Occurrence and Dynamism of Lactic Acid Bacteria in Distinct Ecological Niches: A Multifaceted Functional Health Perspective

1A historical metabolic-based (and somewhat pleonasmic) consensus definition of lactic acid bacteria (LAB) is a broad group of bacteria characterized by the formation of lactic acid as a sole or main (over 50%) end product of carbohydrate utilization. However, LAB more strictly correspond to members of the order Lactobacillales from a taxonomic point of view. The important taxonomic and physiological diversity of LAB representatives is, however, not convenient when addressing specific ecological niches and roles and applications of LAB. Indeed, LAB adapt to various conditions and change their metabolism accordingly; they cover a varied range of genera including species of lactobacilli, enterococci, lactococci, pediococci, streptococci, tetragenococci, vagococci, leuconostocs, oenococci, carnobacteria, and weissella. The LAB thus constitutes a very heterogeneous group and are often misleadingly circumscribed to lactobacilli only. In contrast, other microbes used in the making of fermented dairy products or claimed as probiotics such as bifidobacteria, propionibacteria, and even brevibacteria, belonging to the anaerobic actinomycetales, are falsely included or assimilated within this group. This is partly due to their overlapping habitat or common properties together with unclear species identity.

2Recent efforts have been undertaken to identify lactobacilli and related species. From eighty identified Lactobacillus species, 15 years ago, we now reach to more than 200, with continuous new discoveries, e.g., Lactobacillus timonensis or Lactobacillus metriopterae due to next-generation sequencing (NGS), clustered regularly interspaced short palindromic repeats (CRISPR)-based methods, and culturomics. This has justified the proposal for a reclassification of the genus. According to the last taxonomic update of the lactobacilli, a dozen clades have been recently organized. The current knowledge on evolution of the genus Lactobacillus, its environmental niches, and the degree of host specificity was recently completed. Ecological differentiation of the genus Carnobacterium was recently established based on comparative genomic analysis.

3The genus Enterococcus encompasses more than 50 species that can also be found in diverse environments, from the soil to the intestine of animals and humans, including the hospital environment, which provide concerns. In addition, enterococci are present as spoilage microflora of processed meats, but, on the other hand, they are important for aroma development and ripening of traditional products such as certain cheeses and sausages. Depending on their origins and evolution, they may act as both commensals and pathogens, and strains are consequently of clinical importance, harboring virulence factors as well as possibly being used as probiotics.

4The various genera, species and even strains of LAB inhabit and cope with specific environments in order to exert dedicated or multiple specific functions according to their structural determinants and/or metabolic pathways. With the exception of enterococci as opportunistic pathogens and the case of pathogenic streptococci, there are only a few reported cases of bacteremia due to LAB. The LAB are regarded as generally recognized as safe (GRAS) because of their ubiquitous use in food and their unique role in the healthy microflora of human mucosal surfaces. To date, 50 LAB strains have obtained the qualified presumption of safety (QPS) status by the European Food Safety Agency, again, comprising mostly lactobacilli spp. (n = 37). However, enterococci have been classified in risk group 2 in the European Directive 93/88.

5The LAB greatly differ in morphology, optimal growth and tolerance temperature, salt and pH tolerance, metabolism, and surface and secreted molecule. They may secrete effector proteins, produce exopolysaccharides (EPS) and generate biofilms, or adhere on abiotic and/or biologic surfaces, depending upon genera, species, or strain. Accordingly, the origins, quantities, the diversity, and abundances of LAB strains in complex ecosystems may greatly impact on the intended effect(s), product(s), and functionality. As a striking example of broad effects, the presence of psychrotrophic Lactobacillus spp. as the prevailing spoilage organisms in packaged cold-stored meat or fish products is unwanted. In contrast, dominance of only a few Lactobacillus species inhabiting human vaginal cavities is essential to maintain a low microbial diversity and prevent further vaginosis. Consequently, LAB, in general, and lactobacilli, in particular, cannot be considered as a whole, and have to be stratified depending on their intrinsic characteristics and potential applications. Hence, up to 25 species are defined as fructophilic LAB that inhabit fructose-rich niches in nature, e.g., flowers, fruits, and fermented foods. These LAB can also be isolated from the gut of bees and flies, and the latter have coevolved to determine microbe–host mutualism. A motile phenotype has been characterized in nearly 15 distinct Lactobacillus species, while motility genes have also been detected in other closely related strains. This will both contribute to select geographical ecological niches and, due to flagellin signalization, to sustain the immune potential of such bacteria.

