Category Archives: Built Environment Microbiology

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 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 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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May 22, 2015

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Several special issues this week: Science features results from the Tara ocean plankton biodiversity expedition, Microbes and Infection has a special on the oral microbiome, and Frontiers bundled several papers under the not-so-pretty name The Human Gutome.

General microbiome

The Microbiome and Autoimmune Disease: Report from a Noel R. Rose Colloquium – Jobert G. Barin – Clinical Immunology

New developments providing mechanistic insight into the impact of the microbiota on allergic disease – Kathy D. McCoy – Clinical Immunology

Review: Self or non-self? The multifaceted role of the microbiota in immune-mediated diseases – Martin A. Kriegel – Clinical Immunology

Human oral microbiome

Special issue of Microbes and Infection (7 papers but most have already been posted in this blog). Editorial with links to 7 papers: A New Frontier: Oral Microbes without Borders – Özlem Yilmaz
Extracellular DNA in oral microbial biofilms – Nicholas S. Jakubovics

Not microbiome but cool: The Diet of Three Medieval Individuals from Caravate (Varese, Italy). Combined Results of ICP-MS Analysis of Trace Elements and Phytolith Analysis Conducted on Their Dental Calculus – A. M. B. Lazzati – International Journal of Osteoarchaeology

Human gut microbiome

Frontiers Research Topic (papers have been posted previously in this blog): The Human Gutome: Nutrigenomics of Host-Microbiome Interactions

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes – Stefanía Magnúsdóttir – Frontiers in Genetics

Model: Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico – Almut Heinken – Applied and Environmental Microbiology

Review: Intestinal microbiota and allergic diseases: A systematic review – L.C.F.L. Melli – Allergologia et Immunopathologia

Human urogenital microbiome

Editorial: Cervicovaginal Microbiota: Simple Is Better – Smita Gopinath – Immunity

Cervicovaginal Bacteria Are a Major Modulator of Host Inflammatory Responses in the Female Genital Tract – Melis N. Anahtar – Immunity

The New World of the Urinary Microbiome in Women – Linda Brubaker, Alan J Wolfe – American Journal of Obstetrics and Gynecology

Plant and soil microbiome

Root-associated bacterial endophytes from Ralstonia solanacearum resistant and susceptible tomato cultivars and their pathogen antagonistic effects – Reshmi Upreti and Pious Thomas – Frontiers in Microbiology

Distinct Circular Single-Stranded DNA Viruses Exist in Different Soil Types – Brian Reavy – Applied and Environmental Microbiology

Water microbiome

Special Science issue: Tara Oceans studies plankton at Planetary Scale – P. Bork- Science

pH levels drive bacterial community structure in sediments of the Qiantang River as determined by 454 pyrosequencing – Shuai Liu – Frontiers in Microbiology

Distribution and diversity of fungi in freshwater sediments on a river catchment scale – Jie Liu – Frontiers in Microbiology

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction
Ping Zhang – Applied and Environmental Microbiology

Extremophile microbiome

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms – Young-Mo Kim – Frontiers in Microbiology

Abundance and Distribution of Dimethylsulfoniopropionate Degradation Genes and the Corresponding Bacterial Community Structure at Dimethyl Sulfide Hot Spots in the Tropical and Subtropical Pacific Ocean – Yingshun Cui – Applied and Environmental Microbiology

Built environment microbiome

Feasibility study involving the search for natural strains of microorganisms capable of degrading graffiti from heritage materials – Patricia Sanmartín – International Biodeterioration & Biodegradation

Bioreactor microbiology

Next-Generation Pyrosequencing Analysis of Microbial Biofilm Communities on Granular Activated Carbon in Treatment of Oil Sands Process-Affected Water – M. Shahinoor Islam – Applied and Environmental Microbiology

Metagenomics

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes – Stefanía Magnúsdóttir – Frontiers in Genetics

Metabolomics

Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters – Tina Netzker – Frontiers in Microbiology

Species interactions differ in their genetic robustness – Lon M. Chubiz – Frontiers in Microbiology

Functional foods

Probiotics for Weight Loss: A Systematic Review and Meta-Analysis – Sunmin Parka, Ji-Hyun Baeb – Nutrition Research

Viruses and phages

Badger, mongoose, otter: Fecal virome analysis of three carnivores reveals a novel nodavirus and multiple gemycircularviruses – Nádia Conceição-Neto – Virology Journal

