Peer review 101, Part 2: Writing the peer review

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This post is part of an online article I wrote for Publons. Publons is an online management system where you can keep track of your peer reviews, and compare your records to others. I wrote the article as a helpful guide for beginning peer reviewers. The article consists of four parts:

  1. How to critically read a manuscript
  2. Writing the peer review
  3. Submitting the peer review
  4. Managing peer review requests

2. Writing the peer review

As I am reading the manuscript for the first time, I will have a text editor open in which I immediately write down small comments on specific parts of the manuscript, such as a typo in line 15 or an unclear sentence in the introduction. While I go through the paper, I will start to write down more general thoughts as well, such as remarks about the length of the introduction or a misinterpretation of results. After reading the whole paper, I will then re-read the abstract to see if it correctly captured hypothesis, experiments, results and interpretation. At the end of my read-through, I try to structure my peer review into three parts.

  • Summary: A couple of sentences describing what the authors did, in my own words. This is especially helpful to refresh your memory when you will be asked to do another round of review on a paper you already reviewed before. Here, I will also give a general opinion about the paper, without mentioning if I think it should be rejected or accepted with edits.
  • General comments: Some broad thoughts about the paper, such as: novelty of the findings, length of discussion, order of results, any concerns about data analysis or interpretation, language issues, etc. I will usually have about 3-5 numbered bullet points here.
  • Specific comments. A numbered list of issues that refer to a very specific portion of the text or figures. Here, I might point out typos, missing definitions or abbreviations, unclear sentences, a missing reference, or suggestions to improve a figure or table. Usually, this part of my review will have about 20 remarks (but sometimes much more!). Even if this part is a long list, most of these points should be very easy to address by the authors.

It is important to number your remarks, making it easier for the authors to respond to each one of them.

In your review, the most important thing to keep in mind is to remain friendly and reasonable. You should feel no regret publishing your review under your full name. On the other hand, you do have the right to ask the authors to make primary data publicly available, perform some small and easy additional experiments or analysis, or change the layout and order of their graphs. Depending on the scope of the journal, it is however not reasonable in most cases to ask the authors to do large amounts of additional work. If you think the science is good, it should be published. There is always a need for additional experiments, but that can be put into another paper.

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Peer review 101, Part 1: How to critically read a manuscript

Posted on by

This post is part of an online article I wrote for Publons. Publons is an online peer review management system where you can keep track of your peer reviews, and compare your records to others. I wrote the article as a helpful guide for beginning peer reviewers. The article consists of four parts:

  1. How to critically read a manuscript
  2. Writing the peer review
  3. Submitting the peer review
  4. Managing peer review requests

Peer review is an essential part of science. It is the part of the scientific process where our peers will have a chance to review our work, check it, comment on it, and – most importantly – determine whether it’s good enough to become a permanent part of the scientific legacy. At the same time, it is also one of the most dreaded parts of science, both for authors, whose work will be scrutinized or could be rejected by competitors, as well as for reviewers, whose inboxes are filled with a never-ending stream of peer review requests.

How to critically read a manuscript

So how do you write a good peer review? To help the inexperienced peer-reviewer, I’ve made a list of general questions to ask when you are reading the paper. Asking these questions should help you form an opinion about the paper, even if you have no idea where to start. It’s the list that I wished I had access to when I started my first peer review. Here we go:

  • Do you have a conflict of interest when reviewing this paper? Do you collaborate with these authors, are they your personal friends, or are they direct competitors? Have you reviewed (and rejected) this paper before? If so, you need to decline this peer review and let the editors know.
  • Do the title and abstract cover the main aspects of the work, would it spark interest to the right audience?
  • Is the Introduction easy to follow for most readers of this particular journal? Does it cite the appropriate papers? Does it provide a hypothesis or aim of the study?
  • Does the Methods section provide enough details for the general reader to repeat the experiments?
  • If you skip the Methods, does the Results section give the right amount of detail to understand the basic details of the experiments?
  • Does the Results refer to the figures in a logical order? Do the numbers in the tables add up correctly? Are any figures/tables mislabeled or unclear?
  • Given the data that was obtained in this study, did the authors perform all the logical analyses? Did they include the proper controls?
  • Does the Discussion address the main findings, and does it give proper recognition to similar work in this field?
  • In general, is the paper easy to follow and does it have a logical flow? Are there any language issues?
  • Did the authors make all their data (e.g. sequence reads, code, questionnaires used) available for the readers?
  • Is this paper novel and an advancement of the field, or have other people done very similar work?
  • Finally (and hopefully you will never have to answer yes to any of these question): Does the paper raise any ethical concerns? Any suspicion of plagiarism (text or experiments), duplicated or tampered images, lack of IRB approval, unethical animal experiments, or “dual use of research concern”?

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August 19, 2015

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Guidelines and principles to use “holobionts”, microbiome and provoking autoimmunity in uveitis, bacteria in confiscated passerines, and ecology of the Miscellaneous Crenarchaeotic Group archaea.

