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

Journal: Frontiers in Immunology

Article Title: The intratumoral microbiome in breast cancer: an actionable component of the tumor immune microenvironment

doi: 10.3389/fimmu.2026.1944056

Figure Lengend Snippet: Principal original studies characterizing the breast tumor microbiota (Reviews, general microbiome studies, studies conducted in other tumor types, and microbiota therapeutic intervention studies summarized in Table 2 were not included).

Article Snippet: Tzeng et al., 2021 ( ) , Human , Fresh-frozen tumor, tumor-adjacent, high-risk, and healthy breast tissue , Mixed subtypes and stages , 16S rRNA sequencing , Tumor tissues showed reduced bacterial diversity and distinct microbial profiles associated with clinicopathological features and local immune signatures. , 16S qPCR to quantify absolute bacterial load. , None , Operating-room environmental controls; buffer-only extraction negatives; water PCR negatives; Zymo microbial-community positive controls..

Techniques: Microbiome, Tissue, Sequencing, Bacteria, Cell Culture, DNA Sequencing, Sterility, Control, Sampling, Produced, Extraction, Immunohistochemistry, Electron Microscopy, Whole-Genome Sequencing, Imaging, Microarray, In Vitro, Binding Assay, Immune Cell, Analysis, Staining, Microscopy, RNA Sequencing, Knockdown, Inhibition, Positive Control, Profiling, Functional Assay, RNAscope, Activation Assay, Negative Control, DNA Extraction, Amplification, Migration, Transcriptomics, Dissection

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: Isolation and characterization of multidrug-resistant Proteus mirabilis from diarrheic sika deer fawns in Northeast China

doi: 10.3389/fcimb.2026.1866786

Figure Lengend Snippet: Neighbor-Joining phylogenetic tree based on 1,341-bp 16S rRNA gene sequences of 75 Proteus mirabilis isolates and reference strains. The tree was constructed in MEGA 12 using the Neighbor-Joining method with 1,000 bootstrap replicates. Bootstrap values ≥50% are shown at the nodes. GenBank accession numbers, where available, are shown in parentheses. Superscript T indicates a type strain. P. mirabilis ATCC 29906 T was included as the type strain, whereas P. mirabilis ATCC 12453 was included as the laboratory reference strain. Type strains of closely related Proteus species were included for species-level comparison. The scale bar represents 0.002 substitutions per site.

Article Snippet: The 16S rRNA phylogenetic tree ( ) showed that all 75 study isolates were positioned within the P. mirabilis lineage containing the type strain ATCC 29906 T , the laboratory reference strain ATCC 12453, and additional P. mirabilis reference sequences, and were separated from the type strains of closely related Proteus species included for comparison.

Techniques: Construct, Comparison