frontiers in Microbiology

Paradox of plant growth promotion potential of rhizobacteria and their actual promotion effect on growth of barley (Hordeum vulgare L.) under salt stress – Massimiliano Cardinale – Microbiological Research

Survey of Annual and Seasonal Fungal Communities in Japanese Prunus mume Orchard Soil by Next-Generation Sequencing – Yoshinao Aoki – Advances in Microbiology

Actinobacterial Diversity in the Sediments of Five Cold Springs on the Qinghai-Tibet Plateau – Jian Yang – Frontiers in Microbiology

Bacterial diversity assessment of pristine mangrove microbial community from dhulibhashani, sundarban using 16S rRNA gene tag sequencing – Pijush Basak – Genomics Data

Microbialites in the shallow-water marine environments of the Holy Cross Mountains (Poland) in the aftermath of the Frasnian–Famennian biotic crisis – Michał Rakociński – Global and Planetary Change

No tillage combined with crop rotation improves soil microbial community composition and metabolic activity – Bingjie Sun – Environmental Science and Pollution Research

Assessing the contribution of fallen autumn leaves to airborne fungi in an urban environment – Peter J. Irga – Urban Ecosystems

Water and extremophile microbiome

Weak Coherence in Abundance Patterns Between Bacterial Classes and Their Constituent OTUs Along a Regulated River – Clara Ruiz-González – Frontiers in Microbiology

Combined Culture-Based and Culture-Independent Approaches Provide Insights into Diversity of Jakobids, an Extremely Plesiomorphic Eukaryotic Lineage – Tomáš Pánek – Frontiers in Microbiology

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics – Kuei-Han Lin – BMC Genomics

Waste treatment

Microbial community structure associated with the high loading anaerobic codigestion of olive mill and abattoir wastewaters – Hana Gannoun – Bioresource Technology

Microbial analysis of in situ biofilm formation in drinking water distribution systems: implications for monitoring and control of drinking water quality – Isabel Douterelo – Environmental Biotechnology

Food microbiology

Pyrosequencing reveals bacterial diversity in Korean traditional wheat-based nuruk – Jyotiranjan Bal – Journal of Microbiology

Metagenomics and bioinformatics

Hunting Down Frame Shifts: Ecological Analysis of Diverse Functional Gene Sequences – Michal Strejcek – Frontiers in Microbiology

GenomeTester4: a toolkit for performing basic set operations – union, intersection and complement on k-mer lists – Lauris Kaplinski – GigaScience

Microbes in the news

Cockroaches communicate via bacteria in their feces – Elizabeth Pennisi – Science Magzine

MSU professor trekking to the Amazon to study bacteria of insects that spread disease
– Anne Cantrell, MSU News Service – Bozeman Daily

Bacterial Biofilms: A Charged Environment – Kathryn Calkins – Biomedical Beat

Maintaining Wellness, Starting From Your Gut – Julie Chen – Huffington Post

Fall into Fungi – Alex Alexiev – MicroBEnet

Caps can play a part in cleaning water, not just bottling it – Jim Johnson – Plastic News

Dirty Yamuna water harbours drug-resistant bacteria – Neetu Chandra Sharma – Daily Mail India

Cooperating bacteria isolate cheaters – Phys.org

What you should know about this ‘new’ STD: interview with Raquel Dardik – Kristine Thomason – CNN

Bacteria Hysteria

Bacteria tests: What’s growing beneath your feet? – Alex Osiadacz – KLTV

Science, publication, and career

Five selfish reasons to work reproducibly – Florian Markowetz – Genome Biology

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December 7, 2015

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Not many new microbiome papers, but a nice oversight of the microbiological quality of Rio de Janeiro’s Guanabara Bay, where the 2016 Olympics will be held.

Also, there was an interesting discussion online yesterday on IBM’s new campaign aimed to get more women interested to join them – which backfired and was pulled. IBM was trying to recruit more women with a video called “Hack a Hairdryer”, showing how you can use a hairdryer to iron your clothes or blow confetti. It was unclear how emphasizing feminine applications was supposed to attract smart women wanting to work at a computer company.

HackAHairDryer

Hack a hairdryer: Campaign aimed at women suddenly backfires – BBC

IBM Asks Women In Tech To Hack Hair Dryers, Women Tweet Back To Tell IBM It’s Not The 1950s – Sarah Buhr – Tech Crunch

Remember Massacred Women Engineers with a Hairdryer Hackathon – Mika McKinnon- Gizmodo

Jobs (posting again)

Two job openings in our lab / UCSF School of Dentistry (San Francisco) for our hyposalivation project: Full time study coordinator and Part time dental assistant (20 hours per week)

Animal microbiome

DGGE: Microbiological quality and bacterial diversity of the tropical oyster Crassostrea rhizophorae in a monitored farming system and from natural stocks – M.T. Silva Neta – Genet. Mol. Res

Plants, roots, and soil microbiome

Soil bacterial community responses to warming and grazing in a Tibetan alpine meadow – Yaoming Li – FEMS Microbiology Ecology

Arbuscular Mycorrhizal Fungi for the Biocontrol of Plant-Parasitic Nematodes: A Review of the Mechanisms Involved – Nele Schouteden – Frontiers in Microbiology

Prokaryotes in Subsoil—Evidence for a Strong Spatial Separation of Different Phyla by Analysing Co-occurrence Networks – Marie Uksa – Frontiers in Microbiology

Water microbiome

Environmental and Sanitary Conditions of Guanabara Bay, Rio de Janeiro – Giovana O. Fistarol – Frontiers in Microbiology

Microbes in the news

Metformin Users Have Different Gut Bugs: The popular type 2 diabetes drug may cause profound changes in patients’ microbiomes – Kerry Grens – The Scientist

Biologists Are Engineering Kill Switches for GM Microbes – Sarah Zhang – Wired

Bacteria containing mcr-1 gene resistant to all known antibiotics found in Denmark – News Australia

‘Bik’s Picks’ blogger describes features of a good microbiome study – Kristina Campbell in Gut microbiota

Microbiology and art

Paper Life – The artist Rogan Brown cuts thousands of microorganisms in paper – Ufunk

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December 3, 2015

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Microbiomes of gallstones, soil along a bike trip, nematodes in cattle, kiddie pools, and 100 years of phage research.