6It has been recognized for a long time that LAB are fascinating and useful bacteria and, now, recent advances in technologies allow addressing the specific mechanisms of the important bacteria–host interactions in appropriate models. The uses of LAB as biotherapeutic agents and probiotics are based on multiple molecules and modes of action that are currently deciphered. Here, we present a short overview dealing with the overall occurrence of LAB in the environment and some of their contributions to health, focusing on strain-dependent effects together with consideration on individual hosts and experimental models.

7The LAB can be found nearly everywhere although their total load and relative abundance in microbial ecosystems are extremely diverse and depend on the specific environment. The selective pressure exerted by these environments is a key driver in the genomic diversity among LAB strains derived from distinct habitats. LAB have been identified in Japanese lakes, with viable cell counts ranging from 1 to 3 log per ml, with a clear seasonal variation. LAB could also be isolated from soils following enrichment protocols. Although soils do not contain large amounts of LAB, they are somewhat more abundant on the plant–soil interface such as the rhizosphere of some trees and comestible fungi. Some of the strains obtained from these niches showed antimicrobial properties. The abundance and diversity of LAB in soils greatly depend on carbon-richness, which is, e.g., greater under fruit–trees and in soils associated with anthropic activities or free-range farming, and after the use of manure. Notably, many halo-tolerant LAB, known to be able to survive and even grow in dry environments, can be recovered from soils when soil acidity may contribute too. It is interesting to note that LAB are also used in agriculture, as biofertilizers, safe biocontrol agents for bacterial and fungal phytopathogens, regulators of abiotic plant stress, and biostimulant agents to ameliorate plant growth (recently reviewed by ). Understanding the phytomicrobiome, including the role of LAB therein is an emerging field with great potential to mitigate plant stress and promote plant resistance and production.

8The LAB only represent a subdominant part of raw vegetables and fruits microorganisms (2 and 4 log cfu per g.), while the microbial autochtonous population varies between 5 and 7 log cfu per g.; hetero-fermentative and homo-fermentative species belonging to Leuconostoc, (mostly L. plantarum), Weissella, Enterococcus, and Pediococcus genera are those most frequently identified as epiphytes within the microbiota, depending on the plant species. We also should consider the low but relevant endophyte LAB representatives when regarding adaptation of LAB to plant niches. Indeed, the capacity to adapt to the intrinsic features of the raw plant matrices and persist stably as endophytes throughout plant phenological stages represent additional criteria for selecting robust LAB candidates. Some LAB found in bakery sourdough are there partly due to contaminating flour and may originate from milling, representing a part of the endophytic microbial community of wheat at very low levels. Moreover, LAB diversity in sourdoughs may also originate from external layers of wheat plant organs (epiphytic) and the bakery environment (the bakers, insects, and nuisance species animals). The ability of LAB to produce organic acids and other antimicrobial substances has made them essential in the preservation of plant-based foods while they also are the most important microbes promoting significant positive changes in healthy aspects of plant foods. Their metabolism throughout fermentation contributes to lowering some toxic and antinutritional factors and promoting bioavailable bioactive compounds. Following either spontaneous fermentation or after intentional inoculation of food products with LAB as starters, the final LAB load in plant products can reach 8 to 9 log per g. Such a high concentration of LAB contributes to the biocontrol of pathogens (Gram-negative bacteria, Listeria monocytogenes) in food as well as to their possible use in probiotic/functional food.

9The natural origin of LAB used in traditional fermented foods, such as sauerkraut, pickles, cheese, sausage, fish, fish- and soy- sauce, sourdough bread, and animal silage, is the corresponding matrix (fruits, cereals, milk, and animal farm environment) or the associated (wooden) material. A plant-based origin for dairy lactococci was nicely demonstrated using genome evolution studies. Starters and ferments have then been isolated, selected, and domesticated over past centuries to control the fermentation processes and standardize the taste and quality of the final products. The final count of LAB in fermented products is highly diverse and ranges from 4 to 5 log to over 9 log of bacteria, depending on product types, fermentation dynamics, and the overall microbial ecology of the products. Moreover, the abundance of other non-LAB, yeasts, and molds in these complex ecosystems, especially in cheeses, needs to be considered. The microbial diversity of fermented food together with some functional properties, including the contribution of some LAB therein, has been extensively reviewed elsewhere. The health benefits of fermented foods and the added value of ingesting LAB in order to either prevent or treat some specific diseases is now generally accepted and beyond discussion. Regardless of their traditional or industrial origins, fermented foods are active sources of LAB, among other microbes, that will enter the digestive tract and possibly exert a positive influence (and even a negative one) on the host.

