Category Archives: Bik’s Non-Microbiology Picks

June 9, 2015

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Job openings for microbiome leaders in Pittsburgh, functional foods and microbial growth, and lots of reviews and editorials.

Jobs

The new Center for Microbiome and Medicine at the University of Pittsburgh is hiring leader(s) in microbiome research

Microbiome of pregnancy and birth

Review: Early microbial contact, breast milk microbiome and child health – S. Rautava – Journal of Developmental Origins of Health and Disease

Human oral microbiome

Screening of Probiotic Candidates in Human Oral Bacteria for the Prevention of Dental Disease – Tomohiko Terai – PLOS ONE

Review: Do oral bacteria alter the regenerative potential of stem cells? A concise review – Kyriaki Chatzivasileiou – Journal of Cellular and Molecular Medicine

Human gut microbiome

Editorial for David et al.’s cholera recovery paper: A gut instinct for recovery – Naomi Attar – Nature Reviews Microbiology

Letter to the Editor: Altered microbiota in microscopic colitis – Hans Fischer – Gut

Letter to the Editor: Colonisation with multidrug-resistant bacteria is associated with increased mortality in patients with cirrhosis – Oliver Waidmann – Gut

Animal microbiome

Review: The animal gut as a melting pot for horizontal gene transfer – N. Shterzer, I. Mizrahi – Canadian Journal of Microbiology

Plant root and soil microbiome

Assessment of rhizospheric culturable bacteria of Phragmites australis and Juncus effusus from polluted sites – Sofia I.A. Pereira – Journal of Basic Microbiology

Review: Dispersing misconceptions and identifying opportunities for the use of ‘omics’ in soil microbial ecology – Nature Reviews Microbiology

Built environment microbiome

The effects of different hygiene procedures in reducing bacterial contamination in a model domestic kitchen – Elin Røssvoll – Journal of Applied Microbiology

Functional foods

Pomegranate Ellagitannins Stimulate Growth of Gut Bacteria In Vitro: Implications for Prebiotic and Metabolic Effects – Zhaoping Li – Anaerobe

Prebiotics Modulate the Effects of Antibiotics on Gut Microbial Diversity and Functioning in Vitro – Laura P. Johnson – Nutrients

Microbes in the news

From World Aquaculture 2015: “The gut microbiome of farmed trout is far more complex than previous research has documented” – Alltech highlights latest research in farmed trout – Undercurrent News

How the ‘Microbiome’ Affects Your Baby’s Birth and Health – Penny Simkin – Seattle PI

MicroBiome Therapeutics Presents Clinical Data On Diabetes Drug NM505 At ADA’s 75th Scientific Sessions And Reports Issuance Of NM505 Patent – PR Newswire

Here’s What Happens When You Culture The Bacteria on an Eight Year Old’s Hand – Marissa Fessenden – Smithsonian

MERS Is Not SARS, but Control Was Poor: Seoul ID Docs – Outbreak claims seventh fatality as specialists acknowledge poor infection control – MedPage Today

Bik’s Picks

Massage-like stroking boosts the immune system in mice – Benjamin Major – Scientific Reports

Just add water: Stanford engineers develop a computer that operates on water droplets – Stanford News

A crummy dinosaur fossil turns out to hold 75 million-year-old blood and proteins – Rachel Feltman – The Washington Post

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June 8, 2015

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General microbiome

Minireview: The brain’s Geppetto—microbes as puppeteers of neural function and behaviour? – Roman M. Stilling – Journal of NeuroVirology

Thesis: Novel computational approaches to investigate microbial diversity – Qingpeng Zhang – Michigan State University

Microbiome of pregnancy and birth

Distinctive Intestinal Lactobacillus Communities in Six-Month-Old Infants From Rural Malawi and South-Western Finland – Aakko, Juhani – Journal of Pediatric Gastroenterology & Nutrition

Antenatal Microbiome: Potential Contributor to Fetal Programming and Establishment of the Microbiome in Offspring – Michelle L. Wright, Angela R. Starkweather – Nursing Research

Review: Should Abnormal Vaginal Flora in 2 nd Trimester of Pregnancy be Treated to Prevent Preterm Labor – Gunjan Kumari, Anjali Tempe – Journal of Medical Sciences

Human oral microbiome

The oral mucosal and salivary microbial community of Behcet’s syndrome and recurrent aphthous stomatitis – Noha Seoudi – Journal of Oral Microbiology

Human gut microbiome

Review: Unraveling the environmental and genetic interactions in atherosclerosis: Central role of the gut microbiota – Elin Org – Atherosclerosis

Review: The Effects of Diet and the Microbiome on Reproduction and Longevity: A Comparative Review Across 5 Continents – Stephanie N. Chilton – Nutrition and Food Sciences

Animal models of microbiome research

Lack of Vitamin D Receptor Causes Dysbiosis and Changes the Functions of the Murine Intestinal Microbiome – Dapeng Jin – Clinical Therapeutics

Animal microbiome

Acromyrmex leaf-cutting ants have simple gut microbiota with nitrogen-fixing potential – Panagiotis Sapountzis – Applied and Environmental Microbiology

Anemone: Response of bacterial colonization in Nematostella vectensis to development, environment and biogeography – Benedikt Mortzfeld – Environmental Microbiology

Plant root and soil microbiome

Responses of bacterial communities in seagrass sediments to polycyclic aromatic hydrocarbon-induced stress – Juan Ling – Ecotoxicology

Analyses of microbial biomass and community diversity in kiwifruit orchard soils of different planting ages – Qingxia Fu – Acta Ecologica Sinica

The effects of the presence of Bt-transgenic oilseed rape in wild mustard populations on the rhizosphere nematode and microbial communities – Yongbo Liu – Science of The Total Environment

Long-term conservation tillage influences the soil microbial community and its contribution to soil CO2 emissions in a Mollisol in Northeast China – Shuxia Jia – Journal of Soils and Sediments

Microbial communities inhabiting oil-contaminated soils from two major oilfields in Northern China: Implications for active petroleum-degrading capacity – Weimin Sun – Journal of Microbiology

Differential degradation of polycyclic aromatic hydrocarbon mixtures by indigenous microbial assemblages in soil – Przemyslaw Sawulski – Letters in Applied Microbiology

A novel salt-tolerant chitobiosidase discovered by genetic screening of a metagenomic library derived from chitin-amended agricultural soil – Mariana Silvia Cretoiu – Applied Microbiology and Biotechnology

