August 26, 2015

Microbes in household dust, oropharynx microbiome in schizophrenia, pneumonia in foals, metabolic footprint of bacteria on plant leaves, and Mozzarella cheese.

Human mouth / respiratory microbiome

Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls – Eduardo Castro-Nallar​ – PeerJ

Human vaginal microbiome

Unravelling the Bacterial Vaginosis-Associated Biofilm: A Multiplex Gardnerella vaginalis and Atopobium vaginae Fluorescence In Situ Hybridization Assay Using Peptide Nucleic Acid Probes – Liselotte Hardy – PLOS ONE

Human gut microbiome

Gut feelings of safety: Tolerance to the microbiota mediated by innate immune receptors – Bartlomiej Swiatczak – Microbiology and Immunology

Animal and bioreactor models

The colonic mucus protection depends on the microbiota – Ana M Rodríguez-Piñeiro – Gut Microbes

Sialic acid catabolism drives intestinal inflammation and microbial dysbiosis in mice
Yen-Lin Huang – Nature Communications

Differential responses of gut microbiota to the same prebiotic formula in oligotrophic and eutrophic batch fermentation systems – Wenmin Long – Scientific Report

Animal microbiome

Composition and Diversity of the Fecal Microbiome and Inferred Fecal Metagenome Does Not Predict Subsequent Pneumonia Caused by Rhodococcus equi in Foals – Canaan M. Whitfield-Cargile – PLOS ONE

Plant, root, and soil microbiome

Metabolic footprint of epiphytic bacteria on Arabidopsis thaliana leaves – Florian Ryffel – The ISME Journal

Diversity of Arbuscular Mycorrhizal Fungi in a Brazilian Atlantic Forest Toposequence – Joice Andrade Bonfim – Microbial Ecology

Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping – Rakesh Santhanam – PNAS

Water microbiome

Marine amoebae with cytoplasmic and perinuclear symbionts deeply branching in the Gammaproteobacteria – Frederik Schulz – Scientific Reports

Built environment microbiome

The ecology of microscopic life in household dust – Albert Barberán – Proceedings B

A Pilot Study on Integrating Videography and Environmental Microbial Sampling to Model Fecal Bacterial Exposures in Peri-Urban Tanzania – Timothy R. Julian – PLOS ONE

Food microbiology

Metabolomics and microbiological profile of Italian mozzarella cheese produced with buffalo and cow milk – Maria Barbara Pisano – Food Chemistry

Microbes in the news

What I Learned From Sequencing the Bacteria in My Apartment – Sarah Zhang – Wired

Thousands of microbes found in house dust – Rebecca Morelle – BBC

Household Dust Packed With Thousands of Microbes – Jennifer Viegas – Discovery

Waikiki Water Tested for Bacteria After Sewage Spill – Caleb Jones – ABC News

Methanotrophs: Could bacteria help protect our environment? – EurekAlert
Is our love affair with antibiotics slowly killing us? – Ailin Quinlan – Independent

Science, publishing, and career

In brief, papers with shorter titles get more citations, study suggests – Dalmeet Singh Chawla

[hr]

August 25, 2015

Microbiome of Polish Cemetery soil, microbiome and risk of Plasmodium infection, interactions between mouse gut microbiota, host Genetics and diet, and the microbiome of air at three different heights.

The microbiome of death

Microbiological Analysis of Necrosols Collected from Urban Cemeteries in Poland – Ireneusz Całkosiński – BioMed Research International

Book: Carrion Ecology, Evolution, and Their Applications – M. Eric Benbow – CRC Press

Pregnancy and birth

Review: Rate of establishing the gut microbiota in infancy has consequences for future health – Shaillay Dogra – Gut Microbes

Editorial with disturbing title: Can establishment of human microbiome be customized after birth with local traditions of first feed and intimate kissing? – Sarman Singh – Journal of Laboratory Physicians

