Category Archives: More Microbes

April 8, 2015

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Events

#UMassMedChat on the microbiome is Thursday at 11:30 a.m.- UMass Center for Microbiome Research to answer questions on gut health

Microbes in the City: Mapping the Urban Genome, Friday, June 19, 2015 – The New York Academy of Sciences

Human respiratory microbiome

Analysis of microbiota in stable patients with chronic obstructive pulmonary disease – Estefania Aguirre – APMIS

Human gut microbiome

Site-specific programming of the host epithelial transcriptome by the gut microbiota – Felix Sommer – Genome Biology

Animal microbiome

Horses and pigs: Lactobacillus ruminis strains cluster according to their mammalian gut source – Michelle M O’ Donnell1 – BMC Microbiology

Turkeys: Rye Affects Bacterial Translocation, Intestinal Viscosity, Microbiota Composition and Bone Mineralization in Turkey Poults – Guillermo Tellez – PLOS ONE

Amphibians: Larval exposure to polychlorinated biphenyl 126 (PCB-126) causes persistent alteration of the amphibian gut microbiota – Kevin D. Kohl – Environmental Toxicology and Chemistry

Tsetse fly: Paternal transmission of a secondary symbiont during mating in the viviparous tsetse fly – Linda De Vooght – Molecular Biology and Evolution

Squid and Vibrio fisheri: Signaling between two interacting sensor kinases promotes biofilms and colonization by a bacterial symbiont – Allison N. Norsworthy and Karen L. Visick – Molecular Microbiology
Sponges: Phylogenetic diversity of sulphate-reducing Desulfovibrio associated with three South China Sea sponges – D. Zhang – Letters in Applied Microbiology

Plant root and soil microbiome

Plant diversity increases soil microbial activity and soil carbon storage – Markus Lange – Nature Communications

Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA
genes in actinobacteria – Marketa Sagova-Mareckova – BMC Microbiology

Water microbiome

Functional Gene Composition, Diversity and Redundancy in Microbial Stream Biofilm Communities – Andrew Dopheide – PLOS ONE

Metabolomics

Distributing a metabolic pathway among a microbial consortium enhances production of natural products – Kang Zhou – Nature Biotechnology

Metabolite-sensing receptors ​GPR43 and ​GPR109A facilitate dietary fibre-induced gut homeostasis through regulation of the inflammasome – Laurence Macia – Nature Communications

Molecular Signatures of Nicotinoid-Pathogen Synergy in the Termite Gut – Ruchira Sen – PLOS ONE

Unique Honey Bee (Apis mellifera) Hive Component-Based Communities as Detected by a Hybrid of Phospholipid Fatty-Acid and Fatty-Acid Methyl Ester Analyses – Kirk J. Grubbs – PLOS ONE

Bioinformatics

A Robust ANOVA Approach to Estimating A Phylogeny from Multiple Genes – Ximing Xu – Molecular Biology and Evolution

More microbiology papers

Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe – Gemma L. Kay – Nature Communications

Microbes in the news

Beneficial bacteria – Ella Nonni – The Cornell Daily Sun

Mapping All The Chemicals And Tiny Bacteria Living On Our Skin – Adele Peters – FastCoExist

uBiome and HelloFlo are teaming up to explore how the vaginal microbiome changes during pregnancy and postpartum

Video: Gut Microbiome and Its Role in Allergy and Asthma – Christine Cole Johnson – JSPRQ.com

Colorado startup’s microbiome-modulating drug could improve metformin tolerability – Meghana Keshavan – MedCityNews

Race to stamp out animal plague begins – Ewen Callaway – Nature

Science, publishing, and career

The future of the postdoc: There is a growing number of postdocs and few places in academia for them to go. But change could be on the way – Kendall Powell – Nature

Opinion: Addressing systemic problems in the biomedical research enterprise – Bruce Alberts – PNAS USA

History: Women at the edge of science – Jennifer Rampling – Nature

Bik’s Picks

Efficacy of Commercial Weight-Loss Programs: An Updated Systematic Review
Kimberly A. Gudzune – Annals of Internal Medicine

Ecology: Recovering the potential of coral reefs – Nicholas K. Dulvy & Holly K. Kindsvater – Nature
Complex organic molecules discovered in infant star system: Hints that building blocks of chemistry of life are universal – Science Daily

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March 30, 2015

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Microbiome in rhinosinusitis patients, microbes in permafrost, and responses of soil to deforestation.

Meetings
London Microbiome Meeting 2015 (LMM2015), St. Thomas’ Hospital, 28 May 2015

Human respiratory microbiome

Sinus microbiota varies among chronic rhinosinusitis phenotypes and predicts surgical outcome – Vijay R. Ramakrishnan – Journal of Allergy and Clinical Immunology

Animal microbiome

Antimicrobial resistance in faecal samples from buffalo, wildebeest and zebra grazing together with and without cattle in Tanzania – A.A.S. Katakweba – Journal of Applied Microbiology

Soil and plant root microbiome

Soil microbiome responses to the short-term effects of Amazonian deforestation –
Acacio A. Navarrete – Molecular Ecology

Reconstructed metagenomes reveal changes of microbial functional profiling during PAHs degradation along a rice (Oryza sativa) rhizosphere gradient – B. Ma – Journal of Applied Microbiology

Profiling bacterial diversity in a limestone cave of the western Loess Plateau of China – Yucheng Wu – Frontiers in Microbiology

Extremophile microbiome

Structure, mineralogy, and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania – Cristian Coman – Frontiers in Microbiology

Shifts in methanogenic community composition and methane fluxes along the degradation of discontinuous permafrost – Mette M. Svenning – Frontiers in Microbiology

Bioreactor microbiome

Analysis of microbial community composition in a lab-scale membrane distillation bioreactor – Q. Zhang – Journal of Applied Microbiology

Food microbiology

Diffusion of solutes inside bacterial colonies immobilized in model cheese depends on their physicochemical properties: a time-lapse microscopy study – Juliane Floury – Frontiers in Microbiology

Metagenomics

It’s a dirty job — A robust method for the purification and de novo genome assembly of Cryptosporidium from clinical material – Sofia Andersson – Journal of Microbiological Methods

Bioinformatics and statistics

Power and Sample-Size Estimation for Microbiome Studies Using Pairwise Distances and PERMANOVA – Brendan J. Kelly – Bioinformatics

More microbe papers

Review: Tackling antibiotic resistance: the environmental framework – Thomas U. Berendonk – Nature Reviews Microbiology

Microbes in the news

You Should Know: Kristina Campbell and The Intestinal Gardener – DNLee – Scientific American
Link to blog: The Intestinal Gardener – Kristina Campbell

Video of the February VLAB meeting at Stanford: Gut-Feeling — Ventures into the Microbiome – Colleen Cutcliffe – VLAB videos

Chronic Rhinosinusitis Varies By Bacterial Microbiome – Vijay R. Ramakrishnan – Medical Research

Doctors: How gut bacteria affects obesity, diabetes, child health – Jondi Gumz – Santa Cruz Sentinel

The bacteria that could make your blue jeans greener – Michael Keller – Green Biz

Bacteria power up by using magnets as batteries – Catherine Brahic – New Scientist

Antibiotics from the medieval medicine cabinet: Could medieval medicine provide new antibiotics to treat deadly modern infections? – CrowdFunder

Science, publishing and career

These scientists studied journalists covering science. Whoa, meta. – Suzanne Jacobs – Grist

Let’s compare the backgrounds of science writers for Fox and NPR – Boing Boing

Mind the (gender) gap: Kew’s records show fewer than 3% of land plant species published by women – Lauren Gardiner – Kew Royal Botanical Gardens

I’m an engineer, not a cheerleader. Let’s abandon silly rules about gender roles. – Sara Sakowitz – Washington Post

Bik’s Picks

Velvet Worms, Squirting Slime – James Gorman – New York Times

An apple a day may not keep the doctor away, study says – Lindsey Tanner – Big Story AP

Family income, parental education related to brain structure in children, adolescents – Science Daily

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March 28, 2015

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Screen Shot 2015-03-28 at 1.00.33 AMFeatured video

I had hoped that this would have been a better video. The opening text/visuals are very confusing, and the cartoon human looks like a sad penguin. Is it supposed to be a human? Or human cells inside the human? Or a bacterium? And why is it looking so sad? #SadPenguin

Video (2014): Microbes: The Residents Living On And Inside You – Carl R. Woese Institute for Genomic Biology

 

