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Rangasamy P, Foo HL, Yusof BNM, Chew SY, Jamil AAM, Than LTL. Probiotic Strain Limosilactobacillus reuteri 29B is Proven Safe and Exhibits Potential Probiotic Traits in a Murine Vaginal Model. Probiotics Antimicrob Proteins 2024; 16:1172-1189. [PMID: 37314695 DOI: 10.1007/s12602-023-10094-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2023] [Indexed: 06/15/2023]
Abstract
Lactobacilli, the most common group of bacteria found in a healthy vaginal microbiota, have been demonstrated to act as a defence against colonisation and overgrowth of vaginal pathogens. These groups of bacteria have sparked interests in incorporating them as probiotics aimed at re-establishing balance within the urogenital ecosystem. In this study, the safety characteristics of Limosilactobacillus reuteri 29B (L29B) strain were evaluated through whole genome sequencing (WGS) and animal study. Cell culture assay and 16S rDNA analysis were done to evaluate the ability of the strain to colonise and adhere to the mouse vaginal tract, and RAST analysis was performed to screen for potential genes associated with probiotic trait. The histological study on the mice organs and blood analysis of the mice showed there was no incidence of inflammation. We also found no evidence of bacterial translocation. The cell culture assay on HeLa cells showed 85% of adhesion, and there was a significant reduction of Candida strain viability in displacement assay. As for the 16S rDNA analysis, there was a significant amount of L29B colonisation of the vaginal microflora. Taken together, the intravaginal administration of L29B significantly reduced the number Enterobacteriaceae and Staphylococcaceae that were present in mouse vaginal tract. It also improved and promoted a balanced vaginal microflora environment without causing any harm or irritation to mice. Limosilactobacillus 29B (L29B) is safe to be administered intravaginally.
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Affiliation(s)
- Premmala Rangasamy
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Hooi Ling Foo
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Research Laboratory of Probiotics and Cancer Therapeutics, UPM-MAKNA Cancer Research Laboratory (CANRES), Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Barakatun Nisak Mohd Yusof
- Department of Dietetic, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Shu Yih Chew
- School of Medicine, International Medical University, 57000, Kuala Lumpur, Malaysia
| | - Amilia Afzan Mohd Jamil
- Department of Obstetrics and Gynaecology (O&G), Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Leslie Thian Lung Than
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
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Iorizzo M, Paventi G, Di Martino C. Biosynthesis of Gamma-Aminobutyric Acid (GABA) by Lactiplantibacillus plantarum in Fermented Food Production. Curr Issues Mol Biol 2023; 46:200-220. [PMID: 38248317 PMCID: PMC10814391 DOI: 10.3390/cimb46010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/23/2024] Open
Abstract
In recent decades, given the important role of gamma-aminobutyric acid (GABA) in human health, scientists have paid great attention to the enrichment of this chemical compound in food using various methods, including microbial fermentation. Moreover, GABA or GABA-rich products have been successfully commercialized as food additives or functional dietary supplements. Several microorganisms can produce GABA, including bacteria, fungi, and yeasts. Among GABA-producing microorganisms, lactic acid bacteria (LAB) are commonly used in the production of many fermented foods. Lactiplantibacillus plantarum (formerly Lactobacillus plantarum) is a LAB species that has a long history of natural occurrence and safe use in a wide variety of fermented foods and beverages. Within this species, some strains possess not only good pro-technological properties but also the ability to produce various bioactive compounds, including GABA. The present review aims, after a preliminary excursus on the function and biosynthesis of GABA, to provide an overview of the current uses of microorganisms and, in particular, of L. plantarum in the production of GABA, with a detailed focus on fermented foods. The results of the studies reported in this review highlight that the selection of new probiotic strains of L. plantarum with the ability to synthesize GABA may offer concrete opportunities for the design of new functional foods.
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Affiliation(s)
| | - Gianluca Paventi
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Via De Sanctis, 86100 Campobasso, Italy; (M.I.); (C.D.M.)
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Liu S, Cheng L, Liu Y, Zhan S, Wu Z, Zhang X. Relationship between Dietary Polyphenols and Gut Microbiota: New Clues to Improve Cognitive Disorders, Mood Disorders and Circadian Rhythms. Foods 2023; 12:foods12061309. [PMID: 36981235 PMCID: PMC10048542 DOI: 10.3390/foods12061309] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/08/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Cognitive, mood and sleep disorders are common and intractable disorders of the central nervous system, causing great inconvenience to the lives of those affected. The gut-brain axis plays a vital role in studying neurological disorders such as neurodegenerative diseases by acting as a channel for a bidirectional information exchange between the gut microbiota and the nervous system. Dietary polyphenols have received widespread attention because of their excellent biological activity and their wide range of sources, structural diversity and low toxicity. Dietary intervention through the increased intake of dietary polyphenols is an emerging strategy for improving circadian rhythms and treating metabolic disorders. Dietary polyphenols have been shown to play an essential role in regulating intestinal flora, mainly by maintaining the balance of the intestinal flora and enhancing host immunity, thereby suppressing neurodegenerative pathologies. This paper reviewed the bidirectional interactions between the gut microbiota and the brain and their effects on the central nervous system, focusing on dietary polyphenols that regulate circadian rhythms and maintain the health of the central nervous system through the gut-brain axis.
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Affiliation(s)
- Siyu Liu
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, China
| | - Lu Cheng
- Department of Food Science, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Yanan Liu
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, China
| | - Shengnan Zhan
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, China
| | - Zufang Wu
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, China
| | - Xin Zhang
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, China
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Shi P, Wei H, Liu X, Dong S, He S, Zeng Y, Yang T, Liu C, Li Y. The Nasal Bacteria Microbiome Comparison Among Fungal Ball Sinusitis, Chronic Sinusitis with Polyps. Indian J Microbiol 2023; 63:120-128. [PMID: 37188229 PMCID: PMC10172428 DOI: 10.1007/s12088-023-01062-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/29/2022] [Indexed: 03/02/2023] Open
Abstract
To evaluate the composition of the microbial community of the middle nasal in paranasal sinus fungus ball (FB), chronic sinusitis with nasal polyps (CRSwNP) and healthy controls, providing new insights into the pathogenesis of FB and CRSwNP. Through 16 s rRNA gene high-throughput sequencing to determine the microbial characterization from patients with FB (n = 29) and CRSwNP (n = 10), and healthy controls (n = 4). The FB group had significantly lower αdiversity and significantly different β diversity compared to the other groups. All three groups mainly consisted of four bacterial phyla (Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria). In the FB group, the highest relative abundance was found in Proteobacteria (47.04%). However, pairwise comparisons resulted in statistically significant differences only for Firmicutes (CRSwNP, p = 0.003, Control, p = 0.008). The CRSwNP group was statistically different from the control group in TM7(p = 0.010), Chloroflexi(p = 0.018) and Bacteroidete(p = 0.027). At the genus level, the FB group had the highest relative abundance of Haemophilus (11.53%), followed by Neisseria (7.39%), and Neisseria abundance (p < 0.001) was significantly different from the remaining two groups. Ruminococcacea abundance (p < 0.001) and Comamonadaceae abundance (p < 0.001) were increased in the CRSwNP group. The relative abundance of Lactobacillus (p < 0.001), Bacteroides S24_7 (p < 0.001), and Desulfovibrio (p < 0.001) was significantly decreased in the FB and CRSwNP groups compared to the control group. The imbalance of the microbial community is related to the pathogenesis of sinusitis.