Human oral microbiome

Alterations of the Subgingival Microbiota in Pediatric Crohn’s Disease Studied Longitudinally in Discovery and Validation Cohorts – Judith Kelsen – Inflammatory Bowel Diseases

Review: Human microbiome: From the bathroom to the bedside – Stephen Malnick, Ehud Melzer – World J Gastrointest Pathophysiol

Human gut microbiota / transcriptomics

Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection – Shibu Yooseph – BMC Genomics

Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota – Guanhui Bao – Frontiers in Microbiology

The Fecal Virome of Children with Hand, Foot, and Mouth Disease that Tested PCR Negative for Pathogenic Enteroviruses – Piyada Linsuwanon – PLOS ONE

Review: Gut microbiota and allogeneic transplantation – Weilin Wang – Journal of Translational Medicine

Animal models

Interactions between Gut Microbiota, Host Genetics and Diet Modulate the Predisposition to Obesity and Metabolic Syndrome – Siegfried Ussar – Cell Metabolism

Physical Activity Differentially Affects the Cecal Microbiota of Ovariectomized Female Rats Selectively Bred for High and Low Aerobic Capacity – Tzu-Wen Liu – PLOS ONE

Animal microbiome

Isolation of oxalotrophic bacteria associated with Varroa destructor mites – M. Maddaloni – Letters in Applied Microbiology

Diversity of bacterial communities in the midgut of Bactrocera cucurbitae (Diptera: Tephritidae) populations and their potential use as attractants – Ashok B. Hadapad – Pest Management Science

Midgut bacterial communities in the giant Asian honeybee (Apisdorsata) across four developmental stages: a comparative study – Prakaimuk Saraithong – Insect Science

Bacterial communities associated with four ctenophore genera from the German Bight (North Sea) – Wenjin Hao – FEMS Microbial Ecology

Plant, root, and soil microbiome
(also see study above filed under Microbiome of Death)

The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon – Wei H. Xu – Frontiers in Microbiology

Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil – Yendi E. Navarro-Noya – Archaea

Molecular characterization of microbial communities in the rhizosphere soils and roots of diseased and healthy Panax notoginseng – Zhaoxiang Wu – Antonie van Leeuwenhoek

The diversity changes of soil microbial communities stimulated by climate, soil type and vegetation type analyzed via a functional gene array – Fu Chen – World Journal of Microbiology and Biotechnology

Water microbiome

Carbon fixation by basalt-hosted microbial communities – Beth N. Orcutt – Frontiers in Microbiology

Annual dynamics of North Sea bacterioplankton: Seasonal variability superimposes short-term variation – Judith Lucas – Microbiology Ecology

Ecology and Distribution of Thaumarchaea in the Deep Hypolimnion of Lake Maggiore
Manuela Coci – Archaea

Viral and grazer regulation of prokaryotic growth efficiency in temperate freshwater pelagic environments – A.S. Pradeep Ram – FEMS Microbiology Ecology

Air / built environment microbiome

Vertical distribution of airborne bacterial communities in an Asian-dust downwind area, Noto Peninsula – Teruya Maki – Atmospheric Environment

Microbiological consequences of indoor composting – Alexandre Naegele – Indoor Air

Extremophiles

Response of the rare biosphere to environmental stressors in a highly diverse ecosystem (Zodletone spring, OK, USA) – Suzanne Coveley – PeerJ

Food microbiology

Wine fermentation microbiome: a landscape from different Portuguese wine appellations – Cátia Pinto – Frontiers in Microbiology

Difference of microbial community stressed in artificial pit muds for Luzhou-flavour liquor brewing revealed by multiphase culture-independent technology – Liqiang Zhang – Journal of Applied Microbiology

Monitoring of Yeast Communities and Volatile Flavor Changes During Traditional Korean Soy Sauce Fermentation – Young-Ran Song – Journal of Food Science

Bioreactor microbiology

Microbial community in a hydrogenotrophic denitrification reactor based on pyrosequencing – Hongyu Wang – Applied Microbiology and Biotechnology

