May 2, 2016

A special issue of Science with 2 papers on lifestyle factors that determine composition of the stool microbiome in large human cohorts, variation in microbiome LPS immunogenicity contributes to autoimmunity, SEM analysis of cave speleothem microbial communities, and saliva bacteria in Chicha (Ecuadorian beer).

Jobs and Events

Early Career Microbiome Meal, during European Respiratory Society Meeting 2016 London, September 2016

Caporaso Lab is hiring a software engineer to work on QIIME and scikit-bio – Greg Caporaso – MicroBEnet

General microbiome

A special Science Issue called The Microbiota At Work:

Introduction: Manipulating the Microbiota – Caroline Ash, Kristen Mueller – Science

Review: Cross-species comparisons of host genetic associations with the microbiome – Julia K. Goodrich – Science

Review: How colonization by microbiota in early life shapes the immune system – Thomas Gensollen – Science

Review: Antibiotic use and its consequences for the normal microbiome – Martin J. Blaser – Science

Review: The healthy human microbiome – Jason Lloyd-Price – Genome Medicine

Pregnancy and birth

Infant formula with galacto-oligosaccharides (OM55N) stimulates the growth of indigenous bifidobacteria in healthy term infants – T. Matsuki – Beneficial Microbes

Human oral microbiome

Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes – Junya Yamagishi – PLOS ONE

Human respiratory microbiome

[PDF] The impact of different methods of DNA extraction on microbial community measures of BALF samples based on metagenomic data – Yan Wen – Am J Transl Res

Human reproductive tract microbiome

[PDF] Barcoded sequencing reveals diverse intrauterine microbiomes in patients suffering with endometrial polyps – Rui-Li Fang – Am J Transl Res

Opinion: Cervicovaginal Microbiomes–Threats and Possibilities – Gregor Reid – Trends in Endocrinology & Metabolism

Review: Foodomics as part of the host-microbiota-exposome interplay – Lorenza Putignani – Journal of Proteomics

Human gut microbiome

Population-level analysis of gut microbiome variation – Gwen Falony – Science

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity – Alexandra Zhernakova – Science

Durable coexistence of donor and recipient strains after fecal microbiota transplantation – Simone S. Li – Science

Review: Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens – Eric G. Pamer – Science

Associations between dietary flavonoid intake and gut microbiota in a group of adults with cystic fibrosis (CF) – L. Li – Journal of Nutrition & Intermediary Metabolism

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans – Tommi Vatanen – Cell

Gut Bacteria Metabolism Impacts Immune Recovery in HIV-infected Individuals – Sergio Serrano-Villar – EBioMedicine

Serologic microbial associated markers can predict Crohn’s disease behaviour years before disease diagnosis – R. S. Choung – Alimentary Pharmacology & Therapeutics

Impact of age and sex on the composition and abundance of the intestinal microbiota in individuals with and without enteric infections – Pallavi Singh – Annals of Epidemiology

Review: Human gut microbiota and healthy aging: Recent developments and future prospective – Manish Kumar – Nutrition an Healthy Aging

Animal and other models

Soluble and Insoluble Fiber Differentially Impact Canine Fecal Microbiome and Circulating Metabolome – Matthew Irick Jackson – The FASEB Journal

Germ-free and antibiotic-treated mice are highly susceptible to epithelial injury in DSS colitis – Cristina Hernández-Chirlaque – Journal of Crohn’s and Colitis

High intensity exercise training increases the diversity and metabolic capacity of the mouse distal gut microbiota during diet-induced obesity – Emmanuel Denou – American Journal of Physiology

Induction of Subacute Ruminal Acidosis Affects the Ruminal Microbiome and Epithelium – Joshua C. Mccann – Frontiers in Microbiology

Review: Oral microbial biofilm models and their application to the testing of anticariogenic agents – Christina P.C. Sim – Journal of Dentistry

Animal microbiome

Patterns of bacteria-host associations suggest different ecological strategies between two reef building cold-water coral species – Anne-Leila Meistertzheim – Deep Sea Research Part I: Oceanographic Research Papers

Plant, root, and soil microbiome

Characterizing and handling different kinds of AM fungal spores in the rhizosphere – Xueguang Sun – World Journal of Microbiology and Biotechnology

Illumina-based analysis of the rhizosphere microbial communities associated with healthy and wilted Lanzhou lily (Lilium davidii var. unicolor) plants grown in the field – Qianhan Shang – World Journal of Microbiology and Biotechnology

Microbial community structures and metabolic profiles response differently to physiochemical properties between three landfill cover soils – Xi-En Long – Environmental Science and Pollution Research

The effects of host age and spatial location on bacterial community composition in the English Oak tree (Quercus robur) – S. Meaden – Environmental Microbiology Reports

Universal indicators for oil and gas prospecting based on bacterial communities shaped by light-hydrocarbon microseepage in China – Chunping Deng – Journal of Microbiology and Biotechnology

Performance of 16s rRNA primer pairs in the study of rhizosphere and endosphere bacterial microbiomes in metabarcoding studies – Bram Beckers – Frontiers in Microbiology

Water and extremophiles

The unexpected extremophile: Tolerance to fluctuating salinity in the green alga Picochlorum – Fatima Foflonker – Algal Research

Microbial communities in a range of carbon dioxide fluxes from a natural volcanic vent in Campo de Calatrava, Spain – Irena Fernández-Montiel – International Journal of Greenhouse Gas Control

On the use of high-throughput sequencing for the study of cyanobacterial diversity in Antarctic aquatic mats – Igor Stelmach Pessi – Journal of Phycology

Quorum sensing plays a complex role in regulating the enzyme hydrolysis activity of microbes associated with sinking particles in the ocean – Andreas Krupke – Frontier in Marine Science

Succession of bacterial community structure during the early stage of biofilm development in the Antarctic marine environment – Yung Mi Lee – Korean Journal of MIcrobiology

Using scanning electron microscopy to study microbial communities in speleothem samples collected from Iron Curtain Cave – Cohord Mason – The Journal of Experimental Microbiology & Immunology

Large differences in potential denitrification and sediment microbial communities across the Laurentian great lakes – Gaston E. Small – Biogeochemistry

Built environment microbiome

Ecological succession of the microbial communities of an air conditioning cooling coil in the tropics – Enzo Acerbi – Indoor Air

Web Alert: Microbiology in archaeology: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology – Lawrence P. Wackett – Environmental Microbiology

Food microbiology

Bacteria associated with human saliva are major microbial components of Ecuadorian indigenous beers (chicha) – Ana L. Freire – PeerJ

A method to isolate bacterial communities and characterize ecosystems from food products: Validation and utilization in as a reproducible chicken meat model – Amélie Rouger – International Journal of Food Microbiology

Bioinformatics and metagenomics

BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design – Christoph Mayer – Molecular Biology and Evolution

