Category Archives: Human oral

March 8, 2016

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A very special edition of Bik’s Picks on this International Women’s Day: Soil decomposition on Mount Kilimanjaro, genome of a Ruminococcus associated with IBS, survival of microbes during the digestion of cheese.

Human oral microbiome

Editorial: Oral Biofilm Architecture at the Microbial Scale – Maria D. Ferrer – Trends in Microbiology

Human reproductive tract microbiome

Cervical Microbiota Associated with Risk of Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses – Chandrika J Piyathilake – Cancer Prevention Research

Human gut microbiome

Isolation and whole genome sequencing of a Ruminococcus-like bacterium, associated with irritable bowel syndrome – Ulla Hynönen – Anaerobe

Opinion: Gut microbiota impact on stroke outcome: Fad or fact? – Katarzyna Winek – J Cereb Blood Flow Metab

Review: Mechanisms linking the gut microbiome and glucose metabolism – Kristina M Utzschneider – J Clin Endocrinol Metab

Review: Gut Microbiome and Kidney Disease in Pediatrics: Does Connection Exist? – Tetyana L. Vasylyeva – Frontiers in Microbiology

Review: The complex interplay of diet, xenobiotics, and microbial metabolism in the gut: Implications for clinical outcomes – Mariia Taguer – Clinical Pharmacology & Therapeutics

Review: Obesity and Asthma: Microbiome-metabolome Interactions – Stephanie A Shore – American Journal of Respiratory Cell and Molecular Biology

Animal models

Gut Microbiota-Induced Immunoglobulin G Controls Systemic Infection by Symbiotic Bacteria and Pathogens – Melody Y. Zeng – Immunity

Plant, root, and soil microbiome

Methodological Guidelines for Accurate Detection of Viruses in Wild Plant Species – Christelle Lacroix – Applied and Environmental Microbiology

Rice bacterial endophytes: isolation of a collection, identification of beneficial strains and microbiome analysis – Iris Bertani – Environmental Microbiology

Sulfur Fertilization Changes the Community Structure of Rice Root-, and Soil-Associated Bacteria – Sachiko Masuda – Microbes and Environments

Do shifts in life strategies explain microbial community responses to increasing nitrogen in tundra soil? – Minna Männistö – Soil Biology and Biochemistry

Temperature sensitivity and enzymatic mechanisms of soil organic matter decomposition along an altitudinal gradient on Mount Kilimanjaro – Еvgenia Blagodatskaya – Scientific Reports

Influence of pesticide seed treatments on rhizosphere fungal and bacterial communities and leaf fungal endophyte communities in maize and soybean – Rachel Nettles – Applied Soil Ecology

Forest understory plant and soil microbial response to an experimentally induced drought and heat-pulse event: the importance of maintaining the continuum – Isabell von Rein – Global Change Biology

Water and extremophile microbiome

Abundance and Biogeography of Picoprasinophyte Ecotypes and Other Phytoplankton in the Eastern North Pacific Ocean – Melinda P. Simmons – Applied and Environmental Microbiology

Metagenomic 16s rrna investigation of microbial communities in the Black Sea estuaries in South-West of Ukraine – Oleksandra Bobrova – Acta Biochimica Polonica

Waste and pollution microbiology

Contaminant-Degrading Microorganisms Identified Using Stable Isotope Probing – Alison M. Cupples – Chemical Engineering & Technology

Food microbiology

Survival of lactic acid and propionibacteria in low- and full-fat Dutch-type cheese during human digestion Ex vivo – Aleksandra Martinovic – Letters in Applied Microbiology

Metagenomics and bioinformatics

Review: Targeted metagenomics of active microbial populations with stable-isotope probing -Sara Coyotzi – Current Opinion in Biotechnology

Infection and microbiology

Diagnosis of Bacterial Bloodstream Infections: A 16S Metagenomics Approach – Saskia Decuypere – PLOS Neglected Tropical Diseases

Microbes in the news

Fibre and protein enhance gut bacteria in children – Malene Sommer Christiansen – Science Nordic

Extreme Microbiome Project Aims to Characterize Microbes Living in Harsh Environments – Monica Heger – Genome Web

UTI bacteria use hooks to hang on inside you when you pee – Clare Wilson – New Scientist

Science, publishing and career

Statistical significance and its part in science downfalls – Hilda Bastian – PLOS Blogs

Microbiology and Nature in Video Games – Alex Alexiev – MicroBEnet

Tricon2016: The Microbiome: Sorting Out the Hype from the Hope – Bonnie Feldman – Storify

Leap day, giant viruses, and gene-editing – Dawn Field – Oxford University Press blog
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March 7, 2016

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Back to our regular program…. Today I’ve included papers on the antibiotic resistome in preterm infants, or in soils, the salt-loving Tamarix, and a critical article about the Microbiome Summit in Forbes.

Pregnancy and birth

Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome – Molly K. Gibson – Nature Microbiology

Human oral microbiome

Microbial Diversity in the Early In Vivo-Formed Dental Biofilm – D. Heller – Applied and Environmental Microbiology

Animal models

Effect of dietary protein sources on the small intestine microbiome of weaned piglets based on high-throughput sequencing – Kefei Cao – Letters in Applied Microbiology

Plant, root, and soil microbiome

Appearance of β-lactam Resistance Genes in Agricultural Soils and Clinical Isolates over the 20th Century – David W. Graham – Scientific Reports

Functional redundancy of linuron degradation in microbial communities of agricultural soil and biopurification systems – Benjamin Horemans – Applied and Environmental Microbiology

Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree – Omri M. Finkel – Applied and Environmental Microbiology

Microbial and Functional Diversity within the Phyllosphere of Espeletia Species in an Andean High-Mountain Ecosystem – Carlos A. Ruiz-Pérez – Applied and Environmental Microbiology

Water and extremophile microbiome

Prokaryotic Community Structure Driven by Salinity and Ionic Concentrations in Plateau Lakes of the Tibetan Plateau – Zhi-Ping Zhong – Applied and Environmental Microbiology

Functional responses of salt marsh microbial communities to long-term nutrient enrichment – Christopher J. Graves – Applied and Environmental Microbiology

Waste, pollution, and bioreactor microbiology

Dynamics of size-fractionated bacterial communities during the coastal dispersal of treated municipal effluents – SiGuang Liu – Applied Microbiology and Biotechnology

Biological Nitrogen Removal in a Photosequencing Batch Reactor with an Algal-Nitrifying Bacterial Consortium and Anammox Granules – Nathan D. Manser – Environmental Science & Technology Letters

Microbes in the news (notice 3 articles on antibiotic resistance from EurekAlert)

Preemies’ gut bacteria reveal vast scope of antibiotic resistance – Washington University School of Medicine – EurekAlert

Antibiotics use affects the abundance of resistant bacteria in soil – Aarhus University – EurekAlert

Daily dose of antibiotics helps bacteria develop multi-drug tolerance – KU Leuven – EurekAlert

Microbiome Monday: The Top Three Questions from Visitors – AMNH

Bacteria-laden mosquitoes can control Zika – Zeenews India

Microbes and art

BioArt : What is our True Relationship with the Human Microbiome? – Labiotech
After every 50 handshakes his assistants (white lab coats) would swab his palms, to use for later analysis of the collective microbiome.