General microbiome

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes – Seth R. Bordenstein , Kevin R. Theis – PLOS Biology

Human eye microbiome

Uveitis (Eye): Microbiota-Dependent Activation of an Autoreactive T Cell Receptor Provokes Autoimmunity in an Immunologically Privileged Site – Reiko Horai – Immunity

Human gut microbiome

Review: Diagnostic and Prognostic Microbial Biomarkers in IBD – Marla Dubinsky – Gastroenterology

Letter to the editor: Can inflammatory bowel disease really be solved by the multiple -omics and meta-omics analyses? – Xiaofa Qin – Immunology Letters

Animal models

In vivo imaging and tracking of host–microbiota interactions via metabolic labeling of gut anaerobic bacteria – Naama Geva-Zatorsky – Nature Medicine

Associative patterns among anaerobic fungi, methanogenic archaea, and bacterial communities in response to changes in diet and age in the rumen of dairy cows – Sanjay Kumar – Frontiers in Microbiology

Diet- and Genetically-Induced Obesity Differentially Affect the Fecal Microbiome and Metabolome in Apc1638N Mice – Anna C. Pfalzer – PLOS ONE

Animal microbiome

Detection of bacteria and fungi and assessment of the molecular aspects and resistance of E. coli isolated from confiscated passerines intended for reintroduction programs – Patricia Braconaro – Microbial Pathogenesis

Mining of luxS genes from rumen microbial consortia by metagenomic and metatranscriptomic approaches – Ines Ghali – Animal Science Journal

Isolation and identification of marine fish tumour (odontoma) associated bacteria – Ramalingam Vijayakumar – Journal of Coastal Life Medicine

A facultative endosymbiont in aphids can provide diverse ecological benefits – E. R. Heyworth andJ. Ferrari – Journal of Evolutionary Biology

Not sure why a study on RNAseq and 16S rRNA PCR on voles in France was published in PLOS NTD: A Comparison between Transcriptome Sequencing and 16S Metagenomics for Detection of Bacterial Pathogens in Wildlife – Maria Razzauti – PLOS Neglected Tropical Diseases

Plant, roots, and soil microbiome

Assembly of Active Bacterial and Fungal Communities Along a Natural Environmental Gradient – Rebecca C Mueller – Microbial Ecology

Effects of imidacloprid on soil microbial communities in different saline soils– Qingming Zhang – Environmental Science and Pollution Research

Water microbiome

Microbial Communities Can Be Described by Metabolic Structure: A General Framework and Application to a Seasonally Variable, Depth-Stratified Microbial Community from the Coastal West Antarctic Peninsula – Jeff S. Bowman – PLOS ONE

Diazotrophic bacterial community variability in a subtropical deep reservoir is correlated with seasonal changes in nitrogen – Lina Wang – Environmental Science and Pollution Research

Built environment microbiome

Assessment of contamination using an ATP bioluminescence assay on doorknobs in a university-affiliated hospital in Japan – Naoko Kajigaya – BMC Research Notes

Diversity and antibiotic resistance profiles of Pseudomonads from a hospital wastewater treatment plant – D.O. Santoro – Journal of Applied Microbiology

Cleanroom Maintenance Significantly Reduces Abundance but Not Diversity of Indoor Microbiomes – Alexander Mahnert – PLOS ONE

Archaea

Insights in the ecology and evolutionary history of the Miscellaneous Crenarchaeotic Group lineage – Mireia Fillol – ISME Journal

Metabolomics

Plasma metabolomic profiles enhance precision medicine for volunteers of normal health –
Lining Guo – PNAS

Techniques

Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome – Luigi Faino – mBio

Microbes in the news

Bacteria’s secret weapon against pesticides and antibiotics revealed – Aarhus University – EurekAlert

Die, Bacteria! Engineered particles deliver targeted antibiotics – Helen Knight – Technology Review

Bacteria with synthetic DNA create protein never found in Nature – For when the usual four nucleotides can’t give you what you want – Alexandra Ossola – PopSci

Second Plague Case Traced to Yosemite National Park – Maggie Fox – NBC News

Science, publishing, and career

Increasing disparities between resource inputs and outcomes, as measured by certain health deliverables, in biomedical research – Anthony Bowena and Arturo Casadevall – PNAS
Return on Investment Slipping in Biomedical Research – Johns Hopkins Bloomberg School of Public Health

Science Week Australia: UNSW moves to strengthen women’s role in science – Marcus Strom – Sydney Morning Herald

Bik’s Picks

Stanford’s Angel of Grief Statue Has Arm Chopped Off By Vandals: The arm, made of fine Italian marble, is worth an estimated $20,000 – NBC Bay Area

Hummingbird tongues are way weirder than we thought – Rachel Feltman – Washington Post

Can’t go to Mars? At least sign the card – Jillian Kestler-D’Amours – The Star

Flying Spiders Found—and They Can Steer in Mid-Air – Traci Watson – National Geographic

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August 18, 2015

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New paper from our lab about human microbiota during pregnancy, association between obesity and cervical microflora, Argentina soil metagenomes, proteomics library, and microbiology during mozzarella cheese making.

