Category Archives: Metagenomics & Bioinformatics

July 26, 2016

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The last common ancestor, pika gut microbiome, fire-fighting chemicals and soil microbiome, improved Illumina-compatible 18S rRNA primers.

Jobs

Verily (Google-associated) is looking for a Microbiome Research Associate

Pregnancy and birth

Probiotic properties of lactic acid bacteria isolated from human milk – N.A. Reis – Journal of Applied Microbiology

Human oral microbiome

High Throughput Quantitative Method for Assessing Coaggregation among Oral Bacterial Species – Elizabeth Levin-Sparenberg – Letters in Applied Microbiology

Periodontal infectogenomics: systematic review of associations between host genetic variants and subgingival microbial detection – Luigi Nibali – Journal of Clinical Periodontology

Human respiratory microbiome

Upper airway viruses and bacteria and clinical outcomes in children with cough – Kerry-Ann F. O’Grady – Pediatric Pulmonology

Human skin microbiome

Hypothesis: The skin microbiome: Is it affected by UV-induced immune suppression? – Vijaykumar Patra – Frontiers in Microbiology

Human gut microbiome

Gut microbiota-host interactions and juvenile idiopathic arthritis – Miika Arvonen – Pediatric Rheumatology

Designing fecal microbiota transplant trials that account for differences in donor stool efficacy – Scott W. Olesen – bioRxiv

Probiotics and the Microbiome in Celiac Disease: A Randomised Controlled Trial – Joanna Harnett – Evidence-Based Complementary and Alternative Medicine

Review: Links Between the Microbiome and Bone – Christopher J Hernandez – Journal of Bone and Mineral Research

Human vaginal microbiome

More Easily Cultivated Than Identified: Classical Isolation With Molecular Identification of Vaginal Bacteria – Sujatha Srinivasan – The Journal of Infectious Diseases

The Effects of Hormones and Vaginal Microflora on the Glycome of the Female Genital Tract: Cervical-Vaginal Fluid – Bernard J. Moncla – PLOS ONE

Review: New Systems for Studying Intercellular Interactions in Bacterial Vaginosis – Melissa M. Herbst-Kralovetz – The Journal of Infectious Diseases

Animal experiments

Lactulose differently modulates the composition of luminal and mucosal microbiota in C57BL/6J mice – Bingyong Mao – Journal of Agricultural and Food Chemistry

American Ginseng Attenuates Colitis Associated Colon Carcinogenesis in Mice: Impact on Gut Microbiota and Metabolomics – Chong-Zhi Wang – Cancer Prevention Research

Alterations of Gut Microbiota After Roux-en-Y Gastric Bypass and Sleeve Gastrectomy in Sprague-Dawley Rats – Yikai Shao – Obesity Surgery

Animal microbiome

Diet diversity is associated with beta but not alpha diversity of pika gut microbiota – Huan Li – Frontiers in Mcrobiology

The Microbial Signature Provides Insight into the Mechanistic Basis of Coral Success across Reef Habitats – Alejandra Hernandez-Agreda – mBio

Perspective: Hominid superorganisms – Julia A. Segre – Science

Plant, root, and soil microbiome

Long-term response of soil microbial communities to fire and fire-fighting chemicals –
A. Barreiro – Biology and Fertility of Soils

Desert Perennial Shrubs Shape the Microbial-Community Miscellany in Laimosphere and Phyllosphere Space – Varsik Martirosyan – Microbial Ecology

Lichen-associated Fungal Community in Hypogymnia hypotrypa (Parmeliaceae, Ascomycota) Affected by Geographic Distribution and Altitude – Yanyan Wang – Frontiers in Microbiology

Water management impacts rice methylmercury and the soil microbiome – Sarah E. Rothenberg – Science of the Total Environment

Ecological restoration of a copper polluted vineyard: Long-term impact of farmland abandonment on soil bio-chemical properties and microbial communities – Luciano Cavani – Journal of Environmental Management

Review: Soil C and N models that integrate microbial diversity – Benjamin P. Louis – Environmental Chemistry Letters

Water and extremophile microbiome

Genomes of Abundant and Widespread Viruses from the Deep Ocean – Carolina Megumi Mizuno – mBio

Microbial communities associated with Antarctic snow pack and their biogeochemical implications – Runa Antony – Microbiological Research

Novel chytrid lineages dominate fungal sequences in diverse marine and freshwater habitats – André M. Comeau – Scientific Reports

Metabolomics

Review: Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health – Pamela Vernocchi – Frontiers in Microbiology

Functional foods

Review: Fermented Foods: Are They Tasty Medicines for Helicobacter pylori Associated Peptic Ulcer and Gastric Cancer? – Mydhily R. B. Nair – Frontiers in Microbiology

Bioinformatics

A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF – Yingnan Cong – Scientific Reports
Exploring lateral genetic transfer among microbial genomes using TF-IDF – Yingnan Cong – Scientific Reports

Techniques

Design and Evaluation of Illumina MiSeq Compatible Primers for the 18S rRNA Gene for Improved Characterization of Mixed Microalgal Communities – Ian M. Bradley – Applied and Environmental Microbiology

More microbiology

Are multi-omics enough? – Cristina Vilanova – Nature Microbiology

Review: Bacterial Communities: Interactions to Scale – Reed M. Stubbendieck – Frontiers in Microbiology

The physiology and habitat of the last universal common ancestor – Madeline C. Weiss – Nature Microbiology

