Role of the normal gut microbiota

Table 1 Advantages and disadvantages of few of the currently available next generation sequencing techniques[15,16]

Techniques used in next generation sequencing	Accuracy	Advantages	Disadvantages
454 Pyrosequencing	99.9%	Less amount of sample, long read lengths, large number of samples can be easily read	Homopolymer errors Expensive
Shot gun Sequencing	98%	Short reads in short time	Assembly process is computationally expensive
Illumina Sequencing (Sequencing by synthesis)	98%	Accurate, quicker, reliable and cheap	Expensive
Pacific Bio Sequencing (single molecule real-time sequencing)	99.9%	Fast and provides long read length	Expensive equipment
Ion Torrent Sequencing (Ion semiconductor)	98%	Fast and less expensive equipment	Multiple monomer errors
SOLiD (Sequencing by Ligation) Sequencing	99.9%	Less expensive when compared to other methods	Slow and difficult to sequence palindromes

Table 2 Types of dietary polyphenols present in various foods and the types of microorganisms those are responsible for the degradation

Polyphenolic compounds	Classes involved	Foods containing polyphenols	Gut bacteria
Flavanols	Kaempferol[51], Quercetin[53], Myricetin[52]	Onions, capers, apples, broccoli, grapes and plums	Bacteroides distasonis, Bacteroides uniformis, Enterococcus casseliflavus and Eubacterium ramulus
Flavanones	Hesperetin, Naringenin[54]	Citrus fruits and tomatoes	Clostridium sps, E. ramulus
Flavan-3-ols	Catechin[55], Epicatechin[56], Gallocatechin[57,58]	Green tea, cocoa, kola, banana, pomegranate	Bifidobacterium infantis and Clostridium coccides
Anthocyanidins	Cyanidin[59], Pelagonidin, Malvidin[60]	Bilberries and all red, blue and purple fruits (especially berries)	Lactobacillus plantarum, L. casei, L. acidophilus and Bifidobacterium longum
Isoflavones	Daidzein[61,62], Geinstein[63], Formononentin[64]	Soy, beans, lentils, chickpea (Fabaceae family)	Lactobacillus and Bifidobacterium
Flavones	Luteolin[65], Apigenin[66]	Cereals, parsley, thyme, celery and citrus fruits	C.orbiscinden, Enterococcus avium
Tannins	Gallo tannins, Ellagitannins[67]	Raseberries, cranberries, strawberries, walnuts, grapes and pomegranate	Butyrivibrio sps
Lignins	Secoisolariciesinol, metaresinol, pinoresinol, larciresinol, isolarciresinol, syringiresinol[68]	Flax seeds, cereals, strawberries, and apricots	Species of Bacteroides, Clostridium, Peptostreptococcus and Eubacterium
Chlorogenic acids	Caffeic acid, feruic acid[69]	Peach, plums and coffee	E. coli, Bifidobacterium sps and L. gasseri