Irritable Bowel Syndrome: Definition, Morbidity, General Treatment Options and Introduction to Microbiome Manipulation
Methodology
The Microbiome in IBS
Taxon | Percentage in IBS | Citations |
---|---|---|
Enterobacteriaceae
| Higher | [38] |
Lactobacillus
| Lower | |
Lactobacillus genus or Lactobacillales order | Higher | |
Bifidobacterium
| Lower | |
Firmicutes/Bacteroides
| Higher | |
Firmicutes/Bacteroides
| Lower | |
Clostridiales
| [31] | |
Ruminococcaceae or Ruminococcus | Higher | |
Erysipelotrichaceae
| [31] | |
Methanogens
| Lower | |
Veillonella
| Higher | |
Faecalibacterium
| Lower |
Therapeutic options in managing the intestinal microbiome in IBS
Pre-, Pro- and Synbiotics
Prebiotics
Prebiotic | Dose (g/day) | Duration | Studied species | Detection method | Affected taxon | Citation |
---|---|---|---|---|---|---|
AX | 10 | 10 days | Total anaerobes, aerobes, bifidobacteria, eubacteria, Bacteroides spp., Clostridium spp., Veillonella, Lactobacillus, Streptococci, Staphylococci, yeasts and molds, Enterobacteriaceae | Specific agar cultures | No differences | [154] |
scFOS | 4 | 2 Weeks | Anaerobes, bifidobacterium and lactobacillus | Specific agar cultures | Increased bifidobacteria and lactobacilli | [155] |
Inulin and FOS | 15 | 45 days | Anaerobes, total aerobes, coliforms, gram-positive cocci, bifidobacteria, Bacteroides, Fusobacteria, lactobacilli and Clostridia | Specific agar cultures | Increased predominance of bifidobacteria | [59] |
FOS | 12.5 | 12 days | Anaerobes and bifidobacteria | Specific agar cultures | Increased bifidobacteria | [156] |
FOS | 4 | 42 days | Anaerobes, enterobacteria and bifidobacteria | Specific agar cultures | Increased bifidobacteria | [157] |
Inulin and lactose | 20–40 | 19 days | Anaerobes, bifidobacteria, lactobacilli and Bacteroides spp | Specific agar cultures | Increased bifidobacteria, decreases enterococci and Fusobacteria | [158] |
GOS | 15 | Lactic acid bacteria and bifidobacteria | Specific agar cultures | Increased fecal lactic acid bacteria | [159] | |
Inulin | 34 | 64 days | Total and bifidobacteria | FISH | Increased bifidobacteria | [160] |
scFOS | 2,5–20 | 14 days | Anaerobes and bifidobacteria | Specific agar cultures | Increased bifidobacteria | [161] |
FOS | 8 | 5 weeks | Anaerobes, Bacteroides, lactobacilli, Coliforms, Clostridium perfringens, bifidobacteria | Specific agar cultures | Increased bifidobacteria | [162] |
FOS | 5 | 3 weeks | Total anaerobes, total aerobes, Bacteroides, bifidobacteria, coliforms | Specific agar cultures | Increased bifidobacteria and Bacteroides | [163] |
Inulin | 8 | 2 weeks | Bifidobacteria, Bacteroides, Clostridia (Clostridium perfringens/histolyticum sub.grp.) and lactobacilli/enterococci | FISH | Increased bifidobacteria | [164] |
FOS | 7 | 42 days | Bifidobacteria, Bacteroides, Clostridia (Clostridium perfringens/histolyticum sub.grp.) and Lactobacillus-Enterococcus spp. | FISH | Increased bifidobacteria | [165] |
scFOS | 8 | 3 weeks | Enterobacteriaceae, bifidobacteria, lactobacilli, Clostridium perfringens, Bacteroides and Enterococci | Specific agar cultures | Increased bifidobacteria | [166] |
Inulin | 9 | 2 weeks | Total bacteria, bifidobacteria, E. rectale/C. coccoides, Bacteroides, eubacteria | FISH, DGGE | Increased bifidobacteria | [167] |
GOS and FOS | 0.4 and 0.8 | 28 days | Bifidobacteria, lactobacilli, Bacteroides, Clostridium species, Escherichia coli, Enterobacter, Citrobacter, Proteus, Klebsiella and Candida | Specific agar cultures | Growth of bifidobacteria and lactobacilli | [168] |
Inulin | 20 g Nutricia inulin (%?) | 3 weeks | Total aerobes, enterobacteria, Enterococcus, Pseudomonas sp., total anaerobes, total Bacteroides, Bacteroides fragilis, Clostridia, lactobacilli, bifidobacteria, yeast and fungi | Specific agar cultures | Decreased Bacteroides fragilis | [169] |
scFOS or GOS | 10 | 6 weeks | Total anaerobes, Bifidobacterium, Bacteroides, Lactobacillus and enterobacteria | Specific agar cultures | Increased fecal bifidobacteria | [170] |
FOS and inulin | 2,8 to 3,4 | 2 weeks | Total anaerobes, Bifidobacterium and Bacteroides, Clostridium difficile, lactobacilli, enterococci, Veillonella by culture. Bifidobacterium genus, Atopobium cluster and Coriobacterium, Escherichia coli, Bacteroides distasonis, B. fragilis, Clostridium histolyticum, C. lituseburense, C. coccoides and Eubacterium rectale, Streptococcus–Lactococcus, Lactobacillus and Enterococcus by FISH | Specific agar cultures and FISH | Increased bacteria | [171] |