Microbial ecology

The Evolution of Quorum Sensing as a Mechanism to Infer Kinship – Jonas Schluter – PLOS Computational Biology

Co-existence facilitates interspecific biofilm formation in complex microbial communities – Jonas S Madsen – Environmental Microbiology

Viruses and phages

Molecular evolution of epizootic hemorrhagic disease viruses in North America based on historical isolates using motif fingerprints – W. C. Wilson – Virus Genes

Techniques

[Video Protocol] Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization – Melis N. Anahtar – Journal of Visualized Experiments

Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes – Junya Yamagishi – PLOS ONE

The impact of different methods of DNA extraction on microbial community measures of BALF samples based on metagenomic data – Yan Wen – Am J Transl Res

Microbes in the news

Your gut bacteria are more than what you eat – Elizabeth Pennisi – Science

With quotes from me! New research confirms thriving gut bacteria is linked to a healthier body – Russell Brandom – The Verge

Want more good bugs in your gut? Try yogurt. And coffee – Patrick Skerrett – STAT News

This Bacteria Strain Offers a Curious Mix of Hope and Danger. The Elizabethkingia strain could cure malaria, but it’s also sickened dozens in Wisconsin – Lisa Margonelli – Slate

Bacteria beneficial to plants have spread across California – UC Riverside study shows spread of Bradyrhizobium has important implications for biofertilizers – EurekAlert

The Benefits of Slathering Your Newborn Baby with Vaginal Bacteria – Rebecca Schiller – Vice Broadly

A Timely Gut Check. At the American Museum of Natural History, meet your microbiome – Ralph Gardner – The Wall Street Journal

A Comprehensive Survey of Pre-Clinical Microbiology Curricula Among United States Medical Schools – Dora Melber – Clinical Infectious Diseases

Mayo Clinic Ventures Firm Explores Commercialization Of Gut Microbe Treatment – Don Jacobson – Twin City Business

Microbes and art

Quilting with soil: soil microorganisms had “painted” their efforts on the cloth in an unexpected variety of colors. – Martha Pings – Soils

Science, publishing, and career

Is most published research really false? – Jeffrey T Leek, Leah R Jager – bioRxiv

Who’s downloading pirated papers? Everyone. In rich and poor countries, researchers turn to the Sci-Hub website – John Bohannon – Science

The frustrated science student behind Sci-Hub – John Bohannon – Science

Plagiarism: A worm poking holes into the quality of our academic work – Christine Osae – The New Times

Bik’s Picks
Doctor ready to perform first human head transplant – Ross Kenneth Urken – News Week

April 27, 2016

Posted on April 27, 2016 by eliesbik

Cervical microbiome during cancer, distinct gut microbiome in kidney stone formers? (unclear due to vaguely formulated control group), culturing marine microbes in artificial seawater, codon usage to predict pathogenicity.

Events

Science Diplomats to present ‘Trust Your Gut: How Helpful Bacteria Impact Health’ – Free talk given 3 times at Yale in May

Pregnancy and birth

News & Views: Immunology: Mum’s microbes boost baby’s immunity – Mihir Pendse & Lora V. Hooper – Nature

Human respiratory microbiome

Culture based: Microbiology of peritonsillar abscess in the South Estonian population – Risto Vaikjärv – Microbial Ecology in Health and Disease

Human reproductive tract microbiome

Cervical Microbiome and Cytokine Profile at Various Stages of Cervical Cancer: A Pilot Study – Astride Audirac-Chalifour – PLOS ONE

Human gut microbiome

Note that the control group is poorly described: Evidence for a distinct gut microbiome in kidney stone formers compared to non-stone formers – Joshua M. Stern – Urolithiasis

Review: Macrobiota — helminths as active participants and partners of the microbiota in host intestinal homeostasis – William C Gause – Current Opinion in Microbiology

Review: The possible mechanisms of the human microbiome in allergic diseases – Kagan Ipci – European Archives of Oto-Rhino-Laryngology

Review: Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production – David Endesfelder – Microbiome

Animal and bioreactor models

Biochar, Bentonite and Zeolite Supplemented Feeding of Layer Chickens Alters Intestinal Microbiota and Reduces Campylobacter Load – Tanka P. Prasai – PLOS ONE

Applying theories of microbial metabolism for induction of targeted enzyme activity in a methanogenic microbial community at a metabolic steady state – Jutta Speda – Applied Microbiology and Biotechnology

A humanized microbiota mouse model of ovalbumin-induced lung inflammation – Marie-Claire Arrieta – Gut Microbes

Plant, root, and soil microbiome

Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria – Edward W. Davis II – PeerJ Preprint

Water and extremophile microbiome

Artificial Seawater Media Facilitate Cultivating Members of the Microbial Majority from the Gulf of Mexico – Michael W. Henson – mSphere

Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes – Jian Yang – Scientific Reports

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations – Alexander J. Probst – Environmental Microbiology

Metabolome-mediated biocryomorphic evolution promotes carbon fixation in Greenlandic cryoconite holes – J.M. Cook – Environmental Microbiology

Pollution and waste microbiology

Microbial density and diversity in constructed wetland systems and the relation to pollutant removal efficiency – Yang Zhang – Water Science & Technology

A mesophilic anaerobic digester for treating food waste: process stability and microbial community analysis using pyrosequencing – Lei Li – Microbial Cell Factories

Microbial ecology

Inhibitory interactions promote frequent bistability among competing bacteria –
Erik S. Wright – Nature Communications

Bioinformatics and metagenomics

Protocol: Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles – Maja Fabijani – Data Mining Techniques for the Life Sciences

Review: High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved – Dmitrij Turaev – Current Opinion in Biotechnology

Microbes in the news

Elizabethkingia: The bacteria strain that could kill you. Or cure malaria. Small Science: Genomic data is showing us how little we know – Lisa Margonelli – Houston Chronicle

New Anti-Biofilm Nano Coating Prevents Bacterial Growth on Metal Surfaces – Azo Nano

Quick mapping of our microbiomes and metabolomes – Science Daily

Viral Skin Infections – Tomislav Meštrović – News Medical

Bacteria pill is ‘better than statins’ in the war on cholesterol, say researchers – Joe Smith – Mirror UK

Bacterial virulence is stimulated by burns – EurekAlert

Science, publishing, and career

Meet The New CEO Of The $22 Billion Genomics Company You’ve Never Heard Of: Francis deSouza to lead Illumina – Christina Farr – Fast Company

What Happened When I Pushed Myself to Interview More Women: Increasing the breadth of sources in journalism – John R. Platt – Motherboard

The quiet revolutionary: How the co-discovery of CRISPR explosively changed Emmanuelle Charpentier’s life. The microbiologist spent years moving labs and relishing solitude. Then her work on gene-editing thrust her into the scientific spotlight – Alison Abbott – Nature

Speak up about subtle sexism in science: Female scientists face everyday, often-unintentional microaggression in the workplace, and it won’t stop unless we talk about it – Tricia Serio – Nature

Bik’s Picks

Effects of a Closed Space Environment on Gene Expression in Hair Follicles of Astronauts in the International Space Station – Masahiro Terada – PLOS ONE

April 19, 2016

Posted on April 19, 2016 by eliesbik

A review about breastmilk with a great name, skin microbiome in different populations, a mouse model for Sjögren’s, the office microbiome, Guam reef sponges, the Alaska tundra ecosystem, and taxonomic classification. Note that I will be traveling internationally in the next couple of days due to (another) tragic family situation, so posting will be irregular. But I will try my best!

