Diet rapidly and reproducibly alters the human gut microbiome

Long-term diet influences the structure and activity of the trillions of microorganisms residing in the human gut1–5, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here, we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila, and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale, and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals2, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi, and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids, and the outgrowth of microorganisms capable of triggering inflammatory bowel disease6. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles

Low-water activity foods: increased concern as vehicles of foodborne pathogens

Foods and food ingredients with low water activity (aw) have been implicated with increased frequency in recent years as vehicles for pathogens that have caused outbreaks of illnesses. Some of these foodborne pathogens can survive for several months, even years, in low-aw foods and in dry food processing and preparation environments. Foodborne pathogens in low-aw foods often exhibit an increased tolerance to heat and other treatments that are lethal to cells in high-aw environments. It is virtually impossible to eliminate these pathogens in many dry foods or dry food ingredients without impairing organoleptic quality. Control measures should therefore focus on preventing contamination, which is often a much greater challenge than designing efficient control measures for high-aw foods. The most efficient approaches to prevent contamination are based on hygienic design, zoning, and implementation of efficient cleaning and sanitation procedures in the food processing environment. Methodologies to improve the sensitivity and speed of assays to resuscitate desiccated cells of foodborne pathogens and to detect them when present in dry foods in very low numbers should be developed. The goal should be to advance our knowledge of the behavior of foodborne pathogens in low-aw foods and food ingredients, with the ultimate aim of developing and implementing interventions that will reduce foodborne illness associated with this food category. Presented here are some observations on survival and persistence of foodborne pathogens in low-aw foods, selected outbreaks of illnesses associated with consumption of these foods, and approaches to minimize safety risk

Persistence and survival of pathogens in dry foods and dry food processing environments

Low-moisture foods and food ingredients, i.e., those appearing to be dry or that have been subjected to a drying process, represent important nutritional constituents of human diets. Some of these foods are naturally low in moisture, such as cereals, honey and nuts, whereas others are produced from high-moisture foods that were deliberately submitted to drying (e.g., egg and milk powders). The addition of large amounts of salt or sugar can also be regarded as a ‘drying’ process by reducing the amount of water available for microbial growth. Some foodborne pathogens can survive for long periods in low-moisture foods and environments, and in some cases at doses that can cause infections. Many microorganisms can resist drying processes, especially after exposure to nonlethal stress conditions, including sub-lethal heat treatment or acidic environments. If dry foods are reconstituted (rehydrated) before consumption, there is a possibility that bacterial pathogens will grow if products are subsequently stored under inappropriate conditions, potentially resulting in populations sufficient to cause infection or intoxication. Food plants, in which low-moisture foods are produced, are difficult to clean and sanitise effectively, and there are instances of persistence of specific strains of pathogens for extended periods of time. Because microorganisms may survive during drying processes or persist in low-moisture foods and dry food processing environments, it is imperative that Good Hygiene Practices (GHPs), GMPs and HACCP systems, with specific attention to preventing survival and persistence of foodborne pathogens, be implemented and effectively maintained on a continuous basis. The ILSI Europe report examines the extent to which the industry uses monitoring programmes to aid in their understanding of the bacterial ecology and niches. The report attempts to identify how this understanding is translated to enhance the microbiological safety of the process, identify where there are gaps/failures in this system and how to remedy them. This report summarises information on the survival of foodborne pathogens in low-moisture foods (aw < 0.85) and in dry food processing environments. Pathogens that have been known to cause outbreaks of infections or intoxications associated with consumption of low-moisture foods, as well as those not yet implicated in outbreaks, are discussed

Safety demonstration of food and feed cultures

Fermented foods have been consumed for more than 10 000 years, making food fermentation probably one of the oldest food technologies implemented by man. Presently, fermented food products are estimated to represent a third of our food intake. The scientific knowledge behind its role and mechanisms of action have only been studied in the past 150 years. Food microbiology has provided many answers behind the roles, modes of action, nutrition, and health effects of fermented foods. Nevertheless, one of the major topics of concern remains the safety demonstration of microbial food cultures. Despite this very long history of traditional use, what is considered fermented in a part of the world is considered spoiled, if not unsafe, in another one. As an example, in late 2017, China blocked the importation of cheeses from Europe due to the presence of microbial food cultures not present in the Chinese 2010 positive list: Penicillium roquefortii, Penicillium camemberti, and the presence in their genomes of mycotoxin genes. This is not unheard of per se, as the Biohazard Panel of the European Food Safety Authority has excluded filamentous fungi from the Qualified Presumption of Safety. The United States (GRAS!– Generally Recognized as Safe) also has a respective procedure in place for the microbial risk assessment of microbial species voluntarily added to the food chain. The International Dairy Federation (IDF), in collaboration with the European Food and Feed Cultures Association, has been working for the past 20 years on an inventory of microbial species with technological properties in fermented foods. Safety demonstration of food and feed cultures through inoculation into a food matrix for use in the food chain is aimed to avoid trade barriers between countries when a history of safe use cannot be established for an indigenous fermented food product on the international market. It is as well important to avoid the pitfalls of cross- over fermentation, when changing the traditional food matrix, and when possible, to also avoid deleterious microbial metabolic activities

Safety demonstration of a microbial species for use in the food chain: Weissella confusa

Due to their traditional use in food fermentation process for centuries, microbial food cultures are considered to have a safe history of use. A specific microbial risk assessment is therefore rarely conducted for fermented foods and their food cultures, inoculated or naturally present. Some of those food cultures have been also considered for their potential health effect as probiotic strain candidates, for which a specific safety demonstration process has been proposed by a joint expert report of FAO and WHO. The European Food Safety Authority (EFSA) Biohazard panel also provides an approach for evaluating the safety of a strain to be added in the food chain, the Qualified Presumption of Safety (QPS). Weissella confusa, former taxon Lactobacillus confusus, is a food culture characterized in the fermentation process of sourdough. Some strains have been recently proposed for their probiotic potential. The species is also documented in recent infection case reports. It is considered nevertheless to be opportunistic as underlying factors have been suggested to explain the infection. We report here the microbial risk assessment of the species, by studying a collection of 26 food and 17 clinical isolates of Weissella confusa. The phenotypic study, genomic characterization and bibliographical survey will allow us to conclude about the safety of the species and confirm its use for food fermentation and consider specific strains for demonstration of their respective health effects as probiotic candidates