Growing fungus and bacteria on textiles for fashion – Yuliasri Perdani – Jakarta Post

Science, publishing, and career

A critical view of the Microbiome Medicine Summit: Keep Calm And Avoid Microbiome Mayhem – Kavin Senapathy – Forbes

Everything Is Crumbling: An influential psychological theory, borne out in hundreds of experiments, may have just been debunked. How can so many scientists have been so wrong? – Daniel Engber – Slate

Not just #creatorgate: Most scandalous retractions in science – SBS

Conferences on Weekends? Good or Bad Idea? Summary of responses to query .. – Jonathan Eisen – Phylogenomics

March 5, 2016

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Lung microbes in Cystic Fibrosis, microbiota of reindeer, strawberry phyllosphere, and microbes in raindust.

Pregnancy and birth

Dynamics of Gut Microbiota According to the Delivery Mode in Healthy Korean Infants – Eun Lee- Allergy Asthma Immunol Res.

Review: Respiratory Microbiome of New-Born Infants – David J. Gallacher – Frontiers in Pediatrics

Review: Bosom Buddies: The Symbiotic Relationship Between Infants and Bifidobacterium longum ssp. longum and ssp. infantis. Genetic and Probiotic Features – Silvia Arboleya – Annual Review of Food Science and Technology

Review: Maternal microbiome – A pathway to preterm birth – Angela E. Vinturache – Seminars in Fetal and Neonatal Medicine

Human respiratory microbiome

Analysis of Lung Microbiota in Bronchoalveolar Lavage, Protected Brush and Sputum Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease – Deborah A. Hogan – PLOS ONE

Human oral microbiome

Levels of Candidate Periodontal Pathogens in Subgingival Biofilm – R.R.D.S Oliveira – Journal of Dental Research

Human gut microbiome

Effects of plant stanol ester consumption on fasting plasma oxy(phyto)sterol concentrations as related to fecal microbiota characteristics – Sabine Baumgartner – The Journal of Steroid Biochemistry and Molecular Biology

Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients – Forbes, Jessica D. – Inflammatory Bowel Diseases

Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis – Ohad Manor – Scientific Reports

Research highlight: Growth impairment in undernourished children – Claire Greenhill – Nature Reviews Endocrinology

Review: Elucidating the role of the host genome in shaping microbiome composition – Emily R. Davenport – Gut Microbes

Review: The Microbiome: A Key Regulator of Stress and Neuroinflammation – Kieran Rea – Neurobiology of Stress

Review: The Brain-Gut-Microbiome Axis: What Role Does it Play in Autism Spectrum Disorder? – Ruth Ann Luna – Current Developmental Disorders Reports

Review: Microbes and the Mind: Emerging Hallmarks of the Gut Microbiota-Brain Axis – Kylynda C. Bauer – Cellular Microbiology

Review: The human gut microbiome and its dysfunctions through the meta-omics prism – Stanislas Mondot – Annals of the New York Academy of Sciences

Animal models

Age, introduction of solid feed and weaning are more important determinants of gut bacterial succession in piglets than breed and nursing mother as revealed by a reciprocal cross-fostering model – Gaorui Bian – Environmental Microbiology

Effects of environmental temperature on the gut microbial communities of tadpoles – Kevin D. Kohl – Environmental Microbiology

Apple-Derived Pectin Modulates Gut Microbiota, Improves Gut Barrier Function, and Attenuates Metabolic Endotoxemia in Rats with Diet-Induced Obesity – Tingting Jiang – MDPI Nutrients

The effects of fecal microbial transplantation on microbiome and immunity in SIV-infected macaques – Tiffany Hensley-McBain – Journal of Virology

Soy Protein Compared with Milk Protein in a Western Diet Increases Gut Microbial Diversity and Reduces Serum Lipids in Golden Syrian Hamsters – Dustie N Butteiger – Journal of Nutrition

Review: The interplay between intestinal bacteria and host metabolism in health and disease: lessons from Drosophila melanogaster – Adam C. N. Wong – Disease Models & Mechanisms

Animal microbiome

New Insights into the Microbiota of the Svalbard Reindeer Rangifer tarandus platyrhynchus – Sylwia Zielińska – Frontiers in Microbiology

Geographically conserved microbiomes of four temperate water tunicates – Patrick L. Cahill – Environmental Microbiology Reports

Twenty five new viruses associated with the Drosophilidae (Diptera) – Claire L Webster – bioRxiv

Plant, root, and soil microbiome

Soil Microbial Community Interactions Under Tillage Systems in Australia – Vivian A. Rincon-Florez – Plant, Soil and Microbes

Variation of Bacterial Community Diversity in Rhizosphere Soil of Sole-Cropped versus Intercropped Wheat Field after Harvest – Zhenping Yang – PLOS ONE

Dispersal of Bacillus subtilis and its effect on strawberry phyllosphere microbiota under open field and protection conditions – Feng Wei – Scientific Reports

Temporally Variable Geographical Distance Effects Contribute to the Assembly of Root-Associated Fungal Communities – Christopher J. Barnes – Frontiers in Microbiology

Elevation gradient of soil bacterial communities in bamboo plantations – Yu-Te Lin – Botanical Studies

Soil microbial functional capacity and diversity in a millet-shrub intercropping system of semi-arid Senegal – S. Diakhaté – Journal of Arid Environments

Bioaugmentation of microbes to restore coastal wetland plants to protect land from coastal erosion – Regina Bledsoe – International Biodeterioration & Biodegradation

Review: Nutrient scavenging activity and antagonistic factors of non-photobiont lichen-associated bacteria: a review – M. Auður Sigurbjörnsdóttir – World Journal of Microbiology and Biotechnology

Water, rain, and extremophile microbiome

Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin – Silke Langenheder – Environmental Microbiology Reports

Comparative summer dynamics of surface cyanobacterial communities in two connected lakes from the west of Ireland – N. Touzet – Science of The Total Environment

Dust Rains Deliver Diverse Assemblages of Microorganisms to the Eastern Mediterranean – Ghida Nouhad Itani – Scientific Reports

Protistan diversity and activity inferred from RNA and DNA at a coastal ocean site in the eastern North Pacific – Sarah K. Hu – FEMS Microbiology Ecology

A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge – Julie L. Meyer – Scientific Reports

Biodigester microbiology

This one sounded wrong: Microbial diversity in an anaerobic digester with biogeographical proximity to geothermal active region – Rishi Mahajan – Environmental Technology

Food microbiology

Impact of mulches and growing season on indicator bacteria survival during lettuce cultivation – Aixia Xu – International Journal of Food Microbiology

Built environment microbiology

Seasonal Dynamics of the Airborne Bacterial Community and Selected Viruses in a Children’s Daycare Center – Aaron J. Prussin II – PLOS ONE

Bioweathering Potential of Cultivable Fungi Associated with Semi-Arid Surface Microhabitats of Mayan Buildings – Benjamín O. Ortega-Morales – Frontiers in Microbiology

Microbiome of death

Review: The Thanatomicrobiome: A Missing Piece of the Microbial Puzzle of Death – Gulnaz T. Javan – Frontiers in Microbiology

Waste and pollution microbiology

Isolation and characterization of yeasts associated with plants growing in heavy-metal- and arsenic-contaminated soils – Juan Ramos-Garza – Canadian Journal of Microbiology

Review: Understanding the development of environmental resistance among microbes: A Review – Jatin Srivastava – CLEAN – Soil, Air, Water

Review: Microbial communities, processes and functions in acid mine drainage ecosystems – Lin-xing Chen – Current Opinion in Biotechnology

Infection microbiology

Absence of Serological Evidence of Rickettsia spp., Bartonella spp., Ehrlichia spp. and Coxiella burnetii Infections in American Samoa – Colleen Lau – Ticks and Tick-borne Diseases

