Exploring diversity and functional traits of lactic acid bacteria in traditional vinegar fermentation: A review.

Vinegar has been used for centuries as a food preservative, flavor enhancer, and medicinal agent. While commonly known for its sour taste and acidic properties due to acetic acid bacteria metabolism, vinegar is also home to a diverse community of lactic acid bacteria (LAB). The main genera found during natural fermentation include Lactobacillus, Lacticaseibacillus, Lentilactobacillus, Limosilactbacillus, Leuconostoc, and Pedicoccus. Many of the reported LAB species fulfill the probiotic criteria set by the World Health Organization (WHO). However, it is crucial to acknowledge that LAB viability undergoes a significant reduction during vinegar fermentation. While containing LAB, none of the analyzed vinegar met the minimum viable amount required for probiotic labeling. To fully unlock the potential of vinegar as a probiotic, investigations should be focused on enhancing LAB viability during vinegar fermentation, identifying strains with probiotic properties, and establishing appropriate dosage and consumption guidelines to ensure functional benefits. Currently, vinegar exhibits substantial potential as a postbiotic product, attributed to the high incidence and growth of LAB in the initial stages of the fermentation process. This review aims to identify critical gaps and address the essential requirements for establishing vinegar as a viable probiotic product. It comprehensively examines various relevant aspects, including vinegar processing, total and LAB diversity, LAB metabolism, the potential health benefits linked to vinegar consumption, and the identification of potential probiotic species.

Brazilian artisanal Colonial cheese: characterization, microbiological safety, and survival of Salmonella enterica serovar Enteritidis during ripening.

The artisanal Colonial cheese is typical of the southern region of Brazil and dates back to the colonization by Italian and German immigrants. Produced with raw milk, it is the main cheese produced by more than 15,200 small rural proprieties. The consumer increasingly appraises food with territorial valorization, demanding specific sanitary norms for this type of cheese. This work aimed to know the physical-chemical characteristics of the cheeses produced in the west of Santa Catarina State, to study the ripening time to reach microbiological safety, and to experimentally observe the survival of Salmonella enterica serovar Enteritidis ATCC 13076 during the ripening. The physical-chemical characterization was performed with 129 samples of cheeses. Five dairies were selected for evaluation of the ripening process. Salmonella survival using a challenge test was performed on three batches prepared in a pilot plant. The cheeses were classified as high (15.4%), medium (74.6%), and low moisture (9.2%), and concerning fat content as semi-fat (37.5%) and fat (62.5%). Salmonella challenge test demonstrated their survival for up to 28 days, depending on the initial contamination. The ripening monitoring showed that thermotolerant coliforms could be a good indicator of the process because they are the most persistent microorganisms.

Fine resolution analysis of bacterial communities associated with Neochloris oleoabundans culture and insights into terpenes as contamination control agents.

Biological contamination is one of the main bottlenecks in microalgae production, reducing quality and productivity and sometimes leading to the complete loss of the cultures. Selecting terpenes can be a pathway toward eco-friendly contamination control in microalgae cultures. This work evaluated the presence of bacterial contaminants in N. oleoabundans cultures through HTS and 16 S analysis and their susceptibility to six natural terpenes (α-pinene, ß-pinene, limonene, trans-cinnamaldehyde, linalool, and eugenol). The principal phyla identified were Proteobacteria, Bacteroidetes, and Actinobacteria, and based on these data, 89 bacterial isolates of seven genera were obtained (36 Aureimonas sp., 27 Microbacterium sp., 5 Pseudomonas sp., 9 Bacillus sp., 14 Shinella sp., 1 Brevundimonas sp., and 1 Exiguobacterium sp.) at 25ºC in the presence of light. It was possible to observe that Beta-pinene 50 mg L- 1 only inhibited Bacillus sp. In contrast, Alpha-pinene, Linalool, and Trans-cinnamaldehyde, at a concentration of 6.25 mg L- 1 efficiently inhibited most isolates. The inhibition percentages found were 79-99%.

Emerging contaminants bioremediation by enzyme and nanozyme-based processes - A review.