Pregnancy and birth

Prophages of the genus Bifidobacterium as modulating agents of the infant gut microbiota – Gabriele Andrea Lugli – Environmental Microbiology

Gut microbiota analysis reveals a marked shift to bifidobacteria by a starter infant formula containing a synbiotic of bovine milk-derived oligosaccharides and Bifidobacterium animalis subsp. lactis CNCM I-3446 – Umberto Simeoni – Environmental Microbiology

Human skin microbiome

Alas no pictures: Microbial colonization of normal skin: direct visualization of 194 skin biopsies – Anika C. Jahns – Anaerobe

Human gut microbiome

Structural robustness of the gut mucosal microbiota is associated with Crohn’s disease remission after surgery – S Mondot – Gut

Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria – Hongzhang Shen – Scientific Reports

Improvement in Human Immune Function with Changes in Intestinal Microbiota by Salacia reticulata Extract Ingestion: A Randomized Placebo-Controlled Trial – Yuriko Oda – PLOS ONE

Establishing a Fecal Microbiota Transplant Service for the treatment of Clostridium difficile Infection – Samuel P. Costello – Clinical Infectious Diseases

Review: From Hype to Hope: The Gut Microbiota in Enteric Infectious Disease –
Peter T. McKenney – Cell

Research Highlight: Can Your Microbiome Tell You What to Eat? – Jairam K.P. Vanamala – Cell Metabolism

Review: Nutrition in cancer patients with cachexia: a role for the gut microbiota? – Laure B. Bindels – Clinical Nutrition Experimental

Review: What’s bugging the gut in OCD? A review of the gut microbiome in obsessive-compulsive disorder – Jasmine Turna – Depression and Anxiety

Book Chapter: Bile Acids, the Microbiome and Metabolic Disease-Implications for Surgery – Cyrus Jahansouz – Metabolic Syndrome and Diabetes

Animal and bioreactor models

Gut Microbiota Orchestrates Energy Homeostasis during Cold – Claire Chevalier – Cell

Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling – Maayan Levy – Cell

Levan Enhances Associated Growth of Bacteroides, Escherichia, Streptococcus and Faecalibacterium in Fecal Microbiota – Kaarel Adamberg – PLOS ONE

Animal microbiome

Cattle: Exploring the Gastrointestinal “Nemabiome”: Deep Amplicon Sequencing to Quantify the Species Composition of Parasitic Nematode Communities – Russell W. Avramenko – PLOS ONE

Seals: Brain Meta-Transcriptomics from Harbor Seals to Infer the Role of the Microbiome and Virome in a Stranding Event – Stephanie M. Rosales – PLOS ONE

Shrimp: Bacterial concentration and diversity in fresh tropical shrimps (Penaeus notialis) and the surrounding brackish waters and sediment – D. Sylvain Dabadé – International Journal of Food Microbiology

Plant, root, and soil microbiome

Science and art: Soil microbial communities along the route of a venturous cycling trip – Magdalena Nagler – Applied Soil Ecology

Disease suppression in winter wheat from novel symbiosis with forest fungi – Mary Ridout – Fungal Ecology

Multifunctionality and diversity of culturable bacterial communities strictly associated with spores of the plant beneficial symbiont Rhizophagus intraradices – Fabio Battini – Microbiological Research

Plant Host Species and Geographic Distance Affect the Structure of Aboveground Fungal Symbiont Communities, and Environmental Filtering Affects Belowground Communities in a Coastal Dune Ecosystem – Aaron S. David – Plant Microbe Interactions

The impact of charcoal and soil mixtures on decomposition and soil microbial communities in boreal forest – Nathalie Pluchon – Applied Soil Ecology

Endophytic Actinobacteria and the Interaction of Micromonospora and Nitrogen Fixing Plants – Martha E. Trujillo – Frontiers in Microbiology

The microbiome and functions of black soils are altered by dibutyl phthalate contamination – Zhigang Wang – Applied Soil Ecology

Microbiological and faunal soil attributes of coffee cultivation under different management systems in Brazil – D.R. Lammel – Brazilian Journal of Biology

Spatial Patterns in Biofilm Diversity across Hierarchical Levels of River-Floodplain Landscapes – Marc Peipoch – PLOS ONE

Extremophile microbiome

Bacterial biogeography influenced by shelf–basin exchange in the Arctic surface sediment at the Chukchi Borderland – Dukki Han – Environmental Microbiology

Built environment microbiology

First microbiota assessments of children’s paddling pool waters evaluated using 16S rRNA gene-based metagenome analysis – Toko Sawabe – Journal of Infection and Public Health

Summary of Sloan symposium: healthy buildings 2015-Europe – Hal Levin – Microbiome

Waste microbiology

Characterization of a microbial consortium that converts mariculture fish waste to biomethane – Brigit Quinn – Aquaculture

More microbiology

Ankyrin-mediated self-protection during cell invasion by the bacterial predator Bdellovibrio bacteriovorus – Carey Lambert – Nature Communications

Phages and viruses

In retrospect: A century of phage lessons – Forest Rohwer & Anca M. Segall – Nature

Science, publishing, and career

Scientific Misconduct: Red Flags: Warning signs that scandal might be brewing in your lab – John R. Thomas Jr – The Scientist

Explaining Retractions: Editors and publishers should use a standardized form to detail why they are pulling papers from the scientific literature – Hervé Maisonneuve and Evelyne Decullier – The Scientist

Self Correction: What to do when you realize your publication is fatally flawed – Kerry Grens – The Scientist

Microbes in the news

Why It’s Time to Map the Microbiome (Kavli Roundtable) – Alan Brown, The Kavli Foundation – LiveScience

Scientists Argue Appendix Might Not Be ‘Irrelevant’ to Our Health, Propose This as the Organ’s Current Function – Liz Klimas – The Blaze

Immune cells make appendix ‘silent hero’ of digestive health – Walter and Eliza Hall Institute – EurekAlert

Bugs Against Disease: Could bacteria help fight colorectal cancer? A collaborative group of Tufts researchers hope to find out – Jacqueline Mitchell – Tufts Now

New research: Intestinal bacteria are affected by antidiabetic drugs – EurekAlert
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December 1, 2015

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African gut microbiota and Entamoeba colonization, cuticular bacteria in social spiders, Arabidopsis leaf and root microbiota, the mineralosphere, bacteria in operating rooms and on a university campus.

Pregnancy and birth

The role of gut microbiota in fetal methylmercury exposure: insights from a pilot study – Sarah E. Rothenberg – Toxicology Letters

Human respiratory microbiome

Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways – Darcy R. Denner – The Journal of Allergy and Clinical Immunology

Human gut microbiome

Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence – Elise R. Morton – PLOS Genetics

Not yet on Nature website: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota – Forslund K – Nature

Gut microbiome in health and disease: Linking the microbiome-gut-brain axis and environmental factors in the pathogenesis of systemic and neurodegenerative diseases – Shivani Ghaisas – Pharmacology & Therapeutics

Book Chapter: Microbiome in the Critically Ill – Meredith Barrett – Nutrition Support for the Critically Ill

Review: The gut microbiome, diet, and links to cardiometabolic and chronic disorders – Judith Aron-Wisnewsky & Karine Clément – Nature Reviews Nephrology

Microbiome and bioreactor models

A distributed cell division counter reveals growth dynamics in the gut microbiota –
Cameron Myhrvold – Nature Communications

Polymicrobial Oral Infection with Four Periodontal Bacteria Orchestrates a Distinct Inflammatory Response and Atherosclerosis in ApoEnull Mice – Sasanka S. Chukkapalli – PLOS ONE

Aflatoxin B1 induced compositional changes in gut microbial communities of male F344 rats – Jincheng Wang – Toxicological Sciences

PhD thesis: Advanced Computational Tools for Analyzing Microbial Communities for Energy Production Environments – Adam Robbins-Pianka – University of Colorado at Boulder

Escherichia coli Nissle 1917 enhances bioavailability of serotonin in gut tissues through modulation of synthesis and clearance – Jonathan Nzakizwanayo – Scientific Reports

Animal microbiome

Cuticular bacteria appear lethal to social spiders in mixed but not monoculture inoculations – Carl N. Keiser – Current Zoology

Plant, root, and soil microbiome

Not yet on Nature website: Functional overlap of the Arabidopsis leaf and root microbiota – Bai Y – Nature

The Mineralosphere Concept: Mineralogical Control of the Distribution and Function of Mineral-associated Bacterial Communities – Stephane Uroz – Trends in Microbiology

Impact of lowland rainforest transformation on diversity and composition of soil prokaryotic communities in Sumatra (Indonesia) – Dominik Schneider – Frontiers in Microbiology

The assessment of epiphytic yeast diversity in sugarcane phyllosphere in Thailand by culture-independent method – Rujikan Nasanit – Fungal Biology

Changes in soil physicochemical and microbial properties along elevation gradients in two forest soils – Lei Hu – Scandinavian Journal of Forest Research

Influence of Cadmium and Glucose on Soil Microbial Communities – Aliya Gilmullina – American Journal of Applied Sciences

Convergence of microbial assimilations of soil carbon, nitrogen, phosphorus, and sulfur in terrestrial ecosystems – Xiaofeng Xu – Scientific Reports

Water microbiome

Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages – Magali Lescot – ISME Journal

Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river – Siavash Atashgahi – Scientific Reports

Built environment microbiology

The first microbial environment of infants born by C-section: the operating room microbes – Hakdong Shin – Microbiome

Microbial biogeography of a university campus – Ashley A. Ross and Josh D. Neufeld – Microbiome

Only on Pubmed as of now: Biofilms in churches built in grottoes – Cennamo P – Science of the Total Environment

Molecular Analysis of Microbial Community Structures in Nigerian Oil Production and Processing Facilities in order to Access Souring Corrosion and Methanogenesis – Chuma Okoro – Corrosion Science

Water heater temperature set point and water use patterns influence Legionella pneumophila and associated microorganisms at the tap – William J. Rhoads – Microbiome

Food microbiology

Selection of aroma compounds for the differentiation of wines obtained by fermenting musts with starter cultures of commercial yeast strains – Florin Vararu – Food Chemistry

Metagenomics and bioinformatics

MetaQUAST: evaluation of metagenome assemblies – Alla Mikheenko – Bioinformatics

Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires – Eugen Bauer – Microbiome

Book Chapter: Predicting the Metagenomics Content with Multiple CART Trees – Dante Travisany – Mathematical Models in Biology

