Tip Carl Zimmer, the microbiome

[Diane]

Tending the Body’s Microbial Garden. Absolutely fascinating. :thumbs_up
Excerpt:

Dr. Fischbach cautions that it may take a while to figure out how to manipulate the microbiome to make people healthy.

And it may take even longer to persuade doctors to think like ecologists.

“The physicians I know really like things that are clear and crisp,” Dr. Fischbach said. “But like any ecosystem, the microbiome is not the kind of place to find simple answers.”

Hmmnn.... yup!

[Jo Bowyer]

Wikipedia.
http://en.wikipedia.org/wiki/Human_microbiome

Structure function and diversity of the healthy human microbiome.
http://www.nature.com/nature/journal...ture11234.html

[Jo Bowyer]

Exercise Is More Effective at Altering Gut Microbial Composition and Producing Stable Changes in Lean Mass in Juvenile versus Adult Male F344 Rats

http://journals.plos.org/plosone/art...l.pone.0125889

Abstract

The mammalian intestine harbors a complex microbial ecosystem that influences many aspects of host physiology. Exposure to specific microbes early in development affects host metabolism, immune function, and behavior across the lifespan. Just as the physiology of the developing organism undergoes a period of plasticity, the developing microbial ecosystem is characterized by instability and may also be more sensitive to change. Early life thus presents a window of opportunity for manipulations that produce adaptive changes in microbial composition. Recent insights have revealed that increasing physical activity can increase the abundance of beneficial microbial species. We therefore investigated whether six weeks of wheel running initiated in the juvenile period (postnatal day 24) would produce more robust and stable changes in microbial communities versus exercise initiated in adulthood (postnatal day 70) in male F344 rats. 16S rRNA gene sequencing was used to characterize the microbial composition of juvenile versus adult runners and their sedentary counterparts across multiple time points during exercise and following exercise cessation. Alpha diversity measures revealed that the microbial communities of young runners were less even and diverse, a community structure that reflects volatility and malleability. Juvenile onset exercise altered several phyla and, notably, increased Bacteroidetes and decreased Firmicutes, a configuration associated with leanness. At the genus level of taxonomy, exercise altered more genera in juveniles than in the adults and produced patterns associated with adaptive metabolic consequences. Given the potential of these changes to contribute to a lean phenotype, we examined body composition in juvenile versus adult runners. Interestingly, exercise produced persistent increases in lean body mass in juvenile but not adult runners. Taken together, these results indicate that the impact of exercise on gut microbiota composition as well as body composition may depend on the developmental stage during which exercise is initiated.

[Matthew Danziger]

SS's own Karen Litzy had a particularly great interview with Dr. John Cryan on her podcast on related topics. I might have to give it another listen myself.

http://podcast.healthywealthysmart.c...in-connection/

[Jo Bowyer]

This is a must listen for classical osteopaths and all fans of gut innervation, bearing in mind Dr Cryan's warning that there is still a dearth of gold standard physiological research in this area.

I see infants, children and adults with abdominal pain as well complex pain thought to be neuromusculoskeletal, which may have a visceral component. I am often asked to give answers to questions for which there is a wealth of opinion but as yet, no hard evidence.

First contact practitioners, have the opportunity to identify cases that require medical/surgical opinion and refer them on early.



Neuroanatomy of visceral nociception: vagal and splanchnic afferent
http://gut.bmj.com/content/51/suppl_1/i2.full

Abstract

Afferent fibres convey sensory information from the upper gastrointestinal tract to the central nervous system but the nature of this information is different for vagal and spinal pathways. Vagal afferents convey predominantly physiological information while spinal afferents are able to encode noxious events. Because of the different response profiles following activation of these pathways, it is likely that vagal and splanchnic afferents play different roles in mediating sensation.

[Diane]

Abdominal Cutaneous Nerve Entrapment Syndrome (ACNES): A Commonly Overlooked Cause of Abdominal Pain (full text)
I look for and treat this first.

