Diet drives convergent evolution of gut microbiomes in bamboo-eating species

Wang, Xiao; Hu, Yibo; Wu, Qi; Nie, Yonggang; Dong, Jiuhong; Ding, Yun; Li, Yan; Wei, Fuwen

doi:10.1007/s11427-020-1750-7

Cited by 56 publications

(56 citation statements)

References 30 publications

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“… 68 - 70 At the same time, many researchers also assume that the same diet can lead to the convergence of the gut microbiota of different individuals (both interspecific and intraspecific). 37 , 46 , 47 As the plateau zokors were subjected into captivity, they have to cope with drastic lifestyle and dietary changes. If diet plays a key role in the formation of microbial communities, then it would be expected that the microbial communities of plateau zokors would converge after exposure to a same diet.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, food is a key factor to determine the gut microbiota composition. 44 - 46 Similar diets appear to drive convergence of gut microbial communities. 37 , 47 Therefore, while designing control experiments on the gut microbiota, according to the requirement of a single variable principle, researchers commonly choose to provide the experimental subjects with the same diet for a specific time after bringing them into the laboratory; consequently, their gut microbiota composition will become stable and consistent before the beginning of control experiments.…”

Section: Introductionmentioning

confidence: 99%

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Gut Microbiome Changes in Captive Plateau Zokors (Eospalax baileyi)

Liu

Song

Yan

et al. 2021

Evol Bioinform Online

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Wild-caught animals must cope with drastic lifestyle and dietary changes after being induced to captivity. How the gut microbiome structure of these animals will change in response receives increasing attention. The plateau zokor ( Eospalax baileyi), a typic subterranean rodent endemic to the Qinghai-Tibet plateau, spends almost the whole life underground and is well adapted to the environmental pressures of both plateau and underground. However, how the gut microbiome of the plateau zokor will change in response to captivity has not been reported to date. This study compared the microbial community structure and functions of 22 plateau zokors before (the WS group) and after being kept in captivity for 15 days (the LS group, fed on carrots) using the 16S rRNA gene via high-throughput sequencing technology. The results showed that the LS group retained 973 of the 977 operational taxonomic units (OTUs) in the WS group, and no new OTUs were found in the LS group. The dominant bacterial phyla were Bacteroides and Firmicutes in both groups. In alpha diversity analysis, the Shannon, Sobs, and ACE indexes of the LS group were significantly lower than those of the WS group. A remarkable difference ( P < 0.01) between groups was also detected in beta diversity analysis. The UPGMA clustering, NMDS, PCoA, and Anosim results all showed that the intergroup difference was significantly greater than the intragroup difference. And compared with the WS group, the intragroup difference of the gut microbiota in the LS group was much larger, which failed to support the assumption that similar diets should drive convergence of gut microbial communities. PICRUSt revealed that although some functional categories displayed significant differences between groups, the relative abundances of these categories were very close in both groups. Based on all the results, we conclude that as plateau zokors enter captivity for a short time, although the relative abundances of different gut microbiota categories shifted significantly, they can maintain almost all the OTUs and the functions of the gut microbiota in the wild. So, the use of wild-caught plateau zokors in gut microbial studies is acceptable if the time in captivity is short.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Gut Microbiome Changes in Captive Plateau Zokors (Eospalax baileyi)

Liu

Song

Yan

et al. 2021

Evol Bioinform Online

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“…In mammals, diet adaptation was considered to be the main driving factor affecting the microbial community structure (Ley et al, 2008;Faith et al, 2011;Muegge et al, 2011;Delsuc et al, 2014), although two recent studies suggested that the impact of host phylogeny and physiology outweighs that of host dietary niche in gut microbiome divergence (Nishida and Ochman, 2018;Amato et al, 2019). Furthermore, a recent study on bamboo-feeding pandas confirmed that the specialized herbivorous diet rather than the host phylogeny was the dominant driver of gut microbiome convergence within beers (Arctoidea) (Huang et al, 2021).…”

Section: Diet and Phylogeny Structure The Gut Bacterial Communitymentioning

confidence: 99%

“…Consistent relationships have been reported where the relationship between host phylogeny and microbiota is similar to or even the same as that between diet and microbiota ( Delsuc et al, 2014 ). However, inconsistent relationships were also found, and a dietary shift was often determined as the dominant driving factor of convergent evolution of the gut microbiota ( Ley et al, 2008 ; Huang et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