Events and conferences

ECCMID: 26th European Congress of Clinical Microbiology and Infectious Diseases: April 2016, Istanbul, Turkey

General microbiome

Review: Fulfilling the Promise of Microbiomics to Revolutionize Medicine – Traci L Testerman – J Microbiol Exp

Review: Cross-kingdom similarities in microbiome functions – Rodrigo Mendes – ISME Journal

Pregnancy and birth microbiome

From our lab: Temporal and spatial variation of the human microbiota during pregnancy – Daniel B. DiGiulio – PNAS

Maternal group B Streptococcus and the infant gut microbiota – A. E. Cassidy-Bushrow – Journal of Developmental Origins of Health and Disease

The stool microbiota of insulin resistant women with recent gestational diabetes, a high risk group for type 2 diabetes – Marina Fugmann – Scientific Reports

Human reproductive tract microbiome

Relationship of Specific Bacteria in the Cervical and Vaginal Microbiotas With Cervicitis – Linda M. Gorgos – Sexually Transmitted Diseases

Changes in vaginal microbiota following antimicrobial and probiotic therapy – Jean M. Macklaim – Microbial Ecology in Health and Disease

Association between obesity and cervical microflora dominated by Lactobacillus iners in Korean women – Hea Young Oh – Journal of Clinical Microbiology

Distribution of human papillomavirus (HPV) genotypes and bacterial vaginosis presence in cervical samples from Paraguayan indigenous – Pamela Mongelos – International Journal of Infectious Diseases

The most common isolated microorganisms and its clinical manifestation in hospitalised women suffering from urogenital diseases in Latvia – Anatolijs Naumčiks – International Journal of Reproduction, Contraception, Obstetrics and Gynecology

Human respiratory microbiome

Conference abstract: Profiling of lung microbial communities in lung cancer and chronic obstructive pulmonary disease patients – Yanhong Liu – Cancer Research

Human oral microbiome

Conference abstract: 16S rRNA saliva analysis unveils differences in the head and neck squamous cell carcinoma microbiome before and after surgical resection – Rafael E. Guerrero-Preston – Cancer Research

Human gut microbiome

Variable alterations of the microbiota, without metabolic or immunological change, following faecal microbiota transplantation in patients with chronic pouchitis – J. Landy – Scientific Reports

Review: Systematic Review of the Relation Between Intestinal Microbiota and Toll-Like Receptors in the Metabolic Syndrome: What Do We Know So Far? – José Pedro Portela-Cidade – GE Portuguese Journal of Gastroenterology

Review: Commensal Microbiome Promotes Resistance to Local and Systemic Infections – Nan Zhang – Chinese Medical Journal

Animal microbiome

High diversity of viable bacteria isolated from lymph nodes of slaughter pigs and its possible impacts for food safety – Evelyne Mann – Journal of Applied Microbiology

Geographic patterns in the bacterial microbiome of the glassy-winged sharpshooter, Homalodisca vitripennis (Hemiptera: Cicadellidae) – E. W. Welch – Symbiosis

Plant, root, and soil microbiome

Using direct amplification and next-generation sequencing technology to explore foliar endophyte communities in experimentally inoculated western white pines – Lorinda S. Bullington – Fungal Ecology

Maize lines with different nitrogen use efficiency select bacterial communities with different β-glucosidase-encoding genes and glucosidase activity in the rhizosphere – Shamina I. Pathan – Biology and Fertility of Soils

Fire severity shapes plant colonization effects on bacterial community structure, microbial biomass, and soil enzyme activity in secondary succession of a burned forest – Joseph E. Knelman – Soil Biology and Biochemistry

Diversity of hydrolases from hydrothermal vent sediments of the Levante Bay, Vulcano Island (Aeolian archipelago) identified by activity-based metagenomics and biochemical characterization of new esterases and an arabinopyranosidase – Antonio Placido – Applied Microbiology and Biotechnology

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe – Jonathan W. Leff – PNAS

Soil Metagenomes from Different Pristine Environments of Northwest Argentina – Christina B. McCarthy – Genome Announcements

Relationships between the density and activity of microbial communities possessing arylsulfatase activity and soil sulfate dynamics during the decomposition of plant residues in soil – Séverine Piutti – European Journal of Soil Biology

Food microbiology

Microbial changes of natural milk cultures for mozzarella cheese during repeated propagation cycles – Angela Guidone – LWT – Food Science and Technology

No paper, just abstract, no pathogens appear to have been found: Culture-independent Pathogenic Bacterial Communities in Bottled Mineral Water – Hamdy A. Hassan – Renewable Energy & Sustainable Development

A diagnosis of the microbiological quality of dehydrated bee-pollen produced in Brazil – Adriane Alexandre Machado De-Melo – Letters in Applied Microbiology

Metagenomics and bioinformatics

HipMer: An Extreme-Scale De Novo Genome Assembler – Evangelos Georganas

Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist – Louis J. Cohen – PNAS

Proteomics and metabolomics

The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity – Samuel H. Payne – Scientific Data

Monitoring microbial metabolites using an inductively coupled resonance circuit – Daniil Karnaushenko – Scientific Reports

Extremophiles

Biotechnological applications of extremophiles, extremozymes and extremolytes – Noura Raddadi – Applied Microbiology and Biotechnology

Microbes in the news

Mothers facing C-sections look to vaginal ‘seeding’ to boost their babies’ health – Aimee Molloy – The Guardian

