Although a number of products are available that offer capsules containing mixtures of various bacteria (such as Lactobacillus Acidophilus, Bifidobacterium Bifidum, Streptococcus Thermophilus and Salivarius, Bacillus Coagulans), all appearing to be safe, my preference is to maintain balance of bacteria in my intestine through eating yogurt and various fermented food (much of it made at home).

All is a matter of balance between the different probiotic strains. Probiotics are there to help the body but if the balance is not maintained then side effects could occur.

Abhishek,

The best way to improve microbial balance would be through diet, obviously the consumption of fermented foods helps balance this out, as well as natural fruits and vegetables. The real risks come down to the manufacturer and are they following all the proper food safety strategies. Contamination with pathogenic organisms is always a risk with all raw or unprocessed foodstuffs and beverages, however the innate conditions of many fermented foods prevent pathogens from being present.

The most common side effects (available on a simple online search as well) include gas and bloating as new microbes process your food differently, other possibilities include infections in immunocompromised people and gastrointestinal distress in various forms.

Any shake up of diet can cause temporary or long term issues. Just like if you switched from salads and chicken to fast food or vise versa.

For a quick assessment, I would read this guide on fermented foods to learn more about various safety issues.

https://foodsafety.wisc.edu/assets/pdf_Files/Fermented_Vegetables.pdf

James

From a food safety perspective, consumers of probiotic products should be concerned about which specific intestinal flora organisms are being introduced into their bodies. The primary questions are: 1) Does the probiotic product list the specific probiotic organisms by name? 2) Will the consumer's digestive system negatively react to the introduction of the specific organisms?
Every human's digestive system can contain up to 10 to the 14th number of bacteria. This bacterial flora is unique to each human being. Maintaining digestive health is key to overall health. Specific, beneficial claims by "health food" products should be carefully considered prior to acceptance and engagement in a dietary regime.

Alvarez, S., Villena, J., & Kitazawa, H. (2014). Probiotics : Immunobiotics and Immunogenics. Boca Raton: CRC Press.
Freitas, A. C., & Silva, J. e. (2014). Probiotic Bacteria : Fundamentals, Therapy, and Technological Aspects. Boca Raton: Pan Stanford.
Preedy, V. R., & Watson, R. R. (2016). Probiotics, Prebiotics, and Synbiotics : Bioactive Foods in Health Promotion. Amsterdam: Academic Press.
Qinghui, M., Jay, K., Christopher M., R., & Xin M., L. (2017). Leaky Gut As a Danger Signal for Autoimmune Diseases. Frontiers In Immunology, Vol 8 (2017), doi:10.3389/fimmu.2017.00598/full

Somewhere between 300^[9]and 1000 different species live in the gut,^[10] with most estimates at about 500.^[29][30] However, it is probable that 99% of the bacteria come from about 30 or 40 species, with Faecalibacterium prausnitzii being the most common species in healthy adults.^{[11][31]
From:} https://en.m.wikipedia.org/wiki/Gut_flora

I think that probiotics generally are safe. However, there are issues with other added ingredients in these supplements. Just as others said, these are not often regulated as well as Rx and you can have all manner of levels of organisms in these pills. Some effective and most not actually. I’m addition, who determines what blend and in what dosage? Do you know what is already there and are targeting or is it a shotgun approach? All important things to consider to not have unintended consequences.