Press: Scientists find Luca, a single-cell, bacterium-like organism that is the common ancestor of all life on Earth – Andrew Griffin – Independent
Behold LUCA, the Last Universal Common Ancestor of Life on Earth – Jason Daley – Smithsonian
Our last common ancestor inhaled hydrogen from underwater volcanoes – Robert F. Service – Science
Meet Luca, the Ancestor of All Living Things – Nicholas Wade – New York Times

Microbes in the news

What your gut microbiome may be telling you – Katrina Clarke – The Record

Healthy microbiome supports antibiotic-free production – World Poultry

Charlottesville Lab to Test Microbiology of Local Breweries – NBC29

Nanostructured bacterial film makes new mortar resistant to water uptake – NanoWerk

Bik’s non-microbiology Picks

The Dutchies are still holding the top positions! A century of trends in adult human height – NCD Risk Factor Collaboration (NCD-RisC) – eLIFE

July 24, 2016

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Songbird, soil nitrogen-cycling around the world, and parasites on an ancient butt-wipe stick.

Pregnancy and birth

Dysfunctional gut microbiota and relative co-abundance network in infantile eczema – Heping Wang – Gut Pathogens

Human oral microbiome

Review: From focal sepsis to periodontal medicine: A century of exploring the role of the oral microbiome in systemic disease – Purnima S Kumar – The Journal of Physiology

Human gut microbiome

Review: The Role of the Gut Microbiome on Chronic Kidney Disease – B. Sampaio-Maia – Advances in Applied Microbiology

Review: The Microbiota, Immunoregulation, and Mental Health: Implications for Public Health – Christopher A. Lowry – Current Environmental Health Reports

Animal and other experiments

Insulin resistance, microbiota and fat distribution changes by a new model of vertical sleeve gastrectomy in obese rats – Nicola Basso – Diabetes

Establishment of microbiota in larval culture of Pacific oyster, Crassostrea gigas – Katia Asmani – Aquaculture

Changes in the structure of the microbial community associated with Nannochloropsis salina following treatments with antibiotics and bioactive compounds – Haifeng Geng – Frontiers in Microbiology

Animal microbiome
Social environment has a primary influence on the microbial and odor profiles of a chemically signaling songbird – Danielle J. Whittaker – Frontiers in Ecology and Evolution

16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife – Maxime Galan – mSystems

Plant, root, and soil microbiome

Global biogeography of microbial nitrogen-cycling traits in soil – Michaeline B. Nelson – PNAS

Mammalian engineers drive soil microbial communities and ecosystem functions across a disturbance gradient – David J Eldridge – Journal of Animal Ecology

Biogeochemical drivers of microbial community convergence across actively retreating glaciers – Sarah C. Castle – Soil Biology and Biochemistry

The structure of bacterial communities along two vertical profiles of a deep colluvial soil – Marketa Sagova-Mareckova – Soil Biology and Biochemistry

Silver nanoparticles, ions and shape governing soil microbial functional diversity: nano shapes micro – Yujia Zhai – Frontiers in Microbiology

Water microbiome

Metagenomic signatures of a tropical mining-impacted stream reveal complex microbial and metabolic networks – Mariana P. Reis – Chemosphere

Effects of Copper, Nickel, and Sulphate from the Smelters at Sudbury, Ontario (Canada) on Microbial Communities in Lakes – Togwell A. Jackson – Geomicrobiology Journal

Archeological microbes

Early evidence for travel with infectious diseases along the Silk Road: Intestinal parasites from 2000 year-old personal hygiene sticks in a latrine at Xuanquanzhi Relay Station in China – Hui-Yuan Yeh – Journal of Archaeological Science: Reports

Press: Ancient Faeces Provide Earliest Evidence of Infectious Disease Being Carried on Silk Road – SciCasts
Ancient bottom wipers yield evidence of diseases carried along the Silk Road – Maev Kennedy – The Guardian

Built environment microbiome

Microorganisms associated with corrosion of structural steel in diverse atmospheres – Laura L. Machuca – International Biodeterioration & Biodegradation

More microbes

Individuals hospitalized with acute mania have increased exposure to antimicrobial medications – Robert Yolken – Bipolar Disorders

Metagenomics and bioinformatics

Multiplexed Metagenomic Deep Sequencing To Analyze the Composition of High-Priority Pathogen Reagents – Michael R. Wilson – mSystems

Microbes in the news

Everyday chemicals may be messing up our microbiomes—but we don’t know – Beth Mole – Ars Technica
The jury is still out on whether antibacterial chemical impacts microbiome or causes resistance – Bob Yirka – Medical Xpress

Some Microbes Have Been With Us Since Before We Existed. Certain gut bacteria have evolved in parallel with apes, so that their family tree perfectly mirrors our own. – Ed Yong – The Atlantic

Plants have a microbiome just like humans — and it could transform how our food is produced – Ariel Schwartz – Tech Insider

New book: The Human Superorganism: How the Microbiome Is Revolutionizing the Pursuit of a Healthy Life – Rodney Dietert
Your Microbes, Yourself. In his new book, Rodney Dietert argues that it’s time to re-configure our relationship with germs: – Louise Fabiani – Pacific Standard

Science, publishing, and career

The Women and the Science
Rachel Ignotofsky tells the stories of 50 women in science in her fantastic new science art book – Scientific American
Women in Science: An Illustrated Who’s Who – Julie Leibach – Science Friday

Women in Science: An Illustrated Who’s Who

July 22, 2016

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Fungi in human GI tract, antibiotics reduce Alzheimer’s lesions in mouse model, cospeciation of primates and gut microbes, dangerous bacteria after sewer spill.

