Do foods like spicy peppers have less bacteria on their interior due to their capsaicin content? Probably not, but it seems like they could. Or I guess in other words: does capcaicin provide any benefit from anti-bacterial properties?
In 2014, a review article was pushlished by the Department of Food Science and Nutrition at the University of Minnesota-Twin Cities, one that outlines studies that (collectively) target the top 14 food-borne pathogens in attempts to identifying any potential antimicrobial properties of chili peppers, given that chili peppers can contain high amounts of capsaicin.
From the abstract of the article:
Chili peppers are used worldwide in foods for their pungent flavor, aroma, and to prolong food spoilage. With capsaicin contents ranging from zero to millions of Scoville heat units, the different varieties offer a wide range of options for people all over the world. In addition to their use in cuisines, chili peppers have been explored for their antimicrobial and antifungal properties.
This review goes over some relevant research that has already been done in this area. In addition it lays the ground for the new research that is emerging testing new varieties of chili peppers for nutrient content, flavor profiles, and for antimicrobial activities against numerous human pathogens.
The fourteen pathogens that were targeted and tested against were chosen due to their high risk of harm to the general public, most especially pregnant women (according to the FDA). To name a few that are well known, there's: Clostridium botulinum; Escherichia coli; Salmonella (enteritidis and typhimurium); Staphylococcus aureus; and Listeria monocytogenes.
After reading the conclusions of several studies that were provided by the review article (as well as the conclusion of the review article itself), it would seem that the current (as of 2014) consensus is that the efficacy of capsaicin (in chili peppers) as an antimicrobial agent is still to be determined. Of the (multiple) studies that were considered, collectively they produced quite mixed results. The reason for this is because each study has their own method for testing the antimicrobial activities of capsaicin, which makes the comparison of results between tests difficult to perform with confidence.
There are a variety of methods for testing the antimicrobial activities of chili peppers. These methods strongly affect the observed levels of inhibition. Various reasons may contribute in the differences between results, including inconsistency between analyzed plant materials.
In these experiments, crude extracts of chili peppers were used; no separation of pepper components was done. Based on the data, it seems that capsaicin had a lesser antimicrobial effect compared to other components of chili pepper extracts. Therefore, future studies should try to determine what compounds in the chili pepper gives the spice its antimicrobial properties, and to do so purification of the extracts is necessary. Capsaicin gives chili peppers the ‘hot’ sensation, which some people might not like. It would, therefore, be beneficial if there is another substance in the pepper that could be used in the food industry as a preservative without the pungent taste and hotness.
So, it would seem that, since the idea of using capsaicin as an antimicrobial agent is (fairly) new, there hasn't been a defined method for testing, and because of that, definitive conclusions aren't able to be made yet.
This 2015 article demonstrated that capsaicin kills streptococci (the bacteria that give you throat infection).
However, relatively high concentrations of capsaicin are necessary to kill these bacteria: The minimal inhibitory concentration was determined to be ~128 µg/ml. given that 6.6mg capsaicin correspond to 100.000 scoville, a bowl (400 ml) full of bacteria-killing chilli would need to contain 7-8 habanero chili peppers - I can't imagine that going down well - particularly not with an already inflamed throat.
Interestingly, the same paper also demonstrated, that lower - more practical - concentrations (8µg/ml or 1/2 habanero per bowl) of capsaicin dramatically reduce the ability of streptococci to enter cells. This means that while capsaicin is likely impractical as an antibiotic, it may actually help your body to fight the disease and/or reduce the risk of contracting a throat infection in the first place.
Yes it has some bacteriostasis and antibacterial properties, The only way for you to find it is to do some Agar and similar tests on chillis to find out about their microbes. You will probably find that some chillis have zero bacteria inside them, and that the surface of all chillis have many species. Seeing as it's a weak antibacterial compound, bacteria will probably have evolved to accompany the plant.
hot chillies don't tend to go mouldy on the plant though. they just dry over time.
Fruit generally don't have many bacteria inside them, for example this study shows that a large proportion of tomatoes don't have bacteria inside them, and the bacteria that get in probably do it through the base of the stem. http://aem.asm.org/content/11/1/7.full.pdf
Humans rarely get infections from eating ou fruit and fresh plants, they are a low microbe environment. even melons, one of the most notorious fruits which are source of deaths and food poisonings, are thought to be from bacteria that grow on the outside of melons.
activities of capsaicin and effects of its antiseptic application to ketchup http://en.cnki.com.cn/Article_en/CJFDTotal-DLJY200903023.htm
Extract the natural antiseptic material in capsicum [J] http://en.cnki.com.cn/Article_en/CJFDTOTAL-ZGTW200008001.htm
Study on Bacteriostatic Action of Capsaicinoid [J] http://en.cnki.com.cn/Article_en/CJFDTotal-SDKX200702008.htm
Study on the bacteriostasis of capsaicin in Capsicum annuum
In vitro activity of capsaicin against Helicobacter pylori https://www.researchgate.net/profile/Fadile_Zeyrek/publication/267209796_In_vitro_activity_of_capsaicin_against_Helicobacter_pylori/links/5447a8540cf2d62c30508fb9.pdf
Antibacterial activity of capsaicin-coated wool fabric