Category Archives: Waste and pollution

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 28, 2016

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Viral sequences in cancers, COPD, and EDGE, an easy online tool for metagenomics analysis.

Jobs

Researcher for a project on the effect of gut microbiome in human behavior – Radboud UMC Nijmegen, The Netherlands

General microbiome

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

Pregnancy and birth

Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants – Natalia Zeber-Lubecka – PLOS ONE

Human respiratory microbiome

Lung microbiome dynamics in chronic obstructive pulmonary disease exacerbations – Zhang Wang – European Respiratory Journal

Human gut microbiome

Presence of Porphyromonas gingivalis in esophagus and its association with the clinicopathological characteristics and survival in patients with esophageal cancer – Shegan Gao – BMC Infectious Agents and Cancer

Human colorectal mucosal microbiota correlates with its host niche physiology revealed by endomicroscopy – Ai-Hua Wang – Scientific Reports

Review: Gut Microbiota of Nonalcoholic Fatty Liver Disease – Reham M. Abdou – Digestive Diseases and Sciences

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

Review: Beyond the gut bacterial microbiota: The gut virome – Paola Columpsi – Journal of Medical Virology

Human tissues and infection

Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers – Jens Friis-Nielsen – MDPI Viruses

Models of microbiome research

Maternal Weaning Modulates Emotional Behavior and Regulates the Gut-Brain – Pamela Farshim – Scientific Reports

Rats: Correlations of Fecal Metabonomic and Microbiomic Changes Induced by High-fat Diet in the Pre-Obesity State – Hong Lin – Scientific Reports

Animal microbiome

18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species – Aitor Albaina – Ecology and Evolution

Plant, root and soil microbiome

Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming – Kai Xue – Nature Climate Change

Online Springer Book: Microbial Inoculants in Sustainable Agricultural Productivity – Springer

Book chapter: Soil Effects of Genetically Modified Trees (GMTs) – Fernando Gallardo – Biosafety of Forest Transgenic Trees

Borderline Products between Bio-fertilizers/ Bio-effectors and Plant Protectants: The Role of Microbial Consortia – Marco Nuti – David Publishing Company

Differences in substrate use efficiency: impacts of microbial community composition, land use management, and substrate complexity – Tobias Bölscher – Biology and Fertility of Soils

Comparing how land use change impacts soil microbial catabolic respiration in Southwestern Amazon – Andre Mancebo Mazzetto – Brazilian Journal of Microbiology

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

Soil and tree species traits both shape soil microbial communities during early growth of Chinese subtropical forests – Zhiqin Pei – Soil Biology and Biochemistry

Water and extremophile microbiome

Functional interactions of archaea, bacteria, and viruses in a hypersaline endolithic community – Alexander Crits-Christoph – Environmental Microbiology

Ecological succession leads to chemosynthesis in mats colonizing wood in sea water – Dimitri Kalenitchenko – The ISME Journal

Chapter One – Geomicrobiology and Metagenomics of Terrestrial Deep Subsurface Microbiomes – M. Itävaara – Advances in Applied Microbiology

Waste and pollution microbiology

Bacterial ecology of abattoir wastewater treated by an anaerobic digestor – Linda Jabari – Brazilian Journal of Microbiology

High-Resolution Phylogenetic Analysis of Residual Bacterial Species of Fouled Membranes after NaOCl Cleaning – Ronald R. Navarro – Water Research

Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis – Firouz Abbasian – Biotechnology Progress

Bioinformatics

Now peer reviewed: cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies – John H. Chase – mSystems

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation – Cecilia Noecker – mSystems

Assessing the performance of DNA barcoding using posterior predictive simulations – Anthony J. Barley – Molecular Ecology

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform – Po-E Li – BioRxiv

GenSeed-HMM: A tool for progressive assembly using profile HMMs as seeds and its application in Alpavirinae viral discovery from metagenomic data – João Marcelo P. Alves – Frontiers in Microbiology

Metabolomics

Human microbial metabolites as a source of new drugs – Somdutta Saha – Drug Discovery Today

More microbiology

Microbiota–mitochondria inter-talk: consequence for microbiota-host interaction – Yann Saint-Georges-Chaumet – Pathogens and Disease

Exploitation by cheaters facilitates the preservation of essential public goods in microbial communities – Clara Moreno-Fenoll – bioRxiv

Accurate and semi-automated analysis of bacterial association with mammalian cells – C.M. Murphy – Journal of Microbiological Methods

Microbes in the news

Fungal DNA, mycotoxins, cat allergens and fatigue in classrooms – Holly Ganz – MicroBEnet

Gum Disease Bacteria Linked to Esophageal Cancer Risk – Newsmax

Video: Virginia Tech scientists turn poo into power – Virginia Tech

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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 15, 2016

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Drosophila longevity, gut immunity in insects, metagenomics and beef production, secure computation, and mutualistic phages.

