Category Archives: Human gut

July 18, 2015

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Microbes lighting up the clouds, bacterial degradation of human bone, and probiotics after colonoscopy.

Microbiome of death

An Investigation Into the Relationship Between Funerary Treatment and Bacterial Bioerosion in European Archaeological Human Bone – T. J. Booth – Archaeometry

Human oral microbiome

Cytokine expression in peri-implant crevicular fluid in relation to bacterial presence
– Stefan Renvert – Journal of Clinical Periodontology

High-quality draft genome sequences of five anaerobic oral bacteria and description of
Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae – Maria V. Sizova – Standards in Genomic Sciences

The metabonomic studies of tongue coating in H.pylori positive chronic gastritis patients – Xuan Liu – Evidence Based Complimentary and Alternative Medicine

Human gut microbiome

Randomized controlled trial of probiotics after colonoscopy – Basil D’Souza – ANZ Journal of Surgery

Animal models of microbiome

Chlorinated Water Modulates the Development of Colorectal Tumors with Chromosomal Instability and Gut Microbiota in Apc-Deficient Mice – Tatsunari Sasada – PLOS ONE

A novel “humanized mouse” model for autoimmune hepatitis and the association of gut microbiota with liver inflammation – Muhammed Yuksel – Hepatology

Modulation of gut microbiota in rats fed high-fat diets by processing whole-grain barley to barley malt – Yadong Zhong – Molecular Nutrition & Food Research

Effects of microcystin-LR on gut microflora in different gut regions of mice – Jing Chen – The Journal of Toxicological Sciences

Animal microbiome

Review: Advancements in Bovine Rumen Microbial Ecology: A Review – Nidhi R. Parmar – Int.J.Curr.Microbiol.App.Sci

Bacteria detected in the honeybee parasitic mite Varroa destructor collected from beehive winter debris – Jan Hubert – Journal of Applied Microbiology

A comparative study on microbiota from the intestine of Prussian carp (Carassius gibelio) and their aquatic environmental compartments, using different molecular methods – Elena N. Kashinskaya – Journal of Applied Microbiology

Response of the bacterial community associated with a cosmopolitan marine diatom to crude oil shows a preference for the biodegradation of aromatic hydrocarbons – Sara Mishamandan – Environmental Microbiology

Host-Specific and pH-Dependent Microbiomes of Copepods in an Extensive Rearing System – Alf Skovgaard – PLOS ONE

Microenvironment and Phylogenetic Diversity of Prochloron Inhabiting the Surface of Crustose Didemnid Ascidians – Daniel A. Nielsen – Environmental Microbiology

Plant, root, and soil microbiome

Editorial: Environmental phytoremediation: plants and microorganisms at work – Antonella Furini – Frontiers in Plant Science

Diversity and distribution of endophytic bacterial community in the Noni (Morinda citrifolia L.) plant – Yang Liu – African Journal of Microbiology Research

Aboveground-belowground biodiversity linkages differ in early and late successional temperate forests – Hui Li – Scientific Reports

Effects of Conservation Agriculture and Fertilization on Soil Microbial Diversity and Activity – Johan Habig – Environments

Resilience and receptivity worked in tandem to sustain a geothermal mat community amidst erratic environmental conditions – Wriddhiman Ghosh – Scientific Reports

Determinants of bacterial communities in Canadian agroforestry systems – Samiran Banerjee – Environmental Microbiology

Indigenous arsenic(V)-reducing microbial communities in redox-fluctuating near-surface sediments of the Mekong Delta – S. C. Ying – Geobiology

Impact of soil salinity on arbuscular mycorrhizal fungi biodiversity and microflora biomass associated with Tamarix articulataVahll rhizosphere in arid and semi-arid Algerian areas – Karima Bencherif – Science of The Total Environment

Water microbiome

Natural aerosols explain seasonal and spatial patterns of Southern Ocean cloud albedo – Daniel T. McCoy – Science Advances

Diversity of bacterioplankton in the surface seawaters of Drake Passage near the Chinese Antarctic station – Mengxin Xing – FEMS Microbiology Letters

Seasonality in molecular and cytometric diversity of marine bacterioplankton: the reshuffling of bacterial taxa by vertical mixing – Francisca C. García – Environmental Microbiology

Synchronized dynamics of bacterial niche-specific functions during biofilm development in a cold seep brine pool – Weipeng Zhang – Environmental Microbiology

Waste treatment microbiology

Changes in bacterial and archaeal communities in anaerobic digesters treating different organic wastes – Young Mo Kim – Chemosphere

The role of starvation in biomass harvesting and lipid accumulation: Co-culture of microalgae–bacteria in synthetic wastewater – Yanjia Xu – Environmental Progress & Sustainable Energy

A high-throughput sequencing study of bacterial communities in an autohydrogenotrophic denitrifying bio-ceramsite reactor– Dan Chen – Process Biochemistry

Food microbiology

Packaging gas selects lactic acid bacterial communities on raw pork – Timo T Nieminen – Journal of Applied Microbiology

Metabolic networks

Enteric Pathogens Exploit the Microbiota-generated Nutritional Environment of the Gut – Alline R. Pacheco – Microbiology Spectrum

Linking metabolite production to taxonomic identity in environmental samples by (MA)LDI-FISH – Martin Kaltenpoth – The ISME Journal

Techniques

Phospholipid fatty acid profiling of microbial communities – a review of interpretations and recent applications – C Willers – Journal of Applied Microbiology

Microbes in the news

Tiny Ocean Microbes are Brightening Up the Sky – Maddie Stone – Gizmodo

Baby’s Microbiome: Why Birth to Age Three Is So Critical For Your Child’s Health – Toni Harman – Huffington Post

These caffeine-addicted beetles are using bacteria to ruin all of our coffee – Elahe Izadi – Washington Post

Unearthing Cornerstones in Root Microbiomes. Defining core members of a microbial community for normal plant growth – Joint Genome Institute

You Need Way More Nutrients for Good Gut Health – Rachael Schultz – Shape

Targeting gut microbiome boosted metformin tolerance – Jennie Smith – Clinical Endocrinology News

Scientist develops model for robots with bacteria-controlled brains – Phys.org

Bik’s Picks

Watch what happens when a spinning basketball gets thrown off a dam – Chris Matyszczyk – CNET

Restaurant Food May Be Unhealthier Than Fast Food – Mandy Oaklander – Time

U.S. Adults Are Not Eating Enough Vegetables, Fruit – Says New Study – Matthew Rideout – The Times Gazette

Sea turtle released off Florida Keys tracked by satellite – Daily Commercial

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July 17, 2015

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Laser Capture Microdissection of tissue from infants with NEC, skin microbiome from Chinese subjects, paromomycin treatment effects on human gut microbiome.

