Table 1.

Effect of mycotoxins on gut microbiota composition.

Species	Exposure *	Method of Aanalyze	Sample Analyzed	Result	Reference
Rat	AFB1: 5, 25, 75 μg/kg BW 28 days	16S rRNA gene sequencing	excreta	Decreased phylogenic diversity No consistent pattern of increase or decrease at phylum level	[144]
Rat	AFB1: 25 μg/kg BW 28 days	16S rRNA gene sequencing	excreta	Firmicutes (82%), Bacteroidetes (13.5%) the most abundant Proteobacteria (3.3%) Actinobacteria (1.7%) and Saccharibacteria (1%) No effect on microbiota richness Increased abundance of Alloprevotella spp decrease in Prevotella_9.	[145]
Rat	DON: 100 μg/kg BW 28 days	RT-PCR	excreta rats inoculated with human fecal flora	Variation of microbiota composition with time Increased concentration of Bacteroides and Prevotella genera on day 10–20 Reduced expression of Escherichia coli on day 27	[146]
Rat	DON: 60, 120 μg/kg BW 40 days	16S rRNA gene sequencing	cecal digesta	Firmicutes and Bacteroidetes were the most abundant Increase in the relative abundance of Coprococcus genus	[147]
Rat	DON: 2, 10 mg/kg feed 28 days	16S rRNA gene sequencing	excreta	No significant alteration of the composition or diversity of the microbiota	[148]
Rat	OTA: 70, 210 μg/kg BW 28 days	16S rRNA gene sequencing	excreta	Reduced within-subject diversity of the microbiota Increased relative abundance of Lactobacillus Reduced relative abundance of Bacteroides, Dorea, Escherichia, Oribacterium, Ruminococcus, and Syntrophococcus	[143]
Mice	AFB1*: 100, 160, 400 μg/kg BW 60 days	16S rRNA gene sequencing	intestinal contents (from jejunum to rectum)	Lactobacillus and Bacteroides are the dominant flora Differences in the relative abundance of bacterial flora Effects are not dose-dependent	[149]
Mice	DON: 1, 5 mg/kg BW 14 days	16S rRNA gene sequencing	excreta	Variation of microbiota composition with time Bacteroidetes, Firmicutes, Proteobacteria and Verrucomicrobia are the dominant bacterial phyla Reduced relative abundance of Bacteroidaceae family and Alistipes genus on day 14.	[150]
Mice	DON: 1, 5 mg/kg BW 14 days	shotgun sequencing	cecal digesta	The most abundant genera were Lactobacillus, Mastadenovirus, Bacteroides, Mucispirillum, and Parabacteroides Increased relative abundance of Firmicutes at low doses Increased relative abundance of Bacteroidetes at high doses	[151]
Mice	DON: 10 μg/kg BW 280 days	16S rRNA gene sequencing	excreta	Bacteria of the Firmicutes phyla are the most abundant Increase of Deferribacteres, Proteobacteria, TM7, Verrucomicrobia, Tenericutes, and Cyanobacteria. Reduced abundance of Actinobacteria and Bacteroidetes Several significant differences in taxonomic abundances at the family and genus levels.	[152]
Mice	ZEN: 10 mg/kg BW 14 days	16S rRNA gene sequencing	colon digesta	Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria were the dominant phyla in the colon Reduced diversity of the microbiota Reduced abundance of Firmicutes, Bacteroidetes	[153]
Rabbit	ZEN: 400, 800, 1600 µg/kg BW 28 days	16S rRNA gene sequencing	cecal digesta	Reduced abundance of Actinobacteria and increase the abundance of Cyanobacteria, Synergistetes, and Proteobacteria. Reduced abundance of Adlercreutzia, Blautia, Desulfitobacter, Lactobacillus, Oxalobacter, and p-75-a5.	[154]
Rabbit	DON: 1.5 mg/kg BW 24 days	16S rRNA gene sequencing	ileal, cecal and colon digesta	Reduced abundance and diversity of the microflora, Firmicutes, Bacteroidetes, and Proteobacteria were the dominant phyla. Reduced relative abundance of Proteobacteria, Actinobacteria, and Cyanobacteria in both the ileum and caecum and increased relative abundance of Firmicutes and Bacteroidetes in the ileum and colon.in the ileum and Increased relative abundance of Ruminococcaceae, Bacteriods, and Lachnospiraleaes in the ileum, caecum, and colon. Ruminococcaceae represented the largest number of bacteria in the three intestinal segments at the genus level.	[155]
Pig	DON: 2.5 mg/kg feed 28 days	Bacterial culture Capillary electrophoresis	excreta	Variation of total aerobic bacterial flora with time Increase in total aerobic mesophilic bacteria max on day 7	[156]
