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Supplemental Digital Content 1. Characteristics and Outcomes of Included Studies Sorted by Mammal Type and Publication Year

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Supplemental Digital Content 1. Characteristics and Outcomes of Included Studies Sorted by Mammal Type and Publication Year Supplemental Digital Content 1. Characteristics and outcomes of included studies sorted by mammal type and publication year. Study (first Control Model: Primary Intervention Dietary Methods Gut microbiome Significant taxonomy Declared author, group? (mammal, study aim and group controls composition measures findings Funding publication (Y/N) age/life stage, design Sources § year) health status, sample size) Murine (Mouse) Evans, Y Adult male To 1. Control Yes, LFD Terminal β-diversity, abundance, 1. Control + HFD: G,O 2014 C57BL/6 determine + HFD and HFD restriction bacterial family and Bacteroidetes mice, healthy, effect of groups. fragment phyla, S24-7 (f) n=48 voluntary 2. Wheel LFD: 10% length bacteroidetes:firmicutes Firmicutes exercise vs. access fat polymorphi Clostridiaceae (f) no access to (WA) + HFD: sm Lachnospiraceae (f) exercise on HFD 60% fat (TRFLP), Ruminococcaceae (f) the intestinal (62% PCR assay, Turicibacteraceae (f) microbiome. 3. Control + saturated; 16S rRNA Erysipelotrichaceae (f) Low-fat diet 35.9% sequencing Actinobacteria (LFD) mono-; of fecal Bifidobacteriaceae (f) 32% poly- contents. 4. WA + unsat- 2. WA + HFD: LFD urated). Bacteroidetes S24-7 (f) Firmicutes Clostridiaceae (f) Lachnospiraceae (f) Ruminococcaceae (f) Lactobacillaceae (f) Turicibacteraceae (f) Erysipelotrichaceae (f) 4. WA + LFD: Bacteroidetes S24-7 (f) Firmicutes Lactobacillaceae (f) Lachnospiraceae (f) Ruminococcaceae (f) Turicibacteraceae (f) 7 Erysipelotrichaceae (f) Actinobacteria Bifidobacteriaceae (f) Kang, Y Adult male To 1. Control + Yes, HFD PCR, 16S Operational taxonomic 1. Control + HFD: G,O 2014 C57BL/6 J determine High-fat and ND rRNA units (OTUs), Firmicutes mice, healthy, interaction diet (HFD) groups. sequencing relative abundance, Streptococcus (g) n=40 between ND: 10% of fecal bacteroidetes:firmicutes Tenericutes habitual 2. F. Ex + fat HFD: contents. and bacterial phyla, dietary HFD 60% fat genus, and family 2. F.Ex + HFD: conditions Bacteroidetes and exercise 3. Control + Firmicutes level on normal diet Streptococcus (g) intestinal (ND) Tenericutes microbiome and behavior 4. Forced 4. F.Ex + ND: exercise Bacteroidetes (F.Ex.) + Firmicutes ND Tenericutes Allen, Y Adult male To compare 1. F.Ex. No, all PCR, 16S OTUs, α-diversity, 1. F.Ex: O 2015† C57BL/6J, effects of were fed a rRNA gene richness & evenness, Firmicutes healthy, n=29 voluntary 2. WA standard sequencing relative abundance, Dorea (g) exercise via chow diet. of fecal and bacteroidetes:firmicutes Coprococcus (g) wheel access 3. Control cecal bacterial genera and Oscillospira (g) (WA.) vs. contents. phyla Ruminococcus (g) F.Ex. on the Butyrivibrio (g) intestinal Tenericutes microbiome. Proteobacteria Nautilia (g) 2. WA Bacteroidetes Prevotella (g) Firmicutes Turicibacter (g) Anaerotruncus (g) Lambert, Y Adult male To compare 1. Control + No, all PCR, 16S Total bacteria, bacterial 1. Control + Db/db: G,O 2015 ‡ C57BL mice, the effect of Db/db were fed a rRNA gene phyla and species, Firmicutes healthy (db/+), F.Ex. on the standard sequencing bacteroidetes:firmicutes Clostridium cluster I (g) and Type 2 intestinal chow diet. relative abundance Clostridium cluster XI (g) 8 Diabetic [T2D microbiome 2. F.Ex + of cecal (db/db)], in T2D mice db/db contents. 