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Fermented Foods, Lactobacillus, and HealthLactobacillus bacteria serve as a gateway for understanding transitoryhost-microbe interactions in the digestive tract

Maria L. Marco and Benjamin L. Golomb

The earliest development of fermented foods,among the most ancient agricultural products,coincided with the rise of civilizations around theworld. According to archeological records, winewas produced during the Neolithic Period from8500 to 4000 BC, while beer and bread were mass-produced shortly thereafter. These foods, as wellas others such as cheese, yogurt, and miso, arementioned in ancient texts, including the Bible,the Iliad, and the Odyssey. Although modernpreservation and processing methods reduced re-liance on these products, fermented foods andbeverages remain an important part of dietsthroughout the world.

In the United States, there is renewed interestin fermented foods for both their artisanal man-ufacture and their capacity to benefıt humanhealth. New companies are popping up to pro-duce a wide range of fermented foods and bever-ages, including pickles, sauerkraut, sourdoughbread, artisanal cheeses, yogurts and kefır, craftbeers, and kombucha (fermented tea). Thesefoods are not only popular, but they are also con-sidered healthy. Indeed, in the absence of scien-tifıcally confırmed health benefıts for most fer-mented foods, consumers are being told thatsome are “probiotic” and “prebiotic.” Many ofthese claims revolve around Lactobacillus species,which are widely used to ferment foods, and therole that these bacteria play as probiotics.

Lactobacillus and closely related lactic acidbacteria (LAB) are the most abundant bacteriaconsumed within regular US diets, with an indi-vidual consumer eating between 106 to 109 livingbacterial cells from various fresh and fermentedfood sources each day. Adding probiotic Lacto-bacillus strains to that mix would provide anopportunity for increasing those numbers con-siderably. However, the study of host-microbeinteractions of ingested probiotic bacteria in theintestine is a relatively new fıeld, much in line

with efforts to understand how the indigenousgut microbiome influences its host. Because Lac-tobacillus species are generally regarded as safefor consumption and do not permanently colo-nize the intestine, studying these bacteria servesas a gateway for investigating transitory host-microbe interactions in the digestive tract. Ulti-mately, doing so will help us to appreciate notonly the microbes on our bodies but also thosethat join us at the dinner table.

The Microbiota of Fermented Foods

The production of fermented foods and bever-ages requires a variety of bacteria, molds, andyeasts. Depending on which foods are being fer-mented and under what conditions, differenttypes of microorganisms tend to proliferate. Be-cause of their metabolic and enzymatic activities,these different microorganisms are mainly re-sponsible for the taste, texture, and aroma prop-erties of the fınal fermented products.

Fermentations can be relatively simple, in-volving only one or two microbial species such asfor yogurt or relatively complex, requiring bothbacterial and fungal populations, sometimes

SUMMARY

➤ Fermented foods and beverages, among the most ancient agriculturalproducts, remain an important part of diets throughout the world.

➤ Although lactic acid bacteria (LAB) may dominate, production of fer-mented foods and beverages depends on a variety of bacteria, molds, andyeasts.

➤ Beyond their direct importance in fermentations, LAB alter foods in waysthat benefit human health.

➤ Probiotics work through three broad mechanisms in the human digestivetract: modifying the indigenous microbiota, stimulating the immune sys-tem, and interacting with the epithelium.

➤ Multiple factors influence Lactobacillus-host interactions within the gastro-intestinal tract.

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growing simultaneously, or in other cases, as withcocoa, in succession. Recent studies using high-throughput DNA sequencing and other methodsshow that even “simple” fermentations can in-volve multiple microbial lineages, contain resi-dent bacteriophages that regulate communitycomposition, undergo elaborate microbial cross-feeding networks, and constitute dynamic habi-tats in which members may compete to succeedone another.

However, even with this breadth of startingmaterials, processing approaches, and microbialcommunity structures, most fermented foods de-pend on LAB, which are saccharolytic membersof the Firmicutes phylum that produce lactic acidand other organic acids as the primary end-prod-ucts of fermentative growth. LAB genera found infoods include Lactobacillus, Leuconostoc, Lacto-coccus, Pediococcus, Weisella, Oenococcus, andCarnobacterium, with Lactobacillus being themost common.