Bacterial community in pregnant women linked to preterm birth, study finds – Erin Digitale – Stanford Medicine
Stanford preterm birth study counters Detroit findings – Karen Bouffard – The Detroit News
Microbe Mix May Play Role In Preterm Birth Risk – Rob Stein – NPR

Biologist investigates how gene-swapping bacteria evade antibiotics – University of Texas at Dallas – EurekAlert

Methane and Climate Change: Arctic Bacteria Might Eat Methane? – Nature World News

How beneficial bacteria protect intestinal cells – Quinn Eastman – Emory News Center

Researchers Identify Metaproteomic Differences between Obese, Non-Obese Individuals – Adam Bonislawski – Genomeweb

How does Cincinnati Children’s Hospital use the microbiome to study lupus? A look inside with Diana Taft – Megan McGrath – DNA Genotek

Science, publishing, and career

A Scientific Look at Bad Science – Bourree Lam – The Atlantic

Bik’s Picks

Photos: Ancient Flowering Plant May Have Lived with Dinosaurs – Live Science

First-Ever Salamander in Amber Found in Caribbean – Richard Farrell – Discovery

Nasa awards $200,000 grant to a research project aimed at turning astronaut poo into food – Independent

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August 17, 2015

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Gut microbiota composition is associated with stool consistency, sequencing the lung microbiome, and the importance of purses as fomites.

Events

Tuesday evening: The Microbiome: An Alien Organ Within the Human Body – OMSI Science Pub (18 August 2015), Portland, OR

Human respiratory microbiome

Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities – Eduardo Castro-Nallar – BMC Medical Genomics

Editorial to the Sze article : Outside In: Sequencing the Lung Microbiome – Michael J. Cox – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Gut microbiota composition associated with stool consistency – E F Tigchelaar – Gut

Review: The role for gut permeability in the pathogenesis of type 1 diabetes – a solid or leaky concept? – Xia Li – Pediatric Diabetes

Animal microbiome

Buccal swabbing as a non-invasive method to determine bacterial, archaeal, and eukaryotic microbial community structure in the rumen – Sandra Kittelmann – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Olive Husk Compost Improves the Quality of Intensively Cultivated Agricultural Soils – María Teresa Moreno – Land Degradation & Development

Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities – Blaire Steven – Applied and Environmental Microbiology

Built environment microbiology

A study to investigate the importance of purses as fomites – Susheela D Biranjia-Hurdoyal – Advanced Biomedical Research

More microbiology

Review: Diagnostics and Discovery in Viral Central Nervous System Infections – Walter Ian Lipkin – Brain Pathology

(Meta)genomics

Getting the genome in shape: the formation of loops, domains and compartments – Britta AM Bouwman – Genome Biology

Microbes in the news

Bug-killing book pages clean murky drinking water: pages can be torn out to filter drinking water – Jonathan Webb – BBC

A geneticist says any new parent should ‘roll their child on floor of the New York subway’ — here’s why – Erin Brodwin – Business Insider

Having your rot on! In your compost pile you will find billions and billions of microbes with a voracious appetite for organic matter – Chuck Martin – Midland Daily News

Bacteria in flowers may boost honeybees’ healthy gut microbes: Honeybees were into probiotics way before they were cool, a new study suggests. – Beth Mole – Science News

The curious meeting of two partners: the squid–vibrio symbiosis – Tim Miyashiro – Society for General Microbiology

Horses: Heaves and Tracheal Microbiomes: Is There a Connection? – Erica Larson – The Horse

What’s on the menu? Bacteria – lots of them – Elisa Ung – North Jersey.com
“menus are usually the most bacteria-laden object on a restaurant table”

Oral bacteria: friends and foes of the mouth – Nikki Natividad – Rappler

TB Traces: The mummy museum in Vác, Hungary, has human remains that helped researchers learn more about the origins of tuberculosis in Europe – The Scientist

Bik’s Picks

The relationship between the season of birth and early-onset food allergies in children –
Kajiyo Tanaka – Pediatric Allergy and Immunology

NASA working on gecko-inspired, sticky-footed robot – Chuck Bednar – Red Orbit

Tour de Turtles: The Race to Save the Turtles and Maybe Humans as Well – Dave Randle – Huffington Post
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August 16, 2015

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So many new papers, that I need to do a Sunday post as well. Human nose microbiota changes during rhinovirus infection. tsrimethylamine and human gut microbiome, gut microbiota in sloths, and effect of timber harvesting on forest soils.

