April 25, 2019

Good morning everyone! (and apologies for the delay, a technical issue regarding the system time difference between Israel and US Pacific time :)).

Due to yesterday extremely rich digest, today’s post will be short- but diverse! Spreading from gut microbiome in infants and beetles, to the effect of microbial communities on sweet wine quality. As a bonus for the upcoming weekend, at the end of the post you’ll find a link to an article listing 10 recommended biotech podcasts.

Happy holidays for all!

General Science and Microbiology

Failure to vaccinate and vaccine failure– Editorial- Nature Microbiology

The problem with unadjusted multiple and sequential statistical testing– Casper Albers- Nature Communications

Human microbiome

**Review – What did we learn from multiple omics studies in asthma?– Olga Ivanova- Allergy

Fecal microbiota transplant for Crohn disease: A study evaluating safety, efficacy, and microbiome profile– Liat Gutin- ueg

Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study– Modupe O. Coker- BJOG

The Gut Microbiome on a Periodized Low-Protein Diet Is Associated With Improved Metabolic Health– Zhencheng Li- Frontiers in Microbiology

Plant microbiome

Characterization of Rhodopseudomonas palustris population dynamics on tobacco phyllosphere and induction of plant resistance to Tobacco mosaic virus infection– Pin Su- bioRxiv

The plant host induces antibiotic production to select the most beneficial colonizers– Ariel Ogran- AEM

Microbial network and soil properties are changed in bacterial wilt susceptible soil– Gaufo Qi- AEM

Water Microbiomes

Fates of antibiotic resistance genes in a distributed swine wastewater treatment plant– Qing-Bin Yuan- Water Environment Research

** Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments– Xiyang Dong- Nature Communications

Animal microbiome

Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle– Ceja Navarro- Nature Microbiology

Gut microbiome-derived phenyl sulfate contributes to albuminuria in diabetic kidney disease– Koichi kikuchi- Nature Communications

Honeybee-specific lactic acid bacterial supplements have no effect on American foulbrood infected honeybee colonies– Jorg G. Stephan- AEM

Food microbiome

Influence of microbial communities on the chemical and sensory features of Falanghina sweet passito wines– F De Fillips- Europe PMC

Microbiome in the News

The Asia Pacific human microbiome market is expected to reach US$ 207.81 Mn in 2025 -Cision

**UPDATED- Critical Reading required– Antibiotics: beneficial side effects are starting to come to light– Claire Bourke- The Conversation. I’m bringing about this post in order to encourage a discussion regarding the issues and claims that were written in this non-scientific article. You’re welcome to share your thoughts about it at the comments section below.

Podcasts

Top 10 Biotech Podcasts to Listen to this Spring– Clara Rodriguez Fernandez- Labiotech.eu

**Personal recommendation- This Week in Microbiolgy (TwiM)

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April 16, 2019

Good morning everyone! Today’s digest will deal a lot of disturbance in various ecosystems- starvation of the oral microbiota, forest fires, elevated CO2 levels and rising temperatures and more. Additionally, interesting pieces about science communication and education are recommended (bottom of the post).

Animal microbiome

Effects of diet on gut microbiota of soil collembolans– Qian Xiang- Science of the Total Environment

Diel population and functional synchrony of microbial communities on coral reefs– Winda Wegley-Kelly- Nature Communications

Human microbiome

Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral microbiota– Jonathon L. Baker- PNAS

Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation– Hyeonsoo Jeong- Scientific Reports

Dysbiosis patterns during re-induction/salvage versus induction chemotherapy for acute leukemia– Armin Rashidi- Scientific Reports

The personalized temporal dynamics of microbiome in the airways of cystic fibrosis patients– Giovanni Baci- bioRxiv

Plant, root and soil microbiome

Maize synthesized benzoxazinoids affect the host associated microbiome- Enoch Narh Kodjordjie- Microbiome

Utilization of carbon sources in the rice rhizosphere and non-rhizosphere soils with different long-term fertilization management– Tang H- J of Basic Microbiology

Effect of forest fire prevention treatments on bacterial communities associated with productive Boletus edulis sites- Olaya Mediavilla- Microbial Biotechnology

Effects of elevated temperature and elevated CO2 on soil nitrification and ammonia-oxidizing microbial communities in field-grown crop– Linh T.T Nguyen- Science of the Total Environment

Phyllosphere epiphytic and endophytic fungal community and network structures differ in a tropical mangrove ecosystem– Hui Yao- Microbiome

Changes in fungal communities across a forest disturbance gradient– Lingling Shi- AEM

Water microbiome

Wetland sediments host diverse microbial taxa capable of cycling alchohols- Paula Dalcin Martins- AEM

Review- The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally– Gregory J. Dick- N. Reviews Microbiology

Bioinformatics

DeeplyEssential: A Deep Neural Network for Predicting Essential Genes in Microbes- Md Abid Hassan- bioRxiv

Microbiome news and science communication

Biotech company launches animal models with custom microbiome profiles

Microbial biotechnology for water treatment- A collection of high-quality websites (from Microbial Biotechnology)

Thematic series on scholarly communications in the digital age

The urgent need for microbiology literacy in society

General microbiology and science, August 26, 2014

Here, we have CRISPRs, phages, marine metagenomics, a universal bacterial/archaeal primer (The One?), single-cell genomics, light and bacteria, and Bik’s Picks.