General human microbiome

Prenatal exposure to systemic antibacterials and overweight and obesity in danish schoolchildren: A prevalence study – A Mor – International Journal of Obesity

Review: Humans as Superorganisms: How Microbes, Viruses, Imprinted Genes, and Other Selfish Entities Shape Our Behavior – Peter Kramer – Perspectives on Psychological Science

Pregnancy and birth microbiome

Application of Laser Capture Microdissection and 16S rRNA Gene PCR in the Analysis of Bacteria Colonizing the Intestinal Tissue of Neonates with Necrotizing Enterocolitis – Jingli Yang – The Pediatric Infectious Disease Journal

Human oral microbiome

Checkerboard Assay: Advanced Caries Microbiota in Teeth with Irreversible Pulpitis –
Isabela N. Rôças – Journal of Endodontics

Human skin microbiome

Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups – Marcus H. Y. Leung – Scientific Reports

Human gut microbiome

Dynamic changes of the luminal and mucosa-associated gut microbiota during and after antibiotic therapy with paromomycin – Femke-Anouska Heinsen – Gut Microbes

Short-term High Fat Diet Increases Postprandial Trimethylamine-N-Oxide in Humans – Nabil E. Boutagy – Nutrition Research

In Brief/ Editorial: Modifying the gut to treat liver diseases – Cláudio Nunes-Alves – Nature Reviews Microbiology

Review: Talking microbes: when gut bacteria interact with diet and host organs – Patrice D. Cani – Molecular Nutrition & Food Research

Review: Metagenomic Surveys of Gut Microbiota – Rahul Shubhra Mandal – Genomics, Proteomics & Bioinformatics

Review: The bilateral responsiveness between intestinal microbes and IgA – Andrew J. Macpherson – Trends in Immunology

Animal and other models

How free of germs is germ-free? Detection of bacterial contamination in a germ free mouse unit – Clinton A Fontaine – Gut Microbes

Microbes & Neurodevelopment – Absence of Microbiota during Early Life Increases Activity-Related Transcriptional Pathways in the Amygdala – Roman M. Stilling – Brain, Behavior, and Immunity

Exoelectrogenic capacity of host microbiota predicts lymphocyte recruitment to the gut – Aaron Conrad Ericsson – Physiological Genomics

Polyphenols-rich fruit in maternal diet modulates inflammatory markers and the gut microbiota and improves colonic expression of ZO-1 in offspring – Carina Almeida Morais – Food Research International

Defined Nutrient Diets Alter Susceptibility to Clostridium difficile Associated Disease in a Murine Model – John H. Moore – PLOS ONE

Soluble Dextrin Fibers Alter Intestinal Microbiota and Reduce Proinflammatory Cytokine Secretion in Male IL-10–Deficient Mice – Rosica Valcheva – The Journal of Nutrition

Kiwifruit fermentation drives positive gut microbial and metabolic changes irrespective of initial microbiota composition – Paul Blatchford – Bioactive Carbohydrates and Dietary Fibre

Animal microbiome

The potential roles of bacterial communities in coral defence: A case study at Talang-talang reef – Felicity W. I. Kuek – Ocean Science Journal

Soil

Land-use system shapes soil bacterial communities in Southeastern Amazon region – Lucas William Mendes – Applied Soil Ecology

Water microbiome

Seasonal progression of microbial communities on the Faroe shelf – Anni Djurhuus – Marine Biology Research

Waste treatment microbiology

Understanding the linkage between elevation and activated sludge bacterial community along a 3600 m elevational gradient in China – Lihua Niu – Applied and Environmental Microbiology

Techniques

Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities – Mads Albertsen – PLOS ONE

Microbial ecology

Interaction networks for identifying coupled molecular processes in microbial communities – Magnus Bosse – BioData Mining

Microbes in the news

10 Ways to Cultivate Good Gut Bacteria and Reduce Depression – Therese Borchard – Everyday Health

Science, publishing, and career

Hundreds sign letter criticizing Science for reinforcing “damaging stereotypes” – Shannon Palus – Retraction Watch

Bik’s Picks

International report confirms: 2014 was Earth’s warmest year on record – NOAA

A second FDA approval frees Theranos to do a blood test outside lab – Roger Parloff – Fortune

Mosquitoes first sniff then attack their host – Dispatch Times

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July 16, 2015

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Biomimetic robot models of host-microbiome interactions, an eukaryotic model for astrobiology, how plants use salicylic acid to sculpt their root microbiome, and how to cook Hadza tubers.

Human oral microbiome

TLR4, NOD1 and NOD2 Mediate Immune Recognition of Putative Newly-Identified Periodontal Pathogens – Julie Marchesan – Molecular Oral Microbiology

Human respiratory microbiome

Intraalveolar Catecholamines and the Human Lung Microbiome – Robert P. Dickson – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Transforming berberine into its intestine-absorbable form by the gut microbiota – Ru Feng – Scientific Reports

I could not find information about primers or sequencing strategy, no ordination plots: Colonic bacterial composition in Parkinson’s disease – Ali Keshavarzian – Movement Disorders

Review: Role of gut microbiota in the modulation of atherosclerosis-associated immune response – Dmitry A. Chistiakov – Frontiers in Microbiology

Review: Potential role of the intestinal microbiota in programming health and disease – Olivier Goulet – Nutrition Reviews

Review: Microbiota and the gut–brain axis – John Bienenstock – Nutrition Reviews

Review: The Blood-Brain Barrier’s Gut Check – Nga Bien-Ly – Science Translational Medicine

Review: The Microbes inside Us and the Race for Colibactin – Helge B. Bode – Angewandte Chemie International Edition

Animal models

Macaques: Persistent effects of early infant diet and associated microbiota on the juvenile immune system – Nicole Narayan – Gut Microbes

Pigs: Wheat and barley differently affect porcine intestinal microbiota – Eva Weiss – Journal of the Science of Food and Agriculture

Rats: Bacterial Flora Changes in Conjunctiva of Rats with Streptozotocin-Induced Type I Diabetes – Chao Yang – PLOS ONE

Animal microbiome

Fish-like marine chordate: Diversity and composition of the bacterial community in Amphioxus feces – Minming Pan – Journal of Basic Microbiology

Plant, root, and soil microbiome

Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa – Sarah L. Lebeis – Science

Silencing a key gene of the common symbiosis pathway in Nicotiana attenuata specifically impairs arbuscular mycorrhizal infection without influencing the root-associated microbiome or plant growth – Karin Groten – Plant, Cell & Environment

Water microbiome

Microbial communities related to biodegradation of dispersed Macondo oil at low seawater temperature with Norwegian coastal seawater – Odd G. Brakstad – Microbial Biotechnology

Extremophile microbiome

UV-resistant yeasts isolated from a high-altitude volcanic area on the Atacama Desert as eukaryotic models for astrobiology – André A. Pulschen – Microbiology Open