2. F.Ex + Db/db: n= ~36 when Bacteroidetes compared to 3.Control+ Bacteroides (g) their healthy db/+ Prevotella (g) and Actinobacteria sedentary 4. F.Ex + Bifidobacterium (s) counterparts. db/+ Proteobacteria Enterobacteriaceae (f) Euryarchaeota Methanobrevibacter (g) 4. F.Ex + Db/+: Bacteroidetes Bacteroides (g) Prevotella (g) Firmicutes Clostridium cluster I (g) Actinobacteria Bifidobacterium (s) Euryarchaeota Methanobrevibacter (g) Campbell, Y Adult male To compare 1. Control + Yes, Terminal OTUs, bacterial genus, 1. Control + HFD- G 2016 C57BL/ the effects of HFD- HFD: restriction phyla, family, species induced obesity: 6NTac, voluntary induced 45% fat, fragment Firmicutes healthy, n=36 exercise vs. obesity and length poly- Clostridiales (o) sedentary ND: 10% morphism time on 2. WA + (TRFLP) 2. WA + HFD-induced intestinal HFD- and pyro- obesity: integrity and induced sequencing Firmicutes intestinal obesity of 16S Clostridales (o) microbiome rRNA fecal Faecalibacterium in lean and 3. Control + contents. prausnitzii (s) obese mice. lean Peptococcus (s) Allobaculum (s) 4. WA + lean 4. WA + lean: Firmicutes Clostridales (o) Faecalibacterium prausnitzii (s) 9 Lachnospiraceae (f) Allobaculum (s) Clostridium (g) Denou, Y Adult male To 1. Control + Yes, PCR, 16S OTUs, α-diversity, 2. Control + HFD: G,O 2016 C57BL/6 determine ND HFD: rRNA bacterial genus, phyla, Bacteroidetes mice, healthy, the effect of 45% fat sequencing relative abundance, Firmicutes n=32 high- 2. Control + and of fecal bacteroidetes:firmicutes intensity HFD standard contents. 3. HIIT HFD-induced interval chow diet. obesity: training 3. HIIT + Bacteroidetes (HIIT) on HFD- Bacteroidales (o) the intestinal induced Firmicutes microbiome obesity after HFD- induced 4. Control + obesity. HFD- induced obesity Houghton, Y PolgA mut/mut To 1. Control No, all PCR, 16S OTUs, α-diversity, 2. F.Ex + Age: G, O 2017 and determine were fed a rRNA of bacterial genus, relative Bacteroidetes wild-type how changes 2. Age + standard fecal abundance, Proteobacteria PolgA +/+, in mitochon- F.Ex. chow diet. contents. bacteroidetes:firmicutes Desulfovibrio (g) mitochondrial drial Firmicutes dysfunction, function of 3. Control + Deferribacteraceae n=19 aging age Mucispirillum (g) colonic epithelium influences gut microbiome composition, and whether or not exercise can modulate observed changes in composition in an 10 accelerated aging model. Lamoureux, Y Adult To measure 1. Control No, all PCR, 16S OTUs, α-diversity, No significant taxonomy G 2017 C57BL/6 effect of were fed a rRNA β-diversity, species findings between any mice, healthy, exercise on 2. WA standard sequencing richness, relative groups. n=42 intestinal chow diet. of fecal abundance, bacterial microbiome 3. F.Ex. samples. phyla. in voluntary and forced moderate intensity exercise. Liu, Y Adult To 1. Sed. No, all 16S rRNA OTUs, α-diversity, 4. F.Ex. O 2017 C57BL/6 investigate were fed a sequencing β-diversity, bacterial Bacteroidetes mice, healthy effects of 2. Sed. + standard of fecal phyla. Butyricimonas (g) n=* exercise on Sham chow diet. samples. Prevotella (g) *Sample size intestinal surgery Verrucomicrobia per group not microbiome (S.sx) Akkermansia (g) reported. after myocardial 3. Sed. + MI 5. F.Ex + S.Sx infarction Bacteroidetes (MI). 