Jobs

Research scientists to engineer microbiome engineering therapies – Eligo Bioscience

General microbiome

Perspective: Is triclosan harming your microbiome? – Alyson L. Yee – Science

Understanding How Microbiomes Influence the Systems they Inhabit: Insight from Ecosystem Ecology – Ed Hall – bioRxiv

Pregnancy and birth microbiome

Midtrimester Cervicovaginal Microbiota: Identification of Microbial Variations Associated with Puerperal Infection at Term – Akila Subramaniam – American Journal of Perinatology

Human mouth microbiome

Salivary and fecal microbiota and metabolome of celiac children under gluten-free diet – Maria De Angelis – International Journal of Food Microbiology

Human respiratory microbiome

Lung Microbiome in HIV Infection – Homer L. Twigg III – Translational Research

Human vaginal microbiome

Proceedings of the 2015 NIH/NIAID Bacterial Vaginosis Expert Consultation – The Journal of Infectious Diseases

Human gut microbiome

Age and gender affect the composition of fungal population of the human gastrointestinal tract – Francesco Strati – Frontiers in Microbiology

A reduction in the butyrate producing species Roseburia spp. and Faecalibacterium prausnitzii is associated with chronic kidney disease progression – Shuanghong Jiang – Antonie van Leeuwenhoek

Review: An update discussion on the current assessment of the safety of veterinary antimicrobial drug residues in food with regard to their impact on the human intestinal microbiome – Carl E. Cerniglia – Drug Testing and Analysis

Animal experiments

Antibiotic-induced perturbations in gut microbial diversity influences neuro-inflammation and amyloidosis in a murine model of Alzheimer’s disease – Myles R. Minter – Scientific Reports

Press: Antibiotics weaken Alzheimer’s disease progression through changes in the gut microbiome – EurekAlert
Could antibiotics reduce levels of Alzheimer’s-causing plaques? – Hannah Nichols – MedicalNewsToday

Pathogenic shifts in endogenous microbiota impede tissue regeneration via distinct activation of TAK1/MKK/p38 – Christopher P Arnold – eLIFE

Bacterial community characterization of water and intestine of the shrimp Litopenaeus stylirostris in a biofloc system – Emilie Cardona – BMC Microbiology

Impact of Helminth Infections and Nutritional Constraints on the Small Intestine Microbiota – Isabella M. Cattadori – PLOS ONE

Nutrient Deprivation Affects Salmonella Invasion and Its Interaction with the Gastrointestinal Microbiota – Sophie Yurist-Doutsch – PLOS ONE

Celecoxib alters the intestinal microbiota and metabolome in association with reducing polyp burden – David C. Montrose – Cancer Prevention Research

Review: Interactions between host genetics and gut microbiome in diabetes and metabolic syndrome – Siegfried Ussar – Molecular metabolism

Animal microbiome

Cospeciation of gut microbiota with hominids – Andrew H. Moeller – Science

Press: Primates, Gut Microbes Evolved Together. Symbiotic gut bacteria evolved and diverged along with ape and human lineages, researchers find – Anna Azvolinsky – The Scientist
Microbes in our guts have been with us for millions of years – Ann Gibbons – Science
Your gut bacteria predates appearance of humans, genetic study finds – Naomi Stewart – The Guardian

A snapshot of the microbiome of Amblyomma tuberculatum ticks infesting the gopher tortoise, an endangered species – Khemraj Budachetri – Ticks and Tick-borne Diseases

Do Vertebrate Gut Metagenomes Confer Rapid Ecological Adaptation? –
Antton Alberdi – Trends in Ecology & Evolution

Vaginal microbial communities from synchronized-heifers and cows with reproductive disorders – Candelaria Gonzalez Moreno – Journal of Applied Microbiology

Review: The woodrat gut microbiota as an experimental system for understanding microbial metabolism of dietary toxins – Kevin D. Kohl – Frontiers in Microbiology

Plant, root, and soil microbiome

Plant Identity Exerts Stronger Effect than Fertilization on Soil Arbuscular Mycorrhizal Fungi in a Sown Pasture – Yong Zheng – Microbial Ecology

Beneficial cyanobacteria and eubacteria synergistically enhance bioavailability of soil nutrients and yield of okra – Mallappa Manjunath – Heliyon

Naming Potentially Endangered Parasites: Foliicolous Mycobiota of Dimorphandra wilsonii, a Highly Threatened Brazilian Tree Species– Meiriele da Silva – PLOS ONE

Contribution of the seed microbiome to weed management – D Müller-Stöver – Weed Research

Mycorrhizal associations of trees have different indirect effects on organic matter decomposition – Melanie K. Taylor – Journal of Ecology

Water and extremophile microbiome

Vancomycin resistant enterococci and bacterial community structure following a sewage spill into an aquatic environment – Suzanne Young – Applied and Environmental Microbiology

Press: USF researchers find dangerous bacteria after sewer spills – EurekAlert
USF researchers say they found dangerous bacteria after sewage spill – Anne Lindberg – Saint Peters Blog

Hospital Effluents Are One of Several Sources of Metal, Antibiotic Resistance Genes, and Bacterial Markers Disseminated in Sub-Saharan Urban Rivers – Amandine Laffite – Frontiers in Microbiology