Pregnancy and birth

Research Highlight: Add the microbiota to your birth plan – Cláudio Nunes-Alves – Nature Reviews Microbiology

Human gut microbiome

Review: Gut microbiome and Metabolic Syndrome – Mohsen Mazidi – Diabetes & Metabolic Syndrome: Clinical Research & Reviews

Review: Role of microbes (probiotics and prebiotics) – D.M.A.E. Jonkers – Best Practice & Research Clinical Gastroenterology

Review: Intestinal Microbiota in Liver Disease – Tanvir R. Haque – Best Practice & Research Clinical Gastroenterology

Models of microbiome research

Folate Acts in E. coli to Accelerate C. elegans Aging Independently of Bacterial Biosynthesis – Bhupinder Virk – Cell Reports

Glucose modulates Drosophila longevity and immunity independent of the microbiota – Anthony Galenza – Biology Open

Bacterial successions in the gastrointestinal tract of broilers – Samir Ranjitkar – Applied and Environmental Microbiology

Triclosan Exposure is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish – Christopher A Gaulke – BioRxiv

Research Highlight: How to extend your stay – Cláudio Nunes-Alves – Nature Reviews Microbiology

Animal microbiome

Review: Gut immunity in Lepidopteran insects – Kai Wu – Developmental & Comparative Immunology

Editorial: Bears Arouse Interest in Microbiota’s Role in Health – Kimberly A. Dill-McFarland – Trends in Microbiology

Plant, root, and soil microbiome

Impact of long-term cropping of glyphosate-resistant transgenic soybean [Glycine max (L.) Merr.] on soil microbiome – Letícia Carlos Babujia – Transgenic Research

Food microbiology

Use of metagenomic shotgun sequencing technology to detect foodborne pathogens within their microbiome in beef production chain – Xiang Yang – Applied and Environmental Microbiology

Microbial dynamics in industrial Blue veined cheeses in different packaging –
P. Duval – International Dairy Journal

Diversity of the microbiota involved in wine and organic apple cider submerged vinegar production as revealed by DHPLC analysis and next-generation sequencing – Janja Trček – International Journal of Food Microbiology

Built environment microbiome

Air dispersed essential oils combined with standard sanitization procedures for environmental microbiota control in nosocomial hospitalization rooms – Fabrizio Gelmini – Complementary Therapies in Medicine

Waste and extremophile microbiology

Anaerobic digestion of biowaste under extreme ammonia concentration: Identification of key microbial phylotypes – Simon Poirier – Bioresource Technology

Bioinformatics and metagenomics

Privacy-Preserving Microbiome Analysis Using Secure Computation – Justin Wagner – Bioinformatics

Phages and viruses

Opinion: The Significance of Mutualistic Phages for Bacterial Ecology and Evolution – Nancy Obeng – Trends in Microbiology

Techniques

Unique sequence characteristics account for good DGGE separation of almost full-length 18S rDNAs – Zhiqing Huang – World Journal of Microbiology and Biotechnology

Microbes in the news

New appreciation for human microbiome leads to greater understanding of human health – University of Oklahoma – EurekAlert

From Huts to Cities: How Changes in Dwellings Have Impacted Microbe Exposure for the Human Immune System – New York University Langone

Researchers outline progress in turning bacteria into mini construction workers – The Construction Index

Can we outrun Zika? Walk this street in Colombia and you’ll see how tough it is – Andrew Joseph – STATnews

Cranberries help urinary tract infections, but not as juice – Yvette Brazier – Medical News Today

Biofilm Formation Hampers Removal of Dangerous Bacteria from Hospital Surfaces – Medical Research

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February 11, 2016

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Sulphate reducing bacteria impair memory in mice, gastric microbiota after partial gastrectomy, geomicrobiology of the earth’s deep subsurface, and a viral genome assembly pipeline.

