16s rrna amplicon sequencing  (Novogene)

Journal: Microbiome

Article Title: Amino acid availability influences Staphylococcus aureus interaction with the nasal microbiota in a strain- and community-specific manner

doi: 10.1186/s40168-026-02563-x

Figure Lengend Snippet: Species composition and structure of 11 nasal communities. A Schematic methodology used to determine nasal community structures and establish the strain collection LaCa. B, C Relative species abundance determined by 16S rRNA gene sequencing of nasal metagenomic DNA ( B ) or by isolation and enumeration of nasal species on plates ( C ), from the nasal microbiomes of eleven healthy volunteers ( A – K ). Each color designates one of the 20 most abundant species across all volunteers. Less abundant species were assigned to “Other species”. Species with a missing or unclear identification were assigned to “Not identified”. Below the bars, “ + ” indicates the volunteers in which S. aureus was detected by both techniques, and numbers correspond to the community state type (CST) assigned to the corresponding community. “a” refers to ambiguous S. aureus carriage (detected by only one method) or CST classification (balanced proportion of several species). Each bar displays the results of one replicate. See also Supplementary Fig. S1 and Tables S1, S2, and S3

Article Snippet: Briefly, for 16S rRNA gene amplicon sequencing, total microbial DNA was extracted from the sample (1 mL Amies medium in which nasal swabs were suspended, or 500 μL of bacterial suspension derived from SynCom cultures) using the HostZero Microbial DNA kit (Zymo Research), including the host DNA depletion step for nasal swab samples.

Techniques: Sequencing, Isolation

Journal: Microbiome

Article Title: Amino acid availability influences Staphylococcus aureus interaction with the nasal microbiota in a strain- and community-specific manner

doi: 10.1186/s40168-026-02563-x

Figure Lengend Snippet: S. aureus and SynComs dynamics in mono- and cocultivation. A Schematic methodology used to study synthetic communities in vitro and in vivo. B Relative species abundance determined by 16S rRNA gene sequencing from frozen SynComs (Input) or SynComs cultivated 72 h on SNM agar in isolation for two biological replicates (R1, R2). Each color designates a species. Less abundant species were assigned to “Other species”. Complete data is detailed in Supplementary Table S4. See also Supplementary Fig. 4. C Heatmap depicting the growth fold-change induced by synthetic culture with five different SynComs (A, B, C, J, K) on SNM agar, for four S. aureus strains. Sa A, Sa B, and Sa C originated from volunteers A, B, and C, respectively. Positive fold-changes (verdigris) and negative fold-changes (red) indicate increases or decreases in S. aureus cell numbers in synthetic culture relative to the monoculture, respectively. Each fold-change is based on four biological replicates. Significant changes are marked with stars (* P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001, 2-way ANOVA). See also Supplementary Fig. S5. D. Barplots depicting the bacterial counts of S. aureus Sa A recovered from the noses of gnotobiotic mice, 7 days after nasal inoculation in isolation or in the presence of three different SynComs. Bars represent the median ± interquartile range from 5 to 6 animals per group. Dashed lines represent the nasal inoculum and the detection limit. Statistical significance is indicated by *** P adj < 0.001 (Kruskal–Wallis with Dunn’s correction)

Article Snippet: Briefly, for 16S rRNA gene amplicon sequencing, total microbial DNA was extracted from the sample (1 mL Amies medium in which nasal swabs were suspended, or 500 μL of bacterial suspension derived from SynCom cultures) using the HostZero Microbial DNA kit (Zymo Research), including the host DNA depletion step for nasal swab samples.

Techniques: In Vitro, In Vivo, Sequencing, Isolation, Co-Cultures