Current or interesting microbiome papers
Interesting article that continues the discussion of redeveloping our medical diagnostic and treatment paradigm to include dysbiosis. Technologies such a multiplexing assays give us the ability to quickly gauge the absence or presence of certain complexes that create an environment for disease. Additionally, the introduction of new vocabulary is essential to further discussions and analysis outside of the traditional medical paradigms.
If certain bacteria do instigate cancer, the finding could lead to new screening methods or treatments
The gut microbiome has stolen the show when it comes to the recent explosion of research on the bacteria that thrive within us. But bacteria also live in a woman’s breast tissue—and the mix of those microbes may have an equally important effect on health, according to a new study in Applied and Environmental Microbiology. The results “suggest that microbes in the breast, even in low amounts, may be playing a role in breast cancer—increasing the risk in some cases and decreasing the risk in other cases,” says Gregor Reid, a professor of microbiology and immunology at Western University in Ontario and the study’s senior author.
One in eight women in the U.S. are diagnosed with breast cancer during their lifetimes, but its origins remain unknown in most cases. Age, genetic predisposition and environmental changes are often implicated—and according to a growing body of research, bacteria may be one of those environmental factors. For instance, as early as the 1960s a number of studies have found that breast-feeding is associated with a lower risk of breast cancer, and more recent work suggests that this may be because breast milk supports the growth of beneficial microorganisms.
Link to full article –
https://www.scientificamerican.com/article/the-breast-has-its-own-microbiome-and-the-mix-of-bacteria-could-prevent-or-encourage-cancer/#
The gut microbiota acts as a real organ. The symbiotic interactions between resident micro-organisms and the digestive tract highly contribute to maintain the gut homeostasis….(continued below in the window)
The intestinal tract represents the largest interface between the external environment and the human body. Nutrient uptake mostly happens in the intestinal tract, where the epithelial surface is constantly exposed to dietary antigens. Since inflammatory response toward these antigens may be deleterious for the host, a plethora of protective mechanisms take place to avoid or attenuate local damage. For instance, the intestinal barrier is able to elicit a dynamic response that either promotes or impairs luminal antigens adhesion and crossing. Regulation of intestinal barrier is crucial to control intestinal permeability whose increase is associated with chronic inflammatory conditions. The cross talk among bacteria, immune, and dietary factors is able to modulate the mucosal barrier function, as well as the intestinal permeability. Several nutritional products have recently been proposed as regulators of the epithelial barrier, even if their effects are in part contradictory. At the same time, the metabolic function of the microbiota generates new products with different effects based on the dietary content. Besides conventional treatments, novel therapies based on complementary nutrients are now growing. Fecal therapy has been recently used for the clinical treatment of refractory Clostridium difficile infection instead of the classical antibiotic therapy. In the present review, we will outline the epithelial response to nutritional components derived from dietary intake and microbial fermentation focusing on the consequent effects on the integrity of the epithelial barrier.
Front Immunol. 2015; 6: 612.
For many reasons I have been interested for the last few years in how agricultural practices affect microbiomes. For example in regard to crops, how do farming practices affect the microbiomes of the plants, the microbiomes of the soil and area around the plants, and the microbiomes of organisms (including humans) who make use of the plants?
I won’t go into all the detail right now for why I am interested in this topic but for some examples of my work in this area see The microbes we eat abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types and Structure, variation, and assembly of the root-associated microbiomes of rice.
Anyway, the reason I am writing this now is that tomorrow I am “testifying” to a NRC Committee about this topic and some related topics. The presentation will be shown live online (register here). And I thought, in the interest of openness, I would post some of what I am thinking about here before hand.
One of the key topics for tomorrow is something I have been snooping around at for a few years – how does glyphosate (the key ingredient of RoundUp and a widely used herbicide) affect microbiomes? I am interested in this from both a scientific point of view (I think it is an interesting topic) and also from a “public policy / education” point of view. I think this is a really good topic to have a public discussion of “microbiomes” and both the importance of microbial communities and the challenges with studying them. So a few years ago I started thinking about working on this and developing a “Citizen Science” project around it. And, well, I am still working on that idea and probably will be trying to launch something in the near future. As a first start I thought it would be good to start to engage the community (researchers, teachers, the public, etc) in a discussion of this topic. So .. this is the beginning of that I guess.
Some questions I think are interesting:
Scientists have captured the first detailed microscopy images of ultra-small bacteria that are believed to be about as small as life can get. The research was led by scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory and the University of California, Berkeley. The existence of ultra small bacteria has been debated for two decades, but there hasn’t been a comprehensive electron microscopy and DNA-based description of the microbes until now.
The cells have an average volume of 0.009 cubic microns (one micron is one millionth of a meter). About 150 of these bacteria could fit inside an Escherichia coli cell and more than 150,000 cells could fit onto the tip of a human hair.
The diverse bacteria were found in groundwater and are thought to be quite common. They’re also quite odd, which isn’t a surprise given the cells are close to and in some cases smaller than several estimates for the lower size limit of life. This is the smallest a cell can be and still accommodate enough material to sustain life. The bacterial cells have densely packed spirals that are probably DNA, a very small number of ribosomes, hair-like appendages, and a stripped-down metabolism that likely requires them to rely on other bacteria for many of life’s necessities.
The bacteria are from three microbial phyla that are poorly understood. Learning more about the organisms from these phyla could shed light on the role of microbes in the planet’s climate, our food and water supply, and other key processes.