Events

Third International Workshop on Biological Soil Crusts, September 26-30, 2016 – Moab, Utah, USA

Human gut microbiota

Gastric microbiota and predicted gene functions are altered after subtotal gastrectomy in patients with gastric cancer – Ching-Hung Tseng – Scientific Reports

Research highlight: Gut microbiota: Microbes offer engineering strategies to combat cancer – Susan E. Erdman – Nature Reviews Gastroenterology & Hepatology

Review: The Reciprocal Interactions between Polyphenols and Gut Microbiota and Effects on Bioaccessibility – Tugba Ozdal – MDPI Nutrients

Review: Learning from microbial strategies for polysaccharide degradation – Glyn R. Hemsworth – Biochemical Society Transactions

Book chapter: Interactions Between Wine Polyphenols and Gut Microbiota – Carolina Cueva – Wine Safety, Consumer Preference, and Human Health

Microbiome models

Mice: Sulfate-reducing bacteria impairs working memory in mice – Nathaniel L. Ritz – Physiology & Behavior

Rats: Whole Rye Consumption Improves Blood and Liver n-3 Fatty Acid Profile and Gut Microbiota Composition in Rats – Fayçal Ounnas – PLOS ONE

Animal microbiome

Nematodes: Microbial communities in Globodera pallida females raised in potato monoculture soil – Caroline Eberlein – Phytopathology

Sponges: Distinctive features of the microbial diversity and the polyketide synthase genes spectrum in the community of the endemic Baikal sponge Swartschewskia papyracea – O. V. Kaluzhnaya – Russian Journal of Genetics

Plant, root, and soil microbiome

Medicago truncatula Gaertn. as a model for understanding the mechanism of growth promotion by bacteria from rhizosphere and nodules of alfalfa – Anna Kisiel – Planta

Relationship between in vitro characterization and comparative efficacy of plant growth-promoting rhizobacteria for improving cucumber salt tolerance – Sajid Mahmood Nadeem – Archives of Microbiology

Geomicrobiology and Metagenomics of Terrestrial Deep Subsurface Microbiomes –
M. Itävaara – Advances in Applied Microbiology

Soil Nitrogen Status Modifies Rice Root Response to Nematode-Bacteria Interactions in the Rhizosphere – Yanhong Cheng – PLOS ONE

Water microbiome

Pollution-induced community tolerance for in situ assessment of recovery in river microbial communities following the ban of the herbicide diuron – Stéphane Pesce – Agriculture, Ecosystems & Environment

Built environment microbiology

Characterization of a drinking water distribution pipeline terminally colonized by Naegleria fowleri – Matthew J. Morgan – Environmental Science & Technology

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

Bioreactor microbiology

Anaerobic digestion of biowaste under extreme ammonia concentration: Identification of key microbial phylotypes – Simon Poirier – Bioresource Technology

Bioinformatics, viruses, metabolomics, and metagenomics

VirusTAP: Viral Genome-Targeted Assembly Pipeline – Akifumi Yamashita – Frontiers in Microbiology

The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production – Tilmann Weber – Synthetic and Systems Biotechnology

Microbes in the news

Inhibiting age-related inflammation maintains healthy gut microbiota and extends lifespan – MedicalXpress

An Occupy Movement for the Symbiome – Marti Davidson Sichel – GenEngNews

Middletown High students make bacteria glow in mobile lab – Sylvia Carignan – Frederick News Post
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Electric-car battery materials could harm key soil bacteria – American Chemical Society

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February 9, 2016

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Human skin metagenome, gout patients, malaria and gut microbes, the secrets of the rhizosphere, and single-stranded DNA phages.

Events

2nd Annual Translational Microbiome Conference – April 20-21 2016, Boston MA

Pregnancy and birth

Longitudinal Prediction of the Infant Gut Microbiome with Dynamic Bayesian Networks – Michael J. McGeachie – Scientific Reports

Review: Gut microbiota and the pathogenesis of necrotizing enterocolitis in preterm neonates – Nadim Cassir – Future Microbiology

Human skin microbiome

Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing – Yu-Chih Tsai – mBio

Human urinary tract microbiome

Male non-gonococcal urethritis: From microbiological etiologies to demographic and clinical features – Shin Ito – International Journal of Urology

Research highlight: Altered gut microbiota in CKD – Jessica K. Edwards – Nature Reviews Nephrology

