Probiotics: Selection, Cultivation, Evaluation and Application

A special issue of Foods (ISSN 2304-8158). This special issue belongs to the section "Food Microbiology".

Deadline for manuscript submissions: closed (30 April 2024) | Viewed by 29509

Special Issue Editors


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Guest Editor
Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
Interests: probiotics; lactic acid bacteria; gut microbiota; next-generation sequencing; health function

E-Mail Website
Guest Editor
Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
Interests: probiotics; lactic acid bacteria; exopolysaccharides; gut microbiota; short-chain fatty acid

Special Issue Information

Dear Colleagues,

The FAO/WHO committee has since defined ‘probiotics’ as a unique group of microbes that confer a range of health benefits on their hosts when consumed. Since then, several studies have investigated the in vitro and in vivo activities of various lactic and non-lactic acid-producing bacteria. There are several factors that researchers in the food and allied sectors use to screen probiotic candidates—antimicrobial protocols, tolerance assays, EPS production, DPPH-IV inhibition, among others. It is noted that some studies have reported conflicting findings, which have prompted further investigations. Probiotics have been recognized to play important roles in health and industry for several years. These include direct and indirect uses such as cholesterol-lowering, anti-inflammatory, and anti-oxidative properties. In addition, the use of molecular tools like next-generation sequencing (NGS) holds great potential in unlocking and understanding the immense possibilities that these sensational microorganisms have. 

Dr. Guicheng Huo
Dr. Bailiang Li
Guest Editors

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Keywords

  • probiotics
  • selection
  • cultivation
  • evaluation
  • application
  • next-generation sequencing

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Published Papers (10 papers)