Comparison between a Broad-Range Real-Time and a Broad-Range End-Point PCR Assays for the Detection of Bacterial 16S rRNA in Clinical Samples – Mariam Meddeb – Annals of Clinical & Laboratory Science

Metagenomics and bioinformatics

Capturing the most wanted taxa through cross-sample correlations – Mathieu Almeida – The ISME Journal

MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation
Gabriele Andrea Lugli – FEMS Microbiology Letters

Sequence techniques

Microbial Ecology in the Era of Next Generation Sequencing – Surajit De Mandal – Omics: Next Generation: Sequencing & Applications

Microbial Ecology

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes? – Emily B. Graham – Frontiers in Microbiology

Microbes in the news

Would you try to vaginally “seed” your baby’s microbiome after a C-section – Jonathan Eisen – The Tree of Life

Science, publishing, and career

This Paper Should Not Have Been Retracted: #HandofGod highlights the worst aspects of science twitter – Andrew David Thaler – Southern Friend Science

The “Creator” paper, Post-pub Peer Review, and Racism Among Scientists – Dr24hours – Complex Roots

UC reclassifies master’s degrees, charges elevated tuition – Nanette Asimov – SF Chronicle

She Wanted to Do Her Research. He Wanted to Talk ‘Feelings.’ – A. Hope Jahren – NY Times

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March 4, 2015

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Long term use of protein pump inhibitors, bovine genetics and microbial methane, fungi for biodegradation, Bayesian fingerprinting.

Human oral microbiome

Impact of smoking on experimental gingivitis. A clinical, microbiological and immunological prospective study – D. C. Peruzzo – Journal of Periodontal Research

Human gut microbiome

A comparison of the gut microbiome between long-term users and non-users of proton pump inhibitors – A. G. Clooney – Alimentary Pharmacology & Therapeutics

Animal microbiome

Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance – Rainer Roehe – PLOS Genetics

When Parasites Are Good for Health: Cestode Parasitism Increases Resistance to Arsenic in Brine Shrimps – Marta I. Sánchez – PLOS Pathogens

Plant, root, and soil microbiome

A New Perspective on Sustainable Soil Remediation—Case Study Suggests Novel Fungal Genera Could Facilitate in situ Biodegradation of Hazardous Contaminants – Lauren M. Czaplicki – Remediation Journal

Fungal effects on plant–plant interactions contribute to grassland plant abundances: evidence from the field – Jonathan A. Bennett – Journal of Ecology

Status of microbial diversity in agroforestry systems in Tamil Nadu, India – Srinivasan Radhakrishnan – Journal of Basic Microbiology

Water microbiome

Microfungi Potentially Pathogenic for Humans Reported in Surface Waters Utilized for Recreation – Anna Biedunkiewicz – CLEAN – Soil, Air, Water

Waste and pollution microbiology

Bait and scrape: An approach for assessing biofilm microbial communities on organic media used for gas-phase biofiltration – Jason P. Oliver – Ecological Engineering

Food microbiology

Review: Microbial Safety of Wood in Contact with Food: A Review – Florence Aviat – Comprehensive Reviews in Food Science and Food Safety

Bioinformatics

Species Identification by Bayesian Fingerprinting: A Powerful Alternative to DNA Barcoding – Ziheng Yang – BioRxiv

blastjs: a BLAST+ wrapper for Node.js – Martin Page – BMC Research Notes

Microbes in the news

uBiome Investigates Health Implications of Seniors’ Changing Microbiomes, Seeks Participants – Benzinga

Mystery bacteria linked to 18 deaths in Wisconsin – CBS News

Includes Pat Schloss: 78 Fellows Elected to the American Academy of Microbiology – ASM

Science, publishing, and career

A Science Journal Invokes ‘the Creator,’ and Science Pushes Back – Madison Kotack – Wired

PLOS ONE retracting paper that cites “the Creator” – Alison McCook – Retraction Watch

#IAmAResearchParasite – Marcia McNutt – Science

Making a game of science – Elizabeth Pennisi – Science

Yes, Even CRISPR Pioneer Jennifer Doudna Experiences Gender Bias – Lisa Potter and Jon Brooks – KQED

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March 3, 2016

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Gut microbiome of Indian Nicobarese tribe, CDI patients’ stories about life before and after stool transplants, cryptic species in Nematoda, and similar fungi at opposite poles.

Pregnancy and birth

Review: The Developing Microbiome of the Preterm Infant – Mara E. DiBartolomeo – Clinical Therapeutics

Gut colonization by aerobic microorganisms is associated with route and type of nutrition in premature neonates – Ülle Parm – Nutrition Research

Human oral microbiome

Influence of a triclosan toothpaste on periodontopathic bacteria and periodontitis progression in cardiovascular patients: a randomized controlled trial – G. J. Seymour – Journal of Periodontal Research

Human respiratory microbiome

Review: Microbes and asthma: Opportunities for intervention – Hermelijn H. Smits – Journal of Allergy and Clinical Immunology

Understanding Persistent Bacterial Lung Infections: Clinical Implications Informed by the Biology of the Microbiota and Biofilms – Alexa A. Pragman – Clinical Pulmonary Medicine

Human gut microbiome

Elucidating the richness of bacterial groups in the gut of nicobarese tribal community – Perspective on their lifestyle transition – Maile Anwesh – Anaerobe

Resistant potato starches (type 4 RS) exhibit varying effects on laxation with and without phylum level changes in microbiota: A randomised trial in young adults – W.J. Dahl – Journal of Functional Foods

Recommended: Fecal microbiota transplantation for recurrent Clostridium difficile infection: The patient experience – Amy L. Pakyz – American Journal of Infection Control

Analysis of Gut Microbiome Reveals Significant Differences Between Men with Chronic Prostatitis/Chronic Pelvic Pain Syndrome and Controls – Daniel A. Shoskes – The Journal of Urology

RiMINI – the influence of rifaximin on minimal hepatic encephalopathy (MHE) and on the intestinal microbiome in patients with liver cirrhosis: study protocol for a randomized controlled trial – Christian Schulz – BMC Trials

Editorial: Dysbiosis in fungal microbiota in IBD – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Models of microbiome research

Functional characterization of inflammatory bowel disease-associated gut dysbiosis in gnotobiotic mice – Hiroko Nagao-Kitamoto – CMGH Cellular and Molecular Gastroenterology and Hepatology

Effect of breast feeding time on physiological, immunological and microbial parameters of weaned piglets in an intensive breeding farm – G.R. García – Veterinary Immunology and Immunopathology

Animal microbiome

Prevalence of potential nitrogen-fixing, green sulfur bacteria in the skeleton of reef-building coral Isopora palifera – Shan-Hua Yang – Limnology and Oceanography

An investigation of the microbiota in uterine flush samples and endometrial biopsies from dairy cows during the first 7 weeks postpartum – Lif Rødtness Vesterby Knudsen – Theriogenology

Coexisting cryptic species of the Litoditis marina complex (Nematoda) show differential resource use and have distinct microbiomes with high intraspecific variability – S Derycke – Molecular Ecology

Hologenome analysis of two marine sponges with different microbiomes – Taewoo Ryu – BMC Genomics

Plant, root, and soil microbiome

Land use change in the Amazon rainforest favors generalist fungi – Rebecca C Mueller – Functional Ecology

Drivers of phosphorus limitation across soil microbial communities – Petr Čapek – Functional Ecology

Effects of changes in straw chemical properties and alkaline soils on bacterial communities engaged in straw decomposition at different temperatures – Guixiang Zhou – Scientific Reports

