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Is The Microbiome An Organ

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The host and gut bacteria share the nutrients from the same digests in the gut, and therefore the host-microbe interaction is indeed a competition, and the performance of host to utilize the nutrients could consequently affect the population of the opponent microbes. For example, the mice lacking APOA1, a major component of high-density lipoprotein , harbored a decreased abundance of Erysipelotrichaceae and increased abundance of Lachnospiraceae . A 16s rRNA-based study has showed that the polymorphism of LCT, a gene encoding lactase for the hydrolysis of lactose, can be linked with the abundance of Bifidobacterium . The genus Blautia has been found to be associated with the polymorphisms of CD36, a gene involved in the absorption of long-chain fatty acid in the gut . The polymorphisms of ALDH1L1, a gene encoding for an aldehyde dehydrogenase involved in the formate oxidation, has also been linked with the order SHA-98, a member of the Christensenellaceae consortium . Thus, the metabolites utilization of host could impact the bacteria on their composition in the gut.

What Is The Gut Microbiome How To Support The Forgotten Organ

Remember learning about cells in your first science class? You probably drew a picture and labeled the parts. Imagine that illustration and think about this: the average human body contains 30-40 trillion cells!;

Whats even more impressive than that is the microorganisms in your body outnumber those trillions of cells. According to the National Institutes of Health, microbes make up between two and six pounds of your bodys mass. And in the gut, these microbes are referred to as the gut microbiome. Maintaining a healthy gut microbiome is essential to good health, but what exactly does it do?

Trillions Of Microbes Live With Us

Scientists have classified more than 10,000 different species of micro-organisms populating our body, amongst which theyve estimated there is up to 100 trillion single micro-organisms. Some recent studies have estimated that number at a lower approximation of around 30 trillion, but it is undoubtedly still a huge population particularly when compared to the number of human cells in the body, which is just 10 trillion.;

Even from a genetic point of view the dimension of the microbiome is impressive, with approximately 3.3 million genes in the microbiome compared to the approximately 22,000 in the human genome.

Bacteria, archaea, fungi, protists and viruses are all different kinds of microbes that compose the wonderful community of our microbiome. They inhabit the different parts of the body the mouth, the skin, the vagina, the uterus, and so on spawning different sub-communities of the human microbiome. But definitely the largest community and probably the most important, is the gut microbiome.

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What Is The Gut Microbiome And How Does It Affect Your Health

Home » Food and Nutrients » What is the Gut Microbiome and How Does it Affect Your Health?

By Harriet Smith, BSc , RD

The gut microbiome has become a hot topic as it is thought to play an important role in good health and disease prevention.

Its made up of trillions of live microbes living within the human intestine known as the gut microbiota.

Here we will explore what the gut microbiome is, how it is related to our health, and how we can best support it.


The Gut Microbiota As A Component Of The Holobiont With Its Host

The Human Microbiome

A more extensive vision of the relationship between our organism and the gut microbiota is the controversial concept of the holobiont, that is, the biologic symbiosis between the host as a whole and his/her gut microbiota, seen as the collective contribution of the eukaryotic and prokaryotic counterparts in a multicellular organism ]. This concept, which attributes to the human gut microbiota a role that far exceeds that of the organ of the body, needs further evaluation, as not all animals need a microbiome ]. Moreover, to make a decision whether the concept of the holobiont is reasonable or not, we have to overcome some points that may be against this concept: The composition of the gut microbiota is probably the result of a process involving ecological, and not host, filtering ], but the holobiont theory infers that host genetics contributes to microbiome composition ]; the composition of the microbiota is fluctuant and, as we will see later, with a double face, favorable or detrimental to the host; the gut microbiota is not a proper part of the host as it is largely interchangeable and shared among different hosts ]; and the components of a holobiont must respond to ecological changes as a unit, and evolve as a hologenome, what is difficult to achieve for the whole microbiota together with its host ].