“…Based on the structure and developmental stage of bamboos, these insects can be divided into leaf-, shoot-, and sap-specialized groups ( Wang et al, 1998 ). A most recent study showed that convergent evolution of gut microbes in pandas, a mammal specialized in bamboo diet, was driven by diet rather than host phylogeny ( Huang et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

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Host Phylogeny and Diet Shape Gut Microbial Communities Within Bamboo-Feeding Insects

et al. 2021

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The gut microbiome plays an important role in a host’s development and adaption to its dietary niche. In this study, a group of bamboo-feeding insects are used to explore the potential role of the gut microbiota in the convergent adaptation to extreme diet specialization. Specifically, using a 16S rRNA marker and an Illumina sequencing platform, we profiled the microbial communities of 76 gut samples collected from nine bamboo-feeding insects, including both hemimetabolous (Orthoptera and Hemiptera) and holometabolous (Coleoptera and Lepidoptera) species, which are specialized in three distinct dietary niches: bamboo leaf, shoot, and sap. The gut microbiota of these insects were dominated by Proteobacteria, Firmicutes, and Bacteroidetes and were clustered into solid (leaf and shoot) and liquid (sap) dietary niches. The gut bacterial communities of insects feeding on solid diet overlapped significantly, even though these insects belong to phylogenetically distant lineages representing different orders. In addition, the presence of cellulolytic bacterial communities within the gut microbiota allows bamboo-feeding insects to adapt to a highly specialized, fiber-rich diet. Although both phylogeny and diet can impact the structure and composition of gut microbiomes, phylogeny is the primary driving force underlying the convergent adaptation to a highly specialized diet, especially when the related insect species harbor similar gut microbiomes and share the same dietary niche over evolutionary timescales. These combined findings lay the foundation for future research on how convergent feeding strategies impact the interplays between hosts and their gut microbiomes and how the gut microbiota may facilitate convergent evolution in phylogenetically distant species in adaptation to the shared diet.

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Effects of host identity on the gut microbiota: A comparative study on three microtinae species

Yao,

Zhao,

Tang

et al. 2024

Anim Models and Exp Med

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BackgroundGut microbiota exert an immense effect on host health and host environmental adaptation. Furthermore, the composition and structure of gut microbiota are determined by the environment and host genetic factors. However, the relative contribution of the environment and host genetic factors toward shaping the structure of gut microbiota has been poorly understood.MethodsIn this study, we characterized the fecal microbial communities of the closely related voles Neodon fuscus, Lasiopodomys brandtii, and L. mandarinus after caged feeding in the laboratory for 6 months, through high‐throughput sequencing and bioinformatics analysis.ResultsThe results of pairwise comparisons of N. fuscus vs. L. brandtii and L. mandarinus vs. L. brandtii revealed significant differences in bacterial diversity and composition after domestication. While 991 same operational taxonomic units (OTUs) were shared in three voles, there were 362, 291, and 303 species‐specific OTUs in N. fuscus, L. brandtii, and L. mandarinus, respectively. The relative abundances of Proteobacteria and Prevotella, which are reported to be enriched in high‐altitude populations, were significantly higher in high‐altitude N. fuscus than in low‐altitude L. brandtii after domestication. Firmicutes, which produce various digestive enzymes for energy metabolism, and Spirochaetes, which can degrade cellulose, were found in higher abundance in subterranean L. mandarinus than that in L. brandtii which dwells on the earth surface.ConclusionOur findings showed that some components of gut microbiota still maintained dominance even when different host species are reared under the same environmental conditions, suggesting that these bacteria are substantially influenced by host factors..

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Diet drives convergent evolution of gut microbiomes in bamboo-eating species

Cited by 56 publications

References 30 publications

Gut Microbiome Changes in Captive Plateau Zokors (Eospalax baileyi)

Gut Microbiome Changes in Captive Plateau Zokors (Eospalax baileyi)

Host Phylogeny and Diet Shape Gut Microbial Communities Within Bamboo-Feeding Insects

Effects of host identity on the gut microbiota: A comparative study on three microtinae species

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