Pregnancy and birth

Review: Breastfed at Tiffany’s – Thierry Hennet – Trends in Biochemical Sciences

Human skin microbiome

Body Site Is a More Determinant Factor than Human Population Diversity in the Healthy Skin Microbiome – Guillermo I. Perez Perez – PLOS ONE

Pathogenic bacteria profile and antimicrobial susceptibility patterns of ear infection at Bahir Dar Regional Health Research Laboratory Center, Ethiopia – Derese Hailu – SpringerPlus

Human oral microbiome (also see Animal models, below)

Comparison of the Oral Microbiome of Siblings Using Next-generation Sequencing: a Pilot Study – Hyo-Seol Lee – Oral Diseases

Human gastric microbiome

Characterisation of the gastrointestinal mucosa-associated microbiota: a novel technique to prevent cross-contamination during endoscopic procedures – E. R. Shanahan – Alimentary Pharmacology & Therapeutics

Human gut microbiome

Conference Abstract: Walnut Consumption Influences the Human Gut Microbiome – Heather M Guetterman – The FASEB Journal

Conference Abstract: Anemia and Iron Status are Predictors of Gut Microbiome Composition and Metabolites in Infants and Children in Rural Kenya – Daniela Paganini – The FASEB Journal

Recurrent Clostridium difficile infection associates with distinct bile acid and microbiome profiles – J. R. Allegretti – Alimentary Pharmacology & Therapeutics

Effects of sardine-enriched diet on metabolic control, inflammation and gut microbiota in drug-naïve patients with type 2 diabetes: a pilot randomized trial – Mariona Balfegó – Lipids in Health and Disease

Review: From gut dysbiosis to altered brain function and mental illness: mechanisms and pathways – G B Rogers – Molecular Psychiatry

Review: Reshaping the gut microbiota: Impact of low calorie sweeteners and the link to insulin resistance? – Jodi E. Nettleton – Physiology & Behavior

Book chapter, some plagiarism: Impact of Probiotics and Gut Microbiota on Host Behavior – Sarabjit Singh Kanwar – Microbes in Food and Health

Animal models of microbiome research

Mouse model: Altered Mucosal Microbiome Diversity and Disease Severity in Sjögren Syndrome – Cintia S. de Paiva – Scientific Reports

Systemic Characterization of an Obese Phenotype in the Zucker Rat Model Defining Metabolic Axes of Energy Metabolism and Host-Microbial Interactions – Jutarop Phetcharaburanin – Journal of Proteome Research

Metagenomic analysis of antibiotic-induced changes in gut microbiota in a pregnant rat model – Imran Khan – Frontiers in Pharmacology

Inflammasome signaling affects anxiety- and depressive-like behavior and gut microbiome composition – M-L Wong – Molecular Psychiatry

Animal microbiome

The reproductive tracts of two malaria vectors are populated by a core microbiome and by gender- and swarm-enriched microbial biomarkers – Nicola Segata – Scientific Reports

In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity – Georg Steinert – PeerJ

Microbiome analysis and detection of pathogenic bacteria of Penaeus monodon from Jakarta Bay and Bali – Vincensius S.P. Oetama – Marine Pollution Bulletin

Diversity of endosymbiont bacteria associated with a non-filarial nematode group – Stela S. Lazarova – Nematology

Master thesis: Effects of Roundup (glyphosate) on gut microorganisms of farm animals – Charlotte Lynggaard Katholm – Aarhus University

Plant, root, and soil microbiome

Functional composition of plant communities determines the spatial and temporal stability of soil microbial properties in a long-term plant diversity experiment – Tanja Strecker – Oikos

Bacterial communities of the cotton aphid Aphis gossypii associated with Bt cotton in northern China – Yao Zhao – Scientific Reports

Soil microbial community composition and respiration along an experimental precipitation gradient in a semiarid steppe – Cancan Zhao – Scientific Reports

Bioaerosol Deposition to Food Crops near Manure Application: Quantitative Microbial Risk Assessment – Michael A. Jahne – Journal of Environmental Quality

Effects of biofumigation using Brassica juncea and Raphanus sativus in comparison to disinfection using Basamid on apple plant growth and soil microbial communities at three field sites with replant disease – Bunlong Yim – Plant and Soil

Bacterial and eukaryal diversity in soils forming from acid mine drainage precipitates under reclaimed vegetation and biological crusts – Claudia Rojas – Applied Soil Ecology

Assessment of Bacterial Communities and Predictive Functional Profiling in Soils Subjected to Short-Term Fumigation-Incubation – Lin Chen – Microbial Ecology

Archaeal communities in the sediments of different mangrove stands at Dongzhaigang, China – Wei Li – Journal of Soils and Sediments

Metagenomics reveals pervasive bacterial populations and reduced community diversity across the Alaska tundra ecosystem – Eric R. Johnston – Frontiers in Microbiology

Water microbiome

Bacterioplankton biogeography in the Atlantic Ocean: a case study of the distance-decay relationship – Mathias Milici – Frontiers in Microbiology

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities – Jeffrey Marlow – Frontiers in Microbiology

Metagenomic analysis of sediments under seaports influence in the Equatorial Atlantic Ocean – Tallita Cruz Lopes Tavares – Science of The Total Environment

Dissolution Tests and Microbial Community Analysis Using the Bottom Sediment before and after a Heavy Storm – Ikuo Tsushima – Journal of Water and Environment Technology

Carbohydrate production by microbial mats communities in tidal flat from Bahía Blanca Estuary (Argentina) – E. M. Fernández – Environmental Earth Sciences

Built environment microbiome

Geography and Location Are the Primary Drivers of Office Microbiome Composition – John Chase – mSystems

Waste and pollution microbiology

Population Dynamics of Bulking and Foaming Bacteria in a Full-scale Wastewater Treatment Plant over Five Years – Xiao-Tao Jiang – Scientific Reports

Quantification of microbial load in diesel storage tanks using culture- and qPCR-based approaches – Pedro M. Martin-Sanchez – International Biodeterioration & Biodegradation

