Early-life gut dysbiosis linked to juvenile mortality in ostriches

Abstract

Background: Imbalances in the gut microbial community (dysbiosis) of vertebrates have been associated with several gastrointestinal and autoimmune diseases. However, it is unclear which taxa are associated with gut dysbiosis, and if particular gut regions or specific time periods during ontogeny are more susceptible. We also know very little of this process in non-model organisms, despite an increasing realization of the general importance of gut microbiota for health.

Methods: Here, we examine the changes that occur in the microbiome during dysbiosis in different parts of the gastrointestinal tract in a long-lived bird with high juvenile mortality, the ostrich (Struthio camelus). We evaluated the 16S rRNA gene composition of the ileum, cecum, and colon of 68 individuals that died of suspected enterocolitis during the first 3 months of life (diseased individuals), and of 50 healthy individuals that were euthanized as age-matched controls. We combined these data with longitudinal environmental and fecal sampling to identify potential sources of pathogenic bacteria and to unravel at which stage of development dysbiosis-associated bacteria emerge.

Results: Diseased individuals had drastically lower microbial alpha diversity and differed substantially in their microbial beta diversity from control individuals in all three regions of the gastrointestinal tract. The clear relationship between low diversity and disease was consistent across all ages in the ileum, but decreased with age in the cecum and colon. Several taxa were associated with mortality (Enterobacteriaceae, Peptostreptococcaceae, Porphyromonadaceae, Clostridium), while others were associated with health (Lachnospiraceae, Ruminococcaceae, Erysipelotrichaceae, Turicibacter, Roseburia). Environmental samples showed no evidence of dysbiosis-associated bacteria being present in either the food, water, or soil substrate. Instead, the repeated fecal sampling showed that pathobionts were already present shortly after hatching and proliferated in individuals with low microbial diversity, resulting in high mortality several weeks later.

Conclusions: Identifying the origins of pathobionts in neonates and the factors that subsequently influence the establishment of diverse gut microbiota may be key to understanding dysbiosis and host development. Video Abstract.

Keywords: Disease; Dysbacteriosis; Gastrointestinal tract; Gut microbiota; Inflammation; Microbial diversity.

Fig. 1

Mortality patterns of ostriches up to 12 weeks of age. a One of the ostrich chicks included in the study at 1 week old. b The cumulative mortality and mortality rate per week. c, d Log-transformed weights over time of control individuals that were randomly selected for euthanization at weeks 2, 4, 6, 8, 10, and 12 (blue lines in c), and individuals that died of suspected disease (red lines in d). Grey lines illustrate weights of all other individuals that survived the whole period. e Photographs during dissection illustrating widespread gut inflammation in a diseased individual (bottom) compared to a control individual (top)

Fig. 2

Principal coordinates analysis (PCoA) plots of Bray–Curtis dissimilarities between the microbiomes of control individuals (blue) and diseased individuals (red). Ellipses denote 90% confidence intervals

Fig. 3

Alpha diversity (Shannon index) during development in the ileum, cecum, and colon. Control individuals are shown in blue and diseased individuals in red. Lines display the fitted local regression smoothing curves and shaded areas the 95% confidence interval. Bottom right panel shows all alpha diversity values together

Fig. 4

The proportion of bacterial classes per individual and gut region, sorted by age (left bars = youngest, right bars = oldest). Left column = control individuals, right column = diseased individuals. Top row = ileum, middle row = cecum, bottom row = colon

Fig. 5

Differentially abundant OTUs (q < 0.01) between control and diseased individuals, separate for the three gut regions. y-axes show taxonomic families and OTUs have been colored at the class level. Positive log₂ fold changes indicate higher OTU abundance in the control individuals and negative log₂ fold changes indicate higher abundance in the diseased individuals. NA = OTUs without family classification

Fig. 6

Abundances (normalised and log-transformed) of two bacterial families associated with disease in the weeks preceding death, measured by repeated fecal sampling of individuals. Points and error bars represent means ± SE

Fig. 7

Environmental sources of bacteria present in the different gut sections. C = control individuals and D = diseased individuals