Due to their widespread occurrence and the inadequate removal efficiencies by conventional wastewater treatment plants, emerging contaminants (ECs) have recently become an issue of great concern. Current ongoing studies have focused on different physical, chemical, and biological methods as strategies to avoid exposing ecosystems to significant long-term risks. Among the different proposed technologies, the enzyme-based processes rise as green biocatalysts with higher efficiency yields and lower generation of toxic by-products. Oxidoreductases and hydrolases are among the most prominent enzymes applied for bioremediation processes. The present work overviews the state of the art of recent advances in enzymatic processes during wastewater treatment of EC, focusing on recent innovations in terms of applied immobilization techniques, genetic engineering tools, and the advent of nanozymes. Future trends in the enzymes immobilization techniques for EC removal were highlighted. Research gaps and recommendations on methods and utility of enzymatic treatment incorporation in conventional wastewater treatment plants were also discussed.

Enhancing the Recovery of Bioactive Compounds of Soybean Fermented with Rhizopus oligosporus Using Supercritical CO2: Antioxidant, Anti-Inflammatory, and Oxidative Proprieties of the Resulting Extract.

The aim of the present study was to evaluate the use of supercritical CO2 combined with cosolvent for the recovery of bioactive compounds of soybean fermented with Rhizopus oligosporus NRRL 2710. Soxhlet extractions using seven different organic solvents (n-hexane, petroleum ether, ethyl acetate, acetone, ethanol, methanol, and water) were initially performed for comparative purposes. The extracts obtained were characterized by physicochemical, antioxidant, total phenolic, and oxidative proprieties. For the Soxhlet extractions, the highest and lowest yields obtained were 45.24% and 15.56%, using methanol and hexane, respectively. The extraction using supercritical CO2 combined with ethanol as a static modifier (scCO2 + EtOH) presented, at a high pressure (25 MPa) and temperature (80 °C), a phenolic compound content of 1391.9 µg GAE g-1 and scavenging of 0.17 g, reaching a 42.87% yield. The extracts obtained by sCO2 + EtOH were characterized by high contents of essential fatty acids (linoleic acid and oleic acid) and bioactive compounds (gallic acid, trans-cinnamic acid, daidzein, and genistein). These extracts also showed a great potential for inhibiting hyaluronidase enzymes (i.e., anti-inflammatory activity). Thermogravimetric analyses of the samples showed similar profiles, with oil degradation values in the range from 145 to 540 °C, indicating progressive oil decomposition with a mass loss ranging from 93 to 98.7%. In summary, this study demonstrated the flexibility of scCO2 + EtOH as a green technology that can be used to obtain high-value-added products from fermented soybean.

What Is Candida Doing in My Food? A Review and Safety Alert on Its Use as Starter Cultures in Fermented Foods.

The use of yeasts as starter cultures was boosted with the emergence of large-scale fermentations in the 20th century. Since then, Saccharomyces cerevisiae has been the most common and widely used microorganism in the food industry. However, Candida species have also been used as an adjuvant in cheese production or as starters for coffee, cocoa, vegetable, meat, beer, and wine fermentations. A thorough screening of candidate Candida is sometimes performed to obtain the best performing strains to enhance specific features. Some commonly selected species include C. pulcherrima (teleomorph Metschnikowia pulcherrima) (wine), C. parapsilosis (teleomorph Monilia parapsilosis) (coffee), C. famata (teleomorph Debaryomyces hansenii) (cheese), and C. zeylanoides (teleomorph Kurtzmaniella zeylanoides) and C. norvegensis (teleomorph Pichia norvegensis) (cocoa). These species are associated with the production of key metabolites (food aroma formation) and different enzymes. However, safety-associated selection criteria are often neglected. It is widely known that some Candida species are opportunistic human pathogens, with important clinical relevance. Here, the physiology and metabolism of Candida species are addressed, initially emphasizing their clinical aspects and potential pathogenicity. Then, Candida species used in food fermentations and their functional roles are reported. We recommended that Candida not be used as food cultures if safety assessments are not performed. Some safety features are highlighted to help researchers choose methods and selection criteria.

Fermented Soy Products and Their Potential Health Benefits: A Review.

In the growing search for therapeutic strategies, there is an interest in foods containing natural antioxidants and other bioactive compounds capable of preventing or reversing pathogenic processes associated with metabolic disease. Fermentation has been used as a potent way of improving the properties of soybean and their components. Microbial metabolism is responsible for producing the ß-glucosidase enzyme that converts glycosidic isoflavones into aglycones with higher biological activity in fermented soy products, in addition to several end-metabolites associated with human health development, including peptides, phenolic acids, fatty acids, vitamins, flavonoids, minerals, and organic acids. Thus, several products have emerged from soybean fermentation by fungi, bacteria, or a combination of both. This review covers the key biological characteristics of soy and fermented soy products, including natto, miso, tofu, douchi, sufu, cheonggukjang, doenjang, kanjang, meju, tempeh, thua-nao, kinema, hawaijar, and tungrymbai. The inclusion of these foods in the diet has been associated with the reduction of chronic diseases, with potential anticancer, anti-obesity, antidiabetic, anticholesterol, anti-inflammatory, and neuroprotective effects. These biological activities and the recently studied potential of fermented soybean molecules against SARS-CoV-2 are discussed. Finally, a patent landscape is presented to provide the state-of-the-art of the transfer of knowledge from the scientific sphere to the industrial application.

