April 30, 2020

Hello everyone! I hope you are all staying safe and healthy.


[Preprint]: Evaluation of 19 antiviral drugs against SARS-CoV-2 Infection – Liu et al.

Multi-site human microbiome

[Preprint] Topologically correct synthetic reconstruction of pathogen social behavior found in deep tissue sites – Clark et al.

Human gut microbiome

Association of Short-Chain Fatty Acids in the Gut Microbiome With Clinical Response to Treatment With Nivolumab or Pembrolizumab in Patients With Solid Cancer Tumors – Nomura et al. – JAMA Network

Genetic and metabolic links between the murine microbiome and memory – Mao et al. – BMC

Drosophila as a model for the gut microbiome – Ludington & Ja – PLOS Pathogens

Human respiratory microbiome

Combined bacterial and fungal targeted amplicon sequencing of respiratory samples: Does the DNA extraction method matter? – Angebault et al. – PLOS One

Human oral microbiome

Oral Microbiome Profiling in Smokers with and without Head and Neck Cancer Reveals Variations Between Health and Disease – Sharma et al. – Cancer Prevention Research

Animal microbiome

Coculturing of Mosquito‐Microbiome Bacteria Promotes Heme Degradation in Elizabethkingia anophelis – Ganely et al. – Chemistry Europe

Plant and soil microbiome

The responses of the soil bacterial communities and enzyme activities to the edaphic properties of coal mining areas in Central China – Sun et al. – PLOS One

Water and extremophile microbiome

Network-directed efficient isolation of previously uncultivated Chloroflexi and related bacteria in hot spring microbial mats – Xian et al – Nature

Microbes in space

Crewmember microbiome may influence microbial composition of ISS habitable surfaces – Avila-Herrera et al. – PLOS One


Structure and conformational cycle of a bacteriophage-encoded chaperonin – Bracher et al. – PLOS One


An open-source robotic platform that enables automated monitoring of replicated biofilm cultivations using optical coherence tomography – Gierl et al. – Nature

COVID-19 and Staying Sane

We are living in an insane time. Within the past month, a lot of the world has been put on lockdown, toilet paper is a rare commodity for some reason, and a new virus is sweeping across the world. For many researchers such as myself, this pandemic has shut down a huge portion of our lives since labs are no longer open. Terrifyingly enough, we now have to get used to doing all our work cooped up in our homes. 

When working at home, it’s extremely easy to beat yourself up for not being as driven or productive as you would like, but here is the most important thing for you to remember: NO ONE IS EXPECTING YOU TO BE AS PRODUCTIVE AS YOU WERE BEFORE. This pandemic is unprecedented, and it is causing everyone’s lives to go haywire. Adjusting to such big changes is hard, and it’s unreasonable for anyone to expect you to maintain the same level of productivity during these crazy times. 

For many researchers, lab work is a huge portion of time that is suddenly gone. At least for me, filling the hole that the lack of research has left has been challenging. However, there are still plenty of opportunities to keep working and building research skills while social distancing. Here are a couple of things: 

  1. Learn a new programming language. Codeacademy is giving away Pro memberships to the first 10,000 people to sign up with a .edu email address because of the COVID-19 pandemic. Although Codeacademy is meant for absolute beginners, it does provide a good jumping-off point into further work with programming. Aside from Codeacademy, Datacamp has courses in data analysis languages as well, covering Python, R, Command-Line, and more. 
  2. Brush up on your bioinformatics. There are some really great resources available online tutorials and example datasets to practice on. Bioconductor, for instance, has a huge list of online resources and example data sets to practice using R as a biologist. There are also many tutorials online for using the command-line in bioinformatics, one of which can be found here
  3. Use your social media as a scientist. Now more than ever, Twitter is the perfect place to read about the newest advances in science and jump in on the discussion as well. Even on topics unrelated to COVID-19, scientific discussion is thriving now more than ever. 
  4. Work on your writing skills. While this is probably obvious to any researcher, I still feel like I should mention this. Take this time to write a new review, finally write that Materials and Methods section, or just finish up anything that might be waiting on your to-do list. 
  5. Find out more about something random that interests you by reading a bunch of literature. Whether this is just catching up on a huge backlog of papers you need to get around to reading, or diving headfirst into a completely new field, 

But what can you do outside of work to stay sane? One great thing you can do to fill this new time is to find a new hobby! Baking bread is weirdly popular now, with my coworkers sharing recipes and pictures of the masterpieces they made (if you’re looking for a neat recipe, check out this one). If you’re also looking to contribute to stopping the spread of COVID-19, you could do something simple like sewing face masks as well.

