A time-lagged association between the gut microbiome, nestling weight and nestling survival in wild great tits

Natal body mass is a key predictor of viability and fitness in many animals. While variation in body mass and therefore viability of juveniles may be explained by genetic and environmental factors, emerging evidence points to the gut microbiota as an important factor influencing host health. The gut microbiota is known to change during development, but it remains unclear whether the microbiome predicts fitness, and if it does, at which developmental stage it affects fitness traits.
We collected data on two traits associated with fitness in wild nestling great tits (Parus major): weight and survival to fledging. We characterised the gut microbiome using 16S rRNA sequencing from nestling faeces and investigated temporal associations between the gut microbiome and fitness traits across development at day 8 (D8) and day 15 (D15) post-hatching. We also explored whether particular microbial taxa were ‘indicator species’ that reflected whether nestlings survived or not.
There was no lin..., Field monitoring and microbiome sampling

Birds were sampled from nine nest box populations across Co. Cork, Ireland, five of these were mixed/deciduous habitats and four were coniferous habitats (see O'Shea et al. (2018)). We collected 204 faecal samples from 150 nestling great tits from 54 nests (see below for the number of samples that were successfully sequenced and sample size per developmental stage) for 16S rRNA gene sequencing in order to map the gastrointestinal microbial communities. During April-June 2016, nest boxes were monitored to determine lay dates, hatching dates and nestling survival. Nestlings aged 8 days (+/- 1 day) (D8) and 15 days (D15) were placed into sterile holding bags inside a heated holding case. Coffee filters were used to line the bags in order to soak up uric acid from the faeces, as uric acid has the potential to affect downstream sequencing (Khan et al., 1991). Samples were collected from nestlings that defaecated naturally within 15-20 minutes of be..., See README.txt for description of variables.

Note, some data subsets were centred and scaled before analyses.