Category Archives: Human oral

February 2, 2016, second edition

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Updated status of the microbial census, bacteria in the nasopharynx, deodorant and armpit microbiome, lichen microbiome, fungi on decomposing forest materials, and metagenomics cover the amplicon gaps. So many papers I had to do a second installment today!

Events and jobs

Microbiology and bioinformatics positions at Whole Biome in San Francisco. Wearing hoodies encouraged.

General microbiome

The status of the microbial census: an update – Patrick D Schloss – BioRxiv

Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes – Kevin R Theis – BioRxiv

Human oral microbiome

Interactions between Streptococcus oralis, Actinomyces oris, and Candida albicans in the development of multispecies oral microbial biofilms on salivary pellicle – Indira M.G. Cavalcanti – Molecular Oral Microbiology

Human respiratory microbiome

Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure – Wouter A. A. de Steenhuijsen Piters – mBio 

Human skin microbiome

The effect of habitual and experimental antiperspirant and deodorant product use on the armpit microbiome – Julie Urban – PeerJ

Skin microbiome surveys are strongly influenced by experimental design – Jacquelyn S. Meisel – Journal of Investigative Dermatology

Unique features of a global human ectoparasite identified through sequencing of the bed bug genome – Joshua B. Benoit – Nature Communications

Human vaginal microbiome

Hormonal Contraceptive Effects on the Vaginal Milieu: Microbiota and Immunity – Jessica Tarleton – Current Obstetrics and Gynecology Reports

Human gut microbiome

Sex differences in the gut microbiome–brain axis across the lifespan – Eldin Jašarević – Philosophical Transactions of the Royal Society B

Very poor English and presentation, does not look peer reviewed: Preliminary analysis showed country-specific gut resistome based on 1267 feces samples – Zhenyu Yang – Gene

Confusing study design and interpretations: Gut Microbiota Linked to Sexual Preference and HIV Infection – Marc Noguera-Julian – EBioMedicine

Sequence-based methods for detecting and evaluating the human gut mycobiome – M.J. Suhr – Letters in Applied Microbiology

Review: Microbiota and arthritis: correlations or cause? – Bravo-Blas, Alberto – Current Opinion in Rheumatology

Perspective: Gut microbiota in 2015: Prevotella in the gut: choose carefully – Ruth E. Ley – Nature Reviews Gastroenterology & Hepatology

Editorial: PPIs alter gut microbiota composition – Nature Reviews Gastroenterology & Hepatology

Review: Samples and techniques highlighting the links between obesity and microbiota –
Emmanouil Angelakis – Microbial Pathogenesis

Animal models of microbiome

Bidirectional interactions between indomethacin and the murine intestinal microbiota – Xue Liang – eLife

 

Mixed feelings about this study that killed turtles to look at effect of probiotics on their shells: Dietary Probiotics Affect Gastrointestinal Microbiota, Histological Structure and Shell Mineralization in Turtles – Mateusz Rawski – PLOS ONE

Animal microbiome

The Role of the Microbial Environment in Drosophila Post-Embryonic Development –
Maura Strigini – Developmental & Comparative Immunology

Plant, root, and soil microbiome

Review about lichen bacterial microbiome: Understanding microbial multi-species symbioses – Ines A. Aschenbrenner – Frontiers in Microbiology

Dead fungal mycelium in forest soil represents a decomposition hotspot and a habitat for a specific microbial community – Vendula Brabcová – New Phytologist

Litter decomposition, residue chemistry and microbial community structure under two subtropical forest plantations: A reciprocal litter transplant study –
Zongming He – Applied Soil Ecology

Disentangling nematode-bacteria interactions using a modular soil model system and biochemical markers – Michael Ackermann – Nematology

Using native trees and cacti to improve soil potential nitrogen fixation during long-term restoration of arid lands – Nguyen E. Lopez-Lozano – Plant and Soil

Warming and nitrogen deposition are interactive in shaping surface soil microbial communities near the alpine timberline zone on the eastern Qinghai–Tibet Plateau, southwestern China – Qinli Xiong – Applied Soil Ecology

Short-term effects of mechanical drainage on fungal and bacterial community structure in a managed grassland soil – B.J. Fay – Applied Soil Ecology

Water and extremophile microbiome

Microbial Communities in Methane- and Short Chain Alkane-Rich Hydrothermal Sediments of Guaymas Basin – Frederick Dowell – Frontiers in Microbiology

Bioreactor and crude oil microbiology

Illumina MiSeq sequencing reveals the key microorganisms involved in partial nitritation followed by simultaneous sludge fermentation, denitrification and anammox process – Bo Wang – Bioresource Technology

Microbial communities of light crude from Nigeria and potential for in situ biodegradation, souring, and corrosion – Okoro Chuma Conlette – Petroleum Science and Technology

Built environment microbiome

Rhinitis, Ocular, Throat and Dermal Symptoms, Headache and Tiredness among Students in Schools from Johor Bahru, Malaysia: Associations with Fungal DNA and Mycotoxins in Classroom Dust – Dan Norbäck – PLOS ONE

Bioinformatics and metagenomics

Metagenomics uncovers gaps in amplicon-based detection of microbial diversity – Emiley A. Eloe-Fadrosh – Nature Microbiology

Development of an Analysis Pipeline Characterizing Multiple Hypervariable Regions of 16S rRNA Using Mock Samples – Jennifer J. Barb – PLOS ONE

Optimization of alignment-based methods for taxonomic binning of metagenomics reads – Magali Jaillard – Bioinformatics

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes – John A Lees – BioRxiv

Proteomics

Review: Recent development of mass spectrometry and proteomics applications in identification and typing of bacteria – Keding Cheng – Proteomics – Clinical Applications

Microbes in the news

Study shows maternal diet alters the breast milk microbiome and microbial gene content – EurekAlert

Deodorant And Antiperspirant Alter The Skin Microbiome, But Researchers Can’t Be Sure Of Long-Term Effects – Stephanie Castillo – Medical Daily