Review: The Virome in Host Health and Disease – Ken Cadwell – Immunity

More microbiology

Editorial: recent discoveries in evolutionary and genomic microbiology – Anton G. Kutikhin and Arseniy E. Yuzhalin – Frontiers in Microbiology

Financial evaluations of antibiotic stewardship programs—a systematic review – Jan-Willem H. Dik – Frontiers in Microbiology

Antagonistic interactions are sufficient to explain self-assemblage of bacterial communities in a homogeneous environment: a computational modeling approach – Román Zapién-Campos – Frontiers in Microbiology

Microbes in the news

What’s Next for the Microbiome? – Jo Handelsman and Elizabeth R. Stulberg – Whitehouse.gov
The White House wants input on the future of microbiome research (by June 15) – Jonathan Eisen – Microbe.net

Ocean’s microbiome has incredible diversity – and human likeness – Colin Barras – New Scientist
Three-year ocean voyage discovered thousands of new, unfamiliar viruses: A study of plankton reveals just how little we know about the ocean – Arielle Duhaime-Ross – The Verge
Scientists Map 5,000 New Ocean Viruses – Carl Zimmer – Quanta Magazine

Help fund koala microbiome study – Andy Fell – Egghead Research at UC Davis

Nurturing a baby’s microbiome, before and after birth – Kate Gammo – Populair Science

Meet the caesarean mums who are ‘seeding their baby’s microbiome’ – Best Daily

Long-gone bacteria blows the whistle on gold deposits – Geology Page

Microbes and money

Why bacteria is becoming big business – Stephen Valdivia – Fortune
Danone’s big bet on tiny bacteria – Erica Fry – Fortune

uBiome Partners with PicnicHealth: Participants diagnosed with Inflammatory Bowel Disease (IBD) will receive a complementary PicnicHealth account as well as a complementary uBiome research kit. – PR Rocket

Science, publishing, and career

(Satire) The Allium Top Tips For Scientists and Engineers – The Allium
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May 16, 2015

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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 15, 2015

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Human skin microbiome

Pilot Study on Novel Skin Care Method by Augmentation with Staphylococcus epidermidis, an Autologous Skin Microbe – A Blinded Randomized Clinical Trial – Yuichi Nodake – Journal of Dermatological Science

Human gut microbiome

Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota – Simone Rampelli – Current Biology

Deviations in human gut microbiota: a novel diagnostic test for determining dysbiosis in patients with IBS or IBD – C. Casén – Alimentary Pharmacology & Therapeutics

Intestinal Blautia is associated with reduced death from graft-versus-host disease – Robert R. Jenq – Biology of Blood and Marrow Transplantation

Pubmed link only: The coeliac stomach: gastritis in patients with coeliac disease – B. Lebwohl – Alimentary Pharmacology & Therapeutics

DGGE: Schisandra chinensis fruit modulates the gut microbiota composition in association with metabolic markers in obese women : a randomized, double-blind placebo controlled study – Mi-young Song – Nutrition Research

Review: Gut microbes, immunity, and spondyloarthritis – Matthew L. Stoll – Clinical Immunology

Microbiome models

Relationships Between Diet-Related Changes in the Gut Microbiome And Cognitive Flexibility – K.R. Magnusson – Neuroscience

Animal microbiome

Aphids: Genetic characterisation of new host-specialised biotypes and novel associations with bacterial symbionts in the pea aphid complex – Jean Peccoud – Insect Conservation and Diversity

Review: The Multi-Tasking Gut Epithelium of Insects – Jia-Hsin Huang – Insect Biochemistry and Molecular Biology

Plant and soil microbiome

On small soil beetles: Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics – Carmelo Andújar – Molecular Ecology

Changes in soil nutrient content and bacterial community after 12 years of organic amendment application to a vineyard – M. E. Calleja-Cervantes – European Journal of Soil Science

Built Environment microbiology

Self-healing bio-concrete uses bacteria to repair itself – Anthony Cuthbertson – International Business Times

Bioreactor microbiology

Rare taxa have potential to make metabolic contributions in enhanced biological phosphorus removal ecosystems – Christopher E. Lawson – Environmental Microbiology

Bioinformatics

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods – Jullien M. Flynn -Ecology and Evolution

More microbiology

Editorial: Sifting out virulent bacteria – Naomi Attar – Nature Reviews Microbiology

