Characterization of the human predominant fecal microbiota - With special focus on the Clostridial clusters IV and XIVa
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School of Chemical Technology |
Doctoral thesis (article-based)
| Defence date: 2012-12-07
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Date
2012
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Language
en
Pages
161 + app. 62
Series
VTT Science, 26
Abstract
The human gut microbiota is considered to be a complex fermentor with a metabolic potential rivaling that of the liver. In addition to its primary function in digestion, it affects the human host in numerous ways: maturation and modulation of the immune system, production of short-chain fatty acids and gases, transformation of bile acids, formation of vitamins, and also potential formation of mutagenic, toxic, and carcinogenic substances. Commensal bacteria are able to modulate the expression of host genes that regulate diverse and fundamental physiological functions. Thus the indigenous microbial community has an important influence on host physiological, nutritional and immunological processes. The primary aim of this study was to characterize human predominant fecal microbiota with a special focus on Clostridial clusters XIV (Lachnospiraceae, Eubacterium rectale – Blautia coccoides group) and IV (Ruminococcaceae, Clostridium leptum group). The specific aims were: 1) To develop molecular methods for characterization of the human predominant fecal microbiota; 2) To assess the specificity, practicality, and usability of the developed methods for human fecal samples in healthy adults, elderly people, and people having IBS; 3) To assess possible confounding factors in the analysis of human fecal samples. Molecular tools were developed for rapid, sensitive, and highly specific characterization of the human predominant fecal and salivary microbiota. DNA- and rRNAbased denaturing gradient gel electrophoresis methods (DGGE) were developed for Eubacterium rectale – Blautia coccoides group (Erec), rRNA-based DGGE method for predominant bacteria, and DNA-based DGGE methods for Clostridium leptum group (Clept) and Bacteroides spp. In addition, quantitative real-time PCR (qPCR) methods targeting predominant bacteria, Erec-group, Clept-group, Bacteroides spp., bifidobacteria, and Atopobium group were developed.Suolistomikrobiston ensisijainen tehtävä on auttaa ruoansulatuksessa; paksusuolen mikrobit käyttävät hyödykseen useita ravintoaineita, jotka eivät imeydy ohutsuolessa. Ihminen puolestaan hyödyntää mikrobien aineenvaihduntatuotteita. Suolistomikrobisto vaikuttaa ihmiseen monella muullakin tavoin: se edesauttaa immuunijärjestelmän kehittymistä, tuottaa kaasuja sekä lyhytketjuisia rasvahappoja, muuttaa sappihappojen muotoa, tuottaa vitamiineja ja muodostaa mahdollisesti myös mutageenisiä, toksisia sekä karsinogeenisiä yhdisteitä. Niinpä ihmisen suolistomikrobistolla on merkittävä vaikutus ihmisen fysiologisiin, ravitsemuksellisiin ja immunologisiin toimintoihin. Tämän tutkimuksen tavoitteena oli kehittää menetelmiä ihmisen suolistomikrobiston tärkeimpien bakteeriryhmien karakterisointiin ja kvantitointiin ja todentaa kehitettyjen menetelmien soveltuvuus ihmisen uloste- ja sylkinäytteiden analysointiin. Tässä työssä kehitettiin spesifiset ja herkät rRNA-pohjaiset PCR – denaturoiva gradientti geeli elektroforeesi (DGGE) -menetelmät vallitsevan bakteeriston ja Eubacterium rectale – Blautia coccoides -klostridiryhmän (Erec) karakterisointiin sekä DNA-pohjaiset PCR-DGGE-menetelmät Clostridium leptum –klostridiryhmän (Clept), sekä Bacteroides-suvun karakterisointiin. Lisäksi kehitettiin reaaliaikaiset PCR-menetelmät (qPCR) vallitsevan bakteeriston, Erec-ryhmän, Clept-ryhmän, Bacteroides-suvun, bifidobakteerien, sekä Atopobium-ryhmän kvantitointiin.Description
Supervising professor
Saarela, Maria, Doc., VTT Technical Research Centre of Finland, FinlandKeywords
human fecal microbiota, human salivary microbiota, DGGE, qPCR, IBS, elderly people, GOS, DNA-extraction, Erec, Clept, Bacteroides spp., bifidobacteria, lactobacill
Other note
Parts
- [Publication 1]: Maukonen J, Satokari R, Mättö J, Söderlund H, Mattila-Sandholm T & Saarela M (2006). Prevalence and temporal stability of selected clostridial groups in irritable bowel syndrome in relation to predominant faecal bacteria. Journal of Medical Microbiology, 55, 625–633.
- [Publication 2]: Maukonen J, Mättö J, Satokari R, Söderlund H, Mattila-Sandholm T & Saarela M (2006). PCR-DGGE and RT-PCR-DGGE show diversity and short-term temporal stability in the Clostridium coccoides – Eubacterium rectale group in the human intestinal microbiota. FEMS Microbiology Ecology, 58, 517–528.
- [Publication 3]: Maukonen J, Mättö J, Kajander K, Mattila-Sandholm T & Saarela M (2008). Diversity and temporal stability of fecal bacterial populations in elderly subjects consuming galacto-oligosaccharide containing probiotic yoghurt. International Dairy Journal, 18, 386–395.
- [Publication 4]: Maukonen J, Mättö J, Suihko M-L & Saarela M (2008). Intra-individual diversity and similarity of salivary and faecal microbiota. Journal of Medical Microbiology, 57, 1560–1568.
- [Publication 5]: Maukonen J, Simões C & Saarela M (2012). The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples. FEMS Microbiology Ecology, 79, 697–708.