Human oral microbiome

Acetaldehyde production by major oral microbes – Keisuke Moritani – Oral Diseases

Prelude to oral microbes and chronic diseases: Past, present and future – Kalina R. Atanasova – Microbes and Infection

Effect of dental cements on peri-implant microbial community: comparison of the microbial communities inhabiting the peri-implant tissue when using different luting cements – Michael Korsch – Clinical Oral Implants Research

Human gut microbiome

Common occurrence of antibacterial agents in human intestinal microbiota – Fatima Drissi – Frontiers in Microbiology

Maintaining gut ecosystems for health: Are transitory food bugs stowaways or part of the crew? – Coline Plé – International Journal of Food Microbiology

Size does not matter: commensal microorganisms forge tumorpromoting inflammation and anti-tumor immunity – Melanie R. Rutkowski – Oncoscience

Review: Time for Food: The Intimate Interplay between Nutrition, Metabolism, and the Circadian Clock – Gad Asher – Cell

Animal microbiome

Horses: Characterization and comparison of the bacterial microbiota in different gastrointestinal tract compartments in horses – M.C. Costa – The Veterinary Journal

Fish: Declining diversity of egg-associated bacteria during development of naturally spawned whitefish embryos (Coregonus spp.) – Laetitia G. E. Wilkins – Aquatic Sciences

Bees (see also under “Other microbiology” below): Characterization of gut bacteria at different developmental stages of Asian honey bees, Apis cerana – Jun Guo – Journal of Invertebrate Pathology

Soil, rock, and marble microbiome

Biofouling of marbles by oxygenic photosynthetic microorganisms – Zeki Karaca – Environmental Science and Pollution Research

Water microbiome

Bacterial diversity of polluted surface sediments in the northern Adriatic Sea determined by pyrosequencing – Marino Korlević – Systematic and Applied Microbiology

Extremophile microbiome

Genomics in a changing Arctic: Critical questions await the molecular ecologist – Stan D. Wullschleger – Molecular Ecology

Microbial diversity on Icelandic glaciers and ice caps – Stefanie Lutz – Frontiers in Microbiology

Other microbiology

Antimicrobial-Induced DNA Damage and Genomic Instability in Microbial Pathogens –
Rebecca S. Shapiro – PLOS Pathogens

Parallel Epigenomic and Transcriptomic Responses to Viral Infection in Honey Bees (Apis mellifera) – David A. Galbraith – PLOS Pathogens

News

Planetary Protection Workshop (Forward Contamination) – Jenna Lang – MicroBEnet

How to keep up with microbial ecology and the built environment: microBEnet is your place – Jonathan Eisen – The Tree of Life

Italian Researchers Publish Array Method to Profile Vaginal Microbiome, Gauge Treatment Response – Molika Ashford – Genome Web

Social constructs and behaviors can predict microbiome composition – American Microbiome Institute

Not a good title: Hunter-Gatherers Have Better Guts Than We Do – Cody Brooks – Clapway

The tiny intruders in YOUR home: Researchers reveal the average house has 8,000 different types of bacteria and bugs – Mark Prigg

Drug metabolism: manipulating the microbiome – Sarah DeWeerdt – Pharmaceutical Journal

A High-Fat Diet May Alter Your Behavior and Your Brain with Changed Gut Bacteria – Catherine Griffin – Science World Report

Surfwear founder’s charity backs UQ researcher in superbug war – University of Queensland

Paywalled: Bacteria: Master Microbial Colonizers – Marcia Stone – BioScience

A Farmer Drilled For Water, But What Came Up Turned This Desert Into An Oasis! – OffGridQuest

Science, publishing and career

BioMed Central retracting 43 papers for fake peer review – Cat Ferguson – Retraction Watch

Bik’s Picks

Crossing fingers can reduce feelings of pain – Science Daily

Giant pandas’ secret social life revealed – Bob Holmes – New Scientist

Watch Scientists Try Everything to Put a Camera on a Manatee – Jane J. Lee – National Geographic

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March 19, 2015

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Just a short digest today!

General microbiome

Review: The role of the microbiota in ageing: current state and perspectives – Denise B. Lynch – Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Human gut microbiome / proteomics

Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota – Alessandro Tanca – Proteomics

Animal microbiome

Abalone: Temporal fluctuation in the abundance of alginate-degrading bacteria in the gut of abalone Haliotis gigantea over 1 year – Reiji Tanaka – Aquaculture Research

Soil microbiome

Native California soils are selective reservoirs for multidrug-resistant bacteria – Amanda C. Hollowell – Environmental Microbiology Reports

Techniques

Growing microbes in millifluidic droplets – Laurent Boitard – Engineering in Life Sciences

Other microbiology

Application of Whole-Genome Sequencing for Bacterial Strain Typing in Molecular Epidemiology – Stephen J. Salipante – Journal of Clinical Microbiology

Microbes in the news

Adventures in exploring the great indoors – Anne A. Madden – Fierer Lab

MO BIO Laboratories, Inc. presents the Second Annual MO BIO Microbiome Awards, offering more than $10,000 in prizes! – MoBio

uBiome — Explore Your Dental Microbiome – IndieGoGo
uBiome Launches World’s First Dental Citizen Science Campaign – Global Newswire

Humans Need ‘Stronger’ Breast-Milk Than Most Mammals – Brian Stallard – Nature World News

Interactive/videos: The good, the bad and the ugly in everyday bacteria – CBC news

Los Alamos scientists develop new method for metagenomic analysis – News Medical Net

This week’s  Google Plus Microbiology Journal club: Cheese Microbe Communities – GPlusMicroJC

Researchers have a gut feeling – could chronic pain be caused by bacteria? – Michael Brooks – New Statesman

MeMed’s blood test accurately distinguishes bacterial and viral infections, research shows – Medical Xpress

Turning the gut microbiome into a chat room – Tina Hesman Saey – ScienceNews

Science, publishing, and career

A grad school survival guide – Andrew Gaudet – Science

Bik’s Picks

The New York Times’ smartwatch cancer article is bad, and they should feel bad – Russell Brandom – The Verge

Unmasked: – What 10 million passwords reveal – about the people who choose them – WP engine

All other languages tired of Python’s sh!t – The Science Web
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March 15, 2015

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Microbiome of pregnancy and birth

The vaginal microbiome during pregnancy and the postpartum period in a European population – David A. MacIntyre – Scientific Reports

Probiotic potential of Enterococcus faecalis strains isolated from meconium – Ahmed Khassaf Al Atyaa – Frontiers in Microbiology

Review: The human neonatal gut microbiome: a brief review – Emily C. Gritz and Vineet Bhandari – Frontiers in Pediatrics

Human gut microbiome

Gut microbiome of the Hadza hunter-gatherers – Stephanie L. Schnorr – Nature Communications

Gut microbiome variations during hematopoietic stem cell transplant in severe combined immunodeficiency – Jonathan P. Lane – Journal of Allergy and Clinical Immunology

Despite the title, this is 16S rRNA gene-based analysis: Metagenomic analysis of the impact of nitrofurantoin treatment on the human faecal microbiota – Jascha Vervoort – Journal of Antimicrobial Chemotherapy

Literature review: Mast Cell Activation Disease and Microbiotic Interactions – Lawrence B. Afrin, Alexander Khoruts- Clinical Therapeutics

Review: Autoimmune host–microbiota interactions at barrier sites and beyond – William E. Ruff, Martin A. Kriegel – Trends in Molecular Medicine

Review: Microbiota Regulation of the Mammalian Gut–Brain Axis – Aurelijus Buroka – Advances in Applied Microbiology

Review: IBD and the Gut Microbiota—from Bench to Personalized Medicine – Emanuelle Bellaguarda, Eugene B. Chang – Current Gastroenterology Reports

Review: Mutualistic presence of normal Flora in Human Intestine: A review – Karishma Kabir Nipa- Journal of Bio-Science

Animal models

Monosodium L-Glutamate and Dietary Fat Differently Modify the Composition of the Intestinal Microbiota in Growing Pigs – Feng Z-M – Obesity Facts

Altered profile of gut microbiota after subchronic exposure to neochamaejasmin A in rats – Lifeng Yan – Environmental Toxicology and Pharmacology

Effects of mulberry (Morus alba L.) leaf polysaccharides on growth performance, diarrhea, blood parameters, and gut microbiota of early-weanling pigs – Xiangjie Zhao – Livestock Science

Effect of grinding or pelleting high grain maize- or barley-based concentrates on rumen environment and microbiota of beef cattle – A. Gimeno – Animal Feed Science and Technology

