Category Archives: Bik’s Non-Microbiology Picks

July 23, 2015

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Proteobacteria in gut dysbiosis, microbes on seagrass, viral dark matter, metabolic ups and downs in the biofilm, bacteria/whiskey/copper, The Brown Lagoon, and I’ll see you in the gut.

Human gut microbiome

Review: Proteobacteria: microbial signature of dysbiosis in gut microbiota – Na-Ri Shin – Trends in Biotechnology

DGGE: Equol status and changes in faecal microbiota in menopausal women receiving long-term treatment for menopause symptoms with a soy-isoflavone concentrate – Lucía Guadamuro – Frontiers in Microbiology

Microbiome models

Editorial with a clever title. Like. Escaping Negative Selection: ILC You in the Gut – Adam M. Farkas – Immunity

Maraviroc modifies gut microbiota composition in a mouse model of obesity: a plausible therapeutic option to prevent metabolic disorders in HIV-infected patients – Patricia Perez-Matute – Rev Esp Quimioter

Plants, roots, and soil microbiome

Oxalate secretion by ectomycorrhizal Paxillus involutus is mineral-specific and controls calcium weathering from minerals – A. Schmalenberger – Scientific Reports

Cultivation-dependent analysis the microbial diversity associated with the seagrass meadows in Xincun Bay, South China Sea (sic) – Yu-Feng Jiang – Ecotoxicology

Unearthing the genomes of plant-beneficial Pseudomonas model strains WCS358, WCS374 and WCS417 – Roeland L. Berendsen – BMC Genomics

Water microbiome

Microbial communities associated with benthic faunal assemblages at cold seep sediments of the Sonora Margin, Guaymas Basin – Perrine Cruaud – Frontiers in Marine Science

Assessment of Zooplankton Community Composition along a Depth Profile in the Central Red Sea – John K. Pearman – PLOS ONE

Waste and bioreactor microbiology

Functionally redundant but dissimilar microbial communities within biogas reactors treating maize silage in co-fermentation with sugar beet silage – Susanne G. Langer – Microbial Biotechnology

Effects of Calamagrostis epigejos, Chamaenerion palustre and Tussilago farfara on nutrient availability and microbial activity in the surface layer of spoil heaps after hard coal mining – Anna M. Stefanowicz – Ecological Engineering

Degradation of Biofumigant Isothiocyanates and Allyl Glucosinolate in Soil and Their Effects on the Microbial Community Composition – Franziska S. Hanschen – PLOS ONE

Assessing hog lagoon waste contamination in the Cape Fear Watershed using Bacteroidetes 16S rRNA gene pyrosequencing – Ann M. Arfken – Applied Microbiology and Biotechnology

Bacterial community structure and predicted alginate metabolic pathway in an alginate-degrading bacterial consortium – Akihisa Kita – Journal of Bioscience and Bioengineering

Metagenomics and bioinformatics

Viral dark matter and virus-host interactions resolved from publicly available microbial genomes – Simon Roux – eLIFE

Conference abstract: MetaFast: fast reference-free graph-based comparison of shotgun
metagenomic data – Sergey V. Kazakov

Microbial Ecology

Metabolic co-dependence gives rise to collective oscillations within biofilms – Jintao Liu – Nature

Neutral Models of Microbiome Evolution – Qinglong Zeng – PLOS Computational Biology

Fitness cost of antibiotic susceptibility during bacterial infection – Damien Roux – Science Translational Medicine

New Paradigms in Sepsis: From Prevention to Protection of Failing Microcirculation –
J. Hawiger – Journal of Thrombosis and Haemostasis

Helicobacter pylori eradication for the prevention of gastric neoplasia – Alexander C Ford – Cochrane Library

Microbes in the news

Mutations that make bacteria resistant to antibiotics might also make them deadlier – Arielle Duhaime-Ross – The Verge

Bacteria are many things, but selfish isn’t one of them, scientists say – Robert Gebelhoff – Washington Post

Ulcer-causing bacteria may be key to stomach cancer: A combination of antibiotics and a drug reducing the production of gastric acid can eliminate the bacteria – Stephen Feller – UPI

Project aims to use probiotic bacteria to protect algal crops and increase ecosystem resilience – Lawrence Livermore National Laboratory

Bacteria makes copper from whisky waste – Tereza Pultarova – E&T Institution for Engineering and Technology

Bik’s Picks – reptile edition

HT Ed Yong: No Motherhood Yet for 100-Year-Old Turtle – John R. Platt – Scientific American

Turns Out Boa Constrictors Might Not Actually Suffocate Their Prey – Hilary Hanson – Huffington Post

A Fossil Snake With Four Legs – Ed Yong – National Geographic
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July 22, 2015

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Disappearance of intestinal diversity with Westernization, microbial responses in the Namib Desert after “wetting events”, how fast do ocean bacteria grow, irradiation of oral microbiota, and paying $8 to read 2 sentences.

