Compositional and predicted functional analysis of the gut microbiota of <i>Radix auricularia</i> (Linnaeus) via high-throughput Illumina sequencing

Hu, Zongfu; Chen, Xi; Chang, Jie; Yu, Jianhua; Tong, Qing; Li, Shuguo; Niu, Huaxin

doi:10.7717/peerj.5537

Cited by 46 publications

(46 citation statements)

References 71 publications

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“…The results showed that unclassified genera of Mycoplasmataceae and Chloroflexaceae, Paracoccus , Microcoleus , Pleurocapsa , etc. were the most abundant genera [14]. In contrast, our study found that Ochrobactrum , Sediminibacterium , Desulfovibrio , an unclassified genus of Aeromonadaceae, and Cloacibacterium were dominant bacteria in the gut of P. canaliculata snails.…”

Section: Discussionmentioning

confidence: 73%

Spatial structure of the microbiome in the gut of Pomacea canaliculata

Lü

et al. 2019

BMC Microbiol

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Background: Gut microbes can contribute to their hosts in food digestion, nutrient absorption, and inhibiting the growth of pathogens. However, only limited studies have focused on the gut microbiota of freshwater snails. Pomacea canaliculata is considered one of the worst invasive alien species in the world. Elucidating the diversity and composition of the microbiota in the gut of P. canaliculata snails may be helpful for better understanding the widespread invasion of this snail species. In this study, the buccal masses, stomachs, and intestines were isolated from seven P. canaliculata snails. The diversity and composition of the microbiota in the three gut sections were then investigated based on high-throughput Illumina sequencing targeting the V3-V4 regions of the 16S rRNA gene.Results: The diversity of the microbiota was highest in the intestine but lowest in the buccal mass. A total of 29 phyla and 111 genera of bacteria were identified in all of the samples. In general, Ochrobactrum, a genus of putative cellulose-degrading bacteria, was the most abundant (overall relative abundance: 13.6%), followed by Sediminibacterium (9.7%), Desulfovibrio (7.8%), an unclassified genus in the family Aeromonadaceae (5.4%), and Cloacibacterium (5.4%). The composition of the microbiota was diverse among the different gut sections. Ochrobactrum (relative abundance: 23.15% ± 7.92%) and Sediminibacterium (16.95 ± 5.70%) were most abundant in the stomach, an unclassified genus in the family Porphyromonadaceae (14.28 ± 7.29%) and Leptotrichia (8.70 ± 4.46%) were highest in the buccal mass, and two genera in the families Aeromonadaceae (7.55 ± 4.53%) and Mollicutes (13.47 ± 13.03%) were highest in the intestine. Conclusions:The diversity and composition of the microbiome vary among different gut sections of P. canaliculata snails. Putative cellulose-degrading bacteria are enriched in the gut of P. canaliculata.

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Section: Discussionmentioning

confidence: 73%

Spatial structure of the microbiome in the gut of Pomacea canaliculata

Lü

et al. 2019

BMC Microbiol

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“…The gut microbial communities of wild frogs were similar in composition between the different developmental stages in frogs in the same habitats and with similar food compositions, or under the regulation of similar physiological processes. Although previous research has confirmed that bacterial communities change during host development and growth (Hu et al, 2018), some studies have shown that bacterial communities are similar between the juvenile and adult stages of certain animal hosts (Xue et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

Effects of Captivity and Season on the Gut Microbiota of the Brown Frog (Rana dybowskii)

Tong

Liu

et al. 2019

Front. Microbiol.

