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Mice were obtained from Jackson Laboratory and bred in the facilities of the NeuroBsik consortium (VU University Amsterdam, The Netherlands or Harlan Laboratories, Horst, The Netherlands; 129S1/SvImJ n = 61, A/J n = 49, BALB/cJ n = 47, C3H/HeJ n = 29, C57BL/6J n = 112, DBA/2J n = 40, FVB/NJ n = 49, NOD/ShiLtJ n = 46) or subjected to experiments 2 weeks after shipment from Jackson laboratories to the testing facility (WSB/EiJ n = 14, PWK/PhJ n = 15 and CAST/EiJ n = 14). Male 8 to 12 week old mice were singly housed on sawdust in standard Makrolon type II cages enriched with cardboard nesting material for at least one week prior to experiments, with water and food ad libitum (7:00/19:00 lights on/off; providing an abrupt phase transition). We only used male mice to avoid possible impact of estrous cycle on longitudinal behavioral assessments. Experiments were carried out in accordance with the European Communities Council Directive of 24 November 1986 (86/609/EEC), and with approval of the local animal care and use committee of the VU University Amsterdam, The Netherlands.

Detailed study design and study procedures have been reported previously (22 (link)). In brief, four-week-old A/J, C57BL/6J, FVB/NJ, and NOD/ShiLtJ mice (The Jackson Laboratory, Bar Harbor, ME) were acclimated for two weeks and then randomized to one of five diets: traditional Mediterranean diet (MeD), Japanese diet (JD), typical American diet (mentioned as Western diet (WD) hereafter), ketogenic diet (KD), or control mouse chow with five mice per diet, sex, and strain (Supplementary Figure 1). Mice were housed five per cage and maintained at 22°C under a 12-h light cycle. The mice were maintained on the experimental human and mouse control diets from 6 to 30 weeks of age. Fecal samples were collected at 30 weeks of age and stored at −80°C until further processing. The final dataset had 16S rRNA gene amplicon sequencing data from 149 mice (n = 27–34 per diet, 27–44 per strain, and 3–10 per diet-strain, Supplementary Table 1). The study protocol was approved by Texas A&M University Institution Animal Care and Use Committee (IACUC) protocol number 2017-0076. All experiments were performed in accordance with relevant guidelines and regulations.

Six to eight-week-old female and male A/J (stock #000646), C57BL/6J (stock #000664), 129S1/SvlmJ (stock #002448), NOD/ShiLtJ (stock #001976), and NZO/HILtJ (stock #002105) inbred mice were purchased from Jackson Laboratories. All mice were housed in HEPA filtration racks in the RBL’s ABSL-3 facility and provided ad lib access to food and water. All mice were infected with recombinant wild-type RVFV ZH501 strain under isoflurane anesthesia via left rear footpad (FP) injection to imitate a mosquito bite. Viral infection doses in these studies ranged from 0.2 to 2,000 TCID₅₀ per animal, which equates to doses ranging from 0.138 to 1,380 PFU per animal (0.69 TCID50 = 1 PFU; Poisson distribution based upon Reed and Muench, 1938 ). Mice received a 20 μl injection of virus diluted in sterile phosphate buffered saline (PBS). For all experiments, daily weights were recorded, and mice were evaluated at least once daily for clinical signs of disease. Mice were euthanized according to a predetermined clinical scoring method (Supplementary Table S1). At the time of euthanasia, mice were anesthetized with isoflurane and blood was collected via cardiac puncture. Following cervical dislocation, liver, spleen, brain, and testes (where applicable) were collected for subsequent RNA extraction and viral RNA load quantitation.