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 Declared author, group? (mammal, study aim and group controls composition measures findings Funding publication (Y/N) age/ 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 mice, healthy, effect of groups. fragment phyla, S24-7 (f) n=48 voluntary 2. Wheel LFD: 10% length bacteroidetes: 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 (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)

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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 , 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. 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 , 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) 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 + n=19 aging age (g) colonic epithelium influences gut microbiome composition, and whether or not exercise can modulate observed changes in composition in an

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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 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)

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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)

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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 Christensenellaceae (f) and low exercise LCR Proteobacteria cardio- alters the Heliobacteraceae (f) respiratory intestinal 3.WA + Desulfovibrionaceae (f) (LCR) rats, microbiome HCR healthy, n=30 in ovari- 3. WA + HCR: ectomized 4. Control + Firmicutes rats with HCR Ruminococcus (f) intrinsically Christensenellaceae (f) HCR and Clostridium (g) LCR fed a Proteobacteria HFD. Heliobacteraceae (f) Desulfovibrionaceae (f) Cyanobacteria

HCR Control Vs LCR Control:

Bacteroidetes Porphyromonadaceae (f) Firmicutes Lachnospiraceae (f) Peptococcaceae (f) Proteobacteria Heliobacter (g)

Mika, Y Male juvenile To 1. WA + No, PCR, 16S OTUs, α-diversity, 1. WA + Juvenile: G 2015 and adult F344 determine Juvenile standard rRNA of β-diversity, evenness, Bacteroidetes rats, healthy, whether chow diet. fecal richness, relative Rikenellaceae g_AF12 n=40 juvenile rats 2. Control + Full samples. abundance, bacterial (g) would Juvenile compo- phyla and genus, Rikenellaceae g_ (g) promote a sition not bacteroidetes:firmicutes Firmicutes leaner 3. WA + provided. Blautia (s) intestinal Adult Anaerostipes (s) microbiome Proteobacteria phenotype 4. Control + Desulfovibrio (s) with from 6- Adult weeks of

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voluntary Euryarchaeota wheel Methanosphaera (s) running compared to 3. WA + Adult: adult Bacteroidetes counterparts. Rikenellaceae g_AF12 (g) Rikenellaceae g_ (g)

Firmicutes Turicibacter (s)

Welly, Y Juvenile male To 1. WA + Yes, 45% PCR, 16S OTUs, bacterial phyla, 1. WA + HFD:‡ G,O 2016 ‡ obesity-prone determine HFD HFD for rRNA of family, genera, and Bacteroidetes CD rats (OP- how the all groups. cecal relative abundance, Rikenellaceae (f) CD), healthy, intestinal 2. Control + contents bacteroidetes:firmicutes S24-7 (f) n=30 microbiome HFD . Firmicutes is altered in Streptooccaceae (f) the presence 3. Control + of energy HFD weight 3. Control + HFD WM: deficits matched Firmicutes created from (WM) Streptococcus (g) exercise versus diet in an obesity- prone phenotype. Batacan, Y Adult male To compare 1. Control + Yes, PCR, 16S OTUs, α-diversity, 5. LIT + ND: O 2017 Wistar Rats, the effects of ND ND and rRNA of β-diversity, richness, Firmicutes healthy, n=57 diet (HFD vs 25% HFD fecal evenness, bacterial Lactobacillus johnsonii (s) ND) and two 2. Control + were used contents species, family, and Clostridium exercise HFD in all class. geopufricans (s) intensities on activity Actinobacteria the intestinal 3. Control + groups. Bifidobacteriaceae (f) microbiome ND Coriobacteriaceae (f) over a 12- Proteobacteria week period. 4. Control + Parasutterella HFD excrementihominis (s) Tenericutes 5. Light- Erysipelotrichaceae (f) intensity

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training 6. LIT + HFD: (LIT) + ND Firmicutes Clostridium (c) 6. LIT + HFD 7. HIIT + ND: Firmicutes 7. HIIT + Clostridium ND saccharolyticum (s) Clostridium 8. HIIT + geopufricans (s) HFD Proteobacteria Parasutterella exrementihominis (s)

8. HIIT + HFD: Firmicutes Clostridium (c)

Feng, Y Adult male To 1. LCR No, PCR, OTUs, α-diversity, HCR + Ex:* 2017 HCR and LCR determine Control + standard 16SRNA β-diversity, Bacteroidetes rats. Exact whether S.sx chow diet. gene and bacteroidetes:firmicutes Firmicutes sample size exercise can Full DNA not specified. prevent post- 2. HCR compo- sequencing *Surgical condition not operative Control + sition not of fecal specified cognitive S.sx provided. contents. decline, neuroinfla- 3. LCR mmation and Control + associated Sx shifts in intestinal 4. HCR microbiome. Control + Sx

5. LCR + F.Ex + S.sx

6. HCR + F.Ex + S.sx

7. LCR +

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F.Ex + Sx

8. HCR + F.Ex + Sx

Canine Kieler, N Adult large- To 1. F.Ex + Yes, all PCR, 16S OTUs, α-diversity, No significant changes to O 2017 and medium- determine if Diet rRNA bacterial phyla and intestinal microbiome as a breed dogs exercise were fed sequencing genus. result of exercise. who were influences 2. Control + same dry of fecal sedentary and shifts on Diet diet food. samples. overweight, intestinal healthy, n=18 microbiome during weight loss protocol.