10Dominance of LAB in the vaginal niche is a characteristic of healthy women, reaching from 70 to up to 90% of resident bacteria, whereas LAB colonization of the genital tract of other mammal species, including primates, is anecdotic and generally below 1% of the relative abundance. This is unique in humans where vaginal fluid generally contains 7 to 8 log of lactobacilli per mL, represented by a dozen or so species most frequently found. However, the normal vaginal flora is usually dominated by one or two out of the major species of lactobacilli (Vaneechoutte, 2017b). In addition, occurrence of other rare Lactobacillus species and other LAB representatives such as Pediococcus acidilactici, Weissella spp. (W. kimchi, W. viridescens), Streptococcus anginosus, and Leuconostoc mesenteroides has also been reported. These observations greatly depend on ethnic groups, individuals, and time, according to pregnancy or menopausal status. Notably, not all Lactobacillus-deficient vaginal microbiotas are adverse. The main benefits of lactobacilli in the vaginal sphere are essentially that they have anti-infectious properties, and can prevent and target bacterial vaginosis, vaginal candidiasis, and sexually transmitted virus and bacterial pathogens. The normobiosis of the vaginal microbial community is based on low pH maintenance (ranging from 3.5 to 4) due to lactate production following glycogen consumption, which is unique in humans, and not necessarily in other animals. Another key factor is hydrogen peroxide production. While 95% of lactobacilli of vaginal origin from healthy women are H2O2-producers, this proportion can drop to 6–20% in the context of vaginosis. Moreover, dominance of L. iners, a non-H2O2 producer, has been associated with poor protection and even a risk-factor in vaginal dysbiosis. However, the specific role of L. iners, which is uncultivable in standard LAB culture media and unable to produce D-lactate, is still on debate. Finally, bacteriocin production is also involved in direct killing of microorganisms by lactobacilli in the vagina although most vaginal LAB isolates do not exhibit bactericidal activity. Anyway, this production is an optional issue in selecting appropriate strains and sustaining the role of probiotics in maintaining vaginal health. As a more indirect mechanism, a recent study has demonstrated that the overall Lactobacillus-associated anti-inflammatory properties in the vaginal mucosa could contribute to lower HIV infectiveness. Collectively, only few LAB species are adapted to dominate the human vaginal cavity in order to preserve health.

11Very recently, raised the question of the importance of Lactobacillus in the intestine of mammals by reviewing the occurrence of LAB in the gastrointestinal tract of distinct vertebrates. In contrast to rodents where LAB can represent 20% to up to 60% of all bacteria, the estimated proportion of LAB in the human proximal small intestine is always subdominant (6%), while their relative abundance in the colon is mostly below 0.5% or non-detectable. LAB have also been detected in substantial amounts in the stomach of humans although the actual numbers are subject to huge variations depending on individuals and their health status, the methodology used, and the type of samples. Depending on genetic backgrounds, the gut microbiota of laboratory mice is highly diverse and the proportion of LAB can range from undetectable to near 100%, ranging from 4.7 to 10.6 log. The gut microbiome of wild wood mice comprises an average of 30% of Lactobacillales, although it dramatically changes with the seasons. Indeed, the proportion of Lactobacillus spp. ranges from 60% in spring to 20% in the fall. The abundance of LAB in the intestinal microbiota of laboratory mice is highly influenced by the diet and can range from 10% Lactobacillales on a normal fiber control diet to 0.5% with low-fiber diet and 40% with a high-fiber diet. Similarly, LAB abundances also vary according to circadian rhythm disturbances.

