Table 1 Summary of the animal studies investigating the effects of fasting on gut microbiota alterations

Sonoyama K, 2009

Male Syrian hamsters (age: 10 weeks)

1. Fed active group (n = 6)

Cecum

16S rRNA clone library and species-specific real-time quantitative PCR

↑Akkermansia muciniphila, a mucin degrader, in fasting group but not in hibernation

2. Fasted active, group (n = 6) fasted 96 h

↑Clostridia in fed active and hibernating group

3. hibernating group (n = 6) maintaining darkness at 4 °C

Kohl KD, 2014

Fish, toads, geckos, quail, mice

Four time points through

Colon & cecum

16S rRNA gene sequencing

In tilapia, quail, and mice: ↓Lactobacillus & Prevotella, ↑ Oscillospira

28 days fasting

In tetrapods ↓ Coprobacillus & Ruminococcus

Li G, 2017

7–8-week-old male C57BL/6 N mice: diet-induced obese model

1. Controls: fed with ad libitum (AL) diet

Cecum

16S rRNA gene amplicon sequencing

↑Firmicutes, ↓ Bacteriodetes and Actinobacteria, ↑ Firmicutes to Bacteroidetes ratio

2. Intermittent fasting (IF): every other day fasting (EODF) regimen

↑ beiging of white adipose tissue and subsequently ameliorate metabolic disorders

McCue MD, 2017

Mice, quail, tilapia, toad, geckos

Mice (3 days fasting), quail (7 days fasting), tilapia & toad (21 days fasting), geckos (28daysfasting)

Feces

16S rRNA sequencing

Alteration in Bacteriodetes, Firmicutes, Proteobacteria, Fusobacteria and Verrucomicrobia

Beli E, 2018

4-month-old db/m (non- diabetic) and db/db (diabetic) mice

1. Controls: fed with ad libitum (AL) diet

Feces

16S rRNA sequencing with the MiSeq platform

↑ Firmicutes, ↓ Bacteroidetes and Verrucomicrobia, ↑gut mucin, goblet cell number, villi length

2. IF: fasted on an every other 24-h interval for 7 months

↓ plasma peptidoglycan, ↑ tauroursodeoxycholate bile acid ↓retinal TNF-α mRNA

Catterson JH, 2018

fruit flies (Drosophila melanogaster)

1. Controls: fed with ad libitum

Blood and tissue

qPCR quantification of bacterial load

↓age-related pathologies,↑ gut barrier function & gut health due to ↓relative bacterial abundance

2. IF: 2-day fed,5-day fasted for 40 days

Cignarella F, 2018

7- week- old Female C57BL/6 J mice: multiple sclerosis (MS) animal model

1. Controls: fed with ad libitum (AL) diet (n = 10)

Feces

16S rRNA gene sequencing

↑Lactobacillaceae, Bacterioidaceae and Prevotellaceae families

2. IF: fasted, fed every other day (n = 10)

↑ketone formation and glutathione metabolism, ↑ anti-oxidative pathways, ↓IL-17 producing T cells & ↑the number of regulatory T cells ↓inflammation, demyelination and axonal damage

Wei S, 2018

6-week-old male C57BL/ksJ-db (db/db) mice: a genetic model of type 2 diabetes

1. Controls: standard chow, free access to food and water

Feces

16S rRNA gene sequencing

↑ Bacteroidetes, ↓Firmicutes & Saccharbacteria. ↑Parabacteroides & Blautia, ↓Prevotellaceae, Alistipes & Ruminococcaceae

2. FMD: fasting with the (30% of the daily calorie intake of control group) for 1 week, followed by ad libitum feeding for another week

↓ fasting blood glucose, ↓hepatic steatosis, ↓loss of pancreatic islets and β cells

Kim JN, 2019

Three ruminally cannulated Holstein steers

1.Controls: the ruminal fluids 2 h after the morning

Rumen

Denaturing gradient gel electrophoresis and quantitative polymerase chain reaction

↓ Anaerovibrio lipolytica, Eubacterium ruminantium, Prevotella albensis, Prevotella ruminicola, and Ruminobacter amylophilus

2.Fasting: the ruminal fluids feeding and 24 h after fasting

Li T, 2019

Crucian Carp fish

1. Controls: fed to satiation twice per day

Gut

16S rRNA gene amplicon sequencing

In IF groups: ↑alpha diversity and ecosystem stability of gut microbiota

2.IF: fasted for 5 days followed by 5 days of re-feeding

↑ Bacteroides, Akkermansia, and Erysipelotrichaceae, ↑growth performances, immune function

3. Long term fasting (LF): not fed anything during the whole experimental period

In LF group: ↑ Proteobacteria, Gammaproteobacteria, Vibrio, other Vibrionaceae

Miyamoto J, 2019

Wild-type and Gpr43 − / − mice

1.IF: alternating 24 h periods (15 cycles for 1 month) of free access to diet followed by 24 h fasting

Cecum

16S rRNA amplicon sequencing

IF group: ↑Bacteroidetes& Verrucomicrobia

2. Eucaloric ketogenic diet: ketogenic diets for 6 weeks

↑total plasma ketone body ↓total plasma & cecal short chain fatty acids (SCFA)