Soil pH is a Key Determinant of Soil Fungal Community Composition in the Ny-Ålesund Region, Svalbard (High Arctic) – Tao Zhang – Frontiers in Microbiology

Diversity of endophytic fungal and bacterial communities in Ilex paraguariensis grown under field conditions – María Laura Pérez – World Journal of Microbiology and Biotechnology

Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches – Steven D. Leavitt – Scientific Reports

Rhizosphere competence of wild-type and genetically-engineered Pseudomonas brassicacearum is affected by the crop species – Stacey Blouin Bankhead – Phytopathology

Actinorhizal Alder Phytostabilization Alters Microbial Community Dynamics in Gold Mine Waste Rock from Northern Quebec: A Greenhouse Study – Katrina L. Callender – PLOS ONE

Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs – A. Ö. C. Dupont – Environmental Microbiology

Water and extremophile microbiome

Diazotroph community structure in the deep oxygen minimum zone of the Costa Rica Dome – Shunyan Cheung – Journal of Plankton Research

Not poles apart: Antarctic soil fungal communities show similarities to those of the distant Arctic – Filipa Cox – Ecology Letters

Food microbiology

Salmonella in Shell Eggs: Mechanisms, Prevention and Detection – Seockmo K – Omics Journal of Nutrition & Food Sciences

Intensive aquaculture selects for increased virulence and interference competition in bacteria – Lotta-Riina Sundberg – Proceedings of the Royal Society B

Application of electrolyzed oxidizing water in production of radish sprouts to reduce natural microbiota – Chunling Zhang – Food Control

Biodiversity of culturable psychrotrophic microbiota in raw milk attributable to refrigeration conditions, seasonality and their spoilage potential – Nuwan R. Vithanage – International Dairy Journal

Microbiological characteristics of fresh tofu produced in small industrial scale and identification of specific spoiling microorganisms (SSO) – Franca Rossi – LWT – Food Science and Technology

Built Environment and Waste Microbiome

The efficacy of disinfectants in the decontamination of dental unit water lines: an in vitro laboratory study – Mrudula Patel – BDJ Open

Review: Bacterial communities in full-scale wastewater treatment systems – Agnieszka Cydzik-Kwiatkowska – World Journal of Microbiology and Biotechnology

Preferential methanogenic biodegradation of short-chain n-alkanes by microbial communities from two different oil sands tailings ponds – Mohd Faidz Mohamad Shahimin – Science of The Total Environment

Microbes in space

Two older papers that showed up in my PubMed alert today:
Review: The Significance of Microbe-Mineral-Biomarker Interactions in the Detection of Life on Mars and Beyond – Wilfred F.M. Röling – Astrobiology
Microbial Ecology of a Crewed Rover Traverse in the Arctic: Low Microbial Dispersal and Implications for Planetary Protection on Human Mars Missions – Andrew C. Schuerger – Astrobiology

Phages and viruses

Diversity of phage infection types and associated terminology: the problem with “Lytic or Lysogenic” – Zack Hobbs – FEMS Microbiology Letters

Techniques

Effect of Freezing Conditions on Fecal Bacterial Composition in Pigs – Barbara U. Metzler-Zebeli – MDPI Animals

Microbes in the news

Astronaut Scott Kelly back on earth, Northwestern profs celebrate – Chicago Sun Times

Microbial Manifesto: The Global Push to Understand the Microbiome (Kavli Roundtable) – Alan Brown – Live Science

‘Gut’ bacteria may help put a kink in family obesity cycle – Science Codex

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March 1, 2016

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Colonization of the mouth in babies, biofilm in dinosaur bone, lichen symbiosis, microbial forensics, horse stool transplants, and ViromeScan.

Pregnancy and birth

Probiotic Supplementation and Late-Onset Sepsis in Preterm Infants: A Meta-analysis – Shripada C. Rao – Pediatrics

Early colonization of the oral cavity in 6- and 12-month-old infants by cariogenic and periodontal pathogens: a case-control study – Vlasta Merglova – Folia Microbiologica

Review: Perinatal nutrition: How to Take Care of the gut microbiota? – Izaskun García-Mantrana – Clinical Nutrition Experimental

Human skin microbiome

Antagonism between Staphylococcus epidermidis and Propionibacterium acnes and its genomic basis – Gitte J. M. Christensen – BMC Genomics

Human oral microbiome

Bacterial community shifts during healing of palatal wounds: comparison of two graft harvesting approaches – Suzanne L. Delima – Journal of Clinical Periodontology

Human gut microbiome

Innate Sensing of the Gut Microbiota: Modulation of Inflammatory and Autoimmune Diseases – Aline Ignacio – Frontiers in Immunology

Does the intestinal microbial community of Korean Crohn’s disease patients differ from that of western patients? – Chang Soo Eun – BMC Gastroenterology

Review: Gut Microbiota Modification: Another Piece in the Puzzle of the Benefits of Physical Exercise in Health? – Begoña Cerdá – Frontiers in Physiology

Editorial: The Microbiome in Critical Illness: Firm Conclusions or Bact to Square One?
John D. Lyons – Digestive Diseases and Sciences

Editiorial: Posttraumatic Stress Disorder Does the Gut Microbiome Hold the Key? –
Sophie Leclercq – Canadian Journal of Psychiatry

Animal models of microbiome research

Cognitive Impairment by Antibiotic-Induced Gut Dysbiosis: Analysis of Gut Microbiota-Brain Communication – Esther E. Fröhlich – Brain, Behavior, and Immunity

Epigenome-Microbiome crosstalk: A potential new paradigm influencing neonatal susceptibility to disease – Rene Cortese – Epigenetics

Animal microbiome

Testing the Hypothesis of Biofilm as a Source for Soft Tissue and Cell-Like Structures Preserved in Dinosaur Bone – Mary Higby Schweitzer – PLOS ONE

The holobiont concept: the case of xylophagous termites and cockroaches – Mercedes Berlanga – Symbiosis

Termites: Characterization of the Core and Caste-Specific Microbiota in the Termite, Reticulitermes flavipes – Jacquelynn Benjamino – Frontiers in Microbiology

The sea cucumber microbiome is so hot right now: Individual Apostichopus japonicus fecal microbiome reveals a link with polyhydroxybutyrate producers in host growth gaps – Yohei Yamazaki – Scientific Reports

Gut bacterial communities across tadpole ecomorphs in two diverse tropical anuran faunas – Miguel Vences – The Science of Nature

Review: Equine faecal microbiota transplant: Current knowledge, proposed guidelines and future directions – K. R. Mullen – Equine Veterinary Education

Plant, root, and soil microbiome

Differential Response of Potato Toward Inoculation with Taxonomically Diverse Plant Growth Promoting Rhizobacteria – Tahir Naqqash – Frontiers in Plant Science

Disentangling the relative importance of host tree community, abiotic environment, and spatial factors on ectomycorrhizal fungal assemblages along an elevation gradient – Shunsuke Matsuoka – FEMS Microbiology Ecology

Changes of soil microbial community under different degraded gradients of alpine meadow – Yaoming Li – Agriculture, Ecosystems & Environment

Responses of Soil Fungal Populations and Communities to the Thinning of Cryptomeria Japonica Forests – Wan-Rou Lin – Microbes and Environments

Land-Cover Legacy Effects on Arbuscular Mycorrhizal Abundance in Human and Wildlife Dominated Systems in Tropical Savanna – Geofrey E. Soka – Advances in Ecology

