Macrobiome – from typo to mainstream use

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This blog used the term “macrobiome” (to indicate animals and plants of the visible type, such as the Borneo pygmy elephants above) back in March 2013.

A quick google search reveals earlier uses of the term on the web. Some, though not all,  appearances of “macrobiome” were typographical errors. In those examples, the writer meant to type “microbiome”. Now, the term macrobiome has become mainstream. It appeared in PNAS a few months ago:

For macrobiome to become widespread, “microbiome” had to become mainstream first. And it has, judging from the volume of interesting results at this year’s gut microbiome themed Keystone conference in Keystone Colorado,  now ongoing.

Poop happens, handwashing often doesn’t

Did you use this device today?


And you washed your hands afterwards? If so, you are in the minority of humans on the planet. Only 19% of people worldwide wash their hands after excreting.

Equally surprising, handwashing campaigns only have limited effectiveness in reducing infectious diarrhea, showing on average a reduction of about 23%.

Read the paper here.

Complete text available here:  Hygiene and health: systematic review of handwashing practices worldwide and update of health effects.

Implication: humans share microbes, including fecal microbes, all the time. Most of the time, the shared microbes do not cause infectious diarrhea. It is interesting to consider that each individual’s microbiota includes many pioneers that disperse and colonize other individuals. Room for thought: is it possible that some microbes benefit if their hosts are less fastidious? Certain microbes would have a potential fitness benefit, perhaps, if they could influence the handwashing habits of their hosts.

Final thought: Going on a trip? Consider New Zealand, highest with estimated 72% handwashing. Bring hand sanitizer, and your own food, when visiting Tanzania, estimated 5%.

Late breaking extra: Too much human feces on Mt Everest report in the Guardian

And this priceless bit from the comments section:

“Anyone contemplating a visit to the subcontinent should consider that 700 million people defecate in the open every day. As dawn blushes the golden mountains with its rosey rays, millions of anuses release to deposit fresh mountains of excrement on every road side, behind every tree, in vegetable patches, on footpaths. Every breath inhales dried and powdered human feces and black soot.”

Anti-inflammatory statin therapy useless in sepsis

A recent meta analysis concluded that statins, though effective at reducing cholesterol, are not helpful in sepsis. Statins have a variety of anti-inflammatory effects that were hypothesized to reduce harmful host inflammation in sepsis. It did not work. Read the results here:

Thomas. Statin therapy in critically-ill patients with severe sepsis: a review and meta-analysis of randomized clinical trials. Minerva Anestesiologica 2015;epublished February 18th

Does this mean inflammation is not on balance bad for us in sepsis? Regulation of inflammation during sepsis might not be out of control at all. Inflammation in sepsis, though apparently costly and sometimes fatal is something that we should not interfere with using drug therapy, except with antibiotics. That conclusion can be derived from the failure of multitudes of anti-inflammatory treatments tried in sepsis, described in Marshall Why have clinical trials in sepsis failed? Trends Mol Med 2014

Old ideas die hard, though, and we will continue to document the failure of these interventions for sepsis on this blog as they are reported.

Quicker to treat kid’s fever than pain

Are our priorities mixed up in the in the emergency department? A recent study suggests so. Dvorkin and colleagues compared how quickly pain and fever is treated in kids in the emergency department. Turns out we treat fever with much greater alacrity, perhaps because of standing orders that allow nurses to treat fever by protocol.  Kids in pain are treated much slower. Why, when increasing evidence supports an infection-fighting host defense role of fever?

From the paper:

“Fever is treated more promptly than pain in the pediatric ED. This difference is associated with prevailing and largely unfounded concerns about fever and the undertreatment of pain (oligoanalgesia).” (emphasis added).

Kudos to these researchers for pointing out that concerns about fever’s harm are unfounded. Unfortunately, it is proving to be difficult to dislodge the misconception among parents and practitioners alike.

Is fever treated more promptly than pain in the pediatric emergency department?
Dvorkin R, Bair J, Patel H, Glantz S, Yens DP, Rosalia A Jr, Marguilies J.
J Emerg Med. 2014 Mar;46(3):327-34. doi: 10.1016/j.jemermed.2013.08.063. Epub 2013 Nov 5.

Yet another reason to avoid unnecessary antibiotics

Z pack

The commonly prescribed medications azithromycin and levofloxacin are probably killing people. A recently study by Rao and colleagues in the Annals of Family Medicine had a pretty eye-popping result:

“Compared with amoxicillin, azithromycin resulted in a statistically significant increase in mortality and arrhythmia risks on days 1 to 5, but not 6 to 10. Levofloxacin, which was predominantly dispensed for a minimum of 10 days, resulted in an increased risk throughout the 10-day period.”