Bacterial communities in oil contaminated soils: Biogeography and co-occurrence patterns – Shuo Jiao – Soil Biology and Biochemistry

Methanogen Population of an Oil Production Skimmer Pit and the Effects of Environmental Factors and Substrate Availability on Methanogenesis and Corrosion Rates – Okoro Chuma Conlette – Microbial Ecology

Phages and viruses

Parasite diversity drives rapid host dynamics and evolution of resistance in a bacteria-phage system – Alex Betts – Evolution

Research highlight: More of the world’s a phage – Naomi Attar – Nature Reviews Microbiology

Bioinformatics and metagenomics

Fast and sensitive taxonomic classification for metagenomics with Kaiju – Peter Menzel – Nature Communications

META-pipe – Pipeline Annotation, Analysis and Visualization of Marine Metagenomic Sequence Data – Espen Mikal Robertsen – ArXiv

Fast and sensitive mapping of nanopore sequencing reads with GraphMap – Ivan Sović – Nature Communications

Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity – Beverly E. Flood – Frontiers in Microbiology

Editorial: A tale of two tardigrades – Thomas A. Richards – PNAS

Review: A guide through a family of phylogenetic dissimilarity measures among sites – Sandrine Pavoine – Oikos

Review: Compositional analysis: a valid approach to analyze microbiome high throughput sequencing data – Gregory B Gloor – Canadian Journal of Microbiology

More microbiology

Accessing Nature’s diversity through metabolic engineering and synthetic biology – Jason R. King – F1000 Research

Utilization and control of ecological interactions in polymicrobial infections and community-based microbial cell factories – Vinoth Wigneswaran – F1000 Research

Microbes in the news

Your Invisible Neighbors: Each City Has Unique Microbes – Katherine Du – NPR

Can the bacteria on your skin reveal where you are from? Floors, walls and people in different cities have distinct microbial ‘signatures’ – Abigail Beall – Daily Mail

6 surprising facts about sugar-laden, virus-fighting breast milk – Megan Thielking – STAT News

Gut microbiota development driven by specific enzyme in breast milk – Yvette Brazier – Medical News Today

Mothers’ milk and the infant gut microbiota: An ancient symbiosis – Science Daily

Microbiome-Brain Research to Get $2.8M Boost from NIDA, NCCIH – Genome Web

Earth Day: New insights into coral health hidden in reefs’ microbiomes – National Science Foundation

Downwind safety on the farm. Manure application research aims to improve food safety – American Society of Agronomy

Heartburn Meds Alter the Gut. Acid blockers reduce the diversity of bacteria in the intestines—and that could lead to trouble – Melinda Wenner Moyer – Scientific American

Bacteria that ‘breathes’ iron: Microbes that might change our search for life in space – Dawn Papple – Inquisitr

Microbes and art
This artist uses bacteria as paint: Paint by Microbes – Steph Yin – PopSci

Science, publishing, and career

From #realtimechem to #whywedoresearch: Who are the Tweeting scientists? – Andrew Marsh – Piirus

Tips for Using Social Media to Promote Your Research – Emma Hedington – NPJ Biofilms and Microbiomes

About Joseph Mercola: Known Quack Forced to Refund Customers for Lying About Effects of Tanning Beds – Bryan Menegus – Gizmodo

Bik’s Picks

Meet the woman who makes fake fingers for Japan’s reformed gangsters – Justin McCurry – The Guardian

April 17, 2016

Posted on April 17, 2016 by eliesbik

General microbiome

Review: The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation – Amy Langdon – Genome Medicine

Human oral microbiome

The predictive value of microbiological findings on teeth, internal and external implant portions in clinical decision making – Luigi Canullo – Clinical Oral Implants Research

Human respiratory microbiome

Airway Microbiota in Severe Asthma and Relationship to Asthma Severity and Phenotypes – Qingling Zhang – PLOS ONE

Effects of a honeybee lactic acid bacterial microbiome on human nasal symptoms, commensals, and biomarkers – Anders Mårtensson – International Forum of Allergy & Rhinology

Human gut microbiome

Consistent Prebiotic Effect on Gut Microbiota With Altered FODMAP Intake in Patients with Crohn’s Disease: A Randomised, Controlled Cross-Over Trial of Well-Defined Diets – Emma P Halmos – Clinical and Translational Gastroenterology

Review: Role of the microbiome in non-gastrointestinal cancers – Meirav Pevsner-Fischer – World Journal of Clinical Oncology

Animal models

Thymol and Carvacrol Affect Hybrid Tilapia through the Combination of Direct Stimulation and an Intestinal Microbiota-Mediated Effect: Insights from a Germ-Free Zebrafish Model – Chao Ra – The Journal of Nutrition

Animal microbiome

Microbial diversity in the digestive tract of two different breeds of sheep – J.-L. Douglas – Journal of Applied Microbiology

The Microbiome of the Uropygial Secretion in Hoopoes Is Shaped Along the Nesting Phase – Ángela Martínez-García – Microbial Ecology

The microbiome associated with equine periodontitis and oral health – Rebekah Kennedy – Veterinary Research

Plant, root, and soil microbiome

Diversity and Composition of the Leaf Mycobiome of Beech (Fagus sylvatica) Are Affected by Local Habitat Conditions and Leaf Biochemistry – Martin Unterseher – PLOS ONE

Unearthing microbial diversity of Taxus rhizosphere via MiSeq high-throughput amplicon sequencing and isolate characterization – Da Cheng Hao – Scientific Reports

High Diversity Revealed in Leaf-Associated Protists (Rhizaria: Cercozoa) of Brassicaceae – Sebastian Ploch – Journal of Eukaryotic Microbiology

Temporal and spatial assessment of microbial communities in commercial silages from bunker silos– J. Kraut-Cohen – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Aquatic fungi: targeting the forgotten in microbial ecology – Hans-Peter Grossart – Current Opinion in MIcrobiology

Mineralogy and Microbial Diversity of the Microbialites in the Hypersaline Storr’s Lake, the Bahamas – Varun G. Paul – Astrobiology

Microbial–meiofaunal interrelationships in coastal sediments of the Red Sea – Hamed A. El-Serehy – Saudi Journal of Biological Sciences

Waste and pollution microbiology

Biological Activity of Autochthonic Bacterial Community in Oil-Contaminated Soil – Agnieszka Wolińska – Water Air Soil Pollution

Bioinformatics

Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0 – Brian R. Granger – PLOS Computational Biology

More microbiology

Antimicrobial activity of extracts from macroalgae Ulva lactuca against clinically important Staphylococci is impacted by lunar phase of macroalgae harvest – A.M. Deveau – Letters in Applied Microbiology

Harnessing the Power of Defensive Microbes: Evolutionary Implications in Nature and Disease Control – Suzanne A. Ford – PLOS Pathogens

Microbes in the news

The Wood Wide Web. A new study shows that trees of different species can exchange large amounts of carbon via the fungal internet that connects their roots. – Ed Yong – The Atlantic

Antibiotics may have lasting impact on the immune system of children – MedicalXpress

Drugs for your gut bugs are on the horizon – Elizabeth Preston – STAT News

A Gut Feeling. See profilee Hans Clevers discuss his work with stem cells and cancer in the small intestine – The Scientist

Qiime2 will revolutionize microbiome bioinformatics – Greg Caporaso – American Gut

Bik’s Picks

Pepper-sprayed students outraged as UC Davis tried to scrub incident from web – Anita Chabria – The Guardian

April 5, 2016

Posted on April 5, 2016 by eliesbik

Differences in myelination and gene expression in prefrontal cortex between GF and conventional mice, migratory passerines, metagenomics of probiotics, and megaviromes.