Book chapter: Irrigation with Treated Wastewater: Potential Impacts on Microbial Function and Diversity in Agricultural Soils – Ana Rita Lopes – The Handbook of Environmental Chemistry 2015

Water microbiome

Response of bacteria and meiofauna to iron oxide colloids in sediments of freshwater microcosms – Sebastian Höss – Environmental Toxicology and Chemistry

Response of rare, common and abundant bacterioplankton to anthropogenic perturbations in a Mediterranean coastal site – Federico Baltar – FEMS Microbiology Ecology

Book Chapter: Marine Litter as Habitat and Dispersal Vector – Tim Kiessling – Marine Anthropogenic Litter

Thesis: Metagenomic profiling of microbial metal interaction in Red Sea deep-anoxic brine pools – Hanna, Mina Magdy Abdelsayed – American University in Cairo

Built environment microbiome

Microbial community composition of a household sand filter used for arsenic, iron, and manganese removal from groundwater in Vietnam – Katja Sonja Nitzsche – Chemosphere

The role of bacterial communities and carbon dioxide on the corrosion of steel – K.M. Usher – Corrosion Science

Extremophile microbiome

Review: Metagenomics of extreme environments – DA Cowan – Current Opinion in Microbiology

Food microbiology

Review: The impact of climate change on existing and emerging microbial threats across the food chain: An island of Ireland perspective – Linda D. Stewart – Trends in Food Science & Technology

Review: Microbial decontamination of food by electron beam irradiation – Hsiang-Mei Lung – Trends in Food Science & Technology

Bioreactor microbiome

Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unraveled with genome-resolved metagenomics – Rose S. Kantor – Environmental Microbiology

Bioinformatics and metagenomics

CCLasso: Correlation Inference for Compositional Data through Lasso – Huaying Fang – Bioinformatics

GAML: genome assembly by maximum likelihood: combination of diverse sequencing datasets into a single assembly – Vladimír Boža – Algorithms for Molecular Biology

Effects of library size variance, sparsity, and compositionality on the analysis of microbiome data – Sophie J Weiss – PeerJ

Review: Identification of Viruses and Viroids by Next-Generation Sequencing and Homology-Dependent and Homology-Independent Algorithms – Qingfa Wu – Annual Reviews Phytopathology

Metabolomics

Mapping microbial response metabolomes for induced natural product discovery – Dagmara K. Derewacz – ACS Chemical Biology
http://pubs.acs.org/doi/abs/10.1021/acschembio.5b00001

Techniques

Analysis of microsamples of human faeces: a non-invasive approach to study the bioavailability of fat-soluble bioactive compounds – E. Hernandez-Alvarez – European Journal of Nutrition

Microbes in the news

Say hello to your little friends: Making sense of gut bacteria – Wency Leung – Globe and Mail

Surfers help science in fight against antibiotic resistant bacteria with their poop – Luigi Lugmayer – i4u

Effects of zinc oxide on intestinal microbiota – All About Feed

Video: Waxworm Bacteria Could Recycle Plastic Trash – NBC News

Is That Water Hot Enough to Kill Germs? – C. Claiborne Ray – New York Times

Gut bacteria play a vital role to your health – Sharon Ní Chonchuir – Irish Examiner

New microscope technique could speed identification of deadly bacteria – EurekAlert

Science, publishing, and career

Better advice for ‘Bothered’ – Science Careers Staff – Science Magazine

Retractions and High Profile Journals – Peter Edmonds

Bik’s Picks

Black Hole Hunters – Dennis Overbye – New York Times

Everything You Need to Know About Bill Nye’s Crazy Experimental Spaceship – Jack Linshi – Time

Under the Sea: Google Views for World Oceans Day – Patrick J. Kiger – Discovery

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June 6, 2015

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A new paper on the microbiome of the human nose, several gut microbiome reviews,  microbiomes of soils and extreme environments, microbiome models and a cool poster about defining OTU. Happy Saturday!

Human oral microbiome

Antimicrobial Effect of a Single Dose of Amoxicillin on the Oral Microbiota – Cecilia Larsson Wexell – Clinical Implant Dentistry and Related Research

Human respiratory microbiome

Staphylococcus aureus and the ecology of the nasal microbiome – Cindy M. Liu – Science Advances

Human gut microbiome

Review: Interactions between Diet, Bile Acid Metabolism, Gut Microbiota, and Inflammatory Bowel Diseases – Devkota S – Digestive Diseases

Review: Gut Microbiota, Cirrhosis, and Alcohol Regulate Bile Acid Metabolism in the Gut – Ridlon J.M – Digestive Diseases

Review: Relationship between Obesity, Gut Microbiome and Hepatocellular Carcinoma Development – Hara E. – Digestive Diseases

Animal models of microbiome research

Absence of the intestinal microbiota exacerbates hepatobiliary disease in a murine model of primary sclerosing cholangitis – James H. Tabibian – Hepatology

Effects of dietary fat profile on gut permeability and microbiota and their relationships with metabolic changes in mice – Yan Y. Lam – Obesity

Animal microbiome

Gut-Associated Bacteria of Dendroctonus valens and their Involvement in Verbenone Production – Letian Xu – Microbial Ecology

Feeding of β-1,3/1,6-glucan increases the diversity of the intestinal microflora of carp (Cyprinus carpio) – V. Jung-Schroers – Aquaculture Nutrition

Changes in coral reef communities across a natural gradient in seawater pH – Hannah C. Barkley – Science Advances

Plant root, soil and sediment microbiome

Symbiosis with an endobacterium increases the fitness of a mycorrhizal fungus, raising its bioenergetic potential – Alessandra Salvioli – ISME Journal

Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes – Margarita Lopez-Fernandez – Microbial Ecology

Is Planktonic Diversity Well Recorded in Sedimentary DNA? Toward the Reconstruction of Past Protistan Diversity – Eric Capo – Microbial Ecology

Water microbiome

Phytoplankton community structure in relation to vertical stratification along a north-south gradient in the Northeast Atlantic Ocean – Kristina D. A. Mojica – Limnology and Oceanography

Extremophile microbiome

Supratidal Extremophiles—Cyanobacterial Diversity in the Rock Pools of the Croatian Adria – Maria Brandes – Microbial Ecology

