Browsing by Subject "Gut microbiota"

While there is no current consensus on what characterizes a heathy gut microbiome, there are evidence supporting the association of high microbial diversity with health stability in the host species. A growing literature suggests that microbial communities can withstand short-term anthropogenic changes with resilience, however enduring long-term changes might have a negative impact on the natural composition of host microbiome. Parasitism and anthropogenic disturbances resulting in habitat degradation might represent two of such long-term challenges to the invisible diversity of microbial communities, with consequences for the fitness of their host species. In this study, I tested whether parasitism by a specialist parasitoid and ecological changes due to anthropogenic habitat degradation affected the microbial community associated with the diapausing larvae of the Glanville Fritillary butterfly (Melitaea cinxia). The larval samples were collected in September 2012 from seven different communes across the Åland islands, from two extreme types of habitat patches (i.e., highly human-impacted habitats versus natural meadows). The parasitoid wasp Hyposoter horticola naturally parasitize approximately a third of the M. cinxia larvae in Åland, giving an opportunity to further investigate how parasitism might affect the larvae-associated bacterial community in this system. The DNA from the gut of each larva was extracted, and the bacterial V5-V6 region of the 16S gene was amplified and sequenced at the Finnish Institute for Molecular Medicine. The sequencing data was prepared for analysis by processing it through Mothur and QIIME2 data cleaning protocols. According to alpha- and beta-diversity metrics analyses, anthropogenic degradation of the habitat did not cause significant changes in the bacterial composition of the microbiota associated with diapausing larvae of M. cinxia, however, parasitism with the parasitoid wasp has a significant negative effect on the beta diversity of the microbial communities associated with the diapausing larvae.

The infant gut microbiota maturation is central to infant health and well-being and has been suggested to have important health impacts in adulthood. While most of the previous research and description of the dynamics of the gut microbiota acquisition and maturation focused on the prokaryotic community; recent studies have suggested the importance of other microbial members in the community. Viruses, specifically bacteriophages (phages), are found in high abundances in the gut microbiota, and may influence prokaryotic composition and the microbiota’s trajectory during infancy. Phages can shape the bacterial community by killing their cellular host but also by modulating their bacterial host fitness in the ecosystem. Additionally, phages can carry genes which have no role in the viral replication machinery, but instead modulate the cellular host metabolism. These genes, termed auxiliary metabolic genes (AMGs), are largely uncharacterized in the human gut, in particular in the context of the infant gut microbiota maturation. In this thesis, we explored the diversity and persistence of AMGs in infant gut microbiota from 3 months to 2 years old and identified and characterized changes in the AMGs repertoire during the infant gut microbiota maturation. This project utilized a subset of the broader Finnish Health and Early Life Microbiota (HELMi) birth cohort study, a Finnish prospective cohort on early life microbiota and health. In this study, we leveraged whole genome shotgun metagenomes from faecal samples of 475 infants collected at four time points, as well as samples from their mothers (n = 304) and fathers (n = 123). The viral sequences in these metagenomes were then identified, annotated, and characterized, allowing us to build a large catalogue of bacteriophage sequences, called the HELMi Bacteriophage Catalogue (HBaC). Next, we assessed the presence of putative AMGs in this phage collection and determined their prevalence in the viral community and dynamics during the gut microbiota maturation. The HBaC contains 145,818 unique species-like viral OTUs (vOTUs) of which a majority are temperate phages, classified as Caudoviricetes. Notably, we observed an increase in phage diversity and richness during the infant gut microbiota maturation and an increase in relative abundance of virulent phages. Further, the viral community composition strongly associated with the observed prokaryotic faecal community types (FCTs). In our phage catalogue, 8 % of the vOTUs carried at least one putative AMGs and the Demerecviridae, Autographiviridae and Herelleviridae families proportionally carried the most. The most common metabolic pathways encoded by these putative AMGs found in HBaC were organic nitrogen metabolism, transport functions and carbon utilization. Interestingly, we observed a change in putative AMGs abundance and function during the infant gut microbiota maturation. In the future, additional analysis exploring the influence of early life exposures on phage and AMGs prevalence and dynamics could help unravel the complex interaction between phages and their bacterial host in the dynamic infant gut microbiota.

The gut microbiota is important for human health, participating in many important functions, such as digestion, and is strongly modulated by the diet. The consumption of red and processed meat should be reduced due to both health and environmental reasons. Red meat could be partially replaced with legumes, as they are rich in protein. In addition, legumes are a good source of fibre and increasing their consumption would increase fibre intake. Here we aimed to study the effects of a partial replacement of red and processed meat with legumes on the gut microbiota composition in Finnish healthy men. The study was a 6-week randomized clinical trial in parallel design and included two groups with diet supplemented either with red and processed meat (760 g/wk) or a lower amount of red and processed meat (200 g/wk) and legume products containing the corresponding amount protein as in 560 grams of red and processed meat. Both diets provided 25% of the participants’ daily protein intake. The microbiota composition was analysed before and at the end of the intervention period from faecal samples. In total 102 participants finished the study. The group with the diet containing legume products showed a significant reduction in alpha diversity (p=0.029) and in the relative abundance of the genus Prevotella (false discovery rate (FDR)-corrected p-value (p-FDR) =0.130) and Ruminococcaceae NK4A214 group (p-FDR=0.130) when comparing before and after the intervention period. No significant changes were seen in the meat-based diet group. When comparing the two diet groups at the end of the intervention period we observed a significantly higher relative abundance of the genus Agathobacter (p-FDR=0.023), Coprococcus ( p-FDR=0.154) and Ruminiclostridium (p-FDR=0.154) in the meat-based diet group, while the genus Bacteroides (p-FDR=0.112) and Ruminococcaceae UCG.013 group (pFDR=0.066) showed higher relative abundance in the legume-based diet group. In conclusion, our results show that even a partial replacement of red and processed meat affects the composition of the gut microbiota.