Events

NAS Meeting: Microbiomes of the Built Environment: From Research to Application – David Coil – MicroBEnet

Human oral microbiome

Impact of age and sex on the composition and abundance of the intestinal microbiota in individuals with and without enteric infections – Pallavi Singh – Annals of Epidemiology

Review [PDF]: Oral Microbial Shift: Factors affecting the Microbiome and Prevention of Oral Disease – Namrata Dagli – Journal of Contemporary Dental Practice

Human reproductive tract microbiome

Review: Incorporating microbiota data into epidemiological models: Examples from vaginal microbiota research – Janneke van de Wijgert – Annals of Epidemiology

Combined effect of diet and cervical microbiome on the risk of cervical intraepithelial neoplasia – Sang-Soo Seo – Clinical Nutrition

Human gut microbiome

Diversified mcr-1-Harbouring Plasmid Reservoirs Confer Resistance to Colistin in Human Gut Microbiota – Huiyan Ye – mBio

Animal models

Regulation of prefrontal cortex myelination by the microbiota – AE Hoban – Translational Psychiatry

Responses of fecal bacterial communities to resistant starch intervention in diabetic rats – Zhongkai Zhou – Starch

Resveratrol Attenuates Trimethylamine-N-Oxide (TMAO)-Induced Atherosclerosis by Regulating TMAO Synthesis and Bile Acid Metabolism via Remodeling of the Gut Microbiota – Ming-liang Chen – mBio

Commentary: Policing of gut microbiota by the adaptive immune system – Laurent Dollé – BMC Medicine

Animal microbiome

Sample processing impacts the viability and cultivability of the sponge microbiome – Ana I. Esteves – Frontiers in Microbiology

Characterization of the gut microbiota of migratory passerines during stopover along the northern coast of the Gulf of Mexico – William B. Lewis – Journal of Avian Biology

Highlight: Microbes matter: herbivore gut endosymbionts play a role in breakdown of host plant toxins – Franziska Beran – Environmental Microbiology

Selective feeding by the giant barrel sponge enhances foraging efficiency – Steven E. McMurray – Limnology and Oceanography

PhD Thesis: Molecular investigation of Australian termites and their gut symbionts – Nurdyana Abdul Rahman – University of Queensland

Plant, root, and soil microbiome

Distance-dependent effects of pathogenic fungi on seedlings of a legume tree: impaired nodule formation and identification of antagonistic rhizosphere bacteria – Lan Liu – Journal of Ecology

Bacterial community dynamics during ensiling of perennial ryegrass at two compaction levels monitored by terminal restriction fragment length polymorphism – K. Graf – Journal of Applied Microbiology

Microsite differentiation drives the abundance of soil ammonia oxidizing bacteria along aridity gradients – Manuel Delgado-Baquerizo – Frontiers in Microbiology

Not exactly microbes but sounded interesting: Do tropical rain forest soils have greater nematode diversity than High Arctic tundra? A metagenetic comparison of Malaysia and Svalbard – Dorsaf Kerfahi – Global Ecology and Biogeography

Use of two spatially separated plant species alters microbial community function in horizontal subsurface flow constructed wetlands – Mark Button – Ecological Engineering

Water microbiome

Spatio-temporal interdependence of bacteria and phytoplankton during a Baltic Sea spring bloom – Carina Bunse – Frontiers in Microbiology

Protist-bacteria associations: Gammaproteobacteria and Alphaproteobacteria are prevalent as digestion-resistant bacteria in ciliated protozoa – Jun Gong – Frontiers in Microbiology

Particulate matter stoichiometry driven by microplankton community structure in summer in the Indian sector of the Southern Ocean – M. Rembauville – Limnology and Oceanography

Waste and pollution microbiome

Functional Metagenomics of a Biostimulated Petroleum-Contaminated Soil Reveals an Extraordinary Diversity of Extradiol Dioxygenases – Laura Terrón-González – Applied and Environmental Microbiology

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community – Christopher L. Hemme – mBio

Built environment microbiome

A novel, optical, on-line bacteria sensor for monitoring drinking water quality – Bo Højris – Scientific Reports

Food and probiotics microbiology

Culture-Independent Metagenomic Surveillance of Commercially Available Probiotics with High-Throughput Next-Generation Sequencing – Jennifer N. Patro – mSphere

Unravelling the effect of clostridia spores and lysozyme on microbiota dynamics in Grana Padano cheese: A metaproteomics approach – Alessio Soggiu – Journal of Proteomics

Viruses and phages / metagenomics

VIP: an integrated pipeline for metagenomics of virus identification and discovery – Yang Li – Scientific Reports

Antibiotic Resistome: Improving Detection and Quantification Accuracy for Comparative Metagenomics – Ali H. A. Elbehery – OMICS

Themed Issue of Current Opinion in Microbiology: Environmental microbiology/Megaviromes
Review: Giants among larges: how gigantism impacts giant virus entry into amoebae – Rodrigo Araújo Lima Rodrigues – Current Opinion in Microbiology
Review: Updating strategies for isolating and discovering giant viruses – Jacques Yaacoub Bou Khalil
Review, but not sure about what: Persistent virus and addiction modules: an engine of symbiosis – Luis P Villarreal

Metabolomics

In silico methods for linking genes and secondary metabolites: The way forward – Shradha Khater – Synthetic and Systems Biotechnology

Techniques and bioinformatics

It’s all relative: analyzing microbiome data as compositions – Gregory B. Gloor – Annals of Epidemiology

Not metagenomics but about a not-clearly defined 16S rRNA gene amplification pipeline. Not a good paper: Snapshot on a pilot metagenomic study for the appraisal of gut microbial diversity in mice, cat and men – Coline Plé – Gastroenterology Research and Practice

More microbiology

Expression of arsenic resistance genes in the obligate anaerobe Bacteroides vulgatus ATCC 8482, a gut microbiome bacterium – Jiajiao Li – Anaerobe