Techniques and other microbiology

Application of iChip to Grow “Uncultivable” Microorganisms and its Impact on Antibiotic Discovery – Rinzhin T. Sherpa – Journal of Pharmacy & Pharmaceutical Sciences

Cultivating the uncultured: growing the recalcitrant cluster-2 Frankia strains – Maher Gtari – Scientific Reports

Isolation of Genetically Tractable Most-Wanted Bacteria by Metaparental Mating – Páraic Ó Cuív – Scientific Reports

Burkholderia bacteria infectiously induce the proto-farming symbiosis of Dictyostelium amoebae and food bacteria – Susanne DiSalvo – PNAS

Science, publishing, and career

A call to arms for women in science – Women’s Agenda
Microbes in the news

The Bacteria That Turn Amoebas Into Farmers – Ed Yong – National Geographic

Testers find twice as many ‘superbugs’ in conventional hamburger as organic ones – Lena H. Sun – Washington Post

Humans carry more antibiotic-resistant bacteria than animals they work with – Medical Xpress
[hr]

August 24, 2015

Microbiome of death

Soil fungal community shift evaluation as a potential cadaver decomposition indicator
Monica Chimutsa – Forensic Science International

Pregnancy and birth

Master Thesis – The Association of Necrotizing Enterocolitis with Integrons and Antibiotic Resistance Genes in the Gut Microbiota of Preterm Infants – Eva Lena F. Estensmo – Norwegian University of Life Sciences

Human respiratory microbiome

Regional Isolation Drives Bacterial Diversification within Cystic Fibrosis Lungs – Peter Jorth – Cell Host & Microbe

Quantitative analysis of pathogens in the lower respiratory tract of patients with chronic obstructive pulmonary disease – Huaying Wang – BMC Pulmonary Medicine

Animal microbiome

Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota – Tobin J Hammer – Peer J

Path analyses of cross-sectional and longitudinal data suggest that variability in natural communities of blood-associated parasites is derived from host characteristics and not interspecific interactions – Carmit Cohen – Parasites & Vectors

Plant, root, and soil microbiome

Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest – Jing Cong – BMC Microbiology

Disentangling the ‘brown world’ faecal-detritus interaction web: dung beetle effects on soil microbial properties – Eleanor M. Slade – Oikos

Taxon-specific responses of soil microbial communities to different soil priming effects induced by addition of plant residues and their biochars – Peng Su – Journal of Soils and Sediments

Research Highlight: Root recruiting – Mirella Bucci – Nature Chemical Biology

Water microbiome

Habitat and water quality variables as predictors of community composition in an Indonesian coral reef: a multi-taxon study in the Spermonde Archipelago – Ana Rita Moura Polónia – Science of the Total Environment

Waste water microbiology

Persistence of Ebola Virus in Sterilized Wastewater – Kyle Bibby – Environmental Science & Technology Letters

Metagenomics and bioinformatics

MetaObtainer: A Tool for Obtaining Specified Species from Metagenomic Reads of Next-generation Sequencing – Weihua Pan – Interdisciplinary Sciences: Computational Life Sciences

Minimum Information about a Biosynthetic Gene cluster – Marnix H Medema – Nature Chemical Biology

Viruses

A protein domain-based view of the virosphere-host relationship – Aare Abroi – Biochimie

Microbes in the news

Add Lots of Microbes to ‘Me, Myself, and I’ – David Salisbury – Futurity

The Microbiome Is Science’s Hot New Kid – Anand Veeravagu and Tessa Anderman – The Daily Beast

Science Briefs: Topography of spinach leaf shelters bacteria – John Bordsen – Charlotte Observer

Inside N.C. Science: Bugs – and mates – attracted by body odor – Sarah Council – Charlotte Observer

Universal flu vaccine comes closer, scientists say – Michelle Roberts – BBC News

Science, publishing, and career

Here’s what two college doctors say freshman need to know – LaTasha Seliby and Ranit Mishori – Washington Post

