Isännän genotyypin ja maternaalitransmission vaikutus villien pikkumetsähiirten (Apodemus sylvaticus) suolistomikrobiomiin : tarkasteltuna ekologisten teorioiden näkökulmasta

Nisäkkäiden suolistomikrobiomilla on monia tärkeitä rooleja isännässä, joihin kuuluvat patogeenien kolonisaation estäminen, suoliston homeostaasin ylläpitäminen, ravinteiden sulattaminen ja jopa isännän käyttäytymiseen vaikuttaminen. Nisäkkäiden suolistomikrobiomin koostumus vaihtelee suuresti yksilöiden ja lajien välillä, sekä ajan kuluessa. Kun nisäkäs syntyy, se saa ensimmäisen, enimmäkseen anaerobisen, suolistomikrobiominsa maternaalitransmission kautta äidiltä synnytyksessä. Bakteerien ensimmäisen transmission jälkeen isännän genotyypistä, erityisesti immuniteettiin liittyvistä geeneistä, tulee tärkeä tekijä, joka auttaa määrittämään, mitkä lajit menestyvät suolistossa. Aikuistuessaan yksilön ikä, sukupuoli, ruokavalio, taudit ja fyysinen kontakti alkavat myös vaikuttaa mikrobiyhteisön koostumukseen. Koska mikrobiomiyhteisö on verrattavissa suurempikokoisiin ekologisiin yhteisöihin, sen rakennetta voidaan selittää ekologisten teorioiden avulla. Esimerkiksi community assembly- teoria voi auttaa erottamaan bakteerien maternaalitransmission vaikutuksia isännän genotyypin vaikutuksista. Community assembly-teorian mukaan lajit, jotka kolonisoivat alueen ensimmäisenä vaikuttavat yhteisön lopulliseen rakenteeseen, kuten maternaalitransmission kautta suolistoon saapuvat bakteerit. Tätä varhaista kolonisaatiota korostavaa teoriaa kutsutaan myös nimellä ”priority effect”. Metacommunity-teorian mukaan taas ekosysteemit koostuvat erilaisista laikuista, jotka lisäävät diversiteettiä ja voivat auttaa kuvaamaan mikrobiomin koostumusta aikuisiällä. Tässä pro gradussa käytän community assembly- ja metacommunity-teoriaa selittämään villien pikkumetsähiirten (Apodemus sylvaticus) suolistomikrobiomin koostumusta. Tutkin erityisesti sitä, vaikuttavatko äidiltä saadut bakteerit vai isännän genotyypin luoma ympäristö (suolisto) enemmän suolistomikrobiomin koostumukseen. Tutkimuskysymykseni ovat: Kuinka suuri osa pikkumetsähiirten suolistomikrobiomin koostumuksesta määräytyy isännän genotyypin mukaan? Vaikuttavatko äidit enemmän kuin isät jälkeläisten suolistomikrobiomiin bakteerien maternaalitransmission kautta? Lähdin vastaamaan tutkimuskysymyksiini keräämällä hiiriltä kudos- ja ulostenäytteitä Wytham Woodsin tutkimusalueelta Oxfordista, Iso-Britanniasta. Wythamista kerätyn aineiston lisäksi minulla oli käytössä vastaavanlainen aineisto toisesta hiiripopulaatiosta Silwood Parkista, Lontoosta. Suoritin DNA eristykset ja rakensin hiirille sukupuun Helsingin yliopiston MES-laboratoriossa alkuvuodesta 2018. Toinen ohjaajani sekvensoi mikrobien DNA:n Lontoossa Royal Veterinary Collegessa samoihin aikoihin. Suolismikrobiomin samankaltaisuutta verrattiin isäntäparien sukulaisuussuhteeseen Mantel-testillä ja ANOVA-testiä käytettiin vertaamaan lineaarisia malleja, joissa oli kontrollitekijöinä myös metadataa (vertasin äiti-poikas-, isä-poikas- ja täyssisarusparien mikrobiomin samankaltaisuutta). Mantel-testin mukaan sukulaisilla oli samankaltaisempi mikrobiomikoostumus kuin ei-sukulaisilla, mutta tulos oli merkitsevä vain Wythamin populaatiossa. Molemmissa populaatiossa mikrobiomin samankaltaisuuteen vaikutti merkitsevästi myös ikä ja hiirten reviirien läheisyys. Yleisesti tulokset näyttivät, että äiti-poikas- ja täyssisaruspareilla oli enemmän samankaltainen mikrobiomi, kuin ei-sukulaisilla (vaikka tämä vaikutus oli merkitsevä vain Wythamissa) ja isä-poikaspareilla oli erilaisempi mikrobiomi, kuin kaikilla muilla pareilla (vaikka tämä vaikutus oli merkitsevä vain Silwoodissa). Kun aineistot yhdistettiin, hiirillä oli merkitsevästi samankaltaisempi mikrobiomi äitinsä, kuin isänsä kanssa. Äiti-poikas- ja täyssisarusparien samankaltaisuus voidaan selittää maternaalitransmission ja synnytyksen jälkeisen fyysisen kontaktin avulla. Koska isän vaikutus poikaseen on puhtaasti geneettinen, ero voisi selittyä eri iän ja fyysisen kontaktin puutteen avulla. Vaihtoehtoisesti on mahdollista, että naaraat valitsevat tietoisesti parittelukumppanin, jolla on erilainen immunogenotyyppi ja siten erilainen mikrobiomi kuin sattumanvaraisesti olisi odotettavissa. Tulosteni perusteella bakteerien maternaalitransmissio synnytyksen aikana ja