Great news: the videos from the Stanford Microbiome Informatics Symposium talks are up! The symposium was held on May 27, and featured Rob Knight, Justin Sonnenburg, Ami Bhatt, David Relman, and Susan Holmes.
You can see videos of the talks here (click on the tab “Videos”).
Thanks, Somalee Datta, Ami Bhatt, Roger Winkelman and team for making this possible.
Happy Independence Day!
I have mentioned this before, but this website not only contains blog posts, but pages with more static information as well. These pages include lists that I compiled of important papers on particular microbiome topics. I call this my Microbiome Paper Collection, and they are listed as pages (not posts) under the Microbiome Collection button in the grey bar under the picture at the top of this page.
Tonight, I’ve updated the collections on the following topics:
Feel free to browse the Collection pages. The lists are not complete, but should be a good start for an overview of important papers. You can always let me know if I missed a paper by leaving a comment.
A short Monday post. Bronchiolitis and virome milestones in infants, and playing drums.
Pregnancy and birth
The Fecal Microbiota Profile and Bronchiolitis in Infants – Kohei Hasegawa – Pediatrics
Editorial: Do Bacteria in the Gut Set the Stage for Who Gets Viral Bronchiolitis and Its Severity? – Patrick C. Seed – Pediatrics
Research Highlight: Distinct Fecal Microbiota Pattern Associated with Infant Bronchiolitis – Christine Judge – NEJM Journal Watch
The Bacterial Microbiome and Virome Milestones of Infant Development – Efrem S. Lim – Trends in MIcrobiology
More microbiology
Is there an Infection Risk when Playing Drums Contaminated with Bacillus anthracis? –
A M Bennett – Journal of Applied Microbiology
Microbes in the news
UI researcher finds link between gut bacteria and MS. MS patients show lower levels of good bacteria – EurekAlert
Microbes in extreme heat and cold hold lessons about life on Earth, and beyond – Don Cowan – The Conversation
Olympic rowers unveil special suits to combat bacteria in Rio – WHEC
Pineapples Can Stop Harmful Bacteria In The Gut – Diane Palmer – Parent Herald
Today I found this new article in Wiley’s Environmental Microbiology:
Web Alert: Synthetic microbial communities: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology – Lawrence P. Wackett – Environmental Microbiology
As is made clear in the title, this is not a regular review or research article, but a list of links to websites on this topic. Unfortunately, some of these links are more helpful than others: not all will take you to the paper itself, some lead to websites of research groups, and one was not written in English. But what is most disturbing to me is that Wiley put this article behind a paywall, so many people will have to pay $38 to have access to this list of links.
This is not the first Link-Fest article that this author wrote; there are now 5 of these published in Environmental Microbiology. I wrote about another one from the same author in April on MicroBE.net. All of these “Web Alert” articles are listed as regular publications in PubMed. It looks as if this author has found an easy way to expand his publication list, and as if Environmental Microbiology has found an easy way to fill their pages and earn more money
If you are interested in this particular topic but don’t have access to this paper, here is MicrobiomeDigest to the rescue. I have copied the list, improved all links to directly go to the publisher’s website, and updated the list with some missing relevant papers. This collection of papers on synthetic microbial consortia is freely available on a new page called Synthetic Microbial Communities.
This might also be a good moment to point out that I have made several of these lists of papers on a particular topic, and that you can find all of them here on my page called Microbiome Collection. You will find many topics here that might be of interest, or a good start to a literature search on a particular subject. And all of them are free! Also note that these are Pages, not Posts. Enjoy!
Update Monday, June 20th at 8 AM: ASM has removed the video from YouTube. Scroll to the end of this post to see ASM’s responses on Twitter.
Update Monday, June 20th at 11 AM: ASM has edited the video to make it solely about explaining your science to a lay person in 30 seconds. See new version here.
I’m a bit upset tonight because of a video by the American Society for Microbiology (ASM). It was brought to my attention by a tweet by @Yersinia / Jane EB Smith:
So I checked out the link, and it leads to a video that ASM has uploaded to YouTube called “Can you explain your science in 30 seconds to your mom?” (UPDATE: link no longer works; video has been removed). The video was created by two ASM staff members (a video producer and a media specialist) during last week’s ASM Microbe 2016 meeting in Boston. It starts with a cartoon of a young male scientist and a voice over with the challenge to “explain your science in 30 seconds”, followed by a dramatic pause, followed by: “TO YOUR MOM?”