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Research

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14 pages, 4641 KiB  
Article
Oral Administration of Lactiplantibacillus plantarum CCFM8661 Alleviates Dichlorvos-Induced Toxicity in Mice
by Weiwei Ma, Yiyang Zhao, Hang Sun, Ziwei Zhang and Lili Huang
Foods 2024, 13(19), 3211; https://doi.org/10.3390/foods13193211 - 9 Oct 2024
Viewed by 1106
Abstract
Dichlorvos (DDVP) is an organophosphorus pesticide commonly used in agriculture for pest control, which may enter the organism from the food chain and cause harm. This study aimed to investigate the mitigation effect of Lactiplantibacillus plantarum CCFM8661 (a strain of the bacteria) on [...] Read more.
Dichlorvos (DDVP) is an organophosphorus pesticide commonly used in agriculture for pest control, which may enter the organism from the food chain and cause harm. This study aimed to investigate the mitigation effect of Lactiplantibacillus plantarum CCFM8661 (a strain of the bacteria) on DDVP toxicity. Sixty male mice were randomly divided into five groups including control (saline), model (DDVP), low-dose, medium-dose, and high-dose groups, and alleviating effect was evaluated by determining body weight, pesticide residues, oxidative stress, and inflammation, and by histological analysis. The results showed that compared with the model group, body weight and acetylcholinesterase activity, and SOD, CAT, T-AOC, and GSH levels significantly increased, and serum DDVP content, MDA level, IL-1β, and TNF-α significantly decreased after administration of the L. plantarum CCFM8661. The study demonstrated that L. plantarum CCFM8661 exhibited a significant detoxification effect on pesticide toxicity in mice, providing a theoretical basis for the application of probiotics in mitigating pesticide-induced damage. Full article
(This article belongs to the Special Issue Probiotics: Selection, Cultivation, Evaluation and Application)
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18 pages, 2293 KiB  
Article
Goat Cheese Produced with Sunflower (Helianthus annuus L.) Seed Extract and a Native Culture of Limosilactobacillus mucosae: Characterization and Probiotic Survival
by Osíris Cordeiro Lima Guimarães, Viviane Maria da Silva Quirino, Alícia Santos de Moura, Joyceana Oliveira Correia, João Ricardo Furtado, Isanna Menezes Florêncio, Márcia Maria Cândido da Silva, Hévila Oliveira Salles, Karina Maria Olbrich dos Santos, Antonio Silvio do Egito and Flávia Carolina Alonso Buriti
Foods 2024, 13(18), 2905; https://doi.org/10.3390/foods13182905 - 13 Sep 2024
Viewed by 1277
Abstract
The microbiological and biochemical properties of a goat cheese produced using Helianthus annuus (sunflower) seed extract as a coagulant and the potentially probiotic autochthonous culture Limosilactobacillus mucosae CNPC007 were examined in comparison to a control cheese devoid of the autochthonous culture. Throughout a [...] Read more.
The microbiological and biochemical properties of a goat cheese produced using Helianthus annuus (sunflower) seed extract as a coagulant and the potentially probiotic autochthonous culture Limosilactobacillus mucosae CNPC007 were examined in comparison to a control cheese devoid of the autochthonous culture. Throughout a 60-day storage period at 6 ± 1 °C, lactobacilli maintained a count of above 8 log CFU/g. Additionally, its viability in cheeses subjected to the in vitro gastrointestinal conditions demonstrated improvement over this period. Specifically, the recovery of lactobacilli above 6 log CFU/g was observed in 16.66% of the samples in the first day, increasing to 66.66% at both 30 and 60 days. While total coliforms were detected in both cheese trials, this sanitary parameter exhibited a decline in L. mucosae cheeses during storage, falling below the method threshold (<3 MPN/g) at 60 days. This observation suggests a potential biopreservative effect exerted by this microorganism, likely attributed to the higher acidity of L. mucosae cheeses at that point (1.80 g/100 g), which was twice that of the control trial (0.97 g/100 g). Furthermore, distinct relative proportions of >30 kDa, 30–20 kDa, and <20 kDa proteins during storage was verified for L. mucosae and control cheeses. Consequently, either the H. annuus seed extract or the L. mucosae CNPC007 autochthonous culture influenced the biochemical properties of the cheese, particularly in terms of proteolysis. Moreover, L. mucosae CNPC007 acidification property resulted in a biopreservative effect throughout the storage period, indicating the potential as a promising source of probiotics for this product. Full article
(This article belongs to the Special Issue Probiotics: Selection, Cultivation, Evaluation and Application)
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16 pages, 2788 KiB  
Article
Genome- and Toxicology-Based Safety Assessment of Probiotic Akkermansia muciniphila ONE Isolated from Humans
by Na Lv, Caiping Wang, Hongtao Zhou, Xin Ma, Xueping Yu and Dayong Ren
Foods 2024, 13(13), 1979; https://doi.org/10.3390/foods13131979 - 24 Jun 2024
Cited by 4 | Viewed by 1674
Abstract