Microbial communities in sediments of Lagos Lagoon, Nigeria: Elucidation of community structure and potential impacts of contamination by municipal and industrial wastes – Chioma C. Obi – Frontiers in Microbiology

Cryoconite pans on Snowball Earth: supraglacial oases for Cryogenian eukaryotes? – P. F. Hoffman – Geobiology

Effects of multiple dimensions of bacterial diversity on functioning, stability and multifunctionality – Fabian Roger – Ecology

Heterotrophic bacteria in Antarctic lacustrine and glacial environments – Johanna Laybourn-Parry – Polar Biology

Microbial diversity and activity in seafloor brine lake sediments (Alaminos Canyon block 601, Gulf of Mexico) – M. Crespo-Medina – Geobiology

Bioinformatics and metagenomics

MetaG: a graph-based metagenomic gene analysis for big DNA data – Linkon Chowdhury – Network Modeling Analysis in Health Informatics and Bioinformatics

DFAST and DAGA: web-based integrated genome annotation tools and resources – Yasuhiro Tanizawa – Bioscience of Microbiota, Food and Health

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion – Inka Vanwonterghem – Environmental Microbiology

Microbes in the news

Breast-feeding the Microbiome (Excerpt from his book) – Ed Yong – New Yorker

Janet Jansson Among Nine Authors of Nature Review Article – PNNL

Northern Arizona University professor Bruce Hungate named a fellow of the American Academy of Microbiology – Arizona Business Daily

UF scientists identify seal as source of new strain of bacteria that caused disease in hunter – Sarah Carey – University of Florida

Gut Bacteria May Drive Inflammation in Sepsis, ARDS – Salynn Boyles – MedPageToday

With Rob Knight as keynote speaker: Fermenting Knowledge at Fermentation Festivals (with Kombucha Recipe) – John D. Ivanko – Mother Earth News

Your death microbiome could catch your killer – Anna Williams – New Scientist

Microbes and money

Osel, Inc. Comments on New Study Showing Role of Vaginal Microbiome in Women’s Health – PharmiWeb

Q&A: Indigo’s CEO Reveals the Strategy Behind Its Plant Microbiome Technology – Olivia Vanni – BostInno

Eminent Harvard Geneticist Professor George Church Joins uBiome Advisory Board – Benzinga

Immuron to Cooperate with Leading Australian Universities on Autism Research – Nasdaq

July 15, 2016

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Symbionts and reproductive oddities, microbiota in a mouse stroke model, the plant holobiont, CRISPR spacer extraction from metagenomes.

General microbiome

Bacterial cell biology outside the streetlight: reproductive oddities displayed by bacteria associated with multicellular eukaryotes – Silvia Bulgheresi – Environmental Microbiology

New book: The Human Microbiota and Chronic Disease: Dysbiosis as a Cause of Human Pathology – Brian Henderson, Luigi Nibali – Wiley

Events

Webinar: The Microbiome and the Environment – July 26 – ACS Publications

Microbiomes of the Built Environment Meeting 2 Webcast Videos and Presentations Now Available! – Jonathan Eisen

Human gut microbiome

Severe Gut Microbiota Dysbiosis Is Associated With Poor Growth in Patients With Short Bowel Syndrome – Hannah G. Piper – Journal of Parenteral & Enteral Nutrition

Review: Corralling Colonic Flagellated Microbiota – Ruth E. Ley – The New England Journal of Medicine

Editorial: Microbiome and mental health in the modern environment – Emily Deans -Journal of Physiological Anthropology

Animal experiments

Microbiota Dysbiosis Controls the Neuroinflammatory Response after Stroke – Vikramjeet Singh – The Journal of Neuroscience

Press: Post-stroke shifts in gut bacteria could cause additional brain injury – Rachel Ehrenberg – Science News
Stroke Alters Gut Microbiome, Impacting Recovery. A bidirectional link between the brain and the gut can improve or worsen brain injury in mice, researchers report – Tanya Lewis – The Scientist

Animal microbiome

Nest Bacterial Environment Affects Microbiome of Hoopoe Eggshells, but Not That of the Uropygial Secretion – Ángela Martínez-García – PLOS ONE

Highly Variable Bacterial Communities Associated with the Octocoral Antillogorgia elisabethae – Veronica Robertson – Microorganisms

Review: Alice in microbes’ land: adaptations and counter-adaptations of vector-borne parasitic protozoa and their hosts – Guy Caljon – FEMS Microbiology Reviews

Plant, root, and soil microbiome

Fires of differing intensities rapidly select distinct soil fungal communities in a Northwest US ponderosa pine forest ecosystem – C. Reazin – Forest Ecology and Management

The enzymatic and physiological response of the microbial community in semiarid soil to carbon compounds from plants – I. F. Torres – European Journal of Soil Science

DGGE: Rhizobacterial Community Structures Associated with Native Plants Grown in Chilean Extreme Environments – Milko A. Jorquera – Microbial Ecology

Review: Plant–microbe partnerships in 2020: The plant holobiont and its interactions determine plant performance. – Birgit Mitter – Microbial Biotechnology

Water and extremophile microbiome

Syntrophic associations from hypersaline soda lakes converting organic acids and alcohols to methane at extremely haloalkaline conditions – Dimitry Y. Sorokin – Environmental Microbiology

Microbialite response to an anthropogenic salinity gradient in Great Salt Lake, Utah – M. R. Lindsay – Geobiology

Chemodenitrification in the cryoecosystem of Lake Vida, Victoria Valley, Antarctica – N. E. Ostrom – GeoBiology

Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly – Tomàs Llorens–Marès – ISME Journal

Metagenomics and bioinformatics

MetaCRAST: Reference-guided extraction of CRISPR spacers from unassembled metagenomes – Abraham G Moller – PeerJ Preprints

Microbes in the news

Yale engineers think our future homes should be designed with microbes in mind – Dyllan Furness – Digital Trends

How to get Funding for your Human Microbiome Startup – Global Engage

 

July 12, 2016

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Two papers on plant/root/soil microbiomes of interest, analysis of transcriptional regulatory networks, and too much non-prescription antibiotic use  in the US.

