Journal: Cell metabolism

Article Title: Intermittent fasting confers protection in CNS autoimmunity by altering the gut microbiota

doi: 10.1016/j.cmet.2018.05.006

Figure Lengend Snippet: Stool samples were collected from the IF and ad libitum groups at T1 (baseline, n=10 in the IF group, n=9 in the ad libitum group), T2 (after 4 weeks on the diet, prior to immunization, n=9 in IF, n=10 in ad libitum) and T3 (clinical EAE, n=10 in IF, n=8 in ad libitum). (A) Non-metric multidimensional scaling (NMDS) plots illustrate microbiome similarity in IF and ad libitum groups (each dot is one sample; X-axis and Y-axis are first and second dimension of microbiome data). At T1, samples from two groups intermingled, indicating similar microbiome (P>0.05, PERMANOVA test). At T2 and T3, samples from the two groups clustered separately, indicating two distinct microbiome communities (P<0.05, PERMANOVA test). (B) Richness is a measure of alpha diversity for microbial community. Bacterial richness increased significantly over the three time points in the IF group, but not in the ad libitum group (linear mixed regression #P<0.05; Y-axis is number of different bacteria families); (C) Blood leptin level was negatively correlated with bacterial richness (r=−0.51; P<0.005, Pearson correlation). (D) Bacterial families with significantly different relative abundance between the two groups at T2 and T3. Reported here only those bacterial families with the same direction of difference at T2 and T3 between the two groups. Y-axis is the relative abundance of the bacterial family (q<0.05, ANCOVA). * q<0.05; ** q<0.01. (E) Pearson or Spearman correlations of corticosterone or leptin and microbiome (data were log transformed). All samples from IF and ad libitum groups are included. (F) Different trajectories of Lactobacillus species in the IF and ad libitum groups were seen over the three time points. In the IF group, L. sp are significantly higher at the T2 and T3 time points (P<0.05, linear mixed regression). In b-d, IF is in grey and ad libitum in black.

Article Snippet: 43820) Sigma-Aldrich Cat 1.03164 Iron(III) chloride Sigma-Aldrich Cat 451649 Hepes Buffer Corning Cat 25060CI Fetal bovine serum, FBS Gibco Cat 2614–079 EDTA 0.5 M Corning Cat 40–034Cl Dithiothreitol (DTT) Bio-Rad Cat 1610610 Percoll GE Healthcare Cat 17-0891-01 Hank’s balanced salt solution (+) Gibco Cat 24020–117 Hank’s balanced salt solution (−) Gibco Cat 14175–079 Critical Commercial Assays Lamina Propria Dissociation Kit, mouse Miltenyi Biotec Cat 130-097-410 Corticosterone EIA Kit Arbor Assays Cat K014-H1 Foxp3 Staining Buffer Set eBioscience Cat 00-5523-00 Mouse Adiponectin ELISA EMD Millipore Cat Mill-EZMADP-60K Mouse Leptin ELISA EMD Millipore Cat Mill-EZML-82K β-Hydroxybutyrate (Ketone Body) Colorimetric Assay Kit Cayman Chemical Company Cat 700190 Adiponectin Human ELISA, High Sensitivity (Sandwich) BioVendor Cat RD191023100 Human Leptin “Dual Range” ELISA EMD Millipore Cat EZHL-80SK Deposited Data 16S and Shotgun microbiome data SRA database PRJNA388060 Experimental Models: Organisms/Strains C57BL/6, Black 6 Jackson Laboratory Cat 000664 Software and Algorithms Metamorph 7.7 software Molecular Devices ftp://ftp.meta.moleculardevices.com/pub/uic/software/CDROM/MM77.iso Kaluza 1.3 BeckmanCoulter https://www.beckman.com/coulter-flow-cytometers/software/kaluza GraphPad Prism, 7 GraphPad Software https://www.graphpad.com/scientific-software/prism/ FlowJo_V10 FlowJo, LLC https://www.flowjo.com/ R for microbiome analysis- R version 3.2.2 (2015-08-14) R team https://www.r-project.org/ SAS v9.4 SAS https://www.sas.com/en_us/software/sas9.html Other Gentle MACS TM Dissociators Miltenyi Biotec Cat 130-096-427 Open in a separate window KEY RESOURCES TABLE

Techniques: Bacteria, Transformation Assay

Journal: Cell metabolism

Article Title: Intermittent fasting confers protection in CNS autoimmunity by altering the gut microbiota

doi: 10.1016/j.cmet.2018.05.006

Figure Lengend Snippet: (A) Comparison of serum levels of leptin and adiponectin on day 15 in RRMS patients in the IF and ad libitum groups in the human trial. (B) At phylum level, the alteration of the gut microbiome after IF for 15 days in RRMS patients (n=5 patients/group, top panel) shows similar trends as that in mice (n=8 mice/group, bottom panel). Y-axis represents the percentage of change of the relative abundance of the gut microbiome. In human studies, the percentage change is calculated based on the microbial abundance at baseline and day 15. In mouse studies, the percent change is calculated based on the microbial abundance on T2 and T3. (c) Levels of serum adiponectin are strongly positively correlated with the relative abundance of Faecalibacterium in the MS study participants (r=0.86, P=0.009 Pearson correlation).

