Tag Archives: irritable bowel syndrome

December 18, 2019

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Good morning/afternoon all microbiome lovers!

Coming back from 4th Thunen Sumposium on Soil Metagenomics (11-13.12, Germany), the first section of today’s digest will highlight some work emphasized during the conference. Pay special attention to Amy Willis work (UoW) dealing with amplification bias in 16S analyses, among else. You are more than welcome to check the conference and the bioinformatic workshops schedule, as you’ll find interesting, inspiring and useful studies and tools that are relevant even if you’re not working on soil-associated habitats.

Have a great day!

Soil Metagenomics insights

Rigorous Statistical Methods for Rigorous Microbiome Science, Amy Willis, mSystems. I highly recommended to be familiar with the Willis lab works and tools, for all of us working with amplicon-sequencing and metagenomics. Amy was kind enough to upload her conference materials to github, using this link.

Additionally, They just started a bio-statistics blog, so check this as well.

Consistent and correctable bias in metagenomic sequencing experiments, Michael R. McLaren, bioRxiv

Understanding and interpreting community sequencing measurements of the vaginal microbiome, HL Berman, BJOG

These two papers are from Benjamin Callahan group (NCSW). Even though he wasn’t at the conference, his work (et al.) were mentioned several times by other speakers, so I decided to emphasize these two papers.

The MG-RAST API explorer: an on-ramp for RESTful query composition, Tobias Paczian, BMC Bioinformatics. Folker Meyer, one of the developers of MG-RAST and its head, was actually at the conference with a great talk about both MG-RAST and the importance of pipelines and common workflow language in computational biology. Check this link and the MG-RAST API explorer, making it so much simpler to search, filter and efficiently use MG-RAST.

TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes, Felipe B Correa, bioRxiv. An amazing tool for searching and filtering soil-associated metagenomes in different databases, plus simple codes for downloading. Take a look at more papers from the de-Rocha group.

Human microbiomoe

**Molecular messages in human microbiota, Matthew T. Henke and Jon Clardy, Science

Resident microbes of lactation rooms and daycares, Diana H. Taft, PeerJ

Female genital tract microbiota affecting the risk of preterm birth: What do we know so far? A Review, O. Tsonis, European J OBG & Reproductive Biology

Differences in Fecal Microbiomes and Metabolomes of People With vs Without Irritable Bowel Syndrome and Bile Acid Malabsorption, Ian B. Jeffery, Gastroenterology

Soil and Plant microbiome

Comparison of Microbial Community of Rhizosphere and Endosphere in Kiwifruit, Min-Jung Kim, Plant Patho J.

Soil microbial communities in diverse agroecosystems exposed to the herbicide glyphosate, Ryan M. Kepler, AEM

Soil exposed to silver nanoparticles reveals significant changes in community structure and altered microbial transcriptional profiles, Matthew J. Meier, Env. Pollution

Animal microbiome

Effects of disease, antibiotic treatment and recovery trajectory on the microbiome of farmed seabass (Dicentrarchus labrax), Danila Rosado, Scientific Reports

Microbiome Digest, November 4, 2014

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Tomorrow, Wednesday November 5, at 1:00pm USA-EST : Upcoming AMA (Ask Me Anything) in reddit/r/science: “Microbiota of the human gut” with my co-worker Les Dethlefsen. Ask him anything! You can submit questions, vote for the best questions, and the top questions will be answered by Les.

Human gut microbiome

* Rapid changes in the gut microbiome during human evolution – Andrew H. Moeller – PNAS USA

“To establish how the gut microbiome has changed since the diversification of human and ape species, we characterized the microbial assemblages residing within hundreds of wild chimpanzees, bonobos, and gorillas.”

and: Human Gut Bacteria Much Different Than Apes – Science 2.0

* Blastocystis Is Associated with Decrease of Fecal Microbiota Protective Bacteria: Comparative Analysis between Patients with Irritable Bowel Syndrome and Control Subjects – Céline Nourrisson – PLOS ONE