Human oral microbiome

Long-term evaluation of the antimicrobial susceptibility and microbial profile of subgingival biofilms in individuals with aggressive periodontitis – Talita Gomes Baêta Lourenco – Brazilian Journal of Microbiology

The human oral metaproteome reveals potential biomarkers for caries disease – Pedro Belda-Ferre – Proteomics

Human respiratory microbiome

Changes in microbiota during experimental human Rhinovirus infection – J. J. Hofstra – BMC Infectious Disease

Human gut microbiome

The Microbiome and Osteosarcopenic Obesity in Older Individuals in Long-Term Care Facilities – Julia E. Inglis – Current Osteoporosis Reports

Review: Microbiology Meets Big Data: The Case of Gut Microbiota–Derived Trimethylamine – Gwen Falony – Annual Review of Microbiology

Review: Gut microbiota modulate the immune effect against hepatitis B virus infection – D. Xu – European Journal of Clinical Microbiology & Infectious Diseases

Microbiome models

Osteopontin Deficiency Accelerates Spontaneous Colitis in Mice with Disrupted Gut Microbiota and Macrophage Phagocytic Activity – Takahiko Toyonaga – PLOS ONE

Prolonged antibiotic treatment induces a diabetogenic intestinal microbiome that accelerates diabetes in NOD mice – Kirsty Brown – ISME Journal

Prebiotic effects of diet supplemented with the cultivated red seaweed Chondrus crispus or with fructo-oligo-saccharide on host immunity, colonic microbiota and gut microbial metabolites – Jinghua Liu – BMC Complementary and Alternative Medicine

Animal microbiome

Metagenome Sequencing of the Greater Kudu (Tragelaphus strepsiceros) Rumen Microbiome – Anita N. Dube – Genome Announcements

Diet specialization selects for an unusual and simplified gut microbiota in two- and three-toed sloths – Kimberly A. Dill-McFarland – Environmental Microbiology

Microbiome Variation Across Amphibian Skin Regions: Implications for Chytridiomycosis Mitigation Efforts – Arnaud Bataille – Microbial Ecology

Plant, root, and soil microbiome

Molecular screening of microbial communities for candidate indicators of multiple metal impacts in marine sediments from Northern Australia – Alyssa M. Cornall – Environmental Toxicology and Chemistry

Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering – Alica Chroňáková – PLOS ONE

Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils – Hilary T C Leung – ISME Journal

Microbial Community Composition and Extracellular Enzyme Activities Associated with Juncus roemerianus and Spartina alterniflora Vegetated Sediments in Louisiana Saltmarshes – Anthony J. Rietl – Microbial Ecology

Water microbiome

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time-series and global field samples – Alma Parada – Environmental Microbiology

Diversity of Synechococcus at the Martha’s Vineyard Coastal Observatory: Insights from Culture Isolations, Clone Libraries, and Flow Cytometry – Kristen R. Hunter-Cevera – Microbial Ecology

Built environment microbiome

The Effectiveness of Three Home Products in Cleaning and Disinfection of S. aureus and E. coli on Home Environmental Surfaces – Nancy Goodyear – Journal of Applied Microbiology

Geochemical influences and mercury methylation of a dental wastewater microbiome – Asha Rani – Scientific Reports

Metagenomics

Research Highlights: An encrypted growth signature – Naomi Attar – Nature Reviews Microbiology

Archaea / Metabolomics

Untargeted metabolomics studies employing NMR and LC–MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis – Timothy Hamerly – Metabolomics

Microbes in the news

Toxoplasma parasite’s greedy appetite may be its downfall – University of Melbourne – EurekAlert

Let’s hope the stock photo was not related to the techniques used in this study:
Computerized ‘fishing expedition’ hooks 12,500 virus genomes – Brooks Hays – UPI

New Beach Act aims for faster results on bacteria tests – Dan Radel – APP.com

Swedish infant infects four others with resistant bacteria – New Straits Times

What’s lurking in your lungs? Surprising findings emerge from U-M microbiome research – Health Canal

Science, publishing, and career

Fixing the Leaky Bucket: What Tech Companies Must Do to Retain Their Best Female Talent – Belle Beth Cooper – Huffington Post

Bik’s Picks

Here’s How To Call The International Space Station – Gizmodo

Playing Tetris for 3 minutes could reduce your worst cravings – IBN Live

Teenagers are making themselves DIY braces and it is horrifying – Amy Willis – Metro.co.uk

How the internet of things is having an impact in Africa – HTXT Africa

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August 15, 2015

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Here is your Saturday edition of the Digest. Four papers today about Arctic water and soil microbes, oral bacteria in placentas, using hand microbiomes to identify human ethnicities, and machine learning classifiers give insights in bacterial vaginosis.

Pregnancy and birth microbiome

Oral bacteria in placental tissues: Increased molecular detection in pregnant periodontitis patients – Vanessa Blanc – Oral Diseases

Human skin microbiome

Hand bacteria as an identifier: a biometric evaluation – Amanda B. Holbert – Network Modeling Analysis in Health Informatics and Bioinformatics

Minireview: From Head to Toe: Mapping Fungi across Human Skin – Tim Sandle – EC Microbiology

Human respiratory microbiome

Impact of cigarette smoking on the middle meatus microbiome in health and chronic rhinosinusitis – Vijay R. Ramakrishnan – International Forum of Allergy & Rhinology

Human gut microbiome

Metagenomic Analysis of Crohn’s Disease Patients Identifies Changes in the Virome and Microbiome Related to Disease Status and Therapy, and Detects Potential Interactions and Biomarkers – Pérez-Brocal, Vicente – Inflammatory Bowel Diseases

Animal models

SIV-infection-driven changes of pattern recognition receptor expression in mesenteric lymph nodes and gut microbiota dysbiosis – Tiffany W. Glavan – Journal of Medical Primatology