Cholesterol Analogs with Degradation-resistant Alkyl Side Chains Are Effective Mycobacterium tuberculosis Growth Inhibitors – Daniel J. Frank – The Journal of Biological Chemistry

Microbiology and art

This Artist Paints With Bacteria, And It’s Strangely Beautiful – Jacqueline Howard – Huffington Post

Microbes in the news

With a quote from me! Gut bacteria regulate nerve fibre insulation – Mo Costandi – The Guardian

Europe’s Microbiology Society’s Annual Conference 2016: the Twitter story – Microbepost

Antibiotic soap can alter a baby’s gut bacteria – Tim Sandle – Digital Journal

The fridge that detects bacteria in your food – NZ Herald

About COPD: Take a deep breath – your lung microbiome will appreciate it – GSK

Microbiome and the modern environment: a global drift toward dysbiosis? – Susan Prescott and Alan Logan – BioMed Central blog

Biofilm researcher: New Faces: Boo Shan Tseng: This Life Sciences professor is all about communities – University of Nevada, Las Vegas

Study by the University of Kaiserslautern: Viruses cause bacteria to produce pink pigments – AlphaGalileo

Promising new method inhibits TB–causing bacteria – Phys.org

Bacteria Hysteria

Do you know how clean your lean workout is? The DEADLY bacteria found in your gym mat – Kat Romero – Express

Bik’s Picks

Cellular telephone use during free-living walking significantly reduces average walking speed – Jacob E. Barkley – BMC Research Notes

So cool: The Cemetery as Archive: A 177-year-old cemetery is preparing to digitize millions of records that shed light on New York City’s shifting demographics – Jessica Leigh Hester

April 4, 2016

Posted on April 4, 2016 by eliesbik

Gut microbiome of Australian sea lions, Trichoderma fungi in endemic plants, and digging for microbial proof of Hannibal’s route over the alps.

Human vaginal microbiome

Comment: Translating the vaginal microbiome: gaps and challenges – Jacques Ravel – Genome Medicine

Human respiratory microbiome

Review: The lung microbiome: the perfect culprit for COPD exacerbations? – Carine Gomez – European Respiratory Journal

Animal models

Frogs: Short-term exposure to coal combustion waste has little impact on the skin microbiome of adult spring peepers, Pseudacris crucifer – Myra C. Hughey – Applied and Environmental Microbiology

Short bowel syndrome (SBS)-associated alterations within the gut-liver axis evolve early and persist long-term in the piglet model of short bowel syndrome – Prue M. Pereira-Fantini – Journal of Gastroenterology and Hepatology

Maternal Antibiotic Treatment Impacts Development of the Neonatal Intestinal Microbiome and Antiviral Immunity – Gabriela Gonzalez-Perez – The Journal of Immunology

Generation and Characterization of Indoor Fungal Aerosols for Inhalation Studies – Anne Mette Madsen – Applied and Environmental Microbiology

Correspondence: The premature invocation of a ‘gut-lung axis’ may obscure the direct effects of respiratory microbiota on pneumonia susceptibility – Robert P Dickson – Gut

Animal microbiome

Colony location and captivity influence the gut microbial community composition of the Australian sea lion (Neophoca cinerea) – Tiffany C. Delport – Applied and Environmental Microbiology

DGGE: Decreased microbial diversity and Lactobacillus group in the intestine of geriatric giant pandas (Ailuropoda melanoleuca) – Zhirong Peng – World Journal of Microbiology and Biotechnology

Germs within Worms: Localization of Neorickettsia sp. within Life Cycle Stages of the Digenean Plagiorchis elegans – Stephen E. Greiman – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Comparison of the abundance and community structure of ammonia oxidizing prokaryotes in rice rhizosphere under three different irrigation cultivation modes – Jinping Zhang – World Journal of Microbiology and Biotechnology

Endemic plants harbour specific Trichoderma communities with an exceptional potential for biocontrol of phytopathogens – Christin Zachow – Journal of Biotechnology

Water microbiome

Diverse and temporally-variable particle-associated microbial communities are insensitive to bulk seawater environmental parameters – Cheuk-Man Yung – Applied and Environmental Microbiology

Pollution and waste microbiology

Similar Microbial Consortia and Genes Are Involved in the Biodegradation of Benzalkonium Chlorides in Different Environments – Emine Ertekin – Environmental Science & Technology

Biofilm and Planktonic Bacterial and Fungal Communities Transforming High-Molecular-Weight Polycyclic Aromatic Hydrocarbons – Benjamin D. Folwell – Applied and Environmental Microbiology

Microbes and art

These petri dish “paintings” reveal the hidden beauty of bacteria – Julia Belluz – Vox

After Effects: A series of architectural scale models constructed with black paper and covered with flour and a layer of mould to create the effect of old abandoned buildings – Daniele Del Nero.

Microbes in the news

Scarlett Fever: A 19th-century disease is on the rise in the UK—and nobody knows why – Akshat Rathi – Quartz

The truth about Hannibal’s route across the Alps. How exactly did the Carthaginian general and his elephants reach Italy? Scientists have got their hands dirty to come up with an answer – Philip Ball – The Guardian

Gender differences in antibiotic prescribing in the community: a systematic review and meta-analysis – Wiebke Schröder – Journal of Antimicrobial Chemotherapy

Microbes Meet Cancer. Understanding cancer’s relationship with the human microbiome could transform immune-modulating therapies – Kate Yandell – The Scientist

Guts and Glory. An open mind and collaborative spirit have taken Hans Clevers on a journey from medicine to developmental biology, gastroenterology, cancer, and stem cells – Anna Azvolinsky – The Scientist

Science, pubilishing, and career

Medscape Physician Compensation Report 2016 – Carol Peckham – MedScape

Bik’s Picks

It turns out this planet has three suns in its sky – Rachel Feltman – Washington Post

March 25, 2016

Posted on March 25, 2016 by eliesbik

A minimal bacterial genome, gut microbes/TMAO/platelets, (pro)phages and genomes, Top 50 unidentified fungi, and Propionibacterium acnes as a contaminant.

