Recipe: How I make yogurt

I’ve been meaning to post this for a long time. The way I make yogurt was inspired by Vaugh Tan (from a meet-up back in 2012!). The philosophy he shared, and to which I already, as a biologist, ascribed to, was to understand fermentation as something a community of different organisms do. For yogurt, different bacteria have peak […]

“Welcome to the Post-Pasteurian Age” (my HealthFOO Ignite talk that never happened)

I was blessed with an invitation to HealthFOO this year, here in nearby Cambridge. Alas, the event was cancelled due to the intense events after the Boston Marathon. But not only was I bummed out that I wasn’t going to spend a fun weekend with follow health enthusiasts, but I also had to cancel my […]

Saturday morning thoughts on the evolutionary history of IBD in Eastern European Jews

Of course, as is usual with me on the weekend, I started reading all my open tabs in my browser. And the first one I read was a paper where they crossed two pure strains of mice and correlated microbiome and genome. Link: PLoS ONE: Murine Gut Microbiota Is Defined by Host Genetics and Modulates […]

The wacky world of horizontal gene transfer, genomic variants, and what we think are microbial species

“The main difference from eukaryotes is that prokaryotic reproduction is independent of DNA acquisition and recombination. Instead, DNA is obtained from fragmented chromosomes obtained via parasexual means (that is, without reproduction). These mechanisms of DNA exchange are not restricted to gene exchange within species, and therefore traits can and do come from highly divergent organisms. […]

Gut microbes and immunity: The hygiene hypothesis, peak antibiotics, and the post-Pasteurian Age

“Exposure to microbes during early childhood is associated with protection from immune-mediated diseases such as inflammatory bowel disease (IBD) and asthma. Here, we show that, in germ-free (GF) mice, invariant natural killer T (iNKT) cells accumulate in the colonic lamina propria and lung, resulting in increased morbidity in models of IBD and allergic asthma compared […]

The Impact of a Consortium of Fermented Milk Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins

“The results also showed that (i) consumption of an FMP containing five bacterial strains was not associated with a statistically significant change in the proportional representation of resident community members within and between individuals; (ii) the appearance and disappearance of strains comprising the FMP consortium did not exhibit familial patterns in the fecal microbiota; and […]

International Human Microbe Program Looks Ahead – ScienceInsider

Indeed, Sharp said at the meeting, patients who come to Cleveland Clinic for treatment of inflammatory bowel disease express their own concerns about such approaches, which could include the use of probiotics, the consumption of live microorganisms, to treat intestinal and other maladies. “Many patients are worried about manipulating their gut microbiota,” Sharp said, adding […]

Dangerous C. difficile infections soar in US, but Massachusetts hospitals have cut germ’s spead – The Boston Globe

“A life-threatening germ that causes diarrhea and spreads easily from doctors’ offices to hospitals and nursing homes has climbed to historic highs nationally, federal disease trackers warned Tuesday, as they pointed to efforts in Massachusetts that have helped slow the rate of infections here.” More on this nasty bug. It’s now getting headlines. Read this […]

A human gut microbial gene catalogue established by metagenomic sequencing : Nature

“Beyond providing the global view of the human gut microbiome, the extensive gene catalogue we have established enables future studies of association of the microbial genes with human phenotypes and, even more broadly, human living habits, taking into account the environment, including diet, from birth to old age. We anticipate that these studies will lead […]

Genome Sequence of E. coli O104:H4 Leads to Rapid Development of a Targeted Antimicrobial Agent against This Emerging Pathogen – PLoS ONE

“A recent widespread outbreak of Escherichia coli O104:H4 in Germany demonstrates the dynamic nature of emerging and re-emerging food-borne pathogens, particularly STECs and related pathogenic E. coli. Rapid genome sequencing and public availability of these data from the German outbreak strain allowed us to identify an O-antigen-specific bacteriophage tail spike protein encoded in the genome. […]