Category Archives: Animal experiments

June 12, 2015

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Effects of drinking donkey milk, archaea and fungi on humans,  microbiomes of olives, spoilt wine, cold deserts, indoor air, strawberry soil, and more.

General microbiome

Review: Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: Towards a systems-level understanding of human microbiomes – Bikel Shirley – Computational and Structural Biotechnology Journal

Review: Mycobiota: Micro-Eukaryotes Inhabiting Our Body as Commensals or
Opportunistic Pathogens – Lisa Rizzetto – Fungal Genomics & Biology

Review: Archaea in and on the Human Body: Health Implications and Future Directions – Mor N. Lurie-Weinberger, Uri Gophna – PLOS Pathogens

Human skin microbiome

Antimicrobial Efficacy of Preservatives used in Skin Care Products on Skin Micro Biota – Chintha Lalitha – International Journal of Science and Research

Review: Beneficial and deleterious bacterial–host interactions in chronic wound pathophysiology – C. Watters – Chronic Wound Care Management and Research

Human gut microbiome

Influence of Proton-Pump Inhibitors on the Luminal Microbiota in the Gastrointestinal Tract – Ayumi Tsuda – Clinical and Translational Gastroenterology

Microbiome models

A host-microbiome interaction mediates the opposing effects of omega-6 and omega-3 fatty acids on metabolic endotoxemia – Kanakaraju Kaliannan – Scientific Reports

In rats: Human, donkey and cow milk differently affects energy efficiency and inflammatory state by modulating mitochondrial function and gut microbiota – Giovanna Trinchese – The Journal of Nutritional Biochemistry

Fish: A multiple endpoint analysis of the effects of chronic exposure to sediment contaminated with Deepwater Horizon oil on juvenile Southern flounder and their associated microbiomes – Nancy J. Brown-Peterson – Aquatic Toxicology

Hops β-acids and zinc bacitracin affect the performance and intestinal microbiota of broilers challenged with Eimeria acervulina and Eimeria tenella – C. Bortoluzzi – Animal Feed Science and Technology

Staphylococcus aureus nasal isolates: The effects of spatial structure, frequency dependence and resistance evolution on the dynamics of toxin-mediated microbial invasions – Ben Libberton – Evolutionary Applications

Animal microbiome

Biodiversity of the Symbiotic Bacteria Associated with Toxic Marine Dinoflagellate Alexandrium tamarense – Xiaoling Zhang – Journal of Biosciences and Medicines

Plant microbiome

Wild trees in the Amazon basin harbor a great diversity of beneficial endosymbiotic fungi: is this evidence of protective mutualism? – Romina Gazis – Fungal Ecology

A Legume Genetic Framework Controls Infection of Nodules by Symbiotic and Endophytic Bacteria – Rafal Zgadzaj – PLOS Genetics

Diversity and spatial distribution of endophytes community composition in noni (Morinda citrifolia L.) – Liu Yang – Journal of Hill Agriculture

Comparisons of microbial abundance and community among different plant species in constructed wetlands in summer – Jian Zhang – Ecological Engineering

Soil (and plant root) microbiome

Impact of cover crop in pre-plant of apple orchards: relationship between crop health, root inhabiting fungi and rhizospheric bacteria – Luisa M. Manici – Journal of Plant Science

Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry – Xiangming Xu – Horticulture Research

Positively Frequency-Dependent Interference Competition Maintains Diversity and Pervades a Natural Population of Cooperative Microbes – Olaya Rendueles – Current Biology

A predictive model for microbial counts on beaches where intertidal sand is the primary source – Zhixuan Feng – Marine Pollution Bulletin

Reintroduction of locally extinct vertebrates impacts arid soil fungal communities – Laurence J. Clarke – Molecular Ecology

A simple experimental set-up to disentangle the effects of altered temperature and moisture regimes on soil organisms – Eveline J. Krab – Methods in Ecology and Evolution

Water microbiome

Identifying homogeneity of multivariate dispersions among biofilm-dwelling microbial communities in colonization surveys for marine bioassessment – Guangjian Xu – Ecological Indicators

Bacterial diversity along a 2600 km river continuum – Domenico Savio – Environmental Microbiology

Minireview: Microbial players involved in the decline of filamentous and colonial cyanobacterial blooms with a focus on fungal parasitism – Mélanie Gerphagnon – Environmental Microbiology

Extremophile microbiome

Bacterial diversity of Drass, cold desert in Western Himalaya, and its comparison with Antarctic and Arctic – Puja Gupta – Archives of Microbiology

