Author Archives: eliesbik

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 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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February 20, 2016

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Effects of ocean acidification, structural proteins in viral dark matter, and microbiome art. Also check out my new post at MicroBE.net with new papers on microbiome of the built environment.

Human respiratory tract microbiome

Review: How Recent Advances in Molecular Tests Could Impact the Diagnosis of Pneumonia – David Murdoch – Expert Review of Molecular Diagnostics

Microbiome models

In vitro fermentation of alginate and its derivatives by human gut microbiota – Miaomiao Li – Anaerobe

Plant, root, and soil microbiome

Changes of soil prokaryotic communities after clear cutting in a karst forest: evidences for cutting-based disturbance promoting deterministic processes – Xiao Zhang – FEMS Microbiology Ecology

Use of mulberry–soybean intercropping in salt–alkali soil impacts the diversity of the soil bacterial community – Xin Li – Microbial Biotechnology

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments – Lidianne L. Rocha – International Journal of Microbiology

Water and ice microbiome

Quantification of the effects of ocean acidification on sediment microbial communities in the environment: the importance of ecosystem approaches – Christiane Hassenrück – FEMS Microbiology Ecology

Bacterial communities from Arctic seasonal sea ice are more compositionally variable than those from multi-year sea ice – Ido Hatam – The ISME Journal

Bioreactor and waste microbiology

Biodegradation of different petroleum hydrocarbons by free and immobilized microbial consortia – Tiantian Shen – Environmental Science: Processes & Impacts

Bioinformatics and metagenomics

Recent Developments in Using Advanced Sequencing Technologies for the Genomic Studies of Lignin and Cellulose Degrading Microorganisms – Ayyappa kumar Sista Kameshwar – International Journal of Biological Sciences

DUDE-Seq: Fast, flexible, and robust denoising of nucleotide sequences – Byunghan Lee – Bioinformatics

HTSFinder: Powerful Pipeline of DNA Signature Discovery by Parallel and Distributed Computing – Ramin Karimi – Evolutionary Bioinformatics

FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance – Syun-ichi Urayama – Microbes and Environments

Based on my old discovery of the mycobacterial CRISPR: SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads – Eryu Xia – Genome Medicine

Microbial ecology

A tradeoff between the ecological and evolutionary stabilities of public goods genes in microbial populations – Joseph Rauch – BioRxiv

Agent Based Modeling of Human Gut Microbiome Interactions and Perturbations – Tatiana Shashkova – PLOS ONE

Proteomics

Illuminating structural proteins in viral “dark matter” with metaproteomics – Jennifer R. Brum – PNAS

Microbes in the news

‘Unhealthy’ Microbiomes Could Promote Metabolic Disease. UCSF Symposium Explores Vulnerability and Malleability of Microbes in Human Gut – Nicholas Weiler – University of California San Francisco

Unusual sugar in leafy greens may help gut bacteria protect health – Catharine Paddock – Medical News Today

One startup’s plan to grow more crops: put the germs back in. Indigo claims it can dramatically boost yields by restoring plant’s microbiome – Ben Popper – The Verge

The intestinal microbiota—a new ally for optimum growth – Medical Xpress

Bacteria In Contact Lenses May Cause Inflammatory Response Leading To Microbial Keratitis / Gross Science Video with Anna Rothschild – Lizette Borreli – Medical Daily

Bacteria Hysteria

Tea crawling with harmful bacteria and food trays covered in faeces: The horror health threats facing airline passengers – The Sun

Microbes and art

Faces of BioArt: Sonja Bäumel’s Microbiome Portraits and Bacterial Clothing – Labiotech

Science, publishing, and career

Put the “Ph” Back in PhD. We need big thinkers, but the current system teaches students to think small – Arturo Casadevall

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February 19, 2016

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My PhD anniversary today! Today I found papers on primary sclerosing cholangitis, fungi from goat guts, dispersal from biofilms.

Human gut microbiome

The gut microbial profile in patients with primary sclerosing cholangitis is distinct from patients with ulcerative colitis without biliary disease and healthy controls – Martin Kummen – Gut

Review: Obesity, Asthma, and the Microbiome – Youngji Cho – Physiology

Microbiology of infection

Bacterial biofilm infection detected in breast implant associated anaplastic large cell lymphoma – Hu, Honghua – Plastic and Reconstructive Surgery

Animal models

Peripheral Lymphoid Volume Expansion and Maintenance Are Controlled by Gut Microbiota via RALDH+ Dendritic Cells – Zongde Zhang – Immunity

Important Metabolic Pathways and Biological Processes Expressed by Chicken Cecal Microbiota – Ondrej Polansky – Applied and Environmental Microbiology

Lingonberries reduce atherosclerosis in Apoe-/- mice in association with altered gut microbiota composition and improved lipid profile – Chrysoula Matziouridou – Molecular Nutrition & Food Research

Emerging role of lipid droplets in Aedes aegypti immune response against bacteria and Dengue virus – Ana Beatriz Ferreira Barletta – Scientific Reports

