Sara Vieira-Silva, João Sabino, Mireia Valles-Colomer, Gwen Falony, Gunter Kathagen, Clara Caenepeel, Isabelle Cleynen, Schalk van der Merwe, Séverine Vermeire, and Jeroen Raes
Halfvarson J, Brislawn CJ, Lamendella R, Vázquez-Baeza Y, Walters WA, Bramer LM, D'Amato M, Bonfiglio F, McDonald D, Gonzalez A, McClure EE, Dunklebarger MF, Knight R, Jansson JK.
2017 Feb 13;2:17004. doi: 10.1038/nmicrobiol.2017.4. PubMed PMID: 28191884
Ni J, Wu GD, Albenberg L, Tomov VT. Nat Rev Gastroenterol Hepatol. 2017 Jul 19. doi:
10.1038/nrgastro.2017.88. [Epub ahead of print] Review. PubMed PMID: 28743984.
Nicholas A Bokulich, Sathish Subramanian, Jeremiah J Faith, Dirk Gevers, Jeffrey I Gordon, Rob Knight, David A Mills & J Gregory Caporaso
- High-quality read length and abundance are the primary factors differentiating correct from erroneous reads produced by Illumina High Throughput Sequencing systems.
- Primary quality-filtering parameters (p, minimal high-quality read length, q Phred score, r maximum of consecutive low-quality calls and n maximum of ambiguous calls allowed) and secondary (c, operational taxonomic unit (OTU) threshold) quality-filtering parameters affect analyses that were tested using separate evaluations.
- Users with majority of high-quality, full-length sequences may use filters for retrieving only full-length sequences with low error rates, potentially increasing the discovery rate of rare OTUs.
Users with shorter reads or reads truncated by early low-quality base calls may change settings so that lower-quality but taxonomically useful reads will be retained, and reliable sequences will be selected based on abundance rather than error probability.
- Other users may be more interested in maximizing read count by increased sample sizes, for which reads should be filtered using primary filters of Phred score and minimum high-quality calls.
---> Recommended settings for Illumina processing in QIIME 1.5.0 are (r = 3; p = 0.75 total read length; q = 3; n = 0; c = 0.005)
- Saulnier at al., Gastroenterology 2011 (PMID:21741921):"PEDIATRIC IBS" by 16s pyrosequencing
Gastrointestinal Microbiome Signatures of Pediatric Patients With Irritable Bowel Syndrome
The authors studied 22 controls and 22 patients (7-12 y), 16s pyrosequencing and PhyloChip. They found greater proportion of gamma-proteobacteria (haemophylus Influenzae) in IBS, a Ruminococcus-like bacteria associated with IBS, several taxa from the Alistipes genus were correlated with pain.
- Rajilić-Stojanović et al., Gastroenterology 2011 (PMID:21820992): "IBS-microbiota" by PHYLOCHIP
Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome.
The authors studied 60 IBS patients ( 25 IBS-D; 18 IBS-C; 19 IBS-A), 16s PhyloChip of 3699 probes (129 genus.lie groups). They found 2 clusters based on health status, a decrease of Bacteroidetes and Actinobacteria (Bifibobacteria), and an increase of Firmicutes. R. gnavus and Blautia are significantly higher in IBS and positively correlated with symptoms. M. smithii was found higher in healthy controls. F prausnitzii was reduced in IBS patients. Several members of Gammaproteobacteria were associated with IBS symptoms.
- Jeffery et al., Gut 2012 (PMID:22180058): "ADULT IBS" by 16s pyrosequencing
An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota
The authors studied 37 IBS patients (15 IBS-D, 10 IBS-C, 12 IBS-A) and 20 controls using 16S rDNA pyrosequencing. Their PCoA projections showed 4 separated clusters for healthy controls and IBS patients (Control, normal-like, cluster 1 and cluster 2 microbiota) [not very convincing, since several samples from healthy controls clustered also within clusters 1 and 2 as shown in figure 1B]. Clucter 1 and 2 showed higher and lower diversity respectively and higher Firmicutes/Bacteroidetes ratio. The authors also found a higher proportion of Bifidobacterium adolescentis, of Clostridium clsuter XIVa in cluster 1, a general decrease in the two genera (Bacteroides and Alistipes), an increase of Firmicutes coupled with a decrease of Bacteroidetes. Proteobacteria abundance was associated with an increased mental component and an increased pain threshold. The correlation between clusters 1 and 2 and the 3 IBS types is not obvious.
- Mättö et al., FEMS Imm. Med. Microb. 2005 (PMID:15747442): "MICROBIOTA STABILITY IN IBS" by culture and DGGE.
Composition and temporal stability of gastrointestinal microbiota in irritable bowel syndrome--a longitudinal study in IBS and control subjects.
The authors analyzed 3 time-points samples from 21 IBS patients and 17 controls using culture and DGGE aproaches. They observed higher numbers of coliforms as well as a higher proportion of facultatively anaerobic bacteria, and a more unstable microbiota in IBS than in control subjects. However, more than half of their IBS patients did take antibiotics during the study.