{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T19:52:40Z","timestamp":1787169160023,"version":"build-2736575974"},"reference-count":58,"publisher":"MDPI AG","issue":"23","license":[{"start":{"date-parts":[[2022,11,29]],"date-time":"2022-11-29T00:00:00Z","timestamp":1669680000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Gruppo Savio (Italy)"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Spore formers are ubiquitous microorganisms commonly isolated from most environments, including the gastro-intestinal tract (GIT) of insects and animals. Spores ingested as food and water contaminants safely transit the stomach and reach the intestine, where some of them germinate and temporarily colonize that niche. In the lower part of the GIT, they re-sporulate and leave the body as spores, therefore passing through their entire life cycle in the animal body. In the intestine, both un-germinated spores and germination-derived cells interact with intestinal and immune cells and have health-beneficial effects, which include the production of useful compounds, protection against pathogenic microorganisms, contribution to the development of an efficient immune system and modulation of the gut microbial composition. We report a genomic and physiological characterization of SF106 and SF174, two aerobic spore former strains previously isolated from ileal biopsies of healthy human volunteers. SF106 and SF174 belong respectively to the B. subtilis and Alkalihalobacillus clausii (formerly Bacillus clausii) species, are unable to produce toxins or other metabolites with cytotoxic activity against cultured human cells, efficiently bind mucin and human epithelial cells in vitro and produce molecules with antimicrobial and antibiofilm activities.<\/jats:p>","DOI":"10.3390\/ijms232314946","type":"journal-article","created":{"date-parts":[[2022,11,30]],"date-time":"2022-11-30T01:52:20Z","timestamp":1669773140000},"page":"14946","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Comparative Genomics and Physiological Characterization of Two Aerobic Spore Formers Isolated from Human Ileal Samples"],"prefix":"10.3390","volume":"23","author":[{"given":"Anella","family":"Saggese","sequence":"first","affiliation":[{"name":"Department of Biology, Federico II University of Naples, 80125 Naples, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosa","family":"Giglio","sequence":"additional","affiliation":[{"name":"Gruppo Savio, Pomezia, 00071 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8967-9483","authenticated-orcid":false,"given":"Nicola","family":"D\u2019Anzi","sequence":"additional","affiliation":[{"name":"Gruppo Savio, Pomezia, 00071 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Loredana","family":"Baccigalupi","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, 80131 Naples, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ezio","family":"Ricca","sequence":"additional","affiliation":[{"name":"Department of Biology, Federico II University of Naples, 80125 Naples, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,11,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"109729","DOI":"10.1016\/j.cellsig.2020.109729","article-title":"Bacillus spore germination: Knowns, unknowns and what we need to learn","volume":"74","author":"Christie","year":"2020","journal-title":"Cell. Signal."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1128\/MMBR.64.3.548-572.2000","article-title":"Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments","volume":"64","author":"Nicholson","year":"2000","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"eaav1024","DOI":"10.1126\/sciadv.aav1024","article-title":"Microbial dormancy in the marine subsurface: Global endospore abundance and response to burial","volume":"5","author":"Hoshino","year":"2019","journal-title":"Sci. Adv."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.fm.2010.03.007","article-title":"Bacillus probiotics","volume":"28","author":"Cutting","year":"2011","journal-title":"Food Microbiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"e1863134","DOI":"10.1080\/19490976.2020.1863134","article-title":"The sporobiota of the human gut","volume":"13","author":"Egan","year":"2021","journal-title":"Gut Microbes"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"498","DOI":"10.3390\/applmicrobiol1030032","article-title":"Spore formers as beneficial microbes for humans and animals","volume":"1","author":"Saggese","year":"2021","journal-title":"Appl. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2344","DOI":"10.1128\/AEM.68.5.2344-2352.2002","article-title":"Bacillus probiotics: Spore germination in the gastrointestinal tract","volume":"68","author":"Casula","year":"2002","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"3819","DOI":"10.1128\/AEM.67.9.3819-3823.2001","article-title":"Fate and dissemination of Bacillus subtilis spores in a murine model","volume":"67","author":"Hoa","year":"2001","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2692","DOI":"10.1128\/JB.188.7.2692-2700.2006","article-title":"The intestinal life cycle of Bacillus subtilis and close relatives","volume":"188","author":"Tam","year":"2006","journal-title":"J. Bacteriol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1118","DOI":"10.4049\/jimmunol.172.2.1118","article-title":"Role of commensal bacteria in development of gut-associated lymphoid tissues and preimmune antibody repertoire","volume":"172","author":"Rhee","year":"2004","journal-title":"J. Immunol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"12082","DOI":"10.1038\/s41598-019-48531-4","article-title":"Bacillus megaterium SF185 spores exert protective effects against oxidative stress in vivo and in vitro","volume":"9","author":"Mazzoli","year":"2014","journal-title":"Sci. Rep."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1016\/j.resmic.2006.06.001","article-title":"Bacillus subtilis spores reduce susceptibility to Citrobacter rodentium-mediated enteropathy in a mouse model","volume":"157","author":"Maurano","year":"2006","journal-title":"Res. Microbiol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"12636","DOI":"10.1038\/s41598-020-69533-7","article-title":"Protective action of Bacillus clausii probiotic strains in an invitro model of Rotavirus infection","volume":"10","author":"Paparo","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"759","DOI":"10.3920\/BM2019.0040","article-title":"Safety and probiotic evaluation of two Bacillus strains producing antioxidant compounds","volume":"10","author":"Kotowicz","year":"2019","journal-title":"Benef. Microbes"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"110676","DOI":"10.1016\/j.foodres.2021.110676","article-title":"Treatment with a spore-based probiotic containing five strains of Bacillus induced changes in the metabolic activity and community composition of the gut microbiota in a SHIME\u00ae model of the human gastrointestinal system","volume":"149","author":"Marzorati","year":"2021","journal-title":"Food Res. Intern."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1111\/j.1574-695X.2008.00415.x","article-title":"Immunostimulatory activity of Bacillus spores","volume":"53","author":"Huang","year":"2008","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1745","DOI":"10.1038\/s41598-018-20153-2","article-title":"Alternative use of Bacillus subtilis spores: Protection against environmental oxidative stress in human normal keratinocytes","volume":"8","author":"Petruk","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Saggese, A., Culurciello, R., Casillo, A., Corsaro, M.M., Ricca, E., and Baccigalupi, L. (2018). A marine isolate of Bacillus pumilus secretes a pumilacidin active against Staphylococcus aureus. Mar. Drugs, 16.","DOI":"10.3390\/md16060180"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Saggese, A., De Luca, Y., Baccigalupi, L., and Ricca, E. (2022). An antimicrobial peptide specifically active against Listeria monocytogenes is secreted by Bacillus pumilus SF214. BMC Microbiol., 22.","DOI":"10.1186\/s12866-021-02422-9"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/j.chom.2007.05.004","article-title":"The Bacillus subtilis quorum-sensing molecule CSF contribute to intestinal homoestasis via OCTN2, a host cell membrane transporter","volume":"1","author":"Fujita","year":"2007","journal-title":"Cell Host Microbe"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"609","DOI":"10.3920\/BM2016.0020","article-title":"Bacillus megaterium SF185 induces stress pathways and affects the cell cycle distribution of human intestinal epithelial cells","volume":"7","author":"Varriale","year":"2016","journal-title":"Benef. Microbes"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"2178","DOI":"10.1111\/j.1365-2672.2008.03934.x","article-title":"Characterization of spore forming Bacilli isolated from the human gastrointestinal tract","volume":"105","author":"Fakhry","year":"2008","journal-title":"J. Appl. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1099\/ijsem.0.003775","article-title":"A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov","volume":"70","author":"Patel","year":"2020","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Manzo, N., D\u2019Apuzzo, E., Coutinho, P.M., Cutting, S.M., Henrissat, B., and Ricca, E. (2011). Carbohydrate-active enzymes from pigmented Bacilli: A genomic approach to assess carbohydrate utilization and degradation. BMC Microbiol., 11.","DOI":"10.1186\/1471-2180-11-198"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Xu, J., Mahowald, M.A., Ley, R.E., Lozupone, C.A., Hamady, M., Martens, E.C., Henrissat, B., Coutinho, P.M., Minx, P., and Latreille, P. (2007). Evolution of Symbiotic Bacteria in the Distal Human Intestine. PLoS Biol., 5.","DOI":"10.1371\/journal.pbio.0050156"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1038\/nrmicro3050","article-title":"The abundance and variety of carbohydrate-active enzymes in the human gut microbiota","volume":"11","author":"Armougom","year":"2013","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Ozer, E.A. (2018). ClustaAGE: A tool for clustering and distribution analysis of bacterial accessory genomic elements. BMC Bioinform., 19.","DOI":"10.1186\/s12859-018-2154-x"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"3053","DOI":"10.1128\/JCM.40.8.3053-3056.2002","article-title":"Enterotoxigenic profiles of food-poisoning and food-borne Bacillus cereus strains","volume":"40","author":"Guinebretiere","year":"2002","journal-title":"J. Clin. Microbiol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"3147","DOI":"10.1128\/AEM.68.6.3147-3151.2002","article-title":"Enterotoxin production in natural isolates of Bacillaceae outside the Bacillus cereus group","volume":"68","author":"Phelps","year":"2002","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1093\/oxfordjournals.jbchem.a135315","article-title":"Subtilosin A, a new antibiotic peptide produced by Bacillus subtilis 168: Isolation, structural analysis, and biogenesis","volume":"98","author":"Babasaki","year":"1985","journal-title":"J. Biochem."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1093\/jac\/dkl495","article-title":"The spectrum of antimicrobial activity of the bacteriocin subtilosin A","volume":"59","author":"Shelburne","year":"2007","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1007\/s12602-016-9242-x","article-title":"Subtilosin Prevents Biofilm Formation by Inhibiting Bacterial Quorum Sensing","volume":"9","author":"Algburi","year":"2017","journal-title":"Probiotics Antimicrob Proteins"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1016\/j.jbiotec.2020.12.017","article-title":"Bacilysin within the Bacillus subtilis group: Gene prevalence versus antagonistic activity against Gram-negative foodborne pathogens","volume":"327","author":"Nannan","year":"2021","journal-title":"J. Biotechnol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1021\/bi3016229","article-title":"Action and Timing of BacC and BacD in the Late Stages of Biosynthesis of the Dipeptide Antibiotic Bacilysin","volume":"52","author":"Parker","year":"2013","journal-title":"Biochemistry"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1926","DOI":"10.1021\/acs.biochem.1c00283","article-title":"Substrate substitution in Kanosamine biosynthesis using phosphonates and phosphite rescue","volume":"60","author":"Vetter","year":"2021","journal-title":"Biochemistry"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"108139","DOI":"10.1016\/j.abb.2019.108139","article-title":"The kanosamine biosynthetic pathway in Bacillus cereus UW85: Functional and kinetic characterization of KabA, KabB, and KabC","volume":"676","author":"Prasertanan","year":"2019","journal-title":"Arch. Biochem. Biophys."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/j.ijmm.2013.08.012","article-title":"Epidermin and gallidermin: Staphylococcal lantibiotics","volume":"304","author":"Gotz","year":"2014","journal-title":"Int. J. Med. Microbiol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1111\/1751-7915.12274","article-title":"Extracellular Streptomyces lividans vesicles: Composition, biogenesis and antimicrobial activity","volume":"8","author":"Schrempf","year":"2015","journal-title":"Microb. Biotechnol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.mib.2017.08.006","article-title":"Bacterial nanotubes: A conduit for intercellular molecular trade","volume":"42","author":"Baidya","year":"2017","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_40","unstructured":"European Food Safety Authority (2021, February 01). Guidance on the Assessment of Bacterial Susceptibility to Antimicrobials of Human and Veterinary Importance. Available online: https:\/\/www.efsa.europa.eu\/sites\/default\/files\/consultation\/120323.pdf."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"202","DOI":"10.3389\/fmicb.2013.00202","article-title":"Antibiotic resistance in probiotic bacteria","volume":"4","author":"Gueimonde","year":"2013","journal-title":"Front. Microbiol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"4595","DOI":"10.1007\/s00253-016-7416-9","article-title":"Integrate genome-based assessment of safety for probiotic strains: Bacillus coagulans GBI-30, 6086 as a case study","volume":"100","author":"Salvetti","year":"2016","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1016\/j.ijmm.2013.02.009","article-title":"Intrinsic antibiotic resistance: Mechanisms, origins, challenges and solutions","volume":"303","author":"Cox","year":"2013","journal-title":"Int. J. Med. Microbiol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1016\/j.jss.2007.04.021","article-title":"Characterization of HCT116 human colon cancer cells in an orthotopic model","volume":"147","author":"Rajput","year":"2008","journal-title":"J. Surg. Res."