April 25, 2016

Just a short digest before I hop onto the plane back home at Amsterdam Airport.

Human gut microbiome

Might be DGGE; not sure (no access for me): Gastrointestinal Hormones, Intestinal Microbiota and Metabolic Homeostasis in Obese Patients: Effect of Bariatric Surgery – Alessandro Federico – In Vivo

Hypothesis: Microbes, molecular mimicry and molecules of mood and motivation – J.A. Morris – Medical Hypotheses

Review: The Intestinal Microbiome and Estrogen Receptor–Positive Female Breast Cancer – Maryann Kwa – Journal of the National Cancer Institute

Review: Pathophysiological role of host microbiota in the development of obesity – Nazarii Kobyliak – Nutrition Journal

Animal models

Fistulated dogs, food withheld for 5 days – not sure if the small gain in knowledge justifies the animal experiment here : The effects of feeding and withholding food on the canine small intestinal microbiota – A.C. Kasiraj – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Non-target impact of fungicide tetraconazole on microbial communities in soils with different agricultural management – Sławomir Sułowicz – Ecotoxicology

Air microbiome

Contribution of vegetation to the microbial composition of nearby outdoor air – Despoina S. Lymperopoulou – Applied and Environmental Microbiology

Microbes in the news

Anorexia may be caused by bacterial infection, say scientists – Sarah Knapton – The Telegraph

Chromosomes Have A Lot to Talk About – Here’s How They Do it – Nandita Jayaraj – The Wire

Science, publishing, and career

Has the time come for preprints in biology? – Needhi Bhalla – bioRxiv

Our image duplication project on bioRxiv

As some of you already know, I have been working on a side-project on scientific misconduct, together with Arturo Casadevall ( Johns Hopkins) and Ferric Fang ( University of Washington). In this project, we screened over 20,000 papers that had been published in 40 different journals for cases of inappropriate image duplication, focusing on photographic images such as Western blots, gels, microscopy/histology, and FACS plots. It took me 2 years of almost all my free time to screen the papers and make reports on the 1 in every 25 papers that showed duplicated images or parts of images.

After sending our manuscript to 3 different journals and receiving 3 rejection letters, we wanted to share our results with a wider (and hopefully more positive) audience. So earlier this week, we posted our manuscript on the preprint server bioRxiv (a very easy and free process!). We have also submitted our ms to journal #4. After all, the fouth time’s a charm, right?

Here is the abstract and link to our preprint (not peer-reviewed). You can leave comments at the bottom.

The Prevalence of Inappropriate Image Duplication in Biomedical Research Publications – Elisabeth M. Bik, Arturo Casadevall, Ferric C. Fang – Preprint on bioRxiv

Inaccurate data in scientific papers can result from honest error or intentional falsification. This study attempted to determine the percentage of published papers containing inappropriate image duplication, a specific type of inaccurate data. The images from a total of 20,621 papers in 40 scientific journals from 1995-2014 were visually screened. Overall, 3.8% of published papers contained problematic figures, with at least half exhibiting features suggestive of deliberate manipulation. The prevalence of papers with problematic images rose markedly during the past decade. Additional papers written by authors of papers with problematic images had an increased likelihood of containing problematic images as well. As this analysis focused only on one type of data, it is likely that the actual prevalence of inaccurate data in the published literature is higher. The marked variation in the frequency of problematic images among journals suggest that journal practices, such as pre-publication image screening, influence the quality of the scientific literature.

Retraction Watch coverage

So far, our manuscript has been featured by a couple of news and science sites. Cat Ferguson of Retraction Watch was the first to cover our study in an article called “One in 25 papers contains inappropriately duplicated images, screen finds“. Cat writes:

Bik’s procedure to find these kinds of duplications is disarmingly simple. She pulls up all the figures in a paper and scans them. It only takes her about a minute to check all the images in a PLoS ONE paper, a little longer for a paper with more complicated figures. In some cases, Bik adjusted the contrast on the image to better spot manipulations.

Some other news sites that covered the study:

Problematic images found in 4% of biomedical papers. Giant survey suggests journals should pay more attention to detecting inappropriate duplications – Monya Baker – Nature News

Many Duplicates Unearthed – GenomeWeb

Repeat Offenders: Scanning the literature, scientists find that nearly 2 percent of papers contain duplicated and manipulated figures – Kerry Grens – The Scientist

Brain station; monkey business; duplication dilemma – Katie Moisse -Spectrum News

Peer Review Fails, Again. I don’t know if the refusal of three (3) journals to date to publish this work or that peer reviewers of the original papers missed the duplication is the sadder news about this paper. – Patrick Durusau – Another Word For It.

