The Human Microbiome from Two Worlds

The human microbiome is a complex combination of microorganisms such as bacteria, fungi and archaea residing in layers of the skin, oral cavity, eyes and gastrointestinal tract. These microorganisms maintain some type of symbiosis with their human hosts, however most are known to be useful and participative in maintaining human health [1]. Although some is known about human microbiomes, in comparison to other biological subjects, it is poorly understood and studied. Nevertheless, as science advances and the human microbiome becomes of more interest, a greater number of studies and research has been done regarding this subject. One unique study preformed by the Department of Microbiology and Immunology at the Stanford University School of Medicine analyzed gut microbiome diversity and composition in healthy children from both the United States and Bangladesh [2].

Description of the human body and the bacteria the predominate in the Human Microbimoe
Source: http://upload.wikimedia.org/wikipedia/en/0/0a/Skin_Microbiome20169-300.jpg

The Study was first proposed when a point was brought up. The previously current understanding of the composition and stability of the human gut was based on healthy infants and adults from developed countries. To combat this, the study used older children and adolescents from developing countries as their subjects. To carry out their study, healthy children, ages 9 to 14 years, who lived in an urban slum in Bangladesh and children of the same age range in an upper-middle class suburban community in the United States were used [2].

Using samples of fecal matter, more than 8,000 gene sequences and over 845,000 pyrosequencing reads were analyzed. It was found that the gut of Bangladeshi children contained a greater diversity of bacterial than the guts of the children from the United States [2]. Moreover it was found that there was a distinct fecal bacteria composition between the two groups. Specifically, Bangladeshi children were enriched in microbiota Prevotella, Butyrivibrio, and Oscillospira. Additionally, Bangladeshi children were found to have less stable bacterial communities from a month to month basis than American children [2]. This study suggests that different environmental along with genetic factors may affect the human microbiome. With research on the human microbiome being so new, hopefully this study peaks the interest of others and further investigations will be done to gain a further understanding.

Venn diagram of the exclusive and shared genera of Bangladeshi and U.S. children [2].

Those Bloody Blood Flukes!

Schistosoma haematobium is a type of parasitic flatworm that has two suckers. They are part of the class trematoda meaning “flukes” or flatworms and are part of the subclass digenea which means they usually have two suckers (one ventral and one oral) and are particular common in the digestive tract [1, 2]. Specifically, Schistosoma haematobium cause a urinary parasitic disease known as urinary schistosomiasis. Urinanry Schistosomiasis is often a chronic disease that causes blood in urine, severe pain, secondary infections, kidney damage, and even cancer [3]. Urinanry Schistosomiasis is an endemic disease many in many countries in Africa, Middle East, and even some parts of Southern Europe [4]. It is estimated that 90 million people are infected with this disease in the endemic areas and over 150,000 people die as a result. There are no other known resivour hosts [3].

Some of the disease locations spread throughout Africa and the South East – source: http://www.path.cam.ac.uk/~schisto/Background/Distribution.html

The life cycle of Schistosoma haematobium has six typical like stages: egg, miracidia, sporocyst, redia, cercariae and adult [1]. Starting when they are free swimming larva known as cercariae, they will burrow into the skin of their final host when a person comes into contact with contaminated water. They then enter the hosts blood stream until they can enter the liver and then grow into adults [4]. The adults coat themselves in host antigens so that the immune system of the host does detect them [3]. Around three weeks later, the matured parasites migrate to the bladder to reproduce. The females then lay their eggs (up to 30 per day) which will migrate into the lumen of the urinary bladder and ureter. Upon urination of the host, the eggs are eliminated and make their way into the water supply. When the eggs hatch in fresh water, they are free swimming miracidia. Miracidia then penetrate into an intermediate snail host. Around 4 weeks after initial penetration of the snail, the miracidia develop into sporocysts and then evolves further into cercariae. The cercariae then shed form the snail and are released into the water, looking for a host so that the process can repeat all over again [3].

Life Cycle of Schistosoma haematobium. Source: http://people.emich.edu/kmcgowa4/images/Schistosoma%20life%20cycle.gif

When adults are in their definitive hosts, symptoms or clinical signs appear at different times throughout their presence. 24 hours after initial occupation, an itchy rash appears on the outer skin of the host where the parasite bore though the skin. One to two months later, the host may exhibit symptoms of fever, hepatitis, and an enlarged liver, spleen, and lymph nodes. Anywhere form 3 months to a year the infected individual may experience painful or difficult urination, blood in urine, urethral obstruction, kidney damage from obstruction of urine, no urination, and/or elephantiasis of penis. Years of infection has also been linked to kidney cancer, but is not known. Drug therapy normally does very well in killing the parasitic worms earlier on, but failure of treatment early can result in irreversible damage to the urinary tract.

Adults Female (L) and Adult Male (R) Schistosoma haematobium. Source: http://pathmicro.med.sc.edu/parasitology/sjapomf.jpg

[1] http://en.wikipedia.org/wiki/Trematoda
[2] http://en.wikipedia.org/wiki/Digenea
[3] http://www.stanford.edu/class/humbio103/ParaSites2004/Schisto/website.html
[4] Janki Trivedi. Schistosoma haematobium, 2013. University of Michigan School of Zoology

Microchimerism in Liver Transplation

It is possible that during pregnancy a small amount of DNA or cells from an individual can be transferred and retained within another individual. Some of the cells from the fetus can be found in the mother years later and some of the mother’s cells can be found in her grown child and this is known as microchimerism [1]. ,is the term used to label the retention and transfer of cells between two genetically different individuals. It is currently believed that microchimerism can benefit as well as negatively impact individuals. These effects are currently being examined specifically in cases regarding autoimmune diseases, degenerative diseases, and even cancer.

Interestingly, microchimerism is not only naturally acquired from pregnancy. Transplantation is another example which results in chimerism [1]. Microchimerism after liver transplantation is thought to promote tissue repair and successful transplants by many, but not by all. Unlike other transplanted organs, the liver has been shown to be capable of prompting tolerance [2]. On the other hand, it can be easily understood how transplants based on genetic matching may contain genetic differences, and with the removal of these cells, may come fewer complications concerning the transplant. In a recent study, a hypothesis regarding liver transplantation and the beneficial/negative effects of chimerism was tested.

With a technique known as short tandem repeats (repeating sequences of 2-6 base pairs) of microdissections of hepatocyte nuclei were examined. are cells that comprise the main tissue of the liver and are involved in many processes including: protein synthesis, protein storage, and detoxification and modification. STR-based genotyping was used to analyze donor hepatocyte replacement by recipient cells in liver transplants in relation to two specific long-term outcomes. These outcomes were either successful, stable transplants or late, dysfunctional liver transplants [2].

Heptatocytes (Liver Cells) [3].

The study was retrospective and used the files of the Department of Diagnostic Pathology of Kyoto University Hospital. From 117 pediatric liver transplants, 24 subjects were selected and divided into two groups [2]. The first group was comprised of 13 people who had survived the initial grafts, who had available records on their 10-year protocol biopsies, and whose liver function tests were normal. They were known as the stable group (SG). The second group contained 11 patients who survived their initial grafts, but who experienced dysfunction after a follow-up period similar to the stable group. This group was known as the late-dysfunctional group (LDG). Three liver tissue samples including the recipient’s original liver, the donor liver (pre-implantation) and the long-term-followed liver were used for detecting graft chimerism. The slides were analyzed under fluorescence microscopy. STR analysis revealed that hepatocyte chimerism occurred in 7 of 13 (54%) SGs and 5 of 11 (45%) LDGs. Although it was found that hepatocyte chimerism was present at high frequencies in human liver transplants of the subjects, it was alsos found that recipient-derived hepatocytes do not seem to correlate long-term liver dysfunction [2].

Live Liver Transplant [4].

[1] Lee Nelson MD. 2008. Microchimerism. Accessed on 11 April 2013
[2] Wulamujiang A, Aya M, Munetaka O, Tatsuaki T, Keiji T, Shinji U, Hironori H. 2012. Frequent hepatocyte chimerism in long-term human liver allografts independent of graft outcome. Transplant Immunology
[3] http://en.wikipedia.org/wiki/Hepatocyte
[4] http://www.impactlab.net/wp-content/uploads/2010/10/liver-transplant.jpg

Metagenomics and Protected Potatoes

is the study of genetic material found directly from environmental samples. Metagenomics allows for the overwhelming amount of microbial diversity to come to light, when previous methods could not. Metagenomics brings the microscopic world of many the living world through a lense, and it is no different when it comes to plants.

Bacterial are endosymbionts that come mostly from the soil and colonize the intercellular spaces and vascular tissues of plants. Plants can be symbiotically related to many different species belonging to different phylogenetic groups and it is reported that many of these symbionts have beneficial effects on their host like plant growth, and pathogen resistance.

Many endophyte growth-promoting bacteria produce 1-1-aminocyclopropane-1-carboxylic acid (ACC) deaminase. Bacterial endophytes with similar can help elevate plants stressed from ACC by cleaving an amino group from ACC. This is helpful as ACC is a predecessor of ethylene which harms plant growth[1]. It was proposed that this deaminase helps to make sure that ethylene levels are not raised to the point of causing root harm. To test this, ACC deaminase genes of bacterial endophytes colonizing potato plants were analyzed.

Field-grown potato plants (Solanun tuberosum L.) were collected at flowering stage, from a conventional farmed field. The stems and roots from several plants were used. After no growth was observed, sufficient DNA was isolated from the stems and roots. Metagenomic DNA isolated from the potato’s stem and roots was analyzed by the results showed that there were actually two different types of ACC deaminases (acdS). Of the 64 clones, fifty-nine showed a95% nucleotide identity tot the acdS gene of Psuedomaonas fluorescnes, while the other five showed a 78% identity to acdS gene Rhizobium sullae[1]. The highe percentages of ACC deaminase give support to the idea that it is acting as a guard of harmful ethylene levels.

Solanum tuberosum roots and budding potatoes [2]

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[1] Nikolic Branislav, Schwab Helmut. (2011) Metagenomic analysis of 1-1-aminocyclopropane-1-carboxylate deaminase gene (acdS) operon of an uncultured bacterial endophyte colonizing Solanun tuberosum L. Archives of microbiology. 193 (9): 665-676
[2] http://media-2.web.britannica.com/eb-media/79/37979-004-9177BAFA.jpg

Liking Lichens

are a composite of organisms that are made up of a fungus and algae growing together in a symbiotic relationship, where food, protection and proper living environments are traded among the partners. Nearly one-fourth of lichen-forming fungi associate with trentepohlialean (genus) algae. Trentepohlia live either symbiotically in lichens or can be free living on terrestrial supports such as tree trunks and wet rocks. Work has been done with this free-living trentepohlialean algae to help provide a phylogenetic placement of their genetic diversity [1].
Foliose Lichen – one of the many types of lichens [2]caption]
Dealing specifically with trenteoihialean algae, sampling was done from various types of lichens over a broad geographical substratum, ecological, and phylogenetic range. Thirty-three collections from twenty-eight species were selected . The algae sequenced was from lichen samples of different fungal lineages. A Sigma REDExtract-N-Amp Plant PCR Kit was used to isolate DNA from the algae and it then went under phylogenetic analysis. The results showed that there was no evidence of a single clade that classifies the lichenized algae. In fact, a wide range of trentepohlialean algae had the ability to associate with the lichenized fungi. The study also showed that different trentepohlialean algae can live in lichens from the same geographical area (i.e the same tree). This suggests that the fungi of lichens can associate with many different types of trentepohialean algae. These findings are very similar to experiments on trebouxiophycean algae and cyanobacteria as well[1].

[1] Nelson, Matthew P. (2011), Phylogenetic diversity of trentepohlialean algae associated with lichen-forming fungi. Journal of Phycology, 47 (2): 282-290
[2] http://botit.botany.wisc.edu/Resources/Toms%20Fungi/Lichens/Foliose_lichen_130_d.gif