Animal microbiome

Earthworms: Taxonomic and functional annotation of gut bacterial communities of Eisenia foetida and Perionyx excavatus – Arjun Singh – Microbiological Research

Plant microbiome

Diversity and community ecology of forest epiphyte testate amoebae from European Russia – Richard J. Payne – European Journal of Protistology

Soil and plant root microbiome

Effects of single-root-grafting, double-root-grafting and compost application on microbial properties of rhizosphere soils in Chinese protected cucumber (Cucumis sativus L.) production systems – Yinan Gao – Scientia Horticulturae

Response of belowground communities to short-term phosphorus addition in a phosphorus-limited woodland – Uffe N. Nielsen – Plant and Soil

Composition of soil microbiome along elevation gradients in southwestern highlands of Saudi Arabia – Muhammad Yasir – BMC Microbiology

Illumina MiSeq sequencing investigation on the contrasting soil bacterial community structures in different iron mining areas – Chen Hong – Environmental Science and Pollution Research

Geomicrobiology of Iron Layers in the Sediment of Lake Superior – M. Dittrich – Aquatic Geochemistry

Water and ice microbiome

Microbial abundance in surface ice on the Greenland Ice Sheet – Marek Stibal – Frontiers in Microbiology

Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing – Chia Sing Chan – Frontiers in Microbiology

Review: New perspectives in benthic deep-sea microbial ecology – Cinzia Corinaldesi – Frontiers in Marine Science

Bioreactor microbiome

The microbial community of a passive biochemical reactor treating arsenic, zinc, and sulfate-rich seepage – Susan Anne Baldwin – Frontiers in Bioengineering and Biotechnology

Food microbiology

Process-driven bacterial community dynamics are key to cured meat colour formation by coagulase-negative staphylococci via nitrate reductase or nitric oxide synthase activities – María Sánchez Mainar, Frédéric Leroy – International Journal of Food Microbiology

Metagenomics and Bioinformatics

Modelling Computational Resources for Next Generation Sequencing Bioinformatics Analysis of 16S rRNA Samples – Matthew J. Wade – ArXiv

Accurate multiplexing and filtering for high-throughput amplicon-sequencing – Philippe Esling – Nucleic Acids Research

Transmission and Microevolution of USA300 MRSA in U.S. Households: Evidence from Whole-Genome Sequencing – Md Tauqeer Alam – mBio

Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population – Jessica Labonté – Frontiers in Microbiology

ISMapper: Identifying insertion sequences in bacterial genomes from short read sequence data – Jane Hawkey – BioRXiv

Perspective: Wiretapping into microbial interactions by single cell genomics – Ramunas Stepanauskas – Frontiers in Microbiology

Perspective: Bridging the knowledge gap: from microbiome composition to function – Jeremiah J Faith – Molecular Systems Biology

Metabolomics and Transcriptomics

Clostridium difficile heterogeneously impacts intestinal community architecture but drives stable metabolome responses – David Rojo – ISME Journal

Study of the diversity and short-chain fatty acids production by the bacterial community in overweight and obese Mexican children – S. Murugesan – European Journal of Clinical Microbiology & Infectious Diseases

Genomic Analysis of Xylose Metabolism in Members of the Deinoccocus-Thermus Phylum from Thermophilic Biomass-Deconstructing Bacterial Consortia – Yu-Wei Wu – BioEnergy Research

Proteomics as the final step in the functional metagenomics study of antimicrobial resistance – Fiona Fouhy – Frontiers in Microbiology

Fish: Proteomic profile of the skin mucus of farmed gilthead seabream (Sparus aurata) – Juan Jurado – Journal of Proteomics

Transcriptomic analysis of three Veillonella spp. present in carious dentine and in the saliva of caries-free individuals – Thuy Do – Frontiers in Cellular and Infection Microbiology

The transcriptional response of microbial communities in thawing Alaskan permafrost soils – M J. Coolen and William D. Orsi – Frontiers in Microbiology

Review: Mucin glycan foraging in the human gut microbiome – Louise Tailford – Frontiers in Genetics

More microbial science

Untangling the origin of viruses and their impact on cellular evolution – Arshan Nasir – Annals of the New York Academy of Sciences

The Great Escape: Pathogen Versus Host – Eric Kong, Mary Ann Jabra-Rizk – PLOS Pathogens

A fantastic voyage for sliding bacteria – Joshua D. Shrout – Trends in Microbiology

CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity – Roger A. Garrett – Life

Etiology of Pericarditis in a prospective cohort of 1162 cases – Frédérique Gouriet – The American Journal of Medicine

Microbes in the news

Overselling the microbiome award: Dr. Raphael Kellman at MindBodyGreen – Jonathan Eisen – The Tree of Life
belongs to:
Why The Microbiome Is Your Key To Glowing Skin & Healthy Weight – Dr. Raphael Kellman – MindBodyGreen

The Era of the Microbiome – SXSW Session on Monday March 16

Mind Altering Microbes: How your gut microbiome may influence your mood – Jill Carnahan

CDC: Misuse of garments may have led to release of bacteria at Tulane lab – Debra Goldschmidt and Ed Payne – CNN

The dawn of the cyborg bacteria is here – Robert Boos – PRI

Famous Microbiologists – Paul Ehrlich – Today we honor Paul Ehrlich who was born on March 14 in 1912 – LumiByte

Science and art – microbial edition

Bacterial Paintings? New Art Uses Tiny Life Forms – Tia Ghose – LiveScience

How microbes inspire art (Video) – BBC

Fungi on Tea – Microbe World

Louis Pasteur T-shirt – The Strange company

Bik’s Picks

Five research papers that revolutionised health – Deborah Cohen – BBC News Health

Folic acid plus blood pressure drug lowers stroke risk: study – Daily Mail

Man Credits Hot Chili Sauce Challenge for Brain Cancer Diagnosis – Youth Health Magazine

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February 25, 2015

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Nature and Scientific American have a joint Microbiome special: “Innovations in the Microbiome” with several overview papers from Rob Knight, Ruth Ley,  Justin Sonnenburg et al. Articles include:

The Microbes Within – David Grogan
Why Microbiome Treatments Could Pay Off Soon – Rob Knight
Your Microbes at Work: Fiber Fermenters Keep Us Healthy
Mental Health: Thinking from the Gut – Charles Schmidt
Gut Microbiome: The Peacekeepers – Moises Velasquez-Manoff
The Gene–Microbe Link – Ruth E. Ley
Microbiome Engineering – Justin L. Sonnenburg
The Diverse Microbiome of the Hunter-Gatherer – Stephanie L. Schnorr

Human oral microbiome

Environment and Colonisation Sequence Are Key Parameters Driving Cooperation and Competition between Pseudomonas aeruginosa Cystic Fibrosis Strains and Oral Commensal Streptococci – Robert A. Whiley – PLOS ONE

Human skin microbiome

Malassezia Intra-Specific Diversity and Potentially New Species in the Skin Microbiota from Brazilian Healthy Subjects and Seborrheic Dermatitis Patients – Renan Cardoso Soares – PLOS ONE

Human gut microbiome

From the Gordon lab: Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy – Andrew L. Kau – Science Translational Medicine

Complementary Amplicon-Based Genomic Approaches for the Study of Fungal Communities in Humans – Timothy Heisel – PLOS ONE

Animal models of microbiome research

Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome – Benoit Chassaing – Nature

Animal microbiome

Heritable symbiosis: The advantages and perils of an evolutionary rabbit hole – Gordon M. Bennett and Nancy A. Moran

Endosymbiont Dominated Bacterial Communities in a Dwarf Spider – Bram Vanthournout, Frederik Hendrickx – PLOS ONE

Phylogenetic diversity of Archaea in the intestinal tract of termites from different lineages – Yu Shi – Journal of Basic Microbiology

Plant microbiome

Intercropped Silviculture Systems, a Key to Achieving Soil Fungal Community Management in Eucalyptus Plantations – Caio T. C. C. Rachid – PLOS ONE

Soil microbiome

Microbial dynamics in glacier forefield soils show succession is not just skin deep – Arwyn Edwards and Sophie Cook – Molecular Ecology

Microbial deposits in the aftermath of the end-Permian mass extinction: A diverging case from the Mineral Mountains (Utah, USA) – Emmanuelle Vennin – Sedimentology

Water microbiome

Characterizing variability in marine protist communities via ARISA fingerprints—a method evaluation – E.S. Kilias – Limnology and Oceanography: Methods