Animal microbiome

Goats! Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes – Kevin V. Solomon – Science

Identification of Specialists and Abundance-Occupancy Relationships among Intestinal Bacteria of Aves, Mammalia, and Actinopterygii – Hyatt C. Green – Applied and Environmental Microbiology

Mucosal immunoglobulins at respiratory surfaces mark an ancient association that predates the emergence of tetrapods – Zhen Xu – Nature Communications

Plant, root, and soil microbiome

Opposing phylogenetic diversity gradients of plant and soil bacterial communities – Marta Goberna – Proceedings of the Royal Society B

Water microbiome

Functional metagenomic screen reveals new and diverse microbial rhodopsins – Alina Pushkarev – The ISME Journal

Ultrafiltration and Microarray for Detection of Microbial Source Tracking Marker and Pathogen Genes in Riverine and Marine Systems – Xiang Li – Applied and Environmental Microbiology

Pathogens in Ornamental Waters: A Pilot Study – Maria Nascimento – MDPI Int. J. Environ. Res. Public Health

More Microbiology

What Makes a Bacterial Species Pathogenic? Comparative Genomic Analysis of the Genus Leptospira – Derrick E. Fouts – PLOS NTD

Go Forth and Colonize: Dispersal from Clinically Important Microbial Biofilms – Priya Uppuluri – PLOS Pathogens

Microbes in the news

Fungi from goats’ guts could lead to better biofuels – Matt McGrath – BBC News

Mapping the microbes in your mouth: We spoke to lead author Dr Gary Borisy about the research published in PNAS this month. – Microbe Post

Penn Study Reveals How Fish Control Microbes Through Their Gills – PennNews

93% of Israel’s Fresh Chicken Has Dangerous Bacteria (Campylobacter) – Forward

Electroporation 2.0: Breaking through the bacteria barrier: New microfluidic device may speed up DNA insertion in bacteria, the first step in genetic engineering – MIT News

Gut Microbes and Milk Compounds Tackle Childhood Malnutrition – Pat Bailey – UC Davis

Porcine Probiotic May Help Protect Gut Health – Susan Bubak – University of Guelph
Could Fecal Transplants From Rich Children Help Starving Kids in Africa? – Kari Paul – Motherboard

BiofilmDNA oral microbial salivary test to be launched by Oravital Inc. during 2016 Chicago Midwinter Meeting – DentistryIQ

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February 18, 2016

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Two papers from the Gordon lab today about malnutrition and gut microbes, connecting gut microbes with host chitin, fur seals, and analyzing soil communities for forensic use.

Pregnancy and birth

(partly in mice) Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children – Laura V. Blanton – Science

Sialylated Milk Oligosaccharides Promote Microbiota-Dependent Growth in Models of Infant Undernutrition – Mark R. Charbonneau – Cell

Editorial: The right gut microbes help infants grow – Elizabeth Pennisi – Science

Stool bacterial load in preterm infants with necrotising enterocolitis – Bashir Abdulkadir – Early Human Development

Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study – Guilherme Calvet – The Lancet Infectious Diseases

Human gut microbiome

Gut Microbiota Predict Pulmonary Infiltrates After Allogeneic Hematopoietic Cell Transplantation – Bianca Harris – Am J Respir Crit Care Med

Members of the Intestinal Microbiota Are Associated with Relapse after Allogeneic Hematopoietic Stem Cell Transplantation – Jonathan U. Peled – Biology of Blood and Marrow Transplantation

Conference abstract: Fecal Microbiota Transplant Is a Potentially Safe and Effective Treatment for Clostridium Difficile Infection in Hematopoietic Stem Cell Recipients – Shannon Falconer – Biology of Blood and Marrow Transplantation

The impact of gut colonization by antibiotic-resistant bacteria on the outcomes of allogeneic hematopoietic stem-cell transplantation: a retrospective, single-center study – Jaroslaw Bilinski – Biology of Blood and Marrow Transplantation

 

PhD Thesis: Temporal Modulation of Gut Microbiome and Metabolome by Morphine – Fuyuan Wang – University of Minnesota

Research highlight: Frailty associated with gut microbiota – Iain Dickson – Nature Reviews Gastroenterology & Hepatology

Review: Exploring the Microbiome in Heart Failure – Takeshi Kitai – Current Heart Failure Reports

Perspective: The microbiome and development of allergic disease – Susan V. Lynch – Current Opinion in Allergy and Clinical Immunology

Hypothesis: The gut microbiota: A puppet master in the pathogenesis of endometriosis? – Matthias W. Laschke – American Journal of Obstetrics and Gynecology

Editorial: Microbiota, Obesity and Malnutrition – Didier Raoult – Microbial Pathogenesis

Review: Protective and Pro-Inflammatory Roles of Intestinal Bacteria – Cynthia Reinoso Webb – Pathophysiology

Models of microbiome

Mice: Hepatic circadian clock oscillators and nuclear receptors integrate microbiome-derived signals – Alexandra Montagner – Scientific Reports

