Measuring the gut microbiome in birds: Comparison of faecal and cloacal sampling

Abstract

The gut microbiomes of birds and other animals are increasingly being studied in ecological and evolutionary contexts. Numerous studies on birds and reptiles have made inferences about gut microbiota using cloacal sampling; however, it is not known whether the bacterial community of the cloaca provides an accurate representation of the gut microbiome. We examined the accuracy with which cloacal swabs and faecal samples measure the microbiota in three different parts of the gastrointestinal tract (ileum, caecum, and colon) using a case study on juvenile ostriches, Struthio camelus, and high-throughput 16S rRNA sequencing. We found that faeces were significantly better than cloacal swabs in representing the bacterial community of the colon. Cloacal samples had a higher abundance of Gammaproteobacteria and fewer Clostridia relative to the gut and faecal samples. However, both faecal and cloacal samples were poor representatives of the microbial communities in the caecum and ileum. Furthermore, the accuracy of each sampling method in measuring the abundance of different bacterial taxa was highly variable: Bacteroidetes was the most highly correlated phylum between all three gut sections and both methods, whereas Actinobacteria, for example, was only strongly correlated between faecal and colon samples. Based on our results, we recommend sampling faeces, whenever possible, as this sample type provides the most accurate assessment of the colon microbiome. The fact that neither sampling technique accurately portrayed the bacterial community of the ileum nor the caecum illustrates the difficulty in noninvasively monitoring gut bacteria located further up in the gastrointestinal tract. These results have important implications for the interpretation of avian gut microbiome studies.

Major shifts in gut microbiota during development and its relationship to growth in ostriches

“…By the ages 8-12 weeks, the dynamic changes of bacterial abundances had stabilized, and juveniles had largely obtained an adult-like gut community, heavily dominated by Clostridia (primarily the families Ruminococcaceae, Lachnospiraceae, and Clostridiaceae; Figure 4). This bacterial composition is similar to that of other hindgut fermenters (O' Donnell, Harris, Ross, & O'Toole, 2017), and to previous general characterizations of faecal and colon microbes in ostriches (Matsui et al, 2010;Videvall et al, 2018).…”

“…72.693) and stored at −20°C within 2 hr of collection. Details of sample collection have been described previously (Videvall, Strandh, Engelbrecht, Cloete, & Cornwallis, 2018). The ostrich chicks were weighed during every sampling event.…”

Early-life gut dysbiosis linked to mass mortality in ostriches

“…Microbial communities were characterized using Illumina MiSeq sequencing to identify the V3 and 379 V4 regions of the 16S rRNA gene. For full details please see Videvall et al (2017Videvall et al ( , 2018. We 380 sequenced a total of 323 ileum, caecum, and colon samples from all individuals that died (n = 68) and 381 all euthanized (control) individuals at 2, 4, 6, 8, and 12 weeks of age (n = 50 in total; ten individuals 382 per week).…”

The development of gut microbiota in ostriches and its association with juvenile growth

“…They were subsequently transported on ice to a laboratory and stored at -20 °C. Detailed sample collection has been described by Videvall et al (2017a). Weight measurements of the ostriches were retrieved during each sampling event.…”

“…earthmicrobiome.org). For full details please see Videvall et al (2017a). Amplicon libraries for sequencing of the 16S rRNA V3 and V4 regions were prepared using Illumina fusion primers containing the target-specific primers Bakt_341F and Bakt_805R (Herlemann et al 2011) according to the Illumina 16S Metagenomic Sequencing Library Preparation Guide (Part # 15044223 Rev.B).…”