I have prescribed a fair amount of azithromycin and levofloxacin over the years, the former more than the latter. No more. The excess deaths appear to be due to cardiac causes.

Read the study here: Azithromycin and Levofloxacin Use and Increased Risk of Cardiac Arrhythmia and Death

Of course, Miriam Barlow showed us years ago that amoxicillin was preferable to other antibiotics (for an entirely different reason – avoiding antibiotic resistance). E. coli harbor a plasmid that can only accommodate one resistance allele at a time. The ancestral beta lactamase (blaTEM) that confers resistance to only to penicillin has a selective advantage over more recently evolved multi-drug resistant beta lactamases, especially when penicillin is given. As a result, a penicillin like amoxicillin selects for E. coli sensitivity to antibiotics in other classes. This is a largely unexplored avenue of preserving drug sensitivity. Perhaps there is a connection between these two findings (probably not!).

Either way, the Rao et al result will give more ammunition to physicians trying to talk their patients out of antibiotics for self-limiting conditions. If an antibiotic is absolutely necessary, perhaps the old standby amoxicillin will do.

Much credit is due to Yosuf Leibman of the EMU Monthly blog for alerting me to this study. The EMU Monthly is a highly, highly recommended site. Check it out.

Interested in how microbes control behavior? Post doc opportunity

Aktipis job announcement

Are you interested in the nexus between gut microbiota, behavior, and evolution? Athena Aktipis PhD may have a job opportunity for you. Athena is my collaborator and co-author on the recent Bioessays article “Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms.” I cut and pasted from the announcement below:

JOB# 11058  Posted 12/31/14

The Department of Psychology at Arizona State University invites applications for a Postdoctoral scholar in Microbiome, Evolution and Behavior. A postdoctoral position is available in Dr. Athena Aktipis’s lab for individuals with a PhD in Biology, Psychology or related discipline to work on the role of the microbiome (and biome) in health and human behavior using an evolutionary approach.  There has been recent rapid progress in our understanding of the importance of the microbiome in human health and the role of the gut-brain axis in shaping cognitive and behavioral predispositions.  This position will use experimental and modeling approaches to investigate the evolutionary pressures and proximate mechanisms shaping human-microbe interactions including addressing questions such as (1) Does the microbiome directly or indirectly influence human eating preferences? (2) Are taste/smell perception and the disgust response influenced by the microbiome? (3) Are human social behaviors and mating behaviors influenced by the microbiome?  To be eligible for these positions, applicants must have training in evolutionary biology and methodological expertise in human laboratory experiments and/or microbiome analysis. Other desired qualifications include training in statistical analysis and computational modeling.

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Dishwashers linked with allergy?


I grew up in a home without an automatic dishwasher, meaning that mealtimes were generally followed by arguments about whose turn it was to wash dishes by hand.

Despite much hand-wringing about hand dishwashing, a new study by Hesselmar and colleagues in the journal Pediatrics indicates that my parents were doing me a favor by reducing my allergy risk. This observational study involved about 1000 Swedish children. Kids whose parents used an automatic dishwasher had an increased risk of developing allergy and asthma. Handwashing was associated with a decreased risk ( odds ratio 0.57; 95% CI: 0.37- 0.85), on par with other protective factors such as eating fermented foods and being breast fed. Hesselmar’s group previously published a study linking the method of pacifier cleaning with allergy in children. Kids whose parents licked a pacifier clean (mouth cleaning), instead of boiling or tap water cleaning, had fewer allergies. In that previous study, dishwashing of pacifiers was linked with higher allergy risk. Hesselmar’s recent study suggests that machine dishwashing in general may be dangerous in terms of allergy and asthma risk in children:

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Of course, it remains to be seen if machine dishwashing has a causal relationship with allergy, or if it is simply linked with another causative factor. The authors speculated that hand dishwashing is associated with increased microbial exposure, which has been shown to be protective against allergic diseases. This idea is called the hygiene hypothesis, which we have covered extensively, e.g. here and here.

As for me, hand dishwashing did no good, at least from an immunologic perspective. I am a sneezing eye-watering allergic mess this time of year.

Read the article here: Hesselmar, Hicke-Roberts, Wennergren. Allergy in Children in Hand Versus Machine Dishwashing. Pediatrics doi: 10.1542/peds.2014-2968