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The gut microbiota of amphibians is affected by exogenous and endogenous factors. We performed a comprehensive analysis using high-throughput sequencing technology and functional predictions and observed general changes in the gut microbiota of frogs in different growth stages, seasons, and growth environments. There were no significant differences in microbial richness and diversity between juvenile and adult wild frogs, between the summer and autumn groups of captive frogs, or between wild and captive frogs. There were significant differences in the gut microbiota community structure of Rana dybowskii between the summer and autumn groups of captive frogs and between wild and captive R. dybowskii , whereas the differences between juvenile and adult wild frogs were not significant. The dominant gut bacterial phyla in frogs from both captive and wild environments included Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Linear discriminant effect size (LEfSe) analysis showed that Bacteroidetes and Firmicutes were significantly enriched in captive and wild R. dybowskii , respectively linear discriminant analysis (LDA > 4). The core operational taxonomical units (OTUs) that were found in >90% of all frogs tested encompassed 15 core OTUs. The captive frogs exhibited 15 core OTUs in addition to the above overall core microbiota, whereas the wild frogs exhibited 19 core OTUs in addition to the above overall core microbiota. Predictions made using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) suggested that eleven KEGG pathways, such as infectious diseases, immune system diseases, metabolism, metabolism of other amino acids, metabolism of cofactors and vitamins, metabolism of terpenoids and polyketides, neurodegenerative diseases, and transport and catabolism, were enriched in captive frogs. The relative abundance of several red-leg-syndrome-related pathogens increased significantly in captive frogs compared with that in wild frogs. To our knowledge, this is the first study on the effects of individual seasons and captivity on the gut microbiota of frogs.

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“…The alpha-diversity indices indicate a high diversity of the O. strigosa bacterial community, as compared with other snail species. For example, there were 7,065 total OTUs in O. strigosa, versus 1,196 OTUs in freshwater snail R. Auricularia [53]. The invasive land snail Achatina fulica only had 228 OTUs [8].…”

Section: Overall Species Microbiomementioning

confidence: 99%

Characterization of the Gut Microbiome in Wild Rocky Mountainsnails (Oreohelix strigosa)

Chalifour

2021

Preprint

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BackgroundThe Rocky Mountainsnail (Oreohelix strigosa) is a terrestrial gastropod of ecological importance in the Rocky Mountains of western United States and Canada. Across the animal kingdom, including in gastropods, gut microbiomes have profound effects on the health of the host. Current knowledge regarding snail gut microbiomes, particularly throughout various life history stages, is limited. Understanding snail gut microbiome composition and dynamics can provide an initial step toward better conservation and management of this species. ResultsIn this study, we employed 16S rRNA gene amplicon sequencing to examine gut bacteria communities in wild-caught O. strigosa populations from the Front Range of Colorado. These included three treatment groups: (1) adult and (2) fetal snails, as well as (3) sub-populations of adult snails that were starved prior to ethanol fixation. Overall, O. strigosa harbors a high diversity of bacteria. We sequenced the V4 region of the 16S rRNA gene on an Illumina MiSeq, and obtained 2,714,330 total reads. We identified a total of 7,056 unique operational taxonomic units (OTUs) belonging to 36 phyla. The core gut microbiome of four unique OTUs accounts for roughly half of all sequencing reads returned and may aid the snails’ digestive processes. Significant differences in microbial composition, as well as richness, evenness, and Shannon Indices were found across the three treatment groups.ConclusionsComparisons of gut microbiomes in O. strigosa adult, fetal, and starved samples provide evidence that the host internal environments influence bacterial community compositions, and that bacteria may be transmitted vertically from parent to offspring. This work provides the first comprehensive report on the structure and membership of bacterial populations in the gastropod family Oreohelicidae and reveals similarities and differences across varying life history metrics. Strong differentiation between these life history metrics demonstrates the need for wider sampling for studies of dynamics of the snail gut microbiome.

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Compositional and predicted functional analysis of the gut microbiota of Radix auricularia (Linnaeus) via high-throughput Illumina sequencing

Cited by 46 publications

References 71 publications

Spatial structure of the microbiome in the gut of Pomacea canaliculata

Spatial structure of the microbiome in the gut of Pomacea canaliculata

Effects of Captivity and Season on the Gut Microbiota of the Brown Frog (Rana dybowskii)

Characterization of the Gut Microbiome in Wild Rocky Mountainsnails (Oreohelix strigosa)

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