Human gut microbiome

Antibiotic Exposure and Juvenile Idiopathic Arthritis: A Case–Control Study – Daniel B. Horton – Pediatrics

Bile diversion to the distal small intestine has comparable metabolic benefits to bariatric surgery – Charles Robb Flynn – Nature Communications

Microbiome changes associated with sustained eradication of Clostridium difficile after single faecal microbiota transplantation in children with and without inflammatory bowel disease – S. K. Hourigan – Alimentary Pharmacology & Therapeutics

Review: Gut Microbiome: Westernization and the Disappearance of Intestinal Diversity – Nicola Segata – Current Biology

Models of microbiome research

Dual zinc transporter systems in Vibrio cholerae promote competitive advantages over gut microbiome – Ying Sheng – Infection and Immunity

Low-dose irradiation affects the functional behavior of oral microbiota in the context of mucositis – Barbara WA Vanhoecke – Experimental Biology and Medicine

You have to pay $8 to read the remaining 2 sentences of this In Brief: Engineered microbes treat experimental hyperammonemia – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Review: The Gut Microbiota of Termites: Digesting the Diversity in the Light of Ecology and Evolution – Andreas Brune and Carsten Dietrich – Annual Review of Microbiology

Plant, root, and soil microbiome

Effects of silver sulfide nanomaterials on mycorrhizal colonization of tomato plants and soil microbial communities in biosolid-amended soil – Jonathan D. Judy – Environmental Pollution

Phylogenic diversity and tissue specificity of fungal endophytes associated with the pharmaceutical plant, Stellera chamaejasme L. revealed by a cultivation-independent approach – Hui Jin – Antonie van Leeuwenhoek

Water regime history drives responses of soil Namib Desert microbial communities to wetting events – Aline Frossard – Scientific Reports

Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility – Acacio Aparecido Navarrete – Antonie van Leeuwenhoek

Water microbiome

Shifts in bacterial community composition associated with increased carbon cycling in a mosaic of phytoplankton blooms – Marine Landa – The ISME Journal

Review: Growth Rates of Microbes in the Oceans – David L. Kirchman – Annual Review of Marine Science

Metagenomics, bioinformatics

Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data – Will Rowe – PLOS ONE

Protective tunicate endosymbiont with extreme genome reduction – Jan-Christoph Kehr – Environmental Microbiology

Metabolomics

Microbial Urease in Health and Disease – Diego Mora – PLOS Pathogens

Techniques

Environmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa; Arcellinida; Hyalospheniidae) – Anush Kosakyan – European Journal of Protistology

Nested PCR Biases in Interpreting Microbial Community Structure in 16S rRNA Gene Sequence Datasets – Guoqin Yu – PLOS ONE

Bacteria in the news

Fungi—key to tree survival in warming forest – Phys.org

Story behind the paper: Backbones of evolutionary history test biodiversity theory for microbes – James O. Dwyer – The Tree of Life

New open source uBiome github repository for data analysis tools – Alexandra Carmichael – uBiome

Bik’s Picks

The picture almost made me cry. Early signs that drug ‘may delay Alzheimer’s decline’ – James Gallagher – BBC News

Earth’s Most Famous Climate Scientist Issues Bombshell Sea Level Warning – Eric Holthaus – Slate

Space travel thins your skin: Spending a significant amount of time in space has several negative effects on the body. The latest discovery: thinner skin – Michelle Starr – CNET

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July 21, 2015

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Microbiome of a dead pig in the snow, two papers on oral microbiome in HIV infection, sweetener consumption and microbiome, proteomics of preterm infant colonization, sequencing platform and primer choices, and including microbial ecology in Pre-med programs.

