Category Archives: Microbes in the News

March 9, 2016

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Two papers on altered microbiome in HIV-infected humans and SIV-infected monkeys, ESBL carriage in hospital wards and medical students, fungus infection affects frog song, and protein recycling in the ocean.

Pregnancy and birth

Gut bacteria dysbiosis and necrotising enterocolitis in very low birthweight infants: a prospective case-control study – Barbara B Warner – The Lancet

Human gut microbiome

Editorial: The HIV-Associated Enteric Microbiome Has Gone Viral – Brent E. Palmer – Cell Host & Microbe

Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome – Cynthia L. Monaco – Cell Host & Microbe

Comparison of the faecal colonization rates with extended-spectrum beta-lactamase producing enterobacteria among patients in different wards, outpatients and screened medical students – Fatemeh Ebrahimi – Microbiology and Immunology

Animal models

SIV Infection-Mediated Changes in Gastrointestinal Bacterial Microbiome and Virome Are Associated with Immunodeficiency and Prevented by Vaccination – Scott A. Handley – Cell Host & Microbe

Animal microbiome

Enhanced call effort in Japanese tree frogs infected by amphibian chytrid fungus –
Deuknam An – Biology Letters

Plant, root, and soil microbiome

Diversity and bioactivity of bacterial endophyte community of Cupressaceae – J. Soltani – Forest Pathology

Leaf litter decomposition in remote oceanic island streams is driven by microbes and depends on litter quality and environmental conditions – Verónica Ferreira – Freshwater Biology

Network modules and hubs in plant-root fungal biomes – Hirokazu Toju – Journal of the Royal Society Interface

Water and extremophile microbiome

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean – William D Orsi – The ISME Journal

Food microbiology

Detection of pathogenic Escherichia coli and microbiological quality of chilled shrimp sold in street markets – Liliana Jose Barbosa – Letters in Applied Microbiology

More microbiology

Antimicrobial activity of extracts from macroalgae Ulva lactuca against clinically-important Staphylococci is impacted by lunar phase of macroalgae harvest – Amy M. Deveau – Letters in Applied Microbiology

Microbes in the news

Bacteria discovered by scientists in London cuts dependence on commercial fertilizers – John Miner – LFPress

Fungus makes tree frogs sing – Nature

Michigan researchers start $9.2M effort to study bacteria – Click on Detroit

“Nightmare Bacteria” Found in Southern California Sewage Treatment Plants – Alexander Haro – The Inertia

Two Starbucks Items Voluntarily Recalled Due to Bacteria, Allergen Risk – Gillian Mohney – ABC News

Science, publishing, and career

Scientific record: Class uncorrected errors as misconduct – Sophien Kamoun – Nature

A Multi-dimensional Investigation of the Effects of Publication Retraction on Scholarly Impact – Xin Shuai – Arxiv

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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 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 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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February 29, 2016

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Update March 2: reformatted to include hyperlinks.

Plant, root, and soil microbiome

Regional Similarity and Consistent Patterns of Local Variation in Beach Sand Bacterial Communities throughout the Northern Hemisphere – Christopher Staley – Applied and Environmental Microbiology

Water and extremophile microbiome

Into the deep: Evaluation of SourceTracker for assessment of faecal contamination of coastal waters – Rebekah Henry – Water Research

Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom – David M. Needham – Nature Microbiology

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

Review: Microbial diversity and functional capacity in polar soils – Thulani Peter Makhalanyane – Current Opinion in Biotechnology

Waste and pollution microbiology

Shifts in microbial communities in bioaugmented grease interceptors removing fat, oil, and grease (FOG) – Xia He – Applied Microbiology and Biotechnology

Built environment microbiome

Environmental Contamination in Households of Patients with Recurrent Clostridium difficile Infection – Megan K. Shaughnessy – Applied and Environmental Microbiology

Food microbiology

Improving functionality of chocolate: A review on probiotic, prebiotic, and/or synbiotic characteristics – Nevzat Konar – Trends in Food Science & Technology

More microbiology

Interaction of Candida albicans with host cells: virulence factors, host defense, escape strategies, and the microbiota – Sarah Höfs – Journal of Microbiology

Microbes in the news

Restoring healthy growth in infants – Andrea Du Toit – Nature Reviews Microbiology

Dangerous intestinal bacteria back in Amarillo – Angelica Brown – Newschannel10

Maine seed potato growers contend with new bacteria – Bangor Daily News

Halifax harbour bacteria ‘zapper’ to be shut off Tuesday – Heide Pearson – Global News CA

In-N-Out Vows To Remove Antibiotics From Meat To Save Us All From Drug Resistant “Superbugs” – Matt Tinoco – LAist

Science, publishing, and career

Pre- or post-publication peer review – Jon Tennant – Science Open

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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 25, 2016

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Two papers about the gut microbiome of Japanese sea cucumbers farmed for food, effects of elevation on forest fungi, pico-eukaryotes under disappearing ice, and nitrification in the San Francisco Bay.