Pyrosequencing-Based Assessment of the Microbial Community Structure of Pastoruri Glacier Area (Huascarán National Park, Perú), a Natural Extreme Acidic Environment – Elena González-Toril – Microbial Ecology

Metagenomics and bioinformatics

Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities – Markus Majaneva

Microbiome models, on computers and in lab dishes, see progress – Jop de Vrieze – Nature Medicine

Don’t miss this cool poster: OTU robustness, reproducibility and ecological consistency in the demarcation of operational taxonomic units – Thomas SB Schmidt

Microbes in the news

Nasal Microbiome Study Examines Influence of Host Genetics, Types of Bacterial Communities – Genome Web

The fastest-growing biome on Earth is in our homes. Forget your kids and pets. Your house’s biodiversity hotspots shelter tons of microorganisms – Mary Jo DiLonardo

Socialising Baboons and Gut Microbes – deSciphered: summarising research with simple graphics

Exploring the Link Between Gut Microbes and Diabetes – Betul Hatipoglu

Kaiser Permanente Fresno uses ‘zapper’ to get rid of deadly bacteria – ABC30

This Man Believes Mushrooms Can Solve Virtually All of Humanity’s Problems: next probiotic? – Munchies

Bik’s Picks

Eating placenta ‘does not benefit health’: There is no scientific evidence that eating the placenta after childbirth can protect women against depression and boost energy, US research suggests –  – BBC News

Ancient Shark Fossil Found in Texas – Deborah Grace – Pioneer News

Video: Robots Falling Down at DARPA Robotics Challenge – IEEE Spectrum – Youtube

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June 5, 2015

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A new test that reveals past viral infections using one drop of blood, subgingival microbiota in HIV-infected adults, and influencing horse behavior through diet.

Human oral microbiome

The oral mucosal and salivary microbial community of Behçet’s syndrome and recurrent aphthous stomatitis – Seoudi N – J Oral Microbiology

Subgingival bacterial community profiles in HIV-infected Brazilian adults with chronic periodontitis – D. C. Ferreira – Journal of Periodontal Research

Human bladder microbiome

Decreased microbiota diversity associated with urinary tract infection in a trial of bacterial interference – Deborah Horwitz – Journal of Infection

Human gut microbiome

Use of T-RFLP and seven restriction enzymes to compare the faecal microbiota of obese and lean Japanese healthy men – T. Kobayashi – Beneficial Microbes

The Gut Microbiome and Childhood Obesity: Connecting the Dots – An interview with Mueller Noel Theodore – Childhood Obesity

Review: Metagenomics of the Human Intestinal tract: From who is there to what is done there – Antonietta Cultrone – Current Opinion in Food Science

Editorial: On the Gut Microbiome-Brain Axis and Altruism – Theoharis C. Theoharides – Clinical Therapeutics

Review: Potential Etiologic Factors of Microbiome Disruption in Autism – Timothy Buie – Clinical Therapeutics

Conference abstract: Dietary supplementation with a type 3 resistant starch induces butyrate producing bacteria within the gut microbiota of human volunteers – J. Kelly – Appetite

Review: Immunogenetic control of the intestinal microbiota – Eric Marietta – Immunology

Book chapter: Fecal Microbiota Transplantation for Clostridium Difficile Infection: A Systematic Review of the Evidence – Dimitri Drekonja – Department of Veterans Affairs

Review: Gut bacteria and cancer – Susan E. Erdman – Biochimica et Biophysica Acta (BBA) – Reviews on Cancer

Review: The Gut Microbiota and Type 1 Diabetes – Elke Gülden – Clinical Immunology

Animal models of microbiome research

Transmissible microbial and metabolomic remodeling by soluble dietary fiber improves metabolic homeostasis – Baokun He – Scientific Reports

Antibiotics promote inflammation through the translocation of native commensal colonic bacteria – Kathryn A Knoop – Gut

Pyrosequencing reveals shifts in the bacterial epimural community relative to dietary concentrate amount in goats – S.U. Wetzels – Journal of Dairy Science

Programming rumen bacterial communities in newborn Merino lambs – I. De Barbieri – Small Ruminant Research

Changes of the hindgut microbiota due to high-starch diet can be associated with behavioral stress response in horses – Alexandra Destrez – Physiology & Behavior

Animal microbiome

Bats: Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies – Mario Carrillo-Araujo – Frontiers in Microbiology

Squirrels: An Invasive Mammal (the Gray Squirrel, Sciurus carolinensis) Commonly Hosts Diverse and Atypical Genotypes of the Zoonotic Pathogen Borrelia burgdorferi Sensu Lato
Caroline Millins – Applied and Environmental Microbiology

Fish: High diversity of skin-associated bacterial communities of marine fishes is promoted by their high variability among body parts, individuals and species – Marlène Chiarello

Snakes: Phylogenetic Analysis of Bacterial Communities in Different Regions of the Gastrointestinal Tract of Agkistrodon piscivorus, the Cottonmouth Snake – Timothy J. Colston – PLOS ONE

Insects: Leaf-Cutter Ant Fungus Gardens Are Biphasic Mixed Microbial Bioreactors That Convert Plant Biomass to Polyols with Biotechnological Applications – Alexandre F. Somera – Applied and Environmental Microbiology

Nematodes: Xenorhabdus bovienii Strain Diversity Impacts Coevolution and Symbiotic Maintenance with Steinernema spp. Nematode Hosts – Kristen E. Murfin – mBio

Coral: Microbial invasion of the Caribbean by an Indo-Pacific coral zooxanthella – D. Tye Pettay – PNAS

Plant root and soil microbiome

Linking jasmonic acid signalling, root exudates and rhizosphere microbiomes – Lilia C Carvalhais – Molecular Plant-Microbe Interactions

Changes in microbial communities along redox gradients in polygonized Arctic wet tundra soils – David A. Lipson – Environmental Microbiology Reports

Two decades of warming increases diversity of a potentially lignolytic bacterial community  – Grace Pold – Frontiers in Microbiology

Water microbiome

Patterns and Determinants of Halophilic Archaea (Class Halobacteria) Diversity in Tunisian Endorheic Salt Lakes and Sebkhet Systems – Afef Najjari – Applied and Environmental Microbiology

Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre – Kristina M. Fontanez – Frontiers in Microbiology

Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center – Karthik Anantharaman – The ISME Journal