Waste management microbiology

Changes in diversity of cultured bacteria resistant to erythromycin and tetracycline in swine manure during simulated composting and lagoon storage – L. Wang – Letters in Applied Microbiology

Functional foods

Assessing digestibility of Hadza tubers using a dynamic in-vitro model – Stephanie L. Schnorr – American Journal of Physical Anthropology

Bioinformatics

Exploring Host-Microbiome Interactions using an in Silico Model of Biomimetic Robots and Engineered Living Cells – Keith C. Heyde – Scientific Reports

K-Pax2: Bayesian identification of cluster-defining amino acid positions in large sequence datasets – Alberto Pessia – Microbial Genomics

Microbes in the news

Healthy Living: Preterm Birth Disparities: Doctor Dunlop and her team have begun a five year study to examine prenatal stress, diet and a woman’s microbiome on birth outcomes – 9&10 News
Five-year study to examine the gut microbiome of premature infants – Matt Wood – Science Life University of Chicago

Plant defense hormones help sculpt root microbiome – Science Daily

Research finds diversifying your diet may make your gut healthier – Science Codex

Do you smoke? UBiome wants to study your mouthome – Claire Maldarelli – Popular Science

Bik’s Picks

Polar Bears Don’t Go Into Hibernation-Like State in Summer, Researchers Say – James Gorman – New York Times

Finally, Bacon-Flavored Health Food Has Arrived: introducing dulse, a seaweed that tastes like bacon – Elizabeth Palermo – Live Science

Why screams are scary (hint: It’s not because they’re loud) – Eryn Brown – Los Angeles Times

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July 15, 2015

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Microbiome and weight loss with genetic and “simple” obesity, gut microbiome in coffee beetle detoxifies caffeine,  and a plant-fungal-bacterial symbiosis.

Jobs

Tenure Track position Environmental Microbiology at Montana State University- Bozeman

Pregnancy and birth microbiome

Late-Onset Bloodstream Infection and Perturbed Maturation of the Gastrointestinal Microbiota in Premature Infants – Alexander G. Shaw – PLOS ONE

Human skin microbiome

Identification of axillary Staphylococcus sp. involved in the production of the malodorous thioalcohol 3-methyl-3-sufanylhexan-1-ol – Daniel Bawdon – FEMS Microbiology Letters

Human gut microbiome

Dietary modulation of gut microbiota contributes to alleviation of both genetic and simple obesity in children – Chenhong Zhang – EBioMedicine

Stool bacteriomic profiling in patients with metastatic renal cell carcinoma receiving vascular endothelial growth factor-tyrosine kinase inhibitors – Sumanta K. Pal – Clinical Cancer Research

Proton Pump Inhibitors Alter Specific Taxa in the Human Gastrointestinal Microbiome: A Crossover Trial – Daniel E. Freedberg – Gastroenterology

Review: The bilateral responsiveness between intestinal microbes and IgA – Andrew J. Macpherson – Trends in Immunology

Animal models

Editorial: Medicinal mushroom reduces obesity by modulating microbiota – David Holmes – Nature Reviews Endocrinology

Bifidobacterium pseudocatenulatum CECT 7765 Reduces Obesity-Associated Inflammation by Restoring the Lymphocyte-Macrophage Balance and Gut Microbiota Structure in High-Fat Diet-Fed Mice – Angela Moya-Pérez – PLOS ONE

Animal microbiome

Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee – Javier A. Ceja-Navarro – Nature Communications

Seasonal and ontogenetic variation of skin microbial communities and relationships to natural disease dynamics in declining amphibians – Ana V. Longo – Royal Society Open Science

Most of the dominant members of amphibian skin bacterial communities can be readily cultured – Jenifer B. Walke – Applied and Environmental Microbiology

Effects of Host Phylogeny and Habitats on Gut Microbiomes of Oriental River Prawn (Macrobrachium nipponense) – Tzong-Der Tzeng – PLOS ONE

Potassium permanganate elicits a shift of the external fish microbiome and increases host susceptibility to columnaris disease – Haitham H. Mohammed – Veterinary Research

Microenvironment and Phylogenetic Diversity of Prochloron Inhabiting the Surface of Crustose Didemnid Ascidians – Daniel A. Nielsen – Environmental Microbiology

Deep Characterization of the Microbiomes of Calophya spp. (Hemiptera: Calophyidae) Gall-Inducing Psyllids Reveals the Absence of Plant Pathogenic Bacteria and Three Dominant Endosymbionts – Will A. Overholt – PLOS ONE

Plant, root, and soil microbiome

Review: What’s inside that seed we brew? A new approach to mining the coffee microbiome – Michael Joe Vaughan

A widespread plant-fungal-bacterial symbiosis promotes plant biodiversity, plant nutrition and seedling recruitment – Marcel GA van der Heijden – The ISME Journal

Terroir is a key driver of seed-associated microbial assemblages – Stephanie Klaedtke – Environmental Microbiology

Water microbiome

Enhanced salinities, as a proxy of seawater desalination discharges, impact coastal microbial communities of the eastern Mediterranean Sea – Natalia Belkin – Environmental Microbiology

Top-down and bottom-up control on bacterial diversity in a western Norwegian deep silled fjord – Julia E. Storesund – FEMS Microbiology Ecology

Built environment microbiome

Using amplicon sequencing to characterize and monitor bacterial diversity in drinking water distribution systems – Jennifer L. A. Shaw – Applied and Environmental Microbiology

Microbes in the news

This Beetle is Ruining Your Coffee With the Help of Bacteria – Ed Yong- National Geographic
Gut microbes enable coffee pest to withstand extremely toxic concentrations of caffeine – Phys.org

Microbiologists Hold the Secrets to Making Perfect Cheese – Sophia Chen – Wired.com

About a study conducted in our lab: Citizen Science: How to be Your Own Research Project – Sally James – Seattle Mag

How To Make Better Health Predictions From Our Gut Microbes – Ed Yong – National Geographic

 

Microbiome Teams Up Against C. diff – Researchers build a mathematical model that can predict whether a mouse will be infected by Clostridium difficile based on the microbes found in its GI tract – Jef Akst – The Scientist

Research Finds Diversifying Your Diet May Make Your Gut Healthier – News Wise

Your Gut and Heart Health Connection – Carra Richling – Huffington Post

Prozac In The Yogurt Aisle: Can ‘Good’ Bacteria Chill Us Out? – Allison Aubrey – NPR

Bacteria could improve cancer detection: University lab is researching cancer utilizing intestinal microbial biomes – Sarah Thamer – MN Daily

Science, publishing, and career

Lifelong learning: Science professors need leadership training – Charles E. Leiserson & Chuck McVinney – Nature

PLOS Ecology Community Needs 2 Community Editors – PLOS

Bik’s Picks

Finally, here are the stunning pictures of Pluto NASA has waited a decade to capture – Rachel Feltman – Washington Post
Alzheimer’s Dementia Pathologies Differ by Race – Nancy A. Melville – Medscape

Oldest sperm ever is discovered in Antarctica, by accident – Will Greenberg – Washington Post

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July 14, 2015

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Antibiotic-induced changes in mouse gut microbiome, the lichen microbiome, and what’s floating in the airplane toilet?