Characterisation of the Physical Composition and Microbial Community Structure of Biofilms within a Model Full-Scale Drinking Water Distribution System – Katherine E. Fish – PLOS ONE

Microbiome of the built environment

Sewage Reflects the Microbiomes of Human Populations – Ryan J. Newton – mBio

Phages and viruses

The targeted recognition of Lactococcus lactis phages to their polysaccharide receptors – Orla McCabe – Molecular Microbiology

Bioinformatics

Tools for Bacterial Comparative Genomics – Kat Holt – Holt Lab

Techniques

Comparison of different methods for the recovery of DNA from spores of mycotoxin producing moulds in spiked food samples – Sabrina Grube – Letters in Applied Microbiology

Metabolomics

Nutritional stress induces exchange of cell material and energetic coupling between bacterial species – Saida Benomar – Nature Communications

Other papers of interest

Climate-driven introduction of the Black Death and successive plague reintroductions into Europe – Boris V. Schmid – PNAS USA

Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs – Eric Londin – PNAS USA

Microbes in the news

Fishing For the Microbes Behind Malnutrition – Ed Yong – National Geographic

4th World Summit ‘Gut Microbiota For Health’ to be held in Barcelona – Phys.org

Indian scientist awarded 1.5 million euros grant to investigate the role of gut microbiota in autoimmune diseases – Economic Times India

Johnson & Johnson Bets On Alzheimer’s Vaccine, Disease Prediction, Human ‘Microbiome’ – Amy Nordrum – International Business Times

Altered microbiome may lead to liver disease in patients with cystic fibrosis – Healio

Cystic Fibrosis Liver Cirrhosis Associated with Intestinal Microbiome – Maureen Newmn – LungDiseaseNews

Linoleic acid role balanced by changes to gut microbiota: Study – Annie-Rose Harrison-Dunn – NutraIngredients

My Microbiome Experience from Start to Results – Alexandra Carmichael – uBiome Blog

Session Report: Citizen Microbiology at Citizen Science 2015 – David Coil – MicroBEnet

Bacteria pipe food to each other using tiny tubes – Francie Diep – Popular Science

CSU study finds that Leprosy bacteria can survive in unusual environments – Emily Vavra – Collegian

Science, publishing and career

Scientists are cautious about public outreach – Chris Woolston – Nature

It’s Time for More Racial Diversity in STEM Toys – Maia Weinstock – Scientific American

Science and art

Science and Culture: Data visualization nurtures an artistic movement – J. D. Talasek – PNAS USA

Bik’s Picks

Wanted: 80,000 British babies for massive study – Helen Pearson – Nature

28.8 million tons of Sahara desert fertilize the Amazon – Deborah Netburn – LA Times

Your Eyelashes Should Be This Long, Science Says – Megan Gannon – Scientific American [hr]

February 10, 2015

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Microbiome of pregnancy and birth

Network analysis suggests a potentially ‘evil’ alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities – Zhanshan (Sam) Ma – Scientific Reports

Human respiratory microbiome

The nasal microbiota in health and disease: variation within and between subjects – Kristi Biswas – Frontiers in Microbiology

Analysis of the nasal vestibule mycobiome in patients with allergic rhinitis – Won Hee Jung – Mycoses

Human oral microbiome

Review: Salivary Diagnostics and the Oral Microbiome – Jennifer E. Kerr – Advances in Salivary Diagnostics

Review: Microbiome of peri-implant infections: lessons from conventional, molecular and metagenomic analyses – Georgios Charalampakis – Virulence

Review: On the dynamics of root canal infections – what we understand and what we don’t – Matthias Zehnder – Virulence

Human gut microbiome

See also Rojo paper under Metabolomics

Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences – Brett Wagner Mackenzie – Frontiers in Microbiology

Dysbiosis gut microbiota associated with inflammation and impaired mucosal immune function in intestine of humans with non-alcoholic fatty liver disease – Weiwei Jiang – Scientific Reports

Intestinal Lesions Are Associated with Altered Intestinal Microbiome and Are More Frequent in Children and Young Adults with Cystic Fibrosis and Cirrhosis – Thomas Flass – PLOS ONE

The impact of oral consumption of Lactobacillus plantarum P-8 on faecal bacteria revealed by pyrosequencing – LY Kwok – Beneficial Microbes

Review: Contribution of diet to the composition of the human gut microbiota – Daniela Graf – Microbial Ecology in Health and Disease

Animal microbiome

Characterization of the Fecal Microbial Communities of Duroc Pigs Using 16S rRNA Gene Pyrosequencing – Edward Alain B. Pajarillo – Asian-Australasian Journal of Animal Sciences

Metagenomic analysis of the gut microbiota of the Timber Rattlesnake, Crotalus horridus – Richard William McLaughlin – Molecular Biology Reports

Larval exposure to polychlorinated biphenyl 126 (PCB-126) causes persistent alteration of the amphibian gut microbiota – Kevin D. Kohl – Environmental Toxicology and Chemistry

Abstract: Bugs in bats 2: Analysis of microbial communities in faecal samples obtained from bats in the Netherlands – JCM Wolkers-Rooijackers – 11th Conference of the Dutch Society for Wildlife Health

Plant microbiome

Rapid quantification of rice root-associated bacteria by flow cytometry – G. Valdameri – Letters in Applied Microbiology

Elevated atmospheric CO2 levels affect community structure of rice root-associated bacteria – Kiwamu Minamisawa – Frontiers in Microbiology

Characterization of Leaf Blade- and Leaf Sheath-Associated Bacterial Communities and Assessment of Their Responses to Environmental Changes in CO2, Temperature, and Nitrogen Levels under Field Conditions – Seishi Ikeda – Microbes and Environments

Soil, sediment, and rock microbiome

Community Structure and Biogeochemical Impacts of Microbial Life on Floating Pumice – J. J. Elser – Applied and Environmental Microbiology

Variability in responses of bacterial communities and nitrogen oxide emission to urea fertilization among various flooded paddy soils – Ning Wang – FEMS Microbiology Ecology

Analysis of Sclerotia-Associated Fungal Communities in Cool-Temperate Forest Soils in North Japan – Anzilni F. Amasya – Microbes and Environments

Water microbiome

Bacterial Diversity in the South Adriatic Sea during a Strong, Deep Winter Convection Year – M. Korlević – Applied and Environmental Microbiology

Viruses and phages

Traces of ATCV-1 associated with laboratory component contamination – Kristín Rós Kjartansdóttir – PNAS USA

Reply to Kjartansdóttir et al.: Chlorovirus ATCV-1 findings not explained by contamination – Robert H. Yolken – PNAS USA

Microbial Ecology

Temporal patterns of rarity provide a more complete view of microbial diversity – Ashley Shade, Jack A. Gilbert – Trends in Microbiology

Metagenomics

Genomes of Planktonic Acidimicrobiales: Widening Horizons for Marine Actinobacteria by Metagenomics – Carolina Megumi Mizuno – mBio

Metabolomics

Ranking the impact of human health disorders on gut metabolism: Systemic lupus erythematosus and obesity as study cases – David Rojo – Scientific Reports

Review: Animals in a bacterial world: opportunities for chemical ecology – Alexandra M. Cantley and Jon Clardy – Natural Product Reports

Bioinformatics

CATCh, an Ensemble Classifier for Chimera Detection in 16S rRNA Sequencing Studies – Mohamed Mysara – Applied and Environmental Microbiology

Techniques

Best practices for sample processing and storage prior to microbiome DNA analysis freeze? buffer? process? – Jonathan Eisen – MicroBEnet

More microbes

Natural Green Coating Inhibits Adhesion of Clinically Important Bacteria – Danielle S. Trentin – Scientific Reports

 

Chemical signature of magnetotactic bacteria – Matthieu Amor – PNAS USA

Microbes in the news

Breastfeeding prepares a baby for solid food – Tim Sandle – Digital Journal

Gut microbiota reveal better ways of detecting (and preventing) colorectal cancer – Kristina Campbell – Microbiome Institute

Our Inner Viruses: Forty Million Years In the Making – Carl Zimmer – National Geographic

Our wine owes a debt to ancient viruses – Andrew Geering – Phys.org

Diet is the Chief Factor Behind Gut Microbiome Diversity, Study Shows – Patricia Inacio – IBD News Today

Citizen Oceanography Meets the Marine Microbiome – Rachelle Lauro – Mission Blue

Fecal Microbiota Transplants: An Insider’s Guide – Monica J. Smith

Science and Art

Researcher Determined to Play Piano Duet With Yellow Slime Mold – The Mary Sue

And the winners of the #spacemicrobes Microbial Playoffs are… – Arvind Suresh – Discover Magazine

A Beautiful Wallpaper Made With Smallpox Vaccine – Joseph Flaherty – Wired.com

Bik’s Picks
Stressed Young Bees Linked To Colony Collapse – Jim Algar – Tech Times

Meet Spot: New Breed of Robot Dog Climbs and Trots – Elizabeth Palermo – Live Science

Australia’s Shocking Rate Of Mammal Extinction Blamed On Cats And Red Foxes Brought Over By European Settlers – Rebekah Marcarelli – Headlines and Global News

[hr]

February 1, 2015

Posted on by

Ah, the revenge of being away from work: my in-box was bursting out of the seams with new papers. Today I am quickly catching up after being offline for just 3 days, and I will skip most formatting to save some time (e.g. I will only do the bare essentials, and won’t add the hyperlinks). Enjoy.