“Here, we first compared the prevalence of Blastocystis among 56 IBS patients (40 IBS with constipation (IBS-C), 9 IBS with diarrhea (IBS-D), 4 mixed IBS (IBS-M) and 3 unsubtyped IBS (IBS-U) according to the Rome III criteria) and 56 control (i.e. without any diagnosed chronic or acute gastrointestinal disorder) subjects. “

Animal models of microbiome research

* Bone Marrow Dendritic Cells from Mice with an Altered Microbiota Provide Interleukin 17A-Dependent Protection against Entamoeba histolytica Colitis – Stacey L. Burgess – mBio

“In studies utilizing a murine model, we demonstrated that colonization of the gut with the commensal Clostridia-related bacteria known as segmented filamentous bacteria (SFB) is protective during E. histolytica infection.”

Animal microbiome

Effect of Copper Treatment on the Composition and Function of the Bacterial Community in the Sponge Haliclona cymaeformis – Ren-Mao Tian – mBio

“16S rRNA gene sequencing results showed that the sponge Haliclona cymaeformis harbored symbiotic sulfur-oxidizing Ectothiorhodospiraceae and photosynthetic Cyanobacteria as dominant species. “

Bioinformatics tools

Massive fungal biodiversity data re-annotation with multi-level clustering – Duong Vu – Scientific Reports

“An implementation of the algorithm allowed clustering of all 344,239 ITS (Internal Transcribed Spacer) fungal sequences from GenBank”

Viruses and phages

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry applied to virus identification – Adriana Calderaro – Scientific Reports

“The results revealed MALDI-TOF MS to be an effective and inexpensive tool for the identification of the three poliovirus serotypes. “

More microbiology

Occurrence and expression of bacterial human virulence gene homologues in natural soil bacteria – Ditte A. Søborg – FEMS Microbial Ecology

“About 25% of the bacterial isolates contained virulence gene homologues representing toxin (hblA, cytK2), adhesin (fimH), regulator (phoQ) and resistance (yfbI) determinants in pathogenic bacteria.”

Science, publishing, and career

* Don’t Worry Your Pretty Little Heads – Rebecca Schuman – Slate

“I don’t understand how they wrote the paper or the op-ed they did while looking at the same results I see in their paper. … Where I come from,” she concludes, “we call that institutional bias.”

Bik’s Picks

Birds found using human musical scales for the first time – Virginia Morell – Science Blog

“The flutelike songs of the male hermit thrush (Catharus guttatus) are some of the most beautiful in the animal kingdom.”

Vaccine-resistant polio strain discovered – Science Daily

“The DNA sequence shows two mutations, unknown until now, of the proteins that form the “shell” (capsid) of the virus.”

The appliance of science: home experiments with your kids – Louise Holden – Irish Times

“Next week is Science Week, and one of the messages that McCarthy is hoping to put out there is that science is for everybody, not just those hoping to work in the sector. Helping your child to become science-literate is a great gift.”

The top 20 catchiest songs of all time, according to science – Michelle Starr – CNET

“A year-long survey by the Museum of Science and Industry in Manchester has revealed the top 10 most persistent earworms — with the Spice Girls topping the list.”

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Microbiome Digest, October 3, 2014

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Antibiotics in the first 24 months of life associated with obesity, Giant Pandas are no cul-de-sac, and microbiome and inflammatory disease. And lots of weekend reads!

Pregnancy and birth

Association of Antibiotics in Infancy With Early Childhood Obesity – L. Charles Bailey – JAMA Pediatrics

“Cumulative exposure to antibiotics was associated with later obesity …; this effect was stronger for broad-spectrum antibiotics”

Human gut microbiome

Faecal microbiota composition and host–microbe cross-talk following gastroenteritis and in postinfectious irritable bowel syndrome – Jonna Jalanka-Tuovinen – Gut

“Using a phylogenetic microarray and selected qPCR assays, we analysed differences in the faecal microbiota of 57 subjects from five study groups”

Animal models of microbiome research

Dietary modulation of the microbiome affects autoinflammatory disease – John R. Lukens – Nature

“Here we show that the intestinal microbiota of diseased Pstpip2cmo mice was characterized by an outgrowth of Prevotella. “

Mammal microbiome

Giant pandas are not an evolutionary cul-de-sac: Evidence from multidisciplinary research
Fuwen Wei – Molecular Biology and Evolution

“The latest and most advanced research shows that giant pandas are successful animals highly adapted to a specialized bamboo diet via morphological, ecological and genetic adaptations and co-adaptation of gut microbiota.”

