Antibiotics, gut microbiota, and irritable bowel syndrome: What are the relations?

Table 1 Gut microbiota functions

Bacterial phylum	Key representatives	Functions
Firmicutes	Members of the genera Enterococcus, Ruminococcus, Clostridium, Lactobacillus, Faecalibacterium, Roseburia, and Eubacterium	Metabolism of amino acids[23,24], carbohydrates[25], bile acids, and their salts[22]. Lipid metabolism and cholesterol synthesis[25]. Synthesis of vitamins К2, B1, B2, B6, B7, B9, and B12[26]. Maintenance of a proper immune response[28,29] and intestinal epithelial barrier integrity[31,32]. Protection against enteric pathogens[33]
Bacteroidetes	Members of the genera Bacteroides and Prevotella	Metabolism of amino acids[24], carbohydrates[25,141], bile acids, and their salts[22,142]. Synthesis of vitamin К2[27]. Regulation of appetite[143]. Maintenance of a proper immune response[28-29] and intestinal epithelial barrier integrity[31]. Protection against enteric pathogens[33]
Actinobacteria	Members of the genera Bifidobacterium and Corynebacterium	Metabolism of bile acids and their salts[22]. Synthesis of vitamins К2, B1, B2, B6, B7, B9, and B12[26]. Protection against enteric pathogens[33]
Proteobacteria	Members of the genera Desulfovibrio, Escherichia, and Shigella	Metabolism of amino acids[144]

Table 2 Compositional changes in gut microbiota in patients with irritable bowel syndrome (common threads)

Ref.	Subjects	Method	Specimen	Diversity	Faecalibacterium	Enterobacteriaceae	Bifidobacterium	Lactobacillus
Dior et al[145], 2016	IBS-D (n = 16), IBS-C (n =15), Controls (n = 15)	Real-time PCR	Stool	No data	−	↑ in IBS-D (Escherichia)	↑ in IBS-C	−
Ringel-Kulka et al[108], 2016	IBS (n = 56), Controls (n = 20)	16S rRNA	Stool	No data	−	−	−	↑
Maharshak et al[102], 2018	IBS-D (n = 23), Controls (n = 24)	16S rRNA	Stool	↓1	↓	↑ (unclassified genus)	−	−
			Colonic biopsy	−1	−	−	−	↑
Gobert et al[146], 2016	IBS-C (n = 33), Controls (n = 58)	16S rRNA	Stool	No data	−	↑	↓	−
Shukla et al[105], 2015	IBS (n = 47), Controls (n = 30)	16S rRNA; real-time PCR	Stool	No data	−	−	↓	−
Su et al[107], 2018	IBS-D (n = 40), Controls (n = 20)	16S rRNA; real-time PCR	Stool	No data	−	−	↓	↓
Zhuang et al[109], 2018	IBS-D (n = 30), Controls (n = 13)	16S rRNA	Stool	−2	−	−	−	↓
Zhong et al[147], 2019	IBS-D (n = 20), Controls (n = 16)	FISH	Colonic biopsy	No data	−	↑ (E. coli)	↓	−
Jeffery et al[100], 2020	IBS (n = 80), Controls (n = 65)	16S rRNA, shotgun sequencing	Stool	↓2	−	−	−	−
Rangel et al[148], 2015	IBS (n = 33), Controls (n = 16)	Microarray analysis	Stool	↓2	↓ (F. prausnitzii)	−	−	−
			Colonic biopsy	−2	−	−	−	−

¹Rarefaction analysis.

²Shannon diversity index.

↓: Decreased abundance; ↑: Increased abundance; –: No significant differences found; IBS: Irritable bowel syndrome; IBS-D: Diarrhea-predominant irritable bowel syndrome; IBS-C: Constipation-predominant irritable bowel syndrome; FISH: Fluorescence in situ hybridization; E. coli: Escherichia coli; F. prausnitzii: Faecalibacterium prausnitzii.

Table 3 Effects of antibiotics on gut microbiota composition (based on culture-independent approaches)

Ref.	Method	Antibiotic	Dosing regimen	Diversity	Compositional changes
Pallav et al[136], 2014	Pyrosequencing	Amoxicillin	250 mg 3 times daily for 7 d	−1,2	↑ Escherichia, Shigella
Kabbani et al[137], 2017	16S rRNA	Amoxicillin-Clavulanate	875/125 mg twice daily for 7 d	↓1,3	↑ Escherichia, Parabacteroides, Enterobacter ↓ Roseburia
Burdet et al[120], 2019	16S rRNA	Ceftriaxone	1 g once daily for 3 d	↓1,4	↓ Firmicutes, Actinobacteria, Bacteroidetes
Raymond et al[135], 2016	Shotgun sequencing	Cefprozil	500 mg twice daily for 7 d	↓5	↑Flavonifractor, Lachnoclostridium, Parabacteroides, ↓Bifidobacteriaceae, Coriobacteriaceae, Eubacteriaceae, Oxalobacteraceae, Pasteurellaceae, Veillonellaceae
Rashid et al[121], 2015	Pyrosequencing	Ciprofloxacin	500 mg twice daily for 10 d	↓1	↑ Bacteroides↓ Faecalibacterium, Alistipes, unculturable Ruminococcaceae
		Clindamycin	150 mg 4 times daily for 10 d	↓1	↓ Roseburia, Lachospira, Coprococcus, Dorea, Ruminococcus
Isaac et al[122], 2017	16S rRNA	Vancomycin	250 mg per os 4 times daily for 2 wk	↓1,4	↑ Escherichia, Shigella, Klebsiella, ↓ Bacteroidetes, Faecalibacterium, Ruminococcus

¹OTU analysis.

²Rarefaction analysis.

³Chao1 index.

⁴Shannon index.

⁵Simpson index.