General microbiome

Review? Discovering Emergent Behavior of Host-Microbiome Interactions with Biomimetic Robotics – Keith C. Heyde, Warren C. Ruder – Biophysical Journal
http://www.sciencedirect.com/science/article/pii/S0006349514046268

Book: Microbiome Community Ecology – Muhammad Saleem – Springer Briefs in Ecology
http://link.springer.com/book/10.1007/978-3-319-11665-5

Human oral microbiome

16S rRNA based microarray analysis of ten periodontal bacteria in patients with different forms of periodontitis – Nursen Topcuoglu, Guven Kulekci – Anaerobe
http://www.sciencedirect.com/science/article/pii/S1075996415000128

Human respiratory microbiome

Dynamics of the nasal microbiota in infancy: A prospective cohort study – Moana Mika – Journal of Allergy and Clinical Immunology
http://www.sciencedirect.com/science/article/pii/S0091674914037099

Review: The microbiome of the upper airways: focus on chronic rhinosinusitis – Thanit Chalermwatanachai – World Allergy Organization Journal
http://link.springer.com/article/10.1186/s40413-014-0048-6/fulltext.html

Human skin microbiome

Mapping axillary microbiota responsible for body odours using a culture-independent approach – Myriam Troccaz – Microbiome Journal
http://www.microbiomejournal.com/content/3/1/3/abstract

The shared microbiota of humans and companion animals as evaluated from Staphylococcus carriage sites – Ana M Misic – Microbiome Journal
http://www.microbiomejournal.com/content/3/1/2/abstract

Insights into bacterial colonization of intensive care patients’ skin: the effect of chlorhexidine daily bathing – N. Cassir – European Journal of Clinical Microbiology & Infectious Diseases
http://link.springer.com/article/10.1007/s10096-015-2316-y

Human gut microbiome

(see also Metagenomics) Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species – Sharon Greenblum – Cell
http://www.sciencedirect.com/science/article/pii/S0092867415000136

Gut microbiota composition correlates with changes in body fat content due to weight loss – M. Remely – Beneficial Microbes
http://wageningenacademic.metapress.com/content/ewq1620085607927/#.VM5HCVWJOuY

Genetic Modifier of the Gut Microbiome, GvHD and Bacterial Translocation Following HSCT – Ahmad Rayes – Biology of Blood and Marrow Transplantation
http://www.sciencedirect.com/science/article/pii/S1083879114008350

A Pilot Study of Donor Enteral Human Milk to Modulate the Gut Microbiome in Children Receiving Stem Cell Transplant – Stella M. Davies – Biology of Blood and Marrow Transplantation
http://www.sciencedirect.com/science/article/pii/S1083879114010441

This might be review (no access from my location): Microbiome, peptide autoantibodies, and eating disorders: a missing link between gut and brain – Akio Inui – Nutrition
http://www.sciencedirect.com/science/article/pii/S0899900715000386

Oral Supplementation with L-Glutamine Alters Gut Microbiota of Obese and Overweight Human Adults: A Pilot Study – Alessandra Zanin Zambom de Souza – Nutrition
http://www.sciencedirect.com/science/article/pii/S0899900715000350

Review: Growth Promotion and Gut Microbiota: Insights from Antibiotic Use – Harald Brüssow – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12786/abstract

Hypothesis: An Agent-Based Modeling Framework for Evaluating Hypotheses on Risks for Developing Autism: Effects of the Gut Microbial Environment – Bronson Weston – Medical Hypotheses
http://www.sciencedirect.com/science/article/pii/S0306987715000481

Hypothesis: Gut feelings: A role for the intestinal microbiota in anorexia nervosa? – Susan C. Kleiman – International Journal of Eating Disorders
http://onlinelibrary.wiley.com/doi/10.1002/eat.22394/abstract

Review??? Beyond Model Systems: Super-Resolving the Subcellular Dynamics of Starch Digestion in the Human Gut Microbiome – Krishanthi S. Karunatilaka – Biophysical Journal
http://www.sciencedirect.com/science/article/pii/S0006349514023030

Review: Intestinal Microbiota And Diet in IBS: Causes, Consequences, or Epiphenomena? – Mirjana Rajilić-Stojanović – American Journal of Gastroenterology
http://www.nature.com/ajg/journal/vaop/ncurrent/full/ajg2014427a.html

Review: H. pylori and its modulation of gastrointestinal microbiota – Christian Schulz – Journal of Digestive Diseases
http://onlinelibrary.wiley.com/doi/10.1111/1751-2980.12233/abstract

Review: Implication of Gut Microbiota in Nonalcoholic Fatty Liver Disease
Jerome Boursier – PLOS Pathogens
http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1004559

Review: The human gut microbiota with reference to autism spectrum disorder: considering the whole as more than a sum of its parts – Michael C. Toh and Emma Allen-Vercoe – Microbial Ecology in Health and Disease
http://www.microbecolhealthdis.net/index.php/mehd/article/view/26309

Review: The role of gut microbiota in the development of type 1, type 2 diabetes mellitus and obesity – Ningwen Tai – Reviews in Endocrine and Metabolic Disorders
http://link.springer.com/article/10.1007/s11154-015-9309-0

Review: Diet, Gut Microbiome, and Bone Health – Connie M. Weaver – Current Osteoporosis Reports
http://link.springer.com/article/10.1007/s11914-015-0257-0

Review: Immunogenic properties of a probiotic component of the human gastrointestinal tract microbiota – I. A. Fedorova, V. N. Danilenko – Biology Bulletin Reviews
http://link.springer.com/article/10.1134/S2079086414060036

Animal models of microbiome

Intestinal Microbial Dysbiosis and Colonic Epithelial Cell Hyperproliferation by Dietary α-Mangostin is Independent of Mouse Strain – Fabiola Gutierrez-Orozco – Nutrients
http://www.mdpi.com/2072-6643/7/2/764/htm

Polyphenol-rich sorghum brans alter colon microbiota and impact species diversity and species richness after multiple bouts of dextran sodium sulfate-induced colitis
Lauren E. Ritchie – FEMS Microbiology Ecology
http://femsec.oxfordjournals.org/content/early/2015/01/14/femsec.fiv008.abstract

Effects of chronic exposure to environmentally relevant concentrations of waterborne depleted uranium on the digestive tract of zebrafish, Danio rerio – Starrlight Augustine – Journal of Environmental Radioactivity
http://www.sciencedirect.com/science/article/pii/S0265931X15000041

Cross-Differentiation from the CD8 Lineage to CD4 T Cells in the Gut-Associated Microenvironment with a Nonessential Role of Microbiota – Jen Bon Lui – Cell Reports
http://www.sciencedirect.com/science/article/pii/S2211124714011061

Administration of probiotics Lactobacillus rhamnosus GG and Lactobacillus gasseri K7 during pregnancy and lactation changes mouse mesenteric lymph nodes and mammary gland microbiota – P. Treven- Journal of Dairy Science
http://www.sciencedirect.com/science/article/pii/S0022030215000417

Animal microbiome

First insights into the microbial diversity in the omasum and reticulum of bovine using Illumina sequencing – Shuai Peng – Journal of Applied Genetics
http://link.springer.com/article/10.1007/s13353-014-0258-1/fulltext.html

Prepartum and Postpartum Rumen Fluid Microbiomes: Characterization and Correlation with Production Traits in Dairy Cows – Fabio S. Lima – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1327.abstract

Relationship between honeybee nutrition and their microbial communities – Miriane Acosta Saraiva – Antonie van Leeuwenhoek
http://link.springer.com/article/10.1007/s10482-015-0384-8