In German: Schummelbilder in vier Prozent aller Veröffentlichungen – Lars Fischer- Spektrum

In Dutch: Veel geknoei met foto’s – Wetenschapsfraude –  Dezelfde foto met een ander bijschrift, is dat een slordigheidje of bewuste misleiding? Het blijkt regelmatig voor te komen – Sander Voormolen – NRC

In Russian: 4% биомедицинских статей содержат некорректные иллюстрации – Scientific Russia

 

 

April 14, 2016

Events

Translational Microbiome Conference, April 20-21, Boston MA

Guggenheim Securities Microbiome Day, April 21, New York. I cannot find a website for the conference, but got several links to press releases from companies that will participate, such as Enterome and Evelo Biosciences

General microbiome

Intricacies of assessing the human microbiome in epidemiological studies – Courtney K. Robinson – Annals of Epidemiology

Pregnancy and birth

Secretory IgA in the Coordination of Establishment and Maintenance of the Microbiota – Oliver Pabst – Trends in Immunology

Human skin microbiome

The microbiological signature of human cutaneous leishmaniasis lesions exhibits restricted bacterial diversity compared to healthy skin – Vanessa R Salgado – Memórias do Instituto Oswaldo Cruz

Human respiratory microbiome

Conference abstract: Analysis of the Sputum Microbiome in the Severe Asthma – Rihuang Qiu – Chest Journal

Human gut microbiome

(also contains animal experiments): Helminth infection promotes colonization resistance via type 2 immunity – Deepshika Ramanan – Science

Assessing the Colonic Microbiota in Children: Effects of Sample Site and Bowel Preparation – Shaw, Alexander G. – Journal of Pediatric Gastroenterology & Nutrition

Editorial: further evidence that proton pump inhibitors may impact on the gut microbiota – A. W. Walker – Alimentary Pharmacology & Therapeutics

Couple of papers from the Didier Raoult lab in New Microbes and New Infections (half of the next issue of that journal is by people from his group)
Isolation of a new species Peptoniphilus phoceensis from the human gut – Gaël Mourembou
Romboutsia timonensis, a new Species isolated from human Gut – Davide Ricaboni
« Bariatricus massiliensis », as a new bacterial species from the human gut microbiota – Simon Bessis

Review: Adaptation of Candida albicans to commensalism in the gut – Daniel Prieto – Future Microbiology

Review: Potential Role of the Microbiome in Barrett’s Esophagus and Esophageal Adenocarcinoma – Erik J. Snider – Digestive Diseases and Sciences

Review: Gut barrier structure, mucosal immunity and intestinal microbiota in the pathogenesis and treatment of HIV infection – Camilla Tincati – AIDS Research and Therapy

Review: Gut microbiota, inflammation and colorectal cancer – Jun Sun – Genes & Diseases

Review: Age-mediated changes in the gastrointestinal tract – Hamid A. Merchant – International Journal of Pharmaceutics

Review: Current Understanding of Dysbiosis in Disease in Human and Animal Models – DeGruttola, Arianna K. – Inflammatory Bowel Diseases

Animal models

Resilience of the intestinal microbiota following pathogenic bacterial infection is independent of innate immunity mediated by NOD1 or NOD2 – Susan J. Robertson – Microbes and Infection

Changes of Mouse Gut Microbiota Diversity and Composition by Modulating Dietary Protein and Carbohydrate Contents: A Pilot Study – Eunjung Kim – Preventive Nutrition and Food Science

Chemopreventive Metabolites Are Correlated with a Change in Intestinal Microbiota Measured in A-T Mice and Decreased Carcinogenesis – Amrita K. Cheema – PLOS ONE

Animal microbiome

Analysis of the rumen bacteria and methanogenic archaea of yak (Bos grunniens) steers grazing on the Qinghai-Tibetan Plateau – Dan Xue – Livestock Science

Evolution of the nasopharyngeal microbiota of beef cattle from weaning to 40 days after arrival at a feedlot – Edouard Timsit – Veterinary Microbiology

The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels – Han Liu – Scientific Reports

Plant, root, and soil microbiome

Multiple effects of a commercial Roundup® formulation on the soil filamentous fungus Aspergillus nidulans at low doses: evidence of an unexpected impact on energetic metabolism – Valérie Nicolas – Environmental Science and Pollution Research

Environmental Filtering Process Has More Important Roles than Dispersal Limitation in Shaping Large-Scale Prokaryotic Beta Diversity Patterns of Grassland Soils – Peng Cao – Microbial Ecology

