Intestinal microbiota development in childhood : Implications for health and disease

This thesis characterises the development of the intestinal microbiota in healthy children. The influence of four common factors potentially modulating the microbiota prenatal stress, breastfeeding duration, antibiotic use, and probiotic use were investigated, as well as the association between early-life microbiota composition and the development of BMI. In addition, the microbiota in healthy children was contrasted with that that of children with inflammatory bowel disease, characterising the association between treatment response and microbiota. The bacterial composition was analysed from faecal samples using two DNA-based methods, a phylogenetic microarray, as well as sequencing of the 16S rRNA gene amplicons. In addition, real-time qPCR was conducted to measure bile-salt hydrolase genes and antibiotic resistance genes. Bacteria were cultured anaerobically for antibiotic susceptibility testing. The results showed that the microbiota in childhood are sensitive to modulating factors, and are predictive of later-life health. Maternal stress during pregnancy was associated with altered microbiota development over the first months of life. Long duration of breastfeeding was associated with slow microbiota maturation, normal BMI, and low antibiotic use in preschool age, if the microbiota were not disrupted by antibiotic use before weaning. The results indicate that some of the benefits of breastfeeding are microbiota-dependent. Early microbiota maturation was associated with fast growth in infancy and increased BMI in preschool age. Antibiotic use emerged as a central regulator of the microbiome, with potential effects on the metabolic development of the child. Lactobacillus rhamnosus GG supplementation prevented some of the penicillin-associated changes, but failed to prevent the macrolide-associated loss of bifidobacteria. The probiotic supplementation also reduced antibiotic use for at least 3 years after the intervention. In IBD patients, the microbiota composition varied along a gradient of intestinal inflammation and resembled the microbiota composition of antibiotic-treated healthy children. High microbiota similarity to non-antibiotic treated healthy controls predicted positive response to anti-TNF-α treatment in IBD patients. This work suggests that maternal wellbeing is the first step towards healthy microbiota in the child. Promoting a natural microbiota development in childhood by breastfeeding, avoiding unnecessary antibiotics, careful selection of the antibiotic when it is needed, and possibly the use of specific probiotic strains, may have long-term health benefits, particularly in terms of weight development and immune health.Työssä selvitettiin lapsen suolistossa elävän bakteeriyhteisön kehitystä ja kehitykseen vaikuttavia tekijöitä, sekä varhaisen suolistobakteeriston ja painoindeksin kehittymisen yhteyksiä. Lisäksi tutkittiin terveiden lasten ja tulehduksellista suolistosairautta sairastavien lasten suolistobakteeriston eroja. Bakteeristoa tutkittiin DNA:han perustuvilla sekvensointi- ja mikrosirumenetelmillä suomalaisten ja hollantilaisten lasten ulostenäytteistä. Tulokset osoittivat, että bakteeriston koostumus lapsuudessa riippuu ulkoisista tekijöistä ja ennustaa lapsen terveyttä. Äidin stressi raskauden aikana näytti häiritsevän vauvan bakteeriston normaalia kehitystä ensimmäisten elinkuukausien aikana. Pitkäkestoinen imetys oli yhteydessä bakteeriston hitaaseen kehittymiseen, normaaliin painoindeksiin, ja vähäiseen antibioottien käyttöön päiväkoti-ikäisillä lapsilla, mikäli bakteeristoa ei häiritty antibiooteilla imetyksen aikana. Tulokset osoittivat, että ainakin osa imetyksen immuunipuolustusta tukevista ja ylipainolta suojaavista hyödyistä saadaan bakteeriston kautta. Bakteeriston nopea kehitys kohti aikuismaista koostumusta oli yhteydessä nopeaan kasvuun vauvaiässä ja kohonneeseen painoindeksiin päiväkoti-iässä. Antibioottien käyttö oli keskeinen bakteeristoa muokkaava tekijä. Tulokset tukevat käsitystä, jonka mukaan antibioottien aikaansaamat muutokset bakteeristossa lisäävät lasten ylipainoriskiä. Lactobacillus rhamnosus GG maitohappobakteerin antaminen päiväkotihoidossa oleville lapsille näytti estävän joitain penisilliini-tyyppisten antibioottien aiheuttamia muutoksia bakteeristossa, mutta ei ehkäissyt makrolidi-antibioottien aiheuttamaa bifidobakteerien vähenemistä. Pitkäaikainen päivittäinen maitohappobakteerilisä myös vähensi lasten antibioottien käyttöä jopa kolme vuotta kokeen loppumisen jälkeen. Tulehduksellisia suolistosairauksia sairastavilla potilailla bakteeriston koostumus oli yhteydessä suoliston tulehdustilaan. Potilaiden suolistobakteeristo muistutti antibiootteja saaneiden terveiden lasten bakteeristoa. Bakteeriston koostumus ennusti potilaan hoitovastetta. Potilaat, joiden bakteeristo oli normaalinkaltainen, hyötyivät anti-TNF-α-hoidosta. Tulokset viittaa siihen, että äidin hyvinvointi on ensimmäinen askel kohti lapsen tervettä bakteeriston kehitystä. Syntymän jälkeen bakteeriston luonnollista kehitystä voidaan tukea pitkällä imetyksellä, välttämällä turhia antibioottikuureja, valitsemalla sopiva antibiootti kun sitä tarvitaan, ja mahdollisesti tiettyjä probioottikantoja käyttämällä