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Affiliation(s)
- Pengyu Shi
- Department of Otolaryngology Head and Neck Surgery, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730 People’s Republic of China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China
- Department of Neurology, Beijing Tongren Hospital Capital Medical University, Beijing, 100730 China
| | - Hongzheng Wei
- Department of Otolaryngology Head and Neck Surgery, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730 People’s Republic of China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China
| | - Xin Liu
- Department of Otolaryngology Head and Neck Surgery, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730 People’s Republic of China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China
| | - Shouxiang Dong
- Department of Otolaryngology Head and Neck Surgery, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730 People’s Republic of China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China
| | - Shuai He
- Department of Otolaryngology Head and Neck Surgery, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730 People’s Republic of China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China
| | - Yun Zeng
- Department of Otolaryngology Head and Neck Surgery, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730 People’s Republic of China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China
| | - Ting Yang
- Department of Otolaryngology Head and Neck Surgery, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730 People’s Republic of China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China
| | - Chengyao Liu
- Department of Otolaryngology Head and Neck Surgery, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730 People’s Republic of China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China
| | - Yunchuan Li
- Department of Otolaryngology Head and Neck Surgery, Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730 People’s Republic of China
- Key Laboratory of Otolaryngology Head and Neck Surgery, Ministry of Education, Capital Medical University, Beijing, China
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Yunes RA, Poluektova EU, Belkina TV, Danilenko VN. Lactobacilli: Legal Regulation and Prospects for New Generation Drugs. APPL BIOCHEM MICRO+ 2022; 58:652-664. [PMID: 36164404 PMCID: PMC9492457 DOI: 10.1134/s0003683822050179] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 11/23/2022]
Abstract
The global probiotics industry has been undergoing major changes in recent years. Approaches to finding and creating new probiotics, as well as a paradigm of their use in food, medicine, and pharmacology are changing. The catalyst proved to be the increasing popularity and availability of omics technologies, in particular, metagenomic studies of human and animal microbiomes. However, the efficiency and safety of drugs based on probiotic strains, as well as their marketing rates, largely depend on the levels of legal and technical regulation in the field. The present review discusses the aspects of legal regulation in Russia, the European Union and the United States, along with the advantages and disadvantages of probiotics and postbiotics. A consensus is emerging that postbiotics have a number of advantages over classical live probiotic cultures. The review also focuses on the lactobacilli family, which includes the largest number of probiotic strains studied so far and still holds a leading position among probiotics. On the legislative front, Russia is often ahead of its time with adopting such laws as the Federal Law No. 492-FZ on biosecurity, which defined the concept of human and animal microbiota and set forth legislative guidelines for its preservation. The new field of research referred to as microbiome nutrigenomics aims to achieve this goal.
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Affiliation(s)
- R. A. Yunes
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - E. U. Poluektova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - T. V. Belkina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - V. N. Danilenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
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6
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Dou W, Abdalla HB, Chen X, Sun C, Chen X, Tian Q, Wang J, Zhou W, Chi W, Zhou X, Ye H, Bi C, Tian X, Yang Y, Wong A. ProbResist: a database for drug-resistant probiotic bacteria. Database (Oxford) 2022; 2022:6665407. [PMID: 35962763 PMCID: PMC9375527 DOI: 10.1093/database/baac064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 07/04/2022] [Accepted: 08/06/2022] [Indexed: 11/13/2022]
Abstract
Drug resistance remains a global threat, and the rising trend of consuming probiotic-containing foods, many of which harbor antibiotic resistant determinants, has raised serious health concerns. Currently, the lack of accessibility to location-, drug- and species-specific information of drug-resistant probiotics has hampered efforts to combat the global spread of drug resistance. Here, we describe the development of ProbResist, which is a manually curated online database that catalogs reports of probiotic bacteria that have been experimentally proven to be resistant to antibiotics. ProbResist allows users to search for information of drug resistance in probiotics by querying with the names of the bacteria, antibiotic or location. Retrieved results are presented in a downloadable table format containing the names of the antibiotic, probiotic species, resistant determinants, region where the study was conducted and digital article identifiers (PubMed Identifier and Digital Object Identifier) hyperlinked to the original sources. The webserver also presents a simple analysis of information stored in the database. Given the increasing reports of drug-resistant probiotics, an exclusive database is necessary to catalog them in one platform. It will enable medical practitioners and experts involved in policy making to access this information quickly and conveniently, thus contributing toward the broader goal of combating drug resistance.
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Affiliation(s)
- Wanying Dou
- Department of Computer Science, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Hemn Barzan Abdalla
- Department of Computer Science, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Xu Chen
- Department of Computer Science, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Changyi Sun
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Xuefei Chen
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Qiwen Tian
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Junyi Wang
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Wei Zhou
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Wei Chi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Xuan Zhou
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Hailv Ye
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
| | - Chuyun Bi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics , Ouhai, Wenzhou, Zhejiang 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center , Ouhai, Wenzhou, Zhejiang 325060, China
| | - Xuechen Tian
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics , Ouhai, Wenzhou, Zhejiang 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center , Ouhai, Wenzhou, Zhejiang 325060, China
| | - Yixin Yang
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics , Ouhai, Wenzhou, Zhejiang 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center , Ouhai, Wenzhou, Zhejiang 325060, China
| | - Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
- Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics , Ouhai, Wenzhou, Zhejiang 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center , Ouhai, Wenzhou, Zhejiang 325060, China
- Department of Computer Science, College of Science and Technology, Wenzhou-Kean University , 88 Daxue Road, Ouhai, Wenzhou, Zhejiang 325060, China
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Keter MT, El Halfawy NM, El-Naggar MY. Incidence of virulence determinants and antibiotic resistance in lactic acid bacteria isolated from food products. Future Microbiol 2022; 17:325-337. [PMID: 35172602 DOI: 10.2217/fmb-2021-0053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Background: Lactic acid bacteria (LAB) confer beneficial health effects in humans. However, the safety of these bacteria and their potential to spread resistance in the environment must be evaluated. Materials & methods: Fifty-three LAB were isolated from different food samples and assessed for the prevalence of virulence determinants and antibiotic resistance profile. Results: Multiple resistance was reported for Lactobacillus brevis MIM04, having revealed phenotypic resistance to vancomycin (MIC >128 μg/ml), ampicillin, cefotaxime, oxacillin and gentamicin. Virulence traits (cylA, gelE, esp and agg) were detected using specific primers. Enterococcus faecium CHE32, Lactobacillus plantarum CHE37 and E. faecium MLK68 lack virulence genes, possess antimicrobial activity and survive in low pH and bile salt conditions. Conclusion: Isolated LAB revealed probiotic properties.