pian sen jälkeen ovat keskeinen mikrobiomin koostumusta määrittävä tekijä ja se mahdollisesti selittää myös aiemmissa tutkimuksissa havaittua geneettistä vaikutusta.The gut microbiome of mammals plays many important roles in the host, including preventing colonization of pathogens, maintaining intestinal homeostasis, helping digest nutrients and even affecting host behavior. The composition of mammalian gut microbiota varies greatly between individuals, species and in time. When a mammal is born, it acquires its first, mostly anaerobic, gut microbiota through maternal transmission in the birth canal. After the initial transmission of bacteria, host genotype, especially genes related to immunity, become an important factor that helps determine which species get to stay in the gut and prosper. In adulthood age, sex, diet, disease and contact with others all become important shapers of microbiome composition. Since microbial communities are comparable to any macroecological communities, they can be explained through ecological theories. For example, community assembly theory can help distinguish the effects of input (e.g. transmission) from selective processes (e.g. filtering host genotype) on gut microbiome composition. Community assembly can lead to multiple stable equilibria determined by which species colonized the area first (“priority effect”), emphasizing the importance of early transmission, such as that maternal transmission birth. Metacommunity theory on the other hand, views a large ecosystem as a mosaic of patches and can be helpful in describing the composition of the microbiome in adult individuals. In this thesis, I use community assembly theory and metacommunity theory as a framework to explore determinants of individual gut microbiome composition in wild European wood mice (Apodemus sylvaticus). Specifically, I set out to investigate how much of the gut microbial community variation was accountable for host relatedness and how much of this effect is due maternal transmission (input) versus host genotype (filtering). To find out more about what affects the composition of the gut microbiome in wild animals, I collected both tissue and microbiome samples from wood mice in the Wytham woods research area near Oxford, Great Britain. In addition to the data collected in Wytham, I was given another similarly collected dataset from Silwood Park. My study questions were: What proportion of gut microbiome composition in wood mice is determined by host genotype? Do mothers affect their offspring’s microbiome more than fathers through maternal transmission of bacteria? DNA extractions and mouse genotyping were done by me in the MES laboratory at the University of Helsinki. Sequencing of microbial DNA was done by my co-supervisor at Royal Veterinary College in London. Microbiome similarity was compared to host genetic relatedness using Mantel test and likelihood ratio tests on linear models with dyadic data (comparing relatedness and microbiome similarity of each pair). According to the results, related individuals had a significantly more similar microbiome in Wytham, but not in Silwood. In both populations, microbiome similarity was also affected significantly by age and home range area. The general trend was, that mother-pup and fullsib pairs had more similar microbiome than unrelated pairs (though this effect was significant only in Wytham) and father-pup pairs had a more different microbiome than unrelated pairs (though this effect was significant only in Silwood). All data combined, mice had significantly more similar microbiome with their mother than father. The higher similarity between mother-pup pairs and full siblings can be explained by maternal transmission and postnatal physical contact. Since the father’s effect is purely genetic, their microbiome differing from their offspring even more than from unrelated individuals could be explained by lack of physical contact and different age. Alternatively, females could even be choosing to mate with males with different immunogenotypes, and thus more different microbiome from themselves than expected by chance. Based on my results, transmission of bacteria during and shortly after birth is a key factor shaping microbiome composition and it might even account for the “genetic” effect seen in previous studies