Human respiratory microbiome

Common Cell Shape Evolution of Two Nasopharyngeal Pathogens – Frédéric J. Veyrier – PLOS Genetics

Human gut microbiome

Trimethylamine-N -oxide: A Novel Biomarker for the Identification of Inflammatory Bowel Disease – Aze Wilson – Digestive Diseases and Sciences

Review: Roles of commensal microbiota in pancreas homeostasis and pancreatic pathologies – Camila Leal-Lopes – Journal of Diabetes Research

Animal models of microbiome research

Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile – Alyxandria M. Schubert – mBio

Animal microbiome

The Apis mellifera Filamentous Virus Genome – Laurent Gauthier – Viruses

Concentrations of viable oil-degrading microorganisms are increased in feces from Calanus finmarchicus feeding in petroleum oil dispersions – Ingvild Fladvad Størdal – Marine Pollution Bulletin

Editorial: Microbial symbiosis of marine sessile hosts- diversity and function – Suhelen Egan – Frontiers in Microbiology

Plant, root, and soil microbiome

Analyzing the antagonistic potential of the lichen microbiome against pathogens by bridging metagenomic with culture studies – Tomislav Cernava – Frontiers in Microbiology

Indigenous trees restore soil microbial biomass at faster rates than exotic species – Chun Li – Plant and Soil

MSc Thesis: Tree Islands of Fertility Structure Bacterial Community Assembly and Functional Genes Contributing to Ecosystem Processes – Tayte Paul Campbell – Brigham Young University

Rhizosphere microbiome selection by Epichloë endophytes of Festuca arundinacea – Elizabeth Lewis Roberts – Plant and Soil

Responses of soil microbial communities and enzyme activities to nitrogen and phosphorus additions in Chinese fir plantations of subtropical China – W. Y. Dong – Biogeosciences Discussions

Water microbiome

Ubiquitous healthy diatoms in the deep sea confirm deep carbon injection by the biological pump – S. Agusti – Nature Communications

Extremophile microbiome

Characterization of the Bacterial and Sulphate Reducing Community in the Alkaline and Constantly Cold Water of the Closed Kotalahti Mine – Malin Bomberg – Minerals

Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes – J. Comte – Biogeosciences Discussions

Built environment and waste microbiome

Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance – Thomas Nordahl Petersen- Scientific Reports

Development of antibiotic resistance genes in microbial communities during long-term operation of anaerobic reactors in the treatment of pharmaceutical wastewater – Sevcan Aydin – Water Research

One-Time Addition of Nano-TiO2 Triggers Short-Term Responses in Benthic Bacterial Communities in Artificial Streams – Alexandra Ozaki – Microbial Ecology

Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure – Li Sun – Microbial Biotechnology

Characterization of the microbial community structure and the physicochemical properties of produced water and seawater from the Hibernia oil production platform – C. William Yeung – Environmental Science and Pollution Research

Archaea

The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales – Zackary J. Jay – Biology Direct

Bioinformatics

Estimating beta diversity for under-sampled communities using the variably weighted Odum dissimilarity index and OTUshuff – Daniel K. Manter – Bioinformatics

Swarm v2: highly-scalable and high-resolution amplicon clustering – Frederic Mahe – PeerJ

Cutting edge: Anatomy of BioJS, an open source community for the life sciences – Guy Yachdav – eLIFE

Metagenomics

Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes – Sari Peura – Scientific Reports

Metabolic networks, proteomics

A Single Host-Derived Glycan Impacts Key Regulatory Nodes of Symbiont Metabolism in a Coevolved Mutualism – Min Pan – mBIO

Extracellular protein analysis of activated sludge and their functions in wastewater treatment plant by shotgun proteomics – Peng Zhang – Scientific Reports

Techniques

Scaffolding of a bacterial genome using MinION nanopore sequencing – E. Karlsson – Scientific Reports

Microbial Ecology

Biodiversity inhibits parasites: Broad evidence for the dilution effect – David J. Civitello – PNAS

Science, publishing, and career

Big Data: Astronomical or Genomical? Projecting to the year 2025, we compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. – Zachary D. Stephens – PLOS Biology

The Outrage Factor – Then and Now: There’s a lot of outrage about outrage storming around women in science and science journalism at the moment. And fear of causing it, too. – Hilda Bastian – PLOS Blogs

Microbes in the news

Aging in Microbes: bacteria are using every trick in the book to get ahead – Josh Mitteldorf

Bik’s Picks

Everything you need to know about Tuesday’s Pluto encounter – Rachel Feltman – Washington Post

Introducing the Pentaquark: Physicists Prove a New Particle Exists – Tanya Basu – Time

Neighborhood greenspace and health in a large urban center : higher health perception if you live near trees – Omid Kardan – Scientific Reports
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July 13, 2015

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Trans-sialidases in human gut microbes, microbiome of the dairy cow’s uterus during metritis, and bacteria getting smaller because of ocean warming.

Jobs

Post-doctoral position is available in the laboratory of Lawrence David at Duke University: to help develop high-throughput microfluidic techniques for investigating bacterial interactions and ecology.

Conferences

Microbiome, Antibiotics and Human Disease, with Michael Fishbach, Martin Blaser, and Julie Segre – Cell Press Webinar July 28, 2015

11 speakers, only 1 woman: Meeting the Microbiome – 12 September 2015 – London, UK – CAM conferences

Microbiome of pregnancy and birth

High rates of Double-Stranded RNA Viruses and Mycoplasma hominis in Trichomonas vaginalis Clinical Isolates in South Brazil – Débora da Luz Becker – Infection, Genetics and Evolution

First Trimester Levels of BV-Associated Bacteria and Risk of Miscarriage Among Women Early in Pregnancy – Deborah B. Nelson – Maternal and Child Health Journal

Human oral microbiome

The impact of smoking and previous periodontal disease on peri-implant microbiota and health: a retrospective study up to 7-year follow-up – Quaranta A. – Annali Di Stomatologia

Human respiratory microbiome

Review: The Etiology and Pathogenesis of Chronic Rhinosinusitis: a Review of Current Hypotheses – Kent Lam – Current Allergy and Asthma Reports

Human gut microbiome

Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation – Louise E. Tailford – Nature Communications

Viewpoint: Helicobacter pylori: enemy, commensal or, sometimes, friend? –  Michael B Whalen – The Journal of Infection in Developing Countries