Pig	DON: 1, 3 mg/kg feed 28 days	16S rRNA gene sequencing	small intestinal lumen digesta	Firmicutes, Proteobacteria, Cyanobacteria and Actinobacteria were the dominant phyla Reduced abundance of Firmicutes and increased abundance of Actinobacteria in duodenum and ileum Reduced abundance of Proteobacteria and increased abundance of Cyanobacteria in duodenum, jejunum, and ileum Lactobacillus, Cupriavidus, Acinetobacter, Burholderia, Staphylococcus, Ochrobactrum, Corynebacterium, and Streptococcus were the predominant generaReduced abundance of Lactobacillus and Cupriavidus and increased abundance of Staphylococcus Reduced abundance of Burkholderia in the duodenum and jejunum, but increased abundance in the ileum	[157]
Pig	DON: 0.61, 1.28, 2.89 mg/kg feed 28 days	16S rRNA gene sequencing	cecal digesta	Reduced abundances of unclassified f_Lachnospiraceae, Phascolarctobacterium and Ruminococcaceae_UCG-014 Increased Prevotella_9 and norank f_Prevotellaceae	[158]
Pig	ZEN: 40 μg/kg BW DON: 12 μg/kg BW ZEN + DON: 40 + 12 μg/kg BW42 days	EcoPlate tests	ascending colon digesta	Variation of total aerobic bacterial flora with time Same effect in nature whatever the toxin Lactic acid bacteria predominant floraDecrease in the number of mesophilic aerobic bacteria Decrease in the level of C. perfringens, E. coli, and Enterobacteriaceae family	[159]
Pig	ZEN: 0.8 mg/kg feed DON: 8 mg/kg feed 7 days	16S rRNA gene sequencing	colon digesta	Firmicutes and Bacteroidetes were the dominant phyla Lactobacillus, Megasphaera, and Faecalibacterium genera, and the unclassified Clostridiaceae family were the most abundant Lactobacillus was particularly more abundant in the DON (7.6%) and ZEN (2.7%) groups than in the control (0.2%).	[160]
Pig	ZEN: 5, 10, 15 µg/kg BW 7, 21, 42 days	Bacterial culture	duodenal cap, third duodenum part, jejunum, caecum, descending colon digesta	Microbial counts, mainly E. coli and Enterococcus faecalis, varied from the proximal to the distal segments of the intestinal tract ZEN affected the colony counts of microbiota rather than diversity Increased yeast and mold counts in all intestinal segments, in particular in the colon	[161]
Pig	DON + ZEN: 3.02 + 0.76 mg/kg feed 7 days Repeated exposure	16S rRNA gene sequencing	excreta	Reduced relative abundances of Ruminococcaceae, Streptococcaceae, and Veillonellaceae and increased Erysipelotrichaceae Microbiota returned to the initial state within 3 weeks after the end of a single or repeated DON/ZEN challenge	[162]
Pig	FB1+FB2: 8.6 + 3.2 mg/kg feed 63 days	Capillary single-stranded conformation polymorphism analysis	excreta	Variation of total aerobic bacterial flora with time Reversible alteration of the microbiota balance	[163]
Pig	FB1: 12 mg/kg feed 0, 8, 15, 22, 29 days	16S rRNA gene sequencing	excreta	Decrease in the diversity index, and shifts and constraints in the structure and the composition of the microbiota after 15 days of exposure that reached maximum after 22 days of exposure Increased Lactobacillus and reduced Lachnospiraceae, Veillonellaceae families, and particularly the genera Mitsuokella, Faecalibacterium, and Roseburia	[164]
Broiler	AFB1: 40 μg/kg feed 21 days	Bacterial culture	ileal digesta	No effect on Lactobacilli, Bifidobacteria, C. perfringens, E. coli	[165]
Broiler	Aflatoxins 0.5, 2 mg/kg feed 7 and 28 days	Bacterial culture	ileal digesta	Increased E. coli, Salmonella, Klebsiella, and total Gram- bacteria at day 28 of exposure Changes persisted for 14 days after exposure stopped	[166,167]
Broiler	AFB1: 1, 1.5, 2 mg/kg feed 21 days	Bacterial culture	cecal digesta	Increased total aerobic bacteria, total Gram - bacteria, variable effect on total lactic acid bacteria Effects are not always dose-dependent	[168]
Broiler	DON: 2.5, 5 and 10 mg/kg feed 35 days	16S rRNA gene sequencing	cecal digesta	Increased relative abundance of Firmicutes (decreased Oscillospira, Clostridiaceae genus, Clostridium, and Ruminococcaceae genera but increased Clostridiales genus) Reduced relative abundance of Proteobacteria	[169]
Broiler	FB1 + FB2: 10.4 + 8.2 mg/kg feed 15 days	16S rRNA gene sequencing	ileal digesta	Reduced abundance of Candidatus Savagella and Lactobaccilus spp., increased total Clostridium perfringens	[170]
Turkey	OTA: 199 to 462 µg/kg feed 21, 42, 63, 105 days	Bacterial culture	jejunum and cecal digesta, excreta	Reduced Lactobacillus spp. and Bifidobacterium spp. in samples of the intestinal content and the excreta after 15 weeks	[171]
Duck	OTA: 235 µg/kg BW 14 days	16S rRNA gene sequencing	excreta	Increased Bacteroidetes (phylum level), Bacteroides (genus level), Bacteroides plebeius (species level)	[172]

* calculated from data provided by the authors.