May 14, 2019

Good morning microbe lovers! This digest presents papers for everyone taste, plus some really nice general microbiology and science papers. Check out cool snow algae microbiome in Antarctica, soil aggregates microbiome, DNA extraction methods in studying animal microbiomes and more.

Don’t forget to spread MD with friends, colleges and others- it really helps us knowing our hard work is actually being read.

General microbiology

Into the wild: microbiome transplant studies need broader ecological reality , Christopher J. Greyson-Gaito, EcoEcoRxiv

Predicting the decision making chemicals used for bacterial growth, Kazuha Ashino, Scientific Reports

A longitudinal big data approach for precision health, Sophia Miryam Schussler-Fiorenza Rose, Nature Medicine

Human Microbiome

Mammographic breast density and its association with urinary estrogens and the fecal microbiota in postmenopausal women, Gieira S. Jones, PLOS One

Periodontal Health and Oral Microbiota in Patients with Rheumatoid Arthritis, K. Erikkson, Journal of Clinical Medicine

Animal Microbiome

Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats, Melissa R. Ingala, Ecology and Evolution

Fungal disease and temperature alter skin microbiome structure in an experimental salamander system, CR Muletz-Wolz, Molecular Ecology

Variations of the intestinal gut microbiota of farmed rainbow trout, Oncorhynchus mykiss (Walbaum), depending on the infection status of the fish, A.N Parshukov, Journal of Applied Microbiology

Responses of microbial community structure in turbot (Scophthalmus maximus) larval intestine to the regulation of probiotic introduced through live feed, Yan Jiang, PLOS One

Assessment of microbial communities on freshly killed wild boar meat by MALDI-TOF MS and 16S rRNA amplicon sequencing, M.F. Peruzy, Int. Food Microbiology

**Methods Impact of DNA extraction methods on the observed microbial communities from the intestinal flora of the penaeid shrimp Litopenaeus vannamei, Boyun Jiang, FEMS Microbiology Letters

Air Microbiome

** Snow algae communities in Antarctica: metabolic and taxonomic composition, Matthew P. Davey, The New Phytologist

Soil and Plants Microbiome

**Minireview Soil aggregate microbial communities: Towards understanding microbiome interactions at biologically relevant scales, Regina L. Wilpiszeski, App. Env. Microbiology

Comparative microbiome analysis of two different long-term pesticide contaminated soils revealed the anthropogenic influence on functional potential of microbial communities, Raj Kumar Regar, Science of the Total Environment

Interpreting distance‐decay pattern of soil bacteria via quantifying the assembly processes at multiple spatial scales, Maomao Feng, MicrobiologyOpen

Complex microbial communities drive iron and sulfur cycling in Arctic fjord sediments, J. Buongiorno, App. Env. Microbiology

Defining the root endosphere and rhizosphere microbiomes from the World Olive Germplasm Collection, Antonio Jose Fernandez-Gonzales, bioRxiv

Microbiome in the news

Human gut microbiome physiology can now be studied in vitro using Organ Chip technology, Phys.org

Inspirotec Inc and Argonne National Laboratory Collaborate on Largest Study to Date of Airborne Allergens and Microbiome in Same Homes, Globenewswire

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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)

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