Habitat environments impacted the gut microbiome of long-distance migratory swan geese but central species conserved

Wu, Yueni; Yang, Yefeng; Cao, Lei; Yin, Huaqun; Xu, Meiying; Wang, Zhujun; Liu, Yangying; Wang, Xin; Deng, Ye

doi:10.1038/s41598-018-31731-9

Cited by 79 publications

(91 citation statements)

References 67 publications

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“…Within the primate clade, similar patterns have been described in the Chlorocebus genus (Trosvik et al, ), Alouatta pigra (Amato et al, ), Lemur catta (Bennett et al, ), and Procolobus gordonorum (Barelli et al, ). GM robustness to habitat disturbance has been reported in parrots ( Strigops habroptilus ; see Perry, Digby, & Taylor, ), but other taxa, including frogs ( Fejervarya limnocharis ; see Chang, Huang, Lin, Huang, & Liao, ), jackals ( Canis mesomelas ; see Menke et al, ), and swan geese ( Anser cygnoides ; see Wu et al, ) show that populations in disturbed habitats exhibit distinct GMs relative to pristine habitat counterparts. While our findings in V. variegata generally fit this narrative, our results indicate that it is not simply the level of habitat disturbance driving GM diversity.…”

Section: Discussionmentioning

confidence: 92%

Extensive variability in the gut microbiome of a highly‐specialized and critically endangered lemur species across sites

Donohue

Asangba

Ralainirina

et al. 2019

American J Primatol

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Deforestation continues to jeopardize Malagasy primates as viable habitats become smaller, more fragmented, and more disturbed. This deforestation can lead to changes in diet, microhabitat, and gene flow between populations of endangered species, and it remains unclear how these changes may affect gut microbiome (GM) characteristics. The black-and-white ruffed lemur (Varecia variegata), which is among Madagascar's most threatened lemur species, provides a critical model for understanding the relationships between historical and on-going deforestation (habitat disturbance), feeding ecology, and GM composition and diversity. We studied four populations inhabiting two rainforests (relatively pristine vs. highly disturbed) in southeastern Madagascar. We conducted full-day focal animal behavioral follows and collected fecal samples opportunistically across a three-month period. Our results indicate that lemurs inhabiting sites characterized by habitat disturbance and low dietary diversity exhibited reduced gut microbial alpha diversity. We also show that these same factors were associated with high community dissimilarity using weighted and unweighted UniFrac metrics. Finally, an indicator species analysis showed that the most pristine site was characterized by an abundance of methanogenic archaea.While it is impossible to disentangle the relative contributions of each confounding variable presented by our sampling design, these results provide crucial information about GM variability, thereby underscoring the importance of monitoring endangered species at the population-level.

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Section: Discussionmentioning

confidence: 92%

Extensive variability in the gut microbiome of a highly‐specialized and critically endangered lemur species across sites

Donohue

Asangba

Ralainirina

et al. 2019

American J Primatol

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“…These are interesting observations considering the hypothesis of environmentally‐ and diet‐derived colonization of the gut microbiome. In addition to humans, in which perinatal factors are believed to play an important role in microbiome seeding (Dominguez‐Bello et al, ), other organisms are reported to have significant seeding from the habitat they live in, including marine organisms (Chen, Chen, Weng, Shaw, & Wang, ), birds (Wu et al, ), and soil‐dwelling arthropods (Degli Esposti & Martinez Romero, ).…”

Section: Discussionmentioning

confidence: 99%

The gut microbiome and metabolome of saddleback tamarins (Leontocebus weddelli): Insights into the foraging ecology of a small‐bodied primate

Garber

Mallott

Porter

et al. 2019

American J Primatol

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Body mass is a strong predictor of diet and nutritional requirements across a wide range of mammalian taxa. In the case of small-bodied primates, because of their limited gut volume, rapid food passage rate, and high metabolic rate, they are hypothesized to maintain high digestive efficiency by exploiting foods rich in protein, fats, and readily available energy. However, our understanding of the dietary requirements of wild primates is limited because little is known concerning the contributions of their gut microbiome to the breakdown and assimilation of macronutrients and energy. To study how the gut microbiome contributes to the feeding ecology of a small-bodied primate, we analyzed the fecal microbiome composition and metabolome of 22 wild saddleback tamarins (adult body mass 360-390 g) in Northern Bolivia. Samples were analyzed using high-throughputIllumina sequencing of the 16 S rRNA gene V3-V5 regions, coupled with GC-MS metabolomic profiling. Our analysis revealed that the distal microbiome of Leontocebus weddelli is largely dominated by two main bacterial genera: Xylanibacter and Hallella (34.7 ± 14.7 and 22.6 ± 12.4%, respectively). A predictive analysis of functions likely carried out by bacteria in the tamarin gut demonstrated the dominance of membrane transport systems and carbohydrate metabolism as the predominant metabolic pathways. Moreover, given a fecal metabolome composed mainly of glucose, fructose, and lactic acid (21.7 ± 15.9%, 16.5 ± 10.7%, and 6.8 ± 5.5%, respectively), the processing of highly fermentable carbohydrates appears to play a central role in the nutritional ecology of these small-bodied primates. Finally, the results also show a potential influence of environmentally-derived bacteria in colonizing the tamarin gut. These results indicate high energetic turnover in the distal gut of Weddell's saddleback tamarin, likely influenced by dominant bacterial taxa that facilitate dietary dependence on highly digestible carbohydrates present in nectar, plant exudates, and ripe fruits.

