TABLE 1.
Classifiers assigned to host genera and yield of the curation process
| No. of: |
|||||||
|---|---|---|---|---|---|---|---|
| Host genus or group | Gram group | Outer architecture | Chemotype | Retrieved phage genomes | Genes detected by annotation | Genes after curation (final) | PF hits |
| Achromobacter | − | Diderm (lipopolysaccharide) | A1γ | 36 | 32 | 10 | 13 |
| Acidovorax | − | Diderm (lipopolysaccharide) | A1γ | 3 | 4 | 2 | 2 |
| Acinetobacter | − | Diderm (lipopolysaccharide) | A1γ | 139 | 152 | 50 | 57 |
| Aeromonas | − | Diderm (lipopolysaccharide) | A1γ | 95 | 77 | 26 | 27 |
| Bacteroides | − | Diderm (lipopolysaccharide) | A1γ | 5 | 6 | 3 | 3 |
| Burkholderia | − | Diderm (lipopolysaccharide) | A1γ | 72 | 61 | 27 | 36 |
| Caulobacter | − | Diderm (lipopolysaccharide) | A1γ | 42 | 58 | 17 | 17 |
| Cellulophaga | − | Diderm (lipopolysaccharide) | A1γ | 52 | 38 | 9 | 9 |
| Cronobacter | − | Diderm (lipopolysaccharide) | A1γ | 45 | 64 | 24 | 26 |
| Enterobacter | − | Diderm (lipopolysaccharide) | A1γ | 1 | 1 | ||
| Enterobacteria | − | Diderm (lipopolysaccharide) | A1γ | 797 | 300 | 3 | 3 |
| Enterovibrio | − | Diderm (lipopolysaccharide) | A1γ | 2 | 2 | ||
| Escherichia | − | Diderm (lipopolysaccharide) | A1γ | 684 | 745 | 211 | 231 |
| Fusobacterium | − | Diderm (lipopolysaccharide) | A1γa | 4 | 3 | 3 | 3 |
| Klebsiella | − | Diderm (lipopolysaccharide) | A1γ | 266 | 259 | 67 | 71 |
| Microcystis | − | Diderm (lipopolysaccharide) | A1γ | 8 | 8 | 5 | 5 |
| Pseudomonas | − | Diderm (lipopolysaccharide) | A1γ | 625 | 485 | 89 | 98 |
| Ralstonia | − | Diderm (lipopolysaccharide) | A1γ | 68 | 21 | 14 | 15 |
| Salmonella | − | Diderm (lipopolysaccharide) | A1γ | 414 | 444 | 90 | 93 |
| Serratia | − | Diderm (lipopolysaccharide) | A1γ | 31 | 40 | 13 | 16 |
| Shewanella | − | Diderm (lipopolysaccharide) | A1γ | 1 | 1 | ||
| Shigella | − | Diderm (lipopolysaccharide) | A1γ | 3 | 3 | ||
| Sphingobium | − | Diderm (lipopolysaccharide) | A1γ | 2 | 2 | 1 | 2 |
| Sphingomonas | − | Diderm (glycosphingolipid) | A1γ | 7 | 2 | 1 | 1 |
| Stenotrophomonas | − | Diderm (lipopolysaccharide) | A1γ | 28 | 25 | 6 | 8 |
| Vibrio | − | Diderm (lipopolysaccharide) | A1γ | 578 | 225 | 76 | 85 |
| Yersinia | − | Diderm (lipopolysaccharide) | A1γ | 70 | 62 | 16 | 16 |
| Arthrobacter | + | Monoderm | A3αb | 316 | 400 | 103 | 161 |
| Bacillus | + | Monoderm | A1α | 348 | 400 | 150 | 286 |
| Bifidobacteriumc | + | Monoderm | A4α | 10 | 2 | 1 | 1 |
| Clostridioides | + | Monoderm | A1γ | 23 | 25 | ||
| Clostridium | + | Monoderm | A1γ | 109 | 174 | 30 | 43 |
| Corynebacterium | + | Diderm (mycolic acid) | A1γ | 40 | 30 | 16 | 24 |
| Cutibacterium | + | Monoderm | A3γ | 65 | 65 | ||
| Enterococcus | + | Monoderm | A3α (E. faecalis), A4α (E. faecium)d | 127 | 150 | 50 | 77 |
| Lacticaseibacillus | + | Monoderm | A4α | 13 | 28 | ||
| Lactiplantibacillus | + | Monoderm | A4α | 18 | 42 | ||
| Lactobacillus | + | Monoderm | A4α | 105 | 133 | 22 | 41 |
| Lactococcus | + | Monoderm | A3α | 388 | 376 | 121 | 144 |
| Leuconostoc | + | Monoderm | A3α | 35 | 45 | 11 | 16 |
| Levilactobacillus | + | Monoderm | A4α | 9 | 14 | ||
| Limosilactobacillus | + | Monoderm | A4α | 6 | 14 | ||
| Listeria | + | Monoderm | A1γ | 75 | 87 | 17 | 32 |
| Mycobacterium | + | Diderm (mycolic acid) | A1γ | 1,990 | 3,596 | 299 | 374 |
| Propionibacterium | + | Monoderm | A3γ | 202 | 214 | 5 | 8 |
| Rhodococcus | + | Diderm (mycolic acid) | A1γ | 70 | 83 | 31 | 70 |
| Staphylococcus | + | Monoderm | A3α | 349 | 456 | 79 | 155 |
| Streptococcus | + | Monoderm | A3α | 1,064 | 739 | 246 | 688 |
| Streptomyces | + | Monoderm | A3γ | 240 | 208 | 97 | 151 |
| Totale | 9,539 | 10,206 | 2,182 | 3,303 | |||
| Gram-negative | 4,071 | 3,113 | 770 | 844 | |||
| Gram-positive | 5,468 | 7,093 | 1,412 | 2,459 | |||
a
Contains lanthionine instead of m-DAP.
b
Although there seems to be some variety in peptidoglycan structure among Arthrobacter, we assigned the most common chemotype.
c
There are several chemotypes within Bifidobacterium, but A4α was assigned to the only Bifidobacterium host entry in our database (Bifidobacterium thermophilus).
d
Phage lysins with unassigned Enterococcus host species were included within E. faecalis.
e
In the last three rows, data are the sum of the column values (phage genomes, genes detected, and genes after curation) or weighted averages (PF hits per protein).