12The mode of delivery (vaginal versus C-section) in humans is important to allow, respectively, high or low levels of Lactobacillales in babies. These differences persist during the first 2 years of life and progressively disappear. Indeed, lactobacilli and enterococci are first colonizers and dominant bacteria, then become subdominant at toddler and adult ages. A metagenomic study identified nearly 60 distinct species of lactobacilli in human fecal samples, not exceeding 0.04% of all bacteria present, corresponding to near 8.5 log cell per g. from an average bacterial load of 12 log. Within this diversity, one or two major species (L. rhamnosus and L. acidophilus) were estimated at 8 log. Of the six most represented species, those estimated from 7.5 log were identified as L. rhamnosus, L. ruminis, L. acidophilus, L. delbrueckii, L. casei, and L. plantarum, while others were detected below 5 log cell per g., close to the detection threshold. In this study, the abundance of enterococci was similar to that of lactobacilli, but commensal streptococci were two to five times more abundant. reported dominance of L. gasseri, L. casei, L. namurensis, L. rogosae, and L. murinus in human fecal samples. Clearly, proportions of LAB and even Lactobacillus species are highly diverse and vary between individuals. This may explain difficulties at comparing microbiome data from healthy controls and patients with distinct pathologies aiming at uncovering a possible protective or even deleterious general role of lactobacilli. Many studies investigating the role of the human gut microbiota in distinct immune-mediated inflammatory diseases have reported either increased, decreased, or unchanged levels of lactobacilli. All in all, no consistent marker for any pathology or a healthy state is simply defined by a specific proportion of Lactobacillus, or even based on the follow-up of the Lactobacillus load for an individual in time. Interestingly, gut remodeling due to a restrictive surgery and leading to short bowel syndrome was accompanied by enrichment of lactobacilli, which may explain the D-lactate acidosis in some subgroups of patients. The in lactobacilli-enriched microbiota in patients suffering from short bowel syndrome may also favor energy recovery occurring after resection. The abundance of enterococci in the human gut, mostly E. faecium and E. faecalis, is estimated between 4 and 6 log bacteria per g. wet weight. It, thus, represents nearly 1% of the relative abundance, which is 10–100 times higher than that of lactobacilli. Although commensal LAB are somewhat subdominant, they clearly play a role in gut physiology with consequences on health and qualitative (species and strain specificity) rather than quantitative aspects (genera and family abundance) should be considered. The interplay between LAB and non-LAB within the gut has not been completely revealed yet. For instance, several authors have highlighted the possible indirect role of LAB in increasing the butyrate content in the feces. This capability is attributed to an initial cleavage of fibers in the large intestine to more fermentable compounds, which are then further converted to butyrate by butyrogenic non-LAB present. Moreover, exogenous LAB, sourced after oral administration of fermented foods or dietary supplements, may reach numbers similar to those of commensals (0.1–1% of the total microbiota present in the gastrointestinal tract, so 5–8 log per g.), depending on dietary habits and geographic areas. Such transitory or “visiting” living microorganisms, also named pseudocommensals or transionts, cannot durably colonize the host. However, provided these bacteria are regularly or even occasionally ingested in sufficient amounts, they can act as symbionts or pathobionts, modulate the gut microbiota, and exert various health effects.

13The exploration of the microbiota in the lung is in its infancy when compared with the microbiomes from the gut or the vaginal cavity. Using 16S metagenomics, the microbiota of the respiratory tract has been described since 2010; it is mainly made up by two phila (Firmicutes and Bacteroidetes) in humans and four phila (Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria) in mice. The load of lung microbiota is estimated to reach around 103–104 cultivable bacteria per gram of lung homogenates in mice. In humans, it has been estimated as a mean of 3 log bacterial genomes per cm2 surface in the upper lobe. The lung microbiota plays a key role in promoting tolerance and is a determinant of maintenance of homeostasis. It remains difficult to define a healthy lung microbiota as of yet, due to its high intervariability as a function of age, diet, or environment, but LAB (Streptococcus, Lactobacillus, and Enterococcus) are prominent members and seem to be actors of respiratory symbiosis and health. As an example, the presence of Enterococcus faecalis decreases with the severity of asthma in the human lung microbiota and the decrease of the bacteria improves the outcomes of asthma in a preclinical mouse model. Nasal administration of Lactobacillus rhamnosus GG protects against influenza virus infection and oral supplementation of Lactobacillus spp also modifies the lung ecosystem. Overall, these data indicate that LAB are major members of lung microbiota and might be useful in future preventive strategies or new therapeutics for respiratory health.