Human vaginal microbiome

Review: Bacterial vaginosis: a critical analysis of current knowledge – D Nasioudis – BJOG

Human gut microbiome

Gut microbiome analysis in neuromyelitis optica reveals over-abundance of Clostridium perfringens – Bruce A.C. Cree – Annals of Neurology

Review: Gut Microbiota and Intestinal Decolonization of Pathogenic Microorganisms – De-Chang Chen – Chinese Medical Journal

Animal experiments

Human Gut-Derived Prevotella histicola Suppresses Inflammatory Arthritis in Humanized Mice – Eric V. Marietta – Arthritis & Rheumatology

Press: Gut bacteria can cause, predict and prevent rheumatoid arthritis – Science Daily

Gastric Bypass Surgery Reverses Diabetic Phenotypes in Bdnf-Deficient Mice – Shujun Jiang – American Journal of Pathology

Press: New study suggests potential role for gut microbiota in diabetes remission after bypass surgery – News Medical

Plant, root, and soil microbiome

Host genotype and age shape the leaf and root microbiomes of a wild perennial plant – Maggie R. Wagner – Nature Communications

Press: Breeding plants with more beneficial bacteria to feed the world won’t be simple, study says – Robin A. Smith – Phys.org

Soil inoculation steers restoration of terrestrial ecosystems – E. R. Jasper Wubs – Nature Plants

Soil microbes transplants could help restore damaged ecosystems – The dirt makes all the difference – Meaghan Lee Callaghan – PopSci

Combined Flux Chamber and Genomics Approach Links Nitrous Acid Emissions to Ammonia Oxidizing Bacteria and Archaea in Urban and Agricultural Soil – Nicole K. Scharko – Environmental Science & Technology

Opinion: Plant microbiota affects seed transmission of phytopathogenic microorganisms – Matthieu Barret – Molecular Plant Pathology

Metagenomics and bioinformatics

A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data – Elizabeth T. Hobbs – Algorithms for Molecular Biology

Metagenome and Metatranscriptome Analyses Using Protein Family Profiles – Cuncong Zhong – PLOS Computational Biology

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights – Edoardo Pasolli – PLOS Computational Biology

Review: Metagenome-wide association studies: fine-mining the microbiome – Jun Wang – Nature Reviews Microbiology

Proteomics

An alignment-free ‘metapeptide’ strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing – Damon H. May – Journal of Proteome Research

Bioreactor microbiology

A light-induced shortcut in the planktonic microbial loop – Robert Ptacnik – Scientific Reports

More microbiology

Non-prescription antimicrobial use in a primary care population in the United States: evidence for action – Roger Zoorob – Antimicrobial Agents and Chemotherapy

Press: Self-prescribing antibiotics is a big problem – American Society for Microbiology – EurekAlert

Transfer of DNA from Bacteria to Eukaryotes – Benoît Lacroix – mBio

Origins of pandemic clones from environmental gene pools – B. Jesse Shapiro – bioRxiv

UTSA professor’s study describes new strategies for investigating microbial outbreaks – EurekAlert

Microbes in the news

Railroad spanning Great Salt Lake helps MSU scientists understand origins of reef-like structures – Skip Anderson – Montana State University

The colon is defended from bacteria by a self-sacrificing sentinel cell – EurekAlert

July 11, 2016

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Poor oral health associated with decreased chance of developing IBD, thumb-sucking associated with decreased chance of developing atopic sensitization, and the core actinobacteriome of rice plants.

Jobs

Senior Scientist intestinal health – Wageningen UR Livestock Research, The Netherlands

Human oral microbiome (sort of)

Inverse Association Between Poor Oral Health and Inflammatory Bowel Diseases – Weiyao Yin – Clinical Gastroenterology and Hepatology

Thumb-Sucking, Nail-Biting, and Atopic Sensitization, Asthma, and Hay Fever – Stephanie J. Lynch – Pediatrics

Human respiratory microbiome

Review: Airway Microbiota and the Implications of Dysbiosis in Asthma – Juliana Durack – Current Allergy and Asthma Reports

Review: Understanding the role of the microbiome in chronic obstructive pulmonary disease: principles, challenges, and future directions – Yvonne J. Huang – Translational Research

Human gut microbiome

Review: Communicating systems in the body: how microbiota and microglia cooperate – Daniel Erny – Immunology

Review: Microbiota at the crossroads of autoimmunity – Oded Shamriz – Autoimmunity Reviews

Animal and bioreactor experiments

Dietary silver nanoparticles can disturb the gut microbiota in mice – Sybille van den Brule – Particle and Fibre Toxicology

Modelling Longitudinal Metabonomics and Microbiota Interactions in C57BL/6 mice fed a high fat diet – Ivan Montoliu – Analytical Chemistry