In this study, the genome of Akkermansia muciniphila ONE (designated AKK ONE) was sequenced, assembled, and analyzed. In addition, the safety of this strain was further evaluated by toxicological studies. The results showed that the AKK ONE genome is contained on a single [...] Read more.
In this study, the genome of Akkermansia muciniphila ONE (designated AKK ONE) was sequenced, assembled, and analyzed. In addition, the safety of this strain was further evaluated by toxicological studies. The results showed that the AKK ONE genome is contained on a single chromosome with a total length of 2,817,524 bp and an average GC content of 55.48%. In total, 2411, 1131, 1168, 1745, and 1402 genes were annotated to the NR, GO, KEGG, COG, and SwissProt database, respectively. Potential resistance genes, adeF, tetW, ANT(3″)-IIa, and aadA1 were detected. AKK ONE was sensitive to ampicillin, ceftriaxone, cefotaxime, meropenem, tetracycline, and chloramphenicol and resistant to moxifloxacin. No potential virulence-related genes were detected. The PathogenFinder database analysis showed that AKK ONE was a non-potential human pathogen. This strain had good gastroenteric fluid tolerance and a weak ability to colonize the gut. No test item-related adverse effects were observed in the acute and subchronic toxicity test. AKK ONE did not display mutagenic activity either. This strain did not change the hematological and clinical biochemical parameters of mice. The weights of the organs were not affected by AKK ONE treatment. These results support that AKK ONE is safe for use as a probiotic at a dose of 8.28 × 109 CFU/kg bw/day. Full article
(This article belongs to the Special Issue Probiotics: Selection, Cultivation, Evaluation and Application)
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13 pages, 10946 KiB  
Article
Polyphenols from Foxtail Millet Improve Non-Alcoholic Fatty Liver Disease by Regulating Intestinal Microbiome in Mice
by Israr Ghani, Yuxuan An, Qinqin Qiao, Shuiling He and Zhuoyu Li
Foods 2024, 13(11), 1683; https://doi.org/10.3390/foods13111683 - 27 May 2024
Cited by 4 | Viewed by 2788
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common chronic hepatic manifestation of metabolic dysfunction for which effective interventions are lacking. The burden of NAFLD is increasing at an alarming rate. NAFLD is frequently associated with morbidities such as dyslipidemia, type 2 diabetes [...] Read more.
Non-alcoholic fatty liver disease (NAFLD) is the most common chronic hepatic manifestation of metabolic dysfunction for which effective interventions are lacking. The burden of NAFLD is increasing at an alarming rate. NAFLD is frequently associated with morbidities such as dyslipidemia, type 2 diabetes mellitus and obesity, etc. The current study explored the potential role of bound polyphenols from foxtail millet (BPIS) in treating mice with NAFLD induced by a high-fat diet (HFD). The results indicated the critical role of BPIS in treating NAFLD by effectively restoring the gut microbiota in C57BL/6 mice that received a high-fat diet (HFD) for 12 weeks. At the same time, 16S rRNA analysis demonstrated that BPIS remodeled the overall structure of the gut microbiota from fatty liver diseases towards that of normal counterparts, including ten phylum and twenty genus levels. Further study found that the expression of tight junction proteins was upregulated in the BPIS-treated group. This study provides new insights into the potential NAFLD protective effects induced by polyphenols of foxtail millet. Full article
(This article belongs to the Special Issue Probiotics: Selection, Cultivation, Evaluation and Application)
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21 pages, 9242 KiB  
Article
Characterization of Genomic, Physiological, and Probiotic Features of Lactiplantibacillus plantarum JS21 Strain Isolated from Traditional Fermented Jiangshui
by Yang Liu, Shanshan Wang, Ling Wang, Hongzhao Lu, Tao Zhang and Wenxian Zeng
Foods 2024, 13(7), 1082; https://doi.org/10.3390/foods13071082 - 1 Apr 2024
Cited by 7 | Viewed by 2674
Abstract
This study aimed to understand the genetic and metabolic traits of a Lactiplantibacillus plantarum JS21 strain and its probiotic abilities through laboratory tests and computer analysis. L. plantarum JS21 was isolated from a traditional fermented food known as “Jiangshui” in Hanzhong city. In [...] Read more.
This study aimed to understand the genetic and metabolic traits of a Lactiplantibacillus plantarum JS21 strain and its probiotic abilities through laboratory tests and computer analysis. L. plantarum JS21 was isolated from a traditional fermented food known as “Jiangshui” in Hanzhong city. In this research, the complete genetic makeup of JS21 was determined using Illumina and PacBio technologies. The JS21 genome consisted of a 3.423 Mb circular chromosome and five plasmids. It was found to contain 3023 protein-coding genes, 16 tRNA genes, 64 rRNA operons, 40 non-coding RNA genes, 264 pseudogenes, and six CRISPR array regions. The GC content of the genome was 44.53%. Additionally, the genome harbored three complete prophages. The evolutionary relationship and the genome collinearity of JS21 were compared with other L. plantarum strains. The resistance genes identified in JS21 were inherent. Enzyme genes involved in the Embden–Meyerhof–Parnas (EMP) and phosphoketolase (PK) pathways were detected, indicating potential for facultative heterofermentative pathways. JS21 possessed bacteriocins plnE/plnF genes and genes for polyketide and terpenoid assembly, possibly contributing to its antibacterial properties against Escherichia coli (ATCC 25922), Escherichia coli (K88), Staphylococcus aureus (CMCC 26003), and Listeria monocytogenes (CICC 21635). Furthermore, JS21 carried genes for Na+/H+ antiporters, F0F1 ATPase, and other stress resistance genes, which may account for its ability to withstand simulated conditions of the human gastrointestinal tract in vitro. The high hydrophobicity of its cell surface suggested the potential for intestinal colonization. Overall, L. plantarum JS21 exhibited probiotic traits as evidenced by laboratory experiments and computational analysis, suggesting its suitability as a dietary supplement. Full article
(This article belongs to the Special Issue Probiotics: Selection, Cultivation, Evaluation and Application)
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13 pages, 6427 KiB  
Article
Systematic Investigation of the Effect of Lactobacillus acidophilus TW01 on Potential Prevention of Particulate Matter (PM)2.5-Induced Damage Using a Novel In Vitro Platform
by Sioumin Luo and Mingju Chen
Foods 2023, 12(17), 3278; https://doi.org/10.3390/foods12173278 - 1 Sep 2023
Cited by 1 | Viewed by 3318
Abstract
Exposure to ambient particulate matter (PM) and cigarette smoking (CS) is a risk factor for respiratory/lung infections and metabolic disorders. Lung–gut axis disruption involving the upregulation of oxidative stress, systemic inflammation, and gut barrier dysfunction by PM is one of the potential mechanisms. [...] Read more.
Exposure to ambient particulate matter (PM) and cigarette smoking (CS) is a risk factor for respiratory/lung infections and metabolic disorders. Lung–gut axis disruption involving the upregulation of oxidative stress, systemic inflammation, and gut barrier dysfunction by PM is one of the potential mechanisms. Thus, we designed a novel in vitro platform for pre-selecting probiotics with potentially protective effects against PM-induced lung damage through the lung–gut axis to reduce animal usage. The results showed that a high dose of Lactobacillus acidophilus TW01 (1 × 108 CFU/mL) inhibited reactive oxygen species (ROS) production. This strain could also reduce respiratory epithelial cell death induced by cigarette smoke extraction (CSE), as well as promoting Caco-2 cell migration in 1 × 106 CFU/mL. Although further animal experiments are needed to validate the in vitro findings, L. acidophilus TW01 is a promising probiotic strain for the potential prevention of PM2.5-induced damage. Full article
(This article belongs to the Special Issue Probiotics: Selection, Cultivation, Evaluation and Application)
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16 pages, 3045 KiB  
Article
Genome Analysis of Bifidobacterium Bifidum E3, Structural Characteristics, and Antioxidant Properties of Exopolysaccharides
by Yingxue Yue, Yuqi Wang, Yu Han, Yifan Zhang, Ting Cao, Guicheng Huo and Bailiang Li
Foods 2023, 12(16), 2988; https://doi.org/10.3390/foods12162988 - 8 Aug 2023
Cited by 11 | Viewed by 2385
Abstract
In this study, the antioxidant properties of intact cells (IC), cell-free supernatant (CFS), and cell-free extracts (CFE) and whole genome sequencing of Bifidobacterium bifidum E3 (B. bifidum E3), as well as the structural characteristics and antioxidant properties of EPS-1, EPS-2, and EPS-3, [...] Read more.
In this study, the antioxidant properties of intact cells (IC), cell-free supernatant (CFS), and cell-free extracts (CFE) and whole genome sequencing of Bifidobacterium bifidum E3 (B. bifidum E3), as well as the structural characteristics and antioxidant properties of EPS-1, EPS-2, and EPS-3, were evaluated. The results revealed that intact cells (IC), cell-free supernatant (CFS), and cell-free extracts (CFE) had potent DPPH (1,1-Diphenyl-2-picrylhydrazyl radical), hydroxyl, and superoxide anion radical scavenging capacities, among which CFS was the best. At the genetic level, we identified a strong carbohydrate metabolism capacity, an EPS synthesis gene cluster, and five sugar nucleotides in B. bifidum E3. Therefore, we extracted cEPS from B. bifidum E3 and purified it to obtain EPS-1, EPS-2, and EPS-3. EPS-1, EPS-2, and EPS-3 were heteropolysaccharides with an average molecular weight of 4.15 × 104 Da, 3.67 × 104 Da, and 5.89 × 104 Da, respectively. The EPS-1 and EPS-2 are mainly comprised of mannose and glucose, and the EPS-3 is mainly comprised of rhamnose, mannose, and glucose. The typical characteristic absorption peaks of polysaccharides were shown in Fourier transform infrared spectroscopy (FT-IR spectroscopy). The microstructural study showed a rough surface structure for EPS-1, EPS-2, and EPS-3. Furthermore, EPS-1, EPS-2, and EPS-3 exhibited potent DPPH, hydroxyl, and superoxide anion radical scavenging capacities. Correlation analysis identified that antioxidant capacities may be influenced by various factors, especially molecular weight, chemical compositions, and monosaccharide compositions. In summary, the EPS that was produced by B. bifidum E3 may provide insights into health-promoting benefits in humans. Full article