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Affiliation(s)
- Mike T Keter
- Department of Microbiology & Biotechnology, Kenyatta University, 43844-00100, Kenya
| | - Nancy M El Halfawy
- Department of Botany & Microbiology, Faculty of Science, Alexandria University, 21568, Egypt
| | - Moustafa Y El-Naggar
- Department of Botany & Microbiology, Faculty of Science, Alexandria University, 21568, Egypt
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8
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Wang Y, Dong J, Wang J, Chi W, Zhou W, Tian Q, Hong Y, Zhou X, Ye H, Tian X, Hu R, Wong A. Assessing the drug resistance profiles of oral probiotic lozenges. J Oral Microbiol 2022; 14:2019992. [PMID: 35024089 PMCID: PMC8745366 DOI: 10.1080/20002297.2021.2019992] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background Probiotic lozenges have been developed to harvest the benefits of probiotics for oral health, but their long-term consumption may encourage the transfer of resistance genes from probiotics to commensals, and eventually to disease-causing bacteria. Aim To screen commercial probiotic lozenges for resistance to antibiotics, characterize the resistance determinants, and examine their transferability in vitro. Results Probiotics of all lozenges were resistant to glycopeptide, sulfonamide, and penicillin antibiotics, while some were resistant to aminoglycosides and cephalosporins. High minimum inhibitory concentrations (MICs) were detected for streptomycin (>128 µg/mL) and chloramphenicol (> 512 µg/mL) for all probiotics but only one was resistant to piperacillin (MIC = 32 µg/mL). PCR analysis detected erythromycin (erm(T), ermB or mefA) and fluoroquinolone (parC or gyr(A)) resistance genes in some lozenges although there were no resistant phenotypes. The dfrD, cat-TC, vatE, aadE, vanX, and aph(3")-III or ant(2")-I genes conferring resistance to trimethoprim, chloramphenicol, quinupristin/dalfopristin, vancomycin, and streptomycin, respectively, were detected in resistant probiotics. The rifampicin resistance gene rpoB was also present. We found no conjugal transfer of streptomycin resistance genes in our co-incubation experiments. Conclusion Our study represents the first antibiotic resistance profiling of probiotics from oral lozenges, thus highlighting the health risk especially in the prevailing threat of drug resistance globally.
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Affiliation(s)
- Yi Wang
- Department of Orthodontics, School and Hospital of Stomatology, Wenzhou Medical University, University Town, Wenzhou, Zhejiang Province, China
| | - Jingya Dong
- Department of Orthodontics, School and Hospital of Stomatology, Wenzhou Medical University, University Town, Wenzhou, Zhejiang Province, China
| | - Junyi Wang
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Wei Chi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Wei Zhou
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Qiwen Tian
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Yue Hong
- Department of Orthodontics, School and Hospital of Stomatology, Wenzhou Medical University, University Town, Wenzhou, Zhejiang Province, China
| | - Xuan Zhou
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Hailv Ye
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
| | - Xuechen Tian
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China.,Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang Province, China
| | - Rongdang Hu
- Department of Orthodontics, School and Hospital of Stomatology, Wenzhou Medical University, University Town, Wenzhou, Zhejiang Province, China
| | - Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China.,Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China.,Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou, Zhejiang Province, China
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9
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Danilenko V, Devyatkin A, Marsova M, Shibilova M, Ilyasov R, Shmyrev V. Common Inflammatory Mechanisms in COVID-19 and Parkinson's Diseases: The Role of Microbiome, Pharmabiotics and Postbiotics in Their Prevention. J Inflamm Res 2021; 14:6349-6381. [PMID: 34876830 PMCID: PMC8643201 DOI: 10.2147/jir.s333887] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/29/2021] [Indexed: 12/14/2022] Open
Abstract
In the last decade, metagenomic studies have shown the key role of the gut microbiome in maintaining immune and neuroendocrine systems. Malfunction of the gut microbiome can induce inflammatory processes, oxidative stress, and cytokine storm. Dysfunction of the gut microbiome can be caused by short-term (virus infection and other infectious diseases) or long-term (environment, nutrition, and stress) factors. Here, we reviewed the inflammation and oxidative stress in neurodegenerative diseases and coronavirus infection (COVID-19). Here, we reviewed the renin-angiotensin-aldosterone system (RAAS) involved in the processes of formation of oxidative stress and inflammation in viral and neurodegenerative diseases. Moreover, the coronavirus uses ACE2 receptors of the RAAS to penetrate human cells. The coronavirus infection can be the trigger for neurodegenerative diseases by dysfunction of the RAAS. Pharmabiotics, postbiotics, and next-generation probiotics, are considered as a means to prevent oxidative stress, inflammatory processes, neurodegenerative and viral diseases through gut microbiome regulation.
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Affiliation(s)
- Valery Danilenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Devyatkin
- Central Clinical Hospital with a Polyclinic CMP RF, Moscow, Russia
| | - Mariya Marsova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | | | - Rustem Ilyasov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
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10
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Averina OV, Poluektova EU, Marsova MV, Danilenko VN. Biomarkers and Utility of the Antioxidant Potential of Probiotic Lactobacilli and Bifidobacteria as Representatives of the Human Gut Microbiota. Biomedicines 2021; 9:1340. [PMID: 34680457 PMCID: PMC8533434 DOI: 10.3390/biomedicines9101340] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/12/2021] [Accepted: 09/22/2021] [Indexed: 12/12/2022] Open
Abstract
Lactobacilli and bifidobacteria are an important part of human gut microbiota. Among numerous benefits, their antioxidant properties are attracting more and more attention. Multiple in vivo and in vitro studies have demonstrated that lactobacilli and bifidobacteria, along with their cellular components, possess excellent antioxidant capacity, which provides a certain degree of protection to the human body against diseases associated with oxidative stress. Recently, lactobacilli and bifidobacteria have begun to be considered as a new source of natural antioxidants. This review summarizes the current state of research on various antioxidant properties of lactobacilli and bifidobacteria. Special emphasis is given to the mechanisms of antioxidant activity of these bacteria in the human gut microbiota, which involve bacterial cell components and metabolites. This review is also dedicated to the genes involved in the antioxidant properties of lactobacilli and bifidobacteria strains as indicators of their antioxidant potential in human gut microbiota. Identification of the antioxidant biomarkers of the gut microbiota is of great importance both for creating diagnostic systems for assessing oxidative stress and for choosing strategies aimed at restoring the normal functioning of the microbiota and, through it, restoring human health. In this review, the practical application of probiotic strains with proven antioxidant properties to prevent oxidative stress is also considered.
