High-throughput sequencing reveals the gut and lung prokaryotic community profiles of the Chinese giant salamander (Andrias davidianus)

Wu, Zhenbing; Gatesoupe, François-Joël; Zhang, Qianqian; Wang, Xiehao; Feng, Yuqing; Wang, Shuyi; Feng, Dongyue; Li, Aihua

doi:10.1007/s11033-019-04972-8

Cited by 7 publications

(5 citation statements)

References 56 publications

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“…First, some Methanothermobacter isolates can grow at 37 °C, but not optimally 33 . Second, Methanothermobacter has been observed in a number of animals including salamanders 34 , trout 35 , chickens 36 and buffalo 37 , but very sparsely and at low abundances. Third, we found Methanothermobacter abundances to correlate with higher body temperatures of avian and some mammalian species which have generally been less-studied, especially in regards to archaeal diversity (Supplementary Figs.…”

Section: Discussionmentioning

confidence: 99%

Vertebrate host phylogeny influences gut archaeal diversity

et al. 2021

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Commonly used 16S rRNA gene primers do not detect the full range of archaeal diversity present in the vertebrate gut. As a result, several questions regarding the archaeal component of the gut microbiota remain, including which Archaea are host-associated, the specificities of such associations and the major factors influencing archaeal diversity. Using 16S rRNA gene amplicon sequencing with primers that specifically target Archaea, we obtained sufficient sequence data from 185 gastrointestinal samples collected from 110 vertebrate species that span five taxonomic classes (Mammalia, Aves, Reptilia, Amphibia and Actinopterygii), of which the majority were wild. We provide evidence for previously undescribed Archaea–host associations, including Bathyarchaeia and Methanothermobacter, the latter of which was prevalent among Aves and relatively abundant in species with higher body temperatures, although this association could not be decoupled from host phylogeny. Host phylogeny explained archaeal diversity more strongly than diet, while specific taxa were associated with both factors, and cophylogeny was significant and strongest for mammalian herbivores. Methanobacteria was the only class predicted to be present in the last common ancestors of mammals and all host species. Further analysis indicated that Archaea–Bacteria interactions have a limited effect on archaeal diversity. These findings expand our current understanding of Archaea–vertebrate associations.

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Section: Discussionmentioning

confidence: 99%

Vertebrate host phylogeny influences gut archaeal diversity

et al. 2021

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“…The intestinal floras were different among different individuals or the same one in different conditions, which were related to ages, diets, health status, and ranging profile ( Korpela et al, 2021 ; Liu et al, 2021 ; Spencer et al, 2021 ; Sztandarski et al, 2022 ). High-throughput sequencing was used to investigate the gut and lung prokaryotic community profiles of adult Chinese giant salamanders at age 3 ( Wu et al, 2019 ). In addition, the previous gut microbiota report of A. davidianu s provided much microbial information related to age changes from age 1 to 4 ( Zhang et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

“…The population and abundance of gut microbes in different habitats vary greatly, and the status also is reflected in the giant salamander under different temperatures and ages ( Zhang et al, 2018 ; Zhu et al, 2021 ). There is a close relationship between intestinal flora and host health ( Wu et al, 2019 ), which mainly reflected that microbes are mainly colonized in the intestinal tract and play key roles in the digestive system ( Gerritsen et al, 2011 ). The complex microbes constitute a microbial community, and the balance contributes to maintaining the host’s gut function, including energy uptake, metabolite production, immune system development, and gastrointestinal diseases ( He, 2012 ).…”

Section: Introductionmentioning

confidence: 99%

Changes of intestinal microbiota in the giant salamander (Andrias davidianus) during growth based on high-throughput sequencing

Cai

Deng²,

Sun³

et al. 2023

Front. Microbiol.