Review: Engineering the Microbiome: a Novel Approach to Immunotherapy for Allergic and Immune Diseases – Nan Shen – Current Allergy and Asthma Reports

Review: Antimicrobial Use, Human Gut Microbiota and Clostridium difficile Colonization and Infection – Caroline Vincent – Antibiotics

Animal models

The microbiota regulates type 2 immunity through RORγt+ T cells – Caspar Ohnmacht – Science

Animal microbiome

Uterine microbiota progression from calving until establishment of metritis in dairy cows – Soo Jin Jeon – Applied and Environmental Microbiology

Preening as a Vehicle for Key Bacteria in Hoopoes – Ángela Martínez-García – Microbial Ecology

Variation in the Microbiota of Ixodes ticks with geography, species and sex – Will Van Treuren – Applied and Environmental Microbiology

The Host as Driver of the Microbiota in the Gut and External Environment of Drosophila melanogaster – Adam C-N Wong – Applied and Environmental Microbiology

An Efficient Strategy Developed for Next-Generation Sequencing of Endosymbiont Genomes Performed Using Crude DNA Isolated from Host Tissues: A Case Study of Blattabacterium cuenoti Inhabiting the Fat Bodies of Cockroaches – Yukihiro Kinjo – Microbes and Environments

Arsenophonus and Sodalis symbionts in louse flies: an analogy to the Wigglesworthia and Sodalis system in tsetse flies – Eva Nováková – Applied and Environmental Microbiology

Review: Microbial metagenomics in aquaculture: a potential tool for a deeper insight into the activity – Marcel Martínez-Porchas – Reviews in Aquaculture

Plant, root, and soil microbiome

High-Throughput Sequencing Reveals Drastic Changes in Fungal Communities in the Phyllosphere of Norway Spruce (Picea abies ) Following Invasion of the Spruce Bud Scale (Physokermes piceae ) – Audrius Menkis – Microbial Ecology

Diversity of endophytic and rhizoplane bacterial communities associated with exotic Spartina alterniflora and native mangrove using Illumina amplicon sequencing – Youwei Hong – Canadian Journal of Microbiology

Communities of Cultivable Root Mycobionts of the Seagrass Posidonia oceanica in the Northwest Mediterranean Sea Are Dominated by a Hitherto Undescribed Pleosporalean Dark Septate Endophyte – Martin Vohník – Microbial Ecology

Precipitation modifies the effects of warming and nitrogen addition on soil microbial communities in northern Chinese grasslands – Naili Zhang – Soil Biology and Biochemistry

Long-term responses of plant growth, soil microbial communities and soil enzyme activities to elevated CO2 and neighbouring plants – Baoli Duan – Agricultural and Forest Meteorology

Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils – Christopher R. Penton – Frontiers in Microbiology

Methanotrophic community abundance and composition in plateau soils with different plant species and plantation ways – Yu Dai – Applied Microbiology and Biotechnology

Water microbiome

More, smaller bacteria in response to ocean’s warming? – Xosé Anxelu G. Morán – Proceedings B

Microbial community changes along the active seepage site of one cold seep in the Red Sea – Huiluo Cao – Frontiers in Microbiology

Spatiotemporal dynamics and determinants of planktonic bacterial and microeukaryotic communities in a Chinese subtropical river – Yongming Wang – Applied Microbiology and Biotechnology

Sediment Ammonia-Oxidizing Microorganisms in Two Plateau Freshwater Lakes at Different Trophic States – Yuyin Yang – Microbial Ecology

Detecting nuisance species using NGST: Methodology shortcomings and possible application in ballast water monitoring – Anastasija Zaiko – Marine Environmental Research

A novel bacterial community index to assess stream ecological health – Kelvin E. M. Lau – Freshwater Biology

Bioreactor microbiome

Functional and taxonomic dynamics of an electricity-consuming methane-producing microbial community – Orianna Bretschger – Bioresource Technology

Microbial community distribution and genetic analysis in a sludge active treatment for a complex industrial wastewater: a study using microbiological and molecular analysis and principal component analysis – Giulio Moretti – Annals of Microbiology

Bioinformatics and metagenomics

A reproducible approach to high-throughput biological data acquisition and integration – Daniela Börnigen – PeerJ

MetaBoot: a machine learning framework of taxonomical biomarker discovery for different microbial communities based on metagenomic data – Xiaojun Wang – PeerJ

Good laboratory practice for clinical next-generation sequencing informatics pipelines –
Amy S Gargis – Nature Biotechnology

Transcriptomics, proteomics, and metabolomics

Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions – Dennis Versluis – Scientific Reports

Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities – Fabian Kohrs – Proteomics

Combining Mass Spectrometric Metabolic Profiling with Genomic Analysis: A Powerful Approach for Discovering Natural Products from Cyanobacteria – Karin Kleigrewe – Journal of Natural Products

Microbial Ecology

Phylogenetic diversity analyses reveal disparity between fungal and bacterial communities during microbial primary succession – Shawn P. Brown – Soil Biology and Biochemistry

Editorial: Stopping superbugs, maintaining the microbiota – Victor Nizet – Science Translational Medicine

Biofilm Formation As a Response to Ecological Competition – Nuno M. Oliveria – PLOS Biology

Pawnobiome: Manipulation of the Hologenome Within One Host Generation and Beyond – Jameson D. Voss – Frontiers in Microbiology

Functional foods

Review: Towards microbial fermentation metabolites as markers for health benefits of prebiotics – Kristin A. Verbeke – Nutrition Research Reviews

Techniques

Blocking primers reduce co-amplification of plant DNA when studying bacterial endophyte communities – Brett E. Arenz – Journal of Microbiological Methods

Microbes in the news

The role of the microbiota in preventing allergies – Medical Xpress

World’s largest steel company to use rabbit gut microbe to cut emissions – Emma Hartley – The Guardian

Paw Prints: Streptococcus bacteria a part of natural flora of cats and dogs – Niki Laviolette – Tribune Star

“I’m treating my son’s autism… with someone else’s faeces” – Liam Quinn – Daily Mail
This celebrity reckons autism can be treated with a poo transplant: is he right? – Clair Weaver – AWW

Navy Researchers Identify Bacteria in Human Serum – Christian Kotanen – Science DOD
surface enhanced Raman scattering (SERS) spectroscopy

Why you can’t just eat one french fry (or donut or slice of pizza) – Katherine Ellen Foley – SBS.com

Genetically Modified Bacteria Could Change Future Drug Treatments – Brandi – Clapway

Scientists at Brown University using federal grant to study mysterious fungus killing bats – The Sun Chronicle

Stop Kissing And Cuddling Chicken To Stop Salmonella Outbreak: CDC – Jill Arce – Tech Times

Bik’s Picks

New Horizons Science Update: Pluto Is The Biggest One Of All – Nadia Drake – National Geographic

Your last chance to see ‘Manhattanhenge’ sunset is tonight – Amanda Schallert – NJ.com

What’s in a name? For newborns, maybe fewer medical errors – Tara Haelle – MS News
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July 9, 2015

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Microbiome in colicky infants, bacterial communities on seaweed, and viral communities in soil.