The scientists report their findings Friday, Feb. 27, in the journal Nature Communications.
http://newscenter.lbl.gov/2015/02/27/ultra-small-bacteria/
Microbiome Restoration Comment – This discovery provides further evidence of the commissural nature of all bacteria. These bacteria were found in a sample of sterile water! The importance of having the right populations and balance are seen throughout nature.
Volume 161, Issue 2, 9 April 2015, Pages 264–276
Jessica M. Yano1,Kristie Yu1,Gregory P. Donaldson1,Gauri G. Shastri1,Phoebe Ann1,Liang Ma2,Cathryn R. Nagler3,Rustem F. Ismagilov2,Sarkis K. Mazmanian1,Elaine Y. Hsiao1, ,
The gastrointestinal (GI) tract contains much of the body’s serotonin (5-hydroxytryptamine, 5-HT), but mechanisms controlling the metabolism of gut-derived 5-HT remain unclear. Here, we demonstrate that the microbiota plays a critical role in regulating host 5-HT. Indigenous spore-forming bacteria (Sp) from the mouse and human microbiota promote 5-HT biosynthesis from colonic enterochromaffin cells (ECs), which supply 5-HT to the mucosa, lumen, and circulating platelets. Importantly, microbiota-dependent effects on gut 5-HT significantly impact host physiology, modulating GI motility and platelet function. We identify select fecal metabolites that are increased by Sp and that elevate 5-HT in chromaffin cell cultures, suggesting direct metabolic signaling of gut microbes to ECs. Furthermore, elevating luminal concentrations of particular microbial metabolites increases colonic and blood 5-HT in germ-free mice. Altogether, these findings demonstrate that Sp are important modulators of host 5-HT and further highlight a key role for host-microbiota interactions in regulating fundamental 5-HT-related biological processes.
Right after birth, trillions of microbes rush into a baby’s gut and start to grow. Most of these critters come from the mom’s skin, birth canal and gut.
But exactly which types of bacteria take up residence in an infant’s gut can depend on the mother’s DNA, scientists reported Thursday.
The study, published in the journal Microbiome, focuses on a microbe called Bifidobacterium that potentially benefits babies.
Bifidobacteria are among the first microbes to show up in a baby’s intestinal tract after birth. Some studies suggest a particular type of Bifidobacteria can prevent infections and help establish the newborn’s immune system.
“It plays a role in preventing infections,” says Zachery Lewis, a graduate student in microbiology at the University of California, Davis, who contributed to the study. “Bifidobacteria sort of push other bacteria out. They lower the gut’s pH, which a lot of pathogens don’t like.”
After birth, Bifidobacterium is one of the first microbes to arrive in a baby’s gut. But not all infants get the microbe at the same time — or in the same amounts.
Microbiome Restoration Comment – Mom’s DNA Alters Baby’s Gut Bacteria
Great article. Encouraging mothers to breast feed is very important. From the minute an infant leaves the safety of its mother’s womb it now has to fend for itself. Breast milk is key to the beginning of a healthy microbiome.
Above images source – microbewiki.kenyon.edu
The Lactobacillus bacterium, stained blue here, colonizes the human gut when people eat yogurt. A new study details how L. rahmnosus, a single-organism probiotic, helps the gut microbiome flourish.
Microbiome Restoration Editors note –
While it may seem that certain bacteria may not produce any exotic or powerful compounds that the body uses directly, it now appears that certain probiotic bacteria act as “traffic cops” or regulators of the other bacteria. It is likely that these are as important as the bacteria that directly produce helpful compounds.
http://www.latimes.com/science/sciencenow/la-sci-sn-gut-probiotic-20150414-story.html
Lactobacillus, also called Döderlein’s bacillus, is a genus of Gram-positive facultative anaerobic or microaerophilic rod-shaped bacteria.[1] They are a major part of the lactic acid bacteria group, named as such because most of its members convert lactose and other sugars to lactic acid. In humans they are present in the vagina[2] and the gastrointestinal tract, where they make up a small portion of the gut flora.[3] They are usually benign, except in the mouth where they have been associated with cavities and tooth decay (dental caries). Many species are prominent in decaying plant material. The production of lactic acid makes its environment acidic, which inhibits the growth of some harmful bacteria. Several members of the genus have had their genome sequenced.
Source – Wikipedia
Lactobacillus reuteri are Gram-positive, rod-shaped, and anaerobic. These heterofermentatic lactic acid bacterium naturally inhabit the gut of a wide range of organisms, including humans, pigs, chickens and mice [2]. They can also be isolated from human breast milk [10]. In vitro, Lactobacillus reuteri grows optimally on MRS media at 37 degrees Celsius [2]. They have also been found to grow in biofilms [1]. The Food and Agricultural Organization of the United Nations describes probiotics as “live microorganisms which when administered in adequate amounts confer a health benefit on the host,” [1] an idea first vocalized by Elie Metchnikoff, in the early 1900’s [7]. L. reuteri produces reuterin, an antimicrobial that inhibits growth of harmful bacteria, fungi, and protozoa. Due to these probiotic properties, L. reuteri is believed to be a promising therapy for the alleviation and reduction of certain illnesses related to gastrointestinal health, oral health, and urogenital health, including infantile colic, eczema, and H. pylori infection [1].
Source – microbewiki.kenyon.edu