Plant, root, and soil microbiome

Diazotrophic bacilli isolated from the sunflower rhizosphere and the potential of Bacillus mycoides B38V as biofertiliser – A. Ambrosini – Annals of Applied Biology

Relationships between Oak powdery mildew incidence and severity and commensal fungi – E. T. Topalidou – Forest Pathology

The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity – Anastasia Bragina – Molecular Ecology

Warming reduces the cover and diversity of biocrust-forming mosses and lichens, and increases the physiological stress of soil microbial communities in a semi-arid Pinus halepensis plantation – Fernando T. Maestre – Frontiers in Microbiology

Microbial Mineral Colonization Across a Subsurface Redox Transition Zone – Brandon Converse – Frontiers in Microbiology

Mutabilis in mutabili: Spatiotemporal dynamics of a truffle colony in soil – Milan Gryndler – Soil Biology and Biochemistry

Water microbiome

Bacterioplankton community shifts associated with epipelagic and mesopelagic waters in the Southern Ocean – Zheng Yu – Scientific Reports

Microbial diversity in a submarine carbonate edifice from the serpentinizing hydrothermal system of the Prony Bay (New Caledonia) over a 6-year period – Anne Poste – Frontiers in Microbiology

Extremophile microbiome: Arctic edition

Microbial activity is not always limited by nitrogen in Arctic tundra soils – Caroline Melle – Soil Biology and Biochemistry

Arctic soil microbial diversity in a changing world – Aimeric Blaud – Research in Microbiology

Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure – Richard Hill – Environmental Microbiology

Diversity of planktonic microorganisms in the Arctic Ocean – Carlos Pedrós-Alió – Progress in Oceanography

Waste treatment microbiology

Shotgun metaproteomic profiling of biomimetic anaerobic digestion processes treating sewage sludge – Ariane Bize – Proteomics

Bioinformatics

Machine learning classifiers provide insight into the relationship between microbial communities and bacterial vaginosis – Daniel Beck – BioData Mining

AmpliSAS: a web server for multilocus genotyping using next-generation amplicon sequencing data – Alvaro Sebastian – Molecular Ecology Resources

Science, publishing, and career

My alma mater, Utrecht University was again voted as the best Dutch university! Academic Ranking of World Universities 2015 – Shanghai Ranking

Microbes in the news

The Microbial Discovery Box: a hands-on activity for science teachers – ASM

Young scientists dreaming big: internship presentation competitions – Uganda Virus Research Institute

Infectious Diseases Like It Hot: How Climate Change Helps Cholera and Salmonella Outbreaks – Marlene Cimons – Think Progress

Before an Animal Disease Becomes a Human Epidemic – Cari Romm – The Atlantic

The dangers of eating snakes: Gauteng pastor encouraged his congregation to eat hair and snakes.

Bik’s Picks

Air Problem Is Worse Than You Think – James Fallows – The Atlantic

Georgia court weighs destiny of 18 captured beluga whales – Rich McKay – Reuters

Los Angeles Throws 96M Balls At California’s Drought Problem – Science Daily

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August 14, 2015

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Two papers on detection of bacteria in blood, vaginal microbiome, a discussion on eukaryotes in the human gut, and fungal communities’ resistance and resilience to wild fires. And some extra non-microbial Bik’s Picks for the weekend!

Human blood / infection microbiome

Bacterial Landscape of Bloodstream Infections in Neutropenic Patients via High Throughput Sequencing – Peter Gyarmati – PLOS ONE

16S rRNA Gene Sequence-Based Identification of Bacteria in Automatically Incubated Blood Culture Materials from Tropical Sub-Saharan Africa – Hagen Frickmann – PLOS ONE

Human vaginal microbiome

A Study of the Vaginal Microbiome in Healthy Canadian Women Utilizing cpn60-Based Molecular Profiling Reveals Distinct Gardnerella Subgroup Community State Types – Arianne Y. K. Albert – PLOS ONE

Human gut microbiome

Are Human Intestinal Eukaryotes Beneficial or Commensals? – Julius Lukeš – PLOS Pathogens

Review: Role of the normal gut microbiota – Sai Manasa Jandhyala – World Journal of Gastroenterology

Review: Paleolithic nutrition for metabolic syndrome: systematic review and meta-analysis – Eric W Manheimer – The American Journal of Clinical Nutrition

Animal models

In Mice: Autophagy Protects against Colitis by the Maintenance of Normal Gut Microflora and Secretion of Mucus – Koichiro Tsuboi – Journal of Biological Chemistry

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungal communities show low resistance and high resilience to wildfire disturbance – Xingjia Xiang – Plant and Soil

From lithotroph- to organotroph-dominant: directional shift of microbial community in sulphidic tailings during phytostabilization – Xiaofang Li – Scientific Reports

Water microbiome

A Dissolved Oxygen Threshold for Shifts in Bacterial Community Structure in a Seasonally Hypoxic Estuary – Rachel L. Spietz – PLOS ONE

Techniques

Collection media and delayed freezing effects on microbial composition of human stool – Roberto Flores – Microbiome

Bioinformatics

Sorting out viral dark matter – Denise Waldron – Nature Reviews Microbiology

Manifold Based Optimization for Single-Cell 3D Genome Reconstruction – Jonas Paulsen – PLOS Computational Biology

Other microbiology

Mycobacterium tuberculosis: Genome watch: Looking at Beijing’s skyline – Dorota Jamrozy & Teemu Kallonen – Nature Reviews Microbiology

Microbes in the news

Feeding My Curiosity – And My Microbes – Alanna Collen – uBiome

Crohn’s and Colitis video featuring Laboratory of Will DePaolo

Bik’s Picks – some extra for you for the weekend!