14Anti-inflammatory properties of LAB have been extensively studied in rodents and to a lesser extent in humans. This is attested by many studies sustaining the protective role of commensal LAB and the benefits brought by exogenous LAB through nutritional and/or probiotic interventions. The overall anti-inflammatory value of LAB is also evidenced by the rarefaction of lactobacilli in the gut of inflammatory bowel disease patients. Moreover, the drop of lactobacilli observed in the fecal microbiota of aging populations can be related to the low-grade inflammation theory, i.e., ‘inflamm-aging’ and frailty. Recently, it was shown that diet-induced exacerbation of experimental colitis is associated with a reduction in Lactobacillus sp. and a lower production of protective short-chain fatty acids, including butyrate. Nevertheless, whether the overall rate of LAB or even a minimal threshold of lactobacilli may or may not represent an indicator for health is not yet clear. The prevalence and richness of Lactobacillales and lactobacilli may either increase or decrease depending on immune disease types and studies, and such changes can be linked to causal events or adaptive processes to counteract the injury. Again, besides genus and species, also strain-level attributes matter when considering immunomodulatory properties of LAB. This has been well documented during the last decades, showing anti-inflammatory probiotic properties of specific lactobacilli based on multiple distinct mechanisms of reducing colitis symptoms in mice. For example (non-exhaustive), a L. plantarum strain was shown to be beneficial against inflammation because of a specific teichoic acid structure, while the anti-inflammatory effect of a strain of L. salivarius was dependent on peptidoglycan. In contrast, the alleviation of colitis was attributed to S-layer proteins of L. acidophilus, pili for a L. rhamnosus strain, and EPS for another L. plantarum. In line with these observations, the structurally different EPS from resident lactobacilli generate different immune responses by dendritic cells while, upon gut inflammation, specific bacterial molecular motifs are absent from lactobacilli isolated from IBD, providing tools for further application based on strain selection. The positive role of H2O2 production to lower inflammation has been reported for L. crispatus and L. rhamnosus. The colitis alleviating property of L. bulgaricus was related to activation of the aryl hydrocarbon receptor pathway in colon cells, in line, the control of inflammation by an L. reuteri intervention was associated to the production of histamine followed by activation of a host epithelial cell receptor. An L. casei strain inhibited the secretion of the pro-inflammatory mediator IP-10 protein at the post-translational level; this inhibition is based on the role of a specific secreted protein by the bacteria. Specific bacterial DNA motifs may also drive some of the immune-stimulatory effects in a toll-like receptor 9-dependent manner. Interestingly, distinct immunological activities through TLR5-signaling caused by flagellins isolated from motile lactobacilli presume a consequence of adaptation to commensalism. Pro-inflammatory LAB, i.e., L. crispatus, were inconsistently reported in murine models of colitis. Given that these observations are rare, one has to keep in mind that such undesirable (and embarrassing) results are difficult to publish and that they may be underestimated. LAB other than lactobacilli can also exert immune effects and strain-dependent impact on the release of pro-inflammatory cytokines and colitis. Strain diversity in such anti-inflammatory properties has been reported for food-derived pediococci and oenococci, carnobacteria, and enterococci. Notably, several strains of Enterococcus spp. are marketed as probiotics, for use in many health purposes both in humans and pets, alone or in combination with other LAB and/or bifidobacteria but most of the Enterococcus species are believed to have no prominent beneficial effect on inflammation as well as on the overall human health.

15No single and unique mechanism of anti-inflammatory effects of LAB can be generalized. The overall combination of anti-inflammatory and anti-oxidative properties with the occurrence of some immune-stimulatory signals of a single LAB strain has to be integrated by the host. Moreover, when interpreting the host’s health, one also should consider the interplay of these specific molecular players with those of other (non-)LAB strains from the microbiota. Consequently, the anticipated effects of a promising strain can either be boosted or diluted, depending on its microbial microenvironment in the gut. In addition, the contribution of the matrix should not be neglected. Together with a high variability in host immune reactivity, it seems difficult to fully predict the performance of individual LAB strains. It is essential to screen LAB strains with valuable properties, but integrative endpoints are necessary to fully characterize the consequences of LAB for health; relevant anti-inflammatory strain selection should thus be based on specific mechanisms and how they may interplay within the microbiota.

16Clear links have been established between gut microbiota, metabolism, and the nutritional status of distinct animals, including farm animals, whose growth performance was empirically boosted either by antibiotics or probiotics for several decades. The key role of gut microbes in the metabolic physiology of the host, throughout evolution, has been demonstrated in drosophila in fish, in rodents and humans. Molecular mechanisms involved multiple signaling pathways such as microbial production of short-chain fatty acids, the control of epithelial integrity (and endotoxemia), and modulation of chronic inflammation, which has been reviewed elsewhere. Microbiota-derived metabolites can also interplay with the regulation of appetite and satiety. They act particularly on intestinal food intake mediators likely GLP1, leptin, and ghrelin. In mammals, disruption of the homeostasis of gut microbiota (dysbiosis), resulting from an imbalance of bacterial strains, may induce physio-pathological processes leading to chronic obesity or metabolic disorders such as type 2 diabetes or metabolic syndromes.

17Gnotobiotic rodents have been used to study the health effects on germ-free (axenic) animals of treatment with specific bacterial strains. The glycolytic activity of Streptococcus thermophilus is improved once inside the digestive tract of mono-associated rats. Colonization of the gut of germ-free mice by microbiota from obese mice significantly increases their total body fat compared with colonization by microbiota from lean mice. In addition, inoculation of both obese mice and humans with microbiota from lean mice or humans, respectively, improves symptoms of metabolic syndrome. Some Lactobacillus species are associated with weight gain, while others are associated with protection against obesity. Compared to lean patients with a normal body mass index, abundance of lactobacilli was higher in obese and lower in anorexic individuals. In contrast, a recent study established a relationship between the high oral Lactobacillus counts and protection to further weight gain, while a lack or a low level of oral lactobacilli may increase the risk of obesity. Higher proportions of lactobacilli were related with type 2-diabetes. Moreover, some lactobacilli were also reported to limit undernutrition and to have growth-promoting effects in mice while a strain of L. reuteri could contribute to preventing cachexia. Data dealing with the occurrence of Lactobacillus spp. in obesity and type 2-diabetes are thus inconsistent, which is most probably related to their low and variable quantity in the gut microbiota. Comparative genomic analyses have shown that Lactobacillus species linked to weight-loss had specific arsenals of genes associated with anti-microbial activities such as bacteriocins. In contrast, weight gain-associated Lactobacillus spp. harbored enzymes involved in lipid metabolism. Besides the species level, the importance of properties at the strain level was revealed using interventions in experimental rodent models.