(This article belongs to the Special Issue Probiotics: Selection, Cultivation, Evaluation and Application)
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25 pages, 2734 KiB  
Article
Screening, Identification and Physiological Characteristics of Lactobacillus rhamnosus M3 (1) against Intestinal Inflammation
by Jiayan Jiang, Ke Li, Yuanliang Wang, Zhongqin Wu, Huiqin Ma, Shilin Zheng and Zongjun Li
Foods 2023, 12(8), 1628; https://doi.org/10.3390/foods12081628 - 12 Apr 2023
Cited by 7 | Viewed by 4503
Abstract
The probiotic role of lactic acid bacteria (LAB) in regulating intestinal microbiota to promote human health has been widely reported. However, the types and quantities of probiotics used in practice are still limited. Therefore, isolating and screening LAB with potential probiotic functions from [...] Read more.
The probiotic role of lactic acid bacteria (LAB) in regulating intestinal microbiota to promote human health has been widely reported. However, the types and quantities of probiotics used in practice are still limited. Therefore, isolating and screening LAB with potential probiotic functions from various habitats has become a hot topic. In this study, 104 strains of LAB were isolated from and identified in traditionally fermented vegetables, fresh milk, healthy infant feces, and other environments. The antibacterial properties—resistance to acid, bile salts, and digestive enzymes—and adhesion ability of the strains were determined, and the biological safety of LAB with better performance was studied. Three LAB with good comprehensive performance were obtained. These bacteria had broad-spectrum antibacterial properties and good acid resistance and adhesion ability. They exhibited some tolerance to pig bile salt, pepsin, and trypsin and showed no hemolysis. They were sensitive to the selected antibiotics, which met the required characteristics and safety evaluation criteria for probiotics. An in vitro fermentation experiment and milk fermentation performance test of Lactobacillus rhamnosus (L. rhamnosus) M3 (1) were carried out to study its effect on the intestinal flora and fermentation performance in patients with inflammatory bowel disease (IBD). Studies have shown that this strain can effectively inhibit the growth of harmful microorganisms and produce a classic, pleasant flavor. It has probiotic potential and is expected to be used as a microecological agent to regulate intestinal flora and promote intestinal health. It can also be used as an auxiliary starter to enhance the probiotic value of fermented milk. Full article
(This article belongs to the Special Issue Probiotics: Selection, Cultivation, Evaluation and Application)
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17 pages, 6283 KiB  
Article
Environment-Related Genes Analysis of Limosilactobacillus fermentum Isolated from Food and Human Gut: Genetic Diversity and Adaption Evolution
by Yan Zhao, Leilei Yu, Fengwei Tian, Jianxin Zhao, Hao Zhang, Wei Chen, Yuzheng Xue and Qixiao Zhai
Foods 2022, 11(19), 3135; https://doi.org/10.3390/foods11193135 - 8 Oct 2022
Cited by 10 | Viewed by 3352
Abstract
Limosilactobacillus fermentum is ubiquitous in traditional fermented vegetables, meat products, and the human gut. It is regarded as a “generally recognized as safe” organism by the US Food and Drug Administration. So far, the genetic features and evolutionary strategies of L. fermentum from [...] Read more.
Limosilactobacillus fermentum is ubiquitous in traditional fermented vegetables, meat products, and the human gut. It is regarded as a “generally recognized as safe” organism by the US Food and Drug Administration. So far, the genetic features and evolutionary strategies of L. fermentum from the human gut and food remain unknown. In this study, comparative genomic analysis of 224 L. fermentum strains isolated from food and human gut (164 L. fermentum strains isolated from human gut was sequenced in our lab) was performed to access genetic diversity and explore genomic features associated with environment. A total of 20,505 gene families were contained by 224 L. fermentum strains and these strains separated mainly into six clades in phylogenetic tree connected with their origin. Food source L. fermentum strains carried more carbohydrate active enzyme genes (belonging to glycosyltransferase family 2, glycoside hydrolase family 43_11, and glycoside hydrolase family 68) compared with that of human gut and L. fermentum derived from food showed higher ability to degrade xylulose and ribose. Moreover, the number of genes encoding otr(A), tetA(46), lmrB, poxtA, and efrB were more abundant in food source L. fermentum, which was consistent with the number of CRISPR spacers and prophages in L. fermentum of food source. This study provides new insight into the adaption of L. fermentum to the food and intestinal tract of humans, suggesting that the genomic evolution of L. fermentum was to some extent driven by environmental stress. Full article
(This article belongs to the Special Issue Probiotics: Selection, Cultivation, Evaluation and Application)
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Review