Lactobacillus plantarum strain maintains growth of infant mice during chronic undernutrition – Martin Schwarzer – Science

Mice: Butyrate production from high-fiber diet protects against lymphoma tumor – Wei Wei – Leukemia & Lymphoma

Drosophila: Sex difference in pathology of the ageing gut mediates the greater response of female lifespan to dietary restriction – Jennifer C Regan – eLIFE

Mice: Treatment with a Monoclonal Anti-IL-12p40 Antibody Induces Substantial Gut Microbiota Changes in an Experimental Colitis Model – Josué Castro-Mejía – Gastroenterology Research and Practice

Mice: Diets enriched with cranberry beans alter the microbiota and mitigate colitis severity and associated inflammation – Jennifer M. Monk – The Journal of Nutritional Biochemistry

Research Highlight: Microbiota promote gut healing – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Gut immunity in a protochordate involves a secreted immunoglobulin-type mediator binding host chitin and bacteria – Larry J. Dishaw – Nature Communications

Characterisation of the faecal bacterial community of wild young South American (Arctocephalus australis) and Subantarctic fur seals (Arctocephalus tropicalis) – Aline Weber Medeiros – FEMS Microbiology Ecology

16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife: the importance of cleaning post-sequencing data before estimating positivity, prevalence and co-infection – Maxime Galan – bioRxiv

Nestedness of hoopoes’ bacterial communities: symbionts from the uropygial gland to the eggshell – Juan J. Soler – Biological Journal of the Linnean Society

Plant, root, and soil microbiome

Biogeographic Patterns Between Bacterial Phyllosphere Communities of the Southern Magnolia (Magnolia grandiflora) in a Small Forest – Bram W. G. Stone – Microbial Ecology

Culturable endophytic bacteria from the salt marsh plant Halimione portulacoides: phylogenetic diversity, functional characterization, and influence of metal(loid) contamination – Cátia Fidalgo – Environmental Science and Pollution Research

Next-Generation Sequencing of the Bacterial 16S rRNA Gene for Forensic Soil Comparison: A Feasibility Study – Ellen M. Jesmok – Journal of Forensic Sciences

Water microbiome

Sediments and Soils Act as Reservoirs for Taxonomic and Functional Bacterial Diversity in the Upper Mississippi River – Christopher Staley – Microbial Ecology

The Influence of Time and Plant Species on the Composition of the Decomposing Bacterial Community in a Stream Ecosystem – Adam S. Wymore – Microbial Ecology

Built environment microbiome

Commentary: Making microbiology of the built environment relevant to design – G. Z. Brown – Microbiome

Food microbiology

Changes of microbial spoilage, lipid-protein oxidation and physicochemical properties during post mortem refrigerated storage of goat meat – Azad Behnan Sabow – Animal Science Journal

Metagenomic analysis of a Mexican ripened cheese reveals a unique complex microbiota – Alejandra Escobar-Zepeda – Food Microbiology

Bioinformatics

An analysis of human microbe–disease associations – Wei Ma – Briefings in Bioinformatics

FN-Identify: Novel Restriction Enzymes-Based Method for Bacterial Identification in Absence of Genome Sequencing – Mohamed Awad – Advances in Bioinformatics

Microbial ecology

Capturing the Dynamic, Heterogeneous Response of Microbes to their Environment in the Human Microbiome – Julie Biteen – Biophysical Journal

Perspective: Microbial community modeling using reliability theory – Julie L Zilles – The ISME Journal

Microbes in the news

Could the right gut microbes help fight childhood malnutrition? – Rachel Feltman – Washington Post

Breast Milk Sugars Support Infant Gut Health – Anna Azvolinsky – The Scientist

Targeting gut microbes may reverse effects of childhood malnutrition
Healthy microbes, breast milk component suggest new treatment approach, mouse study shows – Julie Evangelou Strait – Washington University

How Microbes Make Malnutrition Worse. And how they can be marshaled to fight it – Ed Yong – The Atlantic

 

The Mushroom Death Suit is the latest in post-mortem, eco-friendly fashion – Atlas Obscura

Through Metagenomics Analysis, Researchers Uncover Zika Virus Genome in Amniotic Fluid – Genome Web

What’s bugging you now? The amazing potential of our bodies’ own bacteria – Trisha Macnair – Spectator Health

Gut bacteria may be the difference between well-fed and malnourished – Jacob Kastrenakes – The Verge

Creative Minds: Bacteria, Gene Swaps, and Human Cancer, featuring Julie Dunning Hotopp – Francis Collins – NIH Director’s Blog

This Startup Wants to Use Bacteria to Revolutionize How Our Food Is Produced – Beth Kowitt – Fortune

Bacteria Hysteria

Dad warns parents about Sistema Twist ‘N’ Sip drink bottles ‘hoarding bacteria’ – Stuff

Breast Milk Bought Online May Contain Bacteria That Could Harm Your Child, Investigation Finds – Inside Edition

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