[Jo Bowyer]

I am lucky enough to have had abdominal wall pain (overuse injury) and a long hx of IBS from childhood to mid 30s. So I have some insider knowledge of both. In my UK practice over the last ten years or so, there has been an increase in pain arising from the gall bladder and occasionally liver, masquerading as MSK pain or presenting along with MSK pain. The gall bladder does not always refer pain to the shoulder and sometimes the wheels of the NHS turn slowly with regards to investigations. Unfortunately some patients give an edited version during case history, especially when it comes to lifestyle choices.

I tend to look for pathology, which is probably a good idea in the UK as our NHS works within financial constraints and there is less routine testing than is customary in Germany and the USA. I am woefully ignorant as to what happens in Canada.

[Diane]

I think we just use the standard medical pain referral charts in Canada;
gallbladder to right side upper and mid back, pancreas to mid back and mid front, anything touching the diaphragm to right shoulder, spleen only to left shoulder, heart usually left but can refer to right and up into neck, prostate to low back, etc..
I don't worry about anything visceral, at all,
1. unless I try (and fail) to make any sort of dint in the pain pattern with the usual, or
2. unless the pain pattern is very weird. Like the woman I saw for "hip pain" that was relieved only by folding her body into full flexion in long sitting. Turned out to be something sinister to do with pelvic organs.

[Jo Bowyer]

Regulation of the stress response by the gut microbiota: Implications for psychoneuroendocrinology

http://www.lynes.uconn.edu/Lynes_Lab...ress%20ms9.pdf

Summary

There is now an expanding volume of evidence to support the view that commensal organisms within the gut play a role in early programming and later responsivity of the stress system. The gut is inhabited by 1013—1014 micro-organisms, which is ten times the number of cells in the human body and contains 150 times as many genes as our genome. It has long been recognised that gut pathogens such as Escherichia coli, if they enter the gut can activate the HPA. However, animals raised in a germ-free environment show exaggerated HPA responses to psychological stress, which normalises with monocolonisation by certain bacterial species including Bifidobacterium infantis. Moreover, increased evidence suggests that animals treated with probiotics have a blunted HPA response. Stress induces increased permeability of the gut allowing bacteria and bacterial antigens to cross the epithelial barrier and activate a mucosal immune response, which in turn alters the composition of the microbiome and leads to enhanced HPA drive. Increasing data from patients with irritable bowel syndrome and major depression indicate that in these syndromes alteration of the HPA may be induced by increased gut permeability. In the case of irritable bowel syndrome the increased permeability can respond to probiotic therapy. Detailed prospective studies in patients with mood disorders examining the gut microbiota, immune parameters and HPA activity are required to throw further light on this emerging area. It is however clear that the gut microbiota must be taken into account when considering the factors regulating the HPA.

[Jo Bowyer]

A unified initiative to harness Earth's microbiomes

http://www.sciencemag.org/content/350/6260/507.full

Despite their centrality to life on Earth, we know little about how microbes (1) interact with each other, their hosts, or their environment. Although DNA sequencing technologies have enabled a new view of the ubiquity and diversity of microorganisms, this has mainly yielded snapshots that shed limited light on microbial functions or community dynamics. Given that nearly every habitat and organism hosts a diverse constellation of microorganisms—its “microbiome”—such knowledge could transform our understanding of the world and launch innovations in agriculture, energy, health, the environment, and more (see the photo). We propose an interdisciplinary Unified Microbiome Initiative (UMI) to discover and advance tools to understand and harness the capabilities of Earth's microbial ecosystems. The impacts of oceans and soil microbes on atmospheric CO2 are critical for understanding climate change (2). By manipulating interactions at the root-soil-microbe interface, we may reduce agricultural pesticide, fertilizer, and water use enrich marginal land and rehabilitate degraded soils. Microbes can degrade plant cell walls (for biofuels), and synthesize myriad small molecules for new bioproducts, including antibiotics (3). Restoring normal human microbial ecosystems can save lives [e.g., fecal microbiome transplantation for Clostridium difficile infections (4)]. Rational management of microbial communities in and around us has implications for asthma, diabetes, obesity, infectious diseases, psychiatric illnesses, and other afflictions (5, 6). The human microbiome is a target and a source for new drugs (7) and an essential tool for precision medicine (8).