Rhizosphere of Avicennia marina (Forsk.) Vierh. as a landmark for polythene degrading bacteria – Mohd. Shahnawaz – Environmental Science and Pollution Research

Wastewater microbiology

Mussel biofiltration effects on attached bacteria and unicellular eukaryotes in fish-rearing seawater – Eleni Voudanta – PeerJ

Characterization of microbial communities in wetland mesocosms receiving caffeine-enriched wastewater – Dongqing Zhang – Environmental Science and Pollution Research

Food microbiology

Bacterial community analysis of Tatsoi cultivated by hydroponics – Ok K. Koo – Journal of Environmental Science and Health, Part B

Heterofermentative lactic acid bacteria dominate in Korean commercial kimchi – Hee-Young Kim – Food Science and Biotechnology

Spatial Distribution of the Metabolically Active Microbiota within Italian PDO Ewes’ Milk Cheeses – Ilaria De Pasquale – PLOS ONE

Effect of postharvest practices on the culturable filamentous fungi and yeast microbiota associated with the pear carpoplane – Quinton Volschenk – Postharvest Biology and Technology

Review: Control of ochratoxin A-producing fungi in grape berry by microbial antagonists: A review – Hongyin Zhang – Trends in Food Science & Technology

More microbiology

Implementing an Antibiotic Stewardship Program: Guidelines by the Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America – Tamar F. Barlam – Clinical Infectious Diseases

Zero-inflated negative binomial mixed model: an application to two microbial organisms important in oesophagitis – R. Fang – Epidemiology and Infection
http://journals.cambridge.org/action/displayAbstract?

Density-Dependent Differentiation of Bacteria in Spatially Structured Open Systems – Jan Ribbe – Biophysical Journal

Opinion: Harnessing the Power of Defensive Microbes: Evolutionary Implications in Nature and Disease Control – Suzanne A. Ford – PLOS Pathogens

Review: Directed evolution and synthetic biology applications to microbial systems – Marcelo C Bassalo – Current Opinion in Biotechnology

Microbes in the news

Gut bacteria could help prevent cancer – Science Daily

AmpliPhi Bio’s bacteriophage cocktail shows encouraging infection-fighting prowess in cystic fibrosis isolates; shares up 13% – Seeking Alpha

What do you want to know about your microbiome? uBiome opens poll on which of 6 top projects should win $100K in research help – Beth Mole – Ars Technica

Worm Infection Counters Inflammatory Bowel Disease by Drastically Changing Gut Microbiome – PR Newswire

The Microbiome: What Is It and How Does It Affect You? – Marsha Nunley – PR web

Science, publishing, and career

Why our peer review system is a toothless watchdog – Ivan Oransky and Adam Marcus – STAT News

Don’t dismiss science fairs. Make them better – Patrick Skerrett – STAT News

Dutch push for a quantum leap in open access – Martin Enserink – Science

Some followers will need to sign up again

Last week I migrated the blog from an independent server to a WordPress server, and it seems that a subset of my followers were not transferred during the migration. In other words, if you had signed up to get an email whenever I posted something new, you might not have received anything in the last week. I am so sorry about that! I actually lost a large number of followers (the list had ~700 followers, and now only has 150).

I tried to figure out how to fix this but could not find an easy solution. For now, it’s probably the best to sign up again. Since I am now on a different server, the “Follow” box is now at the bottom right.

It looks like this: Screen Shot 2016-04-06 at 05.42PM, Apr 06

Click on it and enter your email, and you should get a confirmation email.

If you don’t see it, that means you are already logged in. Sometimes, signing in in Incognito mode might help to sign up again.

Again, my apologies! Let me know if you still are having troubles.

Elies

 

New server, new look

 

UPDATE: if you don’t receive email alerts for new posts anymore, you will have to sign up again. I am terribly sorry, but somehow the server transfer did not transfer my loyal subscribers. See this post here how to fix this.

I just migrated the MicrobiomeDigest site to a new server, now hosted at WordPress. The old server went down too many times and did not allow updating the themes or plugins anymore. As of now, I have chosen the free WordPress hosting plan, which might involve an occasional ad on the site. If the ads get too annoying, I will consider buying a plan, because I don’t want to pollute this site too much. We’ll see.

I have also been playing a bit with themes and looks, but have not yet found a perfect layout yet. Suggestions and comments are always welcome! For now, enjoy the new site!

The picture at the top is one that I took at Micropia, the Amsterdam microbial museum. Highly recommended!

A big thanks to Gerard Harbers for all his help!

Elies Bik