Human respiratory microbiome

Review: Microbiome, biofilms, and pneumonia in the ICU – Massimiliano Pirrone – Current Opinion in Infectious Diseases

Human gut microbiome

Intestinal Microbiota Distinguish Gout Patients from Healthy Humans – Zhuang Guo – Scientific Reports

Effect of Proton Pump Inhibitors and Antibiotics on the Gut Microbiome of Hospitalised Older Persons – Caoilfhionn O’Donoghue – Journal of Infection

Editorial: A metabolic bridge between microbiota and humans – Kiyoshi Takeda – Nature Reviews Immunology

Review: The Gut Microbiome: Potential Innovations for the Understanding and Treatment of Psychopathology – Matilda E. Nowakowski – Canadian Psychology/Psychologie canadienne

Review: Metabolic modeling with big data and the gut microbiome – Jaeyun Sung – Applied & Translational Genomics

Review: The influence of commensal bacteria on infection with enteric viruses – Stephanie M. Karst – Nature Reviews Microbiology

Review: One more role for the gut: microbiota and blood brain barrier – Laure Michel – Annals of Translational Medicine

Review: Expanding role of gut microbiota in lipid metabolism – Anatole Ghazalpour – Current Opinion in Lipidology

Models of microbiome research

Mice: Composition of the gut microbiota modulates the severity of malaria – Nicolas F. Villarino – PNAS

Mice: Lambda Interferon Restructures the Nasal Microbiome and Increases Susceptibility to Staphylococcus aureus Superinfection – Paul J. Planet – mBio

Dogs: Longitudinal evaluation of the skin microbiome and association with microenvironment and treatment in canine atopic dermatitis – Charles W. Bradley – Journal of Investigative Dermatology

Goats: The effect of helminth infection on the microbial composition and structure of the caprine abomasal microbiome – Robert W. Li – Scientific Reports

More goats: Grain-rich diets altered the colonic fermentation and mucosa-associated bacterial communities and induced mucosal injuries in goats – Huimin Ye – Scientific Reports

Rats: The Colonic Microbiome and Epithelial Transcriptome Are Altered in Rats Fed a High-Protein Diet Compared with a Normal-Protein Diet – Chunlong Mu – The Journal of Nutrition

Rats: Resistant Starch Alters Gut Microbiome and Metabolomics Profiles Concurrent with Amelioration of Chronic Kidney Disease in Rats – Dorothy A. Kieffer – American Journal of Physiology – Renal Physiology
http://ajprenal.physiology.org/content/early/2016/02/01/ajprenal.00513.2015.abstract

Drosophila: From pathogens to microbiota: how Drosophila intestinal stem cells react to gut microbes – Alessandro Bonfini – Developmental & Comparative Immunology

Animal microbiome

Host plant determines the population size of an obligate symbiont Buchnera aphidicola in aphids – Yuan-Chen Zhang – Applied and Environmental Microbiology

Altered Carbohydrates Allocation by Associated Bacteria-fungi Interactions in a Bark Beetle-microbe Symbiosis – Fangyuan Zhou – Scientific Reports

Plant, root, and soil microbiome

Soil amendments yield persisting effects on the microbial communities—a 7-year study – Catherine L. Reardon – Applied Soil Ecology

Microbial genetic and enzymatic responses to an anthropogenic phosphorus gradient within a subtropical peatland – Elise Morrison – Geoderma

Salinity altered root distribution and increased diversity of bacterial communities in the rhizosphere soil of Jerusalem artichoke – Hui Yan – Scientific Reports

Development of oligonucleotide microarrays for simultaneous multi-species identification of Phellinus tree-pathogenic fungi – Yuh Tzean – Microbial Biotechnology

Dilution reveals how viral lysis and grazing shape microbial communities – Jacob A. Cram – Limnology and Oceanography

Response of Soil Bacterial Community Structure to Land-use Conversion of Natural Forests in Maoershan National Forest Park, China – Fanjuan Meng – Molecular Soil Biology

Editorial: Unlocking the Secrets of the Rhizosphere – Susanne C. Brink – Trends in Plant Science

Spotlight: The soil-borne supremacy – Corné M.J. Pieterse – Trends in Plant Science

Water and pollution microbiome

Temporal and spatial changes of microbial community in an industrial effluent receiving area in Hangzhou Bay – Yan Zhang – Journal of Environmental Sciences