Built environment microbiome

Indoor air bacterial communities in Hong Kong households assemble independently of occupant skin microbiomes – David Wilkins – Environmental Microbiology

Food microbiology

Potential spoilage yeasts in winery environments: Characterization and proteomic analysis of Trigonopsis cantarellii – Cauré Portugal – International Journal of Food Microbiology

Microbiota and Metabolome of Un-started and Started Greek-type Fermentation of Bella di Cerignola Table Olives – Maria De Angelis – Food Microbiology

Functional foods

Probiotic BIFICO cocktail ameliorates Helicobacter pylori induced gastritis – Hong-Jing Yu – World Journal of Gastroenterology

Review: Prebiotics, gut microbiota and metabolic risks: Unveiling the relationship – Adeela Yasmin – Journal of Functional Foods

Review: Current evidence on the use of probiotics in liver diseases – Norberto C. Chávez-Tapia – Journal of Functional Foods

Metagenomics 

Review: Methylotrophs in natural habitats: current insights through metagenomics – Ludmila Chistoserdova – Applied Microbiology and Biotechnology

Metabolomics

Editorial: Microbial metabolite triggers antimicrobial defense – Sky W. Brubaker, Denise M. Monack – Science

Microbes in the news

Soil microbial community variation correlates most strongly with plant species identity – AOB blog

Pew Names 22 Top Scientists as Scholars in the Biomedical Sciences: topics range from microbiome, to mosquito’s preferences – Pew Trusts
and: Microbiology professor becomes UC Merced’s first Pew scholar: Clarissa Nobile receives award for biofilm research – UC Merced

2015 ISCB Overton Prize Awarded to Curtis Huttenhower – Christiana N. Fogg, Diane E. Kovats – PLOS Computational Biology

“Genes in Space” Student Finalists Announced: Tarun Srinivasan, of Houston, TX, plans to examine effects on the gut microbiome of spending time on the ISS – Ricki Lewis – PLOS Blogs

Method reveals what bacteria sense in their surroundings – Leila Gray – UW Health Sciences NewsBeat

“ticks had a microbiome rich in pathogens, including Bartonella”: Ticks’ Migration Linked to Changes in Disease Prevalence – Jacquelyn Gray – HCP Live

Like “kopi luwak” coffee, just bigger: Elephant poop coffee, Thailand’s new delicacy – Doug Powell – BarfBlog

New Tool To Monitor Harmful Bacteria: Scientists offer more accurate health risk prediction model to better inform beach closure decisions – Rosenstiel School of Marine & Atmospheric Science

#EULAR2015: First gut microbiota alterations described in systemic sclerosis patients – Karen Blum – PM360online

Some good information here about bacteria in our gut: Six myths about digestion that just won’t die – ITClips

How does Swiss cheese gets its holes?: by carbon-dioxide-burping microbe Propionibacterium freudenreichii – Nicola Twilly – New Yorker

Product candidate to target specific elimination of Streptococcus mutans may alter oral microbiome to provide long-lasting benefits – Dentistry iQ

Fungus among us, but what kind? Typing error spawns retraction for mushroom paper – Retraction Watch

Science, publishing, and career

Business decisions: stories about the entrepreneurial learning curve – Jeffrey Mervis – Science

Bik’s Picks

Polar bear caught eating dolphins and freezing the leftovers – Penny Sarchet – New Scientist

There’s A Link Between Cat Ownership And Schizophrenia – Leigh Weingus – Huffington Post

“Advice to interns: work hard and make your mark.” New planet discovered by 15-year-old intern – Monica Sarkar – CNN

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June 11, 2015

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Exciting edition today, with microbiomes from scorpions, kombucha, Korean infants, and a Yosemite lake.

Pregnancy and birth

Comparison of the gut microbiota profile in breast-fed and formula-fed Korean infants using pyrosequencing – Sang A Lee – Nutrition Research and Practice

Human skin microbiome

Review: Effects of Fermented Dairy Products on Skin: A Systematic Review – Alexandra R. Vaughn – The Journal of Alternative and Complementary Medicine

Human gut microbiome

The Fecal Microbiome in Pediatric Patients With Short Bowel Syndrome – Zev H. Davidovics – Journal of Parental & Enteral Nutrition

Review: Association of the Intestinal Microbiota and Obesity – Andrea A. López-Cepero, Cristina Palacios – Puerto Rico Health Sciences Journal

Microbiome models

Alteration of the rat cecal microbiome during colonization with the helminth Hymenolepis diminuta – Erin A McKenney – Gut Microbes

Bacterial sensing underlies artificial sweetener-induced growth of gut Lactobacillus –
Kristian Daly – Environmental Microbiology