Human gut microbiome

Comment: Faecal microbiota transplantation is promising but not a panacea – Michael J. Sadowsky – Nature Microbiology

Models of microbiome research

In chicken (since that is not clear from the title): Bacteria within the Gastrointestinal Tract Microbiota Correlated with Improved Growth and Feed Conversion: Challenges Presented for the Identification of Performance Enhancing Probiotic Bacteria – Dragana Stanley – Frontiers in Microbiology

Animal microbiome

Gut bacterial diversity of farmed sea cucumbers Apostichopus japonicus with different growth rates – Yujie Sha – Microbiology

Characterization of the gut bacterial community of the Japanese sea cucumber Apostichopus japonicus – E. A. Bogatyrenko – Microbiology

Ants: Yeast communities of Formica aquilonia colonies – I. A. Maksimova – Microbiology

Plant, root, and soil microbiome

Antibiotics Resistance in Rhizobium: Type, Process, Mechanism and Benefit for Agriculture – Judith Naamala – Current Microbiology

Fungi in Costa Rica: Belowground responses to elevation in a changing cloud forest – Caitlin I. Looby – Ecology and Evolution

Water and extremophile microbiome

Characterization of the structure of the prokaryotic complex of Antarctic permafrost by molecular genetic techniques – N. A. Manucharova – Microbiology

Biogeography and Photosynthetic Biomass of Arctic Marine Pico-Eukaroytes during Summer of the Record Sea Ice Minimum 2012 – Katja Metfies – PLOS ONE

Variable Nitrification Rates Across Environmental Gradients in Turbid, Nutrient-Rich Estuary Waters of San Francisco Bay – Julian Damashek – Estuaries and Coasts

Bioreactors and waste microbiology

Effects of different bulking agents on the maturity, enzymatic activity, and microbial community functional diversity of kitchen waste compost – Xiaojuan Wang – Environmental Technology

Prevalence of plasmid-mediated multidrug resistance determinants in fluoroquinolone-resistant bacteria isolated from sewage and surface water – Adriana Osińska – Environmental Science and Pollution Research

Bioinformatics and metagenomics

Comparing different mapping software using anvi’o – A. Murat Eren – Meren Lab blog

Microbes in the news

VCU spotlights internship focused on microbiology at Ardent Craft Ales: 26-year-old Ben Stone is helping the brewery with the finer points of its microbiology – Trevor Dickerson – RVA News

Ikea plans mushroom-based packaging as eco-friendly replacement for polystyrene
Swedish retail giant looks at biodegradable fungus-based packaging to replace polystyrene, which is tricky to recycle – Emily Gosden – The Telegraph

Virginia Tech scientists discover way to track, stop human, agricultural viruses – Augusta Free Press

Microbiology professor James Holden speaks about the intersection of science and religion – Tara Dowd – Daily Collegian

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February 24, 2016

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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 23, 2016

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An introduction to 16S rRNA gene sequencing, gut microbiome disruptions in long-term care, microbial responses to oil contamination, colors and k-mers, and how to build your own Winogradsky column.

Jobs and events

PhD position on metagenomics-driven natural product discovery from plant microbiomes – Wageningen University, The Netherlands

Festival of Genomics: Has microbiome session, 27-29 June 2016, Boston

Human skin microbiome

Good introduction for other sample types too! Research Techniques Made Simple: Bacterial 16S Ribosomal RNA Gene Sequencing in Cutaneous Research – Jay-Hyun Jo – Journal of Investigative Dermatology

Human gut microbiome

Intestinal microbiome disruption in patients in a long-term acute care hospital: A case for development of microbiome disruption indices to improve infection prevention – Alison Laufer Halpin – American Journal of Infection Control

Association of dietary type with fecal microbiota and short chain fatty acids in vegans and omnivores – Alina Reiss – Journal of International Society of Microbiota

Microbiome models

Aging and serum MCP-1 are associated with gut microbiome composition in a murine model – Melissa N. Conley – PeerJ Preprint

Isolation and Characterization of a Novel Gammaherpesvirus from a Microbat Cell Line – Reed S. Shabman – mSphere

