Diversity and function of the avian gut microbiota

Abstract

The intestinal microbiota have now been shown to largely affect host health through various functional roles in terms of nutrition, immunity, and other physiological systems. However, the majority of these studies have been carried out in mammalian hosts, which differ in their physiological traits from other taxa. For example, birds possess several unique life history traits, such as hatching from eggs, which may alter the interactions with and transmission of intestinal microbes compared to most mammals. This review covers the diversity of microbial taxa hosted by birds. It also discusses how avian microbial communities strongly influence nutrition, immune function, and processing of toxins in avian hosts, in manners similar to and different from mammalian systems. Finally, areas demanding further research are identified, along with descriptions of existing techniques that could be employed to answer these questions.

Influence of Hand Rearing and Bird Age on the Fecal Microbiota of the Critically Endangered Kakapo

“…Bacteroidetes-associated OTUs occurred in an individualspecific manner, so although Bacteroidetes were observed in many samples, no Bacteroidetes OTUs were classified in the kakapo core microbiota. In other avian systems, the most abundant bacterial phyla detected with molecular methods are the Firmicutes and Bacteroidetes, followed by Actinobacteria and Proteobacteria (26), which is notably different from the bacterial community profile of the kakapo. The functional implications of this differing community composition compared to those of other herbivorous birds are a matter for future investigation, and knowledge of the core bacteria that comprise the kakapo microbiota will be of benefit for potential future kakapo bacteriotherapy and probiotic development (25).…”

“…Our previous research into the GI tract-associated bacteria of the kakapo revealed a community dominated by only a few operational taxonomic units (OTUs), mainly from the phyla Proteobacteria and Firmicutes and apparently lacking in archaea (12,25). The kakapo GI tract appears to have a low phylum-level diversity of bacteria compared to other birds (25,26), and this has led to speculation of a population bottleneck for the gut microbiota. The kakapo microbiota is not well understood, but it is likely that current management practices have an impact on the microbial community, as kakapos are removed from the wild and given veterinary care at the first sign of sickness (27).…”

Dietary energy level affects the composition of cecal microbiota of starter Pekin ducklings

“…Previous studies revealed that Firmicutes and Bacteroidetes are the dominant phyla in organisms such as birds, zebrafish, and mammals (Ley et al 2008;Kohl 2012;Semova et al 2012), which are known for fermentative metabolism and degra- Figure 1. Genus abundance variation box plot for the 15 most abundant genera of Pekin duck cecal microbiota as determined by sequence abundance.…”

Effects of immune supplementation and immune challenge on bacterial assemblages in the avian cloaca

“…Ornithologists are increasingly interested in the physiological relationships between birds and the microbes that they harbor (Kohl 2012). To shed light on these relationships, investigators continue to develop, refine, and employ a variety of molecular genetic techniques, including denaturing gradient gel electrophoresis (DGGE), which can be useful alternatives to culture-based bacteriological techniques (van der Wielen et al 2002;Grizard et al 2014).…”