Events

Altering the Microbiome: Can it Impact Health? Sept 24, 2015. Call for Abstracts- Deadline August 3, 2015

Microbiome of pregnancy and birth

Probiotic Lactobacillus rhamnosus GG therapy and microbiological programming in infantile colic: a randomized, controlled trial – Anna Pärtty – Pediatric Research

Human respiratory microbiome
The Lung Microbiome: New Principles for Respiratory Bacteriology in Health and Disease – Robert P. Dickson – PLOS Pathogens

Human gut microbiome

Interactions between the intestinal microbiota and bile-acids in gallstones patients – Nirit Keren – Environmental Microbiology Reports

Plant, root, and soil microbiome

Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography – Ezequiel M. Marzinelli – Environmental Microbiology

Ecotoxicological assessment of soil microbial community tolerance to glyphosate – Marco Allegrini – Science of The Total Environment

Dynamics of autochthonous soil viral communities parallels dynamics of host communities under nutrient stimulation – Sharath Srinivasiah – FEMS Microbiology Ecology

Water microbiome

Zonation of bacterioplankton communities along aging upwelled water in the northern Benguela upwelling – Benjamin Bergen – Frontiers in Microbiology

Extremophile microbiome

Temporal evolution of bacterial communities associated with the in situ wetland-based remediation of a marine shore porphyry copper tailings deposit – N. Diaby – Science of The Total Environment

 

Bioinformatics

Web Resources for Microbial Data – Qinglan Sun – Genomics, Proteomics & Bioinformatics

The unifrac significance test is sensitive to tree topology – Catherine A. Lozupone – BMC Bioinformatics

Microbes in the news

Researchers discover how bacteria sweet-talk their way into plants – Aarhus University – EurekAlert

Probiotics—for plants: Helpful bacteria promote growth, less fertilizer on crops – Phys.org

Designer microbiome: MIT biologists program common gut bacteria – Eryn Brown – LA Times

Certain species dominate oral microbiome in patients with Sjögren’s syndrome – Healio

Science, publishing, and career

How to fail better (and even succeed!) in the academic job market – Dr. Acclimatrix – Tenure She Wrote

Bik’s Picks

Science reveals how giant pandas survive on a bamboo diet – Karen Kaplan – LA Times

Patients can spot trouble with new dental implants – Lisa Rapaport – Reuters

This jumping, squishy robot looks like a tiny UFO – Rachel Feltman – Washington Post
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July 8, 2015

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Just a short post today. PLOS ONE has a paper about burn victims and gut microbiome, in which both humans as well as mice were studied, but I really disliked the mouse experiments, where mice were deliberately burned (by shaving them and dipping them in near-boiling water). As a scientist, I realize that animal experiments can be useful, but I very much dislike animal studies that involve deliberate burns, enormous tumors, and parabiosis. I hope that these types of experiments can soon be replaced by more animal-friendly versions.

In other news: a bacterium on satellite survived entry into the Earth’s atmosphere. How cool is that?

Human respiratory microbiome

Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients – Wouter A A de Steenhuijsen Piters – The ISME Journal

Human/animal model gut microbiome

I really dislike the mouse part of this paper: Burn Injury Alters the Intestinal Microbiome and Increases Gut Permeability and Bacterial Translocation – Zachary M. Earley – PLOS ONE

Animal microbiome

Diet shapes the gut microbiome of pigs during nursing and weaning – Steven A. Frese – Microbiome

Plant, root, and soil microbiome

Editorial: Symbiosis: Receptive to infection – Sharon R. Long – Nature

Receptor-mediated exopolysaccharide perception controls bacterial infection – Y. Kawaharada – Nature

Water microbiome

Genomics and Ecophysiology of Heterotrophic Nitrogen-Fixing Bacteria Isolated from Estuarine Surface Water – Mikkel Bentzon-Tilia – mBio

More microbiology

Eye-like ocelloids are built from different endosymbiotically acquired components –
Gregory S. Gavelis – Nature

Spore-Forming Thermophilic Bacterium within Artificial Meteorite Survives Entry into the Earth’s Atmosphere on FOTON-M4 Satellite Landing Module – Alexander Slobodkin – PLOS ONE

Microbes in the news

Justin and Erica Sonnenburg: The Gut Connection – The Insight

Together bacteria invade antibiotic landscapes – Phys.org

Now You Can Buy Shampoo and Cleanser That Promote the Growth of “Good” Bacteria – L.V. Anderson – Slate

Just How Gross Is It to Leave Your Toothbrush In The Bathroom? – Lindsay Colameo – Allure

Science, publishing, and career

Postdocs will be getting a raise – Justin Kiggins – The Spectroscope
and
Will Obama’s revamp of the overtime rules mean postdocs are paid more? – Drugmonkey

Bik’s Picks

Shark selfies: Shark Files: Baited Cameras to Count World Sharks – Lori Cuthbert – Discovery

Scientists Discover a ‘Complex Cocktail of Many Chemicals’ in Snail Venom That Could Treat Cancer, Pain and Addiction – Liz Klimas – The Blaze

These Plastic Chemicals May Be Just As Dangerous As What They Replace – Justin Worland – Time

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July 7, 2015

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A personal perspective on microbiome research, phenotypic heterogeneity in microorganisms, ruling out viruses as causes for necrotizing enterocolitis, and Robert Edgar’s USEARCH.

Job openings

Philipps-Universität Marburg and the Max-Planck Institute for Terrestrial Microbiology are looking for 2 postdocs (one experimentalist and one bioinformatician)

General microbiome

Personal perspective: From cell biology to the microbiome: An intentional infinite loop – Wendy S. Garrett – Journal of Cell Biology

Microbiome of pregnancy and birth

Cytomegalovirus and other common enteric viruses are not commonly associated with Necrotizing Enterocolitis – Thomas Skeath – Acta Paediatrica

Viremia during pregnancy and risk of childhood leukemia and lymphomas in the offspring: Nested case-control study – Davit Bzhalava – International Journal of Cancer

Human oral microbiome

The Oral Bacterial Communities of Children with Well-Controlled HIV Infection and without HIV Infection – Brittany E. Goldberg – PLOS ONE

Human respiratory microbiome

Sputum Bacterial and Fungal Dynamics during Exacerbations of Severe COPD – Jin Su – PLOS ONE

Human gut microbiome

Chemotherapy-driven dysbiosis in the intestinal microbiome – E. Montassier – Alimentary Pharmacology & Therapeutics