Animal microbiome

Review: Molecular trophic markers in marine food webs and their potential use for coral ecology – Miguel Costa Leal – Marine Genomics

Plant, root, and soil microbiome

Microbial diversity in European alpine permafrost and active layers – Beat Frey – FEMS Microbiology Ecology

Responses of microbial community from tropical pristine coastal soil to crude oil contamination – Daniel Morais – PeerJ

Zinc treatment increases the titer of ‘Candidatus Liberibacter asiaticus’ in HLB-affected citrus plants while affecting the bacterial microbiomes – Muqing Zhang – Journal of Applied Microbiology

Draft Genome Sequences of Two Vibrio splendidus Strains, Isolated from Seagrass Sediment – Ruth D. Lee – Genome Announcements

Draft Genome Sequences of Two Pseudoalteromonas Strains Isolated from Roots and Leaf Blades of the Seagrass Zostera marina – Alexandra Alexiev – Genome Announcements

Deep RNA-Seq profile reveals biodiversity, plant–microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues – Sandeep Chakraborty – AMB Express

Water microbiome

Environmental heterogeneity among lakes promotes hyper β-diversity across phytoplankton communities – Selma Maloufi – Freshwater Biology

Bacterial community structure and variation in a full-scale seawater desalination plant for drinking water production – A. Belila – Water Research

Bimodal occupancy-frequency distributions uncover the importance of regional dynamics in shaping marine microbial biogeography – Markus V. Lindh – BioRxiv

Microbial Ecology

Eco-evolutionary dynamics in a coevolving host–virus system – Jens Frickel – Ecology Letters

Bioinformatics and metagenomics

Succinct Colored de Bruijn Graphs – Keith Belk – BioRxiv preprint

Metapalette: A k-mer painting approach for metagenomic taxonomic profiling and quantification of novel strain variation – David Koslicki – ArXiv

Microbes in the news

Grow a bacterial zoo in a bottle: How to build your own Winogradsky column – Steph Yin – Popular Science

Exploring the Humane and Canine Microbiome: Q&A with Dr. Robynne Chutkan – Claudia Kawczynska – The Bark

Ancient bacteria in Utah waters blamed for deaths of pets, people – Todd Tanner – Fox13

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February 22, 2016

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Effect of oxylate on microbiome of an herbivorous woodrat, sequencing 16S rRNA genes with the PacBio SMRT, and big differences in soil diversity caused by choice of extraction method.

Animal models

Metagenomic analysis of rumen microbial population in dairy heifers fed a high grain diet supplemented with dicarboxylic acids or polyphenols – Roberta De Nardi – BMC Veterinary Research

Woodrat: The Effect of Dietary Oxalate on the Gut Microbiota of the Mammalian Herbivore Neotoma albigula – Aaron W. Miller – Applied and Environmental Microbiology

Built environment microbiome

Complementary microorganisms in highly corrosive biofilms from an offshore oil production facility – Adrien Vigneron – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Dominant tree species and soil type affect fungal community structure in a boreal peatland forest – Hui Sun – Applied and Environmental Microbiology

Review: A review of the environmental implications of in situ remediation by nanoscale zero valent iron (nZVI): Behavior, transport and impacts on microbial communities – Emilie Lefevre – Science of the Total Environment

Water microbiome

Diversity, Productivity and Stability of an Industrial Microbial Ecosystem – Doruk Beyter – Applied and Environmental Microbiology

Food microbiology

Illuminating Anaerobic Microbial Community and Co-occurrence Patterns across a Quality Gradient in Chinese Liquor Fermentation Pit Muds – Xiaolong Hu – Applied and Environmental Microbiology

Techniques

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system – Patrick D. Schloss – PeerJ

Estimates of the bacterial ribosome content and diversity in soils are significantly affected by different nucleic acid extraction methods – Pia K. Wüst – Applied and Environmental Microbiology

Bioinformatics and metagenomics

MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression – Minji KimB – BMC ioinformatics

EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation – Evangelos Pafilis – Database

More microbiology

Organization of DNA in a bacterial nucleoid – Michael Y. Tolstorukov – BMC Microbiology

Microbes in the news

Coevolution and the Microbiome – David Baltrus – My Chrobial Romance

Bacteria Are Present in Kidney Stones and May Contribute to Their Formation – Nationwide Children’s

Fatal disease by Salmonella bacteria killing California songbirds – Robert V. Boyd – Microcap Magazine

Synchrotron Being Used to Research Neutralizing Ulcer Bacteria – Adam Brilz
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