Journal: medRxiv

Article Title: Integrative Genomic, Transcriptomic, and Microbiome Profiles of Colon Cancer by Ancestry Provide Insights into Molecular Distinctions

doi: 10.64898/2026.03.25.26349226

Figure Lengend Snippet: A) Alpha diversity (Observed richness, Shannon index) in tumor vs. non-tumor samples (n = 32, 31), and tumors stratified by location (right, n = 16; left, n = 16) or stage (early, n = 22; late, n = 10). B) Differential abundance analysis at the species level comparing tumor vs non-tumor (left), right vs left tumor (middle), and early vs late stage tumor (right). Volcano plots highlight significantly enriched taxa (FDR < 0.05). C) Phylum-level taxonomic composition in tumor and non-tumor tissues, showing enrichment of Fusobacteriota in tumors. D) Genus-level composition of tumors stratified by Fusobacterium nucleatum detection by qPCR (positive vs. negative). E) Top species enriched in tumors from African (AFRg) and European (EURg) ancestry patients (n = 68, WGS); dot size reflects significance (–log10 FDR); colors denote ancestry specificity (red = AFR only, purple = shared). F) Oral-origin taxa significantly enriched in tumors based on presence/absence data and annotation using the Human Oral Microbiome Database (HOMD v16.01). Bar length indicates log2 odds ratio of presence in tumor vs non-tumor (Fisher’s exact test). 16S rRNA sequencing was performed in a sub-cohort of 32 patients (A–D), and WGS in 68 patients (E–F) from the P-1000 cohort.

Article Snippet: For absolute quantification, microbial genomic DNA of F. nucleatum subsp. nucleatum strain VPI 4355 (ATCC # 25586D-5) was used to prepare the standard curve and as a positive control; the negative control was sterile H 2 O.

Techniques: Sequencing

Journal: Microorganisms

Article Title: In Vitro Inhibition of Pathogens by Polyols: Optical Density-Based Screening and Implications for the Oral–Systemic Axis

doi: 10.3390/microorganisms14040884

Figure Lengend Snippet: Endpoint OD600 of Fusobacterium nucleatum at 25.5 h across polyol concentrations. Bars show mean ± SD ( n = 3). Different letters within a concentration indicate Tukey’s HSD groupings ( p < 0.05). The dashed line indicates the untreated control mean. The untreated control mean OD was 1.070 +/− 0.485, whereas that of erythritol 1% was 1.823 +/− 0.163 and that of erythritol 2% was 1.413 +/− 0.374; for D-mannose 1%, the mean OD was 1.577 +/− 0.091, and for D-mannose 2%, it was 1.427 +/− 0.087.

Article Snippet: The following microorganisms were evaluated: Streptococcus mutans (ATCC 25175), Streptococcus anginosus (ATCC 700231), Candida albicans (ATCC 18804), and Fusobacterium nucleatum subsp. nucleatum (ATCC 23726).

Techniques: Concentration Assay, Control

Journal: bioRxiv

Article Title: Growth rate alterations of human colorectal cancer cells by 157 gut bacteria

doi: 10.1101/2019.12.14.876367

Figure Lengend Snippet: Growth rate scores of six human cell lines upon treatment with bacterial cells and secretomes. (A) Heatmap indicating low and high growth rate scores, respectively red and blue. Bacteria are sorted within bacterial families by the average growth rate score. Red numbered octagons highlight the strains discussed in the text: Bacteroides sp. 2_1_22 (1) , B. fragilis K570 clinda R (ETBF) (2), B. sp. 4_1_36 (3), Clostridium septicum (Mace 1889) Ford 1927 (4), C. sp. D5 (5), Escherichia coli D9 (6), Klebsiella sp. 1_1_55 (7), E. coli 4_1_47FAA (8), F. nucleatum DSM 15643 (ATCC 25586) (9), F. nucleatum DSM 20482 (ATCC 10953) (10), F. necrophorum subsp. funduliforme 1_1_36S (11), F. nucleatum subsp. animalis 11_3_2 (12), Lachnospiraceae bacterium 8_1_57FAA (13), L. bacterium 3_1_46FAA (14), Streptococcus bovis 1212 (15), S. bovis 1459 (16), S. bovis 1417 (17), S. bovis 207 (18), Pediococcus acidilactici 7_4 (19), Pseudomonas sp. 2_1_26 (20), D. sp. 6_1_46AFAA (21), Ralstonia sp. 5_2_56FAA (22), Ruminococcaceae bacterium D16 (23), Synergistes sp. 3_1_syn1 (24), Desulfovibrio sp. 3_1_syn3 (25) , Propionibacterium sp. 5_U_42AFAA (26), and Eubacterium sp . 3_1_31 (27). Highlighted with asterisks are cases that correspond to the 5% extremes of the z-score distribution. (B) Distribution of the growth rate scores for bacterial cells and secretomes.

Article Snippet: We purchased 96 bacterial strains from the reference catalogue of the Human Microbiome Project (HMP, Prof. Dr. Emma Allen-Vercoe from the University of Guelph in Guelph, Canada); 24 bacteria were kindly provided by Prof. Dr. Cynthia L. Sears from Johns Hopkins Medical Institutions, Baltimore, MD, USA; five strains were purchased from DSMZ ( Clostridium septicum (Macé 1889) Ford 1927 DSM7534, C. difficile (Hall and O’Toole 1935) Lawson et al. 2016 DSM27543 (known as Clostridium difficile 630, PMID: 6870225), Fusobacterium nucleatum Knorr 1922 DSM15643, Fusobacterium nucleatum subsp. polymorphum (ex Knorr 1922) Dzink et al. 1990 DSM20482, and Peptostreptococcus stomatis Downes and Wade 2006 DSM17678); one strain from ATCC ( Streptococcus agalactiae ATCC13813); and 31 bacteria were in stock at the Radboud University Medical Center in Nijmegen, The Netherlands ( – ).

Techniques: