Whoa.... a recent study examined food microbiomes (community of microbes) of some foods and found that the foods contained many species of microbes - hundreds of species! The foods examined were a variety of masala spice mixes, cilantro, smoked salmon, cucumbers, and mung bean sprouts. Other studies have also found large numbers of bacterial species in all sorts of foods, including raw fruits and vegetables, cheeses, and fermented foods, such as kimchi. There are also bacterial differences between conventional and organic foods. No wonder it's good to eat a diverse diet - all those microbes that you're ingesting! A diverse gut microbial community in humans is considered healthy by researchers.
The researchers (all associated with the US FDA - Food and Drug Administration) looked at the bacterial "species richness" (number of different bacterial species) normally found on the 5 types of foods. They used modern genetic sequencing methods to analyze the food microbiomes and found a LOT of bacterial species ("high bacterial diversity"), as well as species unique to the different foods sampled - whether animal or plant based foods. They found not only beneficial species, but also species associated with food spoilage. Every food had some bacteria that could eventually lead to food spoilage (which makes sense - eventually all foods can spoil). Also, how the food was handled and packaged, as well as moisture levels, influenced the bacterial species found in the foods.
The masala spice mixes were especially rich in bacterial species (from from 968 to 1097) and in unique species (19), but the mixes also contained as many as 17 ingredients. Cucumbers had between 227 and 423 bacterial species, and 216 to 573 species for cilantro. Smoked salmon samples had fewer species - ranging from 89 to 181 species. An example of the diversity is that the cucumber microbiome is comprised of species within Proteobacteria (45 to 85%), Firmicutes (2 to 40%), Actinobacteria (8 to 31%), and Bacteroidetes (0 to 2%).
I don't know if one can ever replenish all the bacteria lost from years of antibiotics (e.g. for sinus infections - both chronic and acute sinusitis), but this is a good reason to eat a variety of foods - for all the species of bacteria. These bacterial species are not found in general probiotic pills - one must eat the foods to ingest the variety and richness of microbes. The researchers wrote: "Once established, the most likely source of new microbes joining our GI microbiome is the food we eat: each food stuff and commodity we consume likely contains a microbiome that passes through our bodies while nutritional ingredients and components are digested."
It is unknown how many of these microbes stick around in our body, but lots of research finds that a diet rich in fruits, vegetables, whole grains, seeds, nuts, legumes, some fish and meat (including poultry), some dairy - are beneficial to our gut microbiome, along with numerous health benefits. The fiber in these foods is also beneficial in that it feeds beneficial microbes. [see category NUTRITION for research, also Feeding Your Gut Microbes page.]
Excerpts from research by Karen G. jarvis et al in Frontiers In Microbiology:
Food microbiome composition impacts food safety and quality. The resident microbiota of many food products is influenced throughout the farm to fork continuum by farming practices, environmental factors, and food manufacturing and processing procedures. Currently, most food microbiology studies rely on culture-dependent methods to identify bacteria. However, advances in high-throughput DNA sequencing technologies have enabled the use of targeted 16S rRNA gene sequencing to profile complex microbial communities including non-culturable members. In this study we used 16S rRNA gene sequencing to assess the microbiome profiles of plant and animal derived foods collected at two points in the manufacturing process; post-harvest/pre-retail (cilantro) and retail (cilantro, masala spice mixes, cucumbers, mung bean sprouts, and smoked salmon).
Our findings revealed microbiome profiles, unique to each food, that were influenced by the moisture content (dry spices, fresh produce), packaging methods, such as modified atmospheric packaging (mung bean sprouts and smoked salmon), and manufacturing stage (cilantro prior to retail and at retail). The masala spice mixes and cucumbers were comprised mainly of Proteobacteria, Firmicutes, and Actinobacteria. Cilantro microbiome profiles consisted mainly of Proteobacteria, followed by Bacteroidetes, and low levels of Firmicutes and Actinobacteria. The two brands of mung bean sprouts and the three smoked salmon samples differed from one another in their microbiome composition, each predominated by either by Firmicutes or Proteobacteria. These data demonstrate diverse and highly variable resident microbial communities across food products, which is informative in the context of food safety, and spoilage where indigenous bacteria could hamper pathogen detection, and limit shelf life.
You are what you eat. This idea, that the food that you consume controls your health, is not novel, and may be attributed to an early monograph on gout by Brillat-Savarin (2010). In recent years, efforts led by the Human Microbiome Project and the MetaHIT consortium have greatly expanded our knowledge of the microbiomes associated with the human host, especially the gastrointestinal (GI) tract (Qin et al., 2010; Human Microbiome Project Consortium, 2012a,b). That knowledge appears to have important consequences for individual human health. This paper explores food microbiomes to identify bacteria that are associated with foods and therefore have the potential to colonize our gastrointestinal tract. ...
... Once established, the most likely source of new microbes joining our GI microbiome is the food we eat: each food stuff and commodity we consume likely contains a microbiome that passes through our bodies while nutritional ingredients and components are digested. It is unclear how much of this inoculum successfully passes through our gastric barrier, reaches our intestine and colon, resulting in colonization. Foods such as fresh produce that are often consumed raw with no kill step also have the potential to alter the microbial composition of our GI tract and, if they harbor pathogens, can cause illness.
The different foods also had bacteria unique to the food - whether plant or animal foods. Some genera were distinct to plant and animal derived foods. For example, Sphingomonas, Pseudomonas, Pantoea, Acinetobacter, and Erwinia were present in all the plant foods; the latter four cause food spoilage. Hafnia and Morganella, both commensals of the human gastrointestinal tract, Brochothrix, linked to meat spoilage, and Photobacterium, a bioluminescent marine bacteria of the Vibrionaceae family, were unique to smoked salmon. The masala spice mixes, which had the highest alpha diversity in our study, harbored 19 unique genera including food spoilage associated bacteria such as Bacillus, and Cronobacter which are known foodborne pathogens, and Pediococcus that is used in food fermentations.
Our findings support a previous microbiome study that demonstrated commodity driven bacterial diversity in conventionally and organically grown fresh fruits and vegetables (Leff and Fierer, 2013). For example, sprouts, spinach, lettuce, tomatoes, peppers, and strawberries, harbored high levels of Enterobacteriaceae and the microbiomes of apples, grapes, peaches, and mushrooms were predominated by Actinobacteria, Firmicutes, Bacteroidetes, and Proteobacteria.