Lactobacillus Is Common in FoodFermentations and Gastrointestinal Tracts

Lactobacillus species are essential agents formaking a variety of plant, dairy, meat, and bever-age products (Fig. 1). Currently, there are 217recognized species of Lactobacillus, and the mostwell-known food-associated species include L.plantarum, L. casei, L. brevis, L. rhamnosus, andL. delbrueckii. A recent genome sequencing effortfocusing on Lactobacillus and other LAB speciesidentifıed more than 44,000 gene families. Thenumber of gene families increased with each ge-nome sequence, indicating that the genetic po-tential has not been completely uncovered forthis genus.

Diversity within the Lactobacillus genus re-flects the assortment of environments fromwhich these species are found. In addition to fer-menting foods, Lactobacillus colonizes humanand animal digestive tracts. Side-by-side with Bi-

FIGURE 1

Popular fermented Western foods involving LAB. LAB are essential for a wide variety of fermented dairy, plant,meat, and beverage products. A representative LAB species responsible for each fermentation type is shown belowthe finished product.

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fıdobacterium, these two genera have been indi-cators of a healthy intestinal microbiome formany years. Lactobacilli typically constituteonly a small fraction (0.1 to 2%) of the totalnumbers of bacteria in the human colon andare thought to be more abundant colonists ofthe small intestine.

Health Benefits of Fermented Foods

Beyond their direct importance in fermenta-tions, LAB alter foods in ways that benefıt humanhealth. For one thing, these bacteria metabolizesugars that are not well tolerated by some humanpopulations. Further, they make organic acidsand antimicrobial peptides that serve as barriersto the growth of spoilage and pathogenic bacteria.LAB fermentations also produce compoundssuch as folic acid or other B vitamins and conju-gated linoleic acid that benefıt consumers.

More recently, experts and consumers in-

creasingly recognize that eating fermented foodsmay help to prevent a variety of chronic diseases.For example, the regular eating of fermenteddairy products is associated with a signifıcantlydecreased risk for developing cardiovascular dis-ease and type II diabetes mellitus. Consumingkimchi, a plant-based fermented food that is astaple in the diet of many Koreans, leads to anincrease in insulin sensitivity and glucose toler-ance in prediabetic adults.

While some fermented foods are pasteurized,roasted, or baked before being consumed, others,such as kimchi and fermented dairy products,serve as a source of living bacteria. These freshlyeaten fermented foods can contain over 1010 LABcells per serving, some of which survive transitthrough the gastrointestinal tract. While suchfood-associated LAB might support humanhealth, the functionality of LAB in the digestivetract is better understood from studies of probi-otic Lactobacillus strains.

FIGURE 2

Factors affecting probiotic function. Factors that might affect probiotic function include the delivery matrixwithin which it is consumed and host factors such as diet, disease status (i.e. gastrointestinal inflammation), age,and genotype.

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Probiotic Lactobacillus

The World Health Organization defınes a probi-otic as a living microorganism that, when con-sumed in suffıcient amounts, confers a healthbenefıt on its host. The term probiotic typically isreserved for specifıc strains investigated in clini-cal studies. However, this defınition can also en-compass bacteria in yogurts that reduce lactoseconcentrations to levels that are acceptable tolactose-intolerant individuals.

Lactobacillus, in particular, are the mostwidely used and best-understood bacteria ap-plied as probiotics for maintaining and improv-ing human health. Some strains of Lactobacillusare effective at preventing and treating antibiotic-associated diarrhea and acute infectious diarrhea,alleviating lactose intolerance, reducing the riskfor necrotizing enterocolitis in infants, and pre-

venting pouchitis, a form of inflammatory boweldisease. Preclinical studies suggest that Lactoba-cillus might also be useful for preventing meta-bolic syndrome, reducing anxiety and depres-sion, reducing atopic disease, and preventingbacterial vaginosis. Although the lactobacillicommonly applied as probiotics are typically dif-ferent from those responsible for fermentingfoods, studies of probiotic strains can help toexplain how dietary LAB might improve condi-tions within the digestive tract as well as systemichealth.