Built environment microbiome

Inflammatory potential in relation to the microbial content of settled dust samples collected from moisture-damaged and reference schools: results of HITEA study – K. Huttunen

Pyrosequencing analysis of bacterial diversity in dental unit waterlines – Damien Costa – Water Research

Viruses and phages

Comprehensive serological profiling of human populations using a synthetic human virome – George J. Xu – Science

Metagenomics and 16S rRNA sequencing

Viewpoint: Improving the quality of genome, protein sequence, and taxonomy databases: a prerequisite for microbiome meta-omics 2.0 – Olivier Pible and Jean Armengaud – Proteomics

Opinion: Confusion about the species richness of human gut microbiota – E. Avershina, K. Rudi – Beneficial Microbes

Metabolomics

Microbial secondary metabolites in homes in association with moisture damage and asthma – P. V. Kirjavainen – Indoor Air

In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum “Latescibacteria” (WS3) – Noha H. Youssef – PLOS ONE

Bioinformatics

BEMOVI, software for extracting behavior and morphology from videos, illustrated with analyses of microbes – Frank Pennekamp – Ecology and Evolution

Techniques

Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase Gene nifH – Bangzhou Zhang – Applied and Environmental Microbiology

Revisiting the Dilution Procedure Used To Manipulate Microbial Biodiversity in Terrestrial Systems – Yan Yan – Applied and Environmental Microbiology

Microbes in the news

How Many Viruses Have Infected You? – Nell GreenfieldBoyce – NPR

A Lifetime of Viruses: Scientists devise an antibody-based test that can generate a person’s complete “viral history” with just one drop of blood. – Amanda B. Keener – The Scientist

Single Test for All Virus Exposure Opens Doors for Researchers – Denise Grady – New York Times

Shielded Microbes Could Spread Life Far Beyond Earth – Elizabeth Howell – Discovery

Unregulated faecal transplants could squander gut-bug promise – New Scientist

Antibiotics affect piglets’ immune system – All About Feed

Good, good, good, good bacteria – Elisabeth Winkler – Sustainable Food Trust

#ASM2015: Many Skin Bacteria Are Dead or Inactive, Study Finds – Health.com

Invasive microbe protects corals from global warming, but at a cost – A’ndrea Elyse Messer, Penn State – Steam Register

Bik’s Picks

India is building millions of toilets. Getting people to use them is a bigger task. – Rama Lakshmi – Washington Post

There Is No Global Warming Hiatus After All – Sarah Zielinski – Smithsonian

New ‘Hellboy’ Dinosaur Unveiled In Scientific Paper With A Romantic Twist – Hilary Hanson – The Huffington Post

Two Newfound Marsupials Do It to Death – Laura Geggel – Discovery

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June 4, 2015

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Smoking changes microbial shifts in mouse gut, root microbiome in sugarcane, microbial life after a volcanic eruption, and disturbing developments in the olive bacterial infection situation in Italy.

Human oral microbiome

Phage-bacteria interaction network in human oral microbiome – Jinfeng Wang – Environmental Microbiology

Models of microbiome research

Precision-guided antimicrobial peptide as a targeted modulator of human microbial ecology – Lihong Guo – PNAS USA

Chronic cigarette smoke exposure induces microbial and inflammatory shifts and mucin changes in the murine gut – Liesbeth Allais – Environmental Microbiology

Use of Germ-Free Animal Models in Microbiota-Related Research – Maha Al-Asmakh – Journal of Microbiology and Biotechnology

Animal microbiome

Use of carbon monoxide and hydrogen by a bacteria-animal symbiosis from seagrass sediments – Manuel Kleiner – Environmental Microbiology

Rodent reservoirs of future zoonotic diseases – Barbara A. Han – PNAS

Plant root and soil microbiome

Evolutionary signals of symbiotic persistence in the legume–rhizobia mutualism – Gijsbert D. A. Werner – PNAS

Inner Mongolian steppe arbuscular mycorrhizal fungal communities respond more strongly to water availability than to nitrogen fertilization – Xiaoliang Li – Environmental Microbiology

The core root microbiome of sugarcanes cultivated under varying nitrogen fertiliser application – Yun Kit Yeoh – Environmental Microbiology

Organic matter quantity and source affects microbial community structure and function following volcanic eruption on Kasatochi Island, Alaska – Lydia H. Zeglin – Environmental Microbiology

Water microbiome

Light availability affects stream biofilm bacterial community composition and function, but not diversity – Karoline Wagner – Environmental Microbiology

Bioreactor microbiome

Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unraveled with genome-resolved metagenomics – Rose S. Kantor – Environmental Microbiology

Metagenomics

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages – Laura A. Hug – – Environmental Microbiology

Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph – Carolina Grob – Environmental Microbiology

Extrachromosomal circular DNA is common in yeast – Henrik D. Møller – PNAS

More microbes

A noisy linear map underlies oscillations in cell size and gene expression in bacteria –
Yu Tanouchi – Nature

The Matrix Reloaded: How Sensing the Extracellular Matrix Synchronizes Bacterial Communities – Nitai Steinberg and Ilana Kolodkin-Gal – Journal of Bacteriology

Measuring ruggedness in fitness landscapes – Jeremy Van Cleve – PNAS

Microbes in the news

Microbiology: Gut Bacteria cooperate when life gets tough – Université du Luxembourg – Alpha Galileo

Does treating koala chlamydia hurt their gut microbes? – Rachel Feltman – Washington Post

Xylella bacteria increasingly affecting olive trees in Southern Europe – Wageningen UR

Italian scientists vilified in wake of olive-tree deaths: Police investigate researchers’ role in devastating bacterial epidemic – Alison Abbott – Nature

Chemists weigh intact virus mixture with mass spectrometer – Science Daily

Swapping Symbionts Enabled Mediterranean Lichen to Conquer the Arctic – Jennifer Frazer – Scientific American

Researchers explain mechanism that makes their mouthwash so effective against tooth decay – Medical Xpress

Microbes and money

Human Microbiome Market – Global Industry Analysis and Forecast to 2020, by Persistence Market Research – MedGadget

Science, publishing, and career

Retracted gay-marriage study debated at misconduct meet-up: Over rum cocktails at the World Conference on Research Integrity, experts discussed what can be learnt from the fallout of a flawed political-science paper – Richard van Noorden – Nature

Bik’s Picks

Scientists use new ‘tool sled’ to collect sea sponges that have potential to combat various diseases – Science Daily

Groundbreaking study to test metabolism of dugongs to see how much food they need to survive – ABC Australia

Seven new species of miniature frogs discovered (and they’re adorable) – Rachel Feltman – Washington Post

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June 3, 2015

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Microbiomes of seahorses, diet and human stool, gut microbes influencing CNS, lichen-associated bacteria, sequencing beer, and news from #ASM2015.