Equine Janabi, Y Adult male To 1. Seasonal No. All PCR, 16S OTUs, α-diversity, β- 2. F. Ex. * O 2016 and female determine control (SC) animals rRNA diversity, relative Bacteroidetes horses (mares the effects of were fed sequencing abundance of bacterial Dysgonomonas (g) and geldings exercise on 2. F.Ex. standard of fecal phyla, genera, and Firmicutes [n=8]), the equine rations of contents. species Clostridium (g) healthy, and intestinal grian and Proteobacteria older seasonal microbiome alfalfa, controls (n=4), over 12- and grass Treponema (g) healthy weeks. ad- * Direction of change libitum. varied based on bi-weekly timepoint over 12-week intervention

Janabi, 2017 Y Adult male To 1. SC 1 No-all PCR, 16S OTUs, α-diversity, β- 1. SC 1 * O and female determine animals rRNA diversity, αrelative Firmicutes horses (mares the acute 2. SC 2 were fed sequencing abundance of bacterial Clostridium (g) and geldings), effect of standard of fecal phyla, genera, and Fusicatenibacter healthy, n=8. exercise on 3. F. Ex 1 ration of contents. species saccharivorans (s)

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the intestinal grain and Spirochaetes microbiome 4. F.Ex 2 alfalfa/ Treponema zioleckii (s) before and grass hay * Direction of change after a 12- ad lib. varied based on bi-weekly week timepoint over 12-week exercise intervention training protocol. Human Clarke, Y Adult male To 1. Rugby No-diets PCR, 16S OTUs, α-diversity, Rugby vs. High BMI G,O 2014 rugby players, determine were rRNA bacterial phyla, family, Bacteroidetes and weight the 2. Low BMI assessed sequencing and genera. RC9 gut group (g) matched high relationship via food of fecal S24-7 (f) and low BMI between 3. High frequen- contents. Firmicutes controls, exercise or BMI cy Succinivibrio (g) healthy, n=83 sedentary question- Succinivibrionaceae (f) time and the naires Verrucomicrobia intestinal (FFQ) Akkermansiaceae (f) microbiota. Akkermansia (g)

Rugby vs. Low BMI: Bacteroidetes Prevotellaceae (f) Prevotella (g) Bacteroides (g) S24-7 (f) Firmicutes Lactobacillaceae (f) Lactobacillus (g) Erysipelotrichaceae (c) Succinivibrionaceae (f) Succinivibrio (g)

Stewart, Y Adults with To 1. T1D No, diets PCR, 16S OTUs, α-diversity, 1. T1D* O 2016 Type 1 determine if were rRNA abundance, bacterial Firmicutes Diabetes the intestinal 2. Non-T1D assessed sequencing phyla and species Lachno-spiraceae (f) (T1D), and microbiome with 24- of fecal Dialister (g) Adult non- of physically hour samples. Actinobacteria diabetic fit adults dietary Actinomyces (g) controls, with recalls. Collinsella (g) managed

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otherwise T1D 2. Non-T1D* healthy, n=20 resembles Firmicutes the intestinal Lachno-spiraceae (f) microbiome Anoxybacillus (g) of physically Clostridium fit adults sensu_stricto (g) without Coprococcus (g) T1D. Actinobacteria Coriobacteriaceae (f) Proteobacteria Aurantimonas (g) Burkholderales (o) Zoogloea (g) Schlegelella (g) Comamonadaceae (f)

*Direction of results not reported.

Allen, Y Normal weight To 1. Sed. + Yes, 3- PCR, 16S OTUs, α-diversity , No significant findings O 2017 and obese determine lean day rRNA β-diversity, bacterial between groups after 6 sedentary influence of control sequencing genera, species weeks of exercise or 6 (sed.) adults, longitudinal 2. Sed. + diet prior weeks of washout. otherwise exercise obese to fecal healthy, n=32. intervention samples. on the 3. Ex. + intestinal lean microbiome where 4. Ex + subjects obese served as their own controls. Bressa, N Females, To obser- 1. Sed No, diets PCR, 16S OTUs, α-diversity, 1. Sed. G, O 2017 premeno- vationally were rRNA β-diversity, bacterial Bacteroidetes pausal, compare the 2. Active charac- sequencing phyla, family, genus, Barnesiellaceae (f) healthy, n=40 intestinal terized and species, Barnesiellaceae microbiome using bacteroidetes:firmicutes unclassified (g) differences FFQs. Odoribacteraceae (f) between Odoribacter (g) sedentary Firmicutes

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and Turicibacter (g) physically Ruminococcaceae active unclassified (g) females. Ruminococcus (g) Proteobacteria Desulfovibrionaceae (g)

2. Active Bacteroidetes Paraprevotella (g) Firmicutes Faecalibacterium prautznnii (s) Roseburia hominis (s) Coprococcus (g) Actinobacteria Bifidobacterium (g) Proteobacteria Haemophilus (g) Verrucomicrobia Akkermansia muciniphila (s)

Paulsen, N Female breast To evaluate 1. BCS No, diets PCR, 16S OTUs, α-diversity, BCS: G, O 2017 cancer the influence were rRNA β-diversity, bacterial No quantitatively survivors of CRF and assessed sequencing phyla, family, order, significant differences. (BCS), psychosocial with 3- and genus otherwise factors on day food healthy, n=12 the intestinal intake microbiome records. in BCS. Significant results are presented by study within the “Significant findings” column. All significant findings are denoted with an arrow indicating the direction of change, and are categorized within their respective phyla, and further characterized where: (c)=Class; (o)= Order; (f)= Family; (g)=Genus; and (s)=Species. ‡Represents results with cecal contents only. † Represents results with fecal and cecal contents. *Denotes a study-specific note within the column.

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