Insights from metagenome-assembled genomes on the genetic stability and safety of over-the-counter probiotic products

Additives EPO, Feed POSUIA, Rychen G, Aquilina G, Azimonti G, Bampidis V et al (2018) Guidance on the characterisation of microorganisms used as feed additives or as production organisms. EFSA J 16:e05206. https://doi.org/10.2903/j.efsa.2018.5206

Article  Google Scholar 

Agius JE, Phalen DN, Rose K, Eden J-S (2021) Genomic insights into the pathogenicity of a novel biofilm-forming Enterococcus sp. bacteria (Enterococcus lacertideformus) identified in reptiles. Front Microbiol 12:635208. https://doi.org/10.3389/fmicb.2021.635208

Article  PubMed  PubMed Central  Google Scholar 

Alayande KA, Aiyegoro OA, Nengwekhulu TM, Katata-Seru L, Ateba CN (2020) Integrated genome-based probiotic relevance and safety evaluation of Lactobacillus reuteri PNW1. PLoS ONE 15:e0235873. https://doi.org/10.1371/journal.pone.0235873

Article  CAS  PubMed  PubMed Central  Google Scholar 

Altermann E, Russell WM, Azcarate-Peril MA, Barrangou R, Buck BL, McAuliffe O, Souther N, Dobson A, Duong T, Callanan M (2005) Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. Proc Natl Acad Sci 102:3906–3912. https://doi.org/10.1073/pnas.0409188102

Article  CAS  PubMed  PubMed Central  Google Scholar 

Amiri S, Mokarram RR, Khiabani MS, Bari MR, Khaledabad MA (2022) Characterization of antimicrobial peptides produced by Lactobacillus acidophilus LA-5 and Bifidobacterium lactis BB-12 and their inhibitory effect against foodborne pathogens. LWT 153:112449. https://doi.org/10.1016/J.LWT.2021.112449

Article  CAS  Google Scholar 

Azevedo AC, Bento CB, Ruiz JC, Queiroz MV, Mantovani HC (2015) Distribution and genetic diversity of bacteriocin gene clusters in rumen microbial genomes. Appl Environ Microbiol 81:7290–7304

Article  CAS  PubMed  PubMed Central  Google Scholar 

Baig MA, Turner MS, Liu SQ, Al-Nabulsi AA, Shah NP, Ayyash MM (2021) Potential probiotic Pediococcus pentosaceus M41 modulates its proteome differentially for tolerances against heat. Cold Acid Bile Stress 12:731410

Google Scholar 

Baker L, Webberley T, Masetti G, Hughes T, Marchesi J, Jack A, Joyce T, Allen M, Plummer S, Michael D (2021) A genome guided evaluation of the Lab4 probiotic consortium. Genomics 113:4028–4038. https://doi.org/10.1016/j.ygeno.2021.08.007

Article  CAS  PubMed  Google Scholar 

Bansal P, Arora M, Gupta V, Maithani M (2019) Bioinformatics-based tools and software in clinical research: a new emerging area. Bioinformatics and drug discovery. Springer, pp 215–230

Chapter  Google Scholar 

Binda S, Hill C, Johansen E, Obis D, Pot B, Sanders ME, Tremblay A, Ouwehand AC (2020) Criteria to qualify microorganisms as “probiotic” in foods and dietary supplements. Front Microbiol. https://doi.org/10.3389/fmicb.2020.01662

Article  PubMed  PubMed Central  Google Scholar 

Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, Van Wezel GP, Medema MH, Weber T (2021) antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucl Acids Res 49:W29–W35. https://doi.org/10.1093/nar/gkab335

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinform 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170

Article  CAS  Google Scholar 

Bonacina J, Suárez N, Hormigo R, Fadda S, Lechner M, Saavedra L (2017) A genomic view of food-related and probiotic Enterococcus strains. DNA Res 24:11–24. https://doi.org/10.1093/dnares/dsw043

Article  CAS  PubMed  Google Scholar 

Bradde S, Nourmohammad A, Goyal S, Balasubramanian V (2020) The size of the immune repertoire of bacteria. Proc Natl Acad Sci 117:5144–5151. https://doi.org/10.1073/pnas.1903666117

Article  CAS  PubMed  PubMed Central  Google Scholar 

Briner AE, Lugli GA, Milani C, Duranti S, Turroni F, Gueimonde M, Margolles A, Van Sinderen D, Ventura M, Barrangou R (2015) Occurrence and diversity of CRISPR–Cas systems in the genus Bifidobacterium. PLoS ONE 10:e0133661. https://doi.org/10.1371/journal.pone.013366

Article  PubMed  PubMed Central  Google Scholar 

Buzikov RM, Piligrimova EG, Shadrin AM (2020) Complete genome sequence of Enterococcus faecium FS86, Used for Propagation of bacteriophages with therapeutic potential. Microbiol Resour Announc 9:e00776-e820. https://doi.org/10.1128/MRA.00776-20

Article  CAS  PubMed  PubMed Central  Google Scholar 

Carpi FM, Coman MM, Silvi S, Picciolini M, Verdenelli MC, Napolioni V (2022) Comprehensive pan-genome analysis of Lactiplantibacillus plantarum complete genomes. J Appl Microbiol 132:592–604. https://doi.org/10.1111/jam.15199

Article  CAS  PubMed  Google Scholar 

Cassir N, Benamar S, La Scola B (2016) Clostridium butyricum: from beneficial to a new emerging pathogen. Clin Microbiol Infect 22:37–45. https://doi.org/10.1016/j.cmi.2015.10.014

Article  PubMed  Google Scholar 

CDC, U. Cronobacter and powdered infant formula investigation. 2022 May 24, 2022 [cited 2022 Sep 22, 2022].