Microbiology of death

Using Bacterial and Necrophagous Insect Dynamics for Post-Mortem Interval Estimation during Cold Season: Novel Case Study in Romania – Lavinia Iancu – Forensic Science International

Pregnancy and birth / Proteomics

Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant – Brandon Brooks

Human oral microbiome

The Oral Microbiome in HIV-positive Individuals – James O. Kistler – Journal of Medical Microbiology

Exploring salivary microbiota in AIDS patients with different periodontal statuses using 454 GS-FLX Titanium pyrosequencing – Fang Zhang – Frontiers in Cellular and Infection Microbiology

Review: Bacteria and Archaea Paleomicrobiology of the Dental Calculus: a Review – Hong T.T. Huynh – Molecular Oral Microbiology

Human urinary tract microbiome

Review: Intracellular Bacterial Communities: A Potential Etiology for Chronic Lower Urinary Tract Symptoms – Victoria C.S. Scott – Urology

Human gut microbiome

High-intensity sweetener consumption and gut microbiome content and predicted gene function in a cross-sectional study of adults in the United States – Cara L. Frankenfeld – Annals of Epidemiology

Pomegranate extract induces ellagitannin metabolite formation and changes stool microbiota in healthy volunteers – Zhaoping Li – Food & Function

Models of microbiome

Neutrophil gelatinase-associated lipocalin regulates gut microbiota of mice – Katsuya Mori – Journal of Gastroenterology and Hepatology

Effect of Dietary Protein Levels on Composition of Odorous Compounds and Bacterial Ecology in Pig Manure – Sungback Cho – Asian Australas. J. Anim. Sci

Animal microbiome

Shotgun Metagenomic Sequencing Reveals Functional Genes and Microbiome Associated with Bovine Digital Dermatitis – Martin Zinicola – PLOS ONE

Diversity and composition of the bacterial community in Amphioxus feces – Minming Pan – Journal of Basic Microbiology

Isolation, characterization, and antibiotic resistance of Vibrio spp. in sea turtles from Northwestern Mexico – Alan A. Zavala-Norzagaray – Frontiers in Microbiology

Microbial Infections Are Associated with Embryo Mortality in Arctic-Nesting Geese – Cristina M. Hansen – Applied and Environmental Microbiology

An insight into the functional role of thioredoxin reductase, a selenoprotein, in maintaining normal native microbiota in the Gulf Coast tick (Amblyomma maculatum) – K. Budachetri – Insect Molecular Biology

Chemotaxis by natural populations of coral reef bacteria – Jessica Tout – The ISME Journal

Review: Exploring the avian gut microbiota: current trends and future directions – David W. Waite – Frontiers in Microbiology

Plant, root, and soil microbiome

Lactic acid bacteria are endophytic components of durum wheat plant following the whole life cycle from plant to flour – Fabio Minervini – Applied and Environmental Microbiology

Application of mesotrione at different doses in an amended soil: Dissipation and effect on the soil microbial biomass and activity – Eva Pose-Juan – Science of The Total Environment

Plant species richness does not attenuate responses of soil microbial and nematode communities to a flood event – Daniela Wagner – Soil Biology and Biochemistry

Declined soil suppressiveness to Fusarium oxysporum by rhizosphere microflora of cotton in soil sickness – Xiaogang Li – Biology and Fertility of Soils

Water / extremophile microbiome

Diversity of methanogens and sulfate-reducing bacteria in the interfaces of five deep-sea anoxic brines of the Red Sea – Yue Guan – Research in Microbiology

Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions – Christopher M. Bellas – Frontiers in Microbiology

A Paleoarchean coastal hydrothermal field inhabited by diverse microbial communities: the Strelley Pool Formation, Pilbara Craton, Western Australia – K. Sugitani – Geobiology

Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents – Daniel C Reed – The ISME Journal

Waste and bioreactor microbiology

GeoChip-based analysis of microbial community of a combined nitritation-anammox reactor treating anaerobic digestion supernatant – Jian Zhao – Water Research

Arsenic toxicity effects on microbial communities and nutrient cycling in indoor experimental channels mimicking a fluvial system – Baigal-Amar Tuulaikhuu – Aquatic Toxicology

Microbial ecology

Review: Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis – Florent Lassalle – Research in Microbiology

Microbiology and Ecology Are Vitally Important to Premedical Curricula – Val H. Smith – Evolution, Medicine, and Public Health

Bioinformatics and metagenomics
MCaVoH: A toolkit for Mining, Classification and Visualization of Human Microbiota –
Maryum Nisar – Journal of Microbiological Methods

An intriguing new bacterial phylum – Naomi Attar – Nature Reviews Microbiology

Metabolic networks

A biosynthetic pathway for a prominent class of microbiota-derived bile acids – A Sloan Devlin – Nature Chemical Biology