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“…The functions of gut microbiota are mainly determined by their composition, which is affected by various factors such as host genetic background, health condition, social behaviour and habitat environment factor [17][18][19][20][21][22][23][24]. Because of the importance of gut microbiota and other microbiome communities, some scientists suggest that the host and its microbiomes are considered as a biological unit subjected to natural selection [25].…”

Section: Introductionmentioning

confidence: 99%

“…Previous research has demonstrated that ruminants depend heavily on gut microbiota to digest fibre in the rumen and use products such as short-chain fatty acids (SCFAs) to meet their energy needs [14,15]. Panda, which do not have a rumen, also rely on their microbiome to degrade hemicellulose and starch in bamboo [16].The functions of gut microbiota are mainly determined by their composition, which is affected by various factors such as host genetic background, health condition, social behaviour and habitat environment factor [17][18][19][20][21][22][23][24]. Because of the importance of gut microbiota and other microbiome communities, some scientists suggest that the host and its microbiomes are considered as a biological unit subjected to natural selection [25].…”

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confidence: 99%

Characterisation of the gut microbial community of rhesus macaques in high-altitude environments

Yao

Dong

et al. 2020

Preprint

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Background: The mammal intestinal microbiota is involved in various physiological processes and plays a key role in host environment adaption. However, for non-human primates (NHPs), little is known about their gut microbial community in high-altitude environments and even less about their adaption to such habitats. We characterised the gut microbial community of rhesus macaques from multiple high-altitude environments and compared it to those of low-altitude populations. Results: We collected faecal samples of rhesus macaques from four high-altitude populations (above 3,000 m) and three low-altitude populations (below 500 m). By calculating the alpha diversity index, we found that high-altitude populations exhibited a higher diversity. Statistical analysis of beta diversity indicated significant differences between high-and low-altitude populations. Significant differences were also detected at the phylum and family levels. At the phylum level, the high-altitude gut microbial community was dominated by Firmicutes (63.42%), while at low altitudes, it was dominated by Bacteroidetes (47.4%). At the family level, the high-altitude population was dominated by Ruminococcaceae (36.2%), while the low-altitude one was dominated by Prevotellaceae (39.6%).Some families, such as Christensenellaceae and Rikenellaceae, were consistently higher abundant in all high-altitude populations. We analysed the overlap of operational taxonomic units (OTUs) in highaltitude populations and determined their core OTUs (shared by all four high-altitude populations).However, when compared with the low-altitude core OTUs, only 65% were shared, suggesting a divergence in core OTUs. Function prediction indicated a significant difference in gene copy number of 35 level-2 pathways between high-and low-altitude populations; 29 of them were higher in high altitudes, especially in membrane transport and carbohydrate metabolism. Conclusions: The gut microbial community of high-altitude rhesus macaques was significantly distinct from that of lowaltitude populations in terms of diversity, composition and function. High-altitude populations were dominated by Firmicutes and Ruminococcace, while in low-altitude populations, Bacteroidetes and Prevotellaceae were dominant. The difference in gut microbiota between these two populations may be caused by differences in host diet, environmental temperature and oxygen pressure. These differentiated gut microbial microorganisms may play a critical role in the adaptive evolution of 4 rhesus macaques to high-altitude environments. BackgroundThe gastrointestinal tract of animals is habited by a complex microbial community, known collectively as the gut or intestinal microbiota. There is increasing evidence that the gut microbial community of animals is involved in a wide range of processes in the host, including health, grow and development as well as behaviour; it can even affect the nervous system by secreting metabolites [1][2][3][4][5][6][7][8][9][10][11]. These microbes can also assist in energy uptake and meta...

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Habitat environments impacted the gut microbiome of long-distance migratory swan geese but central species conserved

Cited by 79 publications

References 67 publications

Extensive variability in the gut microbiome of a highly‐specialized and critically endangered lemur species across sites

Extensive variability in the gut microbiome of a highly‐specialized and critically endangered lemur species across sites

The gut microbiome and metabolome of saddleback tamarins (Leontocebus weddelli): Insights into the foraging ecology of a small‐bodied primate

Characterisation of the gut microbial community of rhesus macaques in high-altitude environments

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