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Despite an increasing appreciation of the importance of host–microbe interaction in healthy growth, information on gut microbiota changes of the Chinese giant salamander (Andrias davidianus) during growth is still lacking. Moreover, it is interesting to identify gut microbial structure for further monitoring A. davidianus health. This study explored the composition and functional characteristics of gut bacteria in different growth periods, including tadpole stage (ADT), gills internalization stage (ADG), 1 year age (ADY), 2 year age (ADE), and 3 year age (ADS), using high-throughput sequencing. The results showed that significant differences were observed in microbial community composition and abundance among different growth groups. The diversity and abundance of intestinal flora gradually reduced from larvae to adult stages. Overall, the gut microbial communities were mainly composed of Fusobacteriota, Firmicutes, Bacteroidota, and Proteobacteria. More specifically, the Cetobacterium genus was the most dominant, followed by Lactobacillus and Candidatus Amphibiichlamydia. Interestingly, Candidatus Amphibiichlamydia, a special species related to amphibian diseases, could be a promising indicator for healthy monitoring during A. davidianus growth. These results could be an important reference for future research on the relationship between the host and microbiota and also provide basic data for the artificial feeding of A. davidianus.

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“…First, some Methanothermobacter isolates can grow at 37°C, but not optimally (33). Second, Methanothermobacter has been observed in a number of animals including salamanders (34), trout (35), chickens (36), buffalo (37) but very sparsely and at low abundances. Third, we found Methanothermobacter abundances to correlate with higher body temperatures of avian and some mammal species which have generally been less-studied, especially in regards to archaeal diversity (Figures S18 & S19).…”

Section: Discussionmentioning

confidence: 99%

Strong influence of vertebrate host phylogeny on gut archaeal diversity

Youngblut

Reischer

Dauser

et al. 2020

Preprint

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Commonly used 16S rRNA gene primers miss much of the archaeal diversity present in the vertebrate gut, leaving open the question of which archaea are host associated, the specificities of such associations, and the major factors influencing archaeal diversity. We applied 16S rRNA amplicon sequencing with Archaea-targeting primers to a dataset of 311 fecal/gut samples spanning 5 taxonomic classes (Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii) and obtained from mainly wild individuals (76% were wild). We obtained sufficient archaeal sequence data from 185 samples comprising 110 species that span all 5 classes. We provide evidence for novel Archaea-host associations, including Bathyarchaeia and Methanothermobacter — the latter of which was prevalent among Aves and enriched in higher body temperatures. Host phylogeny more strongly explained archaeal diversity than diet, while specific taxa were associated with each factor. Co-phylogeny was significant and strongest for mammalian herbivores. Methanobacteria was the only class predicted to be present in the last command ancestors of mammals and all host species. Archaea-Bacteria interactions seem to have a limited effect on archaeal diversity. These findings substantially expand on the paradigm of Archaea-vertebrate associations and the factors that explain those associations.SignificanceArchaea play key roles in the vertebrate gut such as promoting bacterial fermentation via consumption of waste products. Moreover, gut-inhabiting methanogenic Archaea in livestock are a substantial source of greenhouse gas production. Still, much is not known of the archaeal diversity in most vertebrates, especially since 16S rRNA sequence surveys often miss much of the archaeal diversity that is present. By applying Archaea-targeted gut microbiome sequencing to a large collection of diverse vertebrates, we reveal new Archaea-host associations such as a high prevalence of Methanothermobacter in birds. We also show that host evolutionary history explains archaeal diversity better than diet, and certain genera in one particular class of Archaea (Methanobacteria) were likely pervasive in the ancestral vertebrate gut.

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High-throughput sequencing reveals the gut and lung prokaryotic community profiles of the Chinese giant salamander (Andrias davidianus)

Cited by 7 publications

References 56 publications

Vertebrate host phylogeny influences gut archaeal diversity

Vertebrate host phylogeny influences gut archaeal diversity

Changes of intestinal microbiota in the giant salamander (Andrias davidianus) during growth based on high-throughput sequencing

Strong influence of vertebrate host phylogeny on gut archaeal diversity

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