Characterization and comparison of gut microbiomes in nine species of parrots in captivity

Liu, Hongyi; Chen, Zhiwei; Gao, Ge; Sun, Cheng‐He; Li, Yudong; Zhu, Ying

doi:10.1007/s13199-019-00613-7

Cited by 19 publications

(20 citation statements)

References 38 publications

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“…Catellicoccus were first described in 2006 following isolation from decomposing sea mammals (Lawson, Collins, Falsen, & Foster, ) and have subsequently been discovered to be a significant member of the gull faecal microbiome (Koskey, Fisher, Traudt, Newton, & McLellan, ; Lu, Santo Domingo, Lamendella, Edge, & Hill, ). Enterococcus , Staphylococcus , Lactobacillus , Enterobacter , Clostridium and Lactococcus were detected in at least one quarter of the samples and are all common gut microbes in birds (e.g., Grond, Perreau, et al, ; Liu et al, ; van Dongen et al, ; Waite & Taylor, ).…”

Section: Discussionmentioning

confidence: 99%

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Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea

et al. 2020

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How the microbiome interacts with hosts across evolutionary time is poorly understood. Data sets including many host species are required to conduct comparative analyses. Here, we analyzed 142 intestinal microbiome samples from 92 birds belonging to 74 species from Equatorial Guinea, using the 16S rRNA gene. Using four definitions for microbial taxonomic units (97%OTU, 99%OTU, 99%OTU with singletons removed, ASV), we conducted alpha and beta diversity analyses. We found that raw abundances and diversity varied between the data sets but relative patterns were largely consistent across data sets. Host taxonomy, diet and locality were significantly associated with microbiomes, at generally similar levels using three distance metrics. Phylogenetic comparative methods assessed the evolutionary relationship between the microbiome as a trait of a host species and the underlying bird phylogeny. Using multiple ways of defining “microbiome traits”, we found that a neutral Brownian motion model did not explain variation in microbiomes. Instead, we found a White Noise model (indicating little phylogenetic signal), was most likely. There was some support for the Ornstein‐Uhlenbeck model (that invokes selection), but the level of support was similar to that of a White Noise simulation, further supporting the White Noise model as the best explanation for the evolution of the microbiome as a trait of avian hosts. Our study demonstrated that both environment and evolution play a role in the gut microbiome and the relationship does not follow a neutral model; these biological results are qualitatively robust to analytical choices.

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Section: Discussionmentioning

confidence: 99%

“…and Lactococcus were detected in at least one quarter of the samples and are all common gut microbes in birds (e.g., Grond, Perreau, et al, 2019;Liu et al, 2019;van Dongen et al, 2013;Waite & Taylor, 2014).…”

Section: Enterococcus Staphylococcus Lactobacillus Enterobacter Cmentioning

confidence: 99%

Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea

et al. 2020

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“…The first phylosymbiosis study on mammalian gut microbiomes [4] demonstrated the effects of animal phylogeny and diet on gut microbial community dissimilarity [12,21,23,39,70,83]. Studies focusing on gut microbiomes of specific animal groups detected phylosymbiosis in American pikas [51] and Peromyscus deer mice [23,52], no phylosymbiosis in western chipmunks [84], and mixed evidence of phylosymbiosis in primates [17,43,44,70], bats [55,85] and birds [62,68,86,87]. A recent large-scale study revealed much stronger effects of host phylogeny and diet on the gut microbiomes of non-flying mammals than those of bats and birds [72].…”

Section: The Prevalence Of Phylosymbiosismentioning

confidence: 99%

An introduction to phylosymbiosis

2020

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Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of a new, cross-system trend in host-associated microbiomes. Defining phylosymbiosis as ‘microbial community relationships that recapitulate the phylogeny of their host’, we review the relevant literature and data in the last decade, emphasizing frequently used methods and regular patterns observed in analyses. Quantitative support for phylosymbiosis is provided by statistical methods evaluating higher microbiome variation between host species than within host species, topological similarities between the host phylogeny and microbiome dendrogram, and a positive association between host genetic relationships and microbiome beta diversity. Significant degrees of phylosymbiosis are prevalent, but not universal, in microbiomes of plants and animals from terrestrial and aquatic habitats. Consistent with natural selection shaping phylosymbiosis, microbiome transplant experiments demonstrate reduced host performance and/or fitness upon host–microbiome mismatches. Hybridization can also disrupt phylosymbiotic microbiomes and cause hybrid pathologies. The pervasiveness of phylosymbiosis carries several important implications for advancing knowledge of eco-evolutionary processes that impact host–microbiome interactions and future applications of precision microbiology. Important future steps will be to examine phylosymbiosis beyond bacterial communities, apply evolutionary modelling for an increasingly sophisticated understanding of phylosymbiosis, and unravel the host and microbial mechanisms that contribute to the pattern. This review serves as a gateway to experimental, conceptual and quantitative themes of phylosymbiosis and outlines opportunities ripe for investigation from a diversity of disciplines.

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“…Several synergistic factors, such as the environment and diet dominate over host genetics in determining gut microbiota composition [29][30][31]. A comparative study of gut microbial diversity among parrot species, indicated the potential role of host ancestry in shaping gut microbiomes [32]. In birds, genetics specialists applied GWASs to demonstrate the relationship between host genotype and gut/reproductive microbiota population [33][34][35][36][37][38].…”

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confidence: 99%

Influence of the digestive/reproductive tract microbiota on chicken egg production beyond host genetics

Tian

Zhu

et al. 2020

Preprint

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Background: The microbiota of the digestive and reproductive systems has a prominent role in animal health and performance, but the extent of its contribution is difﬁcult to determine. In chickens, the effect of host genetics on the reproductive and digestive tract microbiota is unclear, and the means by which digestive/reproductive microbiomes help improve egg production in chicken are unknown.Results: To gain insight into this, we examined genomes from 128 chickens reared under identical conditions and described their digestive (crop, gizzard and small intestine) and reproductive tract (vagina, uterus and isthmus) microbiota. Although the diversity, composition and predicted function of the digestive and reproductive tract microbiota exhibited notable microbiota variation substantially between different parts, host genetics had limited effects on the reproductive and digestive tract microbial community. The digestive and reproductive tract microbiota had a significant effect on egg production (accounting for 52.31% - 98.86% of the variance), after correcting for host genetic effects; in particular, the uterus and isthmus microbiota accounted for an average of 93.59% and 98.86%, respectively, of variance in egg production. We further identiﬁed four reproductive tract microbial species which were related to immune system, Bacteroides fragilis, Bacteroides salanitronis, Bacteroides barnesiae and Clostridium leptum, that were signiﬁcantly positively correlated with egg production. Chickens with a lower abundance of these species had produced signiﬁcantly fewer eggs at 300 days of age (37.13 vs. 113.75) than those with a higher abundance of these microorganisms. These taxa indicate potential roles play in promoting reproductive performance. Especially uterus and isthmus tract microbiota were major factors in regulating the chicken egg production.Conclusions: Host genetics has limited effect on digestive/reproductive microbiome composition. The distinct site-associated chicken microbiome may be determined by the differences of their physical function. These ﬁndings may help design strategies for controlling and altering the digestive/reproductive tract microbiota in chickens to improve egg production.

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Characterization and comparison of gut microbiomes in nine species of parrots in captivity

Cited by 19 publications

References 38 publications

Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea

Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea

An introduction to phylosymbiosis

Influence of the digestive/reproductive tract microbiota on chicken egg production beyond host genetics

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