Early life colonization of the human gut : microbes matter everywhere

Microbes colonising the infant intestine, especially bacteria, are considered important for metabolic and immunological programming in early life, potentially affecting the susceptibility of the host to disease. We combined published data to provide a global view of microbiota development in early life. The results support the concept that the microbiota develops with age in an orchestrated manner, showing common patterns across populations. Furthermore, infants are colonised at birth by specific, selected maternal faecal bacteria and likely their bacteriophages. Therefore, infants are adapted to receiving specific bacterial signals, partly derived from the maternal microbiota, at successive immunological time windows during early development. Birth by caesarean section compromises the initial vertical transmission of microbes whereas antibiotic use shifts the microbiota away from the normal developmental pattern. These disruptions alter the microbial signals that the host receives, potentially affecting child development.Peer reviewe

Dietary proteins and food-related reward signals

Proteins play a crucial role in almost all biological processes. Dietary proteins are generally considered as energy yielding nutrients and as a source of amino acids for various purposes. In addition, they may have a role in food-related reward signals. The purpose of this review was to give an overview of the role of dietary proteins in food-related reward and possible mechanisms behind such effects. Dietary proteins may elicit food-related reward by several different postprandial mechanisms, including neural and humoral signals from the gastrointestinal tract to the brain. In order to exert rewarding effects, protein have to be absorbed from the intestine and reach the target cells in sufficient concentrations, or act via receptors ad cell signalling in the gut without absorption. Complex interactions between different possible mechanisms make it very difficult to gain a clear view on the role and intesity of each mechanism. It is concluded that, in principle, dietary proteins may have a role in food-related reward. However, the evidence is based mostly on experiments with animal models and one should be careful in drawing conclusions of clinical relevance

Infant gut microbiota restoration : state of the art

The gut microbiota has a central role in the programming of the host's metabolism and immune function, with both immediate and long-term health consequences. Recent years have witnessed an accumulation of understanding of the process of the colonization and development of the gut microbiota in infants. The natural gut microbiota colonization during birth is frequently disrupted due to C-section birth or intrapartum or postpartum antibiotic exposure, and consequently aberrant gut microbiota development is common. On a positive note, research has shown that restoration of normal gut microbiota development is feasible. We discuss here the current understanding of the infant microbiota, provide an overview of the sources of disturbances, and critically evaluate the evidence on early life gut microbiota restoration for improved health outcomes by analyzing published data from infant gut microbiota restoration studies.Peer reviewe

Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling

The use of relative abundance data from next generation sequencing (NGS) can lead to misinterpretations of microbial community structures, as the increase of one taxon leads to the concurrent decrease of the other(s) in compositional data. Although different DNA- and cell-based methods as well as statistical approaches have been developed to overcome the compositionality problem, and the biological relevance of absolute bacterial abundances has been demonstrated, the human microbiome research has not yet adopted these methods, likely due to feasibility issues. Here, we describe how quantitative PCR (qPCR) done in parallel to NGS library preparation provides an accurate estimation of absolute taxon abundances from NGS data and hence provides an attainable solution to compositionality in high-throughput microbiome analyses. The advantages and potential challenges of the method are also discussed.Peer reviewe

Even low-grade inflammation impacts on small intestinal function

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Dietary factors and fluctuating levels of melatonin

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Determinants of bacterial and fungal microbiota in Finnish home dust : Impact of environmental biodiversity, pets, and occupants

The indoors is where many humans spend most of their time, and are strongly exposed to indoor microbiota, which may have multifaceted effects on health. Therefore, a comprehensive understanding of the determinants of indoor microbiota is necessary. We collected dust samples from 295 homes of families with young children in the Helsinki region of Finland and analyzed the bacterial and fungal composition based on the 16S rRNA and ITS DNA sequences. Microbial profiles were combined with extensive survey data on family structure, daily life, and physical characteristics of the home, as well as additional external environmental information, such as land use, and vegetational biodiversity near the home. Using permutational multivariate analysis of variance we explained 18% of the variation of the relative abundance between samples within bacterial composition, and 17% of the fungal composition with the explanatory variables. The fungal community was dominated by the phyla Basidiomycota, and Ascomycota; the bacterial phyla Proteobacteria, Firmicutes, Cyanobacteria, and Actinobacteria were dominant. The presence of dogs, multiple children, and firewood were significantly associated with both the fungal and bacterial composition. Additionally, fungal communities were associated with land use, biodiversity in the area, and the type of building, while bacterial communities were associated with the human inhabitants and cleaning practices. A distinction emerged between members of Ascomycota and Basidiomycota, Ascomycota being more abundant in homes with greater surrounding natural environment, and potential contact with the environment. The results suggest that the fungal composition is strongly dependent on the transport of outdoor environmental fungi into homes, while bacteria are largely derived from the inhabitants.Peer reviewe

Determinants of bacterial and fungal microbiota in Finnish home dust : Impact of environmental biodiversity, pets, and occupants

The indoors is where many humans spend most of their time, and are strongly exposed to indoor microbiota, which may have multifaceted effects on health. Therefore, a comprehensive understanding of the determinants of indoor microbiota is necessary. We collected dust samples from 295 homes of families with young children in the Helsinki region of Finland and analyzed the bacterial and fungal composition based on the 16S rRNA and ITS DNA sequences. Microbial profiles were combined with extensive survey data on family structure, daily life, and physical characteristics of the home, as well as additional external environmental information, such as land use, and vegetational biodiversity near the home. Using permutational multivariate analysis of variance we explained 18% of the variation of the relative abundance between samples within bacterial composition, and 17% of the fungal composition with the explanatory variables. The fungal community was dominated by the phyla Basidiomycota, and Ascomycota; the bacterial phyla Proteobacteria, Firmicutes, Cyanobacteria, and Actinobacteria were dominant. The presence of dogs, multiple children, and firewood were significantly associated with both the fungal and bacterial composition. Additionally, fungal communities were associated with land use, biodiversity in the area, and the type of building, while bacterial communities were associated with the human inhabitants and cleaning practices. A distinction emerged between members of Ascomycota and Basidiomycota, Ascomycota being more abundant in homes with greater surrounding natural environment, and potential contact with the environment. The results suggest that the fungal composition is strongly dependent on the transport of outdoor environmental fungi into homes, while bacteria are largely derived from the inhabitants.Peer reviewe

Cohort profile: Finnish Health and Early Life Microbiota (HELMi) longitudinal birth cohort

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