Research Article: Longitudinal microbiome profiling reveals impermanence of probiotic bacteria in domestic pigeons

Longitudinal microbiome profiling reveals impermanence of probiotic bacteria in domestic pigeons

Date Published: June 17, 2019

Publisher: Public Library of Science

Author(s): Kirsten Grond, Julie M. Perreau, Wesley T. Loo, A. James Spring, Colleen M. Cavanaugh, Sarah M. Hird, Juan J. Loor.

http://doi.org/10.1371/journal.pone.0217804

Abstract

Probiotics are bacterial species or assemblages that are applied to animals and plants with the intention of altering the microbiome in a beneficial way. Probiotics have been linked to positive health effects such as faster disease recovery times in humans and increased weight gain in poultry. Pigeon fanciers often feed their show pigeons probiotics with the intention of increasing flight performance. The objective of our study was to determine the effect of two different probiotics, alone and in combination, on the fecal microbiome of Birmingham Roller pigeons. We sequenced fecal samples from 20 pigeons divided into three probiotic treatments, including prior to, during, and after treatment. Pre-treatment and control group samples were dominated by Actinobacteria, Firmicutes, Proteobacteria, and Cyanobacteria. Administration of a probiotic pellet containing Enterococcus faecium and Lactobacillus acidophilus resulted in increase in average relative abundance of Lactobacillus spp. from 4.7 ± 2.0% to 93.0 ± 5.3%. No significant effects of Enterococcus spp. were detected. Probiotic-induced shifts in the microbiome composition were temporary and disappeared within 2 days of probiotic cessation. Administration of a probiotic powder in drinking water that contained Enterococcus faecium and three Lactobacillus species had minimal effect on the microbiome. We conclude that supplementing Birmingham roller pigeons with the probiotic pellets, but not the probiotic powder, temporarily changed the microbiome composition. A next step is to experimentally test the effect of these changes in microbiome composition on host health and physical performance.

Partial Text

Vertebrates house large and diverse communities of commensal and pathogenic bacteria on and within their bodies, the “microbiome” (reviewed in [1,2]). Generally, the majority of these bacteria reside within the lower intestinal tract in numbers that can equal the total number of host body cells [3]. Many studies in model systems have found an important role for the gut microbiome in host health [4,5], and research has aimed to define the features of a healthy microbiome [4,6,7]. Imbalances in the microbiome, referred to as dysbiosis, are associated with a variety of human diseases including obesity and inflammatory bowel disease [8,9]. Several causes of dysbiosis have been described in mammals, including host genetic factors, pathogen infections, repeated antibiotic treatments, and changes in host diet [10–13]. The microbiome has been relatively well described in humans and mammalian model organisms, but remains poorly described in birds [14–16].

For the 20 pigeons studied, 232 fecal samples were sequenced, as well as a field negative control and PCR negative control. A total of 87 ASV’s were identified as contaminants by the decontam package in the negative field and PCR control and were removed from the data set (S1 Table). After this quality control, a total of 5,762,142 sequences remained for fecal samples (range: 30–117,236 seqs/sample). All samples with fewer than 1,000 reads were excluded, resulting in 207 fecal samples used in further analyses (for sample sizes per treatment/timepoint, see S2 Table).

There is intense interest in how the microbiome interacts with host health and physical performance. Probiotics are an appealing therapy for health issues because they are convenient and could alter dysbiotic states to a more favorable one. Probiotics are readily used in humans [51], but studies showing their effectiveness in animals are mixed [27,52]. Here, we conducted a longitudinal study investigating whether pigeon microbiomes are altered by two different popular pigeon probiotics, Blue Seal probiotic pellets and Probios probiotic powder. The control group’s microbiomes did not significantly change over the course of the experiment. Adding probiotic pellets to the diet significantly changed the fecal microbiome of Birmingham Roller pigeons, but we detected no effect of the probiotic powder on the fecal microbiome. We hypothesize that the ineffectiveness of the probiotic powder to shape the microbiome may be due to the administration method: the powder was dissolved in the water of the pigeons, and may not have been ingested in sufficient amounts to cause a detectable change in microbiome.

Related Research: Microbiome Profiling by Illumina Sequencing of Combinatorial Sequence-Tagged PCR Products

Keywords: microbiome profiling, probiotic bacteria

Source:

http://doi.org/10.1371/journal.pone.0217804


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