Human gut microbiome

Fecal Microbiota in Healthy Subjects Following Omnivore, Vegetarian and Vegan Diets: Culturable Populations and rRNA DGGE Profiling – Ilario Ferrocino – PLOS ONE

Animal models of microbiome research

Host microbiota constantly control maturation and function of microglia in the CNS – Daniel Erny – Nature Neuroscience

Effects of Dietary Linseed Oil and Propionate Precursors on Ruminal Microbial Community, Composition, and Diversity in Yanbian Yellow Cattle – Xiang Z. Li – PLOS ONE

Animal microbiome

A Metagenomic Survey of Viral Abundance and Diversity in Mosquitoes from Hubei Province – Chenyan Shi – PLOS ONE

Comparison of the Intestinal Bacterial Flora in Healthy and Intestinal-diseased Seahorses Hippocampus trimaculatus, Hippocampus erectus, and Hippocampus spinosissimus – Feng Li – Journal of the World Aquaculture Society

Plant and soil microbiome

Analysis of the Peltigera membranacea metagenome indicates that lichen-associated bacteria are involved in phosphate solubilization – Margrét Auður Sigurbjörnsdóttir – Microbiology

Arbuscular Mycorrhizal Fungi Community Structure, Abundance and Species Richness Changes in Soil by Different Levels of Heavy Metal and Metalloid Concentration – Ramasamy Krishnamoorthy – PLOS ONE

Built environment microbiome

Chamber Bioaerosol Study: Outdoor Air and Human Occupants as Sources of Indoor Airborne Microbes – Rachel I. Adams – PLOS ONE

Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing – Wuttichai Mhuantong – PLOS ONE

Metagenomic Insights into the Bioaerosols in the Indoor and Outdoor Environments of Childcare Facilities – Su-Kyoung Shin – PLOS ONE

Food microbiology

PCR-DGGE assessment of the bacterial diversity in Spanish-style green table-olive fermentations – Helena Lucena-Padrós – International Journal of Food Microbiology

Microbial ecology

Perspectives on the context-dependency of stream community responses to contaminants – William H. Clements – Freshwater Biology

Metacommunity speciation models and their implications for diversification theory – Nicolas Hubert – Ecology Letters

The complex relationship between microbial growth rate and yield and its implications for ecosystem processes – David A. Lipson – Frontiers in Microbiology

Techniques

The Effect of Sampling and Storage on the Fecal Microbiota Composition in Healthy and Diseased Subjects – Danyta I. Tedjo – PLOS ONE

Microbes in the news

Sequence your beer: BeerDeCoded: the 1,000 beer genomes

#ASM2015 – Soil microbes ally with plants to fight disease and tolerate stress – Phys.org

#ASM2015 video: A Critical Role of the Plant Microbiome for Immunocompetency – ASM

#ASM2015: Share a Bathroom With Other People? Here’s Something You May or May Not Want to Know About Your Toothbrush – Liz Klimas – The Blaze

All About Flora: How Important Gut Health Really Is. Don’t be grossed out – those little guys living in your guts are your friends – Lacie Glover – US News
Ancient algae found deep in tropical glacier – Biology News

Microbes, biodiversity and the benefits of getting dirty – David Suzuki – National Observer

Former COD Theater Major Researches Microbiology in South Africa – Mitchell11 – Chicago Tribune

Interview with Jessica Richman of uBiome – Tracy Mac – The Power of Poop

Bacteria study may curb antibiotics use – Jeremy Watson – The Times

Could remnants of the earliest life be preserved in volcanic glass? Controversy about microbial “biotextures” – Shalini Saxena – ArsTechnica

Science, publishing, and career

Why we should help people understand our scientific literature – R. W. Abrams – Conservation Biology

Announcing mSystems™: a new ASM open-access journal launching in early 2016 with Jack Gilbert as Founding Editor in Chief – ASM

Scientists Behaving Badly (On Social Media) – Brett Buttliere – PLOS Blogs

Publons and the American Society for Microbiology announce pilot partnership – ASM

Helpful websites for women scientists interested in fellowships, scholarships and funding opportunities – ASM

Bik’s Picks

Chimps Can’t Cook, But Maybe They’d Like To – Michael D. Lemonick – National Geographic

20-year-old invents ingenious system to rid ocean of trash – Olivia Solon – Mirror

Sea lions injured in chlorine attack return to ocean (video) – Chicago Tribune

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June 2, 2015

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General human microbiome

The human microbiome in hematopoiesis and hematological disorders – Veronica E. Manzo and Ami S. Bhatt – Blood

Special issue of Microbial Ecology in Health and Disease: Editorial: We all need friends – Jørgen Valeur

Early Factors Leading to Later Obesity: Interactions of the Microbiome, Epigenome, and Nutrition – Lilly Chang, Josef Neu – Current Problems in Pediatric and Adolescent Health Care

Microbiome of pregnancy and birth

Opportunities to assess factors contributing to the development of the intestinal microbiota in infants living in developing countries – Dennis Lang – Microbial Ecology in Health and Disease

Review: Factors affecting infant gut microbiota and possible consequences for health
Merete Eggesbø – Microbial Ecology in Health and Disease

Human gut microbiome

Draft Genome Sequences of 24 Microbial Strains Assembled from Direct Sequencing from 4 Stool Samples – Patricio Jeraldo – Genome Announcements

Book Chapter: Physiology of Digestion and Absorption: The Functional Interdependence Between Food and the Gut – Stephen J. D. O’Keefe – The Principles and Practice of Nutritional Support

Review: With a little help from my enteric microbial friends – Ben Berkhout – Frontiers in Medicine

Editorial: AI-2 to the rescue against antibiotic-induced intestinal dysbiosis? – Zhongke Sun – Trends in Microbiology

Microbiome models

Evidence from Animal Models: Is a Restricted or Conventional Intestinal Microbiota Composition Predisposing to Risk for High-LET Radiation Injury? – Irene Maier – Radiation Research