Understanding the Effects of Self-Induced Anaerobic Fermentation on Coffee Beans Quality: Microbiological, Metabolic, and Sensory Studies.

In this study, an investigation of the microbial community structure and chemical changes in different layers of a static coffee beans fermentation tank (named self-induced anaerobic fermentation-SIAF) was conducted at different times (24, 48, and 72 h). The microbial taxonomic composition comprised a high prevalence of Enterobacteriaceae and Nectriaceae and low prevalence of lactic acid bacteria and yeast, which greatly differs from the traditional process performed in open tanks. No major variation in bacterial and fungal diversity was observed between the bottom, middle, and top layers of the fermentation tank. On the other hand, the metabolism of these microorganisms varied significantly, showing a higher consumption of pulp sugar and production of metabolites in the bottom and middle layers compared to the top part of the fermentation tank. Extended processes (48 and 72 h) allowed a higher production of key-metabolites during fermentation (e.g., 3-octanol, ethyl acetate, and amyl acetate), accumulation in roasted coffee beans (acetic acid, pyrazine, methyl, 2-propanone, 1-hydroxy), and diversification of sensory profiles of coffee beverages compared to 24 h of fermentation process. In summary, this study demonstrated that SIAF harbored radically different dominant microbial groups compared to traditional coffee processing, and diversification of fermentation time could be an important tool to provide coffee beverages with novel and desirable flavor profiles.

Bioprospecting lipid-producing microorganisms: From metagenomic-assisted isolation techniques to industrial application and innovations.

Traditionally, lipid-producing microorganisms have been obtained via conventional bioprospecting based on isolation and screening techniques, demanding time and effort. Thus, high-throughput sequencing combined with conventional microbiological approaches has emerged as an advanced and rapid strategy for recovering novel oleaginous microorganisms from target environments. This review highlights recent developments in lipid-producing microorganism bioprospecting, following (i) from traditional cultivation techniques to state-of-the-art metagenomics approaches; (ii) related topics on workflow, next-generation sequencing platforms, and knowledge bioinformatics; and (iii) biotechnological potential of the production of docosahexaenoic acid (DHA) by Aurantiochytrium limacinum, arachidonic acid (ARA) by Mortierella alpina and biodiesel by Rhodosporidium toruloides. These three species have been shown to be highly promising and studied in research articles, patents and commercialized products. Trends, innovations and future perspectives of these microorganisms are also addressed. Thus, these microbial lipids allow the development of food, feed and biofuels as alternative solutions to animal and vegetable oils.

Agro-industrial wastewater in a circular economy: Characteristics, impacts and applications for bioenergy and biochemicals.

The generation of agroindustrial byproducts is rising fast worldwide. The slaughter of animals, the production of bioethanol, and the processing of oil palm, cassava, and milk are industrial activities that, in 2019, generated huge amounts of wastewaters, around 2448, 1650, 256, 85, and 0.143 billion liters, respectively. Thus, it is urgent to reduce the environmental impact of these effluents through new integrated processes applying biorefinery and circular economy concepts to produce energy or new products. This review provides the characteristics of some of the most important agro-industrial wastes, including their physicochemical composition, worldwide average production, and possible environmental impacts. In addition, some alternatives for reusing these materials are addressed, focusing mainly on energy savings and the possibilities of generating value-added products. Finally, this review considers recent research and technological innovations and perspectives for the future.

Detection of Enteric Viruses and Core Microbiome Analysis in Artisanal Colonial Salami-Type Dry-Fermented Sausages from Santa Catarina, Brazil.