Beard bacteria could lead to new antibiotics – Matthew Stock – Reuters

Science, publishing, and career

“Those who can, publish. Those who can’t, blog.” Jingmai O’Connor – Current Biology

Chill out about Jingmai O’Connor’s criticism of bloggers – Jeremy Fox – Dynamic Ecology

Paul Knoepfler: Stem cell scientist finds his ‘niche’ in blogging – Karen Weintraub – STAT News

How to (not) write a microbiome grant, part I

How to (not) write a microbiome grant, part II. A deeper dive on preliminary data – David Baltrus – My Chrobial Romance

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February 2, 2016

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Events

Note: website was working yesterday, but not this morning. I hope to fix this soon. SCDA Workshop on Statistical and Algorithmic Challenges in Microbiome Data Analysis, Feb 25-26, New York

Pregnancy and birth microbiome

Not carefully worded, and not novel: New Insight into the Analysis of Amniotic Fluid Microflora using 16S rRNA Sequencing – Young-Ah You – JMM Case Reports

Human oral microbiome

Perspective: What Are We Learning and What Can We Learn from the Human Oral Microbiome Project? – Benjamin Cross – Current Oral Health Reports

Animal microbiome

Increasing the Richness of Culturable Arsenic-Tolerant Bacteria from Theonella swinhoei by Addition of Sponge Skeleton to the Growth Medium – Keren Ray – Microbial Ecology

Comparative studies of the composition of bacterial microbiota associated with the ruminal content, ruminal epithelium and in the faeces of lactating dairy cows –
Jun-hua Liu – Microbial Biotechnology

Experimental exposure to trace metals affects plumage bacterial community in the feral pigeon – M. Chatelain – Journal of Avian Biology

Plant, root, and soil microbiome

Effects of biogas and raw slurries on grass growth and soil microbial indices – Stefanie Wentzel – Journal of Plant Nutrition and Soil Science

Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression – Menno van der Voor – Ecology Letters

Impact of grassland management regimes on bacterial endophyte diversity differs with grass species – Franziska Wemheuer – Letters in Applied Microbiology

Novel soil fumigation method for suppressing cucumber Fusarium wilt disease associated with soil microflora alterations – Rong Li – Applied Soil Ecology

Water and extremophile microbiome

‘Candidatus Kryptonia’: Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs – Emiley A. Eloe-Fadrosh – Nature Communications

Novel Virophages Discovered in a Freshwater Lake in China – Chaowen Gong – Frontiers in Microbiology

Metagenomics and bioinformatics

Studying long 16S rDNA sequences with ultrafast-metagenomic sequence classification using exact alignments (Kraken) – Fabiola Valenzuela-González – Journal of Microbiological Methods

Opinion: From barcodes to genomes: extending the concept of DNA barcoding – Eric Coissac – Molecular Ecology

More microbes

Streptomyces thermoautotrophicus does not fix nitrogen – Drew MacKellar – Scientific Reports

Microbes in the news

How to (not) write a microbiome grant, Part I by David Baltrus

Does Having a C-Section Alter Baby’s First Microbiome? – Brian Handwerk – Smithsonian

Vaginal Microbes Can Be Partially Restored to C-Section Babies – Heather Buschman – UC San Diego Health

George Weinstock Discusses the Human Microbiome at Eastern – Michael Rouleau – Connecticut State University

‘Holy grail’ bacteria for crop farming debunked by scientists – Hayley Dunning – Imperial College London

Orange slime confirmed to be iron bacteria: Crenothrix polyspora – Herald Net

Iranian Researchers: Extraction of gold, copper from e-waste by two types of bacteria – The Iran Project

Microbes in an ancient mummy : We spoke to study author and microbiologist Dr Frank Maixner about the significance of this new research – MicrobePost
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January 25, 2016

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Today’s digest features biogeography of the human mouth, MALDI-TOF-MS, and microbes from ancient halite. OK, it is technically already Tuesday, but I was busy life tweeting from the Microbiome Symposium today at Stanford. The symposium featured many of the microbiome stars of our University – see my combined life tweets during the conference at Storify

Events

Gut microbiota in health and disease – from concept to evidence – March 17, 2016, Stockholm, Sweden. The symposium will be webcasted live at kva.se and will later be available as video-on-demand at kvatv.se.

Human oral microbiome

Biogeography of a human oral microbiome at the micron scale – Jessica L. Mark Welch – PNAS

Animal models of microbiome research

Experimental modulation of external microbiome affects nestmate recognition in harvester ants (Pogonomyrmex barbatus) – Andy Dosmann – PeerJ

Review: Incorporating the gut microbiota into models of human and non-human primate ecology and evolution – Katherine R. Amato – American Journal of Physical Anthropology

Animal microbiome

Faecal contamination of echinoderms: first report of heavy Escherichia coli loading of sea urchins from a natural growing area – M. Bouchoucha – Letters in Applied Microbiology

Extremophile microbiome

Review: Buried Alive: Microbes from Ancient Halite – Salla T. Jaakkola – Trends in Microbiology

Food microbiology

Effect of X-ray treatments on Escherichia coli O157:H7, Listeria monocytogenes, Shigella flexneri, Salmonella enterica and inherent microbiota on whole mangoes – B.S.M. Mahmoud – Letters in Applied Microbiology

Techniques

Advantage of MALDI-TOF-MS over biochemical-based phenotyping for microbial identification illustrated on industrial applications – S.K. Urwyler – Letters in Applied Microbiology

More microbiology

Fueling the Bio-economy: European Culture Collections and Microbiology Education and Training – André Antunes – Trends in Microbiology

Microbes in the news

Do probiotics cure asthma? Don’t believe the hype: Jonathan Eisen awards “prizes” to those who “oversell the microbiome” – Emma Bryce – Wired

The Forest In Your Mouth – Ed Yong – Phenomena National Geographic

Take your kids to the bugs on a Sunday afternoon – Micropia, the world’s only microbe zoo in Amsterdam – Mathias Grote – ASM Blog

IS-diagnostics Publishes Validation of PCR-Based Clinical Metagenomic MDx –  Madeleine Johnson – Genome Web

Bacteria Hysteria

Bacteria won’t wash, with the Brushield toothbrush cover – GizMag

Science, publishing, and career

#ResearchParasites and #ScienceColonialism – featuring Tweets from @DNLee5 & some discussion – Jonathan Eisen – Storify

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January 23, 2016

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Maturation of the mucin layer, periodontitis in Sjögren’s, Caenorhabditis elegans gut microbiota assembly, the rice-osphere, archaea in moonmilk, and microbial arsenic metabolism.