General microbiome

Review: Speciation by Symbiosis: The Microbiome and Behavior – J. Dylan Shropshire – BioRxiv

Human gut microbiome
Research highlight: Gut microbes modulate platelet function and thrombosis risk – Irene Fernández-Ruiz – Nature Reviews Cardiology

Combination of human and mouse studies: Gut Microbial Metabolite TMAO Enhances Platelet Hyperreactivity and Thrombosis Risk – Weifei Zhu – Cell

Animal microbiome

Comparison of Fecal Microbiota between German Holstein Dairy Cows with and without Left-Sided Displacement of the Abomasum – Eun-Sik Song – Journal of Clinical Microbiology

Plant, root, and soil microbiome

Infection with a Shoot-Specific Fungal Endophyte (Epichloë) Alters Tall Fescue Soil Microbial Communities – Xavier Rojas – Microbial Ecology

Distribution patterns of microbial communities in ultramafic landscape: a metagenetic approach highlights the strong relationships between diversity and environmental traits – L Bordez – Molecular Ecology

Spatial and temporal variation of cultivable communities of co-occurring endophytes and pathogens in wheat – Morgane Comby – Frontiers in Microbiology

Plant Growth-Promoting Rhizobacteria Inoculation to Enhance Vegetative Growth, Nitrogen Fixation and Nitrogen Remobilisation of Maize under Greenhouse Conditions – Khing Boon Kuan – PLOS ONE

Microbial control of soil organic matter mineralisation responses to labile carbon in subarctic climate change treatments – Kathrin Rousk – Global Change Biology

Water microbiome

Effects of temperature and nutrients on changes in genetic diversity of bacterioplankton communities in a semi-closed bay, South Korea – Hyun Jung Kim – Marine Pollution Bulletin

Built environment microbiome

Imported anthropogenic bacteria may survive the Antarctic winter and introduce new genes into local bacterial communities – Kristian Brat – Polish Polar Research

Waste and pollution microbiome

Consistency between health risks and microbial response mechanism of various petroleum components in a typical wastewater-irrigated farmland – Juan Zhang – Journal of Environmental Management

Metagenomics and bioinformatics

DUDes: a top-down taxonomic profiler for metagenomics – Vitor C. Piro – Bioinformatics

Viruses

Genetic and life-history traits associated with the distribution of prophages in bacteria – Marie Touchon – The ISME Journal

Hyperexpansion of RNA Bacteriophage Diversity – Siddharth R. Krishnamurthy – PLOS Biology

Fungi

Top 50 most wanted fungi – Henrik Nilsson – MycoKeys

Book: Biology of Microfungi – Editors: De-Wei Li – Springer

Book: The Mycota: Environmental and Microbial Relationships – Editors: Irina S. Druzhinina, Christian P. Kubicek – Springer

Techniques

Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing – Mohammad R. Hasan – Journal of Clinical Microbiology

Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples – Andries E. Budding – Journal of Clinical Microbiology

Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing – Sarah Mollerup

More microbiology

531 kb (473 genes): Design and synthesis of a minimal bacterial genome – Clyde A. Hutchison III – Science

How clonal are bacteria over time? – B. Jesse Shapiro – BioRxiv preprint

Microbes in the news

This man-made cell has the smallest genome ever — but a third of its genes are a mystery – Rachel Feltman – Washington Post

The Mysterious Thing About a Marvelous New Synthetic Cell – Ed Yong – The Atlantic

After 20 Year Quest, Biologists Create Synthetic Bacteria With No Extra Genes – Matthew Herper – Forbes

Scientists Create Tiniest Life Form Yet, Not Sure What It Is – Eric Roston – Bloomberg

Microbes can play games with the mind – Laura Sanders – Science News

SDSU researcher examines link between gut bacteria and metabolic disease – Adriana Millar – The Daily Aztec

What gut bacteria can teach us about cancer treatment: Studies probe link between gut bacteria and treatment effectiveness – Jenn Savedge – Mother Nature Network

Elizabethkingia: Senator seeks answers from CDC on mystery bacteria – Jonathan Stefonek – Daily Register

Study finds vast diversity among viruses that infect bacteria – EurekAlert

Bik’s Picks

Comb jelly ‘anus’ guts ideas on origin of through-gut – Amy Maxmen – Science

Funding Freeze Hits Natural History Museum Collections – Ed Yong – The Atlantic
[hr]

March 16, 2016

Posted on March 16, 2016 by eliesbik

Events

Strategies & Techniques for Analyzing Microbial Population Structures (STAMPS) Course 8/3-8/13 – MicroBEnet

Human skin microbiome

An in Vitro Model for the Human Cutaneous Microbial Ecosystem – Danique A. van der Krieken – Acta Dermato-Venereologica

Human oral microbiome

Interactions between Streptococcus oralis, Actinomyces oris, and Candida albicans in the development of multispecies oral microbial biofilms on salivary pellicle – I.M.G. Cavalcanti – Molecular Oral Microbiology

Human respiratory tract microbiome

High genetic diversity of Staphylococcus aureus strains colonising the nasopharynx of Gambian villagers before widespread use of pneumococcal conjugate vaccines – Chinelo Ebruke – BMC Microbiology

Human gut microbiome

Note: data segregate according to study: Gene expression profiling gut microbiota in different races of humans – Lei Chen – Scientific Reports

Review: A healthy gastrointestinal microbiome is dependent on dietary diversity – Mark L. Heiman

Review: Gut Microbiota and Obesity: Potential Therapeutic Targets and Probiotic
Nicole D. White – American Journal of Life Sciences

Animal models

Fuzhuan tea consumption imparts hepatoprotective effects and alters intestinal microbiota in high saturated fat diet-fed rats – Michelle T. Foster – Molecular Nutrition & Food Research

Long-term effects of early life microbiota disturbance on adaptive immunity in laying
K. Simon – Poultry Science

Rapid evolution of microbe-mediated protection against pathogens in a worm host –
Kayla C King – ISME Journal

Impact of 4-epi-oxytetracycline on the gut microbiota and blood metabolomics of Wistar rats
Hongxing Han – Scientific Reports

Animal microbiome

Genomic Analysis of Companion Rabbit Staphylococcus aureus – Mark A. Holmes – PLOS ONE

Plant, root, and soil microbiome

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants – Tao Ding – PLOS ONE

Water and extremophile microbiome

Ecosystem function decays by fungal outbreaks in Antarctic microbial mats – David Velázquez – Scientific Reports

Multi-laboratory survey of qPCR enterococci analysis method performance in U.S. coastal and inland surface waters – Richard A. Haugland – Journal of Microbiological Methods

Built environment microbiome

Potentially harmful secondary metabolites produced by indoor Chaetomium species on artificially and naturally contaminated building materials – I. Došen – Indoor AIr

Food microbiology

Helicobacter pylori in bottled mineral water: genotyping and antimicrobial resistance properties – Reza Ranjbar – BMC Microbiology

Effects of Temperature on Bacterial Communities and Metabolites during Fermentation of Myeolchi-Aekjeot, a Traditional Korean Fermented Anchovy Sauce – Ji Young Jung – PLOS ONE

Viruses and phages

The Formulation of Bacteriophage in a Semi Solid Preparation for Control of Propionibacterium acnes Growth – Teagan L. Brown – PLOS ONE

News & Views: Microbial oceanography: Viral strategies at sea – T. Frede Thingstad – Nature

Lytic to temperate switching of viral communities – B. Knowles – Nature

Microbial Ecology

Closely coupled evolutionary history of ecto- and endosymbionts from two distantly related animal phyla – Judith Zimmerman – Molecular Ecology