Enhanced virome sequencing using targeted sequence capture – Todd N. Wylie – Genome Research

Biofilms and infection

Multi-species biofilms in ecology, medicine, and biotechnology – A. N. Nozhevnikova – Microbiology

Bacterial infection remodels the DNA methylation landscape of human dendritic cells –
Alain Pacis – Genome Research

Survival with a Helping Hand: Campylobacter and Microbiota – Ivana Indikova – Frontiers in Microbiology

Microbes in the news

Microbiome Startup uBiome Will Sequence Poop for the CDC – Sarah Zhang – Wired

Dr. Elizabeth Lindsey, gastroenterologist: FACES of Nashville – Liza Graves – Style

Microbiome Monday: The Bacteria and “The Guinea Pig Doctor” – American Museum of Natural History

The beloved pioneer bread that smells like feet and breaks food safety rules – Natalie Zarrelli – Atlas Obscura

Peer review

Want me to review your manuscript for free? Then be polite… – Ian M Mackay – Virology Down Under
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November 30, 2015

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Red algae growing in sea otter fur, noroviruses in a Thai river, virus dispersal by hand drying, and the dark side of salad.

Jobs and events

Postdoctoral Position, Evolutionary Genomics, University of California, Davis – Gregory Lanzaro – Phylogenomics

“The Dark Side of Salad: Internalization & Movement of Human Pathogenic Bacteria in Plants,” Guest Speaker: Dr. Amanda Deering – December 2, 2015, Purdue University

General microbiome

Review: Functions of innate immune cells and commensal bacteria in gut homeostasis – Hisako Kayama – Journal of Biochemistry

Human stomach microbiome

Identification of low abundance microbiome in clinical samples using whole genome sequencing – Chao Zhang – Genome Biology

Human gut microbiome

Review: The antimicrobial effects of rifaximin on the gut microbiota – H. L. DuPont – Part of a special issue: “Understanding mechanisms of the actions of rifaximin in selected gastrointestinal diseases “- Alimentary Pharmacology & Therapeutics

Animal models

Influence of Flaxseed Oil on Fecal Microbiota, Egg Quality and Fatty Acid Composition of Egg Yolks in Laying Hens – Jun-Yeong Lee – Current Microbiology

Duodenojejunal Bypass Leads to Altered Gut Microbiota and Strengthened Epithelial Barriers in Rats – Po-Jen Yang – Obesity Surgery

Animal microbiome

Characterization of the putatively introduced red alga Acrochaetium secundatum (Acrochaetiales, Rhodophyta) growing epizoically on the pelage of southern sea otters (Enhydra lutris nereis) – Gena B. Bentall – Marine Mammal Science

The mechanism for microsporidian parasite suppression of the hindgut bacteria of the migratory locust Locusta migratoria manilensis – Shu-qian Tan – Scientific Reports

Comparative Analysis of Microbial Diversity in Termite Gut and Termite Nest Using Ion Sequencing – Arumugam Manjula – Current Microbiology

Plant, root, and soil microbiology

Seasonal dynamics of the soil microbial community: assimilation of old and young carbon sources in a long-term field experiment as revealed by natural 13C abundance – G. Börjesson – European Journal of Soil Science

Aboveground litter quality is a better predictor than belowground microbial communities when estimating carbon mineralization along a land-use gradient – Nicolas Fanin – Soil Biology and Biochemistry

Effect of rice straw application on microbial community and activity in paddy soil under different water status – Fuxia Pan – Environmental Science and Pollution Research

Determinants of the biodiversity patterns of ammonia-oxidizing archaea community in two contrasting forest stands – Jie Chen – Journal of Soils and Sediments

Water and extremophile microbiome

Assessment of bacterial species present in Pasig River and Marikina River soil using 16S rDNA phylogenetic analysis – Maria Constancia O. Carrillo – International Journal of Philippine Science and Technology

Environmental switching during biofilm development in a cold seep system and functional determinants of species sorting – Weipeng Zhang – Molecular Ecology

Molecular detection and characterization of noroviruses in river water near Thailand – K. Inoue – Letters in Applied Microbiology

Biogeochemistry and microbial diversity in the marine cavity beneath the McMurdo Ice Shelf, Antarctica – Trista J. Vick-Majors – Limnology and Oceanography

Waste microbiology

New insights into the genetic and metabolic diversity of thiocyanate-degrading microbial consortia – Mathew P. Watts – Applied Microbiology and Biotechnology

Diversity and Distribution of Arsenic-Related Genes Along a Pollution Gradient in a River Affected by Acid Mine Drainage – Angélique Desoeuvre – Microbial Ecology

Seasonal variations of microbial community in a full scale oil field produced water treatment plant – Q. Xie – Global Journal of Environmental Science and Management

Built environment microbiology

Microbial dynamics in mixed culture biofilms of bacteria surviving sanitation of conveyor belts in salmon processing plants – Solveig Langsrud – Journal of Applied Microbiology

Evaluation of the potential for virus dispersal during hand drying: a comparison of three methods – Patrick T. Kimmitt – Journal of Applied Microbiology

Metabolomics

Review: Genome-scale modelling of microbial metabolism with temporal and spatial resolution – Michael A. Henson – Biochemical Society Transactions

Bioinformatics and metagenomics

Assessing the Unseen Bacterial Diversity in Microbial Communities – Alejandro Caro-Quintero – Genome Biology Evolution

Finding New Order in Biological Functions from the Network Structure of Gene Annotations – Kimberly Glass – PLOS Computational Biology

Microbes in the news

Bacteria on the Brain: A brilliant surgeon offered an untested treatment to dying patients. Was it innovation or overreach? – Emily Eakin – The New Yorker

