atcc 49726  (ATCC)

Journal: mSystems

Article Title: Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses

doi: 10.1128/msystems.01132-24

Figure Lengend Snippet: The four nasal Corynebacterium species have core genomes that have leveled off and pangenomes that remain open. (A) All four species have a core genome that has leveled off using a Tettelin curve fit model. (Ai) The C. propinquum core genome ( n = 19) leveled off at ~12 genomes. (Aii) The C. pseudodiphtheriticum core genome ( n = 42) leveled off at ~19 genomes. (Aiii) The C. accolens core genome ( n = 33) leveled off at ~21 genomes. (Aiv) The C. tuberculostearicum core genome ( n = 8) leveled off at ~7 genomes. Two best-fit curve line models are shown for the core genome: Tettelin (red) and Willenbrock (blue). ( B ) The pangenomes for the four Corynebacterium species ( i–vi ) remain open as indicated by the continuous steep slope of the best-fit line shown in purple. Core and pangenome size estimations were calculated from 10 random genome samplings (represented by gray dots) using the OMCL algorithm predicted GCs with GET_HOMOLOGUES v24082022.

Article Snippet: A combined pangenome was also computed for 107 strains: the 102 nasal Corynebacterium genomes selected for metabolic analysis (Cac_ATCC_49726 & Cps_090104 were excluded) plus 5 Corynebacterium listed in .

Techniques:

Journal: mSystems

Article Title: Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses

doi: 10.1128/msystems.01132-24

Figure Lengend Snippet: Basic genomic information for four common human nasal-associated Corynebacterium species

Article Snippet: A combined pangenome was also computed for 107 strains: the 102 nasal Corynebacterium genomes selected for metabolic analysis (Cac_ATCC_49726 & Cps_090104 were excluded) plus 5 Corynebacterium listed in .

Techniques:

Journal: mSystems

Article Title: Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses

doi: 10.1128/msystems.01132-24

Figure Lengend Snippet: Pangenomic estimation of human nasal-associated Corynebacterium species based on three different platforms

Article Snippet: A combined pangenome was also computed for 107 strains: the 102 nasal Corynebacterium genomes selected for metabolic analysis (Cac_ATCC_49726 & Cps_090104 were excluded) plus 5 Corynebacterium listed in .

Techniques:

Journal: mSystems

Article Title: Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses

doi: 10.1128/msystems.01132-24

Figure Lengend Snippet: GCs assigned to COG metabolism categories are overrepresented in the persistent compared to the accessory genomes of each species indicating limited strain-specific metabolism. We identified the COG functional annotations for GCs using anvi’o and then used PPanGGOLiN to assign GCs to the persistent vs accessory genome. ( A ) Over one-third of the GCs in each species ( i–iv ) were assigned as uninformative (black), ambiguous (dark gray), or unclassified (gray) across both the persistent and accessory genomes. The combined percentage of each of these categories out of all the genes per species was 38.1% Cpr , 37.9% Cps , 37.1% Cac , and 38.3% Ctu . For each species, the percentage of GCs with an informative COG assignment was higher in the persistent genome, 64.9% Cpr (1262), 65.3% Cps (1156), 64.7% Cac (1300), and 63.5% Ctu (1264), than in the accessory genome, with 28.9% Cpr (336), 29.9% Cps (543), 25.7% Cac (363), and 35.6% Ctu (326). ( B ) Functional enrichment of GCs in the persistent vs the accessory genome for the different COG categories. Metabolic COG categories, for example, those involved in energy production (pale orange), or amino acid (yellow), nucleotide (gold), carbohydrate (khaki), and lipid metabolism (dark salmon), were enriched in the persistent genome of each species. By contrast, mobilome (bright orange) and to a lesser extent defense mechanisms were enriched in the accessory genomes. Each Corynebacterium species shared similar COG functional enrichment ratios of GCs in its persistent vs its accessory genome.

Article Snippet: A combined pangenome was also computed for 107 strains: the 102 nasal Corynebacterium genomes selected for metabolic analysis (Cac_ATCC_49726 & Cps_090104 were excluded) plus 5 Corynebacterium listed in .