Women, minorities still underrepresented in medical specialties – Megan Brooks – Reuters

Bik’s Picks

Japanese Spacecraft Delivers Mice, Booze and More to ISS – Sarah Lewin – NBC News

Biologists Have Spotted the First Wolf Pack in California in 100 Years – Marissa Fessenden – Smithsonian

Get the Bunsen burner out: It’s time to concoct dinner – Nancy Szokan – Washington Post

[hr]

August 22, 2015

The microbiology of pig carcasses in streams, machine learning classifiers and bacterial vaginosis, and chestnut leaf extracts inhibiting Staphylococcus aureus growth.

Microbiome of death

The Potential of High-throughput Metagenomic Sequencing of Aquatic Bacterial Communities to Estimate the Postmortem Submersion Interval – Mark Eric Benbow – Journal of Forensic Sciences

Pregnancy and birth

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

Review: Congenital Chagas disease as an ecological model of interactions between Trypanosoma cruzi parasites, pregnant women, placenta and fetuses – Yves Carlier – Acta Tropica

Animal models

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development – Adam R Burns – The ISME Journal

Plant, root, and soil microbiome

Editorial: Plant microbiome blueprints – Cara H. Haney – Science

Castanea sativa (European Chestnut) Leaf Extracts Rich in Ursene and Oleanene Derivatives Block Staphylococcus aureus Virulence and Pathogenesis without Detectable Resistance – Cassandra L. Quave – PLOS ONE

Water microbiome

Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics – Jennifer R. Brum – The ISME Journal

Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter – Jürg B Logue – The ISME Journal

Microbes in the news

Chestnut leaves yield extract that disarms deadly staph bacteria – Phys.org

TSRI Scientists Discover Mechanism Behind Antibiotic-Resistance In Bacteria – Guneet Bhatia – IBD Times

King of fermentation brings together microbiology, food & community – Shady Grove Oliver – KTOO

Science, publishing and career

The Hidden Bias of Science’s Universal Language: The vast majority of scientific papers today are published in English. What gets lost when other languages get left out? – Adam Huttner-Koros – The Atlantic

Bik’s Picks

Minneapolis woman is raising 400 monarch butterflies in her home – Aimee Blanchette – Star Tribune

Climate Change To Blame For Dogs’ Evolution From Cats – J.R. Duren – Immortal

Google Chrome spellchecks multiple languages at once – Steve Dent – Engadget

[hr]

August 21, 2015

Gut microbiota in Malaysian children, humanized microbiota mice, and ecosystem productivity in surface marine waters. Happy weekend!

Human respiratory microbiome

Association of Mucosal Organisms with Patterns of Inflammation in Chronic Rhinosinusitis – Thanit Chalermwatanachai – PLOS ONE

Human gut microbiome

Relatively little data given on socioeconomic status, but that appears to be much greater factor than ehtnicity – if you read scarce information in methods.
Effect of ethnicity and socioeconomic variation to the gut microbiota composition among pre-adolescent in Malaysia – Chun Wie Chong – Scientific Reports

Review: Intestinal Fucose as a Mediator of Host–Microbe Symbiosis – Joseph M. Pickard – The Journal of Immunology

Animal models

Characterization of the Genital Microenvironment of Female Rhesus Macaques Prior to and After SIV Infection – Whitney A. Nichols – American Journal of Reproductive Immunology

Humanized microbiota mice as a model of recurrent Clostridium difficile disease – James Collins – Microbiome

Water microbiome

Ecosystem productivity is associated to bacterial phylogenetic distance in surface marine waters – Pierre E. Galand – Molecular Ecology

Waste water microbiology

Thesis: The Effects of Perturbations on Microbial Community Dynamics and Process Performance in Wastewater Bioreactors – Hari Seshan – University of California, Davis

Techniques

Review: Molecular biology-based methods for quantification of bacteria in mixed culture: perspectives and limitations – Karthiga Nagarajan – Applied Microbiology and Biotechnology