Article Snippet: 43820) Sigma-Aldrich Cat 1.03164 Iron(III) chloride Sigma-Aldrich Cat 451649 Hepes Buffer Corning Cat 25060CI Fetal bovine serum, FBS Gibco Cat 2614–079 EDTA 0.5 M Corning Cat 40–034Cl Dithiothreitol (DTT) Bio-Rad Cat 1610610 Percoll GE Healthcare Cat 17-0891-01 Hank’s balanced salt solution (+) Gibco Cat 24020–117 Hank’s balanced salt solution (−) Gibco Cat 14175–079 Critical Commercial Assays Lamina Propria Dissociation Kit, mouse Miltenyi Biotec Cat 130-097-410 Corticosterone EIA Kit Arbor Assays Cat K014-H1 Foxp3 Staining Buffer Set eBioscience Cat 00-5523-00 Mouse Adiponectin ELISA EMD Millipore Cat Mill-EZMADP-60K Mouse Leptin ELISA EMD Millipore Cat Mill-EZML-82K β-Hydroxybutyrate (Ketone Body) Colorimetric Assay Kit Cayman Chemical Company Cat 700190 Adiponectin Human ELISA, High Sensitivity (Sandwich) BioVendor Cat RD191023100 Human Leptin “Dual Range” ELISA EMD Millipore Cat EZHL-80SK Deposited Data 16S and Shotgun microbiome data SRA database PRJNA388060 Experimental Models: Organisms/Strains C57BL/6, Black 6 Jackson Laboratory Cat 000664 Software and Algorithms Metamorph 7.7 software Molecular Devices ftp://ftp.meta.moleculardevices.com/pub/uic/software/CDROM/MM77.iso Kaluza 1.3 BeckmanCoulter https://www.beckman.com/coulter-flow-cytometers/software/kaluza GraphPad Prism, 7 GraphPad Software https://www.graphpad.com/scientific-software/prism/ FlowJo_V10 FlowJo, LLC https://www.flowjo.com/ R for microbiome analysis- R version 3.2.2 (2015-08-14) R team https://www.r-project.org/ SAS v9.4 SAS https://www.sas.com/en_us/software/sas9.html Other Gentle MACS TM Dissociators Miltenyi Biotec Cat 130-096-427 Open in a separate window KEY RESOURCES TABLE

Techniques: Comparison

Journal: Cell metabolism

Article Title: Intermittent fasting confers protection in CNS autoimmunity by altering the gut microbiota

doi: 10.1016/j.cmet.2018.05.006

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: 43820) Sigma-Aldrich Cat 1.03164 Iron(III) chloride Sigma-Aldrich Cat 451649 Hepes Buffer Corning Cat 25060CI Fetal bovine serum, FBS Gibco Cat 2614–079 EDTA 0.5 M Corning Cat 40–034Cl Dithiothreitol (DTT) Bio-Rad Cat 1610610 Percoll GE Healthcare Cat 17-0891-01 Hank’s balanced salt solution (+) Gibco Cat 24020–117 Hank’s balanced salt solution (−) Gibco Cat 14175–079 Critical Commercial Assays Lamina Propria Dissociation Kit, mouse Miltenyi Biotec Cat 130-097-410 Corticosterone EIA Kit Arbor Assays Cat K014-H1 Foxp3 Staining Buffer Set eBioscience Cat 00-5523-00 Mouse Adiponectin ELISA EMD Millipore Cat Mill-EZMADP-60K Mouse Leptin ELISA EMD Millipore Cat Mill-EZML-82K β-Hydroxybutyrate (Ketone Body) Colorimetric Assay Kit Cayman Chemical Company Cat 700190 Adiponectin Human ELISA, High Sensitivity (Sandwich) BioVendor Cat RD191023100 Human Leptin “Dual Range” ELISA EMD Millipore Cat EZHL-80SK Deposited Data 16S and Shotgun microbiome data SRA database PRJNA388060 Experimental Models: Organisms/Strains C57BL/6, Black 6 Jackson Laboratory Cat 000664 Software and Algorithms Metamorph 7.7 software Molecular Devices ftp://ftp.meta.moleculardevices.com/pub/uic/software/CDROM/MM77.iso Kaluza 1.3 BeckmanCoulter https://www.beckman.com/coulter-flow-cytometers/software/kaluza GraphPad Prism, 7 GraphPad Software https://www.graphpad.com/scientific-software/prism/ FlowJo_V10 FlowJo, LLC https://www.flowjo.com/ R for microbiome analysis- R version 3.2.2 (2015-08-14) R team https://www.r-project.org/ SAS v9.4 SAS https://www.sas.com/en_us/software/sas9.html Other Gentle MACS TM Dissociators Miltenyi Biotec Cat 130-096-427 Open in a separate window KEY RESOURCES TABLE

Techniques: Purification, Virus, Amplification, Sequencing, Recombinant, Staining, Enzyme-linked Immunosorbent Assay, Colorimetric Assay, Software, Gentle