General human microbiome

The Human Microbiome and Public Health: Social and Ethical Considerations – Kieran C. O’Doherty – American Journal of Public Health

Pregnancy and birth

Review: Mucin–Microbiota Interaction During Postnatal Maturation of the Intestinal Ecosystem: Clinical Implications – Sana Rokhsefat- Digestive Diseases and Sciences

Human oral microbiome

Periodontitis prevalence and serum antibody reactivity to periodontal bacteria in primary Sjögren’s syndrome: a pilot study – Bozo Lugonja – Journal of Periodontology

Temporal Stability of the Salivary Microbiota in Oral Health – Daniel Belstrøm – PLOS ONE

Review: Immune dysregulation mediated by the oral microbiome: potential link to chronic inflammation and atherosclerosis – C. Slocum – Journal of Internal Medicine

Human gut microbiome

Review: Microbiota manipulation for weight change – Tal Dror – Microbial Pathogenesis

Review: Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances – M. P. Francino – Frontiers in Microbiology

Models of microbiome research

Modulating the Gut Microbiota Improves Glucose Tolerance, Lipoprotein Profile and Atherosclerotic Plaque Development in ApoE-Deficient Mice – Ida Rune – PLOS ONE

Dysbiosis of the fecal microbiota in the TNBS-induced Crohn’s disease mouse model – Qing He – Applied Microbiology and Biotechnology

Animal microbiome

Note that the worms did not develop into adults without having veggies to eat: Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments – Maureen Berg – The ISME Journal

Plant, root, and soil microbiome

Rice-osphere? Rice Genotype Differences in Tolerance of Zinc-Deficient Soils: Evidence for the Importance of Root-Induced Changes in the Rhizosphere – Asako Mori – Frontiers in Plant Science

A perspective on inter-kingdom signaling in plant–beneficial microbe interactions – Amanda Rosier – Plant Molecular Biology

Chemotaxis signaling systems in model beneficial plant–bacteria associations – Birgit E. Scharf – Plant Molecular Biology

Water and extremophile microbiome

Deciphering associations between dissolved organic molecules and bacterial communities in a pelagic marine system – Helena Osterholz – The ISME Journal

Unique pioneer microbial communities exposed to volcanic sulfur dioxide – Reiko Fujimura – Scientific Reports

Archaeal Distribution in Moonmilk Deposits from Alpine Caves and Their Ecophysiological Potential – Christoph Reitschuler – Microbial Ecology

Chemotaxis toward phytoplankton drives organic matter partitioning among marine bacteria – Steven Smriga – PNAS

Review: The microbial genomics of arsenic – Jérémy Andres – FEMS Microbiology Reviews

Food microbiology

Kombucha tea fermentation: Microbial and biochemical dynamics – Somnath Chakravorty – International Journal of Food Microbiology

PCR-denaturing gradient gel electrophoresis analysis of microbial community in soy-daddawa, a Nigerian fermented soybean (Glycine max (L.) Merr.) condiment – Obinna T. Ezeokoli – International Journal of Food Microbiology

Check your fridge for Thanksgiving leftovers: Direct Dynamic Kinetic Analysis and Computer Simulation of Growth of Clostridium perfringens in Cooked Turkey during Cooling – Lihan Huang – Journal of Food Science

Bioinformatics, metagenomics, and protocols

Protocol collection: Microbial Environmental Genomics (MEG)
MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function – Kevin P. Keegan
Reconstruction of Transformation Processes Catalyzed by the Soil Microbiome Using Metagenomic Approaches – Anne Schöler
Hybridization of Environmental Microbial Community Nucleic Acids by GeoChip – Joy D. Van Nostrand
Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning – Céline Ribière
Fungal Communities in Soils: Soil Organic Matter Degradation – Tomáš Větrovský
GenoSol Platform: A Logistic and Technical Platform for Conserving and Exploring Soil Microbial Diversity – Samuel Dequiedt

Microbes in the news

Exploring the human gut microbiome. Scientific interest in this diverse world of bacteria has flipped from fear to fascination – Sabin Russell – Fred Hutch

Fungi Prevalent in Urine of Women With Chronic Pelvic Pain – Pam Harrison – MedPageToday

Microscopic subway passengers with a ticket to ride: Interview with Chris Mason – Labnews

To Fight Growing Threat From Germs, Scientists Try Old-Fashioned Killer – Gautam Naik – The Wall Street Journal

http://www.cnn.com/2016/01/22/health/flint-water-legionnaires-disease/Flint hospital reports finding Legionnaires’ bacteria in water – Ralph Ellis – CNN

Breast milk protein could be used in fight against antibiotic resistance – The Guardian

Listeria outbreak: Dole packaged salad linked to 12 bacteria infections and one death – John Houck – Inquisitr

Science, publishing, and career

By a 13 year old girl: Letter to BBC Wildlife Magazine on sexism in nature conservation – Mya-Rose Craig – BirdGirl

Bik’s Picks

Secular trends in family dinner frequency among adolescents – Kathryn Walton – BMC Research Notes
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January 22, 2016

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Viruses in desert soils, pneumonia etiology, and a concerning editorial in NEJM.