High-fiber and high-protein diets shape different gut microbial communities, which ecologically behave similarly under stress conditions, as shown in a gastrointestinal simulator – Massimo Marzorati – Molecular Nutrition & Food Research

Plant, root, and soil microbiome

Plant and insect microbial symbionts alter the outcome of plant-herbivore-parasitoid interactions: implications for invaded, agricultural and natural systems – Alison E Bennett – Journal of Ecology

Influences of plant type on bacterial and archaeal communities in constructed wetland treating polluted river water – Yan Long – Environmental Science and Pollution Research

Illumina-based analysis of core actinobacteriome in roots, stems, and grains of rice – Wenfeng Wang – Microbiological Research

Water microbiome

Comparative metagenome of a stream impacted by the urbanization phenomenon – Julliane Dutra Medeiros – Brazilian Journal of Microbiology

Drinking water systems

A modified weighted mixture model for the interpretation of spatial and temporal changes in the microbial communities in drinking water reservoirs using compositional phospholipid fatty acid data – I. Stanimirova – Talanta

Bioinformatics

An automated system for evaluation of the potential functionome: MAPLE version 2.1.0 – Hideto Takami – DNA Research

Microbes in the news

You Can Contract Fatal Bacteria Just By Sniffing – Angela Chen – Gizmodo
Deadly bug strikes in a day – New pathway discovered for bacteria – EurekAlert

Tiny bacteria-powered ‘windfarm’ for your phone? – Science Daily
Scientists show how bacteria can power micro-machines – Indiana Express

Antibiotic resistance discovered in the guts of ancient mummies – Andy Coghlan – New Scientist

Antibiotic-resistant bacteria have been around for centuries – Karen Graham – Digital Journal

Seres initiates first clinical trial of synthetic microbiome therapy for C. difficile – Healio

July 9, 2016

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Bacteroidales from homeothermic animals, 136 microbial genomes from the Red Sea, corrosion of concrete sewers, and the microbiology lab in 2050 (still sexist!).

Pregnancy and birth

Integrated network-diversity analyses suggest suppressive effect of Hodgkin’s lymphoma and slightly relieving effect of chemotherapy on human milk microbiome – Zhanshan (Sam) Ma – Scientific Reports

Review: The Microbiome, Antibiotics, and Health of the Pediatric Population – Ravi S Misra- EC Microbiology

Human oral microbiome

Metagenomic Analysis of Sputum Microbiome as a Tool Towards Culture-independent Pathogen Detection of Patients with Ventilator-associated Pneumonia – Qiulong Yan – American Journal of Respiratory and Critical Care Medicine

Human respiratory microbiome

Smoking Cessation and the Microbiome in Induced Sputum Samples from Cigarette Smoking Asthma Patients – Christian Munck – PLOS ONE

Association of sputum microbiota profiles with severity of community-acquired pneumonia in children – Melinda M. Pettigrew – BMC Infectious Diseases

Human gut microbiome

Review: Polysaccharide degradation by the intestinal microbiota and its influence on human health and disease – Darrell W. Cockburn – Journal of Molecular Biology

Review: Microbiota at the crossroads of autoimmunity – Oded Shamriz – Autoimmunity Reviews

Editorial: A Role for Chemists in Microbiome Research – Courtney C. Aldrich – ACD Infectious Diseases

Animal experiments

Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection – Alison Morris – Microbiome

Animal microbiome

Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals – Kate L. Ormerod – Microbiome

Biodiversity and Activity of the Gut Microbiota across the Life History of the Insect Herbivore Spodoptera littoralis – Bosheng Chen – Scientific Reports

Long-term effect of heavy-metal pollution on diversity of gastrointestinal microbial community of Bufo raddei – Wenya Zhang – Toxicology Letters

Plants, roots, and soil microbiome

Multiscale assemblage of an ectomycorrhizal fungal community: The influence of host functional traits and soil properties in a 10-ha miombo forest – David Bauman – FEMS Microbiology Ecology

Impact of Soil Salinity on the Structure of the Bacterial Endophytic Community Identified from the Roots of Caliph Medic (Medicago truncatula) – Mahmoud W. Yaish – PLOS ONE

Diversity of fungal endophytes in recent and ancient wheat ancestors Triticum dicoccoides and Aegilops sharonensis – Maya Ofek-Lalzar – FEMS Microbiology Ecology

The effect of bullet removal and vegetation on mobility of Pb in shooting range soils – Abioye O. Fayiga – Chemosphere

Water and extremophile microbiome

A catalogue of 136 microbial draft genomes from Red Sea metagenomes – Mohamed F. Haroon – Scientific Data

A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples – Miguel I. Uyaguari-Diaz – Microbiome

Hydrocarbon biodegradation by Arctic sea-ice and sub-ice microbial communities during microcosm experiments, Northwest Passage (Nunavut, Canada) – Marie-Ève Garneau – FEMS Microbiology Ecology

Built environment microbiome

Wastewater Enhanced Microbial Corrosion of Concrete Sewers – Guangming Jiang – Environmental Science & Technology

Bioreactors

The bioleaching potential of a bacterial consortium – Mauricio Latorre – Bioresource Technology

Biofilms

DGGE: Representative sampling of natural biofilms: influence of substratum type on the bacterial and fungal communities structure – Jennifer Hellal – SpringerPlus

