How Dietary Fats Influence the Microbiome
The types of fat that we consume in our diet tend to affect the makeup of our gut Microbiome. There are two major types of dietary fats. Saturated (or bad fats) and unsaturated fats. Saturated fats that come from animal-based foods like beef, whole-fat milk, cheese, and butter have a negative impact on the gut microbiota and lead to obesity. In contrast, unsaturated plant-based fats (like fish oil) play a vital role in maintaining a balance of healthy gut flora, and so do not contribute to obesity. How do dietary fats alter the gut Microbiome? Alternatively, how does the gut Microbiome influence the metabolism of dietary fat?
Gut Microbiome Communicates with the Dietary Fats
Scientists have been able to locate a crosstalk between the microbiota and dietary fats.  Dietary consumption of saturated fats lowers the level of healthy gut bacteria. The altered Microbiome is then capable of harvesting energy from the dietary fat.  Additionally, overweight/obese individuals with metabolic disorder exhibit higher proportion of unhealthy gut bacteria that are capable of harvesting surplus energy from the dietary nutrients. This is probably due to the reduced metabolism of dietary fats in obese individuals. Hence, the microbiota and dietary fats can be considered as a two-way traffic where the Microbiome influences the metabolism of dietary fats or vice versa, consumption of dietary fats plays a role in shaping our Microbiome.
A High-Fat Diet Induces the Release of Inflammatory Substances in Blood
When the dietary intake of saturated fats is considerably on the higher side, the gut bacteria trigger the release of several inflammation-promoting substances. These substances are the culprit behind obesity and long-standing metabolic diseases (including insulin resistance). More interestingly, it is found that regular intake of saturated fats is associated with increased levels of inflammation-promoting substances in the blood regardless of whether the Microbiome is altered or not. A study supporting this notion showed that germfree mice (i.e. mice not exposed to a Microbiome) are protected against obesity induced by a high fat, sugar-rich diet despite not having any exposure to a Microbiome.  A high fat diet induced inflammation and its crosstalk with the gut microbes has been traced to a rise in special immune sensors in the gut called Toll-like receptors. 
Increased Dietary Fat Lowers the Microbial diversity
A high-fat diet also reduces the diversity of the Microbiome. Microbial diversity is the inhabitation of the gut by trillions of diverse bacterial species. Normally, a healthy gut (which is obviously due to a healthy diet) has abundant amounts of good microbes called Bacteroidetes. These bacteria fight inflammation and obesity. On the other hand, a high-fat diet reduces the levels of Bacteroidetes while correspondingly raising the levels of the hostile gut microbes known as Firmicutes. These bacteria (as opposed to Bacteroidetes) drive inflammation and obesity. 
Switching from a low-fat plant-based diet to a high-fat, sugar-rich “Western” diet shifts the structure and composition of the microbiota as early as 24 hours. The good news is that despite being on a high-fat diet, you can still prevent obesity. Apart from regular exercising, this is by the use of probiotics or prebiotics (containing short-chain fructooligosaccharides) that help ferment the gut bacteria to produce short chain fatty acids. These indigestible carbs being high in fiber are protective against diet-induced obesity. 
Dr. Rasheed Huma
- Caesar R, Tremaroli V, Kovatcheva-Datchary P, Cani PD, Bäckhed F. Crosstalk between Gut Microbiota and Dietary Lipids Aggravates WAT Inflammation through TLR Signaling. Cell Metabolism. 2015;22(4):658-668. doi:10.1016/j.cmet.2015.07.026.
- The Human Microbiome, Diet, and Health: Workshop Summary.
- Bäckhed F, Manchester JK, Semenkovich CF, Gordon JI. Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proceedings of the National Academy of Sciences of the United States of America. 2007;104(3):979-984. doi:10.1073/pnas.0605374104.
- Kuo S-M. The Interplay Between Fiber and the Intestinal Microbiome in the Inflammatory Response. Advances in Nutrition. 2013;4(1):16-28. doi:10.3945/an.112.003046.
- Lu Y, Fan C, Li P, Lu Y, Chang X, Qi K. Short Chain Fatty Acids Prevent High-fat-diet-induced Obesity in Mice by Regulating G Protein-coupled Receptors and Gut Microbiota. Scientific Reports. 2016;6:37589. doi:10.1038/srep37589.