Low and high SOS (LSO and HSO) | 1.5 or 3 | 30 days | Total bacteria and bifidobacteria | Specific agar cultures | Increased bacteria with both LSO and HSO; increased bifidobacteria only with HSO | [172] |
scFOS | 8 | 4 weeks | Total anaerobes, Bifidobacterium, Clostridium spp. and enterobacteria | Specific agar cultures | Increased fecal bifidobacteria | [173] |
XOS | 3.8 | 3 weeks | Bifidobacterium, C. perfringens | Specific agar cultures | Increased bifidobacteria | [174] |
Inulin | 7.7 then 15.4 | 3 weeks | Bacteria, Clostridium coccoides/Eubacterium rectale, Bacteroides/Prevotella (Bacteroides fragilis group and Bacteroides distasonis), Faecalibacterium prausnitzii, bifidobacteria, Atopobium, Clostridium histolyticum, Clostridium lituseburense by FISH. Enterobacteriaceae, lactobacilli, enterococci and Clostridium perfringens and yeasts by specific culture | FISH and specific agar cultures | Increased bifidobacteria and decreased Bacteroides | [175] |
Inulin | 5–8 | 2 weeks | Bacteroides/Prevotella, Bifidobacterium genus, Clostridium perfringens histolyticum subgroup and Lactobacillus/Enterococcus | FISH | Increased bifidobacteria | [176] |
GOS, FOS | 03-ene | 3 months | Bifidobacteria, Clostridia and E.coli | FISH | Increased Bifidobacterium; decreased E. coli and Clostridium | [177] |
Inulin/FOS | 10 | 4 weeks | V3 profiles. Specifically, Bifidobacterium by qPCR | DGGE and qPCR | Increased bifidobacteria | [178] |
GOS | 3.6–7 | 7 days | Bifidobacterium genus, Clostridium perfringens/histolyticum subgroup, Bacteroides–Prevotella and Lactobacillus/Enterococcus spp | FISH | Bifidogenic effect | [179] |
GOS, FOS | 6 g/l ratio 9:1 | 27 weeks | Bifidobacterium, Clostridium histolyticum/Clostridium lituseburense, E. coli | FISH | Increased Bifidobacterium; decreased Clostridium | [180] |
FOS and inulin | 11.1:3.6 | 6 weeks |
Bifidobacterium
| qPCR | “Nearly significant” increased Bifidobacterium | [181] |
AXOS | 10 | 21 days | Total bacteria, Bifidobacterium spp., Bifidobacterium adolescentis, Lactobacillus spp., Roseburia–Eubacterium rectale, enterobacteria | qPCR | Increased bifidobacteria; decreased lactobacilli | [182] |
FOS and inulin | 6.8 ± 1.5 | 2 weeks | Bifidobacteria, lactobacilli and enterococci, Bacteroides and Clostridia coccoides–Eubacterium rectale | FISH | No differences | [183] |
FOS and inulin | Not indicated | 1–2 weeks | Bifidobacteria, lactobacilli, Clostridia, Bacteroides and Faecalibacterium prausnitzii | FISH | Decreased F. prausnitzii | [184] |
β-GOS (BimunoTM) | 5.5 | 5–10 weeks | Bifidobacterium spp., Bacteroides spp., Atopobium cluster, Lactobacillus/Enterococcus spp., Fecalibacterium prausnitzii cluster, Roseburia/Eubacterium rectale group, Clostridium coccoides/E. rectale group, Clostridium histolyticum group, E. coli, Desulfovibrio spp. | FISH | Increased bifidobacteria and Bacteroides. Atopobium cluster increased in the follow-up | [72] |
GOS | Escalating from 1.5 to 15 | 36 days | 16 s rRNA gene v1-v2 amplicon | 454 Genome Sequencer FLX Titanium | Increased Bifidobacterium, Faecalibacterium and Lactobacillus | [185] |
Inulin/FOS | 16 | 3 months | 1100 Intestinal bacterial phylotypes | Human Intestinal Tract Chip (HITChip) and qPCR | Increased Bifidobacterium, Faecalibacterium prausnitzii, Lactobacillus spp.; decreased Bacteroides intestinalis and vulgatus. | [186] |
GOS | 10 | 4 weeks | 16 s rRNA Gene v1-v2 amplicon | Illumina MiSeq | Increased Bifidobacteriaceae; decreased lachnospiraceae, Ruminococcaceae, Peptostreptococcaceae, Erysipelotrichaceae, Porphyromonadaceae | [187] |
FOS and GOS | 2 weeks | 16 s rRNA gene v4 amplicon | Ion Torrent | FOS increased Bifidobacterium; FOS decreased abundance of Phascolarctobacterium, Enterobacter, Turicibacter, Coprococcus and Salmonella. GOS increased Bifidobacterium; GOS decreased Ruminococcus, Dehalobacterium, Synergistes and Holdemania. | [188] | |
Inulin | 8 | 16 weeks | 16 s rRNA gene v3-v4 amplicon | Illumina MiSeq | Increased Bifidobacterium spp (Bifidobacterium adolescentis and Bifidobacterium longum); decreased Clostridium cluster XI, Faecalibacterium prausnitzii, Bacteroides vulgatus, Ruminococcus gauvreauii (all differences before correction) | [189] |
FOS and inulin | 16 | 9 weeks | 16 s rRNA gene v3-v4 amplicon | Illumina MiSeq | Increased Bifidobacterium | [190] |
Inulin | 12 | 4 weeks | 16 s rRNA gene v4 amplicon | Illumina MiSeq | Increased Bifidobacerium and anaerostipes; decreased Bilophila | [191] |