February 28, 2020

Good morning/afternoon y’all! today’s digest features some interesting-to-read genral biotech and ecology papers, as weel as the first gene catalouge of the vaginal microbiome, American pets microbiome revealed, cool microbiome engineering for biocontrol purpose in agriculture, a bunch of salt- and sweet-water microbiome studies and more!

Have a great weekend! put the guilt aside and enjoy some time with your spouse, family, pets, hobbies and anything else that you enjoy!

General Science

is is a very cool paper, beuatifuly presenting the connection and applicatino of two very ‘hot’ topics in today biotechnology world- AI and drug discovery:A Deep Learning Approach to Antibiotic Discovery- A Deep Learning Approach to Antibiotic Discovery, Jonathan M. Stokes, Cell

** Novel Outlook in Microbial Ecology: Nonmutualistic Interspecies Electron Transfer, Roman Moscoviz, Trends in Microbiology

A solution to minimum sample size for regressions, David J. Jenkins , PLOS One

The relationship between the host genome, microbiome, and host phenotype, Harald Brussow, Env. Micro.

Human microbiome

** A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina, Bing Ma, Nature Communications

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention, Jessica A. Grembi, Sci. Rep.

Analysis of healthy reference ranges for clinically relevant gut microbial indicators: A large web-based cohort study in Japan, Satoshi Watanabe , bioRxiv

Short chain fatty acids produced by colonizing intestinal commensal bacterial interaction with expressed breast milk are anti-inflammatory in human immature enterocytes, Nan Zheng, PLOS One

Animal microbiome

Characterization of gut microbiomes of household pets in the United States using a direct-to-consumer approach, Aashish R. Jha, PLOS One

Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome, Samuel J. Bowers, PLOS One

Insect microbiome

**Engineering bacterial symbionts of nematodes improves biocontrol potential of the western corn rootworm, Ricardo A. R. Machado, Nature Biotechnology

Plant and soil microbiome

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome, Siwen Deng , bioRxiv

Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes, Yuting Liang , Env. Micro.

Network analysis infers the wilt pathogen invasion associated with non-detrimental bacteria, Qiolong Hu , npj biofims and microbiomes

Marine microbiome

Exploring the resistome, virulome and microbiome of drinking water in environmental and clinical settings, Marcela Franca Dias, Water Research

Niche partitioning of methane-oxidizing bacteria along the oxygen–methane counter gradient of stratified lakes, Magdalena J. Mayr, ISME

A metagenomic assessment of microbial eukaryotic diversity in the global ocean, Aleix Obiol, Mol. Eco. Res.

Ocean acidification affects microbial community and invertebrate settlement on biofilms, Katie S. Nelson, Sci. Rep.

Understanding and creating biocementing beachrocks via biostimulation of indigenous microbial communities, Asha A. Ramachandran , Env. Biotech.

August 23, 2019

Good morning everyone!

This post is written from lovely NYC, quite a distance from my hometown in Israel. If you’re working on microbial ecology in the city and care for a cup of coffee (on me!) and a rather interesting chat about science, entreprenurship and agriculture- please contact me via barakdror@outlook.com or just find me on Linkedin.

Today post will feature highly recommended podcast, a great antimicrobial resistance review paper, Cocaine effect on gut microbiota, some cool bioinformatics tools papers, fascinating animal microbiome studies and more.

Resources and Podcast

I’m a huge fan of the This Week in Microbiology podcast. On their 201 episode the team hosted Prof. Mark Martin (U of Puget Sound) with some great list of papers for 1st year undergrads- but it is a great opportunity to read about general concepts and direction in micrboiology. I truely enjoed both the episode and the recommended papers.

15 Biotech-Themed Online Courses to Try at Home

Antibiotic Resistance

Defining and combating antibiotic resistance from One Health and Global Health perspectives, Sara Hernando-Amado, Nature Microbiology


An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data, Chenhao Li, Microbiome

Analysing complex metagenomic data with MicroWineBar, Franziska Klincke ,bioRxiv

A systematic NGS-based approach for contaminant detection and functional inference, Sung-Joon Park, bioRxiv

Human and Animal microbiome

Cocaine Induces Inflammatory Gut Milieu by Compromising the Mucosal Barrier Integrity and Altering the Gut Microbiota Colonization, Ernest T. Chivero, Scientific Reports

Influence of the microbiota-gut-brain axis on behavior and welfare in farm animals: A review, Narjis Kraimi, Physiology & Behavior

Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system, Yaron Krotman, bioRxiv

Non‐random associations of maternally transmitted symbionts in insects: The roles of drift versus biased co‐transmission and selection, Hugo Mathe-Hubert, Molecular Ecology

The microbiome of the Melitaea cinxia butterfly shows marked variation but is only little explained by the traits of the butterfly or its host plant, G. Minard, Environmental Microbiology

Food microbiome

The occurrence of Listeria monocytogenes is associated with built environment microbiota in three tree fruit processing facilities, Xiaoqing Tan, Microbiome

Environmental microbiome

Marine-freshwater prokaryotic transitions require extensive changes in the predicted proteome, Pedro J. Cabello-Yeves, Microbiome

Taxonomic and functional characterization of a microbial community from a volcanic englacial ecosystem in Deception Island, Antarctica, Emma Martinez-Alonso, Scientific Reports