Probiotics work through three broad mecha-nisms in the human digestive tract: modifıcationof the indigenous microbiota composition orfunction, stimulation of the immune system, andinteraction with the epithelium. Beyond thesegeneral functional categories, there remains the

FIGURE 3

Food-microbe and host-microbe interactions of LAB. L. casei BL23 modifies its cell surface composition, increasesfatty acid metabolism, and produces proteins to counter stress during growth in milk. L. lactis KF147 upregulatesgenes for the breakdown of complex plant polysaccharides and heightened oxidative stress resistance duringgrowth on plant tissues. In the small intestine, L. plantarum WCFS1 encounters oxidative stress and metabolizeshost-derived glycans. In the large intestine, L. plantarum modifies its cell surface and secretome, consumes dietarycarbohydrates, and produces alternate fermentation end-products.

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need to study the precise effectors made by pro-biotics and corresponding host pathways that re-spond to them. Thus far, the main Lactobacillusprobiotic effectors are cell surface-associated andsecreted proteins as well as small metabolites andpolysaccharides. Several of these effectors wereshown to bind to receptors on intestinal cells tomodify cell turnover, tight junction protein local-ization, and immune response pathways.

Factors Affecting Probiotic Lactobacillus

Various external factors influence Lactobacillus-host interactions within the gastrointestinal tract(Fig. 2). We are interested in understanding howLAB such as Lactobacillus adapt to and behave infoods and the digestive tract.

For example, dairy products are a natural hab-itat for certain LAB and a common means fordelivering probiotic Lactobacillus in foods. Whencells of L. casei are in milk, we fınd that proteinsfor modifying cell surfaces, metabolizing fatty ac-ids, transporting and metabolizing amino acids,and transport of inorganic ions are abundant(Fig. 3). We fınd that these milk-associated pro-teins enable L. casei to survive in milk also helpcells from this strain to persist in the murineintestine. Remarkably, ingesting L. casei in milkimproves its capacity to reduce inflammatory re-sponses. Such delivery vehicle-dependent differ-ences in probiotic effıcacy might apply to thebehavior of Lactobacillus when delivered to hu-man populations in fermented dairy products.

Other LAB are more commonly consumed in

AUTHOR PROFILE

Marco: from Pickle Making to Backpacking without Cell Phones

Maria Marco’s grandmother made pickles, introducing hergranddaughter early to food microbiology. “I always thoughtit was rather mystical how she took the cucumbers from hergarden and changed them into pickles,” Marco recalls. “It wasonly later that I learned that she was fermenting them.”

Marco’s research focus is on lactic acid bacteria (LAB) atUniversity of California (UC) Davis, where she is an AssociateProfessor in the Department of Food Science and Technology.She and her collaborators investigate the ecology and molec-ular genetics of LAB, which are essential for fermentingfoods. The practical applications of her work, she says, “aremany and include improved and new fermented foodsensory qualities and extending shelf-life,” as well as “im-proved methods for delivery of probiotic Lactobacillus toensure efficacy.”

Marco, 43, the oldest of three children, grew up in Leech-burg, Pa., a small coal mining-steel mill town near Pittsburgh.Her father was in the insurance business, her mother a musicteacher. They encouraged her “to do many different types ofactivities ranging from science camps, gymnastics, competi-tive dancing, art lessons, softball, and concert, marching, andjazz band,” she says. “I really benefited from the exposure toso many different academic and extracurricular activities. Icertainly grew up with the impression that I could do anythingI set my mind to.”

Her high school science teachers had a lasting impact onher career choice, Marco says. “I knew I wanted to studybiology because of my excellent science teachers in highschool. In college, I refined this view and was excited when I

found microbiology and learned about the far-reaching im-pacts of microbes.” She earned her B.S. in microbiology in1995 from the University of Pennsylvania, and her Ph.D., alsoin microbiology, in 2002 from UC Berkeley. While an under-graduate, she studied in Australia, calling that “a transforma-tive time,” she says. “I’m the only one in my family to havemoved away from Pennsylvania. For this reason and my loveof science, I’m the ‘black sheep.’”

