16S rRNA gene-based microbiota profiles from diverse avian faeces are largely independent of DNA preservation and extraction method

Edwards, Johnson; Hoffbeck, Carmen; West, Annie G.; Pas, An; Taylor, Michael W.

doi:10.3389/fmicb.2023.1239167

Cited by 5 publications

(1 citation statement)

References 37 publications

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“…They inhabit mainly lakes, rivers, and beaches, feeding on plants on the water’s surface as well as on plants on land. The global population of Eurasian wigeons is estimated at 2.8–3.3 million individuals ( 4 ).…”

Section: Announcementmentioning

confidence: 99%

16S rRNA amplicon sequencing of intestinal microbiota in Eurasian Wigeon around Osaka, Japan

Kenzaka,

Nishiguchi,

Nishikawa

2024

Microbiol Resour Announc

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Section: Announcementmentioning

confidence: 99%

16S rRNA amplicon sequencing of intestinal microbiota in Eurasian Wigeon around Osaka, Japan

Kenzaka,

Nishiguchi,

Nishikawa

2024

Microbiol Resour Announc

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Microbial DNA extraction method for avian feces and preen oil from diverse species

Russell,

Kenna,

Huynh

et al. 2024

Ecology and Evolution

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As DNA sequencing technology continues to rapidly improve, studies investigating the microbial communities of host organisms (i.e., microbiota) are becoming not only more popular but also more financially accessible. Across many taxa, microbiomes can have important impacts on organismal health and fitness. To evaluate the microbial community composition of a particular microbiome, microbial DNA must be successfully extracted. Fecal samples are often easy to collect and are a good source of gut microbial DNA. Additionally, interest in the avian preen gland microbiome is rapidly growing, due to the importance of preen oil for many aspects of avian life. Microbial DNA extractions from avian fecal and preen oil samples present multiple challenges, however. Here, we describe a modified PrepMan Ultra Sample Preparation Reagent microbial DNA extraction method that is less expensive than other commonly used methodologies and is highly effective for both fecal and preen oil samples collected from a broad range of avian species. We expect our method will facilitate microbial DNA extractions from multiple avian microbiome reservoirs, which have previously proved difficult and expensive. Our method therefore increases the feasibility of future studies of avian host microbiomes.

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The influence of biotic and abiotic factors on the bacterial microbiome of gentoo penguins (Pygoscelis papua) in their natural environment

Kaczvinsky,

Levy,

Preston

et al. 2024

Sci Rep

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The microbiome is a key factor in the health, well-being, and success of vertebrates, contributing to the adaptive capacity of the host. However, the impact of geographic and biotic factors that may affect the microbiome of wild birds in polar environments is not well defined. To address this, we determined the bacterial 16S rRNA gene sequence profiles in faecal samples from pygoscelid penguin populations in the Scotia Arc, focusing on gentoo penguins. This mesopredatory group breeds in defined colonies across a wide geographic range. Since diet could influence microbiome structure, we extracted dietary profiles from a eukaryotic 18S rRNA gene sequence profile. The bacterial microbiome profiles were considered in the context of a diverse set of environmental and ecological measures. Integrating wide geographic sampling with bacterial 16S and eukaryotic 18S rRNA gene sequencing of over 350 faecal samples identified associations between the microbiome profile and a suite of geographic and ecological factors. Microbiome profiles differed according to host species, colony identity, distance between colonies, and diet. Interestingly there was also a relationship between the proportion of host DNA (in relation to total 18S rRNA gene signal) and the microbiome, which may reflect gut passage time. Colony identity provided the strongest association with differences in microbiome profiles indicating that local factors play a key role in the microbiome structure of these polar seabirds. This may reflect the influence of local transfer of microbes either via faecal-oral routes, during chick feeding or other close contact events. Other factors including diet and host species also associate with variation in microbiome profile, and in at least some locations, the microbiome composition varies considerably between individuals. Given the variation in penguin microbiomes associated with diverse factors there is potential for disruption of microbiome associations at a local scale that could influence host health, productivity, and immunological competence. The microbiome represents a sensitive indicator of changing conditions, and the implications of any changes need to be considered in the wider context of environmental change and other stressors.

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16S rRNA gene-based microbiota profiles from diverse avian faeces are largely independent of DNA preservation and extraction method

Cited by 5 publications

References 37 publications

16S rRNA amplicon sequencing of intestinal microbiota in Eurasian Wigeon around Osaka, Japan

16S rRNA amplicon sequencing of intestinal microbiota in Eurasian Wigeon around Osaka, Japan

Microbial DNA extraction method for avian feces and preen oil from diverse species

The influence of biotic and abiotic factors on the bacterial microbiome of gentoo penguins (Pygoscelis papua) in their natural environment

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