Social networks strongly predict the gut microbiota of wild mice

The mammalian gut teems with microbes, yet how hosts acquire these symbionts remains poorly understood. Research in primates suggests that microbes can be picked up via social contact, but the role of social interactions in non-group-living species remains underexplored. Here, we use a passive tracking system to collect high resolution spatiotemporal activity data from wild mice (Apodemus sylvaticus). Social network analysis revealed social association strength to be the strongest predictor of microbiota similarity among individuals, controlling for factors including spatial proximity and kinship, which had far smaller or nonsignificant effects. This social effect was limited to interactions involving males (male-male and male-female), implicating sex-dependent behaviours as driving processes. Social network position also predicted microbiota richness, with well-connected individuals having the most diverse microbiotas. Overall, these findings suggest social contact provides a key transmission pathway for gut symbionts even in relatively asocial mammals, that strongly shapes the adult gut microbiota. This work underlines the potential for individuals to pick up beneficial symbionts as well as pathogens from social interactions.Peer reviewe

Synchronous seasonality in the gut microbiota of wild mouse populations

The gut microbiome performs many important functions in mammalian hosts, with community composition shaping its functional role. However, the factors that drive individual microbiota variation in wild animals and to what extent these are predictable or idiosyncratic across populations remains poorly understood. Here, we use a multi-population dataset from a common rodent species (the wood mouse, Apodemus sylvaticus), to test whether a consistent “core” gut microbiota is identifiable in this species, and to what extent the predictors of microbiota variation are consistent across populations. Between 2014 and 2018 we used capture-mark-recapture and 16S rRNA profiling to intensively monitor two wild wood mouse populations and their gut microbiota, as well as characterising the microbiota from a laboratory-housed colony of the same species. Although the microbiota was broadly similar at high taxonomic levels, the two wild populations did not share a single bacterial amplicon sequence variant (ASV), despite being only 50km apart. Meanwhile, the laboratory-housed colony shared many ASVs with one of the wild populations from which it is thought to have been founded decades ago. Despite not sharing any ASVs, the two wild populations shared a phylogenetically more similar microbiota than either did with the colony, and the factors predicting compositional variation in each wild population were remarkably similar. We identified a strong and consistent pattern of seasonal microbiota restructuring that occurred at both sites, in all years, and within individual mice. While the microbiota was highly individualised, some seasonal convergence occurred in late winter/early spring. These findings reveal highly repeatable seasonal gut microbiota dynamics in multiple populations of this species, despite different taxa being involved. This provides a platform for future work to understand the drivers and functional implications of such predictable seasonal microbiome restructuring, including whether it might provide the host with adaptive seasonal phenotypic plasticity

Maternal transmission gives way to social transmission during gut microbiota assembly in wild mice

Abstract Background The mammalian gut microbiota influences a wide array of phenotypes which are relevant to fitness, yet knowledge about the transmission routes by which gut microbes colonise hosts in natural populations remains limited. Here, we use an intensively studied wild population of wood mice (Apodemus sylvaticus) to examine how vertical (maternal) and horizontal (social) transmission routes influence gut microbiota composition throughout life. Results We identify independent signals of maternal transmission (sharing of taxa between a mother and her offspring) and social transmission (sharing of taxa predicted by the social network), whose relative magnitudes shift as hosts age. In early life, gut microbiota composition is predicted by both maternal and social relationships, but by adulthood the impact of maternal transmission becomes undetectable, leaving only a signal of social transmission. By exploring which taxa drive the maternal transmission signal, we identify a candidate maternally-transmitted bacterial family in wood mice, the Muribaculaceae. Conclusion Overall, our findings point to an ontogenetically shifting transmission landscape in wild mice, with a mother’s influence on microbiota composition waning as offspring age, while the relative impact of social contacts grows