Energy Metabolism: Analyzing KEGG Pathways

The microbiome opens the pathway to understanding how the body works more and more every day. With a Thryve Gut Test, we have the ability to analyze your DNA and look deep into many physiological functions carried out by your system on a molecular level. Thanks to these advancements in technology and following KEGG pathway maps, we can determine how efficiently your body metabolizes energy. Let’s take a look at the biomarkers for energy metabolism and how Thryve Inside can help you feel focus, alert, and ready to crush it all day long.

What is Energy Metabolism?

energy metabolism photosynthesis
ATP is money for growth!

Energy is the driving force behind everything. It’s the juice that keeps us, our bacteria, and our cells going. So, we all need adequate energy to ensure that all parties are happy. The process of breaking down this energy, conserving it, and using it is known as energy metabolism.

If energy were currency, the dollar bill of the gut biome would be adenosine triphosphate (ATP). ATP consumed from plants and animals is encased inside of nutrients. As we digest food, this ATP is released into our bloodstream, where it powers cells to proliferate, muscles to keep us walking, and generates nerve cell reactions [1].

How Do You Metabolize Energy?

Energy metabolism is a complex process. Our immaculately designed body is ready to take on this challenge. It has all the bases covered, allowing us to convert nutrients into energy through many means.

fermented fruits and vegetables
Out gut is like a prepper’s basement

Your body creates ATP through:

The first two processes are aerobic. They need oxygen to happen. The latter occurs in the small intestine. Fermentation doesn’t require oxygen. Instead, intestinal flora feast on fibers. In turn, they produce metabolites that provide the body energy.

One meta-analysis of energy metabolism and stomach bacteria stated,

“Commensal bacteria ferment carbohydrates, principally non-digestible carbohydrates that are not used by the host, into CO2, H2 and CH4 and short-chain fatty acids (SCFAs) primarily acetate, propionate and butyrate. Most of these SCFAs produced in the intestine are then absorbed by the host and contribute to its energy [2].”

Microb Cell Fact

Undeniably, food is our primary source of energy. We get energy from carbohydrates, fats, and amino acids that we consume in our diet. So, every bite you take kickstarts the energy metabolism process. The question is, are you consuming the right foods to produce energy?

Oxidative Phosphorylation

When we consume foods, our body breaks down the carbohydrates to its simplest form. Simple sugars, like glucose and fructose, go through glycolysis. Depending on the reactions that happen, different enzymes that carry out their own functions are produced. In terms of ATP production, glycolysis produces nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FADH2).

It do be like that with
NADH and FADH2

NADH and FADH2 are the life of the party. They get around many mitochondria, and are known to leave electrons in their wake. Once a little oxygen gets into the mitochondria, the organelle secretes a proton into the system.

This proton will interact with different enzymes and other cofactors in the system, including adenosine diphosphate (ADP). ADP is like an uncharged battery. When it’s ready for a charge, it gets converted into ATP thanks to the proton bringing this energy source into the mitochondria. It then gets converted into ATP [3]. About 26 to 30 ATP will be a result of the oxidative phosphorylation process [4].

Photosynthesis – Food and Energy Metabolism

photosynthesis energy metabolism
Plants love them some sun

We depend on the sun for energy. The sun charges our agriculture. This complex process might ring back days of grade school past. It’s known as photosynthesis.

Energy sources from the sun are known as photons. When photons touch a leaf, it causes a reaction in the leaf’s light-harvesting complexes. These are also known as protein antennas.

Protein Antennas

energy metabolism
The light spectrum influences a lot

A plant’s light-harvesting complexes are a variety of chlorophyll and protein molecules. They live on thylakoids, which are little sacs inside the chloroplast, which is where photosynthesis occurs [5].

Many of these light-harvesting complexes are pigments. Up to 500 different pigments are present to absorb the spectrum of colors emitted from white light. These nutrients are essential for transferring energy back to the system.

Light-harvesting complexes also include antioxidants, such as carotenoids. Seeing as light can cause oxidative damage, having antioxidants present helps keep the pigments healthy. In turn, energy metabolism runs smoothly.

Activating Light-Harvesting Complexes

Once activated, light-harvesting complexes ignite a chain of reactions that causes the plant to release oxygen from water molecules [6]. What’s leftover are charged particles that plants store as ATP.

Just like we try to make using carbs more efficient, so do plants. They break down the energy sources into simple carbs. Plants will use some of the carbs for their own energy supplies. The rest is fair game for us.