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Affiliation(s)
- Olga V. Averina
- Vavilov Institute of General Genetics, Russion Academy of Sciences, 119991 Moscow, Russia; (E.U.P.); (M.V.M.); (V.N.D.)
| | - Elena U. Poluektova
- Vavilov Institute of General Genetics, Russion Academy of Sciences, 119991 Moscow, Russia; (E.U.P.); (M.V.M.); (V.N.D.)
| | - Mariya V. Marsova
- Vavilov Institute of General Genetics, Russion Academy of Sciences, 119991 Moscow, Russia; (E.U.P.); (M.V.M.); (V.N.D.)
| | - Valery N. Danilenko
- Vavilov Institute of General Genetics, Russion Academy of Sciences, 119991 Moscow, Russia; (E.U.P.); (M.V.M.); (V.N.D.)
- Institute of Ecology, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
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11
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Ojha AK, Shah NP, Mishra V. Conjugal Transfer of Antibiotic Resistances in Lactobacillus spp. Curr Microbiol 2021; 78:2839-2849. [PMID: 34076710 DOI: 10.1007/s00284-021-02554-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 05/26/2021] [Indexed: 11/26/2022]
Abstract
Lactic acid bacteria (LAB) are a heterogeneous group of bacteria which are Gram-positive, facultative anaerobes and non-motile, non-spore forming, with varied shapes from cocci to coccobacilli and bacilli. Lactobacillus is the largest and most widely used bacterial species amongst LAB in fermented foods and beverages. The genus is a common member of human gut microbiome. Several species are known to provide benefits to the human gut via synergistic interactions with the gut microbiome and their ability to survive the gut environment. This ability to confer positive health effects provide them a status of generally recognized as safe (GRAS) microorganisms. Due to their various beneficial characteristics, other factors such as their resistance acquisition were overlooked. Overuse of antibiotics has made certain bacteria develop resistance against these drugs. Antibiotic resistance was found to be acquired mainly through conjugation which is a type of lateral gene transfer. Several in vitro methods of conjugation have been discussed previously depending on their success to transfer resistance. In this review, we have addressed methods that are employed to study the transfer of resistance genes using the conjugation phenomenon in lactobacilli.
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Affiliation(s)
- Anup Kumar Ojha
- National Institute of Food Technology Entrepreneurship and Management (NIFTEM), Sonipat, Haryana, 131028, India
| | - Nagendra Prasad Shah
- Food and Nutritional Sciences, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, China
| | - Vijendra Mishra
- National Institute of Food Technology Entrepreneurship and Management (NIFTEM), Sonipat, Haryana, 131028, India.
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12
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De Boeck I, Spacova I, Vanderveken OM, Lebeer S. Lactic acid bacteria as probiotics for the nose? Microb Biotechnol 2021; 14:859-869. [PMID: 33507624 PMCID: PMC8085937 DOI: 10.1111/1751-7915.13759] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 12/11/2022] Open
Abstract
Several studies have recently pointed towards an increased occurrence and prevalence of several taxa of the lactic acid bacteria (LAB) in the microbiota of the upper respiratory tract (URT) under healthy conditions versus disease. These include several species of the Lactobacillales such as Lacticaseibacillus casei, Lactococcus lactis and Dolosigranulum pigrum. In addition to physiological studies on their potential beneficial functions and their long history of safe use as probiotics in other human body sites, LAB are thus increasingly to be explored as alternative or complementary treatment for URT diseases. This review highlights the importance of lactic acid bacteria in the respiratory tract and their potential as topical probiotics for this body site. We focus on the potential probiotic properties and adaptation factors that are needed for a bacterial strain to optimally exert its beneficial activity in the respiratory tract. Furthermore, we discuss a range of in silico, in vitro and in vivo models needed to obtain better insights into the efficacy and adaptation factors specifically for URT probiotics. Such knowledge will facilitate optimal strain selection in order to conduct rigorous clinical studies with the most suitable probiotic strains. Despite convincing evidence from microbiome association and in vitro studies, the clinical evidence for oral or topical probiotics for common URT diseases such as chronic rhinosinusitis (CRS) needs further substantiation.
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Affiliation(s)
- Ilke De Boeck
- Department of Bioscience EngineeringUniversity of AntwerpGroenenborgerlaan 171AntwerpB‐2020Belgium
| | - Irina Spacova
- Department of Bioscience EngineeringUniversity of AntwerpGroenenborgerlaan 171AntwerpB‐2020Belgium
| | - Olivier M. Vanderveken
- ENT, Head and Neck Surgery and Communication DisordersAntwerp University HospitalEdegemBelgium
- Faculty of Medicine and Health SciencesTranslational NeurosciencesUniversity of AntwerpAntwerpBelgium
| | - Sarah Lebeer
- Department of Bioscience EngineeringUniversity of AntwerpGroenenborgerlaan 171AntwerpB‐2020Belgium
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13
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Fusco V, Fanelli F, Chieffi D. Authenticity of probiotic foods and dietary supplements: A pivotal issue to address. Crit Rev Food Sci Nutr 2021; 62:6854-6871. [PMID: 33819118 DOI: 10.1080/10408398.2021.1907300] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The market of probiotic foods and supplements is growing rapidly but frequently the commercialized products are not compliant with their labels in terms of claimed probiotic strain(s) and labeled number of viable probiotic cells, thus mining the authenticity of these probiotic products.In this review, we provide an up-to-date overview of: (i) the current regulatory aspects, (ii) the consistency of probiotic foods and supplements with their labels, (iii) the implications of mislabeling on the quality, safety and functionality of these products and (iv) the available and most promising methods to assess the authenticity of these products, taking into account the need to discriminate among the different physiological states probiotics might be in the carrier matrices. It arises that authenticity of probiotic foods and supplements is an urgent issue, of industrial and legislation relevance, that need to be addressed. A plethora of methods are available to reach this goal, each with its own advantages and disadvantages. Protocols that combine the use of propidium monoazide (PMA) with metagenomics or polyphasic approaches including the PMA real time PCR or flow cytometry (for the viability assessment) and the whole genome sequence analysis (for the identification and typing of the probiotic strain) are the most promising that should be standardized and used by producers and regulators.