Human oral microbiome

Microbiological analysis after complete or partial removal of carious dentin using two different techniques in primary teeth: A randomized clinical trial – Deepak Kumar Singhal – Dental Research Journal

Human respiratory microbiome

The Modern Quest for the “Holy Grail” of Pneumonia Etiology – Seema Jain – Clinical Infectious Diseases

Plant, root, and soil microbiome

Review: Diversity and Ecology of Viruses in Hyperarid Desert Soils – Olivier Zablocki – Applied and Environmental Microbiology

Use of Substrate-Induced Gene Expression in Metagenomic Analysis of an Aromatic Hydrocarbon-Contaminated Soil – Matthew J. Meier – Applied and Environmental Microbiology

Techniques / phages and viruses

Isolation of Polyvalent Bacteriophages by Sequential Multiple-Host Approaches – Pingfeng Yu – Applied and Environmental Microbiology

More microbiology

Tuberculosis in Newborns: The Lessons of the “Lübeck Disaster” (1929–1933) – Gregory J. Fox – PLOS Pathogens

Microbes in the news

For children: Understanding Marine Microbes, the Driving Engines of the Ocean – Anna Kopf

15 min podcast: A Microbiome Is Born – Science Friday

Good Bacteria for Good Skin – Beauty brands say there is a beneficial effect when probiotics and fermented ingredients are applied topically – Fiorella Valdesolo – Wall Street Journal

Your DNA could make you resistant to certain bacteria – gene expression could help explain why some people are more immune to infection than others – Alexandra Ossola – Popular Science

Science, publishing, and career

An editorial in NEJM called Data Sharing, written by Dan L. Longo and Jeffrey M. Drazen, caused a lot of concern because it calls scientists who use other people’s published data “parasites”. Some reactions:

Data Scientists = Research Parasites? – David Shaywitz – Forbes

Research “parasitism” and authorship rights – Leonid Schneider – For Better Science

Attack of the Research Parasites – Derek Lowe – Science Magazine blogs

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January 21, 2016

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Beards and MRSA in hospital workers, dysbiosis in Crohns Disease, non-absorbable antibiotics affect offspring in mice, bacterial sunscreens, and bacteria found in a sick-making building.

Events

2nd Annual Microbiome Symposium – January 25, 2016 – Stanford University, Palo Alto, CA

Pregnancy and birth

A necrotizing enterocolitis-associated gut microbiota is already present in the meconium: results of a prospective study – Fardou H. Heida – Clinical Infectious Diseases

Human oral microbiome

Salivary pathogen and serum antibody to assess the progression of chronic periodontitis: a 24-mo prospective multicenter cohort study – T. Morozumi – Journal of Periodontal Research

Human skin microbiome

Bacterial ecology of hospital workers’ facial hair: a cross-sectional study – E. Wakeam – Journal of hospital infection

Human respiratory microbiome

Correlation of the lung microbiota with metabolic profiles in bronchoalveolar lavage fluid in HIV infection – Sushma K. Cribbs – Microbiome

Human gut microbiome

Changes in Colonic Bile Acid Composition following Fecal Microbiota Transplantation Are Sufficient to Control Clostridium difficile Germination and Growth – Alexa R. Weingarden – PLOS ONE

Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn’s Disease – Takahashi K – Digestion

Detecting Microbial Dysbiosis Associated with Pediatric Crohn Disease Despite the High Variability of the Gut Microbiota – Feng Wang – Cell Reports

DNA fingerprinting approaches to trace Escherichia coli sharing between dogs and owners  – Z. Naziri – Journal of Applied Microbiology

Altered intestinal microbiota as a major driving force in alcoholic steatohepatitis – Herbert Tilg – Gut

Impact of Surotomycin on the Gut Microbiota of Healthy Volunteers in a Phase 1 Clinical Trial – Diane M. Citron – Antimicrobial Agents and Chemotherapy

Microbiome animal and bioreactor models

Administration of Non-Absorbable Antibiotics to Pregnant Mice to Perturb the Maternal Gut Microbiota Is Associated with Alterations in Offspring Behavior – Shiro Tochitani – PLOS ONE

Degradation of chondroitin sulfate by the gut microbiota of Chinese individuals –
Qingsen Shang – International Journal of Biological Macromolecules

Streptococcus pneumoniae colonization disrupts the microbial community within the upper respiratory tract of aging mice – Netusha Thevaranjan – Infection and Immunity

Assessing microbial competition in a hydrogen-based membrane biofilm reactor (MBfR) using multidimensional modeling – Kelly J. Martin – Biotechnology and Bioengineering

Animal microbiome

Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs – Pedro R. Frade – PLOS ONE

Plant, root, and soil microbiome

Bacteria increase arid-land soil surface temperature through the production of sunscreens – Estelle Couradeau – Nature Communications

Historical and current climate drive spatial and temporal patterns in fungal endophyte diversity – Hannah Giauque – Fungal Ecology

Location, location, location: priority effects in wood decay communities may vary between sites – Jennifer Hiscox – Environmental Microbiology

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation – Matthew T. Agler – PLOS Biology

Effect of altitude and season on microbial activity, abundance and community structure in Alpine forest soils – José A. Siles – FEMS Microbiology Ecology

Effects of manure and mineral fertilization strategies on soil antibiotic resistance gene levels and microbial community in a paddy–upland rotation system – Hui Lin – Environmental Pollution

Bacterial community compositions in sediment polluted by perfluoroalkyl acids (PFAAs) using Illumina high-throughput sequencing – Yajun Sun – Environmental Science and Pollution Research

Large amounts of easily decomposable carbon stored in subtropical forest subsoil is associated with r-strategy-dominated soil microbes – Yuping Chen – Soil Biology and Biochemistry

Water, waste, and extremophile microbiome

Effects of anthropogenic heavy metal contamination on litter decomposition in streams – A meta-analysis – Verónica Ferreira – Environmental Pollution

Investigation of the microbial community in the Odisha hot spring cluster based on the cultivation independent approach – Archana Singh – Genomics Data

Analysis of bacterial diversity in two oil blocks from two low-permeability reservoirs with high salinities – Meng Xiao – Scientific Reports