Animal models of microbiome research

Perilipin-2 Modulates Lipid Absorption and Microbiome Responses in the Mouse Intestine – Daniel N. Frank – PLOS ONE

Animal microbiome

NGS metabarcoding proves successful for quantitative assessment of symbiont abundance: the case of feather mites on birds – J. Diaz-Real

Genetic Structure and Antimicrobial Resistance of Escherichia coli and Cryptic Clades in Birds with Diverse Human Associations – Michaela D. J. Blyton – Applied and Environmental Microbiology

Coral transplantation triggers shift in microbiome and promotion of coral disease associated potential pathogens – Jordan M. Casey – Scientific Reports

Plant, root, and soil microbiome

Metabarcoding Analysis of Fungal Diversity in the Phyllosphere and Carposphere of Olive (Olea europaea) – Ahmed Abdelfattah – PLOS ONE

High carbon use efficiency in soil microbial communities is related to balanced growth, not storage compound synthesis – Paul Dijkstra – Soil Biology and Biochemistry

Earthworms modify microbial community structure and accelerate maize stover decomposition during vermicomposting – Yuxiang Chen – Environmental Science and Pollution Research

Water microbiome

Microbial Communities Associated with Zones of Elevated Magnetic Susceptibility in Hydrocarbon-contaminated Sediments – Carol L. Beaver – Geomicrobiology Journal

Bacterial diversity differences along an epigenic cave stream reveal evidence of community dynamics, succession, and stability – Kathleen Brannen-Donnelly – Frontiers in Microbiology

Firmicutes is an Important Component of Microbial Communities in Water-Injected and Pristine Oil Reservoirs; Western Siberia, Russia – Yulia Frank – Geomicrobiology Journal

Functional interactions among filamentous Epsilonproteobacteria and Bacteroidetes in a deep-sea hydrothermal vent biofilm – Runar Stokke – Environmental Microbiology

Temporal Study of the Microbial Diversity of the North Arm of Great Salt Lake, Utah, U.S. – Swati Almeida-Dalmet – Microorganisms

Diversity of the Sediment Microbial Community in the Aha Watershed (Southwest China) in Response to Acid Mine Drainage Pollution Gradients – Weimin Sun – Applied and Environmental Microbiology

Microbial Transport, Retention, and Inactivation in Streams: A Combined Experimental and Stochastic Modeling Approach – Jennifer D. Drummond – Environmental Science & Technology

Extremophile microbiome

Ribosomal tag pyrosequencing of DNA and RNA reveals ‘rare’ taxa with high protein synthesis potential in the sediment of a hypersaline lake in Western Australia – Pascal Weigold – Geomicrobiology Journal

Microbial Diversity in Engineered Haloalkaline Environments Shaped by Shared Geochemical Drivers Observed in Natural Analogues – Talitha C. Santini – Applied and Environmental Microbiology

Built environment microbiome

A New Perspective on Microbiome and Resource Management in Wastewater Systems – Veera Gnaneswar Gude – Biotechnology & Biomaterials

Microbial Ecology

A functional perspective on phenotypic heterogeneity in microorganisms – Martin Ackermann – Nature Reviews Microbiology

Bioinformatics and statistics

USEARCH: Error filtering, pair assembly, and error correction for next-generation sequencing reads – Robert C. Edgar – Bioinformatics

Assessment and Selection of Competing Models for Zero-Inflated Microbiome Data – Lizhen Xu – PLOS ONE

Metabolomics and metatranscriptomics

Functional metabolomics: from biomarker discovery to metabolome reprogramming – Bo Peng – Protein & Cell

Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation – Michael Reck – BMC Genomics

Hydrodynamic chronoamperometry for probing kinetics of anaerobic microbial metabolism – case study of Faecalibacterium prausnitzii – Antonin Prévoteau – Scientific Reports

Techniques

A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes – Craig W. Herbold – Frontiers in Microbiology

This paper is not novel at all: An improved method for bacterial identification through 16S rDNA sequencing using double set of primers: a case study – Amanat Ali – Pak. J. Agri. Sci.,

Microbes in the news

How Bacteria Make This Underground, Awe-Inspiring Cave Shine Gold – Michele Lent Hirsch – Smithsonian

Bacteria in a bottle? AOBiome offers ways to stay clean without traditional soap – Nidhi Subbaraman – The Boston Globe

uBiome to Award Grant of up to $100k for Groundbreaking Microbiome Research – PR Web

Bik’s Picks

NASA Releases Time-Lapse Video Of Mars Rover Opportunity’s Journey: 11 Years In Just 8 Minutes – Jim Algar – Tech Times

Self-Driving ‘Robocabs’ Could Help Curb Global Warming – Wendy Koch – National Geographic

‘Vampires’ keep doctors in the dark for fear of stereotyping: study – Reuters

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July 6, 2015

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Oral microbiomes of dogs and their owners, airway mycobiome in CF patients, memory B cells and antibodies to gut microbiota, and yogurt containing seawater (?).

Human oral microbiome

Comparison of the Oral Microbiomes of Canines and Their Owners Using Next-Generation Sequencing – Changin Oh – PLOS ONE

Systemic immunity shapes the oral microbiome and susceptibility to bisphosphonate-associated osteonecrosis of the jaw – Shirin Kalyan – Journal of Translational Medicine

Review: Oral malodorous gases and oral microbiota: From halitosis to carcinogenesis – Naoko Tanda – Journal of Oral Biosciences

Human respiratory microbiome

A cohort study of the airway mycobiome in adult cystic fibrosis patients: differences in community structure of fungi compared to bacteria reveal predominance of transient fungal elements – Rolf Kramer – Journal of Clinical Microbiology

Review: The role of the local microbial ecosystem in respiratory health and disease – Wouter A. A. de Steenhuijsen Piters – Philosophical Transactions B

Review: The mechanism or mechanisms driving atopic asthma initiation: The infant respiratory microbiome moves to center stage – Patrick G. Holt – Journal of Allergy and Clinical Immunology

Human gut microbiome

Diversification of memory B cells drives the continuous adaptation of secretory antibodies to gut microbiota – Cornelia Lindner – Nature Immunology

Dietary modulation of the gut microbiota – a randomised controlled trial in obese postmenopausal women – Lena K. Brahe – British Journal of Nutrition

Anti-TNF treatment with adalimumab induces changes in the microbiota of Crohn’s disease – Busquets David – Journal of Crohn’s and Colitis

Effects of high doses of vitamin D3 on mucosa-associated gut microbiome vary between regions of the human gastrointestinal tract – Mina Bashir – European Journal of Nutrition

Review: Suppression of inflammation by helminths: a role for the gut microbiota? – Paul Giacomin – Philosophical Transactions B

Review: Immune-microbiota interactions in health and disease – Noah W. Palm – Clinical Immunology