Intestinal microbiota and immune related genes in sea cucumber (Apostichopus japonicus) response to dietary β-glucan supplementation – Gang Yang – Biochemical and Biophysical Research Communications
http://www.sciencedirect.com/science/article/pii/S0006291X15001047

Microbiome affects egg carotenoid investment, nestling development and adult oxidative costs of reproduction in Great tits – Staffan Jacob – Functional Ecology
http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.12404/abstract

Review: Dietary fibre and the importance of the gut microbiota in feline nutrition: a review
Kristel Rochus – Nutrition Research Reviews
http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=9534845&fileId=S0954422414000213

Plant microbiome

T Bacterial Communities Associated with Surfaces of Leafy Greens: Shift in Composition and Decrease in Richness over Time – Merete Wiken Dees – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1530.abstract

Soil, rock, and sediment microbiome

Long-term forest soil warming alters microbial communities in temperate forest soils – Kristen M. DeAngelis – Frontiers in Microbiology
http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00104/abstract

This one was submitted in June 2013, but just published: Soil microbial community structure and activity in a 100-year-old fertilization and crop rotation experiment – Cancan Zhao – Journal of Plant Ecology
http://jpe.oxfordjournals.org/content/early/2015/01/28/jpe.rtv007.abstract

Interrogation of Chesapeake Bay sediment microbial communities for intrinsic alkane-utilizing potential under anaerobic conditions – Jamie M. Johnson – FEMS Microbiology Ecology
http://femsec.oxfordjournals.org/content/early/2014/12/24/femsec.fiu035.abstract

Short-term effects of soil amendment with meadowfoam seed meal on soil microbial composition and function – Suphannika Intanon – Applied Soil Ecology
http://www.sciencedirect.com/science/article/pii/S0929139315000104

Molecular diversity of arbuscular mycorrhizal fungi at a large-scale antimony mining area in southern China – Yuan Wei – Journal of Environmental Sciences
http://www.sciencedirect.com/science/article/pii/S100107421500008X

Assessing Fungal Community Structure from Mineral Surfaces in Kartchner Caverns Using Multiplexed 454 Pyrosequencing – Michael Joe Vaughan – Microbial Ecology
http://link.springer.com/article/10.1007/s00248-014-0560-9

Effects of increasing precipitation on soil microbial community composition and soil respiration in a temperate desert, Northwestern China – Gang Huang – Soil Biology and Biochemistry
http://www.sciencedirect.com/science/article/pii/S003807171500019X

Review: Microbial ecology of hot desert edaphic systems – Thulani P. Makhalanyane – FEMS Microbiology Reviews
http://femsre.oxfordjournals.org/content/early/2015/01/23/femsre.fuu011.abstract

Water microbiome

Synchronous shifts in dissolved organic carbon bioavailability and bacterial community responses over the course of an upwelling-driven phytoplankton bloom – Emma K. Wear – Limnology and Oceanography
http://onlinelibrary.wiley.com/doi/10.1002/lno.10042/abstract

Comparison of the microbial communities of hot springs waters and the microbial biofilms in the acidic geothermal area of Copahue (Neuquén, Argentina) – María Sofía Urbieta – Extremophiles
http://link.springer.com/article/10.1007/s00792-015-0729-2

Environmental controls on intragroup diversity of the uncultured benthic archaea of the miscellaneous Crenarchaeotal group lineage naturally enriched in anoxic sediments of the White Oak River estuary (North Carolina, USA) – Cassandre Sara Lazar – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12659/abstract

Methane oxidation pathways and associated methanotrophic communities in the water column of a tropical lake – Prosper K. Zigah – – Limnology and Oceanography
http://onlinelibrary.wiley.com/doi/10.1002/lno.10035/abstract

Seasonal assemblages and short-lived blooms in coastal north-west Atlantic Ocean bacterioplankton – Heba El-Swais – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12629/abstract

Environmental rather than spatial factors structure bacterioplankton communities in shallow lakes along a > 6000 km latitudinal gradient in South America – Caroline Souffreau – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12692/abstract

Microbial Contamination of Drinking Water and Human Health from Community Water Systems
Nicholas J. Ashbolt – Current Environmental Health Reports
http://link.springer.com/article/10.1007/s40572-014-0037-5

Book Chapter: Microbial Bioprospecting in Marine Environments – Mariana Lozada, Hebe M. Dionisi – Hb25_Springer Handbook of Marine Biotechnology
http://link.springer.com/chapter/10.1007/978-3-642-53971-8_11

Bioreactor microbiome

Long-term monitoring reveals stable and remarkably similar microbial communities in parallel full-scale biogas reactors digesting energy crops – Rico Lucas – FEMS Microbiology Ecology
http://femsec.oxfordjournals.org/content/early/2015/01/11/femsec.fiv004.abstract

The fate of oxytetracycline in two-phase and single-phase anaerobic cattle manure digesters and its effects on microbial communities – Çağrı Akyol – Journal of Chemical Technology and Biotechnology
http://onlinelibrary.wiley.com/doi/10.1002/jctb.4649/abstract

Identification of the microbial community composition and structure of coal-mine wastewater treatment plants – Qiao Ma – Microbiological Research
http://www.sciencedirect.com/science/article/pii/S0944501315000105

New steady-state microbial community compositions and process performances in
biogas reactors induced by temperature disturbances – Gang Luo – Biotechnology for Biofuels

Click to access s13068-014-0182-y.pdf

Archaea

Diversity of Methane-Cycling Archaea in Hydrothermal Sediment Investigated by General and Group-Specific PCR Primers – Mark A. Lever and Andreas P. Teske – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1426.abstract

Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter – WIlliam D Orsi – ISME Journal
http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2014260a.html

Bioinformatics

Integrating Multi-omic features exploiting Chromosome Conformation Capture data – Ivan Merelli – Frontiers in Genetics
http://journal.frontiersin.org/Journal/10.3389/fgene.2015.00040/abstract

Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach – Philippe Rocca-Serra – Database
http://database.oxfordjournals.org/content/2015/bau132.full

Koonkie: An Automated Software Tool for Processing Environmental
Sequence Information using Hadoop – Dongjae Kim – ASE360
http://www.ase360.org/bitstream/handle/123456789/164/P9.pdf?sequence=1&isAllowed=y

MetAmp: combining amplicon data from multiple markers for OTU analysis – Ilya Y. Zhbannikov,, James A. Foster – Bioinformatics

Click to access bioinformatics.btv049.full.pdf

MetaAB – A Novel Abundance-Based Binning Approach for Metagenomic Sequences
Van-Vinh Le – Nature of Computation and Communication
Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering
http://link.springer.com/chapter/10.1007/978-3-319-15392-6_13

NCBI BLAST+ integrated into Galaxy – Peter J. A. Cock – BioRxiv

Click to access 014043.full.pdf

Metagenomics

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species – Sharon Greenblum – Cell
http://www.sciencedirect.com/science/article/pii/S0092867415000136

Integrated metagenomics and network analysis of soil microbial community of the forest timberline – Junjun Ding – Scientific Reports
http://www.nature.com/srep/2015/150123/srep07994/full/srep07994.html

Book Chapter: Marine Sponge Metagenomics – Valliappan Karuppiah, Zhiyong Li – Hb25_Springer Handbook of Marine Biotechnology
http://link.springer.com/chapter/10.1007/978-3-642-53971-8_17

Ecological and genetic interactions between cyanobacteria and viruses in a low-O2 mat community inferred through metagenomics and metatranscriptomics – Alexander A. Voorhies – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12756/abstract

Metagenomic analysis reveals adaptations to a cold adapted lifestyle in a low temperature acid mine drainage stream – Maria Liljeqvist – FEMS Microbiology Ecology
http://femsec.oxfordjournals.org/content/early/2015/01/27/femsec.fiv011.abstract

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes – Manuel Kleiner – BMC Genomics

Click to access s12864-014-1207-4.pdf

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking – Yuji Sekiguchi – PeerJ
https://peerj.com/articles/740/

The effects of variable sample biomass on comparative metagenomics – Meghan Chafee – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12668/abstract

Review: Functional genomic and metagenomic approaches to understanding gut microbiota–animal mutualism – Sang Sun Yoon – Current Opinion in Microbiology
http://www.sciencedirect.com/science/article/pii/S1369527415000089

Book Chapter: Marine Metagenome and Supporting Technology – Tetsushi Mori – Hb25_Springer Handbook of Marine Biotechnology
http://link.springer.com/chapter/10.1007/978-3-642-53971-8_19