Plant microbiome

Multi-symbiotic systems: functional implications of the coexistence of grass–endophyte and legume–rhizobia symbioses – Pablo A. García Parisi – Oikos

“After five months, we quantified the number of nodules in Trifolium roots, shoot biomass of both plant species, and the contribution of atmospheric nitrogen fixation vs. soil nitrogen uptake to above ground nitrogen in each plant species. “

Microbes in the news

Young companies, big ideas – The 2014 edition of the CNN 10: Startups – CNN

“Her doubts were assuaged when supporters donated $350,000 to help launch her startup, uBiome. Now, two years later, uBiome is exploring an emerging field of human biology while giving users a glimpse into how their bodies work.”

No women, unfortunately! And they did not accept my application to be a judge either. MO BIO Laboratories, Inc. announces Microbiome Awards winners – PR NewsWire

“MO BIO Laboratories, Inc. is proud to announce the winners of the MO BIO Microbiome Awards, which provide young, extraordinary scientists with funding and recognition to carry out scientific work in the field of microbiome research.”

Super-bacteria are growing in space … and we’re the ones breeding them – Meera Senthilingam – CNN

“You might think of space as a germ-free environment, but microbes can be carried to space inside human gut flora as well as in food and water and once up there, can be expelled by humans in their breath.”

There’s a simple way to stop the spread of antibiotic-resistant bacteria – Melinda Mary Pettigrew – Washington Post

“The issue boils down to this: we use too many antibiotics. Studies show that up to half of all antibiotics are prescribed unnecessarily.”

Across Indian zoos, rat pee spreading bacteria, killing big cats: Scientists – Priyangi Agarwal – The Times of India

“The leptospirosis bacteria, found in rodent urine, makes its way into blood samples of zoo animals and causes higher morbidity and mortality, scientists at the Indian Veterinary Research Institute (IVRI) in Bareilly have found. “

Brazil releases ‘good’ mosquitoes to fight dengue fever – BBC

“Brazilian researchers in Rio de Janeiro have released thousands of mosquitoes infected with bacteria that suppress dengue fever. The hope is they will multiply, breed and become the majority of mosquitoes, thus reducing cases of the disease.“

Science, Publishing, and Career

Young, Brilliant and Underfunded – Andy Harris – New York Times

“The bulk of that money goes to researchers who are in many cases esteemed in their fields — but also, in many cases, beyond the age when most scientists make their most important contributions to their fields.”

Why women leave tech: It’s the culture, not because ‘math is hard’ – Kieran Snyder – Fortune

“Stories from 716 women who left tech show that the industry’s culture is the primary culprit, not any issues related to science education.”

Satire: Tips For Working With A Lab Partner – FakeScience

Bik’s Picks

Is this the end of autumn as we know it? – Stephanie Pappas – BBC Earth

“The study of the basic triggers of autumnal leaf changes, never mind the impact of climate change on these, is still in its infancy in part because scientists have traditionally focused their attentions on the seasonal changes in March and April than those later in the year.”

The Incredible Rubber Glove – Olga Khazan – The Atlantic

“Basic protective gear was revolutionary for 19th-century medicine, and health workers trying to stop Ebola are recognizing its importance all over again.”

This Is Why Your Voice Sounds So Frickin’ Weird To You – Macrina Cooper-White – The Huffington Post

“Have you ever listened to a recording of your own voice and thought, “Whoa. Do I really sound like that?” Well, it’s time to face the music. You really do.”

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