Microbiome

Mike the Mad Biologist

Category archives for Microbiome

A Handy Transformation for Microbiome Data

When worked on the human microbiome, I regularly confronted a problem with the data. Species frequencies are almost never normally distributed (‘the bell curve’), and if you want to use standard statistical techniques the data should be normally distributed. The second problem is that the data often have a lot of zero values. That is,…

…someone makes an animated cartoon about it. Charlie Foster sends us this clever little animation about the human gut microbiome, narrated by ‘Barry fragilis’ (Barry is, of course, short for Bacteroides). Anyway, enjoy:

Nick Loman listed the fifty most sequenced bacterial genomes according to NCBI. A reader at Nick’s blog came up with an improved list–one that reflects the genomes for which we actually have data (depending on who is doing the sequencing, a project will be registered with NCBI, often months before any sequencing is done). Here’s…

One of the issues I’ve discussed repeatedly is how resources–money–need to be shifted from data generation to data processing and analysis. This report about the Earth Microbiome Project, which will characterize 10,000 environmental (e.g., soil, water) samples is encouraging. Someone must have learned something from the last few years of microbiome work:

Whenever a new discipline, especially one using a ‘sexy’ technology, is brought to bear on human disease, it seems to be oversold in what it will actually accomplish. In addition, every problem is suddenly viewed through that lens, that if we understand how phenomenon X influences something, then WE CAN HAZ CUREZ. I’m worried that…

I don’t see the need to redescribe the recent paper about the discovery of bacteria that can might replace, in extremis, phosphorus with arsenic, which was overhyped by NASA, was poorly covered by most journalists, and which has compromising methodological problems (for good coverage, read here, here, and here; and snark). But what the paper…

How to Take a Government-Approved Poop

Shamelessly stolen from Dr. Isis Yes, you read the title correctly. As I’ve mentioned before, I’m involved with the Human Microbiome Project, which examines how the microbes that live on and in us affect human health and disease. One of the things we do is look at human gut communities. In most cases, examining the…

A couple of weeks ago I attended the Human Microbiome Research Conference. At that meeting, one talk by Bruce Birren (and covered by Jonathan Eisen) mentioned something that was completely overlooked by the attendees. Now, I don’t blame them, since what Birren mentioned was about bacterial genomics, not the human microbiome. But here’s what I…

One of the common sayings in microbiology that drives me up a wall is the notion that 99% of all bacteria can’t be grown in the lab. This false statement stems from the observation that if you take any sample (soil, water, clinical samples) and look under a microscope we see many more bacterial cells…

Programming Note: Microbiome Meeting

I’ll be at the Human Microbiome Research Conference for a few days. But don’t worry, this blog will keep on rollin’.