Methanogenic food web in the gut contents of methane-emitting earthworm Eudrilus eugeniae from Brazil – Kristin Schulz – The ISME Journal

Auxotrophy and intra-population complementary in the ‘interactome’ of a cultivated freshwater model community – Sarahi L Garcia – Molecular Ecology

Techniques

Primer and platform effects on 16S rRNA tag sequencing – Julien Tremblay – Frontiers in Microbiology

Microbes in the news

Programming Bacteria to Kill Cancer Cells – Lecia Bushak – Newsweek

Scientists keep finding more evidence that bacteria in your stomach are connected to your mood – Kevin Loria – Business Insider

#BacteriaHysteria: The even grosser cause behind gross smelling feet – Stephanie Bell-Flynt

Bik’s Picks
One Migration from Siberia Peopled the Americas: Study – Discovery

Study: Women With Mild Memory Problem Worsen Faster Than Men – Lauran Neergaard – ABC News

Marijuana helps broken bones heal, says Israeli scientific team – Ruth Schuster – Haaretz

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July 20, 2015

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Transcriptomics in periodontitis, stool consistency, truffles, ginger and pigs, and salt deserts.

Events (repeat posts)

Free Cell Press Webinar: Microbiome, Antibiotics and Human Disease with human microbiome leaders Martin Blaser, Michael Fischbach and Julie Segre – July 28, 2015, noon EST

Multi-omics for Microbiomes Conference, September 14-16, 2015, Three Rivers Convention Center, Kennewick, WA
Human oral microbiome / transcriptomics

Small RNA transcriptome of the oral microbiome during periodontitis progression – Ana E. Duran-Pinedo – Applied and Environmental Microbiology

Human gut microbiome

Solid evidence: Stool consistency as a major confounding factor affecting microbiota composition: an ignored variable? – Jack A Gilbert – Gut

Review [PDF]: Beyond gut microbiota: understanding obesity and type 2 diabetes – Eva Lau – Hormones

Models of microbiome research

Ginger and inulin: Assessment of Fecal Microflora Changes in Pigs Supplemented with Herbal Residue and Prebiotic – Ashis Kumar Samanta – PLOS ONE

Plant, root, and soil microbiome (and extremophiles!)

The role of the microbiome of truffles in aroma formation: a meta-analysis approach -Maryam Vahdatzadeh – Applied and Environmental Microbiology

Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes – Yayoi Takeuchi – Systematic and Applied Microbiology

A snapshot of microbial communities from the Kutch: one of the largest salt deserts in the World – Aanal S. Pandit – Extremophiles

Temporal patterns of prokaryotic abundance, community structure and microbial activity in glacier foreland soils – Katrin Hofmann – Antonie van Leeuwenhoek

Built environment microbiome

Winner of today’s Longest Title Award: Intensive care unit environmental surfaces are contaminated by multidrug-resistant bacteria in biofilms: combined results of conventional culture, pyrosequencing, scanning electron microscopy, and confocal laser microscopy – H. Hu – Journal of Hospital Infection

Waste treatment microbiology

High prevalence of type 41 and high sequence diversity of partial hexon gene of human adenoviruses in municipal raw sewage and activated sludge – Hsion-Wen Kuo – Journal of Applied Microbiology

Acute Gastrointestinal Illness Risks in North Carolina Community Water Systems: A Methodological Comparison – Nicholas B. DeFelice – Environmental Science & Technology

Metagenomics

Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data – Jason W. Sahl – Genome Biology

Microbial Ecology

Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection – Nobuto Takeuchi – BMC Biology

Techniques

A method to analyze, sort, and retain viability of obligate anaerobic microorganisms from complex microbial communities – Anne W. Thompson – Journal of Microbiological Methods

Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in mouse feces – Yun-wen Yang – Applied and Environmental Microbiology

Antibiotics

Prevalence of Parental Misconceptions About Antibiotic Use – Louise Elaine Vaz – Pediatrics

Microbes in the news

Ginger and prebiotic promote good bacteria in pigs – All About Feed

How plants keep bad bacteria out – ZeeNews India

Parental Knowledge About Appropriate Antibiotic Use Still Poor – Diana Phillips – Medscape

Bik’s Picks

Can’t get Kylie out of your head? Blame the shape of your brain – Sam Wong – New Scientist

Seti: Search for alien life receives $100m boost – Clive Cookson – Financial Times

Remembering the Apollo 11 Moon Landing With the Woman Who Made It Happen – Lily Rothman – Time

Endangered dragonflies, raised in captivity over several years, being released – Dispatch Times

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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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