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Gut Microbiome: Fundamentals And Functions

Most microorganisms in the gut are bacteria . In the general public view, bacteria have been perceived as harmful to our health, but modern bacteriology argues there exists a spectrum of good to bad bacterial types depending on their influence on the host. In fact, most gut microbiota are completely harmless or beneficial , and relatively few types of bacteria pose a modest degree of risk or disease . Most of the time, as in the case of the diverse gut bacteria, harmful bacteria are suppressed, and we live in harmony and balance with our numerous gut bacteria . However, when the gut ecosystem undergoes abnormal changes, the pathobionts become overpopulated, and the gut bacterial composition becomes unbalanced . Then, this imbalance may grow to create a disease-related microbiota community and coordinate inflammatory reactions or toxin release.

The Relationship Between The Gut Microbiota And The Host Is Unbalanced

One consequence of the concept of the microbiota as an organ is to consider its bidirectional relationship with all organs of the human body, including the brain. The relationship with the brain, called the gutmicrobiotabrain axis or gutbrain axis ], has been suggested to be involved in the pathogenesis of chronic inflammatory, neurodegenerative, diseases such as Alzheimer’s disease, Parkinson’s disease, MS, amyotrophic lateral sclerosis, and autism spectrum disorders ].

The correlation of these diseases with intestinal dysbiosis and inflammation and the fact that gut microbiota is essential to trigger inflammation ] suggest a direct, though complementary, role of the dysbiotic microbiota in the onset of neuroinflammatory diseases ]. The opposite direction, from the brain to the microbiota, is different.

Changes in peristalsis may affect the rate at which nutrients pass through the intestine and impaired intestinal transit may influence the gut microbiota. The first can alter the normal functioning of the second, interfere with its rhythms, and therefore disturb peristalsis, the production of acids, enzymes, hormones, and cytokines. Vice versa, diet and intestinal disorders can produce their effects on the central brain and may also be linked to changes in mood.

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Linking Gut Microbiota And Ad Pathogenesis

As we discussed above, accumulating data support the potential contribution of the gut microbiome to AD pathology, but there are still many unanswered questions: what microbiological pathways are actually involved in pathogenesis? How is the gut microbiome able to modulate AD pathogenesis in the brain that is located distally and protected by the BBB? These are fundamentally challenging questions to address because genetic and environmental risk factors can modulate various steps in microbiotagutbrain communication, and vice versa . Therefore, it is conceivable that such complex interplay may give rise to numerous putative pathways, for which several hypotheses have emerged over the years.

Gut Microbiota: The Unknown Organ That Maintains Our Health

How Bacteria Rule Over Your Body â The Microbiome

For a large portion of society it is still unknown that a whole universe of life forms is active within our intestines, receiving the name of gut microbiota, a vital organ that is receiving the attention of the world’s most qualified experts.

For a large portion of society it is still unknown that a whole universe of life forms is active within our intestines, receiving the name of gut microbiota. The tens of trillions of bacteria composing this living community form together what is currently considered by experts as a new organ carrying out specific functions which are key to maintaining an optimal health.

Gut microbiota development starts after birth, since we are all born sterile. This means that the composition of the microbiota is strongly influenced by external factors including conditions of birth, diet, environment or use of antibiotic drugs.;Helping regulate the bodys energy supply and protecting us against intruders are two vital functions performed by gut microbiota: 70% of our immune cells and more than 100 million neurons connected with the brain live in our intestine!

The vast community composing gut microbiota includes at least 1000 bacteria types, weights between 1.5 and 2kg, comprises more than 3.3 million genes, which is 150 times more than in the human genome! Scientific research around gut microbiota is currently booming; and experts from different disciplines are working together to increase knowledge of this vital organ.

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The Gut Microbiome May Benefit Heart Health

Interestingly, the gut microbiome may even affect heart health .

A recent study in 1,500 people found that the gut microbiome played an important role in promoting good HDL cholesterol and triglycerides .

