You may have heard the saying that “a butterfly flaps its wings and…” insert your absurd unintended, chaotic, massive consequence here (e.g., a hurricane). We may not have much control over butterflies, but we do make choices as industries, governments, and individuals on which products we produce, regulate, and consume. Examples of such products that …
Some new papers that may be of interest to people: FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus. Statistical Methods for Functional Metagenomic Analysis Based on Next-Generation Sequencing Data PhD thesis from Pookhao, Naruekamol Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data Parallel-META 2.0: Enhanced …
Well this is very interesting. The FDA has announced a competition: U.S. Food and Drug Administration | 2014 Food Safety Challenge. From their site Summary While the American food supply is among the safest in the world, the Centers for Disease Control and Prevention (CDC) estimates that 1 in 6 Americans is sickened by foodborne illness …
scikit-bio is a library for building bioinformatics tools and workflows in Python. It’s already a core dependency of QIIME, is extensively used in An Introduction to Applied Bioinformatics, and was the subject of my talk at SciPy 2014 (video) this past July. One of our focuses with scikit-bio is to make its functionality very accessible …
This article, “Urban microbiomes and urban ecology: How do microbes in the built environment affect human sustainability in cities?” certainly gets points for an intriguing title. Though it is sadly closed-access. I haven’t read the whole article, but it’s basically a review of a lot of microbiology of the built environment literature, especially as it relates …
We recently submitted a paper to biorxiv on the estimation of average genome size from shotgun metagenomics data and it’s application to the human microbiome (http://biorxiv.org/content/biorxiv/early/2014/09/11/009001.full.pdf). It is currently undergoing peer review. This study was motivated by the troubling observation that many universal single-copy genes appear to vary significantly across metagenomes. How can this be? …
We recently published a paper (http://mbio.asm.org/content/5/4/e01564-14) reporting that plants grown indoors have different leaf-surface (phyllosphere) bacterial communities than those grown outdoors. We found that Romaine lettuce grown in environmental chambers contains 10- to 100-fold lower numbers of bacteria than age-matched, field-grown lettuce. The bacterial diversity on laboratory-grown lettuce plants was also significantly lower and contained …
Researchers in Egypt did a fascinating study recently on probiotics for fish. They tested the effect of three different types of Psuedomonas fluorescens on two pathogens that affect tilapia in the Nile (P. angulliseptica and S. faecium). Their aim was to find a more eco-friendly way of controlling the pathogens in aquaculture compared to chemical antimicrobials. The probiotic was indeed …
Nice new paper that may be of interest: PLOS Pathogens: From Dandruff to Deep-Sea Vents: Malassezia-like Fungi Are Ecologically Hyper-diverse by Anthony Amend. Malassezia are commonly found in many studies of human skin and when they have been found in other places sometimes it is thought that they are vagrants having come from the skin of humans or …
Note – Jonathan Eisen invited Jack Gilbert to write a post about the Earth Microbiome Project especially in light of the recent paper on the topic by Gilbert et al. (see Eisen’s blog post about this paper here). Post by Jack Gilbert submitted by email to Jonathan Eisen. The Earth Microbiome Project started as …