Ecobiotherapy Rich in Firmicutes Decreases Susceptibility to Colitis in a Humanized Gnotobiotic Mouse Model – Jane M. Natividad – Inflammatory Bowel Diseases

Animal microbiome

Species-specific diversity of novel bacterial lineages and differential abundance of predicted pathways for toxic compound degradation in scorpion gut microbiota –
Luis M. Bolaños – Environmental Microbiology

Water microbiome

Changing composition of microbial communities indicates seepage fluid difference of the Thuwal Seeps in the Red Sea – Bo Yang – Antonie van Leeuwenhoek

Microbial diversity and community structure along a lake elevation gradient in Yosemite National Park, California, USA – Curtis J. Hayden – Environmental Microbiology

Food microbiology

Metabarcoding of the kombucha microbial community grown in different microenvironments – Oleg N Reva – AMB Express

More microbiology

I thought this was a very attractive paper: Single-cell genomics of uncultivated deep-branching magnetotactic bacteria reveals a conserved set of magnetosome genes – Sebastian Kolinko – Environmental Microbiology

Review: Small but Mighty: Cell Size and Bacteria – Petra Anne Levin and Esther R. Angert – Cold Spring Harbor Perspectives in Biology

Preview: Bacteria Moving into Focus of Human Cancer – Francesco Boccellato, Thomas F. Meyer – Cell Host & Microbe

Microbes in the news

Microbe-mediated adaptation to a novel diet: Symbiotic bacteria enabled bugs to feed on plant seeds and promoted species diversity – Max Planck Institute for Chemical Ecology

Bespoke diets based on gut microbes could help beat disease and obesity – Ian Sample – The Guardian

Engineers create origami paper-based bacteria-powered battery – Nanowerk

Journal club: Response to May 29, 2015 Journal Club: “Modulation of Post-Antibiotic Bacterial Community Reassembly and Host Response by Candida Albicans” – Human Microbiome Journal Club

Alberta researchers hot on the trail of deadly bacteria: detection time of E. coli in meat cut in half – Alexis Kienlen – Alberta Farmer

Sauerkraut Could Be The Secret To Curing Social Anxiety – Carolyn Gregoire – Huffington Post

Microbiomes might differ between mice: Reproducibility: Use mouse biobanks or lose them – Kent Lloyd – Nature

ESCMID introduces two new study groups to create networks for forensic and veterinary microbiology – News Medical

Science, publishing, and career

Nobel Laureate Resigns Post After Comments on Female Scientists – Dan Bilefsky – New York Times

Funny article, in response to Tim Hunt’s comments: Female scientists post ‘distractingly sexy’ photos – BBC News

African academics challenge homophobic laws – Scientific report demolishes assertions used to back criminalization of homosexuality – Linda Nordling – Nature

Workforce: The joys of research in retirement – Klaus Wittmaack – Nature

Bik’s Picks

Population genomics of Bronze Age Eurasia: low-coverage genomes from 101 ancient humans from across Eurasia – Morten E. Allentoft – Nature

#CureBatten: Celebrities rally for sisters battling rare brain disease – Chris Serico – Today

Three cheers for Samantha Cristoforetti, smasher of space records – Rachel Feltman – Washington Post

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June 10, 2015

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Another load of microbiome reviews, historical responses of microbes to mercury in soil layers, and different pictures of microbial diversity using culture or molecular techniques.

Microbiome of pregnancy and health

Review: Lungs, Microbes and the Developing Neonate – Warner B.B., Hamvas A. – Neonatology

Review: Placentophagy: therapeutic miracle or myth? – Cynthia W. Coyle – Archives of Women’s Mental Health

Review: Preterm delivery and intimacy during pregnancy: interaction between oral, vaginal and intestinal microbiomes – Herrera Morban DA – Medwave

Human gut microbiome

Review: Monitoring host responses to the gut microbiota – Joshua S Lichtman, Justin L Sonnenburg and Joshua E Elias – The ISME Journal

Review: Intestinal Fucose as a Mediator of Host–Microbe Symbiosis – Joseph M. Pickard and Alexander V. Chervonsky – The Journal of Immunology

Review: Novel players in coeliac disease pathogenesis: role of the gut microbiota – Elena F. Verdu – Nature Reviews Gastroenterology & Hepatology

Review: Gut Microbiome-Brain Communications Regulate Host Physiology and Behavior – Sun Hye Lee and Claire B. de La Serre – Journal of Nutritional Health & Food Science