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19 pages, 1845 KiB  
Review
Advances in Genetic Tools and Their Application in Streptococcus thermophilus
by Ruiting Zhao, Zouquan Chen, Jie Liang, Jiaxin Dou, Fangyu Guo, Zhenshang Xu and Ting Wang
Foods 2023, 12(16), 3119; https://doi.org/10.3390/foods12163119 - 19 Aug 2023
Cited by 6 | Viewed by 4975
Abstract
Streptococcus thermophilus is a traditional starter. Nowadays, key aspects of S. thermophilus physiology have been revealed concerning the phenotypic traits relevant for industrial applications, including sugar metabolism, protein hydrolysis, and the production of important metabolites that affect the sensory properties of fermented foods [...] Read more.
Streptococcus thermophilus is a traditional starter. Nowadays, key aspects of S. thermophilus physiology have been revealed concerning the phenotypic traits relevant for industrial applications, including sugar metabolism, protein hydrolysis, and the production of important metabolites that affect the sensory properties of fermented foods as well as the original cooperation with Lactobacillus delbrueckii subsp. bulgaricus. Moreover, significant advances have been made in the synthetic biology toolbox of S. thermophilus based on technological advances in the genome and its sequencing and synthesis. In this review, we discuss the recently developed toolbox for S. thermophilus, including gene expression toolsets (promoters, terminators, plasmids, etc.) and genome editing tools. It can be used for both functionalized foods and therapeutic molecules for consumers. The availability of new molecular tools, including the genome editing toolbox, has facilitated the engineering of physiological studies of S. thermophilus and the generation of strains with improved technical and functional characteristics. Full article
(This article belongs to the Special Issue Probiotics: Selection, Cultivation, Evaluation and Application)
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