Marco is married to Johan Leveau, Associate Professor ofplant pathology at UC Davis, whom she met at Berkeley.Together they moved to the Netherlands, where she startedworking on LAB and probiotics. “The more I learned about thisgroup of bacteria, the more I appreciated my grandmother,whose pickle recipes were never written down but ratherpassed down based on tradition.” She did postdoctoral re-search there from 2002–2005, and between 2006 and 2008she worked as a project manager at NIZO food research inEde, and from 2007–2008 as a project leader at TI Food &Nutrition in nearby Wageningen. That year, she moved to UCDavis, and was promoted in 2015 to associate professor.

Marco and her husband have two sons, 9 and 12. In herspare time, she enjoys staying active but typically is a “soccermom” on the weekends. The family also goes “camping andbackpacking a few times a year,” she says. “The great thing. . .is that there is no cell phone service [and] it forces us to putdown our devices and be in the moment.”

Marlene CimonsMarlene Cimons lives and writes in Bethesda, Md.

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fermented plant foods. To measure how theyadapt for growth on plant tissues, we studiedLactococcus lactis, another LAB commonly foundin fermented foods. Transcript and metabolitelevels of L. lactis after growth in a leaf tissue lysateof Arabidopsis thaliana showed that this LABmetabolizes sucrose, fructose, arabinose, ribose,cellobiose, and hemicellulose (Fig. 3). Cells of L.lactis growing in this plant tissue lysate also ex-press genes encoding enzymes involved in oxida-tive stress pathways and for modifying cell enve-lope composition. Among these plant-induciblegenes is a hybrid nonribosomal protein synthe-tase/polyketide synthase system. Such systemsare responsible for producing secondary metab-olites such as siderophores that can confer highlyspecifıc, plant-dependent traits, and in the case ofL. lactis synthesize a molecule involved in reac-tive oxygen species tolerance, according to ourpreliminary results.

Once ingested, cells of LAB encounter newconditions that influence their behavior. Lacto-bacilli are metabolically active in the intestine,expressing genes that depend on intestinallocation and the health status of the host. Forexample, when residing in the ileum of rhesusmacaques, L. plantarum actively express genesencoding enzymes for degrading host-derivedglycans such as sialic acid. This behavior appearsto be conserved among other bacteria within thesmall intestine because the metatranscriptomesof the indigenous bacteria were also enrichedwith transcripts for fucose, aminosugars, andsialic acid metabolism pathways (Fig. 3).

In contrast, cells of L. plantarum respond dif-ferently when they are within the distal intestine.

In this case, cells of L. plantarum more activelymodify their cell surface composition and pro-duce antimicrobial peptides (Fig. 3). Host dietfurther influences the activity and function of L.plantarum in the distal intestine.Maria L. Marco is an Associate Professor in the Department ofFood Science and Technology, University of California, Davis,and Benjamin L. Golomb received his Ph.D. in 2016 andcurrently is a Scientist at Bayer Crop Science, West Sacramento,Calif.

Suggested Reading

An SY, Lee MS, Jeon JY, et al. 2013. Benefıcial effects offresh and fermented kimchi in prediabetic individu-als. Ann. Nutr. Metab. 63:111–119.

Chilton SN, Burton JP, Reid G. 2015. Inclusion of fer-mented foods in food guides around the world. Nutri-ent 7:390 – 404.

Erkus O, de Jager VCL, Spus M, van Alen-Boerrigter IJ,van Rijswijck IMH, Hazelwood L, Janssen PWM,van Hijum SAFT, Kleerebezem M, Smid EJ. 2013.Multifactorial diversity sustains microbial communitystability. ISME J. 7:2126 –2136.

Golomb BL, Marco ML. 2015. Lactococcus lactis metab-olism and gene expression during growth on planttissues. J. Bacteriol. 197:371–381.

Lee B, Yin X, Griffey SM, Marco ML. 2015. Attenuationof colitis by Lactobacillus casei BL23 is dependent onthe dairy delivery matrix. Appl. Environ. Microbiol.81:6425– 6435.

Marco ML, Tachon S. 2013. Environmental factors influ-encing the effıcacy of probiotic bacteria. Curr. Opin.Biotechnol. 24:207–213.

Sun ZH, Harris HMB, McCann A, et al. 2015. Expand-ing the biotechnology potential of lactobacilli throughcomparative genomics of 213 strains and associatedgenera. Nature Commun. 6:8322.

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