My italics

[Jo Bowyer]

The effect of habitual and experimental antiperspirant and deodorant product use on the armpit microbiome

https://peerj.com/articles/1605/

Abstract

An ever expanding body of research investigates the human microbiome in general and the skin microbiome in particular. Microbiomes vary greatly from individual to individual. Understanding the factors that account for this variation, however, has proven challenging, with many studies able to account statistically for just a small proportion of the inter-individual variation in the abundance, species richness or composition of bacteria. The human armpit has long been noted to host a high biomass bacterial community, and recent studies have highlighted substantial inter-individual variation in armpit bacteria, even relative to variation among individuals for other body habitats. One obvious potential explanation for this variation has to do with the use of personal hygiene products, particularly deodorants and antiperspirants. Here we experimentally manipulate product use to examine the abundance, species richness, and composition of bacterial communities that recolonize the armpits of people with different product use habits. In doing so, we find that when deodorant and antiperspirant use were stopped, culturable bacterial density increased and approached that found on individuals who regularly do not use any product. In addition, when antiperspirants were subsequently applied, bacterial density dramatically declined. These culture-based results are in line with sequence-based comparisons of the effects of long-term product use on bacterial species richness and composition. Sequence-based analyses suggested that individuals who habitually use antiperspirant tended to have a greater richness of bacterial OTUs in their armpits than those who use deodorant. In addition, individuals who used antiperspirants or deodorants long-term, but who stopped using product for two or more days as part of this study, had armpit communities dominated by Staphylococcaceae, whereas those of individuals in our study who habitually used no products were dominated by Corynebacterium. Collectively these results suggest a strong effect of product use on the bacterial composition of armpits. Although stopping the use of deodorant and antiperspirant similarly favors presence of Staphylococcaceae over Corynebacterium, their differential modes of action exert strikingly different effects on the richness of other bacteria living in armpit communities.

[Jo Bowyer]

Microbiota in Breast Milk of Chinese Lactating Mothers

http://journals.plos.org/plosone/art...l.pone.0160856

Abstract

The microbiota of breast milk from Chinese lactating mothers at different stages of lactation was examined in the framework of a Maternal Infant Nutrition Growth (MING) study investigating the dietary habits and breast milk composition in Chinese urban mothers. We used microbiota profiling based on the sequencing of fragments of 16S rRNA gene and specific qPCR for bifidobacteria, lactobacilli and total bacteria to study microbiota of the entire breast milk collected using standard protocol without aseptic cleansing (n = 60), and the microbiota of the milk collected aseptically (n = 30). We have also investigated the impact of the delivery mode and the stage of lactation on the microbiota composition. The microbiota of breast milk was dominated by streptococci and staphylococci for both collection protocols and, in the case of standard collection protocol, Acinetobacter sp. While the predominance of streptococci and staphylococci was consistently reported previously for other populations, the abundance of Acinetobacter sp. was reported only once before in a study where milk collection was done without aseptic cleansing of the breast and rejection of foremilk. Higher bacterial counts were found in the milk collected using standard protocol. Bifidobacteria and lactobacilli were present in few samples with low abundance. We observed no effect of the stage of lactation or the delivery mode on microbiota composition. Methodological and geographical differences likely explain the variability in microbiota composition reported to date.

Mothers who are unable to breastfeed are often made to feel inadequate by peers and by HCPs. While there is evidence for the many benefits of breast feeding, mothers should also be advised that present day formula milk is excellent in composition.