Tuomas Aivelo

Population- and Individual-Level Dynamics of the Intestinal Microbiota of a Small Primate

ABSTRACT Longitudinal sampling for intestinal microbiota in wild animals is difficult, leading to a lack of information on bacterial dynamics occurring in nature. We studied how the composition of microbiota communities changed temporally in free-ranging small primates, rufous mouse lemurs (Microcebus rufus). We marked and recaptured mouse lemurs during their mating season in Ranomafana National Park in southeastern mountainous rainforests of Madagascar for 2 years and determined the fecal microbiota compositions of these mouse lemurs with MiSeq sequencing. We collected 160 fecal samples from 71 animals and had two or more samples from 39 individuals. We found small, but statistically significant, effects of site and age on microbiota richness and diversity and effects of sex, year, and site on microbiota composition, while the within-year temporal trends were less clear. Within-host microbiota showed pervasive variation in intestinal bacterial community composition, especially during the second study year. We hypothesize that the biological properties of mouse lemurs, including their small body size and fast metabolism, may contribute to the temporal intraindividual-level variation, something that should be testable with more-extensive sampling regimes. IMPORTANCE While microbiome research has blossomed in recent years, there is a lack of longitudinal studies on microbiome dynamics on free-ranging hosts. To fill this gap, we followed mouse lemurs, which are small heterothermic primates, for 2 years. Most studied animals have shown microbiota to be stable over the life span of host individuals, but some previous research also found ample within-host variation in microbiota composition. Our study used a larger sample size than previous studies and a study setting well suited to track within-host variation in free-ranging mammals. Despite the overall microbiota stability at the population level, the microbiota of individual mouse lemurs can show large-scale changes in composition in time periods as short as 2 days, suggesting caution in inferring individual-level patterns from population-level data.

Tracking year-to-year changes in intestinal nematode communities of rufous mouse lemurs (Microcebus rufus).

While it is known that intestinal parasite communities vary in their composition over time, there is a lack of studies addressing how variation in component communities (between-hosts) manifests in infracommunities (within-host) during the host lifespan. In this study, we investigate the changes in the intestinal parasite infracommunities in wild-living rufous mouse lemurs (Microcebus rufus) from Ranomafana National Park in southeastern Madagascar from 2010 to 2012. We used high-throughput barcoding of the 18S rRNA gene to interrogate parasite community structure. Our results show that in these nematode communities, there were two frequently occurring putative species and four rarer putative species. All putative species were randomly distributed over host individuals and they did not occur in clear temporal patterns. For the individuals caught in at least two different years, there was high turnover of putative species and high variation in fecal egg counts. Our study shows that while there was remarkable variation in infracommunities over time, the component community was relatively stable. Nevertheless, the patterns of prevalence varied substantially between years in each component community.

Séance: reference-based phylogenetic analysis for 18S rRNA studies

BackgroundMarker gene studies often use short amplicons spanning one or more hypervariable regions from an rRNA gene to interrogate the community structure of uncultured environmental samples. Target regions are chosen for their discriminatory power, but the limited phylogenetic signal of short high-throughput sequencing reads precludes accurate phylogenetic analysis. This is particularly unfortunate in the study of microscopic eukaryotes where horizontal gene flow is limited and the rRNA gene is expected to accurately reflect the species phylogeny. A promising alternative to full phylogenetic analysis is phylogenetic placement, where a reference phylogeny is inferred using the complete marker gene and iteratively extended with the short sequences from a metagenetic sample under study.ResultsBased on the phylogenetic placement approach we built Séance, a community analysis pipeline focused on the analysis of 18S marker gene data. Séance combines the alignment extension and phylogenetic placement capabilities of the Pagan multiple sequence alignment program with a suite of tools to preprocess, cluster and visualise datasets composed of many samples. We showcase Séance by analysing 454 data from a longitudinal study of intestinal parasite communities in wild rufous mouse lemurs (Microcebus rufus) as well as in simulation. We demonstrate both improved OTU picking at higher levels of sequence similarity for 454 data and show the accuracy of phylogenetic placement to be comparable to maximum likelihood methods for lower numbers of taxa.ConclusionsSéance is an open source community analysis pipeline that provides reference-based phylogenetic analysis for rRNA marker gene studies. Whilst in this article we focus on studying nematodes using the 18S marker gene, the concepts are generic and reference data for alternative marker genes can be easily created. Séance can be downloaded from http://wasabiapp.org/software/seance/.