Techniques: Functional Assay

Journal: mSystems

Article Title: Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses

doi: 10.1128/msystems.01132-24

Figure Lengend Snippet: List of estimated complete KEGG modules. Module ID numbers are colored based on their KEGG module subcategory; red: “amino acid metabolism,” dark teal: “biosynthesis of terpenoids and polyketides,” green: “carbohydrate metabolism,” gray: “energy metabolism,” dark orange: “lipid metabolism,” orange: “metabolism of cofactors and vitamins,” yellow: “nucleotide metabolism.” Complete KEGG modules shared by D. pigrum and all four Corynebacterium species are highlighted in pale yellow. Complete KEGG modules shared by the majority (≥78%) of the 27 D. pigrum strain genomes are highlighted in light blue. PRPP is 5-phosphoribosyl diphosphate, DAP is diaminopimelate, FMN is flavin mononucleotide, FAD is flavin adenine dinucleotide, ACP is acyl-carrier protein, HMP is 4-amino-5-hydroxymethyl-2-methylpyrimidine, HET is 5-(2-hydroxyethyl)-4-methylthiazole, and TMP is thiamine monophosphate.

Article Snippet: A combined pangenome was also computed for 107 strains: the 102 nasal Corynebacterium genomes selected for metabolic analysis (Cac_ATCC_49726 & Cps_090104 were excluded) plus 5 Corynebacterium listed in .

Techniques:

Journal: mSystems

Article Title: Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses

doi: 10.1128/msystems.01132-24

Figure Lengend Snippet: C. tuberculostearicum accumulates intracellular glycogen. ( A ) Growth curves for each of the nasal Corynebacterium species at 34°C in a MOPs-buffered CDM with all 20 amino acids and 5% glucose, with C. glutamicum as a positive control for the assay. C. propinquum and C. pseudodiphtheriticum reached stationary phase at a lower optical density at wavelength 600 nm (OD 600 ) than did C. tuberculostearicum and C. accolens , with C. glutamicum T reaching the highest. ( B ) Overall, C. tuberculostearicum accumulated more intracellular glycogen than the other three nasal species ( P -value range 0.033 to 0.009), and less than C. glutamicum ( P = 6.64 × 10 −10 ). Intracellular glycogen content was quantified in µg/mL at timepoints between 24 and 48 hours. Statistics were done using a linear mixed model with species as a fixed effect and time points as a random effect. Boxplots show the median with the first and third quartiles. Data ( A and B ) are from n = 3 independent experiments. Species labels: C. propinquum KPL3953 ( Cpr ) , C. pseudodiphtheriticum KPL1989 ( Cps ) , C. accolens KPL1818 ( Cac ) , C. tuberculostearicum MSK074 ( Ctu ), and C. glutamicum DSM 20300 T ( Cgl ).

Article Snippet: A combined pangenome was also computed for 107 strains: the 102 nasal Corynebacterium genomes selected for metabolic analysis (Cac_ATCC_49726 & Cps_090104 were excluded) plus 5 Corynebacterium listed in .

Techniques: Positive Control

Journal: mSystems

Article Title: Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses

doi: 10.1128/msystems.01132-24

Figure Lengend Snippet: Each of the four nasal Corynebacterium species encodes for an increased metabolic capacity compared to D. pigrum . This heatmap shows stepwise module completeness averaged by KEGG module subcategory (x-axis labels) for each of four nasal Corynebacterium species (average genome size, 2.3–2.5 Mb) and for D. pigrum (avg. genome size 1.9 Mb). Average stepwise completion scores were calculated including only modules detected in at least one of the analyzed genomes. The color legend on the bottom represents KEGG module categories and corresponds with the colors in . (P) and (S) indicate Pathway and Signature modules, respectively. Species labels: C. propinquum ( Cpr ) , C. pseudodiphtheriticum (Cps), C. accolens (Cac), C. tuberculostearicum (Ctu ), and D. pigrum ( Dpi ).

Article Snippet: A combined pangenome was also computed for 107 strains: the 102 nasal Corynebacterium genomes selected for metabolic analysis (Cac_ATCC_49726 & Cps_090104 were excluded) plus 5 Corynebacterium listed in .

Techniques: