Prebiotics and Pasture Raised Chicken

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egg-1175620_1280There seems to be a trend amongst millennials today that has its roots in a simpler time, the need for “happy” food. What do I mean by “happy” food? Well, food that is harvested from grass-fed cows and free-range chickens, food that is organic, food that is hormone free, and food that is harvested from animals that lived a “happy” life. However, happiness comes at a cost. Unless you’re one of the homesteading types, then you have most likely taken trip in the past week to pick up a carton of eggs. As you may have noticed there is a substantial price difference in a dozen conventional eggs and a dozen free-range or cage-free eggs. There is a reason for this, a team of researchers from the University of Arkansas explain that these non conventional farming methods result in a greater prevalence of foodborne pathogens and diminished health status. Essentially, choosing to raise grass-fed or free-range animals is comes at a risk to the farmer, a risk of losing more animals to disease as well as a lesser yield in comparison to conventional farming methods. Naturally, farmers also have to eat, and in order to recoup the cost of these risks, we the consumer are forced to pay a premium in order to eat as if we were on the Oregon Trail.

Park et al. recently published a study in Plos One examining the effects of prebiotics on the microbiome of free-range chickens. With the hopes of limiting the prevalence of pathogenic bacteria, feed additives, such as prebiotics, may be able to reduce the cost to farmer and consumers alike by increasing the yield and overall health of the animals. In order to examine the gut microbiota of these naked neck chickens, Park et al. decided to take advantage of next generation sequencing and perform 16s rRNA gene sequencing to complete this phylogenetic study. 16s rRNA sequencing and the microbiome have been the focus of several human studies, and as the sequencing technology continues to advance, it is exciting to see 16s rRNA gene sequencing be taken advantage of in such a capacity. DNA was extracted from the ceca of 45 birds assigned to three different groups and the V4 region of the 16s rRNA gene sequenced using the Illumina MiSeq technology. As a result, Park et al. were able to analyze gastrointestinal microbiota of the three groups and determine that “there was a significant increase in genus Faecalibacterium” which is known to be related to increased health of the host. 



Your Microbiome: An Early Indicator of Type II Diabetes?

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The National Diabetes Statistics Report (2014) put out by the Center for Disease Control indicates that 29.1 million people in the United States have diabetes. The number of individuals that are considered prediabetic are even more staggering, 86 million people, or 1 out of 3 adults are considered to be prediabetic. In adults, approximately 95% of all patients diagnosed with diabetes are diagnosed with type 2 diabetes. Fortunately, with proper measures, such as weight loss, increased exercise, and a healthy diet, individuals with prediabetes can delay or even prevent the onset of type 2 diabetes. However, 9 out of 10 individuals considered to be prediabetic do not know that they are at risk.

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A team of researchers from The Broad Institute partnered with researchers from Seoul National University in order to investigate whether or not the associated imbalance of microbes within the gut microbiota of individuals with type 2 diabetes is present prior to disease onset. Yassour et al. recently published their findings in Genome Medicine, where they were able to perform shotgun metagenomic sequencing on 36 stool samples collected from 20 monozygotic Korean twins. While most metagenomic microbiome studies examine a diseased population and compare the detected microbial diversity with that of a healthy population, Yassour et al, concluded that this study design is unable to determine the relationship between the microbial ecology of the gut and the disease state, be it causal or responsive. Yassour et al. report both positive and negative correlations in biomarkers associated with type 2 diabetes, “functional changes in the gut microbiome at higher sub-clinical values of BMI, FBS, and triglycerides resembled the signatures found in patients with established IBD or T2D, suggesting a shared response to oxidative stress in the gut, induced even at low levels of inflammation or immune activation.” The results from this study and others exploring the host microbiota indicate the presence of a relationship between the gut response and disease state of the host.



Can Tsunamis Alter Iron Levels?

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Natural disasters can have lasting effects on the local population, infrastructure, and economy, but what about the ecological effects? Scientists from the University of Tokyo recently published their findings examining the effects of the 2011 Great East Japan Earthquake tsunami on the microbial characteristics of the soil surrounding the city of Sendai (Japan). The tsunami was triggered by the 9.0 magnitude earthquake that struck off the coast of Sendai, Miyagi.


Hiraoka et al. describe that lasting microbial affects documented subsequent to the Indian Ocean tsunami of December, 26 2004. Where previous studies, such as those focusing on the aforementioned tsunami, have only taken advantage of 16s rRNA sequencing, Hiraoka et al. made the decision to look at the microbial population structure via 16s rRNA sequencing as well as at the genomic level via whole-genome and shotgun metagenome sequencing methods. Soil samples were taken from Hiyoriyama and Amamiya and Arthrobacter isolates were sequenced using the PacBio RS II, 454 GS FLX+, and Ion PGM platforms. As a result of whole-genome sequencing, the research team from the University of Tokyo was able to determine that the Arthrobacter strains detected in the soil samples affected by the tsunami lacked an iron-chelating gene found in Arthrobacter strains detected in soil samples unaffected by the tsunami. This suggests that the soil contained an increased amount of iron, which was confirmed by chemical analysis.

This study is a great example as to how not only 16s rRNA sequencing, but whole genome sequencing and shotgun metagenomic sequencing is crucial in understanding how natural disasters alter the microbial ecosystem.


Uncovering the Microbiome, Exploring the Virome

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frog-927768_1920Researchers from the University of Puerto Rico in conjunction with faculty from California Polytechnic State University have expanded the knowledge of the human microbiome of ancient cultures by characterizing endogenous retroviruses in coprolites. In today’s culture, the human microbiome has become an expanding area of research and what affects the microbiome can have on gastrointestinal conditions such as crohn’s disease and irritable bowel syndrome. But what about diet? This is the question that is presented by this study published by Plos One. Scientists are continually trying to gather as much information about ancient civilizations as possible, from what tools they were able to use to the complexities of their social interactions. The particular diet of these cultures however can be challenging to ascertain due to the organic therefore decomposable nature of the samples necessary to complete such a study.

Rivera-Perez et al. were able to extract DNA from coprolites, or fossilized feces, from two ancient caribbean cultures, the Saladoid and Huecoid. Nine coprolites were collected and used to create two separate DNA composites for sequencing. This study employed the use of non-target specific metagenomic analyses. The metagenome analysis of these two samples was completed by the MR DNA Research Lab using Illumina’s MiSeq system.  Metagenomic analysis indicates that the diet of these two cultures was comprised of birds, fish, and amphibians. River-Perez et al. state that to the best of their knowledge, the consumption of amphibians had previously been unreported. Rivera-Perez et al. go on to state, “the presence of host-specific viral and proviral DNA can help validate hypotheses generated by other methods and disciplines studying the diets and customs of ancient specimens.”



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