Review: Dust Devil: The Life and Times of the Fungus That Causes Valley Fever – Eric R. G. Lewis – PLOS Pathogens

Microbes in the news

Decode your kitty’s microbiome – participate in some Cat-izen science – Alexandra Ossola –
Popular science

BacteriaHysteria

Faecal matter on plane tray tables, unwashed blankets… and 80 million bacteria on suitcases: The dirty secrets of air travel revealed – John Hutchinson – Daily Mail

Science, publishing, and career

“Reframing my track record undoubtedly helped. Here’s how I did it.” Accounting for career breaks – Emily Nicholson – Science

Bik’s Picks

Denver Zoo Penguins Go ‘Extinct’ For Endangered Species Day – CBS Denver

A Simple Hand-Grip Test Could Predict Your Risk For Heart Disease And Death – Anna Almendrala – Huffington Post

An astronaut’s surprisingly helpful guide to pooping in space – Elahe Izadi – Washington Post

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May 12, 2015

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Microbiome of pregnancy and birth

Metagenomic Analysis of Milk of Healthy and Mastitis-Suffering Women – Esther Jiménez – Journal of Human Lactation

Human oral microbiome

Abstract: Changes In The Oral Microbiome Of HIV-Infected Individuals May Alter Nitrogen Metabolism And The Enterosalivary Circulation Of Nitrate – Carl D. Koch – Am J Respir Crit Care Med

Human respiratory microbiome

Conference abstracts in Am J Respir Crit Care Med:

Human gut microbiome

Metabolism Links Bacterial Biofilms and Colon Carcinogenesis – Caroline H. Johnson – Cell Metabolism

Review: The gut microbiome: What do we know? – Francisco Guarner – Clinical Liver Disease

Review: A model for the role of gut bacteria in the development of autoimmunity for type 1 diabetes – Austin G. Davis-Richardson – Diabetologia

Functional foods

Review: A breakthrough in probiotics: Clostridium butyricum regulates gut homeostasis and anti-inflammatory response in inflammatory bowel disease – Takanori Kanai – Journal of Gastroenterology

Animal models of microbiome research

Phylum Level Change in the Cecal and Fecal Gut Communities of Rats Fed Diets Containing Different Fermentable Substrates Supports a Role for Nitrogen as a Factor Contributing to Community Structure – Martin Kalmokoff – Nutrients

Animal microbiome

Variation in koala microbiomes within and between individuals: effect of body region and captivity status – Niccoló Alfano – Scientific Reports

Plants and soil microbiome

Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota – Mizue Naito – PNAS

Transcriptome diversity among rice root types during asymbiosis and interaction with arbuscular mycorrhizal fungi – Caroline Gutjahr – PNAS
Reintroduction of locally extinct vertebrates impacts arid soil fungal communities –
Laurence J. Clarke – Molecular Ecology

Compartmentalized and contrasted response of ectomycorrhizal and soil fungal communities of Scots pine forests along elevation gradients in France and Spain
Ana Rincón – Environmental Microbiology

Impact of tropical lowland rainforest conversion into rubber and oil palm plantations on soil microbial communities – Valentyna Krashevska – Biology and Fertility of Soils

Masters Thesis: The establishment of apple orchards as temperate forest garden systems and their impact on indigenous bacterial and fungal population abundance in Southern Ontario, Canada – Paul Wartman – University of Guelph, Canada

Review: Plant growth promoting rhizobacteria and sustainable agriculture: A review –
Muhammad Arslan Ashraf – African Journal of Microbiology Research

Water microbiome

Organic and inorganic composition and microbiology of produced waters from Pennsylvania shale gas wells – Denise M. Akob – Applied Geochemistry

Perspective: Using dispersants after oil spills: impacts on the composition and activity of microbial communities – Sara Kleindienst – Nature Reviews Microbiology

Not sure if these are small enough (20-500 um) to be classified as microbes: Metagenetic tools for the census of marine meiofaunal biodiversity: An overview – Laura Carugati – Marine Genomics

Extremophile microbiome

Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator-prey genotypes – Naseer Sangwan – Environmental Microbiology Reports

Comparison of Archaeal and Bacterial Diversity in Methane Seep Carbonate Nodules and Host Sediments, Eel River Basin and Hydrate Ridge, USA – Olivia U. Mason – Microbial Ecology

Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species – Nur A. Hasan – PNAS

Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time – Cody S. Sheik – Frontiers in Microbiology

Built environment microbiome

Forensic analysis of the microbiome of phones and shoes – Simon Lax – Microbiome

The Actinobacterial Colonization of Etruscan Paintings – Marta Diaz-Herraiz – Scientific Reports

Food microbiology

Molecular Analysis of Skin Bacterial Assemblages from Codfish and Pollock after Dry-Salted Fish Production – Natalia Pegoraro

Viruses and phages

Infection of phytoplankton by aerosolized marine viruses – Shlomit Sharoni – PNAS

Archaea

The two-domain tree of life is linked to a new root for the Archaea – Kasie Raymann – PNAS

Review: Archaeal Lineages within the Human Microbiome: Absent, Rare or Elusive?
Hans-Peter Horz – Life

Review: The interplay between nucleoid organization and transcription in archaeal genomes – Eveline Peeters – Nature Reviews Microbiology

Metagenomics and bioinformatics

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data – Kathrin P. Aßhauer – Bioinformatics

ProtPhylo: identification of protein–phenotype and protein–protein functional associations via phylogenetic profiling – Yiming Cheng – Nucleic Acids Research

IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data – Adrian Baez-Ortega – Bioinformatics

Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors – Mark B. Smith – mBio

Manuscript: Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant – Andreas Bremges

Review: The integration of sequencing and bioinformatics in metagenomics – Firouz Abbasian – Reviews in Environmental Science and Bio/Technology

Book Chapter: Protocols and Methods for the in Silico Reconstruction of the Origin and Evolution of Metabolic Pathways – Luana Presta – Briefs in Molecular Science 2015

Book Chapter: Molecular Screening of Azurin-Like Anticancer Bacteriocins from Human Gut Microflora Using Bioinformatics – Van Duy Nguyen – Advanced Computational Methods for Knowledge Engineering

Other microbial papers of interest

Bacterial Swarms Recruit Cargo Bacteria To Pave the Way in Toxic Environments – Alin Finkelshtein – mBio

Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association – Gloria Torres-Cortés – PNAS

Perspective: Resilience vs. historical contingency in microbial responses to environmental change – Christine V. Hawkes – Ecology Letters

A tortoise–hare pattern seen in adapting structured and unstructured populations suggests a rugged fitness landscape in bacteria – Joshua R. Nahum – PNAS

Microbes in the news
Can The Microbes You Leave Behind Be Used to Identify You? – Ed Yong – National Geographic

Forbidden Data: Wyoming wants to conceal the fact that many of its streams are contaminated by E. coli bacteria – Slate

UGSG looks at microbiology, chemistry of Pa. fracked wells – Bob Downing – Ohio.com

Chinese breast milk discovery strengthens case for probiotics in infant formula: Chr Hansen – By Mark Astley – Dairy Reporter

Researchers find metabolic link between bacterial ‘biofilms’, colon cancer – Medical Xpress

Accessing the Hidden Kingdom: Fungal ITS Reference Sequences – NCBI Insights
#BacteriaHysteria

Germ City: Bacteria thriving at the makeup counter: 30% of used makeup samples in stores contain bacteria – PIX11

Tests found bacteria on popular single-serve coffeemakers – Your Central Valley

Bik’s Picks

De novo synthesis of a sunscreen compound in vertebrates – Andrew R Osborn – eLIFE

Chemical messages in 170-year-old champagne bottles from the Baltic Sea: Revealing tastes from the past – Philippe Jeandet – PNAS

Unraveling ancient Egypt’s animal mummy mystery: Roughly a third of the animal mummies examined were completely empty – Michael E. Miller – Washington Post

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May 7, 2015

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Events

Human Gut Microbiome and Diseases Congress – 25-26 June 2015, Milano, Italy

Pregnancy and birth microbiome

The Canadian Healthy Infant Longitudinal Development (CHILD) birth cohort study: assessment of environmental exposures – Tim K Takaro – Journal of Exposure Science and Environmental Epidemiology

The Impact of Infancy Antibiotic Intake on Childhood Obesity; Review of Studies – Mohammad Reza Vafa – Advances in Obesity, Weight Management & Control

Human respiratory microbiome

The Host Response to the Lung Microbiome in Chronic Obstructive Pulmonary Disease
Marc A Sze – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Approaches to studying and manipulating the enteric microbiome to improve autism symptoms – Richard E. Frye – Microbial Ecology in Health and Disease