Rumen Microbiome from Steers Differing in Feed Efficiency – Phillip R. Myer – PLOS ONE

Changes in the composition of intestinal fungi and their role in mice with dextran sulfate sodium-induced colitis – Xinyun Qiu – Scientific Reports

Microbiota prevents cholesterol loss from the body by regulating host gene expression in mice – Chun-Yan Zhong – Scientific Reports

Animal microbiome

Early-life establishment of the swine gut microbiome and impact on host phenotypes – Núria Mach – Environmental Microbiology Reports

Lifestyle Evolution in Cyanobacterial Symbionts of Sponges – Ilia Burgsdorf – mBio

Plant microbiome

Antagonistic interactions between endophytic cultivable bacterial communities isolated from the medicinal plant Echinacea purpurea – Isabel Maida – Environmental Microbiology

Soil microbiome

Distinct soil bacterial communities along a small-scale elevational gradient in alpine tundra – Congcong Shen – Frontiers in Microbiology

Carcass mass has little influence on the structure of gravesoil microbial communities – Sophie Weiss – International Journal of Legal Medicine

Impact of different cropping conditions and tillage practices on the soil fungal abundance of a Phaeozem luvico – Romina P. Gomez – Spanish Journal of Agricultural Research

Biological activity and microbial genetic diversity of bare-fallow and grassland soils – Anna Kot – Acta Agriculturae Scandinavica, Section B — Soil & Plant Science

Masters Thesis: Assessing soil microbial tolerance to salt – Arpita Maheshwari – Lund University

Water microbiome

Microbial metagenomics in the Baltic Sea: Recent advancements and prospects for environmental monitoring – Karolina Ininbergs – AMBIO

Characterizing microbial communities dedicated for conversion of coal to methane in situ and ex situ – Ji Zhang – International Journal of Coal Geology

Dynamics of the bacterial and archaeal communities in the northern South China Sea revealed by 454 pyrosequencing of the 16S rRNA gene – Xia Xiaomin – Deep Sea Research Part II: Topical Studies in Oceanography

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

Review: Biodiversity, community structure and function of biofilms in stream ecosystems – Katharina Besemer – Research in Microbiology

Built environment microbiome

pecunia non olet? Screening Currency Notes for Microbial Pathogens and Antibiotic Resistance Genes Using a Shotgun Metagenomic Approach – Saakshi Jalali – PLOS ONE

Phages and viruses

Dark matter of the biosphere: The amazing world of bacteriophage diversity – Graham F. Hatfull – Journal of Virology

Bioinformatics and metagenomics

VirSorter: mining viral signal from microbial genomic data – Simon Roux – PeerJ

Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction – David Laehnemann – Briefings in Bioinformatics

FCMM: A comparative metagenomic approach for functional characterization of multiple metagenome samples – Jongin Lee – Journal of Microbiological Methods

PuzzleCluster: A Novel Unsupervised Clustering Algorithm for Binning DNA Fragments in Metagenomics – Current Bioinformatics

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi – Leho Tedersoo – MycoKeys

ANCOM: Analysis of composition of microbiomes: a novel method for studying microbial composition – Siddhartha Mandal – Microbial Ecology in Health and Disease

Transcriptomics and Metabolomics

MetabNet: an R package for metabolic association analysis of high-resolution metabolomics data – Karan Uppal – Frontiers in Bioengineering and Biotechnology

Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism – Anna Edlund – ISME Journal

Review: Enteric short-chain fatty acids: microbial messengers of metabolism, mitochondria, and mind: implications in autism spectrum disorders – Derrick F. MacFabe – Microbial Ecology in Health and Disease

Techniques

Co-extraction of DNA and PLFA from soil samples – Sheridan Brewer – Journal of Microbial Methods

Microbial ecology

Editorial: Flexible gene pools: hard to interpret the diversity often observed in microbial communities – Michael M. Desai – Science

Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche – Michael J. Rosen – Science

Microbes in the news

Good craft beer can be spoiled by bacteria – Phys.org / American Society for Microbiology

Treating Koala STDs May also Quash Their Essential Gut Microbes – Katherine Harmon Courage – Scientific American

New study: Gut bacteria cooperate when life gets tough – EurekAlert

Metabolic activity and health of the skin microbiome – Medical Xpress / American Society for Microbiology

Is our first line of defense sleeping on the job? – Science Daily / American Society for Microbiology

Growing Up In an UnSterile World –The Importance of a Healthy Gut Through the Lifespan – Sarah Lobisco – Dr. Lobisco

Citizen Scientists Send Microbes Into Space – Science 2.0

Methanogens: Earth organisms survive under low-pressure Martian conditions – Science Daily

Why is the H-pylori bacteria developing a liking for Mumbai police? – Santosh Andhale – DNA India

Book review: The great microbial beauty – Vittorio Capozzi – Trends in Microbiology

Science, publishing, and career

Plagiarism is the most common cause of retractions in BioMed Central journals:
Retractions Often Due to Plagiarism: Study – Kerry Grens – The Scientist

Bik’s Picks: not-microbial science

Giant Sawfish Have Virgin Births, Rewrite Biology Textbooks – Charles Q. Choi – Live Science

These newly discovered marsupials basically sex each other to death – Elahe Izadi – Washington Post

Seals Help Scientists Probe Remote Seas – Discovery

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Another June 1, 2015

Posted on by

Here’s the second update of today, completing the backlog because of my travels. 

Human skin microbiome

The Cutaneous Microbiome in Outpatients Presenting With Acute Skin Abscesses – James M. Horton – Journal of Infectious Diseases

Book chapter: Skin Microbiota and Attractiveness to Mosquitoes – Niels O. Verhulst, Willem Takken – Encyclopedia of Metagenomics

Human gut microbiome

High prevalence of cannabis use among Aka foragers of the Congo Basin and its possible relationship to helminthiasis – Casey J. Roulette – American Journal of Human Biology

Hospitalization Type Predicts Risk of Subsequent Severe Sepsis – Hallie C Prescott – American Journal of Respiratory and Critical Care Medicine

Review: Harnessing the Microbiome to Enhance Cancer Immunotherapy – Michelle H. Nelson – Journal of Immunology Research

Review: The functional impact of the intestinal microbiome on mucosal immunity and systemic autoimmunity – Randy S. Longman – Current Opinion in Rheumatology

Review: The intestinal microbiome in spondyloarthritis – Tejpal Gill – Current Opinion in Rheumatology