Microbial fermentation plays an important role in the manufacturing of artisanal sausages and can have major effects on product quality and safety. We used metagenomics and culture-dependent methods to study the presence of Hepatitis E virus (HEV) and Rotavirus-A (RV-A), and fungal and bacterial communities, in artisanal Colonial salami-type dry-fermented sausages in Santa Catarina state, Brazil. Lactic acid bacteria (LAB) and yeast dominated the microbiome. Latilactobacillus sakei and Debaryomyces hansenii were ubiquitous and the most abundant species. The DNA of some foodborne pathogens was found in very low concentrations although viable cells of most of these species were undetectable by cultivation methods. The characteristics of the raw material and hygiene of the artisanal sausage manufacturing process resulted in high loads of beneficial microorganisms and the absence of HEV and RV-A viruses as determined by RT-qPCR assays. In conclusion, high LAB load in sausages was more relevant to preventing pathogen growth than the ripening time and/or physicochemical characteristics. However, the presence of Clostridium spp. and other pathogens in some samples must be taken into account for the development of future preservation methods; appropriate LAB starter cultures and health surveillance are required in the production process to prevent foodborne outbreaks.

Integrating metagenetics and high-throughput screening for bioprospecting marine thraustochytrids producers of long-chain polyunsaturated fatty acids.

Omega-3 produced by marine thraustochytrids has appeared as an alternative to fish oil and an eco-friendly solution to overfishing. Herein, an integrative analysis of metagenetics and high-throughput screening was used for bioprospecting marine thraustochytrids from southern Brazil mangrove and coastal seawater. All sampled environments showed biodiversity and abundance of SAR clade. Environmental samples detected with potential lipid-accumulating labyrinthulomycetes were further processed for direct plating and pollen baiting isolation. Microtiter plate system and fluorescence spectroscopy were combined for high-throughput screening of 319 isolates to accumulate lipids. Twenty isolates were selected for submerged cultivation and lipid characterization. Among them, B36 isolate, identified as Aurantiochytrium sp. by 18s rRNA sequencing, achieved the highest biomass (25.60 g/l CDW) and lipids (17.12 g/l CDW). This lipid content had a high biological value with 44.37% LC-PUFAs and 34.6% DHA, which can be used as a sustainable source in vegan, seafood-free and animal feed diets.

Viruses in fermented foods: are they good or bad? Two sides of the same coin.

The emergence of Coronavirus disease 2019 as a global pandemic has increased popular concerns about diseases caused by viruses. Fermented foods containing high loads of viable fungi and bacteria are potential sources for virus contamination. The most common include viruses that infect bacteria (bacteriophage) and yeasts reported in fermented milks, sausages, vegetables, wine, sourdough, and cocoa beans. Recent molecular studies have also associated fermented foods as vehicles for pathogenic human viruses. Human noroviruses, rotavirus, and hepatitis virus have been identified in different fermented foods through multiple routes. No severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) virus or close members were found in fermented foods to date. However, the occurrence/persistence of other pathogenic viruses reveals a potential vulnerability of fermented foods to SARS-CoV-2 contamination. On the other side of the coin, some bacteriophages are being suggested for improving the fermentation process and food safety, as well as owing potential probiotic properties in modern fermented foods. This review will address the diversity and characteristics of viruses associated with fermented foods and what has been changed after a short introduction to the most common next-generation sequencing platforms. Also, the risk of SARS-CoV-2 transmission via fermented foods and preventive measures will be discussed.

Facility-specific 'house' microbiome ensures the maintenance of functional microbial communities into coffee beans fermentation: implications for source tracking.

This work aimed at studying the unconfirmed hypothesis predicting the existence of a connection between coffee farm microbiome and the resulting spontaneous fermentation process. Using Illumina-based amplicon sequencing, 360 prokaryotes and 397 eukaryotes were identified from coffee fruits and leaves, over-ripe fruits, water used for coffee de-pulping, depulped coffee beans, soil, and temporal fermentation samples at an experimental farm in Honduras. Coffee fruits and leaves were mainly associated with high incidence of Enterobacteriaceae, Pseudomonas, Colletotrichum, and Cladosporium. The proportion of Enterobacteriaceae was increased when leaves and fruits were collected on the ground compared to those from the coffee tree. Coffee farm soil showed the richest microbial diversity with marked presence of Bacillus. Following the fermentation process, microorganisms present in depulped coffee beans (Leuconostoc, Gluconobater, Pichia, Hanseniaspora, and Candida) represented more than 90% of the total microbial community, which produced lactic acid, ethanol, and several volatile compounds. The community ecology connections described in this study showed that coffee fruit provides beneficial microorganisms for the fermentation process. Enterobacteria, Colletotrichum, and other microbial groups present in leaves, fruit surface, over-ripe fruits, and soil may transfer unwanted aromas to coffee beans, so they should be avoided from having access to the fermentation tank.

