Table 6.

Influence of NE challenge on gut microbiota and the modulation effect by probiotics.

S/N	Response to NE Challenge	Probiotic Strain	Response to Dietary Probiotics	Ref
1	Decreased Actinobacteria, Lactobacillacae and Firmicutes (Clostridia)	Multi strains of Lactobacillus	Increased Actinobacteria, Lactobacillacae and Firmicutes (Clostridia)	[13]
2	Decreased Lachnospiraceae_UCG_010, Clostridiales_vadinBB60 and Ruminococcaceae_NK4A214_	B. licheniformis	Increased Lachnospiraceae_UCG_010, Clostridiales_vadinBB60 and Ruminococcaceae_NK4A214	[19]
3	Reduced Firmicutes, increased genera; Turicibacter, Streptococcus, Enterococcus and Clostridium	B. licheniformis H2	Reduced Proteobacteria, increased Lactobacillus and Bacillus	[21]
4	Increased Clostridium sensu stricto-1 and reduced Lactobacillus	B. licheniformis	Reduced Clostridium sensu stricto 1 and Escherichia-Shigella; increased Lactobacillus	[23]
5	Reduced cecal Lactobacillus and Bifidobacterium; increased cecal coliform	B. coagulans	Reversed the trend	[25]
6	Increased Candidatus Arthromitus unclassified Brachybacterium and decreased Lactobacillus sp. KC45b	C. butyricum	Probiotics reversed all; increased Weissella thailandensis and Pediococcus acidilactici	[26]
7	Increased Dorea, Bacteroides, Eubacterium, Caldanaerocella and Enterococcus	B. subtilis	Decreased Dorea, Ruminococcus and Proteobacteria	[32]
8	Increased Romboutsia, f_Lachnospiraceae and Ruminococcus_torques group, and decreased Lactobacillus. Lower ileal Bacteriodetes and cecal Proteobacteria on day 28	L. fermentum, B. coagulans	Probiotics reversed it; decreased Faecalibacterium spp. and f_Peptostreptococcaceae	[33]
9	Increased proliferation of CP; reduced L. salivarius and B. fidobacterium	Bacillus subtilis DSM 32315.	Reduced proliferation of CP; increased L. Salivarius and B. fidobacterium	[52]
10	Increased Prevotellacea, Muribaculacea, Rominiclostridium 9, Oscillibacter, RuminococcaceaeUCG_014, ASF356, Clostridium sensu stricto 1,	Multi strain	Decreased the abundance of the pathogens; increased ileum Firmicutes and Lactobacillus	[53]
11	Increased Enterococcus, Escherichia/Shigella, Barnesiella, Desulfovibrio and Campylobacter; reduced Lactobacillus and Bacteriodes	Primlac: multi strain probiotics	Reduced Enterococcus, Escherichia/Shigella, Barnesiella, Desulfovibrio and Campylobacter; increased Lactobacillus and Bacteriodes	[94]
12	Reduced Ruminococcaceae and Bifidobacterium	B. subtilis DSM29784	Increased Ruminococcaceae and Bifidobacterium,	[95]
13	Reduced Lactobacillus	E. faecium	Reversed the negative effect	[112]
14	Increased lachnopiraceae and Ruminococcaceae	B. subtilis DSM 32315	Increased L. johnsonii and Salivarius; reduced CP alpha toxin	[113]
15	Increased CP coliforms in the ileum and cecum	Bacteriophage	Reduced CP coliforms in the ileum and cecum	[118]
16	Increase in Escherichia coli, Staphylococcus aureus, Salmonella typhimurium and C. perfringens.	Bacillus. Surfactin (fermented product)	In vitro reduction in Escherichia coli, Staphylococcus aureus, Salmonella typhimurium and C. perfringens	[119]
17	NE reduced Faecalibacterium	B. subtilis 29784	Increased Butyricicoccus and Faecalibacterium genera	[122]
18	Reduced Bacteriodetes, C. cluster IV and C. cluster XIVa, Lactobacillus, increased Streptococcus spp. Enterobacteriaceae	Lactobacillus johnsonii. LB 15	Increased Lactobacillus, C. cluster IV and C. cluster XIVa, reduced Streptococcus and Enterobacteriaceae	[123]