Certain unhealthy species in the gut microbiome may also contribute to heart disease by producing trimethylamine N-oxide .

TMAO is a chemical that contributes to blocked arteries, which may lead to heart attacks or stroke.

Certain bacteria within the microbiome convert choline and L-carnitine, both of which are nutrients found in red meat and other animal-based food sources, to TMAO, potentially increasing risk factors for heart disease .

However, other bacteria within the gut microbiome, particularly Lactobacilli, may help reduce cholesterol when taken as a probiotic .


Certain bacteria within the gut microbiome can produce chemicals that may block arteries and lead to heart disease. However, probiotics may help lower cholesterol and the risk of heart disease.

Differences In Microbiome Community Across Body Sites

The results showed differentiations in body site-associated microbiome in grass carp and southern catfish . In order to further quantify sources of the differences in microbiome communities in the cohabiting grass carp and southern catfish, a subsample of the data set that included two fish species or each fish species was used for microbial analysis. The fish microbiome was significantly affected not only by fish species but also by body sites . The analyses of overall compositions by ANOSIM tests showed high microbiome variations among body sites in grass carp and southern catfish . In pairwise a posteriori tests of PERMANOVA, the microbiome communities in any two body sites were statistically different . The communities between external body sites were less similar than those between internal body sites. The microbiome between the same type of body sites was generally more similar than that between the different types of body sites . In southern catfish, external microbiome within specific body sites had higher interindividual variability than their internal microbiome . Compared to southern catfish, grass carp had the smaller interindividual dissimilarities of the microbiome among body sites and that were comparable among the organs except for anterior intestine.

Table 1. Body site-driven microbiome differences in co-cultured grass carp and southern catfish.

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Does The Gut Microbiota Have A Structure

If the microbiota is an organ, it must have a structure. With regard to its own organization, the gut microbiota does not seem to organize itself like the organs of our body. When it takes on an organized structure, it does so with the strategy of the colonizers and therefore to occupy space and to improve its defense capabilities, not in order to cooperate with the host. Therefore, the human gut microbiota is not something with a well-defined structure on which to rely and work with.

As for the already mentioned eubiotic and dysbiotic conditions, the microbiota can exist in two different states of organization. Indeed, the bacteria usually oscillate between a motile state, with single cell swimming, and a sessile state, with cell forming a chain or sometimes more complex structures ]. Each of these states offers unique advantages and is more suited to the particular current situation.

Tools For Microbial Analysis

The gut microbiome: the role of a virtual organ in the ...

The importance of metagenomics, meta-transcriptomics and metabolomics approaches as the tool for the study of microbes have also been considered . The identification of about 70% of human microbiota, which was not possible by the existing conventional microbiological methods, has been made possible by the development of the advanced techniques of metagenomic, metatranscriptomic, metabolomic . Metagenomic is a biotechnological perspective of studying the genomic structure of the DNA directly extracted from their natural source . These novel methods have been used by scientist to provide evidence for existence of genes of above one thousand microbial species residing in our body. The metagenomic approach has the potential to discover genes, gene families, and their encoded proteins which are entirely new and which might be of great importance in the field of biotechnological and pharmaceutical science. It allows us to explore the composition of a microbial community .

Fig. 1

Illustration of different available methods to answer the questions related to the human associated microbiome analyses. Arrow indicating the different questions and, other side their equivalent methods to get respective answers mentioned. The questions such as a who are there in? b What they are doing in? c How they are performing to the ecosystem?

Table 1 Online Genome Database for the human microbiomeFig. 2

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Good Microbes Fortify Our Immune System And Help Our Digestion

Most of the bacteria populating our gut represent a beneficial relationship to our body. Bifidobacterium and Lactobacillus are some of these good bacteria . Digesting fibres that our small gut normally cannot break down, they manufacture particularly helpful byproducts for us: the short chain fatty acids.;

As described by scientists at the Imperial College of London, the short chain fatty acids produced primarily from the microbial fermentation of dietary fibre appear to be key mediators of the beneficial effects elicited by the gut microbiome.