Microbiome models

Thesis: Alterations in the Fecal Microbiome of Healthy Horses in Response to Antibiotic Treatment – Rachel Sarah Liepman – Ohio State University

Thesis: Effects of Maternal Dietary Yeast Supplementation on Foal Growth and Microbial
Diversity of the Hindgut in Quarter Horse Mares and Their Offspring – Elizabeth Rebecca Share – Ohio State University

Soil, plant root, and rock microbiome

Fungal invasion of the rhizosphere microbiome – Emilie Chapelle – ISME Journal

Shifts in the phylogenetic structure of arbuscular mycorrhizal fungi in response to experimental nitrogen and carbon dioxide additions – Rebecca C. Mueller – Oecologia

Archean (3.33 Ga) microbe-sediment systems were diverse and flourished in a hydrothermal context – Frances Westall – Geology

Crop rotational diversity enhances belowground communities and functions in an agroecosystem – L. K. Tiemann – Ecology Letters

Evaluation of culture-based techniques and 454 pyrosequencing for the analysis of fungal diversity in potting media and organic fertilizers – Abdullah M. Al-Sadi – Journal of Applied Microbiology

Water microbiome

Aquifer community structure in dependence of lithostratigraphy in groundwater – Andrea Beyer – Environmental Science and Pollution Research

Microbial diversity in the deep-sea sediments of Iheya North and Iheya Ridge, Okinawa Trough – Jian Zhang – Microbiological Research

Urbanisation and earthquake disturbance influence microbial nutrient limitation in streams – Emma R. Moffett – Freshwater Biology

On the use of the serial dilution culture method to enumerate viable phytoplankton in natural communities of plankton subjected to ballast water treatment – John J. Cullen, Hugh L. MacIntyre – Journal of Applied Phycology

Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics – Rendy Ruvindy – ISME Journal

Carbon export efficiency and phytoplankton community composition in the Atlantic sector of the Arctic Ocean – Frédéric A. C. Le Moigne – Journal of Geophysical Research – Oceans

Extremophile microbiome

Photoadaptation to the polar night by phytoplankton in a permanently ice-covered Antarctic lake – Morgan-Kiss R. M.- Limnology and Oceanography

Biodegradation: Updating the concepts of control for microbial clean-up in contaminated aquifers – Rainer Udo Meckenstock – Environmental Science & Technology

Bioreactor microbiome

Multi-system Nernst–Michaelis–Menten model applied to bioanodes formed from sewage sludge – Mickaël Rimboud – Bioresource Technology

Community shifts in a well-operating agricultural biogas plant: how process variations are handled by the microbiome – Susanne Theuerl – Applied Microbiology and Biotechnology

Review: Tolerance engineering in bacteria for the production of advanced biofuels and chemicals – Aindrila Mukhopadhyay – Trends in Microbiology

Viruses and phages

When Competing Viruses Unify: Evolution, Conservation, and Plasticity of Genetic Identities – Luis P. Villarreal, Guenther Witzany – Journal of Molecular Evolution

Metagenomics and bioinformatics

Large-scale Machine Learning for Metagenomics Sequence Classification – Kévin Vervier – ArXiv

Review: Metagenomics as a tool for the investigation of uncultured microorganisms – N. V. Ravin – Russian Journal of Genetics

Metabolomics

Metabolic dynamics analysis by massive data integration: application to tsunami-affected field soils in Japan – Tatsuki Ogura – ACS Chemical Biology

Review: Defining the Metabolome: Size, Flux, and Regulation – Nicola Zamboni – Molecular Cell

Techniques

Review: High-Throughput Sequencing Technologies – Jason A. Reuter – Molecular Cell

Microbes in the news

One Week Change In My Microbiome – Richard Sprague – uBiome blog

Unconscious use of ‘medical marijuana? ‘ Hunter-gatherer cannabis use linked to fewer internal parasites – Science Daily

Touchy Feely: Physical contact helps determine who’s present among baboons’ gut bacteria – Kerry Grens – The Scientist

Mysteries of cat, human health revealed through microbiome – Meredith Knight – Genetic Literacy Project

Gut check: Does a hospital stay set patients up for sepsis by disrupting the body’s microbiome? – Kara Gavin – University of Michigan

Immunotherapy: Target the Gut in Patients with Multiple Sclerosis – Linda G. Hughes – HCP Live

Q&A With Pavan Bhargava of Johns Hopkins University School of Medicine: Studying the Microbiome in Treatment of Multiple Sclerosis – Adam Hochron – HCP Live

Contact Lenses Can Change the Ocular Microbiome – Amanda B. Keener – The Scientist

Microbiome and money

Synthetic Biologics to Host Microbiome Analyst & Investor Meeting – Market Watch

Science, publishing, and career

Scientists Who Cheat – The Editorial Board – New York Times

Michael LaCour Probably Fabricated a Document About Research Integrity – Jesse Singal – New York Magazine

Bik’s Picks

What’s Old Is New Again: Revolutionary new methods for extracting, purifying, and sequencing ever-more-ancient DNA have opened an unprecedented window into the history of life on Earth – Bob Grant – The Scientist

See The Tiny Origami Robot That’s Going Viral — Folds Itself, Walks, Swims, And Dissolves [Video] – Inquisitr

Quick to laugh or smile? It may be in your genes – Science Daily

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May 16, 2015

Posted on by

Posting might be irregular in the coming days because of international travel, but I will try to keep you all updated as best as I can.