Phytochemical analysis and biological activities of in vitro cultured Nidularium procerum, a bromeliad vulnerable to extinction.

This study reports the first phytochemical and biological characterization in treatment of adrenocortical carcinoma cells (H295R) of extracts from Nidularium procerum, an endemic bromeliad of Atlantic Forest vulnerable to extinction. Extracts of dry leaves obtained from in vitro-grown plants were recovered by different extraction methods, viz., hexanoic, ethanolic, and hot and cold aqueous. Chromatography-based metabolite profiling and chemical reaction methods revealed the presence of flavonoids, steroids, lipids, vitamins, among other antioxidant and antitumor biomolecules. Eicosanoic and tricosanoic acids, α-Tocopherol (vitamin E) and scutellarein were, for the first time, described in the Nidularium group. Ethanolic and aqueous extracts contained the highest phenolic content (107.3 mg of GAE.100 g-1) and 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH) radical scavenging activity, respectively. The immunomodulatory and antitumoral activities of aqueous extracts were assessed using specific tests of murine macrophages modulation (RAW 264.7) and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay against adrenocortical carcinoma cell line, respectively. The aqueous extract improved cell adhesion and phagocytic activities and phagolysossomal formation of murine macrophages. This constitutes new data on the Bromeliaceae family, which should be better exploited to the production of new phytomedicines for pharmacological uses.

A comparative study of extraction techniques for maximum recovery of bioactive compounds from Ganoderma lucidum spores / Estudio comparativo de técnicas de extracción para la máxima recuperación de compuestos bioactivos a partir esporas de Ganoderma lucidum

SUMMARY This study aimed at evaluating effective methods for breaking the hard and insoluble spores of Ganoderma lucidum to recover functional biomolecules. Rupture techniques were evaluated such as manual maceration (RM), maceration with spheres of various materials (BR), and microwave exposure plus maceration with steel/ chrome spheres (MBR1). Spore rupture was evaluated using UV-Vis spectroscopy, which showed vibrations of 2955, 1642, 1240, 1080 and 1746 cm-1 corresponding to changes in spore walls. The MBR1 extract contained the largest amounts of carbohydrates (19.80 mg.g-1 spores) and polyphenols (2.21 mg.g-1 spores), whereas the BR extract had higher antioxidant activity (57.22%Inb DPPH). The MBR1 and BR extracts contained 62.2 and 73.5% glucose, respectively. Both methods also involved significant extraction of carbohydrates and proteins. The best way to extract biomolecules from spore walls is to perform a microwave heat treatment and break the walls with steel/chrome spheres; this produces large quantities of carbohydrates with antioxidant properties.

RESUMEN El objetivo de este estudio fue evaluar varios métodos de ruptura de las esporas de Ganoderma lucidum y extraer sus propiedades bioactivas. Para este propósito se evaluaron diferentes técnicas de rompimiento como: la maceración manual (RM), la maceración con esferas de diversos materiales (BR) y la exposición a microondas junto la maceración de las esporas con esferas de acero/cromo (MBR1). La ruptura de las esporas fue evaluada por espectroscopia UV-Vis, la cual mostró que las vibraciones 2955, 1642, 1240, 1080 y 1746 cm-1 correspondieron a cambios estructurales en las paredes de las esporas. El extracto MBR1 presento el mayor contenido de carbohidratos (19,80 mg.g-1) y polifenoles (2,21 mg.g-1), mientras que el extracto BR tuvo una mayor actividad antioxidante (57,22% Inb DPPH). Los extractos MBR1 y BR también presentaron en el análisis de monosacáridos un 62,2 y 73,5% de contenido glucosa. Como conclusión la mejor metodología para extraer biomoléculas de las paredes de las esporas de G. lucidum fueron el tratamiento térmico con microondas y la ruptura de las paredes con esferas de acero/cromo, porque este proceso permitió la extracción de una mayor cantidad de carbohidratos con posibles propiedades antioxidantes.

Microalgal biomass pretreatment for integrated processing into biofuels, food, and feed.

Microalgae are sources of nutritional products and biofuels. However, their economical processing is challenging, because of (i) the inherently low concentration of biomass in algal cultures, below 0.5%, (ii) the high-water content in the harvested biomass, above 70%; and (iii) the variable intracellular content and composition. Cell wall structure and strength vary enormously among microalgae, from naked Dunaliella cells to robust Haematococcus cysts. High-value products justify using fast and energy-intensive processes, ranging from 0.23 kWh/kg dry biomass in high-pressure homogenization, to 6 kWh/kg dry biomass in sonication. However, in biofuels production, the energy input must be minimized, requiring slower, thermal or chemical pretreatments. Whichever the primary fraction of interest, the spent biomass can be processed into valuable by-products. This review discusses microalgal cell structure and composition, how it affects pretreatment, focusing on technologies tested for large scale or promising for industrial processes, and how these can be integrated into algal biorefineries.