Transcriptomics, metabolomics

Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen – Xin Dai – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1375.abstract

Genomic Potential for Polysaccharide Deconstruction in Bacteria – Renaud Berlemont and Adam C. Martiny – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1513.abstract

Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor – Masaru K Nobu – ISME Journal
http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2014256a.html

Perturbations of tyrosine metabolism promote the indolepyruvate pathway via tryptophan in host and microbiome – Ilya Gertsman – Molecular Genetics and Metabolism
http://www.sciencedirect.com/science/article/pii/S109671921500027X

Gut Symbionts from Distinct Hosts Exhibit Genotoxic Activity via Divergent Colibactin Biosynthesis Pathways – Philipp Engel – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1502.abstract

Transcriptome analyses to investigate symbiotic relationships between marine – Sergio Balzano – Frontiers in Microbiology
http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00098/abstract

Perturbations of tyrosine metabolism promote the indolepyruvate pathway via tryptophan in host and microbiome – Ilya Gertsman – Molecular Genetics and Metabolism
http://www.sciencedirect.com/science/article/pii/S109671921500027X

Human metabolic, mineral, and microbiota fluctuations across daily nutritional intake visualized by a data-driven approach – Takuma Misawa – Journal of Proteome Research
http://pubs.acs.org/doi/abs/10.1021/pr501194k

Review: Prospects and challenges for fungal metatranscriptomics of complex communities – Cheryl R. Kuske – Fungal Ecology

Microbial Ecology

Disturbance opens recruitment sites for bacterial colonization – David Vuono – BioRxiv
http://biorxiv.org/content/early/2015/01/27/014456

Review: High-throughput DNA barcoding for ecological network studies – Hirokazu Toju – Population Ecology
http://link.springer.com/article/10.1007/s10144-014-0472-z

Book Chapter: For Three Billion Years, Microorganisms Were the Only Inhabitants of the Earth
Jean-Claude Bertrand – Environmental Microbiology: Fundamentals and Applications
http://link.springer.com/chapter/10.1007/978-94-017-9118-2_4

Book Chapter: Microbiome Ecosystem Ecology: Unseen Majority in an Anthropogenic Ecosystem- Muhammad Saleem – Microbiome Community Ecology
http://link.springer.com/chapter/10.1007/978-3-319-11665-5_1

More microbes

Introduction to a special issue of PLOS Pathogens: The Importance of Pathogen Load – Aubrey J. Cunnington – PLOS Pathogens
http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1004563

Microbes in the news

Satire: Secret Microbiome Forensic Study Reveals DeflateGate Culprit – Megabiome.net

Secret microbiome forensic study reveals #deflategate culprit

Among gut microbes, strains, not just species, matter – MedicalXpress
http://medicalxpress.com/news/2015-01-gut-microbes-strains-species.html

Analysis Highlights Strain Diversity in Gut Microbiome – GenomeWeb
https://www.genomeweb.com/genetic-research/analysis-highlights-strain-diversity-gut-microbiome

Jonathan Eisen and Jessica Richman on the Microbiome – Kevin Bonham – Scientific American
http://blogs.scientificamerican.com/food-matters/2015/01/30/jonathan-eisen-and-jessica-richman-on-the-microbiome/

Part-Time Pooping: A New Way to Make an Extra $13,000 a Year – Everyday Health
http://www.everydayhealth.com/columns/daily-checkup/part-time-pooping-new-way-make-extra-money-year/

OpenBiome will pay for poo – Helen Clark – GizMag
http://www.gizmag.com/openbiome-fecal-transplant/35845/

January 2015 Update on American Gut, British Gut and Australian Gut Human Microbiome Projects – IBS Impact
https://ibsimpact.wordpress.com/2015/01/30/january-2015-update-on-american-gut-british-gut-and-australian-gut-human-microbiome-projects/

The Microbiome – New Research On Inflammatory Bowel Disease May Foreshadow Autism? – Teresa Conrick – Age of Autism
http://www.ageofautism.com/2015/01/the-microbiome-new-research-on-inflammatory-bowel-disease-may-foreshadow-autism.html

The microbiome of the upper airways: focus on chronic rhinosinusitis – 7th Space
http://7thspace.com/headlines/503056/the_microbiome_of_the_upper_airways_focus_on_chronic_rhinosinusitis.html

Germ Theory: What You May Not Know About The Bacteria Crawling Around Your Bathroom – Justin Caba – Medical Daily
http://www.medicaldaily.com/pulse/germ-theory-what-you-may-not-know-about-bacteria-crawling-around-your-bathroom-319884

Altered gut microbiota seen in patients with psoriatic arthritis – Healio.com
http://www.healio.com/rheumatology/psoriatic-arthritis/news/online/%7B0dd6068d-11b8-4e05-82f2-7713d4f28749%7D/altered-gut-microbiota-seen-in-patients-with-psoriatic-arthritis

The Human Microbiome: Biomedical Implications and Birth of a Market – Overview – PRNewsWIre
http://www.prnewswire.co.uk/news-releases/the-human-microbiome-biomedical-implications-and-birth-of-a-market—overview-290212581.html

Meet Dr. Armpit, changing body odor with bacteria – Fast Company
http://www.fastcompany.com/3041388/body-week/meet-dr-armpit-changing-body-odor-with-bacteria

Gut bacteria byproduct linked to chronic kidney disease for the first time – Medical Xpress
http://medicalxpress.com/news/2015-01-gut-bacteria-byproduct-linked-chronic.html

Does draft beer give you a worse hangover? We came across people from the beer industry and beer drinkers who claimed the bacteria in those lines contributes to a hangover. – Jace Larson – Click 2 Houston
http://www.click2houston.com/news/does-draft-beer-give-you-a-worse-hangover/31037044

Bik’s Picks

Face blindness predicted by structural differences in the brain, Stanford neuroscientists discover – Leslie Willoughby – Stanford News
http://news.stanford.edu/news/2015/january/face-blind-brain-013015.html

[hr]

January 14, 2015

Posted on by

Human gut microbiome

Review: Fusobacterium and Escherichia: models of colorectal cancer driven by microbiota and the utility of microbiota in colorectal cancer screening – Andrea Leung – Expert Review of Gastroenterology & Hepatology

Animal microbiome

Passage of Wolbachia pipientis through Mutant Drosophila melanogaster Induces Phenotypic and Genomic Changes – Irene L. G. Newton and Kathy B. Sheehan – Applied and Environmental Microbiology

Water microbiome

Alternative Fecal Indicators and Their Empirical Relationships with Enteric Viruses, Salmonella enterica, and Pseudomonas aeruginosa in Surface Waters of a Tropical Urban Catchment – L. Liang – Applied and Environmental Microbiology

Genomic and proteomic characterization of “Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean – Alyson E. Santoro – PNAS USA

More microbiology

Innate sensing of microbial products promotes wound-induced skin cancer – Esther Hoste – Nature Communications

Identifying strains that contribute to complex diseases through the study of microbial inheritance – Jeremiah J. Faith – PNAS USA

Long-term phenotypic evolution of bacteria – Germán Plata – Nature

Co-infection alters population dynamics of infectious disease – Hanna Susi – Nature Communications

Ferment in the family tree – Nathaniel J. Dominy – PNAS USA

Infection and Host response

Profiling lymphocyte interactions at the single-cell level by microfluidic cell pairing – Burak Dura – Nature Communications

B-cell repertoire responses to varicella-zoster vaccination in human identical twins
Chen Wang – PNAS USA

Metabolomics

Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi – Ralph A. Cacho – Frontiers in Microbiology

The chemistry of negotiation: Rhythmic, glycan-driven acidification in a symbiotic conversation – Julia A. Schwartzman – PNAS USA

Microbes in the news

I love this title! Featuring Margaret McFall-Ngai: Microbiology: Here’s looking at you, squid – Ed Yong – Nature

How Bread, Beer, and Soy Sauce Changed the Human Microbiome – Francie Diep – Popular Science

Early human microbiome studies may aid modern nutrition science – Nathan Gray – Nutraingredients

Understanding the personalities of bacteria – Phys.org

2014: The Year of the Virus – Joan B. Rose – Huffington Post

Have viruses made us smarter? ‘Junk’ virus genes in our DNA may have helped our brain cells evolve – By Victoria Woollaston – Daily Mail

With Vedanta Deal, Johnson & Johnson Marks Big-Pharma Milestone in the Microbiome – Alex Lash – Xconomy