Review: Biliary Mucosal Barrier and Microbiome – Verdier J – Viszeralmedizin

Review: From Next-Generation Sequencing to Systematic Modeling of the Gut Microbiome – Boyang Ji and Jens Nielsen – Frontiers in Microbiology

Animal and other models of microbiome research

Bioimage analysis of Shigella infection reveals targeting of colonic crypts – Ellen T. Arena – PNAS

Animal microbiome

Filamentous fungi isolated from the fur microbiota of callitrichids kept in captivity in Brazil – de Freitas RA – J Zoo Wildl Med

Plant root and soil microbiome

Microbial response to simulated global change is phylogenetically conserved and linked with functional potential – Anthony S Amend – The ISME Journal

Microbial and biochemical basis of a Fusarium wilt-suppressive soil – Jae-Yul Cha – The ISME Journal

Microbial DNA records historical delivery of anthropogenic mercury – Alexandre J Poulain – The ISME Journal

Riverbed methanotrophy sustained by high carbon conversion efficiency – Mark Trimmer – The ISME Journal

Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils – Franck O. P. Stefani – PLOS ONE

Crop monoculture rather than agriculture reduces the spatial turnover of soil bacterial communities at a regional scale – Eva L. M. Figuerola – Environmental Microbiology

Bacteria and fungi associated with isoprene consumption in soil – Christopher M. Gray – Elementa-Science of the Anthropocene

Microbial rRNA:rRNA gene ratios may be unexpectedly low due to extracellular DNA preservation in soils – Glade Dlott – Journal of Microbiological Methods

Differences in microbial community composition between injection and production water samples of water flooding petroleum reservoirs – P. K. Gao – Biogeosciences

Commentary: Scrambled and not-so-tiny genomes of fungal endosymbionts – Chih-Horng Kuo – PNAS

Water microbiome

Sampling the Sea Surface Microlayer – Michael Cunliffe, Oliver Wurl – Springer Protocols
Built environment microbiome

Book chapter: Bacteria and Fungi in Green Roof Ecosystems – Krista L. McGuire – Green Roof Ecosystems

Extremophile microbiome

Application of artificial neural networks as a tool for moisture prediction in microbially colonized halite in the Atacama Desert – K. Wierzchos – Journal of Geophysical Research – Biogeosciences

Bioreactor microbiology

Methanobacterium Dominates Biocathodic Archaeal Communities in Methanogenic Microbial Electrolysis Cells – Michael Siegert – ACS Sustainable Chemistry & Engineering

Metagenomics and bioinformatics

ProDeGe: a computational protocol for fully automated decontamination of genomes – Kristin Tennessen – The ISME Journal

RNeXML: a package for reading and writing richly annotated phylogenetic, character, and trait data in R – Carl Boettiger – arXiv

PrimerView: high-throughput primer design and visualization – Damien M. O’Halloran – Source Code for Biology and Medicine

Techniques

Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi – Giovanna Carpi – BMC Genomics

Cultivation of Environmental Bacterial Communities as Multispecies Biofilms – Marc A. Demeter – Springer Protocols Handbook

Microbes in the news

Brits will swab surfers’ butts to understand antibiotic-resistant bacteria – Alexandra Ossola – Popular Science

You’ve been invaded – by your Microbiome! Video with Rob Knight – UCSD TV

Understanding the nasal microbiome – American Microbiome Institute

How gut bacteria affects your health: What we know, what we don’t – Emily Kaiser – MPR News

The Secrets of Ocular Microbiomes – Mark B. Abelson – Review of Ophthalmology

Nice graphics: To the Phyllosphere and Beyond! – Ben Wolfe – Lucky Peach

Meanwhile in the Future: When Antibiotics Stop Working – Rose Eveleth – Gizmodo

Obesity and Microbiota: What’s Hype, What’s Helpful? – Jeannette Y. Wick – HCP Live

Science, publishing, and career

Nobel Prize Winner Tim Hunt Shocks Journalists With Sexist Comments – Cat Ferguson – BuzzFeed Science

Career coaching for scientists – Joanne Kamens – Nature Biotechnology

Intel Capital Creates $125M Fund for Women-, Minority-led Startups – Deborah Gage – Wall Street Journal

UTHealth’s Kevin Morano, microbiologist receives prestigious teaching honor by Minnie Stevens Piper Foundation – EurekAlert

Bik’s Picks

Caffeine acts through neuronal adenosine A2A receptors to prevent mood and memory dysfunction triggered by chronic stress – Manuella P. Kaster – PNAS

Chimps dig palm wine, new study finds: And in case you were wondering, the apes did occasionally get tipsy – Amina Khan – Los Angeles Times

This new Google-backed app will identify a bird just from a photo – Quartz

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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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