We’ve Used Up Our Annual Supply of Earth’s Resources—And It’s Only August – Maddie Stone – Gizmodo

Drones could be stressing out wildlife, scientists suggest – Chelsea Harvey – Washington Post

Low-fat diets ‘better than cutting carbs’ for weight loss – James Gallagher – BBC News

Google’s Life Sciences division to build a miniature glucose tracker – Mona Lalwani – EnGadget

Why scientists got an alligator to inhale helium – Rachel Feltman – Washington Post

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August 13, 2015

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Fecal microbiota transplants also work with frozen stool, rhizobacterial communities on red pepper plants, effect of vaginal ring contraceptives, and the cilantro microbiome.

Pregnancy and birth microbiome

Maternal group B Streptococcus and the infant gut microbiota – A. E. Cassidy-Bushrow – Journal of Developmental Origins of Health and Disease

Not a microbiome paper, but of interest: Cesarean Section Delivery is not a Risk Factor for Development of IBD: A Population-based Analysis – Charles N. Bernstein – Clinical Gastroenterology and Hepatology

Human gut microbiome

Faecal microbiota transplant for recurrent Clostridium difficile infection using long-term frozen stool is effective: clinical efficacy and bacterial viability data – S. P. Costello – Alimentary Pharmacology & Therapeutics

Review: Colonization Resistance of the Gut Microbiota against Clostridium difficile – Ana Elena Pérez-Cobas – Antibiotics

Review: Microbiome and Asthma: What Have Experimental Models Already Taught Us?
R. Bonamichi-Santos – Journal of Immunology Research

Human reproductive microbiome

Effects of a One Year Reusable Contraceptive Vaginal Ring on Vaginal Microflora and the Risk of Vaginal Infection: An Open-Label Prospective Evaluation – Yongmei Huang – PLOS ONE

Animal models

Lessons from the Drosophila microbiota – Emma L Walton – Biomedical Journal

Studying host-microbiota interactions in Drosophila melanogaster – Jean Kanellopoulos – Biomedical Journal

Impact of Selection for Digestive Efficiency on Microbiota Composition in the Chicken –
Sandrine Mignon-Grasteau – PLOS ONE

Animal microbiome

Deep insights into carbohydrate metabolism in the rumen of mehsani buffalo at different diet treatments – Nidhi R. Parmar – Genomics Data

Metagenomics: Microbiome analyses of pacific white shrimp (Litopenaeus Vannamei) collected from disparate geographical locations – Arun S. Seetharam – Genomics Data

Classifying the bacterial gut microbiota of termites and cockroaches: a curated phylogenetic reference database (DictDb) – Aram Mikaelyan – Systematic and Applied Microbiology

Plant, root, and soil microbiome

Rhizobacterial Communities and Red Pepper (Capsicum annum) Yield under Different Cropping Systems – Byung Kwon Jung – International Journal of Agriculture & Biology

Soil Microbial Community Structure and Metabolic Activity of Pinus elliottii Plantations across Different Stand Ages in a Subtropical Area – Zeyan Wu – PLOS ONE

Microbiomes and potential metabolic pathways of pristine and anthropized Brazilian mangroves – Vanessa L.R. Nogueira – Regional Studies in Marine Science

Phylogenetic Characterization and Community Diversity of Hydrocarbon-Utilizing
Bacteria in Soil Microcosms Enriched with Aromatic Hydrocarbons – Ola Olapade A – Bioremediation & Biodegradation

Review: The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes – Pablo R. Hardoim – Microbiology and Molecular Biology Reviews

Water microbiome

Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake – A. López-Bueno – Molecular Ecology

Causes and consequences of habitat fragmentation in river networks – Matthew R. Fuller – Annals of the New York Academy of Sciences

Capability of the natural microbial community in a river water ecosystem to degrade the drug naproxen – Paola Grenni – Environmental Science and Pollution Research

Food microbiology

Cilantro microbiome before and after nonselective pre-enrichment for Salmonella using 16S rRNA and metagenomic sequencing – Karen G. Jarvis – BMC Microbiology

Changes in the microbial communities of air-packaged and vacuum-packaged common carp (Cyprinus carpio) stored at 4 °C – Yuemei Zhang – Food Microbiology

Metagenomics

An Overview of Genome Organization and How We Got There: from FISH to Hi-C – James Fraser – Microbiology and Molecular Biology Reviews

Microbes in the news

Statistical Advances Help Unlock Mysteries of the Human Microbiome – Infection Control Today

Seeking samples from FIV positive kitties – Holly Ganz – MicroBEnet

NOFA Says ‘Heal the Climate, Heal Ourselves’ – EcoRI news

Guest Post — The Emergent Microbiome: A Revolution for the Life Sciences – Part II, 2015 Patent Trends – Jessica Miles and Anthony D Sabatelli – JDsupra