Legionnaires’ Disease Bacteria Found In Minneapolis Hospital Water Samples – Angela Laguipo – Tech Times

The four bugs that protect us from asthma – Elizabeth Finkel – Cosmos Magazine
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November 28, 2015

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Events

2nd Microbiome R&D and Business Collaboration Congress – Early registration ends Monday – February/March 2016, Kuala Lumpur, Malaysia

Human oral microbiome

Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project – Zongxin Ling – Scientific Reports

Human gut microbiome

Altered Fecal Microbiota in Paediatric Inflammatory Bowel Disease – Johanna Maukonen – Journal of Crohn’s and Colitis

Microbiome models

Perspective: Could microbial therapy boost cancer immunotherapy? – Alexandra Snyder – Science

Chronic Zinc Deficiency Alters Chick Gut Microbiota Composition and Function – Spenser Reed – Nutrients

Microbiota is an essential element for mice to initiate a protective immunity against Vaccinia virus – Maurício T. Lima – FEMS Microbiology Ecology

Impacts of Extended Laboratory Rearing on Female Fitness in Florida Colonies of the Parasitoid Spalangia cameroni (Hymenoptera: Pteromalidae) With an Analysis of Wolbachia Strains – E.T. Machtinger – Annals of the Entomological Society of America

Animal microbiome

Fish: Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures – Laetitia G. E. Wilkins – Scientific Reports

Termites: Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites – Karen Rossmassler – Microbiome

Ticks: Emerging horizons for tick-borne pathogens: from the ‘one pathogen–one disease’ vision to the pathobiome paradigm – Muriel Vayssier-Taussat – Future Microbiology

Beetles: Surveying the endomicrobiome and ectomicrobiome of bark beetles: The case of Dendroctonus simplex – Audrey-Anne Durand – Scientific Reports

Coral: Bacterial predation in a marine host-associated microbiome – Rory M Welsh – The ISME Journal

Plant, root, and soil microbiome

Illumina High-Throughput Sequencing and Comparative Analysis of Bacterial Communities in Cherry Orchard Soil – Lingzhi Liu – Toxicological & Environmental Chemistry

Water microbiome

Interannual and cyclone-driven variability in phytoplankton communities of a tropical coastal lagoon – Suchismita Srichandan – Marine Pollution Bulletin

New insights into relationships between active and dormant organisms, phylogenetic diversity and ecosystem productivity – Jacob A. Cram – Molecular Ecology

Metagenomic Analysis of Upwelling-Affected Brazilian Coastal Seawater Reveals Sequence Domains of Type I PKS and Modular NRPS – Rafael R. C. Cuadrat – International Journal of Molecular Sciences

Assessment of bacterial species present in Pasig River and Marikina River soil using 16S rDNA phylogenetic analysis – Maria Constancia O. Carrillo – International Journal of Philippine Science and Technology

Bacterial community composition of an urban river in the North West Province, South Africa, in relation to physico-chemical water quality – K. Jordaan – Environmental Science and Pollution Research

Extremophile microbiome

The impact of temperature on microbial diversity and AOA activity in the Tengchong Geothermal Field, China – Haizhou Li – Scientific Reports

Built environment microbiome

Characterizing the Bacterial Communities in Retail Stores in the United States – A Hoisington – Indoor Air

Viruses and phages

A New Zamilon-like Virophage Partial Genome Assembled from a Bioreactor Metagenome – Meriem Bekliz – Frontiers in Microbiology

Bioinformatics and metagenomics

Bayesian identification of bacterial strains from sequencing data – Aravind Sankar – ArXiv

Microbial Ecology

Resource limitation drives spatial organization in microbial groups – Sara Mitri – The ISME Journal

Genome-scale modelling of microbial metabolism with temporal and spatial resolution – Michael A. Henson – Biochemical Society Transactions

Biofilms / Infection microbiology

Microbial biofilms associated with intravascular catheter-related bloodstream infections in adult intensive care patients – L. Zhang – European Journal of Clinical Microbiology & Infectious Diseases

Review: The limitations of in vitro experimentation in understanding biofilms and chronic infection – Aled E L Roberts – BioRxiv

Review: The Application of Metagenomic Approaches in the Management of Infectious
Diseases – Jinhua Wu – Tropical Medicine & Surgery

Food microbiology

Sourdough microbial community dynamics: An analysis during French organic bread-making processes – Emilie Lhomme – Food Microbiology

Bacteria in the news

Woolly rhino bacteria cleans up oil spills – Energy Global

A personal touch to wine microbiology – Kyanah Lawson – Food Magazine

Arizona inspectors find Theranos lab issues – AZ Central

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November 26, 2015

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Happy Thanksgiving, everyone! NCBI’s Pubmed nor Google Alerts did not take any holiday, so here is a post stuffed (pun intended) with new papers. For today, I got the microbiome of turkey, red wine, and coprolites. And strain-level variation in human-associated bacteria, cat periodontitis, and historical penguin activity too!