We then consume these photosynthesized foods comprised of these carbs. Our body then goes through the carbohydrate metabolism process, which will then kickstart this energy metabolism process.

Carbon Fixation in Photosynthetic Organisms

We look at carbon dioxide as waste. Plants see it as gaseous gold. So, it’s in their best interest to hoard as much carbon as possible. Therefore, they adhere (or fixate) inorganic carbon molecules (derived from CARBON dioxide) to carbohydrates for future use. For them to do this, they must put the carbon dioxide through the Calvin Cycle.

Calvin Cycle

The goal of the Calvin Cycle is to isolate carbon for future energy use. When a plant has excess carbon dioxide, the spare CO2 molecules get acquainted with an enzyme known as ribulose-1,5-bisphosphate carboxylase (RuBisCO) [7].

Have you heard the new one by
RuBP-CO2?

RuBisco introduces the altered CO2 compound to another molecule known as ribulose-1,5-bisphosphate (RuBP). When these two interact, the Calvin Cycle is on!

The RuBP-CO2 collab is hotter than Ed Sheeran and Justin Beiber. The intermediate molecule is then broken into two separate three-carbon molecules. That’s why the Calvin Cycle is also known as the C3 Cycle.

These trios of carbon compounds are known as phosphoglycerate (3PG). 3PG gets transformed into glyceraldehyde 3-phosphate (Ga3-P). These are plant starches that we consume for energy. If the plant doesn’t convert 3PG to Ga3-P, then it gets recycled back to RuBP, so the Calvin Cycle can live on!

Carbon Fixation in Stomach Bacteria

Plants and humans aren’t the only living beings that experience energy metabolism. Microorganisms also rely on carbon. Therefore, microbes also implement carbon fixation processes.

Besides the Calvin Cycle, microorganisms can conduct carbon fixation through five other processes:

  • Reductive Tricarboxylic Acid Cycle
  • 3-Hydroxypropionate Bi-cycle
  • Wood-Ljungdahl Pathway
  • Dicarboxylate/4-hydroxybutyrate cycle
  • 4-hydroxybutyrate cycle

A meta-analysis on the carbon fixation of prokaryotes noted,

“Navel marine ultrasmall prokaryotes were demonstrated to collectively harbor the genes required for carbon fixation, in particular the “energetically efficient” dicarboxylate/4-hydroxybutyrate pathway and the 4-hydroxybutyrate pathway. This contrasted with the known carbon metabolic pathways associated with Candidate Phyla Radiation (CPR) members in aquifers, where they are described as degraders [8].”

Genome Biol Evol. 

Understanding how these things work on a microscopic level is essential in tailoring gut biome health protocols. We’re hoping to figure out ways to make your cells become more energy-efficient, so you have the power necessary to slay the day.

Methane Metabolism

Got methane?

All living things create waste, including the stomach bacteria (namely archaea) in our system. They metabolize methane the most efficiently. So, when they break down carbon, that’s the type of simple gas they choose. This process is known as methanogenesis.

Living beings that partake in methanogenesis include:

  • Methanotrophs – Prokaryotes
  • Methanogens – Bacteria/Arcahea
  • Methylotrophs – Microorganisms That Operate On 1 Carbon Molecule

We release outside our backend. That’s why we use your stool to extract DNA for microbiome testing. Key influencers leave their footprints in your stool sample.

Nitrogen Metabolism

This part of energy metabolism is very complex. Nitrogen is usually affixed in the proteins we consume. Within these protein sources lies usable ammonia (NH3) [9]. Ammonia is not a source of nitrogen directly from the earth. It’s the result of microbial activity.

Microbes ingest atmospheric nitrogen from our inhales. Nitrogen is vital for life, so it’s in the best interest of microbes to make it last. So, they break it down into the simple form of ammonia. The ammonia is then stored in amino acids so that it can be used for energy later. This energy-saving mechanism is called nitrogen fixation.

Nitrogen Metabolism and Amino Acids

salmon Mediterranean diet
Eat a balanced diet of fat and lean proteins

We need 20 amino acids for human functioning. All by nine can be created inside of our own bodies. These are known as nonessential amino acids. Nonessential amino acids require nitrogen for this process to happen.

Humans must consume essential amino acids through diet. This will help keep nitrogen levels adequate to ensure everything is running optimally. Most of these foods are found in animal fats. However, there are many plant-based proteins that you can eat, too.