Response of Soil Microbial Properties to Long-Term Application of Organic and Inorganic Amendments in a Tropical Soil (Saria, Burkina Faso) – Ndeye Hélène Diallo-Diagne – OJSS

Microspatial variability in community structure and photophysiology of calcified macroalgal microbiomes revealed by coupling of hyperspectral and high-resolution fluorescence imaging – R. G. Perkin – Scientific Reports

Lichen: Understanding Microbial Multi-Species Symbioses – Ines A. Aschenbrenner – Frontiers in Microbiology

Water and extremophile microbiome

Protist metabarcoding and environmental biomonitoring: time for change – J. Pawlowski – European Journal of Protistology

Biogeochemical and microbial variation across 5500 km of Antarctic surface sediment implicates organic matter as a driver of benthic community structure – Deric R. Learman – Frontiers in Microbiology

Book Chapter: Life in the Anoxic Sub-Seafloor Environment: Linking Microbial Metabolism and Mega Reserves of Methane Hydrate – Varsha Honkalas – Advances in Biochemical Engineering/Biotechnology

Waste and pollution microbiology

Potential Impacts of PCBs on Sediment Microbiomes in a Tropical Marine Environment – James S. Klaus – MDPI J. Mar. Sci. Eng.

Microbial Community Structure of Activated Sludge in Treatment Plants with Different Wastewater Compositions – Nataliya M. Shchegolkova – Frontiers in Microbiology

Food microbiology

Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate – Francesca De Filippis – Scientific Reports

Forensic microbiology

Review: Expansion of Microbial Forensics – Sarah E. Schmedes – Journal of Clinical Microbiology

Bioinformatics, viruses, metagenomics

ViromeScan: a new tool for metagenomic viral community profiling – Simone Rampelli – BMC Genomics

MIMIVIRE is a defence system in mimivirus that confers resistance to virophage – Anthony Levasseur – Nature

More microbiology

Culture-independent method for identification of microbial enzyme-encoding genes by activity-based single-cell sequencing using a water-in-oil microdroplet platform – Kazuki Nakamura – Scientific Reports

Expanding the Diet for DIET: Electron Donors Supporting Direct Interspecies Electron Transfer (DIET) in Defined Co-Cultures – Li-Ying Wang – Frontiers in Microbiology

Microbes and infection

Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts – Liang Ma – Nature Communications

Microbes in the news

NASA’s lab rat: What astronaut Scott Kelly’s year in space can teach us – Sharon Begley – STAT news

Video: Bacteria Can Be Your Best Friend, interview with Ned Ruby and Margaret McFall-Ngai – ThinkTech Hawaii

Inside the secret defense systems of giant viruses – Carl Zimmer – STATnews

How Gut Microbiota Impacts HIV Disease. A new understanding of the role gut microbiota plays in HIV disease is beginning to emerge, suggesting potential new strategies to manage the infection – Bob Roehr – Scientific American

The Case of the Missing Microbes – Kevin Bonham – Scientific American

Faecal transplants could be useful in treating diarrhoea in horses – review – Horse Talk

Antibiotic use in preschoolers alters intestinal microbiome, increases disease risk – Healio

Altering the Gut Microbiome with Early Life Exercise – HCP Live

Obstructive sleep apnea raises hypertension risk, a possible link with gut bacteria: Study– Devon Andre – Belmarra Health

Tipping the Balance in Microbiome Standoffs.The Human Microbiome May Dispose Us toward Health or Illness On The Basis Of Tiny Shifts in Microbial Subpopulations – MaryAnn Labant – GenEngNews

Fighting Infections with Viruses, as Antibiotics Fail – NewsMax

HU develops Jerusalem sewage viruses to kill off resistant dental bacteria – Jerusalem Post

Turning bacteria into ‘SWARMBOTS’: Groups of microbes could be engineered to help combat harmful bugs in the gut – Daily Mail

Bacteria or Virus? New Tests May Identify What’s Causing Your Infection – The Wall Street Journal

Science, publishing, and career

I’m quoted here too: Blatt is back: “open debate cornerstone of scientific process” – Leonid Schneider- For Better Science

An introvert goes conferencing – Strategies to cope – Stephen B Heard – Scientist Sees Squirrel

Bik’s Picks

Ever Wonder What a Neanderthal Considered a Delicacy? – Erika Engelhaupt – National Geographic

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February 26, 2016

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IVF outcomes, large oral microbiota study, Pygmies and Bantu, GF animal models, correlation detection strategies, and sashimi in Portugal.

General microbiome

Opinion: Manipulating Bacterial Communities by in situ Microbiome Engineering – Ravi U. Sheth – Trends in Genetics

Pregnancy and birth

Transition from infant- to adult-like gut microbiota – E. Avershina – Environmental Microbiology

Abnormal vaginal microbiota may be associated with poor reproductive outcomes: A prospective study in IVF patients – T. Haahr – Human Reproduction

Human oral microbiome

Bacterial diversity in saliva and oral health-related conditions: the Hisayama Study – Toru Takeshita – Scientific Reports

Human gut microbiome

Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns – Andres Gomez – Cell Reports

Inflammatory Bowel Disease Affects the Outcome of Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection – Alexander Khoruts – Clinical Gastroenterology and Hepatology

Gut microbiota composition and relapse risk in pediatric MS: A pilot study – Helen Tremlett – Journal of the Neurological Sciences

Analysis of Gastric Microbiota by Pyrosequencing: Minor Role of Bacteria Other Than Helicobacter pylori in the Gastric Carcinogenesis – Hyun Jin Jo – Helicobacter

Review: Crohn’s Disease: Evolution, Epigenetics, and the Emerging Role of Microbiome-Targeted Therapies – Ersilia M. DeFilippis – Current Gastroenterology Reports

Review: Immune recognition and response to the intestinal microbiome in type 1 diabetes – Alexandra Paun – Journal of Autoimmunity

Review: Intestinal microbiota: from sequencing to function – Julia-Stefanie Frick – International Journal of Medical Microbiology

Models of microbiome research

Growing up in a Bubble: Using Germ-Free Animals to Assess the Influence of the Gut Microbiota on Brain and Behaviour – Pauline Luczynski – International Journal of Neuropsychopharmacology

Vancomycin treatment alters humoral immunity and intestinal microbiota in an aged mouse model of Clostridium difficile infection – Edward van Opstal – The Journal of Infectious Diseases

Culex quinquefasciatus larval microbiomes vary with instar and exposure to common wastewater contaminants – Marcus J. Pennington – Scientific Reports

Microbial succession in response to pollutants in batch-enrichment culture – Shuo Jiao – Scientific Reports

Manipulation of the gut microbiota using resistant starch is associated with protection against colitis-associated colorectal cancer in rats – Ying Hu – Carcinogenesis

Animal microbiome

Managing Amphibian Disease with Skin Microbiota – Douglas C. Woodhams – Trends in Microbiology

Plant, root, and soil microbiome

Fungal phylogenetic diversity drives plant facilitation – Alicia Montesinos-Navarro – Oecologia

Positive plant–soil feedbacks of the invasive Impatiens glandulifera and their effects on above-ground microbial communities – Z Pattison – Weed Research

Bacterial community dissimilarity between the surface and subsurface soils equals horizontal differences over several kilometers in the western Tibetan Plateau – Haiyan Chu – Environmental Microbiology

Spatial scale drives patterns in soil bacterial diversity – Sarah L. O’Brien – Environmental Microbiology

Detection of short-term cropping system-induced changes to soil bacterial communities differs among four molecular characterization methods – David S. Duncan – Soil Biology and Biochemistry