General microbiome

Nurturing the microbiome field: It is exciting to see the nucleus of a grand vision for the field, but we must make the fundamentals of the scientific method central to our mission – Pat Schloss – Science

Book: Microbial Endocrinology: Interkingdom Signaling in Infectious Disease and Health
Chapters include:

Pregnancy and birth

Preterm gut microbiota and metabolome following discharge from intensive care – Christopher J. Stewart – Scientific Reports

The role of gut microbiota in fetal methylmercury exposure: Insights from a pilot study – Toxicology Letters

Assessing the Intestinal Microbiota in the SHINE Trial – Ethan K. Gough – Clinical Infectious Diseases

Gravidas with Class III Obesity: Evaluating the Abdominal Skin Microbiota Above and Below the Panniculus – Rodney K Edwards – The Journal of Maternal-Fetal & Neonatal Medicine
Review: A Review of Antibiotic Use in Pregnancy – P. Brandon Bookstaver – Pharmacotherapy

Review: On the origin of species: Factors shaping the establishment of infant’s gut microbiota – Niels van Best – Birth Defects Research Part C: Embryo Today: Reviews

Review: Molecular characterization of the human microbiome from a reproductive perspective – Amir Mor – Fertility and Sterility

Review: Reproductive tract microbiome in assisted reproductive technologies – Jason M. Franasiak – Fertility and Sterility

Review: Gynecologic health and disease in relation to the microbiome of the female reproductive tract – Katherine A. Green – Fertility and Sterility

Human skin microbiome

Genetic associations and shared environmental effects on the skin microbiome of Korean twins – Jiyeon Si – BMC Genomics

Human respiratory microbiome

The Sputum Microbiome in Chronic Obstructive Pulmonary Disease Exacerbations
Yvonne J. Huang – Annals of the American Thoracic Society

Review: Clinical Insights into Pulmonary Exacerbations in Cystic Fibrosis from the Microbiome. What Are We Missing? – Fiona J. Whelan – Annals of the American Thoracic Society

Human oral microbiome

Microbiome of titanium and zirconia dental implants abutments – Cássio do Nascimento – Dental Materials

Human gut microbiome

Microbiota and food residues including possible evidence of pre-mammalian hair in Upper Permian coprolites from Russia – Piotr Bajdek – Lethaia

Red wine polyphenols modulate fecal microbiota and reduce markers of the metabolic syndrome in obese patients – Moreno-Indias Isabel – Food & Function

The human gut microbial ecology associated with overweight and obesity determines ellagic acid metabolism – María V. Selma – Food & Function

The severity of NAFLD is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota – Jérôme Boursier – Hepatology

Differences of microbiota in small bowel and faeces between irritable bowel syndrome patients and healthy subjects – Chen-Shuan Chung – Scandinavian Journal of Gastroenterology

Methodology, Not Concept of Fecal Microbiota Transplantation, Affects Clinical Findings – Bota Cui – Gastroenterology

The Gut-Liver Axis in Primary Sclerosing Cholangitis – Bertus Eksteen – Clinics in Liver Disease

Animal models

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota – Marie Vétizou – Science

Antepartum Antibiotic Treatment Increases Offspring Susceptibility to Experimental Colitis: A Role of the Gut Microbiota – Peris Mumbi Munyaka – PLOS ONE

Metabolomic study on the faecal extracts of atherosclerosis mice and its application in a Traditional Chinese Medicine – Feng Tian – Journal of Chromatography B

Animal microbiome

Temporal Relationships Exist Between Cecum, Ileum, and Litter Bacterial Microbiomes in a Commercial Turkey Flock, and Subtherapeutic Penicillin Treatment Impacts Ileum Bacterial Community Establishment – Jessica L. Danzeisen – Frontiers in Veterinary Science

A Pyrosequencing Investigation of Differences in the Feline Subgingival Microbiota in Health, Gingivitis and Mild Periodontitis – Stephen Harris – PLOS ONE

Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species – Katherine R. Amato – Oecologia

Plant, root, and soil microbiome

Bacterial diversity is strongly associated with historical penguin activity in an Antarctic lake sediment profile – Renbin Zhu – Scientific Reports

Elk, sagebrush, and saprotrophs: indirect top-down control on microbial community composition and function – Anna R. Peschel – Ecology

Effect of soil salinity and nutrient levels on the community structure of the root-associated bacteria of the facultative halophyte, Tamarix ramosissima, in southwestern United States – Takeshi Taniguchi – Journal of General and Applied Microbiology

Metagenomic insights into communities, functions of endophytes, and their associates with infection by root-knot nematode, Meloidogyne incognita, in tomato roots – Bao-Yu Tia – Scientific Reports

Effect of rice straw application on microbial community and activity in paddy soil under different water status – Fuxia Pan – Environmental Science and Pollution Research

Mapping the Centimeter-Scale Spatial Variability of PAHs and Microbial Populations in the Rhizosphere of Two Plants – Amélia Bourceret – PLOS ONE

Diversity of bacterial endophytes in 3 and 15 year-old grapevines of Vitis vinifera cv. Corvina and their potential for plant growth promotion and phytopathogen control – Marco Andreolli – Microbiological Research

Review: Functions, mechanisms and regulation of endophytic and epiphytic microbial communities of plants – Charles W. Bacon – Symbiosis

Review: Culture-independent discovery of natural products from soil metagenomes – Micah Katz – Journal of Industrial Microbiology & Biotechnology

Built environment microbiology

ISS: Extracellular Lipase and Protease Production from a Model Drinking Water Bacterial Community Is Functionally Robust to Absence of Individual Members – Graham G. Willsey – PLOS ONE

Food microbiology

Bacterial Ecology of Fermented Cucumber Rising pH Spoilage as Determined by Nonculture-Based Methods – Eduardo Medina – Journal of Food Science

Microbial Ecology

Complete nitrification by Nitrospira bacteria – Holger Daims – Nature

Does Microbial Diversity Confound General Predictions? – Marie Duhamel – Trends in Plant Science

Metagenomics and bioinformatics

Population genetic analyses of metagenomes reveal extensive strain-level variation in prevalent human-associated bacteria – Stephen Nayfach – BioRxiv

Techniques

Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi – Kevin V. Solomon – Anaerobe

