Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese

Drovetski, Sergei V.; O’Mahoney, Michael; Ransome, Emma; Matterson, Kenan O.; Lim, Haw Chuan; Chesser, R. Terry; Graves, Gary R.

doi:10.1038/s41598-018-21892-y

Cited by 25 publications

(38 citation statements)

References 47 publications

(79 reference statements)

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“…[32]. Contrary to our results, Canada geese (Branta canadensis) harboured a higher bacterial diversity in their lower than upper GIT [33]. However, we did detect a similar low diversity in the small intestine in our study as in the duodenum of Canada geese [33] and in the ileum of Ostriches (Struthio camelus) [34].…”

Section: Discussioncontrasting

confidence: 99%

“…Contrary to our results, Canada geese (Branta canadensis) harboured a higher bacterial diversity in their lower than upper GIT [33]. However, we did detect a similar low diversity in the small intestine in our study as in the duodenum of Canada geese [33] and in the ileum of Ostriches (Struthio camelus) [34]. The small intestine is thought to be the gut section that supports the least microorganisms, due to its high concentration of enzymes [35] and the low pH in the anterior section: the gizzard [36].…”

Section: Discussioncontrasting

confidence: 99%

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Spatial heterogeneity of the shorebird gastrointestinal microbiome

2020

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The gastrointestinal tract (GIT) consists of connected structures that vary in function and physiology, and different GIT sections potentially provide different habitats for microorganisms. Birds possess unique GIT structures, including the oesophagus, proventriculus, gizzard, small intestine, caeca and large intestine. To understand birds as hosts of microbial ecosystems, we characterized the microbial communities in six sections of the GIT of two shorebird species, the Dunlin and Semipalmated Sandpiper, identified potential host species effects on the GIT microbiome and used microbial source tracking to determine microbial origin throughout the GIT. The upper three GIT sections had higher alpha diversity and genus richness compared to the lower sections, and microbial communities in the upper GIT showed no clustering. The proventriculus and gizzard microbiomes primarily originated from upstream sections, while the majority of the large intestine microbiome originated from the caeca. The heterogeneity of the GIT sections shown in our study urges caution in equating data from faeces or a single GIT component to the entire GIT microbiome but confirms that ecologically similar species may share many attributes in GIT microbiomes.

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Section: Discussioncontrasting

confidence: 99%

Section: Discussioncontrasting

confidence: 99%

Spatial heterogeneity of the shorebird gastrointestinal microbiome

2020

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“…Previous studies on wild birds have demonstrated low bacterial diversity and community composition differences in the midgut region (stomach and small intestine) compared to the crop microbiota. This suggests that the highly-acidic conditions in the midgut region acts as a barrier for environmental and foodborne bacteria [14,66,76,77]. This is further evident when we look at previously published mealworm gut microbiomes [78], where only a small fraction of the microbiome consists of bacterial genera that we identi ed in the gut microbiomes of mealworm-fed P. major.…”

Section: P Major Gut Microbiomes Respond To Diet Changes But Not Asmentioning

confidence: 74%

“…The seed diet led to a signi cant increase in relative abundance of the genera Fusobacterium (Fusobacteria), Blautia (Firmicutes), and Ruminococcus (Firmicutes). Some Fusobacterium members are animal pathogens [63], but their consistent presence in wild bird guts [2,14,64,65], especially in herbivorous species [64][65][66], suggests a possible symbiotic role. Bacteria from the genus Blautia may facilitate the metabolism of plant secondary metabolites [67,68], consistent with an increase in the relative abundance of this genus in birds feeding on seeds.…”

Section: P Major Gut Microbiomes Respond To Diet Changes But Not Asmentioning

confidence: 99%

Flexibility and resilience of Great tit (Parus major) gut microbiomes to changing diets

Bodawatta

Freiberga

Puzejova

et al. 2020

Preprint

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Background: Gut microbial communities play important roles in nutrient management and can change in response to host diets. The extent of this flexibility and the concomitant resilience is largely unknown in wild animals. To begin untangling the dynamics of avian-gut microbiome symbiosis associated with diet changes, we exposed Parus major (Great tits) fed with a standard diet (seeds and mealworms) to either a mixed (seeds, mealworms and fruits), a seed, or a mealworm diet for four weeks, and examined the flexibility of gut microbiomes to these compositionally different diets. To assess microbiome resilience (recovery potential), all individuals were subsequently reversed to a standard diet for another four weeks. Cloacal microbiomes were collected weekly and characterised through sequencing the v4 region of the 16S rRNA gene using Illumina MiSeq. Results: Initial microbiomes changed significantly with the diet manipulation but the communities did not differ significantly between the three diet groups (mixed, seed and mealworm), despite multiple diet-specific changes of specific bacterial genera. Reverting birds to the standard diet led to only a partial recovery in gut community compositions. The majority of the bacterial taxa that increased significantly during diet manipulation decreased in relative abundances after reversion to the standard diet; however, bacterial taxa that decreased during the manipulation rarely increased after diet reversal.Conclusions: The gut microbial response and partial resilience to dietary changes support that gut bacterial communities of P. major play a role in accommodating dietary changes experienced by wild avian hosts. This may be a contributing factor to the relaxed association between microbiome composition and bird phylogeny. Our findings further imply that interpretations of wild bird gut microbiome analyses from single-time point sampling, especially for omnivorous species or species that have changing seasonal diets, should be done with caution. The partial community recovery implies that ecologically relevant diet changes (e.g., seasonality and migration) open up gut niches that may be filled by previously abundant microbes or replaced by different symbiont lineages, which has important implications for the integrity and specificity of long-term avian-symbiont associations.

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“…Replicate samples from a single intestine were sequenced to elucidate the microvariation that occurs within the intestine. Variation in microbiota between discrete organs of the gastrointestinal tract has been demonstrated in diverse taxa e.g., in snakes (Colston, Noonan, & Jackson, 2015), in humans (Costello et al, 2009), in geese (Drovetski et al, 2018), in alligators (Keenan, Engel, & Elsey, 2013), and in teleost fish (Pratte, Besson, Hollman, & Stewart, 2018). However, few studies have looked at the variation within a single organ.…”

Section: Sample Versus Pcr Replicatesmentioning

confidence: 99%

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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Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese

Cited by 25 publications

References 47 publications

Spatial heterogeneity of the shorebird gastrointestinal microbiome

Spatial heterogeneity of the shorebird gastrointestinal microbiome

Flexibility and resilience of Great tit (Parus major) gut microbiomes to changing diets

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

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