Water and extremophile microbiome

Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs – Jacob P. Beam – Frontiers in Microbiology

Food microbiology

Influence of season and type of restaurants on sashimi microbiota – S. Miguéis – The European Journal of Public Health

Mitigation of Biofilm Formation on Corrugated Cardboard Fresh Produce Packaging Surfaces Using a Novel Thiazolidinedione Derivative Integrated in Acrylic Emulsion Polymers – Michael Brandwein – Frontiers in Microbiology

Psychrophile spoilers dominate the bacterial microbiome in musculature samples of slaughter pigs – Evelyne Mann – Meat Science

Bioinformatics

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision – Sophie Weiss – The ISME Journal

ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses – Jennifer Fouquier – Microbiome

An algorithm for designing minimal microbial communities with desired metabolic capacities – Alexander Eng – Bioinformatics

Posted this previously, but now peer reviewed: Comparison of three clustering approaches for detecting novel environmental microbial diversity – Dominik Forster – PeerJ

Techniques

High-resolution microbiota flow cytometry reveals dynamic colitis-associated changes in fecal bacterial composition – Jakob Zimmermann – European Journal of Immunology

More microbiology

Phenotypic Heterogeneity and the Evolution of Bacterial Life Cycle –
Jordi van Gestel – PLOS Computational Biology
Microbes in the news

Human Gut Microbiome Evolution: From Hunter-Gatherers to a Western Lifestyle – Discover

Giving up hunting and gathering changed our gut microbiome – Eric Smillie – Newsweek

The social microbiome of the social honey bee – Irene Newton – MicroBEnet

Video: The Microbiome Project: Surgery – Jack Gilbert and colleagues discuss – Argonne National Laboratory

Newly discovered microbes in marine sponges, turtles, rockfish, and termites – Microbe Post

Penn Researcher Contributes Engineering Expertise to Solving Dental Maladies – University of Pennsylvania

Living bacteria-powered lights hit the market – New Scientist

What Are You Smoking? Bacteria Found at Local Hookah Bars – Bianca Lopez – University of Tampa

Science, publishing, and career

“That was a really bad Friday for us:” WIRED warns four stories were plagiarized – Ivan Oransky – Retraction Watch

Bik’s picks

Arctic shipworm discovery alarms archaeologists: a new species of the wood-chomping mollusks is loose in the Arctic – Eli Kintisch – Science

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February 24, 2016

Posted on by

Women in space, cacti, celiac disease, and traveling dust.

Event

Not endorsing – full of quackery and folks trying to sell their books and food supplements, little science: Microbiome Medicine Summit

Human oral microbiome

Review: Porphyromonas gingivalis: An Overview of Periodontopathic Pathogen below the Gum Line – Kah Yan How – Frontiers in Microbiology

Human reproductive tract microbiome

The potential influence of the microbiota and probiotics on women during long spaceflights – Camilla Urbaniak – Future Medicine

Human gut microbiome

Study of duodenal bacterial communities by 16S rRNA gene analysis in adults with active celiac disease versus non celiac disease controls – Esther Nistal – Journal of Applied Microbiology

High Molecular Weight Barley β-Glucan Alters Gut Microbiota Toward Reduced Cardiovascular Disease Risk – Yanan Wang – Frontiers in Microbiology

Review: A glance at … dietary emulsifiers, the human intestinal mucus and microbiome, and dietary fiber – Michael J. Glade – Nutrition

Review: Chemical conversations in the gut microbiota – Jessica A. Thompson – Gut Microbes

Review: Atopic dermatitis and the intestinal microbiota in humans and dogs – J. Mark Craig – Veterinary Medicine and Science

Animal models

Composition of fecal microbiota of laboratory mice derived from Japanese commercial breeders using 16S rRNA gene clone libraries – Ryoko Nozu – Journal of Veterinary Medical Science

Animal microbiome

News in livestock research — use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals – Simon Deusch – Computational and Structural Biotechnology Journal

Plant, root, and soil microbiome

The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity – Citlali Fonseca-García – Frontiers in Microbiology

Comparison of Fungal Community in Black Pepper-Vanilla and Vanilla Monoculture Systems Associated with Vanilla Fusarium Wilt Disease –
Wu Xiong – Frontiers in Microbiology

Bacterial-Plant-Interactions: Approaches to Unravel the Biological Function of Bacterial Volatiles in the Rhizosphere – Marco Kai – Frontiers in Microbiology

Short-Term Rhizosphere Effect on Available Carbon Sources, Phenanthrene Degradation, and Active Microbiome in an Aged-Contaminated Industrial Soil – François Thomas – Frontiers in Microbiology

Changes in rhizosphere bacterial gene expression following glyphosate treatment – Molli M. Newman – Science of the Total Environment

Pepino (Solanum muricatum) planting increased diversity and abundance of bacterial communities in karst area – Jinxiang Hu – Scientific Reports

Friend or foe? Biological and ecological traits of the European ash dieback pathogen Hymenoscyphus fraxineus in its native environment – Michelle Cleary – Scientific Report

An interdomain network: the endobacterium of a mycorrhizal fungus promotes antioxidative responses in both fungal and plant hosts – Candida Vannini – New Phytologist

Water and extremophile microbiome

The effect of temperature change on the microbial diversity and community structure along the chronosequence of the sub-arctic glacier forefield of Styggedalsbreen (Norway) – Alejandro Mateos-Rivera – FEMS Microbiology Ecology

Water level changes affect carbon turnover and microbial community composition in lake sediments – Lukas Weise – FEMS Microbiology Ecology

Evaluation of the treatment performance and microbial communities of a combined constructed wetland used to treat industrial park wastewater – Ming Xu – Environmental Science and Pollution Research

Bacterial Composition and Survival on Sahara Dust Particles Transported to the European Alps – Marco Meola – Frontiers in Microbiology

Review: Bridging the divide: a model-data approach to Polar and Alpine microbiology – James A. Bradley – FEMS Microbiology Ecology

Bioinformatics and metagenomics

ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses – Jennifer Fouquier – Microbiome

More microbiology

Peracetic Acid Treatment Generates Potent Inactivated Oral Vaccines from a Broad Range of Culturable Bacterial Species – Kathrin Moor – Frontiers in Immunology

Microbes in the news

Bacteria From the Sahara Desert Found on Swiss Glaciers – Nellie Van Driska – GlacierHub

Wolbachia Bacteria Could Be Answer To Malaria, Dengue: Bill Gates – NDTV

Student Research Focus: Drew Gukeisen discovers and visualizes new virus – Indiana University SouthEast

Bacteria swabbing trend for newborns medically in doubt – Carina Storrs – CNN

Microbes and art

Navel gazing: portraits of the bacteria in our belly buttons – in pictures by Joana Ricou – The Guardian

Science, publishing, and career

Activism: Frustrated postdocs rise up – Paul Smaglik – Nature

Don’t trust an image in a scientific paper? Manipulation detective’s company wants to help – Retraction Watch
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February 17, 2016

Posted on by

Microbial biomarkers for diabetes, gut sialidases,  pathogens in stranded sea turtles, microbial biodeterioration of an ancient staircase, and how bacterial stay in shape.

Events

‘Microbiome-based Foods for Health and Sustainability’ workshop, 23 February, Brussels – APC Microbiome Institute

Call for Entries! ASM’s 2016 Agar Art Contest. Deadline: May 6.