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Affiliation(s)
- Vincenzina Fusco
- National Research Council of Italy, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
| | - Francesca Fanelli
- National Research Council of Italy, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
| | - Daniele Chieffi
- National Research Council of Italy, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
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14
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Identification of New Potential Biotherapeutics from Human Gut Microbiota-Derived Bacteria. Microorganisms 2021; 9:microorganisms9030565. [PMID: 33803291 PMCID: PMC7998412 DOI: 10.3390/microorganisms9030565] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 02/07/2023] Open
Abstract
The role of the gut microbiota in health and disease is well recognized and the microbiota dysbiosis observed in many chronic diseases became a new therapeutic target. The challenge is to get a better insight into the functionality of commensal bacteria and to use this knowledge to select live biotherapeutics as new preventive or therapeutic products. In this study, we set up a screening approach to evaluate the functional capacities of a set of 21 strains isolated from the gut microbiota of neonates and adults. For this purpose, we selected key biological processes involved in the microbiome-host symbiosis and known to impact the host physiology i.e., the production of short-chain fatty acids and the ability to strengthen an epithelial barrier (Caco-2), to induce the release of the anti-inflammatory IL-10 cytokine after co-culture with human immune cells (PBMC) or to increase GLP-1 production from STC-1 endocrine cell line. This strategy highlighted fifteen strains exhibiting beneficial activities among which seven strains combined several of them. Interestingly, this work revealed for the first time a high prevalence of potential health-promoting functions among intestinal commensal strains and identified several appealing novel candidates for the management of chronic diseases, notably obesity and inflammatory bowel diseases.
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15
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Aziz G, Tariq M, Zaidi AH. Mining indigenous honeybee gut microbiota for Lactobacillus with probiotic potential. MICROBIOLOGY-SGM 2021; 167. [PMID: 33587693 DOI: 10.1099/mic.0.001032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The present study was done to explore the diversity of lactic acid bacteria (LAB) associated with the gastrointestinal tract (GIT) of honeybee species endemic to northeastern Pakistan. Healthy worker bees belonging to Apis mellifera, A. dorsata, A. cerana and A. florea were collected from hives and the surroundings of a major apiary in the region. The 16S rRNA amplicon sequencing revealed a microbial community in A. florea that was distinct from the others in having an abundance of Lactobacillus and Bifidobacteria. However, this was not reflected in the culturable bacteria obtained from these species. The isolates were characterized for safety parameters, and 20 LAB strains deemed safe were evaluated for resistance to human GIT stresses like acid and bile, adhesion and adhesiveness, and anti-pathogenicity. The five most robust strains, Enterococcus saigonensis NPL780a, Lactobacillus rapi NPL782a, Lactobacillus kunkeei NPL783a, and NPL784, and Lactobacillus paracasei NPL783b, were identified through normalized Pearson (n) principal components analysis (PCA). These strains were checked for inhibition of human pathogens, antibiotic resistance, osmotic tolerance, metabolic and enzymatic functions, and carbohydrate utilization, along with antioxidative and cholesterol-removing potential. The findings suggest at least three strains (NPL 783a, 784 and 782a) as candidates for further in vitro and in vivo investigations of their potential health benefits and application as novel probiotic adjuncts.
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Affiliation(s)
- Ghazal Aziz
- Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad 45650, Pakistan.,National Probiotic Lab-NIBGE, Jhang Road, Faisalabad 38000 (Punjab), Pakistan
| | - Muhammad Tariq
- Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad 45650, Pakistan.,National Probiotic Lab-NIBGE, Jhang Road, Faisalabad 38000 (Punjab), Pakistan
| | - Arsalan Haseeb Zaidi
- National Probiotic Lab-NIBGE, Jhang Road, Faisalabad 38000 (Punjab), Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad 45650, Pakistan
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16
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Cunningham M, Azcarate-Peril MA, Barnard A, Benoit V, Grimaldi R, Guyonnet D, Holscher HD, Hunter K, Manurung S, Obis D, Petrova MI, Steinert RE, Swanson KS, van Sinderen D, Vulevic J, Gibson GR. Shaping the Future of Probiotics and Prebiotics. Trends Microbiol 2021; 29:667-685. [PMID: 33551269 DOI: 10.1016/j.tim.2021.01.003] [Citation(s) in RCA: 226] [Impact Index Per Article: 75.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/15/2022]
Abstract
Recent and ongoing developments in microbiome science are enabling new frontiers of research for probiotics and prebiotics. Novel types, mechanisms, and applications currently under study have the potential to change scientific understanding as well as nutritional and healthcare applications of these interventions. The expansion of related fields of microbiome-targeted interventions, and an evolving landscape for implementation across regulatory, policy, prescriber, and consumer spheres, portends an era of significant change. In this review we examine recent, emerging, and anticipated trends in probiotic and prebiotic science, and create a vision for broad areas of developing influence in the field.
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Affiliation(s)
- Marla Cunningham
- Department of Science and Innovation, Metagenics, PO Box 675, Virginia BC, QLD, 4014, Australia.
| | - M Andrea Azcarate-Peril
- UNC Departments of Medicine and Nutrition, Microbiome Core Facility, University of North Carolina, Chapel Hill, NC, USA
| | | | - Valerie Benoit
- Bell Institute of Health and Nutrition, General Mills, Minneapolis, MN, USA
| | | | - Denis Guyonnet
- Diana Nova, Symrise Nutrition, Clichy-la-Garenne, France
| | - Hannah D Holscher
- Department of Food Science and Human Nutrition and Division of Nutritional Sciences, University of Illinois, Urbana, IL, USA
| | - Kirsty Hunter
- Department of Sport Science, Nottingham Trent University, UK
| | - Sarmauli Manurung
- Emerging Sciences Research, Reckitt Benckiser, Nijmegen, The Netherlands
| | - David Obis
- Danone Nutricia Research, Palaiseau Cedex, France
| | | | - Robert E Steinert
- R&D Human Nutrition and Health, DSM Nutritional Products Ltd, Basel, Switzerland; Department of Surgery, Division of Visceral and Transplantation Surgery, University Hospital Zürich, Switzerland
| | - Kelly S Swanson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Douwe van Sinderen
- Microbiology BioSciences Institute, University College Cork, Cork, Ireland
| | - Jelena Vulevic
- veMico Ltd, Reading, UK; Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | - Glenn R Gibson
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK
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17
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Zommiti M, Feuilloley MGJ, Connil N. Update of Probiotics in Human World: A Nonstop Source of Benefactions till the End of Time. Microorganisms 2020; 8:E1907. [PMID: 33266303 PMCID: PMC7760123 DOI: 10.3390/microorganisms8121907] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 02/06/2023] Open
Abstract
Lactic acid bacteria (LAB) are known for their biotechnological potential. Moreover, LAB are distinguished by amazing criteria: Adjusting the intestinal environment, inhibiting pathogenic microbes in the gastrointestinal tract, ability to reduce pathogen adhesion activity, improving the balance of the microbiota inside the intestine, capabilities of regulating intestinal mucosal immunity, and maintaining intestinal barrier function. The escalating number of research and studies about beneficial microorganisms and their impact on promoting health has attracted a big interest in the last decades. Since antiquity, various based fermented products of different kinds have been utilized as potential probiotic products. Nevertheless, the current upsurge in consumers' interest in bioalternatives has opened new horizons for the probiotic field in terms of research and development. The present review aims at shedding light on the world of probiotics, a continuous story of astonishing success in various fields, in particular, the biomedical sector and pharmaceutical industry, as well as to display the importance of probiotics and their therapeutic potential in purpose to compete for sturdy pathogens and to struggle against diseases and acute infections. Shadows and future trends of probiotics use are also discussed.