18Significant research efforts over the recent decades have been devoted to the development of effective treatments for obesity and metabolic disorders, using probiotics to mitigate dysbiosis and its impact on metabolism. Several studies have shown that ingestion of LAB by rodents reduced weight gain and improved the metabolic profile (blood glucose level, insulin, leptin), oxidative stress, and hepatic inflammation in various models such as mice fed with a high fat diet (HFD); Leprdb/db mice (lacking the functional, full-length Ob-Rb leptin receptor), streptozotocin (STZ)-induced diabetic mice fed an HFD, STZ-diabetic rats, and rats fed with a diet high in fructose. These experiments mostly underlined the role of L. rhamnosus, L. plantarum, L. gasseri, L. casei L. mali, L. fermentum, and L. reuteri strains alone or in combination with other strains. Again, not all Lactobacilli are able to control obesity and adiposity and some, i.e., an L. salivarius strain known as a probiotic for anti-inflammatory properties in mice, could not alleviate diet-induced obesity and insulin resistance, while a strain of L. rhamnosus did. Similar results have also been observed in clinical trials. For example, glycemia and cholesterol levels were reduced in elderly subjects after a month of daily consumption of a combination of L. acidophilus and B. bifidum strains, while a reduction was observed of oxidative stress and glycemia levels in type-2 diabetes patients after 6 weeks of daily consumption of a probiotic dairy product containing L. acidophilus and B. lactis. The beneficial effects of various species of Lactobacilli on obesity throughout clinical interventions have not been demonstrated nor reviewed yet. One possible explanation of metabolic disorders alleviation is that probiotics, and especially LAB, could reduce the absorption and conversion of food into useable energy and subsequent fat storage, resulting in anti-obesity, anti-inflammatory, and anti-diabetic effects in mice and humans. The current molecular hypothesis of anti-obesity mechanisms involves the specific role of short-chain fatty acids and the host cell receptors FFAR2 and FFAR3, the contribution of bile-salt hydrolases from LAB, and further bile signature signaling of FXR and TGR5 receptors as well as LAB metabolites as antagonists of AhR. However, no clear explanation is achieved yet.

19In addition, LAB strains that either lower pathogen or even pathobiont numbers, those that strengthen the gut barrier and reduce LPS-endotoxemia, and the anti-inflammatory strains are also valuable candidates against obesity.

20Lactic acid bacteria are also able to produce conjugated linoleic acids, gamma-aminobutyric acid (GABA) and may contribute to signal the neuroendocrine and vascular systems. More studies are necessary to determine the best strains, optimal dose, and treatment time to achieve beneficial outcomes for obesity, type-2 diabetes, non-alcoholic fatty liver disease (NAFLD) and decipher the corresponding mechanism(s). Collectively, those data should shed light on selected probiotic strains as important tools to prevent and treat patients with metabolic disorders and cardiovascular diseases.

21Besides the widely known lactic acid and H2O2-mediated anti-bacterial, anti-viral, and anti-fungal properties of LAB, specific bacteriocin-based mechanisms can control bacterial growth in distinct environments. Bacteriocins are ribosomally synthesized peptides or proteins that exhibit bactericidal or bacteriostatic activities. The classification of bacteriocins is a long-term matter of debate. Lately, a large scientific consortium proposed a new classification in which post-translationally modified bacteriocins of less than 10 kDa are considered as Ribosomally synthesized and Post-translationally modified Peptides (RiPPs). This new classification was slightly modified to embrace all bacteriocins leading to three classes, where class I are RiPPs, class II are unmodified bacteriocins (less than 10 kDa), and the class III are large bacteriocins.

22Bacteriocins are found in almost every examined taxa. Their likely ubiquitous nature suggests they play a major role in shaping bacterial communities: they may serve as anticompetitors preventing invasion of a bacterium into an established community and could reciprocally allow a bacterium to invade a community. Intuitively, their activity should lead to diversity reduction; however, experimental and modeling data suggest that under certain circumstances, bacteriocin production can promote diversity providing that taxonomic diversity is mirrored by bacteriocin-encoding gene diversity.