Occurrence of mycotoxins and yeasts and moulds identification in corn silages in tropical climate – B.F. Carvalho – Journal of Applied Microbiology

Food microbiology

Molecular diversity of bacteria in commercially available ‘‘Spirulina’’ food supplements – Elisabeth Vardaka – PeerJ

Ineffective hand washing and the contamination of carrots after using a field latrine – J M Monaghan – Letters in Applied Microbiology

Microbiological characterization using combined culture dependent and independent approaches of Casizolu pasta filata cheese – N.P. Mangia – Journal of Applied Microbiology

Microbial dynamics in mixed culture biofilms of bacteria surviving sanitation of conveyor belts in salmon-processing plants – S. Langsrud – Journal of Applied Microbiology

Built environment microbiology

Bacteria in a water-damaged building: associations of actinomycetes and non-tuberculous mycobacteria with respiratory health in occupants – J.-H. Park – Indoor Air

Bioinformatics and metagenomics

Review: Application of multivariate statistical techniques in microbial ecology – O. Paliy – Molecular Ecology

More microbiology

Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus – Kirsten I Bos – eLIFE

Review: Within-host evolution of bacterial pathogens – Xavier Didelot – Nature Reviews Microbiology

This is NOT novel and methods are missing essential steps: A novel method to assess the biodiversity of parasites using 18S rDNA Illumina sequencing; parasitome analysis method – Akina Hino – Parasitology International

Microbes in the news

Found: Desert Hot Spots Just For Microbes – Sarah Laskow – Atlas Obscura

Beards may be more hygienic and bacteria-resistant than shaven skin, study finds – Kate Ng – Independent
Beards may not be that gross, after all – Rachel Thompson – Mashable
Are beards good for your health? – BBC News Magazine

Bacteria or virus? New diagnostic tool could curb antibiotic overuse – Eric Boodman – STAT news

Getting to know the real you – how seriously should we take the health of our internal aliens? – LabNews UK

Probiotics come with bold health claims, but the science is shaky – Megan Scudellari – STAT news

Weekend binges just as bad for the gut as a regular junk food diet, study suggests – Dan Wheelahan – Medical Xpress

Can our gut microbiota contribute to the effect healthy foods have on us? – Gut Microbiota WorldWatch

Science, publishing, and career

Are results in top journals to be trusted? – SK – Economist

The best academic acknowledgements ever – Glen Wright – Times Higher Education
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January 20, 2016

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Virome of children with diarrhea, bacterial communities in black truffles, arsenic biogeochemistry in an acid vapor-formed spring, distribution of microbes in microenvironments, and retraction of a PLOS ONE air microbiome paper.

Jobs and events

New job openings at Whole Biome: develops therapeutics and diagnostics targeting human microbiome, casual culture, and artisanal coffee

Human oral microbiome

Exploration of Human Salivary Microbiomes—Insights into the Novel Characteristics of Microbial Community Structure in Caries and Caries-Free Subjects – Jianye Zhou – PLOS ONE

Human respiratory microbiome

COPD is characterized by increased detection of Haemophilus influenzae, Streptococcus pneumoniae and a deficiency of Bacillus species – Jodie L. Simpson – Respirology

Human gut microbiome

The fecal virome of South and Central American children with diarrhea includes small circular DNA viral genomes of unknown origin – Tung Gia Phan – Archives of Virology

Perspective: Gut microbiota and aging – Paul W. O’Toole – Science

Review: Studies on Modulation of Gut Microbiota by Wine Polyphenols: From Isolated Cultures to Omic Approaches – Montserrat Dueñas – MDPI Antioxidants

Animal models

Postnatal Hematopoiesis and Gut Microbiota in NOD Mice Deviate from C57BL/6 Mice – Dina Silke Malling Damlund – Journal of Diabetes Research

Bacterial profile and bone healing in rats receiving cancer therapeutic doses of bisphosphonates and corticosteroids: a pilot study – Z. Jabbour – International Journal of Oral & Maxillofacial Surgery

Interaction between dietary lipids and gut microbiota regulates hepatic cholesterol metabolism – Robert Caesar – Journal of Lipid Research

Gut Microbiota Regulates K/BxN Autoimmune Arthritis through Follicular Helper T but Not Th17 Cells – Katharine E. Block – The Journal of Immunology

Editorial: Of Bugs and Drugs: How the Microbiome Controls Responsiveness to Antitumor Immunotherapy – Mandy L. Ford – American Journal of Transplantation

Animal microbiome

Most Low-Abundance “Background” Symbiodinium spp. Are Transitory and Have Minimal Functional Significance for Symbiotic Corals – Moo Joon Lee – Microbial Ecology

Isolation and assessment of gut bacteria from the Formosan subterranean termite, Coptotermes formosanus (Isoptera: Rhinotermitidae), for paratransgenesis research and application – Chinmay V. Tikhe – Insect Science

Plant, root, and soil microbiome

Black truffle: Temporal changes of bacterial communities in the Tuber melanosporum ectomycorrhizosphere during ascocarp development – Aurélie Deveau – Mycorrhiza

Isolation of N2-fixing rhizobacteria from Lolium perenne and evaluating their plant growth promoting traits – Antonio Castellano-Hinojosa – Journal of Basic Microbiology

Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees – J. B. Vincent – Molecular Ecology

Water, waste, and extremophile microbiome

Metagenome-scale analysis yields insights into the structure and function of microbial communities in a copper bioleaching heap – Xian Zhang – BMC Genetics

Microbial Community Structure and Arsenic Biogeochemistry in an Acid Vapor-Formed Spring in Tengchong Geothermal Area, China – Zhou Jiang – PLOS ONE

Phylogenetic conservation of freshwater lake habitat preference varies between abundant bacterioplankton phyla – Marian L. Schmidt – Environmental Microbiology

Food and cigarette microbiome

Characterization of Bacterial Communities in Selected Smokeless Tobacco Products Using 16S rDNA Analysis – Robert E. Tyx – PLOS ONE

More microbes

Divorcing strain classification from species names – David Baltrus

Distributions of Virus-Like Particles and Prokaryotes within Microenvironments – Lisa M. Dann – PLOS ONE

Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli –
Sophie J. Weiss – PLOS ONE

Microbes in the news

Satire: Dung Beetle A Bit Fed Up With Diet – The Allium

How Climate Change Endangers Microbes–And Why That’s Not a Good Thing – Aspen T. Reese – Scientific American

CDC issues guidance to help monitor pregnant women for Zika virus – Helen Branswell – STATnews

Microbes and art

These Close-Up Shots Of Kitchen Mold Are Oddly Appealing: Nikita Teryoshin, Max Slobodda / Küchendienst – FastCoDesign

Science, publishing, and career

Here are the 10 — yes, 10 — reasons PLOS ONE retracted this paper (“Metagenomic Human Repiratory Air in a Hospital Environment”) – Shannon Palus – Retraction Watch

Ten easy ways you can support diversity in academia in 2016 – Jacquelyn Gyll – The Contemplative Mammoth

Bik’s Picks

When chickens go wild. The feral chickens of Kauai provide a unique opportunity to study what happens when domesticated animals escape and evolve – Ewen Callaway – Nature
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January 19, 2016

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Microbiota manipulation during stem cell transplants, meh-crobial diversity in digestive tract of two sheep breeds, eukaryotes within pitcher plants,  South Atlantic Ocean, and soil affected by the 2011 Japan Tsunami.

Events

ISME16, Montreal, Canada, 21 – 26 August 2016. Registration and Submissions now open. The deadline for submitting your abstract is 18 March.

ASM Career Development Grants for Postdoctoral Women – up to 4 awards of $1,500 each. Deadline for Nominations: February 1, 2016.

Fellowships by L’Oréal USA For Women In Science. Deadline Feb 5, 2016. Program awards five women postdoctoral scientists annually with grants of $60,000 each, in any specialty.

Human oral microbiome

Salivary bacterial fingerprints of established oral disease revealed by the Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) technique – Daniel Belstrøm – Journal of Oral Microbiology

Human gut microbiome

Sleep quality and the treatment of intestinal microbiota imbalance in Chronic Fatigue Syndrome: A pilot study – Melinda L. Jackson – Sleep Science

Fecal microbiota transplantation: A ‘How-To’ guide for nurses – Sharyn Leis – Collegian Journal

Review: Microbiota Manipulation With Prebiotics and Probiotics in Patients Undergoing Stem Cell Transplantation – Tessa M. Andermann – Current Hematologic Malignancy Reports

Review: Epigenetic Regulation of Enteric Neurotransmission by Gut Bacteria – Tor C. Savidge – Frontiers in Cellular Neuroscience

Bioreactor and animal models

Microbial Metabolism Shifts Towards an Adverse Profile with Supplementary Iron in the TIM-2 In vitro Model of the Human Colon – Guus A. M. Kortman – Frontiers in Microbiology

Video: A Novel Bioreactor for High Density Cultivation of Diverse Microbial Communities – Jacob R. Price – JOVE

Atlantic Salmon (Salmo salar L.) Gastrointestinal Microbial Community Dynamics in Relation to Digesta Properties and Diet – Kamarul Zaman Zarkasi – Microbial Ecology

Animal microbiome

Microbial diversity in the digestive tract of two different breeds of sheep – J.-L. Douglas – Journal of Applied Microbiology

Dynamics of Bacterial Community Composition in the Malaria Mosquito’s Epithelia – Majoline T. Tchioffo – Frontiers in Microbiology

Microbiota Plays a Role in Oral Immune Priming in Tribolium castaneum – Momir Futo – Frontiers in Microbiology

Plant, root, and soil microbiome

Dynamics of Viral Abundance and Diversity in a Sphagnum-Dominated Peatland: Temporal Fluctuations Prevail Over Habitat – Flore Ballaud – Frontiers in Microbiology

Biogeographic barriers drive co-diversification within associated eukaryotes of the Sarracenia alata pitcher plant system – Jordan D. Satler – PeerJ

Expanding our Understanding of the Seaweed Holobiont: RNA Viruses of the Red Alga Delisea pulchra – Tim Lachnit – Frontiers in Microbiology

New Methods To Unravel Rhizosphere Processes – Eva Oburger – Trends in Plant Science

Soil microbial responses to forest floor litter manipulation and nitrogen addition in a mixed-wood forest of northern China – Xiao-Lu Sun – Scientific Reports

Unraveling the Functions of the Macroalgal Microbiome – Ravindra Pal Singh – Frontiers in Microbiology

Water and extremophile microbiome

Diversity and bioprospection of fungal community present in oligotrophic soil of continental Antarctica – Valéria M. Godinho – Extremophiles

Novel Barite Chimneys at the Loki’s Castle Vent Field Shed Light on Key Factors Shaping Microbial Communities and Functions in Hydrothermal Systems – Ida H. Steen – Frontiers in Microbiology

High Diversity of Anaerobic Alkane-Degrading Microbial Communities in Marine Seep Sediments Based on (1-methylalkyl)succinate Synthase Genes – Marion H. Stagars – Frontiers in Microbiology

Nutrient limitation of microbial phototrophs on a debris-covered glacier – J.L. Darcy – Soil Biology and Biochemistry

Large-scale distribution of microbial and viral populations in the South Atlantic Ocean – Daniele De Corte – Environmental Microbiology Reports

Selective Pressure of Temperature on Competition and Cross-Feeding within Denitrifying and Fermentative Microbial Communities – Anna Hanke – Frontiers in Microbiology

A Lipid-Accumulating Alga Maintains Growth in Outdoor, Alkaliphilic Raceway Pond with Mixed Microbial Communities – Tisza A. S. Bell – Frontiers in Microbiology

Genomic Reconstruction of an Uncultured Hydrothermal Vent Gammaproteobacterial Methanotroph (Family Methylothermaceae) Indicates Multiple Adaptations to Oxygen Limitation – Connor T. Skennerton – Frontiers in Microbiology

Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami – Satoshi Hiraoka – BMC Genomics

Oil reservoir microbiome

Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs – Ping Hu – mBio

Food microbiology

Dynamic changes in microbiota and mycobiota during spontaneous ‘Vino Santo Trentino’ fermentation – Irene Stefanini – Microbial Biotechnology

Other microbiology and techniques

Perspective: Adapting Koch’s postulates – Allyson L. Byrd, Julia Segre – Science

Depletion of human DNA in spiked clinical specimens to improve the sensitivity of pathogen detection by next generation sequencing – Mohammad R. Hasan – Journal of Clinical Microbiology

Evaluation of a new device to simplify and standardize stool sample preparation for viral molecular testing with limited hands-on-time – Linda Feghoul – Journal of Clinical Microbiology

Review: Polymicrobial Biofilm Studies: from Basic Science to Biofilm Control – Hubertine ME Willems – Current Oral Health Reports

Review: Laser microdissection: A promising tool for exploring microorganisms and their interactions with hosts – Oleg V. Podgorny – Journal of Microbiological Methods

Book: Applications of Mass Spectrometry in Microbiology – Plamen Demirev, Todd R Sandrin – Springer

Metagenomics and bioinformatics

Searching more genomic sequence with less memory for fast and accurate metagenomic profiling – Shea N Gardner – bioRxiv

An evaluation of the accuracy and speed of metagenome analysis tools – Stinus Lindgreen – Scientific Reports

Motif-based text mining of microbial metagenome redundancy profiling data for disease classification – Yin Wang – BioMed Research International

Metabolic pathways

Metabolic traits of an uncultured archaeal lineage -MSBL1- from brine pools of the Red Sea – Romano Mwirichia – Scientific Reports

Microbes in the news

Looking at the Microbiota to Improve Intestinal Transplantation Results – Jeannette Y. Wick – HCP Live

Why do I have to share my body with so many bugs? – Michael Mosley – BBC

How Bitter Taste Receptors Defend the Body against Bacteria – Robert J Lee – Scientific American

White Paper: The Future of Microbiome Research: Out of the Lab and Into the Clinic – Global Engage

How chicory may help fight plague bacteria – Jason Tetro – Popular Science

Lethal bacteria in Christmas Island feral cats sparks warning (Leptospira) – Nicolas Perpitch – ABC Australia

Microbes and art

Subvisual Subway: The Art of New York City’s Bacterial World – Emily Driscoll – Science Friday

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January 16, 2016

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Gut microbiota in acute malnutrition, social behavior and the chimpanzee pan-microbiome, arctic marine fungi, and learning ecological networks.

General microbiome

Immune-Microbiota Interactions: Dysbiosis as a Global Health Issue – Alan C. Logan – Current Allergy and Asthma Reports

Human oral microbiome

Long-term prospective cohort study on dental implants: clinical and microbiological parameters – Henri Tenenbaum – Clinical Oral Implants Research

Human reproductive tract microbiome

Alterations in the Genital Microbiota in Women With Spinal Cord Injury – Pires, Cristhiane V.G. – Obstetrics & Gynecology

Human gut microbiome

Gut Microbiota in Children Hospitalized with Oedematous and Non-Oedematous Severe Acute Malnutrition in Uganda – Kia Hee Schultz Kristensen – PLOS Neglected Tropical Diseases

Editorial: Confounding Effects of Metformin on the Human Gut Microbiome in Type 2 Diabetes – Adil Mardinoglu – Cell Metabolism

Review: Impact of high fat diets, prebiotics and probiotics on gut microbiota and immune function, with relevance to elderly populations – Yue Liu – Nutrition and Aging

Review: Transkingdom control of viral infection and immunity in the mammalian intestine – Julie K. Pfeiffer – Science

Review: Micromanagement in the gut: microenvironmental factors govern colon mucosal biofilm structure and functionality – Rosemarie De Weirdt – NPJ Biofilms and Microbiomes

Animal models

In rats: Alternating or continuous exposure to cafeteria diet leads to similar shifts in gut microbiota compared to chow diet – Nadeem O. Kaakoush – Molecular Nutrition & Food Research

In mice: Streptomycin treatment alters the intestinal microbiome, pulmonary T cell profile and airway hyperresponsiveness in a cystic fibrosis mouse model – Mark Bazett – Scientific Reports

Animal microbiome

Social behavior shapes the chimpanzee pan-microbiome – Andrew H. Moeller – Science Advances

Environmental drivers of microbial community shifts in the giant barrel sponge, Xestospongia muta, over a shallow to mesophotic depth gradient – Kathleen M. Morrow – Environmental Microbiology

Feeding cessation alters host morphology and bacterial communities in the ascidian Pseudodistoma crucigaster – Susanna López-Legentil – Frontiers in Zoology

Plant, root, and soil microbiome

Uncultivated margins are source of soil microbial diversity in an agricultural landscape –
Luciana D’Acunto – Agriculture, Ecosystems & Environment

Editorial: Deep influence of soil microbes – Karl Gruber – Nature Plants

Review: Soil microbes and community coalescence – Matthias C. Rillig – Pedobiologia

Water and extremophile microbiome

Linkages between mineralogy, fluid chemistry, and microbial communities within hydrothermal chimneys from the Endeavor Segment, Juan de Fuca Ridge – T. J. Lin – Geochemistry, Geophysiscs, Geosystems

Exploration of microbial diversity and community structure of Lonar Lake: the only hypersaline meteorite crater lake within basalt rock – Dhiraj Paul – Frontiers in Microbiology

Vertical segregation and phylogenetic characterization of ammonia-oxidizing bacteria and archaea in the sediment of a freshwater aquaculture pond – Shimin Lu – Frontiers in Microbiology

Chytrids Dominate Arctic Marine Fungal Communities – B.T. Hassett – Environmental Microbiology