Bioinformatics and metagenomics

GUTSS: An Alignment-Free Sequence Comparison Method for Use in Human Intestinal Microbiome and Fecal Microbiota Transplantation Analysis – Mitchell J. Brittnacher – PLOS ONE

Icarus: visualizer for de novo assembly evaluation – Alla Mikheenko – Bioinformatics

deBGA: read alignment with de Bruijn Graph-based seed and extension – Bo Liu – Bioinformatics

ConsPred – a rule-based (re-)annotation framework for prokaryotic genomes – Thomas Weinmaier – Bioinformatics

Proteomics

Review: Metaproteomic data analysis at a glance: advances in computational microbial community proteomics – Expert Review of Proteomics

Bik’s Picks

A typical day working in a laboratory in 2050: Are microbiologists becoming chemists and serene workers? – Daniele Sohier – Current Opinion in Food Science

Napa native on space mission showed early signs of promise – Jonathan Bloom – ABC News

 

 

July 8, 2016

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The highly anticipated microbiome statistical workflow from the Holmes lab at Stanford, lichen planus, chronic lung disease, and the beneficial microbes of buildings.

Bioinformatics

Preprint, awaiting peer review: Bioconductor workflow for microbiome data analysis: from raw reads to community analyses  – Ben J. Callahan – F1000 Research

Human oral microbiome

The presence of bacteria within tissue provides insights into the pathogenesis of oral lichen planus – Yun Sik Choi – Scientific Reports

Human respiratory microbiome

The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx – R. L. Marsh – Microbiome

Review: Commensal–Pathogen Interactions along the Human Nasal Passages – Silvio D. Brugger – PLOS Pathogens

Animal experiments

Structural Change in Microbiota by a Probiotic Cocktail Enhances the Gut Barrier and Reduces Cancer via TLR2 Signaling in a Rat Model of Colon Cancer – Eugene Dogkotenge Kuugbee – Digestive Diseases and Sciences

Adaptive immunity against gut microbiota enhances apoE-mediated immune regulation and reduces atherosclerosis and western-diet-related inflammation – Diego Saita – Scientific Reports

Animal microbiome

The Fecal Microbial Communities of Dairy Cattle Shedding Shiga Toxin–Producing Escherichia coli or Campylobacter jejuni – Dong Hee-Jin – Foodborne Pathogens and Disease

Press: Microbiology of cattle poop – Doug Powell – BarfBlog

Characterization of the microbial communities along the gastrointestinal tract of sheep by 454 pyroseqencing analysis – Jin Wang – Asian-Australasian Journal of Animal Sciences

Microbial Composition in Different Gut Locations of Weaning Piglets Receiving Antibiotics – Kaifeng Li – Asian-Australasian Journal of Animal Sciences

Plant, root, and soil microbiome

Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities – James P. J. Hall – PNAS

Built environment microbiome

Review: Buildings, Beneficial Microbes, and Health – Jordan Peccia – Trends in Microbiology

Press: Invite good bacteria into home: scientists – MSN
Should architecture take our microbial health into account? – Coby McDonald – Popular Science

Microbes in the news

Gut Bacteria Are Different in People With Chronic Fatigue Syndrome – Nicholas Bakalar – NY Times

An Algorithm To Predict Which Bacteria Are Good For You. For a more targeted microbiome fix than a fecal transplant – Alexandra Ossola – Vocativ

Purdue students hope new bacteria stops toxic algae blooms – Washington Times

Japanese and Chinese scientists team up against infectious diseases – Tetsuya Abe – Nikkei Asian Review

The Microbiome’s New Frontier: The Rest of the Animal Kingdom – Conservation Magazine

July 7, 2016

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Genetic variation and airway microbiome, Thai vegetarians, social wasps carry local yeast strains, classifying infections by host response, profiling of arbuscular mycorrhizal fungi.

Pregnancy and birth

Research Highlight: First steps in the infant gut microbiota – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Human respiratory microbiome

Host genetic variation in mucosal immunity pathways influences the upper airway microbiome – Catherine Igartua – bioRxiv

Human gut microbiome

A Disease-associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients – Jonathan P. Jacobs – CMGH Cellular and Molecular Gastroenterology and Hepatology

Microbial community of healthy Thai vegetarians and non-vegetarians, their core gut microbiota and pathogens risk – Supatjaree Ruengsomwong – Journal of Microbiology and Biotechnology

Animal experiments

Personality composition alters the transmission of cuticular bacteria in social groups – Carl N. Keiser – Biology Letters

Oat products modulate the gut microbiota and produce anti-obesity effects in obese rats – Ji-lin Dong – Journal of Functional Foods

Animal microbiome

Social wasp intestines host the local phenotypic variability of Saccharomyces cerevisiae strains – Leonardo Dapporto – Yeast

Spatial and temporal investigation of the microbiome of the Caribbean octocoral Erythropodium caribaeorum – Erin P McCauley – FEMS Microbiology Ecology

Bacterial and fungal symbionts of parasitic Dendroctonus bark beetles – Loïc Dohet – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Active microorganisms in forest soils differ from the total community yet are shaped by the same environmental factors: the influence of pH and soil moisture – Karl J. Romanowicz – FEMS Microbiology Ecology

High-resolution community profiling of arbuscular mycorrhizal fungi – Klaus Schlaeppi – New Phytologist

Mycorrhizal associations and soil properties of native Allanblackia stuhlmannii stands in the Eastern Usambara Mountains, Tanzania – P. Fransson – Annals of Applied Biology