Animal models

Lentinula edodes-derived polysaccharide rejuvenates mice in terms of immune responses and gut microbiota – Xiaofei Xu – Food and Function

Effect of Lactobacillus plantarum FH185 on the Reduction of Adipocyte Size and Gut Microbial Changes in Mice with Diet-induced Obesity – Sun-Young Park – Korean Journal for Food Science of Animal Resources

In vitro probiotic characteristics of Lactobacillus plantarum ZDY 2013 and its modulatory effect on gut microbiota of mice – Renhui Huang – Journal of Dairy Science

Reduced airway microbiota diversity is associated with elevated allergic respiratory inflammation – Wenkai Yu – Annals of Allergy, Asthma & Immunology

The prebiotics 3’Sialyllactose and 6’Sialyllactose diminish stressor-induced anxiety-like behavior and colonic microbiota alterations: evidence for effects on the gut-brain axis – Andrew J. Tarr – Brain, Behavior, and Immunity

Effect of yogurt containing deep sea water on health-related serum parameters and intestinal microbiota in mice – Sun Moon Kang – Journal of Dairy Science

Animal microbiome

In situ identification and quantification of starch-hydrolyzing bacteria attached to barley and corn grain in the rumen of cows fed barley-based diets – Yun Xia – FEMS Microbiology Ecology

Developmental Dynamic Analysis of the Excreted Microbiome of Chickens Using Next-Generation Sequencing – Lim S. – Journal of Molecular Microbiology and Biotechnology

Wolbachia influences the production of octopamine and affects Drosophila male aggression – Chelsie E. Rohscheib – Applied and Environmental Microbiology

Expanding the Entamoeba Universe: New Hosts Yield Novel Ribosomal Lineages – Alison S. Jacob – Journal of Eukaryotic Microbiology

Interactions between multiple helminths and the gut microbiota in wild rodents – Jakub Kreisinger – Philosophical Transactions B

Plant, root, and soil microbiome

The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes – Pablo R. Hardoim – Microbiology and Molecular Biology Reviews

The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time – Britt Koskella – Philosophical Transactions B

Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States – Ederson da C. Jesus – GCB Bioenergy

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota –
Eduard Vico Oton – The ISME Journal

Composition of soil microbial communities in the rhizosphere of cucumber cultivars with differing nitrogen acquisition efficiency – Xingang Zhou – Applied Soil Ecology

Differential Decay of Wastewater Bacteria and Change of Microbial Communities in Beach Sand and Seawater Microcosms – Qian Zhang – Environmental Science & Technology

New traceability strategies based on a biological Bar Code by PCR-DGGE using bacterial and yeast communities for determining farming type of peach – Ahmed El Shobaky – Egyptian Journal of Basic and Applied Sciences

Optimization of biostimulant for bioremediation of contaminated coastal sediment by response surface methodology (RSM) and evaluation of microbial diversity by pyrosequencing – Bakthavachallam Subha – Marine Pollution Bulletin

Water microbiome

Metagenomic study of red biofilms from Diamante Lake reveals ancient arsenic bioenergetics in haloarchaea – Nicolás Rascovan – ISME Journal

Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis – Benjamin Bolduc – The ISME Journal

Built Environment Microbiome

Bacteriological assessment of the hospital environment in two referral hospitals in Yaoundé-Cameroon – Kamga Hortense Gonsu – Pan African Medical Journal

Green spaces and cognitive development in primary schoolchildren – Payam Dadvand – PNAS

Food microbiology

Source Tracking and Succession of Kimchi Lactic Acid Bacteria during Fermentation –
Se Hee Lee – Journal of Food Science

House microbiotas as sources of lactic acid bacteria and yeasts in traditional Italian sourdoughs – Fabio Minervini – Food Microbiology

Proteomics

Estimating the computational limits of detection of microbial non-model organisms – Mathias Kuhring – Proteomics

Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation – Bernhard Tschitschko – The ISME Journal

Microbial Ecology

Paleobiological Perspectives on Early Microbial Evolution – Andrew H. Knoll – Cold Spring Harbor Perspectives in Biology

Review: Building the microbiome in health and disease: niche construction and social conflict in bacteria – Luke McNally – Philosophical Transactions B

Hypothesis: Restriction modification systems as engines of diversity – Kim Sneppen – Frontiers in Microbiology

Review: A Replisome’s journey through the bacterial chromosome – Thomas R. Beattie – Frontiers in Microbiology

Bioinformatics and metagenomics

Horizontal gene transfer in an acid mine drainage microbial community – Jiangtao Guo – BMC Genomics

ISQuest: Finding Insertion Sequences in Prokaryotic Sequence Fragment Data – Abhishek Biswas – Bioinformatics

Comparing K-mer based methods for improved classification of 16S sequences – Hilde Vinje – BMC Bioinformatics

Databases for Microbiologists – Igor B. Zhulin – Journal of Bacteriology

Techniques

Here, there, and everywhere: From PCRs to next‐generation sequencing technologies and sequence databases, DNA contaminants creep in from the most unlikely places – Karl Gruber – EMBO Reports

Microbes in the news

Bacteria ‘Fight Club’ could help find new cures for diseases – Alexandra Ossola – Popular Science
Sold on Symbiosis: A love of the ocean lured Nicole Dubilier into science; gutless sea worms and their nurturing bacterial symbionts keep her at the leading edge of marine microbiology – Anna Azvolinsky – The Scientist

Terroir: how fungi, yeasts and bacteria affect the taste of your wine – Max Allen – The Australian

Brookline’s Maya Sekhar wins grand prize at state science fair (work on phages)

Almost half of Americans don’t understand threat of antibiotic resistance – Ginger Skinner – Consumer Reports

The Human Microbiome: do not underestimate microbes! – John Dalton – David Game College

Faecal transplants, diet on trend as society embraces gut health – Hamish Fitzsimmons – ABC.au

Aquarium Microbiome Project – Shedd Aquarium – YouTube

The Microbiology Weekly – Cesar Sanchez

This Bacteria-Slaying Light Fixture Is Perfectly Safe For Humans – Andrew Liszewski – Gizmodo

Researcher finds bacteria in pistachio trees – Angela Simental – Las Cruces Sun

Bacteria-Eating Viruses Could Be New Ally Against Superbugs In A ‘Post-Antibiotic Era’ – Ben Hirschler – Reuters / Huffington Post

Linking the microbiome and colorectal cancer: an author Q+A – Sophie Marchant – BioMedCentral blogs

Bik’s Picks

US Fish & Wildlife struggles to save remaining polar bears – Sam Catherman – News Quench

Professor: Nothing Fishy About Portuguese Man o’ War at Jersey Shore – NBC

Japan And The U.S. Are Going To Have An Actual Giant Robot Battle – Damon Beres – The Huffington Post

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