4. F.Ex, Sphingobacteriales (o) Firmicutes 5. F.Ex + Erysipelotrichaceae (f) S.sx Verrucomicrobia Akkermansia (g) 6. F.Ex + MI 6. F.Ex + MI Proteobacteria Phenylobacterium (g) Roseateles (g) Murine (Rat) Matsumoto, Y Adult male To 1.Control Yes, all PCR, 16S Bacterial species, and 2. WA: Not 2008 ‡ Wistar rats, determine were fed a rRNA n-butyrate producing Firmicutes declared healthy, n=14 the effect of 2.WA 25% sequencing bacteria. Ruminococcus WA on the casein- of cecal hydrogenotroplicus (s) intestinal sucrose contents. Clostridium (g) microbiome. diet. SM7/11 (s) Lactobacillus gasseri (s) T2-87 (f) 11 Proteobacteria Escherichia coli (s) Queipo- Y Adult male To 1. Activity- Yes, ABA PCR, 16S Diversity, abundance, 1. ABA: G,O Ortun͂ o, Dawley rats, determine based groups sequencing phyla and genera-level Bacteroidetes 2013 healthy, n=40 the effects of anorexia had food of fecal bacteria, Bacteroides (g) physical (ABA) access contents. bacteroidetes:firmicutes Prevotella (g) activity and restricted Firmicutes nutrition 2. Control + to 1 Clostridium (g) status on the ABA hour/day. Enterococcus (g) intestinal B. Coccoides-E. rectale (s) microbiome. 3. WA + ad Lactobacillus (g) libitum (ad Actinobacteria lib) feeding Bifidobacterium (g) Proteobacteria 4. Control + Heliobacter (g) ad lib Euryarchaeota feeding. M. smithii (s) 2. Control + ABA: Firmicutes Enterococcus (g) B. Coccoides-E. rectale (s) Lactobacillus (g) Actinobacteria Bifidobacterium (g) Euryarchaeota M. smithii (s) 3. WA. + ad lib: Bacteroidetes Bacteroides (g) Prevotella (g) Firmicutes Clostridium(g) Enterococcus (g) B. Coccoides-E. rectale (s) Lactobacillus (g) Actinobacteria Bifidobacterium (g) 12 4. Control + ad lib: Bacteroidetes Bacteroides (g) Prevotella (g) Firmicutes Clostridium (g) Actinobacteria Bifidobacteria (g) Proteobacteria Heliobacter (g) Petriz, Y Zucker and To 1. F.Ex + None, and Pyro- OTUs, α-diversity, 1. F.Ex + Non-obese: G,O 2014 Wistar Rats, determine Non-obese diet sequencing, bacterial species Firmicutes obese, non- the effect of compo- PCR, 16S richness, bacterial Streptococcus (g) obese, or F. Ex. on the 2. F.Ex + sition not rRNA of phyla, relative hyper-tensive, intestinal Obese reported. fecal abundance 2. F.Ex + Obese: n=9, sex not microbiome contents. Firmicutes specified. in the 3. F. Ex + Streptococcus presence of Hyper- alactolyticus (s) known tensive Lactobacillus (g) disease Ruminococcus gnavus (s) genotypes. Ruminococcus flavefaciens (s) Actinobacteria Bifidobacterium animalis (s) Bifidobacterium pseudolongum (s) Proteobacteria Pseudomonas (g) Aggregatibacter pnemotropica (s) 3. F. Ex + Hypertensive: Firmicutes Allobaculum (g) Proteobacteria Aggregatibacter (g) Sutturella (g) 13 Liu, Y Female high To 1. + WA Yes, 45% PCR, 16S OTUs, α-diversity, 1. WA + LCR: G 2015 ‡ cardio- determine LCR HFD after rRNA of β-diversity, bacterial Firmicutes respiratory how OVX. cecal phyla, species richness, Ruminococcus (f) capcity (HCR) voluntary 2. Control + contents. bacteroidetes:firmicutes
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