Diversity and temporal stability of bacterial communities in a model passerine bird, the zebra finch

Abstract

The composition and dynamics of the gastrointestinal bacterial communities in birds is determined by both host-specific and environmental exposure factors yet these are poorly understood. We selected the zebra finch, Taeniopygia guttata, as the host species to examine the diversity and temporal stability of the faecal microflora in a bird, owing to its importance as a model organism in avian ecology, neuroscience and evolution studies. The stability of the gut bacterial community of individual male and female zebra finches was assessed through repeat faecal sampling via culture and temperature gradient gel electrophoresis and partial sequencing of PCR-amplified eubacterial 16S rRNA gene products. Nineteen bacterial genera were detected across all samples (n = 99), with each bird carrying on average six operational taxonomic units. Using a novel statistical approach, we showed that bacterial assemblages and community richness varied between individual birds but remained stable over time within individuals. Neither the composition nor richness of bacterial communities differed significantly between the sexes. Our results show that zebra finches housed together under controlled conditions show consistent variation between individuals in their gut microflora that is not attributable to differences in host exposure to environmental microbial sources. Future studies could usefully explore the origin of this individual-specific variation and its consequences for host fitness and sexual selection.

Characterizing the avian gut microbiota: membership, driving influences, and potential function

“…In agreement with our previous observations of low microbial diversity within the kakapo hindgut (Waite et al, 2012, 2013), the diversity estimators for kakapo were among the lowest observed. Consistent with previously reported mammalian findings (Ley et al, 2008a), and with more targeted avian studies (Zhu et al, 2002; Lucas and Heeb, 2005; Banks et al, 2009; Benskin et al, 2010), the host organism was the strongest driver of community structure in the clone-library data and second strongest in the short-read data (Table 3). Other factors were still significantly associated with shaping the gut community but their fit to the data was lower.…”

“…Specific studies have addressed areas of avian microbial ecology, such as the variation in microbial diversity along the GI tract (Bjerrum et al, 2006; Gong et al, 2007; Torok et al, 2008; Waite et al, 2012), the influence of diet (Rubio et al, 1998; Blanco et al, 2006; Torok et al, 2008; Janczyk et al, 2009; Hammons et al, 2010), age (Van Der Wielen et al, 2002; Godoy-Vitorino et al, 2010; Van Dongen et al, 2013) or other host-specific factors (Zhu et al, 2002; Lucas and Heeb, 2005; Banks et al, 2009; Benskin et al, 2010; Wienemann et al, 2011). While there is extensive evidence that microbial colonization of the GI tract brings benefits to the host bird (Jin et al, 1998; Torok et al, 2008; Angelakis and Raoult, 2010; Torok et al, 2011; Zhang et al, 2011; Cao et al, 2012; Stanley et al, 2012), there are also pathways through which the normal colonization of microbes can be of detriment to the host (Ford and Coates, 1971; Potti et al, 2002; Cao et al, 2012; Singh et al, 2013).…”

Gut Bacterial Diversity of the House Sparrow (Passer domesticus) Inferred by 16S rRNA Sequence Analysis

“…Chicken guts are dominated by Firmicutes [62,76], while turkeys' intestinal communities can be dominated either by Firmicutes [37] or Bacteroidetes [62]. In the few wild birds that have been studied, bacterial communities were dominated by Firmicutes; however the second dominant phylum varied: Actinobacteria in Adelaide Penguins and Proteobacteria in Zebra-Finches [6,8]. In the Hoatzin (Ophistocomus hoatzin) a folivorous bird with crop microbial fermentation [20], the microbial community of the crop was dominated by Firmicutes and Bacteroidetes [20,21,22] while the bacterial communities of the foregut were dominated by Bacteroidetes and Actinobacteria, and contained a lower proportion of Firmicutes and Proteobacteria [21].…”

“…Together these two groups comprise over 96% of all bacterial sequences in the complete gut. The dominance of Firmicutes and Proteobacteria in the intestinal bacterial communities has been reported for other birds like Zebra Finches [8], as well as wild and captive parrots [73]. Because Proteobacteria is a group with a high functional diversity [29], the dominance of Proteobacteria in the House Sparrow gut could be related to its omnivorous diet that includes seeds, insects, fruits, and a large diversity of human food scraps including meat [9,11,49].…”

Full Issue

“…Birds that defecated during this time were removed for processing, and the feces was transferred to a sterile 2 mL collection tube. Fecal samples are commonly used as proxies for gut microbiotas and allow repeat sampling from the same individual (Benskin et al 2010, De Filippo et al 2010, Degnan et al 2012, Dimitriu et al 2013. Feces was stored in a cooler on ice until the end of the day when it was frozen at À208C until DNA was extracted.…”