Human oral microbiome

Intracerebral hemorrhage and deep microbleeds associated with cnm-positive Streptococcus mutans; a hospital cohort study – Shuichi Tonomura – Scientific Reports

Review: Oral Microbiome: Contributions to Local and Systemic Infections – Kerri T. Simpson – Current Oral Health Reports

Human gut microbiome

Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes – Moran Yassour – Genome Medicine

Postoperative changes in fecal bacterial communities and fermentation products in obese patients undergoing bilio-intestinal bypass – Vania Patrone – Frontiers in Microbiology

The Effects of Bowel Preparation on Microbiota-Related Metrics Differ in Health and in Inflammatory Bowel Disease and for the Mucosal and Luminal Microbiota Compartments – Rima M Shobar – Clinical and Translational Gastroenterology

Registered report: Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma – John Repass – eLIFE

Review: Sialidases from gut bacteria: a mini-review – Nathalie Juge – Biochemical Society Transactions

Review: Akkermansia muciniphila and its role in regulating host functions – Muriel Derrien – Microbial Pathogenesis

Models of microbiome research

Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice – Jun Li – PNAS

The bacterial microbiome of Dermacentor andersoni ticks influences pathogen susceptibility – Cory A Gall – ISME Journal

Have clay will lay: Chicken: Dietary supplementation with the clay mineral palygorskite affects performance and beneficially modulates caecal microbiota in laying pullets – S. Chalvatzi – Journal of Applied Microbiology

Animal microbiome

Bacterial agents in 248 ticks removed from people from 2002 to 2013 – Camille Aubry – Ticks and Tick-borne Diseases

Bacterial and viral pathogens detected in sea turtles stranded along the coast of Tuscany, Italy – G. Fichi – Veterinary Microbiology

Poor English (but US lab): Identification of Host-Specific Genetic Markers within 16S rDNA Intervening Sequences of 73 Genera of Fecal Bacteria – Zhenyu Shen – Omics’ Journal of Data Mining in Genomics & Proteomics

Editorial: Developmental biology: Females have a lot of guts – Justin Fear – Nature

The sexual identity of adult intestinal stem cells controls organ size and plasticity – Bruno Hudry – Nature

Plant, root, and soil microbiome

Bacterial predator–prey dynamics in microscale patchy landscapes – Felix J. H. Hol – Proceedings of the Royal Society B

Variation in soil microbial communities associated with critically endangered Wollemi pine affects fungal, but not bacterial, assembly within seedling roots – J.L. Rigg – Pedobiologia

The Effects of Nitrogen Fertilizer on Soil Microbial Communities Under Conventional and Conservation Agricultural Managements in a Tropical Clay-Rich Ultisol – Miura, Toshiko – Soil Science

Cover Crop and Irrigation Effects on Soil Microbial Communities and Enzymes in Semiarid Agroecosystems of the Central Great Plains of North America – Francisco J. Calderón – Pedosphere

Effect of soil disinfection with chemical and biological methods on bacterial communities – Md Rokunuzzaman – Egyptian Journal of Basic and Applied Sciences

Water and extremophile microbiome

Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines – Charlotte D. Vavourakis – Frontiers in Microbiology

Characterization of bacterial communities in wetland mesocosms receiving pharmaceutical-enriched wastewater – Dongqing Zhang – Ecological Engineering

Microbial Community Profile and Water Quality in a Protected Area of the Caatinga Biome – Fabyano Alvares Cardoso Lopes – PLOS ONE

Thesis: Tightly-coupled sulfur-cycling microbial mats of the White Point hydrothermal vent field, CA: An analog for deep-sea vents – Priscilla J Miranda – California State University Long Beach

Thesis: The microbial diversity and function of Arctic supraglacial biomes – Stefanie Lutz – University of Leeds

Built environment microbiome

Biodeterioration Risk Threatens the 3100 Year Old Staircase of Hallstatt (Austria): Possible Involvement of Halophilic Microorganisms – Guadalupe Piñar – PLOS ONE

The Black Yeast Exophiala dermatitidis and Other Selected Opportunistic Human Fungal Pathogens Spread from Dishwashers to Kitchens – Jerneja Zupančič – PLOS ONE

Bioinformatics and metagenomics

IMP: a pipeline for reproducible integrated metagenomic and metatranscriptomic analyses – Shaman Narayanasamy – BioRxiv

Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads – Yvan Le Bras – GigaScience

Shannon: An Information-Optimal de NovoRNA-Seq Assembler – Sreeram Kannan – BioRxiv

RECKONER: Read Error Corrector Based on KMC – Maciej Długosz – ArXiv

A benchmark study on error-correction by read-pairing and tag-clustering in amplicon-based deep sequencing – Tian-Hao Zhang – BMC Genomics

More microbiology

HT: Liz Costello: Universal resilience patterns in complex networks – Jianxi Gao – Nature

Microbially assisted recording of the Earth’s magnetic field in sediment – Xiangyu Zhao – Nature Communications

High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection – Jeroen De Smet – The ISME Journal

Discovery of cahuitamycins as biofilm inhibitors derived from a convergent biosynthetic pathway – Sung Ryeol Park – Nature Communications

Review: Staying in Shape: the Impact of Cell Shape on Bacterial Survival in Diverse Environments – Desirée C. Yang – Microbiology and Molecular Biology Reviews

Microbes in the news

Oral bacteria linked to risk of stroke – Betty Coffman – University of Louisville

Opportunistic Fungal Pathogens in Dishwashers and Kitchens – Alex Alexiev – MicroBEnet

UVA: Bacteria Overgrowth Could Be Major Cause of Stunting in Children – University of Virginia Health System – NBC29

A new method to dramatically improve the sequencing of metagenomes – EurekAlert

What your gut bacteria can tell you about type 2 diabetes – MedicalXpress

New anti-biofilm compounds show promise against drug-resistant bacteria linked to hospital infections – Ian Demsky – University of Michigan

Crowdfunding project: How Insects and Bacteria Can Solve Murder Mysteries: estimate the time since death (TSD) at a crime scene – Experiment

Crowdfunding project: E pluribus unum: how honey bee bacteria coordinate behaviors – Irene Newton – Experiment

uBiome Named One of World’s Top 10 Most Innovative Companies in Healthcare by Fast Company – PR Web

MIT Spinout Synlogic Grabs $40M To Program Microbes Into Living Drugs – Luke Timmerman – Forbes

Science, publishing, and career

Biologists urged to hug a preprint: ASAPbio meeting discusses the ins and outs of posting work online before peer review – Ewen Callaway – Nature

Accelerating Science with Preprints – Peter Binfield – PeerJ Blog

XY Bias: How Male Biology Students See Their Female Peers. In three large classes, men overrated the abilities of male students above equally talented and outspoken women – Ed Yong – The Atlantic

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February 13, 2016

Posted on by

Fungal communities of bark beetles, microbiome in rhinosinusitis, deep-sea chemolithoautotrophic communities, talking walls (microbes in houses), and, for Valentine’s Day: cocoa bean fermentation. 