The two ASM staff members then enter the Boston conference building and challenge 8 young scientists to do an elevator pitch. Most of them fail the test. But one scientist does really well, and she wins the contest.
But back to the title of the video. The question apparently assumes that moms are, well, not that smart. And that moms will look completely puzzled when you tell them your science. And that moms wear purple flowery dresses.
Since the ASM conference was during the Father’s Day weekend, why didn’t the video makers use the title “Can you explain your science in 30 seconds to your dad?” Did they think that that challenge would sound easier?
Anyway, it’s just a little annoyance. Just one of those many tiny disappointments women in science feel almost daily. By itself, it’s not even worth mentioning. But all these tiny sad moments do add up, especially when we see that biology labs and conference halls are filled with at least 50% women, but when the speaker podiums and panel tables only filled up with less than 30% women.
Dear American Society for Microbiology, I really love you for all you have done for women in science, but this video sets you back at least 20 years, and is a disappointment for the many women who are a member of the ASM.
Next morning update: ASM has removed the video. They don’t offer any apologies to moms, but they will try to do better in the future. Here are their replies on Twitter.
And here is their official reply on the Youtube comments: 
Your Saturday Microbiome Digest: CSF metagenomics in multiple sclerosis, Caenorhabditis elegans responses to bacteria, and archaeal communities in permafrost.
Infection and microbes
Only microbial contamination found: Metagenomic Analysis of Cerebrospinal Fluid from Patients with Multiple Sclerosis – Karol Perlejewski – Advances in Experimental Medicine and Biology
Review: The regulation of host defences to infection by the microbiota – Rebecca L. Brown – Immunology
Animal and in vitro experiments
Microbial Community Transplant Results in Increased and Long-Term Oxalate Degradation – Aaron W. Miller – Microbial Ecology
Differential Utilization of Basic Proline-Rich Glycoproteins During Growth of Oral Bacteria in Saliva – Yuan Zhou – Applied and Environmental Microbiology
Caenorhabditis elegans responses to bacteria from its natural habitats – Buck S. Samuel – PNAS
Plant, root, and soil microbiome
Presence and persistence of viable, clinically relevant Legionella pneumophila bacteria in garden soil in the Netherlands – E. van Heijnsbergen – Applied and Environmental Microbiology
Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons – C. Ryan Pento – Frontiers in Microbiology
Monitoring fungi in ecological restorations of coastal Indiana, U.S.A. – Peter G. Avis – Restoration Ecology
Review: Resilience of Soil Microbial Communities to Metals and Additional Stressors: DNA-Based Approaches for Assessing “Stress-on-Stress” Responses – Hamed Azarbad – MDPI International Journal of Molecular Sciences
Water and extremophile microbiome
Archaeal communities of Arctic methane-containing permafrost – Victoria Shcherbakova – FEMS Microbiology Ecology
Microbial community diversity, structure, and assembly across oxygen gradients in meromictic marine lakes, Palau – Matthew S. Meyerhof – Environmental Microbiology
Bioreactor microbiology
An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant – Vera Ortseifen – Journal of Biotechnology
Bioinformatics
Finds microbial interactions based on PubMed abstracts, so basically finding interactions that were already published (???): @MInter: Automated Text-mining of Microbial Interactions – Lim Kun Ming Kenneth – Bioinformatics
More microbiology
In situ replication rates for uncultivated bacteria in microbial communities – Christopher T Brown – bioRxiv
Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities – Sebastian Germerodt – PLOS Computational Biology
Microbes in the news
UWM professor taking a deeper dive on beach pollution data – Milwaukee-Wisconsin Journal Sentinel
The medical revolution that delves into humans’ inner aliens – Robert Matthews – The National
Brewing on the wild side: IU’s Dr. Matthew L. Bochman – Rita Kohn – Nuvo.net
Fecal bacteria and antibiotic resistance genes found in water samples from fly-in Northern Manitoba – Ian Graham – Thompson Citizen
CosmosID, BioCollective Collaborate on Microbiome Analysis Kit – GenomeWeb
Welcome to my brain: I was looking at a map of the San Francisco Bay Area today, near SFO International airport and it really looked like bacteriophage T4. Here you go:
Detlef Weigel (@PlantEvolution) attended me on Twitter to a nice #LabStockPhotoFail in the New York Times – who should know better than to blindly use stock photos with incorrect labels. His tweet included a screenshot of the New York Times article, in which an image of a protein gel is used to portray a DNA sequence.