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Marzorati, M., Van den Abbeele, P., Bubeck, S.S., Bayne, T., Krishnan, K., Young, A., Mehta, D., and DeSouza, A. (2020). Bacillus subtilis HU58 and Bacillus coagulans SC208 Probiotics Reduced the Effects of Antibiotic-Induced Gut Microbiome Dysbiosis in An M-SHIME \u00ae Model. Microorganisms, 8.","DOI":"10.3390\/microorganisms8071028"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"2429","DOI":"10.1099\/ijs.0.009126-0","article-title":"Phylogeny and molecular taxonomy of the Bacillus subtilis species complex and description of Bacillus subtilis subsp. inaquosorum subsp. nov","volume":"59","author":"Rooney","year":"2009","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/s12934-017-0691-z","article-title":"Beneficial effects on host energy metabolism of short-chain fatty acids and vitamins produced by commensal and probiotic bacteria","volume":"16","author":"LeBlanc","year":"2013","journal-title":"Microb. Cell Fact."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"118","DOI":"10.3390\/nu3010118","article-title":"Folate production by probiotic bacteria","volume":"3","author":"Rossi","year":"2011","journal-title":"Nutrients"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"107453","DOI":"10.1016\/j.biotechadv.2019.107453","article-title":"Microbial production of vitamin K2: Current status and future prospects","volume":"39","author":"Ren","year":"2020","journal-title":"Biotechnol. Adv."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1016\/j.ajhg.2011.11.011","article-title":"Lipoic Acid Synthetase Deficiency Causes Neonatal-Onset Epilepsy, Defective Mitochondrial Energy Metabolism, and Glycine Elevation","volume":"89","author":"Mayr","year":"2011","journal-title":"Am. J. Hum. Genet."},{"key":"ref_51","unstructured":"Harwood, C.R., and Cutting, S.M. (1990). Sporulation, Germination, and Outgrowth. Molecular Biological Methods for Bacillus, John Wiley and Sons."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1513","DOI":"10.1128\/JB.00023-16","article-title":"CotG-Like Modular Proteins Are Common among Spore-Forming Bacilli","volume":"198","author":"Saggese","year":"2016","journal-title":"J. Bacteriol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"fnw049","DOI":"10.1093\/femsle\/fnw049","article-title":"MEGAnnotator: A user-friendly pipeline for microbial genomes assembly and annotation","volume":"363","author":"Lugli","year":"2016","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1901","DOI":"10.1128\/aem.55.8.1901-1906.1989","article-title":"Antibacterial activity of Lactobacillus sake isolated from meat","volume":"55","author":"Shillinger","year":"1989","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Zanfardino, A., Migliardi, A., D\u2019Alonzo, D., Lombardi, A., Varcamonti, M., and Cordone, A. (2016). Inactivation of MSMEG_0412 gene drastically affects surface related properties of Mycobacterium smegmatis. BMC Microbiol., 16.","DOI":"10.1186\/s12866-016-0888-z"},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Vittoria, M., Saggese, A., Di Gregorio Barletta, G., Castaldi, S., Isticato, R., Baccigalupi, L., and Ricca, E. (2022). Sporulation efficiency and spore quality in a human intestinal isolate of Bacillus cereus. bioRxiv.","DOI":"10.1101\/2022.06.22.497182"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/j.anaerobe.2011.05.017","article-title":"The human commensal Bacteroides fragilis binds intestinal mucin","volume":"17","author":"Huang","year":"2011","journal-title":"Anaerobe"},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Maia, A.R., Reyes-Ram\u00edrez, R., Pizarro-Guajardo, M., Saggese, A., Castro-C\u00f3rdova, P., Isticato, R., Ricca, E., Paredes-Sabja, D., and Baccigalupi, L. (2020). Induction of a Specific Humoral Immune Response by Nasal Delivery of Bcla2ctd of Clostridioides difficile. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21041277"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/23\/14946\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:29:15Z","timestamp":1760146155000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/23\/14946"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,29]]},"references-count":58,"journal-issue":{"issue":"23","published-online":{"date-parts":[[2022,12]]}},"alternative-id":["ijms232314946"],"URL":"https:\/\/doi.org\/10.3390\/ijms232314946","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,29]]}}}