Microbes in the news

Autoimmune eye infection caused by bacteria in the gut – Mohan Garikiparithi – Bel Marra Health

The Brain-Gut Axis, Part 3 – The Gut Microbiota In Disease – Sara Adaes – Brain Blogger

Workshop on microbiology conducted – The Hindu

Podcast: Forensic Microbiology Part 2: Secrets of Soil – SocGenMicro at Soundcloud

How long have primates been infected with viruses related to HIV? – EurekAlert

Bik’s Picks

‘Mutant’ Lice More Hype Than Headache: Treatment failure doesn’t equal clinical resistance – Hanneke Weitering – MedPageToday

Doctors Behaving Badly: Annals of Internal Medicine published an anonymous essay recounting two appalling incidents – Roni Caryn Rabin – New York Times

Humans are now a unique class of ‘super-predators’ thanks to ‘wickedly efficient killing technology’: study – Randy Shore – National Post

Most Of Us Have Disgusting Contact Lens Habits – Rachael Rettner – LiveScience

[hr]

August 20, 2015

Jobs

Jobs at Technical University of Denmark: Three PhD scholarships at the interface of synthetic biology, metagenomics and bacterial evolution

Pregnancy and birth

The Placental Microbiome Varies in Association with Low Birth Weight in Full-Term Neonates – Jia Zheng – Nutrients

Impact of mode of delivery on the milk microbiota composition of healthy women – R. Cabrera-Rubio – Journal of Developmental Origins of Health and Disease

Human oral microbiome

Dental plaque as a biofilm and a microbial community – implications for treatment – P.D. Marsh – Journal of Oral Biosciences

Human gut microbiome

Low Level Engraftment and Improvement following a Single Colonoscopic Administration of Fecal Microbiota to Patients with Ulcerative Colitis – Christopher J. Damman – PLOS ONE

The presence of Oxalobacter formigenes in the microbiome of healthy young adults – Clea Barnett – The Journal of Urology

The gut microbial community in metabolic syndrome patients is modified by diet – Carmen Haro – The Journal of Nutritional Biochemistry

Review: Intestinal Microbiota and Celiac Disease: Cause, Consequence or Co-Evolution? – María Carmen Cenit – Nutrients

Review: The intestinal microbiome in human disease and how it relates to arthritis and spondyloarthritis – Mary-Ellen Costello – Best Practice & Research Clinical Rheumatology

Editorial: Getting Healthier Through Microbiome Makeover – Duc Hong Le – EBioMedicine

Review: Nutritional Modulation of Gut Microbiota – The Impact on Metabolic Disease Pathophysiology – Patricia Ojeda – The Journal of Nutritional Biochemistry

Animal models

Interactions between Gut Microbiota, Host Genetics and Diet Modulate the Predisposition to Obesity and Metabolic Syndrome – Siegfried Ussar – Cell Metabolism

IL-21 and probiotic therapy improve Th17 frequencies, microbial translocation, and microbiome in ARV-treated, SIV-infected macaques – A M Ortiz – Mucosal Immunology

Animal microbiome

The rectal microbiota of cats infected with feline immunodeficiency virus infection and uninfected controls – JS Weese – Veterinary Microbiology

Bartonella Infection among Cats Adopted from a San Francisco Shelter, Revisited – Drew A. Fleischman – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter – Lucia Žifčáková – Environmental Microbiology

Diversity and complexity of microbial communities from a chlor-alkali tailings dump – Cyril Zappelini – Soil Biology and Biochemistry

Different impacts of native and exotic earthworms on rhizodeposit carbon sequestration in a subtropical soil – Jinhua Huang – Soil Biology and Biochemistry

Polycyclic aromatic hydrocarbons degradation and microbial community shifts during co-composting of creosote-treated wood – Stefano Covino – Journal of Hazardous Materials