23There are three major already established or future applications of bacteriocins. They can be used as biopreservative agents, as probiotic-promoting factors, and as antibiotics. Although two bacteriocins, nisin and pediocin, are allowed as food preservatives, bacteriocins are mainly indirectly used through producer strains. These strains are included into ready-to-eat food in order to produce bacteriocins in situ and are mainly used to target Listeria monocytogenes. Bacteriocin-producing LAB are also promising probiotic candidates for humans and animals. Proof of concept was demonstrated by showing that bacteriocin production by L. salivarius UCC118 allows protecting mice from L. monocytogenes infection. Several studies revealed that bacteriocin production results in changes in the gut microbiota structures leading to the idea of using bacteriocins as tools for targeted manipulation of gut microbiota.

24Besides biopreservation and probiotic-promoting factors, bacteriocins are considered as a means to fight against emerging multidrug resistant pathogens. A promising strategy consists in combining the use of bacteriocin with other antimicrobials to reduce the frequency of resistant variants appearing and/or to increase the antimicrobial potency.

25All these possible applications fuel active research, aiming at identifying new bacteriocins. Despite the tremendous literature describing new bacteriocins, new ones with interesting novel structures and unique activity are still being discovered. The challenge is now to design strategies that allow to avoid already reported bacteriocins. The traditional approach, isolating a strain exhibiting antagonistic activity followed by purification of the active compound prior characterization, is time-consuming, expensive, and tedious. Therefore, new workflows were developed that include steps dedicated to assess the novelty of bacteriocin candidates. One strategy combines liquid chromatography/mass spectrometry with principal component analyses of the antimicrobial spectrum of each bacteriocin-producing LAB strain. There are also in silico strategies based on genome mining that allow identifying candidate genes specifying putative bacteriocin proteins with novel structures.

26The LAB, among other bacteria, have been suggested as tools for detoxification of several xenobiotics and pollutants such as pesticides, toxins, and heavy metals. Whereas bioremediation is actively used in the environmental industry for many years, in vivo applications of LAB to reduce contaminant bioavailability are only in the early stages of development. Proof of concept has already been established, however, using distinct animal models and pilot clinical studies. For example, specific Lactobacillus spp. and Leuconostoc isolated from kimchi possessing an organophosphorus hydrolase gene were able to degrade pesticides such as chlorpyrifos and parathion. In this context, resistance to insecticides (chlorpyrifos, fipronil) was associated with the presence of Lactobacillales in the midgut of insects. Recent data support the use of an L. rhamnosus strain to reduce absorption and subsequent toxicity of organophosphate pesticide and neonicotinoid to Drosophila melanogaster. These are encouraging results that might be helpful in the fight against the current worldwide environmental threat of bees dying from these toxic compounds. They also suggest further examining the use of supplements for human, livestock, or apiary foods with selected probiotic microorganisms.

27Lactic acid bacteria have also shown potential in mitigating toxic effects of distinct mycotoxins such as aflatoxins (B1, F1 and M1), patulin, ochratoxin A, and deoxinivalenol in food and feed. Certain Pediococcus spp. have mycotoxin adsorbing and degrading properties. Reducing aflatoxin bioavailability was reported in rats and in mice, but yet no clinical data are available on the use of LAB as detoxifying probiotics in humans. Other toxic substances can be handled by LAB. Acrylamide-binding ability by LAB was found to be both concentration- and strain-dependent, in vitro as well as in a gastric digestion stimulator; the binding was mostly based on teichoic acid properties of specific strains. These results are promising for further actions and research to reduce exposure and bioavailability of such carcinogenic compounds.

28Bioremediation of heavy metal (HM) and other hazardous and toxic metals such as chromium (CrVI) and aluminum, and, to a lesser extent, copper and cobalt, is challenging. The bioremediation is based on specific capacities of microorganisms to immobilize and/or inactivate pollutants by various passive (biosorption, complexation) or active transport (internalization, efflux/uptake ratio) mechanisms, including distinct bioprocesses (oxido-reduction, demethylation, e.g., for CH3-mercury) to lower HM bioavailability. Efforts have mostly focused on LAB and related species, and these have shown that selected lactobacilli (and bifidobacteria) can sequester lead (Pb) and cadmium (Cd) divalent cations and mercury (Hg) salts. A key point is the huge variations in binding capacity among LAB species and even strains. This variability is partly caused by the high diversity of ionisable compounds on the surface of Gram-positive bacteria. For example, EPS and teichoic acids comprise negatively charged groups (hydroxyl, carboxyl, phosphate) as potential ligands for divalent metal cations (such as Pb2+, Cd2+, Hg2+). In contrast, peptidoglycan and a mosaic of specific surface proteins (e.g., S-layer proteins) have positive charges, which can explain affinity toward arsenate As(V). Since the last decade, bioremediation of HMs and tolerance of humans to HMs through microbial processes using food-grade microorganisms have been highlighted. This concept can also be applied in vivo ‘inside the digestive tract.’ Commensal intestinal microorganisms play a positive role in the interactions with HMs, as demonstrated by we and others. Provided that microbial species meet criteria for safe dietary use, transitory microorganisms may do at least as well or even better than the resident flora. Various selected food microbes can thus prevent the absorption of HMs by the body and remove them upon defecation. Promising proof of concept of efficiency was demonstrated in preclinical models of acute and chronic HM toxicity in mice for cadmium, chromium, and aluminum. Likewise, a first clinical pilot study showed reduced circulating levels of toxic HMs in pregnant women and children living in a contaminated area: by using a designed fermented milk with a selected probiotic L. rhamnosus-supplemented yogurt the bioaccumulation of mercury and arsenic could be reduced. This work clearly illustrates the promising concept of using probiotics in a nutritional strategy against xenobiotics.