Built environment microbiome

Bacterial Monitoring in the International Space Station-“Kibo” Based on rRNA Gene Sequence – Nobuyasu Yamaguchi – Transactions of the Japan Society for Aeronautical and Space Sciences

Metagenomics and bioinformatics

Safe and complete contig assembly via omnitigs – Alexandru I. Tomescu – ArXiv

More microbiology and ecology

How clonal are bacteria over time? – B. Jesse Shapiro – BioRxiv

Transcription Factors Exhibit Differential Conservation in Bacteria with Reduced Genomes – Edgardo Galán-Vásquez – PLOS ONE

Learning Ecological Networks from Next-Generation Sequencing Data – Corinne Vacher – Advances in Ecological Research

Microbes in the news

Chimps Share Microbes When Socializing – Kate Yandell – The Scientist

How Your Social Life Changes Your Microbiome – Ed Yong – The Atlantic

Social Contact Helps Beneficial Gut Bacteria Spread – Brian Handwerk – Smithsonian

Prevent severe diarrhea by controlling levels of specific gut bacteria – Bel Marra Health

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January 14, 2016

Posted on by

Sorry for a late post today – I had a lot of meetings. Here is what I found:

Gut microbiota shaped via fecal microRNA, the microgenderome, dysbiosis in Vitiligo skin lesions, metatranscriptomics, and an 18th century Yersinia pestis.

General microbiome

Perspective: Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease – Niv Zmora – Cell Host & Microbe

The Human Microbiome: Opportunities for Dynamics, Systems, and Control
(based on the IFAC blog post Translate or Die) – Travis E. Gibson – Submitted to ACC 2016

Human skin microbiome

Microbial community profiling shows dysbiosis in the lesional skin of Vitiligo subjects – Parul Ganju – Scientific Reports

Human oral microbiome

Diversity and homogeneity of oral microbiota in healthy Korean pre-school children using pyrosequencing – Soo Eon Lee – Acta Odontologica Scandinavica

Short-term effects of povidone iodine and sodium fluoride therapy on plaque levels and microbiome diversity – C Reilly – Oral Diseases

Commentary: A new association for the oral metagenome – Nicholas S Jakubovics – Oral Diseases

Human vaginal microbiome

Review: Vaginal microbiota and microbiome:- Role in health and disease – Dr Amit A. Rangari – Indian Journal of Basic and Applied Medical Research;

Human gut microbiome

Support for the Microgenderome: Associations in a Human Clinical Population – Amy Wallis – Scientific Reports

Impact of increasing fruit and vegetables and flavonoid intake on the human gut microbiota – Annett Klinder – Food & Function

Colonization potential to reconstitute a microbe community in patients detected early after fecal microbe transplant for recurrent C. difficile – Ranjit Kumar – BMC Microbiology

Review: The microbiome and its implications in intestinal transplantation – Kroemer, Alexander – Current Opinion in Organ Transplantation

Animal models

Genetic and Metabolic Signals during Acute Enteric Bacterial Infection Alter the Microbiota and Drive Progression to Chronic Inflammatory Disease – Karishma Kamdar – Cell Host & Microbe

The Host Shapes the Gut Microbiota via Fecal MicroRNA – Shirong Liu – Cell Host & Microbe

Animal microbiome

The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica – Ngare Wilkinson – Applied Microbiology and Biotechnology

Plant, root, and soil microbiome

Culturable endophytic bacterial communities associated with field grown soybean – Karla Bianca de Almeida Lopes – Journal of Applied Microbiology

Historical precipitation predictably alters the shape and magnitude of microbial functional response to soil moisture – Colin Averill – Global Change Biology

Water and waste microbiome

Development of new host-specific Bacteroides qPCRs for the identification of fecal contamination sources in water – Marta Gómez-Doñate – Microbiology Open

Bacterial diversity in oil-polluted marine coastal sediments – Alejandro Acosta-González – Current Opinion in Biotechnology

Spatial and temporal variability of bacterial communities in high alpine water spring sediments – Alfonso Esposito – Research in Microbiology

Biogeochemical, Isotopic and Bacterial Distributions Trace Oceanic Abyssal Circulation – Angelo Rubino – PLOS ONE

Metagenomics, metatranscriptomics, and bioinformatics

Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus – Kirsten I Bos – BioRxiv

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality – Yue Jiang – BMC Microbiome Journal

Viral metagenomics and blood safety – V. Sauvage – Transfusion Clinique et Biologique

Microbes in the news

Does our Microbiome Control Us or Do We Control It? – Dina Fine Maron – Scientific American

Your gut’s trick for controlling the bacteria that live in it – New Scientist

Mammals shape their microbiome to prevent disease – Science Codex

Low-Fiber Diets Cause Waves of Extinction in the Gut – Ed Yong – The Atlantic

Bad diets today can alter our great-great-grandkids’ biology – Katherine Ellen Foley – Quartz

Thoughtful and balanced comparison: mothur and QIIME – Pat Schloss – Mothur blog

Modifying the structure of wood alters plant microbiome – Science Daily

Gut Microbiome Similar in Formula- and Combination-Fed Babies – Troy Brown – MedScape

Eglin medical group first to find bacteria unseen in humans: Borrelia turicatae – Ilka Cole – US Air Force

Protecting the infant microbiome – Kathryn Kos – Examiner

Microbiology and art

Sunshine and microbiology inspire Reading artist’s work – Francesca Perryman – Get Reading

Science, publishing, and career

Re: Your Recent Email to Your Professor: Students who use emojis in their emails and write “heeeeelp!” in the subject line don’t necessarily know better.  – Paul T. Corrigan and Cameron Hunt McNabb – Inside Higher Education

ORCID: Publishers embrace scheme to end name confusion – John Bohannon – Science

Give teachers a physics test from a woman and they’ll give her worse grades – John Timmer – Ars Technica

Astronomy’s snowballing sexual harassment scandal picks up even more cases – Rachel Feltman – Washington Post

Bik’s Picks

Inside the Eye: Nature’s Most Exquisite Creation – Ed Yong – National Geographic
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