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Consequently, characterizing their diversity is important for understanding the microbiome in health and disease. Whole genome sequences from 181<jats:italic>Neisseria<\/jats:italic>isolates were examined, including those of three well-defined species (<jats:italic>N. meningitidis; N. gonorrhoeae;<\/jats:italic>and<jats:italic>Neisseria polysaccharea<\/jats:italic>) and genomes of isolates unassigned to any species (<jats:italic>Nspp)<\/jats:italic>. Sequence analysis of ribosomal genes, and a set of core (cgMLST) genes were used to infer phylogenetic relationships. Average Nucleotide Identity (ANI) and phenotypic data were used to define species clusters, and morphological and metabolic differences among them. Phylogenetic analyses identified two polyphyletic clusters (<jats:italic>N. polysaccharea<\/jats:italic>and<jats:italic>Nspp<\/jats:italic>.), while, cgMLST data grouped<jats:italic>Nspp<\/jats:italic>isolates into nine clusters and identified at least three<jats:italic>N. polysaccharea<\/jats:italic>clusters. ANI results classified<jats:italic>Nspp<\/jats:italic>into seven putative species, and also indicated at least three putative<jats:italic>N. polysaccharea<\/jats:italic>species. Electron microscopy identified morphological differences among these species. This genomic approach provided a consistent methodology for species characterization using distinct phylogenetic clusters. Seven putative novel<jats:italic>Neisseria<\/jats:italic>species were identified, confirming the importance of genomic studies in the characterization of the genus<jats:italic>Neisseria<\/jats:italic>.<\/jats:p>","DOI":"10.1038\/s41598-019-50203-2","type":"journal-article","created":{"date-parts":[[2019,9,24]],"date-time":"2019-09-24T10:03:28Z","timestamp":1569319408000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":45,"title":["Genomic characterization of novel Neisseria species"],"prefix":"10.1038","volume":"9","author":[{"given":"Kanny","family":"Diallo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jenny","family":"MacLennan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1623-0295","authenticated-orcid":false,"given":"Odile B.","family":"Harrison","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chisomo","family":"Msefula","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samba O.","family":"Sow","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Doumagoum M.","family":"Daugla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Errin","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline","family":"Trotter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Calman A.","family":"MacLennan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7069-5958","authenticated-orcid":false,"given":"Julian","family":"Parkhill","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ray","family":"Borrow","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian M.","family":"Greenwood","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6321-5138","authenticated-orcid":false,"given":"Martin C. 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