29Opportunities to use LAB for health are quite unlimited as the role of intestinal microbiota has now been clearly highlighted in various diseases and pathologies, including those affecting organs at distant sites, cancers, neurologic, and psychological disorders. Some examples are abdominal hyperalgesia and pain that can be controlled by specific strains of lactobacilli targeting nociceptive signals and these strains have been proposed in treatment of irritable bowel syndrome. Interestingly, in the 2014-clinical study, an L. acidophilus strain was clinically effective, but failed to attenuate pain in patients when co-administered with another bacterial strain (Bifidobacterium lactis). The results suggest a diversion effect and caution should be taken when using mixtures of strains. In cancer, a higher enterococci count was correlated with a lower risk of colorectal cancer development. Some reports showed an inverse correlation of fecal enterococci with colon adenomas, while another study suggested a deleterious role of E. faecalis in colorectal cancer development. Selected LAB, such as Enterococcus hirae, can be also used to boost cancer chemotherapy, while appropriate strains may also play a role in immune cell regulation and exhibit anti-oxidative and antigenotoxic effects.

30Other examples of innovative use of LAB as probiotics are in modulating central nervous system functions and behavior symptoms such as chronic fatigue, depression, and anxiety, although clinical data are yet not fully convincing. The results have led to the definition of ‘Psychobiotics’ as a novel class of psychotropic treatments employing bacteria with neuroendocrine and behavioral properties. Functional magnetic resonance imaging has been used for the first time to measure brain activation triggered by probiotic LAB. A deeper understanding of the relationships between the LAB (within the gut or ingested) and the host, if they do really exist and what are the mechanisms, is required to develop microbial-based therapeutic strategies for brain disorders. Indeed, emerging applications are still on examination, partly due to the lack of consistent studies, appropriate study designs, and the selection of the proper strain(s).

31The LAB are multifaceted microorganisms that have existed on earth for several millions of years, with tens of thousands of years of shared history with animals and humans. They have been used for the production of fermented foods for centuries, and more or less actively developed as probiotics for several decades (Figure 1). LAB may strongly be part of the health concept for livestock rearing and in food and feed production. An outstanding effort has been made these last years, using extended omics approaches, to build the knowledge and further tools to elucidate the contribution of LAB in health and diseases. We are now facing the daunting task of integrating of all this information for general application as well as for individual use (“my personalized LAB”). Indeed, separately, LAB can either contribute to induce Th1 or Th2 immune responses; they may also induce specific or non-specific regulatory T cells, which may or may not be required by the host. Similarly, LAB have the potential to favor either weight loss or weight gain. LAB abundance is sometimes diminished or increased depending on diseases. The central role of LAB within the microbiota, providing antimicrobials, also raises the question of the control of ecological niches, which can be advantageous or not. Berstad argued that ‘we should stop thinking of LAB as always being friendly.’ Indeed, few data exist on the long-term impact of LAB, considering their possible capacity to destabilize the microbiota, and the “paradox” to use them empirically in multiple pathologies and combined (metabolic, immune, psychological) disorders. Nevertheless, LAB are our obligate partners and we have to cope with these microorganisms. Dissociating the common and specific interactions of LAB strains, -species and -genera within the whole of the microbiota in which they partake is still necessary to identify regulatory mechanisms, respectively, involved in distinct organs, systems, and hosts. Definitely, integrative system biology approaches are required to achieve the ultimate goal of applying LAB for personalized medicine. It comprises using omics technologies on the LAB as well as on the host and including foodomics and nutrigenomics, together with appropriate basic and integrative models and tools to appraise the overall functionality of LAB.

32BF, FG, MT, and FB prepared the manuscript and all co-authors contributed to editing and critical reviewing thereof.

33The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.