Scientists developing Teflon for bacteria – Amanda Schupak – CBS News

Understanding the personalities of bacteria – Phys.org

#BacteriaHysteria – beautiful, not filthy! Smartphone bacteria ‘prints’ show how filthy your mobile really is – Rob Waugh – Metro

Science, publishing and career

A generation at risk: Young investigators and the future of the biomedical workforce – Ronald J. Daniels – PNAS USA

Work–life balance: Lab life with kids – Kendall Powell – Nature

Bik’s Picks

‘I can haz genomes’: cats claw their way into genetics – Canine dominance bows to tabby chic as cat sequencing takes off – Ewen Callaway – Nature
and
Out of the bag: The preference for either cats or dogs affects science more than you might think– Nature

Geographically varying associations between personality and life satisfaction in the London metropolitan area – Markus Jokela – PNAS USA

Very important science: Watch a chainsaw made with shark teeth slice through salmon – Francie Diep – Popular Science

[hr]

January 13, 2015

Posted on by

Human oral microbiome

The Biofilm Community: Rebels with a Cause – A. Wilson Aruni – Current Oral Health Reports

Human respiratory microbiome

Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age – J C Stearns – The ISME Journal

Recombination is a key driver of genomic and phenotypic diversity in a Pseudomonas aeruginosa population during cystic fibrosis infection – Sophie E. Darch – Scientific Reports

Human gut microbiome

Effect of Exclusive Enteral Nutrition on the Microbiota of Children With Newly Diagnosed Crohn’s Disease – Nadeem O. Kaakoush – Clinical and Translational Gastroenterology

The intestinal microbiota: its role in health and disease – Luc Biedermann, Gerhard Rogler – European Journal of Pediatrics

Geographical patterns of the standing and active human gut microbiome in health and IBD – Ateequr Rehman – Gut

Severity of atopic disease inversely correlates with intestinal microbiota diversity and butyrate-producing bacteria – L. Nylund – Allergy

The influence of the microbiota on the immune response to transplantation – Bartman, Caroline – Current Opinion in Organ Transplantation

Animal models of microbiome research

The enduring importance of animal models in understanding periodontal disease – George Hajishengallis – Virulence

Animal microbiome

Similarities and seasonal variations in bacterial communities from the blood of rodents and from their flea vectors – Carmit Cohen – The ISME Journal

Molecular analysis of cecal and tracheal microbiome of heat-stressed broilers supplemented with prebiotic and probiotic – Muhammad U. Sohail – Avian Pathology

Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies – Karen E Sullam – The ISME Journal

Composition and predicted functional ecology of mussel-associated bacteria in Indonesian marine lakes – Daniel F. R. Cleary – Antonie van Leeuwenhoek

Deep down on a Caribbean reef: lower mesophotic depths harbor a specialized coral-endosymbiont community – Pim Bongaerts – Scientific Reports

Soil microbiome

Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach – Giovanni Bacci – Antonie van Leeuwenhoek

Role of RNase on microbial community analysis in the rice and wheat plants soil by 16S rDNA-DGGE – Md. Mizanur Rahman – Journal of Crop Science and Biotechnology

Field-based evidence for consistent responses of bacterial communities to copper contamination in two contrasting agricultural soils – Jing Li – Frontiers in Microbiology

Evident bacterial community changes but only slight degradation when polluted with pyrene in a red soil – Gaidi Ren – Frontiers in Microbiology

Soil bacterial and fungal communities respond differently to various isothiocyanates added for biofumigation – Ping Hu – Frontiers in Microbiology

Seasonal dynamics of bacterial and archaeal methanogenic communities in flooded rice fields and effect of drainage – Björn Breidenbach and Ralf Conrad – Frontiers in Microbiology

Biogeography and biophysicochemical traits link N2O emissions, N2O emission potential and microbial communities across New Zealand pasture soils – Sergio E. Morales – Soil Biology and Biochemistry

Formation of iron-rich shelled structures (IRSS) by microbial communities – David C. Fernández-Remolar – Journal of Geophysical Research: Biogeosciences

Effects of alkyl-imidazolium ionic liquid [Omim]Cl on the functional diversity of soil microbial communities – Pengpeng Guo – Environmental Science and Pollution Research

Cyanobacteria drive community composition and functionality in rock-soil interface communities – Angel Valverde – Molecular Ecology

Separation of soil microbial community structure by aggregate size to a large extent under agricultural practices during early pedogenesis of a Mollisol – Na Li – Applied Soil Ecology

Microbial community structure of anoxic-oxic-settling-anaerobic sludge reduction process revealed by 454-pyrosequencing – Zhen Zhou – Chemical Engineering Journal

Conservation tillage positively influences the microflora and microfauna in the black soil of Northeast China – Shixiu Zhang – Soil and Tillage Research

Resuscitation of the rare biosphere contributes to pulses of ecosystem activity – Zach Aanderud – Frontiers in Microbiology

Water microbiome

Drinking water microbiology — from measurement to management – Caitlin R Proctor, Frederik Hammes – Current Opinion in Biotechnology

Microbial biogeography of drinking water: patterns in phylogenetic diversity across space and time – Guus Roeselers – Environmental Microbiology

Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid-Ocean Ridge – Håkon Dahle – The ISME Journal
http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2014247a.html

Metagenomics

Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics – Tomàs Llorens-Marès – The ISME Journal

Environmental Metagenomics: The Data Assembly and Data Analysis Perspectives – Vinay Kumar – Journal of The Institution of Engineers (India): Series A

Metagenome assembly through clustering of next-generation sequencing data using protein sequences – Mikang Sim, Jaebum Kim – Journal of Microbiological Methods

Metagenomic Insights into the Effects of Fructo-oligosaccharides (FOS) on the Composition of Fecal Microbiota in Mice – Bingyong Mao – Journal of Agricultural and Food Chemistry

Diagnosis of Neuroinvasive Astrovirus Infection in an Immunocompromised Adult With Encephalitis by Unbiased Next-Generation Sequencing – Samia N. Naccache – Clinical Infectious Diseases

Unbiased Next-Generation Sequencing and New Pathogen Discovery: Undeniable Advantages and Still-Existing Drawbacks – Arianna Calistri and Giorgio Palù – Clinical Infectious Diseases

Identification of diverse circular single-stranded DNA viruses in adult dragonflies and damselflies (Insecta: Odonata) of Arizona and Oklahoma, USA – Anisha Dayaram – Infection, Genetics and Evolution

Metabolomics

Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology – Marco Fondi and Pietro Liò – BioRxiv

Techniques

Accounting for uncertainty in DNA sequencing data – Jason A. O’Rawe – Trends in Genetics

More microbes
3D-Printed Microfluidic Device for the Detection of Pathogenic Bacteria Using Size-based Separation in Helical Channel with Trapezoid Cross-Section – Wonjae Lee – Scientific Reports

Microbes in the news

UCSD hires star biologist Rob Knight – Gary Robbins – UT San Diego

Drug developed out of microbiome studies advances in phase I trial – Stephanie M. Lee – SF Gate
and
Second Genome’s gut check uncovers a possible drug for bowel disease – Ron Leuty – San Francisco Business Times

The Megabiome – It’s not micro anymore – Megabiome.net

Are We Really 10% Human and 90% Bacteria? Exploring The Microbiome… (with Jessica Richman and Jonathan Eisen) – Tim Ferriss Show – Four Hour Workweek

Mounting Research Shows Gut-Brain Connection – Traci Pedersen – Psych Central

Microbiota organization influences colorectal cancers – Nicola Garrett – Family Practice News

“MyNewGut”: New project explores role of gut microbiota in preventing diet- and brain-related diseases – News-Medical.net

Joint Pain, From the Gut – David Kohn – The Atlantic

A Lamp Whose Light Comes From Bioluminescent Bacteria – Liz Stinson – Wired.com

Pieter Dorrestein Recognized by Pharmacology Society – Heather Buschman – UC San Diego

Science, publishing and career

Post publication peer review comes of age – Emma Stoye – Chemistry World

What Tech Conferences Need to Stop for Women to Contribute More – Kellyn Pot’Vin-Gorman – LinkedIn

Bik’s Picks

Because our lab is close: Jeepers! New Look at ‘Creeping’ San Andreas Fault
by Becky Oskin – LiveScience
http://www.livescience.com/49435-san-andreas-fault-less-creepy.html

These scientists raised bot fly larvae in their own bodies — on purpose – Rachel Feltman – The Washington Post

Today in Adorable Science: Disney Has Created a L’il Turtle Robot to Draw Doodles in the Sand – Carolyn Cox – The Mary Sue

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