Bioinformatics

RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to
Yanming Zhang – Nucleic Acids Research

Techniques

The US Culture Collection Network lays the foundation for progress in preservation of valuable microbial resources – Kevin McCluskey – Phytopathology

Assessing the impact of long term frozen storage of faecal samples on protein concentration and protease activity – Laura S. Morris – Journal of Microbiological Methods

A modified micro chamber agar spot slide culture technique for microscopic examination of filamentous fungi – Peralam Yegneswaran Prakash – Journal of Microbiological Methods

Microbes in the news

uBiome is World’s First Company to Appoint Citizen-Scientist-in-Residence – PR Web

Incredible images reveal bacteria motor parts in unprecedented detail – Science Codex

Ancient Bacteria With Photosynthesis Were Much More Common Than Previously Thought, Study Finds – Catherine Griffin – HNGN

Viral Remnants Help Regulate Human Immunity: Endogenous retroviruses in the human genome can regulate genes involved in innate immune responses – Jyoti Madhusoodanan – The Scientist

Plastic That Mimics Insect Wings Kills Bacteria, University of California, Irvine Study – Biospace

Early heavy metal exposure can cause permanent changes to gut microbiome and cause a host of diseases – Dave Mihalovic – SOTT

Slice of PLOS: Bacteria’s Social Media – Lauren Richardson – PLOS ONE

“Unsurprisingly, Perlmutter has his critics.” Neurologist David Perlmutter gets to the guts of brain health with surprising advice – SMH.com

Opinion: A Mother’s Microbes: On “vaginal seeding” and the challenge of evidence-based parenting – Rob Knight and Jack Gilbert – The Scientist

Australian Scientists Discover How Gut Bacteria May Prevent Stomach Cancer – MSN

Reduction in dietary diversity impacts richness of human gut microbiota – Science Codex
http://www.nature.com/articles/srep23075

Press might be overinterpreting Mouse seminal microbiome study:
Scientists discover microbiome that may be responsible for male reproductive disorders – EurekAlert

Seminal work. How unruly data led MU scientists to discover a new microbiome – Roger Meissen – Decoding Science

Microbiome: This Type Of Bacteria May Increase Risk Of Reproductive Disorders – Kathleen Lees – HNGN

Science, publishing, and career

Handful of Biologists Went Rogue and Published Directly to Internet – Amy Harmon

Peer-Led Team Learning Helps Minority Students Succeed – Julia J. Snyder – PLOS Biology

Video parody: PloS ANNA VS ELSAvier – For The First Time – Luisa Hugerth -YouTube

Bik’s Picks

A Month in Mammoth. Two sleep researchers braved the subterranean environment of a Kentucky cave to see if they could train their bodies to abandon the cyclical rhythms of the 24-hour day – The Scientist

Night Night, Flipper – Watch underwater footage of a dolphin sleeping in the wild – The Scientist

Scientists Find That Getting Multiple Tattoos Strengthens Your Immune System – Kelly Tatera – Science Explorer

[hr]

March 13, 2016

Posted on March 13, 2016 by eliesbik

General microbiome

Review: Engineering Human Microbiota: Influencing Cellular and Community Dynamics for Therapeutic Applications – S. Woloszynek – International Review of Cell and Molecular Biology

Pregnancy and birth / Human vaginal microbiome

Review: The vaginal microbiota, host defense and reproductive physiology – Steven B Smith – The Journal of Physiology

Human gut microbiome

Review: Brain-Gut-Microbiota axis: Challenges for Translation in Psychiatry – John R. Kelly – Annals of Epidemiology

Editorial: The microbiome in celiac disease: Beyond diet-genetic interactions – Jose U. Scher – Cleveland Clinic Journal of Medicine
Animal models

Age, introduction of solid feed and weaning are more important determinants of gut bacterial succession in piglets than breed and nursing mother as revealed by a reciprocal cross-fostering model – Gaorui Bian – Environmental Microbiology

Heat-treated high-fat diet modifies gut microbiota and metabolic markers in apoe−/− mice – Nittaya Marungruang – Nutrition & Metabolism

Animal microbiome

Characterization of pollen and bacterial community composition in brood provisions of a small carpenter bee – Quinn S. McFrederick – Molecular Ecology

Plant, root, and soil microbiome

Cry1Ac Transgenic Sugarcane Does Not Affect the Diversity of Microbial Communities and Has No Significant Effect on Enzyme Activities in Rhizosphere Soil within One Crop Season – Dinggang Zhou – Frontiers in Plant Science

Succession of soil microbial communities and enzyme activities in artificial soils – Franziska Ditteric – Pedobiologia

Effect of copper and zinc on microbial tolerance to triclosan in two soil types – Gerty J. H. P. Gielen – Journal of Soils and Sediments

Microbial enzymes as an early warning management tool for monitoring mining site soils – Mohammad Wahsha – CATENA

Water and glacier microbiome

Bacterial communities potentially involved in iron-cycling in Baltic Sea and North Sea sediments revealed by pyrosequencing – Carolina Reyes – FEMS Microbiology Ecology

The Differing Biogeochemical and Microbial Signatures of Glaciers and Rock Glaciers – Timothy S. Fegel – Journal of Geophysical Research

Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon – Florent E. Angly – PeerJ

Infection microbiology

Whole genome sequencing identifies a novel species of the genus Capnocytophaga isolated from dog and cat bite wounds in humans – Salah Zangena – Scientific Reports

Viruses

RNA viruses as major contributors to Antarctic virioplankton – Jaclyn A Miranda – Environmental Microbiology

Review: Giant viruses of amoebas: an update – Sarah Aherfi – Frontiers in Microbiology

Microbial Ecology

Review: Dancing with the Stars: How Choreographed Bacterial Interactions Dictate Nososymbiocity and Give Rise to Keystone Pathogens, Accessory Pathogens, and Pathobionts – George Hajishengallis – Trends in Microbiology

Metagenomics and bioinformatics

LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly – Paola Bonizzoni – Journal of Computational Biology

Microbes in the news

Cool Citizen Microbiology Project in Spain With Great Engagement – David Coil – Microbenet

Podcast: The Bacteria Behind Your Favorite Blues, Bries, and More – Science Friday

Science, publishing and career

Scientists who tweet: 3 Fred Hutch researchers talk about getting #science out into the world, 140 characters at a time – Mary Engel – Fred Hutch

This Student Adds A Woman In Science To Wikipedia Every Time She’s Harassed Online – Kelly Oakes – BuzzFeed

Bik’s Picks

Neandertals’ large lower thorax may represent adaptation to high protein diet – Miki Ben-Dor – American Journal of Physical Anthropology

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Microbiome Digest – Bik's Picks

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

Category Archives: Bik’s Non-Microbiology Picks

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