One of the most important things you have to do during this time is to take mental health days. This could be as simple as just taking one day a week to not think about work and focus on relaxing. These breaks can go a long way in reminding you that work doesn’t control your life, even though it might seem like that now more than ever. 

This is a difficult time for everyone, and learning how to adapt to a life without physical work is extremely challenging. By taking small steps, we can all learn to adapt and come out of this pandemic as stronger researchers.

March 29, 2020

I hope everyone is staying safe and healthy during this pandemic. Today’s digest will start with a few articles on COVID-19 before moving on to microbiome papers.


Preprint: A proposal of alternative primers for the ARTIC Network’s multiplex PCR to improve coverage of SARS-CoV-2 genome sequencing – Itokawa et al.

Preprint: FDA approved drugs with broad anti-coronaviral activity inhibit SARS-CoV-2 in vitro – Weston et al.

Protein Structure and its Sequence Reanalysis of 2019-nCov Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1 – Zhang et al. – ACS Publications

General Microbiome

Antithetic population response to antibiotics in a polybacterial community – Laporta & Ojalvo – ScienceAdvances

Review: Toward a dynamical understanding of microbial communities – Rainey & Quistad – Royal Society Publishing

Pregnancy and early life

Beyond the Bacterial Microbiome: Virome of Human Milk and Effects on the Developing Infant – Mohandas & Pannaraj – Karger

Human vaginal microbiome

Cervicovaginal microbiome and natural history of HPV in a longitudinal study – Usyk et al. – PLOS Pathogens

Vaginal Microbiome of Pregnant Indian Women: Insights into the Genome of Dominant Lactobacillus Species – Mehta et al. – Springer Link

Human gut microbiome

Review: Current explorations of nutrition and the gut microbiome: a comprehensive evaluation of the review literature – Frame & Jackson – Nutrition Reviews

Metaproteomics characterizes human gut microbiome function in colorectal cancer – Long et al. – Nature

The effects of daily fasting hours on shaping gut microbiota in mice – Li et al. – BMC Microbiology

Human oral microbiome

Spatial Ecology of the Human Tongue Dorsum Microbiome – Wilbert et al. – Cell Reports

Effects of Chlorhexidine mouthwash on the oral microbiome – Bescos et al. – Scientific Reports

Animal microbiome

Microbiome diversity and composition varies across body areas in a freshwater turtle – McKnight et al. – Microbiology Society

Gut microbiota shifts in the giant tiger shrimp, Penaeus monodon, during the postlarvae, juvenile, and adult stages – Cicala et al. – Springer Link

Plant and soil microbiome

Community-driven Metadata Standards for Agricultural Microbiome Research – Dundore-Arias et al. – APS Publications

Do cover crops benefit soil microbiome? A meta-analysis of current research – Kim et al. – ScienceDirect

Water and extremophile microbiome

Linking regional shifts in microbial genome adaptation with surface ocean biochemistry – Garcia et al. – The Royal Society Publishing

The potential impact of bacterial communities exposed to crude oil and light on the growth of the harmful algal blooming species Karenia brevis (Dinophyceae) – Park & Buskey – CSIRO Publishing


Machine-learning pattern recognition and differential network analysis of gastric microbiome in the presence of proton pump inhibitor treatment or Helicobacter pylori infection – Ciucci et al.

Infrared absorptions as indicators for Pseudomonas aeruginosa and Acinetobacter baumannii – Yamamoto et al.

Evidence for a growth zone for deep subsurface microbial clades in near-surface anoxic sediments – Lloyd et al.

A potent antibiofilm agent inhibits and eradicates mono- and multi-species biofilms – Long et al.