Table 1.
Whole-genome assembly statistics of each of 40 L. buchneri genomes.
Fig 1.
SNP-based phylogenetic tree of 40 L. buchneri isolates and their isolation sources.
Fig 2.
Average nucleotide identity based heat map and clustering of 40 L. buchneri genomes.
The color gradient from red to dark blue shows a higher trend in percent identity.
Fig 3.
PCoA graph of Jaccard distances based on shared genes among 40 L. buchneri genomes analyzed.
Each colored box shows a unique isolation source.
Fig 4.
BLAST Ring Image Generator analysis of 39 L. buchneri genomes against reference genome ATCC 4005.
The innermost ring shows the location of the genome. Prophages and genomic islands were depicted outside of the rings.
Fig 5.
(A) Distribution of the coding sequences across core and pangenome.
(B) Number of core genes (light green curve) vs pan genes (dark blue curve). (C) Flower plot of core and unique gene families of 40 L. buchneri isolates.
Fig 6.
(A) CAZyme heat map of 40 L. buchneri strains.
The color gradient from lighter to darker colors represent the abundance of CAZymes found in each genome. GH: Glycoside hydrolase, GT: Glycosyltransferase, CE: Carbohydrate esterase, AA: Auxiliary activity, CBM: Carbohydrate binding module. R programming language [10] (version 4.1.1) was used to draw the heatmap. (B) Functional COG analysis across core and pangenomes of 40 L. buchneri strains. (Core genes (Red), Accessory genes (Dark blue).
Fig 7.
(A) Phylogenetic tree of 3366 different Cas9s cataloged in Uniprot and 33 LbCas9s.
Widely characterized effectors and LbCas9s are denoted with additional lines. (B) Phylogenetic tree of 33 LbCas9s based on primary amino acid sequence similarity. Colors denote different groups identified by CRISPRviz regarding repeat and spacer similarity.
Fig 8.
(A) Heatmap of all spacers with significant hits, identified by PAMPredict, when searched against IMGVR and IMGPR databases.
Target samples are binned into categories instead of displaying the individual strain information. Dendrograms show the relationships within spacers and hits. (B) In silico predicted PAM sequence as determined by the alignment of 7 different protospacer-flanking sequences. (C) The genomic context of 4 distinct phages from human gut microbiome targeted by spacers are shown. In sequence alignment, the top strands represent the phage (protospacer) and bottom strands represent the spacer sequences.
Fig 9.
(A) Categorization of L. buchneri strains based on their sources of isolation. (B) Representative schematic of the potential lifecycle of L. buchneri strains starting as part of starter cultures used in kefir and silage. Bacteriophages that are targeted by CRISPR resistome are indicated by their sources of isolation. Vertical colored bars below phages represent spacer numbers and identities targeting each phage. (Phage, cucumber, tomato, stool, and sewage icons are sourced from flaticon.com).