Monthly Archives: April 2015

Bacterial composition following fecal microbiota transplantation

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Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection

Alexa Weingarden1,7†, Antonio González2, Yoshiki Vázquez-Baeza3†, Sophie Weiss4, Gregory Humphry5, Donna Berg-Lyons5, Dan Knights6,7, Tatsuya Unno7, Aleh Bobr8, Johnthomas Kang7,8, Alexander Khoruts7,8, Rob Knight2,9,10 and Michael J Sadowsky1,7*

Abstract

Background: Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection (CDI) that often fails standard antibiotic therapy. Despite its widespread recent use, however, little is known about the stability of the fecal microbiota following FMT.

Results: Here we report on short- and long-term changes and provide kinetic visualization of fecal microbiota composition in patients with multiply recurrent CDI that were refractory to antibiotic therapy and treated using FMT. Fecal samples were collected from four patients before and up to 151 days after FMT, with daily collections until 28 days and weekly collections until 84 days post-FMT. The composition of fecal bacteria was characterized using high throughput 16S rRNA gene sequence analysis, compared to microbiota across body sites in the Human Microbiome Project (HMP) database, and visualized in a movie-like, kinetic format. FMT resulted in rapid normalization of bacterial fecal sample composition from a markedly dysbiotic state to one representative of normal fecal microbiota. While the microbiome appeared most similar to the donor implant material 1 day post-FMT, the composition diverged variably at later time points. The donor microbiota composition also varied over time. However, both post-FMT and donor samples remained within the larger cloud of fecal microbiota characterized as healthy by the HMP.

Conclusions: Dynamic behavior is an intrinsic property of normal fecal microbiota and should be accounted for in comparing microbial communities among normal individuals and those with disease states. This also suggests that more frequent sample analyses are needed in order to properly assess success of FMT procedures.

Keywords: Short- and long-term changes in microbiota following FMT

Complete Paper in PDF

 

Dr. Oz Endorses Fecal Transplants

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Dr. Oz Endorses Fecal Transplants

Well we can now say that fecal transplants have become mainstream.  Featured in a recent episode of the Dr. Oz Show, Dr. Oz and his medical experts describe and endorse the use of fecal transplants as a way to combat stubborn intestinal pathogens.  Video, about 2 minutes in, has some great animation and descriptions about the process.  They also interview a patient who successfully recovered from a c.diff infection using following a fecal transplant.  Good watch and it is nice to see fecal transplants receiving much needed media attention.

America’s Wackiest Health Trends

http://www.doctoroz.com/episode/americas-wackiest-health-trends-tested

Ultra Small Bacteria Found at the Lower Size Limit of Life

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This cryo-electron tomography image reveals the internal structure of an ultra-small bacteria cell like never before. The cell has a very dense interior compartment and a complex cell wall. The darker spots at each end of the cell are most likely ribosomes. The image was obtained from a 3-D reconstruction. The scale bar is 100 nanometers. (Credit: Berkeley Lab)

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.

Indigenous Bacteria from the Gut Microbiota Regulate Host Serotonin Biosynthesis

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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, ,

Received 25 September 2014, Revised 16 December 2014, Accepted 18 February 2015, Available online 9 April 2015
Published: April 9, 2015

Highlights

  • •Gut microbes regulate levels of 5-HT in the colon and blood
  • •Spore-forming bacteria modulate metabolites that promote colon 5-HT biosynthesis
  • •Microbiota-dependent changes in 5-HT impact GI motility and hemostasis
  • •Altering the microbiota could improve 5-HT-related disease symptoms

Summary

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.

Full-size image (60 K)

 

Bundle Of Joyful Microbes: Mom’s DNA Alters Baby’s Gut Bacteria

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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.i

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.

Dr. Gary Gaugler/Science Source

“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.

npr.org

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.

Key probiotic helps by orchestrating others gut bacteria

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Lactobacillus.jpg

Bacteria.pngAbove 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