Sulfur Metabolism

All living beings metabolize sulfur. It’s crucial for many aspects, including creating biotin. So, you definitely want a functioning sulfur metabolism for your all-natural beauty routine!

Our systems can oxidize sulfur for future use. These compounds may become a variety of sulfates and sulfides. Cells can then transform the oxidated sulfur into ATP [10].

sulfur for energy metabolism
Onions are rich in sulfur

Amazingly enough, our body stores sulfur for energy-producing dissimilatory pathways and the assimilatory pathways that consume energy.

In the assimilatory pathway lies many stomach bacteria that rely on sulfides. Many of these sulfides don’t leave the pathway. So, we share some of our energy with bacteria to keep them happy, and they clean their plates.

Meanwhile, the sulfates used in the dissimilatory pathway provides us with amino acids that contain sulfur, including:

  • Methionine
  • Cysteine
  • Homocysteine
  • Taurine

You can also get many of these amino acids from eating a diet with dish, lean meat, and cheese.

Analyze Your Energy Metabolism

Feeling low on energy? Your energy metabolism might be a bit off. The best way to find out if this is happening is to get your gut tested. Using KEGG pathways, we can map out where the deficiencies are. That way, we can get your gut health on the right track. From there, you will produce natural energy that will sustain you throughout the day!

Thryve Probiotics Gut Health

Resources

[1] Khakh, B. S., & Burnstock, G. (2009). The double life of ATP. Scientific American301(6), 84–92. https://doi.org/10.1038/scientificamerican1209-84.

[2] LeBlanc, J. G., Chain, F., Martín, R., Bermúdez-Humarán, L. G., Courau, S., & Langella, P. (2017). Beneficial effects on host energy metabolism of short-chain fatty acids and vitamins produced by commensal and probiotic bacteria. Microbial cell factories16(1), 79. https://doi.org/10.1186/s12934-017-0691-z.

[3] Bonora, M., Patergnani, S., Rimessi, A., De Marchi, E., Suski, J. M., Bononi, A., Giorgi, C., Marchi, S., Missiroli, S., Poletti, F., Wieckowski, M. R., & Pinton, P. (2012). ATP synthesis and storage. Purinergic signalling8(3), 343–357. https://doi.org/10.1007/s11302-012-9305-8.

[4] Berg JM, Tymoczko JL, Stryer L. Biochemistry. 5th edition. New York: W H Freeman; 2002. Chapter 18, Oxidative Phosphorylation. Available from: https://www.ncbi.nlm.nih.gov/books/NBK21208/.

[5] Brotosudarmo, Tatas Hardo Panintingjati, et al. “Chloroplast Pigments: Structure, Function, Assembly and Characterization.” IntechOpen, IntechOpen, 5 Nov. 2018, www.intechopen.com/books/plant-growth-and-regulation-alterations-to-sustain-unfavorable-conditions/chloroplast-pigments-structure-function-assembly-and-characterization.

[6] Barros, Tiago, and Werner Kühlbrandt. “Crystallisation, Structure and Function of Plant Light-Harvesting Complex II.” Biochimica Et Biophysica Acta (BBA) – Bioenergetics, Elsevier, 25 Mar. 2009, www.sciencedirect.com/science/article/pii/S000527280900098X.

[7] Erb, Tobias J, and Jan Zarzycki. “A Short History of RubisCO: the Rise and Fall (?) of Nature’s Predominant CO2 Fixing Enzyme.” Current Opinion in Biotechnology, Elsevier Current Trends, 29 Aug. 2017, www.sciencedirect.com/science/article/pii/S095816691730099X.

[8] Lannes, Romain, et al. “Carbon Fixation by Marine Ultrasmall Prokaryotes.” Genome Biology and Evolution, Oxford University Press, 1 Apr. 2019, www.ncbi.nlm.nih.gov/pubmed/30903144.

[9] Bernhard, A. (2010) The Nitrogen Cycle: Processes, Players, and Human Impact. Nature Education Knowledge 3(10):25.

[10] Parrino, V, et al. “ATP Production from the Oxidation of Sulfide in Gill Mitochondria of the Ribbed Mussel Geukensia Demissa.” The Journal of Experimental Biology, U.S. National Library of Medicine, July 2000, www.ncbi.nlm.nih.gov/pubmed/10862733.