Plant root and soil microbiome

Heading to the Origins – Rice Microbiome as Functional Extension of the Host – Pablo R. Hardoim – Journal of Rice Research

Inoculation of Phaseolus vulgaris with the nodule-endophyte Agrobacterium sp. 10C2 affects richness and structure of rhizosphere bacterial communities and enhances nodulation and growth – Saif-Allah Chihaoui – submitted paper

Biochar in Co-Contaminated Soil Manipulates Arsenic Solubility and Microbiological Community Structure, and Promotes Organochlorine Degradation – Samuel J. Gregory – PLOS ONE

Microbial quality of soil from the Pampa biome in response to different grazing pressures – Rafael S. Vargas – Genetics and Molecular Biology

Built environment microbiome

Dysbiotic drift: mental health, environmental grey space, and microbiota – Alan C Logan – Journal of Physiological Anthropology

Extremophiles

Sub-Ice Microalgal and Bacterial Communities in Freshwater Lake Baikal, Russia – Maria V. Bashenkhaeva – Microbial Ecology

Phages and viruses

Protist predation can select for bacteria with lowered susceptibility to infection by lytic phages – Anni-Maria Örmälä-Odegrip – BMC Evolutionary Biology

Microbial Ecology

Evolutionary ecology of microorganisms: from the tamed to the wild – Jay T Lennon – PeerJ

Metagenomics and bioinformatics

MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation – Yu-Chieh Liao – Journal of Microbiological Methods

PrePrint: Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree – Yu-Qing Qiu – IEEE/ACM Transactions on Computational Biology and Bioinformatics

Metabolomics

Effects of Uremic Toxins from the Gut Microbiota on Bone: A Brief Look at Chronic Kidney Disease – Ana Paula Black – Therapeutic Apheresis and Dialysis

Microbes in the news

Ulcer-causing bacteria induces stomach stem cell growth in mice, researchers find – Stanford Medicine

Newly named bacteria help honey bee larvae thrive – Kim Kaplan – Phys.org

The smell of death: Scientist reveals how 400 compounds mix to create heady mixture of scents as bacteria rips apart rotting flesh – Moheb Costandi – Daily Mail

Eat your vegetables, feed your microbiome – David Charbonneau – EyeViewKamloops

Microbiome Portrait Experiment for High School Students – Tufts

Bacteria redefine reinforced concrete – RSC Advances Blog

Possible role of gut bacteria in autism – Science Daily

Environmental exposures study tracks more than 3,200 Canadian babies – Simon Fraser University

Final Report Summary – TORNADO (Molecular Targets Open for Regulation by the gut flora – New Avenues for improved Diet to Optimize European health) – CORDIS Europa

Measles Vaccination Saves You From More Than Measles – Maggie Fox – NBC News

Microbes and money

‘Gut microbiome’ startup moving to science accelerator, seeks study volunteers: Prince William Science Accelerator – ISOThrive – Inside Nova

UBiome Seeks Academic Partnerships with the Launch of the uBiome Academic Consortium – WDRB

Science, publishing, and career

Science forum: RIPOSTE: a framework for improving the design and analysis of laboratory-based research – Nicholas G D Masca – eLife

Bik’s Picks

Listen To These Eerie ‘X-Files’ Sounds Recorded At The Edge Of Space – Macrina Cooper-White – Huffington Post

Finding That Babies Born at 22 Weeks Can Survive Could Change Abortion Debate – Lucy Westcott – Newsweek

Samantha Cristoforetti: 5 Memorable Moments From the Italian Astronaut’s Time in Space – Alyssa Newcomb – ABC News
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May 4, 2015

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Grant opportunities

Newborn and Infant Gut Health – Application deadline : May 13, 2015 – Bill & Melinda Gates Foundation

Events

Free Webinar: The Human Microbiome: Beyond the Gut – May 5, 2:30 pm ET – The Scientist

General microbiome

Review: Sequencing and beyond: integrating molecular ‘omics’ for microbial community profiling – Eric A. Franzosa – Nature Reviews Microbiology

Reproductive Parasitism: Maternally Inherited Symbionts in a Biparental World
Gregory D.D. Hurst and Crystal L. Frost – Cold Spring Harbor Perspectives in Biology