Chen L, Gu Q, Li P, Chen S, Li Y (2019) Genomic analysis of Lactobacillus reuteri WHH 1689 reveals its probiotic properties and stress resistance. Food Sci Nutr 7:844–857. https://doi.org/10.1002/fsn3.934

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cosentino S, Voldby Larsen M, Møller Aarestrup F, Lund O (2013) PathogenFinder-distinguishing friend from foe using bacterial whole genome sequence data. PLoS ONE 8:e77302. https://doi.org/10.1371/journal.pone.0077302

Article  CAS  PubMed  PubMed Central  Google Scholar 

Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, Rocha EPC, Vergnaud G, Gautheret D, Pourcel C (2018) CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucl Acids Res 46:W246–W251. https://doi.org/10.1093/nar/gky425

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cui Y, Hu T, Qu X, Zhang L, Ding Z, Dong A (2015) Plasmids from food lactic acid bacteria: diversity, similarity, and new developments. Int J Mol Sci 16:13172–13202. https://doi.org/10.3390/ijms160613172

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cui Y, Xu T, Qu X, Hu T, Jiang X, Zhao C (2016) New insights into various production characteristics of Streptococcus thermophilus strains. IJMS 17(10):1701

Article  PubMed  PubMed Central  Google Scholar 

Daliri, E.B.-M., B.H. Lee, and D.H. Oh 2019 Safety of probiotics in health and disease. Role Funct Food Sec Global Health. 603–622.

Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R, Butler RM, Chlenski P, Conrad N, Dickerman A, Dietrich EM (2020) The PATRIC bioinformatics resource center: expanding data and analysis capabilities. Nucl Acids Res 48:D606–D612. https://doi.org/10.1093/nar/gkz943

Article  CAS  PubMed  Google Scholar 

De Filippis F, Pasolli E, Ercolini D (2020) The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health. FEMS Microbiol Rev 44:454–489. https://doi.org/10.1093/femsre/fuaa015

Article  CAS  PubMed  PubMed Central  Google Scholar 

De Jesus LCL, Aburjaile FF, Sousa TDJ, Felice AG, Soares SDC, Alcantara LCJ, Azevedo VADC (2022) Genomic characterization of Lactobacillus delbrueckii strains with probiotics properties. Front Bioinfo. https://doi.org/10.3389/fbinf.2022.912795

Article  Google Scholar 

Doster E, Lakin SM, Dean CJ, Wolfe C, Young JG, Boucher C, Belk KE, Noyes NR, Morley PS (2019) MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data. Nucl Acids Res 48:D561–D569. https://doi.org/10.1093/nar/gkz1010

Article  CAS  PubMed Central  Google Scholar 

EFSA (2012) EFSA panel on additives products or substances used in animal feed guidance on the safety assessment of Enterococcus faecium in animal nutrition. EFSA J 10:2682. https://doi.org/10.2903/j.efsa.2012.2682

Article  CAS  Google Scholar 

EFSA (2021) Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 14: suitability of taxonomic units notified to EFSA until March 2021. EFSA J 19:e06689. https://doi.org/10.2903/j.efsa.2021.6689

Article  CAS  Google Scholar 

FAO/WHO (2002) Joint FAO/WHO working group report on drafting guidelines for the evaluation of probiotics in food. 30.

Fatahi-Bafghi M, Naseri S, Alizehi A (2022) Genome analysis of probiotic bacteria for antibiotic resistance genes. Anton Leeuw 115:375–389. https://doi.org/10.1007/s10482-021-01703-7

Article  CAS  Google Scholar 

Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, Tolstoy I, Tyson GH, Zhao S, Hsu CH, McDermott PF, Tadesse DA, Morales C, Simmons M, Tillman G, Wasilenko J, Folster JP, Klimke W (2019) Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates. Antimicrob Agents Chemother. https://doi.org/10.1128/aac.00483-19

Article  PubMed  PubMed Central  Google Scholar 

Fukao M, Oshima K, Morita H, Toh H, Suda W, Kim SW, Suzuki S, Yakabe T, Hattori M, Yajima N (2013) Genomic analysis by deep sequencing of the probiotic Lactobacillus brevis KB290 harboring nine plasmids reveals genomic stability. PLoS ONE 8:e60521. https://doi.org/10.1371/journal.pone.0060521

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fusco V, Fanelli F, Chieffi D (2021) Authenticity of probiotic foods and dietary supplements: a pivotal issue to address. Crit Rev Food Sci Nutr. https://doi.org/10.1080/10408398.2021.1907300

Article  PubMed  Google Scholar 

Galdeano CM, Cazorla SI, Dumit JML, Vélez E, Perdigón G (2019) Beneficial effects of probiotic consumption on the immune system. Food Funct 74:115–124

Google Scholar 

Garcia-Gutierrez E, O’Connor PM, Colquhoun IJ, Vior NM, Rodríguez JM, Mayer MJ, Cotter PD, Narbad A (2020) Production of multiple bacteriocins, including the novel bacteriocin gassericin M, by Lactobacillus gasseri LM19, a strain isolated from human milk. Appl Microbiol Biotechnol 104:3869–3884. https://doi.org/10.1007/s00253-020-10493-3

Article  CAS 

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