The source of the stock photo was listed as Science Source, which describes themselves as “The best in stock photography, specializing in Science, Medical and Nature images and video”. Not a site where you would expect to see this:
Note: the “DNA gel” photo has been quickly replaced as of today in both the New York Times article as well as on the Science Source website.
Here is a link to the New York Times article as it appeared yesterday, as archived by the WayBack Machine on Archive.org.
Two beautiful examples of the intersection of microbes and art:A Synthetic Biologist’s Beautiful Palette of Bacteria Art – Noémie Jennifer – The Creators Project
Tal Danino grows various strains of bacteria into detailed, microscopic patterns that pull you in close. During a recent residency at Eyebeam in New York City, he researched how bacteria could be used as inks in various printing processes, like silkscreening or stamping. The resulting series of works, Microuniverses, is a marriage of nature and engineering—in the artist’s words, “you can control these patterns, but then they evolve on their own.” The concept of “controlling universes” is part of Danino’s day job. As the director of the Synthetic Biological Systems Laboratory at Columbia University, Danino is figuring out how to program bacteria so it can detect and treat diseases in our bodies.
It’s The Zika Virus In Action, Drawn By A Scientist-Artist – Maggie Zackowitz – NPR
A watercolor by scientist-artist David S. Goodsell just might make the Zika virus easier to visualize. The painting, which depicts an area about 110 nanometers wide (a nanometer is a billionth of a meter), shows the virus in the process of infecting a cell. (…) Of course the comic book-bright structures shown in the painting aren’t so simple and colorful in real, microscopic life. “These things are actually smaller than the wavelength of light, so they don’t really have a color,” Goodsell says. He chose his own color palette to highlight the function of each component — and to make them look beautiful.
Feces for forensic investigations, respiratory tract microbiome in premature infants, soil microbes in cereal rotation, sourdough microbiota, kombucha bacteria making cellulose, GutCyc metabolic models, and 157 new microbial genomes from biogas reactors.
Pregnancy and birth
The Microbiome of the Lower Respiratory Tract in Premature Infants with and without Severe Bronchopulmonary Dysplasia – Takashi Imamura – American Journal of Perinatology
High fecal IgA is associated with reduced Clostridium difficile colonization in infants – Sarah L. Bridgman – Microbes and Infection
Human gut microbiome
Microbial population analysis improves the evidential value of faecal traces in forensic investigations – Frederike C. A. Quaak – International Journal of Legal Medicine
Composition and function of the pediatric colonic mucosal microbiome in untreated patients with ulcerative colitis – Rajesh Shah – Gut Microbes
Active and Secretory IgA-Coated Bacterial Fractions Elucidate Dysbiosis in Clostridium difficile Infection – Mária Džunková – mSphere
Review: Tolerance to the Intestinal Microbiota Mediated by ROR(γt)+ Cells – Caspar Ohnmacht – Trends in Immunology
Review: Vegetarian diets and gut microbiota: important shifts in markers of metabolism and cardiovascular disease – Vinicius A. do Rosario – Nutrition Reviews
Review: Microbiome and its Impact on Gastrointestinal Atopy – Amanda B. Muir – Allergy
Review: Gut microbiota and inflammatory joint diseases – Maxime Breban – Joint Bone Spine
Review: Faecal microbiota transplantation: applications and limitations in treating gastrointestinal disorders – Hani Sbahi – BMJ Open Gastroenterology
Book chapter with not a lot of data: Gut Microbiota: A Possible Role in the Pathogenesis of Multiple Sclerosis – Takashi Yamamura – Neuro-Immuno-Gastroenterology
Review: Recent Advances and Understanding of Using Probiotic-Based Interventions to Restore Homeostasis of the Microbiome for the Prevention/Therapy of Bacterial Diseases – Jan S. Suchodolski – Microbiology Spectrum
Review: The human gut microbiome impacts health and disease – Stanislav Dusko Ehrlich – Comptes Rendus Biologies
Animal microbiology
Analysis of cultivable microbiota and diet intake pattern of the long-lived naked mole-rat – Tewodros Debebe – Gut Pathogens
