Means and methods for classifying microbes

A kit comprising a set of pure microbial cultures or stocks thereof, wherein said set comprises at least 2, 10, 15 or 50 target microbes selected from a group consisting of at least one of the following (i) to (iv):

• (i) Acinetobacter johnsonii, Acinetobacter tjernbergiae, Arthrobacter chlorophenolicus, Bacillus subtilis, Caulobacter crescentus, Cryptococcus albidus, Escherichia coli, Escherichia coli MG1655, Escherichia coli DH5a, Lactococcus lactis, Pseudomonas knackmussii, Pseudomonas migulae, Pseudomonas putida, Pseudomonas veronii, Sphingomonas wittichii, Sphingomonas yanoikuyae, and any subpopulation thereof;
• (ii) Stenotrophomonas rhizophila, Kocuria rhizophila, and Paenibacillus polymyxa, and any subpopulation thereof;
• (iii) Bacteroides cellulosilyticus, Bacteroides caccae, Parabacteroides distasonis, Ruminococcus torques, Clostridium scindens, Collinsella aerofaciens, Bacteroides thetaiotaomicron, Bacteroides vulgatus, Bacteroides ovatus, Bacteroides uniformis, Eumicrobe rectale, Clostridium spiroforme, Faecalimicrobe prausnitzii, Ruminococcus obeum, Dorea longicatena, Clostridioides difficile, Escherichia coli, Klebsiella sp., Salmonella sp., and any subpopulation thereof, preferably at least Clostridioides difficile, Clostridium scindens, Escherichia coli, Klebsiella sp., and/or Salmonella sp., and any subpopulation thereof;
• (iv) Bacteroides fragilis, Bacteroides vulgatus, Bifidobacterium adolescentis, Clostridioides difficile, Enterococcus faecalis, Lactobacillus plantarum, Enterobacter cloacae, Escherichia coli, Helicobacter pylori, Salmonella enterica subsp. Entérica, Yersinia enterocolitica, Fusobacterium nucleatum, Bifidobacterium longum, and any subpopulation thereof.

A computer-readable storage medium containing data of a plurality of cells of a plurality of target microbes for generating a classifier for at least one target microbe, wherein said data comprise for each cell of said target microbes

• (a) a label which identifies the type of the cell, and
• (b) an input vector which comprises a plurality of cytometric parameters of said cell,
• wherein said parameters have been determined by flow cytometry;
• and wherein said target microbes comprise at least 2, 10, 15 or 50 target microbes selected from a group consisting of at least one of the following (i) to (iv):
• (i) Acinetobacter johnsonii, Acinetobacter tjernbergiae, Arthrobacter chlorophenolicus, Bacillus subtilis, Caulobacter crescentus, Cryptococcus albidus, Escherichia coli, Escherichia coli MG1655, Escherichia coli DH5a, Lactococcus lactis, Pseudomonas knackmussii, Pseudomonas migulae, Pseudomonas putida, Pseudomonas veronii, Sphingomonas wittichii, Sphingomonas yanoikuyae, and any subpopulation thereof;
• (ii) Stenotrophomonas rhizophila, Kocuria rhizophila, and Paenibacillus polymyxa, and any subpopulation thereof;
• (iii) Bacteroides cellulosilyticus, Bacteroides caccae, Parabacteroides distasonis, Ruminococcus torques, Clostridium scindens, Collinsella aerofaciens, Bacteroides thetaiotaomicron, Bacteroides vulgatus, Bacteroides ovatus, Bacteroides uniformis, Eumicrobe rectale, Clostridium spiroforme, Faecalimicrobe prausnitzii, Ruminococcus obeum, Dorea longicatena, Clostridioides difficile, Escherichia coli, Klebsiella sp., Salmonella sp., and any subpopulation thereof;
• (iv) Bacteroides fragilis, Bacteroides vulgatus, Bifidobacterium adolescentis, Clostridioides difficile, Enterococcus faecalis, Lactobacillus plantarum, Enterobacter cloacae, Escherichia coli, Helicobacter pylori, Salmonella enterica subsp. Entérica, Yersinia enterocolitica, Fusobacterium nucleatum, Bifidobacterium longum, and any subpopulation thereof.