Waste microbiology

Occurrence of and Sequence Variation among F-Specific RNA Bacteriophage Subgroups in Feces and Wastewater of Urban and Animal Origins – C. Hartard – Applied and Environmental Microbiology

Pathogenic Enteric Viruses and Microbial Indicators during Secondary Treatment of Municipal Wastewater – Naim Montazeri – Applied and Environmental Microbiology

Metaproteomics of activated sludge from a wastewater treatment plant – A pilot study – Sebastian Püttker – Proteomics

Food microbiology

Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains – M. van den Broek – Applied and Environmental Microbiology

Not sure why the title is between quotes: “Spoilage of vacuum-packed beef by the yeast Kazachstania psychrophila” – Jan Kabisch – Food Microbiology

Microbiota of Minas cheese as influenced by the nisin producer Lactococcus lactis subsp. lactis GLc05 – Luana Martins Perin – International Journal of Food Microbiology

Microbes in the news

Does This Phylum Make Me Look Fat? – Katherine Harmon Courage – NPR

Stanford researchers find surprising level of tick-borne disease risk on local trails – Rob Jordan

What Gut Bacteria Can Teach Us About Eating Disorders: uBiome and University of North Carolina Launch Groundbreaking Study – Global News Wire

[hr]

Peer review 101, Part 4: Managing peer review requests

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

Peer review is a great way to become a better scientist. By regularly doing peer reviews, you will start to think like the peer reviewer who will criticize your paper, so it will make you a better writer. It is an essential part of being a scientist. And, to be honest: it can feel really great to be in the power seat sometimes! But, remember to always stay friendly and polite.

4. Managing peer review requests

Which and how many peer reviews should you perform? Most junior scientists will start to get peer review requests after publishing their first paper as a first author. Often, you will get asked if one of your papers is listed in the references of the manuscript, so the new study will be in your field. You should only accept the peer review if you feel you have expertise in the topic of the paper, even if you are not an expert in all the techniques used. Typically, a manuscript will be sent out to about 3 reviewers, so as a rule-of –thumb you should perform 3 times more reviews than the amount of manuscripts you typically submit per year. More is better! Once you have peer-reviewed for a journal, the journal will ask you again, but usually only once or twice a year. The more papers you have published, the more requests you will get. You do not have to accept all of them, though. I’ll try to only have 2 ongoing peer reviews at the time; if I get more requests, I will turn them down until I have finished the previous ones. However, I will always accept requests to re-review a manuscript for the second time, and give priority to requests from journals where I serve in the editorial board.

Publons has been a great resource for me to keep track of all my peer reviews. It is a nice way to get recognition for all the work we peer reviewers do, mostly anonymously. In addition, it is great to compare my acceptance rate and length of peer reviews to that of others, and to have a feel for how many reviews other scientists perform, and for which journals. I can highly recommend signing up!

[hr]

Peer review 101, Part 3: Submitting the peer review

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

3. Submitting the peer review

Once you have written your review, you will have to upload it into the journal’s reviewer interface. Most of them will have a box where you can assign the paper to one of 4 categories: accept without edits (only to be selected if you reviewed The Perfect Paper!), accept with minor edits (addressing typos, unclear sentences, or a small figure edit), accept with major edits (addressing bigger issues such as changes to introduction scope, interpretation of results, additional graphs or analyses) or reject (if the manuscript was not novel at all, not suitable for the scope of that journal, or contains plagiarism or other questionable practices). Most of the papers I have reviewed were classified as “accept with major edits”; I have selected the “reject” category less often. On the journal’s website, there is usually also a box where you can give specific comments to the editor; these will not be forwarded to the authors. Here you can state your personal opinion, or any issues you do not want to share with the authors. Your peer review will go into the section labeled “comments to the authors” – often by simply copy/pasting it into the appropriate box. Even if I think a paper should be rejected, I like to share my thoughts about the manuscript here, so that the authors can improve their paper before submitting it somewhere else.

[hr]

Peer review 101, Part 2: Writing the peer review

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.

[hr]

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

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”?

[hr]