Hierarchical neighbor effects on mycorrhizal community structure and function – Holly V. Moeller – Ecology and Evolution

Review: The role of plant-microbiome interactions in weed establishment and control – F. Trognitz – FEMS Microbiology Ecology

Water and extremophile microbiome

Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya – Anne Kelly Kambura – BMC Microbiology

Spatial distribution of aquatic marine fungi across the western Arctic and sub-arctic – Brandon T. Hassett – Environmental Microbiology

Metagenomics and bioinformatics

Metagenome Mining: A Sequence Directed Strategy for the Retrieval of Enzymes for Biocatalysis – Jack W. E. Jeffries – Chemistry Select

Reaching saturation in 16S rRNA sequences: After All, Only Millions? – Rudolf Amann – mBio

More microbiology

Robust classification of bacterial and viral infections via integrated host gene expression diagnostics – Timothy E. Sweeney – Science Translational Medicine

Press: A Blood Test To Determine When Antibiotics Are Warranted: Scientists can assay gene activity to distinguish between bacterial and viral infections – Alison F. Takemura – The Scientist

Editorial: Linking Ecosystem Function to Microbial Diversity – Anne E. Bernhard – Frontiers in Microbiology

Microbes in the news

Meet Angus, the C. difficile-sniffing dog trained to detect superbugs – CBC News

Researchers, farmers collaborate to prevent E. coli – Science Daily

How the bacterial protective shell is adapted to challenging environments – Phys.org

Could E.Coli be used to fight disease? Bacteria could transport next-generation vaccines, experts reveal – Daily Mail

Single microbe may restore social behaviors in mice – Ann Griswold – Spectrum

High Demand For Antibiotics Leads To Growth In Microbiology Culture Industry In United States – MedGadget

Discovery of new bacterium brings laurels to Palamuru University – The Hindu

July 5, 2016

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Circadian rhythm, resistant starch, mock communities, sea turtle microbiome, tea rhizosphere.

General microbiome

Review: The Metronome of Symbiosis: Interactions Between Microbes and the Host Circadian Clock – Elizabeth A. C. Heath-Heckman – Integrative & Comparative Biology

Human oral microbiome

Microbial Ecosystem Analysis in Root Canal Infections Refractory to Endodontic Treatment – Luiz Carlos Feitosa Henriques – Journal of Endodontics

Human gut microbiome

Impact of dietary resistant starch type 4 on human gut microbiota and immunometabolic functions – Bijaya Upadhyaya – Scientific Reports

Press: Essential Science: Taking on metabolic disorders with starch – Tim Sandle – Digital Journal

Editorial: serologic microbial-associated markers to predict Crohn’s disease behaviour – A. G. Fraser – Alimentary Pharmacology & Therapeutics

Review: Microbiota and Liver – Kazumichi Abe – The Liver in Systemic Diseases

Animal experiments

A Role for Timp3 in Microbiota-Driven Hepatic Steatosis and Metabolic Dysfunction – Maria Mavilio – Cell Reports

Animal microbiome

A first insight into the gut microbiota of the sea turtle Caretta caretta – Khaled F. Abdelrhman – Frontiers in Microbiology

News and views: Co-evolution of marine worms and their chemoautotrophic bacterial symbionts: unexpected host switches explained by ecological fitting? – A. Brune – Molecular Ecology

Bacterial communities of oceanic sea star (Asteroidea: Echinodermata) larvae – Madeline R. Galac – Marine Biology

Gut bacteria differentially affect egg production in the anautogenous mosquito Aedes aegypti and facultatively autogenous mosquito Aedes atropalpus (Diptera: Culicidae) – Kerri L. Coon – Parasites & Vectors

Review: Better with your parasites? Lessons for behavioural ecology from evolved dependence and conditionally helpful parasites – Kelly L. Weinersmith – Animal Behaviour

Plant, root, and soil microbiome

Response of soil properties and microbial communities to agriculture: Implications for primary productivity and soil health indicators – Pankaj Trivedi – Frontiers in Plant Science

Variations of rhizosphere bacterial communities in tea (Camellia sinensis L.) continuous cropping soil by high-throughput pyrosequencing approach – Yanchun Li – Journal of Applied Microbiology

Water and extremophile microbiome

Oil sands tailings ponds harbour a small core prokaryotic microbiome and diverse accessory communities – S.L. Wilson – Journal of Biotechnology

The Ocean Microbiome: Metabolic Engine of the Marine Carbon Cycle – Elizabeth B. Kujawinski – Microbe

Biofilms

Relevant for Cystic Fibrosis: Temperate phages both mediate and drive adaptive evolution in pathogen biofilms – Emily V. Davies – PNAS

Press: Tiny viruses speed-up evolution of bacteria causing infections in cystic fibrosis patients – News Medical

Techniques

Droplet barcoding for massively parallel single-molecule deep sequencing –
Freeman Lan – Nature Communications

Transcriptomics

Comparative transcriptomics across the prokaryotic tree of life – Ofir Cohen – Nucleic Acids Research

Bioinformatics and metagenomics

PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets – Shareef M. Dabdoub – Scientific Reports

Optimization of 16S amplicon analysis using mock communities: implications for
estimating community diversity – Andrew Krohn – PeerJ

Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data – Philip T. L. C. Clausen – Journal of Antimicrobial Chemotherapy

A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies – Shalabh Thakur – BMC Bioinformatics

Editorial: Nucleic Acids Research annual Web Server Issue in 2016 – Nucleic Acids Research