Acetate, propionate and butyrate, for example, are short chain fatty acids that trigger a stabilising effect on our immune system, lowering the inflammatory responses and promoting tolerance and homeostasis. Essentially, they balance the whole system. The short chain fatty acidsare also known for regulating food intake, helping us to control weight.

Gut Flora And Gut Health: The Microbiome As An Endocrine Organ

Officially the endocrine system is made up of a network of glands that secrete hormones to regulate bodily functions, including growth and metabolism. These glands include the hypothalamus, pineal gland, pituitary gland, thyroid, ovaries, testes, and more.; We dont usually count the human gastrointestinal tract as an endocrine organ, but with 30 trillion plus bacteria encompassing hundreds or thousands of bacterial taxa, and continually converting nutritional cues into hormone-like symbols that impact the human host, its fair to regard the gut as a command and control center in the body.;

The microbiome is constantly making compounds, some of which are;biologically active and act like hormones. They fulfill all the requirements of a hormone: a biologically active entity that diffuses in the bloodstream and act on a distant site. Debra Beck from one of last Augusts articles in the American College of Cardiologys journal

Not that I knew one iota about this last fact in 1976 for Petes sake I was only nine years old but it shows you that despite not being officially considered one of the ENDOCRINE ORGANS, people have been talking about THE GUT as a hormone-producing gland for a very long time .;

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Dna Extraction And 16s Rrna Gene Pcr Amplification

Genomic DNA was extracted from the fish and feed samples using QIAamp DNA Stool Mini Kit and from the water samples using Mo PowerWater DNA Isolation kits following the manufacturerâs protocol with minor modifications to increase DNA yield, including resuspension in 100 μl TE buffer solution. The V4-V5 region of the bacteria was PCR-amplified with the bar coded-primers . PCR reactions consisted of 50 μl mixtures with 100 ng DNA templates, 0.4 μM forward and reverse primers, 2.5 U of GoTaq Flexi Polymerase , 200 μM deoxynucleoside triphosphate , and 2 mM MgCl2. Each sample was amplified in duplicate PCR, and then the PCR products were combined into one final pool in equal concentration. PCR conditions were: a denaturation step of 94°C for 5 min, followed by 25 cycles at 94°C for 30 s, 55°C for 30 s, 72°C for 60 s, and a final extension at 72°C for 5 min. Unique combinations of all used forward and reverse primers as negative control and one positive control with water as a template were carried out at each 96-well plate. PCR products were purified using Qiagen Gel Extraction Kit according to the manufacturerâs instructions and then quantified using PicoGreen reagent. The paired-end sequencing was performed on an Illumina HiSeq platform .

Microbiome Association With Diseases

Meet Your Microbiome!

As described above microorganisms present in the gut of the living organisms contribute to health or cause disease of these organisms by interplay with their immune system. Microbiome is developed at birth according to host interaction but later it is evolved and modified by surrounding factors like environmental and diet. The variation in genetic expression of different individuals is thought to be linked with different microbial composition . Genotype of the host affects the composition of gut microbes. Even mutation of a single gene can cause modification in the structure of gut microbiota. The exact mechanism of association between the gut microbes and the genotype of host is still unknown. Bifidobacteria are highly prevalent beneficial bacteria in gut microbiome and are associated with lactase non-persistent genotype. This genotype is responsible for the synthesis of lactase enzyme which helps to digest the lactose, present in the milk. Absence of this enzyme leads to lactose intolerance in different organisms. So it is important to investigate susceptibility of different underlying pathological conditions by studying microbiomes association with genotype and environmental factors that vary among different human populations .

Different studies showed that metabolic disorders are largely congenital and are associated with different microbiomes. For example, gut microbiomes have been linked to metabolic disorders and obesity .

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