Ajit J Shah, H. Shah, Malcom Ward, I. Dekio, Lyna Selami, O. Belgacem, L. Duncan, K. Bruce, Zhen Xu, Hermine V. Mkrtchyan, R. Cave, Laila M. N. Shah, S. Gharbia
{"title":"MALDI-TOF MS and currently related proteomic technologies in reconciling bacterial systematics.","authors":"Ajit J Shah, H. Shah, Malcom Ward, I. Dekio, Lyna Selami, O. Belgacem, L. Duncan, K. Bruce, Zhen Xu, Hermine V. Mkrtchyan, R. Cave, Laila M. N. Shah, S. Gharbia","doi":"10.1079/9781789244984.0093","DOIUrl":"https://doi.org/10.1079/9781789244984.0093","url":null,"abstract":"Abstract\u0000 This book chapter presents an overview and discussion of the use of MALDI-TOF MS for fungal identification. The major known limitations of the technique for fungal taxonomy, and how to overcome these, are also discussed. Moreover, this should guarantee that spectra deposited in such MALDI-TOF MS database would remain public, preferably in open free access. To avoid misidentification, these stored spectra must be curated and based on well-established standard operating procedures. The number of spectra available within species needs to be increased to accommodate the diversity and geographic differences, unique strain traits and the varied culture conditions and procedures in order to establish a single public and open access MALDITOF MS database. This could then be used with metadata analysis and artificial intelligence algorithms, to provide reliable fungal identification.","PeriodicalId":169682,"journal":{"name":"Trends in the systematics of bacteria and fungi","volume":"35 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124098698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Where to now?","authors":"P. Bridge, E. Stackebrandt, David Smith","doi":"10.1079/9781789244984.0320","DOIUrl":"https://doi.org/10.1079/9781789244984.0320","url":null,"abstract":"Abstract\u0000 This chapter provides information on the status quo of molecular assessment of prokaryotes, fungi and yeast. The recent developments in sequencing approaches to assess the diversity of cultured and not-as-yet-cultured organisms and metagenomes, together with the most widely applied algorithms for gene annotation and the pros and cons of defining taxon ranks, are outlined and discussed.","PeriodicalId":169682,"journal":{"name":"Trends in the systematics of bacteria and fungi","volume":"2013 8","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"120968557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genomes reveal the cohesiveness of bacterial species taxa and provide a path towards describing all of bacterial diversity.","authors":"F. Cohan","doi":"10.1079/9781789244984.0282","DOIUrl":"https://doi.org/10.1079/9781789244984.0282","url":null,"abstract":"Abstract\u0000 This book chapter argues that bacterial systematists of the mid-20th century fortuitously created a species-level systematics that actually fits an important universal theory of speciation by discussing taxonomy would allow us to infer the important characteristics of any unknown organism once we classify it to species. It turns out, unexpectedly, that bacterial species taxa share a species-like property with the species taxa of zoology and botany. While recombination within species taxa of all these groups fails to prevent diversification within species, recombination nevertheless appears to act universally as a force of cohesion within species taxa. That is, recurrent recombination within species limits neutral sequence divergence within species taxa of plants, animals, and bacteria; recombination also allows a sharing of generally adaptive genes across a species range. The 95% ANI criterion that demarcates the traditionally defined species taxa of bacteria fortuitously also yields groups of bacteria that are subject to the species-like property of cohesion, where recombination prevents neutral sequence divergence among ecotypes within a species. Use of the ANI criterion, then, not only provides an easily used algorithm for demarcating bacterial species; it also places bacterial demarcation on the same theory-based foundation as the species taxonomy of animals and plants.","PeriodicalId":169682,"journal":{"name":"Trends in the systematics of bacteria and fungi","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128446562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}