Phages and CRISPRs

Abundant and Diverse Clustered Regularly Interspaced Short Palindromic Repeat Spacers in Clostridium difficile Strains and Prophages Target Multiple Phage Types within This Pathogen – Katherine R. Hargreaves – mBio

“We detected multiple matches between spacers and regions in 31 C. difficile phage and prophage genomes”

Evolutionary consequences of intra-patient phage predation on microbial populations
Kimberley D Seed – eLife

“Here, we show that predatory interactions of a phage with an important environmentally transmitted pathogen, Vibrio cholerae, can modulate the evolutionary trajectory of this pathogen during the natural course of infection within individual patients.”

Metagenomics

* Marine metagenomics, a valuable tool for enzymes and bioactive compounds discovery
Rosalba Barone – Frontiers in Marine Science

“We report examples of several hydrolytic enzymes and natural products isolated by functional sequenced-based and function- screening strategies assisted by new high-throughput DNA sequencing technology and recent bioinformatics tools.”

Bioinformatics

Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data – Peter Skewes-Cox – PLOS ONE

“Here, we constructed HMMER3-compatible profile hidden Markov models (profile HMMs) from all the virally annotated proteins in RefSeq in an automated fashion using a custom-built bioinformatic pipeline. “

 

Techniques

I hope they developed two primers, not just one! Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing – Shunsuke Takahashi – PLOS ONE

“Here, we designed a universal primer based on the V3-V4 hypervariable region of prokaryotic 16S rDNA for the simultaneous detection of Bacteria and Archaea in fecal samples from crossbred pigs (Landrace×Large white×Duroc) using an Illumina MiSeq next-generation sequencer.”

A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods – Charles F. A. de Bourcy – PLOS ONE

“Here, we compare three state-of-the-art methods on both bulk and single-cell samples of E. coli DNA: Multiple Displacement Amplification (MDA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC), and the PicoPLEX single-cell WGA kit (NEB-WGA). “

This abstract is so vague, I am not sure where to file this under – A Robust and Adaptable High Throughput Screening Method to Study Host-Microbiota Interactions in the Human Intestine – Tomas de Wouters – PLOS ONE

“In this study, we developed a robust and reproducible methodology to combine these two biological systems for high throughput application”

LC Sciences and Norgen Biotek will be conducting a free informational webinar describing 16S rRNA Sequencing and presenting a few application examples.

“If you are interested in attending the webinar, simply reply to news@lcsciences.com and we would be happy to send the webinar details.”

More microbiology

The Immune System in Children with Malnutrition — A Systematic Review
Maren Johanne Heilskov Rytter – PLOS ONE

“A systematic literature search was done in PubMed, and additional articles identified in reference lists and by correspondence with experts in the field. “

Photodynamic Therapy Using Systemic Administration of 5-Aminolevulinic Acid and a 410-nm Wavelength Light-Emitting Diode for Methicillin-Resistant Staphylococcus aureus-Infected Ulcers in Mice – Kuniyuki Morimoto – PLOS ONE

“5-aminolevulinic acid photodynamic therapy accelerated wound healing and decreased bacterial counts on ulcer surfaces; in contrast, vancomycin treatment did not accelerate wound healing.”

Light Scattering Sensor for Direct Identification of Colonies of Escherichia coli Serogroups O26, O45, O103, O111, O121, O145 and O157 – Yanjie Tang- PLOS ONE

“SMAC was chosen for exhaustive scatter image library development, and 36 additional strains of O157:H7 and 11 non-O157 serovars were examined, with each serogroup producing unique differential scatter patterns.”

Science and publishing

Protecting human research participants in the age of big data – Susan T. Fiskea, and Robert M. Hauser – PNAS USA

“IRB review does not apply to Facebook and other private enterprises, yet they generate data that can benefit humanity”

Bik’s Picks

Magpies don’t like shiny things – Sarah Zielinski – Science News

“Magpies deserve our apology. Apparently humans have been unnecessarily maligning the birds for centuries. “

Richard III ate like a king before biting the dust – Bruce Bower – Science News

“Well-known royal’s brief reign included a sudden shift to fancy food and drink”

What type of researcher are you? Take the Quiz – Roche Life Science

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