Editorial: Microbial ecology: Algae feed a shift on coral reefs – Melissa Garren – Nature Microbiology
Grandeur Alliances: Symbiont Metabolic Integration and Obligate Arthropod Hematophagy – Rita V.M. Rio – Trends in Parasitology
Plant, root, and soil microbiome
Pastures to woodlands: changes in soil microbial communities and carbon following reforestation – T.R. Cavagnaro – Applied Soil Ecology
The legacy effect of cover crops on soil fungal populations in a cereal rotation – Andrew P. Detheridge – Agriculture, Ecosystems & Environment
Microbial utilization of double-labeled aspen litter in boreal aspen and spruce soils – Charlotte E. Norris – Soil Biology and Biochemistry
Isolating a functionally relevant guild of fungi from the root microbiome of Populus – Gregory Bonito – Fungal Ecology
Review – Lichen-Associated Bacteria as a Hot Spot of Chemodiversity: Focus on Uncialamycin, a Promising Compound for Future Medicinal Applications – Delphine Parrot – Planta Med
Book Chapter: Plant-Rhizobacteria Interaction and Drought Stress Tolerance in Plants – Cohen Ana Carmen – Drought Stress Tolerance in Plants, Vol 1
Water microbiology
Response of bacterial communities from California coastal waters to alginate particles and an alginolytic Alteromonas macleodii strain – Maximilian Mitulla – Environmental Microbiology
Food microbiology
New insight into microbial diversity and functions in traditional Vietnamese alcoholic fermentation – Vu Nguyen Thanh – International Journal of Food Microbiology
Evolution of sourdough microbiota in spontaneous sourdoughs started with different plant materials – Valery Ripari – International Journal of Food Technology
Review: Drivers for the establishment and composition of the sourdough lactic acid bacteria biota – Marco Gobbetti – International Journal of Food Microbiology
Pollution and waste microbiology
Deeper insight into the structure of the anaerobic digestion microbial community; the biogas microbiome database is expanded with 157 new genomes – Laura Treu – Bioresource Technology
Differential impacts of willow and mineral fertilizer on bacterial communities and biodegradation in diesel fuel oil-contaminated soil – Mary-Cathrine C. Leewis – Frontiers in Microbiology
Spatial variation of microbial community structure in the Zijinshan commercial copper heap bioleaching plant – Xingyu Liu – Minerals Engineering
Techniques
Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples – Angela Glassing – Gut Pathogens
Viruses
A metagenomic comparison of endemic viruses from broiler chickens with runting stunting syndrome and from normal birds – Ryan Devaney – Avian Pathology
Bioinformatics
GutCyc: a Multi-Study Collection of Human Gut Microbiome Metabolic Models – Aria S. Hahn – bioRxiv
metaBIT, an integrative and automated metagenomic pipeline for analyzing microbial profiles from high-throughput sequencing shotgun data – Guillaume Louvel – Molecular Ecology Resources
A resource-frugal probabilistic dictionary and applications in (meta)genomics – Camille Marchet – arXiv
Book Chapter: An Efficient Algorithm for Finding All Pairs k-Mismatch Maximal Common Substrings – Sharma V. Thankachan – Bioinformatics Research and Applications
More microbiology
Engineering control of bacterial cellulose production using a genetic toolkit and a new cellulose-producing strain – Michael Florea – PNAS
Bacteria In Kombucha Tea Could Be Key To Materials Useful For Mars Mission – Ted Ranosa – Tech Times
Engineering ‘tea bacteria’ could lead to advanced materials – Colin Smith – Imperial College London
Microbes in the news
This genetically engineered bacteria can inhale CO2 and produce energy – Futurism
Harvard Scientist Engineers Bacterium That Inhales CO2, Produces Energy – Jeff McMahon – Forbes
Daily Beast Fails in Its Reporting on Probiotics – David Wild – Gastroenterology & Endoscopy News
Why Ice Cream And Peanut Butter May Promote Gut Inflammation – Both contain emulsifiers, which are added to improve texture and extend shelf life – Rachael Rettner – Huffington Post
Scientists find novel enzymes encoded by giant virus – TASS Russian News Agency
Science, publishing and career
We need to do more for women in science – H. Ahmed – Science
Microbiome Digest - Bik's Picks 