Journal: Frontiers in physiology

Article Title: Gut microbiota depletion minimally affects the daily voluntary wheel running activity and food anticipatory activity in female and male C57BL/6J mice.

doi: 10.3389/fphys.2023.1299474

Figure Lengend Snippet: FIGURE 1 The experimental procedure for microbiota depletion and feeding schedule. The days of beginning of ad libitum feeding (ALI, ALII), timed restricted feeding (TRF), food deprivation (FD) and collection of cecum and feces are indicated with the arrows.

Article Snippet: Extracted fecal DNA samples were shipped to Transnetyx Microbiome (Cordova, TN) for library preparation and whole-genome sequencing.

Techniques:

Journal: Frontiers in physiology

Article Title: Gut microbiota depletion minimally affects the daily voluntary wheel running activity and food anticipatory activity in female and male C57BL/6J mice.

doi: 10.3389/fphys.2023.1299474

Figure Lengend Snippet: FIGURE 5 Relative abundances of microbiota taxa from control and antibiotic-treated mice. Plot representing bacterial load in control (A) and antibiotics- treated (B) mice. Antibiotics depleted majority of gut microbiota. The “Mouse proportion” represents the number of reads that map to the One Codex database mouse genome divided by the total number of reads, while the “Bacterial proportion” represents the number of reads that map to bacteria at the taxonomic rank divided by the total number of reads. The “Other” category includes any reads classified as non-bacterial microorganisms. Taxonomic analysis showing gut microbiota population shifts at Family level. Relative abundance of top 15 families of microbial taxa in control (C), and antibiotics-treated (D) are shown. Lachnospiraceae (indicated as green) was present in all control mice but depleted in antibiotics treated mice. Erysipelotrichaceae was not detected in both control and antibiotics-treated mice. Top 15 orders and genus were shown in Supplementary Figure S5A–D. The number in the brackets represents NCBI taxonomic ID.

Article Snippet: Extracted fecal DNA samples were shipped to Transnetyx Microbiome (Cordova, TN) for library preparation and whole-genome sequencing.

Techniques: Control, Bacteria

Journal:

Article Title: Elucidation of Listeria monocytogenes Contamination Routes in Cold-Smoked Salmon Processing Plants Detected by DNA-Based Typing Methods

doi: 10.1128/AEM.67.6.2586-2595.2001

Figure Lengend Snippet: Adapter and primer oligonucleotides used for AFLP DNA typing of L. monocytogenes from cold-smoked salmon processing plants

Article Snippet: Genomic DNA were extracted from strains of L. monocytogenes by using an Easy-DNA kit (Invitrogen, De Schelp, The Netherlands) according to the manufacturer's instructions.

Techniques: Sequencing

Journal:

Article Title: Elucidation of Listeria monocytogenes Contamination Routes in Cold-Smoked Salmon Processing Plants Detected by DNA-Based Typing Methods

doi: 10.1128/AEM.67.6.2586-2595.2001

Figure Lengend Snippet: Combined dendrogram for 30 L. monocytogenes isolates analyzed by RAPD, AFLP, and PFGE typing. The dendrogram was constructed with GelCompar and Bionumerics (Applied Maths) software by using the Dice correlation and cluster analysis by the unweighted pair group method using arithmetic averages. Percentages of similarity are shown above the dendrogram. The molecular sizes of RAPD, AFLP, and PFGE DNA ranged from 200 to 2,000 bp, from 40 to 500 bp, and from 50 to 400 kb, respectively. The origins of strains are shown in Table ​Table77.

Article Snippet: Genomic DNA were extracted from strains of L. monocytogenes by using an Easy-DNA kit (Invitrogen, De Schelp, The Netherlands) according to the manufacturer's instructions.

Techniques: Construct, Software