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Affiliation(s)
- Mohamed Zommiti
- Unité de Protéomique Fonctionnelle et Potentiel Nutraceutique de la Biodiversité de Tunisie, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université Tunis El-Manar, Tunis 1006, Tunisia
| | - Marc G. J. Feuilloley
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM) EA 4312, Université de Rouen Normandie, Normandie Université, F-27000 Evreux, France; (M.G.J.F.); (N.C.)
| | - Nathalie Connil
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM) EA 4312, Université de Rouen Normandie, Normandie Université, F-27000 Evreux, France; (M.G.J.F.); (N.C.)
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18
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Ghosh TS, Arnoux J, O’Toole PW. Metagenomic analysis reveals distinct patterns of gut lactobacillus prevalence, abundance, and geographical variation in health and disease. Gut Microbes 2020; 12:1-19. [PMID: 32985923 PMCID: PMC7524322 DOI: 10.1080/19490976.2020.1822729] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Lactobacilli are exploited extensively for food fermentation and biotechnology. Some food and gut isolates have been developed as probiotics, for which species that may be commensal to the human host are considered desirable. However, the robustness of defining original niches for lactobacilli - food, environment, the gut - is questionable, and culture-independent analyses of prevalence in different human populations is lacking. Here we analyzed the abundance of lactobacilli in 6,154 subjects from a database of highly curated fecal shotgun metagenomics data spanning 25 nationalities, with ages ranging from infancy to 102 years. Twenty-five species were detected, which we assigned into low, medium, and high prevalence groups. The microbiome of apparently healthy individuals could be categorized into 6 clusters or Lactobacillotypes (LbTypes), with three of the Lbtypes being dominated by L.delbrueckii, L.ruminis, L.casei, and the other three comprising a combination of different species. These Lactobacillus clusters exhibit distinct global abundance patterns. The cluster prevalences also display distinct age-specific trends influenced by geography, with overall lactobacillus prevalence increasing significantly with age in North America and Europe but declining with age in non-Westernized societies. Regression analysis stratified by regional location identified distinct associations of the Lactobacillotypes with age, BMI, and gender. Cirrhosis, fatty-liver, , IBD and T2D were characterized by net gain of lactobacilli, whereas hypertension patients harbored depleted lactobacillus levels. Collectively these data indicate that the species abundance of gut lactobacilli is moderated by geography, diet, and interaction with the whole microbiome, and has strong interactions with diseases associated with a western lifestyle.
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Affiliation(s)
- Tarini Shankar Ghosh
- Department: School of Microbiology and APC Microbiome Ireland Institution, University College Cork, Cork, Ireland
| | - Jerome Arnoux
- Department: School of Microbiology and APC Microbiome Ireland Institution, University College Cork, Cork, Ireland,Department: UFR des Sciences et Techniques Institution, Université De Rouen, Normandie, France
| | - Paul W. O’Toole
- Department: School of Microbiology and APC Microbiome Ireland Institution, University College Cork, Cork, Ireland,CONTACT Paul W. O’Toole School of Microbiology and APC Microbiome Ireland, Cork, Ireland
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Sirichoat A, Flórez AB, Vázquez L, Buppasiri P, Panya M, Lulitanond V, Mayo B. Antibiotic Susceptibility Profiles of Lactic Acid Bacteria from the Human Vagina and Genetic Basis of Acquired Resistances. Int J Mol Sci 2020; 21:E2594. [PMID: 32276519 PMCID: PMC7178285 DOI: 10.3390/ijms21072594] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/01/2020] [Accepted: 04/07/2020] [Indexed: 12/29/2022] Open
Abstract
Lactic acid bacteria can act as reservoirs of antibiotic resistance genes that can be ultimately transferred to pathogens. The present work reports on the minimum inhibitory concentration (MIC) of 16 antibiotics to 25 LAB isolates of five Lactobacillus and one Bifidobacterium species from the human vagina. Acquired resistances were detected to kanamycin, streptomycin, chloramphenicol, gentamicin, and ampicillin. A PCR analysis of lactobacilli failed to identify genetic determinants involved in any of these resistances. Surprisingly, a tet(W) gene was detected by PCR in two Bifidobacterium bifidum strains, although they proved to be tetracycline-susceptible. In agreement with the PCR results, no acquired genes were identified in the genome of any of the Lactobacillus spp. strains sequenced. A genome analysis of B. bifidum VA07-1AN showed an insertion of two guanines in the middle of tet(W) interrupting the open reading frame. By growing the strain in the presence of tetracycline, stable tetracycline-resistant variants were obtained. An amino acid substitution in the ribosomal protein S12 (K43R) was further identified as the most likely cause of VA07-1AN being streptomycin resistance. The results of this work expand our knowledge of the resistance profiles of vaginal LAB and provide evidence for the genetic basis of some acquired resistances.
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Affiliation(s)
- Auttawit Sirichoat
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares, s/n, 33300 Villaviciosa, Asturias, Spain; (A.S.); (A.B.F.); (L.V.)
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Ana Belén Flórez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares, s/n, 33300 Villaviciosa, Asturias, Spain; (A.S.); (A.B.F.); (L.V.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Lucía Vázquez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares, s/n, 33300 Villaviciosa, Asturias, Spain; (A.S.); (A.B.F.); (L.V.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Pranom Buppasiri
- Department of Obstetrics and Gynecology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Marutpong Panya
- College of Medicine and Public Health, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand;
| | - Viraphong Lulitanond
- Department of Microbiology and Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares, s/n, 33300 Villaviciosa, Asturias, Spain; (A.S.); (A.B.F.); (L.V.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
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20
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Pot B, Salvetti E, Mattarelli P, Felis GE. The potential impact of the Lactobacillus name change: The results of an expert meeting organised by the Lactic Acid Bacteria Industrial Platform (LABIP). Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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21
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James A, Wang Y. Characterization, health benefits and applications of fruits and vegetable probiotics. CYTA - JOURNAL OF FOOD 2019. [DOI: 10.1080/19476337.2019.1652693] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Armachius James
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, P.R. China
| | - Yousheng Wang
- Beijing Advanced Innovation Centre for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, P.R. China
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22
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Börner RA, Kandasamy V, Axelsen AM, Nielsen AT, Bosma EF. Genome editing of lactic acid bacteria: opportunities for food, feed, pharma and biotech. FEMS Microbiol Lett 2019; 366:5251984. [PMID: 30561594 PMCID: PMC6322438 DOI: 10.1093/femsle/fny291] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/16/2018] [Indexed: 12/16/2022] Open
Abstract
This mini-review provides a perspective of traditional, emerging and future applications of lactic acid bacteria (LAB) and how genome editing tools can be used to overcome current challenges in all these applications. It also describes available tools and how these can be further developed, and takes current legislation into account. Genome editing tools are necessary for the construction of strains for new applications and products, but can also play a crucial role in traditional ones, such as food and probiotics, as a research tool for gaining mechanistic insights and discovering new properties. Traditionally, recombinant DNA techniques for LAB have strongly focused on being food-grade, but they lack speed and the number of genetically tractable strains is still rather limited. Further tool development will enable rapid construction of multiple mutants or mutant libraries on a genomic level in a wide variety of LAB strains. We also propose an iterative Design–Build–Test–Learn workflow cycle for LAB cell factory development based on systems biology, with ‘cell factory’ expanding beyond its traditional meaning of production strains and making use of genome editing tools to advance LAB understanding, applications and strain development.
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Affiliation(s)
- Rosa A Börner
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
| | - Vijayalakshmi Kandasamy
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
| | - Amalie M Axelsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
| | - Alex T Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
| | - Elleke F Bosma
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kongens Lyngby, Denmark
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23
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Effects of new technology on the current manufacturing process of yogurt-to increase the overall marketability of yogurt. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.03.058] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Bengoa AA, Iraporda C, Acurcio LB, de Cicco Sandes SH, Costa K, Moreira Guimarães G, Esteves Arantes RM, Neumann E, Cantini Nunes Á, Nicoli JR, Garrote GL, Abraham AG. "Physicochemical, immunomodulatory and safety aspects of milks fermented with Lactobacillus paracasei isolated from kefir". Food Res Int 2019; 123:48-55. [PMID: 31284997 DOI: 10.1016/j.foodres.2019.04.041] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/11/2019] [Accepted: 04/17/2019] [Indexed: 12/31/2022]
Abstract
The use of Lactobacillus paracasei strains isolated from kefir grains as starters for the development of functional dairy products was evaluated. The physicochemical and immunomodulatory properties of milks fermented with L. paracasei CIDCA8339, CIDCA83123 and CIDCA83124 were analyzed. The three strains produced bioactive metabolites during fermentation, since the fermented milk supernatants were able to downregulate >75% of the induced innate immune response in vitro. Although all strains presented absence of hemolytic activity and susceptibility to antibiotics, L. paracasei CIDCA8339 presented more attractive probiotic and technological properties. Mice consuming the fermented milk with L. paracasei CIDCA 8339 did not present significant modifications in sIgA levels or TNF-α, TGF-β and IL-10 mRNA expression in ileum. Additionally, a decrease of INF-γ level in ileum and no microbiological translocation to liver and spleen was observed. These results demonstrate that L. paracasei CIDCA8339 represents a safe promising potential probiotic strain for the development of functional foods.
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Affiliation(s)
- Ana A Bengoa
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos (CIDCA, UNLP-CIC-CONICET), La Plata, Argentina
| | - Carolina Iraporda
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos (CIDCA, UNLP-CIC-CONICET), La Plata, Argentina; Departamento de Ingeniería Química y Tecnología de los Alimentos, Facultad de Ingeniería de Olavarría, (FIO, UNCPBA), Olavarría, Argentina
| | - Leonardo B Acurcio
- Department of Microbiology, Biological Science Institute (ICB, UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Sávio H de Cicco Sandes
- Department of General Biology, Biological Science Institute (ICB, UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Karen Costa
- Department of Microbiology, Biological Science Institute (ICB, UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Gabriele Moreira Guimarães
- Department of Microbiology, Biological Science Institute (ICB, UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Rosa M Esteves Arantes
- Department of General Pathology, Biological Science Institute (ICB, UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Elisabeth Neumann
- Department of Microbiology, Biological Science Institute (ICB, UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Álvaro Cantini Nunes
- Department of General Biology, Biological Science Institute (ICB, UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Jaques R Nicoli
- Department of Microbiology, Biological Science Institute (ICB, UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Graciela L Garrote
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos (CIDCA, UNLP-CIC-CONICET), La Plata, Argentina
| | - Analía G Abraham
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos (CIDCA, UNLP-CIC-CONICET), La Plata, Argentina; Área Bioquímica y Control de Alimentos, Facultad de Ciencias Exactas (UNLP), La Plata, Argentina.
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25
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Influence of Media Heat Sterilization Process on Growth Performance of Representative Strains of the Genus Lactobacillus. FERMENTATION-BASEL 2019. [DOI: 10.3390/fermentation5010020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Lactic acid bacteria (LAB) are widely applied microorganisms in food, feed, and beverage applications, where they can provide essential functionality for product modification, increase product shelf life, or act as beneficial organisms after consumption. Among these, strains of the genus Lactobacillus are often used as starters, probiotics, or biopreservatives. For all these types of bacterial preparations, a transportable shelf-stable form of concentrated bacteria, preserving their intrinsic properties, is essential for commercial distribution. Former studies revealed a relationship between the culture medium, cellular morphology, and the robustness of Lactobacillus acidophilus NCFM (name derived from North Carolina Food Microbiology) cultures. Due to these insights, a multitude of Lactobacillus strains representative of the genus were screened regarding their sensitivity to thermal medium pretreatment possibly accompanied by the alteration of their chemical composition, such as the formation of Maillard reaction products (MRPs). This study reveals a quite diverse and different growth behavior of those strains in the form of altered or non-altered cell concentrations and the size distributions of the populations, whereby five strains of the L. delbrueckii group in particular showed increased cell concentrations combined with decreased mean cell volumes. The results are of both scientific and industrial relevance, as they highlight the necessity to consider and understand the effects of media sterilization for the applied production strain.
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Campedelli I, Mathur H, Salvetti E, Clarke S, Rea MC, Torriani S, Ross RP, Hill C, O'Toole PW. Genus-Wide Assessment of Antibiotic Resistance in Lactobacillus spp. Appl Environ Microbiol 2019; 85:e01738-18. [PMID: 30366997 PMCID: PMC6293106 DOI: 10.1128/aem.01738-18] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/10/2018] [Indexed: 11/20/2022] Open
Abstract
Lactobacillus species are widely used as probiotics and starter cultures for a variety of foods, supported by a long history of safe usage. Although more than 35 species meet the European Food Safety Authority (EFSA) criteria for qualified presumption of safety status, the safety of Lactobacillus species and their carriage of antibiotic resistance (AR) genes is under continuing ad hoc review. To comprehensively update the identification of AR in the genus Lactobacillus, we determined the antibiotic susceptibility patterns of 182 Lactobacillus type strains and compared these phenotypes to their genotypes based on genome-wide annotations of AR genes. Resistances to trimethoprim, vancomycin, and kanamycin were the most common phenotypes. A combination of homology-based screening and manual annotation identified genes encoding resistance to aminoglycosides (20 sequences), tetracycline (18), erythromycin (6), clindamycin (60), and chloramphenicol (42). In particular, the genes aac(3) and lsa, involved in resistance to aminoglycosides and clindamycin, respectively, were found in Lactobacillus spp. Acquired determinants predicted to code for tetracycline and erythromycin resistance were detected in Lactobacillus ingluviei, Lactobacillus amylophilus, and Lactobacillus amylotrophicus, flanked in the genome by mobile genetic elements with potential for horizontal transfer.IMPORTANCELactobacillus species are generally considered to be nonpathogenic and are used in a wide variety of foods and products for humans and animals. However, many of the species examined in this study have antibiotic resistance levels which exceed those recommended by the EFSA, suggesting that these cutoff values should be reexamined in light of the genetic basis for resistance discussed here. Our data provide evidence for rationally revising the regulatory guidelines for safety assessment of lactobacilli entering the food chain as starter cultures, food preservatives, or probiotics and will facilitate comprehensive genotype-based assessment of strains for safety screening.
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Affiliation(s)
| | - Harsh Mathur
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Cork, Ireland
| | - Elisa Salvetti
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Siobhán Clarke
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Cork, Ireland
| | - Mary C Rea
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Cork, Ireland
| | - Sandra Torriani
- Department of Biotechnology, University of Verona, Verona, Italy
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul W O'Toole
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
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27
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Viability of Lactobacillus plantarum NCIMB 8826 in fermented apple juice under simulated gastric and intestinal conditions. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.06.036] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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28
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Abdelazez A, Abdelmotaal H, Evivie SE, Melak S, Jia FF, Khoso MH, Zhu ZT, Zhang LJ, Sami R, Meng XC. Screening Potential Probiotic Characteristics of Lactobacillus brevis Strains In Vitro and Intervention Effect on Type I Diabetes In Vivo. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7356173. [PMID: 30327780 PMCID: PMC6169223 DOI: 10.1155/2018/7356173] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/21/2018] [Accepted: 08/08/2018] [Indexed: 12/30/2022]
Abstract
Diabetes has become the third most serious threat to human health, after cancer and cardiovascular disease. Notably, Lactobacillus brevis is the most common species of LAB that produces γ-aminobutyric acid (GABA). The aim of this study is to clarify the effect of time, strain types, antibiotic concentrations, different levels of pH, and intestinal juices in aerobic or anaerobic conditions and the effect of interactions between these factors on the potential properties of KLDS 1.0727 and KLDS 1.0373, furthermore, antagonistic activity against foodborne pathogens. Moreover, another aim is to study the capability of KLDS 1.0727 and KLDS 1.0373 strains as gad gene carriers to express GABA that reduce the risk of type 1 diabetes in C57BL/6 mice as diabetic models. The obtained results exhibited the surprising tolerance of Lactobacillus brevis strains in vitro digestion models mimicking the conditions of the gastrointestinal tract, further, large antagonistic activity against foodborne pathogeneses. In vivo results displayed the significant effect on glucose level reduction, blood plasma, and histological assays of mice organs. As recommended, the use of Lactobacillus brevis strains should be widely shared in the market as a natural source of GABA in pharmaceutical and food applications.
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Affiliation(s)
- Amro Abdelazez
- Key Laboratory of Dairy Science of Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Department of Dairy Microbiology, Animal Production Research Institute, Agriculture Research Centre, Dokki, Giza 12618, Egypt
| | - Heba Abdelmotaal
- Department of Microbiology, Soil, Water, Environment, and Microbiology Research Institute, Agriculture Research Center, Giza 12619, Egypt
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Smith Etareri Evivie
- Key Laboratory of Dairy Science of Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Department of Animal Science, Faculty of Agricultural, University of Benin, 1154, Benin City, Edo State, Nigeria
| | - Sherif Melak
- Department of Animal Science and Biotechnology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Department of Sheep and Goat, Animal Production Research Institute, Agriculture Research Centre, Dokki, Giza 12618, Egypt
| | - Fang-Fang Jia
- Key Laboratory of Dairy Science of Ministry of Education, Northeast Agricultural University, Harbin 150030, China
| | - Mir Hassan Khoso
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Zong-Tao Zhu
- Key Laboratory of Dairy Science of Ministry of Education, Northeast Agricultural University, Harbin 150030, China
| | - Lu-Ji Zhang
- Key Laboratory of Dairy Science of Ministry of Education, Northeast Agricultural University, Harbin 150030, China
| | - Rokayya Sami
- Department of Food Science and Nutrition, Taif University, Taif, Al-huwayah 888, Saudi Arabia
| | - Xiang-Chen Meng
- Key Laboratory of Dairy Science of Ministry of Education, Northeast Agricultural University, Harbin 150030, China
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Salvetti E, Harris HMB, Felis GE, O'Toole PW. Comparative Genomics of the Genus Lactobacillus Reveals Robust Phylogroups That Provide the Basis for Reclassification. Appl Environ Microbiol 2018; 84:e00993-18. [PMID: 29915113 PMCID: PMC6102987 DOI: 10.1128/aem.00993-18] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/12/2018] [Indexed: 12/12/2022] Open
Abstract
The genus Lactobacillus includes over 200 species that are widely used in fermented food preservation and biotechnology or that are explored for beneficial effects on health. Naming, classifying, and comparing lactobacilli have been challenging due to the high level of phenotypic and genotypic diversity that they display and because of the uncertain degree of relatedness between them and associated genera. The aim of this study was to investigate the feasibility of dividing the genus Lactobacillus into more homogeneous genera/clusters, exploiting genome-based data. The relatedness of 269 species belonging primarily to the families Lactobacillaceae and Leuconostocaceae was investigated through phylogenetic analysis (by the use of ribosomal proteins and housekeeping genes) and the assessment of the average amino acid identity (AAI) and the percentage of conserved proteins (POCP). For each subgeneric group that emerged, conserved signature genes were identified. Both distance-based and sequence-based metrics showed that the Lactobacillus genus was paraphyletic and revealed the presence of 10 methodologically consistent subclades, which were also characterized by a distinct distribution of conserved signature orthologues. We present two ways to reclassify lactobacilli: a conservative division into two subgeneric groups based on the presence/absence of a key carbohydrate utilization gene or a more radical subdivision into 10 groups that satisfy more stringent criteria for genomic relatedness.IMPORTANCE Lactobacilli have significant scientific and economic value, but their extraordinary diversity means that they are not robustly classified. The 10 homogeneous genera/subgeneric entities that we identify here are characterized by uniform patterns of the presence/absence of specific sets of genes which offer potential as discovery tools for understanding differential biological features. Reclassification/subdivision of the genus Lactobacillus into more uniform taxonomic nuclei will also provide accurate molecular markers that will be enabling for regulatory approval applications. Reclassification will facilitate scientific communication related to lactobacilli and prevent misidentification issues, which are still the major cause of mislabeling of probiotic and food products reported worldwide.
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Affiliation(s)
- Elisa Salvetti
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Hugh M B Harris
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Giovanna E Felis
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Paul W O'Toole
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
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