Jobs and events

Postdoc opportunity, University of Notre Dame: 20,000 longitudinal gut microbiome samples from wild baboons

Pregnancy and birth

Review: Prevention of Necrotizing Enterocolitis Through Manipulation of the Intestinal Microbiota of the Premature Infant – Kannikar Vongbhavit – Clinical Therapeutics

Human oral microbiome

Analysis of bacterial community profiles of endodontically infected primary teeth using pyrosequencing – Kwan Hee Yun – International Journal of Paediatric Dentistry

Human respiratory microbiome

Composition and dynamics of the respiratory tract microbiome in intubated patients – Brendan J. Kelly – Microbiome Journal

Metagenomic Sequencing of the Chronic Obstructive Pulmonary Disease Upper Bronchial Tract Microbiome Reveals Functional Changes Associated with Disease Severity – Simon J. S. Cameron- PLOS ONE

The bacterial microbiome in chronic rhinosinusitis: Richness, diversity, postoperative changes, and patient outcomes – Edward John Cleland – American Journal of Rhinology & Allergy

Review: Microbiome of the paranasal sinuses: Update and literature review – Jivianne T. Lee – American Journal of Rhinology & Allergy

Editorial: The microbiome of the sinuses and its relevance in health and disease – Simon A. Carney

Human reproductive tract microbiome

Molecular detection of intrauterine microbial colonization in women with endometriosis – Khaleque N. Khan – European Journal of Obstetrics & Gynecology and Reproductive Biology

Review: The Basics of Bacteriuria: Strategies of Microbes for Persistence in Urine – Deepak S. Ipe – Frontiers in Cellular and Infection Microbiology

Review: The Human Microbiome during Bacterial Vaginosis – Andrew B. Onderdonk – Clinical Microbiology Reviews

Human gut microbiome

Allergy associations with the adult fecal microbiota: Analysis of the American Gut Project – Xing Hua – EBioMedicine

An Integrated Metabolomic and Microbiome Analysis Identified Specific Gut Microbiota Associated with Fecal Cholesterol and Coprostanol in Clostridium difficile Infection – Vijay C. Antharam – PLOS ONE

Review: The Role of Probiotics on the Microbiota: Effect on Obesity – Esther Nova – Nutrition in Clinical Practice

Editorial: Policing of gut microbiota by the adaptive immune system – Laurent Dollé – BMC Medicine

Review: Fostering of advanced mutualism with gut microbiota by Immunoglobulin A – Duncan B. Sutherland – Immunological Reviews

Perspective: The Second Brain: Is the Gut Microbiota a Link Between Obesity and Central Nervous System Disorders? – Javier Ochoa-Repáraz – Current Obesity Reports

Review: Butyrate, Neuroepigenetics and the Gut Microbiome: Can a High Fiber Diet Improve Brain Health? – Megan W. Bourassa – Neuroscience Letters

Gut passage

Colonic response to laxative ingestion as assessed by MRI differs in constipated irritable bowel syndrome compared to functional constipation – C. Lam – Neurogastroenterology & Motility

How do primates affect seed germination? A meta-analysis of gut passage effects on neotropical plants – Lisieux F. Fuzessy – Oikos

Models of microbiome research

Drosophila: Effects of co-occurring Wolbachia and Spiroplasma endosymbionts on the Drosophila immune response against insect pathogenic and non-pathogenic bacteria – Upasana Shokal – BMC Microbiology

Rats: Diet-induced changes in maternal gut microbiota and metabolomic profiles influence programming of offspring obesity risk in rats – Heather A. Paul – Scientific Reports

Thesis, mice: The effects of nicotine on the gut microbiome and the serum metabolite profile of mice – Ridwan Amin Mahbub – University of Georgia

Contains several cases of image duplication (might be error): Dietary Fiber Intake Regulates Intestinal Microflora and Inhibits Ovalbumin-Induced Allergic Airway Inflammation in a Mouse Model – Zhiyu Zhang – PLOS ONE

Animal microbiome

Metabarcoding of fungal communities associated with bark beetles – Kirsten E. Miller – Ecology and Evolution

Deep 16S rRNA gene sequencing of anterior foregut microbiota from the blue-green sharpshooter (Graphocephala atropunctata) – E. E. Rogers – Journal of Applied Entomology

A bacterial filter protects and structures the gut microbiome of an insect – Michele Caroline Lanan – The ISME Journal

Plant, root, and soil microbiome

Isolation and Identification of Plant Growth Promoting Rhizobacteria from Cucumber Rhizosphere and Their Effect on Plant Growth Promotion and Disease Suppression – Shaikhul Islam – Frontiers in Microbiology

Microbial biomass and soil organic carbon accumulation on a former lakebed near Novosibirsk, Russia – Mikhail. V. Yakutin – Journal of Plant Nutrition and Soil Science

A cost-effective and efficient strategy for Illumina sequencing of fungal communities: A case study of beech endophytes identified elevation as main explanatory factor for diversity and community composition – A.B. Siddique – Fungal Ecology

Primer: Networking in the Plant Microbiome – Marcel G. A. van der Heijden – PLOS Biology

Thesis: Next generation sequencing on soil samples from Etosha National Park: Diversity studies of an anthrax reservoir – Valseth, Karoline

Water and extremophile microbiome

Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent – Caroline S Fortunato – The ISME Journal

Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt – Sean P Jungbluth – The ISME Journal

Context dependency in biodiversity patterns of central German stream metacommunities – Jonathan D. Tonkin – Freshwater Biology

Microbial community composition in the marine sediments of Jeju Island: next-generation sequencing surveys – Heebok Choi – Journal of Microbiology and Biotechnology

Effects of temperature stress and aquarium conditions on the red macroalga Delisea pulchra and its associated microbial community – Enrique Zozaya-Valdés – Frontiers in Microbiology

Using in situ bacterial communities to monitor contaminants in river sediments – Yuwei Xie – Environmental Pollution

DGGE: Effects of fullerene (C60), multi-wall carbon nanotubes (MWCNT), single wall carbon nanotubes (SWCNT) and hydroxyl and carboxyl modified single wall carbon nanotubes on riverine microbial communities – J. R. Lawrence – Environmental Science and Pollution Research

Built environment microbiome

Walls talk: Microbial biogeography of homes spanning urbanization – Jean F. Ruiz-Calderon – Science Advances

Microbial communities affecting albumen photography heritage: a methodological survey – Andrea Puškárová – Scientific Reports

Food microbiology

Characterization of microbiota in Plaisentif cheese by high-throughput sequencing –
Alessandra Dalmasso – LWT-Food Science and Technology

Metagenomic analysis of viruses associated with field-grown and retail lettuce identifies human and animal viruses – Tiong Gim Aw – International Journal of Food Microbiology

Bacterial diversity of floor drain biofilms and drain waters in a Listeria monocytogenes contaminated food processing environment – Monika Dzieciol

Review: The cocoa bean fermentation process: from ecosystem analysis to starter culture development – L. De Vuyst – Journal of Applied Microbiology

Techniques

Oufti: an integrated software package for high-accuracy, high-throughput quantitative microscopy analysis – Ahmad Paintdakhi – Molecular Microbiology

Viruses and phages

Perspective: A Virological Perspective on Cancer – Blossom Damania – PLOS Pathogens

Bioinformatics and metagenomics

Fast search of thousands of short-read sequencing experiments – Brad Solomon – Nature Biotechnology

Open-Source Sequence Clustering Methods Improve the State Of the Art – Evguenia Kopylova

Editorial: Bacterial Speciation: Genetic Sweeps in Bacterial Species -Frederick M. Cohan – Current Biology

Microbes in the news

Walls talk – or at least hold many secrets a wall whisperer can reveal – Jonathan Eisen – MicroBEnet

Country microbes, city microbes—where you live can change how you get sick – Annalee Newitz – Ars Technica

Urbanization Leads to Change in Type of Bacteria in the Home – Lauran Neergaard – ABC News

Fun list: Ranking the Top 10 Best Bacteria on Earth – Ben Guarino – Inverse

Science, publishing and career

The Research Pirates of the Dark Web – Kaveh Waddell  – The Atlantic

Researcher illegally shares millions of science papers free online to spread knowledge – Science Alert

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