Collecting Fecal Samples for Microbiome Analyses in Epidemiology Studies – Rashmi Sinha – Cancer Epidemiology, Biomarkers & Prevention

Microbes in the news

Is Double-Dipping Okay? CFUs in 4 types of dips after double dipping – Digg

New Research Reveals Bacteria Associated With Feline Gum Disease for the First Time – PR Newswire

Mission space food: Sugar-growing bacteria go into orbit – Clare Wilson – New Scientist

Your Coffee Machine Is a Breeding Ground for Caffeine-Resistant Bacteria – Matthew Braga – Motherboard

Your Poop Knows Best–New Study Shows Microbiome Can Help Predict Health Responses to Certain Foods – Patrick Mustain – Scientific American

Science, publishing, and career

China pursues fraudsters in science publishing – Mara Hvistendahl – Science
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November 25, 2015 – another digest

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Two digests today, to catch up with all literature that came out earlier this week. Gut microbiota of patients with stroke or TIAs, symbiosis within symbiosis, the coffee-machine microbiome, and chocolate making with yeasts.

Human gut microbiome

Dysbiosis of Gut Microbiota With Reduced Trimethylamine‐N‐Oxide Level in Patients With Large‐Artery Atherosclerotic Stroke or Transient Ischemic Attack – Jia Yin – Journal of the American Heart Association

Siri, What Should I Eat? – Reiner Jumpertz von Schwartzenberg, Peter J. Turnbaugh – Cell

Human skin microbiome

Microbiologic Safety of the Transareolar Approach in Breast Augmentation – Dana Mihaela Jianu – Aesthetic Surgery Journal

Microbiome models

Microbiota’s No Wasting Policy – Miguel P. Soares – Cell

Animal microbiome

Vaginal Microbiome Characterization of Nellore Cattle Using Metagenomic Analysis
Mateus Laguardia-Nascimento – PLOS ONE

Review: The natural occurrence of secondary bacterial symbionts in aphids – Sharon E. Zytynska – Ecological Entomology

Plant, root, and soil microbiome

Symbiosis within Symbiosis: Evolving Nitrogen-Fixing Legume Symbionts
Philippe Remigi – Trends in Microbiology

Soil microbial response to tetracycline in two different soils amended with cow manure – Luigi Chessa – Environmental Science and Pollution Research

Reviews: Friends or foes? Emerging insights from fungal interactions with plants – Susanne Zeilinger – FEMS Microbiology Reviews

Review: Extinction risk of soil biota – worrying paucity of existing information – Stavros D. Veresoglou – Nature Communications

Extremophile microbiome

Integrated ‘Omics’, Targeted Metabolite and Single-cell Analyses of Arctic Snow Algae Functionality and Adaptability – Stefanie Lutz – Frontiers in Microbiology

Water microbiome

Extracellular Lipase and Protease Production from a Model Drinking Water Bacterial Community Is Functionally Robust to Absence of Individual Members – Graham G. Willsey – PLOS ONE

Built environment microbiome

The coffee-machine bacteriome: biodiversity and colonisation of the wasted coffee tray leach – Cristina Vilanova – Scientific Reports

Food microbiology

Tuning chocolate flavor through development of thermotolerant Saccharomyces cerevisiae starter cultures with increased acetate ester production – Esther Meersman – Applied and Environmental Microbiology

Microbial genomes and ecology

Migration and horizontal gene transfer divide microbial genomes into multiple niches –
Rene Niehus – Nature Communications

The Good, the Bad, and the Tiny: A Simple, Mechanistic-Probabilistic Model of Virus-Nutrient Colimitation in Microbes – B. B. Cael – PLOS ONE

Microbes are trophic analogs of animals – Shawn A. Steffan – PNAS

Animal–microbe interactions and the evolution of nervous systems – Heather L. Eisthen – Philosophical Transactions B

Molecular operational taxonomic units as approximations of species in the light of evolutionary models and empirical data from Fungi – Martin Ryberg – Molecular Ecology

Review: Metagenomic cross-talk: the regulatory interplay between immunogenomics and the microbiome – Maayan Levy – Genome Medicine

Metagenomics and bioinformatics

Large-scale Machine Learning for Metagenomics Sequence Classification – Kévin Vervier – Bioinformatics

Techniques

Comparative Evaluation of DNA Extraction Methods from Feces of Multiple Host Species for Downstream Next-Generation Sequencing – Marcia L. Hart – PLOS ONE

Bacteria in the news

Your gut bacteria are controlling your appetite, study finds – Bec Crew – ScienceAlert

Beastly bacteria on extinct ancient carcasses offers ‘cure’ for modern oil pollution – Vera Salnitskaya – The Siberian Times

This ‘Plant Lamp’ uses bacteria to generate electricity – Sean Buckley – EnGadget
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November 25, 2015

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My apologies for 2 missed posts (due to overseas family circumstances). Gut microbiota of infants with botulism, gut microbial diversity in US Midwest population, decomposing pig carcasses, oil-degrading microbes and sunlight.

Events

5th Annual Microbiology of the Built Environment Conference – June 1-3 2016, Boulder, CO

Jobs

Our lab at Stanford University is hiring a Clinical Study Coordinator to be based out of UCSF School of Dentistry. Great position for someone who eventually wants to go to medical or dental school.