Built environment microbiome

Metagenomic Analysis Indicates Epsilonproteobacteria as a Potential Cause of Microbial Corrosion in Pipelines Injected with Bisulfite – Dongshan An – Frontiers in Microbiology

Viruses and phages

Viral metagenomics: are we missing the giants? – S Halary – Current Opinion in Microbiology

Single-Stranded DNA Phages: From Early Molecular Biology Tools to Recent Revolutions in Environmental Microbiology – Anna J. Székely – FEMS Microbiology Letters

Sequencing techniques

A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms – Nagaraju Indugu – PeerJ

Bioinformatics and metagenomics

Improved environmental genomes via integration of metagenomic and single-cell assemblies – Daniel R. Mende – Frontiers in Microbiology

PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes – Ivan Gregor- PeerJ

Estimating and comparing microbial diversity in the presence of sequencing errors – Chun-Huo Chiu – PeerJ

Metabolomics

Metabolic modeling with big data and the gut microbiome – Jaeyun Sung – Applied & Translational Genomics

More microbiology

Cyanobacteria use micro-optics to sense light direction – Nils Schuergers – eLIFE

Ultrasensitive Detection of Bacteria by Targeting Abundant Transcripts – Xinhui Wang – Scientific Reports

Microbes in the news

Pill measures gut gas – Swallowable tool may eventually help reveal digestive problems – Sarah Schwartz – Science News

Gut environment could reduce severity of malaria – EurekAlert

Great stockphoto: Hibernation Helpers: Gut microbes may help regulate the metabolic changes a bear experiences before and during hibernation, scientists show – Catherine Offord – The Scientist

The complex marketing of “probiotic” cosmetics – Éva Lagarde – Premium Beauty News

Plants trick bacteria into attacking too soon – Chris Samoray – Science News

Obstructive sleep apnea-induced hypertension linked to gut microbiome – Baylor College of Medicine

Includes Rob Knight. HT: Tomer Altman. Deepak Chopra Convenes 30+ of the World’s Preeminent Thought Leaders, Philosophers, Scientists, Musicians and Artists to Explore Consciousness at a 3-Day Symposium This Fall – PR Newswire

Researchers identify most dangerous strains of often-deadly bacteria – University of Maryland – EurekAlert

Science, publishing, and career

Harvard Medical School students decry lack of diversity – Melissa Baily – STATnews

I make an appearance here: Getting credit for peer review – Sandeep Ravindran – Science

Change the system to halt harassment – Joan Schmelz – Nature

Bik’s Picks

The peptidergic control circuit for sighing – Peng Li – Nature

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February 8, 2016

Posted on by

Plasmid-mediated salt tolerance in the gut microbiota, Tuft cells and immunity, microbes of the Cerrado, impact of sequencing technique on microbiota analysis, and a new microbiome tool on the cloud.

Events

Introducing Nephele, NIAID’s new cloud-based microbiome analysis tool. Webinar on March 7. See also under Bioinformatics below.

Human oral microbiome

Research highlight: FISHing in the oral microbiota – Naomi Attar – Nature Reviews Microbiology

Human gut microbiome

Intestinal microbiota in inflammatory bowel disease and carcinogenesis: Implication for therapeutics – Steven D. Bruner – Clinical Pharmacology & Therapeutics

Evidence for plasmid mediated salt tolerance in the human gut microbiome and potential mechanisms – Eileen Broaders – FEMS Microbiology Ecology

Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD – Thomas Lee – Gut

Review: Novel Strategies for Applied Metagenomics – Moore-Connors, Jessica M. – Inflammatory Bowel Diseases

Research highlight: ntestinal microbiota in inflammatory bowel disease and carcinogenesis: Implication for therapeutics – Steven D. Bruner – Clinical Pharmacology & Therapeutics

Models of microbiome research

Tuft cells, taste-chemosensory cells, orchestrate parasite type 2 immunity in the gut – Michael R. Howitt – Science

Effects of dietary resistant starch content on metabolic status, milk composition, and microbial profiling in lactating sows and on offspring performance – H. Yan – Journal of Animal Physiology and Animal Nutrition

Beneficial Effects of Fecal Microbiota Transplantation on Ulcerative Colitis in Mice – Zhihui Tian – Digestive Diseases and Sciences