How to select a probiotic? A review and update of methods and criteria.

International competition within the dairy market and increasing public awareness about the importance of functional food consumption are providing new challenges for innovation in the probiotic sector. In this context, countless references are currently dedicated to the selection and characterization of new species and more specific strains of probiotic bacteria. In general, these studies adopt basic selection criteria established by the World Health Organization (WHO), including host-associated stress resistance, epithelium adhesion ability, and antimicrobial activity. These aspects are applied to ensure that the candidate probiotic could withstand the stressful conditions of the human digestive system and exert functional proprieties. However, it cannot be assumed that these novel microbial strains are capable of offering several biological benefits attributed to probiotics. Additionally, safety-associated selection criteria, such as plasmid-associated antibiotic resistance spreading and enterotoxin production, are often neglected. This article reviews the recent developments in the processes, strategies, and methods, such as anticarcinogenic, antidepression, antianxiety, antiobesity, antidiabetic, immunostimulatory, and cholesterol-lowering assessments, to select probiotic strains with the ultimate objective of assisting future probiotic microbe evaluation studies.

Microbiological, biochemical, and functional aspects of sugary kefir fermentation - A review.

Sugary kefir beverage is produce by fermenting raw sugar solution with kefir grains, the latter consisting of polysaccharide and microorganisms. This beverage, with great consumption in countries such as USA, Japan, France, and Brazil, represents a promising market to functional cultured drinks. This paper reviews the microbial diversity and interaction, kinetics, safety, and bioactivities of sugary kefir fermentation. The literature reviewed here demonstrates that sugary kefir possesses a similar microbial association relative to traditional milk kefir fermentation, especially among lactic acid bacteria and yeast species, such as Lactobacillus, Leuconostoc, Kluyveromyces, Pichia, and Saccharomyces. However, a selective pressure at species level is generally observed, as, for example, the stimulation of Saccharomyces species metabolism, leading to a high content of alcohol in the final product. This also seems to stimulate the growth of acetic acid bacteria that benefit of increased ethanol production to acetic acid metabolism. Existing reports have suggested important bioactivities associated with sugary kefir beverage consumption, such as antimicrobial, antiedematogenic, anti-inflammatory, antioxidant, cicatrizing, and healing activities. Other alternative non-dairy substrates, such as fruits, vegetables, and molasses, have also been tested for adaptation of kefir grains and production of functional beverages with distinct sensory characteristics. This diversification is of crucial importance for the production of new probiotic products to provide people with special needs (lactose intolerance) and vegan consumers.

Potential applications of plant probiotic microorganisms in agriculture and forestry.

Agriculture producers, pushed by the need for high productivity, have stimulated the intensive use of pesticides and fertilizers. Unfortunately, negative effects on water, soil, and human and animal health have appeared as a consequence of this indiscriminate practice. Plant probiotic microorganisms (PPM), also known as bioprotectants, biocontrollers, biofertilizers, or biostimulants, are beneficial microorganisms that offer a promising alternative and reduce health and environmental problems. These microorganisms are involved in either a symbiotic or free-living association with plants and act in different ways, sometimes with specific functions, to achieve satisfactory plant development. This review deals with PPM presentation and their description and function in different applications. PPM includes the plant growth promoters (PGP) group, which contain bacteria and fungi that stimulate plant growth through different mechanisms. Soil microflora mediate many biogeochemical processes. The use of plant probiotics as an alternative soil fertilization source has been the focus of several studies; their use in agriculture improves nutrient supply and conserves field management and causes no adverse effects. The species related to organic matter and pollutant biodegradation in soil and abiotic stress tolerance are then presented. As an important way to understand not only the ecological role of PPM and their interaction with plants but also the biotechnological application of these cultures to crop management, two main approaches are elucidated: the culture-dependent approach where the microorganisms contained in the plant material are isolated by culturing and are identified by a combination of phenotypic and molecular methods; and the culture-independent approach where microorganisms are detected without cultivating them, based on extraction and analyses of DNA. These methods combine to give a thorough knowledge of the microbiology of the studied environment.