Parasite–microbiota interactions potentially affect intestinal communities in wild mammals

Detecting interaction between species is notoriously difficult, and disentangling species associations in host-related gut communities is especially challenging. Nevertheless, due to contemporary methods, including metabarcoding and 16S sequencing, collecting observational data on community composition has become easier and much more common. We studied the previously collected datasets of intestinal bacterial microbiota and parasite compositions within longitudinally followed mouse lemurs by analysing the potential interactions with diversity metrics and novel joint species distribution modelling. Both methods showed statistical association between certain parasite species and bacterial microbiota composition. Unicellular Eimeria sp. had an effect on diversity of gut microbiota. The cestode Hymenolepis diminuta had negative associations with several bacterial orders, whereas closely related species Hymenolepis nana had positive associations with several bacterial orders. Our results reveal potential interactions between some, but not all, intestinal parasites and gut bacterial microbiota. Host variables contributed over half of the total variation explained with the model, and sex was the most important single host variable; especially with microbiota, there were sex-related differences in the community composition. This study shows how joint species distribution modelling can incorporate both within-host dynamics of several taxa and host characteristics to model potential interactions in intestinal community. These results provide new hypothesis for interactions between and among parasites and bacterial microbiota to be tested further with experimental studies.

Teachers\' approaches to genetics teaching mirror their perceptions of teaching controversial, societal and sensitive issues

The skills to understand genetic phenomena and transfer knowledge to real world situations are an important part of 21st century scientific literacy. While socio-scientific issues (SSI) are emphasized and impediments to considering SSI are widely studied, science teachers have low interest in adopting SSI in teaching. Little is known about how teachers choose content for their teaching, although this is the process in which curricula translates to teaching practice. We studied how teachers choose content for biology courses on cells, heredity, and biotechnology by interviewing ten Finnish upper-secondary school teachers. We asked which content they perceived as the most important and studied how they described teaching genetically modified organisms, hereditary disorders, and complex human traits. We used content analysis to build a tentative model of variables influencing teachers’ choices. We found three main categories of the most important contents: development of phenotype, inheritance and continuity, and gene function. While teachers mentioned that SSI are important, they were never mentioned among the important contexts. Teachers differed in how they described teaching: some embraced human-related content while others described avoidance due to content or pedagogy-related issues. The tentative model of teachers’ choices included national-level factors, which were common to all teachers, school-level factors as the local context and personal-level factors. We classified teachers’ perceptions to Developmental, Structural and Hereditary approaches in genetics teaching which contained not only the perceptions of the most important content, but also teacher inclinations towards teaching human genetics and perceptions of students’ interest in different topics. Teachers’ perceptions were strongly linked with teachers’ likelihood to discuss human genetics. Experience played a part in which approach teachers had, and contrary to previous research, the less experienced teachers were most open to discussing human genetics. Our results suggest that curriculum is an important tool encouraging teachers to adopt SSI-oriented teaching. Disclosure of conflicts of interest: T.A. has participated in writing biology textbooks for upper-secondary school biology for eOppi Oy and has received monetary compensation. None of the teachers involved in this study used biology textbooks from eOppi Oy.Science education strives to increase interest in science and facilitate active citizenship. Thus, the aspects of personal and societal relevance are increasingly emphasised in science curricula. Still, little is known about how teachers choose content for their teaching, although their choices translate curricula to teaching practice. We explored how teachers choose genetics content and contexts for biology courses on cells, heredity, and biotechnology by interviewing ten Finnish upper-secondary school teachers. We specifically studied how the teachers described teaching on genetically modified organisms, hereditary disorders, and human traits as teachers have different amounts of freedom in choosing contents and contexts in these themes. We analysed interviews with theory-guiding content analysis and found consistent patterns in teachers9 perceptions of the main themes in genetics teaching, teacher inclinations towards teaching genetics in human context and perceptions of students9 interest in different topics. These patterns, which we call emphasis of content in genetics teaching could be classified to Developmental, Structural and Hereditary. Teachers with Developmental emphasis embraced teaching genetics in human context while teachers with Structural emphasis avoided them. Contrary to previous research, the less experienced teachers were most open to discussing human genetics. In general, teachers9 justified their choices by national, local school, and teacher9s personal-level factors. While teachers mentioned that societal and personal contexts are important, at the same time teachers never framed main themes in genetics with these contexts. We conclude that more emphasis should be put on how teachers handle issues with societal or personal relevance.