A Genetically Modified Yeast Turns Sugar Into Painkillers: Stanford scientists have engineered a strain of yeast that can produce opiates on its own – Adam Hoffman – Smithsonian

Science, publishing, and career

What is the future of Science? This guy might know! Podcast with Francis Collins, NIH Director – Michael DL Johnson – Black Science Blog

Bik’s Picks

Longer-term outcome in the prevention of psychotic disorders by the Vienna omega-3 study – G. Paul Amminger – Nature Communications

Music as an aid for postoperative recovery in adults: a systematic review and meta-analysis – Jenny Hole – The Lancet

How can ants tell each other apart? Why, with their crazy refined sense of smell. – Elahe Izadi – Washington Post

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August 12, 2015

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Drug metabolism by gut microbiota, nature vs. nurture in inbred strains of mice, gnotobiotic Drosophila, bat virome, and influence of protist predation on marine microbiomes.

General microbiome

Short-chain fatty acids in control of body weight and insulin sensitivity – Emanuel E. Canfora – Nature Reviews Endocrinology

Pregnancy and birth microbiome

Streptococcal Diversity of Human Milk and Comparison of Different Methods for the Taxonomic Identification of Streptococci – Virginia Martín – Journal of Human Lactation

Human gut microbiome

Editorial: Drug Metabolism by the Host and Gut Microbiota: A Partnership or Rivalry?
Hollie I Swanson – Drug Metabolism and Disposition
Review: Mechanisms of How the Intestinal Microbiota Alters the Effects of Drugs and Bile Acids – Curtis D. Klaassen – Drug Metabolism and Disposition

Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing – Chika Kasai – BMC Gastroenterology

Animal and other models

Microbiota in 110 diverse inbred strains of mice: Genetic and environmental control of host-gut microbiota interactions – Elin Org – Genome Research

Co-culturing Escherichia coli O157:H7 with a non-pathogenic E. coli strain increases toxin production and virulence in a germ-free mouse model – Kakolie Goswami – Infection and Immunity

Ovariectomy results in differential shifts in gut microbiota in low versus high aerobic capacity rats – Kimberly A. Cox-York – Physiological Reports

Studying host-microbiota mutualism in Drosophila: Harnessing the power of gnotobiotic flies – Dali Ma – Biomedical Journal

MyD88 Signaling Regulates Steady-State Migration of Intestinal CD103+ Dendritic Cells Independently of TNF-α and the Gut Microbiota – Karin Hägerbrand – The Journal of Immunology

Animal microbiome

Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases – Zhiqiang Wu – ISME Journal

Plant, root, and soil microbiome

Host promiscuity in symbiont associations can influence exotic legume establishment and colonization of novel ranges – Metha M. Klock – Diversity and Distributions

Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure – Richard Hill – Environmental Microbiology

Water microbiome

Marine bacterial community structure resilience to changes in protist predation under phytoplankton bloom conditions – Federico Baltar – ISME Journal

Waste and water treatment microbiology

The activated sludge ecosystem contains a core community of abundant organisms – Aaron M Saunders – ISME Journal

Core-satellite populations and seasonality of water meter biofilms in a metropolitan drinking water distribution system – Fangqiong Ling – ISME Journal

More microbes

Levels and limits in artificial selection of communities – Manuel Blouin – Ecology Letters

Editorial: Origin of the Yeast Whole-Genome Duplication – Kenneth H. Wolfe – PLOS Biology
Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker’s Yeast Lineage – Marina Marcet-Houben – PLOS Biology

Microbes in the news

Global Human Microbiome Market: Asia is expected to show high growth rates by 2020 – MedGadget

Things I Tell My Mom: Five ways for you to participate in science – Cathy Seiler – Ahwatukee Foothills News

Why making and taking fermented drinks is becoming popular again – John McKenna – The Irish Times

Protein Goes Green: Can Algae Become The Next Soy? – Jessie Rack – NPR

Cultured Coffee offers the flavor of poop-brewed coffee without the crap – TJ Dietsch – Geek

Making kefir at home is easy, healthy – Kit Waskom Pollard – Baltimore Sun

‘Genomic Archaeology’ Reveals That Lager Yeast Was Born More Than Once – Andrea Alfano -Tech Times

Researchers resurrect extinct virus to use for gene therapy: Evolutionary ancestors remade based on current viruses – Ars Technica

Science, publishing, and career

Make Peer Review Public: How to make science faster and more robust – Adam Marcus and Ivan Oransky – Slate

Despite concerted effort, barriers to women in science remain – Jennifer Ann Thomson – The Conversation

Outreach: Primary School outreach – inspiring young minds with science – Mariya Lobanovska – SGM

Physics: She did it all: Val Gibson enjoys the autobiography of Mary K. Gaillard, the first female physics professor at Berkeley – Val Gibson – Nature

Bik’s Picks

Octopus Genome Offers Insights Into One Of Ocean’s Cleverest Oddballs – Nell Greenfieldboyce – NPR

Meteor time! How to watch the big Perseid shower – Paul Rogers – San Jose Mercury News

MIT tackling more serious science: they program beer-delivering robots – ZME Science

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