Human oral microbiome

Increased infection with key periodontal pathogens during gestational diabetes mellitus – Himabindu Gogeneni – Journal of Clinical Periodontology

Human respiratory microbiome

Airway microbiota and acute respiratory infection in children – Kohei Hasegawa – Expert Review of Clinical Immunology

Human gut microbiome

Microbiota—implications for immunity and transplantation – Jonathan S. Bromberg – Nature Reviews Nephrology

Poster: Association of classical microbiology and 16S rDNA metagenetic Aanalysis to evaluate the presence of Clostridium difficile ina a belgian nursing home (sic) – Rodriguez Diaz, Cristina – 5th International Human Microbiome Congres

Review: Probiotics, antibiotics and the immune responses to vaccines – Ira Praharaj – Philosophical Transactions B

Microbiome models

Exposure to soil, house dust, and decaying plants increases gut microbial diversity and decreases serum IgE levels in BALB/c mice – Dongrui Zhou – Environmental Microbiology

Water microbiome

Metagenomics reveals the high PAH-degradation potential of abundant uncultured bacteria from chronically-polluted subantarctic and temperate coastal marine environments – Claudia L. Loviso – Journal of Applied Microbiology

Plant root and soil microbiome

Early rhizosphere microbiome composition is related to the growth and Zn uptake of willows introduced to a former landfill – Terrence H. Bell – Environmental Microbiology

Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa – S. Geisen – Molecular Ecology

Soil microbial communities vary as much over time as with chronic warming and nitrogen additions – Alexandra R. Contosta – Soil Biology and Biochemistry

Soil ecotoxicity assessment of glyphosate use under field conditions: microbial activity and community structure of Eubacteria and ammonia oxidizing bacteria – María C. Zabaloy – Pest Management Science

Changes in soil aggregation and microbial community structure control carbon sequestration after afforestation of semiarid shrublands – N. Garcia-Francoa – Soil Biology and Biochemistry

Air microbiome

Challenges and Opportunities of Airborne Metagenomics – Hayedeh Behzad – Genome Biology and Evolution

Food microbiology

Bacteriophages isolated from chicken meat and the horizontal transfer of antimicrobial resistance genes– Amira Shousha – Applied and Environmental Microbiology

Techniques

A simple method of normalization of DNA extraction for improving the quantitative detection of soil-borne plant pathogenic oomycetes by real-time PCR – M. Li – Letters in Applied Microbiology

Microbes in the news

The kittybiome Project – background and some plans – Jonathan Eisen – MicroBEnet

Science, publishing, and career

Why Medicine is Plagued with Fake Research – Chloe Della Costa – Business Cheat Sheet

Physics Paper on the Higgs Boson Has Record 5,154 Authors – Softpedia (link to actual pdf)

Bik’s Picks

Giant Squid Lore and Legends Date Back Centuries – Benjamin Radford – Discovery

Cocaine Use Could be Determined by a Fingerprint, New Study – Silvia Fernandez – Pierce Pioneer

New map shows most distinct causes of death by state – Marilyn Malara – UPI

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May 14, 2015

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General microbiome

Yesterday’s Cell Host & Microbe issue contains a special on “The Host-Microbiota Balance”. Lots of great papers and editorials here! Several papers are listed below in their respective categories, or I already included them in previous posts.

Microbiota and Host Nutrition across Plant and Animal Kingdoms – Stéphane Hacquard – Cell Host & Microbe

Microbiota and Autoimmunity: Exploring New Avenues – Leonid A. Yurkovetskiy – Cell Host & Microbe

Pregnancy and birth

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life – Fredrik Bäckhed – Cell Host & Microbe – with editorial: Birth of the Infant Gut Microbiome: Moms Deliver Twice! – Steven A. Frese, David A. Mills – Cell Host & Microbe

Restricted access: Bacterial communities in neonatal feces are similar to mothers’ placentae – Xu-Dong Dong – Canadian Journal of Infectious Diseases & Medical Microbiology

Review: Antibiotics, Pediatric Dysbiosis, and Disease – Pajau Vangay – Cell Host & Microbe

Human oral microbiome

Pseudomonas aeruginosa and Periodontal Pathogens in the Oral Cavity and Lungs of Cystic Fibrosis Patients: a Case-Control Study – Rocio Rivas Caldas – Journal of Clinical Microbiology

Human gut microbiome

Review: An Integrative View of Microbiome-Host Interactions in Inflammatory Bowel Diseases – Marta Wlodarska – Cell Host & Microbe

Review: Control of Brain Development, Function, and Behavior by the Microbiome – Timothy R. Sampson, Sarkis K. Mazmanian – Cell Host & Microbe

Review: Microbiota in Allergy and Asthma and the Emerging Relationship with the Gut Microbiome – Kei E. Fujimura – Cell Host & Microbe

Editorial: Prevention: Tending the gut. Drugs, lifestyle changes and other measures might lower the risk of colorectal cancer — but the evidence is a long time coming. – Lauren Gravitz – Nature

Editorial: Microbiome: Microbial mystery. Gut bacteria have an important but elusive role in the formation of colorectal cancer. – Sarah DeWeerdt – Nature

Animal models

Editorial: Message in a Biota: Gut Microbes Signal to the Circadian Clock – Emily V. Marcinkevicius, Mimi M. Shirasu-Hiza – Cell Host & Microbe

Animal microbiome

Coprophilic dipteran community associated with horse dung in Malaysia – C.C. Heo – Halteres

Water microbiome

Bacteria in the injection water differently impacts the bacterial communities of production wells in high-temperature petroleum reservoirs – Hongyan Ren – Frontiers in Microbiology

Assessment of nitrogen and sulphur cycle bacteria and shrimp production in ponds treated with biological products – Thangapalam Jawahar Abraham – Journal of Coastal Life Medicine

 

More microbiology

Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons – Kelly M. Wetmore – mBio

Microbes in the news

Maturation of the Infant Microbiome – Kerry Grens – The Scientist
Infant antibiotic use linked to adult diseases – Science Daily

Bacteria on shoes could help forensic teams catch suspects – Stefano Vanin – The Conversation
Forensic scientists could use bacteria to catch criminals – Brooks Hays – UPI

The microbiome and the midnight snack: How gut microbes influence the body’s clock – Matt Wood – ScienceLife

Bacteria the Newest Tool in Detecting Environmental Damage – University of Tennessee

Bacteria May Be Remaking Drugs in Sewage: Microbes that clean our water may also be piecing some pharmaceuticals back together – Brian Bienkowski – Scientific American

If Microbes Could Tweet… Small Things Considered – Daniel P. Haeusser

Microbiology: Fungus against the wall. Paul O’Maille – Nature

Science, publishing, and career

“It’s invigorating to be around that student energy the first time they learn about science,” Adjunct teaching: For love of the lecture – Kendall Powell – Nature

This scientific paper has 2,863 authors. How? – Danielle Wiener-Bronner – Fusion

Bik’s Picks

MIT And UC Berkeley Duking It Out Over CRISPR – Cas 9 – Clayton Browne – Value Walk

Survey: Almost half of all bee hives in the U.S. died in the past year – Mashable

Scientists have discovered the first fully warm-blooded fish – Chelsea Harvey – Washington Post
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