Human oral microbiome

Editorial: Defining functional signatures of dysbiosis in periodontitis progression
Gary P Wang – Genome Medicine
belongs to:
Functional signatures of oral dysbiosis during periodontitis progression revealed by microbial metatranscriptome analysis – Susan Yost – Genome Medicine

Human gut microbiome

Intestinal dysbiosis in children with short bowel syndrome is associated with impaired outcome – Helene Engstrand Lilja – Microbiome

Intestinal Microbiota Signatures Associated With Histological Liver Steatosis in Pediatric-Onset Intestinal Failure – Katri Korpela – Journal of Parenteral & Enteral Nutrition

Differences of the Fecal Microflora With Clostridium difficile Therapies – Thomas J. Louie – Clinical Infectious Diseases

Review: The human gut resistome – Willem van Schaik – Philosophical Transactions B

Animal models

The intestinal microbiota influences Campylobacter jejuni colonization and extra-intestinal dissemination in mice – Jason L. O’Loughlin – Applied and Environmental Microbiology

Animal microbiome

Fish: Selection in the host structures the microbiota associated with developing cod larvae (Gadus morhua) – Ingrid Bakke – Environental Microbiology

Plant and soil microbiome

Crustose coralline algal species host distinct bacterial assemblages on their surfaces – Jennifer M Sneed – The ISME Journal

Influence of plant communities and soil properties during natural vegetation restoration on arbuscular mycorrhizal fungal communities in a karst region – Yueming Liang – Ecological Engineering

Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape – Florentin Constancias – Microbiology Open

Predictable communities of soil bacteria in relation to nutrient concentration and successional stage, in a laboratory culture experiment – Woojin Song – Environmental Microbiology

Water microbiome

Accumulation of Clinically Relevant Antibiotic Resistant Genes, Bacterial load and Metals from a Freshwater Lake Sediments in Central Europe – Naresh Devarajan – Environmental Science & Technology

Effects of Heavy Metal and Nutrients on Benthic Microbial Communities in Freshwater Sediment of Poyang Lake (China) – Cho Yu – Journal of Residuals Science & Technology

Review: Stream microbial diversity responds to environmental changes: Review and synthesis of existing research – Lydia Zeglin – Frontiers in Microbiology

Built environment microbiome

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

Bioreactor microbiology

Bacterial community structure in treated sewage sludge with mesophilic and thermophilic anaerobic digestion – Hana Stiborova – Folia Microbiologica

Performance and microbial community dynamics in bioaugmented aerated filter reactor treating with coking wastewater – Shengnan Shi – Bioresource Technology

Phages and viruses

My life with Mu – Ariane Toussaint – Bacteriophage

Fungi

Fungal artificial chromosomes for mining of the fungal secondary metabolome – Jin Woo Bok – BMC Genomics

Review: The Human Mycobiome – Patrick C. Seed – Cold Spring Harbor Perspectives in Medicine

Antibiotic resistance

Antibiotic resistance genes in the environment: prioritizing risks – Johan Bengtsson-Palme & D. G. Joakim Larsson – Nature Reviews Microbiology

Review: The human gut resistome – Willem van Schaik – Philosophical Transactions B

Metagenomics

Under-detection of endospore-forming Firmicutes in metagenomic data – Sevasti Filippidou – Computational and Structural Biotechnology Journal

Microbes in the news

Each Vineyard Has a Unique Microbiome – University of Chicago – The Epoch Times

Viruses: You’ve heard the bad; here’s the good – American Society for Microbiology – Science Daily

Silver turns bacteria into deadly zombies – Emily Conover – Science Magazine

Rare plague outbreak in Colorado linked to pit bull, CDC says – CNN Wire

Science, publishing, and career

A time limit on postdoctoral contracts: The French experience – Elisabeth Pain – Science Careers

Follow the Funding – Bob Grant – The Scientist

Women Scientists Share Their Awful Stories Of Sexism In Publishing – Cat Ferguson – BuzzFeed Science

Science and art

The Microbiome Votes: I mixed my microbiome with the candidates and asked them to vote – Exploring the Invisible

Bik’s Picks

Horribly bleak study sees ‘empty landscape’ as large herbivores vanish at startling rate – Fred Barbash and Justin Wm. Moyer – Washington Post

Here’s How Coffee Cups in Space Could Help Save Lives on Earth – Helen Regan – Time

Why Hawaiians are protesting construction of the world’s second-largest telescope – Joseph Stromberg – Vox.com

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