The gut bacteria and the genes that they carry—collectively known as the “gut microbiome”—have a significant impact on your health, including the health of your heart. An imbalanced gut microbiome can wreak havoc on your heart. Hence, the key to a healthy heart may simply lie in the health of the bacteria residing in your gut. While several dietary and lifestyle approaches are employed to improve the gut microbiome and the associated heart health, the consumption of indigestible dietary fibers called prebiotics is also a proven strategy to accomplish this goal.
Prebiotics are utilized by the microbial communities within your gut as a source of fuel to drive their growth. They belong to the category of macronutrients called complex carbohydrates. These supplements are fiber-rich and not capable of being digested by the enzymes in our digestive tract. Instead, the microbes in the small intestine split them up (a process called fermentation), yielding fatty acids with fewer carbon atoms called short-chain fatty acids (or SCFAs).
How Prebiotics Benefit Heart?
Prebiotics can fight Obesity
Unfortunately, our current Western diet consists largely of fats, animal protein, and simple carbs, all of which screw up the balance of the gut microbiome, wiping out the good bacteria whereas allowing the bad ones to flourish and grow. On the other hand, research shows that replacing high-fat diets with prebiotics or fermentable fibers can raise the levels of healthy bugs within your gut. The fermentable fibers then work both directly and indirectly through a healthy gut microbiome to fight obesity, which is a known risk factor for heart disease. By helping you lose some weight, prebiotics can ward off heart disease or prevent a pre-existing heart problem from worsening. 
Some Proven Direct effects of Prebiotics on Obesity
Being complex carbs, prebiotics break-down at a slower rate and are not converted into fat. As a rule of thumb, the quicker the carb breaks down, the more readily, it is converted to fat.
Prebiotics also appear to suppress the activity of nerve cells in the appetite-stimulating centers of your brain.  The less you gobble, the more unlikely you’ll be putting up more weight.
Moreover, the addition of a prebiotic called oligofructose into your diet can curb hunger and fill your tummy up quite faster by reducing the levels of your hunger hormone, ghrelin as well as boosting the amount of peptide YY, a chemical that suppresses appetite. This effect of fructooligosaccharides was documented in a study carried out on obese adults. Adding this prebiotic into their diet for three weeks resulted in significant weight loss along with weight-friendly changes in the levels of appetite hormones. 
Prebiotics can lower bad cholesterol levels indirectly
By promoting a healthy gut microbiome, prebiotics can indirectly reduce bad cholesterol levels, which are also a major risk factor for heart disease. How? To be absorbed into the blood, cholesterol uses bonded bile acids. However, gut microbiota accelerates the splitting of the bonds between bile acids. Once un-bonded by the gut bacteria, bile acids cannot be absorbed into the blood and are instead lost in your stool. The liver can form more bile acids from cholesterol. Thus, after the loss of bile acids in feces, your liver starts using the circulating cholesterol to make up for the lost bile acids. This, in turn, reduces the cholesterol levels in your blood.  This is the primary mechanism of action of dietary fibers and some probiotics, in particular, L. reuteri NCIMB 30242 to lower the bad cholesterol levels and save your heart from long-term damage.
Prebiotics may help against Diabetes
High blood sugar levels are another factor that put the arteries supplying your heart at risk of developing blood clots and triggering heart problems like angina and heart attacks. The SCFAs generated from prebiotic fibers and healthy gut bacteria can make your body cells more sensitive to insulin so that it can stabilize the deranged blood sugar levels.  Having controlled blood sugars further cuts your risk of developing heart disease.
In addition, prebiotics may provide protection against products called Advanced Glycation End Products (or AGEs), which could otherwise cause widespread damage in a person with diabetes. A healthy gut microbiome supported by prebiotic addition may hamper the build-up of AGEs in people with prediabetes (raised blood sugar levels, which are not high enough to be labeled as diabetes).  This prevents its progression to full-blown diabetes and the subsequent negative effects of raised blood sugars on your heart.
In a nutshell
Prebiotics can optimize the health of your gut microbiome, which, in turn, can improve the health of your heart.
- Tuohy KM, Fava F, Viola R. ‘The way to a man’s heart is through his gut microbiota’–dietary pro- and prebiotics for the management of cardiovascular risk. Proc Nutr Soc. 2014;73(2):172-85. doi: 10.1017/S0029665113003911.
- Arora T, Loo RL, Anastasovska J, et al. Differential Effects of Two Fermentable Carbohydrates on Central Appetite Regulation and Body Composition. Tomé D, ed. PLoS ONE. 2012;7(8):e43263. doi:10.1371/journal.pone.0043263.
- Parnell JA, Reimer RA. Weight loss during oligofructose supplementation is associated with decreased ghrelin and increased peptide YY in overweight and obese adults. Am J Clin Nutr. 2009;89(6):1751-9. doi: 10.3945/ajcn.2009.27465.
- Kim YA, Keogh JB, Clifton PM. Probiotics, prebiotics, synbiotics and insulin sensitivity. Nutr Res Rev. 2018;31(1):35-51. doi: 10.1017/S095442241700018X.
- Kellow NJ, Coughlan MT, Savige GS, Reid CM. Effect of dietary prebiotic supplementation on advanced glycation, insulin resistance and inflammatory biomarkers in adults with pre-diabetes: a study protocol for a double-blind placebo-controlled randomised crossover clinical trial. BMC Endocrine Disorders. 2014;14:55. doi:10.1186/1472-6823-14-55.