Pregnancy and birth

The relationship between early-life environment, the epigenome and the microbiota – Amber V Majnik – Epigenomics

Human oral microbiome

The impact of different DNA extraction methods on the analysis of microbial diversity of oral saliva from healthy youths by polymerase chain reaction-denaturing gradient gel electrophoresis – Ming Chen – Journal of Dental Sciences

Human gut microbiome

Characterizing the fecal microbiota of infants with botulism – T. Brian Shirey – Microbiome

Early-Life Exposure to Antibiotics, Alterations in the Intestinal Microbiome, and Risk of Metabolic Disease in Children and Adults – Sushmita G. Yallapragada – Pediatric Annals

Impact of demographics on human gut microbial diversity in a US Midwest population – Jun Chen – PeerJ Preprint

Review: Feeding the brain and nurturing the mind: Linking nutrition and the gut microbiota to brain development – Manu S. Goyal – PNAS

Review: Metagenomic cross-talk: the regulatory interplay between immunogenomics and the microbiome – Maayan Levy – Genome Medicine

Review: The relationship between early-life environment, the epigenome and the microbiota – Amber V Majnik – Future Medicine

Microbiome models

Gut Commensal E. coli Proteins Activate Host Satiety Pathways following Nutrient-Induced Bacterial Growth – Jonathan Breton – Cell Metabolism

Plant, root, and soil microbiome

From Rare to Dominant: A Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation – Sebastián Fuentes – Applied and Environmental Microbiology

Metabarcoding analysis of Phytophthora diversity using genus specific primers and 454 pyrosequencing – Maria I Prigigallo – Phytopathology

Structures of microbial communities in alpine soils: seasonal and elevational effects – Anna Lazzaro – Frontiers in Microbiology

Effects of long-term radionuclide and heavy metal contamination on the activity of microbial communities, inhabiting uranium mining impacted soils – Silvena Boteva – Environmental Science and Pollution Research

The community structures of prokaryotes and fungi in mountain pasture soils are highly correlated and primarily influenced by pH – Anders Lanzen – Frontiers in Microbiology

Water microbiome

Application of Microfluidic QPCR (MFQPCR) Technique to Monitor Bacterial Pathogens in Beach Water and Complex Environmental Matrices – Muruleedhara Byappanahalli – Environmental Science & Technology Letters

Natural sunlight shapes crude oil-degrading bacterial communities in northern Gulf of Mexico surface waters – Hernando P. Bacosa – Frontiers in MIcrobiology

Bacterioplankton community resilience to ocean acidification: evidence from microbial network analysis – Yu Wang – ICES Journal of Marine Sciences

Microbial Diversity and Bioactive Substances in Disease Suppressive Composts from India – C. M. Mehta – Compost Science & Utilization

Extremophile microbiome

Microbial metagenomics of oil sands tailings ponds: small bugs, big data – Julia M. Foght – Genome

Built environment microbiome

Changes in Microbes of the Built Environment in Early Stages of Urbanization – Maria Gloria Dominguez-Bello

Microbiome of death

The impact of carrion decomposition on the fatty acid methyl ester (FAME) profiles of soil microbial communities in southern Canada – Heloise Breton – Canadian Society of Forensic Science Journal

Metagenomics and bioinformatics

Assembly: a resource for assembled genomes at NCBI – Nucleic Acid Research

Web Resources for Metagenomics Studies – Pravin Dudhagara – Genomics, Proteomics & Bioinformatics

Metagenome Analysis Exploiting High-Throughput Chromosome Conformation Capture (3C) Data – Martial Marbouty – Trends in Genetics

EBI metagenomics in 2016 – an expanding and evolving resource for the analysis and archiving of metagenomic data – Alex Mitchell – Nucleic Acids Research

probeBase—an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016 – Daniel Greuter – Nucleic Acids Research

Microbial ecology / more microbiology

Review: Microbial Invasions: The Process, Patterns, and Mechanisms – Cyrus Alexander Mallon – Trends in Microbiology

Review: Microbial diversity — exploration of natural ecosystems and microbiomes –
Sean M Gibbons – Current Opinion in Genetics & Development

Microbes As Friends, Not Foes: Shifting the Focus from Pathogenesis to Symbiosis – Sheila A. Homburger – The American Biology Teacher

Microbes in the news

Leading Antibiotic Doomsayer Mellows on Infection Armageddon – Michael Byrne – Motherboard
and
I believed we would face an antibiotics apocalypse – until now – Richard James – The Guardian

Tardigrades: Inside the Bizarre Genome of the World’s Toughest Animal – Ed Yong – The Atlantic

C&EN Talks With Microbiome Surveyor Stefanie Kandels-Lewis: The laboratory technician turned fixer kept the Tara Oceans project, an expedition to map the oceans’ microbial populations, afloat for four years – Sarah Everts – C&EN

Kiwi scientists invent stomach ulcer cure – Olivia Wannan – Stuff NZ

A Doctor Wrestles With Whether To Keep Wearing His White Coat – John Henning Schumann – NPR

When will the world wake up to the potential of poo power? – John Vidal – The Guardian

At TEDMED 2015: How microbiome studies could improve the future of humanity – ScopeBlog

Two Types of Diet May Protect Against Type 2 Through Regulation of Gut Microbiota – Diabetes in Control

Symberix lands two SBIRs for GI drug that targets the microbiome – Meghana Keshavan – MedCity News

Diet study overturns all we know about healthy eating – Israel21c

Liberia monitors over 150 Ebola contacts as virus re-emerges – James Harding Giahyue – Reuters

Now We Can Use Microbes to Make Designer Chocolate Flavors – Esther Inglis-Arkell – Gizmodo

Fossils show sign of ancient vampire microbes – Punctures in fossils suggest predation drove the evolution of self-defense systems – Thomas Sumner – Student Science

Science, publishing and career

Stepping Away from the Lab:Emilie, Can I Ask You? Why I made the decision to leave academic research and become an editor.- Cell

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