Plant, root, and soil microbiome

Soil bacterial communities associated with natural and commercial Cyclopia spp. – Anneke Postma – FEMS Microbiology Ecology

Diversity and functional traits of culturable microbiome members, including cyanobacteria in the rice phyllosphere – Siddarthan Venkatachalam – Plant Biology

Microbial Diversity in Cerrado Biome (Neotropical Savanna) Soils – Alinne Pereira de Castro – PLOS ONE

Dissipation and effects of tricyclazole on soil microbial communities and rice growth as affected by amendment with alperujo compost – M. García-Jaramillo – Science of The Total Environment

Opinion: Plant microbiota affects seed transmission of phytopathogenic micro-organisms – Matthieu Barret – Molecular Plant Pathology

Built environment microbiome

Indoor microbial communities: Influence on asthma severity in atopic and nonatopic children – Karen C. Dannemiller – The Journal of Allergy and Clinical Immunology

Antibiotics in drinking water in Shanghai and its contribution to antibiotic exposure of school children – Hexing Wang – Environmental Science & Technology

Pollution and waste microbiology

Characterisation of biofilm and planktonic bacterial and fungal communities transforming high molecular weight polycyclic aromatic hydrocarbons – Benjamin D Folwell – Applied and Environmental Microbiology

Shift in antibiotic resistance gene profiles associated with nanosilver during wastewater treatment – Yanjun Ma – FEMS Microbiology Ecology

Evaluating the Metal Tolerance Capacity of Microbial Communities Isolated from Alberta Oil Sands Process Water – Mathew L. Frankel- PLOS ONE

Nutrient and metal pollution of the eastern Gulf of Finland coastline: Sediments, macroalgae, microbiota – Yulia Gubelit – Science of the Total Environment

Impacts of pristine and transformed Ag and Cu engineered nanomaterials on surficial sediment microbial communities appear short-lived – Joe D Moore – Environmental Science & Technology

Food microbiology

Diversity and Stability of Lactic Acid Bacteria in Rye Sourdoughs of Four Bakeries with Different Propagation Parameters – Ene Viiard – PLOS ONE

Techniques

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis – Adam G. Clooney – PLOS ONE

Don’t put all your eggs in one basket: a cost-effective and powerful method to optimize primer choice for rRNA environmental community analyses using the Fluidigm Access Array – Shawn P. Brown – Molecular Ecology Resources

Probiotics

Probiotic and Functional Characterization of Bifidobacteria of Indian Human Origin – Nancy Awasti – Journal of Applied Microbiology

Bioinformatics

Nephele, microbiome analysis without boundaries. NIAID’s new tool offering cloud-based storage, file transfer, and analysis.

Note: 16S is not the same as metagenomics: Vikodak – A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets – Sunil Nagpal – PLOS ONE

Microbes in the news

Smart Science: Wolbachia Bacteria Might Stop Zika and Dengue Viruses – Judy Stone – Forbes

The science of treating depression during pregnancy – Josie Glausiusz – Quartz

GIANTmicrobes – When Teachers Throw Things – Anne Estes

Gut bacteria may influence alcoholics’ liver damage – Kathryn Doyle – Reuters
Scientists Seek Answers on Zika in Other Viruses – Carl Zimmer – New York Times

Bears’ Hibernation Linked To Unusual Changes In Their Gut Microbes – Samantha Mathewson – Nature World News

Bears hibernate ‘with bacterial help’ – Jonathan Webb – BBC News

The Tardigrade story a.k.a. Open Science Wins – Surya Saha – Storify

This Bacteria-Powered Microrobot Navigates via Electric Fields – Michael Byrne – Motherboard

Sainsbury’s Recall Camembert Cheese Products Over Food Poisoning Concerns – Natasha Hinde – The Huffington Post UK

EFSA update: Fully defining microbiota cause-and-effect: Yolanda Sanz provides update –
Will Chu – Nutraingredients

Satire: Trump Proposes Ban On All Microbiome Researchers “Until We Know What They Are Up To” “When I become president, we are going to make American poo great once again.” – The Allium

Bacteria Hysteria

What’s hiding in your handbag? Contact 6 tests purses for bacteria – Katrina Cravy – Fox

Bik’s Picks

Natural History Museums Are Teeming With Undiscovered Species – Ed Yong – The Atlantic

New species of tarantula found near Folsom Prison named for Johnny Cash – Rachel Feltman – Washington Post

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