Park S, 2019

Male Sprague Dawley rats: Alzheimer’s disease (AD) model

1. Controls: normal diet

Feces

16S rRNA amplicon sequencing

IF group: ↓ Clostridales, ↑Lactobacillales

2. Ketogenic diet

Ketogenic group: ↑the relative counts of Proteobacteria especially Enterobacteriales

3. High carbohydrate diet

IF and high carbohydrate groups, but not ketogenic group:

4.IF: normal diet with intermittent fasting

↓ the hippocampal amyloidβ deposition,↑ memory function

Rangan P, 2019

8-weeks-old female C57BL/6 mice: inflammatory bowel diseases mouse model

1. Controls: standard diet

Feces

16S rRNA gene sequencing

FMD: ↑ Microbial strains associated with Tcell regulation and gut regeneration

2. Fasting-mimicking diet (FMD): control diet plus 2 cycles of FMD

↓ intestinal inflammation, ↑stem cell number,

3. water-only fasting (WF): control diet plus 2 cycles of WF

↑ Bifidobacteriaceae, ↓Lactobacillaceae

WF: ↑regenerative, ↓ inflammatory markers without reversing pathology

Zhou ZH, 2019

6-week-old male C57BL/6 J mice Parkinson’s disease (PD) model

1. Controls: normal diet (12 kcal/day)

feces

16S and 18S rRNA gene sequencing

FMD: ↑ Firmicutes, Tenericutes, Opisthokonta, ↓Proteobacteria

2. Fasting-mimicking diet (FMD) day 1: 50% of the standard daily calorie intake day 2–3: 10% of the standard daily calorie intake

↑neuroprotective effect for PD

Deng Y, 2020

3-week-old male C57BL/6 J mice:diet-induced obese model

1.controls: fed with ad libitum (AL) diet (n = 15)

feces

16S rDNA gene amplicon sequencing

↑community diversity in gut flora

2. IF: 24-h fasting for 30 days (n = 15)

↓ Firmicutes to Bacteroidetes ratio

↑ Allobaculum

↓fat accumulation, ↑ white fat conversion to beige

Li L, 2020

7-week-old male C57BL/6JLvri mice

1. Controls: fed with ad libitum (AL) diet (n = 15)

Feces

next-generation sequencing

↑level of Akkermansia & ↓level of Alistipe in 16 h fasting group

2. IF: divided in 3 groups of fasting: 12, 16 and 20 h (n = 15 per group)

of 16S r RNA gene amplicons

↓ cumulative food intake in the 16 and 20 h fasting groups

Liu Z, 2020

homozygous Leprdb/db mice (diabetic), heterozygous Leprdb/m, mice (non- diabetic)

1.controls: fed with ad libitum (AL) diet

Feces

16S rRNA gene v3–v4 amplicon

↑ villi length and the muscularis thickness. ↓ gut leakage, ↑cognitive function

2. IF: deprived of food for 24 h for 28-day

Sequencing

↑ microbiome alpha diversity

↑Lactobacillus and butyrate-producing Odoribacter. ↓Enterococcus, Streptococcus, Candidatus Arthromitus, Rummeliibacillus, Enterococcaceae, Leuconostocaceae

Ye Y, 2020

8-week-old male Kunming mice

1. High-fat diet ad libitum

Feces

16S rRNA gene V3–V4

↓ weight gain, ↓liver steatosis, ↓hepatic levels of triglycerides

2. Time-restricted high-fat diet restricted to an 8-h temporal window per day for 8 weeks

Sequencing

↑ Bacteroidetes, ↓ Firmicutes

Zhang X, 2020

7–8 week –old male C57BL/6 mice: colitis mouse model

1.Controls: standard diet

Feces

16S rRNA gene

ADF, TRF & IER: ↑Escherichia

2. Alternate-day fasting (ADF): 24 h feeding/fasting

sequencing

TRF and IER: ↓Escherichia

3. Time restricted feeding (TRF): fed 8 h per day, fed at 24:00 p.m. and fasting at 8:00 a.m. in the morning

TRF and IER, but not ADF: ↓Gammaproteobacteria, Enterobacteriaceae, Shigella & Escherichia coli,↑ Christensenellaceae

4. Intermittent energy fasting (IER): two cycles of four days of IER diet from day 11–14 and day 29–32

↑SCFAs generation-related microbes: Rikenellaceae, Lactobacillus, Coproccus & Ruminococcus

IER but not TRF and ADF: ↓Peptostreptococcaceae

Shi H, 2021

5 weeks old, WKY and SHRSP hypertensive stroke-prone rats

1. Controls: ad libitum feeding 2.every other day fasting (EODF) group: alternating 24 h of ad libitum food access followed by 24 h fasting for 10 weeks

Cecum & plasma

Shotgun sequence analysis of the microbiota and untargeted metabolomics

↑Bacteriodetes & Actinobacteria, ↓proteobacteria

↑ microbial bile acid metabolism genes: 7α-dehydroxylase and bile salt hydrolase

↓ body weight & systolic blood pressure